@article{bowler2025treating,
  title={Treating gaps and biases in biodiversity data as a missing data problem},
  author={Bowler, Diana E and Boyd, Robin J and Callaghan, Corey T and Robinson, Robert A and Isaac, Nick JB and Pocock, Michael JO},
  journal={Biological Reviews},
  volume={100},
  number={1},
  pages={50--67},
  year={2025},
  publisher={Wiley Online Library},
doi={10.1111/brv.13127}
}

@article{Shoari2018_mnar,
author = {Shoari, Niloofar and Dubé, Jean-Sébastien},
title = {Toward improved analysis of concentration data: Embracing nondetects},
journal = {Environmental Toxicology and Chemistry},
volume = {37},
number = {3},
pages = {643-656},
doi = {10.1002/etc.4046},
year = {2018}
}

@article{Newman2023,
author = {Newman, Ken and King, Ruth and Elvira, Víctor and de Valpine, Perry and McCrea, Rachel S. and Morgan, Byron J. T.},
title = {State-space models for ecological time-series data: Practical model-fitting},
journal = {Methods in Ecology and Evolution},
volume = {14},
number = {1},
pages = {26-42},
keywords = {hidden Markov model, Kalman filter, Laplace approximation, likelihood-free methods, Markov chain Monte Carlo, sampling-based methods, sequential Monte Carlo},
doi = {10.1111/2041-210X.13833},
year = {2023}
}


@article{Sotto2011_mnar,
title = {MCMC-based estimation methods for continuous longitudinal data with non-random (non)-monotone missingness},
journal = {Computational Statistics & Data Analysis},
volume = {55},
number = {1},
pages = {301-311},
year = {2011},
issn = {0167-9473},
doi = {10.1016/j.csda.2010.04.026},
author = {Cristina Sotto and Caroline Beunckens and Geert Molenberghs and Michael G. Kenward}
}

@article{McCall2014_mnar,
    author = {McCall, Matthew N. and McMurray, Helene R. and Land, Hartmut and Almudevar, Anthony},
    title = {On non-detects in qPCR data},
    journal = {Bioinformatics},
    volume = {30},
    number = {16},
    pages = {2310-2316},
    year = {2014},
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btu239}
}

@article{Soldaat2007,
author = {Soldaat, Leo and Visser, Hans and van Roomen, Marc and van Strien, Arco},
title = {Smoothing and trend detection in waterbird monitoring data using structural time-series analysis and the Kalman filter.},
journal = {Journal of Ornithology},
volume = {148},
number = {Suppl 2},
pages = {351–357},
doi = {10.1007/s10336-007-0176-7},
year = {2007}
}


@Misc{rstan_package,
    title = {{RStan}: the {R} interface to {Stan}},
    author = {{Stan Development Team}},
    note = {R package version 2.32.6},
    year = {2024},
    url = {https://mc-stan.org/},
}

@article{burkner2017brms,
  title={brms: An R package for Bayesian multilevel models using Stan},
  author={B{\"u}rkner, Paul-Christian},
  journal={Journal of statistical software},
  volume={80},
  pages={1--28},
  year={2017}
}


@article{ricker1954stock,
  title={Stock and recruitment},
  author={Ricker, William Edwin},
  journal={Journal of the Fisheries Board of Canada},
  volume={11},
  number={5},
  pages={559--623},
  year={1954},
  publisher={NRC Research Press Ottawa, Canada},
doi={10.1139/f54-039}
}

@article{bender1984perturbation,
  title={Perturbation experiments in community ecology: theory and practice},
  author={Bender, Edward A and Case, Ted J and Gilpin, Michael E},
  journal={Ecology},
  volume={65},
  number={1},
  pages={1--13},
  year={1984},
  publisher={Wiley Online Library}
}


@article{Sinclair2003,
    author = {Sinclair, A. and Mduma, S. and Brashares, J.},
    title = {Patterns of predation in a diverse predator–prey system},
    journal = {Nature},
    volume = {425},
    pages = {288-290},
    year = {2003},
    doi = {10.1038/nature01934}
}

@article{Buma2017,
author = {Buma, Brian and Bisbing, Sarah and Krapek, John and Wright, Glenn},
title = {A foundation of ecology rediscovered: 100 years of succession on the {W}illiam {S}. {C}ooper plots in {G}lacier {B}ay, {A}laska},
journal = {Ecology},
volume = {98},
number = {6},
pages = {1513-1523},
keywords = {chronosequence, community dynamics, glacial recession, permanent plot, primary succession, relay floristics, repeat survey, successional theory, vegetation development, William S. Cooper},
doi = {10.1002/ecy.1848},
abstract = {Abstract Understanding plant community succession is one of the original pursuits of ecology, forming some of the earliest theoretical frameworks in the field. Much of this was built on the long-term research of William S. Cooper, who established a permanent plot network in Glacier Bay, Alaska, in 1916. This study now represents the longest-running primary succession plot network in the world. Permanent plots are useful for their ability to follow mechanistic change through time without assumptions inherent in space-for-time (chronosequence) designs. After 100-yr, these plots show surprising variety in species composition, soil characteristics (carbon, nitrogen, depth), and percent cover, attributable to variation in initial vegetation establishment first noted by Cooper in the 1916–1923 time period, partially driven by dispersal limitations. There has been almost a complete community composition replacement over the century and general species richness increase, but the effective number of species has declined significantly due to dominance of Salix species which established 100-yr prior (the only remaining species from the original cohort). Where Salix dominates, there is no establishment of “later” successional species like Picea. Plots nearer the entrance to Glacier Bay, and thus closer to potential seed sources after the most recent glaciation, have had consistently higher species richness for 100 yr. Age of plots is the best predictor of soil N content and C:N ratio, though plots still dominated by Salix had lower overall N; soil accumulation was more associated with dominant species. This highlights the importance of contingency and dispersal in community development. The 100-yr record of these plots, including species composition, spatial relationships, cover, and observed interactions between species provides a powerful view of long-term primary succession.},
year = {2017}
}


@article{Adler2009,
author = {Adler, Peter B. and HilleRisLambers, Janneke and Levine, Jonathan M.},
title = {Weak effect of climate variability on coexistence in a sagebrush steppe community},
journal = {Ecology},
volume = {90},
number = {12},
pages = {3303-3312},
keywords = {climate variability, coexistence, competition, population growth, sagebrush steppe, survival},
doi = {10.1890/08-2241.1},
url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/08-2241.1},
eprint = {https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1890/08-2241.1},
abstract = {Climate variability, which is expected to increase in the future, can promote coexistence through a mechanism called the storage effect. Currently, we have little understanding of how the importance of the storage effect varies among ecosystems. We tested for the three conditions of the storage effect in a sagebrush steppe plant community in Idaho (USA) by combining long-term observational data with statistical models. The four sagebrush steppe species that we studied satisfied the first two conditions of the storage effect: a long-lived life stage and species-specific responses to the environment. But the critical third condition, environment-competition covariance, was very weak in this community. While the direction of the covariance was consistent with a stabilizing effect of variability (stronger competition in more favorable years), its magnitude was small, reflecting low temporal variability in both competition and species responses to the environment. Consistent with this result, simulations of species population growth rates when rare showed that climate variability had no consistent stabilizing effect on coexistence. This case study provides an important reminder that species-specific responses to the environment are not sufficient for coexistence via the storage effect. Instead, the magnitude of temporal variability in species performance also plays an important role. Comparison of our results with those from a similar study in Kansas mixed prairie suggests that temporal variability in species performance may reflect both the strength of environmental variability as well as life history strategies.},
year = {2009}
}



@article{Likens1970,
author = {Likens, Gene E. and Bormann, F. Herbert and Johnson, Noye M. and Fisher, D. W. and Pierce, Robert S.},
title = {Effects of Forest Cutting and Herbicide Treatment on Nutrient Budgets in the Hubbard Brook Watershed-Ecosystem},
journal = {Ecological Monographs},
volume = {40},
number = {1},
pages = {23-47},
doi = {10.2307/1942440},
url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.2307/1942440},
eprint = {https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.2307/1942440},
abstract = {All vegetation on Watershed 2 of the Hubbard Brook Experimental Forest was cut during November and December of 1965, and vegetation regrowth was inhibited for two years by periodic application of herbicides. Annual stream—flow was increased 33 cm or 39\% the first year and 27 cm or 28\% the second year above the values expected if the watershed were not deforested. Large increases in streamwater concentration were observed for all major ions, except NH4+, SO4 = and HCO3—, approximately five months after the deforestation. Nitrate concentrations were 41—fold higher than the undisturbed condition the first year and 56—fold higher the second. The nitrate concentration in stream water has exceeded, almost continuously, the health levels recommended for drinking water. Sulfate was the only major ion in stream water that decreased in concentration after deforestation. An inverse relationship between sulfate and nitrate concentrations in stream water was observed in both undisturbed and deforested situations. Average streamwater concentrations increased by 417\% for Ca++, 408\% for Mg++, 1558\% for K+ and 177\% for Na+ during the two years subsequent to deforestation. Budgetary net losses from Watershed 2 in kg/ha—yr were about 142 for NO3—N, 90 for Ca++, 36 for K+, 32 for SiO2—Si, 24 for Al+++, 18 for Mg++, 17 for Na+, 4 for Cl—, and 0 for SO4—S during 1967—68; whereas for an adjacent, undisturbed watershed (W6) net losses were 9.2 for Ca++, 1.6 for K+, 17 for SiO2—Si, 3.1 for A1+++, 2.6 for Mg++, 7.0 for Na+, 0.1 for C1—, and 3.3 for SO4—S. Input of nitrate—nitrogen in precipitation normally exceeds the output in drainage water in the undisturbed ecosystems, and ammonium—nitrogen likewise accumulates in both the undisturbed and deforested ecosystems. Total gross export of dissolved solids, exclusive of organic matter, was about 75 metric tons/km2 in 1966—67, and 97 metric tons/km2 in 1967—68, or about 6 to 8 times greater than would be expected for an undisturbed watershed. The greatly increased export of dissolved nutrients from the deforested ecosystem was due to an alteration of the nitrogen cycle within the ecosystem. The drainage streams tributary to Hubbard Brook are normally acid, and as a result of deforestation the hydrogen ion content increased by 5—fold (from pH 5.1 to 4.3). Streamwater temperatures after deforestation were higher than the undisturbed condition during both summer and winter. Also in contrast to the relatively constant temperature in the undisturbed streams, streamwater temperature after deforestation fluctuated 3—4°C during the day in summer. Electrical conductivity increased about 6—fold in the stream water after deforestation and was much more variable. Increased streamwater turbidity as a result of the deforestation was negligible, however the particulate matter output was increased about 4—fold. Whereas the particulate matter is normally 50\% inorganic materials, after deforestation preliminary estimates indicate that the proportion of inorganic materials increased to 76\% of the total particulates. Supersaturation of dissolved oxygen in stream water from the experimental watersheds is common in all seasons except summer when stream discharge is low. The percent saturation is dependent upon flow rate in the streams. Sulfate, hydrogen ion and nitrate are major constituents in the precipitation. It is suggested that the increase in average nitrate concentration in precipitation compared to data from 1955—56,as well as the consistent annual increase observed from 1964 to 1968, may be some measure of a general increase in air pollution.},
year = {1970}
}



@article{Hughes2017,
    author = {Hughes, Brent B. and Beas-Luna, Rodrigo and Barner, Allison K. and Brewitt, Kimberly and Brumbaugh, Daniel R. and Cerny-Chipman, Elizabeth B. and Close, Sarah L. and Coblentz, Kyle E. and de Nesnera, Kristin L. and Drobnitch, Sarah T. and Figurski, Jared D. and Focht, Becky and Friedman, Maya and Freiwald, Jan and Heady, Kristen K. and Heady, Walter N. and Hettinger, Annaliese and Johnson, Angela and Karr, Kendra A. and Mahoney, Brenna and Moritsch, Monica M. and Osterback, Ann-Marie K. and Reimer, Jessica and Robinson, Jonathan and Rohrer, Tully and Rose, Jeremy M. and Sabal, Megan and Segui, Leah M. and Shen, Chenchen and Sullivan, Jenna and Zuercher, Rachel and Raimondi, Peter T. and Menge, Bruce A. and Grorud-Colvert, Kirsten and Novak, Mark and Carr, Mark H.},
    title = {Long-Term Studies Contribute Disproportionately to Ecology and Policy},
    journal = {BioScience},
    volume = {67},
    number = {3},
    pages = {271-281},
    year = {2017},
    month = {02},
    abstract = {As the contribution for long-term ecological and environmental studies (LTEES) to our understanding of how species and ecosystems respond to a changing global climate becomes more urgent, the relative number and investment in LTEES are declining. To assess the value of LTEES to advancing the field of ecology, we evaluated relationships between citation rates and study duration, as well as the representation of LTEES with the impact factors of 15 ecological journals. We found that the proportionate representation of LTEES increases with journal impact factor and that the positive relationship between citation rate and study duration is stronger as journal impact factor increases. We also found that the representation of LTEES in reports written to inform policy was greater than their representation in the ecological literature and that their authors particularly valued LTEES. We conclude that the relative investment in LTEES by ecologists and funders should be seriously reconsidered for advancing ecology and its contribution to informing environmental policy.},
    issn = {0006-3568},
    doi = {10.1093/biosci/biw185},
    url = {10.1093/biosci/biw185},
    eprint = {https://academic.oup.com/bioscience/article-pdf/67/3/271/10864103/biw185.pdf},
}


@incollection{lebreton1990modelling,
  title={Modelling density dependence, environmental variability, and demographic stochasticity from population counts: an example using Wytham Wood great tits},
  author={Lebreton, Jean-Dominique},
  booktitle={Population biology of passerine birds: An integrated approach},
  pages={89--102},
  year={1990},
  publisher={Springer}
}

@article{chen2013ecological,
  title={Ecological Monitoring Using Wireless Sensor Networks-—Overview, Challenges, and Opportunities},
  author={Chen, Chia-Pang and Chuang, Cheng-Long and Jiang, Joe-Air},
  journal={Advancement in Sensing Technology: New Developments and Practical Applications},
  pages={1--21},
  year={2013},
  publisher={Springer},
doi={10.1007/978-3-642-32180-1}
}


@article{gelman2020bayesian,
  title={Bayesian workflow},
  author={Gelman, Andrew and Vehtari, Aki and Simpson, Daniel and Margossian, Charles C and Carpenter, Bob and Yao, Yuling and Kennedy, Lauren and Gabry, Jonah and B{\"u}rkner, Paul-Christian and Modr{\'a}k, Martin},
  journal={arXiv preprint arXiv:2011.01808},
  year={2020}
}


@article{vitale_modelling_2019,
	title = {Modelling random uncertainty of eddy covariance flux measurements},
	volume = {33},
	issn = {1436-3240},
	url = {https://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=DOISource&SrcApp=WOS&KeyAID=10.1007%2Fs00477-019-01664-4&DestApp=DOI&SrcAppSID=6Cta8CBBwfoZtT7dWTy&SrcJTitle=STOCHASTIC+ENVIRONMENTAL+RESEARCH+AND+RISK+ASSESSMENT&DestDOIRegistrantName=Springer-Verlag},
	doi = {10.1007/s00477-019-01664-4},
	abstract = {The eddy-covariance (EC) technique is considered the most direct and reliable method to calculate flux exchanges of the main greenhouse gases over natural ecosystems and agricultural fields. The resulting measurements are extremely important to characterize ecosystem exchanges of carbon, water, energy and other trace gases, and are widely used to validate or constrain parameter of land surface models via data assimilation techniques. For this purpose, the availability of both complete half-hourly flux time series and its associated uncertainty is mandatory. However, uncertainty estimation for EC data is challenging because the standard procedures based on repeated sampling are not suitable for this kind of measurements, and the presence of missing data makes it difficult to build any sensible time series model with time-varying second-order moments that can provide estimates of total random uncertainty. To overcome such limitations, this paper describes a new method in the context of the strategy based on the model residual approach proposed by Richardson et al. (Agric For Meteorol 148(1): 38-50, 2008). The proposed approach consists in (1) estimating the conditional mean process as representative of the true signal underlying observed data and (2) estimating the conditional variance process as representative of the total random uncertainty affecting EC data. The conditional mean process is estimated through the multiple imputation algorithm recently proposed by Vitale et al. (J Environ Inform https,:il doi .org/10.3808/jei.201800391, 2018). The conditional variance process is estimated through the stochastic volatility model introduced by Beltratti and Morana (Econ Notes 30(2): 205-234, 2001). This strategy is applied to ten sites that are part of FLUXNET2015 dataset, selected in such a way to cover various ecosystem types under different climatic regimes around the world. The estimated uncertainty is compared with estimates by other well-established methods, and it is demonstrated that the scaling relationship between uncertainty and flux magnitude is preserved. Additionally, the proposed strategy allows obtaining a complete half-hourly time series of uncertainty estimates, which are expected to be useful for many users of EC flux data.},
	language = {English},
	number = {3},
	urldate = {2021-09-16},
	journal = {Stochastic Environmental Research and Risk Assessment},
	author = {Vitale, Domenico and Bilancia, Massimo and Papale, Dario},
	month = mar,
	year = {2019},
	note = {Place: New York
Publisher: Springer
WOS:000463874500006},
	keywords = {Conditional heteroskedasticity, Ecology, Eddy covariance, Global warming, Net ecosystem exchange, Time series, Uncertainty, bayesian-inference, carbon-dioxide exchange, co2 flux, forest, long-term measurements, missing data, multiple imputation, net ecosystem exchange, semiarid woodland, water},
	pages = {725--746},
}

@article{thurstan_nineteenth_2016,
	title = {Nineteenth century narratives reveal historic catch rates for {Australian} snapper ({Pagrus} auratus)},
	volume = {17},
	issn = {1467-2979},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/faf.12103},
	doi = {10.1111/faf.12103},
	abstract = {Snapper (Pagrus auratus) is widely distributed throughout subtropical and temperate southern oceans and forms a significant recreational and commercial fishery in Queensland, Australia. Using data from government reports, media sources, popular publications and a government fisheries survey carried out in 1910, we compiled information on individual snapper fishing trips that took place prior to the commencement of fisherywide organized data collection, from 1871 to 1939. In addition to extracting all available quantitative data, we translated qualitative information into bounded estimates and used multiple imputation to handle missing values, forming 287 records for which catch rate (snapper fisher−1 h−1) could be derived. Uncertainty was handled through a parametric maximum likelihood framework (a transformed trivariate Gaussian), which facilitated statistical comparisons between data sources. No statistically significant differences in catch rates were found among media sources and the government fisheries survey. Catch rates remained stable throughout the time series, averaging 3.75 snapper fisher−1 h−1 (95\% confidence interval, 3.42–4.09) as the fishery expanded into new grounds. In comparison, a contemporary (1993–2002) south-east Queensland charter fishery produced an average catch rate of 0.4 snapper fisher−1 h−1 (95\% confidence interval, 0.31–0.58). These data illustrate the productivity of a fishery during its earliest years of development and represent the earliest catch rate data globally for this species. By adopting a formalized approach to address issues common to many historical records – missing data, a lack of quantitative information and reporting bias – our analysis demonstrates the potential for historical narratives to contribute to contemporary fisheries management.},
	language = {en},
	number = {1},
	urldate = {2021-09-16},
	journal = {Fish and Fisheries},
	author = {Thurstan, Ruth H. and Campbell, Alexander B. and Pandolfi, John M.},
	year = {2016},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/faf.12103},
	keywords = {Catch per unit effort, historical ecology, multiple imputation, narrative accounts, qualitative data},
	pages = {210--225},
}

@article{hossie_confronting_2021,
	title = {Confronting Missing Ecological Data in the Age of Pandemic Lockdown},
	volume = {9},
	issn = {2296-701X},
	url = {https://www.frontiersin.org/article/10.3389/fevo.2021.669477},
	doi = {10.3389/fevo.2021.669477},
	abstract = {The COVID-19 pandemic profoundly affected research in ecology and evolution, with lockdowns resulting in the suspension of most research programs and creating gaps in many ecological datasets. Likewise, monitoring efforts directed either at tracking trends in natural systems or documenting the environmental impacts of anthropogenic activities were largely curtailed. In addition, lockdowns have affected human activity in natural environments in ways that impact the systems under investigation, rendering many widely used approaches for handling missing data (e.g., available case analysis, mean substitution) inadequate. Failure to properly address missing data will lead to bias and weak inference. Researchers and environmental monitors must ensure that lost data are handled robustly by diagnosing patterns and mechanisms of missingness and applying appropriate tools like multiple imputation, full-information maximum likelihood, or Bayesian approaches. The pandemic has altered many aspects of society and it is timely that we critically reassess how we treat missing data in ecological research and environmental monitoring, and plan future data collection to ensure robust inference when faced with missing data. These efforts will help ensure the integrity of inference derived from datasets spanning the COVID-19 lockdown and beyond.},
	urldate = {2021-09-16},
	journal = {Frontiers in Ecology and Evolution},
	author = {Hossie, Thomas J. and Gobin, Jenilee and Murray, Dennis L.},
	year = {2021},
	pages = {542},
}

@article{kim_transcending_2018,
	title = {Transcending data gaps: a framework to reduce inferential errors in ecological analyses},
	volume = {21},
	issn = {1461-0248},
	shorttitle = {Transcending data gaps},
	doi = {10.1111/ele.13089},
	abstract = {The analysis of functional diversity (FD) has gained increasing importance due to its generality and utility in ecology. In particular, patterns in the spatial distribution and temporal change of FD are being used to predict locations and functional groups that are immediately vulnerable to global changes. A major impediment to the accurate measurement of FD is the pervasiveness of missing data in trait datasets. While such prevalent data gaps can engender misleading inferences in FD analyses, we currently lack any practical guide to handle missing data in trait datasets. Here, we identify significant mismatches between true FD and values derived from datasets that contain missing data. We demonstrate that imputing missing data with a phylogeny-informed approach reduces the risk of misinterpretation of FD patterns, and provides baseline information against which central questions in ecology can be evaluated.},
	language = {en},
	number = {8},
	urldate = {2021-09-16},
	journal = {Ecology Letters},
	author = {Kim, Sun W. and Blomberg, Simon P. and Pandolfi, John M.},
	year = {2018},
	
	keywords = {Functional biogeography, functional diversity, functional trait, imputation, trait database},
	pages = {1200--1210},
}
@book{gelman_data_2006,
	address = {Cambridge ; New York},
	edition = {1st edition},
	title = {Data {Analysis} {Using} {Regression} and {Multilevel}/{Hierarchical} {Models}},
	isbn = {978-0-521-68689-1},
	abstract = {Data Analysis Using Regression and Multilevel/Hierarchical Models is a comprehensive manual for the applied researcher who wants to perform data analysis using linear and nonlinear regression and multilevel models. The book introduces a wide variety of models, whilst at the same time instructing the reader in how to fit these models using available software packages. The book illustrates the concepts by working through scores of real data examples that have arisen from the authors' own applied research, with programming codes provided for each one. Topics covered include causal inference, including regression, poststratification, matching, regression discontinuity, and instrumental variables, as well as multilevel logistic regression and missing-data imputation. Practical tips regarding building, fitting, and understanding are provided throughout. Author resource page: http://www.stat.columbia.edu/{\textasciitilde}gelman/arm/},
	language = {English},
	publisher = {Cambridge University Press},
	author = {Gelman, Andrew and Hill, Jennifer},
	month = dec,
	year = {2006},
}

@article{smith_carbon-13_1981,
	title = {Carbon-13 isotopic fractionation as a measure of aquatic metabolism},
	volume = {294},
	copyright = {1981 Nature Publishing Group},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/294252a0},
	doi = {10.1038/294252a0},
	abstract = {The fixation of dissolved CO2 in organic matter during photosynthesis preferentially removes 12C from the water, causing the remaining HCO−3 to become enriched in the less abundant isotope, 13C. Respiration later releases part of this CO2 back into the water. Metabolically active aquatic communities thus can generate variations in both the chemical1–3 and isotopic4–7 compositions of the water surrounding them. We describe here experiments designed to establish the isotopic fractionation of carbon by the metabolism of two common coral reef organisms. We then show that the fractionation coefficient obtained for the metabolism of those organisms is also applicable to a reef community and may be used to estimate the metabolic rate of the community.},
	language = {en},
	number = {5838},
	urldate = {2021-08-27},
	journal = {Nature},
	author = {Smith, S. V. and Kroopnick, P.},
	month = nov,
	year = {1981},
	note = {Bandiera\_abtest: a
Cg\_type: Nature Research Journals
Number: 5838
Primary\_atype: Research
Publisher: Nature Publishing Group},
	pages = {252--253},
}

@article{benson_solubility_1979,
	title = {The solubility and isotopic fractionation of gases in dilute aqueous solution. {I}. {Oxygen}},
	volume = {8},
	issn = {1572-8927},
	url = {10.1007/BF01033696},
	doi = {10.1007/BF01033696},
	abstract = {A very precise and accurate new method is described for determination of the Henry coefficient k and the isotopic fractionation of gases dissolved in liquids. It yields fully corrected values for k at essentially infinite dilution. For oxygen the random error for k is less than 0.02\%, which is an order of magnitude better than the best previous measurements on that or any other gas. Extensive tests and comparison with other work indicate that systematic errors probably are negligible and that the accuracy is determined by the precision of the measurements. In the virial correction factor (1+λPt), where Pt is the total pressure of the vapor phase, the coefficient λ for oxygen empirically is a linear decreasing function of the temperature over the range 0–60°C. The simple three-term power series in 1/T proposed by Benson and Krause,\$\${\textbackslash}ln k = a\_0  + a\_1 /T + a\_2 /T{\textasciicircum}2 \$\$},
	language = {en},
	number = {9},
	urldate = {2021-08-27},
	journal = {Journal of Solution Chemistry},
	author = {Benson, Bruce B. and Krause, Daniel and Peterson, Mark A.},
	month = sep,
	year = {1979},
	pages = {655--690},
}

@article{benson_concentration_1984,
	title = {The concentration and isotopic fractionation of oxygen dissolved in freshwater and seawater in equilibrium with the atmosphere1},
	volume = {29},
	issn = {1939-5590},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.1984.29.3.0620},
	doi = {10.4319/lo.1984.29.3.0620},
	abstract = {Previous work on the solubility of oxygen in freshwater has been extended to seawater. Measurements of the Henry coefficient in the ranges 0° {\textless} t {\textless} 45°C and 0{\textless} S {\textless} 50 fit the Setschenow relationship for the variation with salinity. The temperature dependence of the Setschenow coefficient for oxygen is found to be K = 0.0225034 ‒ 13.6083/T + 2,565.68/T2. The equation for the Henry coefficient as a function of temperature and salinity is used to calculate values for unit standard atmospheric concentrations (USAC) in freshwater and seawater in equilibrium with air at a total pressure of 1 atmosphere. It is estimated that the possible error in the new USAC values is no greater than ±0.1\% and probably less. Tables and equations are presented for obtaining accurate USAC values in the ranges 0° {\textless} t {\textless} 40°C and 0 {\textless} S {\textless} 40. Simple procedures are given for calculating standard atmospheric concentrations at pressures different from 1 atm. The presence of sea salt has a negligible effect on the fractionation of the oxygen isotopes during solution.},
	language = {en},
	number = {3},
	urldate = {2021-08-27},
	journal = {Limnology and Oceanography},
	author = {Benson, Bruce B. and Krause, Daniel},
	year = {1984},
	note = {\_eprint: https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.4319/lo.1984.29.3.0620},
	pages = {620--632},
}

@article{knox_kinetic_1992,
	title = {Kinetic isotopic fractionation during air-water gas transfer of {O2}, {N2}, {CH4}, and {H2}},
	volume = {97},
	issn = {2156-2202},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/92JC00949},
	doi = {10.1029/92JC00949},
	abstract = {We present experimental results that show that the kinetic isotopic fractionation during gas exchange is 0.9972 ± 0.0002 for oxygen, 0.9992 ± 0.0002 for methane, 0.9987 ± 0.0001 for nitrogen and 0.982 ± 0.002 for hydrogen, and that the equilibrium fractionation between water and gas phases is 1.037 for hydrogen. We show that the isotopic fractionation during gas transfer for these gases is not equal to the square root of their reduced mass in water, as would be predicted by an extension of the kinetic theory of ideal gases to dissolved gases. The use of isotopes as tracers of biogeochemical gases requires knowledge of the fractionation factor for air-water gas transfer; there have been few direct measurements of these factors.},
	language = {en},
	number = {C12},
	urldate = {2021-08-27},
	journal = {Journal of Geophysical Research: Oceans},
	author = {Knox, M. and Quay, P. D. and Wilbur, D.},
	year = {1992},
	note = {\_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/92JC00949},
	pages = {20335--20343},
}

@article{schneider_climate_2017,
	title = {Climate goals and computing the future of clouds},
	volume = {7},
	copyright = {2017 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	issn = {1758-6798},
	url = {https://www.nature.com/articles/nclimate3190},
	doi = {10.1038/nclimate3190},
	abstract = {How clouds respond to warming remains the greatest source of uncertainty in climate projections. Improved computational and observational tools can reduce this uncertainty. Here we discuss the need for research focusing on high-resolution atmosphere models and the representation of clouds and turbulence within them.},
	language = {en},
	number = {1},
	urldate = {2021-08-27},
	journal = {Nature Climate Change},
	author = {Schneider, Tapio and Teixeira, João and Bretherton, Christopher S. and Brient, Florent and Pressel, Kyle G. and Schär, Christoph and Siebesma, A. Pier},
	month = jan,
	year = {2017},
	note = {Bandiera\_abtest: a
Cg\_type: Nature Research Journals
Number: 1
Primary\_atype: Comments \& Opinion
Publisher: Nature Publishing Group
Subject\_term: Atmospheric dynamics;Climate and Earth system modelling;Research data
Subject\_term\_id: atmospheric-dynamics;climate-and-earth-system-modelling;research-data},
	pages = {3--5},
}

@article{gudmundsson_globally_2021,
	title = {Globally observed trends in mean and extreme river flow attributed to climate change},
	volume = {371},
	copyright = {Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. https://www.sciencemag.org/about/science-licenses-journal-article-reuseThis is an article distributed under the terms of the Science Journals Default License.},
	issn = {0036-8075, 1095-9203},
	url = {https://science.sciencemag.org/content/371/6534/1159},
	doi = {10.1126/science.aba3996},
	abstract = {Change of flow
Anthropogenic influence on climate has changed temperatures, precipitation, atmospheric circulation, and many other related physical processes, but has it changed river flow as well? Gudmundsson et al. analyzed thousands of time series of river flows and hydrological extremes across the globe and compared them with model simulations of the terrestrial water cycle (see the Perspective by Hall and Perdigão). They found that the observed trends can only be explained if the effects of climate change are included. Their analysis shows that human influence on climate has affected the magnitude of low, mean, and high river flows on a global scale.
Science, this issue p. 1159; see also p. 1096
Anthropogenic climate change is expected to affect global river flow. Here, we analyze time series of low, mean, and high river flows from 7250 observatories around the world covering the years 1971 to 2010. We identify spatially complex trend patterns, where some regions are drying and others are wetting consistently across low, mean, and high flows. Trends computed from state-of-the-art model simulations are consistent with the observations only if radiative forcing that accounts for anthropogenic climate change is considered. Simulated effects of water and land management do not suffice to reproduce the observed trend pattern. Thus, the analysis provides clear evidence for the role of externally forced climate change as a causal driver of recent trends in mean and extreme river flow at the global scale.
The fingerprint of anthropogenic climate change is apparent in river flow and hydrological extremes at the global scale.
The fingerprint of anthropogenic climate change is apparent in river flow and hydrological extremes at the global scale.},
	language = {en},
	number = {6534},
	urldate = {2021-08-27},
	journal = {Science},
	author = {Gudmundsson, Lukas and Boulange, Julien and Do, Hong X. and Gosling, Simon N. and Grillakis, Manolis G. and Koutroulis, Aristeidis G. and Leonard, Michael and Liu, Junguo and Schmied, Hannes Müller and Papadimitriou, Lamprini and Pokhrel, Yadu and Seneviratne, Sonia I. and Satoh, Yusuke and Thiery, Wim and Westra, Seth and Zhang, Xuebin and Zhao, Fang},
	month = mar,
	year = {2021},
	pmid = {33707264},
	note = {Publisher: American Association for the Advancement of Science
Section: Report},
	pages = {1159--1162},
}

@article{gomez-gener_integrating_2021,
	title = {Integrating {Discharge}-{Concentration} {Dynamics} {Across} {Carbon} {Forms} in a {Boreal} {Landscape}},
	volume = {57},
	issn = {1944-7973},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020WR028806},
	doi = {10.1029/2020WR028806},
	abstract = {The flux of terrestrial carbon across land-water boundaries influences the overall carbon balance of landscapes and the ecology and biogeochemistry of aquatic ecosystems. The local consequences and broader fate of carbon delivered to streams is determined by the overall composition of carbon inputs, including the balance of organic and inorganic forms. Yet, our understanding of how hydrologic fluxes across different land-water interfaces regulate carbon supply remains poor. We used 7 years of data from three boreal catchments to test how different land-water interfaces (i.e., forest, wetland, and lake) modulate concentration-discharge (C-Q) relationships for dissolved organic carbon (DOC), carbon dioxide (CO2), and methane, as well as the balance among forms (e.g., DOC:CO2). Seasonal patterns in concentrations and C-Q relationships for individual carbon forms differed across catchments. DOC varied between chemostasis and transport limitation in the forest catchment, between supply limitation and chemostasis in the wetland catchment, and was persistently chemostatic in the lake outlet stream. Carbon gases were supply limited overall, but exhibited chemostasis or transport limitation in the forest and wetland catchments linked to elevated flow in summer and autumn. Unique C-Q relationships for individual forms reflected the properties of different interfaces and underpinned changes in the composition of lateral carbon supply. Accordingly, DOC dominated the carbon flux during snowmelt, whereas gas evasion increased in relative importance during other times of the year. Integrating the C-Q dynamics of individual carbon forms provides insight into the shifting composition of lateral export, and thus helps to predict how hydrologic changes may alter the fate of carbon supplied to streams.},
	language = {en},
	number = {8},
	urldate = {2021-08-27},
	journal = {Water Resources Research},
	author = {Gómez-Gener, Lluís and Hotchkiss, Erin R. and Laudon, Hjalmar and Sponseller, Ryan A.},
	year = {2021},
	note = {\_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2020WR028806},
	keywords = {biogeochemistry, boreal, carbon, carbon dioxide, catchment, dissolved organic carbon, floods, headwater, hydrology, landscape, methane, seasonal variability, stream},
	pages = {e2020WR028806},
}

@article{farrell_variation_2018,
	title = {Variation in {Detrital} {Resource} {Stoichiometry} {Signals} {Differential} {Carbon} to {Nutrient} {Limitation} for {Stream} {Consumers} {Across} {Biomes}},
	volume = {21},
	issn = {1435-0629},
	url = {10.1007/s10021-018-0247-z},
	doi = {10.1007/s10021-018-0247-z},
	abstract = {Stoichiometric ratios of resources and consumers have been used to predict nutrient limitation across diverse terrestrial and aquatic ecosystems. In forested headwater streams, coarse and fine benthic organic matter (CBOM, FBOM) are primary basal resources for the food web, and the distribution and quality of these organic matter resources may therefore influence patterns of secondary production and nutrient cycling within stream networks or among biomes. We measured carbon (C), nitrogen (N), and phosphorus (P) content of CBOM and FBOM and calculated their stoichiometric ratios (C/N, C/P, N/P) from first- to fourth-order streams from tropical montane, temperate deciduous, and boreal forests, and tallgrass prairie, to compare the magnitude and variability of these resource types among biomes. We then used the ratios to predict nutritional limitations for consumers of each resource type. Across biomes, CBOM had consistently higher \%C and \%N, and higher and more variable C/N and C/P than FBOM, suggesting that microbial processing results in more tightly constrained elemental composition in FBOM than in CBOM. Biome-specific differences were observed in \%P and N/P between the two resource pools; CBOM was lower in \%P but higher in N/P than FBOM in the tropical montane and temperate deciduous forest biomes, while CBOM was higher in \%P but similar in N/P than FBOM in the grassland and boreal forest biomes. Stable 13C isotopes suggest that FBOM likely derives from CBOM in tropical and temperate deciduous forest, but that additional non-detrital components may contribute to FBOM in boreal forests and grasslands. Comparisons of stoichiometric ratios of CBOM and FBOM to estimated needs of aquatic detritivores suggest that shredders feeding on CBOM are more likely to experience nutrient (N and/or P) than C limitation, whereas collector–gatherers consuming FBOM are more likely to experience C than N and/or P limitation. Our results suggest that differences in basal resource elemental content and stoichiometric ratios have the potential to affect consumer production and ecosystem rates of C, N, and P cycling in relatively consistent ways across diverse biomes.},
	language = {en},
	number = {8},
	urldate = {2021-08-26},
	journal = {Ecosystems},
	author = {Farrell, Kaitlin J. and Rosemond, Amy D. and Kominoski, John S. and Bonjour, Sophia M. and Rüegg, Janine and Koenig, Lauren E. and Baker, Christina L. and Trentman, Matt T. and Harms, Tamara K. and McDowell, William H.},
	month = dec,
	year = {2018},
	pages = {1676--1691},
}

@article{rubin_inference_1976,
	title = {Inference and missing data},
	volume = {63},
	issn = {0006-3444},
	url = {10.1093/biomet/63.3.581},
	doi = {10.1093/biomet/63.3.581},
	abstract = {When making sampling distribution inferences about the parameter of the data, θ, it is appropriate to ignore the process that causes missing data if the missing data are ‘missing at random’ and the observed data are ‘observed at random’, but these inferences are generally conditional on the observed pattern of missing data. When making direct-likelihood or Bayesian inferences about θ, it is appropriate to ignore the process that causes missing data if the missing data are missing at random and the parameter of the missing data process is ‘distinct’ from θ. These conditions are the weakest general conditions under which ignoring the process that causes missing data always leads to correct inferences.},
	number = {3},
	urldate = {2021-04-21},
	journal = {Biometrika},
	author = {Rubin, D. B.},
	month = dec,
	year = {1976},
	pages = {581--592},
}

@book{mcknight_missing_2007,
	title = {Missing {Data}: {A} {Gentle} {Introduction}},
	isbn = {978-1-59385-393-8},
	shorttitle = {Missing {Data}},
	url = {https://www.guilford.com/books/Missing-Data/McKnight-McKnight-Sidani-Figueredo/9781593853938},
	abstract = {While most books on missing data focus on applying sophisticated statistical techniques to deal with the problem after it has occurred, this volume provides a methodology for the control and prevention of missing data. In clear, nontechnical language, the authors help the reader understand the different types of missing data and their implications for the reliability, validity, and generalizability of a study’s conclusions.},
	language = {en-US},
	urldate = {2021-08-24},
	publisher = {Guilford Press},
	author = {McKnight, P.E. and McKnight, K.M. and Sidani, S and Figueredo, A. J.},
	year = {2007},
}

@book{allison_missing_2002,
	address = {2455 Teller Road, Thousand Oaks California 91320 United States of America},
	title = {Missing {Data}},
	isbn = {978-0-7619-1672-7 978-1-4129-8507-9},
	url = {http://methods.sagepub.com/book/missing-data},
	urldate = {2021-08-24},
	publisher = {SAGE Publications, Inc.},
	author = {Allison, Paul},
	year = {2002},
	doi = {10.4135/9781412985079},
}

@book{little_statistical_2002,
	edition = {Second},
	title = {Statistical {Analysis} with {Missing} {Data}},
	isbn = {978-1-119-01356-3},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9781119013563.ch1},
	abstract = {Standard statistical methods have been developed to analyze rectangular data sets. Traditionally, the rows of the data matrix represent units, also called cases, observations, or subjects depending on context, and the columns represent variables measured for each unit. The entries in the data matrix are nearly always real numbers, either representing the values of essentially continuous variables, such as age and income, or representing categories of response, which may be ordered (e.g., level of education) or unordered . This chapter discusses some important patterns, and formalizes the idea of missing-data mechanisms. A different issue concerns the mechanisms that lead to missing data, and in particular the question of whether the fact that variables are missing is related to the underlying values of the variables in the data set. Missing-data mechanisms are crucial since the properties of missing-data methods depend very strongly on the nature of the dependencies in these mechanisms.},
	language = {en},
	urldate = {2021-08-24},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Little, Roderick J. A. and Rubin, Donald B.},
	year = {2002},
	doi = {10.1002/9781119013563.ch1},
	note = {Section: 1
\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781119013563.ch1},
	keywords = {data matrix, data sets, missing-data mechanisms, statistical methods},
}

@incollection{noauthor_front_2002,
	title = {Front {Matter}},
	isbn = {978-1-119-01356-3},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9781119013563.fmatter},
	abstract = {The prelims comprise: Half-Title Page Series Page Title Page Copyright Page Contents Preface},
	language = {en},
	urldate = {2021-08-24},
	booktitle = {Statistical {Analysis} with {Missing} {Data}},
	publisher = {John Wiley \& Sons, Ltd},
	year = {2002},
	doi = {10.1002/9781119013563.fmatter},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781119013563.fmatter},
	pages = {i--xv},
}

@article{helman_fractionation_2005,
	title = {Fractionation of the {Three} {Stable} {Oxygen} {Isotopes} by {Oxygen}-{Producing} and {Oxygen}-{Consuming} {Reactions} in {Photosynthetic} {Organisms}},
	volume = {138},
	issn = {1532-2548, 0032-0889},
	url = {https://academic.oup.com/plphys/article/138/4/2292/6112998},
	doi = {10.1104/pp.105.063768},
	abstract = {Abstract
            The triple isotope composition (δ 17O and δ 18O) of dissolved O2 in the ocean and in ice cores was recently used to assess the primary productivity over broad spatial and temporal scales. However, assessment of the productivity with the aid of this method must rely on accurate measurements of the 17O/16O versus 18O/16O relationship in each of the main oxygen-producing and -consuming reactions. Data obtained here showed that cleavage of water in photosystem II did not fractionate oxygen isotopes; the δ 18O and δ 17O of the O2 evolved were essentially identical to those of the substrate water. The fractionation slopes for the oxygenase reaction of Rubisco and respiration were identical (0.518 ± 0.001) and that of glycolate oxidation was 0.503 ± 0.002. There was a considerable difference in the slopes of O2 photoreduction (the Mehler reaction) in the cyanobacterium Synechocystis sp. strain PCC 6803 (0.497 ± 0.004) and that of pea (Pisum sativum) thylakoids (0.526 ± 0.001). These values provided clear and independent evidence that the mechanism of O2 photoreduction differs between higher plants and cyanobacteria. We used our method to assess the magnitude of O2 photoreduction in cyanobacterial cells maintained under conditions where photorespiration was negligible. It was found that electron flow to O2 can be as high as 40\% that leaving photosystem II, whereas respiratory activity in the light is only 6\%. The implications of our findings to the evaluation of specific O2-producing or -consuming reactions, in vivo, are discussed.},
	language = {en},
	number = {4},
	urldate = {2021-08-17},
	journal = {Plant Physiology},
	author = {Helman, Yael and Barkan, Eugeni and Eisenstadt, Doron and Luz, Boaz and Kaplan, Aaron},
	month = aug,
	year = {2005},
	pages = {2292--2298},
}

@article{guy_photosynthetic_1993,
	title = {Photosynthetic {Fractionation} of the {Stable} lsotopes of {Oxygen} and {Carbon}'},
	volume = {101},
	language = {en},
	author = {Guy, Robert D and Fogel, Marilyn L. and Berry, Joseph A.},
	year = {1993},
	pages = {37--47},
}

@article{stevens_oxygen_nodate,
	title = {Oxygen {Isotope} {Fractionation} during {Photosynthesis} in a {Blue}-{Green} and a {Green} {Alga}},
	abstract = {Oxygen isotope fractionation (180/160) at the natural abundance level has been measured during photosynthesis of a blue-green and a green alga. When sufficient attention is paid to removal of contaminating air 02 before and during the experiments, then the photosynthetic 02 evolved, as compared to the water 02, had an average difference of -0.36\%0 for a blue-green alga and -0.80\%0 for a green alga. These experiments suggest that there is no reason to invoke an inverse isotope effect in photosynthesis as part of the explanation for the 180 enrichment in atmospheric 02 relative to 02 in oceanic waters. In addition, in an indirect way, the experiments also support the argument that the bulk of 02 evolved during photosynthesis comes fronm water. A 10\%s contribution of 02 arising froni CO2 would have been detectable in the present work.},
	language = {en},
	author = {Stevens, Catherine L R and Schultz, David and Baalen, Chase Van and Parker, Patrick L},
	pages = {4},
}

@article{luz_isotopic_2011,
	title = {The isotopic composition of atmospheric oxygen},
	volume = {25},
	issn = {1944-9224},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2010GB003883},
	doi = {10.1029/2010GB003883},
	abstract = {Atmospheric O2 is almost 24‰ more enriched in 18O than seawater, and this enrichment is known as the Dole effect. For a long time it has been accepted that there is no oxygen isotope fractionation in photosynthesis, and thus the Dole effect should be the result of preferential terrestrial and marine respiratory consumption of 16O over 18O, and also several permil enrichment of leaf water from which terrestrial photosynthesis produces 18O enriched O2. This concept has led to the understanding that the record of past Dole effect variations was strongly affected by changes in the ratio of photosynthetic production between land and sea. However, recent studies in our lab have led to two major new observations: (1) O2 produced by certain marine phytoplankton, representing important groups of primary producers, is significantly enriched (up to 6‰) in 18O with respect to the substrate seawater and (2) effective oxygen isotope fractionation in soil respiration is considerably smaller than the intrinsic respiratory fractionation. Here we take these two observations into account and show that the magnitudes of the terrestrial and marine components of the Dole effect are close, and both are close to the measured Dole effect. As a result, the magnitude of the global Dole effect should not be sensitive to past changes in the ratio of land-to-sea photosynthetic rates. Instead of the land-sea control, variations in low-latitude hydrology, and possibly changes of fractionations in the marine biosphere, are more important in regulating the magnitude of the Dole effect and its past variations.},
	language = {en},
	number = {3},
	urldate = {2021-08-17},
	journal = {Global Biogeochemical Cycles},
	author = {Luz, Boaz and Barkan, Eugeni},
	year = {2011},
	note = {\_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2010GB003883},
	keywords = {Dole effect, atmospheric δ18O, dissolved O2 and δ18O, ice cores δ18O, soil air δ18O, δ17O and δ18O in photosynthesis},
}

@article{finlay_controls_2003,
	title = {Controls of streamwater dissolved inorganic carbon dynamics in a forested watershed},
	volume = {62},
	issn = {1573-515X},
	url = {10.1023/A:1021183023963},
	doi = {10.1023/A:1021183023963},
	abstract = {Iinvestigated controls of stream dissolved inorganic carbon (DIC) sources andcycling along a stream size and productivity gradient in a temperate forestedwatershed in northern California. Dissolved CO2 (CO2(aq))dynamics in heavily shaded streams contrasted strongly with those of larger,open canopied sites. In streams with canopy cover {\textgreater} 97\%, CO2 (aq)was highest during baseflow periods (up to 540 μM) and wasnegatively related to discharge. Effects of algal photosynthesis on CO2(aq) were minimal and stream CO2 (aq) was primarily controlledby groundwater CO2 (aq) inputs and degassing losses to theatmosphere. In contrast to the small streams, CO2 (aq) in larger,open-canopied streams was often below atmospheric levels at midday duringbaseflow and was positively related to discharge. Here, stream CO2(aq) was strongly influenced by the balance between autotrophic andheterotrophic processes. Dynamics of HCO3− werelesscomplex. HCO3− and Ca2+ were positivelycorrelated, negatively related to discharge, and showed no pattern with streamsize. Stable carbon isotope ratios of DIC (i.e. δ13C DIC)increased with stream size and discharge, indicating contrasting sources of DICto streams and rivers. During summer baseflows, δ13C DIC were13C-depleted in the smallest streams (minimum of−17.7‰) due to the influence of CO2 (aq) derived frommicrobialrespiration and HCO3− derived from carbonateweathering. δ13C DIC were higher (up to −6.6‰)inthe larger streams and rivers due to invasion of atmospheric CO2enhanced by algal CO2 (aq) uptake. While small streams wereinfluenced by groundwater inputs, patterns in CO2 (aq) and evidencefrom stable isotopes demonstrate the strong influence of stream metabolism andCO2 exchange with the atmosphere on stream and river carbon cycles.},
	language = {en},
	number = {3},
	urldate = {2021-08-17},
	journal = {Biogeochemistry},
	author = {Finlay, Jacques C.},
	month = mar,
	year = {2003},
	pages = {231--252},
}

@article{zeng_controls_2011,
	title = {Controls on the origin and cycling of riverine dissolved inorganic carbon in the {Brazos} {River}, {Texas}},
	volume = {104},
	issn = {1573-515X},
	url = {10.1007/s10533-010-9501-y},
	doi = {10.1007/s10533-010-9501-y},
	abstract = {Rivers draining watersheds that include carbonate bedrock or organic matter (OM)-rich sedimentary rocks frequently have 14C-depleted dissolved inorganic carbon (DIC) relative to rivers draining carbonate- and OM-free watersheds, due to dissolution of carbonate and/or decomposition of ancient OM. However, our results from a subtropical river, the Brazos River in Texas, USA, show that in this watershed human activities appear to dominate basin lithology in controlling the origin and metabolism of DIC. The middle Brazos flows through limestone and coal-bearing bedrock, but DIC isotope data suggest no limestone dissolution or respiration of ancient OM, and instead reflect efficient air–water CO2 exchange, degradation of relatively young OM and photosynthesis in the river as a result of river damming and urban treated wastewater input. The lower Brazos drains only small areas of carbonate and coal-bearing bedrock, but DIC isotope data suggest the strong influence of carbonate dissolution, with a potentially minor contribution from decomposition of old soil organic matter (SOM). Oyster shells and crushed carbonate minerals used in road construction are likely sources of carbonate in the lower Brazos, in addition to natural marl and pedogenic carbonate. Additionally, the generally low pCO2 and high DIC concentration in the Brazos River lead to a low CO2 outgassing:DIC export ratio, distinguishing the Brazos River from other rivers.},
	language = {en},
	number = {1},
	urldate = {2021-08-17},
	journal = {Biogeochemistry},
	author = {Zeng, Fan-Wei and Masiello, Caroline A. and Hockaday, William C.},
	month = jul,
	year = {2011},
	pages = {275--291},
}

@article{herczeg_stable_1987,
	title = {A stable carbon isotope study of dissolved inorganic carbon cycling in a softwater lake},
	volume = {4},
	issn = {1573-515X},
	url = {10.1007/BF02187369},
	doi = {10.1007/BF02187369},
	abstract = {The dissolved inorganic carbon (DIC) cycle in a softwater lake was studied using natural variations of the stable isotopes of carbon,12C and13C. During summer stratification there was a progressive decrease in epilimnion DIC concentration with a concomitant increase in δ13CDIC), due to preferential uptake of12C by phytoplankton and a change in the dominant CO2 source from inflow andin situ oxidation to invasion from the atmosphere. There was an increase in hypolimnion DIC concentration throughout summer with a concomitant general decrease in δ13CDIC from oxidation of the isotopically light particulate organic carbon that sank down through the thermocline from the epilimnion.},
	language = {en},
	number = {3},
	urldate = {2021-08-17},
	journal = {Biogeochemistry},
	author = {Herczeg, Andrew L.},
	month = oct,
	year = {1987},
	pages = {231--263},
}

@article{campeau_multiple_2017,
	title = {Multiple sources and sinks of dissolved inorganic carbon across {Swedish} streams, refocusing the lens of stable {C} isotopes},
	volume = {7},
	copyright = {2017 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-017-09049-9},
	doi = {10.1038/s41598-017-09049-9},
	abstract = {It is well established that stream dissolved inorganic carbon (DIC) fluxes play a central role in the global C cycle, yet the sources of stream DIC remain to a large extent unresolved. Here, we explore large-scale patterns in δ13C-DIC from streams across Sweden to separate and further quantify the sources and sinks of stream DIC. We found that stream DIC is governed by a variety of sources and sinks including biogenic and geogenic sources, CO2 evasion, as well as in-stream processes. Although soil respiration was the main source of DIC across all streams, a geogenic DIC influence was identified in the northernmost region. All streams were affected by various degrees of atmospheric CO2 evasion, but residual variance in δ13C-DIC also indicated a significant influence of in-stream metabolism and anaerobic processes. Due to those multiple sources and sinks, we emphasize that simply quantifying aquatic DIC fluxes will not be sufficient to characterise their role in the global C cycle.},
	language = {en},
	number = {1},
	urldate = {2021-08-17},
	journal = {Scientific Reports},
	author = {Campeau, Audrey and Wallin, Marcus B. and Giesler, Reiner and Löfgren, Stefan and Mörth, Carl-Magnus and Schiff, Sherry and Venkiteswaran, Jason J. and Bishop, Kevin},
	month = aug,
	year = {2017},
	note = {Bandiera\_abtest: a
Cc\_license\_type: cc\_by
Cg\_type: Nature Research Journals
Number: 1
Primary\_atype: Research
Publisher: Nature Publishing Group
Subject\_term: Carbon cycle;Geochemistry
Subject\_term\_id: carbon-cycle;geochemistry},
	pages = {9158},
}

@article{dupuis_bayesian_2007,
	title = {A {Bayesian} {Approach} to the {Multistate} {Jolly}–{Seber} {Capture}–{Recapture} {Model}},
	volume = {63},
	issn = {1541-0420},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/j.1541-0420.2007.00815.x},
	doi = {10.1111/j.1541-0420.2007.00815.x},
	abstract = {This article considers a Bayesian approach to the multistate extension of the Jolly–Seber model commonly used to estimate population abundance in capture–recapture studies. It extends the work of George and Robert (1992, Biometrika79, 677–683), which dealt with the Bayesian estimation of a closed population with only a single state for all animals. A super-population is introduced to model new entrants in the population. Bayesian estimates of abundance are obtained by implementing a Gibbs sampling algorithm based on data augmentation of the missing data in the capture histories when the state of the animal is unknown. Moreover, a partitioning of the missing data is adopted to ensure the convergence of the Gibbs sampling algorithm even in the presence of impossible transitions between some states. Lastly, we apply our methodology to a population of fish to estimate abundance and movement.},
	language = {en},
	number = {4},
	urldate = {2021-08-17},
	journal = {Biometrics},
	author = {Dupuis, Jerome A. and Schwarz, Carl James},
	year = {2007},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1541-0420.2007.00815.x},
	keywords = {Abundance, Bayesian estimates, Capture–recapture, Missing data, Multistate model, Stratified Jolly–Seber model},
	pages = {1015--1022},
}

@article{mcclintock_bridging_2017,
	title = {Bridging the gaps in animal movement: hidden behaviors and ecological relationships revealed by integrated data streams},
	volume = {8},
	issn = {2150-8925},
	shorttitle = {Bridging the gaps in animal movement},
	url = {http://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecs2.1751},
	doi = {10.1002/ecs2.1751},
	abstract = {Inferences about animal behavior from movement models typically rely solely on location data, but auxiliary biotelemetry and environmental data are powerful and readily available resources for incorporating much more behavioral realism. Integrating multiple data streams can not only reveal hidden behaviors and ecological relationships that would otherwise be difficult or impossible to infer from location data alone, but also facilitate more realistic path reconstruction that respects important ecological features while bridging the information gaps that commonly arise due to measurement error or missing data. Using the bearded seal (Erignathus barbatus), a benthic predator associated with Arctic sea ice, we demonstrate how integrating location, dive activity, land cover, bathymetry, and sea ice data in a unified modeling framework allowed us to identify novel behavior states, such as hauling out on seasonal sea ice and those associated with competing foraging strategies (i.e., benthic vs. mid-water prey). By utilizing multiple data streams, ecologists can move beyond conventional two-state models (“foraging” and “transit”) and address more interesting hypotheses about activity budgets, resource selection, and many other areas of movement and behavioral ecology. The generality of our approach provides broad applicability to marine and terrestrial species, as well as many types of biotelemetry and environmental data.},
	language = {en},
	number = {3},
	urldate = {2021-08-17},
	journal = {Ecosphere},
	author = {McClintock, Brett T. and London, Joshua M. and Cameron, Michael F. and Boveng, Peter L.},
	year = {2017},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ecs2.1751},
	keywords = {animal location data, bearded seal, hidden Markov, switching behavior, telemetry},
	pages = {e01751},
}

@article{dupuis_bayesian_2007-1,
	title = {A {Bayesian} {Approach} to the {Multistate} {Jolly}–{Seber} {Capture}–{Recapture} {Model}},
	volume = {63},
	issn = {1541-0420},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/j.1541-0420.2007.00815.x},
	doi = {10.1111/j.1541-0420.2007.00815.x},
	abstract = {This article considers a Bayesian approach to the multistate extension of the Jolly–Seber model commonly used to estimate population abundance in capture–recapture studies. It extends the work of George and Robert (1992, Biometrika79, 677–683), which dealt with the Bayesian estimation of a closed population with only a single state for all animals. A super-population is introduced to model new entrants in the population. Bayesian estimates of abundance are obtained by implementing a Gibbs sampling algorithm based on data augmentation of the missing data in the capture histories when the state of the animal is unknown. Moreover, a partitioning of the missing data is adopted to ensure the convergence of the Gibbs sampling algorithm even in the presence of impossible transitions between some states. Lastly, we apply our methodology to a population of fish to estimate abundance and movement.},
	language = {en},
	number = {4},
	urldate = {2021-08-17},
	journal = {Biometrics},
	author = {Dupuis, Jerome A. and Schwarz, Carl James},
	year = {2007},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1541-0420.2007.00815.x},
	keywords = {Abundance, Bayesian estimates, Capture–recapture, Missing data, Multistate model, Stratified Jolly–Seber model},
	pages = {1015--1022},
}

@article{clark_hierarchical_2005,
	title = {Hierarchical {Bayes} for {Structured}, {Variable} {Populations}: {From} {Recapture} {Data} to {Life}-{History} {Prediction}},
	volume = {86},
	issn = {1939-9170},
	shorttitle = {Hierarchical {Bayes} for {Structured}, {Variable} {Populations}},
	url = {http://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/04-1348},
	doi = {10.1890/04-1348},
	abstract = {Understanding population dynamics requires models that admit the complexity of natural populations and the data ecologists obtain from them. Populations possess structure, which may be defined as “fixed” stages through which individuals pass, with superimposed variability among individuals and groups. Data contain missing values and inaccurate censuses. From limited data ecologists attempt to predict life history schedules and population growth. We extend the “missing value” framework for Bayesian analysis of structured populations to admit the heterogeneity in demography and the limitations of data that are typical of ecological populations. Our hierarchical treatment of capture–recapture data allows inference on demographic rates contained in matrix transition models for populations that may be stratified by location and by other variables. Simulations with artificial data sets demonstrate the ability of the Bayesian model to successfully estimate underlying parameters, even with incomplete census data. In contrast, traditional nonhierarchical models may lead to biased parameter estimates because of variation in recapture rates of individuals. Analyses of published demographic data on Common Terns and Taitu Hills rats illustrate the utility of the model. Predictive distributions of maturation age, survivorship, and population growth demonstrate profound impacts of population and data complexity.},
	language = {en},
	number = {8},
	urldate = {2021-08-17},
	journal = {Ecology},
	author = {Clark, James S. and Ferraz, Gonçalo and Oguge, Nick and Hays, Helen and DiCostanzo, Joseph},
	year = {2005},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1890/04-1348},
	keywords = {Markov chain Monte Carlo, capture–recapture data, matrix population models, population viability analysis, random effects, stratification, terns and rats},
	pages = {2232--2244},
}

@article{colchero_bayesian_2012,
	title = {Bayesian inference on age-specific survival for censored and truncated data},
	volume = {81},
	issn = {1365-2656},
	url = {http://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2656.2011.01898.x},
	doi = {10.1111/j.1365-2656.2011.01898.x},
	abstract = {1. Traditional estimation of age-specific survival and mortality rates in vertebrates is limited to individuals with known age. Although this subject has been studied extensively using effective capture–recapture and capture–recovery models, inference remains challenging because of large numbers of incomplete records (i.e. unknown age of many individuals) and because of the inadequate duration of the studies. 2. Here, we present a hierarchical model for capture–recapture/recovery (CRR) data sets with large proportions of unknown times of birth and death. The model uses a Bayesian framework to draw inference on population-level age-specific demographic rates using parametric survival functions and applies this information to reconstruct times of birth and death for individuals with unknown age. 3. We simulated a set of CRR data sets with varying study span and proportions of individuals with known age, and varying recapture and recovery probabilities. We used these data sets to compare our method to a traditional CRR model, which requires knowledge of individual ages. Subsequently, we applied our method to a subset of a long-term CRR data set on Soay sheep. 4. Our results show that this method performs better than the common CRR model when sample sizes are low. Still, our model is sensitive to the choice of priors with low recapture probability and short studies. In such cases, priors that overestimate survival perform better than those that underestimate it. Also, the model was able to estimate accurately ages at death for Soay sheep, with an average error of 0·94 years and to identify differences in mortality rate between sexes. 5. Although many of the problems in the estimation of age-specific survival can be reduced through more efficient sampling schemes, most ecological data sets are still sparse and with a large proportion of missing records. Thus, improved sampling needs still to be combined with statistical models capable of overcoming the unavoidable limitations of any fieldwork. We show that our approach provides reliable estimates of parameters and unknown times of birth and death even with the most incomplete data sets while being flexible enough to accommodate multiple recapture probabilities and covariates.},
	language = {en},
	number = {1},
	urldate = {2021-08-17},
	journal = {Journal of Animal Ecology},
	author = {Colchero, Fernando and Clark, James S.},
	year = {2012},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2656.2011.01898.x},
	keywords = {Bayesian inference, age-specific survival, capture–recapture/recovery data, maximum likelihood},
	pages = {139--149},
}

@article{dupuis_bayesian_1995,
	title = {Bayesian {Estimation} of {Movement} and {Survival} {Probabilities} from {Capture}- {Recapture} {Data}},
	volume = {82},
	issn = {0006-3444},
	url = {https://www.jstor.org.weblib.lib.umt.edu:8080/stable/2337343},
	doi = {10.2307/2337343},
	abstract = {The Arnason--Schwarz model is usually used for estimating survival and movement probabilities of animal populations from capture-recapture data. The missing data structure of this capture-recapture model is exhibited and summarised via a directed graph representation. Taking advantage of this structure we implement a Gibbs sampling algorithm from which Bayesian estimates and credible intervals for survival and movement probabilities are derived. Convergence of the algorithm is proved using a duality principle. We illustrate our approach through a real example.},
	number = {4},
	urldate = {2021-08-17},
	journal = {Biometrika},
	author = {Dupuis, Jerome A.},
	year = {1995},
	note = {Publisher: [Oxford University Press, Biometrika Trust]},
	pages = {761--772},
}

@article{ellington_using_2015,
	title = {Using multiple imputation to estimate missing data in meta-regression},
	volume = {6},
	issn = {2041-210X},
	doi = {10.1111/2041-210X.12322},
	abstract = {There is a growing need for scientific synthesis in ecology and evolution. In many cases, meta-analytic techniques can be used to complement such synthesis. However, missing data are a serious problem for any synthetic efforts and can compromise the integrity of meta-analyses in these and other disciplines. Currently, the prevalence of missing data in meta-analytic data sets in ecology and the efficacy of different remedies for this problem have not been adequately quantified. We generated meta-analytic data sets based on literature reviews of experimental and observational data and found that missing data were prevalent in meta-analytic ecological data sets. We then tested the performance of complete case removal (a widely used method when data are missing) and multiple imputation (an alternative method for data recovery) and assessed model bias, precision and multimodel rankings under a variety of simulated conditions using published meta-regression data sets. We found that complete case removal led to biased and imprecise coefficient estimates and yielded poorly specified models. In contrast, multiple imputation provided unbiased parameter estimates with only a small loss in precision. The performance of multiple imputation, however, was dependent on the type of data missing. It performed best when missing values were weighting variables, but performance was mixed when missing values were predictor variables. Multiple imputation performed poorly when imputing raw data which were then used to calculate effect size and the weighting variable. We conclude that complete case removal should not be used in meta-regression and that multiple imputation has the potential to be an indispensable tool for meta-regression in ecology and evolution. However, we recommend that users assess the performance of multiple imputation by simulating missing data on a subset of their data before implementing it to recover actual missing data.},
	language = {en},
	number = {2},
	urldate = {2021-08-17},
	journal = {Methods in Ecology and Evolution},
	author = {Ellington, E. Hance and Bastille-Rousseau, Guillaume and Austin, Cayla and Landolt, Kristen N. and Pond, Bruce A. and Rees, Erin E. and Robar, Nicholas and Murray, Dennis L.},
	year = {2015},
	keywords = {complete case removal, ecological synthesis, meta-analysis, meta-regression, missing data, model selection, multiple imputation, partial data},
	pages = {153--163},
}

@article{penone_imputation_2014,
	title = {Imputation of missing data in life-history trait datasets: which approach performs the best?},
	volume = {5},
	issn = {2041-210X},
	shorttitle = {Imputation of missing data in life-history trait datasets},
	url = {http://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.12232},
	doi = {10.1111/2041-210X.12232},
	abstract = {Despite efforts in data collection, missing values are commonplace in life-history trait databases. Because these values typically are not missing randomly, the common practice of removing missing data not only reduces sample size, but also introduces bias that can lead to incorrect conclusions. Imputing missing values is a potential solution to this problem. Here, we evaluate the performance of four approaches for estimating missing values in trait databases (K-nearest neighbour (kNN), multivariate imputation by chained equations (mice), missForest and Phylopars), and test whether imputed datasets retain underlying allometric relationships among traits. Starting with a nearly complete trait dataset on the mammalian order Carnivora (using four traits), we artificially removed values so that the percent of missing values ranged from 10\% to 80\%. Using the original values as a reference, we assessed imputation performance using normalized root mean squared error. We also evaluated whether including phylogenetic information improved imputation performance in kNN, mice, and missForest (it is a required input in Phylopars). Finally, we evaluated the extent to which the allometric relationship between two traits (body mass and longevity) was conserved for imputed datasets by looking at the difference (bias) between the slope of the original and the imputed datasets or datasets with missing values removed. Three of the tested approaches (mice, missForest and Phylopars), resulted in qualitatively equivalent imputation performance, and all had significantly lower errors than kNN. Adding phylogenetic information into the imputation algorithms improved estimation of missing values for all tested traits. The allometric relationship between body mass and longevity was conserved when up to 60\% of data were missing, either with or without phylogenetic information, depending on the approach. This relationship was less biased in imputed datasets compared to datasets with missing values removed, especially when more than 30\% of values were missing. Imputations provide valuable alternatives to removing missing observations in trait databases as they produce low errors and retain relationships among traits. Although we must continue to prioritize data collection on species traits, imputations can provide a valuable solution for conducting macroecological and evolutionary studies using life-history trait databases.},
	language = {en},
	number = {9},
	urldate = {2021-08-17},
	journal = {Methods in Ecology and Evolution},
	author = {Penone, Caterina and Davidson, Ana D. and Shoemaker, Kevin T. and Marco, Moreno Di and Rondinini, Carlo and Brooks, Thomas M. and Young, Bruce E. and Graham, Catherine H. and Costa, Gabriel C.},
	year = {2014},
	keywords = {Phylopars, body mass, carnivores, kNN, longevity, missForest, multivariate imputation by chained equations, phylogeny, root mean squared error},
	pages = {961--970},
}

@article{johnson_handling_2021,
	title = {Handling missing values in trait data},
	volume = {30},
	issn = {1466-8238},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/geb.13185},
	doi = {10.1111/geb.13185},
	abstract = {Aim Trait data are widely used in ecological and evolutionary phylogenetic comparative studies, but often values are not available for all species of interest. Traditionally, researchers have excluded species without data from analyses, but estimation of missing values using imputation has been proposed as a better approach. However, imputation methods have largely been designed for randomly missing data, whereas trait data are often not missing at random (e.g., more data for bigger species). Here, we evaluate the performance of approaches for handling missing values when considering biased datasets. Location Any. Time period Any. Major taxa studied Any. Methods We simulated continuous traits and separate response variables to test the performance of nine imputation methods and complete-case analysis (excluding missing values from the dataset) under biased missing data scenarios. We characterized performance by estimating the error in imputed trait values (deviation from the true value) and inferred trait–response relationships (deviation from the true relationship between a trait and response). Results Generally, Rphylopars imputation produced the most accurate estimate of missing values and best preserved the response–trait slope. However, estimates of missing data were still inaccurate, even with only 5\% of values missing. Under severe biases, errors were high with every approach. Imputation was not always the best option, with complete-case analysis frequently outperforming Mice imputation and, to a lesser degree, BHPMF imputation. Mice, a popular approach, performed poorly when the response variable was excluded from the imputation model. Main conclusions Imputation can handle missing data effectively in some conditions but is not always the best solution. None of the methods we tested could deal effectively with severe biases, which can be common in trait datasets. We recommend rigorous data checking for biases before and after imputation and propose variables that can assist researchers working with incomplete datasets to detect data biases and minimize errors.},
	language = {en},
	number = {1},
	urldate = {2021-08-17},
	journal = {Global Ecology and Biogeography},
	author = {Johnson, Thomas F. and Isaac, Nick J. B. and Paviolo, Agustin and González-Suárez, Manuela},
	year = {2021},
	keywords = {BHPMF, MAR, MCAR, MNAR, Rphylopars, functional trait, imputation, life-history trait, missing data, multiple imputation chained equations},
	pages = {51--62},
}

@article{padilla_space-time_2020,
	title = {Space-time autoregressive estimation and prediction with missing data based on {Kalman} filtering},
	volume = {31},
	issn = {1099-095X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/env.2627},
	doi = {10.1002/env.2627},
	abstract = {We propose a Kalman filter algorithm to provide a formal statistical analysis of space-time data with an autoregressive structure in time. The Kalman filter technique allows to capture the temporal dependence as well as the spatial correlation structure through state-space equations, and it is aimed to perform statistical inference in terms of parameter estimation and prediction at unobserved locations. We thus develop space-time estimation and prediction methods in the presence of missing data, through the Kalman filter, in order to obtain accurate estimates of model parameters and reliable space-time predictions. Our findings are illustrated through an application on daily air temperatures in some regions of southern Chile, where the dataset shows a number of missing data in many locations.},
	language = {en},
	number = {7},
	urldate = {2021-08-12},
	journal = {Environmetrics},
	author = {Padilla, Leonardo and Lagos-Álvarez, Bernado and Mateu, Jorge and Porcu, Emilio},
	year = {2020},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/env.2627},
	keywords = {autoregressive space-time model, general expectation-maximization algorithm, maximum likelihood, missing data, state-space system},
	pages = {e2627},
}

@article{borcard_partialling_1992,
	title = {Partialling out the {Spatial} {Component} of {Ecological} {Variation}},
	volume = {73},
	issn = {1939-9170},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.2307/1940179},
	doi = {10.2307/1940179},
	abstract = {A method is proposed to partition the variation of species abundance data into independent components: pure spatial, pure environmental, spatial component of environmental influence, and undetermined. The new method uses pre—existing techniques and computer programs of canonical ordination. The intrinsic spatial component of community structure is partialled out of the species—environment relationship in order to see if the environmental control model still holds. The method is illustrated using oribatid mites in a peat blanket, forest vegetation data, and aquatic heterotrophic bacteria. In this latter example, the new method is shown to be complementary to another approach based on partial Mantel tests.},
	language = {en},
	number = {3},
	urldate = {2021-08-12},
	journal = {Ecology},
	author = {Borcard, Daniel and Legendre, Pierre and Drapeau, Pierre},
	year = {1992},
	note = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.2307/1940179},
	pages = {1045--1055},
}

@article{dale_spatial_2002,
	title = {Spatial autocorrelation and statistical tests in ecology},
	volume = {9},
	issn = {1195-6860},
	url = {10.1080/11956860.2002.11682702},
	doi = {10.1080/11956860.2002.11682702},
	abstract = {The presence of positive spatial autocorrelation in ecological data causes parametric statistical tests to give more apparently significant results than the data justify, which is a serious problem for both statistical and ecological interpretation. In this paper, we review this problem and some of the statistical approaches that have been used to address it, concentrating on statistical methods rather than on sampling or experimental design. We then describe in more detail the technique of adjusting the “effective sample size” based on the autocorrelation structure of the data. Unfortunately, the effective sample size cannot be reliably estimated from the data, and therefore this approach may not be a general solution to the problem. An alternative approach is to determine a parametric model of the data and its spatial autocorrelation structure, and then to use a Monte Carlo approach to generate the distribution of the test statistic of interest using that model. We suggest that this latter approach should be used in situations in which no robust analytically derived solution is available.},
	number = {2},
	urldate = {2021-08-12},
	journal = {Écoscience},
	author = {Dale, Mark R.T. and Fortin, Marie-Josée},
	month = jan,
	year = {2002},
	note = {Publisher: Taylor \& Francis
\_eprint: 10.1080/11956860.2002.11682702},
	keywords = {Effective sample size, Monte Carlo methods, Méthodes de Monte Carlo, Permutation avec contraintes, Restricted randomization, Sous-échantillonnage, Subsampling, Taille utile de l’échantillon},
	pages = {162--167},
}

@article{fieberg_understanding_2012,
	title = {Understanding the causes and consequences of animal movement: a cautionary note on fitting and interpreting regression models with time-dependent covariates},
	volume = {3},
	issn = {2041-210X},
	shorttitle = {Understanding the causes and consequences of animal movement},
	url = {https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/j.2041-210X.2012.00239.x},
	doi = {10.1111/j.2041-210X.2012.00239.x},
	abstract = {New technologies have made it possible to simultaneously, and remotely, collect time series of animal location data along with indicators of individuals' physiological condition. These data, along with animal movement models that incorporate individual physiological and behavioural states, promise to offer new insights into determinants of animal behaviour. Care must be taken, however, when attempting to infer causal relationships from biotelemetry data. The possibility of unmeasured confounders, responsible for driving both physiological measurements and animal movement, must be considered. Further, response values may be predictive of future covariate values . When this occurs, the covariate process is said to be endogenous with respect to the response variable, which has implications for both choosing statistical estimation targets and also estimators of these quantities. We explore models that attempt to relate = log(daily movement rate) to = log(average daily heart rate) using data collected from a black bear (Ursus americanus) population in Minnesota. The regression parameter for was 0·19 and statistically different from 0 (P {\textless} 0·001) when daily measurements were assumed to be independent, but residuals were highly autocorrelated. Assuming an autoregressive model (ar(1)) for the residuals, however, resulted in a negative slope estimate (-0·001) that was not statistically different from 0. The sensitivity of regression parameters to the assumed error structure can be explained by exploring relationships between lagged and current values of x and y and between parameters in the independence and ar(1) models. We hypothesize that an unmeasured confounder may be responsible for the behaviour of the regression parameters. In addition, measurement error associated with daily movement rates may also play a role. Similar issues often arise in epidemiological, biostatistical and econometrics applications; directed acyclical graphs, representing causal pathways, are central to understanding potential problems (and their solutions) associated with modelling time-dependent covariates. In addition, we suggest that incorporating lagged responses and lagged predictors as covariates may prove useful for diagnosing when and explaining why some conclusions are sensitive to model assumptions.},
	language = {en},
	number = {6},
	urldate = {2021-08-12},
	journal = {Methods in Ecology and Evolution},
	author = {Fieberg, J. and Ditmer, M.},
	year = {2012},
	note = {\_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/j.2041-210X.2012.00239.x},
	keywords = {arima, autocorrelation, black bear, causal inference, distributed lag, endogeneity, heart rate, temporal confounding, time series},
	pages = {983--991},
}

@article{hefley_basis_2017,
	title = {The basis function approach for modeling autocorrelation in ecological data},
	volume = {98},
	issn = {1939-9170},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecy.1674},
	doi = {10.1002/ecy.1674},
	abstract = {Analyzing ecological data often requires modeling the autocorrelation created by spatial and temporal processes. Many seemingly disparate statistical methods used to account for autocorrelation can be expressed as regression models that include basis functions. Basis functions also enable ecologists to modify a wide range of existing ecological models in order to account for autocorrelation, which can improve inference and predictive accuracy. Furthermore, understanding the properties of basis functions is essential for evaluating the fit of spatial or time-series models, detecting a hidden form of collinearity, and analyzing large data sets. We present important concepts and properties related to basis functions and illustrate several tools and techniques ecologists can use when modeling autocorrelation in ecological data.},
	language = {en},
	number = {3},
	urldate = {2021-08-12},
	journal = {Ecology},
	author = {Hefley, Trevor J. and Broms, Kristin M. and Brost, Brian M. and Buderman, Frances E. and Kay, Shannon L. and Scharf, Henry R. and Tipton, John R. and Williams, Perry J. and Hooten, Mevin B.},
	year = {2017},
	note = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.1674},
	keywords = {Bayesian model, autocorrelation, collinearity, dimension reduction, semiparametric regression, spatial statistics, time series},
	pages = {632--646},
}

@article{lichstein_spatial_2002,
	title = {Spatial {Autocorrelation} and {Autoregressive} {Models} in {Ecology}},
	volume = {72},
	issn = {1557-7015},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/0012-9615%282002%29072%5B0445%3ASAAAMI%5D2.0.CO%3B2},
	doi = {10.1890/0012-9615(2002)072[0445:SAAAMI]2.0.CO;2},
	abstract = {Recognition and analysis of spatial autocorrelation has defined a new paradigm in ecology. Attention to spatial pattern can lead to insights that would have been otherwise overlooked, while ignoring space may lead to false conclusions about ecological relationships. We used Gaussian spatial autoregressive models, fit with widely available software, to examine breeding habitat relationships for three common Neotropical migrant songbirds in the southern Appalachian Mountains of North Carolina and Tennessee, USA. In preliminary models that ignored space, the abundance of all three species was correlated with both local- and landscape-scale habitat variables. These models were then modified to account for broadscale spatial trend (via trend surface analysis) and fine-scale autocorrelation (via an autoregressive spatial covariance matrix). Residuals from ordinary least squares regression models were autocorrelated, indicating that the assumption of independent errors was violated. In contrast, residuals from autoregressive models showed little spatial pattern, suggesting that these models were appropriate. The magnitude of habitat effects tended to decrease, and the relative importance of different habitat variables shifted when we incorporated broadscale and then fine-scale space into the analysis. The degree to which habitat effects changed when space was added to the models was roughly correlated with the amount of spatial structure in the habitat variables. Spatial pattern in the residuals from ordinary least squares models may result from failure to include or adequately measure autocorrelated habitat variables. In addition, contagious processes, such as conspecific attraction, may generate spatial patterns in species abundance that cannot be explained by habitat models. For our study species, spatial patterns in the ordinary least squares residuals suggest that a scale of 500–1000 m would be appropriate for investigating possible contagious processes.},
	language = {en},
	number = {3},
	urldate = {2021-08-12},
	journal = {Ecological Monographs},
	author = {Lichstein, Jeremy W. and Simons, Theodore R. and Shriner, Susan A. and Franzreb, Kathleen E.},
	year = {2002},
	note = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1890/0012-9615\%282002\%29072\%5B0445\%3ASAAAMI\%5D2.0.CO\%3B2},
	keywords = {CAR model, Moran's I, Neotropical migrant songbirds, habitat model, landscape effects, spatial autocorrelation, spatial autoregressive model, trend surface analysis},
	pages = {445--463},
}

@article{zhang_carbon_nodate,
	title = {Carbon isotope fractionation during gas-water exchange and dissolution of {CO},},
	abstract = {The kinetic and equilibrium fractionation effects for 13C during CO* gas transfer ( ck and c{\textasciitilde}\_{\textasciitilde}) have been measured in acidified distilled water. The equilibrium fractionation effects between bicarbonate and carbonate and gaseous COP (+c03mp and cCOJ\_)\$ have been measured in NaHC03 and NaHCOj + Na2C03 solutions, respectively, from 5” to 25°C. The measured fractionations, except cC03\_g,agreed with earlier work to within 0.2\%0. cco,\_\%was about 2\%0 smaller than most values previously reported. The temperature dependence of the fractionation for 13Cbetween bicarbonate and carbonate and gaseous CO* was found to be cHC03\_g= -(0.141 ? O.O03)T(“C) + (10.78 ? 0.05)\%0 and cc09-g = -(0.052 -C O.O3)T(“C) + (7.22 4 0.46)\%0, respectively. The fractionation during gas dissolution was E{\textasciitilde}-{\textasciitilde} = - (0.0049 2 O.O03)T(“C) - ( 1.31 + 0.06)\%0 and the kinetic effect during gas transfer, ckr was -0.81 ? 0.16\%0 at 21°C and -0.95 2 0.20\%0 at 5°C. The equilibrium fractionation between total DIC in seawater and CO2 in air ( cD’ccg)was measured and compared with that calculated from the concentration of aqueous COz, HCO;, and CO; and individual fractionations between the three C species and CO2 gas. The measured and calculated results showed a significant difference of up to 0.2\%0. We hypothesize that carbonate ion complexes likely complicate the calculation of cDlcg from individual C species. We obtain the following empirical function of to’c\_\%in seawater vs. temperature and the carbonate fraction (fco,), cu’c-g = (0.014 + 0.01 )Tfco, - (0.105 -C 0.002)T + (10.53 ? 0.05)\%0, when 0.05 {\textless} fco, {\textless} 0.20 and 5°C {\textless} T {\textless} 25°C.},
	language = {en},
	author = {Zhang, J and Quay, P D},
	pages = {8},
}

@article{porter_new_2009,
	title = {New {Eyes} on the {World}: {Advanced} {Sensors} for {Ecology}},
	volume = {59},
	issn = {0006-3568},
	shorttitle = {New {Eyes} on the {World}},
	url = {10.1525/bio.2009.59.5.6},
	doi = {10.1525/bio.2009.59.5.6},
	abstract = {Innovative uses of advanced sensors and sensor networks are starting to be translated into new ecological knowledge. These sensors are providing a new set of “eyes” through which researchers may observe the world in new ways, extend spatial and temporal scales of observation, more accurately estimate what cannot be observed, and, most important, obtain unexpected results or develop new paradigms. Automated sensors are widely deployed by members of the Organization of Biological Field Stations, yet some needs—particularly for chemical and biological sensors—are not currently being met. There are additional opportunities for developing sensor networks at synoptic, regional, continental, and global scales. Although we are seeing more uses of sensor systems and, in particular, sensor networks, the opportunities for these systems are just beginning to be realized, with much more work to be done, including formulation of new questions, development of new sensors, better software, and new ways for researchers to work together across large distances.},
	number = {5},
	urldate = {2021-08-09},
	journal = {BioScience},
	author = {Porter, John H. and Nagy, Eric and Kratz, Timothy K. and Hanson, Paul and Collins, Scott L. and Arzberger, Peter},
	month = may,
	year = {2009},
	pages = {385--397},
}

@article{koschorreck_technical_2021,
	title = {Technical note: {CO}$_{\textrm{2}}$ is not like {CH}$_{\textrm{4}}$ – limits of and corrections to the headspace method to analyse \textit{p}{CO}$_{\textrm{2}}$ in fresh water},
	volume = {18},
	issn = {1726-4170},
	shorttitle = {Technical note},
	url = {https://bg.copernicus.org/articles/18/1619/2021/},
	doi = {10.5194/bg-18-1619-2021},
	abstract = {{\textless}p{\textgreater}{\textless}strong class="journal-contentHeaderColor"{\textgreater}Abstract.{\textless}/strong{\textgreater} Headspace analysis of CO{\textless}span class="inline-formula"{\textgreater}$_{\textrm{2}}${\textless}/span{\textgreater} frequently has been used to quantify the concentration of CO{\textless}span class="inline-formula"{\textgreater}$_{\textrm{2}}${\textless}/span{\textgreater} in fresh water. According to basic chemical theory, not considering chemical equilibration of the carbonate system in the sample vials will result in a systematic error. By analysing the potential error for different types of water and experimental conditions, we show that the error incurred by headspace analysis of CO{\textless}span class="inline-formula"{\textgreater}$_{\textrm{2}}${\textless}/span{\textgreater} is less than 5 \% for typical samples from boreal systems which have low alkalinity ({\textless}span class="inline-formula"{\textgreater}\<{\textless}/span{\textgreater} 900 {\textless}span class="inline-formula"{\textgreater}µ{\textless}/span{\textgreater}mol L{\textless}span class="inline-formula"{\textgreater}$^{\textrm{−1}}${\textless}/span{\textgreater}), with pH {\textless}span class="inline-formula"{\textgreater}\<{\textless}/span{\textgreater} 7.5, and high {\textless}span class="inline-formula"{\textgreater}\textit{p}{\textless}/span{\textgreater}CO{\textless}span class="inline-formula"{\textgreater}$_{\textrm{2}}${\textless}/span{\textgreater} ({\textless}span class="inline-formula"{\textgreater}\>{\textless}/span{\textgreater} 1000 {\textless}span class="inline-formula"{\textgreater}µ{\textless}/span{\textgreater}atm). However, the simple headspace calculation can lead to high error (up to {\textless}span class="inline-formula"{\textgreater}−{\textless}/span{\textgreater}300 \%) or even impossibly negative values in highly undersaturated samples equilibrated with ambient air, unless the shift in carbonate equilibrium is explicitly considered. The precision of the method can be improved by lowering the headspace ratio and/or the equilibration temperature. We provide a convenient and direct method implemented in an R script or a JMP add-in to correct CO{\textless}span class="inline-formula"{\textgreater}$_{\textrm{2}}${\textless}/span{\textgreater} headspace results using separately measured alkalinity.{\textless}/p{\textgreater}},
	language = {English},
	number = {5},
	urldate = {2021-08-05},
	journal = {Biogeosciences},
	author = {Koschorreck, Matthias and Prairie, Yves T. and Kim, Jihyeon and Marcé, Rafael},
	month = mar,
	year = {2021},
	note = {Publisher: Copernicus GmbH},
	pages = {1619--1627},
}

@article{kaandorp_time_2021,
	title = {Time lags of nitrate, chloride, and tritium in streams assessed by dynamic groundwater flow tracking in a lowland landscape},
	volume = {25},
	issn = {1607-7938},
	url = {https://hess.copernicus.org/articles/25/3691/2021/},
	doi = {10.5194/hess-25-3691-2021},
	abstract = {Abstract. Surface waters are under pressure from diffuse pollution from agricultural activities, and groundwater is known to be a connection between the agricultural fields and streams. This paper is one of the first to calculate long-term in-stream concentrations of tritium, chloride, and nitrate using dynamic groundwater travel time distributions (TTDs) derived from a distributed, transient, 3D groundwater flow model using forward particle tracking. We tested our approach in the Springendalse Beek catchment, a lowland stream in the east of the Netherlands, for which we collected a long time series of chloride and nitrate concentrations (1969–2018). The Netherlands experienced a sharp decrease in concentrations of solutes leaching to groundwater in the 1980s due to legislations on the application of nitrogen to agricultural fields. Stream measurements of chloride and nitrate showed that the corresponding trend reversal in the groundwater-fed stream occurred after a time lag of 5–10 years. By combining calculated TTDs with the known history of nitrogen and chloride inputs, we found that the variable contribution of different groundwater flow paths to stream water quality reasonably explained the majority of long-term and seasonal variation in the measured stream nitrate concentrations. However, combining only TTDs and inputs underestimated the time lag between the peak in nitrogen input and the following trend reversal of nitrate in the stream. This feature was further investigated through an exploration of the model behaviour under different scenarios. A time lag of several years, and up to decades, can occur due to (1) a thick unsaturated zone adding a certain travel time, (2) persistent organic matter with a slow release of N in the unsaturated zone, (3) a long mean travel time (MTT) compared to the rate of the reduction in nitrogen application, (4) areas with a high application of nitrogen (agricultural fields) being located further away from the stream or drainage network, or (5) a higher presence of nitrate attenuating processes close to the stream or drainage network compared to the rest of the catchment. By making the connection between dynamic groundwater travel time distributions and in-stream concentration measurements, we provide a method for validating the travel time approach and make the step towards application in water quality modelling and management.},
	language = {en},
	number = {6},
	urldate = {2021-07-05},
	journal = {Hydrology and Earth System Sciences},
	author = {Kaandorp, Vince P. and Broers, Hans Peter and van der Velde, Ype and Rozemeijer, Joachim and de Louw, Perry G. B.},
	month = jun,
	year = {2021},
	pages = {3691--3711},
}

@techreport{lafon_fire_2017,
	address = {Asheville, NC},
	title = {Fire history of the {Appalachian} region: a review and synthesis},
	shorttitle = {Fire history of the {Appalachian} region},
	url = {https://www.fs.usda.gov/treesearch/pubs/53589},
	abstract = {The importance of fire in shaping Appalachian vegetation has become increasingly apparent over the last 25 years. This period has seen declines in oak (Quercus) and pine (Pinus) forests and other fire-dependent ecosystems, which in the near-exclusion of fire are being replaced by fire-sensitive mesophytic vegetation. These vegetation changes imply that Appalachian vegetation had developed under a history of burning before the fire-exclusion era, a possibility that has motivated investigations of Appalachian fire history using proxy evidence. Here we synthesize those investigations to obtain an up-to-date portrayal of Appalachian fire history. We organize the report by data type, beginning with studies of high-resolution data on recent fires to provide a context for interpreting the lower-resolution proxy data. Each proxy is addressed in a subsequent chapter, beginning with witness trees and continuing to fire-scarred trees, stand age structure, and soil and sediment charcoal. Taken together, these proxies portray frequent burning in the past. Fires had occurred at short intervals (a few years) for centuries before the fire-exclusion era.},
	language = {en},
	number = {SRS-GTR-219},
	urldate = {2021-06-21},
	institution = {U.S. Department of Agriculture, Forest Service, Southern Research Station},
	author = {Lafon, Charles W. and Naito, Adam T. and Grissino-Mayer, Henri D. and Horn, Sally P. and Waldrop, Thomas A.},
	year = {2017},
	doi = {10.2737/SRS-GTR-219},
	pages = {SRS--GTR--219},
}

@article{armatas_importance_nodate,
	title = {The {Importance} of {Water}-{Based} {Ecosystem} {Services} {Derived} from the {Shoshone} {National} {Forest}},
	language = {en},
	author = {Armatas, Christopher Aden},
	pages = {494},
}

@article{armatas_opportunities_2016,
	title = {Opportunities to utilize traditional phenological knowledge to support adaptive management of social-ecological systems vulnerable to changes in climate and fire regimes},
	volume = {21},
	issn = {1708-3087},
	url = {https://www.jstor.org/stable/26270350},
	abstract = {ABSTRACT. The field of adaptive management has been embraced by researchers and managers in the United States as an approach to improve natural resource stewardship in the face of uncertainty and complex environmental problems. Integrating multiple knowledge sources and feedback mechanisms is an important step in this approach. Our objective is to contribute to the limited literature that describes the benefits of better integrating indigenous knowledge (IK) with other sources of knowledge in making adaptive-management decisions. Specifically, we advocate the integration of traditional phenological knowledge (TPK), a subset of IK, and highlight opportunities for this knowledge to support policy and practice of adaptive management with reference to policy and practice of adapting to uncharacteristic fire regimes and climate change in the western United States.},
	number = {1},
	urldate = {2021-06-21},
	journal = {Ecology and Society},
	author = {Armatas, Christopher A. and Venn, Tyron J. and McBride, Brooke B. and Watson, Alan E. and Carver, Steve J.},
	year = {2016},
	note = {Publisher: Resilience Alliance Inc.},
}

@article{feck_response_2004,
	title = {Response of {American} dippers ({Cinclus} mexicanus) to variation in stream water quality},
	volume = {49},
	issn = {1365-2427},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2427.2004.01254.x},
	doi = {10.1111/j.1365-2427.2004.01254.x},
	abstract = {1. Semi-aquatic birds may be sensitive to altered water quality. While avian species are not used in the bioassessment of streams, they may complement the more common use of benthic macroinvertebrates and fish. We estimated the extent to which water quality can predict attributes of the populations of one common semi-aquatic bird, the American dipper (Cinclus mexicanus). 2. First, we estimated dipper presence/absence in relation to water quality as measured by a multimetric assessment index and individual bioassessment metrics. Second, we estimated dipper territory area and reproductive success in response to variation in water quality. We studied the diet, territory area and fecundity of dippers and sampled benthic macroinvertebrates, water chemistry and physical variables at 32 sites with and 17 sites without nesting dippers. 3. Dipper presence was only weakly related to chemical, physical and commonly recorded bioassessment metrics such as per cent Ephemeroptera, Plecoptera and Trichoptera (\%EPT). Dippers were strongly related to the abundance of their common prey, Drunella and Heptageniidae, which are only a small component of the commonly recorded bioassessment metrics. The variances in territory area and reproductive success were weakly predicted by water quality variables. 4. Dipper presence reflected disturbance as measured by their common prey, showing that lower abundance of these stream invertebrates affected this semi-aquatic bird. We suggest dipper presence/absence might be used in multimetric indices of biotic integrity for the bioassessment of streams.},
	language = {en},
	number = {9},
	urldate = {2021-06-21},
	journal = {Freshwater Biology},
	author = {Feck, Jules and Hall, Robert O.},
	year = {2004},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2427.2004.01254.x},
	keywords = {American dippers, benthic macroinvertebrates, bioassessment, sedimentation, terrestrial/aquatic linkages},
	pages = {1123--1137},
}

@article{epanchin_nonnative_2010,
	title = {Nonnative trout impact an alpine-nesting bird by altering aquatic-insect subsidies},
	volume = {91},
	copyright = {© 2010 by the Ecological Society of America},
	issn = {1939-9170},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/09-1974.1},
	doi = {10.1890/09-1974.1},
	abstract = {Adjacent food webs may be linked by cross-boundary subsidies: more-productive donor systems can subsidize consumers in less-productive neighboring recipient systems. Introduced species are known to have direct effects on organisms within invaded communities. However, few studies have addressed the indirect effects of nonnative species in donor systems on organisms in recipient systems. We studied the direct role of introduced trout in altering a lake-derived resource subsidy and their indirect effects in altering a passerine bird's response to that subsidy. We compared the abundance of aquatic insects and foraging Gray-crowned Rosy-Finches (Leucosticte tephrocotis dawsoni, “Rosy-Finch”) at fish-containing vs. fishless lakes in the Sierra Nevada Mountains of California (USA). Introduced trout outcompeted Rosy-Finches for emerging aquatic insects (i.e., mayflies). Fish-containing lakes had 98\% fewer mayflies than did fishless lakes. In lakes without fish, Rosy-Finches showed an aggregative response to emerging aquatic insects with 5.9 times more Rosy-Finches at fishless lakes than at fish-containing lakes. Therefore, the introduction of nonnative fish into the donor system reduced both the magnitude of the resource subsidy and the strength of cross-boundary trophic interactions. Importantly, the timing of the subsidy occurs when Rosy-Finches feed their young. If Rosy-Finches rely on aquatic-insect subsidies to fledge their young, reductions in the subsidy by introduced trout may have decreased Rosy-Finch abundances from historic levels. We recommend that terrestrial recipients of aquatic subsidies be included in conservation and restoration plans for ecosystems with alpine lakes.},
	language = {en},
	number = {8},
	urldate = {2021-06-21},
	journal = {Ecology},
	author = {Epanchin, Peter N. and Knapp, Roland A. and Lawler, Sharon P.},
	year = {2010},
	note = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1890/09-1974.1},
	keywords = {Callibaetis ferrugineus, Oncorhynchus mykiss, Passeriformes, Salvelinus fontinalis, aquatic-insect emergence, aquatic-terrestrial linkages, density-mediated indirect effect, ecosystem boundary, ecosystem subsidy, fish stocking, food web, land–water interface},
	pages = {2406--2415},
}

@article{holtgrieve_coherent_2011,
	title = {A {Coherent} {Signature} of {Anthropogenic} {Nitrogen} {Deposition} to {Remote} {Watersheds} of the {Northern} {Hemisphere}},
	volume = {334},
	copyright = {Copyright © 2011, American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	url = {https://science.sciencemag.org/content/334/6062/1545},
	doi = {10.1126/science.1212267},
	abstract = {{\textless}p{\textgreater}Humans have more than doubled the amount of reactive nitrogen (Nr) added to the biosphere, yet most of what is known about its accumulation and ecological effects is derived from studies of heavily populated regions. Nitrogen (N) stable isotope ratios ($^{\textrm{15}}$N:$^{\textrm{14}}$N) in dated sediments from 25 remote Northern Hemisphere lakes show a coherent signal of an isotopically distinct source of N to ecosystems beginning in 1895 ± 10 years (±1 standard deviation). Initial shifts in N isotope composition recorded in lake sediments coincide with anthropogenic CO$_{\textrm{2}}$ emissions but accelerate with widespread industrial Nr production during the past half century. Although current atmospheric Nr deposition rates in remote regions are relatively low, anthropogenic N has probably influenced watershed N budgets across the Northern Hemisphere for over a century.{\textless}/p{\textgreater}},
	language = {en},
	number = {6062},
	urldate = {2021-06-21},
	journal = {Science},
	author = {Holtgrieve, Gordon W. and Schindler, Daniel E. and Hobbs, William O. and Leavitt, Peter R. and Ward, Eric J. and Bunting, Lynda and Chen, Guangjie and Finney, Bruce P. and Gregory-Eaves, Irene and Holmgren, Sofia and Lisac, Mark J. and Lisi, Peter J. and Nydick, Koren and Rogers, Lauren A. and Saros, Jasmine E. and Selbie, Daniel T. and Shapley, Mark D. and Walsh, Patrick B. and Wolfe, Alexander P.},
	month = dec,
	year = {2011},
	pmid = {22174250},
	note = {Publisher: American Association for the Advancement of Science
Section: Report},
	pages = {1545--1548},
}

@article{bogan_biodiversity_2019,
	title = {Biodiversity value of remnant pools in an intermittent stream during the great {California} drought},
	volume = {29},
	issn = {1099-0755},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1002/aqc.3109},
	doi = {10.1002/aqc.3109},
	abstract = {In many intermittent streams, remnant pools persist after flow ceases and provide refuge for aquatic organisms able to tolerate stagnant water conditions. The conservation value of these pools may be greatly under-appreciated, especially in regions with a Mediterranean climate, where perennial streams have been substantially modified or disturbed by human activities. Fish, amphibians, aquatic reptiles, and aquatic invertebrates were sampled from 15 remnant pools and three seeps at Coyote Creek, California, USA, in the late summer of 2014, during the height of the most intense drought that California has experienced in 500 years. Patterns of vertebrate and invertebrate species richness and community composition were compared with abiotic factors (e.g. water quality and habitat size). Thirteen vertebrate species and 172 invertebrate taxa were identified from remnant pools and seeps. Overall vertebrate richness and composition were not correlated with abiotic factors, but fish species richness increased with remnant pool size and depth. Invertebrate taxon richness increased with pool size. Invertebrate community composition differed by habitat type (pool versus seep) and gradients in composition were correlated with several abiotic factors (e.g. pool size, substrate, and canopy cover). Remnant pools at Coyote Creek supported a full assemblage of native fishes and numerous imperilled taxa, including California red-legged frogs and California floater mussels. Nearly all native fishes and imperilled taxa are absent from artificially perennial and urbanized reaches of Coyote Creek just a few kilometres downstream of the study area. Remnant pools in intermittent streams should be a focus of conservation efforts in regions with a Mediterranean climate, especially during extreme droughts. Native fauna adapted to harsh intermittent flow regimes can thrive in these habitats, whereas non-native taxa may fare poorly. Furthermore, remnant pools supported by deep groundwater sources, such as those along geological faults, may provide both ecological refuge and evolutionary refugia for freshwater biota.},
	language = {en},
	number = {6},
	urldate = {2021-06-19},
	journal = {Aquatic Conservation: Marine and Freshwater Ecosystems},
	author = {Bogan, Michael T. and Leidy, Robert A. and Neuhaus, Linnea and Hernandez, Christopher J. and Carlson, Stephanie M.},
	year = {2019},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/aqc.3109},
	keywords = {amphibians, aquatic invertebrates, drought, drying, fishes, refuge, refugia, reptiles},
	pages = {976--989},
}

@article{rust_wildfire_2019,
	title = {Wildfire impacts on water quality, macroinvertebrate, and trout populations in the {Upper} {Rio} {Grande}},
	volume = {453},
	issn = {0378-1127},
	url = {https://www.sciencedirect.com/science/article/pii/S0378112719304219},
	doi = {10.1016/j.foreco.2019.117636},
	abstract = {Forest fires affect water quality in disrupted watersheds, which can impact aquatic ecosystems including sensitive macroinvertebrates and fish. The West Fork Complex (WFC) fire consumed 44,360 ha of forest in the state of Colorado during the summer of 2013. Damage to the soils was of moderate to high severity in the majority (60\%) of the area. The fire surrounded the headwaters of the Rio Grande, affecting water quality and habitat critical to aquatic insects and fish. The current research investigates whether there was a measurable effect on the water quality, insect diversity and fish populations within and downstream of the burn area. Parameters important to the survival of aquatic life, such as discharge, temperature, dissolved oxygen, pH, conductivity, total dissolved solids, total suspended solids, and concentrations of metals and nutrients were measured regularly in the Rio Grande and some of its tributaries for three years after the fire. Macroinvertebrate and fish populations were sampled annually. Precipitation, flow and turbidity data revealed monsoon rain events delivered sediments into the Rio Grande and its tributaries from steep, severely burned hillslopes. The monsoon events caused acute and dramatic fish kills, where hundreds of trout were reported killed in one tributary in a single day event. Turbidity was observed as high as 505 NTU in the impacted stream during the fish kill event and turbidity regularly reached 3000 NTU during subsequent precipitation events. Despite elevated turbidity levels that persisted for three years downstream of severely burned areas, the aquatic ecosystem appears to have recovered. Insect diversity and fish populations recovered to pre-fire levels and were similar to control sites within three years. Results indicate aquatic ecosystems can be resilient to largescale disturbances, such as wildfire.},
	language = {en},
	urldate = {2021-06-18},
	journal = {Forest Ecology and Management},
	author = {Rust, Ashley J. and Randell, Jackie and Todd, Andrew S. and Hogue, Terri S.},
	month = dec,
	year = {2019},
	pages = {117636},
}

@article{hallema_assessment_2017,
	title = {Assessment of wildland fire impacts on watershed annual water yield: {Analytical} framework and case studies in the {United} {States}: {Wildland} fire impacts on annual water yield: {Framework} and case studies},
	volume = {10},
	issn = {19360584},
	shorttitle = {Assessment of wildland fire impacts on watershed annual water yield},
	url = {http://doi.wiley.com/10.1002/eco.1794},
	doi = {10.1002/eco.1794},
	abstract = {More than 50\% of water supplies in the conterminous United States originate on forestland or rangeland and are potentially under increasing stress as a result of larger and more severe wildfires. Little is known, however, about the long‐term impacts of fire on annual water yield and the role of climate variability within this context. We here propose a framework for evaluating wildland fire impacts on streamflow that combines double‐mass analysis with new methods (change point analysis, climate elasticity modeling, and process‐based modeling) to distinguish between multiyear fire and climate impacts. The framework captures a wide range of fire types, watersheds characteristics, and climate conditions using streamflow data, as opposed to other approaches requiring paired watersheds. The process is illustrated with three case studies. A watershed in Arizona experienced a +266\% increase in annual water yield in the 5 years after a wildfire, where +219\% was attributed to wildfire and +24\% to precipitation trends. In contrast, a California watershed had a lower (−64\%) post‐fire net water yield, comprised of enhanced flow (+38\%) attributed to wildfire offset (−102\%) by lower precipitation in the post‐fire period. Changes in streamflow within a watershed in South Carolina had no apparent link to periods of prescribed burning but matched a very wet winter and reports of storm damage. The presented framework is unique in its ability to detect and quantify fire or other disturbances, even if the date or nature of the disturbance event is uncertain, and regardless of precipitation trends.},
	language = {en},
	number = {2},
	urldate = {2021-06-18},
	journal = {Ecohydrology},
	author = {Hallema, Dennis W. and Sun, Ge and Caldwell, Peter V. and Norman, Steven P. and Cohen, Erika C. and Liu, Yongqiang and Ward, Eric J. and McNulty, Steven G.},
	month = mar,
	year = {2017},
	pages = {e1794},
}

@misc{noauthor_lack_nodate,
	title = {Lack of eutrophication in a tallgrass prairie ecosystem over 27 years - {McLauchlan} - 2014 - {Ecology} - {Wiley} {Online} {Library}},
	url = {https://esajournals-onlinelibrary-wiley-com.weblib.lib.umt.edu:2443/doi/full/10.1890/13-1068.1?sid=vendor%3Adatabase},
	urldate = {2021-06-18},
}

@article{worrall_time_2004,
	title = {Time series analysis of long-term river dissolved organic carbon records},
	volume = {18},
	issn = {1099-1085},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/hyp.1321},
	doi = {10.1002/hyp.1321},
	abstract = {Two long records of dissolved organic carbon (DOC) concentrations in river water were examined by a detailed time series analysis in order to shed light on the mechanisms generating observed increases in DOC concentrations across the UK. The records date back as far as 1962 and come from catchments 589 and 818 km2 in area. The DOC records were compared with others taken simultaneously for flow, pH, alkalinity, air temperature and rainfall, and in one of the catchments also for turbidity and conductivity. All records were examined by the seasonal Kendall test; frequency distributions of daily DOC measurements were examined; annual cycles were calculated, Autoregressive and impulse functions were derived for DOC against flow records. The time series analysis shows that: (i) DOC trends cannot be readily explained by trends in flow, pH, alkalinity, turbidity or conductivity; (ii) there is a significant increase in carbon flux from these catchments; (iii) maximum and minimum components of the annual distribution of daily readings both show increases in DOC, implying that DOC flux is increasing for differing hydrological pathways; (iv) increases in DOC concentrations coincide with increases in temperature, though the biggest increases in temperature are in the winter months when such increases might be expected to have less effect on DOC production; (v) change in trend, and therefore flux, was observed to occur after a severe drought in 1976. The study suggests that there are real, significant increases in carbon loss from upland peat catchments and that climate is a major driver, especially a severe drought. Severe drought triggering changes in the DOC flux might be attributed to enzymic latch mechanisms. Copyright © 2004 John Wiley \& Sons, Ltd.},
	language = {en},
	number = {5},
	urldate = {2021-06-17},
	journal = {Hydrological Processes},
	author = {Worrall, Fred and Burt, Tim},
	year = {2004},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/hyp.1321},
	keywords = {UK, dissolved organic carbon (DOC), river water},
	pages = {893--911},
}

@article{likens_effects_1970,
	title = {Effects of {Forest} {Cutting} and {Herbicide} {Treatment} on {Nutrient} {Budgets} in the {Hubbard} {Brook} {Watershed}-{Ecosystem}},
	volume = {40},
	issn = {0012-9615},
	url = {https://www.jstor.org/stable/1942440},
	doi = {10.2307/1942440},
	abstract = {All vegetation on Watershed 2 of the Hubbard Brook Experimental Forest was cut during November and December of 1965, and vegetation regrowth was inhibited for two years by periodic application of herbicides. Annual stream-flow was increased 33 cm or 39\% the first year and 27 cm or 28\% the second year above the values expected if the watershed were not deforested. Large increases in streamwater concentration were observed for all major ions, except NH"4+, SO"4 = and HCO"3{\textasciicircum}-, approximately five months after the deforestation. Nitrate concentrations were 41-fold higher than the undisturbed condition the first year and 56-fold higher the second. The nitrate concentration in stream water has exceeded, almost continuously, the health levels recommended for drinking water. Sulfate was the only major ion in stream water that decreased in concentration after deforestation. An inverse relationship between sulfate and nitrate concentrations in stream water was observed in both undisturbed and deforested situations. Average streamwater concentrations increased by 417\% for Ca{\textasciicircum}+{\textasciicircum}+, 408\% for Mg{\textasciicircum}+{\textasciicircum}+, 1558\% for K{\textasciicircum}+ and 177\% for Na{\textasciicircum}+ during the two years subsequent to deforestation. Budgetary net losses from Watershed 2 in kg/ha-yr were about 142 for NO"3-N, 90 for Ca{\textasciicircum}+{\textasciicircum}+, 36 for K{\textasciicircum}+, 32 for SiO"2-Si, 24 for Al{\textasciicircum}+{\textasciicircum}+{\textasciicircum}+, 18 for Mg{\textasciicircum}+{\textasciicircum}+, 17 for Na{\textasciicircum}+, 4 for Cl{\textasciicircum}-, and 0 for SO"4-S during 1967-68; whereas for an adjacent, undisturbed watershed (W6) net losses were 9.2 for Ca{\textasciicircum}+{\textasciicircum}+, 1.6 for K{\textasciicircum}+, 17 for SiO"2-Si, 3.1 for A1{\textasciicircum}+{\textasciicircum}+{\textasciicircum}+, 2.6 for Mg{\textasciicircum}+{\textasciicircum}+, 7.0 for Na{\textasciicircum}+, 0.1 for C1{\textasciicircum}-, and 3.3 for SO"4-S. Input of nitrate-nitrogen in precipitation normally exceeds the output in drainage water in the undisturbed ecosystems, and ammonium-nitrogen likewise accumulates in both the undisturbed and deforested ecosystems. Total gross export of dissolved solids, exclusive of organic matter, was about 75 metric tons/km{\textasciicircum}2 in 1966-67, and 97 metric tons/km{\textasciicircum}2 in 1967-68, or about 6 to 8 times greater than would be expected for an undisturbed watershed. The greatly increased export of dissolved nutrients from the deforested ecosystem was due to an alteration of the nitrogen cycle within the ecosystem. The drainage streams tributary to Hubbard Brook are normally acid, and as a result of deforestation the hydrogen ion content increased by 5-fold (from pH 5.1 to 4.3). Streamwater temperatures after deforestation were higher than the undisturbed condition during both summer and winter. Also in contrast to the relatively constant temperature in the undisturbed streams, streamwater temperature after deforestation fluctuated 3-4@?C during the day in summer. Electrical conductivity increased about 6-fold in the stream water after deforestation and was much more variable. Increased streamwater turbidity as a result of the deforestation was negligible, however the particulate matter output was increased about 4-fold. Whereas the particulate matter is normally 50\% inorganic materials, after deforestation preliminary estimates indicate that the proportion of inorganic materials increased to 76\% of the total particulates. Supersaturation of dissolved oxygen in stream water from the experimental watersheds is common in all seasons except summer when stream discharge is low. The percent saturation is dependent upon flow rate in the streams. Sulfate, hydrogen ion and nitrate are major constituents in the precipitation. It is suggested that the increase in average nitrate concentration in precipitation compared to data from 1955-56,as well as the consistent annual increase observed from 1964 to 1968, may be some measure of a general increase in air pollution.},
	number = {1},
	urldate = {2021-06-17},
	journal = {Ecological Monographs},
	author = {Likens, Gene E. and Bormann, F. Herbert and Johnson, Noye M. and Fisher, D. W. and Pierce, Robert S.},
	year = {1970},
	note = {Publisher: Ecological Society of America},
	pages = {23--47},
}

@article{benito_ecological_2020,
	title = {Ecological memory at millennial time-scales: the importance of data constraints, species longevity and niche features},
	volume = {43},
	copyright = {© 2019 The Authors. Ecography published by John Wiley \& Sons on behalf of Nordic Society Oikos},
	issn = {1600-0587},
	shorttitle = {Ecological memory at millennial time-scales},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ecog.04772},
	doi = {10.1111/ecog.04772},
	abstract = {Ecological memory describes how antecedent conditions drive the dynamics of an ecological system. Palaeoecological records are paramount to understand ecological memory at millennial time-scales, but the concept is widely neglected in the literature, and a formal approach is lacking. Here, we fill such a gap by introducing a quantitative framework for ecological memory in palaeoecology, and assessing how data constraints and taxa traits shape ecological memory patterns. We simulate the population dynamics and pollen abundance of 16 virtual taxa with different life and niche traits as a response to an environmental driver. The data is processed to mimic a realistic sediment deposition and sampled at increasing depth intervals. We quantify ecological memory with Random Forests, and assess how data properties and taxa traits shape ecological memory. We find that life-span and niche features modulate the relative importance of the antecedent values of the driver and the pollen abundance over periods of 240 yr and longer. Additionally, we find that accumulation rate and decreasing pollen-sampling resolution inflate the importance of antecedent pollen abundance. Our results suggest that: 1) ecological memory patterns are sensitive to varying accumulation rates. A better understanding on the numerical basis of this effect may enable the assimilation of ecological memory concepts and methods in palaeoecology; 2) incorporating niche theory and models is essential to better understand the nature of ecological memory patterns at millennial time-scales. 3) Long-lived generalist taxa are highly decoupled from the environmental signal. This finding has implications on how we interpret the abundance-environment relationship of real taxa with similar traits, and how we use such knowledge to forecast their distribution or reconstruct past climate.},
	language = {en},
	number = {1},
	urldate = {2021-06-17},
	journal = {Ecography},
	author = {Benito, Blas M. and Gil-Romera, Graciela and Birks, H. John B.},
	year = {2020},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ecog.04772},
	keywords = {Random Forest, ecological niche, mechanistic models, palaeopalynology, population dynamics, virtual species},
	pages = {1--10},
}

@article{schweiger_importance_2019,
	title = {The importance of ecological memory for trophic rewilding as an ecosystem restoration approach},
	volume = {94},
	copyright = {© 2018 Cambridge Philosophical Society},
	issn = {1469-185X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/brv.12432},
	doi = {10.1111/brv.12432},
	abstract = {Increasing human pressure on strongly defaunated ecosystems is characteristic of the Anthropocene and calls for proactive restoration approaches that promote self-sustaining, functioning ecosystems. However, the suitability of novel restoration concepts such as trophic rewilding is still under discussion given fragmentary empirical data and limited theory development. Here, we develop a theoretical framework that integrates the concept of ‘ecological memory’ into trophic rewilding. The ecological memory of an ecosystem is defined as an ecosystem's accumulated abiotic and biotic material and information legacies from past dynamics. By summarising existing knowledge about the ecological effects of megafauna extinction and rewilding across a large range of spatial and temporal scales, we identify two key drivers of ecosystem responses to trophic rewilding: (i) impact potential of (re)introduced megafauna, and (ii) ecological memory characterising the focal ecosystem. The impact potential of (re)introduced megafauna species can be estimated from species properties such as lifetime per capita engineering capacity, population density, home range size and niche overlap with resident species. The importance of ecological memory characterising the focal ecosystem depends on (i) the absolute time since megafauna loss, (ii) the speed of abiotic and biotic turnover, (iii) the strength of species interactions characterising the focal ecosystem, and (iv) the compensatory capacity of surrounding source ecosystems. These properties related to the focal and surrounding ecosystems mediate material and information legacies (its ecological memory) and modulate the net ecosystem impact of (re)introduced megafauna species. We provide practical advice about how to quantify all these properties while highlighting the strong link between ecological memory and historically contingent ecosystem trajectories. With this newly established ecological memory–rewilding framework, we hope to guide future empirical studies that investigate the ecological effects of trophic rewilding and other ecosystem-restoration approaches. The proposed integrated conceptual framework should also assist managers and decision makers to anticipate the possible trajectories of ecosystem dynamics after restoration actions and to weigh plausible alternatives. This will help practitioners to develop adaptive management strategies for trophic rewilding that could facilitate sustainable management of functioning ecosystems in an increasingly human-dominated world.},
	language = {en},
	number = {1},
	urldate = {2021-06-17},
	journal = {Biological Reviews},
	author = {Schweiger, Andreas H. and Boulangeat, Isabelle and Conradi, Timo and Davis, Matt and Svenning, Jens-Christian},
	year = {2019},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/brv.12432},
	keywords = {adaptive management, alternative stable states, anachronism, ecological memory, ecosystem assembly, extinction debt, megafauna, resilience, restoration ecology, rewilding},
	pages = {1--15},
}

@article{martinuzzi_scenarios_2015,
	title = {Scenarios of future land use change around {United} {States}’ protected areas},
	volume = {184},
	issn = {0006-3207},
	url = {https://www.sciencedirect.com/science/article/pii/S0006320715000828},
	doi = {10.1016/j.biocon.2015.02.015},
	abstract = {Land use change around protected areas can diminish their conservation value, making it important to predict future land use changes nearby. Our goal was to evaluate future land use changes around protected areas of different types in the United States under different socioeconomic scenarios. We analyzed econometric-based projections of future land use change to capture changes around 1260 protected areas, including National Forests, Parks, Refuges, and Wilderness Areas, from 2001 to 2051, under different land use policies and crop prices. Our results showed that urban expansion around protected areas will continue to be a major threat, and expand by 67\% under business-as-usual conditions. Concomitantly, a substantial number of protected areas will lose natural vegetation in their surroundings. National land-use policies or changes in crop prices are not likely to affect the overall pattern of land use, but can have effects in certain regions. Discouraging urbanization through zoning, for example, can reduce future urban pressures around National Forests and Refuges in the East, while the implementation of an afforestation policy can increase the amount of natural vegetation around some Refuges throughout the U.S. On the other hand, increases in crop prices can increase crop/pasture cover around some protected areas, and limit the potential recovery of natural vegetation. Overall, our results highlight that future land-use change around protected areas is likely to be substantial but variable among regions and protected area types. Safeguarding the conservation value of protected areas may require serious consideration of threats and opportunities arising from future land use.},
	language = {en},
	urldate = {2021-06-16},
	journal = {Biological Conservation},
	author = {Martinuzzi, Sebastián and Radeloff, Volker C. and Joppa, Lucas N. and Hamilton, Christopher M. and Helmers, David P. and Plantinga, Andrew J. and Lewis, David J.},
	month = apr,
	year = {2015},
	keywords = {Anthropogenic threat, Econometric model, Land-use change, Protected areas},
	pages = {446--455},
}

@techreport{hallema_wildland_2019,
	address = {Asheville, NC},
	title = {Wildland fire impacts on water yield across the contiguous {United} {States}},
	url = {https://www.fs.usda.gov/treesearch/pubs/58095},
	abstract = {Wildland fires in the contiguous United States (CONUS) have increased in size and severity, but much remains unclear about the impact of fire size and burn severity on water supplies used for drinking, irrigation, industry, and hydropower. While some have investigated large-scale fire patterns, long-term effects on runoff, and the simultaneous effect of fire and climate trends on surface water yield, no studies account for all these factors and their interactions at the same time. In this report, we present critical new information for the National Cohesive Wildland Fire Management Strategy—a first-time CONUS-wide assessment of observed and potential wildland fire impacts on surface water yield. First, we analyzed data from 168 fire-affected locations, collected between 1984 and 2013, with machine learning and used climate elasticity models to correct for the local climate baseline impact. Stream gage data show that annual river flow increased most in the Lower Mississippi and Lower and Upper Colorado water resource regions, however they do not show which portion of this increase is caused by fire and which portion results from local climate trends. Our machine learning model identified local climate trends as the main driver of water yield change and determined wildland fires must affect at least 19 percent of a watershed {\textgreater} 10 km2 to change its annual water yield. A closer look at 32 locations with fires covering at least 19 percent of a watershed {\textgreater}10 km2 revealed that wildfire generally enhanced annual river flow. Fires increased river flow relatively the most in the Lower Colorado, Pacific Northwest, and California regions. In the Lower Colorado and Pacific Northwest regions, flow increased despite post-fire drought conditions. In southern California, post-fire drought effects masked the flow enhancement attributed to wildfire, meaning that annual water yield declined but not as much as expected based on the decline in precipitation. Prescribed burns in the Southeastern United States did not produce a widespread effect on river flow, because the area affected was typically too small and characterized by only low burn severity. In the second stage of the assessment, we performed full-coverage simulations of the CONUS with the Water Supply Stress Index (WaSSI) hydrologic model (88,000 HUC-12-level watersheds) for the period between 2001 and 2010. This enables us to fill in the gaps of areas with scarce data and to identify regions with large potential increases in post-fire annual water yield (+10 to +50 percent): mid- to high-elevation forests in northeastern Washington, northwestern Montana, central Minnesota, southern Utah, Colorado, and South Dakota, and coastal forests in Georgia and northern Florida. A hypothetical 20-percent forest burn impact scenario for the CONUS suggests that surface yield can increase up to +10 percent in most watersheds, and even more in some watersheds depending on climate, soils, and vegetation. The insights gained from this quantitative analysis have major implications for flood mitigation and watershed restoration, and are vital to forest management policies aimed at reducing fire impact risk and improving water supply under a changing climate.},
	language = {en},
	number = {SRS-GTR-238},
	urldate = {2021-06-16},
	institution = {U.S. Department of Agriculture, Forest Service, Southern Research Station},
	author = {Hallema, Dennis and Sun, Ge and Caldwell, Peter and Robinne, Francois-Nicolas and Bladon, Kevin D. and Norman, Steve and Liu, Yongqiang and Cohen, Erika C. and McNulty, Steve},
	year = {2019},
	doi = {10.2737/SRS-GTR-238},
	pages = {SRS--GTR--238},
}

@techreport{hallema_wildland_2019-1,
	address = {Asheville, NC},
	title = {Wildland fire impacts on water yield across the contiguous {United} {States}},
	url = {https://www.fs.usda.gov/treesearch/pubs/58095},
	abstract = {Wildland fires in the contiguous United States (CONUS) have increased in size and severity, but much remains unclear about the impact of fire size and burn severity on water supplies used for drinking, irrigation, industry, and hydropower. While some have investigated large-scale fire patterns, long-term effects on runoff, and the simultaneous effect of fire and climate trends on surface water yield, no studies account for all these factors and their interactions at the same time. In this report, we present critical new information for the National Cohesive Wildland Fire Management Strategy—a first-time CONUS-wide assessment of observed and potential wildland fire impacts on surface water yield. First, we analyzed data from 168 fire-affected locations, collected between 1984 and 2013, with machine learning and used climate elasticity models to correct for the local climate baseline impact. Stream gage data show that annual river flow increased most in the Lower Mississippi and Lower and Upper Colorado water resource regions, however they do not show which portion of this increase is caused by fire and which portion results from local climate trends. Our machine learning model identified local climate trends as the main driver of water yield change and determined wildland fires must affect at least 19 percent of a watershed {\textgreater} 10 km2 to change its annual water yield. A closer look at 32 locations with fires covering at least 19 percent of a watershed {\textgreater}10 km2 revealed that wildfire generally enhanced annual river flow. Fires increased river flow relatively the most in the Lower Colorado, Pacific Northwest, and California regions. In the Lower Colorado and Pacific Northwest regions, flow increased despite post-fire drought conditions. In southern California, post-fire drought effects masked the flow enhancement attributed to wildfire, meaning that annual water yield declined but not as much as expected based on the decline in precipitation. Prescribed burns in the Southeastern United States did not produce a widespread effect on river flow, because the area affected was typically too small and characterized by only low burn severity. In the second stage of the assessment, we performed full-coverage simulations of the CONUS with the Water Supply Stress Index (WaSSI) hydrologic model (88,000 HUC-12-level watersheds) for the period between 2001 and 2010. This enables us to fill in the gaps of areas with scarce data and to identify regions with large potential increases in post-fire annual water yield (+10 to +50 percent): mid- to high-elevation forests in northeastern Washington, northwestern Montana, central Minnesota, southern Utah, Colorado, and South Dakota, and coastal forests in Georgia and northern Florida. A hypothetical 20-percent forest burn impact scenario for the CONUS suggests that surface yield can increase up to +10 percent in most watersheds, and even more in some watersheds depending on climate, soils, and vegetation. The insights gained from this quantitative analysis have major implications for flood mitigation and watershed restoration, and are vital to forest management policies aimed at reducing fire impact risk and improving water supply under a changing climate.},
	language = {en},
	number = {SRS-GTR-238},
	urldate = {2021-06-16},
	institution = {U.S. Department of Agriculture, Forest Service, Southern Research Station},
	author = {Hallema, Dennis and Sun, Ge and Caldwell, Peter and Robinne, Francois-Nicolas and Bladon, Kevin D. and Norman, Steve and Liu, Yongqiang and Cohen, Erika C. and McNulty, Steve},
	year = {2019},
	doi = {10.2737/SRS-GTR-238},
	pages = {SRS--GTR--238},
}

@article{hallema_assessment_2017-1,
	title = {Assessment of wildland fire impacts on watershed annual water yield: {Analytical} framework and case studies in the {United} {States}},
	volume = {10},
	copyright = {Copyright © 2016 John Wiley \& Sons, Ltd.},
	issn = {1936-0592},
	shorttitle = {Assessment of wildland fire impacts on watershed annual water yield},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/eco.1794},
	doi = {10.1002/eco.1794},
	abstract = {More than 50\% of water supplies in the conterminous United States originate on forestland or rangeland and are potentially under increasing stress as a result of larger and more severe wildfires. Little is known, however, about the long-term impacts of fire on annual water yield and the role of climate variability within this context. We here propose a framework for evaluating wildland fire impacts on streamflow that combines double-mass analysis with new methods (change point analysis, climate elasticity modeling, and process-based modeling) to distinguish between multiyear fire and climate impacts. The framework captures a wide range of fire types, watersheds characteristics, and climate conditions using streamflow data, as opposed to other approaches requiring paired watersheds. The process is illustrated with three case studies. A watershed in Arizona experienced a +266\% increase in annual water yield in the 5 years after a wildfire, where +219\% was attributed to wildfire and +24\% to precipitation trends. In contrast, a California watershed had a lower (−64\%) post-fire net water yield, comprised of enhanced flow (+38\%) attributed to wildfire offset (−102\%) by lower precipitation in the post-fire period. Changes in streamflow within a watershed in South Carolina had no apparent link to periods of prescribed burning but matched a very wet winter and reports of storm damage. The presented framework is unique in its ability to detect and quantify fire or other disturbances, even if the date or nature of the disturbance event is uncertain, and regardless of precipitation trends.},
	language = {en},
	number = {2},
	urldate = {2021-06-16},
	journal = {Ecohydrology},
	author = {Hallema, Dennis W. and Sun, Ge and Caldwell, Peter V. and Norman, Steven P. and Cohen, Erika C. and Liu, Yongqiang and Ward, Eric J. and McNulty, Steven G.},
	year = {2017},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/eco.1794},
	keywords = {United States, change point analysis, climate change, climate elasticity, hydrologic disturbance, prescribed burning, wildfire},
	pages = {e1794},
}

@article{mcbride_participatory_2017,
	title = {Participatory {Geographic} {Information} {Systems} as an {Organizational} {Platform} for the {Integration} of {Traditional} and {Scientific} {Knowledge} in {Contemporary} {Fire} and {Fuels} {Management}},
	volume = {115},
	issn = {0022-1201},
	url = {https://academic.oup.com/jof/article/115/1/43-50/4599757},
	doi = {10.5849/jof.14-147},
	language = {en},
	number = {1},
	urldate = {2021-06-16},
	journal = {Journal of Forestry},
	author = {McBride, Brooke Baldauf and Sanchez-Trigueros, Fernando and Carver, Stephen J. and Watson, Alan E. and Stumpff, Linda Moon and Matt, Roian and Borrie, William T.},
	month = jan,
	year = {2017},
	pages = {43--50},
}

@article{kalman_filter_1960,
	title = {A New Approach to Linear Filtering and Prediction Problems},
	volume = {82},
	doi = {10.1115/1.3662552},
	language = {en},
	number = {1},
	journal = {Journal of Basic Engineering},
	author = {Kalman, Rudolf E.},
	year = {1960},
	pages = {35--45},
}

@article{holden_effects_2007,
	title = {Effects of {Multiple} {Wildland} {Fires} on {Ponderosa} {Pine} {Stand} {Structure} in {Two} {Southwestern} {Wilderness} {Areas}, {USA}},
	volume = {3},
	copyright = {2007 The Author(s)},
	issn = {1933-9747},
	url = {https://fireecology.springeropen.com/articles/10.4996/fireecology.0302018},
	doi = {10.4996/fireecology.0302018},
	abstract = {The effects of 30 years (1972–2003) of Wildland Fire Use for Resource Benefit (WFU) fires on ponderosa pine forest stand structure were evaluated in the Gila Wilderness, New Mexico, and the Saguaro Wilderness, Arizona. Tree density, diameter-class distributions, basal area, and stand density index were compared among areas that burned with different frequencies since 1972 and areas that burned mid-century (1940–1950) and again during the WFU era (1972–2003). In both the Saguaro Wilderness and the Gila Wilderness, significantly fewer small-diameter (5 cm to 22.5 cm) trees occurred in areas that burned multiple times since 1972 compared to areas that were unburned (p {\textless} 0.05) during this time. The density of large-diameter ({\textgreater}45 cm diameter breast height) trees in the Gila Wilderness was highly variable and did not differ significantly among fire treatments (p {\textgreater} 0.32). In the Saguaro Wilderness, significantly more large-diameter trees ({\textgreater}45 cm dbh) occurred in areas that burned mid-century and again during WFU than in all other fire treatments. Mean 10-year basal area increment growth rates (1840 to the present) of trees in the Gila Wilderness that experienced mid-century fires suggest that those fires may have had a thinning effect. Ponderosa pine forests in the Gila Wilderness and Saguaro Wilderness are structurally diverse and resistant to fires burning during the natural fire season, suggesting that repeated WFU fires have restored forest resilience to fire.},
	language = {en},
	number = {2},
	urldate = {2021-06-16},
	journal = {Fire Ecology},
	author = {Holden, Zachary A. and Morgan, Penelope and Rollins, Matthew G. and Kavanagh, Kathleen},
	month = dec,
	year = {2007},
	note = {Number: 2
Publisher: SpringerOpen},
	pages = {18--33},
}

@article{messager_global_2021,
	title = {Global prevalence of non-perennial rivers and streams},
	volume = {594},
	copyright = {2021 The Author(s), under exclusive licence to Springer Nature Limited},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/s41586-021-03565-5},
	doi = {10.1038/s41586-021-03565-5},
	abstract = {Flowing waters have a unique role in supporting global biodiversity, biogeochemical cycles and human societies1–5. Although the importance of permanent watercourses is well recognized, the prevalence, value and fate of non-perennial rivers and streams that periodically cease to flow tend to be overlooked, if not ignored6–8. This oversight contributes to the degradation of the main source of water and livelihood for millions of people5. Here we predict that water ceases to flow for at least one day per year along 51–60 per cent of the world’s rivers by length, demonstrating that non-perennial rivers and streams are the rule rather than the exception on Earth. Leveraging global information on the hydrology, climate, geology and surrounding land cover of the Earth’s river network, we show that non-perennial rivers occur within all climates and biomes, and on every continent. Our findings challenge the assumptions underpinning foundational river concepts across scientific disciplines9. To understand and adequately manage the world’s flowing waters, their biodiversity and functional integrity, a paradigm shift is needed towards a new conceptual model of rivers that includes flow intermittence. By mapping the distribution of non-perennial rivers and streams, we provide a stepping-stone towards addressing this grand challenge in freshwater science.},
	language = {en},
	number = {7863},
	urldate = {2021-06-16},
	journal = {Nature},
	author = {Messager, Mathis Loïc and Lehner, Bernhard and Cockburn, Charlotte and Lamouroux, Nicolas and Pella, Hervé and Snelder, Ton and Tockner, Klement and Trautmann, Tim and Watt, Caitlin and Datry, Thibault},
	month = jun,
	year = {2021},
	note = {Number: 7863
Publisher: Nature Publishing Group},
	pages = {391--397},
}

@article{stevens_impact_2004,
	title = {Impact of {Nitrogen} {Deposition} on the {Species} {Richness} of {Grasslands}},
	volume = {303},
	copyright = {American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	url = {https://science.sciencemag.org/content/303/5665/1876},
	doi = {10.1126/science.1094678},
	abstract = {{\textless}p{\textgreater}A transect of 68 acid grasslands across Great Britain, covering the lower range of ambient annual nitrogen deposition in the industrialized world (5 to 35 kg Nha$^{\textrm{–1}}$ year$^{\textrm{–1}}$), indicates that long-term, chronic nitrogen deposition has significantly reduced plant species richness. Species richness declines as a linear function of the rate of inorganic nitrogen deposition, with a reduction of one species per 4-m$^{\textrm{2}}$ quadrat for every 2.5 kg Nha$^{\textrm{–1}}$ year$^{\textrm{–1}}$ of chronic nitrogen deposition. Species adapted to infertile conditions are systematically reduced at high nitrogen deposition. At the mean chronic nitrogen deposition rate of central Europe (17 kg Nha$^{\textrm{–1}}$ year$^{\textrm{–1}}$), there is a 23\% species reduction compared with grasslands receiving the lowest levels of nitrogen deposition.{\textless}/p{\textgreater}},
	language = {en},
	number = {5665},
	urldate = {2021-06-16},
	journal = {Science},
	author = {Stevens, Carly J. and Dise, Nancy B. and Mountford, J. Owen and Gowing, David J.},
	month = mar,
	year = {2004},
	pmid = {15031507},
	note = {Publisher: American Association for the Advancement of Science
Section: Report},
	pages = {1876--1879},
}

@article{smith_wildfire_2011,
	title = {Wildfire effects on water quality in forest catchments: {A} review with implications for water supply},
	volume = {396},
	issn = {0022-1694},
	shorttitle = {Wildfire effects on water quality in forest catchments},
	url = {https://www.sciencedirect.com/science/article/pii/S0022169410006748},
	doi = {10.1016/j.jhydrol.2010.10.043},
	abstract = {Wildfires burn extensive forest areas around the world each year. In many locations, fire-prone forest catchments are utilised for the supply of potable water to small communities up to large cities. Following wildfire, increased erosion rates and changes to runoff generation and pollutant sources may greatly increase fluxes of sediment, nutrients and other water quality constituents, potentially contaminating water supplies. Most research to date has focused on suspended sediment exports and concentrations after wildfire. Reported first year post-fire suspended sediment exports varied from 0.017 to 50tha−1year−1 across a large range of catchment sizes (0.021–1655km2). This represented an estimated increase of 1–1459 times unburned exports. Maximum reported concentrations of total suspended solids in streams for the first year after fire ranged from 11 to ∼500,000mgL−1. Similarly, there was a large range in first year post-fire stream exports of total N (1.1–27kgha−1year−1) and total P (0.03–3.2kgha−1year−1), representing a multiple change of 0.3–431 times unburned, while NO3- exports of 0.04–13.0kgha−1year−1 (3–250 times unburned) have been reported. NO3-, NO2-, and NH3/NH4+ concentrations in streams and lakes or reservoirs may increase after wildfire but appear to present a generally low risk of exceeding drinking water guidelines. Few studies have examined post-fire exports of trace elements. The limited observations of trace element concentrations in streams after wildfire found high levels (well over guidelines) of Fe, Mn, As, Cr, Al, Ba, and Pb, which were associated with highly elevated sediment concentrations. In contrast, Cu, Zn, and Hg were below or only slightly above guideline values. Elevated Na+, Cl− and SO42- solute yields have been recorded soon after fire, while reports of concentrations of these constituents were mostly confined to coniferous forest areas in North America, where maximum sampled values were well below recommended limits. Likewise, reported wildfire effects on dissolved organic carbon were generally minor and elevated concentrations largely reflected background conditions. Available cyanide concentrations in small streams may approach levels of concern soon after fire, but increases are likely to be of short duration. Post-fire concentrations of polycyclic aromatic hydrocarbons in streams have been found to increase but remained within the recommended limit. Large increases in exports and concentrations of some constituents after wildfire indicate the potential for impacts on water supply from forest catchments. In response, various water treatment measures may be required and in the absence of adequate treatment facilities or alternative sources, water supplies may be vulnerable to disruption.},
	language = {en},
	number = {1},
	urldate = {2021-06-16},
	journal = {Journal of Hydrology},
	author = {Smith, Hugh G. and Sheridan, Gary J. and Lane, Patrick N. J. and Nyman, Petter and Haydon, Shane},
	month = jan,
	year = {2011},
	keywords = {Nutrients, Suspended sediment, Trace elements, Water quality, Water supply, Wildfire},
	pages = {170--192},
}

@article{rust_evaluating_2019,
	title = {Evaluating the factors responsible for post-fire water quality response in forests of the western {USA}},
	volume = {28},
	issn = {1049-8001},
	url = {http://www.publish.csiro.au/?paper=WF18191},
	doi = {10.1071/WF18191},
	abstract = {Wildfires commonly increase nutrient, carbon, sediment and metal inputs to streams, yet the factors responsible for the type, magnitude and duration of water quality effects are poorly understood. Prior work by the current authors found increased nitrogen, phosphorus and cation exports were common the first 5 post-fire years from a synthesis of 159 wildfires across the western United States. In the current study, an analysis is undertaken to determine factors that best explain post-fire streamwater responses observed in those watersheds. Increased post-fire total nitrogen and phosphorus loading were proportional to the catchment extent of moderate and high burn severity. While post-fire dissolved metal concentrations were correlated with pre-fire soil organic matter. Total metal concentration increased where post-fire Normalised Difference Vegetation Index, a remote sensing indicator of live green vegetation, was low. When pre-fire soil field capacity exceeded 17\%, there was a 750\% median increase in total metals export to streams. Overall, the current analysis identified burn severity, post-fire vegetation cover and several soil properties as the key variables explaining extended post-fire water quality response across a broad range of conditions found in the western US.},
	language = {en},
	number = {10},
	urldate = {2021-06-16},
	journal = {International Journal of Wildland Fire},
	author = {Rust, Ashley J. and Saxe, Samuel and McCray, John and Rhoades, Charles C. and Hogue, Terri S.},
	year = {2019},
	pages = {769},
}

@article{smith_wildfire_2011-1,
	title = {Wildfire effects on water quality in forest catchments: {A} review with implications for water supply},
	volume = {396},
	issn = {0022-1694},
	shorttitle = {Wildfire effects on water quality in forest catchments},
	url = {https://www.sciencedirect.com/science/article/pii/S0022169410006748},
	doi = {10.1016/j.jhydrol.2010.10.043},
	abstract = {Wildfires burn extensive forest areas around the world each year. In many locations, fire-prone forest catchments are utilised for the supply of potable water to small communities up to large cities. Following wildfire, increased erosion rates and changes to runoff generation and pollutant sources may greatly increase fluxes of sediment, nutrients and other water quality constituents, potentially contaminating water supplies. Most research to date has focused on suspended sediment exports and concentrations after wildfire. Reported first year post-fire suspended sediment exports varied from 0.017 to 50tha−1year−1 across a large range of catchment sizes (0.021–1655km2). This represented an estimated increase of 1–1459 times unburned exports. Maximum reported concentrations of total suspended solids in streams for the first year after fire ranged from 11 to ∼500,000mgL−1. Similarly, there was a large range in first year post-fire stream exports of total N (1.1–27kgha−1year−1) and total P (0.03–3.2kgha−1year−1), representing a multiple change of 0.3–431 times unburned, while NO3- exports of 0.04–13.0kgha−1year−1 (3–250 times unburned) have been reported. NO3-, NO2-, and NH3/NH4+ concentrations in streams and lakes or reservoirs may increase after wildfire but appear to present a generally low risk of exceeding drinking water guidelines. Few studies have examined post-fire exports of trace elements. The limited observations of trace element concentrations in streams after wildfire found high levels (well over guidelines) of Fe, Mn, As, Cr, Al, Ba, and Pb, which were associated with highly elevated sediment concentrations. In contrast, Cu, Zn, and Hg were below or only slightly above guideline values. Elevated Na+, Cl− and SO42- solute yields have been recorded soon after fire, while reports of concentrations of these constituents were mostly confined to coniferous forest areas in North America, where maximum sampled values were well below recommended limits. Likewise, reported wildfire effects on dissolved organic carbon were generally minor and elevated concentrations largely reflected background conditions. Available cyanide concentrations in small streams may approach levels of concern soon after fire, but increases are likely to be of short duration. Post-fire concentrations of polycyclic aromatic hydrocarbons in streams have been found to increase but remained within the recommended limit. Large increases in exports and concentrations of some constituents after wildfire indicate the potential for impacts on water supply from forest catchments. In response, various water treatment measures may be required and in the absence of adequate treatment facilities or alternative sources, water supplies may be vulnerable to disruption.},
	language = {en},
	number = {1},
	urldate = {2021-06-16},
	journal = {Journal of Hydrology},
	author = {Smith, Hugh G. and Sheridan, Gary J. and Lane, Patrick N. J. and Nyman, Petter and Haydon, Shane},
	month = jan,
	year = {2011},
	keywords = {Nutrients, Suspended sediment, Trace elements, Water quality, Water supply, Wildfire},
	pages = {170--192},
}

@article{diamond_metabolic_nodate,
	title = {Metabolic regime shifts and ecosystem state changes are decoupled in a large river},
	volume = {n/a},
	copyright = {© 2021 Association for the Sciences of Limnology and Oceanography.},
	issn = {1939-5590},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lno.11789},
	doi = {10.1002/lno.11789},
	abstract = {Aquatic ecosystem recovery from anthropogenic degradation can be hampered by internal feedbacks that stabilize undesirable states. The challenges of managing and predicting alternative states in lakes are well known, but state shifts in rivers and their attendant effects on ecosystem function remain understudied despite strong recent evidence that such shifts can and do occur. Using three decades of measurements of key state variables such as turbidity, nutrient concentrations, Corbicula fluminea clam densities, and chlorophyll a, including hourly dissolved oxygen, we investigated a sudden shift from phytoplankton to macrophyte dominance in the middle Loire River (France), and its associated effects on the rivers metabolic regime. We show, instead, that despite large and synchronous shifts across all state variables, changes in gross primary production and ecosystem respiration were modest (25\% and 14\% declines, respectively) and that these shifts lagged the ecosystem state changes by a decade or more. The shift to a macrophyte-dominated state reduced the sensitivity of primary production to abiotic drivers, altered element cycling efficiency, flipped the net carbon balance from positive to negative, and, crucially, weakened the temporal coupling between production and respiration. This weakened coupling, detected using Granger causality, increased the temporal autocorrelation of net ecosystem production, yielding a robust early warning indicator of both state- and metabolic-shifts that may provide valuable guidance for river restoration.},
	language = {en},
	number = {n/a},
	urldate = {2021-06-04},
	journal = {Limnology and Oceanography},
	author = {Diamond, Jacob S. and Moatar, Florentina and Cohen, Matthew J. and Poirel, Alain and Martinet, Cécile and Maire, Anthony and Pinay, Gilles},
	note = {\_eprint: https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.1002/lno.11789},
}

@article{eyre_comparison_nodate,
	title = {Comparison of {Isotope} {Pairing} and {N2}:{Ar} {Methods} for {Measuring} {Sediment} {Denitrification}—{Assumptions}, {Modifications}, and {Implications}},
	abstract = {Denitrification has been measured during the last few years using two different methods in particular: isotope pairing measured on a triple-collector isotopic ratio mass spectrometer and N2:Ar ratios measured on a membrane inlet mass spectrometer (MIMS). This study compares these two techniques in short-term batch experiments. Rates obtained using the original N2:Ar method were up to 3 to 4 times higher than rates obtained using the isotope pairing technique due to O2 reacting with the N2 during MIMS analysis. Oxygen combines with N2 within the mass spectrometer ion source forming NO؉ which reduces the N2 concentration. The decrease in N2 is least at lower O2 concentrations and since oxygen is typically consumed during incubations of sediment cores, the result is often a pseudo-increase in N2 concentration being interpreted as denitrification activity. The magnitude of this oxygen effect may be instrument specific. The reaction of O2 with N2 and the subsequent decrease in N2 was only partly corrected using an O2 correction curve for the relationship between N2 and O2 concentrations. The O2 corrected N2:Ar denitrification rates were lower, but still did not match the isotope pairing rates and the variability between replicates was much higher. Using a copper reduction column heated to 600؇C to remove all of the O2 from the sample before MIMS analysis resulted in comparable rates (slightly lower), and comparable variability between replicates, to the isotope pairing technique. The N2:Ar technique determines the net N2 production as the difference between N2 production by denitrification and N2 consumption by Nfixation, while N-fixation has little effect on the isotope pairing technique which determines a rate very close to the gross N2 production. When the two different techniques were applied on the same sediment, the small difference in rates obtained by the two methods seemed to reflect N-fixation as also supported from measurements of ethylene production in acetylene enriched sediment cores. The N2:Ar and isotope pairing techniques may be combined to provide simultaneous measurements of denitrification and N-fixation. Both techniques have several assumptions that must be met to achieve accurate rates; a number of tests are outlined that can be applied to demonstrate that these assumptions are being meet.},
	language = {en},
	author = {Eyre, Bradley D and Rysgaard, SøREN and Dalsgaard, Tage and Christensen, Peter Bondo},
	pages = {11},
}

@article{robertson_application_2019,
	title = {Application of the isotope pairing technique in sediments: {Use}, challenges, and new directions},
	volume = {17},
	copyright = {© 2019 The Authors. Limnology and Oceanography: Methods published by Wiley Periodicals, Inc. on behalf of Association for the Sciences of Limnology and Oceanography.},
	issn = {1541-5856},
	shorttitle = {Application of the isotope pairing technique in sediments},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lom3.10303},
	doi = {10.1002/lom3.10303},
	abstract = {Determining accurate rates of benthic nitrogen (N) removal and retention pathways from diverse environments is critical to our understanding of process distribution and constructing reliable N budgets and models. The whole-core 15N isotope pairing technique (IPT) is one of the most widely used methods to determine rates of benthic nitrate-reducing processes and has provided valuable information on processes and factors controlling N removal and retention in aquatic systems. While the whole core IPT has been employed in a range of environments, a number of methodological and environmental factors may lead to the generation of inaccurate data and are important to acknowledge for those applying the method. In this review, we summarize the current state of the whole core IPT and highlight some of the important steps and considerations when employing the technique. We discuss environmental parameters which can pose issues to the application of the IPT and may lead to experimental artifacts, several of which are of particular importance in environments heavily impacted by eutrophication. Finally, we highlight the advances in the use of the whole-core IPT in combination with other methods, discuss new potential areas of consideration and encourage careful and considered use of the whole-core IPT. With the recognition of potential issues and proper use, the whole-core IPT will undoubtedly continue to develop, improve our understanding of benthic N cycling and allow more reliable budgets and predictions to be made.},
	language = {en},
	number = {2},
	urldate = {2021-06-02},
	journal = {Limnology and Oceanography: Methods},
	author = {Robertson, Elizabeth K. and Bartoli, Marco and Brüchert, Volker and Dalsgaard, Tage and Hall, Per O. J. and Hellemann, Dana and Hietanen, Susanna and Zilius, Mindaugas and Conley, Daniel J.},
	year = {2019},
	note = {\_eprint: https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.1002/lom3.10303},
	pages = {112--136},
}

@article{odonnell_coupling_2019,
	title = {Coupling {Concentration}- and {Process}-{Discharge} {Relationships} {Integrates} {Water} {Chemistry} and {Metabolism} in {Streams}},
	volume = {55},
	copyright = {©2019. American Geophysical Union. All Rights Reserved.},
	issn = {1944-7973},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2019WR025025},
	doi = {10.1029/2019WR025025},
	abstract = {Stream ecosystem processes, such as metabolism, are dynamically impacted by flow intensity. Therefore, without integrating ecosystem processes with water quality, we miss opportunities to develop frameworks to understand metabolic responses to changing flow. Flow simultaneously affects the material transport and biological opportunities for material transformation. Combining the strengths of ecohydrology and stream ecology to understand how flow variation alters ecosystem processes, we analyzed more than 5 years of water quality and stream metabolism data. We created segmented process-discharge (P-Q) relationships to examine how metabolism rates vary across discharge and compared them to concentration-discharge (C-Q) relationships to explore the dynamic effects of discharge on processes and physicochemical parameters. Within the segmented P-Q relationships, we found the behavior of ecosystem respiration (ER), gross primary production (GPP), and net ecosystem production (NEP) to be different at high and low flows with varying degrees of statistical significance, demonstrating the potential for divergent metabolic responses across changing flows. GPP declined with increasing discharge. The rate of ER declined with discharge initially but then became unchanging at higher flows. NEP reflected the divergent trends between ER and GPP, as the relationship of NEP to Q was flat at lower discharge and declined at higher flows. Interrelated physicochemical parameters and ecosystem processes, such as pH and NEP, had mirrored responses to discharge. Coupling analyses of flow, water quality, and metabolism offers a more complete picture of interrelated ecosystem processes, allowing for a better understanding of ecosystem response to the physical and chemical changes that occur across flows.},
	language = {en},
	number = {12},
	urldate = {2021-06-02},
	journal = {Water Resources Research},
	author = {O'Donnell, B. and Hotchkiss, E. R.},
	year = {2019},
	note = {\_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2019WR025025},
	keywords = {C-Q, catchment, concentration-discharge, metabolism},
	pages = {10179--10190},
}

@article{burris_effects_1981,
	title = {Effects of oxygen and inorganic carbon concentrations on the photosynthetic quotients of marine algae},
	volume = {65},
	issn = {0025-3162, 1432-1793},
	url = {http://link.springer.com/10.1007/BF00397114},
	doi = {10.1007/BF00397114},
	abstract = {The photosynthetic quotients of the marine prymnesiophyte Pavlova lutheri and the marine dinoflagellate Glenodinum sp. were measured at different concentrations of dissolved oxygen and inorganic carbon. Dissolved oxygen concentration appeared to be the most important factor controlling the photosynthetic quotient, Photosynthetic quotients generally were between 1.0 and 1.8 at oxygen concentrations less than saturation, were approximately 1.0 at oxygen saturation, and generally were from 0.1 to 1.0 at oxygen concentrations greater than saturation. The photosynthetic quotients greater than 1.0 were not caused by lipid synthesis. They may have been partially caused by the presence of KNO3 rather than an ammonium salt in the growth media. The lowered photosynthetic quotients at higher oxygen concentrations were probably caused by algal photorespiration.},
	language = {en},
	number = {3},
	urldate = {2021-06-01},
	journal = {Marine Biology},
	author = {Burris, J. E.},
	month = dec,
	year = {1981},
	pages = {215--219},
}

@misc{noauthor_influence_nodate,
	title = {The  influence of irradiance on the apparent photosynthetic quotient in the unicellular alga {Pycnococcus} provasolii},
	url = {https://www.ehu.eus/eu/web/marineestuarineplankton/argitalpenak/-/asset_publisher/vC61/content/publicacion_the_influence_of_irradiance_on_the_apparent_photosynthetic_quotient_in_the_unicellular_alga_pycnococcus_provasolii},
	abstract = {The influence of irradiance on the apparent photosynthetic quotient in the unicellular alga Pycnococcus provasolii Egileak: A. Iriarte Urtea: 1999 Aldizkaria: Cahiers de Biologie Marine...},
	language = {en},
	urldate = {2021-06-01},
	journal = {Zooplanktonaren Ekologia Ikerketa Taldea},
}

@book{kirk_light_1994,
	address = {Cambridge},
	edition = {2},
	title = {Light and {Photosynthesis} in {Aquatic} {Ecosystems}},
	url = {https://www.cambridge.org/core/books/light-and-photosynthesis-in-aquatic-ecosystems/C19B28AE07B1CDEBDA5593194DE4E304},
	abstract = {Penetration of light into aquatic ecosystems is greatly affected by the absorption and scattering processes that take place within the water. Thus within any water body, the intensity and colour of the light field changes greatly with depth and this has a marked influence on both the total productivity of, and the kinds of plant that predominate in, the ecosystem. This study presents an integrated and coherent treatment of the key role of light in aquatic ecosystems. It ranges from the physics of light transmission within water, through the biochemistry and physiology of aquatic photosynthesis, to the ecological relationships which depend on the underwater light climate.},
	urldate = {2021-06-01},
	publisher = {Cambridge University Press},
	author = {Kirk, John T. O.},
	year = {1994},
	doi = {10.1017/CBO9780511623370},
}

@article{saderne_total_2021,
	title = {Total alkalinity production in a mangrove ecosystem reveals an overlooked {Blue} {Carbon} component},
	volume = {6},
	copyright = {© 2020 The Authors. Limnology and Oceanography Letters published by Wiley Periodicals LLC on behalf of Association for the Sciences of Limnology and Oceanography.},
	issn = {2378-2242},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lol2.10170},
	doi = {10.1002/lol2.10170},
	abstract = {Mangroves have the capacity to sequester organic carbon (Corg) in their sediments permanently. However, the carbon budget of mangroves is also affected by the total alkalinity (TA) budget. Principally, TA emitted from carbonate sediment dissolution is a perennial sink of atmospheric CO2. The assessment of the TA budget of mangrove carbonate sediments in the Red Sea revealed a large TA emission of 403 ± 17 mmol m−2 d−1, independent of light, seasons, or the presence of pneumatophores, compared to −36 ± 10 mmol m−2 d−1 in lagoon sediment. We estimate the TA emission from carbonate dissolution in Red Sea mangroves supported a CO2 uptake of 345 ± 15 gC m−2 yr−1, 23-fold the Corg burial rate of 15 gC m−2 yr−1. The focus on Corg burial in sediments may substantially underestimate the role of mangroves in CO2 removal. Quantifying the role of mangroves in climate change mitigation requires carbonate dissolution to be included in assessments.},
	language = {en},
	number = {2},
	urldate = {2021-05-19},
	journal = {Limnology and Oceanography Letters},
	author = {Saderne, Vincent and Fusi, Marco and Thomson, Timothy and Dunne, Aislinn and Mahmud, Fatima and Roth, Florian and Carvalho, Susana and Duarte, Carlos M.},
	year = {2021},
	note = {\_eprint: https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.1002/lol2.10170},
	pages = {61--67},
}

@article{zatkos_geophysical_2021,
	title = {Geophysical templates modulate the structure of stream food webs dominated by omnivory},
	volume = {12},
	copyright = {© 2021 The Authors.},
	issn = {2150-8925},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecs2.3444},
	doi = {10.1002/ecs2.3444},
	abstract = {Food webs show the architecture of trophic relationships, revealing the biodiversity and species interactions in an ecosystem. Understanding which factors modulate the structure of food webs offers us the ability to predict how they will change when influential factors are altered. To date, most of the research about food webs has focused on species interactions whereas the influences of surrounding environments have been overlooked. Here, using network analysis, we identified how the structure of aquatic food webs varied across a range of geophysical conditions within a whole stream system. Within a headwater basin in the Cascade Mountain Range, Oregon, USA, macroinvertebrate and vertebrate composition was investigated at 18 sites. Predator–prey interactions were compiled based on existing literature and dietary analysis. Several structural network metrics were calculated for each food web. We show that the structure of food webs was predictable based on geophysical features at both local (i.e., slope) and broader (i.e., basin size) spatial extents. Increased omnivory, greater connectance, shorter path lengths, and ultimately greater complexity and resilience existed downstream compared to upstream in the stream network. Surprisingly, the variation in food web structure was not associated with geographic proximity. Structural metric values and abundance of omnivory suggest high levels of stability for these food webs. There is a predictable variation in the structure of food webs across the network that is influenced by both longitudinal position within streams and patchy discontinuities in habitat. Hence, findings illustrate that the slightly differing perspectives from the River Continuum Concept, Discontinuity Patch Dynamics, and Process Domains can be integrated and unified using food web networks. Our analyses extend ecologists’ understanding of the stability of food webs and are a vital step toward predicting how webs and communities may respond to both natural disturbances and current global environmental change.},
	language = {en},
	number = {3},
	urldate = {2021-05-18},
	journal = {Ecosphere},
	author = {Zatkos, Lauren and Arismendi, Ivan and Johnson, Sherri L. and Penaluna, Brooke E.},
	year = {2021},
	note = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1002/ecs2.3444},
	keywords = {community complexity, connectance, food web theory, headwater streams, network analysis, omnivory, stability, watershed},
	pages = {e03444},
}

@article{aho_highest_nodate,
	title = {Highest rates of gross primary productivity maintained despite {CO2} depletion in a temperate river network},
	volume = {n/a},
	copyright = {© 2021 The Authors. Limnology and Oceanography Letters published by Wiley Periodicals LLC on behalf of Association for the Sciences of Limnology and Oceanography.},
	issn = {2378-2242},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lol2.10195},
	doi = {10.1002/lol2.10195},
	abstract = {Aquatic primary productivity produces oxygen (O2) and consumes carbon dioxide (CO2) in a ratio of 1.2. However, in aquatic ecosystems, dissolved CO2 concentrations can be low, potentially limiting primary productivity. Here, results show that a large drainage basin maintains its highest levels of gross primary productivity (GPP) when dissolved CO2 is diminished or undetectable due to photosynthetic uptake. Data show that, after CO2 is depleted, bicarbonate, an ionized form of inorganic carbon, supports these high levels of productivity. In fact, outputs from a process-based model suggest that bicarbonate can support up to 58\% of GPP under the most productive conditions. This is the first evidence that high levels of aquatic GPP are sustained in a riverine drainage network despite CO2 depletion, which has implications for freshwater ecology, biogeochemistry, and isotopic analysis.},
	language = {en},
	number = {n/a},
	urldate = {2021-05-13},
	journal = {Limnology and Oceanography Letters},
	author = {Aho, Kelly S. and Hosen, Jacob D. and Logozzo, Laura A. and McGillis, Wade R. and Raymond, Peter A.},
	note = {\_eprint: https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.1002/lol2.10195},
}

@article{nimick_diel_2003,
	title = {Diel cycles in dissolved metal concentrations in streams: {Occurrence} and possible causes},
	volume = {39},
	copyright = {Copyright 2003 by the American Geophysical Union.},
	issn = {1944-7973},
	shorttitle = {Diel cycles in dissolved metal concentrations in streams},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2002WR001571},
	doi = {10.1029/2002WR001571},
	abstract = {Substantial diel (24-hour) cycles in dissolved (0.1-μm filtration) metal concentrations were observed during low flow for 18 sampling episodes at 14 sites on 12 neutral and alkaline streams draining historical mining areas in Montana and Idaho. At some sites, concentrations of Cd, Mn, Ni, and Zn increased as much as 119, 306, 167, and 500\%, respectively, from afternoon minimum values to maximum values shortly after sunrise. Arsenic concentrations exhibited the inverse temporal pattern with increases of up to 54\%. Variations in Cu concentrations were small and inconsistent. Diel metal cycles are widespread and persistent, occur over a wide range of metal concentrations, and likely are caused primarily by instream geochemical processes. Adsorption is the only process that can explain the inverse temporal patterns of As and the divalent metals. Diel metal cycles have important implications for many types of water-quality studies and for understanding trace-metal mobility.},
	language = {en},
	number = {9},
	urldate = {2021-05-13},
	journal = {Water Resources Research},
	author = {Nimick, David A. and Gammons, Christopher H. and Cleasby, Thomas E. and Madison, James P. and Skaar, Don and Brick, Christine M.},
	year = {2003},
	note = {\_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2002WR001571},
	keywords = {Montana, arsenic, cadmium, manganese, sorption, zinc},
}

@article{tredennick_practical_nodate,
	title = {A practical guide to selecting models for exploration, inference, and prediction in ecology},
	volume = {n/a},
	copyright = {© 2021 The Authors. Ecology published by Wiley Periodicals LLC on behalf of Ecological Society of America.},
	issn = {1939-9170},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecy.3336},
	doi = {10.1002/ecy.3336},
	abstract = {Selecting among competing statistical models is a core challenge in science. However, the many possible approaches and techniques for model selection, and the conflicting recommendations for their use, can be confusing. We contend that much confusion surrounding statistical model selection results from failing to first clearly specify the purpose of the analysis. We argue that there are three distinct goals for statistical modeling in ecology: data exploration, inference, and prediction. Once the modeling goal is clearly articulated, an appropriate model selection procedure is easier to identify. We review model selection approaches and highlight their strengths and weaknesses relative to each of the three modeling goals. We then present examples of modeling for exploration, inference, and prediction using a time series of butterfly population counts. These show how a model selection approach flows naturally from the modeling goal, leading to different models selected for different purposes, even with exactly the same data set. This review illustrates best practices for ecologists and should serve as a reminder that statistical recipes cannot substitute for critical thinking or for the use of independent data to test hypotheses and validate predictions.},
	language = {en},
	number = {n/a},
	urldate = {2021-05-05},
	journal = {Ecology},
	author = {Tredennick, Andrew T. and Hooker, Giles and Ellner, Stephen P. and Adler, Peter B.},
	note = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.3336},
	keywords = {model selection, prediction, validation, variable selection},
	pages = {e03336},
}

@article{bostrom_bioavailability_1988,
	title = {Bioavailability of different phosphorus forms in freshwater systems},
	volume = {170},
	doi = {doi.org/10.1007/BF00024902},
	abstract = {The recent literature on the bioavailability of different forms of P in freshwater systems is reviewed. Bioavailable P is defined as the sum of immediately available P and the P that can be transformed into an available form by naturally occurring processes. Methods used to estimate the bioavailable P pool, which vary between studies largely depending on the time perspective applied, are critically evaluated.},
	language = {en},
	journal = {Hydrobiologia},
	author = {Boström, Bengt and Persson, Gunnar and Broberg’, Brita},
	year = {1988},
	pages = {133--155},
}

@article{vance_comparative_2021,
	title = {A {Comparative} {Assessment} of {Gap}-filling {Techniques} for {Ocean} {Carbon} {Time} {Series}},
	issn = {1726-4170},
	url = {https://bg.copernicus.org/preprints/bg-2021-78/},
	doi = {10.5194/bg-2021-78},
	abstract = {{\textless}p{\textgreater}{\textless}strong class="journal-contentHeaderColor"{\textgreater}Abstract.{\textless}/strong{\textgreater} Regularized time series of ocean carbon data are necessary for assessing seasonal dynamics, annual budgets, interannual variability and long-term trends. There are, however, no standardized methods for imputing gaps in ocean carbon time series, and only limited evaluation of the numerous methods available for constructing uninterrupted time series. A comparative assessment of eight imputation models was performed using data from seven long-term monitoring sites. Multivariate linear regression (MLR), mean imputation, linear interpolation, spline interpolation, Stineman interpolation, Kalman filtering, weighted moving average and multiple imputation by chained equation (MICE) models were compared using cross-validation to determine error and bias. A bootstrapping approach was employed to determine model sensitivity to varied degrees of data gaps and secondary time series with artificial gaps were used to evaluate impacts on seasonality and annual summations and to estimate uncertainty. All models were fit to DIC time series, with MLR and MICE models also applied to field measurements of temperature, salinity and remotely sensed chlorophyll, with model coefficients fit for monthly mean conditions. MLR estimated DIC with a mean error of 8.8 umol kg$^{\textrm{\−1}}$ among 5 oceanic sites and 20.0 ummol kg$^{\textrm{\−1}}$ among 2 coastal sites. The empirical methods of MLR, MICE and mean imputation retained observed seasonal cycles over greater amounts and durations of gaps resulting in lower error in annual budgets, outperforming the other statistical methods. MLR had lower bias and sampling sensitivity than MICE and mean imputation and provided the most robust option for imputing time series with gaps of various duration.{\textless}/p{\textgreater}},
	language = {English},
	urldate = {2021-04-29},
	journal = {Biogeosciences Discussions},
	author = {Vance, Jesse M. and Currie, Kim and Zeldis, John and Dillingham, Peter and Law, Cliff S.},
	month = apr,
	year = {2021},
	note = {Publisher: Copernicus GmbH},
	pages = {1--32},
}

@incollection{nakagawa_missing_2015,
	title = {Missing data: mechanisms, methods, and messages},
	isbn = {978-0-19-179648-7},
	language = {en\_US},
	booktitle = {Ecological Statistics: Contemporary theory and application},
	publisher = {Oxford University Press},
	author = {Nakagawa, Shinichi},
	year = {2015},
	pages = {81--105},
  editor={Fox, Gordon A.  AND Negrete-Yankelevich, Simoneta AND Sosa, Vinicio J.},
doi={10.1093/acprof:oso/9780199672547.003.0005}
}

@article{graham_missing_2009,
	title = {Missing Data Analysis: {Making} It Work in the Real World},
	volume = {60},
	shorttitle = {Missing {Data} {Analysis}},
	doi = {10.1146/annurev.psych.58.110405.085530},
	abstract = {This review presents a practical summary of the missing data literature, including a sketch of missing data theory and descriptions of normal-model multiple imputation (MI) and maximum likelihood methods. Practical missing data analysis issues are discussed, most notably the inclusion of auxiliary variables for improving power and reducing bias. Solutions are given for missing data challenges such as handling longitudinal, categorical, and clustered data with normal-model MI; including interactions in the missing data model; and handling large numbers of variables. The discussion of attrition and nonignorable missingness emphasizes the need for longitudinal diagnostics and for reducing the uncertainty about the missing data mechanism under attrition. Strategies suggested for reducing attrition bias include using auxiliary variables, collecting follow-up data on a sample of those initially missing, and collecting data on intent to drop out. Suggestions are given for moving forward with research on missing data and attrition.},
	number = {1},
	urldate = {2021-04-21},
	journal = {Annual Review of Psychology},
	author = {Graham, John W.},
	year = {2009},
	pmid = {18652544},
	pages = {549--576},
}

@article{nakagawa_missing_2008,
	title = {Missing inaction: the dangers of ignoring missing data},
	volume = {23},
	issn = {0169-5347},
	shorttitle = {Missing inaction},
	url = {https://www.sciencedirect.com/science/article/pii/S0169534708002772},
	doi = {10.1016/j.tree.2008.06.014},
	abstract = {The most common approach to dealing with missing data is to delete cases containing missing observations. However, this approach reduces statistical power and increases estimation bias. A recent study shows how estimates of heritability and selection can be biased when the ‘invisible fraction’ (missing data due to mortality) is ignored, thus demonstrating the dangers of neglecting missing data in ecology and evolution. We highlight recent advances in the procedures of handling missing data and their relevance and applicability.},
	language = {en},
	number = {11},
	urldate = {2021-04-21},
	journal = {Trends in Ecology \& Evolution},
	author = {Nakagawa, Shinichi and Freckleton, Robert P.},
	month = nov,
	year = {2008},
	pages = {592--596},
}

@book{fox_ecological_2015,
	title = {Ecological {Statistics}: {Contemporary} theory and application},
	isbn = {978-0-19-967254-7},
	shorttitle = {Ecological {Statistics}},
	url = {https://oxford.universitypressscholarship.com/view/10.1093/acprof:oso/9780199672547.001.0001/acprof-9780199672547},
	language = {en},
	urldate = {2021-04-21},
	publisher = {Oxford University Press},
	editor = {Fox, Gordon A. and Negrete-Yankelevich, Simoneta and Sosa, Vinicio J.},
	month = jan,
	year = {2015},
	doi = {10.1093/acprof:oso/9780199672547.001.0001},
	doi = {10.1093/acprof:oso/9780199672547.001.0001},
}

@misc{noauthor_multiple_nodate,
	title = {Multiple {Imputation} for {Nonresponse} in {Surveys} {\textbar} {Wiley}},
	url = {https://www.wiley.com/en-us/Multiple+Imputation+for+Nonresponse+in+Surveys-p-9780471655749},
	abstract = {Demonstrates how nonresponse in sample surveys and censuses can be handled by replacing each missing value with two or more multiple imputations. Clearly illustrates the advantages of modern computing to such handle surveys, and demonstrates the benefit of this statistical technique for researchers who must analyze them. Also presents the background for Bayesian and frequentist theory. After establishing that only standard complete-data methods are needed to analyze a multiply-imputed set, the text evaluates procedures in general circumstances, outlining specific procedures for creating imputations in both the ignorable and nonignorable cases. Examples and exercises reinforce ideas, and the interplay of Bayesian and frequentist ideas presents a unified picture of modern statistics.},
	language = {en-us},
	urldate = {2021-04-21},
	journal = {Wiley.com},
}

@article{newcomer_hysteresis_2021,
	title = {Hysteresis {Patterns} of {Watershed} {Nitrogen} {Retention} and {Loss} {Over} the {Past} 50 years in {United} {States} {Hydrological} {Basins}},
	volume = {35},
	copyright = {© 2021. American Geophysical Union. All Rights Reserved.},
	issn = {1944-9224},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020GB006777},
	doi = {10.1029/2020GB006777},
	abstract = {Patterns of watershed nitrogen (N) retention and loss are shaped by how watershed biogeochemical processes retain, biogeochemically transform, and lose incoming atmospheric deposition of N. Loss patterns represented by concentration, discharge, and their associated stream exports are important indicators of integrated watershed N retention behaviors. We examined continental United States (CONUS) scale N deposition (e.g., wet and dry atmospheric deposition), vegetation trends, and stream trends as potential indicators of watershed N-saturation and retention conditions, and how watershed N retention and losses vary over space and time. By synthesizing changes and modalities in watershed nitrogen loss patterns based on stream data from 2200 U.S. watersheds over a 50 years record, our work revealed two patterns of watershed N-retention and loss. One was a hysteresis pattern that reflects the integrated influence of hydrology, atmospheric inputs, land-use, stream temperature, elevation, and vegetation. The other pattern was a one-way transition to a new state. We found that regions with increasing atmospheric deposition and increasing vegetation health/biomass patterns have the highest N-retention capacity, become increasingly N-saturated over time, and are associated with the strongest declines in stream N exports—a pattern, that is, consistent across all land cover categories. We provide a conceptual model, validated at an unprecedented scale across the CONUS that links instream nitrogen signals to upstream mechanistic landscape processes. Our work can aid in the future interpretation of in-stream concentrations of DOC and DIN as indicators of watershed N-retention status and integrators of watershed hydrobiogeochemical processes.},
	language = {en},
	number = {4},
	urldate = {2021-04-19},
	journal = {Global Biogeochemical Cycles},
	author = {Newcomer, Michelle E. and Bouskill, Nicholas J. and Wainwright, Haruko and Maavara, Taylor and Arora, Bhavna and Siirila‐Woodburn, Erica R. and Dwivedi, Dipankar and Williams, Kenneth H. and Steefel, Carl and Hubbard, Susan S.},
	year = {2021},
	note = {\_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2020GB006777},
	keywords = {Watersheds, catchment scale nitrogen retention, ecosystem variability, nitrogen dynamics, watershed N hysteresis, watershed exports},
	pages = {e2020GB006777},
}

@article{gomez-gener_global_2021,
	title = {Global carbon dioxide efflux from rivers enhanced by high nocturnal emissions},
	copyright = {2021 The Author(s), under exclusive licence to Springer Nature Limited},
	issn = {1752-0908},
	url = {https://www.nature.com/articles/s41561-021-00722-3},
	doi = {10.1038/s41561-021-00722-3},
	abstract = {Carbon dioxide (CO2) emissions to the atmosphere from running waters are estimated to be four times greater than the total carbon (C) flux to the oceans. However, these fluxes remain poorly constrained because of substantial spatial and temporal variability in dissolved CO2 concentrations. Using a global compilation of high-frequency CO2 measurements, we demonstrate that nocturnal CO2 emissions are on average 27\% (0.9 gC m−2 d−1) greater than those estimated from diurnal concentrations alone. Constraints on light availability due to canopy shading or water colour are the principal controls on observed diel (24 hour) variation, suggesting this nocturnal increase arises from daytime fixation of CO2 by photosynthesis. Because current global estimates of CO2 emissions to the atmosphere from running waters (0.65–1.8 PgC yr−1) rely primarily on discrete measurements of dissolved CO2 obtained during the day, they substantially underestimate the magnitude of this flux. Accounting for night-time CO2 emissions may elevate global estimates from running waters to the atmosphere by 0.20–0.55 PgC yr−1.},
	language = {en},
	urldate = {2021-04-15},
	journal = {Nature Geoscience},
	author = {Gómez-Gener, Lluís and Rocher-Ros, Gerard and Battin, Tom and Cohen, Matthew J. and Dalmagro, Higo J. and Dinsmore, Kerry J. and Drake, Travis W. and Duvert, Clément and Enrich-Prast, Alex and Horgby, Åsa and Johnson, Mark S. and Kirk, Lily and Machado-Silva, Fausto and Marzolf, Nicholas S. and McDowell, Mollie J. and McDowell, William H. and Miettinen, Heli and Ojala, Anne K. and Peter, Hannes and Pumpanen, Jukka and Ran, Lishan and Riveros-Iregui, Diego A. and Santos, Isaac R. and Six, Johan and Stanley, Emily H. and Wallin, Marcus B. and White, Shane A. and Sponseller, Ryan A.},
	month = apr,
	year = {2021},
	note = {Publisher: Nature Publishing Group},
	pages = {1--6},
}

@article{dugan_slow_nodate,
	title = {The slow and steady salinization of {Sparkling} {Lake}, {Wisconsin}},
	volume = {n/a},
	copyright = {© 2021 The Authors. Limnology and Oceanography Letters published by Wiley Periodicals LLC on behalf of Association for the Sciences of Limnology and Oceanography.},
	issn = {2378-2242},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lol2.10191},
	doi = {10.1002/lol2.10191},
	abstract = {The concentrations of conservative solutes in seepage lakes are determined by the relative inputs of precipitation vs. groundwater. In areas of road salt application, seepage lakes may be at high risk of salinization depending on groundwater flow. Here, we revisit a 1992 analysis on the salinization of Sparkling Lake, a deep seepage lake in Northern Wisconsin. The original analysis predicted a rapid increase in chloride concentrations before reaching a steady steady of 8 mg L−1 by 2020. Forty years of monitoring Sparkling Lake show that rather than reaching a dynamic equilibrium, chloride concentrations have steadily increased. We update the original box model approach by adding a soil reservoir component that shows the slow steady rise in chloride is the result of terrestrial retention. For freshwater rivers and lakes, chloride retention on the landscape will both delay chloride impairment and prolong recovery and must be considered when modeling future chloride contamination risk.},
	language = {en},
	number = {n/a},
	urldate = {2021-04-13},
	journal = {Limnology and Oceanography Letters},
	author = {Dugan, Hilary A. and Rock, Linnea A.},
	note = {\_eprint: https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.1002/lol2.10191},
}

@article{crawford_long-term_2020,
	title = {Long-{Term} {Trends} in {Acid} {Precipitation} and {Watershed} {Elemental} {Export} {From} an {Alpine} {Catchment} of the {Colorado} {Rocky} {Mountains}, {USA}},
	volume = {125},
	copyright = {©2020. American Geophysical Union. All Rights Reserved.},
	issn = {2169-8961},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020JG005683},
	doi = {10.1029/2020JG005683},
	abstract = {Acid deposition associated with precipitation is an ecological problem that has affected watersheds in industrialized parts of North America and Europe, but remote landscapes, such as the Colorado Rocky Mountains, have also been impacted. The deposition of strong acids, including nitric and sulfuric acids, has decreased substantially over the past 30 years at Niwot Ridge, a high-alpine watershed of Colorado. The pH of precipitation has followed these declines and has increased to 5.5. Meanwhile, NH4+, another important constituent of acid/base balance, and a fertilizing nutrient, has more than doubled in precipitation between 1984 and 2017. A statistical model of long-term water chemistry concentrations and loads revealed a variety of trends in watershed export of acids and bases, some of which were unexpected, and remain unexplained. For example, despite declining sulfate deposition, sulfate export has increased. On the other hand, watershed nitrate export has remained constant despite decreases in atmospheric deposition, while watershed NH4+ export has increased, albeit minimally, relative to total nitrogen export. Watershed pH and alkalinity appear to have stabilized in response to decreased acid precipitation, which may be explained by geochemical processes, such as carbonate weathering. Overall, in this high-alpine watershed, atmospheric deposition is trending toward preindustrial conditions, and there is a need to conduct targeted, process-based studies to determine the mechanisms underlying these trends. The unexpected watershed responses that we identify here require a new framework for understanding acid precipitation recovery.},
	language = {en},
	number = {11},
	urldate = {2021-04-12},
	journal = {Journal of Geophysical Research: Biogeosciences},
	author = {Crawford, John T. and Hinckley, Eve-Lyn S. and Neff, Jason C.},
	year = {2020},
	keywords = {acid rain, deposition, nitrogen, recovery, sulfur, watershed},
	pages = {e2020JG005683},
}

@article{schichtel_long-term_2019,
	title = {Long-term trends of wet inorganic nitrogen deposition in {Rocky} {Mountain} {National} {Park}: {Influence} of missing data imputation methods and associated uncertainty},
	volume = {687},
	issn = {0048-9697},
	shorttitle = {Long-term trends of wet inorganic nitrogen deposition in {Rocky} {Mountain} {National} {Park}},
	url = {https://www.sciencedirect.com/science/article/pii/S0048969719326725},
	doi = {10.1016/j.scitotenv.2019.06.104},
	abstract = {Excess reactive nitrogen (Nr) deposition is occurring in Rocky Mountain National Park and impacting sensitive ecosystems. In 2006, the National Park Service, State of Colorado, and Environmental Protection Agency established the goal to reduce Nr deposition to below the ecosystem critical load by 2032. Progress is tracked using 5-year averages of annual wet inorganic nitrogen (IN) deposition measured at Loch Vale, Colorado, by the National Atmospheric Deposition Program (NADP). This remote high alpine site is challenging to operate, and large fractions of the annual precipitation, at times {\textgreater}40\%, had invalid IN concentrations. Annual wet IN deposition is calculated using the NADP protocol, which replaces missing concentrations with the annual precipitation-weighted mean (PWM) concentration of valid samples. This protocol does not account for seasonal variations in IN concentrations and the inverse relationship between concentration and precipitation amounts. Invalid samples occurred more frequently in the winter and at high and low precipitation amounts, and the NADP protocol generally overestimated annual deposition rates, by as much as 20\%. Here, a new method for imputing missing weekly IN concentrations that accounts for their seasonal and precipitation dependence is introduced. Using a bootstrapping analysis shows that the new method reduced the errors in the annual deposition rates by about 30\% compared to the NADP protocol and the biases were near zero. The overall trend in the wet IN deposition rates was found to be flat from 1990 to 2017, but the nitrate contribution decreased about 33\%, which was offset by a nearly equal increase in ammonium wet deposition. These trends are consistent with known changes in nitrate and ammonium precursor emissions. The long-term trends in the annual IN deposition rates were similar using both data imputation methods, but the 2013–2017 average was about 10\% smaller using the new method.},
	language = {en},
	urldate = {2021-04-12},
	journal = {Science of The Total Environment},
	author = {Schichtel, Bret A. and Gebhart, Kristi A. and Morris, Kristi H. and Cheatham, James R. and Vimont, John and Larson, Robert S. and Beachley, Gregory},
	month = oct,
	year = {2019},
	keywords = {Bootstrapping, Critical loads, Reactive nitrogen deposition, Uncertainty, Wet deposition trends},
	pages = {817--826},
}

@article{schichtel_long-term_2019-1,
	title = {Long-term trends of wet inorganic nitrogen deposition in {Rocky} {Mountain} {National} {Park}: {Influence} of missing data imputation methods and associated uncertainty},
	volume = {687},
	issn = {0048-9697},
	shorttitle = {Long-term trends of wet inorganic nitrogen deposition in {Rocky} {Mountain} {National} {Park}},
	url = {https://www.sciencedirect.com/science/article/pii/S0048969719326725},
	doi = {10.1016/j.scitotenv.2019.06.104},
	abstract = {Excess reactive nitrogen (Nr) deposition is occurring in Rocky Mountain National Park and impacting sensitive ecosystems. In 2006, the National Park Service, State of Colorado, and Environmental Protection Agency established the goal to reduce Nr deposition to below the ecosystem critical load by 2032. Progress is tracked using 5-year averages of annual wet inorganic nitrogen (IN) deposition measured at Loch Vale, Colorado, by the National Atmospheric Deposition Program (NADP). This remote high alpine site is challenging to operate, and large fractions of the annual precipitation, at times {\textgreater}40\%, had invalid IN concentrations. Annual wet IN deposition is calculated using the NADP protocol, which replaces missing concentrations with the annual precipitation-weighted mean (PWM) concentration of valid samples. This protocol does not account for seasonal variations in IN concentrations and the inverse relationship between concentration and precipitation amounts. Invalid samples occurred more frequently in the winter and at high and low precipitation amounts, and the NADP protocol generally overestimated annual deposition rates, by as much as 20\%. Here, a new method for imputing missing weekly IN concentrations that accounts for their seasonal and precipitation dependence is introduced. Using a bootstrapping analysis shows that the new method reduced the errors in the annual deposition rates by about 30\% compared to the NADP protocol and the biases were near zero. The overall trend in the wet IN deposition rates was found to be flat from 1990 to 2017, but the nitrate contribution decreased about 33\%, which was offset by a nearly equal increase in ammonium wet deposition. These trends are consistent with known changes in nitrate and ammonium precursor emissions. The long-term trends in the annual IN deposition rates were similar using both data imputation methods, but the 2013–2017 average was about 10\% smaller using the new method.},
	language = {en},
	urldate = {2021-04-12},
	journal = {Science of The Total Environment},
	author = {Schichtel, Bret A. and Gebhart, Kristi A. and Morris, Kristi H. and Cheatham, James R. and Vimont, John and Larson, Robert S. and Beachley, Gregory},
	month = oct,
	year = {2019},
	keywords = {Bootstrapping, Critical loads, Reactive nitrogen deposition, Uncertainty, Wet deposition trends},
	pages = {817--826},
}

@article{horgby_dynamics_2019,
	title = {Dynamics and potential drivers of {CO2} concentration and evasion across temporal scales in high-alpine streams},
	volume = {14},
	issn = {1748-9326},
	url = {https://iopscience.iop.org/article/10.1088/1748-9326/ab5cb8/meta},
	doi = {10.1088/1748-9326/ab5cb8},
	language = {en},
	number = {12},
	urldate = {2021-04-07},
	journal = {Environmental Research Letters},
	author = {Horgby, Åsa and Gómez-Gener, Lluís and Escoffier, Nicolas and Battin, Tom J.},
	month = dec,
	year = {2019},
	note = {Publisher: IOP Publishing},
	pages = {124082},
}

@article{horgby_unexpected_2019,
	title = {Unexpected large evasion fluxes of carbon dioxide from turbulent streams draining the world’s mountains},
	volume = {10},
	copyright = {2019 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-019-12905-z},
	doi = {10.1038/s41467-019-12905-z},
	abstract = {Inland waters, including streams and rivers, are active components of the global carbon cycle. Despite the large areal extent of the world’s mountains, the role of mountain streams for global carbon fluxes remains elusive. Using recent insights from gas exchange in turbulent streams, we found that areal CO2 evasion fluxes from mountain streams equal or exceed those reported from tropical and boreal streams, typically regarded as hotspots of aquatic carbon fluxes. At the regional scale of the Swiss Alps, we present evidence that emitted CO2 derives from lithogenic and biogenic sources within the catchment and delivered by the groundwater to the streams. At a global scale, we estimate the CO2 evasion from mountain streams to 167 ± 1.5 Tg C yr−1, which is high given their relatively low areal contribution to the global stream and river networks. Our findings shed new light on mountain streams for global carbon fluxes.},
	language = {en},
	number = {1},
	urldate = {2021-04-07},
	journal = {Nature Communications},
	author = {Horgby, Åsa and Segatto, Pier Luigi and Bertuzzo, Enrico and Lauerwald, Ronny and Lehner, Bernhard and Ulseth, Amber J. and Vennemann, Torsten W. and Battin, Tom J.},
	month = oct,
	year = {2019},
	note = {Number: 1
Publisher: Nature Publishing Group},
	pages = {4888},
}

@article{noble_planned_2018,
	title = {Planned missing data design: stronger inferences, increased research efficiency and improved animal welfare in ecology and evolution},
	copyright = {© 2018, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NoDerivs 4.0 International), CC BY-ND 4.0, as described at http://creativecommons.org/licenses/by-nd/4.0/},
	shorttitle = {Planned missing data design},
	url = {https://www.biorxiv.org/content/10.1101/247064v1},
	doi = {10.1101/247064},
	abstract = {{\textless}h3{\textgreater}Abstract{\textless}/h3{\textgreater} {\textless}p{\textgreater}Ecological and evolutionary research questions are increasingly requiring the integration of research fields along with larger datasets to address fundamental local and global scale problems. Unfortunately, these agendas are often in conflict with limited funding and a need to balance animal welfare concerns.{\textless}/p{\textgreater}{\textless}p{\textgreater}Planned missing data design (PMDD), where data are randomly and deliberately missed during data collection, is a simple and effective strategy to working under greater research constraints while ensuring experiments have sufficient power to address fundamental research questions. Here, we review how PMDD can be incorporated into existing experimental designs by discussing alternative design approaches and evaluating how data imputation procedures work under PMDD situations.{\textless}/p{\textgreater}{\textless}p{\textgreater}Using realistic examples and simulations of multilevel data we show how a variety of research questions and data types, common in ecology and evolution, can be aided by utilizing a PMDD and data imputation procedures. More specifically, we show how PMDD can improve statistical power in detecting effects of interest even with high levels (50\%) of missing data and moderate sample sizes. We also provide examples of how PMDD can facilitate improved animal welfare all the while reducing research costs and constraints that would make endeavours for integrative research challenging.{\textless}/p{\textgreater}{\textless}p{\textgreater}Planned missing data designs are still in their infancy and we discuss some of the difficulties in their implementation and provide tentative solutions. Nonetheless, data imputation procedures are becoming more sophisticated and more easily implemented and it is likely that PMDD will be an effective and powerful tool for a wide range of experimental designs, data types and problems common in ecology and evolution.{\textless}/p{\textgreater}},
	language = {en},
	urldate = {2021-04-05},
	journal = {bioRxiv},
	author = {Noble, Daniel W. A. and Nakagawa, Shinichi},
	month = jan,
	year = {2018},
	note = {Publisher: Cold Spring Harbor Laboratory
Section: New Results},
	pages = {247064},
}

@article{onkelinx_working_2017,
	title = {Working with population totals in the presence of missing data comparing imputation methods in terms of bias and precision},
	volume = {158},
	issn = {2193-7206},
	url = {10.1007/s10336-016-1404-9},
	doi = {10.1007/s10336-016-1404-9},
	abstract = {Missing observations in water bird censuses are commonly handled using the Underhill index or the birdSTATs tool which enables the use of TRIM under the hood. Multiple imputation is a standard technique for handling missing data that is rarely used in the field of ecology, but is a well known statistical technique in the fields of medical and social sciences. The purpose of this paper is to compare these three methods in terms of bias and variance. The bias in the Underhill method depends on the algorithm and starting values. birdSTATs and multiple imputation are unbiased in the case of missing values that are missing completely at random; more missing values implies less information, and so wider confidence intervals are expected as the missingness increases. The Underhill method and birdSTATs tool underestimate the variance; omitting data from a complete dataset and applying the Underhill index or birdSTATs tool results in smaller confidence intervals. Multiple imputation with an adequate imputation model provides wider confidence intervals. Biased parameter estimates with underestimated variance can potentially lead to incorrect management and policy conclusions. Hence, we dissuade the use of Underhill indices or the birdSTATs tool to handle missing data, rather we suggest that multiple imputation is a more robust alternative, even in suboptimal conditions.},
	language = {en},
	number = {2},
	urldate = {2021-04-05},
	journal = {Journal of Ornithology},
	author = {Onkelinx, Thierry and Devos, Koen and Quataert, Paul},
	month = apr,
	year = {2017},
	pages = {603--615},
}

@article{bokde_novel_2018,
	title = {A novel imputation methodology for time series based on pattern sequence forecasting},
	volume = {116},
	issn = {0167-8655},
	url = {https://www.sciencedirect.com/science/article/pii/S0167865518306500},
	doi = {10.1016/j.patrec.2018.09.020},
	abstract = {The Pattern Sequence Forecasting (PSF) algorithm is a previously described algorithm that identifies patterns in time series data and forecasts values using periodic characteristics of the observations. A new method for univariate time series is introduced that modifies the PSF algorithm to simultaneously forecast and backcast missing values for imputation. The imputePSF method extends PSF by characterizing repeating patterns of existing observations to provide a more precise estimate of missing values compared to more conventional methods, such as replacement with means or last observation carried forward. The imputation accuracy of imputePSF was evaluated by simulating varying amounts of missing observations with three univariate datasets. Comparisons of imputePSF with well-established methods using the same simulations demonstrated an overall reduction in error estimates. The imputePSF algorithm can produce more precise imputations on appropriate datasets, particularly those with periodic and repeating patterns.},
	language = {en},
	urldate = {2021-04-05},
	journal = {Pattern Recognition Letters},
	author = {Bokde, Neeraj and Beck, Marcus W. and Martínez Álvarez, Francisco and Kulat, Kishore},
	month = dec,
	year = {2018},
	keywords = {Data mining, Forecasting, Imputation, Time series},
	pages = {88--96},
}

@article{taugourdeau_filling_2014,
	title = {Filling the gap in functional trait databases: use of ecological hypotheses to replace missing data},
	volume = {4},
	copyright = {© 2014 The Authors. Ecology and Evolution published by John Wiley \& Sons Ltd.},
	issn = {2045-7758},
	shorttitle = {Filling the gap in functional trait databases},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.989},
	doi = {10.1002/ece3.989},
	abstract = {Functional trait databases are powerful tools in ecology, though most of them contain large amounts of missing values. The goal of this study was to test the effect of imputation methods on the evaluation of trait values at species level and on the subsequent calculation of functional diversity indices at community level using functional trait databases. Two simple imputation methods (average and median), two methods based on ecological hypotheses, and one multiple imputation method were tested using a large plant trait database, together with the influence of the percentage of missing data and differences between functional traits. At community level, the complete-case approach and three functional diversity indices calculated from grassland plant communities were included. At the species level, one of the methods based on ecological hypothesis was for all traits more accurate than imputation with average or median values, but the multiple imputation method was superior for most of the traits. The method based on functional proximity between species was the best method for traits with an unbalanced distribution, while the method based on the existence of relationships between traits was the best for traits with a balanced distribution. The ranking of the grassland communities for their functional diversity indices was not robust with the complete-case approach, even for low percentages of missing data. With the imputation methods based on ecological hypotheses, functional diversity indices could be computed with a maximum of 30\% of missing data, without affecting the ranking between grassland communities. The multiple imputation method performed well, but not better than single imputation based on ecological hypothesis and adapted to the distribution of the trait values for the functional identity and range of the communities. Ecological studies using functional trait databases have to deal with missing data using imputation methods corresponding to their specific needs and making the most out of the information available in the databases. Within this framework, this study indicates the possibilities and limits of single imputation methods based on ecological hypothesis and concludes that they could be useful when studying the ranking of communities for their functional diversity indices.},
	language = {en},
	number = {7},
	urldate = {2021-04-05},
	journal = {Ecology and Evolution},
	author = {Taugourdeau, Simon and Villerd, Jean and Plantureux, Sylvain and Huguenin‐Elie, Olivier and Amiaud, Bernard},
	year = {2014},
	keywords = {Functional diversity, LEDA database, imputation methods, missing data, plant functional trait},
	pages = {944--958},
}

@article{nakagawa_model_2011,
	title = {Model averaging, missing data and multiple imputation: a case study for behavioural ecology},
	volume = {65},
	issn = {1432-0762},
	shorttitle = {Model averaging, missing data and multiple imputation},
	url = {10.1007/s00265-010-1044-7},
	doi = {10.1007/s00265-010-1044-7},
	abstract = {Model averaging, specifically information theoretic approaches based on Akaike’s information criterion (IT-AIC approaches), has had a major influence on statistical practices in the field of ecology and evolution. However, a neglected issue is that in common with most other model fitting approaches, IT-AIC methods are sensitive to the presence of missing observations. The commonest way of handling missing data is the complete-case analysis (the complete deletion from the dataset of cases containing any missing values). It is well-known that this results in reduced estimation precision (or reduced statistical power), biased parameter estimates; however, the implications for model selection have not been explored. Here we employ an example from behavioural ecology to illustrate how missing data can affect the conclusions drawn from model selection or based on hypothesis testing. We show how missing observations can be recovered to give accurate estimates for IT-related indices (e.g. AIC and Akaike weight) as well as parameters (and their standard errors) by utilizing ‘multiple imputation’. We use this paper to illustrate key concepts from missing data theory and as a basis for discussing available methods for handling missing data. The example is intended to serve as a practically oriented case study for behavioural ecologists deciding on how to handle missing data in their own datasets and also as a first attempt to consider the problems of conducting model selection and averaging in the presence of missing observations.},
	language = {en},
	number = {1},
	urldate = {2021-04-05},
	journal = {Behavioral Ecology and Sociobiology},
	author = {Nakagawa, Shinichi and Freckleton, Robert P.},
	month = jan,
	year = {2011},
	pages = {103--116},
}

@article{segatto_metabolic_2021,
	title = {The {Metabolic} {Regimes} at the {Scale} of an {Entire} {Stream} {Network} {Unveiled} {Through} {Sensor} {Data} and {Machine} {Learning}},
	issn = {1435-0629},
	url = {10.1007/s10021-021-00618-8},
	doi = {10.1007/s10021-021-00618-8},
	abstract = {Streams and rivers form dense networks that drain the terrestrial landscape and are relevant for biodiversity dynamics, ecosystem functioning, and transport and transformation of carbon. Yet, resolving in both space and time gross primary production (GPP), ecosystem respiration (ER) and net ecosystem production (NEP) at the scale of entire stream networks has been elusive so far. Here, combining Random Forest (RF) with time series of sensor data in 12 reach sites, we predicted annual regimes of GPP, ER, and NEP in 292 individual stream reaches and disclosed properties emerging from the network they form. We further predicted available light and thermal regimes for the entire network and expanded the library of stream metabolism predictors. We found that the annual network-scale metabolism was heterotrophic yet with a clear peak of autotrophy in spring. In agreement with the River Continuum Concept, small headwaters and larger downstream reaches contributed 16\% and 60\%, respectively, to the annual network-scale GPP. Our results suggest that ER rather than GPP drives the metabolic stability at the network scale, which is likely attributable to the buffering function of the streambed for ER, while GPP is more susceptible to flow-induced disturbance and fluctuations in light availability. Furthermore, we found large terrestrial subsidies fueling ER, pointing to an unexpectedly high network-scale level of heterotrophy, otherwise masked by simply considering reach-scale NEP estimations. Our machine learning approach sheds new light on the spatiotemporal dynamics of ecosystem metabolism at the network scale, which is a prerequisite to integrate aquatic and terrestrial carbon cycling at relevant scales.},
	language = {en},
	urldate = {2021-04-05},
	journal = {Ecosystems},
	author = {Segatto, Pier Luigi and Battin, Tom J. and Bertuzzo, Enrico},
	month = apr,
	year = {2021},
}

@article{hui_gap-filling_2004,
	title = {Gap-filling missing data in eddy covariance measurements using multiple imputation ({MI}) for annual estimations},
	volume = {121},
	issn = {0168-1923},
	url = {https://www.sciencedirect.com/science/article/pii/S0168192303001588},
	doi = {10.1016/S0168-1923(03)00158-8},
	abstract = {Missing data is a ubiquitous problem in evaluating long-term experimental measurements, such as those associated with the FluxNet project, due to the equipment failures, system maintenance, power-failure, and lightning strikes among other things. To estimate annual values of net ecosystem carbon exchange (NEE), latent heat flux (LE) and sensible heat flux (H), such gaps in the measured data must be filled or imputed. So far, no standardized method has been accepted and the imputation methods used are largely dependent on the researchers’ choice. Here, we used multiple imputation (MI) to gap-fill the missing data for annual estimations of NEE, LE and H at three flux sites associated with the FluxNet effort. MI is a Monte Carlo technique in which the missing values are replaced by several simulated values. Each data set imputed is a complete one where the observed values are the same as those in the original data set; only the missing values are different. Thus, the normal statistical analysis (e.g. annual total calculation) can be applied to each data set separately. The results of each analysis can be recombined into one summary. We applied the MI method to eddy covariance measurements collected from Walker Branch Watershed (WBW) site (a deciduous forest), Duke site (a coniferous forest) and Niwot site (a subalpine forest). Results showed that annual estimations of NEE, LE and H by MI were comparable to other imputation methods but MI was much easier to apply because of readily available software and standard algorithms. Besides the normal statistical analyses, MI also provided confidence intervals for each estimated parameter. This confidence interval is most useful when assessing energy, water, and carbon balance closures at a given tower site. Significant differences in annual NEE, LE and H were found among years at the three AmeriFlux sites. NEE at the Niwot Ridge site was lower and LE and H were higher than at the other two sites. With the available software and realistic gap-filling capability, MI has the potential to become a standardized method to gap-fill eddy covariance flux data for annual estimations and to improve the analysis of uncertainties associated with annual estimations of NEE, LE and H from regional and global flux networks.},
	language = {en},
	number = {1},
	urldate = {2021-04-02},
	journal = {Agricultural and Forest Meteorology},
	author = {Hui, Dafeng and Wan, Shiqiang and Su, Bo and Katul, Gabriel and Monson, Russell and Luo, Yiqi},
	month = jan,
	year = {2004},
	keywords = {Eddy covariance, Latent heat, Missing data, Multiple imputation, Net ecosystem carbon exchange, Regression analysis, Sensible heat},
	pages = {93--111},
}

@article{jankowski_aquatic_nodate,
	title = {Aquatic ecosystem metabolism as a tool in environmental management},
	volume = {n/a},
	copyright = {© 2021 Wiley Periodicals LLC. This article has been contributed to by US Government employees and their work is in the public domain in the USA.},
	issn = {2049-1948},
	url = {https://pericles.pericles-prod.literatumonline.com/doi/abs/10.1002/wat2.1521},
	doi = {10.1002/wat2.1521},
	abstract = {Recent advances in high-frequency environmental sensing and statistical approaches have greatly expanded the breadth of knowledge regarding aquatic ecosystem metabolism—the measurement and interpretation of gross primary productivity (GPP) and ecosystem respiration (ER). Aquatic scientists are poised to take advantage of widely available datasets and freely-available modeling tools to apply functional information gained through ecosystem metabolism to help inform environmental management. Historically, several logistical and conceptual factors have limited the widespread application of metabolism in management settings. Benefitting from new instrumental and modeling tools, it is now relatively straightforward to extend routine monitoring of dissolved oxygen (DO) to dynamic measures of aquatic ecosystem function (GPP and ER) and key physical processes such as gas exchange with the atmosphere (G). We review the current approaches for using DO data in environmental management with a focus on the United States, but briefly describe management frameworks in Europe and Canada. We highlight new applications of diel DO data and metabolism in regulatory settings and explore how they can be applied to managing and monitoring ecosystems. We then review existing data types and provide a short guide for implementing field measurements and modeling of ecosystem metabolic processes using currently available tools. Finally, we discuss research needed to overcome current conceptual limitations of applying metabolism in management settings. Despite challenges associated with modeling metabolism in rivers and lakes, rapid developments in this field have moved us closer to utilizing real-time estimates of GPP, ER, and G to improve the assessment and management of environmental change. This article is categorized under: Water and Life {\textgreater} Conservation, Management, and Awareness},
	language = {en},
	number = {n/a},
	urldate = {2021-04-02},
	journal = {WIREs Water},
	author = {Jankowski, Kathi Jo and Mejia, Francine H. and Blaszczak, Joanna R. and Holtgrieve, Gordon W.},
	keywords = {aquatic, dissolved oxygen, ecosystem metabolism, environmental management},
	pages = {e1521},
}

@article{pedersen_hierarchical_2019,
	title = {Hierarchical generalized additive models in ecology: an introduction with mgcv},
	volume = {7},
	issn = {2167-8359},
	shorttitle = {Hierarchical generalized additive models in ecology},
	url = {https://peerj.com/articles/6876},
	doi = {10.7717/peerj.6876},
	abstract = {In this paper, we discuss an extension to two popular approaches to modeling complex structures in ecological data: the generalized additive model (GAM) and the hierarchical model (HGLM). The hierarchical GAM (HGAM), allows modeling of nonlinear functional relationships between covariates and outcomes where the shape of the function itself varies between different grouping levels. We describe the theoretical connection between HGAMs, HGLMs, and GAMs, explain how to model different assumptions about the degree of intergroup variability in functional response, and show how HGAMs can be readily fitted using existing GAM software, the mgcv package in R. We also discuss computational and statistical issues with fitting these models, and demonstrate how to fit HGAMs on example data. All code and data used to generate this paper are available at: github.com/eric-pedersen/mixed-effect-gams.},
	language = {en},
	urldate = {2021-04-01},
	journal = {PeerJ},
	author = {Pedersen, Eric J. and Miller, David L. and Simpson, Gavin L. and Ross, Noam},
	month = may,
	year = {2019},
	note = {Publisher: PeerJ Inc.},
	pages = {e6876},
}

@article{simpson_modelling_2018,
	title = {Modelling {Palaeoecological} {Time} {Series} {Using} {Generalised} {Additive} {Models}},
	volume = {6},
	issn = {2296-701X},
	url = {https://www.frontiersin.org/articles/10.3389/fevo.2018.00149/full},
	doi = {10.3389/fevo.2018.00149},
	abstract = {In the absence of annual laminations, time series generated from lake sediments or other similar stratigraphic sequences are irregularly spaced in time, which complicates formal analysis using classical statistical time series models. In lieu, statistical analyses of trends in palaeoenvironmental time series, if done at all, have typically used simpler linear regressions or (non-) parametric correlations with little regard for the violation of assumptions that almost surely occurs due to temporal dependencies in the data or that correlations do not provide estimates of the magnitude of change, just whether or not there is a linear or monotonic trend. Alternative approaches have used LOESS-estimated trends to justify data interpretations or test hypotheses as to the causal factors without considering the inherent subjectivity of the choice of parameters used to achieve the LOESS fit (e.g. span width, degree of polynomial). Generalized additive models (GAMs) are statistical models that can be used to estimate trends as smooth functions of time. Unlike LOESS, GAMs use automatic smoothness selection methods to objectively determine the complexity of the fitted trend, and as formal statistical models, GAMs, allow for potentially complex, non-linear trends, a proper accounting of model uncertainty, and the identification of periods of significant temporal change. Here, I present a consistent and modern approach to the estimation of trends in palaeoenvironmental time series using GAMs, illustrating features of the methodology with two example time series of contrasting complexity; a 150-year bulk organic matter δ15N time series from Small Water, UK, and a 3000-year alkenone record from Braya-Sø, Greenland. I discuss the underlying mechanics of GAMs that allow them to learn the shape of the trend from the data themselves and how simultaneous confidence intervals and the first derivatives of the trend are used to properly account for model uncertainty and identify periods of change. It is hoped that by using GAMs greater attention is paid to the statistical estimation of trends in palaeoenvironmental time series leading to more a robust and reproducible palaeoscience.},
	language = {English},
	urldate = {2021-04-01},
	journal = {Frontiers in Ecology and Evolution},
	author = {Simpson, Gavin L.},
	year = {2018},
	note = {Publisher: Frontiers},
	keywords = {Spline, environmental change, generalized additive models, simultaneous interval, time series},
}

@article{enders_bayesian_2013,
	title = {A {Bayesian} {Approach} for {Estimating} {Mediation} {Effects} {With} {Missing} {Data}},
	volume = {48},
	issn = {0027-3171},
	url = {10.1080/00273171.2013.784862},
	doi = {10.1080/00273171.2013.784862},
	abstract = {Methodologists have developed mediation analysis techniques for a broad range of substantive applications, yet methods for estimating mediating mechanisms with missing data have been understudied. This study outlined a general Bayesian missing data handling approach that can accommodate mediation analyses with any number of manifest variables. Computer simulation studies showed that the Bayesian approach produced frequentist coverage rates and power estimates that were comparable to those of maximum likelihood with the bias-corrected bootstrap. We share an SAS macro that implements Bayesian estimation and use 2 data analysis examples to demonstrate its use.},
	number = {3},
	urldate = {2021-03-31},
	journal = {Multivariate Behavioral Research},
	author = {Enders, Craig K. and Fairchild, Amanda J. and MacKinnon, David P.},
	month = may,
	year = {2013},
	pmid = {24039298},
	pages = {340--369},
}

@article{kong_sequential_1994,
	title = {Sequential Imputations and {Bayesian} Missing Data Problems},
	volume = {89},
	issn = {0162-1459},
	url = {https://amstat.tandfonline.com/doi/abs/10.1080/01621459.1994.10476469},
	doi = {10.1080/01621459.1994.10476469},
	abstract = {For missing data problems, Tanner and Wong have described a data augmentation procedure that approximates the actual posterior distribution of the parameter vector by a mixture of complete data posteriors. Their method of constructing the complete data sets is closely related to the Gibbs sampler. Both required iterations, and, similar to the EM algorithm, convergence can be slow. We introduce in this article an alternative procedure that involves imputing the missing data sequentially and computing appropriate importance sampling weights. In many applications this new procedure works very well without the need for iterations. Sensitivity analysis, influence analysis, and updating with new data can be performed cheaply. Bayesian prediction and model selection can also be incorporated. Examples taken from a wide range of applications are used for illustration.},
	number = {425},
	urldate = {2021-03-31},
	journal = {Journal of the American Statistical Association},
	author = {Kong, Augustine and Liu, Jun S. and Wong, Wing   Hung},
	month = mar,
	year = {1994},
	note = {Publisher: Taylor \& Francis},
	pages = {278--288},
}

@misc{tjo_bayesian_nodate,
	title = {Bayesian modeling with {R} and {Stan} (5): {Time} series with seasonality},
	shorttitle = {Bayesian modeling with {R} and {Stan} (5)},
	url = {https://tjo-en.hatenablog.com/entry/2015/08/18/123000},
	abstract = {In the previous post, we successfully estimated a model with a nonlinear trend by using Stan. But please remember this is a time series dataset. Does it include any other kind of nonlinear components? Yes, we have to be careful for seasonality. Actually when I generate the dataset, I added a seasona…},
	language = {en},
	urldate = {2021-03-31},
	journal = {Data Scientist TJO in Tokyo},
	author = {{TJO}},
}

@article{bertschinger_bayesian_2021,
	title = {Bayesian estimation and likelihood-based comparison of agent-based volatility models},
	volume = {16},
	issn = {1860-7128},
	url = {10.1007/s11403-020-00289-z},
	doi = {10.1007/s11403-020-00289-z},
	abstract = {The statistical description and modeling of volatility plays a prominent role in econometrics, risk management and finance. GARCH and stochastic volatility models have been extensively studied and are routinely fitted to market data, albeit providing a phenomenological description only. In contrast, agent-based modeling starts from the premise that modern economies consist of a vast number of individual actors with heterogeneous expectations and incentives. Observed market statistics then emerge from the collective dynamics of many actors following heterogeneous, yet simple rules. On the one hand, such models generate volatility dynamics, qualitatively matching several stylized facts. On the other hand, they illustrate the possible role of different mechanisms, such as chartist trading and herding behavior. Yet, rigorous and quantitative statistical fits are still mostly lacking. Here, we propose Hamiltonian Monte Carlo, an efficient and scalable Markov chain Monte Carlo algorithm, as a general method for Bayesian inference of agent-based models. In particular, we implement several models by Vikram and Sinha, Franke and Westerhoff and Alfarano, Lux and Wagner in Stan, an accessible probabilistic programming language for Bayesian modeling. We also compare the performance of these models with standard econometric models of the GARCH and stochastic volatility families. We find that the best agent-based models are on par with stochastic volatility models in terms of predictive likelihood, yet exhibit challenging posterior geometries requiring care in model comparison and sophisticated sampling algorithms.},
	language = {en},
	number = {1},
	urldate = {2021-03-31},
	journal = {Journal of Economic Interaction and Coordination},
	author = {Bertschinger, Nils and Mozzhorin, Iurii},
	month = jan,
	year = {2021},
	pages = {173--210},
}

@article{chatzilena_contemporary_2019,
	title = {Contemporary statistical inference for infectious disease models using {Stan}},
	volume = {29},
	issn = {1755-4365},
	url = {https://www.sciencedirect.com/science/article/pii/S1755436519300325},
	doi = {10.1016/j.epidem.2019.100367},
	abstract = {This paper is concerned with the application of recent statistical advances to inference of infectious disease dynamics. We describe the fitting of a class of epidemic models using Hamiltonian Monte Carlo and variational inference as implemented in the freely available Stan software. We apply the two methods to real data from outbreaks as well as routinely collected observations. Our results suggest that both inference methods are computationally feasible in this context, and show a trade-off between statistical efficiency versus computational speed. The latter appears particularly relevant for real-time applications.},
	language = {en},
	urldate = {2021-03-31},
	journal = {Epidemics},
	author = {Chatzilena, Anastasia and van Leeuwen, Edwin and Ratmann, Oliver and Baguelin, Marc and Demiris, Nikolaos},
	month = dec,
	year = {2019},
	keywords = {Automatic differentiation variational inference, Epidemic models, Hamiltonian Monte Carlo, No-U-turn sampler, Stan},
	pages = {100367},
}

@article{song_analysis_2002,
	title = {Analysis of structural equation model with ignorable missing continuous and polytomous data},
	volume = {67},
	issn = {1860-0980},
	url = {10.1007/BF02294846},
	doi = {10.1007/BF02294846},
	abstract = {The main purpose of this article is to develop a Bayesian approach for structural equation models with ignorable missing continuous and polytomous data. Joint Bayesian estimates of thresholds, structural parameters and latent factor scores are obtained simultaneously. The idea of data augmentation is used to solve the computational difficulties involved. In the posterior analysis, in addition to the real missing data, latent variables and latent continuous measurements underlying the polytomous data are treated as hypothetical missing data. An algorithm that embeds the Metropolis-Hastings algorithm within the Gibbs sampler is implemented to produce the Bayesian estimates. A goodness-of-fit statistic for testing the posited model is presented. It is shown that the proposed approach is not sensitive to prior distributions and can handle situations with a large number of missing patterns whose underlying sample sizes may be small. Computational efficiency of the proposed procedure is illustrated by simulation studies and a real example.},
	language = {en},
	number = {2},
	urldate = {2021-03-31},
	journal = {Psychometrika},
	author = {Song, Xin-Yuan and Lee, Sik-Yum},
	month = jun,
	year = {2002},
	pages = {261--288},
}

@article{junger_imputation_2015,
	title = {Imputation of missing data in time series for air pollutants},
	volume = {102},
	issn = {1352-2310},
	url = {https://www.sciencedirect.com/science/article/pii/S1352231014009145},
	doi = {10.1016/j.atmosenv.2014.11.049},
	abstract = {Missing data are major concerns in epidemiological studies of the health effects of environmental air pollutants. This article presents an imputation-based method that is suitable for multivariate time series data, which uses the EM algorithm under the assumption of normal distribution. Different approaches are considered for filtering the temporal component. A simulation study was performed to assess validity and performance of proposed method in comparison with some frequently used methods. Simulations showed that when the amount of missing data was as low as 5\%, the complete data analysis yielded satisfactory results regardless of the generating mechanism of the missing data, whereas the validity began to degenerate when the proportion of missing values exceeded 10\%. The proposed imputation method exhibited good accuracy and precision in different settings with respect to the patterns of missing observations. Most of the imputations obtained valid results, even under missing not at random. The methods proposed in this study are implemented as a package called mtsdi for the statistical software system R.},
	language = {en},
	urldate = {2021-03-31},
	journal = {Atmospheric Environment},
	author = {Junger, W. L. and Ponce de Leon, A.},
	month = feb,
	year = {2015},
	keywords = {Air pollution, Data imputation, EM algorithm, Environmental epidemiology, Missing data, Particulate matter, Time series},
	pages = {96--104},
}

@article{maldonado_experimental_nodate,
	title = {An {Experimental} {Comparison} of {Methods} to {Handle} {Missing} {Values} in {Environmental} {Datasets}},
	abstract = {This paper reports on a comparison of different techniques to handle missing data in a real environmental dataset containing missing values. In particular, we handled a dataset related to a surface water quality index. The chosen techniques were regression imputation by linear regression, a model tree and a Bayesian network; multiple imputation by chained equations; and data augmentation by a Bayesian network. The models were tested by analyzing the predictive maps and by comparing the density function of the predicted variable with the observed one. The experimental results showed that the imputation by linear regression and the multiple imputation by chained equations maintained the characteristics of the response variable more than the remaining models.},
	language = {en},
	author = {Maldonado, A D and Aguilera, P A and Salmeron, A},
	pages = {9},
}

@article{scutari_bayesian_2019,
	title = {Bayesian {Network} {Models} for {Incomplete} and {Dynamic} {Data}},
	url = {http://arxiv.org/abs/1906.06513},
	abstract = {Bayesian networks are a versatile and powerful tool to model complex phenomena and the interplay of their components in a probabilistically principled way. Moving beyond the comparatively simple case of completely observed, static data, which has received the most attention in the literature, in this paper we will review how Bayesian networks can model dynamic data and data with incomplete observations. Such data are the norm at the forefront of research and in practical applications, and Bayesian networks are uniquely positioned to model them due to their explainability and interpretability.},
	urldate = {2021-03-31},
	journal = {arXiv:1906.06513 [math, stat]},
	author = {Scutari, Marco},
	month = oct,
	year = {2019},
	note = {arXiv: 1906.06513},
	keywords = {Mathematics - Statistics Theory, Statistics - Machine Learning, Statistics - Methodology},
}

@article{racault_impact_2014,
	title = {Impact of missing data on the estimation of ecological indicators from satellite ocean-colour time-series},
	volume = {152},
	issn = {0034-4257},
	url = {https://www.sciencedirect.com/science/article/pii/S0034425714002041},
	doi = {10.1016/j.rse.2014.05.016},
	abstract = {Ocean-colour remote sensing provides high-resolution and global-coverage of chlorophyll concentration, which can be used to estimate ecological indicators and to study inter-annual and long-term trends in the state of the marine ecosystem. To date, the record of ocean-colour observations is a rich one, including data from a number of sensors spanning more than three decades. The ESA Ocean-Colour Climate Change Initiative has advanced seamless merging of ocean-colour observations from missions during the period 1990s to 2010s. However, comparison of these more recent observations with records from 1970s to 1980s remains a complex undertaking, particularly for absolute values of chlorophyll concentration, primarily due to differences in the sensors. A further impediment to the analysis of the past records is the non-uniform distribution of gaps in the observations, in both time and space dimensions, when data from two or more sensors are compared. Here, we use the CZCS gap distribution from the Coastal Zone Color Scanner (CZCS, 1978–1986) as a mask to evaluate the impact that missing data may have on the estimation of six ecological indicators, when using the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) data set. Specifically, we evaluate the precision and accuracy of indicators by computing the root-mean-square-error (RMSE) and the bias arising purely from missing data. We develop an original resampling method allowing comparison of indicator estimates between SeaWiFS reference time-series and SeaWiFS time-series with CZCS-like gaps. We reduce some of the sampling gaps by applying a linear interpolation procedure, and compute multi-year averages of the indicators for every one-by-one degree pixel where sufficient data are available. Indicators from SeaWiFS reference and SeaWiFS with CZCS-like gaps are compared. Lowest uncertainty arising from missing data is observed in the indicators of annual mean and median chlorophyll concentration (global mean RMSE of 8\% and {\textbar}bias{\textbar} ≤1\%), whilst higher uncertainty is recorded for the peak chlorophyll values and the duration of the phytoplankton growing period (global mean RMSE of 33 and 47\% respectively and {\textbar}bias{\textbar} ≤20\%). Timing of initiation of the increasing phase of chlorophyll concentration in the seasonal cycle and timing of peak chlorophyll are subject to a global mean RMSE of nearly two months and a bias of two weeks or less. The present quantitative evaluation of uncertainty due to missing data demonstrates that, when pooled to create a nine-year climatology at 8-day temporal resolution, the coverage of CZCS is adequate for many climate-related studies on the marine ecosystem. Phytoplankton annual mean biomass can be estimated with low error in approximately 95\% of the global oceans (i.e. regions where the indicators can be estimated with RMSE values of less than 30\% and bias within ±10\%), and the phenological patterns can be estimated with low error in approximately 25\% of the global oceans.},
	language = {en},
	urldate = {2021-03-31},
	journal = {Remote Sensing of Environment},
	author = {Racault, Marie-Fanny and Sathyendranath, Shubha and Platt, Trevor},
	month = sep,
	year = {2014},
	keywords = {CZCS, Chlorophyll-a, Ecological indicators, Missing data, Phenology, SeaWiFS, Uncertainty},
	pages = {15--28},
}

@article{nakagawa_model_2011-1,
	title = {Model averaging, missing data and multiple imputation: a case study for behavioural ecology},
	volume = {65},
	issn = {1432-0762},
	shorttitle = {Model averaging, missing data and multiple imputation},
	url = {10.1007/s00265-010-1044-7},
	doi = {10.1007/s00265-010-1044-7},
	abstract = {Model averaging, specifically information theoretic approaches based on Akaike’s information criterion (IT-AIC approaches), has had a major influence on statistical practices in the field of ecology and evolution. However, a neglected issue is that in common with most other model fitting approaches, IT-AIC methods are sensitive to the presence of missing observations. The commonest way of handling missing data is the complete-case analysis (the complete deletion from the dataset of cases containing any missing values). It is well-known that this results in reduced estimation precision (or reduced statistical power), biased parameter estimates; however, the implications for model selection have not been explored. Here we employ an example from behavioural ecology to illustrate how missing data can affect the conclusions drawn from model selection or based on hypothesis testing. We show how missing observations can be recovered to give accurate estimates for IT-related indices (e.g. AIC and Akaike weight) as well as parameters (and their standard errors) by utilizing ‘multiple imputation’. We use this paper to illustrate key concepts from missing data theory and as a basis for discussing available methods for handling missing data. The example is intended to serve as a practically oriented case study for behavioural ecologists deciding on how to handle missing data in their own datasets and also as a first attempt to consider the problems of conducting model selection and averaging in the presence of missing observations.},
	language = {en},
	number = {1},
	urldate = {2021-03-31},
	journal = {Behavioral Ecology and Sociobiology},
	author = {Nakagawa, Shinichi and Freckleton, Robert P.},
	month = jan,
	year = {2011},
	pages = {103--116},
}

@article{trentman_agricultural_2021,
	title = {Agricultural layering explains variation in sediment {P} dynamics in streams draining two distinct agricultural biomes},
	volume = {83},
	issn = {1420-9055},
	url = {10.1007/s00027-020-00764-6},
	doi = {10.1007/s00027-020-00764-6},
	abstract = {Phosphorus (P) enrichment of headwater agricultural streams due to the runoff of fertilizers can lead to the eutrophication of downstream aquatic ecosystems. Agriculture is intensive but heterogeneous in the Mississippi River Basin, with a mixture of pasture, row crops, and patches of confined animal feedlot operations (CAFOs). Many studies have evaluated how a single form of agricultural land use can affect sediment response to P loading, but few have considered the role of agricultural layering (i.e., one vs. two forms of agriculture in the same watershed). We used a synoptic sampling approach to determine the effect of agricultural layering on sediment P cycling in two watersheds in Arkansas (AR) and Michigan (MI). We sampled stream sediments from 10 sites in each watershed across two seasons; sampling from sites draining row crop vs. row crop plus a dairy in MI, and from sites draining chicken CAFOs vs. chicken CAFOs with pasture in AR. The proportion of bioavailable P was highest in MI and lowest in AR sediments, likely due to enhanced runoff of P rich sediment from row crops in MI, compared to sites in AR that were still predominantly forested, despite isolated CAFOs. Sediment P retention capacity was lowest downstream of sites with row crop + dairy in MI and highest at sites draining CAFOs alone in AR. Finally, substrate size differences between watersheds likely influences the reach-scale potential P retention capacity. Overall, we show that agricultural layering along with underlying geology can explain drivers influencing sediment P dynamics in agricultural streams.},
	language = {en},
	number = {1},
	urldate = {2021-03-19},
	journal = {Aquatic Sciences},
	author = {Trentman, Matt T. and Tank, Jennifer L. and Braund, Danielle and Entrekin, Sally A.},
	year = {2021},
	pages = {7},
}

@article{shangguan_autonomous_2021,
	title = {Autonomous in situ measurements of freshwater alkalinity},
	volume = {19},
	copyright = {© 2020 The Authors. Limnology and Oceanography: Methods published by Wiley Periodicals LLC. on behalf of Association for the Sciences of Limnology and Oceanography.},
	issn = {1541-5856},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lom3.10404},
	doi = {10.1002/lom3.10404},
	abstract = {Total alkalinity (AT) is an important parameter in the study of aquatic biogeochemical cycles, chemical speciation modeling, and many other important fundamental and anthropogenic (e.g., industrial) processes. We know little about its short-term variability, however, because studies are based on traditional bottle sampling typically with coarse temporal resolution. In this work, an autonomous AT sensor, named the Submersible Autonomous Moored Instrument for Alkalinity (SAMI-alk), was tested for freshwater applications. A comprehensive evaluation was conducted in the laboratory using freshwater standards. The results demonstrated excellent precision and accuracy (± 0.1\%–0.4\%) over the AT range from 800 to 3000 μmol L−1. The system had no drift over an 8 d test and also demonstrated limited sensitivity to variations in temperature and ionic strength. Three SAMI-alks were deployed for 23 d in the Clark Fork River, Montana, with a suite of other sensors. Compared to discrete samples, in situ accuracy for the three instruments were within 10–20 μmol L−1 (0.3–0.6\%), indicating good performance considering the challenges of in situ measurements in a high sediment, high biofouling riverine environment with large and rapid changes in temperature. These data reveal the complex AT dynamics that are typically missed by coarse sampling. We observed AT diel cycles as large as 60–80 μmol L−1, as well as a rapid change caused by a runoff event. Significant errors in inorganic carbon system modeling result if these short-term variations are not considered. This study demonstrates both the feasibility of the technology and importance of high-resolution AT measurements.},
	language = {en},
	number = {2},
	urldate = {2021-03-26},
	journal = {Limnology and Oceanography: Methods},
	author = {Shangguan, Qipei and Lai, Chun-Ze and Beatty, Cory M. and Young, Fischer L. and Spaulding, Reggie S. and DeGrandpre, Michael D.},
	year = {2021},
	pages = {51--66},
}

@article{rowland_lake_2021,
	title = {Lake {Erie} tributary nutrient trend evaluation: {Normalizing} concentrations and loads to reduce flow variability},
	volume = {125},
	issn = {1470-160X},
	shorttitle = {Lake {Erie} tributary nutrient trend evaluation},
	url = {https://www.sciencedirect.com/science/article/pii/S1470160X21002661},
	doi = {10.1016/j.ecolind.2021.107601},
	abstract = {Establishing tributary load (i.e., the mass exported over a period of time) targets to reduce anthropogenic nutrient inputs to receiving waters — and thus eutrophication — is a common mitigation strategy in freshwater and coastal ecosystems. However, detecting and quantifying trends can be difficult because annual precipitation strongly influences tributary flow (e.g., average daily stream discharge). This may obscure trends as wet years tend to produce high tributary loads despite management activities to reduce nutrient export, and dry years typically generate low loads, even without management of nutrients. Furthermore, flow and nutrient concentrations are often correlated. Earlier efforts to reduce the effect of flow variability on tributary nutrient assessment were limited by computational and methodological constraints, until the weighted regressions on time, discharge, and season (WRTDS) method was introduced in 2010. Here we use WRTDS to assess nutrient concentration and load changes from 1982 to 2018 in three tributaries to the western basin of Lake Erie, of the Laurentian Great Lakes. Generally, trends revealed by flow-normalization do not contradict those of non-normalized metrics; however flow-normalization made the patterns more perceptible than in non-normalized metrics and reduced the influence of a particularly wet or dry period at the end of records on long-term trend analysis. We demonstrate that using WRTDS for flow-normalization removed the noise arising from annual precipitation variability and makes tributary nutrient trend evaluation more straightforward.},
	language = {en},
	urldate = {2021-03-24},
	journal = {Ecological Indicators},
	author = {Rowland, Freya E. and Stow, Craig A. and Johnson, Laura T. and Hirsch, Robert M.},
	month = jun,
	year = {2021},
	keywords = {Long-term data, Monitoring, Nutrients, Statistics, Streams, Time-series analysis},
	pages = {107601},
}

@article{ogle_ensuring_2020,
	title = {Ensuring identifiability in hierarchical mixed effects {Bayesian} models},
	volume = {30},
	copyright = {© 2020 by the Ecological Society of America},
	issn = {1939-5582},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/eap.2159},
	doi = {10.1002/eap.2159},
	abstract = {Ecologists are increasingly familiar with Bayesian statistical modeling and its associated Markov chain Monte Carlo (MCMC) methodology to infer about or to discover interesting effects in data. The complexity of ecological data often suggests implementation of (statistical) models with a commensurately rich structure of effects, including crossed or nested (i.e., hierarchical or multi-level) structures of fixed and/or random effects. Yet, our experience suggests that most ecologists are not familiar with subtle but important problems that often arise with such models and with their implementation in popular software. Of foremost consideration for us is the notion of effect identifiability, which generally concerns how well data, models, or implementation approaches inform about, i.e., identify, quantities of interest. In this paper, we focus on implementation pitfalls that potentially misinform subsequent inference, despite otherwise informative data and models. We illustrate the aforementioned issues using random effects regressions on synthetic data. We show how to diagnose identifiability issues and how to remediate these issues with model reparameterization and computational and/or coding practices in popular software, with a focus on JAGS, OpenBUGS, and Stan. We also show how these solutions can be extended to more complex models involving multiple groups of nested, crossed, additive, or multiplicative effects, for models involving random and/or fixed effects. Finally, we provide example code (JAGS/OpenBUGS and Stan) that practitioners can modify and use for their own applications.},
	language = {en},
	number = {7},
	urldate = {2021-03-24},
	journal = {Ecological Applications},
	author = {Ogle, Kiona and Barber, Jarrett J.},
	year = {2020},
	keywords = {MCMC, crossed effects, equifinality, fixed effects, hierarchical model, identifiability, multi-level model, nested effects, prior distribution, random effects, sum-to-zero, sweeping},
	pages = {e02159},
}

@article{shinohara_composition_2018,
	title = {The composition of particulate phosphorus: {A} case study of the {Grand} {River}, {Canada}},
	volume = {44},
	issn = {0380-1330},
	shorttitle = {The composition of particulate phosphorus},
	url = {https://www.sciencedirect.com/science/article/pii/S0380133018300418},
	doi = {10.1016/j.jglr.2018.03.006},
	abstract = {We examined the fractions of particulate phosphorus (PP) in the lower reaches of the Grand River, Canada, to test the hypothesis that the river is a source of both particulate-bound orthophosphate and labile species of PP. At the mouth of the Grand River, the proportion of particulate organic P (POP) was, on average, 57.7\% of total PP, which was significantly higher than the proportion of particulate inorganic P (PIP) in PP. Analysis with 31P nuclear magnetic resonance (NMR) spectroscopy showed that the proportion of P species other than orthophosphate in the NaOH- EDTA extract was 1.75 times greater than that of orthophosphate. Labile P species (e.g. nucleotides and pyrophosphate) were present in the NMR spectrum; whereas, refractory organic P (myo-inositol hexakisphosphate) was absent. These results suggest that during winter and spring, the Grand River supplies primarily bioavailable phosphorus species in organic forms to Lake Erie, rather than inorganic orthophosphate. These results suggest that labile organic P is contained in PP rather than alkaline extractable inorganic P. Future studies should examine POP species in other rivers of the Lake Erie watershed.},
	language = {en},
	number = {3},
	urldate = {2021-03-19},
	journal = {Journal of Great Lakes Research},
	author = {Shinohara, Ryuichiro and Ouellette, Lance and Nowell, Peter and Parsons, Chris T. and Matsuzaki, Shin-ichiro S. and Paul Voroney, R.},
	month = jun,
	year = {2018},
	keywords = {Labile phosphorus, Organic phosphorus, P nuclear magnetic resonance (NMR), Suspended particles},
	pages = {527--534},
}

@article{lai_autonomous_2018,
	title = {Autonomous {Optofluidic} {Chemical} {Analyzers} for {Marine} {Applications}: {Insights} from the {Submersible} {Autonomous} {Moored} {Instruments} ({SAMI}) for {pH} and {pCO2}},
	volume = {4},
	issn = {2296-7745},
	shorttitle = {Autonomous {Optofluidic} {Chemical} {Analyzers} for {Marine} {Applications}},
	url = {https://www.frontiersin.org/articles/10.3389/fmars.2017.00438/full},
	doi = {10.3389/fmars.2017.00438},
	abstract = {The commercial availability of inexpensive fiber optics and small volume pumps in the early 1990’s provided the components necessary for the successful development of low power, low reagent consumption, autonomous optofluidic analyzers for marine applications. It was evident that to achieve calibration-free performance, reagent-based sensors would require frequent renewal of the reagent by pumping the reagent from an impermeable, inert reservoir to the sensing interface. Pumping also enabled measurement of a spectral blank further enhancing accuracy and stability. The first instrument that was developed based on this strategy, the Submersible Autonomous Moored Instrument for CO2 (SAMI-CO2), uses a pH indicator for measurement of the partial pressure of CO2 (pCO2). Because the pH indicator gives an optical response, the instrument requires an optofluidic design where the indicator is pumped into a gas permeable membrane and then to an optical cell for analysis. The pH indicator is periodically flushed from the optical cell by using a valve to switch from the pH indicator to a blank solution. Because of the small volume and low power light source, over 8,500 measurements can be obtained with a {\textasciitilde}500 mL reagent bag and 8 alkaline D-cell battery pack. The primary drawback is that the design is more complex compared to the single-ended electrode or optode that is envisioned as the ideal sensor. The SAMI technology has subsequently been used for the successful development of autonomous pH and total alkalinity analyzers. In this manuscript, we will discuss the pros and cons of the SAMI pCO2 and pH optofluidic technology and highlight some past data sets and applications for studying the carbon cycle in aquatic ecosystems.},
	language = {English},
	urldate = {2021-03-18},
	journal = {Frontiers in Marine Science},
	author = {Lai, Chun-Ze and DeGrandpre, Michael D. and Darlington, Reuben C.},
	year = {2018},
	note = {Publisher: Frontiers},
	keywords = {Carbon Cycle, Sensors, biogeochemistry, chemical, marine, optofluidics},
}

@article{simpson_sediment_nodate,
	title = {Sediment phosphorus buffering in streams at baseflow: {A} meta-analysis},
	volume = {n/a},
	copyright = {© 2021 The Authors. Journal of Environmental Quality © 2021 American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America},
	issn = {1537-2537},
	shorttitle = {Sediment phosphorus buffering in streams at baseflow},
	url = {https://acsess.pericles-prod.literatumonline.com/doi/abs/10.1002/jeq2.20202},
	doi = {10.1002/jeq2.20202},
	abstract = {Phosphorus (P) pollution of surface waters remains a challenge for protecting and improving water quality. Central to the challenge is understanding what regulates P concentrations in streams. This quantitative review synthesizes the literature on a major control of P concentrations in streams at baseflow—the sediment P buffer—to better understand streamwater–sediment P interactions. We conducted a global meta-analysis of sediment equilibrium phosphate concentrations at net zero sorption (EPC0), which is the dissolved reactive P (DRP) concentration toward which sediments buffer solution DRP. Our analysis of 45 studies and {\textgreater}900 paired observations of DRP and EPC0 showed that sediments often have potential to remove or release P to the streamwater (83\% of observations), meaning that “equilibrium” between sediment and streamwater is rare. This potential for P exchange is moderated by sediment and stream characteristics, including sorption affinity, stream pH, exchangeable P concentration, and particle sizes. The potential for sediments to modify streamwater DRP concentrations is often not realized owing to other factors (e.g., hydrologic interactions). Sediment surface chemistry, hyporheic exchange, and biota can also influence the potential exchange of P between sediments and the streamwater. Methodological choices significantly influenced EPC0 determination and thus the estimated potential for P exchange; we therefore discuss how to measure and report EPC0 to best suit research objectives and aid in interstudy comparison. Our results enhance understanding of the sediment P buffer and inform how EPC0 can be effectively applied to improve management of aquatic P pollution and eutrophication.},
	language = {en},
	number = {n/a},
	urldate = {2021-03-18},
	journal = {Journal of Environmental Quality},
	author = {Simpson, Zachary P. and McDowell, Richard W. and Condron, Leo M. and McDaniel, Marshall D. and Jarvie, Helen P. and Abell, Jonathan M.}
}

@article{ravishankar_resistance_2020,
	title = {Resistance {Mechanisms} of {Saccharomyces} cerevisiae to {Commercial} {Formulations} of {Glyphosate} {Involve} {DNA} {Damage} {Repair}, the {Cell} {Cycle}, and the {Cell} {Wall} {Structure}},
	volume = {10},
	issn = {2160-1836},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7263678/},
	doi = {10.1534/g3.120.401183},
	abstract = {The use of glyphosate-based herbicides is widespread and despite their extensive use, their effects are yet to be deciphered completely. The additives in commercial formulations of glyphosate, though labeled inert when used individually, have adverse effects when used in combination with other additives along with the active ingredient. As a species, Saccharomyces cerevisiae has a wide range of resistance to glyphosate-based herbicides. To investigate the underlying genetic differences between sensitive and resistant strains, global changes in gene expression were measured, when yeast were exposed to a glyphosate-based herbicide (GBH). Expression of genes involved in numerous pathways crucial to the cell’s functioning, such as DNA replication, MAPK signaling, meiosis, and cell wall synthesis changed. Because so many diverse pathways were affected, these strains were then subjected to in-lab-evolutions (ILE) to select mutations that confer increased resistance. Common fragile sites were found to play a role in adaptation to resistance to long-term exposure of GBHs. Copy number increased in approximately 100 genes associated with cell wall proteins, mitochondria, and sterol transport. Taking ILE and transcriptomic data into account it is evident that GBHs affect multiple biological processes in the cell. One such component is the cell wall structure which acts as a protective barrier in alleviating the stress caused by exposure to inert additives in GBHs. Sed1, a GPI-cell wall protein, plays an important role in tolerance of a GBH. Hence, a detailed study of the changes occurring at the genome and transcriptome levels is essential to better understand the effects of an environmental stressor such as a GBH, on the cell as a whole.},
	number = {6},
	urldate = {2021-03-15},
	journal = {G3: Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Ravishankar, Apoorva and Pupo, Amaury and Gallagher, Jennifer E. G.},
	month = apr,
	year = {2020},
	pmid = {32299824},
	pmcid = {PMC7263678},
	pages = {2043--2056},
}

@article{botstein_yeast_2011,
	title = {Yeast: {An} {Experimental} {Organism} for 21st {Century} {Biology}},
	volume = {189},
	issn = {1943-2631},
	shorttitle = {Yeast},
	url = {10.1534/genetics.111.130765},
	doi = {10.1534/genetics.111.130765},
	abstract = {In this essay, we revisit the status of yeast as a model system for biology. We first summarize important contributions of yeast to eukaryotic biology that we anticipated in 1988 in our first article on the subject. We then describe transformative developments that we did not anticipate, most of which followed the publication of the complete genomic sequence of Saccharomyces cerevisiae in 1996. In the intervening 23 years it appears to us that yeast has graduated from a position as the premier model for eukaryotic cell biology to become the pioneer organism that has facilitated the establishment of the entirely new fields of study called “functional genomics” and “systems biology.” These new fields look beyond the functions of individual genes and proteins, focusing on how these interact and work together to determine the properties of living cells and organisms.},
	number = {3},
	urldate = {2021-03-15},
	journal = {Genetics},
	author = {Botstein, David and Fink, Gerald R},
	month = nov,
	year = {2011},
	pages = {695--704},
}

@article{shepherd_development_2021,
	title = {Development of a yeast-based assay for bioavailable phosphorous},
	url = {http://biorxiv.org/content/early/2021/03/02/2021.02.28.433264.abstract},
	doi = {10.1101/2021.02.28.433264},
	abstract = {Preventing eutrophication of inland freshwater ecosystems requires quantifying the phosphorous (P) content of the streams and rivers that feed them. Typical methods for measuring P assess soluble reactive P (SRP) or total P (TP) and require expensive analytical techniques that produce hazardous waste. Here we present a novel method for measuring the more relevant bioavailable P (BAP); this assay utilizes the growth of familiar baker’s yeast, avoids production of hazardous waste, and reduces cost relative to measurements of SRP and TP. The yeast BAP (yBAP) assay takes advantage of the observation that yeast density at saturating growth increases linearly with provided P. We show that this relationship can be used to measure P in freshwater in concentration ranges relevant to eutrophication. In addition, we measured yBAP in water containing known amount of fertilizer and in samples from agricultural waterways. We observed that the majority of yBAP values were between those obtained from standard SRP and TP measurements, demonstrating that the assay is compatible with real-world settings. The cost-effective and nonhazardous nature of the yeast-based assay suggests that it could have utility in a range of settings, offering added insight to identify water systems at risk of eutrophication from excess phosphorus.Competing Interest StatementThe authors have declared no competing interest.},
	journal = {bioRxiv},
	author = {Shepherd, Heather A.M. and Trentman, Matt T. and Tank, Jennifer L. and Praner, Jennifer and Cervantes, Anissa and Chaudhary, Priya and Gezelter, Jonah and Marrs, Allyson J. and Myers, Kathryn A. and Welsh, Jonathan R. and Wu, Yueh-Fu O. and Goodson, Holly V.},
	month = jan,
	year = {2021},
	pages = {2021.02.28.433264},
}

@article{beel_emerging_2021,
	title = {Emerging dominance of summer rainfall driving {High} {Arctic} terrestrial-aquatic connectivity},
	volume = {12},
	copyright = {2021 Crown},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-021-21759-3},
	doi = {10.1038/s41467-021-21759-3},
	abstract = {Hydrological transformations induced by climate warming are causing Arctic annual fluvial energy to shift from skewed (snowmelt-dominated) to multimodal (snowmelt- and rainfall-dominated) distributions. We integrated decade-long hydrometeorological and biogeochemical data from the High Arctic to show that shifts in the timing and magnitude of annual discharge patterns and stream power budgets are causing Arctic material transfer regimes to undergo fundamental changes. Increased late summer rainfall enhanced terrestrial-aquatic connectivity for dissolved and particulate material fluxes. Permafrost disturbances ({\textless}3\% of the watersheds’ areal extent) reduced watershed-scale dissolved organic carbon export, offsetting concurrent increased export in undisturbed watersheds. To overcome the watersheds’ buffering capacity for transferring particulate material (30 ± 9 Watt), rainfall events had to increase by an order of magnitude, indicating the landscape is primed for accelerated geomorphological change when future rainfall magnitudes and consequent pluvial responses exceed the current buffering capacity of the terrestrial-aquatic continuum.},
	language = {en},
	number = {1},
	urldate = {2021-03-12},
	journal = {Nature Communications},
	author = {Beel, C. R. and Heslop, J. K. and Orwin, J. F. and Pope, M. A. and Schevers, A. J. and Hung, J. K. Y. and Lafrenière, M. J. and Lamoureux, S. F.},
	month = mar,
	year = {2021},
	note = {Number: 1
Publisher: Nature Publishing Group},
	pages = {1448},
}

@article{mcgill_you_nodate,
	title = {You are welcome here: {A} practical guide to diversity, equity, and inclusion for undergraduates embarking on an ecological research experience},
	volume = {n/a},
	copyright = {© 2021 The Authors. Ecology and Evolution published by John Wiley \& Sons Ltd.},
	issn = {2045-7758},
	shorttitle = {You are welcome here},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.7321},
	doi = {10.1002/ece3.7321},
	abstract = {As we build a more diverse, equitable, and inclusive culture in the ecological research community, we must work to support new ecologists by empowering them with the knowledge, tools, validation, and sense of belonging in ecology to succeed. Undergraduate research experiences (UREs) are critical for a student's professional and interpersonal skill development and key for recruiting and retaining students from diverse groups to ecology. However, few resources exist that speak directly to an undergraduate researcher on the diversity, equity, and inclusion (DEI) dimensions of embarking on a first research experience. Here, we write primarily for undergraduate readers, though a broader audience of readers, especially URE mentors, will also find this useful. We explain many of the ways a URE benefits undergraduate researchers and describe how URE students from different positionalities can contribute to an inclusive research culture. We address three common sources of anxiety for URE students through a DEI lens: imposter syndrome, communicating with mentors, and safety in fieldwork. We discuss the benefits as well as the unique vulnerabilities and risks associated with fieldwork, including the potential for harassment and assault. Imposter syndrome and toxic field experiences are known to drive students, including students from underrepresented minority groups, out of STEM. Our goal is to encourage all students, including those from underrepresented groups, to apply for UREs, build awareness of their contributions to inclusion in ecology research, and provide strategies for overcoming known barriers.},
	language = {en},
	number = {n/a},
	urldate = {2021-03-11},
	journal = {Ecology and Evolution},
	author = {McGill, Bonnie M. and Foster, Madison J. and Pruitt, Abagael N. and Thomas, Samantha Gabrielle and Arsenault, Emily R. and Hanschu, Janaye and Wahwahsuck, Kynser and Cortez, Evan and Zarek, Kaci and Loecke, Terrance D. and Burgin, Amy J.},
	keywords = {diversity, ecology, equity, inclusion, undergraduate research experience},
}

@article{hart_working_2017,
	title = {Working {Across} {Contexts}: {Practical} {Considerations} of {Doing} {Indigenist}/{Anti}-{Colonial} {Research}},
	volume = {23},
	issn = {1077-8004},
	shorttitle = {Working {Across} {Contexts}},
	url = {10.1177/1077800416659084},
	doi = {10.1177/1077800416659084},
	abstract = {Although Indigenous scholars have been documenting Indigenous research methodologies, little has been written on the practical considerations of doing research across Indigenous/Settler contexts. As a small social work research team (two Cree researchers and one Settler) exploring Indigenous aging, our work crossed several contexts: academic and community, social locations within the team, and epistemes. Centering the research on an Indigenist, anti-colonial framework allowed us to highlight and correct for colonial power dynamics throughout the project. By enacting Indigenism together, we found that Indigenous and Settler researchers can create a space of deep learning and knowledge co-creation with communities. However, this work was challenging, risky, and at times difficult. Learning to navigate some of these complexities required ongoing attention to our relational accountabilities. We detail lessons learned from each of our perspectives, concluding with implications, community obligations, and directions for future research.},
	language = {en},
	number = {5},
	urldate = {2021-02-26},
	journal = {Qualitative Inquiry},
	author = {Hart, Michael A. and Straka, Silvia and Rowe, Gladys},
	month = jun,
	year = {2017},
	note = {Publisher: SAGE Publications Inc},
	keywords = {Indigenous approaches to knowledge, Indigenous critical theory, decolonizing the academy, ethnicity and race, methods of inquiry, pedagogy, reconceptualizing collaboration},
	pages = {332--342},
}

@article{simpson_modelling_2018-1,
	title = {Modelling {Palaeoecological} {Time} {Series} {Using} {Generalised} {Additive} {Models}},
	volume = {6},
	issn = {2296-701X},
	url = {https://www.frontiersin.org/articles/10.3389/fevo.2018.00149/full},
	doi = {10.3389/fevo.2018.00149},
	abstract = {In the absence of annual laminations, time series generated from lake sediments or other similar stratigraphic sequences are irregularly spaced in time, which complicates formal analysis using classical statistical time series models. In lieu, statistical analyses of trends in palaeoenvironmental time series, if done at all, have typically used simpler linear regressions or (non-) parametric correlations with little regard for the violation of assumptions that almost surely occurs due to temporal dependencies in the data or that correlations do not provide estimates of the magnitude of change, just whether or not there is a linear or monotonic trend. Alternative approaches have used LOESS-estimated trends to justify data interpretations or test hypotheses as to the causal factors without considering the inherent subjectivity of the choice of parameters used to achieve the LOESS fit (e.g. span width, degree of polynomial). Generalized additive models (GAMs) are statistical models that can be used to estimate trends as smooth functions of time. Unlike LOESS, GAMs use automatic smoothness selection methods to objectively determine the complexity of the fitted trend, and as formal statistical models, GAMs, allow for potentially complex, non-linear trends, a proper accounting of model uncertainty, and the identification of periods of significant temporal change. Here, I present a consistent and modern approach to the estimation of trends in palaeoenvironmental time series using GAMs, illustrating features of the methodology with two example time series of contrasting complexity; a 150-year bulk organic matter δ15N time series from Small Water, UK, and a 3000-year alkenone record from Braya-Sø, Greenland. I discuss the underlying mechanics of GAMs that allow them to learn the shape of the trend from the data themselves and how simultaneous confidence intervals and the first derivatives of the trend are used to properly account for model uncertainty and identify periods of change. It is hoped that by using GAMs greater attention is paid to the statistical estimation of trends in palaeoenvironmental time series leading to more a robust and reproducible palaeoscience.},
	language = {English},
	urldate = {2021-02-22},
	journal = {Frontiers in Ecology and Evolution},
	author = {Simpson, Gavin L.},
	year = {2018},
	note = {Publisher: Frontiers},
	keywords = {Spline, environmental change, generalized additive models, simultaneous interval, time series},
}

@article{wang_simple_2020,
	title = {A simple new approach to variable selection in regression, with application to genetic fine mapping},
	volume = {82},
	copyright = {© 2020 The Authors Journal of the Royal Statistical Society: Series B (Statistical Methodology) Published by John Wiley \& Sons Ltd on behalf of Royal Statistical Society.},
	issn = {1467-9868},
	url = {https://rss.onlinelibrary.wiley.com/doi/abs/10.1111/rssb.12388},
	doi = {10.1111/rssb.12388},
	abstract = {We introduce a simple new approach to variable selection in linear regression, with a particular focus on quantifying uncertainty in which variables should be selected. The approach is based on a new model—the ‘sum of single effects’ model, called ‘SuSiE’—which comes from writing the sparse vector of regression coefficients as a sum of ‘single-effect’ vectors, each with one non-zero element. We also introduce a corresponding new fitting procedure—iterative Bayesian stepwise selection (IBSS)—which is a Bayesian analogue of stepwise selection methods. IBSS shares the computational simplicity and speed of traditional stepwise methods but, instead of selecting a single variable at each step, IBSS computes a distribution on variables that captures uncertainty in which variable to select. We provide a formal justification of this intuitive algorithm by showing that it optimizes a variational approximation to the posterior distribution under SuSiE. Further, this approximate posterior distribution naturally yields convenient novel summaries of uncertainty in variable selection, providing a credible set of variables for each selection. Our methods are particularly well suited to settings where variables are highly correlated and detectable effects are sparse, both of which are characteristics of genetic fine mapping applications. We demonstrate through numerical experiments that our methods outperform existing methods for this task, and we illustrate their application to fine mapping genetic variants influencing alternative splicing in human cell lines. We also discuss the potential and challenges for applying these methods to generic variable-selection problems.},
	language = {en},
	number = {5},
	urldate = {2021-02-10},
	journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
	author = {Wang, Gao and Sarkar, Abhishek and Carbonetto, Peter and Stephens, Matthew},
	year = {2020},
	keywords = {Genetic fine mapping, Linear regression, Sparsity, Variable selection, Variational inference},
	pages = {1273--1300},
}

@article{pedersen_hierarchical_2019-1,
	title = {Hierarchical generalized additive models in ecology: an introduction with mgcv},
	volume = {7},
	issn = {2167-8359},
	shorttitle = {Hierarchical generalized additive models in ecology},
	url = {https://peerj.com/articles/6876},
	doi = {10.7717/peerj.6876},
	abstract = {In this paper, we discuss an extension to two popular approaches to modeling complex structures in ecological data: the generalized additive model (GAM) and the hierarchical model (HGLM). The hierarchical GAM (HGAM), allows modeling of nonlinear functional relationships between covariates and outcomes where the shape of the function itself varies between different grouping levels. We describe the theoretical connection between HGAMs, HGLMs, and GAMs, explain how to model different assumptions about the degree of intergroup variability in functional response, and show how HGAMs can be readily fitted using existing GAM software, the mgcv package in R. We also discuss computational and statistical issues with fitting these models, and demonstrate how to fit HGAMs on example data. All code and data used to generate this paper are available at: github.com/eric-pedersen/mixed-effect-gams.},
	language = {en},
	urldate = {2021-02-10},
	journal = {PeerJ},
	author = {Pedersen, Eric J. and Miller, David L. and Simpson, Gavin L. and Ross, Noam},
	month = may,
	year = {2019},
	note = {Publisher: PeerJ Inc.},
	pages = {e6876},
}

@article{moritz_comparison_2015,
	title = {Comparison of different Methods for Univariate Time Series Imputation in {R}},
	url = {http://arxiv.org/abs/1510.03924},
	abstract = {Missing values in datasets are a well-known problem and there are quite a lot of R packages offering imputation functions. But while imputation in general is well covered within R, it is hard to find functions for imputation of univariate time series. The problem is, most standard imputation techniques can not be applied directly. Most algorithms rely on inter-attribute correlations, while univariate time series imputation needs to employ time dependencies. This paper provides an overview of univariate time series imputation in general and an in-detail insight into the respective implementations within R packages. Furthermore, we experimentally compare the R functions on different time series using four different ratios of missing data. Our results show that either an interpolation with seasonal kalman filter from the zoo package or a linear interpolation on seasonal loess decomposed data from the forecast package were the most effective methods for dealing with missing data in most of the scenarios assessed in this paper.},
	urldate = {2021-02-08},
	journal = {arXiv:1510.03924 [cs, stat]},
	author = {Moritz, Steffen and Sardá, Alexis and Bartz-Beielstein, Thomas and Zaefferer, Martin and Stork, Jörg},
	month = oct,
	year = {2015},
	note = {arXiv: 1510.03924},
	keywords = {Computer Science - Other Computer Science, Statistics - Applications},
}

@article{lao_influence_2020,
	title = {The influence of artificial light at night and polarized light on bird-building collisions},
	volume = {241},
	issn = {0006-3207},
	url = {https://www.sciencedirect.com/science/article/pii/S0006320719312339},
	doi = {10.1016/j.biocon.2019.108358},
	abstract = {Collisions with buildings annually kill up to 1 billion birds in the United States. Bird-building collisions primarily occur at glass surfaces: birds often fail to perceive glass as a barrier and appear to be attracted to artificial light emitted from windows. However, some aspects of avian vision are poorly understood, including how bird responses to different types of light influence building collisions. Some evidence suggests birds can detect polarized light, which may serve as a cue to assist with migration orientation and/or detect water bodies. Dark, reflective surfaces, including glass, reflect high degrees of polarized light, causing polarized light pollution (PLP). However, no studies have analyzed the relationship between bird collisions and PLP reflected from buildings. Additionally, while artificial light at night (ALAN) is frequently implicated as a major factor influencing bird-building collisions, few studies have analyzed this relationship. We investigated both types of light pollution—PLP and ALAN—and their association with bird collisions at 48 façades of 13 buildings in Minneapolis, Minnesota, USA. We found that the area of glass emitting ALAN was the most important factor influencing collisions, and that this effect of ALAN was independent of overall glass area; this result provides strong support for turning off lights at night to reduce bird-building collisions. Although we found no relationship between PLP and collisions, additional research is needed to better understand bird responses to polarized light. Fully understanding how different aspects of light influence bird-building collisions can inform conservation efforts to reduce this major threat to birds.},
	language = {en},
	urldate = {2021-02-08},
	journal = {Biological Conservation},
	author = {Lao, Sirena and Robertson, Bruce A. and Anderson, Abigail W. and Blair, Robert B. and Eckles, Joanna W. and Turner, Reed J. and Loss, Scott R.},
	month = jan,
	year = {2020},
	keywords = {Artificial light at night, Avian mortality, Bird-building collisions, Bird-window collisions, Light pollution, Polarized light},
	pages = {108358},
}

@article{iannucci_biogeochemical_nodate,
	title = {Biogeochemical responses over 37 years to manipulation of phosphorus concentrations in an {Arctic} river: {The} {Upper} {Kuparuk} {River} {Experiment}},
	volume = {n/a},
	copyright = {This article is protected by copyright. All rights reserved.},
	issn = {1099-1085},
	shorttitle = {Biogeochemical responses over 37 years to manipulation of phosphorus concentrations in an {Arctic} river},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/hyp.14075},
	doi = {10.1002/hyp.14075},
	abstract = {The climate of the Arctic region is changing rapidly, with important implications for permafrost, vegetation communities, and transport of solutes by streams and rivers to the Arctic Ocean. While research on Arctic streams and rivers has accelerated in recent years, long-term records are relatively rare compared to temperate and tropical regions. We began monitoring the upper Kuparuk River in 1983 as part of a long-term, low-level, whole-season phosphorus enrichment of a 4-6 km experimental reach, which was subsequently incorporated into the Arctic Long-Term Ecological Research (Arctic LTER) program. The phosphorus enrichment phase of the Upper Kuparuk River Experiment (UKRE) ran continuously for 34 seasons, fundamentally altering the community structure and function of the fertilized reach. The objectives of this paper are to 1) update observations of the environmental conditions in the Kuparuk River region as revealed by long-term, catchment-level monitoring, 2) compare long-term trends in biogeochemical characteristics of phosphorus-enriched and reference reaches of the Kuparuk River, and 3) report results from a new “ReFertilization” experiment. During the UKRE, temperature and discharge did not change significantly, though precipitation increased slightly. However, the UKRE revealed unexpected community state changes attributable to phosphorus enrichment (e.g., appearance of colonizing bryophytes) and long-term legacy effects of these state changes after cessation of the phosphorus enrichment. The UKRE also revealed important biogeochemical trends (e.g., increased nitrate flux and benthic C:N, decreased DOP flux). The decrease in DOP is particularly notable in that this may be a pan-Arctic trend related to permafrost thaw and exposure to new sources of iron that reduce phosphorus mobility to streams and rivers. The trends revealed by the UKRE would have been difficult or impossible to identify without long-term, catchment level research and may have important influences on connections between Arctic headwater catchments and downstream receiving waters, including the Arctic Ocean. This article is protected by copyright. All rights reserved.},
	language = {en},
	number = {n/a},
	urldate = {2021-02-08},
	journal = {Hydrological Processes},
	author = {Iannucci, Frances M. and Beneš, Joshua and Medvedeff, Alexander and Bowden, William B.},
	pages = {e14075},
}

@article{runge_inferring_2019,
	title = {Inferring causation from time series in {Earth} system sciences},
	volume = {10},
	copyright = {2019 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-019-10105-3},
	doi = {10.1038/s41467-019-10105-3},
	abstract = {The heart of the scientific enterprise is a rational effort to understand the causes behind the phenomena we observe. In large-scale complex dynamical systems such as the Earth system, real experiments are rarely feasible. However, a rapidly increasing amount of observational and simulated data opens up the use of novel data-driven causal methods beyond the commonly adopted correlation techniques. Here, we give an overview of causal inference frameworks and identify promising generic application cases common in Earth system sciences and beyond. We discuss challenges and initiate the benchmark platform causeme.netto close the gap between method users and developers.},
	language = {en},
	number = {1},
	urldate = {2021-02-04},
	journal = {Nature Communications},
	author = {Runge, Jakob and Bathiany, Sebastian and Bollt, Erik and Camps-Valls, Gustau and Coumou, Dim and Deyle, Ethan and Glymour, Clark and Kretschmer, Marlene and Mahecha, Miguel D. and Muñoz-Marí, Jordi and van Nes, Egbert H. and Peters, Jonas and Quax, Rick and Reichstein, Markus and Scheffer, Marten and Schölkopf, Bernhard and Spirtes, Peter and Sugihara, George and Sun, Jie and Zhang, Kun and Zscheischler, Jakob},
	month = jun,
	year = {2019},
	note = {Number: 1
Publisher: Nature Publishing Group},
	pages = {2553},
}

@article{trentman_cover_2020,
	title = {Cover crops and precipitation influence soluble reactive phosphorus losses via tile drain discharge in an agricultural watershed},
	volume = {34},
	copyright = {© 2020 John Wiley \& Sons Ltd},
	issn = {1099-1085},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/hyp.13870},
	doi = {10.1002/hyp.13870},
	abstract = {Subsurface tile drainage speeds water removal from agricultural fields that are historically prone to flooding. While managed drainage systems improve crop yields, they can also contribute tothe eutrophication of downstream ecosystems, as tile-drained systems are conduits for nutrients to adjacent waterways. The changing climate of the Midwestern US has already altered precipitation regimes which will likely continue into the future, with unknown effects on tile drain water and nutrient loss to waterways. Adding vegetative cover (i.e., as winter cover crops) is one approach that can retain water and nutrients on fields to minimize export via tile drains. In the current study, we evaluate the effect of cover crops on tile drain discharge and soluble reactive phosphorus (SRP) loads using bi-monthly measurements from 43 unique tile outlets draining fields with or without cover crops in two watersheds in northern Indiana. Using four water years of data (n = 844 measurements), we examined the role of short-term antecedent precipitation conditions and variation in soil biogeochemistry in mediating the effect of cover crops on tile drain flow and SRP loads. We observed significant effects of cover crops on both tile drain discharge and SRP loads, but these results were season and watershed specific. Cover crop effects were identified only in spring, where their presence reduced tile drain discharge in both watersheds and SRP loads in one watershed. Varying effects on SRP loads between watersheds were attributed to different soil biogeochemical characteristics, where soils with lower bioavailable P and higher P sorption capacity were less likely to have a cover crop effect. Antecedent precipitation was important in spring, and cover crop differences were still evident during periods of wet and dry antecedent precipitation conditions. Overall, we show that cover crops have the potential to significantly decrease spring tile drain P export, and these effects are resilient to a wide range of precipitation conditions.},
	language = {en},
	number = {23},
	urldate = {2021-02-03},
	journal = {Hydrological Processes},
	author = {Trentman, Matt T. and Tank, Jennifer L. and Royer, Todd V. and Speir, Shannon L. and Mahl, Ursula H. and Sethna, Lienne R.},
	year = {2020},
	keywords = {agriculture, cover crops, phosphorus, precipitation},
	pages = {4446--4458},
}

@article{dodds_eutrophication_2009,
	title = {Eutrophication of {U}.{S}. {Freshwaters}: {Analysis} of {Potential} {Economic} {Damages}},
	volume = {43},
	issn = {0013-936X, 1520-5851},
	shorttitle = {Eutrophication of {U}.{S}. {Freshwaters}},
	url = {https://pubs.acs.org/doi/10.1021/es801217q},
	doi = {10.1021/es801217q},
	language = {en},
	number = {1},
	urldate = {2021-02-03},
	journal = {Environmental Science \& Technology},
	author = {Dodds, Walter K. and Bouska, Wes W. and Eitzmann, Jeffrey L. and Pilger, Tyler J. and Pitts, Kristen L. and Riley, Alyssa J. and Schloesser, Joshua T. and Thornbrugh, Darren J.},
	month = jan,
	year = {2009},
	pages = {12--19},
}

@article{perez_extreme_2021,
	title = {Extreme temperature events alter stream ecosystem functioning},
	volume = {121},
	issn = {1470-160X},
	url = {http://www.sciencedirect.com/science/article/pii/S1470160X20309237},
	doi = {10.1016/j.ecolind.2020.106984},
	abstract = {Extreme temperature events have increased in intensity, duration and frequency in the last century, with potential consequences on organisms and ecosystems. In many streams, leaf litter of terrestrial origin is a key resource for microorganisms and some detritivores, and its decomposition has a main role on ecosystem functioning and is often used as an indicator of ecological integrity. As litter is often exposed to atmospheric conditions before entering the stream, extreme warming and freezing events may alter its physicochemical structure and affect decomposition and associated detritivores. We tested this prediction in a microcosm experiment by exposing litter of three tree species (in single-species treatments and the 3-species mixture) to different temperature pre-treatments: heating (40 °C), freezing (−20 °C) and both (heating followed by freezing). We then examined changes in litter traits due to leaching (72 h), litter decomposition in the absence and presence of detritivores, and detritivore growth (28 d), with focus on mass and nutrient (nitrogen and phosphorus) changes. Nutrient leaching was promoted mostly by the heating pre-treatment, which apparently produced lower-quality litter. However, microbial activity mostly resulted in litter mass and nutrient gain, which were reinforced by the heating pre-treatment, while freezing had the opposite effect. When detritivores were present, decomposition showed high variation among litter types but, again, the heating and freezing pre-treatments tended to reduce and enhance nutrient loss, respectively. The greatest and more consistent effects occurred for detritivore growth, which was reduced by temperature pre-treatments, particularly in the highest-quality litter type. In general, the sequential application of heating and freezing pre-treatments showed no synergistic effect, and the litter mixture showed similar responses to single-species treatments. Our results demonstrate that short-term extreme temperatures can modify litter quality in riparian soils and have subsequent effects on its decomposition within the stream and associated fauna, potentially altering stream food webs, ecosystem functioning and biogeochemical cycles.},
	language = {en},
	urldate = {2021-02-02},
	journal = {Ecological Indicators},
	author = {Pérez, Javier and Correa-Araneda, Francisco and López-Rojo, Naiara and Basaguren, Ana and Boyero, Luz},
	month = feb,
	year = {2021},
	keywords = {Climate change, Conservation/biodiversity, Decomposition, Functional indicator, Invertebrates, Nutrient cycling, Running waters/rivers/streams},
	pages = {106984},
}

@article{yao_using_nodate,
	title = {Using stacking to average {Bayesian} predictive distributions},
	abstract = {Bayesian model averaging is flawed in the M-open setting in which the true data-generating process is not one of the candidate models being fit. We take the idea of stacking from the point estimation literature and generalize to the combination of predictive distributions. We extend the utility function to any proper scoring rule and use Pareto smoothed importance sampling to efficiently compute the required leave-one-out posterior distributions. We compare stacking of predictive distributions to several alternatives: stacking of means, Bayesian model averaging (BMA), Pseudo-BMA using AIC-type weighting, and a variant of Pseudo-BMA that is stabilized using the Bayesian bootstrap. Based on simulations and real-data applications, we recommend stacking of predictive distributions, with bootstrapped-Pseudo-BMA as an approximate alternative when computation cost is an issue.},
	language = {en},
	author = {Yao, Yuling and Vehtari, Aki and Simpson, Daniel and Gelman, Andrew},
	pages = {30},
}

@article{wit_land-use_2020,
	title = {Land-use dominates climate controls on nitrogen and phosphorus export from managed and natural {Nordic} headwater catchments},
	volume = {34},
	copyright = {© 2020 The Authors. Hydrological Processes published by John Wiley \& Sons Ltd.},
	issn = {1099-1085},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/hyp.13939},
	doi = {10.1002/hyp.13939},
	abstract = {Agricultural, forestry-impacted and natural catchments are all vectors of nutrient loading in the Nordic countries. Here, we present concentrations and fluxes of total nitrogen (totN) and phosphorus (totP) from 69 Nordic headwater catchments (Denmark: 12, Finland:18, Norway:17, Sweden:22) between 2000 and 2018. Catchments span the range of Nordic climatic and environmental conditions and include natural sites and sites impacted by agricultural and forest management. Concentrations and fluxes of totN and totP were highest in agricultural catchments, intermediate in forestry-impacted and lowest in natural catchments, and were positively related \%agricultural land cover and summer temperature. Summer temperature may be a proxy for terrestrial productivity, while \%agricultural land cover might be a proxy for catchment nutrient inputs. A regional trend analysis showed significant declines in N concentrations and export across agricultural (−15 μg totN L−1 year−1) and natural (−0.4 μg NO3-N L−1 year−1) catchments, but individual sites displayed few long-term trends in concentrations (totN: 22\%, totP: 25\%) or export (totN: 6\%, totP: 9\%). Forestry-impacted sites had a significant decline in totP (−0.1 μg P L−1 year−1). A small but significant increase in totP fluxes (+0.4 kg P km−2 year−1) from agricultural catchments was found, and countries showed contrasting patterns. Trends in annual concentrations and fluxes of totP and totN could not be explained in a straightforward way by changes in runoff or climate. Explanations for the totN decline include national mitigation measures in agriculture international policy to reduced air pollution and, possibly, large-scale increases in forest growth. Mitigation to reduce phosphorus appears to be more challenging than for nitrogen. If the green shift entails intensification of agricultural and forest production, new challenges for protection of water quality will emerge possible exacerbated by climate change. Further analysis of headwater totN and totP export should include seasonal trends, aquatic nutrient species and a focus on catchment nutrient inputs.},
	language = {en},
	number = {25},
	urldate = {2021-02-02},
	journal = {Hydrological Processes},
	author = {Wit, Heleen A. de and Lepistö, Ahti and Marttila, Hannu and Wenng, Hannah and Bechmann, Marianne and Blicher‐Mathiesen, Gitte and Eklöf, Karin and Futter, Martyn N. and Kortelainen, Pirkko and Kronvang, Brian and Kyllmar, Katarina and Rakovic, Jelena},
	year = {2020},
	keywords = {agriculture, bioeconomy, forest, forestry, long-term trend, mitigation, monitoring, stream},
	pages = {4831--4850},
}

@article{jabiol_variable_2020,
	title = {Variable temperature effects between heterotrophic stream processes and organisms},
	volume = {65},
	copyright = {© 2020 John Wiley \& Sons Ltd.},
	issn = {1365-2427},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/fwb.13520},
	doi = {10.1111/fwb.13520},
	abstract = {Temperature is known to stimulate metabolism with cascading effects on multiple biological processes. These effects may, however, vary across processes, types of organisms or levels of biological organisation. They can also vary with nutrient availability, with potentially stronger temperature effects when nutrients are not limiting. This context dependence of temperature effects on processes challenges our ability to anticipate their consequences on ecosystems in a changing world. In headwater streams, the decomposition of allochthonous leaf litter, driven by both microbial decomposers and invertebrates, is known to respond to both temperature and nutrient availability. These food webs are highly tractable and a useful model system to investigate the variations of temperature effects on processes across types of organisms (microbes versus invertebrates), resource availability levels (nutrient concentration), and levels of biological organisation (from individual to ecosystem). In a microcosm experiment, we measured the effects of temperature and nitrogen availability (four levels each) on respiration rates of litter-consuming microbes and invertebrates and their decomposition activity in different contexts of food web complexity. The latter included one treatment without invertebrate detritivore (microbial decomposers only), three single invertebrate taxa (Gammarus, Potamophylax, and Sericostoma) treatments, and one mixed invertebrate taxa treatment (three-species altogether). Microbial processes increased nearly exponentially with temperature (Arrhenius model, activation energy (± 95\% confidence interval) = 0.56 ± 0.53 and 1.00 ± 0.23 eV for litter decomposition and respiration), while invertebrate-driven processes increased (activation energy from 0.47–1.15 eV) up to a maximal value at an intermediate temperature (c. 11–15°C depending on species and process), above which process rates decreased. By contrast, litter consumption in mixed invertebrate species treatments was not significantly influenced by temperature, because of a negative effect of species mixing occurring above 12°C. Nitrogen had a weaker influence, only slightly stimulating litter consumption by mixed-species invertebrates, which limited the scope for synergies with temperature effects. Our results raise issues about how aquatic litter consumers meet their energy requirements at high temperature and suggest that a general consequence of warming could be loss of carbon through mineralisation in headwater stream food webs. In several aspects, our results deviate from expectations based on universal relationships between temperature and individual metabolism (e.g. metabolic theory of ecology), suggesting that we may need to develop less simplistic assumptions to predict the consequence of warming on ecosystem processes.},
	language = {en},
	number = {9},
	urldate = {2021-02-01},
	journal = {Freshwater Biology},
	author = {Jabiol, Jérémy and Gossiaux, Alice and Lecerf, Antoine and Rota, Thibaut and Guérold, François and Danger, Michaël and Poupin, Pascal and Gilbert, Franck and Chauvet, Eric},
	year = {2020},
	keywords = {decomposers, litter decomposition, nitrogen, respiration, temperature},
	pages = {1543--1554},
}

@article{hooten_guide_2015,
	title = {A guide to {Bayesian} model selection for ecologists},
	volume = {85},
	copyright = {© 2015 by the Ecological Society of America},
	issn = {1557-7015},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/14-0661.1},
	doi = {10.1890/14-0661.1},
	abstract = {The steady upward trend in the use of model selection and Bayesian methods in ecological research has made it clear that both approaches to inference are important for modern analysis of models and data. However, in teaching Bayesian methods and in working with our research colleagues, we have noticed a general dissatisfaction with the available literature on Bayesian model selection and multimodel inference. Students and researchers new to Bayesian methods quickly find that the published advice on model selection is often preferential in its treatment of options for analysis, frequently advocating one particular method above others. The recent appearance of many articles and textbooks on Bayesian modeling has provided welcome background on relevant approaches to model selection in the Bayesian framework, but most of these are either very narrowly focused in scope or inaccessible to ecologists. Moreover, the methodological details of Bayesian model selection approaches are spread thinly throughout the literature, appearing in journals from many different fields. Our aim with this guide is to condense the large body of literature on Bayesian approaches to model selection and multimodel inference and present it specifically for quantitative ecologists as neutrally as possible. We also bring to light a few important and fundamental concepts relating directly to model selection that seem to have gone unnoticed in the ecological literature. Throughout, we provide only a minimal discussion of philosophy, preferring instead to examine the breadth of approaches as well as their practical advantages and disadvantages. This guide serves as a reference for ecologists using Bayesian methods, so that they can better understand their options and can make an informed choice that is best aligned with their goals for inference.},
	language = {en},
	number = {1},
	urldate = {2021-01-29},
	journal = {Ecological Monographs},
	author = {Hooten, M. B. and Hobbs, N. T.},
	year = {2015},
	keywords = {Akaike information criterion, Bayes factors, cross-validation, deviance information criterion, model averaging, multi-model inference, regularization, shrinkage},
	pages = {3--28},
}

@article{hall_gas_2020,
	title = {Gas exchange in streams and rivers},
	volume = {7},
	issn = {2049-1948},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/wat2.1391},
	doi = {10.1002/wat2.1391},
	abstract = {Gas exchange across the air–water boundary of streams and rivers is a globally large biogeochemical flux. Gas exchange depends on the solubility of the gas of interest, the gas concentrations of the air and water, and the gas exchange velocity (k), usually normalized to a Schmidt number of 600, referred to as k600. Gas exchange velocity is of intense research interest because it is problematic to estimate, is highly spatially variable, and has high prediction error. Theory dictates that molecular diffusivity and turbulence drives variation in k600 in flowing waters. We measure k600 via several methods from direct measures, gas tracer experiments, to modeling of diel changes in dissolved gas concentrations. Many estimates of k600 show that surface turbulence explains variation in k600 leading to predictive models based upon geomorphic and hydraulic variables. These variables include stream channel slope and stream flow velocity, the product of which, is proportional to the energy dissipation rate in streams and rivers. These empirical models provide understanding of the controls on k600, yet high residual variation in k600 show that these simple models are insufficient for predicting individual locations. The most appropriate method to estimate gas exchange depends on the scientific question along with the characteristics of the study sites. We provide a decision tree for selecting the best method to estimate k600 for individual river reaches to scaling to river networks. This article is categorized under: Water and Life {\textgreater} Nature of Freshwater Ecosystems Science of Water {\textgreater} Water Quality Water and Life {\textgreater} Methods},
	language = {en},
	number = {1},
	urldate = {2021-01-25},
	journal = {WIREs Water},
	author = {Hall, Robert O. and Ulseth, Amber J.},
	year = {2020},
	keywords = {energy dissipation rate, gas exchange, gas tracer experiments, hydraulics, k600, river metabolism, rivers, scaling, streams},
	pages = {e1391},
}

@article{trentman_using_2020,
	title = {Using path analysis to determine interacting effects of biotic and abiotic factors on patch-scale biogeochemical rates in a prairie stream},
	volume = {82},
	issn = {1420-9055},
	url = {10.1007/s00027-020-0702-8},
	doi = {10.1007/s00027-020-0702-8},
	abstract = {Biogeochemical rates within streams vary with ecosystem properties including the distribution of fishes. While many studies investigate the singular effect of fishes on ecosystem components, there is a limited understanding of how fish presence interacts with other ecosystem properties to affect ecosystem structure and function. Here, we used path analyses to elucidate direct and indirect effects of fish presence, and other ecosystem properties on ecosystem respiration (ER), gross primary production (GPP), and ammonium uptake. Experimental responses of fish removal on patch scale (300 cm2) benthic rates of ER, GPP, and ammonium uptake were measured at two sites in a prairie stream. The effect of fish was determined by comparing substrata from field exclosures with fish absent to substrata exposed to fish. Total path model-explained variance was greatest for ER (R2 = 0.55) and least for ammonium uptake (R2 = 0.36) and GPP (R2 = 0.34). Fish decreased algal biomass and directly increased all biogeochemical rates. The relative importance of the different abiotic ecosystem properties varied by process; however, FBOM and substrata size were important for most rates. This study provides evidence for predominantly direct effects of fish on both stream structure and function in a prairie stream. Our results emphasize that interactions between biotic and abiotic factors should be considered when determining drivers of biogeochemical activity. We suggest that simple linear food webs that consist of top–down or bottom–up control are not always sufficient to describe animal effects on ecosystem rates.},
	language = {en},
	number = {2},
	urldate = {2021-01-14},
	journal = {Aquatic Sciences},
	author = {Trentman, Matt T. and Dodds, Walter K. and Gido, Keith B. and Rüegg, Janine and Ruffing, Claire M.},
	month = feb,
	year = {2020},
	pages = {26},
}

@article{dodds_n_2002,
	title = {N uptake as a function of concentration in streams},
	volume = {21},
	issn = {0887-3593},
	url = {https://www.journals.uchicago.edu/doi/full/10.2307/1468410},
	doi = {10.2307/1468410},
	abstract = {Detailed studies of stream N uptake were conducted in a prairie reach and gallery forest reach of Kings Creek on the Konza Prairie Biological Station. Nutrient uptake rates were measured with multiple short-term enrichments of NO3− and NH4+ at constant addition rates in the spring and summer of 1998. NH4+ uptake was also measured with 15N-NH4+ tracer additions and short-term unlabeled NH4+ additions at 12 stream sites across North America. Concurrent addition of a conservative tracer was used to account for dilution in all experiments. NH4+ uptake rate per unit area (Ut) was positively correlated to nutrient concentration across all sites (r2 = 0.41, log–log relationship). Relationships between concentration and Ut were used to determine whether the uptake was nonlinear (i.e., kinetic uptake primarily limited by the biotic capacity of microorganisms to accumulate nutrients) or linear (e.g., limited by mass transport into stream biofilms). In all systems, Ut was lower at ambient concentrations than at elevated concentrations. Extrapolation from uptake measured from a series of increasing enrichments could be used to estimate ambient Ut. Linear extrapolation of Ut assuming the relationship passes through the origin and rates measured at 1 elevated nutrient concentration underestimated ambient Ut by ∼3-fold. Uptake rates were saturated under some but not all conditions of enrichment; in some cases there was no saturation up to 50 μmol/L. The absolute concentration at which Ut was saturated in Kings Creek varied among reaches and nutrients. Uptake rates of NH4+ at ambient concentrations in all streams were higher than would be expected, assuming Ut does not saturate with increasing concentrations. At ambient nutrient concentrations in unpolluted streams, Ut is probably limited to some degree by the kinetic uptake capacity of stream biota. Mass transfer velocity from the water column is generally greater than would be expected given typical diffusion rates, underscoring the importance of advective transport. Given the short-term spikes in nutrient concentrations that can occur in streams (e.g., in response to storm events), Ut may not saturate, even at high concentrations.},
	number = {2},
	urldate = {2021-01-14},
	journal = {Journal of the North American Benthological Society},
	author = {Dodds, Walter K. and López, Amanda J. and Bowden, William B. and Gregory, Stan and Grimm, Nancy B. and Hamilton, Stephen K. and Hershey, Anne E. and Martí, Eugenia and McDowell, William H. and Meyer, Judy L. and Morrall, Donna and Mulholland, Patrick J. and Peterson, Bruce J. and Tank, Jennifer L. and Valett, H. Maurice and Webster, Jackson R. and Wollheim, Wilfred},
	month = jun,
	year = {2002},
	note = {Publisher: The University of Chicago Press},
	pages = {206--220},
}

@article{ardon_experimental_nodate,
	title = {Experimental nitrogen and phosphorus enrichment stimulates multiple trophic levels of algal and detrital-based food webs: a global meta-analysis from streams and rivers},
	issn = {1469-185X},
	shorttitle = {Experimental nitrogen and phosphorus enrichment stimulates multiple trophic levels of algal and detrital-based food webs},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/brv.12673},
	doi = {10.1111/brv.12673},
	abstract = {Anthropogenic increases in nitrogen (N) and phosphorus (P) concentrations can strongly influence the structure and function of ecosystems. Even though lotic ecosystems receive cumulative inputs of nutrients applied to and deposited on land, no comprehensive assessment has quantified nutrient-enrichment effects within streams and rivers. We conducted a meta-analysis of published studies that experimentally increased concentrations of N and/or P in streams and rivers to examine how enrichment alters ecosystem structure (state: primary producer and consumer biomass and abundance) and function (rate: primary production, leaf breakdown rates, metabolism) at multiple trophic levels (primary producer, microbial heterotroph, primary and secondary consumers, and integrated ecosystem). Our synthesis included 184 studies, 885 experiments, and 3497 biotic responses to nutrient enrichment. We documented widespread increases in organismal biomass and abundance (mean response = +48\%) and rates of ecosystem processes (+54\%) to enrichment across multiple trophic levels, with no large differences in responses among trophic levels or between autotrophic or heterotrophic food-web pathways. Responses to nutrient enrichment varied with the nutrient added (N, P, or both) depending on rate versus state variable and experiment type, and were greater in flume and whole-stream experiments than in experiments using nutrient-diffusing substrata. Generally, nutrient-enrichment effects also increased with water temperature and light, and decreased under elevated ambient concentrations of inorganic N and/or P. Overall, increased concentrations of N and/or P altered multiple food-web pathways and trophic levels in lotic ecosystems. Our results indicate that preservation or restoration of biodiversity and ecosystem functions of streams and rivers requires management of nutrient inputs and consideration of multiple trophic pathways.},
	language = {en},
	urldate = {2021-01-14},
	journal = {Biological Reviews},
	author = {Ardón, Marcelo and Zeglin, Lydia H. and Utz, Ryan M. and Cooper, Scott D. and Dodds, Walter K. and Bixby, Rebecca J. and Burdett, Ayesha S. and Shah, Jennifer Follstad and Griffiths, Natalie A. and Harms, Tamara K. and Johnson, Sherri L. and Jones, Jeremy B. and Kominoski, John S. and McDowell, William H. and Rosemond, Amy D. and Trentman, Matt T. and Horn, David Van and Ward, Amelia},
	keywords = {decomposition, ecosystem metabolism, eutrophication, lotic, nutrient criteria, primary and secondary production},
}

@article{istvanovics_coupled_2018,
	title = {Coupled simulation of high-frequency dynamics of dissolved oxygen and chlorophyll widens the scope of lake metabolism studies},
	volume = {63},
	copyright = {© 2017 The Authors Limnology and Oceanography published by Wiley Periodicals, Inc. on behalf of Association for the Sciences of Limnology and Oceanography},
	issn = {1939-5590},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lno.10615},
	doi = {10.1002/lno.10615},
	abstract = {High frequency time series of dissolved oxygen (DO), delayed chlorophyll fluorescence (Chl) and relevant background variables were recorded on nearly 900 d during 7 yr in large, shallow, meso-eutrophic Lake Balaton (Hungary). Novel models were developed for coupled simulation of diel dynamics of DO and Chl using sequential learning and uncertainty assessment in a Bayesian framework. Despite the generally good model fit for both variables, the uncertainty of the metabolic estimates was high, due primarily to the identification problem of individual metabolic processes. Deviations between observed and simulated DO concentrations suggested that neglect of transient stratification might be responsible for the bulk of the systematic model errors. Net ecosystem production (NEP) was uncertain. Unless air-water oxygen exchange can be estimated from direct measurements, the free-water DO method cannot reliably estimate NEP. Gross primary production (GPP) could satisfactorily be hindcasted assuming non-linear multiplicative dependence on Chl, water temperature and light. Hindcast of community respiration (CR) was less successful, possibly due to the impact of local benthic respiration. Results suggested a major shift in lake metabolism at about 16°C. Below and above this temperature, 70\% and 90\% of net primary production could be utilized by heterotrophs within a day, respectively. Indirect evidence suggested that biomass-specific net primary production was determined by phosphorus. The large difference between reproductive rates and net growth rates estimated from GPP and Chl and from daily change in Chl, respectively indicated that loss rates of phytoplankton were as important determinants of algal dynamics as reproductive rates.},
	language = {en},
	number = {1},
	urldate = {2021-01-13},
	journal = {Limnology and Oceanography},
	author = {Istvánovics, Vera and Honti, Márk},
	year = {2018},
	pages = {72--90},
}

@article{ives_detecting_2012,
	title = {Detecting dynamical changes in nonlinear time series using locally linear state-space models},
	volume = {3},
	copyright = {Copyright: © 2012 Ives and Dakos.},
	issn = {2150-8925},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/ES11-00347.1},
	doi = {10.1890/ES11-00347.1},
	abstract = {Interest is growing in methods for predicting and detecting regime shifts—changes in the structure of dynamical processes that cause shifts among alternative stable states. Here, we use locally linear, autoregressive state-space models to statistically identify nonlinear processes that govern the dynamics of time series. We develop both time-varying and threshold models. In time-varying autoregressive models with p time lags, AR(p), and vector autoregressive models for n-dimensional systems of order p = 1, VAR(1), we assume that coefficients vary with time. We can infer an approaching regime shift if the coefficients indicate critical slowing down of the local dynamics of the system. In self-excited threshold models, we assume that the time series is governed by two autoregressive processes; the state variable switches between them when the time series crosses a threshold value. We use the existence of a statistically significant threshold as an indicator of alternative stable states. All models are fit to data using a state-space form that incorporates measurement error, and maximum likelihood estimation allows for statistically testing alternative hypotheses about the processes governing dynamics. Our model-based approach for forecasting regime shifts and identifying alternative stable states overcomes limitations of other common metric-based approaches and is a useful addition to the toolbox of methods for analyzing nonlinear time series.},
	language = {en},
	number = {6},
	urldate = {2021-01-13},
	journal = {Ecosphere},
	author = {Ives, Anthony R. and Dakos, Vasilis},
	year = {2012},
	keywords = {Kalman filter, SETAR, SETARSS, TVAR, TVARSS, alternative stable states, critical slowing down, critical transition, early warning signals, regime shift, threshold autoregressive models, time-varying autoregressive models},
	pages = {art58},
}

@article{rowland_recent_2020,
	title = {Recent {Patterns} in {Lake} {Erie} {Phosphorus} and {Chlorophyll} a {Concentrations} in {Response} to {Changing} {Loads}},
	volume = {54},
	issn = {0013-936X},
	url = {10.1021/acs.est.9b05326},
	doi = {10.1021/acs.est.9b05326},
	abstract = {Despite the initial success of extensive efforts to reduce phosphorus (P) loading to Lake Erie as a part of the Great Lakes Water Quality Agreement, Lake Erie appears to be undergoing a re-eutrophication and it is plagued by harmful algal blooms. To offer insights into potential lake responses under differing Maumee River loads and reveal recent changes with time, we explored patterns in phosphorus and chlorophyll a data from 2008 to 2018 collected in western Lake Erie near the mouth of the Maumee River. We found high, but relatively stable Maumee River and lake concentrations of total P (TP) and soluble reactive P (SRP) with no discernable annual or seasonal patterns. Maumee spring TP load was not strongly related to lake TP, and lake SRP concentrations were positively but weakly related to SRP loads. Lake TP was a strong predictor of chlorophyll a, but the relationship was weaker at sites closer to the Maumee. These results highlight spatial differences both in P concentration and the relationship between TP and chlorophyll a, and these indicate that spring phosphorus loads are a weak algal biomass predictor in the portion of the western basin of Lake Erie represented by these sampling stations.},
	number = {2},
	urldate = {2021-01-11},
	journal = {Environmental Science \& Technology},
	author = {Rowland, Freya E. and Stow, Craig A. and Johengen, Thomas H. and Burtner, Ashley M. and Palladino, Danna and Gossiaux, Duane C. and Davis, Timothy W. and Johnson, Laura T. and Ruberg, Steve},
	month = jan,
	year = {2020},
	note = {Publisher: American Chemical Society},
	pages = {835--841},
}

@article{gelman_prior_nodate,
	title = {Prior distributions for variance parameters in hierarchical models},
	abstract = {Various noninformative prior distributions have been suggested for scale parameters in hierarchical models. We construct a new folded-noncentral-t family of conditionally conjugate priors for hierarchical standard deviation parameters, and then consider noninformative and weakly informative priors in this family. We use an example to illustrate serious problems with the inverse-gamma family of “noninformative” prior distributions. We suggest instead to use a uniform prior on the hierarchical standard deviation, using the half-t family when the number of groups is small and in other settings where a weakly informative prior is desired. We also illustrate the use of the half-t family for hierarchical modeling of multiple variance parameters such as arise in the analysis of variance.},
	language = {en},
	author = {Gelman, Andrew},
	pages = {19},
}

@article{gelman_beyond_2017,
	title = {Beyond subjective and objective in statistics},
	volume = {180},
	issn = {09641998},
	url = {http://doi.wiley.com/10.1111/rssa.12276},
	doi = {10.1111/rssa.12276},
	abstract = {Decisions in statistical data analysis are often justified, criticized, or avoided using concepts of objectivity and subjectivity. We argue that the words “objective” and “subjective” in statistics discourse are used in a mostly unhelpful way, and we propose to replace each of them with broader collections of attributes, with objectivity replaced by transparency, consensus, impartiality, and correspondence to observable reality, and subjectivity replaced by awareness of multiple perspectives and context dependence. The advantage of these reformulations is that the replacement terms do not oppose each other and that they give more specific guidance about what statistical science strives to achieve. Instead of debating over whether a given statistical method is subjective or objective (or normatively debating the relative merits of subjectivity and objectivity in statistical practice), we can recognize desirable attributes such as transparency and acknowledgment of multiple perspectives as complementary goals. We demonstrate the implications of our proposal with recent applied examples from pharmacology, election polling, and socioeconomic stratification.},
	language = {en},
	number = {4},
	urldate = {2021-01-05},
	journal = {Journal of the Royal Statistical Society: Series A (Statistics in Society)},
	author = {Gelman, Andrew and Hennig, Christian},
	month = oct,
	year = {2017},
	pages = {967--1033},
}

@article{gabry_visualization_2019,
	title = {Visualization in {Bayesian} workflow},
	volume = {182},
	copyright = {© 2019 Royal Statistical Society},
	issn = {1467-985X},
	url = {https://rss.onlinelibrary.wiley.com/doi/abs/10.1111/rssa.12378},
	doi = {10.1111/rssa.12378},
	abstract = {Bayesian data analysis is about more than just computing a posterior distribution, and Bayesian visualization is about more than trace plots of Markov chains. Practical Bayesian data analysis, like all data analysis, is an iterative process of model building, inference, model checking and evaluation, and model expansion. Visualization is helpful in each of these stages of the Bayesian workflow and it is indispensable when drawing inferences from the types of modern, high dimensional models that are used by applied researchers.},
	language = {en},
	number = {2},
	urldate = {2021-01-05},
	journal = {Journal of the Royal Statistical Society: Series A (Statistics in Society)},
	author = {Gabry, Jonah and Simpson, Daniel and Vehtari, Aki and Betancourt, Michael and Gelman, Andrew},
	year = {2019},
	keywords = {Bayesian data analysis, Statistical graphics, Statistical workflow},
	pages = {389--402},
}

@article{gelman_prior_2017,
	title = {The {Prior} {Can} {Often} {Only} {Be} {Understood} in the {Context} of the {Likelihood}},
	volume = {19},
	issn = {1099-4300},
	url = {http://www.mdpi.com/1099-4300/19/10/555},
	doi = {10.3390/e19100555},
	abstract = {A key sticking point of Bayesian analysis is the choice of prior distribution, and there is a vast literature on potential defaults including uniform priors, Jeffreys’ priors, reference priors, maximum entropy priors, and weakly informative priors. These methods, however, often manifest a key conceptual tension in prior modeling: a model encoding true prior information should be chosen without reference to the model of the measurement process, but almost all common prior modeling techniques are implicitly motivated by a reference likelihood. In this paper we resolve this apparent paradox by placing the choice of prior into the context of the entire Bayesian analysis, from inference to prediction to model evaluation.},
	language = {en},
	number = {10},
	urldate = {2021-01-05},
	journal = {Entropy},
	author = {Gelman, Andrew and Simpson, Daniel and Betancourt, Michael},
	month = oct,
	year = {2017},
	pages = {555},
}

@article{mulholland_effects_2006,
	title = {Effects of light on {NO3}− uptake in small forested streams: diurnal and day-to-day variations},
	volume = {25},
	issn = {2161-9549, 2161-9565},
	shorttitle = {Effects of light on {NO3}− uptake in small forested streams},
	url = {https://bioone.org/journals/freshwater-science/volume-25/issue-3/0887-3593(2006)25[583:EOLONU]2.0.CO;2/Effects-of-light-on-NO3-uptake-in-small-forested-streams/10.1899/0887-3593(2006)25[583:EOLONU]2.0.CO;2.full},
	doi = {10.1899/0887-3593(2006)25[583:EOLONU]2.0.CO;2},
	abstract = {We investigated the effects of autotrophy on short-term variations in nutrient dynamics by measuring diurnal and day-to-day variations in light level, primary productivity, and NO3− uptake during early and late spring in 2 forested streams, the East and West Forks of Walker Branch in eastern Tennessee, USA. We predicted that diurnal and day-to-day variations in NO3− uptake rate would be larger in the West Fork than in the East Fork in early spring because of higher rates of primary productivity resulting from a more stable substratum in the West Fork. We also predicted minimal diurnal variations in both streams in late spring after forest leaf emergence when light levels and primary productivity are uniformly low. Reach-scale rates of gross primary production (GPP) were determined using the diurnal dissolved O2 change technique, and reach-scale rates of NO3− uptake were determined by tracer 15N-NO3− additions. In the West Fork, significant diurnal and day-to-day variations in NO3− uptake were related to variations in light level and primary productivity in early spring but not in late spring, consistent with our predictions. In early spring, West Fork NO3− uptake rates were 2 to 3× higher at midday than during predawn hours and 50\% higher on 2 clear days than on an overcast day several days earlier. In the East Fork, early spring rates of GPP were 4 to 5× lower than in the West Fork and diurnal and day-to-day variations in NO3− uptake rates were {\textless}30\%, considerably lower than in the West Fork. However, diurnal variations in NO3− uptake rates were greater in late spring in the East Fork, possibly because of diurnal variation in water temperature. Our results indicate the important role of autotrophs in nutrient uptake in some forested streams, particularly during seasons when forest vegetation is dormant and light levels are relatively high. Our results also have important implications for longer-term assessments of N cycling in streams that rely on daytime measurements or measurements only under limited weather conditions (i.e., clear days).},
	number = {3},
	urldate = {2020-12-30},
	journal = {Freshwater Science},
	author = {Mulholland, Patrick J. and Thomas, Steven A. and Valett, H. Maurice and Webster, Jackson R. and Beaulieu, Jake},
	month = sep,
	year = {2006},
	note = {Publisher: Society for Freshwater Science},
	pages = {583--595},
}

@article{green_predicting_nodate,
	title = {Predicting high-frequency variation in stream solute concentrations with water quality sensors and machine learning},
	volume = {n/a},
	copyright = {© 2020 John Wiley \& Sons Ltd},
	issn = {1099-1085},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/hyp.14000},
	doi = {10.1002/hyp.14000},
	abstract = {Stream solute monitoring has produced many insights into ecosystem and Earth system functions. Although new sensors have provided novel information about the fine-scale temporal variation of some stream water solutes, we lack adequate sensor technology to gain the same insights for many other solutes. We used two machine learning algorithms – Support Vector Machine and Random Forest – to predict concentrations at 15-min resolution for 10 solutes, of which eight lack specific sensors. The algorithms were trained with data from intensive stream sensing and manual stream sampling (weekly) for four full years in a hydrologic reference stream within the Hubbard Brook Experimental Forest in New Hampshire, USA. The Random Forest algorithm was slightly better at predicting solute concentrations than the Support Vector Machine algorithm (Nash-Sutcliffe efficiencies ranged from 0.35 to 0.78 for Random Forest compared to 0.29 to 0.79 for Support Vector Machine). Solute predictions were most sensitive to the removal of fluorescent dissolved organic matter, pH and specific conductance as independent variables for both algorithms, and least sensitive to dissolved oxygen and turbidity. The predicted concentrations of calcium and monomeric aluminium were used to estimate catchment solute yield, which changed most dramatically for aluminium because it concentrates with stream discharge. These results show great promise for using a combined approach of stream sensing and intensive stream discrete sampling to build information about the high-frequency variation of solutes for which an appropriate sensor or proxy is not available.},
	language = {en},
	number = {n/a},
	urldate = {2020-12-18},
	journal = {Hydrological Processes},
	author = {Green, Mark B. and Pardo, Linda H. and Bailey, Scott W. and Campbell, John L. and McDowell, William H. and Bernhardt, Emily S. and Rosi, Emma J.},
	keywords = {biogeochemistry, machine learning, stream solutes, water quality},
	pages = {e14000},
}

@article{canadell_daily_nodate,
	title = {Daily entropy of dissolved oxygen reveals different energetic regimes and drivers among high-mountain stream types},
	volume = {n/a},
	copyright = {© 2020 The Authors. Limnology and Oceanography published by Wiley Periodicals LLC. on behalf of Association for the Sciences of Limnology and Oceanography.},
	issn = {1939-5590},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lno.11670},
	doi = {10.1002/lno.11670},
	abstract = {High-resolution time series of dissolved oxygen (DO) have revealed different ecosystem energetics regimes across various stream types. Ecosystem energetic regimes are relevant to better understand the transformation and retention of nutrients and carbon in stream ecosystems. However, the patterns and controls of stream energetics in high-mountain landscapes remain largely unknown. Here we monitored percent DO saturation (every 10 min) over 2 years in a glacier-fed, krenal (groundwater-fed) and a nival (snowmelt-fed) stream as they are typical for the high mountains. We used daily Shannon entropy to explore the temporal dynamics of stream water DO and to infer information on the ecosystem energetics and on the potential drivers. We found that discharge modulated the drivers of DO variations at daily and seasonal scales. Elevated bed movement along with high turbidity and very high gas exchange rates drove the daily DO patterns in the glacier-fed stream during snow and ice melt, whereas light seemed to drive DO dynamics in the krenal and nival streams. We found a window of favorable conditions for potential gross primary production (GPP) during the onset of the snowmelt in the glacier-fed stream, whereas potential GPP seemed to extend over longer periods in the krenal and nival streams. Our findings suggest how the energetic regimes of these high-mountain streams may change in the future as their biological and physical drivers change owing to climate warming.},
	language = {en},
	number = {n/a},
	urldate = {2020-12-17},
	journal = {Limnology and Oceanography},
	author = {Canadell, Marta Boix and Gómez‐Gener, Lluís and Clémençon, Mélanie and Lane, Stuart N. and Battin, Tom J.}
}

@article{groisman_changes_2012,
	title = {Changes in {Intense} {Precipitation} over the {Central} {United} {States}},
	volume = {13},
	issn = {1525-7541, 1525-755X},
	url = {https://journals.ametsoc.org/view/journals/hydr/13/1/jhm-d-11-039_1.xml},
	doi = {10.1175/JHM-D-11-039.1},
	abstract = {{\textless}section class="abstract"{\textgreater}{\textless}h2 class="abstractTitle text-title my-1" id="d1588e2"{\textgreater}Abstract{\textless}/h2{\textgreater}{\textless}p{\textgreater}In examining intense precipitation over the central United States, the authors consider only days with precipitation when the daily total is above 12.7 mm and focus only on these days and multiday events constructed from such consecutive precipitation days. Analyses show that over the central United States, a statistically significant redistribution in the spectra of intense precipitation days/events during the past decades has occurred. Moderately heavy precipitation events (within a 12.7–25.4 mm day$^{\textrm{−1}}$ range) became less frequent compared to days and events with precipitation totals above 25.4 mm. During the past 31 yr (compared to the 1948–78 period), significant increases occurred in the frequency of “very heavy” (the daily rain events above 76.2 mm) and extreme precipitation events (defined as daily and multiday rain events with totals above 154.9 mm or 6 in.), with up to 40\% increases in the frequency of days and multiday extreme rain events. Tropical cyclones associated with extreme precipitation do not significantly contribute to the changes reported in this study. With time, the internal precipitation structure (e.g., mean and maximum hourly precipitation rates within each preselected range of daily or multiday event totals) did not noticeably change. Several possible causes of observed changes in intense precipitation over the central United States are discussed and/or tested.{\textless}/p{\textgreater}{\textless}/section{\textgreater}},
	language = {EN},
	number = {1},
	urldate = {2020-12-15},
	journal = {Journal of Hydrometeorology},
	author = {Groisman, Pavel Ya and Knight, Richard W. and Karl, Thomas R.},
	month = feb,
	year = {2012},
	note = {Publisher: American Meteorological Society
Section: Journal of Hydrometeorology},
	pages = {47--66},
}

@article{williams_changing_2020,
	title = {Changing {Rainfall} {Patterns} {Over} the {Western} {Lake} {Erie} {Basin} (1975–2017): {Effects} on {Tributary} {Discharge} and {Phosphorus} {Load}},
	volume = {56},
	copyright = {Published 2020. This article is a U.S. Government work and is in the public domain in the USA.},
	issn = {1944-7973},
	shorttitle = {Changing {Rainfall} {Patterns} {Over} the {Western} {Lake} {Erie} {Basin} (1975–2017)},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2019WR025985},
	doi = {10.1029/2019WR025985},
	abstract = {In agricultural watersheds, shifting climate and hydrologic patterns present an immediate and future risk to both farm productivity and downstream aquatic ecosystems. Here, our objective was to evaluate long-term spatiotemporal trends in rainfall amount and intensity within the Maumee River-Lake Erie system and quantify the effects of rainfall patterns on streamflow and phosphorus loading. Across the watershed, annual rainfall increased by 102 ± 115 mm (11 ± 13\%) from 1975–2017. Heavy (25.4–76.2 mm) and very heavy ({\textgreater}76.2 mm) rainfall accounted for most of the increase in total rainfall, with observed increases of 45 ± 32\% that occurred primarily during spring and summer. Trends in streamflow for 12 monitored subwatersheds generally followed patterns in rainfall, as discharge increased by 19 ± 32\%. Discharge-to-rainfall ratio increased in 9 of 12 subwatersheds despite no change or increases in watershed storage capacity, suggesting that increasing rainfall intensity that exceeds short-term watershed storage capacity (i.e., during/immediately following the rainfall event) may control patterns of discharge more than long-term gains in watershed storage (i.e., changes in soil water holding capacity). Long-term trends in phosphorus (total phosphorus and soluble reactive phosphorus) load indicate that changes in rainfall amount and intensity have substantially contributed to increased loading through increased discharge volumes. Differences in total phosphorus and soluble reactive phosphorus concentration trends also highlight how concomitant changes in rainfall and land management practices have influenced loading. Findings therefore suggest that changing patterns in rainfall amount and intensity have and will likely continue to pose a significant challenge to conservation efforts in agricultural landscapes aiming to decrease phosphorus delivery to surface waters.},
	language = {en},
	number = {3},
	urldate = {2020-12-15},
	journal = {Water Resources Research},
	author = {Williams, Mark R. and King, Kevin W.},
	year = {2020},
	keywords = {climate change, long-term trend, rainfall intensity, subsurface drainage, watershed monitoring},
	pages = {e2019WR025985},
}

@article{atlas_indigenous_2020,
	title = {Indigenous {Systems} of {Management} for {Culturally} and {Ecologically} {Resilient} {Pacific} {Salmon} ({Oncorhynchus} spp.) {Fisheries}},
	issn = {0006-3568},
	url = {10.1093/biosci/biaa144},
	doi = {10.1093/biosci/biaa144},
	abstract = {Pacific salmon (Oncorhynchus spp.) are at the center of social–ecological systems that have supported Indigenous peoples around the North Pacific Rim since time immemorial. Through generations of interdependence with salmon, Indigenous Peoples developed sophisticated systems of management involving cultural and spiritual beliefs, and stewardship practices. Colonization radically altered these social–ecological systems, disrupting Indigenous management, consolidating authority within colonial governments, and moving most harvest into mixed-stock fisheries. We review Indigenous management of salmon, including selective fishing technologies, harvest practices, and governance grounded in multigenerational place-based knowledge. These systems and practices showcase pathways for sustained productivity and resilience in contemporary salmon fisheries. Contrasting Indigenous systems with contemporary management, we document vulnerabilities of colonial governance and harvest management that have contributed to declining salmon fisheries in many locations. We suggest that revitalizing traditional systems of salmon management can improve prospects for sustainable fisheries and healthy fishing communities and identify opportunities for their resurgence.},
	number = {biaa144},
	urldate = {2020-12-11},
	journal = {BioScience},
	author = {Atlas, William I and Ban, Natalie C and Moore, Jonathan W and Tuohy, Adrian M and Greening, Spencer and Reid, Andrea J and Morven, Nicole and White, Elroy and Housty, William G and Housty, Jess A and Service, Christina N and Greba, Larry and Harrison, Sam and Sharpe, Ciara and Butts, Katherine I R and Shepert, William M and Sweeney-Bergen, Elissa and Macintyre, Donna and Sloat, Matthew R and Connors, Katrina},
	month = dec,
	year = {2020},
}

@article{risse-buhl_hydromorphologic_2020,
	title = {Hydromorphologic {Sorting} of {In}-{Stream} {Nitrogen} {Uptake} {Across} {Spatial} {Scales}},
	issn = {1435-0629},
	url = {10.1007/s10021-020-00576-7},
	doi = {10.1007/s10021-020-00576-7},
	abstract = {Nitrogen (N) uptake is a key process in stream ecosystems that is mediated mainly by benthic microorganisms (biofilms on different substrata) and has implications for the biogeochemical fluxes at catchment scale and beyond. Here, we focused on the drivers of assimilatory N uptake, especially the effects of hydromorphology and other environmental constraints, across three spatial scales: micro, meso and reach. In two seasons (summer and spring), we performed whole-reach 15N-labelled ammonium injection experiments in two montane, gravel-bed stream reaches with riffle–pool sequences. N uptake was highest in epilithic biofilms, thallophytes and roots (min–max range 0.2–545.2 mg N m−2 day−1) and lowest in leaves, wood and fine benthic organic matter (0.05–209.2 mg N m−2 day−1). At the microscale, N uptake of all primary uptake compartments except wood was higher in riffles than in pools. At the mesoscale, hydromorphology determined the distribution of primary uptake compartments, with fast-flowing riffles being dominated by biologically more active compartments and pools being dominated by biologically less active compartments. Despite a lower biomass of primary uptake compartments, mesoscale N uptake was 1.7–3.0 times higher in riffles than in pools. At reach scale, N uptake ranged from 79.6 to 334.1 mg N m−2 day−1. Highest reach-scale N uptake was caused by a bloom of thallopyhtes, mainly filamentous autotrophs, during stable low discharge and high light conditions. Our results reveal the important role of hydromorphologic sorting of primary uptake compartments at mesoscale as a controlling factor for reach-scale N uptake in streams.},
	language = {en},
	urldate = {2020-12-10},
	journal = {Ecosystems},
	author = {Risse-Buhl, Ute and Anlanger, Christine and Noss, Christian and Lorke, Andreas and von Schiller, Daniel and Weitere, Markus},
	month = dec,
	year = {2020},
}

@article{trentman_using_2020-1,
	title = {Using path analysis to determine interacting effects of biotic and abiotic factors on patch-scale biogeochemical rates in a prairie stream},
	volume = {82},
	issn = {1420-9055},
	url = {10.1007/s00027-020-0702-8},
	doi = {10.1007/s00027-020-0702-8},
	abstract = {Biogeochemical rates within streams vary with ecosystem properties including the distribution of fishes. While many studies investigate the singular effect of fishes on ecosystem components, there is a limited understanding of how fish presence interacts with other ecosystem properties to affect ecosystem structure and function. Here, we used path analyses to elucidate direct and indirect effects of fish presence, and other ecosystem properties on ecosystem respiration (ER), gross primary production (GPP), and ammonium uptake. Experimental responses of fish removal on patch scale (300 cm2) benthic rates of ER, GPP, and ammonium uptake were measured at two sites in a prairie stream. The effect of fish was determined by comparing substrata from field exclosures with fish absent to substrata exposed to fish. Total path model-explained variance was greatest for ER (R2 = 0.55) and least for ammonium uptake (R2 = 0.36) and GPP (R2 = 0.34). Fish decreased algal biomass and directly increased all biogeochemical rates. The relative importance of the different abiotic ecosystem properties varied by process; however, FBOM and substrata size were important for most rates. This study provides evidence for predominantly direct effects of fish on both stream structure and function in a prairie stream. Our results emphasize that interactions between biotic and abiotic factors should be considered when determining drivers of biogeochemical activity. We suggest that simple linear food webs that consist of top–down or bottom–up control are not always sufficient to describe animal effects on ecosystem rates.},
	language = {en},
	number = {2},
	urldate = {2020-12-09},
	journal = {Aquatic Sciences},
	author = {Trentman, Matt T. and Dodds, Walter K. and Gido, Keith B. and Rüegg, Janine and Ruffing, Claire M.},
	month = feb,
	year = {2020},
	pages = {26},
}

@article{summers_long-term_2020,
	title = {Long-term data reveal highly-variable metabolism and transitions in trophic status in a montane stream},
	volume = {39},
	issn = {2161-9549},
	url = {https://www.journals.uchicago.edu/doi/full/10.1086/708659},
	doi = {10.1086/708659},
	abstract = {In streams, gross primary production (GPP) and ecosystem respiration (ER) (i.e., stream metabolism) control the transport and fate of nutrients and organic carbon and vice versa. The importance of short-term and local factors in driving these processes is well known in the literature. However, little information exists regarding the extent of temporal variability of stream metabolism and how both local physicochemical and broad-scale climatic drivers affect this variability. We used 7 years of field data from an open-canopy headwater stream ecosystem in the southwestern United States to quantify the extent of seasonal and inter-annual variability in stream metabolism (GPP, ER, and net ecosystem production [NEP]) and to assess if temporal variation in these processes was related to the magnitude of snowmelt runoff. In spring, seasonal mean ER (p = 0.025, r2 = 0.67) and NEP (p = 0.004, r2 = 0.83) were more strongly related to discharge (Q) than GPP (p = 0.19, r2 = 0.32), potentially because of an increased influx of nutrients and organic carbon during years with higher snowmelt runoff. There were no strong relationships between seasonal mean GPP and Q, light, temperature, turbidity, and specific conductance (p ≥ 0.27, r2 ≤ 0.18). Our long-term data revealed unanticipated shifts from autotrophic to heterotrophic status within and across years. However, this variability was not strongly associated with environmental factors at either local (i.e., Q or photosynthetically-active radiation) or global (i.e., El Niño-Southern Oscillation) scales. Previous paradigms hold that local attributes dictated by geographic and landscape positioning (e.g., light and temperature regimes) control the trophic status of streams, but our findings suggest that complex combinations of spatiotemporally-variable factors, such as snow accumulation and melting, and their role in connecting terrestrial and aquatic ecosystems can lead to substantial within-stream variation in autotrophic or heterotrophic status.},
	number = {2},
	urldate = {2020-12-09},
	journal = {Freshwater Science},
	author = {Summers, Betsy M. and Horn, David J. Van and González-Pinzón, Ricardo and Bixby, Rebecca J. and Grace, Michael R. and Sherson, Lauren R. and Crossey, Laura J. and Stone, Mark C. and Parmenter, Robert R. and Compton, T. Scott and Dahm, Clifford N.},
	month = mar,
	year = {2020},
	note = {Publisher: The University of Chicago Press},
	pages = {241--255},
}

@article{allen_river_2020,
	title = {River ecosystem conceptual models and non-perennial rivers: {A} critical review},
	volume = {7},
	copyright = {© 2020 Wiley Periodicals LLC.},
	issn = {2049-1948},
	shorttitle = {River ecosystem conceptual models and non-perennial rivers},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/wat2.1473},
	doi = {10.1002/wat2.1473},
	abstract = {Conceptual models underpin river ecosystem research. However, current models focus on continuously flowing rivers and few explicitly address characteristics such as flow cessation and drying. The applicability of existing conceptual models to nonperennial rivers that cease to flow (intermittent rivers and ephemeral streams, IRES) has not been evaluated. We reviewed 18 models, finding that they collectively describe main drivers of biogeochemical and ecological patterns and processes longitudinally (upstream-downstream), laterally (channel-riparian-floodplain), vertically (surface water-groundwater), and temporally across local and landscape scales. However, perennial rivers are longitudinally continuous while IRES are longitudinally discontinuous. Whereas perennial rivers have bidirectional lateral connections between aquatic and terrestrial ecosystems, in IRES, this connection is unidirectional for much of the time, from terrestrial-to-aquatic only. Vertical connectivity between surface and subsurface water occurs bidirectionally and is temporally consistent in perennial rivers. However, in IRES, this exchange is temporally variable, and can become unidirectional during drying or rewetting phases. Finally, drying adds another dimension of flow variation to be considered across temporal and spatial scales in IRES, much as flooding is considered as a temporally and spatially dynamic process in perennial rivers. Here, we focus on ways in which existing models could be modified to accommodate drying as a fundamental process that can alter these patterns and processes across spatial and temporal dimensions in streams. This perspective is needed to support river science and management in our era of rapid global change, including increasing duration, frequency, and occurrence of drying. This article is categorized under: Water and Life {\textgreater} Nature of Freshwater Ecosystems Water and Life {\textgreater} Stresses and Pressures on Ecosystems Science of Water {\textgreater} Hydrological Processes},
	language = {en},
	number = {5},
	urldate = {2020-12-09},
	journal = {WIREs Water},
	author = {Allen, Daniel C. and Datry, Thibault and Boersma, Kate S. and Bogan, Michael T. and Boulton, Andrew J. and Bruno, Daniel and Busch, Michelle H. and Costigan, Katie H. and Dodds, Walter K. and Fritz, Ken M. and Godsey, Sarah E. and Jones, Jeremy B. and Kaletova, Tatiana and Kampf, Stephanie K. and Mims, Meryl C. and Neeson, Thomas M. and Olden, Julian D. and Pastor, Amandine V. and Poff, N. LeRoy and Ruddell, Benjamin L. and Ruhi, Albert and Singer, Gabriel and Vezza, Paolo and Ward, Adam S. and Zimmer, Margaret},
	year = {2020},
	keywords = {conceptual model, ecosystem, nonperennial, river, stream},
	pages = {e1473},
}

@article{francoeur_short-term_2006,
	title = {Short-term {Effects} of {Elevated} {Velocity} and {Sediment} {Abrasion} on {Benthic} {Algal} {Communities}},
	volume = {561},
	issn = {1573-5117},
	url = {10.1007/s10750-005-1604-4},
	doi = {10.1007/s10750-005-1604-4},
	abstract = {Of the mechanisms that remove benthic algae during flood disturbances, relatively little is known about the effects of sediment scour. We investigated suspended sediment scour using naturally colonized benthic algal communities exposed to realistic velocities and suspended sediment concentrations in a laboratory flowtank. Increased velocity alone removed benthic algal biomass, and high suspended sediment concentrations further increased algal removal. Efficacy of biomass removal by velocity and suspended sediments was community-specific; communities with a tightly adherent cohesive mat physiognomy were resistant to removal, despite taxonomic similarity to easily disturbed communities. In addition, some taxa were more susceptible to removal by disturbance than others. The duration of scour and physical refugia on the substratum also influenced algal biomass removal. Our results indicate that suspended sediment scour may be an important mechanism for algal removal during flood events, and some variability in biomass removal among flood events may be the result of differences in suspended sediment load.},
	language = {en},
	number = {1},
	urldate = {2020-12-09},
	journal = {Hydrobiologia},
	author = {Francoeur, Steven N. and Biggs, Barry J. F.},
	month = may,
	year = {2006},
	pages = {59--69},
}

@misc{zhao_effects_2019,
	type = {Research {Article}},
	title = {Effects of {Rainfall} {Intensity} and {Vegetation} {Cover} on {Erosion} {Characteristics} of a {Soil} {Containing} {Rock} {Fragments} {Slope}},
	url = {https://www.hindawi.com/journals/ace/2019/7043428/},
	abstract = {Rainfall events coupled with shallow and gravelly sloping farmland have led to serious soil erosion and associated problems in the Three Gorges reservoir. Previous studies have shown that the use of vegetation is an effective way to control soil erosion. Therefore, an artificial, simulated rainfall experiment study is conducted to determine the effect of rainfall intensity and vegetation cover on runoff volume, sediment load, and runoff hydraulics characteristics. The experiment consists of seven vegetation treatments subjected to three rainfall intensities on a soil that contains rock fragments on a slope of 30°. The results indicate that the runoff volume and sediment load of the bare plot were greater than those of vegetation-covered plots under three different rainfall intensities. When Cynodon dactylon and Indigofera amblyantha were applied together, the plot displayed the best performance for soil loss control, with a reduction of 87.88\%–99.11\%. According to a redundancy analysis, the change in rainfall intensity had the least impact on the Reynolds number and the runoff volume of the herb-shrub mixed plot in this study. These findings suggest that the effect of combining Cynodon dactylon and Indigofera amblyantha and increasing the vegetation coverage is an effective solution for soil and water loss conservation. The application of this method can alleviate environmental stress on the Three Gorges reservoir.},
	language = {en},
	urldate = {2020-12-09},
	journal = {Advances in Civil Engineering},
	author = {Zhao, Bingqin and Zhang, Lun and Xia, Zhenyao and Xu, Wennian and Xia, Lu and Liang, Yongzhe and Xia, Dong},
	month = sep,
	year = {2019},
	doi = {10.1155/2019/7043428},
	doi = {10.1155/2019/7043428},
	note = {ISSN: 1687-8086
Pages: e7043428
Publisher: Hindawi
Volume: 2019},
}

@article{kaye_using_2017,
	title = {Using cover crops to mitigate and adapt to climate change. {A} review},
	volume = {37},
	issn = {1773-0155},
	url = {10.1007/s13593-016-0410-x},
	doi = {10.1007/s13593-016-0410-x},
	abstract = {Cover crops have long been touted for their ability to reduce erosion, fix atmospheric nitrogen, reduce nitrogen leaching, and improve soil health. In recent decades, there has been resurgence in cover crop adoption that is synchronous with a heightened awareness of climate change. Climate change mitigation and adaptation may be additional, important ecosystem services provided by cover crops, but they lie outside of the traditional list of cover cropping benefits. Here, we review the potential for cover crops to mitigate climate change by tallying all of the positive and negative impacts of cover crops on the net global warming potential of agricultural fields. Then, we use lessons learned from two contrasting regions to evaluate how cover crops affect adaptive management for precipitation and temperature change. Three key outcomes from this synthesis are (1) Cover crop effects on greenhouse gas fluxes typically mitigate warming by {\textasciitilde}100 to 150 g CO2 e/m2/year, which is higher than mitigation from transitioning to no-till. The most important terms in the budget are soil carbon sequestration and reduced fertilizer use after legume cover crops. (2) The surface albedo change due to cover cropping, calculated for the first time here using case study sites in central Spain and Pennsylvania, USA, may mitigate 12 to 46 g CO2 e/m2/year over a 100-year time horizon. And (3) Cover crop management can also enable climate change adaptation at these case study sites, especially through reduced vulnerability to erosion from extreme rain events, increased soil water management options during droughts or periods of soil saturation, and retention of nitrogen mineralized due to warming. Overall, we found very few tradeoffs between cover cropping and climate change mitigation and adaptation, suggesting that ecosystem services that are traditionally expected from cover cropping can be promoted synergistically with services related to climate change.},
	language = {en},
	number = {1},
	urldate = {2020-12-09},
	journal = {Agronomy for Sustainable Development},
	author = {Kaye, Jason P. and Quemada, Miguel},
	month = jan,
	year = {2017},
	pages = {4},
}

@article{alnoee_macrophytes_2020,
	title = {Macrophytes enhance reach-scale metabolism on a daily, seasonal and annual basis in agricultural lowland streams},
	volume = {83},
	issn = {1420-9055},
	url = {10.1007/s00027-020-00766-4},
	doi = {10.1007/s00027-020-00766-4},
	abstract = {In many lowland streams, macrophytes are highly abundant and play a key role in ecosystem structure and function. However, no studies on annual stream metabolism have been conducted in streams with significant macrophyte abundance, despite the well-known effect on both gross primary production (GPP) and ecosystem respiration (ER). Macrophyte abundance in temperate streams is strongly seasonal, with highest biomass during summer and lowest during winter. We expected that this phenological pattern would drive annual fluctuations in GPP and ER. We measured daily metabolism for one year in two stream reaches, one with and one without macrophytes. Our results demonstrated that annual, aggregated GPP and ER were 2.2 and 1.3 times higher in the macrophyte reach. Furthermore, while daily GPP was the same between the two reaches during winter where biomass was negligible, GPP was higher during spring, summer and fall for the macrophyte reach. The range in daily ER was more constrained during summer, but more variable during fall and winter in the macrophyte reach relative to the non-macrophyte reach. Macrophyte abundance and chlorophyll-a controlled 80\% of the variation in annual GPP for the macrophyte reach. Similarly, 63\% of the variation in annual ER was controlled by macrophyte abundance together with discharge in the macrophyte reach. Although macrophytes enhanced GPP on an annual and seasonal time scale in agricultural lowland streams, both reaches were heterotrophic (i.e., GPP {\textless} ER) reflecting high organic matter supply from the landscape and in-stream retention and decomposition of organic matter within the macrophyte beds.},
	language = {en},
	number = {1},
	urldate = {2020-12-09},
	journal = {Aquatic Sciences},
	author = {Alnoee, Anette Baisner and Levi, Peter S. and Baattrup-Pedersen, Annette and Riis, Tenna},
	month = nov,
	year = {2020},
	pages = {11},
}

@article{obrien_aquatic_2014,
	title = {Aquatic {Macrophytes} {Alter} {Metabolism} and {Nutrient} {Cycling} in {Lowland} {Streams}},
	volume = {17},
	issn = {1435-0629},
	url = {10.1007/s10021-013-9730-8},
	doi = {10.1007/s10021-013-9730-8},
	abstract = {Macrophytes influence the physical, chemical, and biological characteristics of lowland streams, so may be critically important in stream management. We investigated the role of macrophytes in regulating metabolism and nutrient cycling in three lowland, agricultural streams. We measured stream metabolism over the growing season and following experimental macrophyte removal, and used short-term nutrient additions of phosphate (P) and ammonium to assess macrophyte influences on nutrient uptake. Primary production was closely correlated with macrophyte cover across all streams and dates, and decreased greatly with macrophyte removal, whereas ecosystem respiration was not correlated with macrophyte cover and was not altered by macrophyte removal. Phosphate uptake velocity was negatively related to primary production, suggesting that macrophyte activity actually slowed P uptake. Ammonium uptake was not correlated with macrophyte cover or metabolism metrics. Stream nitrate concentrations typically exceeded concentrations of incoming groundwater, suggesting little net nitrate retention in these macrophyte-dominated streams. Phosphorous demand by macrophytes was 10-fold lower than observed uptake rates, indicating that macrophyte P demand was much lower than that of other stream biota. Nitrogen demand by macrophytes was nearly equal to ammonium uptake and was not sufficient to affect the high nitrate flux. These results indicate that macrophytes drive ecosystem metabolism but have limited influence on water column nutrient concentrations because macrophyte demand is much lower than the supply available from the water column. Thus macrophytes in our streams had a large impact on stream trophic state, but offered little potential to influence nutrient removal via management.},
	language = {en},
	number = {3},
	urldate = {2020-12-08},
	journal = {Ecosystems},
	author = {O’Brien, Jonathan M. and Lessard, Joanna L. and Plew, David and Graham, S. Elizabeth and McIntosh, Angus R.},
	month = apr,
	year = {2014},
	pages = {405--417},
}

@article{genzoli_shifts_2016,
	title = {Shifts in {Klamath} {River} metabolism following a reservoir cyanobacterial bloom},
	volume = {35},
	issn = {2161-9549},
	url = {https://www.journals.uchicago.edu/doi/10.1086/687752},
	doi = {10.1086/687752},
	abstract = {Sources of C and the location of production in rivers can influence trophic state. Despite major alterations to large rivers, data describing metabolic balance and partitioning in these rivers are sparse. We quantified ecosystem metabolism in the Lower Klamath River, USA, before and after a reservoir-derived cyanobacterial bloom. We calculated daily whole-river metabolism at 3 reaches on the Klamath River below Iron Gate Dam from May–October 2012. We measured planktonic metabolism biweekly from June to October to partition the source (planktonic or benthic) of whole-river gross primary production (GPPTotal) and ecosystem respiration (ERTotal) prior to and during the cyanobacterial bloom. Whole-river ecosystem metabolism in the Klamath River varied seasonally, with low GPPTotal and ERTotal in spring and autumn (May, June, October means = 4.4, –2.9 g O2 m−2 d−1), and high GPPTotal and ERTotal during summer (July–September means = 8.0, –6.8 g O2 m−2 d−1). Within sites, daily variation in ERTotal was coupled with daily variation in GPPTotal, suggesting a dominant role of autotrophs in ERTotal. Average rates of GPPTotal declined from up- to downriver sites, driving parallel declines in net ecosystem production. After the bloom, planktonic production and respiration increased 2–4× over nonbloom rates, whereas whole-river metabolism was relatively stable because of compensatory declines in benthic metabolism. Minimum daily dissolved O2 concentration (DO) declined with increasing GPPTotal. This pattern strengthened during the bloom, showing that DO, a regulated water-quality variable, was tightly linked to C-cycling processes in the river. The bloom changed the location (planktonic vs benthic) of production and respiration in the river and decreased DO minima, but not rates of whole-river metabolism. Location of primary production had only subtle effects on ecosystem metabolism compared to seasonal changes in metabolism.},
	number = {3},
	urldate = {2020-12-07},
	journal = {Freshwater Science},
	author = {Genzoli, Laurel and Hall, Robert O.},
	month = jun,
	year = {2016},
	note = {Publisher: The University of Chicago Press},
	pages = {795--809},
}

@article{herreid_divergent_2020,
	title = {Divergent {Controls} on {Stream} {Greenhouse} {Gas} {Concentrations} {Across} a {Land}-{Use} {Gradient}},
	issn = {1435-0629},
	url = {10.1007/s10021-020-00584-7},
	doi = {10.1007/s10021-020-00584-7},
	abstract = {Inland waters can be significant sources of carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) to the atmosphere. However, considerable uncertainty remains in regional and global estimates of greenhouse gas (GHG) emissions from freshwater ecosystems, particularly streams. Controls on GHG production in streams, such as water chemistry and sediment characteristics, are also poorly understood. The main objective of this study was to quantify spatial and temporal variability in GHG concentrations in 20 streams across a landscape with considerable variation in land use and land cover in New England, USA. Stream water was consistently supersaturated in CO2, CH4, and N2O, suggesting that these small streams are sources of GHGs to the atmosphere in this landscape. Results show that concentrations of dissolved CO2, CH4 and N2O differed in their spatial and temporal patterns and in their relationship to stream chemistry. Both bivariate and multivariate analyses revealed a unique combination of predictor variables for each gas, suggesting variation in the landscape attributes and in-stream processes that control GHG concentrations. Although hydrologic conditions did not explain variation among sites, temporal patterns in GHG concentrations align with seasonal phenologies in flow and temperature. We developed a conceptual model based on these data that describes the spatial variability in GHG production from streams and that can elucidate the dominant controls on each gas. Developing an understanding of the factors controlling GHG dynamics in streams can help assess and predict how fluvial ecosystems will respond to changes in climate and land use and can be used to incorporate emissions from streams into regional and global GHG emission inventories.},
	language = {en},
	urldate = {2020-12-03},
	journal = {Ecosystems},
	author = {Herreid, Allison M. and Wymore, Adam S. and Varner, Ruth K. and Potter, Jody D. and McDowell, William H.},
	month = dec,
	year = {2020},
}

@article{ruegg_thinking_nodate,
	title = {Thinking like a consumer: {Linking} aquatic basal metabolism and consumer dynamics},
	volume = {n/a},
	issn = {2378-2242},
	shorttitle = {Thinking like a consumer},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lol2.10172},
	doi = {10.1002/lol2.10172},
	abstract = {The increasing availability of high-frequency freshwater ecosystem metabolism data provides an opportunity to identify links between metabolic regimes, as gross primary production and ecosystem respiration patterns, and consumer energetics with the potential to improve our current understanding of consumer dynamics (e.g., population dynamics, community structure, trophic interactions). We describe a conceptual framework linking metabolic regimes of flowing waters with consumer community dynamics. We use this framework to identify three emerging research needs: (1) quantifying the linkage of metabolism and consumer production data via food web theory and carbon use efficiencies, (2) evaluating the roles of metabolic dynamics and other environmental regimes (e.g., hydrology, light) in consumer dynamics, and (3) determining the degree to which metabolic regimes influence the evolution of consumer traits and phenology. Addressing these needs will improve the understanding of consumer biomass and production patterns as metabolic regimes can be viewed as an emergent property of food webs.},
	language = {en},
	number = {n/a},
	urldate = {2020-12-02},
	journal = {Limnology and Oceanography Letters},
	author = {Rüegg, Janine and Conn, Caitlin C. and Anderson, Elizabeth P. and Battin, Tom J. and Bernhardt, Emily S. and Canadell, Marta Boix and Bonjour, Sophia M. and Hosen, Jacob D. and Marzolf, Nicholas S. and Yackulic, Charles B.},
}

@article{bonjour_influence_2020,
	title = {Influence of fishes on macroinvertebrate communities and insect emergence production in intermittent stream refuges},
	volume = {65},
	copyright = {© 2020 John Wiley \& Sons Ltd.},
	issn = {1365-2427},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/fwb.13509},
	doi = {10.1111/fwb.13509},
	abstract = {Drying intermittent stream networks often have permanent water refuges that are important for recolonisation. These habitats may be hotspots for interactions between fishes and invertebrates as they become isolated, but densities and diversity of fishes in these refuges can be highly variable across time and space. Insect emergence from streams provides energy and nutrient subsidies to riparian habitats. The magnitude of such subsidies may be influenced by in-stream predators such as fishes. We examined whether benthic macroinvertebrate communities, emerging adult insects, and algal biomass in permanent grassland stream pools differed among sites with naturally varying densities of fishes. We also manipulated fish densities in a mesocosm experiment to address how fishes might affect colonisation during recovery from hydrologic disturbance. Fish biomass had a negative impact on invertebrate abundance, but not biomass or taxa richness, in natural pools. Total fish biomass was not correlated with total insect emergence in natural pools, but orangethroat darter (Etheostoma spectabile) biomass was inversely correlated with emerging Chironomidae biomass and individual midge body size. The interaction in our models between predatory fish biomass and date suggested that fishes may also delay insect emergence from natural pools, altering the timing of aquatic–terrestrial subsidies. There was an increase over time in algal biomass (chlorophyll-a) in mesocosms, but this did not differ among fish density treatments. Regardless, fish presence in mesocosms reduced the abundance of colonising insects and total invertebrate biomass. Mesocosm invertebrate communities in treatments without fishes were characterised by more Chironomidae, Culicidae, and Corduliidae. Results suggest that fishes influence invertebrates in habitats that represent important refuges during hydrologic disturbance, hot spots for subsidy exports to riparian food webs, and source areas for colonists during recovery from hydrologic disturbance. Fish effects in these systems include decreasing invertebrate abundance, shifting community structure, and altering patterns of invertebrate emergence and colonisation.},
	language = {en},
	number = {8},
	urldate = {2020-12-02},
	journal = {Freshwater Biology},
	author = {Bonjour, Sophia M. and Whiles, Matt R. and Gido, Keith B.},
	year = {2020},
	keywords = {benthos, ecosystem, fresh waters, other species interactions, predation},
	pages = {1412--1428},
}

@article{jones_stream_2020,
	title = {Stream {Microbial} {Community} {Structured} by {Trace} {Elements}, {Headwater} {Dispersal}, and {Large} {Reservoirs} in {Sub}-{Alpine} and {Urban} {Ecosystems}},
	volume = {11},
	issn = {1664-302X},
	url = {https://www.frontiersin.org/articles/10.3389/fmicb.2020.491425/full?utm_source=S-TWT&utm_medium=SNET&utm_campaign=ECO_FCIMB_XXXXXXXX_auto-dlvrit},
	doi = {10.3389/fmicb.2020.491425},
	abstract = {Stream bacterioplankton communities, a crucial component of aquatic ecosystems and surface water quality, are shaped by environmental selection (i.e., changes in taxa abundance associated with more or less favorable abiotic conditions) and passive dispersal (i.e., organisms’ abundance and distribution is a function of the movement of the water). These processes are a function of hydrologic conditions such as residence time and water chemistry, which are mediated by human infrastructure. To quantify the role of environmental conditions, dispersal, and human infrastructure (dams) on stream bacterioplankton, we measured bacterioplankton community composition in rivers from sub-alpine to urban environments in three watersheds (Utah, USA) across three seasons. Of the 43 environmental parameters measured (including physicochemical parameters, solute concentrations, and catchment characteristics), trace element concentrations explained the most variability in bacterioplankton community composition using Redundancy Analysis ordination. Trace elements may correlate with bacterioplankton due to the commonality in source of water and microorganisms, and/or environmental selection creating more or less favorable conditions for bacteria. Bacterioplankton community diversity decreased downstream along parts of the stream continuum but was disrupted where large reservoirs increased water residence time by orders of magnitude, potentially indicating a shift in the relative importance of environmental selection and dispersal at these sites. Reservoirs also had substantial effects on community composition, dissimilarity (Bray-Curtis distance) and species interactions as indicated by co-occurrence networks. Communities downstream of reservoirs were enriched with anaerobic Sporichthyaceae, methanotrophic Methylococcaceae, and iron-transforming Acidimicrobiales, suggesting alternative metabolic pathways became active in the hypolimnion of large reservoirs. Our results identify that human activity affects river microbial communities, with potential impacts on water quality through modified biogeochemical cycling.},
	language = {English},
	urldate = {2020-12-01},
	journal = {Frontiers in Microbiology},
	author = {Jones, Erin Fleming and Griffin, Natasha and Kelso, Julia E. and Carling, Gregory T. and Baker, Michelle A. and Aanderud, Zachary T.},
	year = {2020},
	note = {Publisher: Frontiers},
	keywords = {Dispersal, Urban, bacterioplankton, community composition, reservoir, species sorting, water chemistry},
}

@article{gardiner_state-space_2019,
	title = {State-space modeling reveals habitat perception of a small terrestrial mammal in a fragmented landscape},
	volume = {9},
	copyright = {© 2019 The Authors. Ecology and Evolution published by John Wiley \& Sons Ltd.},
	issn = {2045-7758},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.5519},
	doi = {10.1002/ece3.5519},
	abstract = {Habitat loss is a major cause of species loss and is expected to increase. Loss of habitat is often associated with fragmentation of remaining habitat. Whether species can persist in fragmented landscapes may depend on their movement behavior, which determines their capability to respond flexibility to changes in habitat structure and spatial distribution of patches. Movement is frequently generalized to describe a total area used, or segmented to highlight resource use, often overlooking finer-scale individual behaviors. We applied hidden Markov models (HMM) to movement data from 26 eastern bettongs (Bettongia gaimardi) in fragmented landscapes. HMMs are able to identify distinct behavior states associated with different movement patterns and discover how these behaviors are associated with habitat features. Three distinct behavior states were identified and interpreted as denning, foraging, and fast-traveling. The probability of occurrence of each state, and of transitions between them, was predicted by variation in tree-canopy cover and understorey vegetation density. Denning was associated with woodland with low canopy cover but high vegetation density, foraging with high canopy cover but low vegetation density, and fast-traveling with low canopy cover and low vegetation density. Bettongs did move outside woodland patches, often fast-traveling through pasture and using smaller stands of trees as stepping stones between neighboring patches. Males were more likely to fast-travel and venture outside woodlands patches, while females concentrated their movement within woodland patches. Synthesis and applications: Our work demonstrates the value of using animal movement to understand how animals respond to variation in habitat structure, including fragmentation. Analysis using HMMs was able to characterize distinct habitat types needed for foraging and denning, and identify landscape features that facilitate movement between patches. Future work should extend the use of individual movement analyses to guide management of fragmented habitat in ways that support persistence of species potentially threatened by habitat loss.},
	language = {en},
	number = {17},
	urldate = {2020-12-01},
	journal = {Ecology and Evolution},
	author = {Gardiner, Riana and Hamer, Rowena and Leos‐Barajas, Vianey and Peñaherrera‐Palma, Cesar and Jones, Menna E. and Johnson, Chris},
	year = {2019},
	keywords = {Hidden Markov Models, conservation, fragmentation, management, movement ecology, restoration},
	pages = {9804--9814},
}

@article{auger-methe_state-space_2016,
	title = {State-space models’ dirty little secrets: even simple linear {Gaussian} models can have estimation problems},
	volume = {6},
	copyright = {2016 The Author(s)},
	issn = {2045-2322},
	shorttitle = {State-space models’ dirty little secrets},
	url = {https://www.nature.com/articles/srep26677},
	doi = {10.1038/srep26677},
	abstract = {State-space models (SSMs) are increasingly used in ecology to model time-series such as animal movement paths and population dynamics. This type of hierarchical model is often structured to account for two levels of variability: biological stochasticity and measurement error. SSMs are flexible. They can model linear and nonlinear processes using a variety of statistical distributions. Recent ecological SSMs are often complex, with a large number of parameters to estimate. Through a simulation study, we show that even simple linear Gaussian SSMs can suffer from parameter- and state-estimation problems. We demonstrate that these problems occur primarily when measurement error is larger than biological stochasticity, the condition that often drives ecologists to use SSMs. Using an animal movement example, we show how these estimation problems can affect ecological inference. Biased parameter estimates of a SSM describing the movement of polar bears (Ursus maritimus) result in overestimating their energy expenditure. We suggest potential solutions, but show that it often remains difficult to estimate parameters. While SSMs are powerful tools, they can give misleading results and we urge ecologists to assess whether the parameters can be estimated accurately before drawing ecological conclusions from their results.},
	language = {en},
	number = {1},
	urldate = {2020-11-30},
	journal = {Scientific Reports},
	author = {Auger-Méthé, Marie and Field, Chris and Albertsen, Christoffer M. and Derocher, Andrew E. and Lewis, Mark A. and Jonsen, Ian D. and Mills Flemming, Joanna},
	month = may,
	year = {2016},
	note = {Number: 1
Publisher: Nature Publishing Group},
	pages = {26677},
}

@article{betancourt_conceptual_2018,
	title = {A {Conceptual} {Introduction} to {Hamiltonian} {Monte} {Carlo}},
	url = {http://arxiv.org/abs/1701.02434},
	abstract = {Hamiltonian Monte Carlo has proven a remarkable empirical success, but only recently have we begun to develop a rigorous understanding of why it performs so well on difficult problems and how it is best applied in practice. Unfortunately, that understanding is confined within the mathematics of differential geometry which has limited its dissemination, especially to the applied communities for which it is particularly important. In this review I provide a comprehensive conceptual account of these theoretical foundations, focusing on developing a principled intuition behind the method and its optimal implementations rather of any exhaustive rigor. Whether a practitioner or a statistician, the dedicated reader will acquire a solid grasp of how Hamiltonian Monte Carlo works, when it succeeds, and, perhaps most importantly, when it fails.},
	urldate = {2020-11-30},
	journal = {arXiv:1701.02434 [stat]},
	author = {Betancourt, Michael},
	month = jul,
	year = {2018},
	note = {arXiv: 1701.02434},
	keywords = {Statistics - Methodology},
}

@article{breed_state-space_2012,
	title = {State-space methods for more completely capturing behavioral dynamics from animal tracks},
	volume = {235-236},
	issn = {0304-3800},
	url = {http://www.sciencedirect.com/science/article/pii/S0304380012001378},
	doi = {10.1016/j.ecolmodel.2012.03.021},
	abstract = {State-space models (SSMs) are now the tools of choice for analyzing animal tracking data. A wide variety of such data are being collected worldwide and modeled using state-space methods to better understand population dynamics, animal behavior and physical and environmental processes. The central goal of such analyses is the estimation of biologically interpretable static parameters. Most approaches implement some form of MCMC or Kalman filter to estimate these parameters. We demonstrate the utility in allowing time-varying (rather than static) parameters to more completely capture dynamic features of the processes of interest, in this case the behavioral dynamics of tracked marine animals. We develop and demonstrate a parameter augmented sequential Monte Carlo method (also referred to as an augmented particle filter or particle smoother (PF or PS)) that allows straightforward estimation of both static and time-varying parameters from tracking data. We focus specifically on temporally irregular GPS data describing marine animal movement with the goal of better understanding the underlying behavioral dynamics. Using tracking data from California sea lions (Zalophus californianus) we demonstrate the approach's ability to detect subtle yet biologically relevant changes in behavior.},
	language = {en},
	urldate = {2020-11-30},
	journal = {Ecological Modelling},
	author = {Breed, Greg A. and Costa, Daniel P. and Jonsen, Ian D. and Robinson, Patrick W. and Mills-Flemming, Joanna},
	month = jun,
	year = {2012},
	keywords = {Behavioral dynamics, GPS tracking, Parameter estimation, Particle filters, Particle smoothers, State augmentation, State-space model},
	pages = {49--58},
}

@article{chang_model_2015,
	series = {Proceedings of the 5th {International} {Billfish} {Symposium}},
	title = {Model selection and multi-model inference for {Bayesian} surplus production models: {A} case study for {Pacific} blue and striped marlin},
	volume = {166},
	issn = {0165-7836},
	shorttitle = {Model selection and multi-model inference for {Bayesian} surplus production models},
	url = {http://www.sciencedirect.com/science/article/pii/S0165783614002781},
	doi = {10.1016/j.fishres.2014.08.023},
	abstract = {Stock assessment typically involves developing a set of alternative models, fitting each to the available data, and then selecting the one that gives the most accurate estimates of management quantities of interest. In this context, it is important to consider model selection uncertainty because ignoring it can lead to unreliable estimates and overconfident inferences. For this study, four Bayesian surplus production models with symmetric or asymmetric production functions and either a constant or hierarchical time-varying intrinsic growth rate (r) were developed using data for Pacific blue marlin (Makaira nigricans) and Western and Central North Pacific striped marlin (Kajikia audax). The uncertainty resulting from model selection was evaluated using Monte Carlo simulation techniques to examine the consistency of model estimates within (self-tests) and among (cross-tests) the alternative models. Specifically, these tests evaluated the performance of the deviance information criterion (DIC) and Bayesian model averaging (BMA). The results of the simulation tests suggested that mis-specification of time-varying r can lead to large estimation errors for biomass and management quantities and that DIC may not reliably identify the true data-generating model. Although BMA did not provide more accurate point estimates than just selecting the data-generating model, it did provide a more accurate characterization of uncertainty in model results. Our study shows the value of using simulations to evaluate model performance and to account for model selection uncertainty.},
	language = {en},
	urldate = {2020-11-30},
	journal = {Fisheries Research},
	author = {Chang, Yi-Jay and Brodziak, Jon and O’Malley, Joseph and Lee, Hui-Hua and DiNardo, Gerard and Sun, Chi-Lu},
	month = jun,
	year = {2015},
	keywords = {Bayesian hierarchical surplus production model, Billfish, Deviance information criterion, Model selection uncertainty, Multi-model inference},
	pages = {129--139},
}

@article{baldwin_bayesian_2018,
	title = {Bayesian state-space models reveal unobserved off-shore nocturnal migration from {Motus} data},
	volume = {386},
	issn = {0304-3800},
	url = {http://www.sciencedirect.com/science/article/pii/S0304380018302692},
	doi = {10.1016/j.ecolmodel.2018.08.006},
	abstract = {Recent advances in wildlife tracking technology, including the Motus system, have allowed researchers to continuously track small organisms with lightweight radio transmitters over large spatial and temporal ranges. The quantity and format of data generated by the Motus system is unprecedented and requires novel statistical methods. Building from the bsam package in R, we propose new biologically informed Bayesian state-space models for animal movement in JAGS that include informed assumptions about behavior. To apply the models, we employed a localization routine on a Motus data set from migrating Red-eyed Vireos (Vireo olivaceus). This allowed us to apply the new models to estimate unobserved locations and behaviors. Directed migratory flights were detected at night and often over water (e.g. the Bay of Fundy, the Long Island Sound and the New York Bight). Migratory flights were not exclusively nocturnal.},
	language = {en},
	urldate = {2020-11-30},
	journal = {Ecological Modelling},
	author = {Baldwin, Justin W. and Leap, Katie and Finn, John T. and Smetzer, Jennifer R.},
	month = oct,
	year = {2018},
	keywords = {Automated telemetry, Bird migration, Motus, Movement ecology, Red-eyed Vireo, State-space models},
	pages = {38--46},
}

@article{best_parameterizations_2020,
	title = {Parameterizations for {Bayesian} state-space surplus production models},
	volume = {222},
	issn = {0165-7836},
	url = {http://www.sciencedirect.com/science/article/pii/S0165783619302668},
	doi = {10.1016/j.fishres.2019.105411},
	abstract = {Bayesian state-space surplus production models are commonly applied in fisheries stock assessment when the only information available is an index of relative abundance. However, even relatively simple models such as these can be computationally expensive to fit, and diagnosing poor fits can be difficult. The Stan software package provides an advanced Markov chain Monte Carlo sampler and diagnostics that are not available in other packages for fitting Bayesian models. Here the sampler diagnostics, efficiency, and posterior inferences are compared among multiple parameterizations of a state-space biomass dynamics model, using both Pella-Tomlinson and Schaefer dynamics. Two parameterizations that prevent predictions of negative biomass are introduced, one of which allows for errors in catch. None of the parameterizations used avoid diagnostic warnings using the default sampler parameter values. Choosing the appropriate parameterization of a model, and paying attention to these diagnostics can increase computational efficiency and make inferences more robust.},
	language = {en},
	urldate = {2020-11-25},
	journal = {Fisheries Research},
	author = {Best, John K. and Punt, André E.},
	month = feb,
	year = {2020},
	keywords = {Bayesian, Markov chain Monte Carlo, Stan, diagnostics, state-space, surplus production model},
	pages = {105411},
}

@article{monnahan_faster_2017,
	title = {Faster estimation of {Bayesian} models in ecology using {Hamiltonian} {Monte} {Carlo}},
	volume = {8},
	copyright = {© 2016 The Authors. Methods in Ecology and Evolution © 2016 British Ecological Society},
	issn = {2041-210X},
	url = {https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.12681},
	doi = {10.1111/2041-210X.12681},
	abstract = {Bayesian inference is a powerful tool to better understand ecological processes across varied subfields in ecology, and is often implemented in generic and flexible software packages such as the widely used BUGS family (BUGS, WinBUGS, OpenBUGS and JAGS). However, some models have prohibitively long run times when implemented in BUGS. A relatively new software platform called Stan uses Hamiltonian Monte Carlo (HMC), a family of Markov chain Monte Carlo (MCMC) algorithms which promise improved efficiency and faster inference relative to those used by BUGS. Stan is gaining traction in many fields as an alternative to BUGS, but adoption has been slow in ecology, likely due in part to the complex nature of HMC. Here, we provide an intuitive illustration of the principles of HMC on a set of simple models. We then compared the relative efficiency of BUGS and Stan using population ecology models that vary in size and complexity. For hierarchical models, we also investigated the effect of an alternative parameterization of random effects, known as non-centering. For small, simple models there is little practical difference between the two platforms, but Stan outperforms BUGS as model size and complexity grows. Stan also performs well for hierarchical models, but is more sensitive to model parameterization than BUGS. Stan may also be more robust to biased inference caused by pathologies, because it produces diagnostic warnings where BUGS provides none. Disadvantages of Stan include an inability to use discrete parameters, more complex diagnostics and a greater requirement for hands-on tuning. Given these results, Stan is a valuable tool for many ecologists utilizing Bayesian inference, particularly for problems where BUGS is prohibitively slow. As such, Stan can extend the boundaries of feasible models for applied problems, leading to better understanding of ecological processes. Fields that would likely benefit include estimation of individual and population growth rates, meta-analyses and cross-system comparisons and spatiotemporal models.},
	language = {en},
	number = {3},
	urldate = {2020-11-25},
	journal = {Methods in Ecology and Evolution},
	author = {Monnahan, Cole C. and Thorson, James T. and Branch, Trevor A.},
	year = {2017},
	keywords = {Bayesian inference, Markov chain Monte Carlo, Stan, hierarchical modelling, no-U-turn sampler},
	pages = {339--348},
}

@article{auger-methe_guide_2020,
	title = {A guide to state-space modeling of ecological time series},
	url = {http://arxiv.org/abs/2002.02001},
	abstract = {State-space models (SSMs) are an important modeling framework for analyzing ecological time series. These hierarchical models are commonly used to model population dynamics, animal movement, and capture-recapture data, and are now increasingly being used to model other ecological processes. SSMs are popular because they are flexible and they model the natural variation in ecological processes separately from observation error. Their flexibility allows ecologists to model continuous, count, binary, and categorical data with linear or nonlinear processes that evolve in discrete or continuous time. Modeling the two sources of stochasticity separately allows researchers to differentiate between biological variation (e.g., in birth processes) and imprecision in the sampling methodology, and generally provides better estimates of the ecological quantities of interest than if only one source of stochasticity is directly modeled. Since the introduction of SSMs, a broad range of fitting procedures have been proposed. However, the variety and complexity of these procedures can limit the ability of ecologists to formulate and fit their own SSMs. We provide the knowledge for ecologists to create SSMs that are robust to common, and often hidden, estimation problems, and the model selection and validation tools that can help them assess how well their models fit their data. In this paper, we present a review of SSMs that will provide a strong foundation to ecologists interested in learning about SSMs, introduce new tools to veteran SSM users, and highlight promising research directions for statisticians interested in ecological applications. The review is accompanied by an in-depth tutorial that demonstrates how SSMs models can be fitted and validated in R. Together, the review and tutorial present an introduction to SSMs that will help ecologists to formulate, fit, and validate their models.},
	urldate = {2020-11-25},
	journal = {arXiv:2002.02001 [q-bio, stat]},
	author = {Auger-Méthé, Marie and Newman, Ken and Cole, Diana and Empacher, Fanny and Gryba, Rowenna and King, Aaron A. and Leos-Barajas, Vianney and Flemming, Joanna Mills and Nielsen, Anders and Petris, Giovanni and Thomas, Len},
	month = nov,
	year = {2020},
	note = {arXiv: 2002.02001},
	keywords = {Quantitative Biology - Populations and Evolution, Quantitative Biology - Quantitative Methods, Statistics - Methodology},
}

@article{moser_mountain_2019,
	title = {Mountain lakes: {Eyes} on global environmental change},
	volume = {178},
	issn = {0921-8181},
	shorttitle = {Mountain lakes},
	url = {http://www.sciencedirect.com/science/article/pii/S0921818118306702},
	doi = {10.1016/j.gloplacha.2019.04.001},
	abstract = {Mountain lakes are often situated in protected natural areas, a feature that leads to their role as sentinels of global environmental change. Despite variations in latitude, mountain lakes share many features, including their location in catchments with steep topographic gradients, cold temperatures, high incident solar and ultraviolet radiation (UVR), and prolonged ice and snow cover. These characteristics, in turn, affect mountain lake ecosystem structure, diversity, and productivity. The lakes themselves are mostly small, and up until recently, have been characterized as oligotrophic. This paper provides a review and update of the growing body of research that shows that sediments in remote mountain lakes archive regional and global environmental changes, including those linked to climate change, altered biogeochemical cycles, and changes in dust composition and deposition, atmospheric fertilization, and biological manipulations. These archives provide an important record of global environmental change that pre-dates typical monitoring windows. Paleolimnological research at strategically selected lakes has increased our knowledge of interactions among multiple stressors and their synergistic effects on lake systems. Lakes from transects across steep climate (i.e., temperature and effective moisture) gradients in mountain regions show how environmental change alters lakes in close proximity, but at differing climate starting points. Such research in particular highlights the impacts of melting glaciers on mountain lakes. The addition of new proxies, including DNA-based techniques and advanced stable isotopic analyses, provides a gateway to addressing novel research questions about global environmental change. Recent advances in remote sensing and continuous, high-frequency, limnological measurements will improve spatial and temporal resolution and help to add records to spatial gaps including tropical and southern latitudes. Mountain lake records provide a unique opportunity for global scale assessments that provide knowledge necessary to protect the Earth system.},
	language = {en},
	urldate = {2020-11-23},
	journal = {Global and Planetary Change},
	author = {Moser, K. A. and Baron, J. S. and Brahney, J. and Oleksy, I. A. and Saros, J. E. and Hundey, E. J. and Sadro, S. and Kopáček, J. and Sommaruga, R. and Kainz, M. J. and Strecker, A. L. and Chandra, S. and Walters, D. M. and Preston, D. L. and Michelutti, N. and Lepori, F. and Spaulding, S. A. and Christianson, K. R. and Melack, J. M. and Smol, J. P.},
	month = jul,
	year = {2019},
	keywords = {Atmospheric deposition, Carbon cycle, Climate change, Dust, Mountain lakes, Paleolimnology, Species invasions},
	pages = {77--95},
}

@article{walker_toward_2019,
	title = {Toward the improvement of total nitrogen deposition budgets in the {United} {States}},
	volume = {691},
	issn = {0048-9697},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969719331717},
	doi = {10.1016/j.scitotenv.2019.07.058},
	abstract = {Frameworks for limiting ecosystem exposure to excess nutrients and acidity require accurate and complete deposition budgets of reactive nitrogen (Nr). While much progress has been made in developing total Nr deposition budgets for the U.S., current budgets remain limited by key data and knowledge gaps. Analysis of National Atmospheric Deposition Program Total Deposition (NADP/TDep) data illustrates several aspects of current Nr deposition that motivate additional research. Averaged across the continental U.S., dry deposition contributes slightly more (55\%) to total deposition than wet deposition and is the dominant process ({\textgreater}90\%) over broad areas of the Southwest and other arid regions of the West. Lack of dry deposition measurements imposes a reliance on models, resulting in a much higher degree of uncertainty relative to wet deposition which is routinely measured. As nitrogen oxide (NOx) emissions continue to decline, reduced forms of inorganic nitrogen (NHx = NH3 + NH4+) now contribute {\textgreater}50\% of total Nr deposition over large areas of the U.S. Expanded monitoring and additional process-level research are needed to better understand NHx deposition, its contribution to total Nr deposition budgets, and the processes by which reduced N deposits to ecosystems. Urban and suburban areas are hotspots where routine monitoring of oxidized and reduced Nr deposition is needed. Finally, deposition budgets have incomplete information about the speciation of atmospheric nitrogen; monitoring networks do not capture important forms of Nr such as organic nitrogen. Building on these themes, we detail the state of the science of Nr deposition budgets in the U.S. and highlight research priorities to improve deposition budgets in terms of monitoring and flux measurements, leaf- to regional-scale modeling, source apportionment, and characterization of deposition trends and patterns.},
	language = {en},
	urldate = {2020-11-23},
	journal = {Science of The Total Environment},
	author = {Walker, J. T. and Beachley, G. and Amos, H. M. and Baron, J. S. and Bash, J. and Baumgardner, R. and Bell, M. D. and Benedict, K. B. and Chen, X. and Clow, D. W. and Cole, A. and Coughlin, J. G. and Cruz, K. and Daly, R. W. and Decina, S. M. and Elliott, E. M. and Fenn, M. E. and Ganzeveld, L. and Gebhart, K. and Isil, S. S. and Kerschner, B. M. and Larson, R. S. and Lavery, T. and Lear, G. G. and Macy, T. and Mast, M. A. and Mishoe, K. and Morris, K. H. and Padgett, P. E. and Pouyat, R. V. and Puchalski, M. and Pye, H. O. T. and Rea, A. W. and Rhodes, M. F. and Rogers, C. M. and Saylor, R. and Scheffe, R. and Schichtel, B. A. and Schwede, D. B. and Sexstone, G. A. and Sive, B. C. and Sosa Echeverría, R. and Templer, P. H. and Thompson, T. and Tong, D. and Wetherbee, G. A. and Whitlow, T. H. and Wu, Z. and Yu, Z. and Zhang, L.},
	month = nov,
	year = {2019},
	keywords = {Ammonia, Dry deposition, Organic nitrogen, Oxidized nitrogen, Reactive nitrogen, Wet deposition},
	pages = {1328--1352},
}

@article{oleksy_nutrients_2020,
	title = {Nutrients and warming interact to force mountain lakes into unprecedented ecological states},
	volume = {287},
	url = {https://royalsocietypublishing.org/doi/full/10.1098/rspb.2020.0304},
	doi = {10.1098/rspb.2020.0304},
	abstract = {While deposition of reactive nitrogen (N) in the twentieth century has been strongly linked to changes in diatom assemblages in high-elevation lakes, pronounced and contemporaneous changes in other algal groups suggest additional drivers. We explored the origin and magnitude of changes in two mountain lakes from the end of the Little Ice Age at ca 1850, to ca 2010, using lake sediments. We found dramatic changes in algal community abundance and composition. While diatoms remain the most abundant photosynthetic organisms, concentrations of diatom pigments decreased while pigments representing chlorophytes increased 200–300\% since ca 1950 and total algal biomass more than doubled. Some algal changes began ca 1900 but shifts in most sedimentary proxies accelerated ca 1950 commensurate with many human-caused changes to the Earth System. In addition to N deposition, aeolian dust deposition may have contributed phosphorus. Strong increases in summer air and surface water temperatures since 1983 have direct and indirect consequences for high-elevation ecosystems. Such warming could have directly enhanced nutrient use and primary production. Indirect consequences of warming include enhanced leaching of nutrients from geologic and cryosphere sources, particularly as glaciers ablate. While we infer causal mechanisms, changes in primary producer communities appear to be without historical precedent and are commensurate with the post-1950 acceleration of global change.},
	number = {1930},
	urldate = {2020-11-23},
	journal = {Proceedings of the Royal Society B: Biological Sciences},
	author = {Oleksy, Isabella A. and Baron, Jill S. and Leavitt, Peter R. and Spaulding, Sarah A.},
	month = jul,
	year = {2020},
	note = {Publisher: Royal Society},
	pages = {20200304},
}

@article{reich_synergistic_2020,
	title = {Synergistic effects of four climate change drivers on terrestrial carbon cycling},
	copyright = {2020 The Author(s), under exclusive licence to Springer Nature Limited},
	issn = {1752-0908},
	url = {https://www.nature.com/articles/s41561-020-00657-1},
	doi = {10.1038/s41561-020-00657-1},
	abstract = {Disentangling impacts of multiple global changes on terrestrial carbon cycling is important, both in its own right and because such impacts can dampen or accelerate increases in atmospheric CO2 concentration. Here we report on an eight-year grassland experiment, TeRaCON, in Minnesota, United States, that factorially manipulated four drivers: temperature, rainfall, CO2 and nitrogen deposition. Net primary production increased under warming, elevated CO2 and nitrogen deposition, and decreased under diminished summer rainfall. Treatment combinations that increased net primary production also increased soil CO2 emissions, but less so, and hence ecosystem carbon storage increased overall. Productivity, soil carbon emissions and plant carbon stock responses to each individual factor were influenced by levels of the other drivers, in both amplifying and dampening ways. Percentage increases in productivity, soil carbon emissions and plant carbon stocks in response to two, three or four global changes experienced jointly were generally much greater than those expected based on the effects of each individual driver alone. Multiple global change drivers had a profound combined influence on observed outcomes that would have been poorly predicted by knowledge of each driver alone. If such interacting impacts of multiple global change drivers on carbon cycling occur widely among ecosystems, accurately projecting biosphere responses to multifactorial global changes will remain a major challenge in the decades ahead.},
	language = {en},
	urldate = {2020-11-23},
	journal = {Nature Geoscience},
	author = {Reich, Peter B. and Hobbie, Sarah E. and Lee, Tali D. and Rich, Roy and Pastore, Melissa A. and Worm, Kally},
	month = nov,
	year = {2020},
	note = {Publisher: Nature Publishing Group},
	pages = {1--7},
}

@article{noauthor_impact_2020,
	title = {Impact factors and mechanisms of dissolved reactive phosphorus ({DRP}) losses from agricultural fields: {A} review and synthesis study in the {Lake} {Erie} basin},
	volume = {714},
	issn = {0048-9697},
	shorttitle = {Impact factors and mechanisms of dissolved reactive phosphorus ({DRP}) losses from agricultural fields},
	url = {https://www.sciencedirect.com/science/article/pii/S0048969720301340},
	doi = {10.1016/j.scitotenv.2020.136624},
	abstract = {Dissolved Reactive Phosphorus (DRP) losses from agricultural fields promote algae growth in water bodies, and may increase the risk of Harmful Algal B…},
	language = {en},
	urldate = {2020-11-23},
	journal = {Science of The Total Environment},
	month = apr,
	year = {2020},
	note = {Publisher: Elsevier},
	pages = {136624},
}

@article{marleau_converting_2020,
	title = {Converting {Ecological} {Currencies}: {Energy}, {Material}, and {Information} {Flows}},
	volume = {35},
	issn = {0169-5347},
	shorttitle = {Converting {Ecological} {Currencies}},
	url = {http://www.sciencedirect.com/science/article/pii/S0169534720302093},
	doi = {10.1016/j.tree.2020.07.014},
	abstract = {Understanding how the three currencies of life – energy, material, and information – interact is a key step towards synthesis in ecology and evolution. However, current theory focuses on the role of matter as a resource and energy, and typically ignores how the same matter can have other important effects as a carrier of information or modifier of the environment. Here we present the hypothesis that the dynamic conversion of matter by organisms among its three currencies mediates the structure and function of ecosystems, and that these effects can even supersede the effects of matter as a resource. Humans are changing the information in the environment and this is altering species interactions and flows of matter within and among ecosystems.},
	language = {en},
	number = {12},
	urldate = {2020-11-19},
	journal = {Trends in Ecology \& Evolution},
	author = {Marleau, Justin N. and Peller, Tianna and Guichard, Frederic and Gonzalez, Andrew},
	month = dec,
	year = {2020},
	keywords = {fluxes, gradients, meta-ecosystems, non-trophic interactions, resources, semiochemicals},
	pages = {1068--1077},
}

@article{ives_detecting_2012-1,
	title = {Detecting dynamical changes in nonlinear time series using locally linear state-space models},
	volume = {3},
	copyright = {Copyright: © 2012 Ives and Dakos.},
	issn = {2150-8925},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/ES11-00347.1},
	doi = {10.1890/ES11-00347.1},
	abstract = {Interest is growing in methods for predicting and detecting regime shifts—changes in the structure of dynamical processes that cause shifts among alternative stable states. Here, we use locally linear, autoregressive state-space models to statistically identify nonlinear processes that govern the dynamics of time series. We develop both time-varying and threshold models. In time-varying autoregressive models with p time lags, AR(p), and vector autoregressive models for n-dimensional systems of order p = 1, VAR(1), we assume that coefficients vary with time. We can infer an approaching regime shift if the coefficients indicate critical slowing down of the local dynamics of the system. In self-excited threshold models, we assume that the time series is governed by two autoregressive processes; the state variable switches between them when the time series crosses a threshold value. We use the existence of a statistically significant threshold as an indicator of alternative stable states. All models are fit to data using a state-space form that incorporates measurement error, and maximum likelihood estimation allows for statistically testing alternative hypotheses about the processes governing dynamics. Our model-based approach for forecasting regime shifts and identifying alternative stable states overcomes limitations of other common metric-based approaches and is a useful addition to the toolbox of methods for analyzing nonlinear time series.},
	language = {en},
	number = {6},
	urldate = {2020-11-18},
	journal = {Ecosphere},
	author = {Ives, Anthony R. and Dakos, Vasilis},
	year = {2012},
	keywords = {Kalman filter, SETAR, SETARSS, TVAR, TVARSS, alternative stable states, critical slowing down, critical transition, early warning signals, regime shift, threshold autoregressive models, time-series, time-varying autoregressive models},
	pages = {art58},
}

@article{oleksy_role_2020,
	title = {The role of warm, dry summers and variation in snowpack on phytoplankton dynamics in mountain lakes},
	volume = {101},
	copyright = {© 2020 The Authors. Ecology published by Wiley Periodicals LLC on behalf of Ecological Society of America},
	issn = {1939-9170},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecy.3132},
	doi = {10.1002/ecy.3132},
	abstract = {Climate change is altering biogeochemical, metabolic, and ecological functions in lakes across the globe. Historically, mountain lakes in temperate regions have been unproductive because of brief ice-free seasons, a snowmelt-driven hydrograph, cold temperatures, and steep topography with low vegetation and soil cover. We tested the relative importance of winter and summer weather, watershed characteristics, and water chemistry as drivers of phytoplankton dynamics. Using boosted regression tree models for 28 mountain lakes in Colorado, we examined regional, intraseasonal, and interannual drivers of variability in chlorophyll a as a proxy for lake phytoplankton. Phytoplankton biomass was inversely related to the maximum snow water equivalent (SWE) of the previous winter, as others have found. However, even in years with average SWE, summer precipitation extremes and warming enhanced phytoplankton biomass. Peak seasonal phytoplankton biomass coincided with the warmest water temperatures and lowest nitrogen-to-phosphorus ratios. Although links between snowpack, lake temperature, nutrients, and organic-matter dynamics are increasingly recognized as critical drivers of change in high-elevation lakes, our results highlight the additional influence of summer conditions on lake productivity in response to ongoing changes in climate. Continued changes in the timing, type, and magnitude of precipitation in combination with other global-change drivers (e.g., nutrient deposition) will affect production in mountain lakes, potentially shifting these historically oligotrophic lakes toward new ecosystem states. Ultimately, a deeper understanding of these drivers and pattern at multiple scales will allow us to anticipate ecological consequences of global change better.},
	language = {en},
	number = {10},
	urldate = {2020-11-18},
	journal = {Ecology},
	author = {Oleksy, Isabella A. and Beck, Whitney S. and Lammers, Roderick W. and Steger, Cara E. and Wilson, Codie and Christianson, Kyle and Vincent, Kim and Johnson, Gunnar and Johnson, Pieter T. J. and Baron, J. S.},
	year = {2020},
	keywords = {alpine, climate change, cryosphere, limnology, mountain lakes, nitrogen deposition, phytoplankton, snowmelt timing},
	pages = {e03132},
}

@article{zhang_approach_2020,
	title = {An approach for decomposing river water-quality trends into different flow classes},
	issn = {0048-9697},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969720370935},
	doi = {10.1016/j.scitotenv.2020.143562},
	abstract = {A number of statistical approaches have been developed to quantify the overall trend in river water quality, but most approaches are not intended for reporting separate trends for different flow conditions. We propose an approach called FN2Q, which is an extension of the flow-normalization (FN) procedure of the well-established WRTDS (“Weighted Regressions on Time, Discharge, and Season”) method. The FN2Q approach provides a daily time series of low-flow and high-flow FN flux estimates that represent the lower and upper half of daily riverflow observations that occurred on each calendar day across the period of record. These daily estimates can be summarized into any time period of interest (e.g., monthly, seasonal, or annual) for quantifying trends. The proposed approach is illustrated with an application to a record of total nitrogen concentration (632 samples) collected between 1985 and 2018 from the South Fork Shenandoah River at Front Royal, Virginia (USA). Results show that the overall FN flux of total nitrogen has declined in the period of 1985–2018, which is mainly attributable to FN flux decline in the low-flow class. Furthermore, the decline in the low-flow class was highly correlated with wastewater effluent loads, indicating that the upgrades of treatment technology at wastewater treatment facilities have likely led to water-quality improvement under low-flow conditions. The high-flow FN flux showed a spike around 2007, which was likely caused by increased delivery of particulate nitrogen associated with sediment transport. The case study demonstrates the utility of the FN2Q approach toward not only characterizing the changes in river water quality but also guiding the direction of additional analysis for capturing the underlying drivers. The FN2Q approach (and the published code) can easily be applied to widely available river monitoring records to quantify water-quality trends under different flow conditions to enhance understanding of river water-quality dynamics.},
	language = {en},
	urldate = {2020-11-16},
	journal = {Science of The Total Environment},
	author = {Zhang, Qian and Webber, James S. and Moyer, Douglas L. and Chanat, Jeffrey G.},
	month = nov,
	year = {2020},
	keywords = {Flow classes, Nitrogen, Trend analysis, WRTDS, Wastewater, Water quality},
	pages = {143562},
}

@article{kincaid_wikipedia_nodate,
	title = {Wikipedia can help resolve information inequality in the aquatic sciences},
	volume = {n/a},
	copyright = {© 2020 The Authors. Limnology and Oceanography Letters published by Wiley Periodicals LLC on behalf of Association for the Sciences of Limnology and Oceanography.},
	issn = {2378-2242},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lol2.10168},
	doi = {10.1002/lol2.10168},
	language = {en},
	number = {n/a},
	urldate = {2020-11-16},
	journal = {Limnology and Oceanography Letters},
	author = {Kincaid, Dustin W. and Beck, Whitney S. and Brandt, Jessica E. and Brisbin, Margaret Mars and Farrell, Kaitlin J. and Hondula, Kelly L. and Larson, Erin I. and Shogren, Arial J.},
}

@article{zakem_redox-informed_2020,
	title = {Redox-informed models of global biogeochemical cycles},
	volume = {11},
	copyright = {2020 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-020-19454-w},
	doi = {10.1038/s41467-020-19454-w},
	abstract = {Microbial activity mediates the fluxes of greenhouse gases. However, in the global models of the marine and terrestrial biospheres used for climate change projections, typically only photosynthetic microbial activity is resolved mechanistically. To move forward, we argue that global biogeochemical models need a theoretically grounded framework with which to constrain parameterizations of diverse microbial metabolisms. Here, we explain how the key redox chemistry underlying metabolisms provides a path towards this goal. Using this first-principles approach, the presence or absence of metabolic functional types emerges dynamically from ecological interactions, expanding model applicability to unobserved environments.},
	language = {en},
	number = {1},
	urldate = {2020-11-10},
	journal = {Nature Communications},
	author = {Zakem, Emily J. and Polz, Martin F. and Follows, Michael J.},
	month = nov,
	year = {2020},
	note = {Number: 1
Publisher: Nature Publishing Group},
	pages = {5680},
}

@article{sparrow_effective_2020,
	title = {Effective ecosystem monitoring requires a multi-scaled approach},
	volume = {95},
	copyright = {© 2020 The Authors. Biological Reviews published by John Wiley \& Sons Ltd on behalf of Cambridge Philosophical Society.},
	issn = {1469-185X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/brv.12636},
	doi = {10.1111/brv.12636},
	abstract = {Ecosystem monitoring is fundamental to our understanding of how ecosystem change is impacting our natural resources and is vital for developing evidence-based policy and management. However, the different types of ecosystem monitoring, along with their recommended applications, are often poorly understood and contentious. Varying definitions and strict adherence to a specific monitoring type can inhibit effective ecosystem monitoring, leading to poor program development, implementation and outcomes. In an effort to develop a more consistent and clear understanding of ecosystem monitoring programs, we here review the main types of monitoring and recommend the widespread adoption of three classifications of monitoring, namely, targeted, surveillance and landscape monitoring. Landscape monitoring is conducted over large areas, provides spatial data, and enables questions relating to where and when ecosystem change is occurring to be addressed. Surveillance monitoring uses standardised field methods to inform on what is changing in our environments and the direction and magnitude of that change, whilst targeted monitoring is designed around testable hypotheses over defined areas and is the best approach for determining the causes of ecosystem change. The classification system is flexible and can incorporate different interests, objectives, targets and characteristics as well as different spatial scales and temporal frequencies, while also providing valuable structure and consistency across distinct ecosystem monitoring programs. To support our argument, we examine the ability of each monitoring type to inform on six key types of questions that are routinely posed for ecosystem monitoring programs, such as where and when change is occurring, what is the magnitude of change, and how can the change be managed? As we demonstrate, each type of ecosystem monitoring has its own strengths and weaknesses, which should be carefully considered relative to the desired results. Using this scheme, scientists and land managers can design programs best suited to their needs. Finally, we assert that for our most serious environmental challenges, it is essential that we include information from each of these monitoring scales to inform on all facets of ecosystem change, and this is best achieved through close collaboration between the scales. With a renewed understanding of the importance of each monitoring type, along with greater commitment to monitor cooperatively, we will be well placed to address some of our greatest environmental challenges.},
	language = {en},
	number = {6},
	urldate = {2020-11-10},
	journal = {Biological Reviews},
	author = {Sparrow, Ben D. and Edwards, Will and Munroe, Samantha E. M. and Wardle, Glenda M. and Guerin, Greg R. and Bastin, Jean-Francois and Morris, Beryl and Christensen, Rebekah and Phinn, Stuart and Lowe, Andrew J.},
	year = {2020},
	keywords = {biodiversity monitoring, collaboration, ecological questions, ecosystem monitoring, environmental change, environmental monitoring, landscape monitoring, research infrastructure, surveillance monitoring, targeted monitoring},
	pages = {1706--1719},
}

@article{pearce_metabolic_2020,
	title = {Metabolic regimes of three mid-order streams in southern {Ontario}, {Canada} exposed to contrasting sources of nutrients},
	volume = {847},
	issn = {1573-5117},
	url = {10.1007/s10750-020-04222-0},
	doi = {10.1007/s10750-020-04222-0},
	abstract = {Light, temperature, and discharge control stream metabolism, but the response of gross primary production (GPP) and ecosystem respiration (ER) to seasonal variation in these physical drivers may differ in accordance with the types of human activities present in the catchment. Our study examined three mid-order streams in southern Ontario, Canada that differed in anthropogenic nutrient sources (i.e., sewage treatment plant effluent, sewage lagoon effluent, and agriculture), but had comparable light, temperature, and discharge regimes. For each stream, GPP and ER were estimated daily from June through November. Comparisons of paired daily metabolic rates revealed pairwise differences among all streams, with streams receiving sewage effluent having greater rates and variability of GPP and ER than the stream draining agricultural land. The two sewage influenced streams differed only in ER. Temporal patterns of GPP and ER were correlated for all streams throughout the study period and were most affected by seasonal variation in temperature, whereby effluent receiving streams responded more rapidly to increases in temperature. Our findings suggest that managers may need to balance effects of human activities with regional environmental constraints on stream metabolism to maintain and enhance the ecological condition and services of stream ecosystems.},
	language = {en},
	number = {8},
	urldate = {2020-11-09},
	journal = {Hydrobiologia},
	author = {Pearce, Nolan J. T. and Thomas, Kathryn E. and Chambers, Patricia A. and Venkiteswaran, Jason J. and Yates, Adam G.},
	month = may,
	year = {2020},
	pages = {1925--1942},
}

@article{myrstener_nutrients_nodate,
	title = {Nutrients influence seasonal metabolic patterns and total productivity of {Arctic} streams},
	volume = {n/a},
	copyright = {© 2020 The Authors. Limnology and Oceanography published by Wiley Periodicals LLC on behalf of Association for the Sciences of Limnology and Oceanography.},
	issn = {1939-5590},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lno.11614},
	doi = {10.1002/lno.11614},
	abstract = {The seasonality of gross primary production (GPP) in streams is driven by multiple physical and chemical factors, yet incident light is often thought to be most important. In Arctic tundra streams, however, light is available in saturating amounts throughout the summer, but sharp declines in nutrient supply during the terrestrial growing season may constrain aquatic productivity. Given the opposing seasonality of these drivers, we hypothesized that “shoulder seasons”—spring and autumn—represent critical time windows when light and nutrients align to optimize rates of stream productivity in the Arctic. To test this, we measured annual patterns of GPP and biofilm accumulation in eight streams in Arctic Sweden. We found that the aquatic growing season length differed by 4 months across streams and was determined largely by the timing of ice-off in spring. During the growing season, temporal variability in GPP for nitrogen (N) poor streams was correlated with inorganic N concentration, while in more N-rich streams GPP was instead linked to changes in phosphorus and light. Annual GPP varied ninefold among streams and was enhanced by N availability, the length of ice-free period, and low flood frequency. Finally, network scale estimates of GPP highlight the overall significance of the shoulder seasons, which accounted for 48\% of annual productivity. We suggest that the timing of ice off and nutrient supply from land interact to regulate the annual metabolic regimes of nutrient poor, Arctic streams, leading to unexpected peaks in productivity that are offset from the terrestrial growing season.},
	language = {en},
	number = {n/a},
	urldate = {2020-11-06},
	journal = {Limnology and Oceanography},
	author = {Myrstener, Maria and Gómez‐Gener, Lluís and Rocher‐Ros, Gerard and Giesler, Reiner and Sponseller, Ryan A.},
}

@article{simpson_biotic_2020,
	title = {The biotic contribution to the benthic stream sediment phosphorus buffer},
	volume = {151},
	issn = {1573-515X},
	url = {10.1007/s10533-020-00709-z},
	doi = {10.1007/s10533-020-00709-z},
	abstract = {Benthic stream sediments interact strongly with phosphorus (P) and can buffer dissolved reactive P (DRP) concentrations. The sediment P buffer can be measured with the sediment equilibrium phosphate concentration at net zero sorption (EPC0), which often correlates well with DRP. Yet, it is unclear how much of this P affinity in sediments is attributable to biotic (microbial P demand) or abiotic (sorption) processes. To clarify the role of biotic processes on EPC0, we used two experiments with benthic sediment from 12 streams. First, sediments sterilized by γ-irradiation increased in EPC0 compared to fresh sediments by a median of 83\%. This increase in EPC0 was likely a result of cell lysis, where microbial biomass P (2.4 to 22.6 mg P kg−1) was re-adsorbed to sediment surfaces. This data also shows that the sediment microbial biomass is a significant, yet under-reported biotic stock of P in streams compared to their photic zone counterpart (i.e., periphyton). In a second experiment, fresh sediment EPC0 was measured after alleviating potential limitation of carbon (C) and nitrogen (N) for microbial growth. Sediment EPC0 did not change with C addition and decreased slightly (0.5 µg P L−1 or {\textasciitilde} 5\% decrease) with N addition, suggesting these sediments strongly buffered DRP towards the EPC0 in spite of biotic demand. Together, these experiments suggest that sediment EPC0 was primarily abiotic in nature but that sediments may subsidize biotic P requirements through desorption. Further work is needed on whether this relation holds for streams with different substrate, geology, and nutrient inputs.},
	language = {en},
	number = {1},
	urldate = {2020-11-05},
	journal = {Biogeochemistry},
	author = {Simpson, Z. P. and McDowell, R. W. and Condron, L. M.},
	month = nov,
	year = {2020},
	pages = {63--79},
}

@article{reid_two-eyed_nodate,
	title = {“{Two}-{Eyed} {Seeing}”: {An} {Indigenous} framework to transform fisheries research and management},
	volume = {n/a},
	copyright = {© 2020 John Wiley \& Sons Ltd},
	issn = {1467-2979},
	shorttitle = {“{Two}-{Eyed} {Seeing}”},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/faf.12516},
	doi = {10.1111/faf.12516},
	abstract = {Increasingly, fisheries researchers and managers seek or are compelled to “bridge” Indigenous knowledge systems with Western scientific approaches to understanding and governing fisheries. Here, we move beyond the all-too-common narrative about integrating or incorporating (too often used as euphemisms for assimilating) other knowledge systems into Western science, instead of building an ethic of knowledge coexistence and complementarity in knowledge generation using Two-Eyed Seeing as a guiding framework. Two-Eyed Seeing (Etuaptmumk in Mi’kmaw) embraces “learning to see from one eye with the strengths of Indigenous knowledges and ways of knowing, and from the other eye with the strengths of mainstream knowledges and ways of knowing, and to use both these eyes together, for the benefit of all,” as envisaged by Elder Dr. Albert Marshall. In this paper, we examine the notion of knowledge dichotomies and imperatives for knowledge coexistence and draw parallels between Two-Eyed Seeing and other analogous Indigenous frameworks from around the world. It is set apart from other Indigenous frameworks in its explicit action imperative—central to Two-Eyed Seeing is the notion that knowledge transforms the holder and that the holder bears a responsibility to act on that knowledge. We explore its operationalization through three Canadian aquatic and fisheries case-studies that co-develop questions, document and mobilize knowledge, and co-produce insights and decisions. We argue that Two-Eyed Seeing provides a pathway to a plural coexistence, where time-tested Indigenous knowledge systems can be paired with, not subsumed by, Western scientific insights for an equitable and sustainable future.},
	language = {en},
	number = {n/a},
	urldate = {2020-11-05},
	journal = {Fish and Fisheries},
	author = {Reid, Andrea J. and Eckert, Lauren E. and Lane, John-Francis and Young, Nathan and Hinch, Scott G. and Darimont, Chris T. and Cooke, Steven J. and Ban, Natalie C. and Marshall, Albert},
	keywords = {Etuaptmumk, Western science, co-production, indigenous knowledge, knowledge coexistence, pluralism},
}

@article{moritz_comparison_nodate,
	title = {Comparison of different {Methods} for {Univariate} {Time} {Series} {Imputation} in {R}},
	abstract = {Missing values in datasets are a well-known problem and there are quite a lot of R packages offering imputation functions. But while imputation in general is well covered within R, it is hard to find functions for imputation of univariate time series. The problem is, most standard imputation techniques can not be applied directly. Most algorithms rely on inter-attribute correlations, while univariate time series imputation needs to employ time dependencies. This paper provides an overview of univariate time series imputation in general and an in-detail insight into the respective implementations within R packages. Furthermore, we experimentally compare the R functions on different time series using four different ratios of missing data. Our results show that either an interpolation with seasonal kalman filter from the zoo package or a linear interpolation on seasonal loess decomposed data from the forecast package were the most effective methods for dealing with missing data in most of the scenarios assessed in this paper.},
	language = {en},
	author = {Moritz, Steffen},
	pages = {20},
}


@article{Little_1992,
	title = {Regression with Missing X’s: A Review},
	volume = {87},
	issn = {},
	url = {},
	doi = {10.1080/01621459.1992.10476282},
	language = {},
	number = {420},
	urldate = {},
	journal = {Journal of the American Statistical Association},
	author = {Little,  Roderick J. A.},
	year = {1992},
	pages = {1227--1237},
}



@article{honaker_what_2010,
	title = {What to Do about Missing Values in Time-Series Cross-Section Data},
	volume = {54},
	issn = {00925853, 15405907},
	url = {http://doi.wiley.com/10.1111/j.1540-5907.2010.00447.x},
	doi = {10.1111/j.1540-5907.2010.00447.x},
	language = {en},
	number = {2},
	urldate = {2020-11-02},
	journal = {American Journal of Political Science},
	author = {Honaker, James and King, Gary},
	month = apr,
	year = {2010},
	pages = {561--581},
}

@article{moritz_imputets_2017,
	title = {{imputeTS}: {Time} {Series} {Missing} {Value} {Imputation} in {R}},
	volume = {9},
	issn = {2073-4859},
	shorttitle = {{imputeTS}},
	url = {https://journal.r-project.org/archive/2017/RJ-2017-009/index.html},
	doi = {10.32614/RJ-2017-009},
	abstract = {The imputeTS package specializes on univariate time series imputation. It offers multiple state-of-the-art imputation algorithm implementations along with plotting functions for time series missing data statistics. While imputation in general is a well-known problem and widely covered by R packages, finding packages able to fill missing values in univariate time series is more complicated. The reason for this lies in the fact, that most imputation algorithms rely on inter-attribute correlations, while univariate time series imputation instead needs to employ time dependencies. This paper provides an introduction to the imputeTS package and its provided algorithms and tools. Furthermore, it gives a short overview about univariate time series imputation in R.},
	language = {en},
	number = {1},
	urldate = {2020-11-02},
	journal = {The R Journal},
	author = {Moritz, Steffen and Bartz-Beielstein, Thomas},
	year = {2017},
	pages = {207},
}

@article{jabiol_variable_2020,
	title = {Variable temperature effects between heterotrophic stream processes and organisms},
	volume = {65},
	copyright = {© 2020 John Wiley \& Sons Ltd.},
	issn = {1365-2427},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/fwb.13520},
	doi = {10.1111/fwb.13520},
	abstract = {Temperature is known to stimulate metabolism with cascading effects on multiple biological processes. These effects may, however, vary across processes, types of organisms or levels of biological organisation. They can also vary with nutrient availability, with potentially stronger temperature effects when nutrients are not limiting. This context dependence of temperature effects on processes challenges our ability to anticipate their consequences on ecosystems in a changing world. In headwater streams, the decomposition of allochthonous leaf litter, driven by both microbial decomposers and invertebrates, is known to respond to both temperature and nutrient availability. These food webs are highly tractable and a useful model system to investigate the variations of temperature effects on processes across types of organisms (microbes versus invertebrates), resource availability levels (nutrient concentration), and levels of biological organisation (from individual to ecosystem). In a microcosm experiment, we measured the effects of temperature and nitrogen availability (four levels each) on respiration rates of litter-consuming microbes and invertebrates and their decomposition activity in different contexts of food web complexity. The latter included one treatment without invertebrate detritivore (microbial decomposers only), three single invertebrate taxa (Gammarus, Potamophylax, and Sericostoma) treatments, and one mixed invertebrate taxa treatment (three-species altogether). Microbial processes increased nearly exponentially with temperature (Arrhenius model, activation energy (± 95\% confidence interval) = 0.56 ± 0.53 and 1.00 ± 0.23 eV for litter decomposition and respiration), while invertebrate-driven processes increased (activation energy from 0.47–1.15 eV) up to a maximal value at an intermediate temperature (c. 11–15°C depending on species and process), above which process rates decreased. By contrast, litter consumption in mixed invertebrate species treatments was not significantly influenced by temperature, because of a negative effect of species mixing occurring above 12°C. Nitrogen had a weaker influence, only slightly stimulating litter consumption by mixed-species invertebrates, which limited the scope for synergies with temperature effects. Our results raise issues about how aquatic litter consumers meet their energy requirements at high temperature and suggest that a general consequence of warming could be loss of carbon through mineralisation in headwater stream food webs. In several aspects, our results deviate from expectations based on universal relationships between temperature and individual metabolism (e.g. metabolic theory of ecology), suggesting that we may need to develop less simplistic assumptions to predict the consequence of warming on ecosystem processes.},
	language = {en},
	number = {9},
	urldate = {2020-10-30},
	journal = {Freshwater Biology},
	author = {Jabiol, Jérémy and Gossiaux, Alice and Lecerf, Antoine and Rota, Thibaut and Guérold, François and Danger, Michaël and Poupin, Pascal and Gilbert, Franck and Chauvet, Eric},
	year = {2020},
	keywords = {decomposers, litter decomposition, nitrogen, respiration, temperature},
	pages = {1543--1554},
}

@article{utz_influence_2020,
	title = {Influence of temperature, precipitation, and cloud cover on diel dissolved oxygen ranges among headwater streams with variable watershed size and land use attributes},
	volume = {82},
	issn = {1420-9055},
	url = {10.1007/s00027-020-00756-6},
	doi = {10.1007/s00027-020-00756-6},
	abstract = {Dissolved oxygen (DO) concentrations in streams are driven by multiple, interacting biotic and abiotic processes. While DO variability largely reflect cyclic patterns of respiration and photosynthesis coupled to diel cycles, physical processes such as floods that disturb biofilms and variation in temperature disrupt such cycles. In urban settings, DO cycles are typically greatly altered by elevating nutrient concentrations and reducing light-shielding riparian vegetation. We analyzed diel variations in DO from sensors distributed throughout six headwater streams to quantify (1) diel DO range patterns among watersheds of varying size and urbanization intensity, (2) the conditions that lead to abrupt declines in diel DO ranges, and (3) the amount of time needed for diel DO ranges to recover post-disturbance. In very small streams, disruptions to diel DO ranges appear to occur following severe fluctuations in atmospheric temperatures while precipitation events were primarily related to diel DO disruptions in larger streams. Precipitation events ≥ 1.5 cm over a 1-day period or ≥ 2.5 over a 2-day period consistently resulted in abrupt depressions of diel DO variations. While we primarily analyzed abiotic variables, we acknowledge that photosynthetic activity producing DO was also an important variable as shown by an analysis of how cloud cover influenced DO variations. Recovery of diel DO ranges to pre-disturbance conditions varied among sites, with the smallest watershed site reaching 50\% pre-disturbance ranges in an average of 4.5 days and the largest and most urban sites reaching the same threshold over an average of 2.1 days. Urban sites typically exhibited greater diel DO ranges but did not exhibit lower precipitation thresholds for resetting diel DO ranges. DO ranges were more likely to be disrupted by precipitation events when water temperatures were cooler, which suggested different impacts of hydrologic controls on DO variations across seasons. Our findings suggest that streams consistently possess discharge thresholds that, if exceeded, lead to abrupt declines in the magnitude of the diel change in DO, but urban streams may show greater variation in diel DO concentrations with implications for fish habitat, redox-sensitive microbial processes, and contaminant transport and transformation.},
	language = {en},
	number = {4},
	urldate = {2020-10-30},
	journal = {Aquatic Sciences},
	author = {Utz, Ryan M. and Bookout, Bethany J. and Kaushal, Sujay S.},
	month = sep,
	year = {2020},
	pages = {82},
}

@article{mcmahon_cultivating_2019,
	title = {Cultivating {Native} {American} scientists: an application of an {Indigenous} model to an undergraduate research experience},
	volume = {14},
	issn = {1871-1510},
	shorttitle = {Cultivating {Native} {American} scientists},
	url = {10.1007/s11422-017-9850-0},
	doi = {10.1007/s11422-017-9850-0},
	abstract = {With growing evidence demonstrating the impact of undergraduate research experiences on educational persistence, efforts are currently being made to expand these opportunities within universities and research institutions throughout the United States. Recruiting underrepresented students into these programs has become an increasingly popular method of promoting diversity in science. Given the low matriculation into postsecondary education and completion rates among Native Americans, there is a great need for Native American undergraduate research internships. Although research has shown that Western education models tend to be less effective with Native populations, the implementation of indigenous epistemologies and pedagogies within higher education, including research experiences, is rare. This study explores the applicability of a cognitive apprenticeship merged with an indigenous approach, the Circle of Courage, to build a scientific learning environment and enhance the academic and professional development of Native students engaged in an undergraduate research experience in the health sciences. Data were drawn from focus groups with 20 students who participated in this program in 2012–2014. Questions explored the extent to which relational bonds between students and mentors were cultivated as well as the impact of this experience on the development of research skills, intellectual growth, academic and professional self-determination, and the attachment of meaning to their research experiences. Data were analyzed via deductive content analysis, allowing for an assessment of how the theoretical constructs inherent to this model (belonging, mastery, independence, and generosity) impacted students. Findings suggest that engaging Native students in research experiences that prioritize the needs of belonging, mastery, independence, and generosity can be a successful means of fostering a positive learning environment, in which students felt like significant members of a research team, developed a greater understanding and appreciation for the role of science in education and its various applications to socially relevant health issues, made more informed decisions about a career in research and the health sciences, and worked toward improving the health and well-being of others while also inspiring hope among their people back home. This study represents an extension of the application of the Circle of Courage to an undergraduate research experience and provides evidence of its ability to be used as a framework for cultivating Native scientists.},
	language = {en},
	number = {1},
	urldate = {2020-10-28},
	journal = {Cultural Studies of Science Education},
	author = {McMahon, Tracey R. and Griese, Emily R. and Kenyon, DenYelle Baete},
	month = mar,
	year = {2019},
	pages = {77--110},
}

@article{bartlett_two-eyed_2012,
	title = {Two-{Eyed} {Seeing} and other lessons learned within a co-learning journey of bringing together indigenous and mainstream knowledges and ways of knowing},
	volume = {2},
	issn = {2190-6491},
	url = {10.1007/s13412-012-0086-8},
	doi = {10.1007/s13412-012-0086-8},
	abstract = {This is a process article for weaving indigenous and mainstream knowledges within science educational curricula and other science arenas, assuming participants include recognized holders of traditional ecological knowledge (we prefer “Indigenous Knowledge” or “Traditional Knowledge”) and others with expertise in mainstream science. It is based on the “Integrative Science” undergraduate program created at Cape Breton University to bring together indigenous and mainstream sciences and ways of knowing, as well as related Integrative Science endeavors in science research, application, and outreach. A brief historical outline for that experiential journey is provided and eight “Lessons Learned” listed. The first, namely “acknowledge that we need each other and must engage in a co-learning journey” is explained as key for the success of weaving efforts. The second, namely “be guided by Two-Eyed Seeing”, is considered the most profound because it is central to the whole of a co-learning journey and the article’s discussion is focussed through it. The eighth lesson, “develop an advisory council of willing, knowledgeable stakeholders”, is considered critical for sustaining success over the long-term given that institutional and community politics profoundly influence the resourcing and recruitment of any academic program and thus can help foster success, or sabotage it. The scope of relevance for Two-Eyed Seeing is broad and its uptake across Canada is sketched; the article also places it in the context of emerging theory for transdisciplinary research. The article concludes with thoughts on why “Two-Eyed Seeing” may seem to be desired or resisted as a label in different settings.Traditional Indian education is an expression of environmental education par excellence. It is an environmental education process that can have a profound meaning for the kind of modern education required to face the challenges of living in the world of the twenty-first century (Cajete (2010), p. 1128, emphasis as in original).As two-eyed seeing implies, people familiar with both knowledge systems can uniquely combine the two in various ways to meet a challenge or task at hand. In the context of environmental crises alone, a combination of both seems essential (Aikenhead and Michell (2011), p. 114).},
	language = {en},
	number = {4},
	urldate = {2020-10-28},
	journal = {Journal of Environmental Studies and Sciences},
	author = {Bartlett, Cheryl and Marshall, Murdena and Marshall, Albert},
	month = nov,
	year = {2012},
	pages = {331--340},
}

@article{michie_application_2018,
	title = {The {Application} of {Both}-{Ways} and {Two}-{Eyed} {Seeing} {Pedagogy}: {Reflections} on {Engaging} and {Teaching} {Science} to {Post}-secondary {Indigenous} {Students}},
	volume = {48},
	issn = {1573-1898},
	shorttitle = {The {Application} of {Both}-{Ways} and {Two}-{Eyed} {Seeing} {Pedagogy}},
	url = {10.1007/s11165-018-9775-y},
	doi = {10.1007/s11165-018-9775-y},
	abstract = {The issue of Indigenous engagement, participation and success in the sciences is a concern both in Australia and in Canada. The authors of this paper have taught Indigenous students in tertiary enabling programs, undergraduate science and science education. Their experiences bridging Indigenous and Western cultures in science and science education through Both-Ways (BW) or Two-Eyed Seeing (TES) pedagogical and methodological approaches form the data for this paper. Their teaching experience with tertiary level Indigenous students using BW/TES pedagogies serves as case studies for the epistemic insight (knowledge about knowledge) they have gained. Each of the case studies considers the role of the Nature of Science (NOS) and potential conflicts through engagement with the two knowledge paradigms. Rather than being in conflict, the two worldviews are seen as complementary, a situation leading to epistemic insight.},
	language = {en},
	number = {6},
	urldate = {2020-10-28},
	journal = {Research in Science Education},
	author = {Michie, Michael and Hogue, Michelle and Rioux, Joël},
	month = dec,
	year = {2018},
	pages = {1205--1220},
}

@misc{noauthor_relationship_nodate,
	title = {Relationship {Between} {Phosphatase} {Activity} and {Phosphorus} {Fractions} in {Agricultural} {Soils}},
	url = {http://connection.ebscohost.com/c/articles/26025494/relationship-between-phosphatase-activity-phosphorus-fractions-agricultural-soils},
	urldate = {2020-10-27},
}

@misc{noauthor_relationship_nodate-1,
	title = {Relationship {Between} {Phosphatase} {Activity} and {Phosphorus} {Fractions} in {Agricultural} {Soils}},
	url = {https://scialert.net/abstract/?doi=ijss.2007.107.118},
	urldate = {2020-10-27},
}

@article{kizilkaya_variation_2010,
	title = {Variation of land use and land cover effects on some soil physico-chemical characteristics and soil enzyme activity},
	volume = {97},
	abstract = {The main objective of this study was to determine some chemical, physical properties and extracellular enzymatic activities of soil modified after forestland transformation into cropland and pasture in ÇankırıUludere watershed. In this study, the changes in the properties of four different pedons classified as Lithic Leptosol (Lithic Xerorthent, LPq), Dystric Cambisol (Typic Dystroxerept, CMd) and Haplic Cambisol (Typic Haploxerept, CMha) located on three adjacent land use types which are native forest, pasture and cultivated fields include some extracellular enzymes, organic matter, pH, EC, CaCO3, bulk density, total porosity, hydraulic conductivity and aggregate stability. The effects of agricultural practices on soil properties taken from each four adjacent land use types were most clearly detected in the past 50 years with the land use change. Land use change and subsequent tillage practices resulted in significant decreases in organic matter, total porosity, total nitrogen and soil aggregates stability. There was also a significant change in bulk density among cultivat, pasture and natural forest soils. Depending upon the increasing in bulk density and disruption of pores by cultivation, total porosity decreased accordingly. The data show that after long term continuous cultivation of the natural forest soils resulted in change in soils both in physical and chemical characteristics. In addition, it was found that changes of land use and land cover associated with organic matter content can alter the soil enzyme activities within the soil profile.},
	language = {en},
	number = {2},
	journal = {Zemdirbyste-Agriculture},
	author = {Kizilkaya, Rıdvan and Dengi̇z, Orhan},
	year = {2010},
	pages = {10},
}

@techreport{noauthor_circular_2018,
	type = {Circular},
	title = {Circular},
	language = {en},
	year = {2018},
	note = {Series: Circular},
}

@article{ibrahim_bayesian_2002,
	title = {Bayesian methods for generalized linear models with covariates missing at random},
	volume = {30},
	issn = {1708-945X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.2307/3315865},
	doi = {10.2307/3315865},
	abstract = {The authors propose methods for Bayesian inference for generalized linear models with missing covariate data. They specify a parametric distribution for the covariates that is written as a sequence of one-dimensional conditional distributions. They propose an informative class of joint prior distributions for the regression coefficients and the parameters arising from the covariate distributions. They examine the properties of the proposed prior and resulting posterior distributions. They also present a Bayesian criterion for comparing various models, and a calibration is derived for it. A detailed simulation is conducted and two real data sets are examined to demonstrate the methodology.},
	language = {en},
	number = {1},
	urldate = {2020-10-23},
	journal = {Canadian Journal of Statistics},
	author = {Ibrahim, Joseph G. and Chen, Ming-Hui and Lipsitz, Stuart R.},
	year = {2002},
	keywords = {Bayesian criterion, Gibbs sampling, Poisson regression, data augmentation, historical data, logistic regression, predictive distribution, prior distribution},
	pages = {55--78},
}

@article{ma_bayesian_2018,
	title = {Bayesian methods for dealing with missing data problems},
	volume = {47},
	issn = {1226-3192},
	url = {http://www.sciencedirect.com/science/article/pii/S1226319218300176},
	doi = {10.1016/j.jkss.2018.03.002},
	abstract = {Missing data, a common but challenging issue in most studies, may lead to biased and inefficient inferences if handled inappropriately. As a natural and powerful way for dealing with missing data, Bayesian approach has received much attention in the literature. This paper reviews the recent developments and applications of Bayesian methods for dealing with ignorable and non-ignorable missing data. We firstly introduce missing data mechanisms and Bayesian framework for dealing with missing data, and then introduce missing data models under ignorable and non-ignorable missing data circumstances based on the literature. After that, important issues of Bayesian inference, including prior construction, posterior computation, model comparison and sensitivity analysis, are discussed. Finally, several future issues that deserve further research are summarized and concluded.},
	language = {en},
	number = {3},
	urldate = {2020-10-22},
	journal = {Journal of the Korean Statistical Society},
	author = {Ma, Zhihua and Chen, Guanghui},
	month = sep,
	year = {2018},
	keywords = {Bayesian approach, Missing data, Missing data model, Non-ignorable missing data mechanism},
	pages = {297--313},
}

@article{choi_comparison_2019,
	title = {A comparison of different methods to handle missing data in the context of propensity score analysis},
	volume = {34},
	issn = {1573-7284},
	url = {10.1007/s10654-018-0447-z},
	doi = {10.1007/s10654-018-0447-z},
	abstract = {Propensity score analysis is a popular method to control for confounding in observational studies. A challenge in propensity methods is missing values in confounders. Several strategies for handling missing values exist, but guidance in choosing the best method is needed. In this simulation study, we compared four strategies of handling missing covariate values in propensity matching and propensity weighting. These methods include: complete case analysis, missing indicator method, multiple imputation and combining multiple imputation and missing indicator method. Concurrently, we aimed to provide guidance in choosing the optimal strategy. Simulated scenarios varied regarding missing mechanism, presence of effect modification or unmeasured confounding. Additionally, we demonstrated how missingness graphs help clarifying the missing structure. When no effect modification existed, complete case analysis yielded valid causal treatment effects even when data were missing not at random. In some situations, complete case analysis was also able to partially correct for unmeasured confounding. Multiple imputation worked well if the data were missing (completely) at random, and if the imputation model was correctly specified. In the presence of effect modification, more complex imputation models than default options of commonly used statistical software were required. Multiple imputation may fail when data are missing not at random. Here, combining multiple imputation and the missing indicator method reduced the bias as the missing indicator variable can be a proxy for unobserved confounding. The optimal way to handle missing values in covariates of propensity score models depends on the missing data structure and the presence of effect modification. When effect modification is present, default settings of imputation methods may yield biased results even if data are missing at random.},
	language = {en},
	number = {1},
	urldate = {2020-10-22},
	journal = {European Journal of Epidemiology},
	author = {Choi, Jungyeon and Dekkers, Olaf M. and le Cessie, Saskia},
	month = jan,
	year = {2019},
	pages = {23--36},
}

@article{jackman_estimation_2000,
	title = {Estimation and {Inference} {Are} {Missing} {Data} {Problems}: {Unifying} {Social} {Science} {Statistics} via {Bayesian} {Simulation}},
	volume = {8},
	issn = {1047-1987},
	shorttitle = {Estimation and {Inference} {Are} {Missing} {Data} {Problems}},
	url = {https://www.jstor.org/stable/25791616},
	abstract = {Bayesian simulation is increasingly exploited in the social sciences for estimation and inference of model parameters. But an especially useful (if often overlooked) feature of Bayesian simulation is that it can be used to estimate any function of model parameters, including "auxiliary" quantities such as goodness-of-fit statistics, predicted values, and residuals. Bayesian simulation treats these quantities as if they were missing data, sampling from their implied posterior densities. Exploiting this principle also lets researchers estimate models via Bayesian simulation where maximum-likelihood estimation would be intractable. Bayesian simulation thus provides a unified solution for quantitative social science. I elaborate these ideas in a variety of contexts: these include generalized linear models for binary responses using data on bill cosponsorship recently reanalyzed in Political Analysis, item—response models for the measurement of respondent's levels of political information in public opinion surveys, the estimation and analysis of legislators' ideal points from roll-call data, and outlier-resistant regression estimates of incumbency advantage in U.S. Congressional elections.},
	number = {4},
	urldate = {2020-10-21},
	journal = {Political Analysis},
	author = {Jackman, Simon},
	year = {2000},
	note = {Publisher: [Oxford University Press, Society for Political Methodology]},
	pages = {307--332},
}

@article{ludtke_regression_2020,
	title = {Regression models involving nonlinear effects with missing data: {A} sequential modeling approach using {Bayesian} estimation},
	volume = {25},
	copyright = {© 2019, American Psychological Association},
	issn = {1082-989X},
	shorttitle = {Regression models involving nonlinear effects with missing data},
	url = {https://search.proquest.com/docview/2320473830/abstract/E821A3D13CBE4F30PQ/1},
	doi = {http://dx.doi.org/10.1037/met0000233},
	abstract = {When estimating multiple regression models with incomplete predictor variables, it is necessary to specify a joint distribution for the predictor variables. A convenient assumption is that this distribution is a joint normal distribution, the default in many statistical software packages. This distribution will in general be misspecified if the predictors with missing data have nonlinear effects (e.g., x2) or are included in interaction terms (e.g., x·z). In the present article, we discuss a sequential modeling approach that can be applied to decompose the joint distribution of the variables into 2 parts: (a) a part that is due to the model of interest and (b) a part that is due to the model for the incomplete predictors. We demonstrate how the sequential modeling approach can be used to implement a multiple imputation strategy based on Bayesian estimation techniques that can accommodate rather complex substantive regression models with nonlinear effects and also allows a flexible treatment of auxiliary variables. In 4 simulation studies, we showed that the sequential modeling approach can be applied to estimate nonlinear effects in regression models with missing values on continuous, categorical, or skewed predictor variables under a broad range of conditions and investigated the robustness of the proposed approach against distributional misspecifications. We developed the R package mdmb, which facilitates a user-friendly application of the sequential modeling approach, and we present a real-data example that illustrates the flexibility of the software. (PsycINFO Database Record (c) 2020 APA, all rights reserved) (Source: journal abstract) Translational Abstract—Regression models testing whether two predictor variables interact to produce an effect on the outcome variable are commonly used in psychology. Often a portion of the participants do not fully complete their responses so their data are missing on one or both of the predictor variables. Although more modern methods of addressing missing data typically lead to more accurate results, the performance of these methods may be greatly diminished when regression models contain interactions or other nonlinear effects. We describe a new sequential modeling approach using multiple imputation that separates the problem into two parts: (a) the substantive regression model of interest and (b) the imputation model; this approach theoretically identifies when the two parts are compatible. When the two parts are compatible, Bayesian estimation can be used to produce accurate results. We show the improved performance of this sequential modeling approach relative to other forms of multiple imputation in four simulation studies under a broad range of conditions. The simulation studies considered most of the types of predictor variables commonly considered in research: normally distributed continuous, skewed continuous, binary, and latent. We developed the R package mdmb, which facilitates a user-friendly application of the sequential modeling approach, and we present a real-data example that illustrates the flexibility of the software. Annotated R computer script for the main analyses is presented in the online supplemental material. (PsycINFO Database Record (c) 2020 APA, all rights reserved)},
	language = {English},
	number = {2},
	urldate = {2020-10-21},
	journal = {Psychological Methods},
	author = {Lüdtke, Oliver and Robitzsch, Alexander and West, Stephen G.},
	month = apr,
	year = {2020},
	note = {Num Pages: 157-181 Place: Washington, US Publisher: American Psychological Association (US)},
	keywords = {Models, Multiple Regression (major), Nonlinear Regression (major), Normal Distribution (major), Simulation (major), Statistical Data, Statistical Estimation (major)},
	pages = {157--181},
}

@article{colchero_basta_2012,
	title = {{BaSTA}: an {R} package for {Bayesian} estimation of age-specific survival from incomplete mark–recapture/recovery data with covariates},
	volume = {3},
	copyright = {© 2012 The Authors. Methods in Ecology and Evolution © 2012 British Ecological Society},
	issn = {2041-210X},
	shorttitle = {{BaSTA}},
	url = {https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/j.2041-210X.2012.00186.x},
	doi = {10.1111/j.2041-210X.2012.00186.x},
	abstract = {1. Understanding age-specific survival in wild animal populations is crucial to the study of population dynamics and is therefore an essential component of several fields including evolution, management and conservation. 2. We present Bayesian survival trajectory analysis (BaSTA), a free open-source software package for estimating age-specific survival from capture–recapture/recovery data under a Bayesian framework. 3. The method copes with low recapture probabilities, unknown ages (e.g. because of left-truncation) and unknown ages at death (e.g. because of right-censoring). It estimates survival and detection parameters as well as the unknown birth and death times (i.e. latent states) while allowing users to test a range of survival models. In addition, the effect of continuous or categorical covariates can be evaluated. 4. This tool facilitates the analysis of age patterns of survival in long-term animal studies and will enable researchers to robustly infer the effect of covariates, even with large amounts of missing data.},
	language = {en},
	number = {3},
	urldate = {2020-10-21},
	journal = {Methods in Ecology and Evolution},
	author = {Colchero, Fernando and Jones, Owen R. and Rebke, Maren},
	year = {2012},
	keywords = {Bayesian inference, R project, capture–recapture, capture–recovery, free software, long-term individual-based data sets, survival analysis},
	pages = {466--470},
}

@article{wohl_carbon_2017,
	title = {Carbon dynamics of river corridors and the effects of human alterations},
	volume = {87},
	copyright = {© 2017 by the Ecological Society of America},
	issn = {1557-7015},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecm.1261},
	doi = {10.1002/ecm.1261},
	abstract = {Research in stream metabolism, gas exchange, and sediment dynamics indicates that rivers are an active component of the global carbon cycle and that river form and process can influence partitioning of terrestrially derived carbon among the atmosphere, geosphere, and ocean. Here we develop a conceptual model of carbon dynamics (inputs, outputs, and storage of organic carbon) within a river corridor, which includes the active channel and the riparian zone. The exchange of carbon from the channel to the riparian zone represents potential for storage of transported carbon not included in the “active pipe” model of organic carbon (OC) dynamics in freshwater systems. The active pipe model recognizes that river processes influence carbon dynamics, but focuses on CO2 emissions from the channel and eventual delivery to the ocean. We also review how human activities directly and indirectly alter carbon dynamics within river corridors. We propose that dams create the most significant alteration of carbon dynamics within a channel, but that alteration of riparian zones, including the reduction of lateral connectivity between the channel and riparian zone, constitutes the most substantial change of carbon dynamics in river corridors. We argue that the morphology and processes of a river corridor regulate the ability to store, transform, and transport OC, and that people are pervasive modifiers of river morphology and processes. The net effect of most human activities, with the notable exception of reservoir construction, appears to be that of reducing the ability of river corridors to store OC within biota and sediment, which effectively converts river corridors to OC sources rather than OC sinks. We conclude by summarizing knowledge gaps in OC dynamics and the implications of our findings for managing OC dynamics within river corridors.},
	language = {en},
	number = {3},
	urldate = {2020-10-20},
	journal = {Ecological Monographs},
	author = {Wohl, Ellen and Hall, Robert O. and Lininger, Katherine B. and Sutfin, Nicholas A. and Walters, David M.},
	year = {2017},
	keywords = {active channel, carbon, dam, land use, riparian zone, river},
	pages = {379--409},
}

@article{ortiz_detecting_2020,
	title = {Detecting changes in statistical indicators of resilience prior to algal blooms in shallow eutrophic lakes},
	volume = {11},
	copyright = {© 2020 The Authors.},
	issn = {2150-8925},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecs2.3200},
	doi = {10.1002/ecs2.3200},
	abstract = {Algal blooms in lakes and reservoirs can be considered regime shifts from a clear-water to algae-dominated state that often occurs abruptly. Under experimental conditions, these regime shifts have been predicted from rises in variance and autocorrelation (generic resilience indicators) of state variables monitored at a high frequency. The goal of this study was to evaluate the behavior of resilience indicators prior to a critical transition in lakes that naturally experience algal blooms. Ambient lake conditions provide several potential hurdles that could inhibit the detection of meaningful changes in resilience indicators prior to a critical transition such as stochastic nutrient loading, spatial complexity, and decreased resilience due to higher baseline nutrient concentrations. We compiled five lake-years of high-frequency monitoring of chlorophyll a, phycocyanin, dissolved oxygen, and pH from four hypereutrophic lakes. Despite the factors that might hinder detecting statistical indicators of changing resilience in hypereutrophic ecosystems, we found that a rise in resilience indicators did occur prior to a critical transition in three out of four possible lake-years, with rise beginning between 5 and 33 d prior. In one lake-year, a critical transition occurred soon after the monitoring began, preventing detection of rising variance or autocorrelation signals which are calculated using a 21-d rolling window. These results add to the growing body of evidence that rises in resilience indicators can be detected in ecosystems prior to a regime shift if monitoring programs are properly designed to capture the dynamics; however, continued research is needed to better understand the conditions under which resilience indicators may be useful as an early warning detection tool for lake management.},
	language = {en},
	number = {10},
	urldate = {2020-10-16},
	journal = {Ecosphere},
	author = {Ortiz, David and Palmer, Jason and Wilkinson, Grace},
	year = {2020},
	keywords = {critical transition, cyanobacteria, early warning indicator, harmful algal bloom, lake, regime shift},
	pages = {e03200},
}

@article{reiners_complementary_1986,
	title = {Complementary {Models} for {Ecosystems}},
	volume = {127},
	issn = {0003-0147},
	url = {https://www.jstor.org/stable/2461647},
	abstract = {The ecosystem level of ecological research is fraught with conceptual difficulties that have contributed to faltering progress in theoretical development. An acceptance of multiple models for different aspects of ecosystems may assist in reducing this confusion. Two complementary models of ecosystems are suggested: the first based on energy, the second based on matter. Whereas the first follows from the second law of thermodynamics, the second complementary model derives from the chemical stoichiometry of the biota. These models can be developed independently but have many points of interaction. These points yield another series of predictions and hypotheses. While these complementary models serve as theoretical structures for much of the body of ecosystem concepts, they are not adequate by themselves. Other complementary models, perhaps centered on explicit linkages at the population and community levels, are necessary.},
	number = {1},
	urldate = {2020-10-15},
	journal = {The American Naturalist},
	author = {Reiners, William A.},
	year = {1986},
	note = {Publisher: [University of Chicago Press, American Society of Naturalists]},
	pages = {59--73},
}

@article{carpenter_stan_2017,
	title = {Stan: {A} probabilistic programming language},
	volume = {76},
	issn = {1548-7660},
	shorttitle = {Stan},
	doi = {10.18637/jss.v076.i01},
	language = {en},
	number = {1},
	urldate = {2020-10-13},
	journal = {Journal of Statistical Software},
	author = {Carpenter, Bob and Gelman, Andrew and Hoffman, Matthew D. and Lee, Daniel and Goodrich, Ben and Betancourt, Michael and Brubaker, Marcus and Guo, Jiqiang and Li, Peter and Riddell, Allen},
	month = jan,
	year = {2017},
	keywords = {Bayesian inference, Stan, algorithmic differentiation, probabilistic programming},
	pages = {1--32},
}

@article{koschorreck_technical_2020,
	title = {Technical note: {CO2} is not like {CH4}; limits of and corrections to the headspace method to analyse {pCO2} in water},
	issn = {1726-4170},
	url = {https://bg.copernicus.org/preprints/bg-2020-307/},
	language = {English},
	urldate = {2020-10-09},
	journal = {Biogeosciences},
	author = {Koschorreck, Matthias and Prairie, Yves T. and Kim, Jihyeon and Marcé, Rafael},
	month = sep,
	year = {2020},
	pages = {1--12},
}

@book{dickson_guide_2007,
	address = {Sidney, BC},
	series = {{PICES} special publication},
	title = {Guide to best practices for ocean {CO2} measurements},
	number = {3},
	publisher = {North Pacific Marine Science Organization},
	editor = {Dickson, Andrew Gilmore and Sabine, Christopher L. and Christian, James Robert and Bargeron, Charlene P.},
	year = {2007},
}

@misc{noauthor_ocads_nodate,
	title = {{OCADS} - {Guide} to {Best} {Practices} for {Ocean} {CO2} {Measurements}},
	url = {http://www.ncei.noaa.gov/},
	language = {en},
	urldate = {2020-10-09},
}

@article{isles_misuse_nodate,
	title = {The misuse of ratios in ecological stoichiometry},
	volume = {n/a},
	copyright = {© 2020 by the Ecological Society of America},
	issn = {1939-9170},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecy.3153},
	doi = {10.1002/ecy.3153},
	abstract = {Ecological stoichiometry is concerned with the ratios of different elements, particularly carbon, nitrogen, and phosphorus. Ratios by their nature do not respond symmetrically to changes in the numerator and denominator and do not follow normal distributions; however, researchers frequently fail to consider these properties in their analyses, which has biased reported results. Calculating means, variance, or linear slopes based on untransformed ratios results in biased results. I demonstrate the consequences of these errors for inferences from stoichiometric analyses using simple examples and several large monitoring data sets. I then review 100 studies in ecological stoichiometry and find that misuse of ratio data is common, with 93\% of studies containing at least one error. These errors may be problematic, particularly in large-scale meta-analyses summarizing data over large ranges. Fortunately, most of these mistakes can be easily avoided by first log transforming elemental ratios. I therefore recommend that, to ensure robust and reproducible results, researchers in ecological stoichiometry should adopt a convention of presenting stoichiometric ratio data as the logarithm of molar ratios in the future. The widespread use of untransformed nitrogen to phosphorus ratio as an indicator of nutrient limitation has likely exaggerated the importance of phosphorus limitation, particularly in freshwater systems.},
	language = {en},
	number = {n/a},
	urldate = {2020-10-09},
	journal = {Ecology},
	author = {Isles, Peter D. F.},
	keywords = {ecological stoichiometry, log transformation, nitrogen to phosphorus ratio, ratio data, stoichiometric plasticity},
	pages = {e03153},
}

@article{myrstener_nutrients_nodate-1,
	title = {Nutrients influence seasonal metabolic patterns and total productivity of {Arctic} streams},
	volume = {n/a},
	copyright = {© 2020 The Authors. Limnology and Oceanography published by Wiley Periodicals LLC on behalf of Association for the Sciences of Limnology and Oceanography.},
	issn = {1939-5590},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lno.11614},
	doi = {10.1002/lno.11614},
	abstract = {The seasonality of gross primary production (GPP) in streams is driven by multiple physical and chemical factors, yet incident light is often thought to be most important. In Arctic tundra streams, however, light is available in saturating amounts throughout the summer, but sharp declines in nutrient supply during the terrestrial growing season may constrain aquatic productivity. Given the opposing seasonality of these drivers, we hypothesized that “shoulder seasons”—spring and autumn—represent critical time windows when light and nutrients align to optimize rates of stream productivity in the Arctic. To test this, we measured annual patterns of GPP and biofilm accumulation in eight streams in Arctic Sweden. We found that the aquatic growing season length differed by 4 months across streams and was determined largely by the timing of ice-off in spring. During the growing season, temporal variability in GPP for nitrogen (N) poor streams was correlated with inorganic N concentration, while in more N-rich streams GPP was instead linked to changes in phosphorus and light. Annual GPP varied ninefold among streams and was enhanced by N availability, the length of ice-free period, and low flood frequency. Finally, network scale estimates of GPP highlight the overall significance of the shoulder seasons, which accounted for 48\% of annual productivity. We suggest that the timing of ice off and nutrient supply from land interact to regulate the annual metabolic regimes of nutrient poor, Arctic streams, leading to unexpected peaks in productivity that are offset from the terrestrial growing season.},
	language = {en},
	number = {n/a},
	urldate = {2020-10-09},
	journal = {Limnology and Oceanography},
	author = {Myrstener, Maria and Gómez‐Gener, Lluís and Rocher‐Ros, Gerard and Giesler, Reiner and Sponseller, Ryan A.}
}

@article{kirk_estimating_2020,
	title = {Estimating {Benthic} {Light} {Regimes} {Improves} {Predictions} of {Primary} {Production} and constrains {Light}-{Use} {Efficiency} in {Streams} and {Rivers}},
	issn = {1432-9840},
	url = {https://link.springer.com/epdf/10.1007/s10021-020-00552-1},
	doi = {10.1007/s10021-020-00552-1},
	abstract = {Light-use efficiency (LUE) describes conversion of incident light into gross primary production (GPP), combining the inherent photosynthetic efficiency of chloroplasts with light-capture ability of the autotrophic community. In lotic ecosystems, LUE is poorly constrained, in part because most studies neglect water-column attenuation. We hypothesized that rigorous quantification of benthic light would (1) improve GPP predictions and (2) constrain cross-site variation in LUE. We used a field-validated light model to successively attenuate open-sky irradiance through the riparian canopy and water column to estimate benthic light at 11 sites spanning discharge and dissolved-color gradients where we simultaneously calculated daily GPP. Our results indicate substantial water-column attenuation (up to 96\% of stream-surface light), implying significant underestimation of LUE using stream-surface light alone. Benthic light dramatically improved GPP predictions, especially after considering mean-light conditions, which we suggest enumerates ecosystem light-capture ability due to biomass density. The model including mean-light effects explained 78\% of GPP variation across sites and yielded a LUE identical to terrestrial ecosystems (1.9\%). Interactions between daily and mean-light only slightly improved model fit (R2 = 0.80), implying higher LUE at sites with higher mean light, but notably reduced LUE variation across sites compared with individual site analyses. This suggests that better representation of benthic light regimes leads to LUE convergence. Our study supports use of a global river LUE to translate large-scale predictions of stream light regimes into expected GPP, from which disturbance and nutrient limitation effects can then be discerned.},
	language = {en},
	urldate = {2020-10-09},
	journal = {Ecosystems},
	author = {Kirk, Lily and Hensley, Robert T. and Savoy, Philip and Heffernan, James B. and Cohen, Matthew J.},
	year = {2020},
}

@article{filazzola_database_2020,
	title = {A database of chlorophyll and water chemistry in freshwater lakes},
	volume = {7},
	copyright = {2020 The Author(s)},
	issn = {2052-4463},
	url = {https://www.nature.com/articles/s41597-020-00648-2},
	doi = {10.1038/s41597-020-00648-2},
	abstract = {Measures of chlorophyll represent the algal biomass in freshwater lakes that is often used by managers as a proxy for water quality and lake productivity. However, chlorophyll concentrations in lakes are dependent on many interacting factors, including nutrient inputs, mixing regime, lake depth, climate, and anthropogenic activities within the watershed. Therefore, integrating a broad scale dataset of lake physical, chemical, and biological characteristics can help elucidate the response of freshwater ecosystems to global change. We synthesized a database of measured chlorophyll a (chla) values, associated water chemistry variables, and lake morphometric characteristics for 11,959 freshwater lakes distributed across 72 countries. Data were collected based on a systematic review examining 3322 published manuscripts that measured lake chla, and we supplemented these data with online repositories such as The Knowledge Network for Biocomplexity, Dryad, and Pangaea. This publicly available database can be used to improve our understanding of how chlorophyll levels respond to global environmental change and provide baseline comparisons for environmental managers responsible for maintaining water quality in lakes.},
	language = {en},
	number = {1},
	urldate = {2020-10-09},
	journal = {Scientific Data},
	author = {Filazzola, Alessandro and Mahdiyan, Octavia and Shuvo, Arnab and Ewins, Carolyn and Moslenko, Luke and Sadid, Tanzil and Blagrave, Kevin and Imrit, Mohammad Arshad and Gray, Derek K. and Quinlan, Roberto and O’Reilly, Catherine M. and Sharma, Sapna},
	month = sep,
	year = {2020},
	note = {Number: 1
Publisher: Nature Publishing Group},
	pages = {310},
}

@article{elser_shifts_2009,
	title = {Shifts in {Lake} {N}:{P} {Stoichiometry} and {Nutrient} {Limitation} {Driven} by {Atmospheric} {Nitrogen} {Deposition}},
	volume = {326},
	copyright = {Copyright © 2009, American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	shorttitle = {Shifts in {Lake} {N}},
	url = {https://science.sciencemag.org/content/326/5954/835},
	doi = {10.1126/science.1176199},
	abstract = {Human activities have more than doubled the amount of nitrogen (N) circulating in the biosphere. One major pathway of this anthropogenic N input into ecosystems has been increased regional deposition from the atmosphere. Here we show that atmospheric N deposition increased the stoichiometric ratio of N and phosphorus (P) in lakes in Norway, Sweden, and Colorado, United States, and, as a result, patterns of ecological nutrient limitation were shifted. Under low N deposition, phytoplankton growth is generally N-limited; however, in high–N deposition lakes, phytoplankton growth is consistently P-limited. Continued anthropogenic amplification of the global N cycle will further alter ecological processes, such as biogeochemical cycling, trophic dynamics, and biological diversity, in the world’s lakes, even in lakes far from direct human disturbance.
Deposition of anthropogenically derived nitrogen can cause phosphorus to become the limiting nutrient of lake phytoplankton.
Deposition of anthropogenically derived nitrogen can cause phosphorus to become the limiting nutrient of lake phytoplankton.},
	language = {en},
	number = {5954},
	urldate = {2020-10-09},
	journal = {Science},
	author = {Elser, James J. and Andersen, Tom and Baron, Jill S. and Bergström, Ann-Kristin and Jansson, Mats and Kyle, Marcia and Nydick, Koren R. and Steger, Laura and Hessen, Dag O.},
	month = nov,
	year = {2009},
	pmid = {19892979},
	note = {Publisher: American Association for the Advancement of Science
Section: Report},
	pages = {835--837},
}

@article{millero_dissociation_2006,
	title = {Dissociation constants of carbonic acid in seawater as a function of salinity and temperature},
	volume = {100},
	issn = {0304-4203},
	url = {http://www.sciencedirect.com/science/article/pii/S0304420305001921},
	doi = {10.1016/j.marchem.2005.12.001},
	abstract = {Potentiometric measurements of the stoichiometric constants on the seawater pH scale for the dissociation of carbonic acid in seawater (K1⁎=[H+][HCO3−]/[CO2] and K2⁎=[H+][CO32−]/[HCO3−]) have been made as a function of salinity (1 to 50) and temperature (0 to 50 °C). The results have been fitted to the equations (T/K)pKi−pKi0=Ai+Bi/T+Ciln⁢T. The values of pKi0 in pure water are taken from the early work of Harned and Davis (1943) and Harned and Scholes (1941)pK10=−126.34048+6320.813/T+19.568224⁢ln⁢TpK20=−90.18333+5143.692/T+14.613358⁢ln⁢T. The value of the adjustable parameters Ai, Bi and Ci for pK1⁎ are given by (σ=0.0054 and N=466)A1=13.4191S0.5+0.0331⁢S−5.33⁢E−05S2B1=−530.123S0.5−6.103⁢SC1=−2.06950S0.5. For pK2⁎ the parameters are given by (σ=0.011 and N=458)A2=21.0894S0.5+0.1248⁢S−3.687⁢E−04S2B2=−772.483S0.5−20.051⁢SC2=−3.3336S0.5. The values of pK1⁎ and pK2⁎ determined in this study are in good agreement with the seawater (SW) measurements of Mehrbach et al. (1973) and Mojica-Prieto and Millero (2002) from S=15 to 45 and 0 to 40 °C. The values of pK1⁎ near S=35 are also in reasonable agreement with the measurements in artificial seawater (ASW) of Goyet and Poisson (1989) and Roy et al. (1993) from 0 to 35 °C. The values of pK2⁎ in real seawater, however, do not agree with the measurement made in artificial seawater at temperatures above 5 °C. Calculations of pK1⁎ and pK2⁎ near 25 °C using an ionic interaction model (Millero and Roy, 1997) suggest that the pK2⁎ results in SW are more reliable than in ASW. The equations from this study should be valid from S=0 to 50 and t=0 to 50 °C for most estuarine and marine waters (check values at S=35 and t=25 °C are pK1⁎=5.8401 and pK2⁎=8.9636).},
	language = {en},
	number = {1},
	urldate = {2020-10-08},
	journal = {Marine Chemistry},
	author = {Millero, Frank J. and Graham, Taylor B. and Huang, Fen and Bustos-Serrano, Héctor and Pierrot, Denis},
	month = jun,
	year = {2006},
	keywords = {Carbonic acid, Dissociation constants, Modeling, Seawater, Titration, p},
	pages = {80--94},
}

@techreport{noauthor_open-file_2010,
	type = {Open-{File} {Report}},
	title = {Open-{File} {Report}},
	language = {en},
	year = {2010},
	note = {Series: Open-File Report},
}

@article{millero_carbonate_2010,
	title = {Carbonate constants for estuarine waters},
	volume = {61},
	issn = {1448-6059},
	url = {https://www.publish.csiro.au/mf/MF09254},
	doi = {10.1071/MF09254},
	abstract = {Intensive studies have been made on the carbonate system in seawater. The thermodynamic constants needed to examine the components of the carbonate system have been developed by several authors. The thermodynamic constants for the dissociation of carbonic acid in seawater have been determined on different pH scales. The two most popular pH scales are the total scale: [H+]T = [H+]F\{1 + [SO42–]T/KHSO4\}) and the seawater scale: [H+]SWS = [H+]F \{1 + βHSO4[SO42–]T/KHSO4 + βHF[F–]T/KHF\}, where the brackets denote concentrations and the subscripts F and T are for free and total concentrations. The values of KHSO4 and KHF are the dissociation constants for HSO4– and HF: As long as the same pH scale and constants for seawater are used, one can evaluate the components of the carbonate system in seawater. Unfortunately, not all the measured and fitted constants have been made for dilute seawater, and thus cannot be used in estuarine waters. In this paper, the measured constants from S = 1 to 50 and t = 0 to 50°C have been determined on the total, seawater and free scale (pHF = –log[H+]F). These stoichiometric constants can now be used to examine the carbonate system in most estuarine waters.},
	language = {en},
	number = {2},
	urldate = {2020-10-08},
	journal = {Marine and Freshwater Research},
	author = {Millero, Frank J.},
	month = mar,
	year = {2010},
	note = {Publisher: CSIRO PUBLISHING},
	pages = {139--142},
}

@article{millero_carbonate_2010-1,
	title = {Carbonate constants for estuarine waters},
	volume = {61},
	issn = {1323-1650},
	url = {http://www.publish.csiro.au/?paper=MF09254},
	doi = {10.1071/MF09254},
	abstract = {As long as the same pH scale and constants for seawater are used, one can evaluate the components of the carbonate system in seawater. Unfortunately, not all the measured and fitted constants have been made for dilute seawater, and thus cannot be used in estuarine waters. In this paper, the measured constants from S = 1 to 50 and t = 0 to 50◦C have been determined on the total, seawater and free scale (pHF = −log[H+]F). These stoichiometric constants can now be used to examine the carbonate system in most estuarine waters.},
	language = {en},
	number = {2},
	urldate = {2020-10-08},
	journal = {Marine and Freshwater Research},
	author = {Millero, Frank J.},
	year = {2010},
	pages = {139},
}

@misc{noauthor_doi101016jmarchem200512001_nodate,
	title = {doi:10.1016/j.marchem.2005.12.001 {\textbar} {Elsevier} {Enhanced} {Reader}},
	shorttitle = {doi},
	url = {https://reader.elsevier.com/reader/sd/pii/S0304420305001921?token=51578643E95F3C47F7E09F081C29A81DF458C2FB45D0C6CD62D8A49966676547C53036641F5808BC15D38CF5DC517B65},
	language = {en},
	urldate = {2020-10-08},
	doi = {10.1016/j.marchem.2005.12.001},
}

@article{gelbrecht_use_1998,
	title = {Use of {GC} and equilibrium calculations of {CO2} saturation index to indicate whether freshwater bodies in north-eastern {Germany} are net sources or sinks for atmospheric {CO2}},
	volume = {361},
	issn = {1432-1130},
	url = {10.1007/s002160050832},
	doi = {10.1007/s002160050832},
	abstract = {The determination of CO2 saturation by two different methods is described for freshwater bodies of differing trophic states, hydrology and chemistry in the North-East of Germany. Direct measurements were carried out by gas chromatography and values were calculated from the dissolved inorganic carbon concentration and pH. These results were in good agreement. In both cases, the CO2 saturation index was calculated from the carbon dioxide/carbonate/hydrogencarbonate equilibrium in water. An overestimation of CO2 saturation index will be caused at pH {\textgreater} 7 by neglecting the calcium forming ion pairs with HCO3– and CO32–. The CO2 saturation patterns exhibited seasonal changes in all the lakes investigated which were variable within each trophic group. A direct relationship was found between the increasing trophic state and undersaturation of CO2 during the periods of high primary production. Thus, with respect to the atmosphere, these freshwater bodies act mostly as sources of CO2. Periods of ice covering and clear-water phases are characterized by high CO2 supersaturation and therefore the surface waters investigated are CO2 sources for short periods only.},
	language = {en},
	number = {1},
	urldate = {2020-10-08},
	journal = {Fresenius' Journal of Analytical Chemistry},
	author = {Gelbrecht, J. and Fait, Martin and Dittrich, Maria and Steinberg, Christian},
	month = apr,
	year = {1998},
	pages = {47--53},
}

@article{noauthor_thermodynamics_1979,
	title = {The thermodynamics of the carbonate system in seawater},
	volume = {43},
	issn = {0016-7037},
	url = {https://www-sciencedirect-com.weblib.lib.umt.edu:2443/science/article/pii/0016703779901844},
	doi = {10.1016/0016-7037(79)90184-4},
	abstract = {The apparent constants (K'i) for the ionization of carbonic acid in seawater at various salinities (S,\%.) have been fit to equations of the form ln K'…},
	language = {en},
	number = {10},
	urldate = {2020-09-25},
	journal = {Geochimica et Cosmochimica Acta},
	month = oct,
	year = {1979},
	note = {Publisher: Pergamon},
	pages = {1651--1661},
}

@article{noauthor_thermodynamics_1979-1,
	title = {The thermodynamics of the carbonate system in seawater},
	volume = {43},
	issn = {0016-7037},
	url = {https://www-sciencedirect-com.weblib.lib.umt.edu:2443/science/article/pii/0016703779901844},
	doi = {10.1016/0016-7037(79)90184-4},
	abstract = {The apparent constants (K'i) for the ionization of carbonic acid in seawater at various salinities (S,\%.) have been fit to equations of the form ln K'…},
	language = {en},
	number = {10},
	urldate = {2020-09-25},
	journal = {Geochimica et Cosmochimica Acta},
	month = oct,
	year = {1979},
	note = {Publisher: Pergamon},
	pages = {1651--1661},
}

@article{filazzola_database_2020-1,
	title = {A database of chlorophyll and water chemistry in freshwater lakes},
	volume = {7},
	copyright = {2020 The Author(s)},
	issn = {2052-4463},
	url = {https://www.nature.com/articles/s41597-020-00648-2},
	doi = {10.1038/s41597-020-00648-2},
	abstract = {Measures of chlorophyll represent the algal biomass in freshwater lakes that is often used by managers as a proxy for water quality and lake productivity. However, chlorophyll concentrations in lakes are dependent on many interacting factors, including nutrient inputs, mixing regime, lake depth, climate, and anthropogenic activities within the watershed. Therefore, integrating a broad scale dataset of lake physical, chemical, and biological characteristics can help elucidate the response of freshwater ecosystems to global change. We synthesized a database of measured chlorophyll a (chla) values, associated water chemistry variables, and lake morphometric characteristics for 11,959 freshwater lakes distributed across 72 countries. Data were collected based on a systematic review examining 3322 published manuscripts that measured lake chla, and we supplemented these data with online repositories such as The Knowledge Network for Biocomplexity, Dryad, and Pangaea. This publicly available database can be used to improve our understanding of how chlorophyll levels respond to global environmental change and provide baseline comparisons for environmental managers responsible for maintaining water quality in lakes.},
	language = {en},
	number = {1},
	urldate = {2020-09-22},
	journal = {Scientific Data},
	author = {Filazzola, Alessandro and Mahdiyan, Octavia and Shuvo, Arnab and Ewins, Carolyn and Moslenko, Luke and Sadid, Tanzil and Blagrave, Kevin and Imrit, Mohammad Arshad and Gray, Derek K. and Quinlan, Roberto and O’Reilly, Catherine M. and Sharma, Sapna},
	month = sep,
	year = {2020},
	note = {Number: 1
Publisher: Nature Publishing Group},
	pages = {310},
}

@article{sander_compilation_2015,
	title = {Compilation of {Henry}'s law constants (version 4.0) for water as solvent},
	volume = {15},
	issn = {1680-7324},
	url = {https://acp.copernicus.org/articles/15/4399/2015/},
	doi = {10.5194/acp-15-4399-2015},
	abstract = {Many atmospheric chemicals occur in the gas phase as well as in liquid cloud droplets and aerosol particles. Therefore, it is necessary to understand the distribution between the phases. According to Henry’s law, the equilibrium ratio between the abundances in the gas phase and in the aqueous phase is constant for a dilute solution. Henry’s law constants of trace gases of potential importance in environmental chemistry have been collected and converted into a uniform format. The compilation contains 17 350 values of Henry’s law constants for 4632 species, collected from 689 references. It is also available at http://www.henrys-law.org.},
	language = {en},
	number = {8},
	urldate = {2020-09-21},
	journal = {Atmospheric Chemistry and Physics},
	author = {Sander, R.},
	month = apr,
	year = {2015},
	pages = {4399--4981},
}

@article{chen_inverse_2014,
	title = {Inverse modeling of dissolved {O2} and δ{18O}-{DO} to estimate aquatic metabolism, reaeration and respiration isotopic fractionation: effects of variable light regimes and input uncertainties},
	volume = {76},
	issn = {1420-9055},
	shorttitle = {Inverse modeling of dissolved {O2} and δ{18O}-{DO} to estimate aquatic metabolism, reaeration and respiration isotopic fractionation},
	url = {10.1007/s00027-014-0337-8},
	doi = {10.1007/s00027-014-0337-8},
	abstract = {A transient model, hereafter referred to as ROM-TM, was developed to quantify river ecosystem metabolic rates and reaeration rates from field observation of changes in dissolved O2 (DO) and the ratio of 18O to 16O in DO (δ18O-DO). ROM-TM applies an inverse modeling approach and is programmed using MATLAB. Parameters describing photosynthesis, ecosystem respiration, gas exchange, and isotopic fractionation, such as maximum photosynthetic rate (Pm), photosynthetic efficiency parameter (a), respiration rate at 20 °C (R20), gas exchange coefficient (K), respiration isotopic fractionation factor (aR), and photorespiration coefficient (βR), can be abstracted by minimizing the sum of square errors between the fitted data and the observed field data. Then DO and δ18O-DO time series can be reconstructed using estimated parameters and input variables. Besides being capable of teasing apart metabolic processes and gas exchange to provide daily average estimates of metabolic parameters at the ecosystem scale, ROM-TM can be used to address issues related to light including light saturation phenomena at the ecosystem level, the effect of cloud cover on the metabolic balance, and photorespiration. Error and uncertainty analysis demonstrates that ROM-TM is stable and robust for the random errors of DO time series. The photosynthetic parameters Pmand a are more sensitive than other parameters to lower-resolution time series data.},
	language = {en},
	number = {3},
	urldate = {2020-09-16},
	journal = {Aquatic Sciences},
	author = {Chen, Gao and Venkiteswaran, Jason J. and Schiff, Sherry L. and Taylor, William D.},
	month = jul,
	year = {2014},
	pages = {313--329},
}

@article{honti_error_2019,
	title = {Error propagation during inverse modeling leads to spurious correlations and misinterpretation of lake metabolism},
	volume = {17},
	copyright = {© 2018 The Authors. Limnology and Oceanography: Methods published by Wiley Periodicals, Inc. on behalf of Association for the Sciences of Limnology and Oceanography.},
	issn = {1541-5856},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lom3.10293},
	doi = {10.1002/lom3.10293},
	abstract = {Inverse modeling is a common practice to decompose observed processes into constituents that are unobservable or difficult to measure. To achieve this goal, a mechanistic model is calibrated to fit the observations and thereby the model produces a coherent set of constituent estimates. A disadvantage of this procedure is that any disagreement between the model assumptions and reality potentially introduces bias and other statistical artifacts into the constituents and their relations. Lake metabolism is recently most often followed by high-frequency measurements of dissolved oxygen, and inverse modeling with simple conceptual models is used to couple oxygen dynamics to ecosystem-wide aggregated metabolic rates, such as net ecosystem production (NEP). These models rely on estimates of gas exchange and community respiration. Using a model of a simple ecosystem and field data, we demonstrate that typical relations between modeled metabolic rates frequently do not follow patterns expected from synthetic ecosystems and that estimation errors strongly influence calculations by producing strong, spurious correlations. Correlation artifacts can be expected during inverse modeling, whenever observed time series are decomposed into poorly known or unmeasured processes that can compensate for the effect of each other.},
	language = {en},
	number = {1},
	urldate = {2020-09-16},
	journal = {Limnology and Oceanography: Methods},
	author = {Honti, Mark and Istvánovics, Vera},
	year = {2019},
	pages = {17--24},
}

@article{alewell_global_2020,
	title = {Global phosphorus shortage will be aggravated by soil erosion},
	volume = {11},
	copyright = {2020 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-020-18326-7},
	doi = {10.1038/s41467-020-18326-7},
	abstract = {Soil phosphorus (P) loss from agricultural systems will limit food and feed production in the future. Here, we combine spatially distributed global soil erosion estimates (only considering sheet and rill erosion by water) with spatially distributed global P content for cropland soils to assess global soil P loss. The world’s soils are currently being depleted in P in spite of high chemical fertilizer input. Africa (not being able to afford the high costs of chemical fertilizer) as well as South America (due to non-efficient organic P management) and Eastern Europe (for a combination of the two previous reasons) have the highest P depletion rates. In a future world, with an assumed absolute shortage of mineral P fertilizer, agricultural soils worldwide will be depleted by between 4–19 kg ha−1 yr−1, with average losses of P due to erosion by water contributing over 50\% of total P losses.},
	language = {en},
	number = {1},
	urldate = {2020-09-16},
	journal = {Nature Communications},
	author = {Alewell, Christine and Ringeval, Bruno and Ballabio, Cristiano and Robinson, David A. and Panagos, Panos and Borrelli, Pasquale},
	month = sep,
	year = {2020},
	note = {Number: 1
Publisher: Nature Publishing Group},
	pages = {4546},
}

@article{bratt_co-limitation_2020,
	title = {Co-limitation by {N} and {P} {Characterizes} {Phytoplankton} {Communities} {Across} {Nutrient} {Availability} and {Land} {Use}},
	volume = {23},
	issn = {1435-0629},
	url = {10.1007/s10021-019-00459-6},
	doi = {10.1007/s10021-019-00459-6},
	abstract = {Historically, freshwater lakes have been widely assumed to be singly limited by phosphorus (P) because the dominant paradigm assumes that nitrogen fixation (N2 fixation) will compensate for any nitrogen (N) deficits. However, a growing body of evidence demonstrates that primary producer response to nutrient manipulation most frequently indicates co-limitation by N and P. Differences in N and P supply ratio have been shown to influence the identity and severity of nutrient limitation, but whether N and P concentration and the ratio of N to P concentrations can explain the frequency of co-limitation in aquatic primary producer assemblages remains unclear, especially in ecosystems subject to human perturbation that strongly increase nutrient availability. We determined how resource availability influences nutrient limitation by N and P of phytoplankton primary production across 12 lakes in Minnesota that vary in watershed land use and lake nutrient levels. We measured epilimnetic lake metabolism and indicators of N2 fixation to evaluate their influence on nutrient limitation status of planktonic algal assemblages. Despite large differences in land use (agricultural, urban, and suburban) and water column N and P availability, planktonic algal response to nutrient manipulation was consistently characterized by co-limitation by N and P across years and months. Neither P availability (as concentrations of total and inorganic forms) nor N2-flux rate predicted responses to nutrient additions. N availability significantly influenced responses of phytoplankton to nutrient additions across years, but this effect was small. The ratio of total N to total P significantly influenced the response to single additions of N and P (these effects were negative and positive, respectively) in summer 2013. Importantly, higher lake primary production and heterocyte count (number of nitrogen fixing cells) were also associated with a stronger, positive response to N + P addition. Overall, these data suggest that planktonic algal assemblages are predominantly characterized by co-limitation by N and P despite large and diverse human impacts on nutrient inputs. Additionally, higher rates of primary production increase the likelihood of co-limitation. Together, these results further support the paradigm shift toward dual management of N and P in aquatic ecosystems.},
	language = {en},
	number = {6},
	urldate = {2020-09-16},
	journal = {Ecosystems},
	author = {Bratt, A. R. and Finlay, J. C. and Welter, J. R. and Vculek, B. A. and Van Allen, R. E.},
	month = sep,
	year = {2020},
	pages = {1121--1137},
}

@article{worrall_dissolved_2020,
	title = {The dissolved organic carbon flux from the {UK} – {A} new {Bayesian} approach to flux calculation},
	volume = {590},
	issn = {0022-1694},
	url = {http://www.sciencedirect.com/science/article/pii/S0022169420309719},
	doi = {10.1016/j.jhydrol.2020.125511},
	abstract = {The study of regional and national-scale fluxes of biogeochemically relevant elements (e.g. carbon) has been hampered by inconsistency of long-term sampling. In this study we solve the issue of sporadic, low-density and low-frequency sampling for nutrients by using Bayesian hierarchical generalised linear modelling. The Bayesian approach means that it is possible to estimate a distribution of the expected value of the nutrient of interest for each location within a survey, no matter whether it was surveyed in a particular year, as long as that site was sampled sometime during the entire study period and that somewhere within the wider survey was sampled in the particular year, i.e. there is no minimum number of samples for a site to be included save that the site was sampled during the entire study period. The method developed was applied to problem of understanding the long-term flux of dissolved organic carbon (DOC) for the UK. The method was applied to 251 monitoring sites across the UK from 1974 to 2019 and the approach was similarly applied to river discharges so as to infill gaps in flow records. The results showed that:I.The annual expected value of the DOC concentration at the UK tidal limit sites has significantly declined over the period from 1974 to 2019.II.Statistically significant changes in DOC concentration were observed over the period from 1974 to 2018 with DOC concentrations rising at the majority sites until the late 1990 s, before declining to a minimum in 2007 with modest increases to 2018.III.The DOC flux from the UK peaked in the year 2000 at 1103 ± 141 ktonnes C/yr (4.5 tonnes C/km2/yr) and reached a minimum of 503 ± 63 ktonnes C/yr (2.1 tonnes C/km2/yr) in 2018.IV.The spatial pattern of DOC export shows large declines in the south and east of the UK where urban centres dominate while catchments in the north of the country show continuing high exports (up to 21 tonnes C/km2/yr) but exports as low as 0.16 tonnes C/km2/yr in eastern England.The flux method developed here makes maximal use of the available data allowing for calculation of long time series, even with sporadic sampling, and gives results with a coherent and consistent measure of their uncertainty.},
	language = {en},
	urldate = {2020-09-15},
	journal = {Journal of Hydrology},
	author = {Worrall, Fred and Howden, Nicholas J. K. and Burt, Tim P.},
	month = nov,
	year = {2020},
	keywords = {Bayesian analysis, DOC trends, Dissolved organic carbon, Time series analysis},
	pages = {125511},
}

@article{geary_guide_2020,
	title = {A guide to ecosystem models and their environmental applications},
	copyright = {2020 The Author(s), under exclusive licence to Springer Nature Limited},
	issn = {2397-334X},
	url = {https://www.nature.com/articles/s41559-020-01298-8},
	doi = {10.1038/s41559-020-01298-8},
	abstract = {Applied ecology has traditionally approached management problems through a simplified, single-species lens. Repeated failures of single-species management have led us to a new paradigm — managing at the ecosystem level. Ecosystem management involves a complex array of interacting organisms, processes and scientific disciplines. Accounting for interactions, feedback loops and dependencies between ecosystem components is therefore fundamental to understanding and managing ecosystems. We provide an overview of the main types of ecosystem models and their uses, and discuss challenges related to modelling complex ecological systems. Existing modelling approaches typically attempt to do one or more of the following: describe and disentangle ecosystem components and interactions; make predictions about future ecosystem states; and inform decision making by comparing alternative strategies and identifying important uncertainties. Modelling ecosystems is challenging, particularly when balancing the desire to represent many components of an ecosystem with the limitations of available data and the modelling objective. Explicitly considering different forms of uncertainty is therefore a primary concern. We provide some recommended strategies (such as ensemble ecosystem models and multi-model approaches) to aid the explicit consideration of uncertainty while also meeting the challenges of modelling ecosystems.},
	language = {en},
	urldate = {2020-09-15},
	journal = {Nature Ecology \& Evolution},
	author = {Geary, William L. and Bode, Michael and Doherty, Tim S. and Fulton, Elizabeth A. and Nimmo, Dale G. and Tulloch, Ayesha I. T. and Tulloch, Vivitskaia J. D. and Ritchie, Euan G.},
	month = sep,
	year = {2020},
	note = {Publisher: Nature Publishing Group},
	pages = {1--13},
}

@article{trentman_seasonal_2020,
	title = {Seasonal evaluation of biotic and abiotic factors suggests phosphorus retention in constructed floodplains in three agricultural streams},
	volume = {729},
	issn = {0048-9697},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969720322610},
	doi = {10.1016/j.scitotenv.2020.138744},
	abstract = {Floodplain restoration constructed via the two-stage ditch in agricultural streams has the potential to enhance nutrient retention and prevent the eutrophication of downstream ecosystems. Identifying the role of biotic and abiotic factors influencing soluble reactive phosphorus (SRP) retention in floodplains is of interest given that changing redox conditions associated with floodplain inundation can result in a release of geochemically sorbed SRP to the water column. In three agricultural waterways (Indiana, USA), we conducted seasonal measurements of a suite of biogeochemical pools (total P, bioavailable P and Fe) and processes (SRP flux and microbial respiration) from multiple floodplain transects, along with their adjacent stream sediments, to determine the role of biotic and abiotic processes on floodplain SRP retention or release. Across floodplain soils, organic matter explained a significant amount of variation in soil respiration, and SRP flux from the water column to the floodplain soils was driven by the molar ratio of Fe: P, with values {\textgreater}6 indicating potential SRP sorption due to increased available sorption sites. We developed a mass balance model at a single site to relate seasonal floodplain processes with water column SRP export, above and below the study reach, using measurements in this study combined with data from the literature. Grab sample data suggest that the reach retained 26\% of incoming SRP, which the mass balance model attributed to seasonal synergy between plant assimilation in spring and summer (removing P from floodplain soils) and abiotic P sorption during winter and spring inundation (adding SRP to the floodplain). Retention of SRP was higher in floodplain soils compared to stream sediments based on the modeled SRP budget. Thus, we suggest that these constructed floodplains will maximize SRP retention from the water column if they inundate regularly, have floodplain soils with Fe:P {\textgreater} 3–6, and that promote sustained plant life.},
	language = {en},
	urldate = {2020-09-13},
	journal = {Science of The Total Environment},
	author = {Trentman, Matt T. and Tank, Jennifer L. and Jones, Stuart E. and McMillan, Sara K. and Royer, Todd V.},
	month = aug,
	year = {2020},
	keywords = {Agriculture, Floodplains, Phosphorus, Streams, Two-stage ditch},
	pages = {138744},
}

@article{young_solubility_nodate,
	title = {{THE} {SOLUBILITY} {OF} {GASES} {IN} {LIQUIDS}},
	language = {en},
	author = {Young, C L and Battino, R and Clever, H L},
	pages = {7},
}

@article{zhang_carbon_1995,
	title = {Carbon isotope fractionation during gas-water exchange and dissolution of {CO2}},
	volume = {59},
	issn = {0016-7037},
	url = {http://www.sciencedirect.com/science/article/pii/001670379591550D},
	doi = {10.1016/0016-7037(95)91550-D},
	abstract = {The kinetic and equilibrium fractionation effects for 13C during CO2 gas transfer (εk and εag−g) have been measured in acidified distilled water. The equilibrium fractionation effects between bicarbonate and carbonate and gaseous C02 (εHCO3−g and εCO3−g) have been measured in NaHC03 and NaHC03 + Na2C03 solutions, respectively, from 5° to 25°C. The measured fractionations, except εCO3−g, agreed with earlier work to within 0.2‰. εCO3−g was about 2‰ smaller than most values previously reported. The temperature dependence of the fractionation for 13C between bicarbonate and carbonate and gaseous CO2 was found to be εHCO3−g = −(0.141 ± 0.003)T(°C) + 0.05)‰ and εCO3−g = −(0.052 ± 0.03) T(°C)E+ (7.22 ± 0.46)‰ respectively. The fractionation during gas dissolution was εCO3−g = −0.03)T(°C) + (1.31 ± 0.06\%. and the kinetic effect during gas transfer, εk, was −0.81 ± 0.16‰ at 21°C and −0.95 ± 0.20‰ at 5°C. The equilibrium fractionation between total DIC in seawater and CO2 in air (εDIC−g) was measured and compared with that calculated from the concentration of aqueous CO2, HC03− and CO3= and individual fractionations between the three C species and CO2 gas. The measured and calculated results showed a significant difference of up to 0.2‰. We hypothesize that carbonate ion complexes likely complicate the calculation of εDIC−g from individual C species. We obtain the following empirical function of εDIC−g in seawater vs. temperature and the carbonate fraction (fCO3), εDIC−g = (0.014 ± 0.01) TfCO3 − (0.105 ± 0.002) T + (10.53 ± 0.05)\%., when 0.05 {\textless} fCO3 {\textless} 0.20and5°C{\textless} T {\textless} 25°C},
	language = {en},
	number = {1},
	urldate = {2020-09-09},
	journal = {Geochimica et Cosmochimica Acta},
	author = {Zhang, J. and Quay, P. D. and Wilbur, D. O.},
	month = jan,
	year = {1995},
	pages = {107--114},
}

@article{miyajima_determining_1995,
	title = {Determining the stable isotope ratio of total dissolved inorganic carbon in lake water by {GC}/{C}/{IIRMS}},
	volume = {40},
	issn = {1939-5590},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.1995.40.5.0994},
	doi = {10.4319/lo.1995.40.5.0994},
	abstract = {A simple, precise method for determining the carbon stable isotope ratio of total dissolved inorganic C (ΣCO2) in freshwater samples is described. Water samples are packed in airtight glass bottles of known inner volume (∼70 ml) with no air bubbles. Subsequently, a headspace of 5.0 ml is created inside each bottle with pure helium gas, and each sample is acidified by adding 0.5 ml of a CO2-free, 6.0 N HCl solution. After the original dissolved CO2 has equilibrated with the headspace gas, a portion of this headspace gas is subsampled and injected into the GC/C/IRMS (gas chromatograph/combustion furnace/isotope-ratio mass spectrometer) system to determine the carbon isotope ratio of the CO2. The isotope ratio of CO2 remaining in the liquid phase is calculated by temperature-dependent isotope discrimination between gas and aqueous phases. The isotope ratio of ΣCO2 of the original sample is then derived assuming isotope mass balance. The analytical precision of this method is ±0.1‰. The method enables a single operator to determine the isotopic ratio in at least 60 lake-water samples within 3 d of sampling.},
	language = {en},
	number = {5},
	urldate = {2020-09-09},
	journal = {Limnology and Oceanography},
	author = {Miyajima, Toshihiro and Miyajima, Yoshihiro and Hanba, Yuko T. and Yoshii, Koichi and Koitabashi, Tadatoshi and Wada, Eitaro},
	year = {1995},
	pages = {994--1000},
}

@article{battino_ostwald_1984,
	title = {The {Ostwald} coefficient of gas solubility},
	volume = {15},
	issn = {03783812},
	url = {https://linkinghub.elsevier.com/retrieve/pii/0378381284870090},
	doi = {10.1016/0378-3812(84)87009-0},
	abstract = {Battino, R., 1984. The Ostwald coefficient of gas solubility. Fhdd Phase Equilibria, 15: 231-240.},
	language = {en},
	number = {3},
	urldate = {2020-09-09},
	journal = {Fluid Phase Equilibria},
	author = {Battino, Rubin},
	month = jan,
	year = {1984},
	pages = {231--240},
}

@article{farquhar_carbon_1989,
	title = {Carbon isotope discrimination and photosynthesis},
	volume = {40},
	language = {en},
	journal = {Annual Review of Plant Physiology and Molecular Biology},
	author = {Farquhar, G D and Ehleringer, I J R and Hubick, K T},
	year = {1989},
	pages = {503--537},
}

@article{millero_thermodynamics_1979,
	title = {The thermodynamics of the carbonate system in seawater},
	abstract = {The apparent constants (Ki) for the ionization of carbonic acid in seawater at various salinities (S, Y,,) have been fit to equations of the form In Ki = In K, + AiS”’ + \&S where Ki is the thermodynamic ionization constant in water, Ai and Bi are adjustable parameters. The temperature dependence (TK) of Ki, Ai and Bi were of the form, o0 + 0,/T + as In T. Equations of similar forms have been used to analyze the ionization constants for water and boric acid and the solubility product of calcite in seawater. The effect of pressure on the apparent constants (KY/K?) have been fit to equations of the form In (KY/K:) = -(AVP + 0.5 AK P’)/RT where the volume (AV) and compressibility (AK) changes are polynomial functions of temperature. The equations generated for variousaCids in seawater have been used to examine the carbonate system in seawater. Equations relating the NBS and Tris pH scales have been derived as well as equations of pH as a function of temperature and pressure. The equations from HANSSON(1972, Ph.D. Thesis, University of Goteborg, Sweden) and MEHRBACHet al. (1973, Limnol. Oceanqr. 18, 897-907) have been used to examine the components of the carbonate system. At a fixed total alkalinity and total carbon dioxide, differences of kO.01 m-equiv kg - 1 in HCO; and CO:- were found; however, the [CO,] and Pco, are nearly the same. The con\&bution of borate ion, B(OH); determined from the equations of HANWN (1972, Ph.D. Thesis, University of Giiteborg, Sweden) and LYMAN (1957, Ph.D. Thesis, University of California, Los Ang-eles) differ by kO.01 m-equiv kg-i for waters with the same salinity and temperature.},
	language = {en},
	author = {Millero, Frank J},
	year = {1979},
	pages = {11},
}

@article{carter_predicting_2012,
	title = {Predicting sediment phosphorus release rates using landuse and water-quality data},
	volume = {31},
	issn = {2161-9549},
	url = {https://www.journals.uchicago.edu/doi/10.1899/11-177.1},
	doi = {10.1899/11-177.1},
	abstract = {We developed a series of models using landuse and water-quality variables to predict sediment P release rates under anoxic conditions in reservoirs. We collected sediment cores from 17 reservoirs in the Central Plains region of the USA, and we measured nutrient release rates under anoxic conditions in laboratory incubation studies. We used corresponding landuse and water-quality data from the reservoirs to develop regression models for predicting P release rates. We used variables that relate directly to trophic state, including \% cropland in the watershed, which explained the greatest amount of variation in release rates. P release rates tended to be higher in reservoirs that had greater \% cropland in the watersheds. We developed additional predictive models using surface total P concentrations and Secchi disk depths. Trophic state was also a good predictor of release rates because more P was released from hypereutrophic reservoirs than from mesotrophic or eutrophic reservoirs. The median release rates for reservoirs representing different trophic state classes (e.g., mesotrophic, eutrophic, and hypereutrophic) were very similar to those previously reported for natural lakes. Our models can be used to predict sediment release rates in individual reservoirs of concern or to screen a large number of reservoirs to help direct resources to those systems that are most vulnerable to internal loading. Models based on landuse characteristics are particularly valuable because these data can be obtained from computer-based assessments and do not require labor-intensive field sampling.},
	number = {4},
	urldate = {2020-09-01},
	journal = {Freshwater Science},
	author = {Carter, Lindsey D. and Dzialowski, Andrew R.},
	month = dec,
	year = {2012},
	note = {Publisher: The University of Chicago Press},
	pages = {1214--1222},
}

@article{kendall_distribution_2001,
	title = {Distribution of oxygen-18 and deuterium in river waters across the {United} {States}},
	volume = {15},
	issn = {1099-1085},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1002/hyp.217},
	doi = {10.1002/hyp.217},
	abstract = {Reconstruction of continental palaeoclimate and palaeohydrology is currently hampered by limited information about isotopic patterns in the modern hydrologic cycle. To remedy this situation and to provide baseline data for other isotope hydrology studies, more than 4800, depth- and width-integrated, stream samples from 391 selected sites within the USGS National Stream Quality Accounting Network (NASQAN) and Hydrologic Benchmark Network (HBN) were analysed for δ18O and δ2H (http://water.usgs.gov/pubs/ofr/ofr00-160/pdf/ofr00-160.pdf). Each site was sampled bimonthly or quarterly for 2·5 to 3 years between 1984 and 1987. The ability of this dataset to serve as a proxy for the isotopic composition of modern precipitation in the USA is supported by the excellent agreement between the river dataset and the isotopic compositions of adjacent precipitation monitoring sites, the strong spatial coherence of the distributions of δ18O and δ2H, the good correlations of the isotopic compositions with climatic parameters, and the good agreement between the ‘national’ meteoric water line (MWL) generated from unweighted analyses of samples from the 48 contiguous states of δ2H=8·11δ18O+8·99 (r2=0·98) and the unweighted global MWL of sites from the Global Network for Isotopes in Precipitation (GNIP) of the International Atomic Energy Agency and the World Meteorological Organization (WMO) of δ2H=8·17δ18O+10·35. The national MWL is composed of water samples that arise in diverse local conditions where the local meteoric water lines (LMWLs) usually have much lower slopes. Adjacent sites often have similar LMWLs, allowing the datasets to be combined into regional MWLs. The slopes of regional MWLs probably reflect the humidity of the local air mass, which imparts a distinctive evaporative isotopic signature to rainfall and hence to stream samples. Deuterium excess values range from 6 to 15‰ in the eastern half of the USA, along the northwest coast and on the Colorado Plateau. In the rest of the USA, these values range from −2 to 6‰, with strong spatial correlations with regional aridity. The river samples have successfully integrated the spatial variability in the meteorological cycle and provide the best available dataset on the spatial distributions of δ18O and δ2H values of meteoric waters in the USA. Published in 2001 by John Wiley \& Sons, Ltd.},
	language = {en},
	number = {7},
	urldate = {2020-08-25},
	journal = {Hydrological Processes},
	author = {Kendall, Carol and Coplen, Tyler B.},
	year = {2001},
	keywords = {USA, deuterium, deuterium excess, oxygen-18, rivers, stable isotopes},
	pages = {1363--1393},
}

@article{bowen_spatial_2002,
	title = {Spatial distribution of ␦{18O} in meteoric precipitation},
	abstract = {Proxy data reflecting the oxygen isotope composition of meteoric precipitation (␦18Oppt) are widely used in reconstructions of continental paleoclimate and paleohydrology. However, actual geographic variation in modern water compositions is difficult to estimate from often sparse data. A first step toward understanding the geologic pattern of change in ␦18Oppt is to describe the modern distribution in terms of principal geographic parameters. To this end, we empirically model relationships between 18O in modern precipitation and latitude and altitude. We then identify geographic areas where large-scale vapor transport patterns give rise to significant deviations from model ␦18Oppt compositions based on latitude and altitude. Model value and residual grids are combined to derive a high-resolution global map of ␦18Oppt that can serve as a spatial reference against which proxy data for paleoprecipitation can be compared. Reiteration of the procedure outlined here, for paleo-␦18Oppt data, may illuminate past changes in the climatic and physiographic parameters controlling the distribution of ␦18O regimes.},
	language = {en},
	author = {Bowen, Gabriel J and Wilkinson, Bruce},
	year = {2002},
	pages = {4},
}

@article{beckmann_-line_2009,
	title = {On-line mass spectrometry: membrane inlet sampling},
	volume = {102},
	issn = {0166-8595},
	shorttitle = {On-line mass spectrometry},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847165/},
	doi = {10.1007/s11120-009-9474-7},
	abstract = {Significant insights into plant photosynthesis and respiration have been achieved using membrane inlet mass spectrometry (MIMS) for the analysis of stable isotope distribution of gases. The MIMS approach is based on using a gas permeable membrane to enable the entry of gas molecules into the mass spectrometer source. This is a simple yet durable approach for the analysis of volatile gases, particularly atmospheric gases. The MIMS technique strongly lends itself to the study of reaction flux where isotopic labeling is employed to differentiate two competing processes; i.e., O2 evolution versus O2 uptake reactions from PSII or terminal oxidase/rubisco reactions. Such investigations have been used for in vitro studies of whole leaves and isolated cells. The MIMS approach is also able to follow rates of isotopic exchange, which is useful for obtaining chemical exchange rates. These types of measurements have been employed for oxygen ligand exchange in PSII and to discern reaction rates of the carbonic anhydrase reactions. Recent developments have also engaged MIMS for online isotopic fractionation and for the study of reactions in inorganic systems that are capable of water splitting or H2 generation. The simplicity of the sampling approach coupled to the high sensitivity of modern instrumentation is a reason for the growing applicability of this technique for a range of problems in plant photosynthesis and respiration. This review offers some insights into the sampling approaches and the experiments that have been conducted with MIMS.},
	number = {2-3},
	urldate = {2020-08-21},
	journal = {Photosynthesis Research},
	author = {Beckmann, Katrin and Messinger, Johannes and Badger, Murray Ronald and Wydrzynski, Tom and Hillier, Warwick},
	month = dec,
	year = {2009},
	pmid = {19653116},
	pmcid = {PMC2847165},
	pages = {511--522},
}

@article{botter_depth_2020,
	title = {Depth of {Solute} {Generation} {Is} a {Dominant} {Control} on {Concentration}-{Discharge} {Relations}},
	volume = {56},
	copyright = {©2020. American Geophysical Union. All Rights Reserved.},
	issn = {1944-7973},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2019WR026695},
	doi = {10.1029/2019WR026695},
	abstract = {Solutes in rivers often come from multiple sources, notably precipitation (above) and generation from the subsurface (below). The question of which source is more influential in shaping the dynamics of solute concentration cannot be easily addressed due to the general lack of input data. An analysis of solute concentrations and their dependence on discharge across 585 catchments in nine countries leads us to hypothesize that both the timing and the vertical distribution of the solute generation are important drivers of solute export dynamics at the catchment scale. We test this hypothesis running synthetic experiments with a tracer-aided distributed hydrological model. The results reveal that the depth of solute generation is the most important control of the concentration-discharge (C-Q) relation for a number of solutes. Such relation shows that C-Q patterns of solute export vary from dilution (Ca2+, Mg2+, K+, Na+, and Cl−) to weakly enriching (dissolved organic carbon). The timing of the input imposes a signature on temporal dynamics, most evident for nutrients, and adds uncertainty in the exponent of the C-Q relation.},
	language = {en},
	number = {8},
	urldate = {2020-08-21},
	journal = {Water Resources Research},
	author = {Botter, M. and Li, L. and Hartmann, J. and Burlando, P. and Fatichi, S.},
	year = {2020},
	keywords = {C-Q relations, catchment transport processes, solute export dynamics, solute input},
	pages = {e2019WR026695},
}

@article{kroopnick_atmospheric_1972,
	title = {Atmospheric {Oxygen}: {Isotopic} {Composition} and {Solubility} {Fractionation}},
	volume = {175},
	issn = {0036-8075},
	shorttitle = {Atmospheric {Oxygen}},
	url = {https://www.jstor.org/stable/1733235},
	abstract = {Atmospheric oxygen has been found to be enriched in oxygen-18 by 23.5 ± 0.3 per mil relative to average ocean water (SMOW). Oxygen dissolved in seawater is further enriched in oxygen-18 by 0.85 per mil at 0 ° C. The temperature dependence of the solubility enrichment is given by ε (per mil) = 0.85- 0.010 t (° C). This result is in good agreement with earlier measurements of the solubility effect in distilled water.},
	number = {4017},
	urldate = {2020-08-20},
	journal = {Science},
	author = {Kroopnick, P. and Craig, H.},
	year = {1972},
	note = {Publisher: American Association for the Advancement of Science},
	pages = {54--55},
}

@article{venkiteswaran_dynamics_2007,
	title = {Dynamics of {Dissolved} {Oxygen} {Isotopic} {Ratios}: {A} {Transient} {Model} to {Quantify} {Primary} {Production}, {Community} {Respiration}, and {Air}-{Water} {Exchange} in {Aquatic} {Ecosystems}},
	volume = {153},
	issn = {0029-8549},
	shorttitle = {Dynamics of {Dissolved} {Oxygen} {Isotopic} {Ratios}},
	url = {https://www.jstor.org/stable/40210874},
	abstract = {Dissolved O₂ is an important aquatic ecosystem health indicator. Metabolic and gas exchange (G) rates, which control O₂ concentration, are affected by nutrient loading and other environmental factors. Traditionally, aquatic metabolism has been reported as primary production:community respiration (P:R) ratios using diel measurements and interpretations of dissolved O₂ and/or CO₂ concentrations, and recently using stable isotopes \$({\textbackslash}delta {\textasciicircum}\{18\} O,{\textbackslash},{\textbackslash}Delta {\textasciicircum}\{17\} O)\$ and steady state assumptions. Aquatic ecosystems, such as rivers and ponds, are not at steady state and exhibit diel changes, so steady state approaches are often inappropriate. A dynamic O₂ stable isotope model (photosynthesis-respiration-gas exchange; PoRGy) is presented here, requiring a minimum of parameters to quantify daily averaged P, R, and G rates under transient field conditions. Unlike steady state approaches, PoRGy can address scenarios with 100\% O₂ saturation but with \${\textbackslash}delta {\textasciicircum}\{18\} O - O\_2\$ values that are not at air equilibrium. PoRGy successfully accounts for isotopic G when applied to an oxygen isotope equilibration laboratory experiment. PoRGy model results closely matched the diel O₂ and \${\textbackslash}delta {\textasciicircum}\{18\} O - O\_2\$ data from three field sites with different P:R:G ratios and various P, R and G rates. PoRGy provides a new research tool to assess ecosystem health and to pose environmental impact-driven questions. Using daily averaged rates was successful and thus they can be used to compare ecosystems across seasons and landscapes.},
	number = {2},
	urldate = {2020-08-20},
	journal = {Oecologia},
	author = {Venkiteswaran, Jason J. and Wassenaar, Leonard I. and Schiff, Sherry L.},
	year = {2007},
	note = {Publisher: Springer},
	pages = {385--398},
}

@article{benson_concentration_1984,
	title = {The concentration and isotopic fractionation of oxygen dissolved in freshwater and seawater in equilibrium with the atmosphere1},
	volume = {29},
	issn = {1939-5590},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.1984.29.3.0620},
	doi = {10.4319/lo.1984.29.3.0620},
	abstract = {Previous work on the solubility of oxygen in freshwater has been extended to seawater. Measurements of the Henry coefficient in the ranges 0° {\textless} t {\textless} 45°C and 0{\textless} S {\textless} 50 fit the Setschenow relationship for the variation with salinity. The temperature dependence of the Setschenow coefficient for oxygen is found to be K = 0.0225034 ‒ 13.6083/T + 2,565.68/T2. The equation for the Henry coefficient as a function of temperature and salinity is used to calculate values for unit standard atmospheric concentrations (USAC) in freshwater and seawater in equilibrium with air at a total pressure of 1 atmosphere. It is estimated that the possible error in the new USAC values is no greater than ±0.1\% and probably less. Tables and equations are presented for obtaining accurate USAC values in the ranges 0° {\textless} t {\textless} 40°C and 0 {\textless} S {\textless} 40. Simple procedures are given for calculating standard atmospheric concentrations at pressures different from 1 atm. The presence of sea salt has a negligible effect on the fractionation of the oxygen isotopes during solution.},
	language = {en},
	number = {3},
	urldate = {2020-08-20},
	journal = {Limnology and Oceanography},
	author = {Benson, Bruce B. and Krause, Daniel},
	year = {1984},
	pages = {620--632},
}

@article{nkoue_ndondo_stable_2020,
	title = {Stable {Carbon} {Isotopes} δ{13C} as a {Proxy} for {Characterizing} {Carbon} {Sources} and {Processes} in a {Small} {Tropical} {Headwater} {Catchment}: {Nsimi}, {Cameroon}},
	issn = {1573-1421},
	shorttitle = {Stable {Carbon} {Isotopes} δ{13C} as a {Proxy} for {Characterizing} {Carbon} {Sources} and {Processes} in a {Small} {Tropical} {Headwater} {Catchment}},
	url = {10.1007/s10498-020-09386-8},
	doi = {10.1007/s10498-020-09386-8},
	abstract = {Stream carbon fluxes are one of the major components in the global C cycle, yet the discrimination of the various sources of stream carbon remains to a large extent unclear and less is known about the biogeochemical transformations that accompany the transfer of C from soils to streams. Here, we used patterns in stream water and groundwater δ13C values in a small forested tropical headwater catchment to investigate the source and contribution from the soil carbon pools to stream organic and inorganic carbon behavior over seasonal scales. Stream organic carbon (DOC and POC) comes mainly from the upper rich soil organic carbon horizons and derived from total organic carbon (TOC) of biogenic source. The isotopic compositions δ13CTOC, δ13CDOC and δ13CPOC of these carbon species were very close (− 30‰ to − 26‰) and typical of the forested C3 vegetation. The relationship observed between DOC and log pCO2 and δ13CDIC indicated that besides the considerable CO2 evasion that occurs as DIC is transported from soils to streams, there were also other processes affecting the stream DIC pool. In-stream mineralization of DOC and mixing of atmospheric carbon had a significant influence on the δ13CDIC values. These processes which varied seasonally with hydrological changes represent the main control on DOC and DIC cycling in the wet tropical milieu. The rapid turnover of carbon on hillside soils, the transformation of TOC to DOC in wetland soils and further mineralization of stream DOC to DIC favor the evasion of C, making the zone a source of carbon to the atmosphere.},
	language = {en},
	urldate = {2020-08-20},
	journal = {Aquatic Geochemistry},
	author = {Nkoue Ndondo, Gustave Raoul and Probst, J.-L. and Ndjama, J. and Ndam Ngoupayou, Jules Remy and Boeglin, J.-L. and Takem, G. E. and Brunet, F. and Mortatti, J. and Gauthier-Lafaye, F. and Braun, J.-J. and Ekodeck, G. E.},
	month = jul,
	year = {2020},
}

@article{duvert_co_2018,
	title = {{CO} 2 evasion along streams driven by groundwater inputs and geomorphic controls},
	volume = {11},
	copyright = {2018 CROWN},
	issn = {1752-0908},
	url = {https://www.nature.com/articles/s41561-018-0245-y},
	doi = {10.1038/s41561-018-0245-y},
	abstract = {Headwaters are hotspots of carbon dioxide (CO2) evasion from rivers. While emerging evidence suggests that groundwater contributes disproportionately to CO2 in headwater streams, the processes of CO2 delivery to streams and subsequent evasion to the atmosphere remain largely unknown. Here we show the variability of CO2 input and evasion fluxes based on coupled measurements of dissolved CO2 along streams and in adjacent groundwater from two headwater catchments of the tropical and temperate zones. We find that the processes can be highly localized in both space and time. Spatially, they are significantly influenced by heterogeneities in the subsurface and stream landscape; temporally, they predominately occur during the transient activation of connected subsurface water flows. We highlight sharp increases and decreases in the stream CO2 flux, and suggest that current models fail to capture the true magnitude of CO2 evasion. The high spatial and temporal variability of CO2 input from groundwater and evasion to the atmosphere makes accurate assessment of CO2 evasion fluxes difficult, and will require a collaborative effort by catchment hydrologists and aquatic ecologists to fully understand the contribution of groundwater to stream CO2 emissions.},
	language = {en},
	number = {11},
	urldate = {2020-08-20},
	journal = {Nature Geoscience},
	author = {Duvert, Clément and Butman, David E. and Marx, Anne and Ribolzi, Olivier and Hutley, Lindsay B.},
	month = nov,
	year = {2018},
	note = {Number: 11
Publisher: Nature Publishing Group},
	pages = {813--818},
}

@article{peeters_lake_2016,
	title = {Lake {Metabolism}: {Comparison} of {Lake} {Metabolic} {Rates} {Estimated} from a {Diel} {CO2}- and the {Common} {Diel} {O2}-{Technique}},
	volume = {11},
	issn = {1932-6203},
	shorttitle = {Lake {Metabolism}},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0168393},
	doi = {10.1371/journal.pone.0168393},
	abstract = {Lake metabolism is a key factor for the understanding of turnover of energy and of organic and inorganic matter in lake ecosystems. Long-term time series on metabolic rates are commonly estimated from diel changes in dissolved oxygen. Here we present long-term data on metabolic rates based on diel changes in total dissolved inorganic carbon (DIC) utilizing an open-water diel CO2-technique. Metabolic rates estimated with this technique and the traditional diel O2-technique agree well in alkaline Lake Illmensee (pH of {\textasciitilde}8.5), although the diel changes in molar CO2 concentrations are much smaller than those of the molar O2 concentrations. The open-water diel CO2- and diel O2-techniques provide independent measures of lake metabolic rates that differ in their sensitivity to transport processes. Hence, the combination of both techniques can help to constrain uncertainties arising from assumptions on vertical fluxes due to gas exchange and turbulent diffusion. This is particularly important for estimates of lake respiration rates because these are much more sensitive to assumptions on gradients in vertical fluxes of O2 or DIC than estimates of lake gross primary production. Our data suggest that it can be advantageous to estimate respiration rates assuming negligible gradients in vertical fluxes rather than including gas exchange with the atmosphere but neglecting vertical mixing in the water column. During two months in summer the average lake net production was close to zero suggesting at most slightly autotrophic conditions. However, the lake emitted O2 and CO2 during the entire time period suggesting that O2 and CO2 emissions from lakes can be decoupled from the metabolism in the near surface layer.},
	language = {en},
	number = {12},
	urldate = {2020-08-14},
	journal = {PLOS ONE},
	author = {Peeters, Frank and Atamanchuk, Dariia and Tengberg, Anders and Encinas-Fernández, Jorge and Hofmann, Hilmar},
	month = dec,
	year = {2016},
	note = {Publisher: Public Library of Science},
	keywords = {Atmospheric layers, Carbon dioxide, Carbonates, Dissolved oxygen, Lakes, Metabolic processes, Respiration, Surface water},
	pages = {e0168393},
}

@article{williams_comparison_1983,
	title = {Comparison of 14 {C} and {O} 2 measurements of phytoplankton production in oligotrophic waters},
	volume = {305},
	copyright = {1983 Nature Publishing Group},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/305049a0},
	doi = {10.1038/305049a0},
	abstract = {Present day estimates of primary phytoplankton production are derived almost exclusively from the results of a single method, the 14C technique. 14C methodology is amenable to routine measurement and also has the requisite sensitivity for the large expanses of ocean characterized by low autotrophic biomass. However, there is still great uncertainty as to its ecological interpretations; for example, whether it is measuring net or gross primary production. We report here the first comparison of planktonic photosynthesis based on 14C assimilation with measurements of oxygen flux for an oligotrophic environment of ocean character. We conclude from the results that there is no evidence of persistent errors of any size, unique to the 14C technique, in the measurement of gross production. We also infer, from a consideration of the rates themselves, that in vitro methodology is not biased with respect to in situ photosynthesis.},
	language = {en},
	number = {5929},
	urldate = {2020-08-14},
	journal = {Nature},
	author = {Williams, P. J. le B. and Heinemann, K. R. and Marra, J. and Purdie, D. A.},
	month = sep,
	year = {1983},
	note = {Number: 5929
Publisher: Nature Publishing Group},
	pages = {49--50},
}

@article{williams_overall_1991,
	title = {Overall planktonic oxygen and carbon dioxide metabolisms: the problem of reconciling observations and calculations of photosynthetic quotients},
	volume = {13},
	issn = {0142-7873},
	shorttitle = {Overall planktonic oxygen and carbon dioxide metabolisms},
	url = {https://academic.oup.com/plankt/article/13/supp1/153/1406071},
	doi = {10.1093/oxfordjournals.plankt.a042366},
	abstract = {Abstract.  Although the photosynthetic quotient (P0) of micro-algae in culture has been studied and characterized, that for natural plankton is poorly understoo},
	language = {en},
	number = {supp1},
	urldate = {2020-08-14},
	journal = {Journal of Plankton Research},
	author = {Williams, P. J. IeB and Robertson, J. E.},
	month = jan,
	year = {1991},
	note = {Publisher: Oxford Academic},
	pages = {153--169},
}

@article{ostrom_evaluation_2005,
	title = {Evaluation of primary production in {Lake} {Erie} by multiple proxies},
	volume = {144},
	issn = {0029-8549, 1432-1939},
	url = {http://link.springer.com/10.1007/s00442-005-0032-5},
	doi = {10.1007/s00442-005-0032-5},
	language = {en},
	number = {1},
	urldate = {2020-08-14},
	journal = {Oecologia},
	author = {Ostrom, Nathaniel E. and Carrick, Hunter J. and Twiss, Michael R. and Piwinski, Leah},
	month = jun,
	year = {2005},
	pages = {115--124},
}

@article{berggren_magnitude_2012,
	title = {Magnitude and regulation of bacterioplankton respiratory quotient across freshwater environmental gradients},
	volume = {6},
	copyright = {2012 International Society for Microbial Ecology},
	issn = {1751-7370},
	url = {https://www.nature.com/articles/ismej2011157},
	doi = {10.1038/ismej.2011.157},
	abstract = {Bacterioplankton respiration (BR) may represent the largest single sink of organic carbon in the biosphere and constitutes an important driver of atmospheric carbon dioxide (CO2) emissions from freshwaters. Complete understanding of BR is precluded by the fact that most studies need to assume a respiratory quotient (RQ; mole of CO2 produced per mole of O2 consumed) to calculate rates of BR. Many studies have, without clear support, assumed a fixed RQ around 1. Here we present 72 direct measurements of bacterioplankton RQ that we carried out in epilimnetic samples of 52 freshwater sites in Québec (Canada), using O2 and CO2 optic sensors. The RQs tended to converge around 1.2, but showed large variability (s.d.=0.45) and significant correlations with major gradients of ecosystem-level, substrate-level and bacterial community-level characteristics. Experiments with natural bacterioplankton using different single substrates suggested that RQ is intimately linked to the elemental composition of the respired compounds. RQs were on average low in net autotrophic systems, where bacteria likely were utilizing mainly reduced substrates, whereas we found evidence that the dominance of highly oxidized substrates, for example, organic acids formed by photo-chemical processes, led to high RQ in the more heterotrophic systems. Further, we suggest that BR contributes to a substantially larger share of freshwater CO2 emissions than presently believed based on the assumption that RQ is ∼1. Our study demonstrates that bacterioplankton RQ is not only a practical aspect of BR determination, but also a major ecosystem state variable that provides unique information about aquatic ecosystem functioning.},
	language = {en},
	number = {5},
	urldate = {2020-08-14},
	journal = {The ISME Journal},
	author = {Berggren, Martin and Lapierre, Jean-François and del Giorgio, Paul A.},
	month = may,
	year = {2012},
	note = {Number: 5
Publisher: Nature Publishing Group},
	pages = {984--993},
}

@article{stewart_physiological_2008,
	title = {Physiological heterogeneity in biofilms},
	volume = {6},
	copyright = {2008 Nature Publishing Group},
	issn = {1740-1534},
	url = {https://www.nature.com/articles/nrmicro1838},
	doi = {10.1038/nrmicro1838},
	abstract = {Bacterial cells growing in biofilms are physiologically distinct from free-swimming planktonic cells. For example, differences have been shown in motility, polysaccharide production, antibiotic tolerance and global proteomic and transcriptomic profiles.Bacterial cells within biofilms can also be physiologically distinct from adjacent cells on a micrometre scale.Chemical heterogeneities are established in biofilms primarily owing to bacterial metabolic activity and solute diffusion. Chemical gradients of oxygen, nutrients, bacterial waste products and bacterial signalling compounds can therefore be established, thereby generating unique environmental conditions for the cells.Bacterial adaptation to chemical gradients in biofilms includes differences in gene expression and protein production. Also relevant are mutation and selection for the fittest organisms in a particular microenvironment, as well as the response that is due to stochastic gene expression.Techniques for characterizing gene expression and physiological activities have been applied to bacterial biofilms to characterize the local activity of cells within biofilms. Examples that used these techniques are discussed, including the advantages and disadvantages of using particular techniques to characterize subsets of cells from within biofilms.},
	language = {en},
	number = {3},
	urldate = {2020-08-14},
	journal = {Nature Reviews Microbiology},
	author = {Stewart, Philip S. and Franklin, Michael J.},
	month = mar,
	year = {2008},
	note = {Number: 3
Publisher: Nature Publishing Group},
	pages = {199--210},
}

@article{wagner_high_2017,
	title = {High light intensity mediates a shift from allochthonous to autochthonous carbon use in phototrophic stream biofilms},
	volume = {122},
	copyright = {©2017. American Geophysical Union. All Rights Reserved.},
	issn = {2169-8961},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2016JG003727},
	doi = {10.1002/2016JG003727},
	abstract = {Changes in the riparian vegetation along stream channels, diurnal light availability, and longitudinal fluctuations in the local light regime in streams influence primary production and carbon (C) cycling in benthic stream biofilms. To investigate the influence of light availability on the uptake dynamics of autochthonous and allochthonous dissolved organic carbon (DOC) in benthic biofilms, we experimentally added 13C-labeled allochthonous DOC to biofilms grown under light intensities ranging from 5 to 152 μmol photons m−2 s−1. We calculated the net C flux, which showed that benthic biofilms released autochthonous DOC across the entire light gradient. Light availability and diurnal light patterns influenced C uptake by benthic biofilms. More allochthonous DOC was respired under low light availability and at night, whereas under high light availability and during the day mainly autochthonous C was respired by the benthic biofilm community. Furthermore, phenol oxidase activity (indicative of allochthonous DOC uptake) was more elevated under low light availability, whereas beta-glucosidase activity (indicative of autochthonous DOC use) increased with light intensity. Collectively, our results suggest that biofilms exposed to high light inputs preferentially used autochthonous DOC, whereas biofilms incubated at attenuated levels showed greater use of allochthonous DOC. This has implications for the spatial dynamics of DOC uptake in streams and speaks against the occurrence of priming effects in algal-dominated stream biofilms.},
	language = {en},
	number = {7},
	urldate = {2020-08-14},
	journal = {Journal of Geophysical Research: Biogeosciences},
	author = {Wagner, Karoline and Bengtsson, Mia M. and Findlay, Robert H. and Battin, Tom J. and Ulseth, Amber J.},
	year = {2017},
	keywords = {allochthonous, autochthonous, benthic biofilms, dissolved organic carbon, light, δ13carbon},
	pages = {1806--1820},
}

@article{bester_metabolic_2010,
	title = {Metabolic {Differentiation} in {Biofilms} as {Indicated} by {Carbon} {Dioxide} {Production} {Rates}},
	volume = {76},
	issn = {0099-2240},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2820951/},
	doi = {10.1128/AEM.01719-09},
	abstract = {The measurement of carbon dioxide production rates as an indication of metabolic activity was applied to study biofilm development and response of Pseudomonas sp. biofilms to an environmental disturbance in the form of a moving air-liquid interface (i.e., shear). A differential response in biofilm cohesiveness was observed after bubble perturbation, and the biofilm layers were operationally defined as either shear-susceptible or non-shear-susceptible. Confocal laser scanning microscopy and image analysis showed a significant reduction in biofilm thickness and biomass after the removal of the shear-susceptible biofilm layer, as well as notable changes in the roughness coefficient and surface-to-biovolume ratio. These changes were accompanied by a 72\% reduction of whole-biofilm CO2 production; however, the non-shear-susceptible region of the biofilm responded rapidly after the removal of the overlying cells and extracellular polymeric substances (EPS) along with the associated changes in nutrient and O2 flux, with CO2 production rates returning to preperturbation levels within 24 h. The adaptable nature and the ability of bacteria to respond to environmental conditions were further demonstrated by the outer shear-susceptible region of the biofilm; the average CO2 production rate of cells from this region increased within 0.25 h from 9.45 ± 5.40 fmol of CO2·cell−1·h−1 to 22.6 ± 7.58 fmol of CO2·cell−1·h−1 when cells were removed from the biofilm and maintained in suspension without an additional nutrient supply. These results also demonstrate the need for sufficient monitoring of biofilm recovery at the solid substratum if mechanical methods are used for biofouling control.},
	number = {4},
	urldate = {2020-08-14},
	journal = {Applied and Environmental Microbiology},
	author = {Bester, Elanna and Kroukamp, Otini and Wolfaardt, Gideon M. and Boonzaaier, Leandro and Liss, Steven N.},
	month = feb,
	year = {2010},
	pmid = {20023078},
	pmcid = {PMC2820951},
	pages = {1189--1197},
}

@article{kroukamp_co2_2009,
	title = {{CO2} {Production} as an {Indicator} of {Biofilm} {Metabolism}},
	volume = {75},
	copyright = {Copyright © 2009 American Society for Microbiology},
	issn = {0099-2240, 1098-5336},
	url = {https://aem.asm.org/content/75/13/4391},
	doi = {10.1128/AEM.01567-08},
	abstract = {Biofilms are important in aquatic nutrient cycling and microbial proliferation. In these structures, nutrients like carbon are channeled into the production of extracellular polymeric substances or cell division; both are vital for microbial survival and propagation. The aim of this study was to assess carbon channeling into cellular or noncellular fractions in biofilms. Growing in tubular reactors, biofilms of our model strain Pseudomonas sp. strain CT07 produced cells to the planktonic phase from the early stages of biofilm development, reaching pseudo steady state with a consistent yield of ∼107 cells·cm−2·h−1 within 72 h. Total direct counts and image analysis showed that most of the converted carbon occurred in the noncellular fraction, with the released and sessile cells accounting for {\textless}10\% and {\textless}2\% of inflowing carbon, respectively. A CO2 evolution measurement system (CEMS) that monitored CO2 in the gas phase was developed to perform a complete carbon balance across the biofilm. The measurement system was able to determine whole-biofilm CO2 production rates in real time and showed that gaseous CO2 production accounted for 25\% of inflowing carbon. In addition, the CEMS made it possible to measure biofilm response to changing environmental conditions; changes in temperature or inflowing carbon concentration were followed by a rapid response in biofilm metabolism and the establishment of new steady-state conditions.},
	language = {en},
	number = {13},
	urldate = {2020-08-14},
	journal = {Applied and Environmental Microbiology},
	author = {Kroukamp, Otini and Wolfaardt, Gideon M.},
	month = jul,
	year = {2009},
	pmid = {19346353},
	note = {Publisher: American Society for Microbiology
Section: PHYSIOLOGY},
	pages = {4391--4397},
}

@article{weiss_carbon_1974,
	title = {Carbon dioxide in water and seawater: the solubility of a non-ideal gas},
	volume = {2},
	issn = {0304-4203},
	shorttitle = {Carbon dioxide in water and seawater},
	url = {http://www.sciencedirect.com/science/article/pii/0304420374900152},
	doi = {10.1016/0304-4203(74)90015-2},
	abstract = {New measurements of the solubility of carbon dioxide in water and seawater confirm the accuracy of the measurements of Murray and Riley, as opposed to those of Li and Tsui. Corrections for non-ideal behavior in the gas phase and for dissociation in distilled water are required to calculate solubility coefficients from these sets of data. Equations for the solubilities of real gases are presented and discussed. Solubility coefficients for carbon dioxide in water and seawater are calculated for the data of Murray and Riley, and are fitted to equations in temperature and salinity of the form used previously to fit the solubilities of other gases.},
	language = {en},
	number = {3},
	urldate = {2020-07-31},
	journal = {Marine Chemistry},
	author = {Weiss, R. F.},
	month = nov,
	year = {1974},
	pages = {203--215},
}

@article{weyhenmeyer_water_2008,
	title = {Water chemical changes along a latitudinal gradient in relation to climate and atmospheric deposition},
	volume = {88},
	issn = {1573-1480},
	url = {10.1007/s10584-007-9331-7},
	doi = {10.1007/s10584-007-9331-7},
	abstract = {Evaluating trends over time (nonparametric Mann–Kendall test) for 18 water chemical variables from 79 reference lakes, distributed all over Sweden, during spring since 1984 showed most significant trends for atmospheric deposition driven sulfate (SO4) concentrations. The decrease in SO4 concentrations was on average 2.7 times higher at lower (56°N to 59°N) than at higher latitudes (60°N to 68°N). This large difference in the rate of change between lower and higher latitudes could not solely be explained by atmospheric deposition as the rates of change in SO4 wet deposition differed by a factor of only 1.5 between lower and higher latitudes. Significantly higher rates of change at lower than at higher latitudes are known from the timing of lake ice breakup, a typical climate change indicator. The rates of change in the timing of lake ice breakup differed by a factor of 2.3 between lower and higher latitudes. Other water chemical variables showing significantly higher rates of change at lower than at higher latitudes were water color (a factor of 3.5), calcium (a factor of 2.9), magnesium (a factor of 5.5) and conductivity (a factor of 5.9). The rates of change of all these variables were strongly related to the rates of change in the timing of lake ice breakup along a latitudinal gradient (R2 = 0.41–0.78, p {\textless} 0.05), suggesting that climatic changes can accelerate atmospheric driven changes at especially lower latitudes. This acceleration will result in more heterogeneous lake ecosystems along a latitudinal gradient.},
	language = {en},
	number = {2},
	urldate = {2020-07-31},
	journal = {Climatic Change},
	author = {Weyhenmeyer, Gesa A.},
	month = may,
	year = {2008},
	pages = {199--208},
}

@article{isles_recent_2018,
	title = {Recent {Synchronous} {Declines} in {DIN}:{TP} in {Swedish} {Lakes}},
	volume = {32},
	copyright = {©2018. American Geophysical Union. All Rights Reserved.},
	issn = {1944-9224},
	shorttitle = {Recent {Synchronous} {Declines} in {DIN}},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2017GB005722},
	doi = {10.1002/2017GB005722},
	abstract = {Declining atmospheric nitrogen (N) deposition in northern Europe and parts of North America, coupled with ongoing changes in climate, has the potential to alter the nutrient limitation status of freshwater ecosystems. In this study we compared time series data of atmospheric N deposition, air temperature, and precipitation with corresponding estimates of dissolved inorganic nitrogen (DIN), total phosphorus (TP), DIN:TP, and total organic carbon from 78 headwater streams and 95 nutrient-poor lakes in Sweden from 1998 to 2013 to assess trends in, and potential drivers of, lake N:P ratios. We found that trends in nutrients were variable at the scale of individual lakes but were highly synchronous at the regional scale, suggesting underlying control by broad-scale environmental drivers mediated by site-specific characteristics. Widespread declines in lake DIN throughout Sweden were correlated with declines in atmospheric N deposition, particularly in northern areas. TP did not have strong directional trends, but interannual variability was synchronous at regional scales, implying that broad-scale climate drivers were affecting these trends. Overall, we observed a significant decline in DIN:TP throughout Sweden over the monitoring period. At the beginning of the study period, 32\% of lakes were N limited and 45\% colimited by N and P. Proportions increased to 63\% of lakes N limited and 20\% colimited by N and P at the end of the study period. These results suggest that N limitation is likely to become more widespread in subarctic and boreal areas of Europe in the future if recent trends continue.},
	language = {en},
	number = {2},
	urldate = {2020-07-31},
	journal = {Global Biogeochemical Cycles},
	author = {Isles, Peter D. F. and Creed, Irena F. and Bergström, Ann-Kristin},
	year = {2018},
	keywords = {DIN:TP, boreal lakes, nitrogen deposition, nitrogen limitation},
	pages = {208--225},
}

@article{siebers_diel_2020,
	title = {Diel cycles of δ{13CDIC} and ecosystem metabolism in ephemeral dryland streams},
	volume = {82},
	issn = {1420-9055},
	url = {10.1007/s00027-020-0708-2},
	doi = {10.1007/s00027-020-0708-2},
	abstract = {Streams in hot, arid environments often exist as a series of isolated pools along main channels. During these periods, shallow alluvial through flow may strongly influence key ecological processes within pools. We measured diel changes in δ13C values of dissolved inorganic carbon (DIC) and dissolved oxygen (DO) in two pools of ephemeral, dryland streams. We quantified alluvial water connectivity through stable isotope analysis (δ18O and δ2H) of pool and alluvial water. We also estimated gross primary productivity (GPP) and ecosystem respiration (ER) rates across a wider set of pools in both streams. δ13CDIC values displayed regular diel cycles, where both pools displayed small but similar daily amplitude (0.7–0.9‰) despite contrasting amplitudes of change in DO (0.8 mg L−1 vs. 2.8 mg L−1) and contrasting alluvial water connectivity (connected vs. disconnected). Water temperature was the strongest predictor of both δ13CDIC values and rates of change in δ13CDIC across both pools. Across both streams, all pools were net heterotrophic. GPP (0.35–1.73 g O2 m−2 d−1) and ER (0.49–2.64 g O2 m−2 d−1) rates were linked to aquatic vegetation cover. The disconnect between diurnal amplitudes of δ13C values and DO concentrations thus suggests that ecological drivers of gas exchange became increasingly localised as pools contracted.},
	language = {en},
	number = {2},
	urldate = {2020-07-31},
	journal = {Aquatic Sciences},
	author = {Siebers, Andre R. and Pettit, Neil E. and Skrzypek, Grzegorz and Dogramaci, Shawan and Grierson, Pauline F.},
	month = feb,
	year = {2020},
	pages = {32},
}

@article{walter_temporal_2020,
	title = {Temporal {Coherence} {Between} {Lake} and {Landscape} {Primary} {Productivity}},
	issn = {1432-9840},
	url = {https://link.springer.com/epdf/10.1007/s10021-020-00531-6},
	doi = {10.1007/s10021-020-00531-6},
	abstract = {Understanding the patterns and drivers of primary productivity is a major goal of ecology, but little is known about whether the primary productivities of different types of ecosystems—here, lakes and the landscapes in which they are embedded—fluctuate in related ways through time. Due to shared climatic variation and well-known connections between lake and terrestrial ecosystems, such as nutrient and resource subsidies, we hypothesized that interannual fluctuations in aquatic and terrestrial primary productivity indices could be coherent. We also expected that lake and watershed characteristics could modify the strength and nature of primary productivity relationships. We applied wavelet coherence analyses to time series of lake chlorophyll-a and satellite-derived NDVI to examine coherence between lakes and land, and used random forest regression and generalized additive models to evaluate why coherence varies among lakes. There can be substantial coherence between lake and terrestrial primary productivity, but the strength and phase (direction and time lag) of this relationship vary widely, and there were marked differences between short (2–4-year periods of oscillation) and long ({\textgreater} 4-year periods of oscillation) timescales. Across all timescales, variables associated with the connectedness of lakes to their watersheds were consistently the important explanatory variables of the strength and phase of coherence. The patterns observed in this study suggest the importance of cross-ecosystem flows, as opposed to shared climatic variation, in determining temporal coherence between lakes and the landscape.},
	language = {en},
	urldate = {2020-07-27},
	journal = {Ecosystems},
	author = {Walter, Jonathan A. and Fleck, Rachel and Kastens, Jude H. and Pace, Michael L. and Wilkinson, Grace M.},
	year = {2020},
}

@article{alexander_how_2020,
	title = {How does climate variability affect water quality dynamics in {Canada}'s oil sands region?},
	volume = {732},
	issn = {0048-9697},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969720325791},
	doi = {10.1016/j.scitotenv.2020.139062},
	abstract = {In Canada's oil sands region, classic boreal hydrology (i.e., winter low flow followed by peaks during spring freshet and then summer flow recession) combined with erosion of both natural and anthropogenically-exposed bitumen results in seasonal and inter-annual variability in stream water chemistry. Using data collected from all seasons over three years (2012–2015), we investigated the mechanisms driving spatial and temporal change in the concentration of 26 water quality parameters for six rivers draining Canada's oil sands region. Mantel tests showed a strong spatial aggregation of climatic drivers (average daily precipitation, accumulated precipitation, snow water equivalent) associated with west versus east discharge patterns. Wavelet analysis highlighted unique watershed attributes, in particular the importance of developed area in lowering responsiveness to seasonal precipitation. Concentrations of most chemical parameters (20 of 23) showed distinct temporal patterns that were correlated with seasonal changes in hydrology which, in turn, were related to changes in weather. Comparison of concentrations observed in this study with those reported in the scientific literature for the same watersheds showed 81\% of comparisons differed significantly. This was likely due to the short duration of previous field campaigns and thus the sampling of a very narrow window of the annual streamflow regime.},
	language = {en},
	urldate = {2020-07-22},
	journal = {Science of The Total Environment},
	author = {Alexander, A. C. and Levenstein, B. and Sanderson, L. A. and Blukacz-Richards, E. A. and Chambers, P. A.},
	month = aug,
	year = {2020},
	keywords = {Climate, Oil sands, Rivers, Seasonal precipitation, Water quality monitoring, Wavelet cycles},
	pages = {139062},
}

@article{mulholland_inter-biome_2001,
	title = {Inter-biome comparison of factors controlling stream metabolism},
	volume = {46},
	issn = {1365-2427},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-2427.2001.00773.x},
	doi = {10.1046/j.1365-2427.2001.00773.x},
	abstract = {1. We studied whole-ecosystem metabolism in eight streams from several biomes in North America to identify controls on the rate of stream metabolism over a large geographic range. The streams studied had climates ranging from tropical to cool-temperate and from humid to arid and were all relatively uninfluenced by human disturbances. 2. Rates of gross primary production (GPP), ecosystem respiration (R) and net ecosystem production (NEP) were determined using the open-system, two-station diurnal oxygen change method. 3. Three general patterns in metabolism were evident among streams: (1) relatively high GPP with positive NEP (i.e. net oxygen production) in early afternoon, (2) moderate primary production with a distinct peak in GPP during daylight but negative NEP at all times and (3) little or no evidence of GPP during daylight and a relatively constant and negative NEP over the entire day. 4. Gross primary production was most strongly correlated with photosynthetically active radiation (PAR). A multiple regression model that included log PAR and stream water soluble reactive phosphorus (SRP) concentration explained 90\% of the variation in log GPP. 5. Ecosystem respiration was significantly correlated with SRP concentration and size of the transient storage zone and, together, these factors explained 73\% of the variation in R. The rate of R was poorly correlated with the rate of GPP. 6. Net ecosystem production was significantly correlated only with PAR, with 53\% of the variation in log NEP explained by log PAR. Only Sycamore Creek, a desert stream in Arizona, had positive NEP (GPP: R {\textgreater} 1), supporting the idea that streams are generally net sinks rather than net sources of organic matter. 7. Our results suggest that light, phosphorus concentration and channel hydraulics are important controls on the rate of ecosystem metabolism in streams over very extensive geographic areas.},
	language = {en},
	number = {11},
	urldate = {2020-07-22},
	journal = {Freshwater Biology},
	author = {Mulholland, P. J. and Fellows, C. S. and Tank, J. L. and Grimm, N. B. and Webster, J. R. and Hamilton, S. K. and Martí, E. and Ashkenas, L. and Bowden, W. B. and Dodds, W. K. and Mcdowell, W. H. and Paul, M. J. and Peterson, B. J.},
	year = {2001},
	keywords = {inter-biome, metabolism, primary production, respiration, stream},
	pages = {1503--1517},
}

@article{appling_metabolic_2018,
	title = {The metabolic regimes of 356 rivers in the {United} {States}},
	volume = {5},
	copyright = {2018 This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply},
	issn = {2052-4463},
	url = {https://www.nature.com/articles/sdata2018292},
	doi = {10.1038/sdata.2018.292},
	abstract = {A national-scale quantification of metabolic energy flow in streams and rivers can improve understanding of the temporal dynamics of in-stream activity, links between energy cycling and ecosystem services, and the effects of human activities on aquatic metabolism. The two dominant terms in aquatic metabolism, gross primary production (GPP) and aerobic respiration (ER), have recently become practical to estimate for many sites due to improved modeling approaches and the availability of requisite model inputs in public datasets. We assembled inputs from the U.S. Geological Survey and National Aeronautics and Space Administration for October 2007 to January 2017. We then ran models to estimate daily GPP, ER, and the gas exchange rate coefficient for 356 streams and rivers across the continental United States. We also gathered potential explanatory variables and spatial information for cross-referencing this dataset with other datasets of watershed characteristics. This dataset offers a first national assessment of many-day time series of metabolic rates for up to 9 years per site, with a total of 490,907 site-days of estimates.},
	language = {en},
	number = {1},
	urldate = {2020-07-22},
	journal = {Scientific Data},
	author = {Appling, Alison P. and Read, Jordan S. and Winslow, Luke A. and Arroita, Maite and Bernhardt, Emily S. and Griffiths, Natalie A. and Hall, Robert O. and Harvey, Judson W. and Heffernan, James B. and Stanley, Emily H. and Stets, Edward G. and Yackulic, Charles B.},
	month = dec,
	year = {2018},
	pages = {180292},
}


@article{palmer_linkages_2019,
	title = {Linkages between flow regime, biota, and ecosystem processes: {Implications} for river restoration},
	volume = {365},
	copyright = {Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. http://www.sciencemag.org/about/science-licenses-journal-article-reuseThis is an article distributed under the terms of the Science Journals Default License.},
	issn = {0036-8075, 1095-9203},
	shorttitle = {Linkages between flow regime, biota, and ecosystem processes},
	url = {https://science.sciencemag.org/content/365/6459/eaaw2087},
	doi = {10.1126/science.aaw2087},
	abstract = {River restoration guided by research
Human activities have altered the flow regimes of many of Earth's rivers, with negative impacts on biodiversity, water quality, and ecological processes. In a Review, Palmer and Ruhi explain how restoration designs now attempt to mimic ecologically important aspects of natural flow regimes, guided by insights into how variations in flow affect biota and ecosystem processes. To be successful, such efforts must go beyond accounting for flood pulses to restore natural flow variability and achieve hydrological connectivity between a river and its surroundings.
Science, this issue p. eaaw2087
Structured Abstract
BACKGROUNDEarly civilizations developed around seasonal river floodplains, and the natural rhythm of rivers remains critical to humans today. We use streams and rivers to meet drinking water, irrigation, and hydropower needs by storing and moving water in complex ways, at the times and places of our choosing. Consequently, many of Earth’s rivers have flow regimes that are “unnatural” in magnitude, frequency, duration, and timing. The rise in river degradation globally has motivated research on the link between hydrologic alteration and declines in valued biota. At the same time, largely fueled by new technologies and methods, research has expanded to understand the patterns in, and drivers of, riverine processes like primary production, in both near-pristine and degraded rivers. A third line of research, stymied by how difficult it has been to restore degraded rivers, has called for process-based restoration, building on knowledge from the other two research thrusts. Today’s hydroecological science seeks to understand the mechanisms whereby flow regimes affect biota and ecosystem processes, and the interplay between them, in a three-way interaction we call the flow-biota-ecosystem processes nexus.
ADVANCESBy shifting the focus from static patterns at sites to dynamic processes along river networks, advances are being made to understand the interactions and feedbacks at the nexus. Fueled by increasingly available time-series data and novel modeling, emerging research ranges from studies on regime-based properties such as flow periodicity and its change, to studies on river network structure and associated spatial variation in flow and water chemistry. These studies demonstrate how flow variability influences long-term persistence of riverine assemblages, and they are disentangling the direct effects of flow on communities and ecosystem processes from its indirect effects (e.g., via species interactions, light-blocking turbidity). Changes in temporal patterns in flow magnitudes can increase risk of community collapse and alter key ecosystem processes such as primary production. Growing research shows that storm flows not only enhance inputs and downstream export of terrestrially derived carbon to rivers but, when associated with sustained hydrologic connectivity with soils, exert particular influence on water chemistry and biogeochemical processes that can influence food webs. Increased availability of environmental sensors has stimulated research, showing that extreme flows may impart disproportionate impacts on stream metabolism, but the relationship can depend on the predictability of those flows. Research combining changes in flow patterns with stable isotope analyses is revealing how temporal fluctuations in habitat, and in the quality and quantity of basal resources, influence trophic pathways and resulting food-web structure. Evidence suggests that restoring particular facets of a flow regime can produce desirable conservation outcomes, but context is paramount. Restoration actions going beyond discrete flow events and enhancing groundwater-influenced river habitat or redirecting subsurface flow paths may be critical in future climates.
OUTLOOKOur understanding of the flow-biota-ecosystem processes nexus is still incomplete and is a frontier research topic. Challenges include connecting organismal and ecosystem-level processes, and understanding the role of microbial communities as intermediaries. Capturing the effects of watershed-level physical and biogeochemical heterogeneity, and parsing out direct, indirect, or cascading effects of flow alteration on biota and processes would also reduce uncertainty in restoration outcomes, particularly in novel, nonstationary environments. Understanding how much flow restoration alone can achieve in urban watersheds is an urgent need, as is translating findings from hydroecology to design green infrastructure and flow release programs from reservoirs. These management tools may offer growing opportunities to experiment with flow regimes, which will assist in refining process-based river restoration. Both solid science, and effective translation into practice will be needed to curb the fast pace of global river ecosystem degradation. {\textless}img class="fragment-image" aria-describedby="F1-caption" src="https://science.sciencemag.org/content/sci/365/6459/eaaw2087/F1.medium.gif"/{\textgreater} Download high-res image Open in new tab Download Powerpoint River flow regimes have shap­ed the life history strategies of plants and animals over evolutionary time scales.River regulation and associated alteration of flow and thermal regimes alter organismal development, often shifting important events such as insect emergence, depicted here by Palingenia mayflies entering their winged, flying stage to mate.PHOTO: CHRISS\_NS/ISTOCKPHOTO.COM
River ecosystems are highly biodiverse, influence global biogeochemical cycles, and provide valued services. However, humans are increasingly degrading fluvial ecosystems by altering their streamflows. Effective river restoration requires advancing our mechanistic understanding of how flow regimes affect biota and ecosystem processes. Here, we review emerging advances in hydroecology relevant to this goal. Spatiotemporal variation in flow exerts direct and indirect control on the composition, structure, and dynamics of communities at local to regional scales. Streamflows also influence ecosystem processes, such as nutrient uptake and transformation, organic matter processing, and ecosystem metabolism. We are deepening our understanding of how biological processes, not just static patterns, affect and are affected by stream ecosystem processes. However, research on this nexus of flow-biota-ecosystem processes is at an early stage. We illustrate this frontier with evidence from highly altered regulated rivers and urban streams. We also identify research challenges that should be prioritized to advance process-based river restoration.},
	language = {en},
	number = {6459},
	urldate = {2020-07-22},
	journal = {Science},
	author = {Palmer, Margaret and Ruhi, Albert},
	month = sep,
	year = {2019},
	pmid = {31604208},
	note = {Publisher: American Association for the Advancement of Science
Section: Review},
}

@article{engel_simplified_2020,
	title = {A simplified approach to detect a significant carbon dioxide reduction by phytoplankton in lakes and rivers on a regional and global scale},
	volume = {107},
	issn = {1432-1904},
	url = {10.1007/s00114-020-01685-y},
	doi = {10.1007/s00114-020-01685-y},
	abstract = {Carbon dioxide (CO2) uptake by phytoplankton can significantly reduce the partial pressure of CO2 (pCO2) in lakes and rivers, and thereby CO2 emissions. Presently, it is not known in which inland waters on Earth a significant pCO2 reduction by phytoplankton is likely. Since detailed, comparable carbon budgets are currently not available for most inland waters, we modified a proxy to assess the pCO2 reduction by phytoplankton, originally developed for boreal lakes, for application on a global scale. Using data from 61 rivers and 125 lakes distributed over five continents, we show that a significant pCO2 reduction by phytoplankton is widespread across the temperate and sub-/tropical region, but absent in the cold regions on Earth. More specifically, we found that a significant pCO2 reduction by phytoplankton might occur in 24\% of the lakes in the temperate region, and 39\% of the lakes in the sub-/tropical region. We also showed that such a reduction might occur in 21\% of the rivers in the temperate region, and 5\% of the rivers in the sub-/tropical region. Our results indicate that CO2 uptake by phytoplankton is a relevant flux in regional and global carbon budgets. This highlights the need for more accurate approaches to quantify CO2 uptake by primary producers in inland waters, particularly in the temperate and sub-/tropical region.},
	language = {en},
	number = {4},
	urldate = {2020-07-22},
	journal = {The Science of Nature},
	author = {Engel, Fabian and Attermeyer, Katrin and Weyhenmeyer, Gesa A.},
	month = jun,
	year = {2020},
	pages = {29},
}

@article{jankowski_watershed_2019,
	title = {Watershed geomorphology modifies the sensitivity of aquatic ecosystem metabolism to temperature},
	volume = {9},
	copyright = {2019 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-019-53703-3},
	doi = {10.1038/s41598-019-53703-3},
	abstract = {The regulation of aquatic carbon cycles by temperature is a significant uncertainty in our understanding of how watersheds will respond to climate change. Aquatic ecosystems transport substantial quantities of carbon to the atmosphere and ocean, yet we have limited understanding of how temperature modifies aquatic ecosystem metabolic processes and contributions to carbon cycles at watershed to global scales. We propose that geomorphology controls the distribution and quality of organic material that forms the metabolic base of aquatic ecosystems, thereby controlling the response of aquatic ecosystem metabolism to temperature across landscapes. Across 23 streams and four years during summer baseflow, we estimated variation in the temperature sensitivity of ecosystem respiration (R) among streams draining watersheds with different geomorphic characteristics across a boreal river basin. We found that geomorphic features imposed strong controls on temperature sensitivity; R in streams draining flat watersheds was up to six times more temperature sensitive than streams draining steeper watersheds. Further, our results show that this association between watershed geomorphology and temperature sensitivity of R was linked to the carbon quality of substrates that changed systematically across the geomorphic gradient. This suggests that geomorphology will control how carbon is transported, stored, and incorporated into river food webs as the climate warms.},
	language = {en},
	number = {1},
	urldate = {2020-07-22},
	journal = {Scientific Reports},
	author = {Jankowski, K. J. and Schindler, D. E.},
	month = nov,
	year = {2019},
	note = {Number: 1
Publisher: Nature Publishing Group},
	pages = {17619},
}

@article{bott_comparison_1978,
	title = {A comparison of methods for measuring primary productivity and community respiration in streams},
	volume = {60},
	issn = {0018-8158, 1573-5117},
	url = {http://link.springer.com/10.1007/BF00018681},
	doi = {10.1007/BF00018681},
	abstract = {Carbon dioxide and oxygen exchange procedures for measuring community metabolism (two open stream methods and three chamber methods) were compared on the same reach of a thirdorder stream . Open stream methods were complicated by high diffusion rates and yielded net community primary productivity estimates lower than those obtained with chamber methods . Chamber methods yielded variable productivity and respiration data . However, when normalized for chlorophyll a, productivity estimates from the chamber methods were within an expected range for the system . Balances of photosynthesis and respiration from the chamber methods were similar between methods and indicated that autotrophic or heterotrophic processes could dominate the system . Considerations in applying the various procedures are discussed .},
	language = {en},
	number = {1},
	urldate = {2020-07-20},
	journal = {Hydrobiologia},
	author = {Bott, T. L. and Brock, J. T. and Cushing, C. E. and Gregory, S. V. and King, D. and Petersen, R. C.},
	month = jul,
	year = {1978},
	pages = {3--12},
}

@article{bott_evaluation_1997,
	title = {An evaluation of techniques for measuring periphyton metabolism in chambers},
	volume = {54},
	abstract = {Experiments were performed to compare 14C uptake, dissolved O2 and CO2 change, and microelectrode techniques for measuring benthic primary productivity and community metabolism at a site on the South Saskatchewan River, Saskatchewan. The highest estimates of primary productivity were obtained with O2 microelectrodes (two to four times higher than simultaneous estimates from bulk-water dissolved O2 measurements), presumably because measurements are biased toward active communities under optimal conditions for photosynthesis. In daytime experiments lasting {\textasciitilde}1.3 and 2.4 h, estimates from 14C uptake were higher than those measured simultaneously from dissolved O2 and CO2 change, suggesting that 14C uptake measured gross primary production (GPP) in these short-term incubations. Differences in experimental water velocity ranging from 0.2 to {\textgreater}6.5 cm⋅s–1 had less of an effect than chlorophyll a concentration on metabolic rates in diel experiments with rocks taken from a site where velocities were from 5.6 to 7.8 cm⋅s–1. There was a potential for phosphorus and possibly NH4 limitation of metabolic activity during long-term incubations. Results highlight areas in which further research is needed when using chambers to determine periphyton metabolism.},
	language = {en},
	author = {Bott, T L and Brock, J T and Baattrup-Pedersen, A and Chambers, P A and Dodds, W K and Himbeault, K T and Lawrence, J R and Planas, D and Snyder, E and Wolfaardt, G M},
	year = {1997},
	pages = {11},
}

@article{oconnor_thresholds_2012,
	title = {Thresholds of flow-induced bed disturbances and their effects on stream metabolism in an agricultural river},
	volume = {48},
	copyright = {This paper is not subject to U.S. copyright. Published in 2012 by the American Geophysical Union},
	issn = {1944-7973},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2011WR011488},
	doi = {10.1029/2011WR011488},
	abstract = {Storm-driven flow pulses in rivers destroy and restructure sediment habitats that affect stream metabolism. This study examined thresholds of bed disturbances that affected patch- and reach-scale sediment conditions and metabolism rates. A 4 year record of discharge and diel changes in dissolved oxygen concentrations (ΔDO) was analyzed for disturbances and recovery periods of the ΔDO signal. Disturbances to the ΔDO signal were associated with flow pulses, and the recovery times for the ΔDO signal were found to be in two categories: less than 5 days (30\% of the disturbances) or greater than 15 days (70\% of the disturbances). A field study was performed during the fall of 2007, which included a storm event that increased discharge from 3.1 to 6.9 m3/s over a 7 h period. During stable flow conditions before the storm, variability in patch-scale stream metabolism values were associated with sediment texture classes with values ranging from −16.4 to 2.3 g O2/m2/d (negative sign indicates net respiration) that bounded the reach-averaged rate of −5.6 g O2/m2/d. Hydraulic modeling of bed shear stresses demonstrated a storm-induced flow pulse mobilized approximately 25\% of the bed and reach-scale metabolism rates shifted from −5 to −40 g O2/m2/d. These results suggest that storm-induced bed disturbances led to threshold behavior with respect to stream metabolism. Small flow pulses resulted in partial-bed mobilization that disrupted stream metabolism by increased turbidity with short recovery times. Large flow pulses resulted in full-bed mobilization that disrupted stream metabolism by destroying periphyton habitats with long recovery times.},
	language = {en},
	number = {8},
	urldate = {2020-07-16},
	journal = {Water Resources Research},
	author = {O'Connor, Ben L. and Harvey, Judson W. and McPhillips, Lauren E.},
	year = {2012},
	keywords = {disturbance, ecosystem stability, hydraulic modeling, sediment texture, stream metabolism, threshold conditions},
}

@article{krogh_membrane_2014,
	title = {Membrane introduction mass spectrometry ({MIMS}): a versatile tool for direct, real-time chemical measurements},
	volume = {49},
	copyright = {Copyright © 2014 John Wiley \& Sons, Ltd.},
	issn = {1096-9888},
	shorttitle = {Membrane introduction mass spectrometry ({MIMS})},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1002/jms.3447},
	doi = {10.1002/jms.3447},
	abstract = {Membrane introduction mass spectrometry (MIMS) is a direct, continuous, on-line measurement technique. It utilizes a membrane to semi-selectively transfer analyte mixtures from a sample to a mass spectrometer, rejecting the bulk of the sample matrix, which can be a gas, liquid or solid/slurry. Analyte selectivity and sensitivity are affected by optimizations at the membrane, ionization and the mass spectrometer levels. MIMS can be roughly classified by the acceptor phase that entrains analyte(s) to the mass spectrometer after membrane transport, either a gaseous acceptor phase (GP-MIMS) or condensed acceptor phase (CP-MIMS). The aim of this article is to provide an introduction to MIMS as a technique and to explore current variants, recent developments and modern applications, emphasizing examples from our group, the Applied Environmental Research Laboratories as well as selected work from others in this emerging area. Also provided is a synopsis of current and future directions for this versatile analytical technique. Copyright © 2014 John Wiley \& Sons, Ltd.},
	language = {en},
	number = {12},
	urldate = {2020-07-15},
	journal = {Journal of Mass Spectrometry},
	author = {Krogh, Erik T. and Gill, Chris G.},
	year = {2014},
	keywords = {condensed phase MIMS (CP-MIMS), direct sample introduction, environmental analysis, membrane inlet mass spectrometry, membrane introduction mass spectrometry (MIMS), qualitative analysis, quantitative analysis, real-time monitoring},
	pages = {1205--1213},
}

@article{kana_determination_2006,
	title = {Determination of denitrification in the {Chesapeake} {Bay} from measurements of {N2} accumulation in bottom water},
	volume = {29},
	issn = {1559-2731},
	url = {10.1007/BF02781991},
	doi = {10.1007/BF02781991},
	abstract = {This study demonstrates the feasibility of using direct N2 measurements in an estuary for determination of denitrification. High precision measurements of dinitrogen: argon ratios (N2∶Ar) were made by membrane inlet mass spectrometry on water samples taken along the length of the Chesapeake Bay in July and October 2004. The N2∶Ar ratio in low salinity surface water was elevated relative to air saturation by 0.3–0.5\% with no systematic change along the length of the Bay. N2∶Ar in high salinity bottom water exhibited a linear increase in the landward direction along a 144-km longitudinal section. In this section of the Bay covering 20\% of the main stem, the bottom water salinity was statistically uniform and the increase in N2∶Ar was in the direction of net residual current flow. The system was analyzed as a capped river with the assumption that N2 entered the water from the underlying sediment where denitrification is known to take place. The rate of denitrification needed to support the measured increase in N2 was calculated using an average residual current velocity and water column depth. The increase in N2 with distance (0.046μmol N l−1 km−1) equated to an average denitrification flux of 73 μmol N m−2 h−1. N2 fluxes determined on sediment cores taken from the source and terminus regions of the delineated water mass were 45±23 and 83±39 μmol N m−2 hr−1, respectively, which were not statistically different from the whole system estimate. The measured change in oxygen concentration within the bottom water was used to estimate nitrogen remineralization and the efficiency of denitrification. Denitrification efficiency (nitrogen denitrified/nitrogen remineralized) was estimated to be in the range of 22–28\% for the bottom water sediment system and 30–37\% considering the sediment zone alone.},
	language = {en},
	number = {2},
	urldate = {2020-07-15},
	journal = {Estuaries and Coasts},
	author = {Kana, Todd M. and Cornwell, Jeffrey C. and Zhong, Liejun},
	month = apr,
	year = {2006},
	pages = {222--231},
}

@article{ferron_application_2016,
	title = {Application of membrane inlet mass spectrometry to measure aquatic gross primary production by the {18O} in vitro method},
	volume = {14},
	copyright = {© 2016 The Authors Limnology and Oceanography: Methods published by Wiley Periodicals, Inc. on behalf of Association for the Sciences of Limnology and Oceanography},
	issn = {1541-5856},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lom3.10116},
	doi = {10.1002/lom3.10116},
	abstract = {The 18O technique is considered the most direct in vitro method for measuring gross primary production (GPP) in aquatic ecosystems. This method measures the 18O enrichment of the dissolved O2 pool through photosynthesis after spiking a water sample with a tracer amount of 18O-labeled water (18O-H2O) and incubating it under natural light conditions. Despite its advantages, the 18O technique has only scarcely been used to measure GPP in the ocean. The lack of 18O-based primary productivity measurements is most likely due to the technical difficulty associated with sample collection, handling, and processing, and to the need of an isotope ratio mass spectrometer (IRMS) for sample analysis, which is not available for the majority of research groups. The current procedure also precludes at sea measurements. In this manuscript, we demonstrate that the biological 18O enrichment of dissolved O2, after incubation of seawater enriched with 18O-H2O, can be precisely measured by shipboard or laboratory-based membrane inlet mass spectrometry (MIMS). The method was validated in the low-productivity oligotrophic North Pacific Subtropical Gyre, where the measured GPP ranged from 0.2 to 1.1 μmol O2 L−1 d−1, with an approximate precision for surface waters of ± 0.02 μmol O2 L−1 d−1. This new approach has the advantages of simple water sample handling and analysis, accurate dissolved gas measurements, capability of analysis on board of a ship, and use of relatively inexpensive instrumentation, and therefore has the potential to improve our understanding of primary production in the ocean and other aquatic environments.},
	language = {en},
	number = {9},
	urldate = {2020-07-15},
	journal = {Limnology and Oceanography: Methods},
	author = {Ferrón, Sara and Valle, Daniela A. del and Björkman, Karin M. and Quay, Paul D. and Church, Matthew J. and Karl, David M.},
	year = {2016},
	pages = {610--622},
}

@article{gauthier_measurement_2018,
	title = {Measurement of {Gross} {Photosynthesis}, {Respiration} in the {Light}, and {Mesophyll} {Conductance} {Using} {H218O} {Labeling1}[{OPEN}]},
	volume = {177},
	issn = {0032-0889},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5933133/},
	doi = {10.1104/pp.16.00741},
	abstract = {H218O labeling and IRMS can be used to measure gross photosynthesis, mesophyll conductance, and respiratory uptake in the light in leaflets exposed to 21\% and 2\% O2., A fundamental challenge in plant physiology is independently determining the rates of gross O2 production by photosynthesis and O2 consumption by respiration, photorespiration, and other processes. Previous studies on isolated chloroplasts or leaves have separately constrained net and gross O2 production (NOP and GOP, respectively) by labeling ambient O2 with 18O while leaf water was unlabeled. Here, we describe a method to accurately measure GOP and NOP of whole detached leaves in a cuvette as a routine gas-exchange measurement. The petiole is immersed in water enriched to a δ18O of ∼9,000‰, and leaf water is labeled through the transpiration stream. Photosynthesis transfers 18O from H2O to O2. GOP is calculated from the increase in δ18O of O2 as air passes through the cuvette. NOP is determined from the increase in O2/N2. Both terms are measured by isotope ratio mass spectrometry. CO2 assimilation and other standard gas-exchange parameters also were measured. Reproducible measurements are made on a single leaf for more than 15 h. We used this method to measure the light response curve of NOP and GOP in French bean (Phaseolus vulgaris) at 21\% and 2\% O2. We then used these data to examine the O2/CO2 ratio of net photosynthesis, the light response curve of mesophyll conductance, and the apparent inhibition of respiration in the light (Kok effect) at both oxygen levels. The results are discussed in the context of evaluating the technique as a tool to study and understand leaf physiological traits.},
	number = {1},
	urldate = {2020-07-15},
	journal = {Plant Physiology},
	author = {Gauthier, Paul P. G. and Battle, Mark O. and Griffin, Kevin L. and Bender, Michael L.},
	month = may,
	year = {2018},
	pmid = {29588336},
	pmcid = {PMC5933133},
	pages = {62--74},
}

@article{krauss_photosynthesis_nodate,
	title = {Photosynthesis in the {Algae}},
	language = {en},
	journal = {WATER PURIFICATION},
	author = {Krauss, Robert W and Palmer, C Mervin and Oswald, William J and Gataas, Harold B},
	pages = {10},
}

@article{romero_changes_1989,
	title = {Changes in {Net} 02 {Exchange} {Induced} by {Inorganic} {Nitrogen} in the {Blue}-{Green} {Alga} {Anacystis} nidulans'},
	abstract = {The response of net 02 exchange to light intensity by intact Anacystis nidulans cells in the presence of saturating NaHCO3 concentrations followed a curve with an inflection near the lightcompensation point. Addition of either KNO3 or NH4CI stimulated 02 uptake in the dark and at light intensities below the lightcompensation point. This resulted in steeper slopes of the curve calculated below and above the light-compensation point. At 02 concentrations limiting dark respiration, addition of inorganic nitrogen had no effect on either dark respiration or 02 exchange in the light. The apparent changes in photosynthetic yield observed under normal 02 concentration disappeared when respiration was limited by 02 availability, indicating that the effects of inorganic nitrogen on 02 exchange at low light intensities are due to stimulation of respiration rather than to increases in photosynthetic yield.},
	language = {en},
	author = {Romero, Jose M and Lara, Catalina and Sivak, Mirta N},
	year = {1989},
	pages = {3},
}

@article{tcherkez_tracking_2017,
	title = {Tracking the origins of the {Kok} effect, 70 years after its discovery},
	volume = {214},
	copyright = {© 2017 The Authors. New Phytologist © 2017 New Phytologist Trust},
	issn = {1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.14527},
	doi = {10.1111/nph.14527},
	language = {en},
	number = {2},
	urldate = {2020-07-15},
	journal = {New Phytologist},
	author = {Tcherkez, Guillaume and Gauthier, Paul and Buckley, Thomas N. and Busch, Florian A. and Barbour, Margaret M. and Bruhn, Dan and Heskel, Mary A. and Gong, Xiao Ying and Crous, Kristine and Griffin, Kevin L. and Way, Danielle A. and Turnbull, Matthew H. and Adams, Mark A. and Atkin, Owen K. and Bender, Michael and Farquhar, Graham D. and Cornic, Gabriel},
	year = {2017},
	keywords = {CO2 assimilation, Kok effect, incident photosynthetically active radiation, light response curve, net photosynthesis},
	pages = {506--510},
}

@article{romeijn_streambed_2019,
	title = {Streambed {Organic} {Matter} {Controls} on {Carbon} {Dioxide} and {Methane} {Emissions} from {Streams}},
	volume = {53},
	issn = {0013-936X},
	url = {10.1021/acs.est.8b04243},
	doi = {10.1021/acs.est.8b04243},
	abstract = {Greenhouse gas (GHG) emissions of carbon dioxide (CO2) and methane (CH4) from streambeds are currently understudied. There is a paucity of research exploring organic matter (OM) controls on GHG production by microbial metabolic activity in streambeds, which is a major knowledge gap given the increased inputs of allochthonous carbon to streams, especially in agricultural catchments. This study aims to contribute to closing this knowledge gap by quantifying how contrasting OM contents in different sediments affect streambed GHG production and associated microbial metabolic activity. We demonstrate, by means of an incubation experiment, that streambed sediments have the potential to produce substantial amounts of GHG, controlled by sediment OM quantity and quality. We observed streambed CO2 production rates that can account for 35\% of total stream evasion estimated in previous studies, ranging between 1.4 and 86\% under optimal conditions. Methane production varied stronger than CO2 between different geologic backgrounds, suggesting OM quality controls between streambed sediments. Moreover, our results indicate that streambed sediments may produce much more CO2 than quantified to date, depending on the quantity and quality of the organic matter, which has direct implications for global estimates of C fluxes in stream ecosystems.},
	number = {5},
	urldate = {2020-07-15},
	journal = {Environmental Science \& Technology},
	author = {Romeijn, Paul and Comer-Warner, Sophie A. and Ullah, Sami and Hannah, David M. and Krause, Stefan},
	month = mar,
	year = {2019},
	note = {Publisher: American Chemical Society},
	pages = {2364--2374},
}

@article{angert_using_2015,
	title = {Using {O} $_{\textrm{2}}$ to study the relationships between soil {CO} $_{\textrm{2}}$ efflux and soil respiration},
	volume = {12},
	issn = {1726-4189},
	url = {https://www.biogeosciences.net/12/2089/2015/},
	doi = {10.5194/bg-12-2089-2015},
	abstract = {Abstract. Soil respiration is the sum of respiration processes in the soil and is a major flux in the global carbon cycle. It is usually assumed that the CO2 efflux is equal to the soil respiration rate. Here we challenge this assumption by combining measurements of CO2 with high-precision measurements of O2. These measurements were conducted on different ecosystems and soil types and included measurements of air samples taken from the soil profile of three Mediterranean sites: a temperate forest and two alpine forests. Root-free soils from the alpine sites were also incubated in the lab. We found that the ratio between the CO2 efflux and the O2 influx (defined as apparent respiratory quotient, ARQ) was in the range of 0.14 to 1.23 and considerably deviated from the value of 0.9 ± 0.1 expected from the elemental composition of average plants and soil organic matter. At the Mediterranean sites, these deviations are explained as a result of CO2 dissolution in the soil water and transformation to bicarbonate ions in these high-pH soils, as well as by carbonate mineral dissolution and precipitation processes. Thus, a correct estimate of the short-term, chamber-based biological respiratory flux in such soils can only be made by dividing the measured soil CO2 efflux by the average (efflux-weighted) soil profile ARQ. Applying this approach to a semiarid pine forest resulted in an estimated short-term biological respiration rate that is 3.8 times higher than the chamber-measured surface CO2. The ARQ values often observed in the more acidic soils were unexpectedly low ({\textless} 0.7). These values probably result from the oxidation of reduced iron, which has been formed previously during times of high soil moisture and local anaerobic conditions inside soil aggregates. The results reported here provide direct quantitative evidence of a large temporal decoupling between soil–gas exchange fluxes and biological soil respiration.},
	language = {en},
	number = {7},
	urldate = {2020-07-15},
	journal = {Biogeosciences},
	author = {Angert, A. and Yakir, D. and Rodeghiero, M. and Preisler, Y. and Davidson, E. A. and Weiner, T.},
	month = apr,
	year = {2015},
	pages = {2089--2099},
}

@article{haggerty_development_2008,
	title = {Development of a “smart” tracer for the assessment of microbiological activity and sediment-water interaction in natural waters: {The} resazurin-resorufin system},
	volume = {44},
	issn = {1944-7973},
	shorttitle = {Development of a “smart” tracer for the assessment of microbiological activity and sediment-water interaction in natural waters},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2007WR006670},
	doi = {10.1029/2007WR006670},
	abstract = {A “smart” tracer is a tracer that provides, directly or through measurement of its concentration or in combination with another compound, at least one “bit” more of information about the environment through which it travels than a conservative tracer. In this study we propose and present the chemical compound resazurin as a smart tracer to assess the coupling between solute transport and microbiological activity in sediment-water interfaces in freshwaters. Resazurin is a weakly fluorescent redox-sensitive dye that undergoes an irreversible reduction to strongly fluorescent resorufin under mildly reducing conditions, most commonly in the presence of living microorganisms. To investigate the suitability of resazurin as a smart tracer, we characterized the decay, sorption, reaction, and transport behavior of resazurin and resorufin in various waters and sediments using laboratory experiments. Results show that resazurin irreversibly and rapidly reacts to resorufin in colonized sediment with pseudo-first-order behavior and a rate coefficient of 1.41 h−1. This reaction is 3 orders of magnitude faster than that in stream water alone, indicating the tracer is sensitive to microbiological activity and associated sediment-water interactions. The compounds are affected by significant sorption, with an approximately linear isotherm and a Kd of 6.63 mL/g for resorufin in sediment with 2.19\% organic carbon. The compounds are stable over weeks in natural water, except in the presence of strong light where significant photochemical decay may occur more rapidly.},
	language = {en},
	number = {4},
	urldate = {2020-07-15},
	journal = {Water Resources Research},
	author = {Haggerty, Roy and Argerich, Alba and Martí, Eugènia},
	year = {2008},
	keywords = {fluorescent tracer, hyporheic zone, microbial respiration and metabolism, phenoxazine, redox, smart tracer},
}

@article{gonzalezpinzon_measuring_2012,
	title = {Measuring aerobic respiration in stream ecosystems using the resazurin-resorufin system},
	volume = {117},
	copyright = {©2012. American Geophysical Union. All Rights Reserved.},
	issn = {2156-2202},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2012JG001965},
	doi = {10.1029/2012JG001965},
	abstract = {The use of smart tracers to study hydrologic systems is becoming more widespread. Smart tracers are compounds that irreversibly react in the presence of a process or condition under investigation. Resazurin (Raz) is a smart tracer that undergoes an irreversible reduction to resorufin (Rru) in the presence of cellular metabolic activity. We quantified the relationship between the transformation of Raz and aerobic bacterial respiration in pure culture experiments using two obligate aerobes and two facultative anaerobes, and in colonized surface and shallow ({\textless}10 cm) hyporheic sediments using reach-scale experiments. We found that the transformation of Raz to Rru was nearly perfectly (minr2 = 0.986), positively correlated with aerobic microbial respiration in all experiments. These results suggest that Raz can be used as a surrogate to measure respiration in situ and in vivoat different spatial scales, thus providing an alternative to investigate mechanistic controls of solute transport and stream metabolism on nutrient processing. Lastly, a comparison of respiration and mass-transfer rates in streams suggests that field-scale respiration is controlled by the slower of respiration and mass transfer, highlighting the need to understand both biogeochemistry and physics in stream ecosystems.},
	language = {en},
	number = {G3},
	urldate = {2020-07-15},
	journal = {Journal of Geophysical Research: Biogeosciences},
	author = {González‐Pinzón, Ricardo and Haggerty, Roy and Myrold, David D.},
	year = {2012},
	keywords = {aerobic respiration, metabolism, resazurin, resorufin, smart tracer, streams},
}

@article{speir_quantifying_2020,
	title = {Quantifying denitrification following floodplain restoration via the two-stage ditch in an agricultural watershed},
	volume = {155},
	issn = {0925-8574},
	url = {http://www.sciencedirect.com/science/article/pii/S0925857420302330},
	doi = {10.1016/j.ecoleng.2020.105945},
	abstract = {In agricultural streams, constructed floodplains have been shown to expand bioreactive surface area and enhance nitrate (NO3−-N) removal via microbial denitrification, thereby reducing export to downstream ecosystems. At the Shatto Ditch Watershed (Indiana, USA), 0.6 km of two-stage ditch was constructed at the watershed outlet in 2007, while an additional 3.7 and 2.7 km were constructed in 2017 and 2018, respectively. We quantified denitrification following floodplain construction using experimental incubations of stream sediments and floodplain soils from Spring 2017 to Spring 2019. We measured dissolved dinitrogen gas (N2) concentrations using membrane inlet mass spectrometry (MIMS) and found that denitrification on unconsolidated stream sediments was minimally impacted by stream dredging during two-stage construction in 2017 and 2018. In contrast, even one year after the 2017 construction, denitrification on floodplain soils fell below detection limits; we finally observed measurable rates in Spring 2019. As predicted, stream sediment denitrification was driven by water column NO3−-N concentration, while organic matter limited denitrification on floodplain soils. Floodplains constructed via the two-stage ditch can increase NO3−-N removal by {\textgreater}20\% in agricultural watersheds, representing an effective ecological engineering solution to combat downstream eutrophication. However, our results also show that denitrification on floodplain soils may take longer to recover from construction-related activities as organic matter builds up more slowly over time. As such, lags in the recovery or enhancement of ecosystem function are important to consider when documenting restoration success.},
	language = {en},
	urldate = {2020-07-15},
	journal = {Ecological Engineering},
	author = {Speir, Shannon L. and Tank, Jennifer L. and Mahl, Ursula H.},
	month = aug,
	year = {2020},
	keywords = {Agriculture, Denitrification, Floodplain restoration, MIMS, Stream, Two-stage ditch},
	pages = {105945},
}

@article{song_continental-scale_2018,
	title = {Continental-scale decrease in net primary productivity in streams due to climate warming},
	volume = {11},
	copyright = {2018 The Author(s)},
	issn = {1752-0908},
	url = {https://www.nature.com/articles/s41561-018-0125-5},
	doi = {10.1038/s41561-018-0125-5},
	abstract = {An increase in stream temperature leads to a convergence of metabolic balance, overall decline in net ecosystem productivity, and higher CO2 emissions from streams, according to analyses of temperature sensitivity of stream metabolism across six biomes.},
	language = {en},
	number = {6},
	urldate = {2020-07-14},
	journal = {Nature Geoscience},
	author = {Song, Chao and Dodds, Walter K. and Rüegg, Janine and Argerich, Alba and Baker, Christina L. and Bowden, William B. and Douglas, Michael M. and Farrell, Kaitlin J. and Flinn, Michael B. and Garcia, Erica A. and Helton, Ashley M. and Harms, Tamara K. and Jia, Shufang and Jones, Jeremy B. and Koenig, Lauren E. and Kominoski, John S. and McDowell, William H. and McMaster, Damien and Parker, Samuel P. and Rosemond, Amy D. and Ruffing, Claire M. and Sheehan, Ken R. and Trentman, Matt T. and Whiles, Matt R. and Wollheim, Wilfred M. and Ballantyne, Ford},
	month = jun,
	year = {2018},
	note = {Number: 6
Publisher: Nature Publishing Group},
	pages = {415--420},
}

@article{kreiling_land_2020,
	title = {Land {Use} {Effects} on {Sediment} {Nutrient} {Processes} in a {Heavily} {Modified} {Watershed} {Using} {Structural} {Equation} {Models}},
	volume = {56},
	issn = {1944-7973},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2019WR026655},
	doi = {10.1029/2019WR026655},
	abstract = {Contemporary land use can affect sediment nutrient processes in rivers draining heavily modified watersheds; however, studies linking land use to sediment nutrient processes in large river networks are limited. In this study, we developed and evaluated structural equation models for denitrification and phosphorus retention capacity to determine direct and indirect linkages between current land use and sediment nutrient processes during base flow in the Fox River watershed, WI, USA. A large spatial-scale dataset used for this study included sediment nitrogen and phosphorus retention measurements and land use information for 106 sites. The structural equation models for the Fox River watershed identified direct links between current land use and in-stream sediment nutrient processes. Subwatersheds with agricultural land consisting of more natural land cover had lower surface water nitrate concentrations and higher denitrification enzyme activity than subwatersheds with less alternative cover. This indicates that best management practices implemented in the Fox River watershed that restore natural land cover can improve water quality through nitrogen removal on the agricultural landscape and in the river network. Best management practices are not having the same measurable effects on phosphorus in the river network, most likely due to legacy phosphorus stored in the sediment.},
	language = {en},
	number = {7},
	urldate = {2020-07-13},
	journal = {Water Resources Research},
	author = {Kreiling, R. M. and Thoms, M. C. and Bartsch, L. A. and Larson, J. H. and Christensen, V. G.},
	year = {2020},
	keywords = {Fox River Basin, best management practices, phosphorus retention, resilience, sediment nutrient dynamics, structural equation modeling},
	pages = {e2019WR026655},
}

@article{ward_nutrient_2018,
	title = {Nutrient uptake during low-level fertilization of a large, seventh-order oligotrophic river},
	volume = {75},
	issn = {0706-652X, 1205-7533},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfas-2017-0062},
	doi = {10.1139/cjfas-2017-0062},
	abstract = {Uptake of nitrogen (total nitrogen (TN), NH4-N, and NO3-N) and phosphorus (total dissolved phosphorus (TDP) and total phosphorus (TP)) was quantified June through September 2009–2011 using whole-river fertilization in a seventh-order, P-limited river (Kootenai River, Idaho, USA), at discharges up to three orders of magnitude greater than previously studied. Mean uptake length (Sw) and uptake velocity (Vf) values were similar for dosed TDP and NH4; both had steep gradients indicating rapid uptake, while NO3-N did not. TP remained higher than reference levels. TN showed no clear pattern. Autotrophs accounted for 28\% of daylight mean NO3-N uptake compared with 72\% by heterotrophs. Nutrient uptake was strongly associated with chlorophyll accrual and epilithon growth rates. Mean midsummer epilithon growth and N rates roughly tripled late summer rates. TDP uptake length (Sw = 5.7 km) showed a slow increase with increasing stream order consistent with published findings. Mean TDP uptake velocity (Vf = 32 mm·min−1) was eight times greater than previously seen in smaller streams. Vf (10.9 ± 5 mm·min−1) and Sw (16.8. ± 7 km) for NO3-N increased with increasing river order and discharge.},
	language = {en},
	number = {4},
	urldate = {2020-07-13},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Ward, Peter R.B. and Anders, Paul J. and Minshall, G. Wayne and Holderman, Charlie and Hoyle, Genevieve M. and Yassien, Hassen},
	month = apr,
	year = {2018},
	pages = {569--579},
}

@article{sarma_continuous_2006,
	title = {Continuous shipboard sampling system for determination of triple oxygen isotopes and {O2}/{Ar} ratio by dual-inlet mass spectrometry},
	volume = {20},
	copyright = {Copyright © 2006 John Wiley \& Sons, Ltd.},
	issn = {1097-0231},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/rcm.2756},
	doi = {10.1002/rcm.2756},
	abstract = {A continuous shipboard sampling system was developed for the determination of the isotopic composition of the triple oxygen isotopes and oxygen to argon (O2/Ar) ratios in dissolved air. In this system, dissolved air is separated by a hollow fiber membrane degassing module. This system collects dissolved air quantitatively and rapidly. The sample flow rate through the membrane is critical for the fractionation of the oxygen isotopes and the O2/Ar ratio and should be {\textless}2 mL/min. Fractionation of oxygen between the liquid and gas phase of the air-saturated water was found to be similar to that of earlier reports. The advantages of this method over existing techniques include rapid collection of samples (30 min/sample), high efficiency in extraction of gases from the liquid phase, and the lack of a sample preparation step (e.g. degassing). Copyright © 2006 John Wiley \& Sons, Ltd.},
	language = {en},
	number = {23},
	urldate = {2020-07-10},
	journal = {Rapid Communications in Mass Spectrometry},
	author = {Sarma, V. V. S. S. and Abe, O. and Yoshida, N. and Saino, T.},
	year = {2006},
	pages = {3503--3508},
}

@article{helman_fractionation_2005,
	title = {Fractionation of the {Three} {Stable} {Oxygen} {Isotopes} by {Oxygen}-{Producing} and {Oxygen}-{Consuming} {Reactions} in {Photosynthetic} {Organisms}},
	volume = {138},
	copyright = {© 2005 American Society of Plant Biologists},
	issn = {0032-0889, 1532-2548},
	url = {http://www.plantphysiol.org/content/138/4/2292},
	doi = {10.1104/pp.105.063768},
	abstract = {The triple isotope composition (δ17O and δ18O) of dissolved O2 in the ocean and in ice cores was recently used to assess the primary productivity over broad spatial and temporal scales. However, assessment of the productivity with the aid of this method must rely on accurate measurements of the 17O/16O versus 18O/16O relationship in each of the main oxygen-producing and -consuming reactions. Data obtained here showed that cleavage of water in photosystem II did not fractionate oxygen isotopes; the δ18O and δ17O of the O2 evolved were essentially identical to those of the substrate water. The fractionation slopes for the oxygenase reaction of Rubisco and respiration were identical (0.518 ± 0.001) and that of glycolate oxidation was 0.503 ± 0.002. There was a considerable difference in the slopes of O2 photoreduction (the Mehler reaction) in the cyanobacterium Synechocystis sp. strain PCC 6803 (0.497 ± 0.004) and that of pea (Pisum sativum) thylakoids (0.526 ± 0.001). These values provided clear and independent evidence that the mechanism of O2 photoreduction differs between higher plants and cyanobacteria. We used our method to assess the magnitude of O2 photoreduction in cyanobacterial cells maintained under conditions where photorespiration was negligible. It was found that electron flow to O2 can be as high as 40\% that leaving photosystem II, whereas respiratory activity in the light is only 6\%. The implications of our findings to the evaluation of specific O2-producing or -consuming reactions, in vivo, are discussed.},
	language = {en},
	number = {4},
	urldate = {2020-07-10},
	journal = {Plant Physiology},
	author = {Helman, Yael and Barkan, Eugeni and Eisenstadt, Doron and Luz, Boaz and Kaplan, Aaron},
	month = aug,
	year = {2005},
	pmid = {16040650},
	note = {Publisher: American Society of Plant Biologists
Section: BIOENERGETICS AND PHOTOSYNTHESIS},
	pages = {2292--2298},
}

@article{cole_carbon_2001,
	title = {Carbon in catchments: connecting terrestrial carbon losses with aquatic metabolism},
	volume = {52},
	issn = {1448-6059},
	shorttitle = {Carbon in catchments},
	url = {https://www.publish.csiro.au/mf/mf00084},
	doi = {10.1071/mf00084},
	abstract = {For a majority of aquatic ecosystems, respiration (R) exceeds autochthonous gross primary production (GPP). These systems have negative net ecosystem production ([NEP]=[GPP]–R) and ratios of [GPP]/R of {\textless}1. This net heterotrophy can be sustained only if aquatic respiration is subsidized by organic inputs from the catchment. Such subsidies imply that organic materials that escaped decomposition in the terrestrial environment must become susceptible to decomposition in the linked aquatic environment. Using a moderate-sized catchment in North America, the Hudson River (catchment area 33500 km2), evidence is presented for the magnitude of net heterotrophy. All approaches (CO2 gas flux; O2 gas flux; budget and gradient of dissolved organic C; and the summed components of primary production and respiration within the ecosystem) indicate that system respiration exceeds gross primary production by {\textasciitilde}200 g C m-2 year-1. Highly 14C-depleted C of ancient terrestrial origin (1000–5000 years old) may be an important source of labile organic matter to this riverine system and support this excess respiration. The mechanisms by which organic matter is preserved for centuries to millennia in terrestrial soils and decomposed in a matter of weeks in a river connect modern riverine metabolism to historical terrestrial conditions.},
	language = {en},
	number = {1},
	urldate = {2020-06-30},
	journal = {Marine and Freshwater Research},
	author = {Cole, Jonathan J. and Caraco, Nina F.},
	year = {2001},
	note = {Publisher: CSIRO PUBLISHING},
	pages = {101--110},
}

@article{odum_primary_1956,
	title = {Primary production in flowing waters},
	volume = {1},
	copyright = {© 1956, by the Association for the Sciences of Limnology and Oceanography, Inc.},
	issn = {1939-5590},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.1956.1.2.0102},
	doi = {10.4319/lo.1956.1.2.0102},
	abstract = {Respiration, photosynthetic production, and diffusion interact to produce the daily curve of oxygen change in a segment of flowing water. Conversely, the observed curves of oxygen in streams can be used to calculate the component rates of production, respiration, and diffusion. New production values obtained with these analyses of oxygen curves from various sources, as well as a few previously existing estimates of primary production, indicate a generally higher rate of production in flowing waters than in other types of aquatic environments. The ratio of total primary production to total community respiration is used to classify communities quantitatively according to their predominantly heterotrophic or autotrophic characteristics. Longitudinal succession within a stream tends to modify the ratio towards unity from higher values for autotrophic and from lower values for heterotrophic communities. The behavior of this ratio is described for the annual cycle in a stream, for the sequence of pollution recovery, and for diverse types of communities.},
	language = {en},
	number = {2},
	urldate = {2020-07-06},
	journal = {Limnology and Oceanography},
	author = {Odum, Howard T.},
	year = {1956},
	pages = {102--117},
}

@article{carter_predicting_2012,
	title = {Predicting sediment phosphorus release rates using landuse and water-quality data},
	volume = {31},
	issn = {2161-9549},
	url = {https://www.journals.uchicago.edu/doi/10.1899/11-177.1},
	doi = {10.1899/11-177.1},
	abstract = {We developed a series of models using landuse and water-quality variables to predict sediment P release rates under anoxic conditions in reservoirs. We collected sediment cores from 17 reservoirs in the Central Plains region of the USA, and we measured nutrient release rates under anoxic conditions in laboratory incubation studies. We used corresponding landuse and water-quality data from the reservoirs to develop regression models for predicting P release rates. We used variables that relate directly to trophic state, including \% cropland in the watershed, which explained the greatest amount of variation in release rates. P release rates tended to be higher in reservoirs that had greater \% cropland in the watersheds. We developed additional predictive models using surface total P concentrations and Secchi disk depths. Trophic state was also a good predictor of release rates because more P was released from hypereutrophic reservoirs than from mesotrophic or eutrophic reservoirs. The median release rates for reservoirs representing different trophic state classes (e.g., mesotrophic, eutrophic, and hypereutrophic) were very similar to those previously reported for natural lakes. Our models can be used to predict sediment release rates in individual reservoirs of concern or to screen a large number of reservoirs to help direct resources to those systems that are most vulnerable to internal loading. Models based on landuse characteristics are particularly valuable because these data can be obtained from computer-based assessments and do not require labor-intensive field sampling.},
	number = {4},
	urldate = {2020-07-03},
	journal = {Freshwater Science},
	author = {Carter, Lindsey D. and Dzialowski, Andrew R.},
	month = dec,
	year = {2012},
	note = {Publisher: The University of Chicago Press},
	pages = {1214--1222},
}

@article{zeng_seasonal_2019,
	title = {Seasonal and diurnal variations in {DIC}, {NO3}− and {TOC} concentrations in spring-pond ecosystems under different land-uses at the {Shawan} {Karst} {Test} {Site}, {SW} {China}: {Carbon} limitation of aquatic photosynthesis},
	volume = {574},
	issn = {0022-1694},
	shorttitle = {Seasonal and diurnal variations in {DIC}, {NO3}− and {TOC} concentrations in spring-pond ecosystems under different land-uses at the {Shawan} {Karst} {Test} {Site}, {SW} {China}},
	url = {http://www.sciencedirect.com/science/article/pii/S0022169419304305},
	doi = {10.1016/j.jhydrol.2019.04.090},
	abstract = {Human activities have altered terrestrial carbon (C) and nitrogen (N) dynamics via changes to land cover and use such as deforestation, agriculture, application of fertilizers, etc. and have influenced the patterns of organic C input and eutrophication in downstream freshwater ecosystems. Biogeochemical cycling of C and N and the related organic carbon (OC) production may display correlated diurnal and seasonal variations due to photosynthesis and respiration in these ecosystems, whose underlying mechanisms still need to be resolved. In this study, we document the diurnal and seasonal variations measured in DIC (dissolved inorganic carbon), NO3−, TOC (total organic carbon) and other related hydrochemical parameters (pH and DO-dissolved oxygen) in five artificial spring-pond ecosystems with differing land-uses in tanks draining into springs and corresponding ponds, constructed at the Shawan Karst Test Site, SW China. It was found that diurnal changes in DIC, NO3− and TOC in all ponds were dominated by aquatic ecosystem metabolism (i.e., photosynthesis and respiration), as evidenced by the pertinent variations in DO and pH. Daily DIC and NO3− uptake and OC production were higher in October (growing period) and lower in January (dormant period), indicating seasonal differences in assimilation that were determined by both changes in weather (temperature and light) and nutrient inputs. Under conditions of bare rock or bare soil, there was very low DIC and NO3− additions to the spring-pond ecosystems, resulting in lower OC productivity in the ponds. Cropped land yielded higher DIC and NO3− to the pond, due to growth of corn and use of fertilizers that enhanced OC production. Highest productivity and densest vegetation cover on tanks with grassland or shrubs (with higher N retention in soils) resulted in higher DIC but limited NO3− addition to the ecosystems downstream. The highest DIC concentration (in the grassland) resulted in maximum OC production in the pond. These results indicate that OC production in the ponds with elevated pH was limited by DIC fertilization. In general, the supply of DIC is not considered to limit aquatic primary productivity because its concentration exceeds that of other plant macronutrients such as NO3 and PO43− by two or three orders of magnitude. Therefore, the carbon limitation detected here may indicate that photoautotrophs in karst dominated aquatic terrains (dominated by Charophyta and Spirogyra) cannot use the total DIC for photosynthesis but only the dissolved CO2, which comprises {\textless}1\% of total DIC at pH {\textgreater} 8.2 that is characteristic in these environments. This may have implications for control of eutrophication in such alkaline aquatic ecosystems, i.e., rates of eutrophication in freshwater ecosystems may be regulated not only by N and/or P but also by C. It is also projected that there will be an increase in OC sequestration with the current land-use and global climate change-driven increases in DIC, due to carbon limitation of aquatic primary production.},
	language = {en},
	urldate = {2020-07-02},
	journal = {Journal of Hydrology},
	author = {Zeng, Sibo and Liu, Huan and Liu, Zaihua and Kaufmann, Georg and Zeng, Qingrui and Chen, Bo},
	month = jul,
	year = {2019},
	keywords = {Aquatic photosynthesis, Carbon limitation, Eutrophication control, Karst surface aquatic ecosystem, Temporal variation, Water quality},
	pages = {811--821},
}

@article{jiang_biogeochemical_2020,
	title = {Biogeochemical and physical controls on the evolution of dissolved inorganic carbon ({DIC}) and δ{13CDIC} in karst spring-waters exposed to atmospheric {CO2}(g): {Insights} from laboratory experiments},
	volume = {583},
	issn = {0022-1694},
	shorttitle = {Biogeochemical and physical controls on the evolution of dissolved inorganic carbon ({DIC}) and δ{13CDIC} in karst spring-waters exposed to atmospheric {CO2}(g)},
	url = {http://www.sciencedirect.com/science/article/pii/S0022169419310297},
	doi = {10.1016/j.jhydrol.2019.124294},
	abstract = {Karst waters (spring-fed streams, lakes and reservoirs) characterized by relatively high concentrations of dissolved inorganic carbon (DIC) and pCO2 significantly impact regional and global carbon cycles by releasing carbon dioxide to the atmosphere. Investigating the transfer of DIC from karst waters to the atmosphere is important to further our understanding of carbon cycling in karst environments. There is still considerable uncertainty about the controls of DIC transfer in karst waters because of challenges associated with investigations that aim to mimic the continuum of changes in DIC concentrations to equilibrium with atmospheric CO2 in natural settings. Laboratory simulations can create controlled conditions that allow targeted investigations. In this study, four tanks were taken to investigate the variations of pCO2, DIC and δ13CDIC when karst spring-waters were exposed to the atmosphere from 40 to 360 h as: (1) agitated water containing Hydrilla verticillata; (2) static water containing Hydrilla verticillata; (3) agitated water without Hydrilla verticillata; and (4) static water without Hydrilla verticillata. The rates of photosynthesis/respiration of submerged plants, CO2 outgassing and carbonate precipitation/dissolution were quantified by a time-stepping chemical/isotopic mass balance model. This experiment was designed to create ideal conditions to estimate the temporal evolution of DIC and δ13CDIC, and investigate mechanisms that control their evolution when karst spring-waters interact with atmospheric CO2. Results show: (1) generally a steep decrease in DIC concentrations and δ13CDIC enrichment; (2) DIC loss and δ13CDIC enrichment are faster in the agitated waters with submerged plants; (3) DIC evolution is mainly controlled by the metabolism of aquatic plants; (4) carbonate precipitation/dissolution and CO2 outgassing has a lower effect on the DIC evolution in waters with submerged plants; (5) δ13CDIC evolution is mainly controlled by the metabolism of submerged plants; (6) CO2 evasion, photosynthesis and δ13CDIC enrichment are accelerated by the agitation of waters. Our analyses show that more than 40\% of the total DIC resulting from carbonate weathering was used for photosynthesis by submerged aquatic plants thereby transforming the DIC into organic carbon (OC), suggesting that intense aquatic photosynthetic activities in continental surface water systems could play an important role as natural carbon sinks.},
	language = {en},
	urldate = {2020-07-02},
	journal = {Journal of Hydrology},
	author = {Jiang, Yongjun and Lei, Jiaqi and Hu, Liuchan and Xiao, Qiong and Wang, Jinliang and Zhang, Cheng and Ali, Hendratta},
	month = apr,
	year = {2020},
	keywords = {Biological process, Chemical process, Dissolved inorganic carbon, Karst spring-waters-atmosphere interaction, Physical process, Stable carbon isotope},
	pages = {124294},
}

@article{parker_diel_2010,
	series = {Rates of {Geochemical} {Processes} and their {Application} to {Natural} {Systems}},
	title = {Diel behavior of stable isotopes of dissolved oxygen and dissolved inorganic carbon in rivers over a range of trophic conditions, and in a mesocosm experiment},
	volume = {269},
	issn = {0009-2541},
	url = {http://www.sciencedirect.com/science/article/pii/S0009254109002939},
	doi = {10.1016/j.chemgeo.2009.06.016},
	abstract = {Rates of diel (24-h) biogeochemical processes in rivers and their effect on daily changes in the concentration of metals and metalloids have been well documented in the literature over the last 20years. Investigations into the effects of these processes on aquatic systems and the underlying mechanisms that control the processes can significantly improve our understanding of how natural aquatic environments function and will respond to changing environmental conditions and anthropogenic impacts. Daily changes in the rates of biogeochemical processes have, more recently, been shown to influence the stable isotope composition of dissolved oxygen and dissolved inorganic carbon in natural waters. Here we present a comprehensive picture of the persistence and reproducibility of diel cycles of the 18O composition of dissolved molecular oxygen (δ18O-DO) and the 13C composition of dissolved inorganic carbon (δ13C-DIC) across five Montana, USA rivers investigated over a 4-year period. A mesocosm experiment showed the same behavior in δ18O-DO and δ13C-DIC as seen in riverine settings across light and dark periods. A cross plot of δ18O-DO and δ13C-DIC from each stream exhibits a clockwise elliptical pattern which is attributed to the daily changes in the balance of metabolic rates as well as air–water gas exchange. The amplitude of the change in the isotope composition is shown to be directly related to the trophic state of the river and a relationship between net productivity and diel changes in δ18O-DO and δ13C-DIC is presented. This relationship between trophic status with δ18O-DO, δ13C-DIC and production emphasizes the significance of how rates of biogeochemical processes in natural systems can influence the daily changes in the composition of surface waters.},
	language = {en},
	number = {1},
	urldate = {2020-07-02},
	journal = {Chemical Geology},
	author = {Parker, Stephen R. and Gammons, Christopher H. and Poulson, Simon R. and DeGrandpre, Michael D. and Weyer, Charmaine L. and Smith, M. Garrett and Babcock, John N. and Oba, Yasuhiro},
	month = jan,
	year = {2010},
	keywords = {Diel, Dissolved inorganic carbon, Dissolved oxygen, Stable isotopes, Trophic state},
	pages = {22--32},
}

@article{glibert_stable_2019,
	title = {Stable isotope tracers: {Enriching} our perspectives and questions on sources, fates, rates, and pathways of major elements in aquatic systems},
	volume = {64},
	copyright = {© 2018 The Authors. Limnology and Oceanography published by Wiley Periodicals, Inc. on behalf of Association for the Sciences of Limnology and Oceanography.},
	issn = {1939-5590},
	shorttitle = {Stable isotope tracers},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lno.11087},
	doi = {10.1002/lno.11087},
	abstract = {Stable isotope applications have evolved from simple characterizations of isotope composition in organisms and organic matter, to highly complex methodologies on scales ranging from individual compounds and cells, to broad ecosystem-level approaches. New techniques are rapidly evolving, allowing novel, difficult, and inconvenient questions to be addressed. This article aims to provide an overarching perspective on how the field has evolved and where it is going with regard to aquatic systems, some of the oceanographic and limnological concepts derived from these approaches, and important challenges. To this end, we highlight a selection of natural abundance and tracer enrichment studies that represent a wide range of stable isotope applications. These include studies of rate processes and biogeochemical cycling, source tracking, food webs, and paleoenvironments. Our coverage of stable isotope applications is by no means complete, but by highlighting a mixture of classic and new applications across a wide range of research areas, our goal is to convey the power of stable isotope tools and the excitement in this rapidly expanding field, while also encouraging the scrutiny and healthy respect for limitations and assumptions necessary to take full advantage of these powerful tools.},
	language = {en},
	number = {3},
	urldate = {2020-07-01},
	journal = {Limnology and Oceanography},
	author = {Glibert, Patricia M. and Middelburg, Jack J. and McClelland, James W. and Zanden, M. Jake Vander},
	year = {2019},
	pages = {950--981},
}

@article{kaplan_untangling_2008,
	title = {Untangling the complex issue of dissolved organic carbon uptake: a stable isotope approach},
	volume = {53},
	copyright = {© 2007 The Authors},
	issn = {1365-2427},
	shorttitle = {Untangling the complex issue of dissolved organic carbon uptake},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2427.2007.01941.x},
	doi = {10.1111/j.1365-2427.2007.01941.x},
	abstract = {1. We estimated uptake of stream water dissolved organic carbon (DOC) through a whole-stream addition of a 13C-DOC tracer coupled with laboratory measurements of bioavailability of the tracer and stream water DOC. 2. The tracer, a leachate of 13C-labelled tree tissues, was added to the head waters of White Clay Creek, Pennsylvania, U.S.A., over a 2-h period and followed 1.27 km downstream to generate mass transfer coefficients for DOC lability classes within the tracer. 3. From the longitudinal 13C uptake curve, we resolved labile and semi-labile DOC classes within the 13C-DOC tracer comprising 82\% and 18\% of the tracer respectively. 4. Plug-flow laboratory bioreactors colonized and maintained with stream water were used to determine the concentration of stream water DOC fractions that had a similar lability to the labile and semi-labile classes within the tracer and we assumed that stream water DOC and tracer DOC with comparable lability fractions in the bioreactors behaved similarly in the stream, i.e. they had the same mass transfer coefficients. 5. A small fraction (8.6\%) of the stream water DOC was labile, travelling 238 m downstream before being taken up. The remaining bioavailable stream water DOC was semi-labile and transported 4.5 km downstream before being taken up. These uptake lengths suggest that the labile DOC is an energy source within a stream reach, while the semi-labile DOC is exported out of the reach to larger rivers and the downstream estuary, where it may provide energy for marine microbial communities or simply be exported to the oceans.},
	language = {en},
	number = {5},
	urldate = {2020-07-01},
	journal = {Freshwater Biology},
	author = {Kaplan, Louis A. and Wiegner, Tracy N. and Newbold, J. D. and Ostrom, Peggy H. and Gandhi, Hasand},
	year = {2008},
	keywords = {bioavailability, dissolved organic carbon, stable isotopes, streams, tracer addition},
	pages = {855--864},
}

@article{tobias_oxygen-18_2007,
	title = {The oxygen-18 isotope approach for measuring aquatic metabolism in high productivity waters},
	volume = {52},
	copyright = {© 2007, by the Association for the Sciences of Limnology and Oceanography, Inc.},
	issn = {1939-5590},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.2007.52.4.1439},
	doi = {10.4319/lo.2007.52.4.1439},
	abstract = {We examined the utility of δ18O2 measurements in estimating gross primary production (P), community respiration (R), and net metabolism (P : R) through diel cycles in a productive agricultural stream located in the midwestern U.S.A. Large diel swings in O2 (±200 µmol L−1) were accompanied by large diel variation in δ18O2 (±10‰). Simultaneous gas transfer measurements and laboratory-derived isotopic fractionation factors for O2 during respiration (αr) were used in conjunction with the diel monitoring of O2 and δ18O2 to calculate P, R, and P :R using three independent isotope-based methods. These estimates were compared to each other and against the traditional “open-channel diel O2-change” technique that lacked δ18O2. A principal advantage of the δ18O2 measurements was quantification of diel variation in R, which increased by up to 30\% during the day, and the diel pattern in R was variable and not necessarily predictable from assumed temperature effects on R. The P, R, and P :R estimates calculated using the isotope-based approaches showed high sensitivity to the assumed system fractionation factor (αr). The optimum modeled ar values (0.986-0.989) were roughly consistent with the laboratory-derived values, but larger (i.e., less fractionation) than αr values typically reported for enzyme-limited respiration in open water environments. Because of large diel variation in O2, P :R could not be estimated by directly applying the typical steady-state solution to the O2 and 18O-O2 mass balance equations in the absence of gas transfer data. Instead, our results indicate that a modified steady-state solution (the daily mean value approach) could be used with time-averaged O2 and δ18O2 measurements to calculate P :R independent of gas transfer. This approach was applicable under specifically defined, net heterotrophic conditions. The diel cycle of increasing daytime R and decreasing nighttime R was only partially explained by temperature variation, but could be consistent with the diel production/consumption of labile dissolved organic carbon from photosynthesis.},
	language = {en},
	number = {4},
	urldate = {2020-07-01},
	journal = {Limnology and Oceanography},
	author = {Tobias, Craig R. and Böhlke, John Karl and Harvey, Judson W.},
	year = {2007},
	pages = {1439--1453},
}

@article{collins_increased_2016,
	title = {Increased {Light} {Availability} {Reduces} the {Importance} of {Bacterial} {Carbon} in {Headwater} {Stream} {Food} {Webs}},
	volume = {19},
	issn = {1432-9840, 1435-0629},
	url = {http://link.springer.com/10.1007/s10021-015-9940-3},
	doi = {10.1007/s10021-015-9940-3},
	language = {en},
	number = {3},
	urldate = {2020-07-01},
	journal = {Ecosystems},
	author = {Collins, Sarah M. and Sparks, Jed P. and Thomas, Steven A. and Wheatley, Sarah A. and Flecker, Alexander S.},
	month = apr,
	year = {2016},
	pages = {396--410},
}

@article{kaplan_untangling_2008-1,
	title = {Untangling the complex issue of dissolved organic carbon uptake: a stable isotope approach},
	volume = {53},
	copyright = {© 2007 The Authors},
	issn = {1365-2427},
	shorttitle = {Untangling the complex issue of dissolved organic carbon uptake},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2427.2007.01941.x},
	doi = {10.1111/j.1365-2427.2007.01941.x},
	abstract = {1. We estimated uptake of stream water dissolved organic carbon (DOC) through a whole-stream addition of a 13C-DOC tracer coupled with laboratory measurements of bioavailability of the tracer and stream water DOC. 2. The tracer, a leachate of 13C-labelled tree tissues, was added to the head waters of White Clay Creek, Pennsylvania, U.S.A., over a 2-h period and followed 1.27 km downstream to generate mass transfer coefficients for DOC lability classes within the tracer. 3. From the longitudinal 13C uptake curve, we resolved labile and semi-labile DOC classes within the 13C-DOC tracer comprising 82\% and 18\% of the tracer respectively. 4. Plug-flow laboratory bioreactors colonized and maintained with stream water were used to determine the concentration of stream water DOC fractions that had a similar lability to the labile and semi-labile classes within the tracer and we assumed that stream water DOC and tracer DOC with comparable lability fractions in the bioreactors behaved similarly in the stream, i.e. they had the same mass transfer coefficients. 5. A small fraction (8.6\%) of the stream water DOC was labile, travelling 238 m downstream before being taken up. The remaining bioavailable stream water DOC was semi-labile and transported 4.5 km downstream before being taken up. These uptake lengths suggest that the labile DOC is an energy source within a stream reach, while the semi-labile DOC is exported out of the reach to larger rivers and the downstream estuary, where it may provide energy for marine microbial communities or simply be exported to the oceans.},
	language = {en},
	number = {5},
	urldate = {2020-07-01},
	journal = {Freshwater Biology},
	author = {Kaplan, Louis A. and Wiegner, Tracy N. and Newbold, J. D. and Ostrom, Peggy H. and Gandhi, Hasand},
	year = {2008},
	keywords = {bioavailability, dissolved organic carbon, stable isotopes, streams, tracer addition},
	pages = {855--864},
}

@article{ulseth_natural_2005,
	title = {Natural abundances of stable isotopes trace anthropogenic {N} and {C} in an urban stream},
	volume = {24},
	issn = {2161-9549, 2161-9565},
	url = {https://bioone.org/journals/Freshwater-Science/volume-24/issue-2/03-080.1/Natural-abundances-of-stable-isotopes-trace-anthropogenic-N-and-C/10.1899/03-080.1.full},
	doi = {10.1899/03-080.1},
	abstract = {Important ecological services of low-order streams are greatly affected by urbanization. North Buffalo Creek, in the headwaters of the Cape Fear River basin in Greensboro, North Carolina, receives point- and nonpoint-source pollutants. Natural abundances of the stable isotopes of C (13C) and N (15N) were used to determine the influence of anthropogenic nutrients on seston δ15N, nutrient concentrations, C/N ratios, and patterns of δ13C and δ15N in foodweb components in North Buffalo Creek during different hydrological conditions. Baseflow seston δ15N varied significantly among sampling sites. Baseflow seston δ15N ranged from 3.7‰ to 4.6‰ at forested sites and was slightly enriched at open sites, and probably reflected nonpoint sources of N in North Buffalo Creek. Seston δ15N also reflected point sources of N in North Buffalo Creek. The most enriched seston δ15N values (8.4‰) were found directly downstream of the Waste Water Treatment Plant (WWTP). Seston δ15N values at the Rankin Mill Road (Rankin) site, several km downstream of the WWTP, also were strongly influenced by effluent from the WWTP. The Summit Avenue site (Summit) received textile effluent until June 2001. Before June 2001, seston 15N at Summit was depleted compared to seston 15N at sites upstream of the plant, probably because the textile effluent was depleted in 15N. During storms, seston δ15N was negatively correlated with nutrient concentrations upstream of the WWTP. However, at Rankin Mill Road, seston δ15N was positively correlated with NO3− flux, which explained 54\% of the variation in seston δ15N. δ15N was not correlated with NH4 and PO4−3 fluxes at Rankin Mill Road. During storms, seston δ15N was influenced partially by nonpoint sources of N, a pattern consistent with observed C/N ratios. δ13C values for most foodweb components and δ15N values for all foodweb components varied significantly between sites, suggesting that sources of C and N differed among sites. Foodweb components at Rankin were enriched in 15N from incorporation of sewage-derived N from the WWTP effluent, whereas, prior to June 2001, foodweb components at Summit appeared to be depleted in 15N from incorporation of textile effluent. Thus, specific influences of point sources of N could be distinguished in foodweb components. Nonpoint sources and stormwater influenced seston δ15N during storm events, but these sources could not be distinguished in consumers by using natural abundances of stable isotopes.},
	number = {2},
	urldate = {2020-07-01},
	journal = {Freshwater Science},
	author = {Ulseth, Amber J. and Hershey, Anne E.},
	month = jun,
	year = {2005},
	note = {Publisher: Society for Freshwater Science},
	pages = {270--289},
}

@article{wiegner_contribution_2005,
	title = {Contribution of dissolved organic {C} to stream metabolism: a mesocosm study using {13C}-enriched tree-tissue leachate},
	volume = {24},
	issn = {0887-3593},
	shorttitle = {Contribution of dissolved organic {C} to stream metabolism},
	url = {https://www.journals.uchicago.edu/doi/abs/10.1899/0887-3593(2005)024%3C0048%3ACODOCT%3E2.0.CO%3B2},
	doi = {10.1899/0887-3593(2005)024<0048:CODOCT>2.0.CO;2},
	abstract = {Dissolved organic C (DOC) is metabolically important in streams, but its contribution to ecosystem metabolism is not well known because it is a complex mixture of mostly unidentified molecules. The uptake of bioavailable DOC in White Clay Creek (WCC), a 3rd-order stream in Pennsylvania, was estimated from the results of an experiment using 13C-labeled tree-tissue leachate and streambed sediments in recirculating mesocosms. The contribution of DOC in transport to stream metabolism was estimated from measurements of 13C-DOC uptake, 12C-DOC concentrations, and diel changes in dissolved O2 in the mesocosms. Eighty percent (±5) of the DOC in the 13C-tree-tissue leachate was bioavailable and belonged to 1 of 2 distinct lability classes, readily and intermediately labile. These components made up 88\% (±0.6) and 12\% (±0.6), respectively, of the biodegradable DOC in the leachate. Uptake mass transfer coefficients for the readily and intermediately labile components were 55 (±24) μm/s and 2.6 (±0.13) μm/s, respectively. Based on our mesocosm measurements, DOC in transport could support 33 to 54\% of the bacterial C demand and up to 51\% of the community respiration in WCC. Extrapolation of our results to WCC indicates that readily and intermediately labile DOC similar in quality to the 13C-DOC would travel 175 and 3692 m downstream in WCC before being taken up by the sediments. These distances represent ∼7\% and {\textgreater}150\% of the length of the 3rd-order reach. Our results suggest that readily labile DOC is an important energy source at the reach scale, whereas intermediately labile DOC serves as an energy subsidy from upstream to downstream reaches.},
	number = {1},
	urldate = {2020-06-30},
	journal = {Journal of the North American Benthological Society},
	author = {Wiegner, Tracy N. and Kaplan, Louis A. and Newbold, J. Denis and Ostrom, Peggy H.},
	month = mar,
	year = {2005},
	note = {Publisher: The University of Chicago Press},
	pages = {48--67},
}

@article{finlay_light-mediated_2011,
	title = {Light-mediated thresholds in stream-water nutrient composition in a river network},
	volume = {92},
	issn = {0012-9658},
	url = {https://www.jstor.org/stable/29779582},
	abstract = {The elemental composition of solutes transported by rivers reflects combined influences of surrounding watersheds and transformations within stream networks, yet comparatively little is known about downstream changes in effects of watershed loading vs. in-channel processes. In the forested watershed of a river under a mediterranean hydrologic regime, we examined the influence of longitudinal changes in environmental conditions on water-column nutrient composition during summer base flow across a network of sites ranging from strongly heterotrophic headwater streams to larger, more autotrophic sites downstream. Small streams (0.1-10 km² watershed area) had longitudinally similar nutrient concentration and composition with low ({\textasciitilde}2) dissolved nitrogen (N) to phosphorus (P) ratios. Abrupt deviations from this pattern were observed in larger streams with watershed areas {\textgreater} 100 km² where insolation and algal abundance and production rapidly increased. Downstream, phosphorus and silica concentrations decreased by {\textgreater}50\% compared to headwater streams, and dissolved organic carbon and nitrogen increased by {\textasciitilde}3-6 times. Decreasing dissolved P and increasing dissolved N raised stream-water N:P to 46 at the most downstream sites, suggesting a transition from N limitation in headwaters to potential P limitation in larger channels. We hypothesize that these changes were mediated by increasing algal photosynthesis and N fixation by benthic algal assemblages, which, in response to increasing light availability, strongly altered stream-water nutrient concentration and stoichiometry in larger streams and rivers.},
	number = {1},
	urldate = {2020-06-30},
	journal = {Ecology},
	author = {Finlay, Jacques C. and Hood, James M. and Limm, Michael P. and Power, Mary E. and Schade, John D. and Welter, Jill R.},
	year = {2011},
	note = {Publisher: Ecological Society of America},
	pages = {140--150},
}

@article{kaylor_relating_2019,
	title = {Relating spatial patterns of stream metabolism to distributions of juveniles salmonids at the river network scale},
	volume = {10},
	copyright = {© 2019 The Authors.},
	issn = {2150-8925},
	url = {http://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecs2.2781},
	doi = {10.1002/ecs2.2781},
	abstract = {Understanding the factors that drive spatial patterns in stream ecosystem processes and the distribution of aquatic biota is important to effective management of these systems and the conservation of biota at the network scale. In this study, we conducted field surveys throughout an extensive river network in NE Oregon that supports diminishing populations of wild salmonids. We collected data on physical habitat, nutrient concentrations, biofilm standing stocks, stream metabolism (gross primary production [GPP] and ecosystem respiration [ER]), and ESA-listed juvenile salmonid density from approximately 50 sites across two sub-basins. Our goals were to (1) to evaluate network patterns in these metrics, and (2) determine network-scale linkages among these metrics, thus providing inference of processes driving observed patterns. Ambient nitrate-N and phosphate-P concentrations were low across both sub-basins ({\textless}40 μg/L). Nitrate-N decreased with watershed area in both sub-basins, but phosphate-P only decreased in one sub-basin. These spatial patterns suggest co-limitation in one sub-basin but N limitation in the other; experimental results using nutrient diffusing substrates across both sub-basins supported these predictions. Solar exposure, temperature, GPP, ER, and GPP:ER increased with watershed area, but biofilm Chl a and ash-free dry mass (AFDM) did not. Spatial statistical network (SSN) models explained between 70\% and 75\% of the total variation in biofilm Chl a, AFDM, and GPP, but only 21\% of the variation in ER. Temperature and nutrient concentrations were the most supported predictors of Chl a and AFDM standing stocks, but these variables explained little of the total variation compared to spatial autocorrelation. In contrast, solar exposure and temperature were the most supported variables explaining GPP, and these variables explained far more variation than autocorrelation. Solar exposure, temperature, and nutrient concentrations explained almost none of the variation in ER. Juvenile salmonids—a key management focus in these sub-basins—were most abundant in cool stream sections where rates of GPP were low, suggesting temperature constraints on these species restrict their distribution to oligotrophic areas where energy production at the base of the food web may be limited.},
	language = {en},
	number = {6},
	urldate = {2020-06-30},
	journal = {Ecosphere},
	author = {Kaylor, Matthew J. and White, Seth M. and Saunders, W. Carl and Warren, Dana R.},
	year = {2019},
	keywords = {biofilm, gross primary production, salmonids, spatial patterns, spatial statistical network models, stream metabolism},
	pages = {e02781},
}

@article{degrandpre_short-term_1998,
	title = {Short-term {pCO2} and {O2} dynamics in {California} coastal waters},
	volume = {45},
	issn = {0967-0645},
	url = {http://www.sciencedirect.com/science/article/pii/S0967064598800064},
	doi = {10.1016/S0967-0645(98)80006-4},
	abstract = {We studied short-term pCO2 and O2 variability in surface waters 30km off Monterey, California from April to May 1995. Sensors for pCO2 and O2 were deployed for 19 days on the manned research platform, R/P FLIP. The sensors were located at 5, 10 and 31m depths. The 31m sensors resided below or within the thermocline, and the 5 and 10m sensors were within the surface mixed layer during the field study. The area was characterized by surface pCO2 undersaturation and O2 supersaturation during the entire period. The average pCO2 levels at 5, 10, and 31m, were 323±18, 326±19, and 452±63μatm, respectively. Much of the short term variability was related to thermocline movement and advection of offshore and coastal upwelled waters around the site. Rates of gas exchange and primary production were determined during periods when advection did not appear to dominate the variability. Air-sea gas exchange models predict an observed decline in O2 supersaturation. Rapid air-sea reequilibration of O2 relative to pCO2 appears to have a significant effect on the pCO2:O2 relationship. Primary production estimates based on CO2 and O2 rates of change match well with shipboard 14C primary production.},
	language = {en},
	number = {8},
	urldate = {2020-06-30},
	journal = {Deep Sea Research Part II: Topical Studies in Oceanography},
	author = {DeGrandpre, M. D. and Hammar, T. R. and Wirick, C. D.},
	month = aug,
	year = {1998},
	pages = {1557--1575},
}

@article{stets_carbonate_2017,
	title = {Carbonate buffering and metabolic controls on carbon dioxide in rivers},
	volume = {31},
	copyright = {©2017. American Geophysical Union. All Rights Reserved.},
	issn = {1944-9224},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2016GB005578},
	doi = {10.1002/2016GB005578},
	abstract = {Multiple processes support the significant efflux of carbon dioxide (CO2) from rivers and streams. Attribution of CO2 oversaturation will lead to better quantification of the freshwater carbon cycle and provide insights into the net cycling of nutrients and pollutants. CO2 production is closely related to O2 consumption because of the metabolic linkage of these gases. However, this relationship can be weakened due to dissolved inorganic carbon inputs from groundwater, carbonate buffering, calcification, and anaerobic metabolism. CO2 and O2 concentrations and other water quality parameters were analyzed in two data sets: a synoptic field study and nationwide water quality monitoring data. CO2 and O2 concentrations were strongly negatively correlated in both data sets (ρ = −0.67 and ρ = −0.63, respectively), although the correlations were weaker in high-alkalinity environments. In nearly all samples, the molar oversaturation of CO2 was a larger magnitude than molar O2 undersaturation. We used a dynamically coupled O2CO2 model to show that lags in CO2 air-water equilibration are a likely cause of this phenomenon. Lags in CO2 equilibration also impart landscape-scale differences in the behavior of CO2 between high- and low-alkalinity watersheds. Although the concept of carbonate buffering and how it creates lags in CO2 equilibration with the atmosphere is well understood, it has not been sufficiently integrated into our understanding of CO2 dynamics in freshwaters. We argue that the consideration of carbonate equilibria and its effects on CO2 dynamics are primary steps in understanding the sources and magnitude of CO2 oversaturation in rivers and streams.},
	language = {en},
	number = {4},
	urldate = {2020-06-30},
	journal = {Global Biogeochemical Cycles},
	author = {Stets, Edward G. and Butman, David and McDonald, Cory P. and Stackpoole, Sarah M. and DeGrandpre, Michael D. and Striegl, Robert G.},
	year = {2017},
	keywords = {biogeochemistry, carbon, metabolism, rivers, streams},
	pages = {663--677},
}

@article{crawford_co2_2014,
	title = {{CO2} and {CH4} emissions from streams in a lake-rich landscape: {Patterns}, controls, and regional significance},
	volume = {28},
	copyright = {©2014. American Geophysical Union. All Rights Reserved.},
	issn = {1944-9224},
	shorttitle = {{CO2} and {CH4} emissions from streams in a lake-rich landscape},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2013GB004661},
	doi = {10.1002/2013GB004661},
	abstract = {Aquatic ecosystems are important components of landscape carbon budgets. In lake-rich landscapes, both lakes and streams may be important sources of carbon gases (CO2 and CH4) to the atmosphere, but the processes that control gas concentrations and emissions in these interconnected landscapes have not been adequately addressed. We use multiple data sets that vary in their spatial and temporal extent during 2001–2012 to investigate the carbon gas source strength of streams in a lake-rich landscape and to determine the contribution of lakes, metabolism, and groundwater to stream CO2 and CH4. We show that streams emit roughly the same mass of CO2 (23.4 Gg C yr−1; 0.49 mol CO2 m−2 d−1) as lakes at a regional scale (27 Gg C yr−1) and that stream CH4 emissions (189 Mg C yr−1; 8.46 mmol CH4 m−2 d−1) are an important component of the regional greenhouse gas balance. Gas transfer velocity variability (range = 0.34 to 13.5 m d−1) contributed to the variability of gas flux in this landscape. Groundwater inputs and in-stream metabolism control stream gas supersaturation at the landscape scale, while carbon cycling in lakes and deep groundwaters does not control downstream gas emissions. Our results indicate the need to consider connectivity of all aquatic ecosystems (lakes, streams, wetlands, and groundwater) in lake-rich landscapes and their connections with the terrestrial environment in order to understand the full nature of the carbon cycle.},
	language = {en},
	number = {3},
	urldate = {2020-06-30},
	journal = {Global Biogeochemical Cycles},
	author = {Crawford, John T. and Lottig, Noah R. and Stanley, Emily H. and Walker, John F. and Hanson, Paul C. and Finlay, Jacques C. and Striegl, Robert G.},
	year = {2014},
	keywords = {carbon dioxide, groundwater, metabolism, methane, streams, upscaling},
	pages = {197--210},
}

@article{vachon_paired_2019,
	title = {Paired {O2}–{CO2} measurements provide emergent insights into aquatic ecosystem function},
	volume = {n/a},
	copyright = {© 2019 The Authors. Limnology and Oceanography published by Wiley Periodicals, Inc. on behalf of Association for the Sciences of Limnology and Oceanography.},
	issn = {2378-2242},
	url = {http://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lol2.10135},
	doi = {10.1002/lol2.10135},
	abstract = {Scientific Significance Statement Metabolic stoichiometry predicts that dissolved oxygen (O2) and carbon dioxide (CO2) in aquatic ecosystems should covary inversely; however, field observations often diverge from theoretical expectations. Here, we propose a suite of metrics describing this O2 and CO2 decoupling and introduce a conceptual framework for interpreting these metrics within aquatic ecosystems. Within this framework, we interpret cross-system patterns of high-frequency O2 and CO2 measurements in 11 northern lakes and extract emergent insights into the metabolic behavior and the simultaneous roles of chemical and physical forcing in shaping ecosystem processes. This approach leverages the power of high-frequency paired O2–CO2 measurements, and yields a novel, integrative aquatic system typology which can also be applicable more broadly to streams and rivers, wetlands and marine systems.},
	language = {en},
	number = {n/a},
	urldate = {2020-04-28},
	journal = {Limnology and Oceanography Letters},
	author = {Vachon, Dominic and Sadro, Steven and Bogard, Matthew J. and Lapierre, Jean-François and Baulch, Helen M. and Rusak, James A. and Denfeld, Blaize A. and Laas, Alo and Klaus, Marcus and Karlsson, Jan and Weyhenmeyer, Gesa A. and Giorgio, Paul A. del},
	year = {2019}
}

@article{hanson_lake_2006,
	title = {Lake {Dissolved} {Inorganic} {Carbon} and {Dissolved} {Oxygen}: {Changing} {Drivers} from {Days} to {Decades}},
	volume = {76},
	copyright = {© 2006 by the Ecological Society of America},
	issn = {1557-7015},
	shorttitle = {Lake {Dissolved} {Inorganic} {Carbon} and {Dissolved} {Oxygen}},
	url = {http://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/0012-9615%282006%29076%5B0343%3ALDICAD%5D2.0.CO%3B2},
	doi = {10.1890/0012-9615(2006)076[0343:LDICAD]2.0.CO;2},
	abstract = {Dissolved inorganic carbon (DIC) and dissolved oxygen (DO) are commonly measured to compute metabolism of aquatic ecosystems. However, concentrations of DIC and DO depend on many factors in addition to ecosystem metabolism, such as water temperature, gas exchange with the atmosphere, abiotic chemical reactions, and inputs in precipitation, groundwater, and surface water. We used 20-year time series from seven lakes to understand how DIC and DO concentrations are controlled as a function of time scale. Diel cycles of both solutes are controlled primarily by metabolism, exchange with the atmosphere, and temperature. At seasonal and annual scales, metabolism is important, but physical processes associated with spring and autumn mixing, as well as solute loading from the watershed, have comparably large effects. At decadal scales, effects of metabolism are negligible. Controls of the two solutes diverge, with variance in DIC explained largely by solute inputs and variance in DO explained largely by water temperature. Like other indicators in many ecosystems, variability of DIC and DO is strongly scale dependent and associated with different drivers depending on the time scale of the analysis.},
	language = {en},
	number = {3},
	urldate = {2020-06-30},
	journal = {Ecological Monographs},
	author = {Hanson, Paul C. and Carpenter, Stephen R. and Armstrong, David E. and Stanley, Emily H. and Kratz, Timothy K.},
	year = {2006},
	keywords = {aquatic ecosystem metabolism, dissolved inorganic carbon (DIC), dissolved oxygen (DO), drivers of DIC and DO, ecosystem drivers, lake concentrations of DIC and DO, long-term ecological research, temporal scale},
	pages = {343--363},
}

@article{torgersen_carbon_2008,
	title = {Carbon and oxygen fluxes from a small pond to the atmosphere: {Temporal} variability and the {CO2}/{O2} imbalance},
	volume = {44},
	copyright = {Copyright 2008 by the American Geophysical Union.},
	issn = {1944-7973},
	shorttitle = {Carbon and oxygen fluxes from a small pond to the atmosphere},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2006WR005634},
	doi = {10.1029/2006WR005634},
	abstract = {Because of the relative strength of sediment processes compared to water column processes, natural and anthropogenic ponds represent an important component of the terrestrial hydrologic cycle and a site for recycling carbon to the atmosphere. Over 250 d of dissolved oxygen and carbon dioxide concentrations were measured on the 0.5 h timescale in a small Connecticut pond. Using approximately 8000 half-hour time intervals, Mirror Lake (Storrs, Connecticut) exhibits net annual fluxes for 2002 and 2003 of 80 and 86 mmol CO2 m−2 d−1 (±26\%) and 25 and −7.5 mmol O2 m−2 d−1 (±20\%), respectively (positive flux is to the atmosphere). The instantaneous (0.5 h) fluxes of both CO2 and O2 to the atmosphere exhibit a standard deviation in the flux (measured every 0.5 h) of the order 100\%, indicating a high degree of daily, weekly, and seasonal variability in the controlling processes, and the two gases rarely follow Redfield ratio stoichiometry. This net carbon flux to the atmosphere agrees with the range of carbon fluxes from various shallow inland aquatic waters. Using CO2 and O2 mass balances, the minimum bacterial production of CO2 in the pond is estimated to be 100 and 81mmol CO2 m−2 d−1 for 2002 and 2003 (same order as the net CO2 flux from the pond), indicating the importance of the bacterial processes in pond carbon dynamics. Bacterial pathways that utilize NO3−1 or fermentation strongly favor CO2 production relative to O2 consumption and may provide a mechanistic explanation for the (instantaneous to annual) CO2 to O2 imbalance relative to the Redfield ratio. Thus, while natural and man-made ponds do provide advantages for flood control, sediment settling, and some degree of contaminant removal, ponds may also provide a locus for the processing of terrestrial carbon into a CO2 source to the atmosphere. Given the number of small ponds and their location in the hydrologic cycle, pond systems represent a coupling of hydrology and the carbon cycle worthy of greater investigation.},
	language = {en},
	number = {2},
	urldate = {2020-06-30},
	journal = {Water Resources Research},
	author = {Torgersen, T. and Branco, B.},
	year = {2008},
	keywords = {carbon cycle, observing networks, ponds},
}

@article{torgersen_carbon_2007,
	title = {Carbon and oxygen dynamics of shallow aquatic systems: {Process} vectors and bacterial productivity},
	volume = {112},
	copyright = {Copyright 2007 by the American Geophysical Union.},
	issn = {2156-2202},
	shorttitle = {Carbon and oxygen dynamics of shallow aquatic systems},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2007JG000401},
	doi = {10.1029/2007JG000401},
	abstract = {In shallow aquatic systems subject to heavy allochthonous (terrestrial) organic loading, bacterial processing of organic matter can be a significant component in the ecosystem C-cycle. Because this bacterial processing of organic matter also produces reduced species (Fe+2, Mn+2, S−2, NH3, etc.), these processes also create an additional chemical oxygen demand. Hence, net ecosystem operation can deviate significantly from the “Redfield Line” defined by the traditional photosynthesis/respiration reaction stoichiometry. Here, a 3D process vector concept is presented in terms of (gas-exchange-corrected) CO2 or O2-TDIC-time to characterize significant bacterial contributions to the net O2 and TDIC dynamics of the ecosystem. The direction of the process vector provides an important clue to the internal process dynamics and the biogeochemical pathways that govern the net ecosystem function. Using instrumented in situ measures of O2 and TDIC in a small pond (ca. 0.7 m deep), this ecosystem is shown to operate significantly off the “Redfield Line” with multiple periods producing a net increase in both (gas-exchange-corrected) O2 and CO2 and exporting of both to the atmosphere. A methodology for the quantification of the minimum bacterially produced TDIC in the ecosystem (MBP) is developed. The rates (38–91 mmoles C m−2 day−1) are consistent with measured carbon fluxes from shallow terrestrial aquatic systems as well as anticipated cell numbers in the sediment that likely contribute to this bacterially produced carbon. The process vector concept can be extended to additional dimensions (CH4, NO3−, NH4+, Fe+2, etc.) and may provide a tool for visualization of observatory data streams.},
	language = {en},
	number = {G3},
	urldate = {2020-06-30},
	journal = {Journal of Geophysical Research: Biogeosciences},
	author = {Torgersen, Thomas and Branco, Brett},
	year = {2007},
	keywords = {aqueous processes, bacterial processes, carbon cycle, oxygen, ponds},
}

@article{power_seasonal_2008,
	title = {Seasonal {Reassembly} of a {River} {Food} {Web}: {Floods}, {Droughts}, and {Impacts} of {Fish}},
	volume = {78},
	copyright = {© 2008 by the Ecological Society of America},
	issn = {1557-7015},
	shorttitle = {Seasonal {Reassembly} of a {River} {Food} {Web}},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/06-0902.1},
	doi = {10.1890/06-0902.1},
	abstract = {Eighteen years of field observations and five summer field experiments in a coastal California river suggest that hydrologic regimes influence algal blooms and the impacts of fish on algae, cyanobacteria, invertebrates, and small vertebrates. In this Mediterranean climate, rainy winters precede the biologically active summer low-flow season. Cladophora glomerata, the filamentous green alga that dominates primary producer biomass during summer, reaches peak biomass during late spring or early summer. Cladophora blooms are larger if floods during the preceding winter attained or exceeded “bankfull discharge” (sufficient to mobilize much of the river bed, estimated at 120 m3/s). In 9 out of 12 summers preceded by large bed-scouring floods, the average peak height of attached Cladophora turfs equaled or exceeded 50 cm. In five out of six years when flows remained below bankfull, Cladophora biomass peaked at lower levels. Flood effects on algae were partially mediated through impacts on consumers in food webs. In three experiments that followed scouring winter floods, juvenile steelhead (Oncorhynchus mykiss) and roach (Lavinia (Hesperoleucas) symmetricus) suppressed certain insects and young-of-the-year fish fry, affecting persistence or accrual of algae positively or negatively, depending on the predator-specific vulnerabilities of primary consumers capable of suppressing algae during a given year. During two post-flood years, these grazers were more vulnerable to small predators (odonates and fish fry, which stocked steelhead always suppressed) than to experimentally manipulated, larger fish, which had adverse effects on algae in those years. During one post-flood year, all enclosed grazers capable of suppressing algae were consumed by steelhead, which therefore had positive effects on algae. During drought years, when no bed-scouring winter flows occurred, large armored caddisflies (Dicosmoecus gilvipes) were more abundant during the subsequent summer. In drought-year experiments, stocked fish had little or no influence on algal standing crops, which increased only when Dicosmoecus were removed from enclosures. Flood scour, by suppressing invulnerable grazers, set the stage for fish mediated effects on algae in this river food web. Whether these effects were positive or negative depended on the predator-specific vulnerabilities of primary consumers that dominated during a given summer.},
	language = {en},
	number = {2},
	urldate = {2020-06-29},
	journal = {Ecological Monographs},
	author = {Power, Mary E. and Parker, Michael S. and Dietrich, William E.},
	year = {2008},
	keywords = {Cladophora glomerata, Lavinia (Hesperoleucas) symmetricus, Mediterranean hydrologic regimes, Oncorhynchus mykiss, algal blooms, context dependency, effect sizes, flood scour, food chain length, interaction strength, long-term studies, predator impacts},
	pages = {263--282},
}

@article{macrae_intra-annual_2007,
	title = {Intra-annual variability in the contribution of tile drains to basin discharge and phosphorus export in a first-order agricultural catchment},
	volume = {92},
	issn = {0378-3774},
	url = {http://www.sciencedirect.com/science/article/pii/S0378377407001424},
	doi = {10.1016/j.agwat.2007.05.015},
	abstract = {This study examines spatiotemporal variability (event-based, seasonal) in the contribution of drainage tiles within a basin to basin hydrologic discharge and soluble reactive phosphorus (SRP) and total phosphorus (TP) export over a period of 1 year. Tile discharge was highly variable at both moderate (wet versus dry periods) and smaller (within-event) temporal scales, accounting for 0–90\% of basin discharge at any given time. An estimated 42\% of basin annual discharge originated from drainage tiles, the majority of which occurred during the winter and spring months. Concentrations of SRP and TP in drainage tile effluent were also highly variable in space and time (1–2850μgSRPL−1, 5–8275μgTPL−1). Higher concentrations of SRP and TP were linked to fields receiving manure compared to fields receiving inorganic fertilizers. SRP export from tiles accounted for 118\% of basin SRP export on average, although their contribution to basin SRP export ranged from 4 to 344\% on 32 discrete dates during which all tiles in the basin were sampled for hydrochemistry. On the same 32 dates, tiles accounted for an average of 43\% of basin TP export, although this ranged from 0 to 200\%. Management options such as tile plugs and optimizing the timing and application rates of fertilizer should be explored to minimize nutrient export from tiles.},
	language = {en},
	number = {3},
	urldate = {2020-06-25},
	journal = {Agricultural Water Management},
	author = {Macrae, M. L. and English, M. C. and Schiff, S. L. and Stone, M.},
	month = sep,
	year = {2007},
	keywords = {Agriculture, Antecedent hydrologic conditions, Hydrology, Management practices, Season, Soluble reactive phosphorus, Tile drainage, Total phosphorus},
	pages = {171--182},
}

@article{rissebuhl_tracking_2012,
	title = {Tracking the autochthonous carbon transfer in stream biofilm food webs},
	volume = {79},
	copyright = {© 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved},
	issn = {1574-6941},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/j.1574-6941.2011.01202.x},
	doi = {10.1111/j.1574-6941.2011.01202.x},
	abstract = {Food webs in the rhithral zone rely mainly on allochthonous carbon from the riparian vegetation. However, autochthonous carbon might be more important in open canopy streams. In streams, most of the microbial activity occurs in biofilms, associated with the streambed. We followed the autochthonous carbon transfer toward bacteria and grazing protozoa within a stream biofilm food web. Biofilms that developed in a second-order stream (Thuringia, Germany) were incubated in flow channels under climate-controlled conditions. Six-week-old biofilms received either 13C- or 12C-labeled CO2, and uptake into phospholipid fatty acids was followed. The dissolved inorganic carbon of the flow channel water became immediately labeled. In biofilms grown under 8-h light/16-h dark conditions, more than 50\% of the labeled carbon was incorporated in biofilm algae, mainly filamentous cyanobacteria, pennate diatoms, and nonfilamentous green algae. A mean of 29\% of the labeled carbon reached protozoan grazer. The testate amoeba Pseudodifflugia horrida was highly abundant in biofilms and seemed to be the most important grazer on biofilm bacteria and algae. Hence, stream biofilms dominated by cyanobacteria and algae seem to play an important role in the uptake of CO2 and transfer of autochthonous carbon through the microbial food web.},
	language = {en},
	number = {1},
	urldate = {2020-05-25},
	journal = {FEMS Microbiology Ecology},
	author = {Risse‐Buhl, Ute and Trefzger, Nicolai and Seifert, Anne-Gret and Schönborn, Wilfried and Gleixner, Gerd and Küsel, Kirsten},
	year = {2012},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1574-6941.2011.01202.x},
	keywords = {PLFA, autochthonous carbon, grazing protozoa, stable isotopes, stream biofilm},
	pages = {118--131},
}

@article{lyon_carbon_2009,
	title = {Carbon cycling within epilithic biofilm communities across a nutrient gradient of headwater streams},
	volume = {54},
	copyright = {© 2009, by the Association for the Sciences of Limnology and Oceanography, Inc.},
	issn = {1939-5590},
	url = {http://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.2009.54.2.0439},
	doi = {10.4319/lo.2009.54.2.0439},
	abstract = {Primary production (PP), nutrient uptake, and carbon (C) cycling within epilithic biofilm communities were assessed in four headwater streams in the Arkansas Ozarks, U.S.A., representing a hundred-fold range in total dissolved nitrogen (TDN) and soluble reactive phosphorus concentrations. Small enclosures containing stream water and rock substrate were incubated for 8 h with 13C-enriched dissolved inorganic C. 13C was measured in dissolved organic carbon (DOC), bulk biofilm, and individual biofilm phospholipid fatty acids (PLFA) as biomarkers for C uptake into autotrophic and heterotrophic microorganisms. Biofilm \%N, chlorophyll content, C-specific biofilm PP, N-specific TDN uptake, and relative abundance of algal PLFA increased with the nutrient gradient represented by the four study streams. Total net DOC release as a proportion of PP was greatest in both the lowest and highest nutrient streams, while the source of released DOC varied with the nutrient gradient. In the most nutrient-rich stream a greater fraction of DOC was comprised of C fixed during the incubation, but in the most nutrient-poor stream released DOC was mainly derived from older biofilm C. Carbon uptake into PLFA increased with the nutrient gradient for algal but not heterotrophic bacterial biomarkers, indicating lower relative incorporation of new PP by biofilm heterotrophs in higher nutrient streams. Results suggest that tight C flow between biofilm autotrophs and heterotrophs may support biofilm nutrient retention in low-nutrient streams while nutrient enrichment may disrupt this coupling and release more new PP as DOC with potential effects on nutrient export to downstream ecosystems.},
	language = {en},
	number = {2},
	urldate = {2020-05-25},
	journal = {Limnology and Oceanography},
	author = {Lyon, David R. and Ziegler, Susan E.},
	year = {2009},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.4319/lo.2009.54.2.0439},
	pages = {439--449},
}

@article{hall_use_1995,
	title = {Use of a {Stable} {Carbon} {Isotope} {Addition} to {Trace} {Bacterial} {Carbon} through a {Stream} {Food} {Web}},
	volume = {14},
	issn = {0887-3593},
	url = {https://www.jstor.org/stable/1467779},
	doi = {10.2307/1467779},
	abstract = {The use of bacterial carbon by stream invertebrates was assessed by dripping $^{\textrm{13}}$C as sodium acetate into a headwater spring at Coweeta Hydrologic Laboratory for three weeks during August 1992. The addition raised the δ $^{\textrm{13}}$C value of dissolved organic carbon from approximately -26‰ to approximately 100‰. Coarse particulate organic matter, fine particulate organic matter (FPOM), and 14 taxa of animals were analyzed by mass spectrometer before and after the $^{\textrm{13}}$C addition. Pre-addition sample δ $^{\textrm{13}}$C ranged from -36‰ to -22‰; post-addition samples ranged from -35‰ to 129‰. Predators contained less $^{\textrm{13}}$C label than collectors, shredders, and scrapers. Shredders were not uniformly labeled, suggesting low use of bacterial carbon. Stenonema (Heptageniidae), a biofilm scraper, was the most highly labeled taxon (up to 128‰), even though biofilm δ $^{\textrm{13}}$C was -16‰. Chironomids and copepods were clearly labeled and had a higher δ $^{\textrm{13}}$C than the FPOM, suggesting preferential assimilation of bacterial carbon relative to FPOM. Although adults and larvae of Optioservus (Elmidae) are believed to be scrapers, the adults were more labeled than the larvae, indicating greater dependence on bacterial carbon. Gut analyses of Optioservus corroborated the stable isotope results: adult guts contained mostly detritus whereas larval guts contained a high proportion of diatoms. This technique is useful for determining the relative differences in bactivory by an assemblage of stream animals.},
	number = {2},
	urldate = {2020-05-25},
	journal = {Journal of the North American Benthological Society},
	author = {Hall, Robert O.},
	year = {1995},
	note = {Publisher: [University of Chicago Press, Society for Freshwater Science]},
	pages = {269--277},
}

@article{hill_changes_2006,
	title = {Changes in carbon stable isotope ratios during periphyton development},
	volume = {51},
	copyright = {© 2006, by the Association for the Sciences of Limnology and Oceanography, Inc.},
	issn = {1939-5590},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.2006.51.5.2360},
	doi = {10.4319/lo.2006.51.5.2360},
	abstract = {Stable isotopes are widely used to infer trophic relationships with little attention paid to temporal variability at the base of the food web. We examined changes in the carbon-stable isotope composition during periphyton development, sampling periphyton that accumulated on ceramic tiles at four stream sites over a 2-month period. Periphyton 13C rose and fell in general concordance with rising and falling biomass at all four sites, resulting in significant correlations between periphyton Δ13C and chlorophyll a (Chl a). Mean Δ13C values at one site rose from -26‰ to -20‰ in 2 weeks, falling back to -24‰ the next week after a large scouring spate. Periphyton 13C also underwent a smaller, longer-term increase that correlated with a gradual rise in stream temperature. Multiple regression analysis with both Chl a and temperature as independent variables accounted for up to 88\% of the temporal variability in Δ13C, with Chl a the largest source of variability. Water velocity, measured on each sampling occasion, was unrelated to temporal changes in 13C. Depletion of inorganic carbon within the periphyton matrix is the probable cause of increasing 13C in periphyton as biomass develops. Rising Δ13C values during periphyton biomass development suggest the possibility of carbon-limited periphyton growth, even in alkaline waters. The strong link between biomass and periphyton 13C helps explain the large range of Δ13C reported for periphyton in streams, where temporal and spatial variability in periphyton biomass are notorious.},
	language = {en},
	number = {5},
	urldate = {2020-05-25},
	journal = {Limnology and Oceanography},
	author = {Hill, Walter R. and Middleton, R. Gerry},
	year = {2006},
	note = {\_eprint: https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.4319/lo.2006.51.5.2360},
	pages = {2360--2369},
}

@article{hotchkiss_whole-stream_2015,
	title = {Whole-stream {13C} tracer addition reveals distinct fates of newly fixed carbon},
	volume = {96},
	copyright = {© 2015 by the Ecological Society of America},
	issn = {1939-9170},
	url = {http://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/14-0631.1},
	doi = {10.1890/14-0631.1},
	abstract = {Many estimates of freshwater carbon (C) fluxes focus on inputs, processing, and storage of terrestrial C; yet inland waters have high rates of internally fixed (autochthonous) C production. Some fraction of newly fixed C may be released as biologically available, dissolved organic C (DOC) and stimulate microbial-driven biogeochemical cycles soon after fixation, but the fate of autochthonous C is difficult to measure directly. Tracing newly fixed C can increase our understanding of fluxes and fate of autochthonous C in the context of freshwater food webs and C cycling. We traced autochthonous C fixation and fate using a dissolved inorganic C stable isotope addition (13CDIC). We added 13CDIC to North Fork French Creek, Wyoming, USA during two days in August. We monitored changes in 13C pools, fluxes, and storage for 44 d after the addition. Two-compartment flux models were used to quantify net release of newly fixed 13CDOC and 13CDIC into the water column. We compared net 13C fixation with tracer 13CDIC removal and gross primary production (GPP) to account for the mass of tracer fixed, released, lost to the atmosphere, and exported downstream. Much of the fixed C turned over rapidly and did not enter longer-term storage pools. Net C fixed was 70\% of GPP measured with O2. Algae likely released the remaining 30\% via 13CDOC exudation and respiration of newly fixed C. Primary producers released 13CDOC at rates of up to 16\% per day during the 13C addition, but exudation of new labile C declined to near zero by day 6. DIC production from newly fixed C accounted for 21\% of ecosystem respiration the day after the 13C addition. All measured organic C (OC) pools were enriched with 13C 1 d after the tracer addition. 20\% of fixed 13C remained in benthic OC by day 44, and average residence time of autochthonous C in benthic OC was 62 d. Newly fixed C had two distinct fates: short-term ({\textless}1 week) exudation and respiration or longer-term storage and downstream export. Autochthonous C in streams likely fuels short-term microbial production and biogeochemical cycling, in addition to providing a longer-term resource for consumers.},
	language = {en},
	number = {2},
	urldate = {2020-05-25},
	journal = {Ecology},
	author = {Hotchkiss, Erin R. and Hall, Robert O.},
	year = {2015},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1890/14-0631.1},
	keywords = {13C tracer, C cycling, DOC exudation, autochthonous, ecosystem metabolism, residence time, stable isotopes, streams},
	pages = {403--416},
}

@article{feijoo_retention_2018,
	title = {Retention and release of nutrients and dissolved organic carbon in a nutrient-rich stream: {A} mass balance approach},
	volume = {566},
	issn = {0022-1694},
	shorttitle = {Retention and release of nutrients and dissolved organic carbon in a nutrient-rich stream},
	url = {http://www.sciencedirect.com/science/article/pii/S0022169418307455},
	doi = {10.1016/j.jhydrol.2018.09.051},
	abstract = {The relevance of fluvial systems to process nutrients and carbon is widely accepted, but their role as sinks and sources of nutrients and dissolved organic carbon (DOC) is still under discussion especially in non-forested and highly productive streams. In this study, we used a mass balance approach at a reach scale in a Pampean stream to elucidate the major sources of water, nutrients and DOC as well as to determine net in-stream retention efficiencies of nutrients and DOC under different hydrological conditions. We measured conductivity, conservative ions (chloride and calcium), soluble reactive phosphorus (SRP), nitrate (NO3), nitrite (NO2), ammonium (NH4) and DOC at the end-point of a reach of Las Flores stream (site A), at two upstream tributaries (B1 and B2), and at each potential hydrological contributors to stream flow (groundwater, overland and subsurface flows, and rainfall). In addition, we monitored one storm event where we collected samples during the rising and the recession limb of the hydrograph. Stream flow originated from groundwater (≈50\%), upstream tributaries (B1 and B2) at baseflow, whereas overland flow contributed {\textgreater}20\% during high flows. During baseflow, groundwater provided NO3 to stream water, while B2, which received a point input of a dairy industry, was the main source of SRP and NH4. Conversely, SRP and NH4 were provided by B1, overland flow and subsurface flow during high flows. Overland flow also contributed DOC during high flow periods. Mass balance estimates revealed that the reach acts as a source of DOC, SRP and NO3 (21.4, 37.4 and 53.5\% mean net in-stream release, respectively) and a sink of NH4 (−36.8\% mean net in-stream retention). Relevant in-stream processes may be nutrient uptake (as in the case of SRP and NH4) and biotic production (DOC), as well as decomposition (SRP) and nitrification (NH4) in this Pampean stream. Our results stress the relevance of nutrient and DOC generation processes within the channel in non-forested and highly productive streams.},
	language = {en},
	urldate = {2020-05-21},
	journal = {Journal of Hydrology},
	author = {Feijoó, Claudia and Messetta, María Laura and Hegoburu, Cecilia and Gómez Vázquez, Alicia and Guerra-López, José and Mas-Pla, Josep and Rigacci, Laura and García, Victoria and Butturini, Andrea},
	month = nov,
	year = {2018},
	keywords = {Groundwater, In-stream processing, Nitrogen, Phosphorus, Storm events},
	pages = {795--806},
}

@article{shin_factors_2020,
	title = {Factors affecting diurnal dissolved inorganic carbon and its isotopic composition in a small stream on a volcanic island in {South} {Korea}},
	volume = {24},
	issn = {1598-7477},
	url = {10.1007/s12303-019-0013-z},
	doi = {10.1007/s12303-019-0013-z},
	abstract = {Water samples were collected hourly at a small stream on Jeju Island, South Korea in both wet and dry seasons to identify the factors affecting dissolved inorganic carbon (DIC) and its isotopic composition (δ13CDIC). In the wet season, dissolved oxygen (DO) displayed a diurnal pattern with lower values in samples collected between sunset and sunrise compared to samples at other times. Likewise, a diurnal pattern was observed for pH, DIC and δ13CDIC. An overall negative correlation between DIC and DO indicated that photosynthesis and respiration in the stream are the main factors controlling DIC concentration and behavior. Notably, samples at night displayed two trends in plots of DO and DIC, with different δ13CDIC values. This was due to CO2 outgassing from the stream to the ambient atmosphere. Partial pressure of CO2 (pCO2), calcite saturation index (SIcalcite), and equilibrium isotope fractionation between HCO3− and CO2 gas were related to the δ13CDIC value, verifying that photosynthesis and respiration determined DIC behavior. In addition to microbial activity, CO2 outgassing contributed to DIC in the stream after respiration and before photosynthesis. In comparison, δ13CDIC values in the dry season were similar to those in the wet season but showed no clear relationship with pCO2 and SIcalcite. Unlike the wet season, this indicated that in the dry season, photosynthesis and respiration are not the dominant processes and that CO2 exchange between the atmosphere and water is more important in determining DIC.},
	language = {en},
	number = {1},
	urldate = {2020-05-21},
	journal = {Geosciences Journal},
	author = {Shin, Woo-Jin and Choi, Seung-Hyun and Ryu, Jong-Sik and Ha, Kyoochul and Lee, Ji-Yeon and Lee, Kwang-Sik},
	month = feb,
	year = {2020},
	pages = {73--83},
}

@article{raven_inorganic_1982,
	title = {Inorganic {C}-{Sources} for {Lemanea}, {Cladophora} and {Ranunculus} in a {Fast}-{Flowing} {Stream}: {Measurements} of {Gas} {Exchange} and of {Carbon} {Isotope} {Ratio} and {Their} {Ecological} {Implications}},
	volume = {53},
	issn = {0029-8549},
	shorttitle = {Inorganic {C}-{Sources} for {Lemanea}, {Cladophora} and {Ranunculus} in a {Fast}-{Flowing} {Stream}},
	url = {https://www.jstor.org/stable/4216650},
	abstract = {CO₂- and O₂-exchange characteristics and δ 13C values have been measured in a rhodophycean haptophyte (Lemanea mamillosa), a chlorophycean haptophyte (Cladophora glomerata) and a magnoliophyte rhizophyte (Ranunculus sp.) from a 5 m stretch of the Dichty Burn near Dundee. Light- and CO₂-saturated rates of photosynthesis are greatest on a dry weight basis for Cladophora and lowest for Lemanea; the order is reversed on a surface area basis. The CO₂ concentration at pH 6.5 at which photosynthesis is half-saturated is 25-40 μM, with Lemanea rather lower than Cladophora or Ranunculus; these half-saturation values are similar to the free CO₂ concentration in the Burn water. Lemanea cannot use HCO3 - in photosynthesis, while Cladophora and Ranunculus can. Despite being within a factor or two of saturation with free CO₂ in terms of the bulk water concentration, the growth habit of Cladophora and, particularly, Ranunculus means that the high water velocity in the Burn does not necessarily prevent C depletion effects around the plants, thus providing a possible role for HCO3 - use by these plants. Lemanea lives in the fastest-growing parts of the Burn, and its growth habit insures that it is exposed to this high water velocity, thus minimising CO₂ depletion during photosynthesis despite the low surface/volume ratio for this plant. δ 13C measurements on the inorganic C in the Burn water are consistent with at least part of its excess (above air-equilibrium) inorganic C levels coming from heterotrophic activity. Lemanea has the most negative δ 13C value of the three plants, consistent with CO₂ use and small diffusion resistances. Ranunculus has the least negative δ 13C value, consistent with some CO₂ depletion and/or HCO3 - use in situ related to a high diffusion resistance in a rhizophyte which does not have to obtain all of its N and P from the bulk water but can obtain some from the sediments. Cladophora is intermediate, suggesting some CO₂ depletion and/or HCO3 - use in this densely growing haptophyte.},
	number = {1},
	urldate = {2020-05-21},
	journal = {Oecologia},
	author = {Raven, John and Beardall, John and Griffiths, Howard},
	year = {1982},
	note = {Publisher: Springer},
	pages = {68--78},
}

@article{gammons_diel_2011,
	series = {Diel {Biogeochemical} {Processes} in {Terrestrial} {Waters}},
	title = {Diel cycling and stable isotopes of dissolved oxygen, dissolved inorganic carbon, and nitrogenous species in a stream receiving treated municipal sewage},
	volume = {283},
	issn = {0009-2541},
	url = {http://www.sciencedirect.com/science/article/pii/S0009254110002457},
	doi = {10.1016/j.chemgeo.2010.07.006},
	abstract = {Diel and synoptic studies were undertaken in Silver Bow Creek, a small, highly eutrophic stream receiving municipal sewage from the city of Butte, Montana, USA. During mid-summer baseflow conditions, oxidation of ammonium from the Butte wastewater treatment plant created a 2-km long reach marked by nightly hypoxia and extreme growth of aquatic plants and algae. Large diel cycles in the concentrations and isotopic compositions of dissolved oxygen (DO) and dissolved inorganic carbon (DIC) were inversely related, and are explained by the daily cycle of photosynthesis and respiration, modified by the effects of nitrification. Nitrification rates were higher during the day than at night due to a combination of higher water temperatures and higher DO concentrations. Changes in nitrification rate imparted diel cycles in the concentrations and N-isotopic compositions of NO3− and NH4+, whereas total dissolved inorganic nitrogen (DIN) concentrations and δ15N-DIN values showed minimal diel variation. δ15N-NH4 steadily increased with distance downstream over a 5km reach, whereas δ15N-NO3 showed a more complex spatial pattern. Plant assimilation caused downstream decreases in DIN and soluble reactive phosphorous: however, it was not possible to determine whether the plants assimilated NO3−, NH4+, or both. An important new finding of this study is the recognition that synoptic and diel changes in δ18O-DO in the zone of active nitrification imparted a corresponding change in δ18O-NO3. Future studies examining the O-isotope composition of nitrate need to consider whether DO has a constant or shifting isotopic composition at the source of nitrification. The results of this study underscore the complex and dynamic interactions between biologically-active solutes in nutrient-rich streams, and also emphasize the importance of recognizing these cycles when collecting samples for scientific or monitoring purposes.},
	language = {en},
	number = {1},
	urldate = {2020-05-21},
	journal = {Chemical Geology},
	author = {Gammons, Christopher H. and Babcock, John N. and Parker, Stephen R. and Poulson, Simon R.},
	month = apr,
	year = {2011},
	keywords = {Ammonium, Diel, Dissolved oxygen, Diurnal, Nitrate, Nitrification, Photosynthesis, Respiration, Stable isotope},
	pages = {44--55},
}

@article{finlay_stable-carbon-isotope_2001,
	title = {Stable-{Carbon}-{Isotope} {Ratios} of {River} {Biota}:implications for {Energy} {Flow} in {Lotic} {Food} {Webs}},
	volume = {82},
	copyright = {© 2001 by the Ecological Society of America},
	issn = {1939-9170},
	shorttitle = {Stable-{Carbon}-{Isotope} {Ratios} of {River} {Biota}},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/0012-9658%282001%29082%5B1052%3ASCIROR%5D2.0.CO%3B2},
	doi = {10.1890/0012-9658(2001)082[1052:SCIROR]2.0.CO;2},
	abstract = {Stable-isotope ratios of carbon (13C/12C or δ13C) have been widely used to determine the energy base of stream food webs, but such use is controversial due to unexplained variability in algal δ13C. I used published δ13C data from temperate headwater streams through medium-sized rivers (0.2–4000 km2 watershed area) collected during summer baseflows and original data from streams in northern California to analyze energy pathways through river food webs. The analyses showed three important results. First, epilithic algal δ13C and watershed area are positively related, suggesting that effects of carbon limitation on algal carbon uptake result in 13C enrichment of algal δ13C in larger, more productive rivers. Second, epilithic algae and terrestrial detritus δ13C values are often distinct in small shaded streams but overlap in some larger unshaded streams and rivers. Measurements of δ13C values may be most useful in distinguishing algal and terrestrial energy sources in unproductive streams with supersaturated dissolved CO2 concentrations, and some productive rivers where CO2 concentrations are low relative to photosynthetic rates. Finally, consumer δ13C values are more strongly related to algal δ13C than terrestrial δ13C. The relative contribution of terrestrial and algal carbon sources often varied by functional feeding group within and between sites. However, with the exception of shredders and scrapers, which respectively relied on terrestrial and algal carbon sources, patterns of consumer δ13C clearly show a transition from terrestrial to algal carbon sources for many lotic food webs in streams with ≥10 km2 watershed area. The observed transition to algal carbon sources is likely related to increasing primary production rates as forest canopy cover declines in larger streams, although decreasing retention or quality of terrestrial carbon may also play a role. Improved analyses of algal δ13C and δ15N combined with quantitative study of organic matter dynamics and food web structure should allow the relative importance of these factors to be distinguished in future food web studies.},
	language = {en},
	number = {4},
	urldate = {2020-05-21},
	journal = {Ecology},
	author = {Finlay, Jacques C.},
	year = {2001},
	note = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1890/0012-9658\%282001\%29082\%5B1052\%3ASCIROR\%5D2.0.CO\%3B2},
	keywords = {algae, carbon limitation, energy flow, lotic food webs, stable-carbon-isotope ratios, terrestrial detritus, watershed area, δ13C},
	pages = {1052--1064},
}

@article{finlay_effects_1999,
	title = {Effects of water velocity on algal carbon isotope ratios: {Implications} for river food web studies},
	volume = {44},
	copyright = {© 1999, by the Association for the Sciences of Limnology and Oceanography, Inc.},
	issn = {1939-5590},
	shorttitle = {Effects of water velocity on algal carbon isotope ratios},
	url = {http://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.1999.44.5.1198},
	doi = {10.4319/lo.1999.44.5.1198},
	abstract = {We used variation in algal d13C between river habitats to study the spatial scale of energy flow through river food webs. We found a strong negative relationship between herbivore d13C (which reflects algal d13C) and water velocity in three productive Northern California rivers but not in unproductive streams. The contrast among habitats suggests that water velocity affects algal d13C most strongly when CO2 availability is low relative to photosynthetic rates. Our results help explain the wide variation in published river biota d13C and show that past studies using carbon isotope analyses may have significantly underestimated the importance of algal-derived carbon to river food webs. While flow-related variation in d13C complicates this common application of carbon isotope analysis, we show that it provides a natural tracer of the flux of algal production derived from different habitats within rivers to higher trophic levels. Measurements of consumer d13C showed that most invertebrate and vertebrate consumers relied on local production, except for filter-feeding insects and steelhead trout, which relied on production derived from multiple sources. Stable carbon isotopes may thus be used to spatially delineate the habitats that support river food webs, providing previously unavailable information for understanding and managing river ecosystems.},
	language = {en},
	number = {5},
	urldate = {2020-05-21},
	journal = {Limnology and Oceanography},
	author = {Finlay, Jacques C. and Power, Mary E. and Cabana, Gilbert},
	year = {1999},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.4319/lo.1999.44.5.1198},
	pages = {1198--1203},
}

@article{hecky_contributions_1995,
	title = {Contributions of {Benthic} {Algae} to {Lake} {Food} {Webs} as {Revealed} by {Stable} {Isotope} {Analysis}},
	volume = {14},
	issn = {0887-3593, 1937-237X},
	url = {https://www.journals.uchicago.edu/doi/10.2307/1467546},
	doi = {10.2307/1467546},
	abstract = {Foodwebs of tropical,temperate,and arcticlakes can be characterizedby the carbon and nitrogenstableisotope ratiosof theirconstituentorganisms.Afterassigningtrophiclevelsusing 815Na, broadrangeof 813Cis observedat the primaryconsumerlevel in nearlyall lakes.Therange of 813Cis on the orderof 20 \%oin tropicallakes Kyoga and Malawiand lakes with low dissolved inorganiccarbonin temperateCanada,but is narrowerin shallowlakesof the Canadianarctic.This broad range exists in ecosystemsin which terrestrialinputs and/or aquaticmacrophytesare often minimal.Theisotopicallylight end of the rangeresultsfromphytoplanktonphotosynthesiswhereas the isotopicallyheavy end representsbenthicalgaephotosynthesizingwithin an unstirredboundary layer.Thisrangeis successfullypredictedby an applicationof a simpleisotopicmodel forphotosyntheticfractionationo, riginallydevelopedfor aquaticmacrophytes,which uses boundarylayerthicknesses reportedfor benthicalgal communities.Whenbenthicphotosynthesisbecomes light-limited in very turbidlakes of the MackenzieDelta, then phytoplanktoniccarbondominatesthe diet of the primaryconsumers.The organismson the primaryconsumertrophiclevel appearfrom their 813C valuesto harvestpreferentiallyeitherplanktonicor benthicalgal carbonbut, in temperateand arctic lakes,higherconsumerlevelsareincreasinglyomnivorous.Thereforetop aquaticpredatorsoftenhave a narrow range of 813C.In temperateand arcticlakes these top predatorshave a 813Cnear the midpointof the range at the primaryconsumerlevel,which would resultfrom nearlyequal dependence on planktonicand benthicalgal carbon.This equal dependencewould not be predictedfrom the relativemagnitudeof planktonicand benthicalgalphotosynthesisas currentlyestimatedin these systems.},
	language = {en},
	number = {4},
	urldate = {2020-05-21},
	journal = {Journal of the North American Benthological Society},
	author = {Hecky, R. E. and Hesslein, R. H.},
	month = dec,
	year = {1995},
	pages = {631--653},
}

@article{song_methods_2016,
	title = {Methods of approximation influence aquatic ecosystem metabolism estimates},
	volume = {14},
	copyright = {© 2016 Association for the Sciences of Limnology and Oceanography},
	issn = {1541-5856},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lom3.10112},
	doi = {10.1002/lom3.10112},
	abstract = {Aquatic ecologists have recently employed dynamic models to estimate aquatic ecosystem metabolism. All approaches involve numerically solving a differential equation describing dissolved oxygen (DO) dynamics. Although the DO differential equation can be solved accurately with linear multistep or Runge–Kutta methods, less accurate methods, such as the Euler method, have been applied. The methods also differ in how discrete temperature and light measurements are used to drive DO dynamics. Here, we used a representative stream DO data set to compare the metabolism estimates generated by multiple Euler based methods and an accurate numerical method. We also compared metabolism estimates using linear, piecewise constant and smoothing spline interpolation of light and temperature. Using observed DO to calculate DO saturation deficit in the Euler method results in a substantial difference in metabolism estimates compared to all other methods. If modeled DO is used to calculate DO saturation deficit, the Euler method introduces smaller error in metabolism estimates, which diminishes as logging interval decreases. Linear and smoothing spline interpolation result in similar metabolism estimates, but differ from estimates based on piecewise constant interpolation. We demonstrate how different computational methods imply distinct assumptions about process and observation error, and conclude that under the assumption of observation error, the best practice is to use the accurate numerical method of solving differential equation with a continuous interpolation of light and temperature. The Euler method will introduce minimal error if it is paired with frequently logged data and DO saturation deficit is computed using modeled DO.},
	language = {en},
	number = {9},
	urldate = {2020-05-19},
	journal = {Limnology and Oceanography: Methods},
	author = {Song, Chao and Dodds, Walter K. and Trentman, Matt T. and Rüegg, Janine and Ballantyne, Ford},
	year = {2016},
	note = {\_eprint: https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.1002/lom3.10112},
	pages = {557--569},
}

@article{raymond_scaling_2012,
	title = {Scaling the gas transfer velocity and hydraulic geometry in streams and small rivers},
	volume = {2},
	copyright = {© 2012 by the Association for the Sciences of Limnology and Oceanography, Inc.},
	issn = {2157-3689},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1215/21573689-1597669},
	doi = {10.1215/21573689-1597669},
	abstract = {Lay Abstract The exchange of gasses between water and air is important to the budgets of carbon, nutrients, and pollutants. This exchange is driven, in part, by the turbulent energy at the air–water interface. Turbulent energy at the air–water interface scales with the gas transfer velocity (k), which can be measured in streams through various methods. We performed a metadata analysis of studies that have measured k in streams using direct gas tracer releases. We evaluated models that predict k based on stream morphology. We found that models that use slope and velocity to predict k perform reasonably well and are consistent with general theory. We also used the data set to provide new stream hydraulic equations that predict stream morphology (width, depth, velocity) based on discharge.},
	language = {en},
	number = {1},
	urldate = {2020-05-18},
	journal = {Limnology and Oceanography: Fluids and Environments},
	author = {Raymond, Peter A. and Zappa, Christopher J. and Butman, David and Bott, Thomas L. and Potter, Jody and Mulholland, Patrick and Laursen, Andrew E. and McDowell, William H. and Newbold, Denis},
	year = {2012},
	note = {\_eprint: https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.1215/21573689-1597669},
	keywords = {CO2, O2, gas exchange, reaeration, turbulence},
	pages = {41--53},
}

@article{marescaux_seasonal_2018,
	title = {Seasonal and spatial variability of the partial pressure of carbon dioxide in the human-impacted {Seine} {River} in {France}},
	volume = {8},
	copyright = {2018 The Author(s)},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-018-32332-2},
	doi = {10.1038/s41598-018-32332-2},
	abstract = {Carbon evasion from rivers is an important component of the global carbon cycle. The intensification of anthropogenic pressures on hydrosystems requires studies of human-impacted rivers to identify and quantify the main drivers of carbon evasion. In 2016 and 2017, four field campaigns were conducted in the Seine River network characterized by an intensively cropped and highly populated basin. We measured partial pressures of carbon dioxide (pCO2) in streams or rivers draining land under different uses at different seasons. We also computed pCO2 from an existing data set (pH, water temperature and total alkalinity) going back until 1970. Here we report factors controlling pCO2 that operate at different time and space scales. In our study, the Seine River was shown to be supersaturated in CO2 with respect to the atmospheric equilibrium, as well as a source of CO2. Our results suggest an increase in pCO2 from winter to summer in small streams draining forests (from 1670 to 2480 ppm), croplands (from 1010 to 1550 ppm), and at the outlet of the basin (from 2490 to 3630 ppm). The main driver of pCO2 was shown to be dissolved organic carbon (DOC) concentrations (R2 = 0.56, n = 119, p {\textless} 0.05) that are modulated by hydro-climatic conditions and groundwater discharges. DOC sources were linked to land use and soil, mainly leaching into small upstream streams, but also to organic pollution, mainly found downstream in larger rivers. Our long-term analysis of the main stream suggests that pCO2 closely mirrors the pattern of urban water pollution over time. These results suggest that factors controlling pCO2 operate differently upstream and downstream depending on the physical characteristics of the river basin and on the intensity and location of the main anthropogenic pressures. The influence of these controlling factors may also differ over time, according to the seasons, and mirror long term changes in these anthropogenic pressures.},
	language = {en},
	number = {1},
	urldate = {2020-05-13},
	journal = {Scientific Reports},
	author = {Marescaux, Audrey and Thieu, Vincent and Borges, Alberto Vieira and Garnier, Josette},
	month = sep,
	year = {2018},
	note = {Number: 1
Publisher: Nature Publishing Group},
	pages = {13961},
}

@article{yoon_technical_2016,
	title = {Technical note: {Assessing} gas equilibration systems for continuous \textit{p} {CO} $_{\textrm{2}}$ measurements in inland waters},
	volume = {13},
	issn = {1726-4189},
	shorttitle = {Technical note},
	url = {https://www.biogeosciences.net/13/3915/2016/},
	doi = {10.5194/bg-13-3915-2016},
	abstract = {Abstract. High-frequency continuous measurements of the partial pressure of CO2 (pCO2) are crucial for constraining the spatiotemporal dynamics of CO2 emissions from inland water systems. However, direct measurements of pCO2 are scarce, and no systematic comparisons have been conducted on the suitability of the widely used measurement systems for continuous underway or long-term deployment in various field conditions. We compared spray- and marble-type equilibrators and a membrane-enclosed CO2 sensor to assess their suitability for continuous long-term or underway pCO2 measurements in an urbanized river system in Korea. Both equilibrators had a shorter response time compared with the membrane-enclosed sensor, and could capture large spatial variations of pCO2 during a transect study along a highly urbanized river reach. The membrane-enclosed sensor based on passive equilibration provided comparable underway measurements along the river sections where pCO2 varied within the sensor detection range. When deployed in a eutrophic river site, the membrane-enclosed sensor was able to detect large diel variations in pCO2. However, biofouling on the membrane could reduce the accuracy of the measurement during long deployments exceeding several days. The overall results suggest that the fast response of the equilibrator systems facilitates capturing large spatial variations in pCO2 during short underway measurements. However, the attendant technical challenges of these systems, such as clogging and desiccant maintenance, have to be addressed carefully to enable their long-term deployment. The membrane-enclosed sensor would be suitable as an alternative tool for long-term continuous measurements if membrane biofouling could be overcome by appropriate antifouling measures such as copper mesh coverings.},
	language = {en},
	number = {13},
	urldate = {2020-05-13},
	journal = {Biogeosciences},
	author = {Yoon, Tae Kyung and Jin, Hyojin and Oh, Neung-Hwan and Park, Ji-Hyung},
	month = jul,
	year = {2016},
	pages = {3915--3930},
}

@article{horgby_unexpected_2019,
	title = {Unexpected large evasion fluxes of carbon dioxide from turbulent streams draining the world’s mountains},
	volume = {10},
	copyright = {2019 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-019-12905-z},
	doi = {10.1038/s41467-019-12905-z},
	abstract = {Inland waters, including streams and rivers, are active components of the global carbon cycle. Despite the large areal extent of the world’s mountains, the role of mountain streams for global carbon fluxes remains elusive. Using recent insights from gas exchange in turbulent streams, we found that areal CO2 evasion fluxes from mountain streams equal or exceed those reported from tropical and boreal streams, typically regarded as hotspots of aquatic carbon fluxes. At the regional scale of the Swiss Alps, we present evidence that emitted CO2 derives from lithogenic and biogenic sources within the catchment and delivered by the groundwater to the streams. At a global scale, we estimate the CO2 evasion from mountain streams to 167 ± 1.5 Tg C yr−1, which is high given their relatively low areal contribution to the global stream and river networks. Our findings shed new light on mountain streams for global carbon fluxes.},
	language = {en},
	number = {1},
	urldate = {2020-05-12},
	journal = {Nature Communications},
	author = {Horgby, Åsa and Segatto, Pier Luigi and Bertuzzo, Enrico and Lauerwald, Ronny and Lehner, Bernhard and Ulseth, Amber J. and Vennemann, Torsten W. and Battin, Tom J.},
	month = oct,
	year = {2019},
	note = {Number: 1
Publisher: Nature Publishing Group},
	pages = {4888},
}

@article{horgby_dynamics_2019,
	title = {Dynamics and potential drivers of {CO2} concentration and evasion across temporal scales in high-alpine streams},
	volume = {14},
	issn = {1748-9326},
	url = {10.1088%2F1748-9326%2Fab5cb8},
	doi = {10.1088/1748-9326/ab5cb8},
	abstract = {Carbon dioxide (CO2) evasion from streams greatly contributes to global carbon fluxes. Despite this, the temporal dynamics of CO2 and its drivers remain poorly understood to date. This is particularly true for high-altitude streams. Using high-resolution time series of CO2 concentration and specific discharge from sensors in twelve streams in the Swiss Alps, we studied over three years the responsiveness of both CO2 concentration and evasion fluxes to specific discharge at annual scales and at the scale of the spring freshet. On an annual basis, our results show dilution responses of the streamwater CO2 likely attributable to limited supply from sources within the catchment. Combining our sensor data with stable isotope analyses, we identify the spring freshet as a window where source limitation of the CO2 evasion fluxes becomes relieved. CO2 from soil respiration enters the streams during the freshet thereby facilitating CO2 evasion fluxes that are potentially relevant for the carbon fluxes at catchment scale. Our study highlights the need for long-term measurements of CO2 concentrations and fluxes to better understand and predict the role of streams for global carbon cycling.},
	language = {en},
	number = {12},
	urldate = {2020-05-12},
	journal = {Environmental Research Letters},
	author = {Horgby, {\textbackslash}AAsa and Gómez-Gener, Lluís and Escoffier, Nicolas and Battin, Tom J.},
	month = dec,
	year = {2019},
	note = {Publisher: IOP Publishing},
	pages = {124082},
}

@article{horgby_high-resolution_2019,
	title = {High-{Resolution} {Spatial} {Sampling} {Identifies} {Groundwater} as {Driver} of {CO2} {Dynamics} in an {Alpine} {Stream} {Network}},
	volume = {124},
	copyright = {©2019. American Geophysical Union. All Rights Reserved.},
	issn = {2169-8961},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2019JG005047},
	doi = {10.1029/2019JG005047},
	abstract = {Inland waters are major sources of CO2 to the atmosphere. The origin of this CO2 is often elusive, especially in high-altitude streams that remain poorly studied at present. Here we study the spatial and seasonal variations in streamwater CO2, its potential sources and drivers in an Alpine stream network (Switzerland). High-resolution sampling combined with stable isotope analysis and mixing models enabled us to capture the fine-scale spatial heterogeneity in streamwater pCO2 as the stream network expanded and contracted during seasons. We identified soil respiration as a major source of CO2 to the stream. We also identified a major groundwater upwelling zone as an ecosystem “control point” that disproportionately influenced stream biogeochemistry. This was particularly pronounced when the stream network expanded during snowmelt, when it covered a five times larger area compared to winter (35,300 m2 compared to 7,100 m2). Downstream from this control point, CO2 evaded rapidly owing to high gas transfer velocity. The stream network was a net source of CO2 to the atmosphere with an average areal evasion flux of 30.1 (18.0–43.1) μmol · m-2 · s-1 and a total flux at network scale ranging from 237 (141–339) kg C/day in winter to 1793 (1069–2565) kg C/day during spring snowmelt. Our study highlights the role of stream network dynamics and control points for the CO2 dynamics in high-altitude streams.},
	language = {en},
	number = {7},
	urldate = {2020-05-12},
	journal = {Journal of Geophysical Research: Biogeosciences},
	author = {Horgby, Åsa and Canadell, Marta Boix and Ulseth, Amber J. and Vennemann, Torsten W. and Battin, Tom J.},
	year = {2019},
	note = {\_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2019JG005047},
	keywords = {CO2 evasion, CO2 sources, control point, headwater stream, hydrological connectivity, stable isotopes},
	pages = {1961--1976},
}

@article{marx_review_2017,
	title = {A review of {CO2} and associated carbon dynamics in headwater streams: {A} global perspective},
	volume = {55},
	copyright = {©2017. American Geophysical Union. All Rights Reserved.},
	issn = {1944-9208},
	shorttitle = {A review of {CO2} and associated carbon dynamics in headwater streams},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2016RG000547},
	doi = {10.1002/2016RG000547},
	abstract = {Terrestrial carbon export via inland aquatic systems is a key process in the global carbon cycle. It includes loss of carbon to the atmosphere via outgassing from rivers, lakes, or reservoirs and carbon fixation in the water column as well as in sediments. This review focuses on headwater streams that are important because their stream biogeochemistry directly reflects carbon input from soils and groundwaters. Major drivers of carbon dioxide partial pressures (pCO2) in streams and mechanisms of terrestrial dissolved inorganic, organic and particulate organic carbon (DIC, DOC, and POC) influxes are summarized in this work. Our analysis indicates that the global river average pCO2 of 3100 ppmV is more often exceeded by contributions from small streams when compared to rivers with larger catchments ({\textgreater} 500 km2). Because of their large proportion in global river networks ({\textgreater} 96\% of the total number of streams), headwaters contribute large—but still poorly quantified—amounts of CO2 to the atmosphere. Conservative estimates imply that globally 36\% (i.e., 0.93 Pg C yr−1) of total CO2 outgassing from rivers and streams originate from headwaters. We also discuss challenges in determination of CO2 sources, concentrations, and fluxes. To overcome uncertainties of CO2 sources and its outgassing from headwater streams on the global scale, new investigations are needed that should include groundwater data. Such studies would also benefit from applications of integral CO2 outgassing isotope approaches and multiscale geophysical imaging techniques.},
	language = {en},
	number = {2},
	urldate = {2020-05-12},
	journal = {Reviews of Geophysics},
	author = {Marx, A. and Dusek, J. and Jankovec, J. and Sanda, M. and Vogel, T. and Geldern, R. van and Hartmann, J. and Barth, J. a. C.},
	year = {2017},
	note = {\_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1002/2016RG000547},
	keywords = {CO2 outgassing, carbon cycle, headwater catchments, river water chemistry, stable isotopes},
	pages = {560--585},
}

@article{kana_membrane_1994,
	title = {Membrane {Inlet} {Mass} {Spectrometer} for {Rapid} {High}-{Precision} {Determination} of {N2}, {O2}, and {Ar} in {Environmental} {Water} {Samples}},
	volume = {66},
	issn = {0003-2700},
	url = {10.1021/ac00095a009},
	doi = {10.1021/ac00095a009},
	number = {23},
	urldate = {2020-05-12},
	journal = {Analytical Chemistry},
	author = {Kana, Todd M. and Darkangelo, Christina. and Hunt, M. Duane. and Oldham, James B. and Bennett, George E. and Cornwell, Jeffrey C.},
	month = dec,
	year = {1994},
	note = {Publisher: American Chemical Society},
	pages = {4166--4170},
}

@article{madinger_linking_2019,
	title = {Linking denitrification with ecosystem respiration in mountain streams},
	volume = {4},
	copyright = {© 2019 The Authors. Limnology and Oceanography published by Wiley Periodicals, Inc. on behalf of Association for the Sciences of Limnology and Oceanography.},
	issn = {2378-2242},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lol2.10111},
	doi = {10.1002/lol2.10111},
	abstract = {Rivers denitrify a portion of their nitrate () load, but estimates are difficult using microcosm or reach-scale measurements that require specific biogeochemical and hydrologic conditions. Measuring reach-scale oxygen (O2) respiration fluxes is easier than nitrogen (N2) fluxes, thus we paired microcosm estimates of denitrification by N2 production with estimates of aerobic respiration. The median molar ratio of ΔN2:−ΔO2 from 13 streams was 0.011 (95\% credible interval 0.0002–0.027 mol:mol). We then measured diel O2 concentrations from 11 streams and converted to ecosystem respiration (ER) using a multiday oxygen model. Given reach-scale ER of −160 mmol O2 m−2 d−1, the estimated median denitrification was 1.5 mmol N2 m−2 d−1 (credible interval (CI): 0.18–4.21) across our streams. Our estimates of denitrification constituted 19\% of gross uptake (CI: 0–51\%). In streams, ΔN2:−ΔO2 was lower than in estuarine and marine ecosystems. Despite multiple sources of error, this approach estimates reach-scale denitrification and variation with concentrations.},
	language = {en},
	number = {5},
	urldate = {2020-05-11},
	journal = {Limnology and Oceanography Letters},
	author = {Madinger, Hilary L. and Hall, Robert O.},
	year = {2019},
	note = {\_eprint: https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.1002/lol2.10111},
	pages = {145--154},
}

@article{parker_dissolved_2014,
	title = {Dissolved oxygen and dissolved inorganic carbon stable isotope composition and concentration fluxes across several shallow floodplain aquifers and in a diffusion experiment},
	volume = {117},
	issn = {1573-515X},
	url = {10.1007/s10533-013-9899-0},
	doi = {10.1007/s10533-013-9899-0},
	abstract = {Recent studies have documented the occurrence of dissolved molecular oxygen (DO) in shallow groundwater that is isotopically lighter than can be explained by atmospheric gas exchange or by biogeochemical reactions that consume 16O16O faster than 16O18O. In the present study, spatial gradients in the isotopic composition of DO (δ18O-DO) and dissolved inorganic carbon (δ13C-DIC) were measured in three shallow floodplain aquifers: (1) the Nyack aquifer, of the Middle Fork of the Flathead River in northwest Montana; (2) the Silver Bow Creek floodplain in southwest Montana; and (3) the Umatilla River floodplain in northeast Oregon. The field data show general trends of increasing DIC concentration, decreasing δ13C-DIC, and decreasing DO concentration with increase in groundwater path length. These trends are consistent with consumption of DO and production of DIC by microbial respiration. Although the expected trend of an increase in δ18O-DO with increase in path length was found at an area adjacent to hyporheic recharge at the Nyack floodplain, the majority of groundwater samples collected at Nyack and from the other sites distal to recharge zones had anomalously low δ18O-DO values well below 24.2 ‰, the value corresponding to atmospheric isotopic equilibrium. At the Nyack site, 3H-3He dates were used to estimate groundwater travel time: all groundwater samples with apparent age {\textgreater}1 year had δ18O-DO{\textless}24.2 ‰. Previously it has been suggested that diffusion of O2 could be a viable mechanism to explain the existence of isotopically light DO in shallow groundwater. To test this hypothesis, laboratory experiments were conducted to measure the isotopic fractionation of O2 as it diffuses from air across a simulated capillary fringe (made from a floating layer of foam beads) into a stirred, initially anoxic, water column. As expected, 16O16O diffused faster than 16O18O, and the magnitude of isotope fractionation associated with diffusion increased with a decrease in temperature. Fractionation factors (α) calculated from these diffusion experiments were 1.0030 at 15–19 °C and 1.0048 at 8 °C. The combined field and laboratory data suggest that diffusion is an important mechanism to maintain aerobic conditions in shallow groundwater systems, allowing microbial respiration to continue at long distances (km scale) from the source of groundwater recharge.},
	language = {en},
	number = {2},
	urldate = {2020-05-11},
	journal = {Biogeochemistry},
	author = {Parker, Stephen R. and Darvis, Marissa N. and Poulson, Simon R. and Gammons, Christopher H. and Stanford, Jack A.},
	month = mar,
	year = {2014},
	pages = {539--552},
}

@article{smith_tracing_2011,
	title = {Tracing dissolved {O2} and dissolved inorganic carbon stable isotope dynamics in the {Nyack} aquifer: {Middle} {Fork} {Flathead} {River}, {Montana}, {USA}},
	volume = {75},
	issn = {0016-7037},
	shorttitle = {Tracing dissolved {O2} and dissolved inorganic carbon stable isotope dynamics in the {Nyack} aquifer},
	url = {http://www.sciencedirect.com/science/article/pii/S0016703711004212},
	doi = {10.1016/j.gca.2011.07.033},
	abstract = {The geochemistry and microbiology of shallow groundwater aquifers is greatly influenced by the concentration of dissolved oxygen gas (DO); however, the mechanisms that consume DO in groundwater (e.g., biotic or abiotic) are often ambiguous. The use of stable isotopes of molecular O2 (δ18O-DO), in conjunction with stable isotopes of dissolved inorganic carbon (δ13C-DIC), has potential to discriminate between the various mechanisms causing DO depletion in subsurface waters. Here we report the results of spatial and seasonal changes in δ18O-DO and δ13C-DIC at the Nyack floodplain aquifer along the Middle Fork of the Flathead River near West Glacier, Montana, USA. Over a short, well constrained flow path (∼100m) near a main recharge zone of the floodplain, the δ18O-DO consistently increased as DO concentrations decreased with distance from the recharge source. Concurrently, DIC concentrations increased and δ13C-DIC values decreased. These observations are explained by community respiration coupled with dissolution of calcite from cobbles in the aquifer matrix. When these results are compared to data from wells distributed over the entire floodplain (several km) a much less predictable relationship was observed between DO concentration and δ18O-DO. Many wells with low DO concentrations (e.g., {\textless}125μmolL−1 or 4mgL−1) had anomalously low δ18O-DO values (e.g., {\textless}20‰). Mass balance calculations show that approximately equal amounts of O2 may be contributed to the aquifer by diffusion from the vadose zone and by advection from the river recharge. Calculations presented here suggest that diffusion across a narrow air–water interface can contribute isotopically light δ18O-DO to the saturated zone. Possible contributions of light δ18O-DO from other processes, such as isotopic exchange and radial oxygen loss from plant roots in or near the water table, are compared and evaluated.},
	language = {en},
	number = {20},
	urldate = {2020-05-08},
	journal = {Geochimica et Cosmochimica Acta},
	author = {Smith, M. Garrett and Parker, Stephen R. and Gammons, Christopher H. and Poulson, Simon R. and Hauer, F. Richard},
	month = oct,
	year = {2011},
	pages = {5971--5986},
}

@article{craig_standard_1961,
	title = {Standard for {Reporting} {Concentrations} of {Deuterium} and {Oxygen}-18 in {Natural} {Waters}},
	volume = {133},
	copyright = {1961 by the American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	url = {http://science.sciencemag.org/content/133/3467/1833},
	doi = {10.1126/science.133.3467.1833},
	abstract = {A standard, based on the set of ocean water samples used by Epstein and Mayeda to obtain a reference standard for oxygen-18 data, but defined relative to the National Bureau of Standards isotopic reference water sample, is proposed for reporting both deuterium and oxygen-18 variations in natural waters relative to the same water. The range of absolute concentrations of both isotopes in meteoric-waters is discussed.},
	language = {en},
	number = {3467},
	urldate = {2020-05-01},
	journal = {Science},
	author = {Craig, Harmon},
	month = jun,
	year = {1961},
	pmid = {17819002},
	note = {Publisher: American Association for the Advancement of Science
Section: Reports},
	pages = {1833--1834},
}

@article{mader_dissolved_2017,
	title = {Dissolved oxygen in water and its stable isotope effects: {A} review},
	volume = {473},
	issn = {0009-2541},
	shorttitle = {Dissolved oxygen in water and its stable isotope effects},
	url = {http://www.sciencedirect.com/science/article/pii/S0009254117305508},
	doi = {10.1016/j.chemgeo.2017.10.003},
	abstract = {Dissolved oxygen (DO) is one of the most commonly measured parameters in aqueous studies, however its sources and sinks such as atmospheric exchange, photosynthesis or respiration often remain unknown. A large number of studies have combined concentration measurements with investigations of stable isotope ratios (18O/16O and 17O/16O) of DO that are expressed as per mille [‰] deviation versus international standards. These isotope shifts can provide important additional information about oxygen sources and sinks, aqueous productivity and also of turnover rates of related material such as carbon. This review provides an overview of oxygen isotope systematics and the Dole effect that is still unresolved and explores the discrepancy between the isotope composition of ocean water and atmospheric O2. Here we summarize the most relevant processes of influence on the isotope composition of DO, including gas-water exchange, photosynthesis and respiration. The latter is known to exert the strongest isotope effects with isotope discriminations of up to −29‰. New developments suggest that they can be cancelled out with recent applications of a 17O excess method for the evaluation of aqueous productivity. Furthermore, variations of DO stable isotope ratios can serve as a valuable additional tracer in a wide range of biogeochemical and aqueous studies. Among aquatic systems lakes, estuarine and shallow groundwater environments are the most challenging reservoirs as they usually expose steep oxygen gradients. So far causes and effects of these gradients remain often unexplored and could be revealed with DO isotope methods. Particularly in groundwater, additional oxygen sources from the soil zone may be quantified with new oxygen isotope signals that were influenced by diffusion. Future investigations of groundwater-surface water interactions and of ecological functions can benefit from this method. Other new applications include investigations of mineral oxidations and of engineered approaches such as photo-bioreactors.},
	language = {en},
	urldate = {2020-04-29},
	journal = {Chemical Geology},
	author = {Mader, Michael and Schmidt, Christian and van Geldern, Robert and Barth, Johannes A. C.},
	month = nov,
	year = {2017},
	keywords = {Aquatic chemistry, Dissolved oxygen, Fractionation, Stable isotopes, Water},
	pages = {10--21},
}

@article{hotchkiss_high_2014,
	title = {High rates of daytime respiration in three streams: {Use} of δ{18OO2} and {O2} to model diel ecosystem metabolism},
	volume = {59},
	copyright = {© 2014, by the Association for the Sciences of Limnology and Oceanography, Inc.},
	issn = {1939-5590},
	shorttitle = {High rates of daytime respiration in three streams},
	url = {http://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.2014.59.3.0798},
	doi = {10.4319/lo.2014.59.3.0798},
	abstract = {Photosynthesis and respiration determine the carbon and oxygen (O2) balance of ecosystems. Current methods used to estimate ecosystem respiration (ER) do not include diel ER fluctuations, which limit testing predictions about short-term drivers of ecosystem metabolism. Diel changes in δ18OO22 can be used to estimate diel ER due to discrimination against δ18OO22 during respiration. We monitored diel δ18OO22, O2, light, and water temperature in three Wyoming streams and measured respiration fractionation (αR) against δ18OO22 in dark benthic flow chambers in two streams. The ranges of measured and literature αR values were used to estimate uncertainty in metabolism parameters associated with not measuring αR directly. Daytime ER was 54–340\% higher than nighttime ER using δ18OO22, but diel ER parameter estimates were highly uncertain relative to traditional estimates of ecosystem metabolism. Diel variations in water temperature only accounted for 4–55\% of the range of diel ER calculated using diel δ18OO22. Measured benthic flow chamber αR varied within the range of literature values: from 0.9755 to 0.9954. Metabolism parameter estimates were very sensitive to choice of αR within the measured and published range of values. The mean and uncertainty of diel ER estimates increased with decreasing αR, with daily ER more than ten times higher given an αR of 0.975 vs. 0.999. Diel changes in ER can be modeled using δ18OO22 and O2, but diel ER estimates depend on the choice of αR, suggesting the need to better understand how αR may vary within spatial and temporal scales appropriate for δ18OO22 metabolism models.},
	language = {en},
	number = {3},
	urldate = {2020-04-29},
	journal = {Limnology and Oceanography},
	author = {Hotchkiss, Erin R. and Hall, Jr, Robert O.},
	year = {2014},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.4319/lo.2014.59.3.0798},
	pages = {798--810},
}

@article{tromboni_respiration_2020,
	title = {Respiration in rivers fractionates stable isotopes of dissolved oxygen; a global investigation on the influences of temperature and flow},
	volume = {147},
	issn = {1573-515X},
	url = {10.1007/s10533-020-00636-z},
	doi = {10.1007/s10533-020-00636-z},
	abstract = {Quantifying ecosystem respiration remains challenging in aquatic ecosystems. Most investigators assume that nighttime and daytime respiration are equal. Recent studies suggest measuring dissolved oxygen isotopes during periods with and without photosynthesis can account for variations in daytime and nighttime respiration. These models are extremely sensitive to the oxygen isotopic fractionation factor (α) value used for respiration, yet almost nothing is known about the variability of α and factors driving that variability. We quantified how α varies with temperature and flow velocity using field measurements, laboratory experiments, and a modeling approach. We measured α in the field using sealed recirculating chambers in 16 rivers from different biomes (temperate, tropical, and sub-arctic) to assess a range of possible α values. The α values were widely variable, and variation was higher among sites in the same biome or ecoregion (e.g. 0.9780 ± 0.005 to 0.9898 ± 0.002 among six desert sites) than across different biomes. Our data revealed that both temperature, flow, and biofilm characteristics produced variations in α, with temperature decreasing and flow increasing it, until leveling off at high flow velocities. Biological and physical processes occurring in the diffusion boundary layer produced variations in α. Our results highlight that environmental conditions produce variable α values, the need for site-specific α measurements, and practical implications for consideration when measuring α in the field. More generally we illustrate an array of factors that can influence isotopic fractionation associated with metabolic activity of biologically active layers that could be important in any diffusion-limited environment.},
	language = {en},
	number = {2},
	urldate = {2020-04-29},
	journal = {Biogeochemistry},
	author = {Tromboni, Flavia and Dodds, Walter K. and Chandra, Sudeep and Poulson, Simon R. and Pandey, Aakash and Schechner, Anne},
	month = jan,
	year = {2020},
	pages = {199--210},
}

@article{bergstrom_atmospheric_2006,
	title = {Atmospheric nitrogen deposition has caused nitrogen enrichment and eutrophication of lakes in the northern hemisphere},
	volume = {12},
	issn = {1365-2486},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2486.2006.01129.x},
	doi = {10.1111/j.1365-2486.2006.01129.x},
	abstract = {We compiled chemical data and phytoplankton biomass (PB) data (chlorophyll a) from unproductive lakes in 42 different regions in Europe and North America, and compared these data to inorganic nitrogen (N) deposition over these regions. We demonstrate that increased deposition of inorganic N over large areas of Europe and North America has caused elevated concentrations of inorganic N in lakes. In addition, the unproductive lakes in high N deposition areas had clearly higher PB relative to the total phosphorus (P) concentrations illustrating that the elevated inorganic N concentrations has resulted in eutrophication and increased biomass of phytoplankton. The eutrophication caused by inorganic N deposition indicates that PB yield in a majority of lakes in the northern hemisphere is (was) limited by N in their natural state. We, therefore, suggest that P limitation largely concerns lakes where the balance between N and P has been changed because of increased anthropogenic input of N.},
	language = {en},
	number = {4},
	urldate = {2020-04-28},
	journal = {Global Change Biology},
	author = {Bergström, Ann-Kristin and Jansson, Mats},
	year = {2006},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2486.2006.01129.x},
	keywords = {chlorophyll a, deposition, eutrophication, limitation, nitrogen, northern lakes, nutrient, phosphorus, phytoplankton},
	pages = {635--643},
}

@article{williams_critical_2017,
	title = {Critical loads of atmospheric {N} deposition for phytoplankton nutrient limitation shifts in western {U}.{S}. mountain lakes},
	volume = {8},
	copyright = {© 2017 Williams et al.},
	issn = {2150-8925},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecs2.1955},
	doi = {10.1002/ecs2.1955},
	abstract = {In many oligotrophic mountain lakes, anthropogenic atmospheric nitrogen (N) deposition has increased concentrations of N, a key limiting nutrient, and thereby shifted phytoplankton biomass growth from N limitation to P limitation. In the western United States, the critical load N deposition rate for these shifts has not been quantified. We synthesized existing mountain lake chemistry, nutrient limitation bioassay, and N deposition data to estimate N critical loads for shifts from N to P limitation of phytoplankton biomass growth. Data from bioassays in 47 mountain lakes were used to define biological (RR-N/RR-P = 1) and chemical (NO3, DIN, DIN:TP) thresholds above which biomass P limitation is more likely than N limitation. Logistic regression was used to calculate critical loads as the total N deposition rate with {\textgreater}50\% probability of exceeding biological or chemical thresholds, and thus where P limitation is more likely than N limitation. Logistic regression models were developed with N deposition as the only predictor and with both N deposition and watershed characteristics as predictors. Logistic model performance was evaluated by comparing predicted and observed chemical threshold exceedances in 108 mountain lakes. Across models, estimated critical loads ranged from 2.8 to 5.2 kg total N·ha−1·yr−1. The best-performing model was a univariate logistic model predicting NO3 threshold exceedance, with N deposition as the only predictor. This model yielded a critical load of 4.1 kg total N·ha−1·yr−1 and accurately predicted NO3 threshold exceedance in 69\% of lakes. We applied this critical load to an independent sample of 385 mountain lakes with NO3 data to estimate the frequency it would fail to predict a limitation shift—cases where the NO3 threshold for biomass shifts was exceeded, but the critical load was not. The false-negative rate was 13\% across the western United States, but was higher (22\%) in the Sierras. Performance analyses suggest a 2.0 kg total N·ha−1·yr−1 critical load may avoid false negatives entirely. Critical loads presented here can be used to assess N deposition impacts on western U.S. mountain lakes, and associated performance information can be used to consider if presented critical loads are adequate for specific management applications.},
	language = {en},
	number = {10},
	urldate = {2020-04-28},
	journal = {Ecosphere},
	author = {Williams, Jason J. and Lynch, Jason A. and Saros, Jasmine E. and Labou, Stephanie G.},
	year = {2017},
	note = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1002/ecs2.1955},
	keywords = {critical load, mountain lakes, nitrogen deposition, phytoplankton},
	pages = {e01955},
}

@article{zhang_concentrations_2019,
	title = {Concentrations, fluxes, and potential sources of nitrogen and phosphorus species in atmospheric wet deposition of the {Lake} {Qinghai} {Watershed}, {China}},
	volume = {682},
	issn = {0048-9697},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969719322636},
	doi = {10.1016/j.scitotenv.2019.05.224},
	abstract = {Plateau lakes are typically dystrophic and are sensitive to small changes in nutrient deposition. With this assumption, we investigated the concentrations, fluxes, and sources of nitrogen (N) and phosphorus (P) in the atmospheric wet deposition (AWD) of the Lake Qinghai Watershed (LQW), which is the largest inland lake in China, for one year from October 2017 to September 2018. The results showed that the annual volume-weighted mean (VWM) concentrations (mg L−1) in the AWD were 1.97 for NH4+-N, 0.55 for NO3−-N, 0.04 for NO2−-N, 0.77 for dissolved organic N (DON), 3.33 for total dissolved N (TDN), 0.30 for dissolved inorganic P (DIP), 0.07 for dissolved organic P (DOP), 0.36 for total dissolved P (TDP), and 0.99 for reactive sulfur (SO42−-S). The annual AWD fluxes of TDN and TDP were 16.82 and 1.86 kg ha−1 yr−1, respectively. Strong dilution effects in the wet season, a long residency time of nutrient-rich aerosols in the dry season, strong ammonia volatilization in the wet and warm seasons, and moisture sources dominated the seasonal or monthly changing characteristics of N and P concentrations in the AWD, including high in the wet season and low in the dry season for NH4+-N, low in the wet season and high in the dry season for NO3−-N, and generally increasing from April to September for DIP and DOP. Precipitation quantity dominated the monthly changes in the N and P fluxes of the AWD, which gradually increased from April to August and then decreased in September. N and P in the AWD mostly originated from anthropogenic sources. High ammonia volatilization from local intense animal husbandry, alkaline soils and lakes led to a relatively high NH4+-N concentration compared with other sites of the Qinghai-Tibet Plateau, China, and in the world. The N/P molar ratio in the precipitation was higher than 16, which might have effect on the aquatic ecosystems of Lake Qinghai. Ammonia volatilization fluxes and atmospheric dry deposition fluxes of N and P should be further studied to completely understand the geochemical cycles of N and P in the LQW.},
	language = {en},
	urldate = {2020-04-28},
	journal = {Science of The Total Environment},
	author = {Zhang, Xuan and Lin, Chunye and Zhou, Xueli and Lei, Kai and Guo, Bobo and Cao, Yuanxin and Lu, Shuang and Liu, Xitao and He, Mengchang},
	month = sep,
	year = {2019},
	keywords = {Atmospheric wet deposition, Lake Qinghai Watershed, Nitrogen, Phosphorus, Source},
	pages = {523--531},
}

@article{trentman_impact_2018,
	title = {The impact of long-term regional air mass patterns on nutrient precipitation chemistry and nutrient deposition within a {United} {States} grassland ecosystem},
	volume = {75},
	copyright = {All rights reserved},
	issn = {1573-0662},
	url = {10.1007/s10874-018-9384-1},
	doi = {10.1007/s10874-018-9384-1},
	abstract = {Changes in the frequency of precipitation as a result of a changing climate, as well as anthropogenic induced deposition of nitrogen (N), both have the potential to alter grassland productivity and diversity. Central U.S. weather patterns are dominated by three major air mass trajectories including regional sources from the Gulf of Mexico (marine tropical, Mt), the Pacific Northwest (mild pacific, mP), and the Desert Southwest (continental tropical, Ct). In this work, the Hybrid Single Particle Lagrangian Integrated Trajectory model was used to determine trends in the proportion of precipitation events from these air mass sources from 1983 to 2006 relative to Konza Prairie Biological Station (KPBS), KS. The annual volume-weighted mean (VWM) concentrations and wet deposition of a variety of precipitation dissolved solutes were linked to source regions north or south of KPBS. The proportion of precipitation events from Mt significantly increased, while the proportion of events from Ct and mP decreased significantly over the study period. The annual VWM concentrations of most solutes were typically higher from precipitation sourced to the north of KPBS. However, wet deposition of four ecologically relevant solutes (NH4+, NO3−, H+, and SO4−2) was higher from events from the southern region, likely due to higher precipitation amounts. The proportion of reduced N increased significantly over the study period but was not affected by source region despite the higher use of fertilizers for agriculture in the northern source region. Given the location of this site relative to three dominant air mass paths, future shifts in these patterns will likely impact wet nutrient deposition.},
	language = {en},
	number = {4},
	urldate = {2020-04-28},
	journal = {Journal of Atmospheric Chemistry},
	author = {Trentman, Matt T.},
	month = dec,
	year = {2018},
	pages = {399--410},
}

@article{zhang_drainage_2017,
	title = {Drainage water management combined with cover crop enhances reduction of soil phosphorus loss},
	volume = {586},
	issn = {0048-9697},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969717302668},
	doi = {10.1016/j.scitotenv.2017.02.025},
	abstract = {Integrating multiple practices for mitigation of phosphorus (P) loss from soils may enhance the reduction efficiency, but this has not been studied as much as individual ones. A four-year study was conducted to determine the effects of cover crop (CC) (CC vs. no CC, NCC) and drainage water management (DWM) (controlled drainage with sub-irrigation, CDS, vs. regular free tile drainage, RFD) and their interaction on P loss through both surface runoff (SR) and tile drainage (TD) water in a clay loam soil of the Lake Erie region. Cover crop reduced SR flow volume by 32\% relative to NCC, regardless of DWM treatment. In contrast, CC increased TD flow volume by 57 and 9.4\% with CDS and RFD, respectively, compared to the corresponding DWM treatment with NCC. The total (SR+TD) field water discharge volumes were comparable amongst all the treatments. Cover crop reduced flow-weighted mean (FWM) concentrations of particulate P (PP) by 26\% and total P (TP) by 12\% in SR, while it didn't affect the FWM dissolved reactive P (DRP) concentration, regardless of DWM treatments. Compared with RFD, CDS reduced FWM DRP concentration in TD water by 19\%, while CC reduced FWM PP and TP concentrations in TD by 21 and 17\%, respectively. Total (SR+TD) soil TP loss was the least with CDS-CC followed by RFD-CC, CDS-NCC, and RFD-NCC. Compared with RFD-NCC, currently popular practice in the region, total TP loss was reduced by 23\% with CDS-CC. The CDS-CC system can be an effective practice to ultimately mitigate soil P loading to water resource.},
	language = {en},
	urldate = {2020-04-28},
	journal = {Science of The Total Environment},
	author = {Zhang, T. Q. and Tan, C. S. and Zheng, Z. M. and Welacky, T. and Wang, Y. T.},
	month = may,
	year = {2017},
	keywords = {Cover crop, Drainage water management, Phosphorus, Surface runoff, Surface water quality, Tile drainage},
	pages = {362--371},
}

@article{ulen_nutrient_1997,
	title = {Nutrient losses by surface run-off from soils with winter cover crops and spring-ploughed soils in the south of {Sweden}},
	volume = {44},
	issn = {0167-1987},
	url = {http://www.sciencedirect.com/science/article/pii/S0167198797000512},
	doi = {10.1016/S0167-1987(97)00051-2},
	abstract = {Winter cover crops are used as a method of reducing nitrogen (N) losses from arable land in several countries, but their effect on phosphorus (P) losses is poorly documented. Run-off and losses of nutrients and soil were measured from a clay loam with autumn-ploughed and spring-ploughed plots and from plots with winter wheat during three winter seasons (1993–1996) in Holland County in south western Sweden. The run-off water was collected in troughs dug into the soil at the end of collecting slopes placed in the experimental plots. As a result of the weather, there was only one winter in which surface run-off occurred to any great extent. On average, 75\% of P was in particulate form (Ppart). Neither winter wheat (Triticum aestivum L.) nor catch crops of English ryegrass (Lolium perenne L.) reduced losses of Ppart when compared with losses from autumn-ploughed soil; and losses from spring-ploughed soil containing stubble and weeds were no lower than those from autumn-ploughed soil. Losses of Ppart from all treatments were moderate considering its low bio-availability. Concentrations of phosphate phosphorus (PO4-P) were low, with a mean 0.04 mg 1−1. Despite a significant increase in losses of PO4-P from spring-ploughed soil covered with stubble and catch crops or weeds compared with that in autumn-ploughed soil, the extra input from this P source was at most 2 g ha−1 yr−1. This mass loss was equal to 0.5 g kg−1 of the total mass of P in the vegetation. Thus, only very small extra P surface losses were found with winter cover crops compared with those with bare soils. N losses in run-off were low in all treatments.},
	language = {en},
	number = {3},
	urldate = {2020-04-28},
	journal = {Soil and Tillage Research},
	author = {Ulén, B.},
	month = dec,
	year = {1997},
	keywords = {Autumn-ploughing, Nutrient losses, Phosphorus losses, Spring-ploughing, Surface run-off, Winter cover crops},
	pages = {165--177},
}

@article{bergstrom_turnover_2015,
	title = {Turnover and {Losses} of {Phosphorus} in {Swedish} {Agricultural} {Soils}: {Long}-{Term} {Changes}, {Leaching} {Trends}, and {Mitigation} {Measures}},
	volume = {44},
	copyright = {© 2015 The Authors.},
	issn = {1537-2537},
	shorttitle = {Turnover and {Losses} of {Phosphorus} in {Swedish} {Agricultural} {Soils}},
	url = {http://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/jeq2014.04.0165},
	doi = {10.2134/jeq2014.04.0165},
	abstract = {Transport of phosphorus (P) from agricultural fields to water bodies deteriorates water quality and causes eutrophication. To reduce P losses and optimize P use efficiency by crops, better knowledge is needed of P turnover in soil and the efficiency of best management practices (BMPs). In this review, we examined these issues using results from 10 Swedish long-term soil fertility trials and various studies on subsurface losses of P. The fertility trials are more than 50 years old and consist of two cropping systems with farmyard manure and mineral fertilizer. One major finding was that replacement of P removed by crops with fertilizer P was not sufficient to maintain soil P concentrations, determined with acid ammonium lactate extraction. The BMPs for reducing P leaching losses reviewed here included catch crops, constructed wetlands, structure liming of clay soils, and various manure application strategies. None of the eight catch crops tested reduced P leaching significantly, whereas total P loads were reduced by 36\% by wetland installation, by 39 to 55\% by structure liming (tested at two sites), and by 50\% by incorporation of pig slurry into a clay soil instead of surface application. Trend analysis of P monitoring data since the 1980s for a number of small Swedish catchments in which various BMPs have been implemented showed no clear pattern, and both upward and downward trends were observed. However, other factors, such as weather conditions and soil type, have profound effects on P losses, which can mask the effects of BMPs.},
	language = {en},
	number = {2},
	urldate = {2020-04-28},
	journal = {Journal of Environmental Quality},
	author = {Bergström, Lars and Kirchmann, Holger and Djodjic, Faruk and Kyllmar, Katarina and Ulén, Barbro and Liu, Jian and Andersson, Helena and Aronsson, Helena and Börjesson, Gunnar and Kynkäänniemi, Pia and Svanbäck, Annika and Villa, Ana},
	year = {2015},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.2134/jeq2014.04.0165},
	pages = {512--523},
}

@article{segatto_modeling_nodate,
	title = {Modeling the coupled dynamics of stream metabolism and microbial biomass},
	volume = {n/a},
	copyright = {© 2020 The Authors. Limnology and Oceanography published by Wiley Periodicals, Inc. on behalf of Association for the Sciences of Limnology and Oceanography.},
	issn = {1939-5590},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lno.11407},
	doi = {10.1002/lno.11407},
	abstract = {Estimating and interpreting ecosystem metabolism remains an important challenge in stream ecology. Here, we propose a novel approach to model, estimate, and predict multiseasonal patterns of stream metabolism (gross primary production [GPP] and ecosystem respiration [ER]) at the reach scale leveraging on increasingly available long-term, high-frequency measurements of dissolved oxygen (DO). The model uses DO measurements to estimate the parameters of a simple ecosystem model describing the underlying dynamics of stream autotrophic and heterotrophic microbial biomass. The model has been applied to four reaches within the Ybbs river network, Austria. Even if microbial biomasses are not observed, that is, they are treated as latent variables, results show that by accounting for the temporal dynamics of biomass, the model reproduces variability in metabolic fluxes that is not explained by fluctuations of light, temperature, and resources. The model is particularly data-demanding: to estimate the 11 parameters used in this formulation, it requires sufficiently long, for example, annual, time series, and significant scouring events. On the other hand, the approach has the potential to separate ER into its autotrophic and heterotrophic components, estimate a richer set of ecosystem carbon fluxes (i.e., carbon uptake, loss, and scouring), extrapolate metabolism estimates for periods when DO measurements are unavailable, and predict how ecosystem metabolism would respond to variations of the driving forces. The model is seen as a building block to develop tools to fully appreciate multiseasonal patterns of metabolic activity in river networks and to provide reliable estimations of carbon fluxes from land to ocean.},
	language = {en},
	number = {n/a},
	urldate = {2020-04-24},
	journal = {Limnology and Oceanography},
	author = {Segatto, Pier Luigi and Battin, Tom J. and Bertuzzo, Enrico},
	note = {\_eprint: https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.1002/lno.11407},
}

@article{wan_inferring_2014,
	title = {Inferring land use and land cover impact on stream water quality using a {Bayesian} hierarchical modeling approach in the {Xitiaoxi} {River} {Watershed}, {China}},
	volume = {133},
	issn = {0301-4797},
	url = {http://www.sciencedirect.com/science/article/pii/S0301479713007287},
	doi = {10.1016/j.jenvman.2013.11.035},
	abstract = {Lake eutrophication has become a very serious environmental problem in China. If water pollution is to be controlled and ultimately eliminated, it is essential to understand how human activities affect surface water quality. A recently developed technique using the Bayesian hierarchical linear regression model revealed the effects of land use and land cover (LULC) on stream water quality at a watershed scale. Six LULC categories combined with watershed characteristics, including size, slope, and permeability were the variables that were studied. The pollutants of concern were nutrient concentrations of total nitrogen (TN) and total phosphorus (TP), common pollutants found in eutrophication. The monthly monitoring data at 41 sites in the Xitiaoxi Watershed, China during 2009–2010 were used for model demonstration. The results showed that the relationships between LULC and stream water quality are so complicated that the effects are varied over large areas. The models suggested that urban and agricultural land are important sources of TN and TP concentrations, while rural residential land is one of the major sources of TN. Certain agricultural practices (excessive fertilizer application) result in greater concentrations of nutrients in paddy fields, artificial grasslands, and artificial woodlands. This study suggests that Bayesian hierarchical modeling is a powerful tool for examining the complicated relationships between land use and water quality on different scales, and for developing land use and water management policies.},
	language = {en},
	urldate = {2020-04-22},
	journal = {Journal of Environmental Management},
	author = {Wan, Rongrong and Cai, Shanshan and Li, Hengpeng and Yang, Guishan and Li, Zhaofu and Nie, Xiaofei},
	month = jan,
	year = {2014},
	keywords = {Land use and land cover, Total nitrogen, Total phosphorus, Water quality, Watershed modeling},
	pages = {1--11},
}

@article{monteith_dissolved_2007,
	title = {Dissolved organic carbon trends resulting from changes in atmospheric deposition chemistry},
	volume = {450},
	issn = {1476-4687},
	url = {http://www.nature.com/articles/nature06316},
	doi = {10.1038/nature06316},
	abstract = {The use of time series data from 522 remote lakes and streams in North America and northern Europe and a simple model shows that dissolved organic carbon concentrations between 1990– 2004 have increased in proportion to the rates at which atmospherically deposited anthropogenic sulphur and sea salt have declined. It is suggested that acid deposition to these ecosystems has been partially buffered by changes in organic acidity and that the rise in dissolved organic carbon is integral to recovery from acidification.},
	language = {en},
	number = {7169},
	urldate = {2020-04-22},
	journal = {Nature},
	author = {Monteith, Donald T. and Stoddard, John L. and Evans, Christopher D. and de Wit, Heleen A. and Forsius, Martin and Høgåsen, Tore and Wilander, Anders and Skjelkvåle, Brit Lisa and Jeffries, Dean S. and Vuorenmaa, Jussi and Keller, Bill and Kopácek, Jiri and Vesely, Josef},
	month = nov,
	year = {2007},
	note = {Number: 7169
Publisher: Nature Publishing Group},
	pages = {537--540},
}

@article{teissier_detailing_2007,
	title = {Detailing biogeochemical {N} budgets in riverine epilithic biofilms},
	volume = {26},
	issn = {2161-9549, 2161-9565},
	url = {https://bioone.org/journals/Freshwater-Science/volume-26/issue-2/0887-3593(2007)26[178:DBNBIR]2.0.CO;2/Detailing-biogeochemical-N-budgets-in-riverine-epilithic-biofilms/10.1899/0887-3593(2007)26[178:DBNBIR]2.0.CO;2.full},
	doi = {10.1899/0887-3593(2007)26[178:DBNBIR]2.0.CO;2},
	abstract = {Dissolved inorganic N fluxes, including nitrification and denitrification rates, were measured in situ under dark and light conditions using epilithic biofilms from a 6th to 8th Strahler-order reach of the River Garonne, France. A broad range of epilithic biofilm biomasses (6–51 g ash-free dry mass [AFDM]/m2) was assessed in 39 benthic chamber experiments. Nitrification was detected in 31 cases (0.1–7.7 mg N m−2 h−1) and caused a net release of NO3– in spite of algal assimilation in light conditions in 5 cases. Denitrification (Dw) (0–8.1 mg N m−2 h−1), which accounted for 83\% of gross NO3– removal in the dark, was a significant, permanent N sink. Calculation of mean (±1 SE) N budgets indicated epilithon release of inorganic N in the dark (1.5 ± 0.3 mg N m−2 h−1) that was significantly related to biofilm mass. Calculation of mean N budgets under light indicated net uptake (1.8 ± 0.4 mg N m−2 h−1). However, a net release was observed when biomass was {\textgreater}40 g AFDM/m2. A calculated daily budget showed evidence for a threshold between photoautotrophy (N assimilation) and heterotrophy (N mineralization) of 23 g AFDM/m2. This threshold approximated mean biomass at low water and may correspond to an equilibrium value for epilithic biomass in the river. A conceptual scheme of the epilithic biofilm function and the consequences on the water-column N content in rivers is proposed.},
	number = {2},
	urldate = {2020-04-22},
	journal = {Freshwater Science},
	author = {Teissier, Samuel and Torre, Mathieu and Delmas, François and Garabétian, Frédéric},
	month = jun,
	year = {2007},
	note = {Publisher: Society for Freshwater Science},
	pages = {178--190},
}

@article{hurlbert_pseudoreplication_1984,
	title = {Pseudoreplication and the {Design} of {Ecological} {Field} {Experiments}},
	volume = {54},
	issn = {0012-9615},
	url = {https://www.jstor.org/stable/1942661},
	doi = {10.2307/1942661},
	abstract = {Pseudoreplication is defined as the use of inferential statistics to test for treatment effects with data from experiments where either treatments are not replicated (though samples may be) or replicates are not statistically independent. In ANOVA terminology, it is the testing for treatment effects with an error term inappropriate to the hypothesis being considered. Scrutiny of 176 experimental studies published between 1960 and the present revealed that pseudoreplication occurred in 27\% of them, or 48\% of all such studies that applied inferential statistics. The incidence of pseudoreplication is especially high in studies of marine benthos and small mammals. The critical features of controlled experimentation are reviewed. Nondemonic intrusion is defined as the impingement of chance events on an experiment in progress. As a safeguard against both it and preexisting gradients, interspersion of treatments is argued to be an obligatory feature of good design. Especially in small experiments, adequate interspersion can sometimes be assured only by dispensing with strict randomization procedures. Comprehension of this conflict between interspersion and randomization is aided by distinguishing pre-layout (or conventional) and layout-specific alpha (probability of type I error). Suggestions are offered to statisticians and editors of ecological journals as to how ecologists' understanding of experimental design and statistics might be improved.},
	number = {2},
	urldate = {2020-04-22},
	journal = {Ecological Monographs},
	author = {Hurlbert, Stuart H.},
	year = {1984},
	note = {Publisher: Ecological Society of America},
	pages = {187--211},
}

@article{qian_continuous_2015,
	title = {A continuous variable {Bayesian} networks model for water quality modeling: {A} case study of setting nitrogen criterion for small rivers and streams in {Ohio}, {USA}},
	volume = {69},
	issn = {1364-8152},
	shorttitle = {A continuous variable {Bayesian} networks model for water quality modeling},
	url = {http://www.sciencedirect.com/science/article/pii/S1364815215000778},
	doi = {10.1016/j.envsoft.2015.03.001},
	abstract = {We present a continuous variable Bayesian networks modeling framework that integrates the graphical representation of a Bayesian networks model with empirical model-developing approach. Our model retains the Bayesian networks model's graphical representation of hypothesized causal connections among important variables and employs conventional statistical modeling approaches for establishing functional relationships among these variables. The modeling framework avoids discretizing continuous variables and the resulting models can be updated over time when new data are available or updated using local data to develop a site-specific model. We illustrate the modeling approach using a data for establishing nutrient criteria in streams and rivers in Ohio, U.S.A.},
	language = {en},
	urldate = {2020-04-22},
	journal = {Environmental Modelling \& Software},
	author = {Qian, Song S. and Miltner, Robert J.},
	month = jul,
	year = {2015},
	keywords = {Bayesian statistics, Biological monitoring, Clean Water Act, Nutrient criteria, Ohio, Simulation, Updating},
	pages = {14--22},
}

@article{holtgrieve_simultaneous_2010,
	title = {Simultaneous quantification of aquatic ecosystem metabolism and reaeration using a {Bayesian} statistical model of oxygen dynamics},
	volume = {55},
	copyright = {© 2010, by the Association for the Sciences of Limnology and Oceanography, Inc.},
	issn = {1939-5590},
	url = {http://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.2010.55.3.1047},
	doi = {10.4319/lo.2010.55.3.1047},
	abstract = {We present a Bayesian statistical model of diel oxygen dynamics in aquatic ecosystems to simultaneously estimate gross primary production, ecosystem respiration, and oxygen exchange with the atmosphere (and their uncertainties) on the basis of changes in dissolved oxygen concentration, water temperature, irradiance, and, if desired, the 18O to 16O ratio (δ18O-O2). We test this model using simulated data with realistic measurement errors to demonstrate that it accurately estimates the model parameters and that parameter uncertainties correctly scale with error in the observations and number of data points. Application of the model to field data from two productive stream ecosystems with substantial daily dissolved oxygen variation quantified the underlying physical and biological factors that control oxygen dynamics in these ecosystems and provided empirical support for a light saturation model of the photosynthesis-irradiance relationships at the ecosystem scale. Although inclusion of δ18O-O2 provides a second oxygen budget, analysis of field data shows that metabolic and reaeration parameters can be accurately estimated by modeling the transient dynamics of dissolved oxygen concentration alone in relation to daily changes in water temperature and light regime. This model is particularly suited to low-gas exchange, high-productivity systems, which have thus far proved challenging to measure ecosystem metabolism accurately. The modeling framework is applicable to single-station, open-system experimental designs and provides a rigorous and generalizable framework for estimating ecosystem metabolism in aquatic ecosystems.},
	language = {en},
	number = {3},
	urldate = {2020-04-22},
	journal = {Limnology and Oceanography},
	author = {Holtgrieve, Gordon W. and Schindler, Daniel E. and Branch, Trevor A. and A'mar, Z. Teresa},
	year = {2010},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.4319/lo.2010.55.3.1047},
	pages = {1047--1063},
}

@article{teissier_simultaneous_2002,
	title = {Simultaneous assessment of nitrification and denitrification on freshwater epilithic biofilms by acetylene block method},
	volume = {36},
	issn = {0043-1354},
	url = {http://www.sciencedirect.com/science/article/pii/S0043135402000982},
	doi = {10.1016/S0043-1354(02)00098-2},
	abstract = {Acetylene (C2H2) inhibits key enzymes involved in nitrification (Ammonium monooxygenase) and denitrification (N2O reductases). Thus an injection of C2H2 at mid time of a batch type incubation make it possible to assess denitrification by measurement of the N2O accumulation as well as nitrification, calculated from the variations of the ammonium flux. As estimated by the “acetylene block technique”, denitrification is known to be only a measure of the denitrification rate supported by nitrate diffusing from the water column (Dw). This paper presents a first application on river epilithic biofilms which proved that the simultaneous measurement of Dw and nitrification allows the estimation of the order of magnitude of total denitrification (Dt) when nitrification is detected in the tested sample. This approach appears to be an easy tool for determination of nitrification and denitrification in natural samples and as thus presents an alternative to isotopic 15N methods.},
	language = {en},
	number = {15},
	urldate = {2020-04-22},
	journal = {Water Research},
	author = {Teissier, S and Torre, M},
	month = sep,
	year = {2002},
	keywords = {Acetylene, Biofilm, Denitrification, Freshwater, Nitrification},
	pages = {3803--3811},
}

@article{belyazid_assessing_2019,
	title = {Assessing the {Effects} of {Climate} {Change} and {Air} {Pollution} on {Soil} {Properties} and {Plant} {Diversity} in {Northeastern} {U}.{S}. {Hardwood} {Forests}: {Model} {Setup} and {Evaluation}},
	volume = {230},
	issn = {1573-2932},
	shorttitle = {Assessing the {Effects} of {Climate} {Change} and {Air} {Pollution} on {Soil} {Properties} and {Plant} {Diversity} in {Northeastern} {U}.{S}. {Hardwood} {Forests}},
	url = {10.1007/s11270-019-4145-6},
	doi = {10.1007/s11270-019-4145-6},
	abstract = {The integrated forest ecosystem model ForSAFE-Veg was used to simulate soil processes and understory vegetation composition at three—sugar maple, beech, yellow birch—hardwood forest sites in the Northeastern United States (one at Hubbard Brook, NH, and two at Bear Brook, ME). Input data were pooled from a variety of sources and proved coherent and consistent. While the biogeochemical component ForSAFE was used with limited calibration, the ground vegetation composition module Veg was calibrated to field relevés. Evaluating different simulated ecosystem indicators (soil solution chemistry, tree biomass, ground vegetation composition) showed that the model performed comparably well regardless of the site’s soil condition, climate, and amounts of nitrogen (N) and sulfur (S) deposition, with the exception of failing to capture tree biomass decline at Hubbard Brook. The model performed better when compared with annual observation than monthly data. The results support the assumption that the biogeochemical model ForSAFE can be used with limited calibration and provide reasonable confidence, while the vegetation community composition module Veg requires calibration if the individual plant species are of interest. The study welcomes recent advances in empirically explaining the responses of hardwood forests to nutrient imbalances and points to the need for more research.},
	language = {en},
	number = {5},
	urldate = {2020-04-22},
	journal = {Water, Air, \& Soil Pollution},
	author = {Belyazid, Salim and Phelan, Jennifer and Nihlgård, Bengt and Sverdrup, Harald and Driscoll, Charles and Fernandez, Ivan and Aherne, Julian and Teeling-Adams, Leslie M. and Bailey, Scott and Arsenault, Matt and Cleavitt, Natalie and Engstrom, Brett and Dennis, Robin and Sperduto, Dan and Werier, David and Clark, Christopher},
	month = apr,
	year = {2019},
	pages = {106},
}

@article{pardo_effects_2011,
	title = {Effects of nitrogen deposition and empirical nitrogen critical loads for ecoregions of the {United} {States}},
	volume = {21},
	copyright = {© 2011 by the Ecological Society of America},
	issn = {1939-5582},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/10-2341.1},
	doi = {10.1890/10-2341.1},
	abstract = {Human activity in the last century has led to a significant increase in nitrogen (N) emissions and atmospheric deposition. This N deposition has reached a level that has caused or is likely to cause alterations to the structure and function of many ecosystems across the United States. One approach for quantifying the deposition of pollution that would be harmful to ecosystems is the determination of critical loads. A critical load is defined as the input of a pollutant below which no detrimental ecological effects occur over the long-term according to present knowledge. The objectives of this project were to synthesize current research relating atmospheric N deposition to effects on terrestrial and freshwater ecosystems in the United States, and to estimate associated empirical N critical loads. The receptors considered included freshwater diatoms, mycorrhizal fungi, lichens, bryophytes, herbaceous plants, shrubs, and trees. Ecosystem impacts included: (1) biogeochemical responses and (2) individual species, population, and community responses. Biogeochemical responses included increased N mineralization and nitrification (and N availability for plant and microbial uptake), increased gaseous N losses (ammonia volatilization, nitric and nitrous oxide from nitrification and denitrification), and increased N leaching. Individual species, population, and community responses included increased tissue N, physiological and nutrient imbalances, increased growth, altered root : shoot ratios, increased susceptibility to secondary stresses, altered fire regime, shifts in competitive interactions and community composition, changes in species richness and other measures of biodiversity, and increases in invasive species. The range of critical loads for nutrient N reported for U.S. ecoregions, inland surface waters, and freshwater wetlands is 1–39 kg N·ha−1·yr−1, spanning the range of N deposition observed over most of the country. The empirical critical loads for N tend to increase in the following sequence for different life forms: diatoms, lichens and bryophytes, mycorrhizal fungi, herbaceous plants and shrubs, and trees. The critical load approach is an ecosystem assessment tool with great potential to simplify complex scientific information and communicate effectively with the policy community and the public. This synthesis represents the first comprehensive assessment of empirical critical loads of N for major ecoregions across the United States.},
	language = {en},
	number = {8},
	urldate = {2020-04-22},
	journal = {Ecological Applications},
	author = {Pardo, Linda H. and Fenn, Mark E. and Goodale, Christine L. and Geiser, Linda H. and Driscoll, Charles T. and Allen, Edith B. and Baron, Jill S. and Bobbink, Roland and Bowman, William D. and Clark, Christopher M. and Emmett, Bridget and Gilliam, Frank S. and Greaver, Tara L. and Hall, Sharon J. and Lilleskov, Erik A. and Liu, Lingli and Lynch, Jason A. and Nadelhoffer, Knute J. and Perakis, Steven S. and Robin-Abbott, Molly J. and Stoddard, John L. and Weathers, Kathleen C. and Dennis, Robin L.},
	year = {2011},
	note = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1890/10-2341.1},
	keywords = {air pollution, atmospheric N deposition, biodiversity, community shifts, natural resource protection, nitrate leaching, nitrogen saturation, plant nitrogen cycling, vegetation type conversion},
	pages = {3049--3082},
}

@article{simon_stream_2010,
	title = {Stream ecosystem response to chronic deposition of {N} and acid at the {Bear} {Brook} {Watershed}, {Maine}},
	volume = {171},
	issn = {1573-2959},
	url = {10.1007/s10661-010-1532-2},
	doi = {10.1007/s10661-010-1532-2},
	abstract = {The Bear Brook Watershed in Maine (BBWM) is a long-term, paired watershed experiment that addresses the effects of acid and nitrogen (N) deposition on whole watersheds. To examine stream response at BBWM, we synthesized data on organic matter dynamics, including leaf breakdown rates, organic matter inputs and standing stocks, macroinvertebrate secondary production, and nutrient uptake in treated and reference streams at the BBWM. While N concentrations in stream water and leaves have increased, the input, standing stocks, and breakdown rates of leaves, as well as macroinvertebrate production, were not responsive to acid and N deposition. Both chronic and acute increases of N availability have saturated uptake of nitrate in the streams. Recent experimental increases in phosphorus (P) availability enhanced stream capacity to take up nitrate and altered the character of N saturation. These results show how the interactive effects of multiple factors, including environmental flow regime, acidification, and P availability, may constrain stream response to chronic N deposition.},
	language = {en},
	number = {1},
	urldate = {2020-04-22},
	journal = {Environmental Monitoring and Assessment},
	author = {Simon, Kevin S. and Chadwick, Michael A. and Huryn, Alexander D. and Valett, H. Maurice},
	month = dec,
	year = {2010},
	pages = {83--92},
}

@article{baron_empirical_2011,
	title = {Empirical {Critical} {Loads} of {Atmospheric} {Nitrogen} {Deposition} for {Nutrient} {Enrichment} and {Acidification} of {Sensitive} {US} {Lakes}},
	volume = {61},
	issn = {0006-3568},
	url = {https://academic.oup.com/bioscience/article/61/8/602/337131},
	doi = {10.1525/bio.2011.61.8.6},
	abstract = {Abstract.  The ecological effects of elevated atmospheric nitrogen (N) deposition on high-elevation lakes of the western and northeastern United States include},
	language = {en},
	number = {8},
	urldate = {2020-04-22},
	journal = {BioScience},
	author = {Baron, Jill S. and Driscoll, Charles T. and Stoddard, John L. and Richer, Eric E.},
	month = aug,
	year = {2011},
	note = {Publisher: Oxford Academic},
	pages = {602--613},
}

@article{baron_interactive_2013,
	title = {The interactive effects of excess reactive nitrogen and climate change on aquatic ecosystems and water resources of the {United} {States}},
	volume = {114},
	issn = {1573-515X},
	url = {10.1007/s10533-012-9788-y},
	doi = {10.1007/s10533-012-9788-y},
	abstract = {Nearly all freshwaters and coastal zones of the US are degraded from inputs of excess reactive nitrogen (Nr), sources of which are runoff, atmospheric N deposition, and imported food and feed. Some major adverse effects include harmful algal blooms, hypoxia of fresh and coastal waters, ocean acidification, long-term harm to human health, and increased emissions of greenhouse gases. Nitrogen fluxes to coastal areas and emissions of nitrous oxide from waters have increased in response to N inputs. Denitrification and sedimentation of organic N to sediments are important processes that divert N from downstream transport. Aquatic ecosystems are particularly important denitrification hotspots. Carbon storage in sediments is enhanced by Nr, but whether carbon is permanently buried is unknown. The effect of climate change on N transport and processing in fresh and coastal waters will be felt most strongly through changes to the hydrologic cycle, whereas N loading is mostly climate-independent. Alterations in precipitation amount and dynamics will alter runoff, thereby influencing both rates of Nr inputs to aquatic ecosystems and groundwater and the water residence times that affect Nr removal within aquatic systems. Both infrastructure and climate change alter the landscape connectivity and hydrologic residence time that are essential to denitrification. While Nr inputs to and removal rates from aquatic systems are influenced by climate and management, reduction of N inputs from their source will be the most effective means to prevent or to minimize environmental and economic impacts of excess Nr to the nation’s water resources.},
	language = {en},
	number = {1},
	urldate = {2020-04-22},
	journal = {Biogeochemistry},
	author = {Baron, J. S. and Hall, E. K. and Nolan, B. T. and Finlay, J. C. and Bernhardt, E. S. and Harrison, J. A. and Chan, F. and Boyer, E. W.},
	month = jul,
	year = {2013},
	pages = {71--92},
}

@article{mohammed_effects_2019,
	title = {Effects of preferential flow on snowmelt partitioning andgroundwater recharge in frozen soils},
	volume = {23},
	url = {https://www.hydrol-earth-syst-sci-discuss.net/hess-2019-169/hess-2019-169.pdf},
	doi = {10.5194/hess-2019-169},
	abstract = {Snowmelt is a major source of groundwater recharge in cold regions. Throughout many landscapes snowmelt occurs when ground is still frozen, thus frozen soil processes play an important role in snowmelt routing, and, by extension, on the timing and magnitude of recharge. This study investigated the vadose zone dynamics governing snowmelt infiltration 10 and groundwater recharge at three grassland sites in the Canadian Prairies over the winter and spring of 2017. The region is characterised by numerous topographic depressions where ponding of snowmelt runoff results in focused infiltration and recharge. Water balance estimates showed infiltration was the dominant sink (35–85\%) of snowmelt under uplands (i.e. areas outside depressions), even when ground was frozen, with soil moisture responses indicating flow through the frozen layer. Refreezing of infiltrated meltwater during winter melt events enhanced runoff generation in subsequent melt events. 15 At one site, time lags of up to 3 days between snowcover depletion on uplands and ponding in depressions demonstrated the role of shallow subsurface flow through frozen soil in routing snowmelt to depressions. At all sites, depression-focused infiltration and recharge began before ground thaw and a significant portion (45–100\%) occurred while the ground was partially frozen. Relatively rapid infiltration rates and non-sequential soil moisture and groundwater responses, observed prior to ground thaw, indicated preferential flow through frozen soils. The preferential flow dynamics are attributed to 20 macropore networks within the grassland soils, which allow infiltrated meltwater to bypass portions of the frozen soil matrix and facilitate both lateral transport of meltwater between topographic positions and groundwater recharge through frozen ground. Both of these flowpaths may facilitate preferential mass transport to groundwater.},
	language = {en},
	number = {12},
	urldate = {2020-01-23},
	journal = {Hydrology and Earth System Sciences},
	author = {Mohammed, Aaron A. and Pavlovskii, Igor and Cey, Edwin E. and Hayashi, Masaki},
	month = apr,
	year = {2019},
	pages = {5017--5031},
}

@article{baeumler_precipitation_2019,
	title = {Precipitation as the {Primary} {Driver} of {Variability} in {River} {Nitrogen} {Loads} in the {Midwest} {United} {States}},
	volume = {56},
	copyright = {© 2019 American Water Resources Association},
	issn = {1752-1688},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/1752-1688.12809},
	doi = {10.1111/1752-1688.12809},
	abstract = {Nitrogen (N) losses from agricultural lands in the Midwest United States are contributing to the expansion of the hypoxic zone in the Gulf of Mexico. This study evaluated the importance of inter-annual variability in precipitation, land cover, and N fertilizer use on NO3 + NO2-N loads in seven United States Midwestern Rivers using the backward stepwise regression analysis. At the annual scale, fluctuations in the current and previous years’ precipitations explained much of the variation in streamflow, baseflow, and N-load. Previous years precipitation effects were associated with fillable soil porosity. In some years, higher residual soil N from previous dry years also contributed to an increase in N-load. Area under soybean production (SOY), a surrogate for replacement of prairies and small grains was generally not a significant explanatory variable. Fertilizer use from 1987 to 2012 was also not a significant explanatory variable in the annual analysis. Precipitation in both the current and previous months and previous year were important in explaining variation in monthly streamflow, baseflow, and N-load. SOY was significant in one or two months from June to August, but had a higher p-value than precipitation. We conclude recent increases in river N-loads are primarily due to wet climate and minimally due to the changes in land cover or N fertilizer use. Under current cropping systems and agronomic N application rates, tile water remediation will be necessary to reduce river N-loads.},
	language = {en},
	number = {1},
	urldate = {2020-02-07},
	journal = {JAWRA Journal of the American Water Resources Association},
	author = {Baeumler, Nathaniel W. and Gupta, Satish C.},
	year = {2019},
	keywords = {N fertilizer use, N-loads, baseflow, evapotranspiration, flow-weighted N concentration, prairies, precipitation, row crops, streamflow, tile drainage},
	pages = {113--133},
}

@article{yang_impact_2020,
	title = {Impact of cover crop on {Corn}-{Soybean} productivity and {Soil} {Water} dynamics under different seasonal rainfall patterns},
	copyright = {This article is protected by copyright. All rights reserved},
	issn = {1435-0645},
	url = {https://acsess.onlinelibrary.wiley.com/doi/abs/10.1002/agj2.20110},
	doi = {10.1002/agj2.20110},
	abstract = {The impact of cover crop (CC) on soil water balance and agricultural production is closely related to rainfall amount, duration, and distribution in rainfed cropping systems. This study used the RZWQM2 model calibrated and validated with 4-yr field measurements to predict the impact of planting a winter wheat (Triticum aestivum L.) CC in a no-till rainfed corn (Zea mays L.)-soybean (Glycine max L.) rotation on soil water balance, crop yield, and grain water-use efficiency (WUE) in northeast Mississippi, USA. Seasonal rainfall for 80 consecutive years (1938 to 2017) was classified as ‘wet’, ‘normal’, and ‘dry’ years using frequency analysis and the data sets matched chronologically to wheat, corn, and soybean growth periods were used as an input parameter in RZWQM2 simulations. During autumn and spring (early October to early April), the CC reduced deep drainage by 69 mm (11\%), 53 mm (15\%), and 51 mm (21\%) mm and increased evapotranspiration by 79 mm (55\%), 81 mm (57\%), and 73 mm (56\%) mm in wet, normal, and dry years, respectively. Averaged across 40 years, the CC decreased surface evaporation by 64 mm (32\%) and 38 mm (24\%) mm for corn and soybean growth periods, respectively. Wheat CC also improved soil water storage in early crop growth period during April-June in any of the three rainfall patterns. Regardless of rainfall patterns, the increase in WUE can be attributed to a decrease in evapotranspiration during cash crop period without sacrificing cash crop yield in the CC system. Introducing CC into cropping systems is beneficial to reduce annual deep drainage and evaporation while maintaining higher crop yields under different rainfall patterns. This article is protected by copyright. All rights reserved},
	language = {en},
	urldate = {2020-02-14},
	journal = {Agronomy Journal},
	author = {Yang, Wei and Feng, Gary and Read, John J. and Ouyang, Ying and Han, Jianjun and Li, Pinfang},
	year = {2020},
	keywords = {Climate variability, agricultural system models, crop rotation, deep drainage, evapotranspiration, rainfall},
	pages = {1--15},
}

@article{mclaughlin_biological_2013,
	title = {Biological lability of dissolved organic carbon in stream water and contributing terrestrial sources},
	volume = {32},
	issn = {2161-9549},
	url = {https://www.journals.uchicago.edu/doi/abs/10.1899/12-202.1},
	doi = {10.1899/12-202.1},
	abstract = {Terrestrial sources of dissolved organic C (DOC) provide energy for stream microbial heterotrophs. Hydrologic conditions alter flow paths to the stream and influence terrestrial source quantity and quality. We used bioreactors to measure biodegradable DOC (BDOC) in water from soils, shallow wells, and spring seeps under baseflow conditions, overland flow during storms, and a stream during base flow and storm flow. Stream DOC concentrations ranged from 0.7 to 15.5 mg C/L and total BDOC ranged from 0.1 to 8.7 mg C/L. Under baseflow conditions, DOC was generally {\textless}2 mg C/L and BDOC was {\textless}0.7 mg C/L. BDOC made up 37.8\% of DOC (8.2\% labile and 29.6\% semilabile constituents) and most DOC (62.2\%) was recalcitrant. Storms increased DOC concentrations 6- to 12-fold and selectively mobilized BDOC increasing concentrations 8- to 27-fold. Labile and semilabile constituents increased 2-fold to 17.3\% and 55.4\%, respectively, so that storm flow DOC was largely biodegradable (73\%). Terrestrial DOC concentrations declined from 2.15 mg C/L in soil water to 1.78 mg C/L in shallow wells to 1.26 mg C/L in spring seeps, and labile BDOC concentrations declined from 0.1 mg C/L in soil water to 0.04 mg C/L in shallow wells but increased to 0.13 mg C/L in spring seeps. Overland flow waters had elevated DOC (11.0 mg C/L) and labile BDOC (1.7 mg C/L) concentrations. Peak storm concentrations for 2 biological reactivity classes were coincident during 2 storms but divergent during another storm, suggesting temporal variation in hydrologic pathways. Our results demonstrate that storms deliver increased BDOC loads to a headwater stream and reveal the temporal variability of labile and semilabile BDOC constituents. Storms increase stream depth and velocity, resulting in increased uptake lengths for BDOC constituents, exporting them from the basin and probably providing a downstream subsidy.},
	number = {4},
	urldate = {2020-04-14},
	journal = {Freshwater Science},
	author = {McLaughlin, Christine and Kaplan, Louis A.},
	month = dec,
	year = {2013},
	note = {Publisher: The University of Chicago Press},
	pages = {1219--1230},
}

@article{saldanha_nutritional_2004,
	title = {Nutritional {Homeostasis} in {Batch} and {Steady}-{State} {Culture} of {Yeast}},
	volume = {15},
	issn = {1059-1524},
	url = {https://www.molbiolcell.org/doi/full/10.1091/mbc.e04-04-0306},
	doi = {10.1091/mbc.e04-04-0306},
	abstract = {We studied the physiological response to limitation by diverse nutrients in batch and steady-state (chemostat) cultures of S. cerevisiae. We found that the global pattern of transcription in steady-state cultures in limiting phosphate or sulfate is essentially identical to that of batch cultures growing in the same medium just before the limiting nutrient is completely exhausted. The massive stress response and complete arrest of the cell cycle that occurs when nutrients are fully exhausted in batch cultures is not observed in the chemostat, indicating that the cells in the chemostat are “poor, not starving.” Similar comparisons using leucine or uracil auxotrophs limited on leucine or uracil again showed patterns of gene expression in steady-state closely resembling those of corresponding batch cultures just before they exhaust the nutrient. Although there is also a strong stress response in the auxotrophic batch cultures, cell cycle arrest, if it occurs at all, is much less uniform. Many of the differences among the patterns of gene expression between the four nutrient limitations are interpretable in light of known involvement of the genes in stress responses or in the regulation or execution of particular metabolic pathways appropriate to the limiting nutrient. We conclude that cells adjust their growth rate to nutrient availability and maintain homeostasis in the same way in batch and steady state conditions; cells in steady-state cultures are in a physiological condition normally encountered in batch cultures.},
	number = {9},
	urldate = {2020-04-10},
	journal = {Molecular Biology of the Cell},
	author = {Saldanha, Alok J. and Brauer, Matthew J. and Botstein, David},
	month = jul,
	year = {2004},
	note = {Publisher: American Society for Cell Biology (mboc)},
	pages = {4089--4104},
}

@misc{noauthor_nutritional_nodate,
	title = {Nutritional {Homeostasis} in {Batch} and {Steady}-{State} {Culture} of {Yeast} {\textbar} {Molecular} {Biology} of the {Cell}},
	url = {https://www.molbiolcell.org/doi/full/10.1091/mbc.e04-04-0306},
	urldate = {2020-04-10},
}

@article{singh_land_2014,
	title = {Land application of poultry manure and its influence on spectrofluorometric characteristics of dissolved organic matter},
	volume = {193},
	issn = {0167-8809},
	url = {http://www.sciencedirect.com/science/article/pii/S0167880914002254},
	doi = {10.1016/j.agee.2014.04.019},
	abstract = {Land application of manure is a common practice that is used to supplement nutrients from fertilizers as well as to reuse and recycle waste in agricultural watersheds. Excess application of manure can however result in elevated exports of organic and inorganic nutrients in runoff. We evaluated the concentration and composition of dissolved organic matter (DOM) in runoff from cropland (corn) receiving poultry manure. Manure was applied once every three years at the rate of 9Mgha−1 in early spring and was incorporated into the soil during application. Surface runoff and soil water sampling was performed for eight natural storm events with one storm event prior to manure application. Samples were collected from the field edge, upland and lowland riparian zones and a receiving stream. Concentrations of dissolved organic carbon (DOC) were highest at the field edge (mean: 94mgL−1) and then declined sharply for the riparian and stream locations. Temporally, DOC concentrations in field runoff were highest for the first storm event following manure application and then declined quickly over the next 1–3 weeks. DOM composition in runoff following manure application had low aromaticity and a microbial/tryptophan-like character. These characteristics evolved with time toward more aromatic, more humic, and a terrestrial-like DOM composition. The decrease in runoff DOM was attributed to sorption and microbial degradation. Our observations suggest that while concentrations of DOM can be low in manure runoff, a short period (1–3 weeks) following manure application could be an environmentally sensitive and vulnerable period for runoff water quality.},
	language = {en},
	urldate = {2020-04-09},
	journal = {Agriculture, Ecosystems \& Environment},
	author = {Singh, Shatrughan and Dutta, Sudarshan and Inamdar, Shreeram},
	month = aug,
	year = {2014},
	keywords = {Agricultural watershed, Dissolved organic matter (DOM), Excitation emission matrices (EEMs), Fluorescence spectroscopy, Poultry manure, Storm events, UV absorbance},
	pages = {25--36},
}

@misc{noauthor_transport_nodate,
	title = {Transport of {N} and {P} in {U}.{S}. streams and rivers differs with land use and between dissolved and particulate forms - {Manning} - - {Ecological} {Applications} - {Wiley} {Online} {Library}},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/eap.2130},
	urldate = {2020-04-08},
}

@article{mehlich_mehlich_1984,
	title = {Mehlich 3 soil test extractant: {A} modification of {Mehlich} 2 extractant},
	volume = {15},
	issn = {0010-3624},
	shorttitle = {Mehlich 3 soil test extractant},
	url = {10.1080/00103628409367568},
	doi = {10.1080/00103628409367568},
	abstract = {The objectives of this study were to modify the Mehlich 2 (M2) extractant to include Cu among the extractable nutrients, retain or enhance the wide range of soils for which it is suitable and minimize it's corrosive properties. The substitution of nitrate for chloride anions and the addition of EDTA accomplished those objectives. The new extracting solution, already designated Mehlich 3 (M3) is composed of 0.2N CH3COOH‐0.25N NH4N03‐0.015NNH4F‐0.013NHN03‐0.001M EDTA. Extractions from 105 soils using M3, M2, Bray 1 (Bl) and Ammonium Acetate (AA) were compared to evaluate the new extractant. The quantity of F extracted by M3 exceeded that by M2 20\% and that by Bl 4\% but the results from all extractions were highly correlated. Extractions of both K and Mg by M3 were 6–8\% higher than those by AA and 3–4\% higher than those by M2, but, again, there was high correlation among methods. Addition of EDTA increased Cu extractions by 170\%, Mn by 50\% and Zn by 25\%. Cu extractions by M3 correlated with those from the Mehlich‐Bowling method. High correlations between Mn, as well as Zn, extracted by M3 and M2 were shown.},
	number = {12},
	urldate = {2020-04-07},
	journal = {Communications in Soil Science and Plant Analysis},
	author = {Mehlich, A.},
	month = dec,
	year = {1984},
	note = {Publisher: Taylor \& Francis
\_eprint: 10.1080/00103628409367568},
	keywords = {Ammonium Acetate, Bray 1, Cu Extraction, EDTA, Mehlich 3},
	pages = {1409--1416},
}

@article{ibrahim_estimation_2019,
	title = {The {Estimation} of {Soil} {Organic} {Matter} {Variation} in {Arid} and {Semi}-{Arid} {Lands} {Using} {Remote} {Sensing} {Data}},
	volume = {10},
	issn = {2156-8359, 2156-8367},
	url = {http://www.scirp.org/journal/doi.aspx?DOI=10.4236/ijg.2019.105033},
	doi = {10.4236/ijg.2019.105033},
	number = {05},
	urldate = {2020-04-07},
	journal = {International Journal of Geosciences},
	author = {Ibrahim, Majed and Ghanem, Fatima and Al-Salameen, Afnan and Al-Fawwaz, Abdallah},
	year = {2019},
	pages = {576--588},
}

@article{elser_global_2007,
	title = {Global analysis of nitrogen and phosphorus limitation of primary producers in freshwater, marine and terrestrial ecosystems},
	volume = {10},
	issn = {1461-0248},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1461-0248.2007.01113.x},
	doi = {10.1111/j.1461-0248.2007.01113.x},
	abstract = {The cycles of the key nutrient elements nitrogen (N) and phosphorus (P) have been massively altered by anthropogenic activities. Thus, it is essential to understand how photosynthetic production across diverse ecosystems is, or is not, limited by N and P. Via a large-scale meta-analysis of experimental enrichments, we show that P limitation is equally strong across these major habitats and that N and P limitation are equivalent within both terrestrial and freshwater systems. Furthermore, simultaneous N and P enrichment produces strongly positive synergistic responses in all three environments. Thus, contrary to some prevailing paradigms, freshwater, marine and terrestrial ecosystems are surprisingly similar in terms of N and P limitation.},
	language = {en},
	number = {12},
	urldate = {2020-04-03},
	journal = {Ecology Letters},
	author = {Elser, James J. and Bracken, Matthew E. S. and Cleland, Elsa E. and Gruner, Daniel S. and Harpole, W. Stanley and Hillebrand, Helmut and Ngai, Jacqueline T. and Seabloom, Eric W. and Shurin, Jonathan B. and Smith, Jennifer E.},
	year = {2007},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1461-0248.2007.01113.x},
	keywords = {Ecosystem, meta-analysis, nitrogen, nutrient limitation, phosphorus, primary production},
	pages = {1135--1142},
}

@article{bossio_role_2020,
	title = {The role of soil carbon in natural climate solutions},
	copyright = {2020 The Author(s), under exclusive licence to Springer Nature Limited},
	issn = {2398-9629},
	url = {https://www.nature.com/articles/s41893-020-0491-z},
	doi = {10.1038/s41893-020-0491-z},
	abstract = {Diverse strategies are needed to mitigate climate change. This study finds that storing carbon in soils represents 25\% of land-based potential, of which 60\% must come from rebuilding depleted carbon stores.},
	language = {en},
	urldate = {2020-04-03},
	journal = {Nature Sustainability},
	author = {Bossio, D. A. and Cook-Patton, S. C. and Ellis, P. W. and Fargione, J. and Sanderman, J. and Smith, P. and Wood, S. and Zomer, R. J. and von Unger, M. and Emmer, I. M. and Griscom, B. W.},
	month = mar,
	year = {2020},
	note = {Publisher: Nature Publishing Group},
	pages = {1--8},
}

@article{smith_eutrophication_2003,
	title = {Eutrophication of freshwater and coastal marine ecosystems a global problem},
	volume = {10},
	issn = {1614-7499},
	url = {10.1065/espr2002.12.142},
	doi = {10.1065/espr2002.12.142},
	abstract = {Humans now strongly influence almost every major aquatic ecosystem, and their activities have dramatically altered the fluxes of growth-limiting nutrients from the landscape to receiving waters. Unfortunately, these nutrient inputs have had profound negative effects upon the quality of surface waters worldwide. This review examines how eutrophication influences the biomass and species composition of algae in both freshwater and costal marine systems.},
	language = {en},
	number = {2},
	urldate = {2020-04-02},
	journal = {Environmental Science and Pollution Research},
	author = {Smith, Val H.},
	month = mar,
	year = {2003},
	pages = {126--139},
}

@article{chen_assessing_2020,
	title = {Assessing connectivity between the river channel and floodplains during high flows using hydrodynamic modeling and particle tracking analysis},
	volume = {583},
	issn = {0022-1694},
	url = {http://www.sciencedirect.com/science/article/pii/S002216942030069X},
	doi = {10.1016/j.jhydrol.2020.124609},
	abstract = {River-floodplain connectivity is vital to hydrological and biogeochemical processes in river corridors over multiple spatiotemporal scales. In the present study, an approach of particle tracking in conjunction with two-dimensional hydrodynamic modeling was developed to study the dynamics of river-floodplain connectivity during flood periods and applied to the study of McCarran Ranch in the lower Truckee River, Nevada, U.S. The hydrodynamic model was calibrated and validated for flood events of different magnitudes of peak flow discharge. The outputs of the hydrodynamic model were further applied to determine the lateral transboundary flux during high flows. Lagrangian particle trajectories were then performed to quantify the flow path length and residence time on floodplains. The exchange frequency between the river mainstem and the floodplain were also examined. The results show that the hydrodynamic model reproduce hydrographs well. The river-floodplain exchange is sensitive to the magnitudes of the flood events. Larger floods cause shorter residence times and flow path lengths on the floodplains but lead to larger transboundary flux within the river reaches. The particle analysis results also show that higher discharge introduces less frequent exchange between the river channel and floodplains. Furthermore, comparison of the river-floodplain exchange properties among river reaches with different levels of sinuosity show that meandering reaches can introduce considerably higher exchange flux than a straight reach, leading to complex exchange behaviors within the river-floodplain system.},
	language = {en},
	urldate = {2020-04-02},
	journal = {Journal of Hydrology},
	author = {Chen, Xiaobing and Chen, Li and Stone, Mark C. and Acharya, Kumud},
	month = apr,
	year = {2020},
	keywords = {Exchange flux, Floods, Hydrodynamic modeling, Particle tracking, River-floodplain connectivity},
	pages = {124609},
}

@article{forsmann_phosphorus_2014,
	title = {Phosphorus release from anaerobic peat soils during convective discharge — {Effect} of soil {Fe}:{P} molar ratio and preferential flow},
	volume = {223-225},
	issn = {0016-7061},
	shorttitle = {Phosphorus release from anaerobic peat soils during convective discharge — {Effect} of soil {Fe}},
	url = {http://www.sciencedirect.com/science/article/pii/S0016706114000524},
	doi = {10.1016/j.geoderma.2014.01.025},
	abstract = {Phosphorus (P) accumulation in drained agricultural lowlands causes a risk for P pollution to the aquatic environment following wetland restoration. While extensive knowledge is available on P sorption and desorption from anaerobic soils, very limited information is available on the interacting influence of soil geochemistry and local scale active flow volume. Combining batch incubation experiments and continuous column discharge experiments, we investigated iron (Fe) reduction and P release from 10 anoxic Fe-dominated (oxalate extractable Fe (Feox) from {\textasciitilde}5500 to 50,000mgkg−1) lowland peat soils (TOC from 5 to 39\%) with a gradient in Fe:P molar ratio (molar ratio between bicarbonate dithionite extractable Fe and P (FeBD:PBD) from 3 to 112) and degree of non-equilibrium (preferential) flow. Short-term batch incubation experiments (21days) indicated that concurrent Fe and P release was controlled by reductive Fe(III) dissolution, and was well predicted from the soil FeBD:PBD molar ratio. Continuous convective column discharge with oxygen-free deionised water at 1mmh−1 for 10 effluent pore volumes resulted in highly variable in situ redox potential (Eh from −200 to 300mV), effluent Fe(II) concentrations (23 to 2000μM) and effluent dissolved reactive phosphorus (DRP) concentrations ({\textless}6.5 to 316μM). Effluent P forms changed from dominantly particular P/dissolved organic P (PP/DOP) to dominantly DRP as Eh decreased in all soils. Total phosphorus (TP) release rates during convective discharge (3–66μmolkg−1day−1) were negatively non-linearly correlated with the soil FeBD:PBD molar ratio, which explained 71–73\% of the variability, and with FeBD:PBD of 10 as a critical threshold ratio. Fe and P release rates from batch experiments were poorly correlated with convective discharge Fe and P release rates, indicating the overall influence of soil structure. Diffusion was found to be the rate-limiting step for P release after prolonged leaching. Although the soil FeBD:PBD molar ratio turned out as a key explanatory parameter in predicting P release rates following rewetting of these peat soils, the results did indicate the influence of preferential flow in decreasing P release rates. Although, sufficient available P is present for leaching in the initial phase after rewetting P enriched lowland soils, we do expect that soils with pronounced preferential flow will become more rapidly exhausted in available P, and hence limit P release after prolonged discharge.},
	language = {en},
	urldate = {2020-04-01},
	journal = {Geoderma},
	author = {Forsmann, Ditte M. and Kjaergaard, Charlotte},
	month = jul,
	year = {2014},
	keywords = {Iron:phosphorus ratio, Peat, Phosphorus release, Preferential flow, Redox dynamic, Wetland restoration},
	pages = {21--32},
}

@incollection{rose_chapter_2014,
	title = {Chapter {Two} - {A} {Meta}-{Analysis} and {Review} of {Plant}-{Growth} {Response} to {Humic} {Substances}: {Practical} {Implications} for {Agriculture}},
	volume = {124},
	shorttitle = {Chapter {Two} - {A} {Meta}-{Analysis} and {Review} of {Plant}-{Growth} {Response} to {Humic} {Substances}},
	url = {http://www.sciencedirect.com/science/article/pii/B9780128001387000024},
	abstract = {The breakdown products of plant and animal remains, extracted in an alkaline solution, are commonly referred to as humic substances (HS). They can be extracted from a wide variety of sources, including subbituminous coals, lignites (brown coals), peat, soil, composts, and raw organic wastes. The application of HS to plants has the potential to improve plant growth, but the extent of plant-growth promotion is inconsistent and relatively unpredictable when compared to inorganic fertilizers. The goal of this review was to determine the magnitude and likelihood of plant-growth response to HS and to rank the factors contributing to positive growth promotion. These factors included the source of the HS, the environmental growing conditions, the type of plant being treated, and the manner of HS application. Literature reports of exogenously applied HS–plant interactions were collated and quantitatively analyzed using meta-analytic and regression tree techniques. Overall, random-effects meta-analysis estimated shoot dry weight increases of 22±4\% and root dry weight increases of 21±6\% in response to HS application. Nevertheless, actual responses varied considerably and were mainly influenced by the source of the HS applied, the rate of HS application, and to a lesser extent, plant type and growing conditions. HS from compost sources significantly outperformed lignite and peat-derived HS in terms of growth promotion, while HS application rate nonlinearly moderated the growth response under different circumstances. Our results demonstrate the difficulty in generalizing recommendations for the use of HS in agriculture; however, some specific suggestions for maximizing the efficacy of HS under certain conditions are offered. We also outline some recent developments in the use of HS as synergists for improving fertilizer use efficiency and the activity of microbial inoculants. Finally, we identify a number of research gaps, which, when addressed, should clarify how, when, and where HS can be best applied for the greatest benefit.},
	language = {en},
	urldate = {2020-04-01},
	booktitle = {Advances in {Agronomy}},
	publisher = {Academic Press},
	author = {Rose, Michael T. and Patti, Antonio F. and Little, Karen R. and Brown, Alicia L. and Jackson, W. Roy and Cavagnaro, Timothy R.},
	editor = {Sparks, Donald L.},
	month = jan,
	year = {2014},
	doi = {10.1016/B978-0-12-800138-7.00002-4},
	keywords = {Compost, Crop stimulant, Humic acid, Lignite, Organic matter, Peat, Soil amendment, Soil carbon},
	pages = {37--89},
}

@article{montalvo_natural_2015,
	title = {Natural {Colloidal} {P} and {Its} {Contribution} to {Plant} {P} {Uptake}},
	volume = {49},
	issn = {0013-936X, 1520-5851},
	url = {https://pubs.acs.org/doi/10.1021/es504643f},
	doi = {10.1021/es504643f},
	abstract = {Phosphorus (P) bioavailability depends on its concentration and speciation in solution. Andisols and Oxisols have very low soil solution concentration of free orthophosphate, as they contain high concentrations of strongly P-sorbing minerals (Al/Fe oxyhydroxides, allophanes). Free orthophosphate is the form of P taken up by plants, but it is not the only P species present in the soil solution. Natural colloidal P (P associated with Al, Fe, and organic matter of sizes ranging from 1 to 1000 nm) constitutes an important fraction of soil solution P in these soils; however, its availability has not been considered. We measured the uptake of P by wheat (Triticum aestivum) from radiolabeled nonfiltered (colloid-containing) and 3-kDa filtered (nearly colloidfree) soil-water extracts from Andisols and Oxisols. In the Andisol extracts, P uptake was up to 5-fold higher from the nonfiltered solutions than the corresponding 3-kDa filtered solutions. In the Oxisol extract, no difference in P uptake between both solutions was observed. Also the diffusional flux of P as measured with the DGT technique was larger in the nonfiltered than in the 3-kDa filtered solutions. Our results suggest that colloidal P from Andisols is not chemically inert and contributes to plant uptake of P.},
	language = {en},
	number = {6},
	urldate = {2020-04-01},
	journal = {Environmental Science \& Technology},
	author = {Montalvo, Daniela and Degryse, Fien and McLaughlin, Mike J.},
	month = mar,
	year = {2015},
	pages = {3427--3434},
}

@article{gerke_acquisition_2015,
	title = {The acquisition of phosphate by higher plants: {Effect} of carboxylate release by the roots. {A} critical review.},
	volume = {178},
	copyright = {Copyright © 2015 WILEY‐VCH Verlag GmbH \& Co. KGaA, Weinheim},
	issn = {1522-2624},
	shorttitle = {The acquisition of phosphate by higher plants},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jpln.201400590},
	doi = {10.1002/jpln.201400590},
	abstract = {Phosphorus is one of the most limiting macronutrients for plant productivity in agriculture worldwide. The main reasons are the limited rock phosphate reserves and the high affinity of phosphate (P) to the soil solid phase, restricting the P availability to the plant roots. Plants can adapt to soils low in available P by changing morphological or/and physiological root features. Morphological changes include the formation of longer root hairs and a higher root : shoot ratio both parameters increasing the root surface which provides the shoot with P. This may be successful if the P availability in soil, i.e., the P concentration of the soil solution is not extremely low ({\textgreater} 1–2 µM P). If the P concentration of the soil solution is lower, the diffusive flux to the root surface will be very low and may not satisfy the P demand of the shoots. Under these conditions plants have developed strategies to increase the rhizosphere soil solution concentration by secreting mobilizing agents. The most effective way of P mobilization is the release of di- and tricarboxylic acid anions, especially oxalate and citrate. Citrate can accumulate in the rhizosphere up to concentrations up to 80 µmol g−1 soil. Cluster root formation is an efficient way of carboxylate accumulation in the cluster root rhizosphere improving P mobilization. Cluster roots strongly improve the acquisition of the mobilized P. Considering a single root, around 80–90\% of the mobilized P diffuses away from the root. From the rhizosphere of cluster roots, most of the mobilized P is taken up by the cluster roots. Both, the strong accumulation of carboxylates in and the effective P uptake from the cluster-root rhizosphere are the basis of the unique ability of P acquisition by cluster root-forming plants. Plants that do not form cluster roots, e.g., red clover, can also accumulate carboxylates in the rhizosphere. Red clover accumulates high quantities of citrate in the rhizosphere soil. Model calculations show that the release of citrate by red clover roots and its accumulation in the rhizosphere strongly improve P acquisition by this plant species in various soils. Similar results are obtained with alfalfa. In sugar beet, oxalate release can strongly contribute to P acquisition. In summary, P acquisition can be strongly improved by the release of carboxylates and should be taken as a challenge for basic and applied research.},
	language = {en},
	number = {3},
	urldate = {2020-04-01},
	journal = {Journal of Plant Nutrition and Soil Science},
	author = {Gerke, Jörg},
	year = {2015},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/jpln.201400590},
	keywords = {humic P-complexes, organic acids, phosphate mobilization, phytate, rhizosphere},
	pages = {351--364},
}

@article{montalvo_natural_2015-1,
	title = {Natural {Colloidal} {P} and {Its} {Contribution} to {Plant} {P} {Uptake}},
	volume = {49},
	issn = {0013-936X},
	url = {10.1021/es504643f},
	doi = {10.1021/es504643f},
	abstract = {Phosphorus (P) bioavailability depends on its concentration and speciation in solution. Andisols and Oxisols have very low soil solution concentration of free orthophosphate, as they contain high concentrations of strongly P-sorbing minerals (Al/Fe oxyhydroxides, allophanes). Free orthophosphate is the form of P taken up by plants, but it is not the only P species present in the soil solution. Natural colloidal P (P associated with Al, Fe, and organic matter of sizes ranging from 1 to 1000 nm) constitutes an important fraction of soil solution P in these soils; however, its availability has not been considered. We measured the uptake of P by wheat (Triticum aestivum) from radiolabeled nonfiltered (colloid-containing) and 3-kDa filtered (nearly colloid-free) soil-water extracts from Andisols and Oxisols. In the Andisol extracts, P uptake was up to 5-fold higher from the nonfiltered solutions than the corresponding 3-kDa filtered solutions. In the Oxisol extract, no difference in P uptake between both solutions was observed. Also the diffusional flux of P as measured with the DGT technique was larger in the nonfiltered than in the 3-kDa filtered solutions. Our results suggest that colloidal P from Andisols is not chemically inert and contributes to plant uptake of P.},
	number = {6},
	urldate = {2020-04-01},
	journal = {Environmental Science \& Technology},
	author = {Montalvo, Daniela and Degryse, Fien and McLaughlin, Mike J.},
	month = mar,
	year = {2015},
	note = {Publisher: American Chemical Society},
	pages = {3427--3434},
}

@article{parsons_sediment_2017,
	title = {Sediment phosphorus speciation and mobility under dynamic redox conditions},
	volume = {14},
	issn = {1726-4189},
	url = {https://www.biogeosciences.net/14/3585/2017/},
	doi = {10.5194/bg-14-3585-2017},
	abstract = {Abstract. Anthropogenic nutrient enrichment has caused phosphorus (P) accumulation in many freshwater sediments, raising concerns that internal loading from legacy P may delay the recovery of aquatic ecosystems suffering from eutrophication. Benthic recycling of P strongly depends on the redox regime within surficial sediment. In many shallow environments, redox conditions tend to be highly dynamic as a result of, among others, bioturbation by macrofauna, root activity, sediment resuspension and seasonal variations in bottom-water oxygen (O2) concentrations. To gain insight into the mobility and biogeochemistry of P under fluctuating redox conditions, a suspension of sediment from a hypereutrophic freshwater marsh was exposed to alternating 7-day periods of purging with air and nitrogen gas (N2), for a total duration of 74 days, in a bioreactor system. We present comprehensive data time series of bulk aqueous- and solid-phase chemistry, solid-phase phosphorus speciation and hydrolytic enzyme activities demonstrating the mass balanced redistribution of P in sediment during redox cycling. Aqueous phosphate concentrations remained low ( ∼  2.5 µM) under oxic conditions due to sorption to iron(III) oxyhydroxides. During anoxic periods, once nitrate was depleted, the reductive dissolution of iron(III) oxyhydroxides released P. However, only 4.5 \% of the released P accumulated in solution while the rest was redistributed between the MgCl2 and NaHCO3 extractable fractions of the solid phase. Thus, under the short redox fluctuations imposed in the experiments, P remobilization to the aqueous phase remained relatively limited. Orthophosphate predominated at all times during the experiment in both the solid and aqueous phase. Combined P monoesters and diesters accounted for between 9 and 16 \% of sediment particulate P. Phosphatase activities up to 2.4 mmol h−1 kg−1 indicated the potential for rapid mineralization of organic P (Po), in particular during periods of aeration when the activity of phosphomonoesterases was 37 \% higher than under N2 sparging. The results emphasize that the magnitude and timing of internal P loading during periods of anoxia are dependent on both P redistribution within sediments and bottom-water nitrate concentrations.},
	language = {en},
	number = {14},
	urldate = {2020-04-01},
	journal = {Biogeosciences},
	author = {Parsons, Chris T. and Rezanezhad, Fereidoun and O\&amp;apos;Connell, David W. and Van Cappellen, Philippe},
	month = jul,
	year = {2017},
	pages = {3585--3602},
}

@article{gerke_concepts_2018,
	title = {Concepts and {Misconceptions} of {Humic} {Substances} as the {Stable} {Part} of {Soil} {Organic} {Matter}: {A} {Review}},
	volume = {8},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	shorttitle = {Concepts and {Misconceptions} of {Humic} {Substances} as the {Stable} {Part} of {Soil} {Organic} {Matter}},
	url = {https://www.mdpi.com/2073-4395/8/5/76},
	doi = {10.3390/agronomy8050076},
	abstract = {In the last three decades, the concept of soil humic substances has been questioned in two main directions. Misinterpretations of CP MAS13C NMR spectroscopy led to the conclusion that soil organic matter is mainly aliphatic, questioning the theory of polymerization of humic substances from phenolic molecules. Conversely, some critics of humic substances assume that a great proportion of aromatic soil organic carbon originates from fire-affected carbon, often termed as black carbon (BC). However, the determination of BC in soil by two widely applied methods, the benzene polycarboxylic acid marker method and the UV method, is not reliable and seems to strongly overestimate the BC content of soils. The concept of humic substances continues to be relevant today. The polymerization of phenolic molecules that originate from the degradation of lignin or synthesis by microorganisms may lead to humic substances which can incorporate a variety of organic and inorganic molecules and elements. The incorporation, e.g., of triazines or surfactants into the humic matrix, leading to bound residues, illustrates that humic substances are important to explain central reactions in soil. Humic substances are also important to understand the availability of plant nutrients in soil, including P, Fe, and Cu, and they may have a direct effect on the growth of higher plants in soil. Therefore, there are good reasons to reformulate or to further develop the concepts and models of humic substances introduced and developed by M. Schnitzer, W. Flaig, W. Ziechmann, and F.J. Stevenson.},
	language = {en},
	number = {5},
	urldate = {2020-04-01},
	journal = {Agronomy},
	author = {Gerke, Jörg},
	month = may,
	year = {2018},
	note = {Number: 5
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {aromatic humic core, black carbon overestimation, humification, misinterpretation of quantitative $^{\textrm{13}}$C NMR spectroscopy, phenolic molecules, polymerization, supramolecular structure},
	pages = {76},
}

@article{nifong_model_2020,
	title = {To model or measure: {Estimating} gas exchange to measure metabolism in shallow, low-gradient stream habitats},
	volume = {39},
	issn = {2161-9549},
	shorttitle = {To model or measure},
	url = {https://www-journals-uchicago-edu.proxy.library.nd.edu/doi/abs/10.1086/707460},
	doi = {10.1086/707460},
	abstract = {Stream metabolism is an important metric of ecosystem function. Accurate estimates of gross primary production (GPP) and respiration (ER) are based on metabolism models that require estimates of gas transfer rates at the surface–water interface. When the gas exchange rate K (d−1) is measured directly from the environment, it can be used with dissolved O2 data to estimate GPP and ER. However, inverse modeling methods can also be used to solve for GPP, ER, and K simultaneously. Estimates of K from inverse models have rarely been compared to direct estimates of K. Additionally, the effects of the method used to estimate K on estimates of ecosystem metabolism are unknown. We compared these methods in shallow, low-gradient, open-canopy experimental streams under a range of hydrologic conditions with (vegetated) and without (unvegetated) instream vegetation. The different methods gave similar results for K estimates in vegetated streams. In unvegetated streams, however, inverse modeling methods that simultaneously estimated K with GPP and ER gave higher K estimates than did our direct measurements. When K was modeled rather than measured, metabolism estimates were higher in unvegetated streams, and model fits struggled to replicate dissolved O2 data. The different methods of estimating K resulted in similar metabolism estimates within vegetated streams. However, the linear relationships between ER and GPP were not significantly different among methods of estimating K for vegetated or unvegetated streams. This study demonstrates that in shallow, low-gradient, open-canopy streams, particularly those with high GPP and low K, practitioners can use inverse modeling approaches to estimate K. Estimates in unvegetated systems, which have lower GPP, may be hindered by uncertainty in measured K in low gas transfer environments or by process errors within existing models.},
	number = {1},
	urldate = {2020-04-01},
	journal = {Freshwater Science},
	author = {Nifong, Rachel L. and Taylor, Jason M. and Yasarer, Lindsey},
	month = mar,
	year = {2020},
	note = {Publisher: The University of Chicago Press},
	pages = {70--85},
}

@article{murphy_changing_2020,
	title = {Changing suspended sediment in {United} {States} rivers and streams: linking sediment trends to changes in land use/cover, hydrology and climate},
	volume = {24},
	issn = {1027-5606},
	shorttitle = {Changing suspended sediment in {United} {States} rivers and streams},
	url = {https://www.hydrol-earth-syst-sci.net/24/991/2020/},
	doi = {10.5194/hess-24-991-2020},
	abstract = {{\textless}p{\textgreater}{\textless}strong{\textgreater}Abstract.{\textless}/strong{\textgreater} Sediment is one of the leading pollutants in rivers and streams across the United States (US) and the world. Between 1992 and 2012, concentrations of annual mean suspended sediment decreased at over half of the 137 stream sites assessed across the contiguous US. Increases occurred at less than 25\&thinsp;\% of the sites, and the direction of change was uncertain at the remaining 25\&thinsp;\%. Sediment trends were characterized using the Weighted Regressions on Time, Discharge, and Season (WRTDS) model, and decreases in sediment ranged from {\textless}span class="inline-formula"{\textgreater}−95{\textless}/span{\textgreater}\&thinsp;\% to {\textless}span class="inline-formula"{\textgreater}−8.5{\textless}/span{\textgreater}\&thinsp;\% of the 1992 concentration. To explore potential drivers of these changes, the sediment trends were (1) parsed into two broad contributors of change, changes in land management versus changes in the streamflow regime, and (2) grouped by land use of the watershed and correlated to concurrent changes in land use or land cover (land use/cover), hydrology and climate variables and static/long-term watershed characteristics. At 83\&thinsp;\% of the sites, changes in land management (captured by changes in the concentration–streamflow relationship over time; C–Q relationship) contributed more to the change in the sediment trend than changes in the streamflow regime alone (i.e., any systematic change in the magnitude, frequency or timing of flows). However, at {\textless}span class="inline-formula"{\textgreater}\&gt;50{\textless}/span{\textgreater}\&thinsp;\% of the sites, changes in the streamflow regime contributed at least a 5\&thinsp;\% change in sediment, and at 11 sites changes in the streamflow regime contributed over half the change in sediment, indicating that at many sites changes in streamflow were not the main driver of changes in sediment but were often an important supporting factor. Correlations between sediment trends and concurrent changes in land use/cover, hydrology and climate were often stronger at sites draining watersheds with more homogenous, human-related land uses (i.e., agricultural and urban lands) compared to mixed-use or undeveloped lands. At many sites, decreases in sediment occurred despite small-to-moderate increases in the amount of urban or agricultural land in the watershed, suggesting conservation efforts and best-management practices (BMPs) used to reduce sediment runoff to streams may be successful, up to a point, as lands are converted to urban and agricultural uses.{\textless}/p{\textgreater}},
	language = {English},
	number = {2},
	urldate = {2020-03-30},
	journal = {Hydrology and Earth System Sciences},
	author = {Murphy, Jennifer C.},
	month = mar,
	year = {2020},
	note = {Publisher: Copernicus GmbH},
	pages = {991--1010},
}

@article{parker_oxygen_2020,
	title = {Oxygen dynamics and evaluation of the single-station diel oxygen model across contrasting geologies},
	volume = {17},
	issn = {1726-4170},
	url = {https://www.biogeosciences.net/17/305/2020/},
	doi = {10.5194/bg-17-305-2020},
	abstract = {{\textless}p{\textgreater}{\textless}strong{\textgreater}Abstract.{\textless}/strong{\textgreater} In aquatic ecosystems, the single-station, single-stage {\textless}span class="inline-formula"{\textgreater}\textit{R}{\textless}/span{\textgreater} diel oxygen model assumes constant ecosystem respiration and aeration rate (notwithstanding temperature effects) over the course of a single night. The validity of this model was assessed for four small streams representing two geologies (Chalk and Greensand) over a 1-year period, by examining the behaviour of the nighttime dissolved oxygen (DO) saturation deficit for each night at points where change in DO is zero. The resulting value was then compared with the corresponding ratio (the regression quotient) obtained from nighttime regression analysis (Hornberger and Kelly, 1975). If model assumptions are correct, then these two values should be equal; where they diverge therefore gives a method of assessing the suitability of the model structure.{\textless}/p{\textgreater} {\textless}p{\textgreater}For two streams (one Chalk and one Greensand), the regression quotient persistently underestimated the observed DO deficit. These two streams showed similar timing patterns of oxygen dynamics with the point of minimum DO occurring relatively quickly after sunset in spring and early summer, although the two Chalk streams were more similar to one another in terms of DO magnitudes. Comparisons between different streams using the single-station model with constant {\textless}span class="inline-formula"{\textgreater}\textit{R}{\textless}/span{\textgreater} and {\textless}span class="inline-formula"{\textgreater}\textit{k}{\textless}/span{\textgreater} on the presumption that it is equally appropriate in all cases may lead to misleading conclusions.{\textless}/p{\textgreater}},
	language = {English},
	number = {2},
	urldate = {2020-03-30},
	journal = {Biogeosciences},
	author = {Parker, Simon J.},
	month = jan,
	year = {2020},
	note = {Publisher: Copernicus GmbH},
	pages = {305--315},
}

@article{cordell_story_2009,
	series = {Traditional {Peoples} and {Climate} {Change}},
	title = {The story of phosphorus: {Global} food security and food for thought},
	volume = {19},
	issn = {0959-3780},
	shorttitle = {The story of phosphorus},
	url = {http://www.sciencedirect.com/science/article/pii/S095937800800099X},
	doi = {10.1016/j.gloenvcha.2008.10.009},
	abstract = {Food production requires application of fertilizers containing phosphorus, nitrogen and potassium on agricultural fields in order to sustain crop yields. However modern agriculture is dependent on phosphorus derived from phosphate rock, which is a non-renewable resource and current global reserves may be depleted in 50–100 years. While phosphorus demand is projected to increase, the expected global peak in phosphorus production is predicted to occur around 2030. The exact timing of peak phosphorus production might be disputed, however it is widely acknowledged within the fertilizer industry that the quality of remaining phosphate rock is decreasing and production costs are increasing. Yet future access to phosphorus receives little or no international attention. This paper puts forward the case for including long-term phosphorus scarcity on the priority agenda for global food security. Opportunities for recovering phosphorus and reducing demand are also addressed together with institutional challenges.},
	language = {en},
	number = {2},
	urldate = {2020-03-18},
	journal = {Global Environmental Change},
	author = {Cordell, Dana and Drangert, Jan-Olof and White, Stuart},
	month = may,
	year = {2009},
	keywords = {Fertilizer, Global food security, Peak phosphorus, Phosphate rock, Phosphorus, Reuse, Scarcity},
	pages = {292--305},
}

@article{summers_long-term_2020,
	title = {Long-term data reveal highly-variable metabolism and transitions in trophic status in a montane stream},
	issn = {2161-9549},
	url = {http://www.journals.uchicago.edu/doi/10.1086/708659},
	doi = {10.1086/708659},
	abstract = {In streams, gross primary production (GPP) and ecosystem respiration (ER) (i.e., stream metabolism) control the transport and fate of nutrients and organic carbon and vice versa. The importance of short-term and local factors in driving these processes is well known in the literature. However, little information exists regarding the extent of temporal variability of stream metabolism and how both local physicochemical and broad-scale climatic drivers affect this variability. We used 7 years of field data from an open-canopy headwater stream ecosystem in the southwestern United States to quantify the extent of seasonal and inter-annual variability in stream metabolism (GPP, ER, and net ecosystem production [NEP]) and to assess if temporal variation in these processes was related to the magnitude of snowmelt runoff. In spring, seasonal mean ER (p = 0.025, r2 = 0.67) and NEP (p = 0.004, r2 = 0.83) were more strongly related to discharge (Q) than GPP (p = 0.19, r2 = 0.32), potentially because of an increased influx of nutrients and organic carbon during years with higher snowmelt runoff. There were no strong relationships between seasonal mean GPP and Q, light, temperature, turbidity, and specific conductance (p ≥ 0.27, r2 ≤ 0.18). Our long-term data revealed unanticipated shifts from autotrophic to heterotrophic status within and across years. However, this variability was not strongly associated with environmental factors at either local (i.e., Q or photosynthetically-active radiation) or global (i.e., El Niño-Southern Oscillation) scales. Previous paradigms hold that local attributes dictated by geographic and landscape positioning (e.g., light and temperature regimes) control the trophic status of streams, but our findings suggest that complex combinations of spatiotemporally-variable factors, such as snow accumulation and melting, and their role in connecting terrestrial and aquatic ecosystems can lead to substantial within-stream variation in autotrophic or heterotrophic status.},
	urldate = {2020-03-17},
	journal = {Freshwater Science},
	author = {Summers, Betsy M. and Horn, David J. Van and González-Pinzón, Ricardo and Bixby, Rebecca J. and Grace, Michael R. and Sherson, Lauren R. and Crossey, Laura J. and Stone, Mark C. and Parmenter, Robert R. and Compton, T. Scott and Dahm, Clifford N.},
	month = mar,
	year = {2020},
	note = {Publisher: The University of Chicago Press},
	pages = {000--000},
}

@article{norberg_effects_2019,
	title = {Effects of cover crops sown in autumn on {N} and {P} leaching},
	volume = {00},
	copyright = {© 2019 British Society of Soil Science},
	issn = {1475-2743},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/sum.12565},
	doi = {10.1111/sum.12565},
	abstract = {A field experiment with separately tile-drained plots was used to study the ability of oilseed radish (Rhaphanus sativus L.), as a cover crop sown after harvest of a main crop of cereals or peas, to reduce nitrogen (N) and phosphorus (P) leaching losses from a clay loam in southern Sweden over 6 years. In addition to oilseed radish in pure stand, two cover crop mixtures (hairy vetch (Vicia villosa) and rye (Secale cereale) for 3 years and oilseed radish in mixture with buckwheat (Fagopyrum esculentum) for 2 years) were tested. The cover crop plots (three replicates per treatment) were compared with unplanted plots as a control. Plots cropped with oilseed radish during autumn (August–November) had significantly smaller yearly mean N concentration in drainage water over 5 of 6 years compared with unplanted controls. Mineral N content in the soil profile in autumn was significantly less in oilseed radish plots than for control plots in all years. The cover crop mixtures of hairy vetch and rye or buckwheat and oilseed radish also showed the potential to reduce soil mineral N in autumn and N concentration in drainage water, compared with unplanted controls. The cover crops had no impact on P leaching. In conclusion, oilseed radish has the ability to reduce leaching losses of N, without increasing the risk of P leaching.},
	language = {en},
	urldate = {2020-02-04},
	journal = {Soil Use and Management},
	author = {Norberg, Lisbet and Aronsson, Helena},
	year = {2019},
	keywords = {N leaching, hairy vetch, oilseed radish, phosphorus, soil N},
	pages = {1--12},
}

@article{clothier_roots_1997,
	title = {{ROOTS}: {THE} {BIG} {MOVERS} {OF} {WATER} {AND} {CHEMICAL} {IN} {SOIL}},
	volume = {162},
	issn = {0038-075X},
	shorttitle = {{ROOTS}},
	url = {https://journals.lww.com/soilsci/Abstract/1997/08000/ROOTS__THE_BIG_MOVERS_OF_WATER_AND_CHEMICAL_IN.2.aspx},
	abstract = {Root water uptake and the dynamic availability of water  to plants is a phenomenon that tends to be overlooked by soil scientists, despite  the often dominant role of roots as a sink for water in the soil. Water taken up  by roots is vital for plant growth and the productive management of soils. In addition,  trapping and consuming water in the rootzone means there is less remaining to act  as a vehicle to carry chemicals beyond the grasp of roots and consign them to either  receiving groundwater bodies or surface reserves. Here we review landmark developments  in the theoretical description of the availability of water to roots. By the 1960s,  thanks to Wilford Gardner and others, we had achieved a good theoretical understanding  of the interplay between soil characteristics and water availability for a single,  isolated, semiinfinite root embedded in a cylinder of soil. We discuss the incorporation  of these simple theoretical notions into the multitude of comprehensive simulation  models of rootzone functioning that followed the democratic spread of computers throughout  the 1970s. Much still remains to be done in linking rootzone form to root functioning,  but technology is coming to the rescue. New techniques are providing improved means  by which we can better observe both the changing spatial form of roots and the temporal  pattern of their functioning. Time Domain Reflectometry for measuring soil water  content close to roots and near the soil surface, in tandem with instantaneous monitoring  of sap flow directly within roots, is providing a sharper view of root functioning.  Mean while improved rhizotrons, along with new techniques of image analysis and topological  description, are providing better descriptions of root system form. We feel that  progress in understanding the role of roots as the big movers of water and chemical  in soil will, in the near future, remain driven by improvements in our ability to  observe the link between rootzone form and function.},
	language = {en-US},
	number = {8},
	urldate = {2020-03-15},
	journal = {Soil Science},
	author = {Clothier, Brent E. and Green, Steve R.},
	month = aug,
	year = {1997},
	pages = {534--543},
}

@article{lamberti_linkages_2010,
	title = {Linkages among aquatic ecosystems},
	volume = {29},
	issn = {0887-3593},
	url = {http://www.journals.uchicago.edu/doi/abs/10.1899/08-166.1},
	doi = {10.1899/08-166.1},
	abstract = {Aquatic ecosystems are almost invariably connected to other ecosystems because the dominant force of water movement facilitates physical, chemical, and biological exchanges among ecosystems. In this sense, we define an ecosystem linkage as any persistent or recurring process or attribute that connects different ecosystems in some manner. We argue that such linkages are integral, even defining, components of aquatic ecosystem structure and function, and therefore, should be evaluated in the course of ecological studies. J-NABS has made significant contributions to our understanding of such linkages. The percentage of all publications in J-NABS addressing some ecological linkage has approached 10\% in recent years. Historically, emphasis was placed on upstream–downstream linkages in flowing waters, and theory (e.g., river continuum, nutrient spiraling) has evolved largely around this phenomenon. However, other linkages among ecosystems have received increased attention in the past 20 y. These linkages include surface–subsurface, lake–stream, river–floodplain, and, more recently, marine–freshwater. We contend that many ecological processes, including primary production, nutrient cycling, organic matter processing, and secondary production, are driven by such exchanges because of the donor-controlled nature of many aquatic ecosystems. Exchanges of materials from aquatic ecosystems to terrestrial systems, caused by flooding, nutrient translocation, or insect emergence, can be substantial. Movement of energy and nutrients from the ocean to freshwaters, such as in the migrations of anadromous fishes, also can be dramatic. Despite increasing evidence of the importance of such linkages, considerable impediments to research, such as journal specialization, lack of interdisciplinary study teams, and limited funding of sufficient duration for such research, exist. Such obstacles are surmountable if investigators continue to emphasize that aquatic ecology will be advanced by the study of such linkages, and that environmental problems are better understood and solved in the context of that knowledge.},
	number = {1},
	urldate = {2020-03-14},
	journal = {Journal of the North American Benthological Society},
	author = {Lamberti, Gary A. and Chaloner, Dominic T. and Hershey, Anne E.},
	month = mar,
	year = {2010},
	note = {Publisher: The University of Chicago Press},
	pages = {245--263},
}

@article{likens_linkages_1974,
	title = {Linkages between {Terrestrial} and {Aquatic} {Ecosystems}},
	volume = {24},
	issn = {0006-3568},
	url = {https://www.jstor.org/stable/1296852},
	doi = {10.2307/1296852},
	abstract = {The gravitational movement of materials in drainage waters from terrestrial ecosystems to aquatic ecosystems is the major land-water linkage in the biosphere. Undisturbed humid terrestrial ecosystems develop tight cycles and tend not to be leaky, but with disturbance losses of water, nutrients, and particulate matter are increased. Eutrophication in downstream aquatic ecosystems may be accelerated by these inputs in addition to the well-known eutrophication effects of urban-industrial wastes. Movement of some air-borne pollutants from terrestrial to aquatic ecosystems is increasing and must be considered as a factor influencing aquatic ecosystems. A holistic view of these land-air-water interactions is required for intelligent management of landscapes.},
	number = {8},
	urldate = {2020-03-14},
	journal = {BioScience},
	author = {Likens, Gene E. and Bormann, F. Herbert},
	year = {1974},
	note = {Publisher: [American Institute of Biological Sciences, Oxford University Press]},
	pages = {447--456},
}

@article{neset_global_2012,
	title = {Global phosphorus scarcity: identifying synergies for a sustainable future},
	volume = {92},
	copyright = {Copyright © 2011 Society of Chemical Industry},
	issn = {1097-0010},
	shorttitle = {Global phosphorus scarcity},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jsfa.4650},
	doi = {10.1002/jsfa.4650},
	abstract = {Global food production is dependent on constant inputs of phosphorus. In the current system this phosphorus is not predominantly derived from organic recycled waste, but to a large degree from phosphate-rock based mineral fertilisers. However, phosphate rock is a finite resource that cannot be manufactured. Our dependency therefore needs to be addressed from a sustainability perspective in order to ensure global food supplies for a growing global population. The situation is made more urgent by predictions that, for example, the consumption of resource intensive foods and the demand for biomass energy will increase. The scientific and societal debate has so far been focussed on the exact timing of peak phosphorus and on when the total depletion of the global reserves will occur. Even though the timing of these events is important, all dimensions of phosphorus scarcity need to be addressed in a manner which acknowledges linkages to other sustainable development challenges and which takes into consideration the synergies between different sustainability measures. Many sustainable phosphorus measures have positive impacts on other challenges; for example, shifting global diets to more plant-based foods would not only reduce global phosphorus consumption, but also reduce greenhouse gas emissions, reduce nitrogen fertiliser demand and reduce water consumption. Copyright © 2011 Society of Chemical Industry},
	language = {en},
	number = {1},
	urldate = {2020-03-13},
	journal = {Journal of the Science of Food and Agriculture},
	author = {Neset, Tina-Simone S. and Cordell, Dana},
	year = {2012},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/jsfa.4650},
	keywords = {food security, peak phosphorus, phosphorus scarcity, sustainable development challenges, synergies},
	pages = {2--6},
}

@article{jarvie_water_2013,
	title = {Water {Quality} {Remediation} {Faces} {Unprecedented} {Challenges} from “{Legacy} {Phosphorus}”},
	volume = {47},
	issn = {0013-936X},
	url = {10.1021/es403160a},
	doi = {10.1021/es403160a},
	number = {16},
	urldate = {2020-03-13},
	journal = {Environmental Science \& Technology},
	author = {Jarvie, Helen P. and Sharpley, Andrew N. and Spears, Bryan and Buda, Anthony R. and May, Linda and Kleinman, Peter J. A.},
	month = aug,
	year = {2013},
	note = {Publisher: American Chemical Society},
	pages = {8997--8998},
}

@article{sharpley_phosphorus_2013,
	title = {Phosphorus {Legacy}: {Overcoming} the {Effects} of {Past} {Management} {Practices} to {Mitigate} {Future} {Water} {Quality} {Impairment}},
	volume = {42},
	issn = {0047-2425},
	shorttitle = {Phosphorus {Legacy}},
	url = {https://dl.sciencesocieties.org/publications/jeq/abstracts/42/5/1308},
	doi = {10.2134/jeq2013.03.0098},
	language = {en},
	number = {5},
	urldate = {2020-03-13},
	journal = {Journal of Environmental Quality},
	author = {Sharpley, Andrew and Jarvie, Helen P. and Buda, Anthony and May, Linda and Spears, Bryan and Kleinman, Peter},
	year = {2013},
	note = {Publisher: The American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.},
	pages = {1308--1326},
}

@article{scholz_approaching_2013,
	title = {Approaching a dynamic view on the availability of mineral resources: {What} we may learn from the case of phosphorus?},
	volume = {23},
	issn = {0959-3780},
	shorttitle = {Approaching a dynamic view on the availability of mineral resources},
	url = {http://www.sciencedirect.com/science/article/pii/S0959378012001264},
	doi = {10.1016/j.gloenvcha.2012.10.013},
	abstract = {This paper elaborates in what way a dynamic perspective on reserves, resources and geopotential is necessary to provide robust estimates on resource availability. We introduce concepts of essentiality, criticality and economic scarcity and discuss for the case of phosphorus (P) how they are defined and may be measured. The case of P is considered in detail as P an essential element for global food security with a highly dissipative use and is geographically unevenly distributed across the globe. We distinguish and relate the complementarity between physical and economic scarcity and discuss limits and potential of static indicators such as static lifetime, Hubbert curve applications, and the Herfindahl–Hirschman-Index of P for predicting future availability of these resources. We reveal that these static indicators are – in general – not valid approaches to predict physical scarcity of resources. Geological data show that though the P reserves have not been systematically and completely assessed on a global scale, the static lifetime of P is high. When acknowledging socio-economic and technological dynamics, and available geological facts, statements predicting physical scarcity or a peak in P production within a few decades are unlikely to be accurate or valid. We elaborate that some simplified indicators such as static lifetime or the Hubbert curve based prediction of peaks may serve as screening indicators preceding early warning research, which may induce increased mining activities, technology innovation or other actions. However, in general, these simplified indicators are not valid approaches to predict physical scarcity of resources. Although one day there may be a supply-driven P production peak, demand-driven production plateaus and multiple peaks are probable in the near future. Given its geopotential, essentiality, and the learning curve of efficient fertilizer use, P is subject to demand-driven market dynamics. Thus, a symmetric decline and unavoidable shortage of P in the next decades are unlikely. This insight does not refute the need to close the anthropogenic P loop. Activities associated with P production and consumption use has a significant pollution potential in part because of the dissipative nature. The paper reveals the necessity to mitigate risks (such as economic scarcity, especially for poor farmers) of both short-term price peaks and longer lasting step-changes in price, e.g. due to knowledge gaps of technological adaptation in energy and water management or other reasons of insufficient supply-demand dynamics management. The complexity of this task necessitates a transdisciplinary approach.},
	language = {en},
	number = {1},
	urldate = {2020-03-13},
	journal = {Global Environmental Change},
	author = {Scholz, Roland W. and Wellmer, Friedrich-Wilhelm},
	month = feb,
	year = {2013},
	keywords = {Criticality, Demand-driven production curve, Herfindahl–Hirschman Index, Peak phosphorus, Phosphorus, Scarcity},
	pages = {11--27},
}

@article{childers_sustainability_2011,
	title = {Sustainability {Challenges} of {Phosphorus} and {Food}: {Solutions} from {Closing} the {Human} {Phosphorus} {Cycle}},
	volume = {61},
	issn = {0006-3568},
	shorttitle = {Sustainability {Challenges} of {Phosphorus} and {Food}},
	url = {https://academic.oup.com/bioscience/article/61/2/117/242667},
	doi = {10.1525/bio.2011.61.2.6},
	abstract = {Abstract.  The Green Revolution has led to a threefold growth in food production in the last 50 to 75 years, but increases in crop production have required a co},
	language = {en},
	number = {2},
	urldate = {2020-03-13},
	journal = {BioScience},
	author = {Childers, Daniel L. and Corman, Jessica and Edwards, Mark and Elser, James J.},
	month = feb,
	year = {2011},
	note = {Publisher: Oxford Academic},
	pages = {117--124},
}

@article{sharpley_modeling_2002,
	title = {Modeling phosphorus transport in agricultural watersheds: {Processes} and possibilities},
	volume = {57},
	copyright = {Copyright 2002 by the Soil and Water Conservation Society},
	issn = {0022-4561, 1941-3300},
	shorttitle = {Modeling phosphorus transport in agricultural watersheds},
	url = {https://www.jswconline.org/content/57/6/425},
	abstract = {ABSTRACT:
Modeling phosphorus (P) loss from agricultural watersheds is key to quantifying the long term water quality benefits of alternative best management practices. Scientists engaged in this endeavor struggle to represent processes controlling P transport at scales and time frames that are meaningful to farmers, resource managers, and policy makers. To help overcome these challenges, we reviewed salient issues facing scientists that model P transport, providing a conceptual framework from which process-based P transport models might be evaluated. Recent advances in quantifying the release of soil P to overland and subsurface flow show that extraction coefficients relating soil and flow P are variable but can be represented as a function of land cover or erosion. Existing information on best management effects on P export should be linked to watershed models to better represent changes in P transport. The main needs of P transport models are inclusion of flexible coefficients relating soil and overland flow P, fertilizer and manure management and P loss, stream channel effects on edge-of-field P losses prior to water body input, and linkage of watershed and water-body response models. However, it is essential that the most appropriate model be carefully selected, according to a user's needs in terms of available input data, level of predictive accuracy, and scale of simulation being considered.},
	language = {en},
	number = {6},
	urldate = {2020-03-13},
	journal = {Journal of Soil and Water Conservation},
	author = {Sharpley, A. N. and Kleinman, P. J. A. and McDowell, R. W. and Gitau, M. and Bryant, R. B.},
	month = nov,
	year = {2002},
	note = {Publisher: Soil and Water Conservation Society
Section: Special Section},
	pages = {425--439},
}

@article{bennett_human_2001,
	title = {Human {Impact} on {Erodable} {Phosphorus} and {Eutrophication}: {A} {Global} {PerspectiveIncreasing} accumulation of phosphorus in soil threatens rivers, lakes, and coastal oceans with eutrophication},
	volume = {51},
	issn = {0006-3568},
	shorttitle = {Human {Impact} on {Erodable} {Phosphorus} and {Eutrophication}},
	url = {https://academic.oup.com/bioscience/article/51/3/227/256199},
	doi = {10.1641/0006-3568(2001)051[0227:HIOEPA]2.0.CO;2},
	abstract = {Human actions—mining phosphorus (P) and transporting it in fertilizers, animal feeds, agricultural crops, and other products—are altering the global P cycle, ca},
	language = {en},
	number = {3},
	urldate = {2020-03-13},
	journal = {BioScience},
	author = {Bennett, Elena M. and Carpenter, Stephen R. and Caraco, Nina F.},
	month = mar,
	year = {2001},
	note = {Publisher: Oxford Academic},
	pages = {227--234},
}

@inproceedings{cooper_future_2011,
	title = {The future distribution and production of global phosphate rock reserves},
	doi = {10.1016/j.resconrec.2011.09.009},
	abstract = {Abstract Phosphorus (P) is essential for crop growth and food production, and most of the phosphorus applied to agricultural land comes from phosphate rock (PR), a non-renewable resource. The distribution of PR reserves and the share of current production are both concentrated in a handful of countries, notably Morocco and China. Individual countries operate their phosphate mining industries at different reserve-to-production (R/P) ratios, which determines the lifetime of PR reserves in that country and, in turn, the global distribution of both reserves and production in the future. This research uses U.S. Geological Survey data (released in January 2011) to derive R/P ratios for individual countries and combines this with a scenario for increasing global demand to investigate how the global distribution of PR reserves and production will change between now and the year 2100. The results show that 70\% of global production is currently produced from reserves which will be depleted within 100 years and combining this with increasing demand will result in a significant global production deficit, which by 2070 will be larger than current production. Morocco, with nearly 77\% of global reserves, will need to increase production by around 700\% by 2075 in order to meet most of this deficit. If this is possible, Morocco will obtain a much greater share of worldwide production, from around 15\% in 2010 to around 80\% by 2100, which implies more control over market prices. Also, since Morocco operates the highest R/P ratio throughout the analysis period, its share of the global reserves continues to increase, from 77\% in 2011 to 89\% by 2100. Overall, the research concludes that, unless additional sources of phosphorus can be accessed or society can significantly increase phosphorus recycling, future global phosphorus security will be increasingly reliant on a single country.},
	author = {Cooper, James Edward and Lombardi, Rachel and Boardman, D. I. and Carliell-Marquet, Cynthia M.},
	year = {2011},
}

@article{simon_disturbance_2006,
	title = {Disturbance, stream incision, and channel evolution: {The} roles of excess transport capacity and boundary materials in controlling channel response},
	volume = {79},
	issn = {0169555X},
	shorttitle = {Disturbance, stream incision, and channel evolution},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0169555X06002583},
	doi = {10.1016/j.geomorph.2006.06.037},
	abstract = {Channel incision is part of denudation, drainage-network development, and landscape evolution. Rejuvenation of fluvial networks by channel incision often leads to further network development and an increase in drainage density as gullies migrate into previously non-incised surfaces. Large, anthropogenic disturbances, similar to large or catastrophic “natural” events, greatly compress time scales for incision and related processes by creating enormous imbalances between upstream sediment delivery and available transporting power. Field examples of channel responses to antrhopogenic and “natural” disturbances are presented for fluvial systems in the mid continent and Pacific Northwest, USA, and central Italy. Responses to different types of disturbances are shown to result in similar spatial and temporal trends of incision for vastly different fluvial systems. Similar disturbances are shown to result in varying relative magnitudes of vertical and lateral (widening) processes, and different channel morphologies as a function of the type of boundary sediments comprising the bed and banks. This apparent contradiction is explained through an analysis of temporal adjustments to flow energy, shear stress, and stream power with time. Numerical simulations of sand-bed channels of varying bank resistance and disturbed by reducing the upstream sediment supply by half, show identical adjustments in flow energy and the rate of energy dissipation. The processes that dominate adjustment and the ultimate stable geometries, however, are vastly different, depending on the cohesion of the channel banks and the supply of hydraulically-controlled sediment (sand) provided by bank erosion.},
	language = {en},
	number = {3-4},
	urldate = {2020-03-13},
	journal = {Geomorphology},
	author = {Simon, Andrew and Rinaldi, Massimo},
	month = sep,
	year = {2006},
	pages = {361--383},
}

@article{carpenter_phosphorus_2008,
	title = {Phosphorus control is critical to mitigating eutrophication},
	volume = {105},
	issn = {0027-8424},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2516213/},
	doi = {10.1073/pnas.0806112105},
	number = {32},
	urldate = {2020-03-13},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Carpenter, Stephen R.},
	month = aug,
	year = {2008},
	pmid = {18685114},
	pmcid = {PMC2516213},
	pages = {11039--11040},
}

@article{rabalais_gulf_2002,
	title = {Gulf of {Mexico} {Hypoxia}, {A}.{K}.{A}. “{The} {Dead} {Zone}”},
	volume = {33},
	url = {10.1146/annurev.ecolsys.33.010802.150513},
	doi = {10.1146/annurev.ecolsys.33.010802.150513},
	abstract = {Abstract The second largest zone of coastal hypoxia (oxygen-depleted waters) in the world is found on the northern Gulf of Mexico continental shelf adjacent to the outflows of the Mississippi and Atchafalaya Rivers. The combination of high freshwater discharge, wind mixing, regional circulation, and summer warming controls the strength of stratification that goes through a well-defined seasonal cycle. The physical structure of the water column and high nutrient loads that enhance primary production lead to an annual formation of the hypoxic water mass that is dominant from spring through late summer. Paleoindicators in dated sediment cores indicate that hypoxic conditions likely began to appear around the turn of the last century and became more severe since the 1950s as the nitrate flux from the Mississippi River to the Gulf of Mexico tripled. Whereas increased nutrients enhance the production of some organisms, others are eliminated from water masses (they either emigrate from the area or die) where the oxygen level falls below 2 mg l−1 or lower for a prolonged period. A hypoxia-stressed benthos is typified by short-lived, smaller surface deposit-feeding polychaetes and the absence of marine invertebrates such as pericaridean crustaceans, bivalves, gastropods, and ophiuroids. The changes in benthic communities, along with the low dissolved oxygen, result in altered sediment structure and sediment biogeochemical cycles. Important fisheries are variably affected by increased or decreased food supplies, mortality, forced migration, reduction in suitable habitat, increased susceptibility to predation, and disruption of life cycles.},
	number = {1},
	urldate = {2020-03-13},
	journal = {Annual Review of Ecology and Systematics},
	author = {Rabalais, Nancy N. and Turner, R. Eugene and Wiseman, William J.},
	year = {2002},
	note = {\_eprint: 10.1146/annurev.ecolsys.33.010802.150513},
	pages = {235--263},
}

@article{nebgen_effects_2019,
	title = {Effects of shading on stream ecosystem metabolism and water temperature in an agriculturally influenced stream in central {Wisconsin}, {USA}},
	volume = {126},
	issn = {0925-8574},
	url = {http://www.sciencedirect.com/science/article/pii/S0925857418304002},
	doi = {10.1016/j.ecoleng.2018.10.023},
	abstract = {Headwater streams with a forested riparian zone and canopy cover have regulated stream temperatures and stream ecosystem metabolism because of shading. Agricultural practices have dramatically altered riparian corridors with the removal of mature vegetation, which consequently alters natural stream processes. The objective of this study was to investigate the effects of shading on stream temperature and ecosystem metabolism in an agriculturally influenced, low order stream. We examined three stream reaches; two in a recently restored stream (Lost Creek) and one in a nearby-unimpacted reference stream (Little Plover River). The two reaches in Lost Creek included a 100-m artificially-shaded stream reach and a control reach immediately upstream of the shaded reach. The Little Plover River included one reference reach with a fully forested canopy. Both streams are located in agricultural watersheds and based on phosphorus levels would be classified as meso-eutrophic. Each stream reach was assessed during stable flow conditions once each month between June and October of 2016. Rates of gross primary production (GPP), ecosystem respiration (ER), and net ecosystem production (NEP) were determined using the open system, two-station diel dissolved oxygen change method, and reaeration (k) was calculated using the nighttime regression method. Based on stream discharge data, we corrected metabolism values for groundwater when inputs exceeded 7\% (Hall and Tank 2005). We also measured water temperature, PAR (photosynthetically active radiation), soluble reactive phosphorus (SRP), periphytic chlorophyll a content, and organic matter content at each site as potential controlling variables. Surprisingly, no significant differences were observed in daily maximum water temperatures among the three sites; however, GPP levels were significantly lower (ANOVA F2,14 = 45.45; p {\textless} 0.001) in the artificially shaded reach and the reference site compared to the control indicating that shading reduced GPP. ER was not significantly different among the reaches and remained relatively low, which resulted in the control reach having a highly positive and significantly higher NEP (ANOVA F2,14 = 17.656 p {\textless} 0.001) compared to the shaded and reference reaches. Redundancy analysis revealed that GPP and NEP were strongly correlated with PAR. Our findings suggest that shading can improve dissolved oxygen dynamics in an agriculturally-influenced stream by lowering GPP.},
	language = {en},
	urldate = {2020-03-13},
	journal = {Ecological Engineering},
	author = {Nebgen, Elizabeth L. and Herrman, Kyle S.},
	month = jan,
	year = {2019},
	keywords = {ER, Eutrophic, GPP, NEP, Organic matter, PAR, Periphyton, SRP, Stream shading, Stream temperature},
	pages = {16--24},
}

@article{karr_water_1978,
	title = {Water {Resources} and the {Land}-{Water} {Interface}},
	volume = {201},
	copyright = {1978 by the American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	url = {https://science.sciencemag.org/content/201/4352/229},
	doi = {10.1126/science.201.4352.229},
	abstract = {Development and implementation of local and regional plans to control nonpoint sources of pollution from agricultural land are major mandates of section 208 of Public Law 92-500. Many planners tend to equate erosion control as measured by the universal soil loss equation with improvements in water quality. Others implement channel management practices which degrade rather than improve water quality and thereby decrease the effectiveness of other efforts to control nonpoint sources. Planners rarely recognize the importance of the land-water interface in regulating water quality in agricultural watersheds. More effective planning can result from the development of "best management systems" which incorporate theory from all relevant disciplines.},
	language = {en},
	number = {4352},
	urldate = {2020-03-12},
	journal = {Science},
	author = {Karr, James R. and Schlosser, Isaac J.},
	month = jul,
	year = {1978},
	pmid = {17778646},
	note = {Publisher: American Association for the Advancement of Science
Section: Articles},
	pages = {229--234},
}

@article{grimm_merging_2003,
	title = {Merging aquatic and terrestrial perspectives of nutrient biogeochemistry},
	volume = {137},
	issn = {1432-1939},
	url = {10.1007/s00442-003-1382-5},
	doi = {10.1007/s00442-003-1382-5},
	abstract = {Although biogeochemistry is an integrative discipline, terrestrial and aquatic subdisciplines have developed somewhat independently of each other. Physical and biological differences between aquatic and terrestrial ecosystems explain this history. In both aquatic and terrestrial biogeochemistry, key questions and concepts arise from a focus on nutrient limitation, ecosystem nutrient retention, and controls of nutrient transformations. Current understanding is captured in conceptual models for different ecosystem types, which share some features and diverge in other ways. Distinctiveness of subdisciplines has been appropriate in some respects and has fostered important advances in theory. On the other hand, lack of integration between aquatic and terrestrial biogeochemistry limits our ability to deal with biogeochemical phenomena across large landscapes in which connections between terrestrial and aquatic elements are important. Separation of the two approaches also has not served attempts to scale up or to estimate fluxes from large areas based on plot measurements. Understanding connectivity between the two system types and scaling up biogeochemical information will rely on coupled hydrologic and ecological models, and may be critical for addressing environmental problems associated with locally, regionally, and globally altered biogeochemical cycles.},
	language = {en},
	number = {4},
	urldate = {2020-03-12},
	journal = {Oecologia},
	author = {Grimm, Nancy B. and Gergel, Sarah E. and McDowell, William H. and Boyer, Elizabeth W. and Dent, C. Lisa and Groffman, Peter and Hart, Stephen C. and Harvey, Judson and Johnston, Carol and Mayorga, Emilio and McClain, Michael E. and Pinay, Gilles},
	month = dec,
	year = {2003},
	pages = {485--501},
}

@article{likens_linkages_1974-1,
	title = {Linkages between {Terrestrial} and {Aquatic} {Ecosystems}},
	volume = {24},
	issn = {0006-3568},
	url = {https://www.jstor.org/stable/1296852},
	doi = {10.2307/1296852},
	abstract = {The gravitational movement of materials in drainage waters from terrestrial ecosystems to aquatic ecosystems is the major land-water linkage in the biosphere. Undisturbed humid terrestrial ecosystems develop tight cycles and tend not to be leaky, but with disturbance losses of water, nutrients, and particulate matter are increased. Eutrophication in downstream aquatic ecosystems may be accelerated by these inputs in addition to the well-known eutrophication effects of urban-industrial wastes. Movement of some air-borne pollutants from terrestrial to aquatic ecosystems is increasing and must be considered as a factor influencing aquatic ecosystems. A holistic view of these land-air-water interactions is required for intelligent management of landscapes.},
	number = {8},
	urldate = {2020-03-12},
	journal = {BioScience},
	author = {Likens, Gene E. and Bormann, F. Herbert},
	year = {1974},
	note = {Publisher: [American Institute of Biological Sciences, Oxford University Press]},
	pages = {447--456},
}

@article{rossini_saccharomyces_1993,
	title = {In {Saccharomyces} cerevisiae, protein secretion into the growth medium depends on environmental factors},
	volume = {9},
	issn = {1097-0061},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/yea.320090110},
	doi = {10.1002/yea.320090110},
	abstract = {In the budding yeast Saccharomyces cerevisiae the cell wall, mainly composed of mannoproteins and glucans, constitutes a barrier to protein excretion in the growth medium. In this paper we have studied the effects of different environmental parameters on excretion of Escherichia coli β-galactosidase obtained by exploiting the glucoamylase II signal sequence. Excretion of the unglycosylated β-galactosidase was detectable only in cells grown in rich medium, was affected by temperature (36°C {\textgreater} 30°C {\textgreater}{\textgreater} 24°C) and slightly stimulated by reducing agents. On the contrary, glycosylated proteins, such as α-galactosidase and glucoamylase II, were excreted to a good extent under all tested conditions of medium composition, growth temperature and pH. These data indicate that optimization of environmental parameters may help the excretion of heterologous proteins, offering advantages for protein purification.},
	language = {en},
	number = {1},
	urldate = {2020-03-12},
	journal = {Yeast},
	author = {Rossini, Dominique and Porro, Danilo and Brambilla, Luca and Venturini, Marina and Ranzi, Bianca Maria and Vanoni, Marco and Alberghina, Lilia},
	year = {1993},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/yea.320090110},
	keywords = {Yeast, physiological modulation, protein excretion},
	pages = {77--84},
}

@article{scavia_assessing_2014,
	title = {Assessing and addressing the re-eutrophication of {Lake} {Erie}: {Central} basin hypoxia},
	volume = {40},
	issn = {0380-1330},
	shorttitle = {Assessing and addressing the re-eutrophication of {Lake} {Erie}},
	url = {http://www.sciencedirect.com/science/article/pii/S0380133014000252},
	doi = {10.1016/j.jglr.2014.02.004},
	abstract = {Relieving phosphorus loading is a key management tool for controlling Lake Erie eutrophication. During the 1960s and 1970s, increased phosphorus inputs degraded water quality and reduced central basin hypolimnetic oxygen levels which, in turn, eliminated thermal habitat vital to cold-water organisms and contributed to the extirpation of important benthic macroinvertebrate prey species for fishes. In response to load reductions initiated in 1972, Lake Erie responded quickly with reduced water-column phosphorus concentrations, phytoplankton biomass, and bottom-water hypoxia (dissolved oxygen {\textless}2mg/l). Since the mid-1990s, cyanobacteria blooms increased and extensive hypoxia and benthic algae returned. We synthesize recent research leading to guidance for addressing this re-eutrophication, with particular emphasis on central basin hypoxia. We document recent trends in key eutrophication-related properties, assess their likely ecological impacts, and develop load response curves to guide revised hypoxia-based loading targets called for in the 2012 Great Lakes Water Quality Agreement. Reducing central basin hypoxic area to levels observed in the early 1990s (ca. 2000km2) requires cutting total phosphorus loads by 46\% from the 2003–2011 average or reducing dissolved reactive phosphorus loads by 78\% from the 2005–2011 average. Reductions to these levels are also protective of fish habitat. We provide potential approaches for achieving those new loading targets, and suggest that recent load reduction recommendations focused on western basin cyanobacteria blooms may not be sufficient to reduce central basin hypoxia to 2000km2.},
	language = {en},
	number = {2},
	urldate = {2020-03-12},
	journal = {Journal of Great Lakes Research},
	author = {Scavia, Donald and David Allan, J. and Arend, Kristin K. and Bartell, Steven and Beletsky, Dmitry and Bosch, Nate S. and Brandt, Stephen B. and Briland, Ruth D. and Daloğlu, Irem and DePinto, Joseph V. and Dolan, David M. and Evans, Mary Anne and Farmer, Troy M. and Goto, Daisuke and Han, Haejin and Höök, Tomas O. and Knight, Roger and Ludsin, Stuart A. and Mason, Doran and Michalak, Anna M. and Peter Richards, R. and Roberts, James J. and Rucinski, Daniel K. and Rutherford, Edward and Schwab, David J. and Sesterhenn, Timothy M. and Zhang, Hongyan and Zhou, Yuntao},
	month = jun,
	year = {2014},
	keywords = {Best management practices, Hypoxia, Lake Erie, Phosphorus load targets},
	pages = {226--246},
}

@article{shinohara_biogenic_2012,
	title = {Biogenic {Phosphorus} {Compounds} in {Sediment} and {Suspended} {Particles} in a {Shallow} {Eutrophic} {Lake}: {A} {31P}-{Nuclear} {Magnetic} {Resonance} ({31P} {NMR}) {Study}},
	volume = {46},
	issn = {0013-936X},
	shorttitle = {Biogenic {Phosphorus} {Compounds} in {Sediment} and {Suspended} {Particles} in a {Shallow} {Eutrophic} {Lake}},
	url = {10.1021/es301887z},
	doi = {10.1021/es301887z},
	abstract = {Differences in biogenic phosphorus (P) compounds between sediment and suspended particles in aquatic environments are important for understanding the mechanisms of internal P loading, but these differences are still unknown. We used solution-state 31P-nuclear magnetic resonance spectroscopy (31P NMR) with NaOH-ethylenediaminetetraacetic extraction to detect the multiple P compounds in suspended particles and sediment in the eutrophic Lake Kasumigaura, including orthophosphate monoesters, orthophosphate diesters, pyrophosphate, and polyphosphate. We tested the hypothesis that there is a significant difference between these groups in suspended particles and sediment. Biogenic P other than orthophosphate was found in significantly higher proportions in suspended particles (74.3\% of total P) than in sediment (25.6\%). Orthophosphate monoesters were comparatively more abundant in suspended particles, as indicated by the ratio of orthophosphate diesters to monoesters (average, 0.31 for suspended particles; 1.05 for sediment). The compounds identified as orthophosphate monoesters by 31P NMR spectroscopy originated mainly from phospholipids (α-glycerophosphate and β-glycerophosphate) and ribonucleic acid (RNA-P), whereas the orthophosphate diesters included mostly DNA (DNA-P). These results suggest that the dynamics of orthophosphate diesters, the production of DNA-P, or the degradation of phospholipids, play an important role in P cycling in Lake Kasumigaura.},
	number = {19},
	urldate = {2020-03-12},
	journal = {Environmental Science \& Technology},
	author = {Shinohara, Ryuichiro and Imai, Akio and Kawasaki, Nobuyuki and Komatsu, Kazuhiro and Kohzu, Ayato and Miura, Shingo and Sano, Tomoharu and Satou, Takayuki and Tomioka, Noriko},
	month = oct,
	year = {2012},
	note = {Publisher: American Chemical Society},
	pages = {10572--10578},
}

@incollection{hladyz_chapter_2011,
	title = {Chapter 4 - {Stream} {Ecosystem} {Functioning} in an {Agricultural} {Landscape}: {The} {Importance} of {Terrestrial}–{Aquatic} {Linkages}},
	volume = {44},
	shorttitle = {Chapter 4 - {Stream} {Ecosystem} {Functioning} in an {Agricultural} {Landscape}},
	url = {http://www.sciencedirect.com/science/article/pii/B9780123747945000043},
	abstract = {The loss of native riparian vegetation and its replacement with non-native species or grazing land for agriculture is a worldwide phenomenon, but one that is prevalent in Europe, reflecting the heavily-modified nature of the continent's landscape. The consequences of these riparian alterations for freshwater ecosystems remain largely unknown, largely because bioassessment has traditionally focused on the impacts of organic pollution on community structure. We addressed the need for a broader perspective, which encompasses changes at the catchment scale, by comparing ecosystem processes in woodland reference sites with those with altered riparian zones. We assessed a range of riparian modifications, including clearance for pasture and replacement of woodland with a range of low diversity plantations, in 100 streams to obtain a continental-scale perspective of the major types of alterations across Europe. Subsequently, we focused on pasture streams, as an especially prevalent widespread riparian alteration, by characterising their structural (e.g. invertebrate and fish communities) and functional (e.g. litter decomposition, algal production, herbivory) attributes in a country (Ireland) dominated by this type of landscape modification, via field and laboratory experiments. We found that microbes became increasingly important as agents of decomposition relative to macrofauna (invertebrates) in impacted sites in general and in pasture streams in particular. Resource quality of grass litter (e.g., carbon : nutrient ratios, lignin and cellulose content) was a key driver of decomposition rates in pasture streams. These systems also relied more heavily on autochthonous algal production than was the case in woodland streams, which were more detrital based. These findings suggest that these pasture streams might be fundamentally different from their native, ancestral woodland state, with a shift towards greater reliance on autochthonous-based processes. This could have a destabilizing effect on the dynamics of the food web relative to the slower, detrital-based pathways that dominate in woodland streams.},
	language = {en},
	urldate = {2020-03-12},
	booktitle = {Advances in {Ecological} {Research}},
	publisher = {Academic Press},
	author = {Hladyz, Sally and Åbjörnsson, Kajsa and Chauvet, Eric and Dobson, Michael and Elosegi, Arturo and Ferreira, Verónica and Fleituch, Tadeusz and Gessner, Mark O. and Giller, Paul S. and Gulis, Vladislav and Hutton, Stephen A. and Lacoursière, Jean O. and Lamothe, Sylvain and Lecerf, Antoine and Malmqvist, Björn and McKie, Brendan G. and Nistorescu, Marius and Preda, Elena and Riipinen, Miira P. and Rîşnoveanu, Geta and Schindler, Markus and Tiegs, Scott D. and Vought, Lena B. -M. and Woodward, Guy},
	editor = {Woodward, Guy},
	month = jan,
	year = {2011},
	doi = {10.1016/B978-0-12-374794-5.00004-3},
	keywords = {Allochthonous subsidies, Aquatic ecosystems, Autochthonous production, EU Water Framework Directive, Food webs, Grass litter, Land-use change, Open-canopy streams, Riparian alteration, Riparian zone},
	pages = {211--276},
}

@article{schroder_improved_2011,
	series = {The {Phosphorus} {Cycle}},
	title = {Improved phosphorus use efficiency in agriculture: {A} key requirement for its sustainable use},
	volume = {84},
	issn = {0045-6535},
	shorttitle = {Improved phosphorus use efficiency in agriculture},
	url = {http://www.sciencedirect.com/science/article/pii/S0045653511001056},
	doi = {10.1016/j.chemosphere.2011.01.065},
	abstract = {Mineral phosphorus (P) fertilizers processed from fossil reserves have enhanced food production over the past 50years and, hence, the welfare of billions of people. Fertilizer P has, however, not only been used to lift the fertility level of formerly poor soils, but also allowed people to neglect the reuse of P that humans ingest in the form of food and excrete again as faeces and urine and also in other organic wastes. Consequently, P mainly moves in a linear direction from mines to distant locations for crop production, processing and consumption, where a large fraction eventually may become either agronomically inactive due to over-application, unsuitable for recycling due to fixation, contamination or dilution, and harmful as a polluting agent of surface water. This type of P use is not sustainable because fossil phosphate rock reserves are finite. Once the high quality phosphate rock reserves become depleted, too little P will be available for the soils of food-producing regions that still require P supplements to facilitate efficient utilization of resources other than P, including other nutrients. The paper shows that the amounts of P applied in agriculture could be considerably smaller by optimizing land use, improvement of fertilizer recommendations and application techniques, modified livestock diets, and adjustment of livestock densities to available land. Such a concerted set of measures is expected to reduce the use of P in agriculture whilst maintaining crop yields and minimizing the environmental impact of P losses. The paper also argues that compensation of the P exported from farms should eventually be fully based on P recovered from ‘wastes’, the recycling of which should be stimulated by policy measures.},
	language = {en},
	number = {6},
	urldate = {2020-03-12},
	journal = {Chemosphere},
	author = {Schröder, J. J. and Smit, A. L. and Cordell, D. and Rosemarin, A.},
	month = aug,
	year = {2011},
	keywords = {Efficiency, Fertilizer, Land use, Manure, Phosphorus, Surplus},
	pages = {822--831},
}

@article{elser_phosphorus_2012,
	series = {Phosphorus biotechnology • {Pharmaceutical} biotechnology},
	title = {Phosphorus: a limiting nutrient for humanity?},
	volume = {23},
	issn = {0958-1669},
	shorttitle = {Phosphorus},
	url = {http://www.sciencedirect.com/science/article/pii/S0958166912000481},
	doi = {10.1016/j.copbio.2012.03.001},
	abstract = {Phosphorus is a chemical element that is essential to life because of its role in numerous key molecules, including DNA and RNA; indeed, organisms require large amounts of P to grow rapidly. However, the supply of P from the environment is often limiting to production, including to crops. Thus, large amounts of P are mined annually to produce fertilizer that is applied in support of the ‘Green Revolution.’ However, much of this fertilizer eventually ends up in rivers, lakes and oceans where it causes costly eutrophication. Furthermore, given increasing human population, expanding meat consumption, and proliferating bioenergy pressures, concerns have recently been raised about the long-term geological, economic, and geopolitical viability of mined P for fertilizer production. Together, these issues highlight the non-sustainable nature of current human P use. To achieve P sustainability, farms need to become more efficient in how they use P while society as a whole must develop technologies and practices to recycle P from the food chain. Such large-scale changes will probably require a radical restructuring of the entire food system, highlighting the need for prompt but sustained action.},
	language = {en},
	number = {6},
	urldate = {2020-03-12},
	journal = {Current Opinion in Biotechnology},
	author = {Elser, James J},
	month = dec,
	year = {2012},
	pages = {833--838},
}

@article{elser_broken_2011,
	title = {A broken biogeochemical cycle},
	volume = {478},
	issn = {1476-4687},
	url = {http://www.nature.com/articles/478029a},
	doi = {10.1038/478029a},
	abstract = {Excess phosphorus is polluting our environment while, ironically, mineable resources of this essential nutrient are limited. James Elser and Elena Bennett argue that recycling programmes are urgently needed.},
	language = {en},
	number = {7367},
	urldate = {2020-03-12},
	journal = {Nature},
	author = {Elser, James and Bennett, Elena},
	month = oct,
	year = {2011},
	note = {Number: 7367
Publisher: Nature Publishing Group},
	pages = {29--31},
}

@article{filippelli_global_2008,
	title = {The {Global} {Phosphorus} {Cycle}: {Past}, {Present}, and {Future}},
	volume = {4},
	issn = {1811-5209},
	shorttitle = {The {Global} {Phosphorus} {Cycle}},
	url = {http://pubs.geoscienceworld.org/elements/article/4/2/89/137768/The-Global-Phosphorus-Cycle-Past-Present-and},
	doi = {10.2113/GSELEMENTS.4.2.89},
	language = {en},
	number = {2},
	urldate = {2020-03-12},
	journal = {Elements},
	author = {Filippelli, Gabriel M.},
	month = apr,
	year = {2008},
	note = {Publisher: GeoScienceWorld},
	pages = {89--95},
}

@article{galloway_nitrogen_2004,
	title = {Nitrogen {Cycles}: {Past}, {Present}, and {Future}},
	volume = {70},
	issn = {1573-515X},
	shorttitle = {Nitrogen {Cycles}},
	url = {10.1007/s10533-004-0370-0},
	doi = {10.1007/s10533-004-0370-0},
	abstract = {This paper contrasts the natural and anthropogenic controls on the conversion of unreactive N2 to more reactive forms of nitrogen (Nr). A variety of data sets are used to construct global N budgets for 1860 and the early 1990s and to make projections for the global N budget in 2050. Regional N budgets for Asia, North America, and other major regions for the early 1990s, as well as the marine N budget, are presented to Highlight the dominant fluxes of nitrogen in each region. Important findings are that human activities increasingly dominate the N budget at the global and at most regional scales, the terrestrial and open ocean N budgets are essentially disconnected, and the fixed forms of N are accumulating in most environmental reservoirs. The largest uncertainties in our understanding of the N budget at most scales are the rates of natural biological nitrogen fixation, the amount of Nr storage in most environmental reservoirs, and the production rates of N2 by denitrification.},
	language = {en},
	number = {2},
	urldate = {2020-03-12},
	journal = {Biogeochemistry},
	author = {Galloway, J. N. and Dentener, F. J. and Capone, D. G. and Boyer, E. W. and Howarth, R. W. and Seitzinger, S. P. and Asner, G. P. and Cleveland, C. C. and Green, P. A. and Holland, E. A. and Karl, D. M. and Michaels, A. F. and Porter, J. H. and Townsend, A. R. and Vöosmarty, C. J.},
	month = sep,
	year = {2004},
	pages = {153--226},
}

@article{tilman_forecasting_2001,
	title = {Forecasting {Agriculturally} {Driven} {Global} {Environmental} {Change}},
	volume = {292},
	issn = {0036-8075},
	url = {https://www.jstor.org/stable/3082735},
	abstract = {During the next 50 years, which is likely to be the final period of rapid agricultural expansion, demand for food by a wealthier and 50\% larger global population will be a major driver of global environmental change. Should past dependences of the global environmental impacts of agriculture on human population and consumption continue, 109 hectares of natural ecosystems would be converted to agriculture by 2050. This would be accompanied by 2.4- to 2.7-fold increases in nitrogen- and phosphorus-driven eutrophication of terrestrial, freshwater, and near-shore marine ecosystems, and comparable increases in pesticide use. This eutrophication and habitat destruction would cause unprecedented ecosystem simplification, loss of ecosystem services, and species extinctions. Significant scientific advances and regulatory, technological, and policy changes are needed to control the environmental impacts of agricultural expansion.},
	number = {5515},
	urldate = {2020-03-12},
	journal = {Science},
	author = {Tilman, David and Fargione, Joseph and Wolff, Brian and D'Antonio, Carla and Dobson, Andrew and Howarth, Robert and Schindler, David and Schlesinger, William H. and Simberloff, Daniel and Swackhamer, Deborah},
	year = {2001},
	note = {Publisher: American Association for the Advancement of Science},
	pages = {281--284},
}

@article{tilman_global_1999,
	title = {Global environmental impacts of agricultural expansion: {The} need for sustainable and efficient practices},
	volume = {96},
	copyright = {Copyright © 1999, The National Academy of Sciences},
	issn = {0027-8424, 1091-6490},
	shorttitle = {Global environmental impacts of agricultural expansion},
	url = {https://www.pnas.org/content/96/11/5995},
	doi = {10.1073/pnas.96.11.5995},
	abstract = {The recent intensification of agriculture, and the prospects of future intensification, will have major detrimental impacts on the nonagricultural terrestrial and aquatic ecosystems of the world. The doubling of agricultural food production during the past 35 years was associated with a 6.87-fold increase in nitrogen fertilization, a 3.48-fold increase in phosphorus fertilization, a 1.68-fold increase in the amount of irrigated cropland, and a 1.1-fold increase in land in cultivation. Based on a simple linear extension of past trends, the anticipated next doubling of global food production would be associated with approximately 3-fold increases in nitrogen and phosphorus fertilization rates, a doubling of the irrigated land area, and an 18\% increase in cropland. These projected changes would have dramatic impacts on the diversity, composition, and functioning of the remaining natural ecosystems of the world, and on their ability to provide society with a variety of essential ecosystem services. The largest impacts would be on freshwater and marine ecosystems, which would be greatly eutrophied by high rates of nitrogen and phosphorus release from agricultural fields. Aquatic nutrient eutrophication can lead to loss of biodiversity, outbreaks of nuisance species, shifts in the structure of food chains, and impairment of fisheries. Because of aerial redistribution of various forms of nitrogen, agricultural intensification also would eutrophy many natural terrestrial ecosystems and contribute to atmospheric accumulation of greenhouse gases. These detrimental environmental impacts of agriculture can be minimized only if there is much more efficient use and recycling of nitrogen and phosphorus in agroecosystems.},
	language = {en},
	number = {11},
	urldate = {2020-03-12},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Tilman, David},
	month = may,
	year = {1999},
	pmid = {10339530},
	note = {Publisher: National Academy of Sciences
Section: Colloquium Paper},
	pages = {5995--6000},
}

@article{vitousek_human_1997,
	title = {Human {Domination} of {Earth}'s {Ecosystems}},
	volume = {277},
	issn = {0036-8075, 1095-9203},
	url = {https://science.sciencemag.org/content/277/5325/494},
	doi = {10.1126/science.277.5325.494},
	abstract = {Human alteration of Earth is substantial and growing. Between one-third and one-half of the land surface has been transformed by human action; the carbon dioxide concentration in the atmosphere has increased by nearly 30 percent since the beginning of the Industrial Revolution; more atmospheric nitrogen is fixed by humanity than by all natural terrestrial sources combined; more than half of all accessible surface fresh water is put to use by humanity; and about one-quarter of the bird species on Earth have been driven to extinction. By these and other standards, it is clear that we live on a human-dominated planet.},
	language = {en},
	number = {5325},
	urldate = {2020-03-12},
	journal = {Science},
	author = {Vitousek, Peter M. and Mooney, Harold A. and Lubchenco, Jane and Melillo, Jerry M.},
	month = jul,
	year = {1997},
	note = {Publisher: American Association for the Advancement of Science
Section: Special Articles},
	pages = {494--499},
}

@article{tilman_forecasting_2001-1,
	title = {Forecasting {Agriculturally} {Driven} {Global} {Environmental} {Change}},
	volume = {292},
	issn = {0036-8075, 1095-9203},
	url = {https://science.sciencemag.org/content/292/5515/281},
	doi = {10.1126/science.1057544},
	abstract = {During the next 50 years, which is likely to be the final period of rapid agricultural expansion, demand for food by a wealthier and 50\% larger global population will be a major driver of global environmental change. Should past dependences of the global environmental impacts of agriculture on human population and consumption continue, 109 hectares of natural ecosystems would be converted to agriculture by 2050. This would be accompanied by 2.4- to 2.7-fold increases in nitrogen- and phosphorus-driven eutrophication of terrestrial, freshwater, and near-shore marine ecosystems, and comparable increases in pesticide use. This eutrophication and habitat destruction would cause unprecedented ecosystem simplification, loss of ecosystem services, and species extinctions. Significant scientific advances and regulatory, technological, and policy changes are needed to control the environmental impacts of agricultural expansion.},
	language = {en},
	number = {5515},
	urldate = {2020-03-12},
	journal = {Science},
	author = {Tilman, David and Fargione, Joseph and Wolff, Brian and D'Antonio, Carla and Dobson, Andrew and Howarth, Robert and Schindler, David and Schlesinger, William H. and Simberloff, Daniel and Swackhamer, Deborah},
	month = apr,
	year = {2001},
	pmid = {11303102},
	note = {Publisher: American Association for the Advancement of Science
Section: Report},
	pages = {281--284},
}

@article{foley_global_2005,
	title = {Global {Consequences} of {Land} {Use}},
	volume = {309},
	copyright = {Copyright American Association for the Advancement of Science Jul 22, 2005},
	issn = {00368075},
	url = {http://search.proquest.com/docview/213600813/abstract/5ED61BE6FF445A4PQ/1},
	abstract = {Land use has generally been considered a local environmental issue, but it is becoming a force of global importance. Worldwide changes to forests, farmlands, waterways, and air are being driven by the need to provide food, fiber, water, and shelter to more than six billion people. Global croplands, pastures, plantations, and urban areas have expanded in recent decades, accompanied by large increases in energy, water, and fertilizer consumption, along with considerable losses of biodiversity. Such changes in land use have enabled humans to appropriate an increasing share of the planet's resources, but they also potentially undermine the capacity of ecosystems to sustain food production, maintain freshwater and forest resources, regulate climate and air quality, and ameliorate infectious diseases. We face the challenge of managing trade-offs between immediate human needs and maintaining the capacity of the biosphere to provide goods and services in the long term. [PUBLICATION ABSTRACT]},
	language = {English},
	number = {5734},
	urldate = {2020-03-11},
	journal = {Science; Washington},
	author = {Foley, Jonathan A. and DeFries, Ruth and Asner, Gregory P. and Barford, Carol and al, et},
	month = jul,
	year = {2005},
	note = {Num Pages: 5
Place: Washington, United States, Washington
Publisher: The American Association for the Advancement of Science
Section: REVIEW},
	keywords = {Biosphere, Ecosystems, Environmental impact, Human influences, Land use, Sciences: Comprehensive Works, Technology: Comprehensive Works},
	pages = {570--4},
}

@article{mortland_influence_1952,
	title = {The {Influence} of {Clay} {Minerals} on the {Enzymatic} {Hydrolysis} of {Organic} {Phosphorus} {Compounds} 1},
	volume = {16},
	issn = {0361-5995},
	url = {https://dl.sciencesocieties.org/publications/sssaj/abstracts/16/1/SS0160010010},
	doi = {10.2136/sssaj1952.03615995001600010004x},
	language = {en},
	number = {1},
	urldate = {2020-03-11},
	journal = {Soil Science Society of America Journal},
	author = {Mortland, Max M. and Gieseking, J. E.},
	month = jan,
	year = {1952},
	note = {Publisher: Soil Science Society of America},
	pages = {10--13},
}

@article{syers_phosphate_1973,
	title = {Phosphate {Chemistry} in {Lake} {Sediments} 1},
	volume = {2},
	issn = {0047-2425},
	url = {https://dl.sciencesocieties.org/publications/jeq/abstracts/2/1/JEQ0020010001},
	doi = {10.2134/jeq1973.00472425000200010001x},
	language = {en},
	number = {1},
	urldate = {2020-03-11},
	journal = {Journal of Environmental Quality},
	author = {Syers, J. K. and Harris, R. F. and Armstrong, D. E.},
	year = {1973},
	note = {Publisher: American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America},
	pages = {1--14},
}

@article{musselman_projected_2018,
	title = {Projected increases and shifts in rain-on-snow flood risk over western {North} {America}},
	volume = {8},
	copyright = {2018 The Author(s)},
	issn = {1758-6798},
	url = {https://www.nature.com/articles/s41558-018-0236-4},
	doi = {10.1038/s41558-018-0236-4},
	abstract = {Rain-on-snow events pose a significant flood risk. High-resolution model simulations reveal that such events will increase in frequency in the higher elevations of western North America, resulting in a 20–200\% enhancement of flood risk.},
	language = {en},
	number = {9},
	urldate = {2020-03-11},
	journal = {Nature Climate Change},
	author = {Musselman, Keith N. and Lehner, Flavio and Ikeda, Kyoko and Clark, Martyn P. and Prein, Andreas F. and Liu, Changhai and Barlage, Mike and Rasmussen, Roy},
	month = sep,
	year = {2018},
	note = {Number: 9
Publisher: Nature Publishing Group},
	pages = {808--812},
}

@article{oldenborg_impact_2019,
	title = {Impact of sediment dredging on sediment phosphorus flux in a restored riparian wetland},
	volume = {650},
	issn = {0048-9697},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969718337495},
	doi = {10.1016/j.scitotenv.2018.09.298},
	abstract = {Many riverine wetlands have been drained for the creation of agricultural land; however, global declines in freshwater biodiversity have begun to motivate wetland restoration projects around the world. Legacy phosphorus (P) increases the risk that wetland restoration may liberate excess P to the water column and connecting waterbodies, resulting in a trade-off of restored habitat for degraded water quality. To avoid this trade-off, we dredged a former agricultural parcel prior to hydrologic reconnection, and evaluated restoration success by comparing sediment P dynamics before and after dredging. First, results from P adsorption isotherm experiments suggested that after dredging, the sediment would act as a sink for dissolved P only when water column soluble reactive phosphorus (SRP) concentrations exceeded 40 μg L−1. Additionally, the dredging depth ({\textasciitilde}1 m on average) exposed sediment with significantly reduced P sorption capacities. Second, P release rates were measured in sediment cores that were incubated under two water temperatures (ambient; +2 °C) and two oxygen levels (oxic; hypoxic). Average maximum total phosphorus (TP) release rates ranged from 40 to 85 mg m−2 d−1 before dredging and from 0 to 7 mg m−2 d−1 after dredging, resulting in a 95–99\% reduction in TP release rates after dredging. Similar reductions were measured also for SRP release rates. The significant reduction in sediment P release after dredging now creates a high potential for this restored wetland to reduce net P loads into downstream waters by facilitating the deposition and burial of particulate P. We conclude that sediment dredging can be a useful technique for balancing the goals of habitat restoration and water quality improvements in wetlands restored on former agricultural lands.},
	language = {en},
	urldate = {2020-03-11},
	journal = {Science of The Total Environment},
	author = {Oldenborg, Kimberly A. and Steinman, Alan D.},
	month = feb,
	year = {2019},
	keywords = {Area of concern, Legacy phosphorus, Water quality, Wetland restoration},
	pages = {1969--1979},
}

@article{miles_spatial_2013,
	title = {Spatial distribution and temporal variability in the forms of phosphorus in the {Beaver} {River} subwatershed of {Lake} {Simcoe}, {Ontario}, {Canada}},
	volume = {3},
	issn = {2044-2041},
	url = {https://www.tandfonline.com/doi/abs/10.5268/IW-3.2.531},
	doi = {10.5268/IW-3.2.531},
	abstract = {Agricultural runoff is an important source of phosphorus (P) to surface waters. This paper investigated the relationship between agricultural land use and the forms of P (i.e., total phosphorus [TP], total dissolved phosphorus [TDP], and soluble reactive phosphorus [SRP]) in streams draining 8 headwater subcatchments in the Beaver River subwatershed, a major inflow to Lake Simcoe, which is a large hard-water lake in south-central Canada. The time period of analysis had a strong influence on the results. There was no relationship between percent total agriculture and average TP when concentrations were averaged over the entire 12-month (Jun 2010–May 2011) monitoring period, whereas there were significant positive correlations between agricultural land use and average TP during the summer season (Jun–Aug). Significant correlations between average stream TDP and SRP and percent pastureland were observed, although relationships were again dependent on the time period of analysis. Concentrations of TP, TDP, and SRP were highly variable over time, with maximum concentrations occurring during the winter months. This was illustrated by a single rain-on-snow event (11 mm) on 5 March 2011, when samples taken 3–4 h apart varied by as much as 100\%. These results indicate that winter storm-targeted sampling is likely necessary to capture the full range of annual variability in P forms and concentrations},
	number = {2},
	urldate = {2020-03-11},
	journal = {Inland Waters},
	author = {Miles, Jennifer J. and Eimers, M. Catherine and North, Rebecca L. and Dillon, Peter J.},
	month = jan,
	year = {2013},
	note = {Publisher: Taylor \& Francis
\_eprint: https://www.tandfonline.com/doi/pdf/10.5268/IW-3.2.531},
	keywords = {Lake Simcoe, headwater streams, land use, phosphorus, rain events, runoff, soluble reactive phosphorus},
	pages = {179--186},
}

@article{darch_meta-analysis_2014,
	title = {A {Meta}-{Analysis} of {Organic} and {Inorganic} {Phosphorus} in {Organic} {Fertilizers}, {Soils}, and {Water}: {Implications} for {Water} {Quality}},
	volume = {44},
	issn = {1064-3389},
	shorttitle = {A {Meta}-{Analysis} of {Organic} and {Inorganic} {Phosphorus} in {Organic} {Fertilizers}, {Soils}, and {Water}},
	url = {10.1080/10643389.2013.790752},
	doi = {10.1080/10643389.2013.790752},
	abstract = {Phosphorus is known to be an important contributor to eutrophication of aquatic systems,1 but the role of organic phosphorus is often overlooked. This review uses a meta-analysis approach to investigate inorganic and organic phosphorus in organic fertilizers, soils and waters, including the quantification of organic phosphorous forms such as monoesters, diesters, and inositol hexakisphosphate. Across these media, organic phosphorus comprised 22–46\% of the total phosphorus (by mass of phosphorus). Bioavailable organic phosphorus appears to be more mobile than recalcitrant forms. Organic phosphorus may represent a significant risk for eutrophication, and the risk may vary according to the season, but conclusions are hampered by a lack of data.},
	number = {19},
	urldate = {2020-03-11},
	journal = {Critical Reviews in Environmental Science and Technology},
	author = {Darch, T. and Blackwell, M. S. A. and Hawkins, J. M. B. and Haygarth, P. M. and Chadwick, D.},
	month = oct,
	year = {2014},
	note = {Publisher: Taylor \& Francis
\_eprint: 10.1080/10643389.2013.790752},
	keywords = {hydrolysis, mobilisation, phosphatase, review, temporal, transport},
	pages = {2172--2202},
}

@article{hupfer_polyphosphate-accumulating_2007,
	title = {Polyphosphate-accumulating microorganisms in aquatic sediments},
	volume = {47},
	issn = {0948-3055, 1616-1564},
	url = {http://www.int-res.com/abstracts/ame/v47/n3/p299-311/},
	doi = {10.3354/ame047299},
	abstract = {The direct contribution of microorganisms to the mobilisation and immobilisation of phosphorus (P) in aquatic sediments has been controversially discussed for more than a decade. Some authors have speculated that the microbial P pool is highly variable in the uppermost sediment layer, especially when excessive P accumulation in the form of polyphosphate (Poly-P) occurs. Poly-P storage is a widespread ability of many different organisms in nature. The phenomenon of Poly-P storage has been technically optimised in wastewater treatment plants (WWTP) providing conditions for enhanced biological phosphorus removal. New insights into the functioning of P elimination in WWTP were strongly linked to the development of novel methods, like 31P nuclear magnetic resonance, for the detection of Poly-P and molecular biological methods for the identification of the specific microorganisms responsible for biological P elimination. Our review summarises current literature on Poly-P in aquatic systems and discusses different potential habitats and mechanisms for Poly-P storage in sediments that are more diverse than in WWTP. Poly-P in sediments may originate from benthic or pelagic hetero- and autotrophic organisms. Poly-P-accumulating organisms in sediments may be of high ecological importance, since they insert phosphorus into the benthic food chain and affect the permanent P mineral deposition in sediments by physiologically inducing rapid P release. Although several studies indicate that Poly-P substantially contributes to total P in the uppermost sediment layer (up to 10\%), its origin and the microorganisms and mechanisms involved in Poly-P storage and cycling are largely unknown. Therefore, we also aim to stimulate future studies focusing on these important areas of sediment research.},
	language = {en},
	urldate = {2020-03-11},
	journal = {Aquatic Microbial Ecology},
	author = {Hupfer, M and Gloess, S and Grossart, Hp},
	month = may,
	year = {2007},
	pages = {299--311},
}

@article{wang_sequential_2013,
	title = {Sequential extraction procedures for the determination of phosphorus forms in sediment},
	volume = {14},
	issn = {1439-863X},
	url = {10.1007/s10201-012-0397-1},
	doi = {10.1007/s10201-012-0397-1},
	abstract = {This article summarizes the main extraction methods for sedimentary phosphorus (P) determination. With sequential chemical extractions, P is supposed to be selectively removed from different compounds in the sediments. Extraction schemes using strong acids and alkaline solutions have been tested on different sediments and found not to extract well-defined fractions. In addition, several systematic errors in these schemes have been detected. Thus, these schemes have been modified and simplified accordingly. The Standards Measurements and Testing Program of the European Commission (SMT) method is a popular modification of these extraction schemes, as it is simple to handle, allows laboratories to achieve reproducible results and could provide a useful tool for routine use by water managers. The SEDEX (sequential extraction method) method, another popular modification, is widely applied in biogeochemical research as it can separate authigenic carbonate fluorapatite from fluorapatite. Other chemical extractions using chelating compounds have attempted to extract P bound with iron and calcium in sediments without disturbing clay-bound or organic P, the purpose being to determine the algal-available non-apatite, apatite and organic fractions of sediment P. All extraction procedures still yield operationally defined fractions and cannot be used for identification of discrete P compounds. Future modifications of the extraction scheme should aim to achieve better extraction efficiency and selectivity, simple handling techniques and methods that can prevent the extracted P from being re-adsorbed onto Fe(OOH) and CaCO3.},
	language = {en},
	number = {2},
	urldate = {2020-03-11},
	journal = {Limnology},
	author = {Wang, Changyou and Zhang, Yong and Li, Hongli and Morrison, R. John},
	month = apr,
	year = {2013},
	pages = {147--157},
}

@article{pacini_speciation_1999,
	title = {Speciation of riverine particulate phosphorus during rain events},
	volume = {47},
	issn = {0168-2563, 1573-515X},
	url = {http://link.springer.com/10.1007/BF00993098},
	doi = {10.1007/BF00993098},
	abstract = {Suspended sediments collected during rain events were analysed to assess the maximum potential bioavailability of particulate phosphorus (PP). Physical (separation by particle size) and chemical (sequential extraction) fractionation techniques were applied. Time differentiated sampling during rain events revealed that changes in the concentrations of soluble and particle bound phosphorus, and in the proportion of different PP phases, are due to the changing contribution of various sources of runoff and to flow related variations in particle size. Size fractionation and the extraction of PP phases, can help to distinguish resuspended sediments from sediments coming directly from outside the channel. In light of a former study, investigating PP sedimentation and transformations within the sediments of Lake Sempach, our results lead to the conclusion that, at least 25\% (particulate inorganic and reductive soluble P) and at most 70\% of the allochthonous PP supply transported during a single rain event, may become bioavailable after early diagenesis in the lake sediments. The uncertainty is due to the unknown time span necessary for the diagenesis, at the lake sediment surface, of particulate organic phosphorus of allochthonous origin.},
	language = {en},
	number = {1},
	urldate = {2020-03-11},
	journal = {Biogeochemistry},
	author = {Pacini, Nic and Gächter, Rene},
	month = oct,
	year = {1999},
	pages = {87--109},
}

@article{parsons_sediment_2017-1,
	title = {Sediment phosphorus speciation and mobility under dynamic redox conditions},
	volume = {14},
	issn = {1726-4170},
	url = {https://www.biogeosciences.net/14/3585/2017/},
	doi = {10.5194/bg-14-3585-2017},
	abstract = {{\textless}p{\textgreater}{\textless}strong{\textgreater}Abstract.{\textless}/strong{\textgreater} Anthropogenic nutrient enrichment has caused phosphorus (P) accumulation in many freshwater sediments, raising concerns that internal loading from legacy P may delay the recovery of aquatic ecosystems suffering from eutrophication. Benthic recycling of P strongly depends on the redox regime within surficial sediment. In many shallow environments, redox conditions tend to be highly dynamic as a result of, among others, bioturbation by macrofauna, root activity, sediment resuspension and seasonal variations in bottom-water oxygen (O$_{\textrm{2}}$) concentrations. To gain insight into the mobility and biogeochemistry of P under fluctuating redox conditions, a suspension of sediment from a hypereutrophic freshwater marsh was exposed to alternating 7-day periods of purging with air and nitrogen gas (N$_{\textrm{2}}$), for a total duration of 74 days, in a bioreactor system. We present comprehensive data time series of bulk aqueous- and solid-phase chemistry, solid-phase phosphorus speciation and hydrolytic enzyme activities demonstrating the mass balanced redistribution of P in sediment during redox cycling. Aqueous phosphate concentrations remained low ( ∼ 2.5 µM) under oxic conditions due to sorption to iron(III) oxyhydroxides. During anoxic periods, once nitrate was depleted, the reductive dissolution of iron(III) oxyhydroxides released P. However, only 4.5 \% of the released P accumulated in solution while the rest was redistributed between the MgCl$_{\textrm{2}}$ and NaHCO$_{\textrm{3}}$ extractable fractions of the solid phase. Thus, under the short redox fluctuations imposed in the experiments, P remobilization to the aqueous phase remained relatively limited. Orthophosphate predominated at all times during the experiment in both the solid and aqueous phase. Combined P monoesters and diesters accounted for between 9 and 16 \% of sediment particulate P. Phosphatase activities up to 2.4 mmol h$^{\textrm{−1}}$ kg$^{\textrm{−1}}$ indicated the potential for rapid mineralization of organic P (P$_{\textrm{o}}$), in particular during periods of aeration when the activity of phosphomonoesterases was 37 \% higher than under N$_{\textrm{2}}$ sparging. The results emphasize that the magnitude and timing of internal P loading during periods of anoxia are dependent on both P redistribution within sediments and bottom-water nitrate concentrations.{\textless}/p{\textgreater}},
	language = {English},
	number = {14},
	urldate = {2020-03-11},
	journal = {Biogeosciences},
	author = {Parsons, Chris T. and Rezanezhad, Fereidoun and O'Connell, David W. and Cappellen, Philippe Van},
	month = jul,
	year = {2017},
	note = {Publisher: Copernicus GmbH},
	pages = {3585--3602},
}

@article{pettersson_phosphorus_1988,
	title = {Phosphorus in sediments — speciation and analysis},
	volume = {170},
	issn = {1573-5117},
	url = {10.1007/BF00024900},
	doi = {10.1007/BF00024900},
	abstract = {Characterization of sediment phosphorus is commonly based on sequential chemical extractions, in which phosphorus is supposed to be selectively removed from different compounds in the sediments. The first extraction schemes were designed to quantify discrete chemical or mineralogical compounds. As extraction schemes have been tested on different sediments, several systematic errors have been detected and the schemes have been modified and simplified accordingly. Other chemical extractions or treatments have attempted to determine phosphorus bound to particles with a certain strength or binding energy, the purpose being to determine the labile, loosely bound, exchangeable, mobile or algal-available fraction of sediment phosphorus. All extraction procedures yield operationally defined fractions and cannot be used for identification of discrete phosphorus compounds. The many methodological modifications make it necessary to be cautious when comparing results from the literature in this field.},
	language = {en},
	number = {1},
	urldate = {2020-03-11},
	journal = {Hydrobiologia},
	author = {Pettersson, Kurt and Boström, Bengt and Jacobsen, Ole-Stig},
	month = dec,
	year = {1988},
	pages = {91--101},
}

@article{gerke_humic_2010,
	title = {Humic ({Organic} {Matter})-{Al}({Fe})-{Phosphate} {Complexes}: {An} {Underestimated} {Phosphate} {Form} in {Soils} and {Source} of {Plant}-{Available} {Phosphate}},
	volume = {175},
	issn = {0038-075X},
	shorttitle = {Humic ({Organic} {Matter})-{Al}({Fe})-{Phosphate} {Complexes}},
	url = {https://journals.lww.com/soilsci/Abstract/2010/09000/Humic__Organic_Matter__Al_Fe__Phosphate_Complexes_.1.aspx},
	doi = {10.1097/SS.0b013e3181f1b4dd},
	abstract = {The chemical interaction between soil organic matter and the orthophosphate anion (phosphate [P]) is important for reactions of P at the soil solid phase, in soil solution, and in natural waters. Humic substances account for an important or dominant part of soil organic matter and of dissolved organic carbon in rivers and lakes. Orthophosphate is not bound directly to the humic molecules, but metals complexed by the humic substances can bind P anions of which Al(III) and Fe(III) seem to be the most important.
        Humic-metal-P associations or complexes (HMEP) are not detected by conventional P speciation procedures in natural water and in soil solution. In addition, HMEP cannot be detected at the soil solid phase by traditional P fractionation procedures. The concentration of free orthophosphate in solution is determined spectrophotometrically by the phosphomolybdate method in its many variations, with organic P being calculated as the difference between total P and inorganic P. During the photometric procedure, more than 50\%, in many cases, more than 80\% of the humic-associated P, is hydrolyzed and therefore considered to be free orthophosphate. This is the main reason why HMEP are often ignored in soil chemistry. Hydrolysis occurs during the analytical speciation of P in soil solution and in soil P fractionation procedures. A step to preseparate according to the molecule mass, for example, by 5,000 to 20,000 Da ultrafiltration or by gel permeation chromatography, is therefore required.
        In natural water and in soil solution, HMEP can account for more than 50\%, in some cases, more than 80\% of the P in solution. Free orthophosphate in solution is often in equilibrium with P in HMEP.
        The potential relevance of HMEP at the soil solid phase can be as follows. If the content of alkaline pyrophosphate-extractable Al + Fe (after McKeague, J. A., J. E. Bryden, and N. N. Miles. 1971. Differentiation of forms of extractable iron and aluminum. Soil Sci. Soc. Am. Proc. 35:33-38) is high compared with that of acid oxalate-extractable Fe + Al (Tamm reagent, after Schwertmann, 1964), then humic-Al(Fe) complexes are important for P sorption and transformation in soil compared with oxides or clay minerals. In soils, evidence exists for the importance of HMEP in Spodosols and Andosols. Humic-P complexes are important with respect to the soil P availability to plant roots. Mobilizing plant species often excrete citrate or oxalate as a result of P deficiency. The P from HMEP is much better mobilized by dibasic and tribasic low-molecular-weight anions than P adsorbed to inorganic surfaces such as goethite or ferrihydrite.},
	language = {en-US},
	number = {9},
	urldate = {2020-03-11},
	journal = {Soil Science},
	author = {Gerke, Jörg},
	month = sep,
	year = {2010},
	pages = {417--425},
}

@article{palmer-felgate_impact_2010,
	title = {Impact of {Point}-{Source} {Pollution} on {Phosphorus} and {Nitrogen} {Cycling} in {Stream}-{Bed} {Sediments}},
	volume = {44},
	issn = {0013-936X},
	url = {10.1021/es902706r},
	doi = {10.1021/es902706r},
	abstract = {Diffusive equilibration in thin films was used to study the cycling of phosphorus and nitrogen at the sediment−water interface in situ and with minimal disturbance to redox conditions. Soluble reactive phosphate (SRP), nitrate, nitrite, ammonium, sulfate, iron, and manganese profiles were measured in a rural stream, 12 m upstream, adjacent to, and 8 m downstream of a septic tank discharge. Sewage fungus adjacent to the discharge resulted in anoxic conditions directly above the sediment. SRP and ammonium increased with depth through the fungus layer to environmentally significant concentrations (440 and 1800 μM, respectively) due to release at the sediment surface. This compared to only 0.8 μM of SRP and 2.0 μM of ammonium in the water column upstream of the discharge. Concomitant removal of ammonium, nitrite and nitrate within 0.5 cm below the fungus−water interface provided evidence for anaerobic ammonium oxidation (anammox). “Hotspots” of porewater SRP (up to 350 μM) at the downstream site demonstrated potential in-stream storage of the elevated P concentrations from the effluent. These results provide direct in situ evidence of phosphorus and nitrogen release from river-bed sediments under anoxic conditions created by sewage-fungus, and highlight the wider importance of redox conditions and rural point sources on in-stream nutrient cycling.},
	number = {3},
	urldate = {2020-03-11},
	journal = {Environmental Science \& Technology},
	author = {Palmer-Felgate, Elizabeth J. and Mortimer, Robert J. G. and Krom, Michael D. and Jarvie, Helen P.},
	month = feb,
	year = {2010},
	note = {Publisher: American Chemical Society},
	pages = {908--914},
}

@article{jarvie_within-river_2006,
	series = {Hydro-ecological functioning of the {Pang} and {Lambourn} catchments, {UK}},
	title = {Within-river nutrient processing in {Chalk} streams: {The} {Pang} and {Lambourn}, {UK}},
	volume = {330},
	issn = {0022-1694},
	shorttitle = {Within-river nutrient processing in {Chalk} streams},
	url = {http://www.sciencedirect.com/science/article/pii/S0022169406001958},
	doi = {10.1016/j.jhydrol.2006.04.014},
	abstract = {This work examines baseflow nutrient concentrations and loads along two rural Chalk streams, the Pang and Lambourn. Soluble reactive phosphorus (SRP) and boron (B) concentrations in these streams were heavily influenced by point-source inputs and the effects of downstream flow accretion and dilution. Unlike B (which is chemically conservative), SRP loads were also strongly influenced by in-stream processing resulting in uptake of SRP, particularly immediately downstream of sewage effluent discharges, where rates of SRP uptake were highest. For the upper River Pang, up to 80\% of SRP loads were lost within 4km downstream of Compton sewage treatment works (STW) and on the River Lambourn up to 55\% of SRP loads were lost within 1.6km downstream of East Shefford STW. In contrast, nitrate (NO3) concentrations at sites along the Pang and Lambourn were largely controlled by groundwater inputs and plant uptake during periods of high photosynthetic activity in spring and summer and silicon (Si) by diatom uptake in April/May. There were net gains in NO3 loads along the river reaches, as a result of volumetric increases in groundwater discharge, and, compared with SRP, the role of in-stream processing of NO3 appeared low. Examination of SRP exchange by bed sediment and uptake of SRP into algal biofilms indicated that biofilms accounted for only a very small percentage of in-stream P-uptake, but that bed sediment SRP-exchanges had a more important control on baseflow SRP concentrations and loads. Point source P remediation at East Shefford STW, by removal of P from final effluent (P-stripping), resulted in 70–90\% reductions in river-water SRP loads. After introduction of P-stripping at East Shefford STW, bed sediments immediately downstream of the STW switched from being net sinks to net sources of SRP. Our results show that, in the immediate aftermath of P-stripping, bed sediment SRP-release was responsible for a 30μg-Pl−1 rise in river-water SRP along this reach. While this increase in SRP concentration, as a result of bed sediment SRP release, is potentially ecologically significant, it is small in relation to the increase in SRP concentrations from effluent prior to P-stripping, which resulted in increases in SRP concentration of up to 500μg-Pl−1. There was a six-month lag between the introduction of P-stripping at East Shefford STW and bed sediment EPC0 recovering to equilibrium levels with the overlying river water (and thus negligible SRP release). Recovery of bed sediments to equilibrium levels is likely to have occurred as a result of winnowing and removal of high-EPC0 sediment and delivery of lower EPC0 sediment from upstream. Under higher/more variable flow conditions and greater rates of in-channel sediment erosion/delivery, more rapid recovery of bed sediment EPC0 levels following P-stripping might be expected.},
	language = {en},
	number = {1},
	urldate = {2020-03-11},
	journal = {Journal of Hydrology},
	author = {Jarvie, Helen P. and Neal, Colin and Jürgens, Monika D. and Sutton, Elizabeth J. and Neal, Margaret and Wickham, Heather D. and Hill, Linda K. and Harman, Sarah A. and Davies, Jennifer J. L. and Warwick, Alan and Barrett, Cyril and Griffiths, Jim and Binley, Andrew and Swannack, Natalie and McIntyre, Neil},
	month = oct,
	year = {2006},
	keywords = {Agriculture, Biofilm, Chalk, Eutrophication, Flux, LOCAR, Lambourn, Nitrogen, Nutrient, Pang, Permeable catchment, Phosphorus, River, Sediment, Sewage},
	pages = {101--125},
}

@article{house_geochemical_2003,
	title = {Geochemical cycling of phosphorus in rivers},
	volume = {18},
	issn = {0883-2927},
	url = {http://www.sciencedirect.com/science/article/pii/S0883292702001580},
	doi = {10.1016/S0883-2927(02)00158-0},
	abstract = {Concentrations of contaminants in fresh waters are controlled, not only by point and diffuse sources within the catchment, but by a multitude of biogeochemical reactions (riverine processes) that may occur in the water column during transport. As an example, the results of mass-balance studies using “snapshot” field sampling techniques for P transport in a large river in Northern England (R. Swale) are summarised to identify the processes that contribute to internal cycling within the river, and their relative size compared with the total export of P. The interaction of P with sediments is an important factor controlling concentrations of soluble P in the water column, during both low and high river-flows, with in-river storage in some instances amounting to {\textgreater}30\% of the load throughput. Antecedent weather conditions are identified as important in controlling the pool of fine sediment and associated P available for remobilisation during storm pulses. Examples of P reactions with sediments that have been identified from field studies are briefly reviewed. Firstly, a mass-balance approach to elucidate the net interaction of P with river bed-sediments is presented and then two specific interactions of P with sediments are discussed: (a) the coprecipitation of phosphate with calcite in lakes during phytoplankton blooms and in benthic algal biofilms on river sediments and (b) the formation of vivianite in the anoxic zone of bed-sediment in eutrophic lakes and rivers. Phosphate coprecipitation with calcite is an important mechanism controlling P concentrations in some hardwater lakes, and has been found to contribute as much as 30\% of the dry mass associated with the colonisation and development of algal biofilms on hardwater river beds. Vivianite has been detected in anoxic river sediments (up to 20\% by mass) receiving treated sewage, although little is known about the conditions of formation and how widespread the occurrence of vivianite is in sediments.},
	language = {en},
	number = {5},
	urldate = {2020-03-11},
	journal = {Applied Geochemistry},
	author = {House, William A.},
	month = may,
	year = {2003},
	pages = {739--748},
}

@article{sharpley_phosphorus_2013-1,
	title = {Phosphorus {Legacy}: {Overcoming} the {Effects} of {Past} {Management} {Practices} to {Mitigate} {Future} {Water} {Quality} {Impairment}},
	volume = {42},
	copyright = {© 2013 The Authors.},
	issn = {1537-2537},
	shorttitle = {Phosphorus {Legacy}},
	url = {https://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/jeq2013.03.0098},
	doi = {10.2134/jeq2013.03.0098},
	abstract = {The water quality response to implementation of conservation measures across watersheds has been slower and smaller than expected. This has led many to question the efficacy of these measures and to call for stricter land and nutrient management strategies. In many cases, this limited response has been due to the legacies of past management activities, where sinks and stores of P along the land–freshwater continuum mask the effects of reductions in edge-of-field losses of P. Accounting for legacy P along this continuum is important to correctly apportion sources and to develop successful watershed remediation. In this study, we examined the drivers of legacy P at the watershed scale, specifically in relation to the physical cascades and biogeochemical spirals of P along the continuum from soils to rivers and lakes and via surface and subsurface flow pathways. Terrestrial P legacies encompass prior nutrient and land management activities that have built up soil P to levels that exceed crop requirements and modified the connectivity between terrestrial P sources and fluvial transport. River and lake P legacies encompass a range of processes that control retention and remobilization of P, and these are linked to water and sediment residence times. We provide case studies that highlight the major processes and varying timescales across which legacy P continues to contribute P to receiving waters and undermine restoration efforts, and we discuss how these P legacies could be managed in future conservation programs.},
	language = {en},
	number = {5},
	urldate = {2020-03-11},
	journal = {Journal of Environmental Quality},
	author = {Sharpley, Andrew and Jarvie, Helen P. and Buda, Anthony and May, Linda and Spears, Bryan and Kleinman, Peter},
	year = {2013},
	note = {\_eprint: https://acsess.onlinelibrary.wiley.com/doi/pdf/10.2134/jeq2013.03.0098},
	pages = {1308--1326},
}

@article{zawal_early_2016,
	title = {Early post-dredging recolonization of caddisflies ({Insecta}: {Trichoptera}) in a small lowland river ({NW} {Poland})},
	volume = {17},
	issn = {1439-863X},
	shorttitle = {Early post-dredging recolonization of caddisflies ({Insecta}},
	url = {10.1007/s10201-015-0466-3},
	doi = {10.1007/s10201-015-0466-3},
	abstract = {An analysis was made of the effect of dredging on the caddisfly fauna (Trichoptera) of the river Krąpiel (north-western Poland) a short time after the intervention. Pronounced changes were observed in the qualitative and quantitative structure and the biodiversity of Trichoptera. These changes should not, however, be characterized as unfavourable from an ecological perspective if we consider only the one group of insects analysed. Some species — Brachycentrus subnubilus and Lepidostoma hirtum — disappeared from the dredged parts of the river, but significantly more appeared, and these were typical river species. This replacement of species can be linked to habitat changes and the uncovering of larger patches of sandy bottom. The recolonizing species included accidental (eurytopic) species, which is typical in ecological succession for periods immediately following disturbances. On balance, despite the replacement of species, there was no decrease in species diversity, and typical river species appeared in larger numbers. In Trichoptera, recolonization following dredging first takes place as a result of drift of larvae, and then via dispersion of adults.},
	language = {en},
	number = {1},
	urldate = {2020-03-11},
	journal = {Limnology},
	author = {Zawal, Andrzej and Czachorowski, Stanisław and Stępień, Edyta and Buczyńska, Edyta and Szlauer-Łukaszewska, Agnieszka and Buczyński, Paweł and Stryjecki, Robert and Dąbkowski, Piotr},
	month = jan,
	year = {2016},
	pages = {71--85},
}

@article{dabkowski_impact_2016,
	title = {The impact of dredging of a small lowland river on water beetle fauna ({Coleoptera})},
	issn = {1723-8633, 1129-5767},
	url = {http://www.jlimnol.it/index.php/jlimnol/article/view/jlimnol.2016.1270},
	doi = {10.4081/jlimnol.2016.1270},
	abstract = {{\textless}p{\textgreater}Using the example of a regulated stretch of the Krąpiel River (NW Poland), an analysis of the impact of dredging on the aquatic beetle (Coleoptera) fauna was made. After dredging the beetle fauna became markedly poorer quantitatively and had lower species diversity. Moreover, the qualitative composition and dominance structure were highly transformed. However, species number and diversity increased rapidly and were restored within just half a year. The structure of the restored fauna was most strongly influenced by vegetation, flow velocity and bottom sediment composition. The first to colonize the river were eurytopic beetles and species typical of small water bodies, which had significant refuges in the form of fish ponds bordering on the river; these species dominated the assemblage throughout the study period. Rheophiles with less dispersal power appeared later, and finally rheobionts, in low numbers but occupying an increasing number of sampling sites. {\textless}/p{\textgreater}},
	urldate = {2020-03-11},
	journal = {Journal of Limnology},
	author = {Dabkowski, Piotr and Buczynski, Paweł and Zawal, Andrzej and Stepien, Edyta and Buczynska, Edyta and Stryjecki, Robert and Czachorowski, Stanislaw and Smietana, Przemyslaw and Szenejko, Magdalena},
	month = apr,
	year = {2016},
}

@article{baczyk_influence_2018,
	title = {Influence of technical maintenance measures on ecological status of agricultural lowland rivers – {Systematic} review and implications for river management},
	volume = {627},
	issn = {0048-9697},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969718302778},
	doi = {10.1016/j.scitotenv.2018.01.235},
	abstract = {Intensification of agriculture and ongoing urban sprawl exacerbate pressures on rivers. Small rivers in agricultural landscapes are especially exposed to excessive technical actions implemented in order to allow for harvesting river water for irrigation, draining agricultural water and receiving sewage. Regular dredging and macrophyte removal strongly interfere with the global need for preserving river biodiversity that allows agricultural lowland rivers to remain refuges for a variety of species, and—accordingly—to keep water bodies resilient for the benefit of society. In order to provide a comprehensive look at the influence of agricultural lowland river management on the ecological status of these water bodies, we conducted a literature review and a meta-analysis. For the structured literature review we selected 203 papers reflecting on the response of aquatic ecosystems to dredging and macrophyte management actions. The database of scientific contributions developed for our study consists of papers written by the authors from 33 countries (first authorship) addressing dredging, macrophyte removal, status of fish and macroinvertebrates as well as the general ecological status of lowland agricultural rivers. We revealed that 96\% of the analyzed papers indicated unilateral, negative responses of aquatic ecosystems, particularly macroinvertebrates, ichthyofauna and macrophyte composition, to maintenance measures. We revealed that studies conducted in the European Union on the ecological status of rivers appeared to significantly increase in quantity after the implementation of the Water Framework Directive. Finally, we concluded that day-to-day management of lowland agricultural rivers requires revision in terms of compliance with environmental conservation requirements and the recurrent implementation of technical measures for river maintenance.},
	language = {en},
	urldate = {2020-03-11},
	journal = {Science of The Total Environment},
	author = {Bączyk, Anna and Wagner, Maciej and Okruszko, Tomasz and Grygoruk, Mateusz},
	month = jun,
	year = {2018},
	keywords = {Agriculture, Ecosystem, Management, River, Water Framework Directive},
	pages = {189--199},
}

@article{audette_speciation_2018,
	title = {Speciation of {Phosphorus} from {Agricultural} {Muck} {Soils} to {Stream} and {Lake} {Sediments}},
	volume = {47},
	issn = {0047-2425},
	url = {http://dl.sciencesocieties.org/publications/jeq/articles/47/4/884},
	doi = {10.2134/jeq2018.02.0068},
	language = {en},
	number = {4},
	urldate = {2020-03-11},
	journal = {Journal of Environmental Quality},
	author = {Audette, Yuki and O’Halloran, Ivan P. and Nowell, Peter M. and Dyer, Richard and Kelly, Ross and Voroney, R. Paul},
	year = {2018},
	note = {Publisher: The American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.},
	pages = {884--892},
}

@article{vidon_storm_2012,
	title = {Storm phosphorus concentrations and fluxes in artificially drained landscapes of the {US} {Midwest}},
	volume = {2012},
	url = {http://www.scirp.org/journal/PaperInformation.aspx?PaperID=20173},
	doi = {10.4236/as.2012.34056},
	abstract = {This study investigates phosphorus (P) concentrations and fluxes in tile drains, overland flow, and streamflow at a high temporal resolution during 7 spring storms in anagricultural watershed in Indiana, USA. Research goals include a better understanding of 1) how bulk precipitation and antecedent moisture conditions affect P concentrations and fluxes at the watershed scale; 2) how P concentrations and fluxes measured in tile drains translate to the whole watershed scale; 3) whether P losses to the stream are significantly affected by overland flow. Results indicate that bulk precipitation and antecedent moisture conditions are not good predictors of SRP or TP losses (either concentration or flux) to the stream. However, along with previously published storm data in this watershed, results indicate a threshold-based behavior whereby SRP and TP fluxes significantly increase with precipitation when bulk precipitation exceeds 4 cm. Although total SRP and TP fluxes are very much driven by flow, SRP and TP fluxes are somewhat limited by the amount of P available for leaching for most storms. On average, SRP fluxes in tile drains are 13\% greater than in the stream, and stream SRP fluxes account for 45\% of TP fluxes at the watershed scale. Our results indicate that when P is the primary concern, best management practices aimed at reducing P losses via tile drains are likely to have the most effect on P exports at the watershed scale.},
	language = {en},
	urldate = {2020-03-11},
	author = {Vidon, Philippe and Hubbard, Hilary and Cuadra, Pilar and Hennessy, Matthew},
	month = jul,
	year = {2012},
	note = {Publisher: Scientific Research Publishing},
}

@article{sharpley_phosphorus_2008,
	title = {Phosphorus {Loss} from an {Agricultural} {Watershed} as a {Function} of {Storm} {Size}},
	volume = {37},
	issn = {1537-2537},
	url = {http://dl.sciencesocieties.org/publications/jeq/abstracts/37/2/362},
	doi = {10.2134/jeq2007.0366},
	language = {en},
	number = {2},
	urldate = {2020-03-11},
	journal = {Journal of Environmental Quality},
	author = {Sharpley, Andrew N. and Kleinman, Peter J. A. and Heathwaite, A. Louise and Gburek, William J. and Folmar, Gordon J. and Schmidt, John P.},
	month = mar,
	year = {2008},
	note = {Publisher: American Society of Agronomy, Crop Science Society of America, Soil Science Society},
	pages = {362--368},
}

@article{outram_antecedent_2016,
	title = {Antecedent conditions, hydrological connectivity and anthropogenic inputs: {Factors} affecting nitrate and phosphorus transfers to agricultural headwater streams},
	volume = {545-546},
	issn = {0048-9697},
	shorttitle = {Antecedent conditions, hydrological connectivity and anthropogenic inputs},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969715311827},
	doi = {10.1016/j.scitotenv.2015.12.025},
	abstract = {This paper examines relationships between rainfall–runoff, catchment connectivity, antecedent moisture conditions and fertiliser application with nitrate-N and total phosphorus (TP) fluxes in an arable headwater catchment over three hydrological years (2012–2014). Annual precipitation totals did not vary substantially between years, yet the timing of rainfall strongly influenced runoff generation and subsequent nitrate-N and TP fluxes. The greatest nitrate-N ({\textgreater}250kgNday−1) and TP ({\textgreater}10kgTPday−1) fluxes only occurred when shallow groundwater was within 0.6m of the ground surface and runoff coefficients were greater than 0.1. These thresholds were reached less frequently in 2012 due to drought recovery resulting in lower annual nitrate-N (7.4kgNha−1) and TP (0.12kgPha−1) fluxes in comparison with 2013 (15.1kgNha−1; 0.21kgPha−1). The wet winter of 2013 with elevated shallow groundwater levels led to more frequent activation of sub-surface pathways and tile drain flow. Throughout the period, dry antecedent conditions had a temporary effect in elevating TP loads. Evidence of TP source exhaustion after consecutive storm events can be attributed to the repeated depletion of temporarily connected critical source areas to the river network via impermeable road surfaces. Fertiliser application varied considerably across three years due to differences in crop rotation between farms, with annual N and P fertiliser inputs varying by up to 21\% and 41\%, respectively. Proportional reductions in annual riverine nitrate-N and TP loadings were not observed at the sub-catchment outlet as loadings were largely influenced by annual runoff. Nitrate loadings were slightly higher during fertiliser application, but there was little relationship between P fertiliser application and riverine TP load. These data indicate that this intensive arable catchment may be in a state of biogeochemical stationarity, whereby legacy stores of nutrients buffer against changes in contemporary nutrient inputs.},
	language = {en},
	urldate = {2020-03-11},
	journal = {Science of The Total Environment},
	author = {Outram, Faye N. and Cooper, Richard J. and Sünnenberg, Gisela and Hiscock, Kevin M. and Lovett, Andrew A.},
	month = mar,
	year = {2016},
	keywords = {Antecedent, Arable, Catchment, Fertiliser, Nitrate, Pathways, Total phosphorus},
	pages = {184--199},
}

@article{sadeghi_non-point_2017,
	title = {Non-point source contribution and dynamics of soluble and particulate phosphorus from main tributaries of the {Zarivar} {Lake} watershed, {Iran}},
	volume = {189},
	issn = {1573-2959},
	url = {10.1007/s10661-017-5937-z},
	doi = {10.1007/s10661-017-5937-z},
	abstract = {The temporal variability of phosphorus (P) transport and the relationships between discharge, suspended sediment concentration and particulate (PP), and soluble (SP) phosphorus were examined. The study was conducted at the event scale in seven tributaries of the Zarivar Lake watershed in Kurdistan Province (Iran) from March 2011 to April 2012. Based on eight runoff events, 82\% of the total P was the PP carried out by suspended sediment. Results showed a high variability of P transport during different runoff events. It was found that soil erosion was the source of the high P load. For all tributaries, PP was linearly related to both discharge and suspended sediment concentration. However, the relationships of SP and PP with discharge and suspended sediment concentration showed different hysteresis patterns. The relationship between PP and discharge was generally characterized by a clockwise pattern (i.e., lower part contribution of the sub-watersheds) but the patterns between SP and discharge were mainly anticlockwise (i.e., upper part contribution of the sub-watersheds or perhaps due to a subsurface flow contribution).},
	language = {en},
	number = {5},
	urldate = {2020-03-11},
	journal = {Environmental Monitoring and Assessment},
	author = {Sadeghi, Seyed Hamidreza and Ebrahimi Mohammadi, Shirko and Singh, Vijay P. and Chapi, Kamran},
	month = apr,
	year = {2017},
	pages = {238},
}

@article{moatar_elemental_2017,
	title = {Elemental properties, hydrology, and biology interact to shape concentration-discharge curves for carbon, nutrients, sediment, and major ions},
	volume = {53},
	copyright = {© 2017. The Authors.},
	issn = {1944-7973},
	url = {http://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2016WR019635},
	doi = {10.1002/2016WR019635},
	abstract = {To investigate the prevalence and cause of concentration-discharge (C-Q) relationships for carbon, nutrients, major ions, and particulates, we analyzed 40 years of water quality data from 293 monitoring stations in France. Catchments drained diverse landscapes and ranged from 50 to 110,000 km2, together covering nearly half of France. To test for differences during low and high flows, we calculated independent C-Q slopes above and below the median discharge. We found that 84\% of all catchment-element combinations were chemodynamic for at least half of the hydrograph and 60\% of combinations showed nonlinear C-Q curves. Only two or three of the nine possible C-Q modalities were manifest for each parameter, and these modalities were stable through time, suggesting that intrinsic and extrinsic elemental properties (e.g., solubility, reactivity, and source dynamics) set basic C-Q templates for each parameter, which are secondarily influenced by biological activity during low flows, and the interaction between hydrology and catchment characteristics at high flows. Several patterns challenged current C-Q views, including low-flow chemostasis for TSS in 66\% of catchments, low-flow biological mediation of in 71\% of catchments, and positive C-Q for dissolved organic carbon independent of catchment size in 80\% of catchments. Efforts to reduce nutrient loading decreased phosphorus concentration and altered C-Q curves, but continued to increase. While C-Q segmentation requires more data than a single analysis, the prevalence of nonlinear C-Q slopes demonstrates the potential information loss associated with linear or monotonic analysis of C-Q relationships, and conversely, the value of long-term monitoring.},
	language = {en},
	number = {2},
	urldate = {2020-03-11},
	journal = {Water Resources Research},
	author = {Moatar, F. and Abbott, B. W. and Minaudo, C. and Curie, F. and Pinay, G.},
	year = {2017},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/2016WR019635},
	keywords = {catchment, chemodynamic, chemostatic, source limitation, transport limitation, water quality},
	pages = {1270--1287},
}

@article{house_hysteresis_1998,
	title = {Hysteresis of the solute concentration/discharge relationship in rivers during storms},
	volume = {32},
	issn = {0043-1354},
	url = {http://www.sciencedirect.com/science/article/pii/S0043135497004739},
	doi = {10.1016/S0043-1354(97)00473-9},
	abstract = {Hysteresis of dissolved calcium, silicon, nitrate, nitrite, ammonium and phosphorus fractions, i.e. soluble reactive phosphorus, total dissolved phosphorus and total phosphorus, in river waters during a major storm event in the R. Swale catchment in Yorkshire (U.K.), are quantified using a semi-empirical model. The model separates point and base-flow contributions of the chemical determinants from diffuse inputs. The magnitude of the diffuse inputs is related to river water discharge so that the size and rotation of the hysteresis loop is characterized by a single parameter. The approach is applied to chemical and water discharge data collected at 2h intervals from three river sites in the catchment over a complete storm hydrograph. The results illustrate hysteresis effects for all the determinants with the majority showing “clockwise” hysteresis, i.e. higher concentrations during the rising limb of the hydrograph compared with those measured during the falling limb. The model parameters, computed by optimizing agreement between the predicted and measured concentration–discharge relationships, are generally consistent with land-use patterns in the catchment. The method has potential for further development to enable comparisons of chemical and nutrient dynamics in river catchments and the assessment of the relative importance of diffuse and point sources during high flow conditions.},
	language = {en},
	number = {8},
	urldate = {2020-03-11},
	journal = {Water Research},
	author = {House, William A. and Warwick, Melanie S.},
	month = aug,
	year = {1998},
	keywords = {ammonium, calcium, diffuse inputs, hysteresis, nitrate, nitrite, nutrients, phosphorus, point inputs, rivers, silicon, storms},
	pages = {2279--2290},
}

@article{bender_phosphorus_2018,
	title = {Phosphorus dynamics during storm events in a subtropical rural catchment in southern {Brazil}},
	volume = {261},
	issn = {0167-8809},
	url = {http://www.sciencedirect.com/science/article/pii/S0167880918301464},
	doi = {10.1016/j.agee.2018.04.004},
	abstract = {The intensification of agricultural activities increases the transfer of phosphorus (P) to surface water bodies causing a wide range of environmental, social and economic problems, such as eutrophication. This paper describes the dynamics of P loss during rainfall events (intra-event) and between events (inter-event) in a rural catchment with intensive soil use in southern Brazil, emphasizing the relationships of the solutes with the hydrosedimentological variables. The information on the magnitude and the pattern of P transport was obtained during eighth significant rainfall events, in addition to the sampling performed during the baseflow period (between events). During the events, we evaluated the transfer dynamics of the total P (TP), dissolved P (DP), particulate P (PP) and suspended sediment concentration (SSC). Phosphorus (dissolved and particulate) is predominantly lost during events. The concentrations of DP and PP were low in samples collected in the period between events, when groundwater flow predominates. There is predominance of subsurface flow for the total volume of DP drained into the catchment. The hysteresis of TP forms a loop in the counterclockwise direction at the moment the soil is exposed by plowing, due to P transfer from the cropland to the water course. The transfer of P occurred predominantly in the particulate form (88\%) due to the high affinity of P with mineral colloids. There was predominance of clockwise hysteresis for TP and SSC during the fallow period and at the beginning of soil mobilization, indicating the presence of P and sediment sources closer to the catchment outlet. However, during the development period of the crop, when the soil was more exposed due to plowing, counterclockwise hysteresis was observed for TP, which indicates a predominance of sources farther from the outlet, such as the cropland. Thus, we believe that efforts towards adopting practices that reduce erosion can contribute to a reduction of P transfer to water sources. Consequently controlling the process of eutrophication.},
	language = {en},
	urldate = {2020-03-11},
	journal = {Agriculture, Ecosystems \& Environment},
	author = {Bender, Marcos Antonio and dos Santos, Danilo Rheinheimer and Tiecher, Tales and Minella, Jean Paolo Gomes and de Barros, Cláudia Alessandra Peixoto and Ramon, Rafael},
	month = jul,
	year = {2018},
	keywords = {Catchment, Rainfall, Runoff, Sediment and phosphorus loss, Soil erosion},
	pages = {93--102},
}

@article{williams_sediment_1989,
	title = {Sediment concentration versus water discharge during single hydrologic events in rivers},
	volume = {111},
	issn = {0022-1694},
	url = {http://www.sciencedirect.com/science/article/pii/0022169489902540},
	doi = {10.1016/0022-1694(89)90254-0},
	abstract = {Relations between sediment concentration (C) and water discharge (Q) for a hydrologic event, such as a flood, are studied qualitatively by analyzing “smoothed” temporal graphs (discharge and concentration vs. time) in terms of mode, spread, and skewness. Comparing CQ ratios at a given discharge on the rising and falling limbs of the discharge hydrograph provides a consistent, reliable method for categorizing C–Q relations. Five common classes of such relations are single-valued (straight or curved), clockwise loop, counterclockwise loop, single-valued plus a loop, and figure eight. Temporal-graph mode and skewness influence the type of relation, whereas temporal-graph spread affects the details of the particular C–Q relation (its graphical breadth, shape, orientation, and plotted location). Field examples of the various types of relations are given, including varieties that heretofore have received little attention, such as the figure eight. Explanations for each type of C–Q relation are discussed.},
	language = {en},
	number = {1},
	urldate = {2020-03-11},
	journal = {Journal of Hydrology},
	author = {Williams, Garnett P.},
	month = jan,
	year = {1989},
	pages = {89--106},
}

@article{bowes_phosphorusdischarge_2005,
	title = {Phosphorus–discharge hysteresis during storm events along a river catchment: the {River} {Swale}, {UK}},
	volume = {39},
	issn = {0043-1354},
	shorttitle = {Phosphorus–discharge hysteresis during storm events along a river catchment},
	url = {http://www.sciencedirect.com/science/article/pii/S0043135404005688},
	doi = {10.1016/j.watres.2004.11.027},
	abstract = {Variations in the concentration of determinands in rivers during storms often result in a hysteresis effect with different concentration during the rising and falling limb of the hydrograph. This is investigated here by measuring total phosphorus, particulate phosphorus and soluble reactive phosphorus at 3-h intervals at three points along the River Swale. Phosphorus concentration–discharge hysteresis from 10 storm events were quantified using an empirical model. The size and direction of the hysteresis loops were described by a response factor, and the slope of the loop quantified by a gradient constant. The modelled loops produced acceptable agreement with the field measurements. Hysteresis patterns for all phosphorus fractions changed markedly downstream, with predominantly anticlockwise trajectories in the upland moors (indicating a slow diffuse phosphorus delivery to the river) and clockwise in the intensively farmed lowland (indicating mobilisation of within-channel and riverbank phosphorus, and rapid inputs from field drains). The size of the hysteresis loops increased downstream, indicating an increased capacity for phosphorus storage and mobilisation within the lower catchment. During a succession of storms, lowland hysteresis loops decreased in magnitude, tending towards anticlockwise behaviour, indicating a depletion of mobile phosphorus from the river channel and margins. The modelling of hysteresis trajectories offers a convenient method of determining the relative contributions of diffuse and within-channel phosphorus sources.},
	language = {en},
	number = {5},
	urldate = {2020-03-11},
	journal = {Water Research},
	author = {Bowes, Michael J. and House, William A. and Hodgkinson, Robin A. and Leach, David V.},
	month = mar,
	year = {2005},
	keywords = {Diffuse inputs, Hysteresis, Nutrients, Phosphorus, Rivers, Storms},
	pages = {751--762},
}

@article{vaughan_high-frequency_2017,
	title = {High-frequency dissolved organic carbon and nitrate measurements reveal differences in storm hysteresis and loading in relation to land cover and seasonality},
	volume = {53},
	copyright = {© 2017. The Authors.},
	issn = {1944-7973},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2017WR020491},
	doi = {10.1002/2017WR020491},
	abstract = {Storm events dominate riverine loads of dissolved organic carbon (DOC) and nitrate and are expected to increase in frequency and intensity in many regions due to climate change. We deployed three high-frequency (15 min) in situ absorbance spectrophotometers to monitor DOC and nitrate concentration for 126 storms in three watersheds with agricultural, urban, and forested land use/land cover. We examined intrastorm hysteresis and the influences of seasonality, storm size, and dominant land use/land cover on storm DOC and nitrate loads. DOC hysteresis was generally anticlockwise at all sites, indicating distal and plentiful sources for all three streams despite varied DOC character and sources. Nitrate hysteresis was generally clockwise for urban and forested sites, but anticlockwise for the agricultural site, indicating an exhaustible, proximal source of nitrate in the urban and forested sites, and more distal and plentiful sources of nitrate in the agricultural site. The agricultural site had significantly higher storm nitrate yield per water yield and higher storm DOC yield per water yield than the urban or forested sites. Seasonal effects were important for storm nitrate yield in all three watersheds and farm management practices likely caused complex interactions with seasonality at the agricultural site. Hysteresis indices did not improve predictions of storm nitrate yields at any site. We discuss key lessons from using high-frequency in situ optical sensors.},
	language = {en},
	number = {7},
	urldate = {2020-03-09},
	journal = {Water Resources Research},
	author = {Vaughan, M. C. H. and Bowden, W. B. and Shanley, J. B. and Vermilyea, A. and Sleeper, R. and Gold, A. J. and Pradhanang, S. M. and Inamdar, S. P. and Levia, D. F. and Andres, A. S. and Birgand, F. and Schroth, A. W.},
	year = {2017},
	note = {\_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1002/2017WR020491},
	keywords = {DOC, high-frequency sensors, hysteresis, land use/land cover, nitrate},
	pages = {5345--5363},
}

@article{lloyd_using_2016,
	title = {Using hysteresis analysis of high-resolution water quality monitoring data, including uncertainty, to infer controls on nutrient and sediment transfer in catchments},
	volume = {543},
	issn = {0048-9697},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969715310093},
	doi = {10.1016/j.scitotenv.2015.11.028},
	abstract = {A large proportion of nutrients and sediment is mobilised in catchments during storm events. Therefore understanding a catchment's hydrological behaviour during storms and how this acts to mobilise and transport nutrients and sediment to nearby watercourses is extremely important for effective catchment management. The expansion of available in-situ sensors is allowing a wider range of water quality parameters to be monitored and at higher temporal resolution, meaning that the investigation of hydrochemical behaviours during storms is increasingly feasible. Studying the relationship between discharge and water quality parameters in storm events can provide a valuable research tool to infer the likely source areas and flow pathways contributing to nutrient and sediment transport. Therefore, this paper uses 2years of high temporal resolution (15/30min) discharge and water quality (nitrate-N, total phosphorus (TP) and turbidity) data to examine hysteretic behaviour during storm events in two contrasting catchments, in the Hampshire Avon catchment, UK. This paper provides one of the first examples of a study which comprehensively examines storm behaviours for up to 76 storm events and three water quality parameters. It also examines the observational uncertainties using a non-parametric approach. A range of metrics was used, such as loop direction, loop area and a hysteresis index (HI) to characterise and quantify the storm behaviour. With two years of high resolution information it was possible to see how transport mechanisms varied between parameters and through time. This study has also clearly shown the different transport regimes operating between a groundwater dominated chalk catchment versus a surface-water dominated clay catchment. This information, set within an uncertainty framework, means that confidence can be derived that the patterns and relationships thus identified are statistically robust. These insights can thus be used to provide information regarding transport processes and biogeochemical processing within river catchments.},
	language = {en},
	urldate = {2020-03-09},
	journal = {Science of The Total Environment},
	author = {Lloyd, C. E. M. and Freer, J. E. and Johnes, P. J. and Collins, A. L.},
	month = feb,
	year = {2016},
	keywords = {Catchment processes, Nutrient transport, Rivers, Storm behaviour, Turbidity, Uncertainty},
	pages = {388--404},
}

@misc{noauthor_storm_nodate,
	title = {Storm phosphorus concentrations and fluxes in artificially drained landscapes of the {US} {Midwest}},
	url = {https://www.scirp.org/html/4-3000280_20173.htm},
	urldate = {2020-03-08},
}

@misc{noauthor_spatial_nodate,
	title = {Spatial contributions of diffuse inputs and within-channel processes to the form of stream water phosphorus over storm events - {ScienceDirect}},
	url = {https://www-sciencedirect-com.proxy.library.nd.edu/science/article/pii/S0022169407006361},
	urldate = {2020-03-08},
}

@misc{noauthor_journal_nodate,
	title = {Journal of {Environmental} {Quality} {Abstract} - {Landscape} and {Watershed} {Processes} {Phosphorus} {Loss} from an {Agricultural} {Watershed} as a {Function} of {Storm} {Size} {\textbar} {Digital} {Library}},
	url = {https://dl-sciencesocieties-org.proxy.library.nd.edu/publications/jeq/abstracts/37/2/362},
	urldate = {2020-03-08},
}

@misc{noauthor_phosphorus_nodate,
	title = {Phosphorus export during storm events from a human perturbed watershed, southeast {China}: {Implications} for coastal ecology - {ScienceDirect}},
	url = {https://www-sciencedirect-com.proxy.library.nd.edu/science/article/pii/S0272771415001018},
	urldate = {2020-03-08},
}

@article{rahutomo_inorganic_2018,
	title = {Inorganic and {Organic} {Phosphorus} in {Sediments} in the {Walnut} {Creek} {Watershed} of {Central} {Iowa}, {USA}},
	volume = {229},
	issn = {1573-2932},
	url = {10.1007/s11270-018-3721-5},
	doi = {10.1007/s11270-018-3721-5},
	abstract = {The dynamics of phosphorus (P) reactions in stream water are important because of their potential to trigger eutrophication. This study aimed to explore the nature of P in sediments associated with Walnut Creek, Jasper County, Iowa. The Walnut Creek watershed supports row crop production, grazing, and riparian buffer zones. The alluvial cross section is composed of a sequence of sediments that contribute differentially to the amounts and forms of P entering the stream. Twenty-five sediment samples collected near Walnut Creek (classified as bank, in-stream, and floodplain deposits) were sequentially extracted for P. Across all 25 samples, the inorganic P (Pi) fractions followed the order Fe-bound Pi {\textgreater} Ca-bound Pi {\textgreater} reductant-soluble Pi {\textgreater} Al-bound Pi {\textgreater} soluble and loosely bound Pi. For the organic (Po) fractions, the order was nonlabile Po {\textgreater} fulvic acid-bound Po {\textgreater} humic acid-bound Po {\textgreater} labile Po {\textgreater} moderately labile Po. The ranges of total P (TP), Mehlich-3-extractable P (P-M3), and ammonium oxalate-extractable P (Pox) were 386 to 1134, 5 to 85, and 60 to 823 mg kg−1, respectively. Among the sample groups, the highest concentrations of TP, P-M3, and Pox were measured in in-stream deposits. Total P was significantly correlated with Fe oxides, clay, and soil organic matter, especially in the bank and floodplain deposits. Because of the potential release of P from these sediments, we can speculate that changes in land use within the riparian areas may, at least initially, have little direct effect on soluble or particulate P loads in Walnut Creek.},
	language = {en},
	number = {3},
	urldate = {2020-03-07},
	journal = {Water, Air, \& Soil Pollution},
	author = {Rahutomo, Suroso and Kovar, John L. and Thompson, Michael L.},
	month = feb,
	year = {2018},
	pages = {72},
}

@article{rahutomo_phosphorus_2019,
	title = {Phosphorus transformations in stream bank sediments in {Iowa}, {USA}, at varying redox potentials},
	volume = {19},
	issn = {1614-7480},
	url = {10.1007/s11368-018-2139-4},
	doi = {10.1007/s11368-018-2139-4},
	abstract = {Stream bank erosion is one of the main sources of suspended sediments in stream water, and it often carries phosphorus with it. With a controlled laboratory study, we investigated the changes in different forms of P in stream bank sediments at varying redox potentials. We hypothesized that there could be increases in labile forms of solid-phase P under low redox conditions.},
	language = {en},
	number = {2},
	urldate = {2020-03-07},
	journal = {Journal of Soils and Sediments},
	author = {Rahutomo, Suroso and Kovar, John L. and Thompson, Michael L.},
	month = feb,
	year = {2019},
	pages = {1029--1039},
}

@article{simpson_phosphorus_2019,
	title = {Phosphorus attenuation in streams by water-column geochemistry and benthic sediment reactive iron},
	issn = {1726-4170},
	url = {https://www.biogeosciences-discuss.net/bg-2019-400/},
	doi = {10.5194/bg-2019-400},
	abstract = {{\textless}p{\textgreater}{\textless}strong{\textgreater}Abstract.{\textless}/strong{\textgreater} Streams can attenuate inputs of phosphorus (P) and, therefore the likelihood of ecosystem eutrophication. This attenuation is, however, poorly understood, particularly in reference to the geochemical mechanisms involved. In our study, we measured P attenuation mechanisms in the form of (1) mineral (co-)precipitation from the water-column and (2) P sorption with benthic sediments. We hypothesized that both mechanisms would vary with catchment geology and, further, that P sorption would depend on reactive Fe content in sediments. We sampled 31 streams at baseflow conditions, covering a gradient of P inputs (via land use), hydrological characteristics, and catchment geologies. Geochemical equilibria in the water-column were measured and benthic sediments ({\textless}\&thinsp;2\&thinsp;mm) were analyzed for sorption properties and P and iron (Fe) fractions. Neither P-containing minerals (e.g., hydroxylapatite) nor calcite-phosphate co-precipitation had the potential to occur. In contrast, in-stream dissolved reactive P (DRP) correlated with labile sediment P (water-soluble and easily reduced Fe-P), but only for streams where hyporheic exchange between the water-column and the coarse sediment porewaters was likely sufficient. The non-labile P fractions contained most of sediment P (generally {\textgreater}\&thinsp;90\&thinsp;\%) and varied with parent geology. Similarly, most sediment Fe was in a recalcitrant form (generally {\textgreater}\&thinsp;90\&ndash;95\&thinsp;\%). However, despite its small contribution to total sediment Fe, the pool of surface-reactive Fe was a strong predictor for sediment P sorption potential. Our results suggest that, in these streams, it is the combination of biogeochemical Fe and P cycles and the exchange with the hyporheic zone that attenuates DRP in baseflow. Such combinations are likely to vary spatiotemporally within a catchment and must be considered alongside inputs of P and sediment if the P concentrations at baseflow \&ndash; and eutrophication risk \&ndash; are to be well managed.{\textless}/p{\textgreater}},
	language = {English},
	urldate = {2020-03-07},
	journal = {Biogeosciences Discussions},
	author = {Simpson, Zachary P. and McDowell, Richard W. and Condron, Leo M.},
	month = oct,
	year = {2019},
	note = {Publisher: Copernicus GmbH},
	pages = {1--35},
}

@article{audette_speciation_2018-1,
	title = {Speciation of {Phosphorus} from {Agricultural} {Muck} {Soils} to {Stream} and {Lake} {Sediments}},
	volume = {47},
	issn = {0047-2425},
	url = {http://dl.sciencesocieties.org/publications/jeq/abstracts/47/4/884},
	doi = {10.2134/jeq2018.02.0068},
	language = {en},
	number = {4},
	urldate = {2020-03-07},
	journal = {Journal of Environmental Quality},
	author = {Audette, Yuki and O’Halloran, Ivan P. and Nowell, Peter M. and Dyer, Richard and Kelly, Ross and Voroney, R. Paul},
	year = {2018},
	note = {Publisher: The American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.},
	pages = {884--892},
}

@article{reid_components_2018,
	title = {Components of {Phosphorus} {Loss} {From} {Agricultural} {Landscapes}, and {How} to {Incorporate} {Them} {Into} {Risk} {Assessment} {Tools}},
	volume = {6},
	issn = {2296-6463},
	url = {https://www.frontiersin.org/articles/10.3389/feart.2018.00135/full},
	doi = {10.3389/feart.2018.00135},
	abstract = {Phosphorus (P) loss to surface freshwater is a key driver of environmental degradation, including blooms of both harmful (e.g. microcystis) and nuisance (e.g. cladophora) algae, along with the development of hypoxic zones that could significantly impact fish habitat . Mitigating P losses from agricultural land will require a detailed understanding of the forms (particulate versus dissolved), sources (soil erosion, desorption of soil P, dissolved P from fertilizer or manure application, or release from frozen vegetation) and transport pathways (surface runoff, or subsurface runoff through tile drains). This paper describes each of these components in detail, and discusses how this can guide the adoption of appropriate beneficial management practices to effectively reduce P losses. Further, it describes how this component structure has been incorporated into the Canadian national Indicator of Risk of Water Contamination by Phosphorus (IROWC-P) as an example of a risk assessment tool.},
	language = {English},
	urldate = {2020-03-07},
	journal = {Frontiers in Earth Science},
	author = {Reid, Keith and Schneider, Kimberly and McConkey, Brian},
	year = {2018},
	note = {Publisher: Frontiers},
	keywords = {Component P Index, Nutrient loss, P source, P transport, Phosphorus, risk assessment tools},
}

@article{rosenberg_coupling_2017,
	title = {Coupling of reactive riverine phosphorus and iron species during hot transport moments: impacts of land cover and seasonality},
	volume = {132},
	issn = {1573-515X},
	shorttitle = {Coupling of reactive riverine phosphorus and iron species during hot transport moments},
	url = {10.1007/s10533-016-0290-9},
	doi = {10.1007/s10533-016-0290-9},
	abstract = {Spring runoff often comprises the majority of annual discharge and riverine phosphorus (P) export due to sustained high flow, and the magnitude of spring runoff can be a strong predictor of receiving water summer harmful algal bloom severity. Yet the loading of reactive forms of P during this time period remains poorly-characterized in time, space and geochemical partitioning. Here, we explore the hypothesis that riverine dissolved and suspended sediment P loads during spring runoff have a particularly high proportion of potentially reactive species due to unique hydrologic pathways and P association with iron (Fe).The concentration, distribution and temporal dynamics of dissolved P (DP), dissolved and colloidal Fe, and redox sensitive suspended sediment P (RSP) and Fe during spring runoff and summer storms were compared in forested and agricultural catchments of the same watershed. The dominant carrier of RSP was Fe (oxy)hydroxides across land cover and season, but Fe (oxy)hydroxide particles and colloids in agricultural catchments were strongly enriched in RSP and DP during spring runoff and summer storms, particularly at the onset of snowmelt. In 2014, 83\% of DP and 74\% of RSP were delivered to Missisquoi Bay during spring runoff. Suspended sediment was significantly more redox sensitive than typically input to limnological models, suggesting that the reactivity of this load may be systematically underestimated. Changes in the timing, provenance and severity of spring runoff associated with climate or land cover change will have dramatic impacts on total riverine P loads and their potential reactivity in receiving water ecosystems.},
	language = {en},
	number = {1},
	urldate = {2020-03-07},
	journal = {Biogeochemistry},
	author = {Rosenberg, Braden D. and Schroth, Andrew W.},
	month = jan,
	year = {2017},
	pages = {103--122},
}

@article{sharpley_transport_1992,
	title = {The {Transport} of {Bioavailable} {Phosphorus} in {Agricultural} {Runoff}},
	volume = {21},
	copyright = {© 1992 American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America},
	issn = {1537-2537},
	url = {https://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/jeq1992.00472425002100010003x},
	doi = {10.2134/jeq1992.00472425002100010003x},
	abstract = {Bioavailable P (BAP) in agricultural runoff represents P potentially available for algal uptake and consists of soluble P (SP) and a variable portion of participate P (PP). Evaluation of the impact of agricultural management on BAP in runoff will aid assessment of the resultant biological productivity of receiving water bodies. Soluble P, PP, and bioavailable PP (BPP) (estimated by NaOH extraction) were determined over a 5-yr period in runoff from 20 unfertilized and fertilized, grassed, and cropped watersheds in the Southern Plains. Soluble P, BPP, and BAP loss in runoff was reduced by practices minimizing erosion and runoff, with respective mean annual amounts ranging from 237 to 122, 1559 to 54, and 1796 to 176 g P ha−1 yr−1 (for peanut-sorghum [Arachis hypogaea L.-Sorghum bicolor (L.) Moench] and native grass watersheds, respectively). However, as vegetative cover improved, BAP (SP plus BPP) comprised a larger portion of total P (TP) loss (29\% for peanut-sorghum and 88\% for native grass). This results from an increasing contribution to BAP of SP (13\% for peanut-sorghum and 69\% for native grass watersheds) and BPP to PP (26\% for peanut-sorghum and 69\% for native grass watersheds). Clearly, P bioavailability is a dynamic function of physiochemical processes controlling erosion, particle size enrichment, P desorption-dissolution reactions, and plant residue breakdown, in addition to soil and fertilizer P management. Hence, the change in trophic state of a water body may not be adequately reflected by TP inputs only. To more reliably evaluate the biological response of a water body to agricultural P inputs, particularly from conservation tillage practices, it may be necessary to determine BAP in runoff.},
	language = {en},
	number = {1},
	urldate = {2020-03-07},
	journal = {Journal of Environmental Quality},
	author = {Sharpley, Andrew N. and Smith, S. J. and Jones, O. R. and Berg, W. A. and Coleman, G. A.},
	year = {1992},
	note = {\_eprint: https://acsess.onlinelibrary.wiley.com/doi/pdf/10.2134/jeq1992.00472425002100010003x},
	pages = {30--35},
}

@article{logan_phosphate_1979,
	title = {Phosphate {Characteristics} and {Bioavailability} of {Suspended} {Sediments} from {Streams} {Draining} into {Lake} {Erie}},
	volume = {5},
	issn = {0380-1330},
	url = {http://www.sciencedirect.com/science/article/pii/S0380133079721368},
	doi = {10.1016/S0380-1330(79)72136-8},
	abstract = {Suspended sediments from major U.S. tributaries draining into Lake Erie were analyzed for phosphorus. Analyses included: sediment concentration, reactive and total filtered P, and total P on water samples. Recovered sediment total P was determined by perchloric and persulfate extraction. Sediment was fractionated for NaOH-P citrate-dithionite-bicarbonate (CDB)-P, HCl-P, and organic P. New York streams had the highest suspended solids and the lowest content of most sediment fractions except HCl-P. NaOH-P and CDB-P were highest in sediments from Ohio tributaries; these fractions are considered to be bioavailable with NaOH-P more available than CDB-P. Digestion with perchloric acid consistently removed more P than the persulfate method. The difference in the two methods was negatively correlated with HCl-P.},
	language = {en},
	number = {2},
	urldate = {2020-03-07},
	journal = {Journal of Great Lakes Research},
	author = {Logan, Terry J. and Oloya, Tom O. and Yaksich, Steve M.},
	month = jan,
	year = {1979},
	pages = {112--123},
}

@article{baker_phosphorus_2014,
	title = {Phosphorus loading to {Lake} {Erie} from the {Maumee}, {Sandusky} and {Cuyahoga} rivers: {The} importance of bioavailability},
	volume = {40},
	issn = {0380-1330},
	shorttitle = {Phosphorus loading to {Lake} {Erie} from the {Maumee}, {Sandusky} and {Cuyahoga} rivers},
	url = {http://www.sciencedirect.com/science/article/pii/S0380133014001178},
	doi = {10.1016/j.jglr.2014.05.001},
	abstract = {Lake Erie has undergone re-eutrophication beginning in the 1990s, even though total phosphorus (TP) loads to the lake continued to slowly decline. Using our 1982 and 2007–10 studies of the bioavailability of dissolved and particulate phosphorus export from major Ohio tributaries, together with our long-term TP and dissolved reactive phosphorus (DRP) loading data, we estimated long-term annual export of dissolved and particulate bioavailable phosphorus. DRP was found to adequately represent dissolved bioavailable export while 26–30\% of the particulate phosphorus (PP) was extractable by 0.1N NaOH, a frequently used indicator of PP bioavailability. During the period of re-eutrophication (1991–2012), DRP export from nonpoint sources in the Maumee and Sandusky rivers increased dramatically while NaOH-PP export had a slight decline for the Maumee and a small increase in the Sandusky. For the Cuyahoga River, both DRP and NaOH-PP increased, but these changes were small in relation to those of the Maumee and Sandusky. During this period, whole lake loading of both non-point and point sources of phosphorus declined. This study indicates that increased nonpoint loading of DRP is an important contributing factor to re-eutrophication. Although nonpoint control programs in the Maumee and Sandusky have been effective in reducing erosion and PP export, these programs have been accompanied by increased DRP export. Future target loads for Lake Erie should focus on reducing bioavailable phosphorus, especially DRP from nonpoint sources. Agricultural P load reduction programs should address both DRP and PP, and take into account the lower bioavailability of PP.},
	language = {en},
	number = {3},
	urldate = {2020-03-07},
	journal = {Journal of Great Lakes Research},
	author = {Baker, D. B. and Confesor, R. and Ewing, D. E. and Johnson, L. T. and Kramer, J. W. and Merryfield, B. J.},
	month = sep,
	year = {2014},
	keywords = {Bioavailable phosphorus, Dissolved phosphorus, Lake Erie re-eutrophication, Nonpoint sources, Particulate phosphorus, Point sources},
	pages = {502--517},
}

@article{pierson_phosphorus_2001,
	title = {Phosphorus and {Ammonium} {Concentrations} in {Surface} {Runoff} from {Grasslands} {Fertilized} with {Broiler} {Litter}},
	volume = {30},
	issn = {1537-2537},
	url = {http://dl.sciencesocieties.org/publications/jeq/abstracts/30/5/1784},
	doi = {10.2134/jeq2001.3051784x},
	language = {en},
	number = {5},
	urldate = {2020-03-07},
	journal = {Journal of Environmental Quality},
	author = {Pierson, S. T. and Cabrera, M. L. and Evanylo, G. K. and Kuykendall, H. A. and Hoveland, C. S. and McCann, M. A. and West, L. T.},
	month = sep,
	year = {2001},
	note = {Publisher: American Society of Agronomy, Crop Science Society of America, Soil Science Society},
	pages = {1784--1789},
}

@article{saleem_loss_2018,
	title = {Loss of phosphorus by runoff from soils after amendment with poultry litter co-composted with crop waste},
	volume = {7},
	issn = {2251-7715},
	url = {10.1007/s40093-018-0207-9},
	doi = {10.1007/s40093-018-0207-9},
	abstract = {The study aimed to assess the influence of poultry litter (PL) after co-composting with sugarcane and cabbage waste on phosphorus (P) losses in runoff from soils under natural rainfall conditions.},
	language = {en},
	number = {3},
	urldate = {2020-03-07},
	journal = {International Journal of Recycling of Organic Waste in Agriculture},
	author = {Saleem, Asma and Irshad, Muhammad and Ping, An and Haroon, Bushra},
	month = sep,
	year = {2018},
	pages = {211--215},
}

@article{sharpley_rainfall_1997,
	title = {Rainfall {Frequency} and {Nitrogen} and {Phosphorus} {Runoff} from {Soil} {Amended} with {Poultry} {Litter}},
	volume = {26},
	issn = {0047-2425},
	url = {http://dl.sciencesocieties.org/publications/jeq/abstracts/26/4/JEQ0260041127},
	doi = {10.2134/jeq1997.00472425002600040026x},
	language = {en},
	number = {4},
	urldate = {2020-03-07},
	journal = {Journal of Environmental Quality},
	author = {Sharpley, Andrew N.},
	year = {1997},
	note = {Publisher: American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America},
	pages = {1127--1132},
}

@article{sauer_runoff_2000,
	title = {Runoff {Water} {Quality} from {Poultry} {Litter}-{Treated} {Pasture} and {Forest} {Sites}},
	volume = {29},
	issn = {0047-2425},
	url = {http://dl.sciencesocieties.org/publications/jeq/abstracts/29/2/JEQ0290020515},
	doi = {10.2134/jeq2000.00472425002900020020x},
	language = {en},
	number = {2},
	urldate = {2020-03-07},
	journal = {Journal of Environmental Quality},
	author = {Sauer, T. J. and Daniel, T. C. and Nichols, D. J. and West, C. P. and Moore, P. A. and Wheeler, G. L.},
	year = {2000},
	note = {Publisher: American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America},
	pages = {515--521},
}

@article{sauer_poultry_1999,
	title = {Poultry {Litter} and {Grazing} {Animal} {Waste} {Effects} on {Runoff} {Water} {Quality}},
	volume = {28},
	copyright = {© 1999 American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America},
	issn = {1537-2537},
	url = {https://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/jeq1999.00472425002800030017x},
	doi = {10.2134/jeq1999.00472425002800030017x},
	abstract = {In complex landscapes with multiple land uses, it is often difficult to identify the source of contaminant loadings. The objective of this study was to compare nutrient runoff as affected by grazing animal depositions vs. poultry litter application. Simulated rainfall was applied twice to 1.5 by 6.0 m runoff plots of tall fescue (Festuca arundinacea Schreb.) with treatments of no waste (CT), dairy calf feces and urine (DFU), poultry litter (PL), and dairy calf feces and urine with poultry litter (DFU + PL). Chemical properties of the runoff samples including pH, electrical conductivity (EC), C, soluble reactive phosphorus (SRP), total nitrogen (TN), NH4-N, NO3-N, K, Mg, S, B, Cu, Fe, Mn, Mo, Na, and Zn were determined. Plots receiving poultry litter had significantly greater losses of most nutrient parameters for both rainfall simulations. For the nutrient parameters of primary interest with regard to water quality, 5.0, 29.5, and 21.9\% of the TN, NH4-N, and SRP applied in the PL treatment were transported in runoff during the first rainfall simulation as compared to 3.9, 5.0, and 15.3\%, respectively, for the DFU treatment. Comparable percentages of the applied nutrients were lost from the PL and DFU treatments even though the PL treatment, with the exception of NH4-N, provided at least six times the amount of each nutrient. A severe rainfall event shortly after poultry litter application produces significantly greater nutrient losses as compared to similar application of grazing animal depositions at the rates used in the experiment.},
	language = {en},
	number = {3},
	urldate = {2020-03-07},
	journal = {Journal of Environmental Quality},
	author = {Sauer, T. J. and Daniel, T. C. and Moore, P. A. and Coffey, K. P. and Nichols, D. J. and West, C. P.},
	year = {1999},
	note = {\_eprint: https://acsess.onlinelibrary.wiley.com/doi/pdf/10.2134/jeq1999.00472425002800030017x},
	pages = {860--865},
}

@article{shigaki_nitrogen_2009,
	title = {Nitrogen {Fate} in {Drainage} {Ditches} of the {Coastal} {Plain} after {Dredging}},
	volume = {38},
	issn = {1537-2537},
	url = {https://dl.sciencesocieties.org/publications/jeq/articles/38/6/2449#ref-29},
	doi = {10.2134/jeq2008.0268},
	language = {en},
	number = {6},
	urldate = {2020-03-06},
	journal = {Journal of Environmental Quality},
	author = {Shigaki, Francirose and Schmidt, John P. and Kleinman, Peter J. A. and Sharpley, Andrew N. and Allen, Arthur L.},
	month = nov,
	year = {2009},
	note = {Publisher: American Society of Agronomy, Crop Science Society of America, Soil Science Society},
	pages = {2449--2457},
}

@article{smith_assessing_2010,
	title = {Assessing {Nutrient} {Transport} {Following} {Dredging} of {Agricultural} {Drainage} {Ditches}},
	volume = {53},
	issn = {2151-0040},
	url = {http://elibrary.asabe.org/abstract.asp??JID=3&AID=29583&CID=t2010&v=53&i=2&T=1},
	doi = {10.13031/2013.29583},
	abstract = {Agricultural drainage ditches are vital for many agricultural landscapes in the U.S. Previous research has indicated that dredging agricultural drainage ditches may degrade water quality. In this study, we monitored nutrient transport in two drainage ditches for six years (2003‐2008), during which two dredging activities occurred. Ditch reach nutrient loads were calculated on a monthly and annual basis for the two ditches, as hydrology and water chemistry were monitored daily during the growing season. When dredging activities occurred within the previous 12 months, reach loads were significantly reduced for all nutrients monitored, with net losses in the dredged reaches of NH4‐N (-94 kg), soluble P (SP; -6.6 kg), and total P (TP; -5.4 kg). When examining annual reach loads, the nutrient losses from recently dredged reaches were generally significantly lower than the other reaches during the same year. The apparent improvements in water chemistry seem to be contrary to earlier reports of potentially degraded water quality immediately after dredging. We attribute this to: (1) oxidation of reduced sediments, (2) deposition of “fresh” sediments, (3) recolonization by filamentous algae and higher plants, and (4) formation of biofilms on the exposed sediments. To avoid the detrimental impacts on water quality immediately after dredging, and to maximize the benefit of ditch recovery, we propose that ditch managers work with agricultural producers to delay nutrient applications to adjacent fields for at least one month after dredging activities. This should allow the ditches sufficient time to recover their ecological function following dredging.},
	language = {en},
	number = {2},
	urldate = {2020-03-06},
	journal = {Transactions of the ASABE},
	author = {Smith, D. R. and Huang, C.},
	year = {2010},
	pages = {429--436},
}

@article{macrae_phosphate_2003,
	title = {Phosphate retention in an agricultural stream using experimental additions of phosphate},
	volume = {17},
	copyright = {Copyright © 2003 John Wiley \& Sons, Ltd.},
	issn = {1099-1085},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/hyp.1356},
	doi = {10.1002/hyp.1356},
	abstract = {In-stream experiments involving additions of phosphate were conducted to determine the soluble reactive phosphorus (SRP) retention potential of a perennial first-order stream that drains a 2·7 km2 agricultural catchment in southern Ontario. SRP retention was determined in relation to highly elevated SRP concentrations under low flow conditions. Point source treatments of phosphate were added to three reaches of this stream during two time periods when baseline SRP concentrations were notably different (early summer and early autumn). The reaches selected varied with respect to streambed shape and gradient, direction of groundwater flow, and channel vegetation type and density. One of the three experimental stream reaches was dredged between the two sampling periods, so that all vegetation and the top 25 cm of sediments were removed. SRP retention in the stream ranged from 0·8 to 24·1 µg m−2 s−1. Dredging the stream sediments did not alter the ability of the stream to remove SRP from the water column. SRP retention over the experimental reaches was generally 5–10\% of the elevated concentration (0·7–4·2 mg l−1, a factor of 8–53 above pre-experiment conditions), although low-flow conditions in the stream were conducive to retention by stream sediments. Copyright © 2003 John Wiley \& Sons, Ltd.},
	language = {en},
	number = {18},
	urldate = {2020-03-06},
	journal = {Hydrological Processes},
	author = {Macrae, M. L. and English, M. C. and Schiff, S. L. and Stone, M. A.},
	year = {2003},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/hyp.1356},
	keywords = {agriculture, experimental point source additions, phosphorus, retention, streams},
	pages = {3649--3663},
}

@article{entrekin_rapid_2011,
	title = {Rapid expansion of natural gas development poses a threat to surface waters},
	volume = {9},
	copyright = {© The Ecological Society of America},
	issn = {1540-9309},
	url = {http://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/110053},
	doi = {10.1890/110053},
	abstract = {Extraction of natural gas from hard-to-reach reservoirs has expanded around the world and poses multiple environmental threats to surface waters. Improved drilling and extraction technology used to access low permeability natural gas requires millions of liters of water and a suite of chemicals that may be toxic to aquatic biota. There is growing concern among the scientific community and the general public that rapid and extensive natural gas development in the US could lead to degradation of natural resources. Gas wells are often close to surface waters that could be impacted by elevated sediment runoff from pipelines and roads, alteration of streamflow as a result of water extraction, and contamination from introduced chemicals or the resulting wastewater. However, the data required to fully understand these potential threats are currently lacking. Scientists therefore need to study the changes in ecosystem structure and function caused by natural gas extraction and to use such data to inform sound environmental policy.},
	language = {en},
	number = {9},
	urldate = {2020-03-06},
	journal = {Frontiers in Ecology and the Environment},
	author = {Entrekin, Sally and Evans-White, Michelle and Johnson, Brent and Hagenbuch, Elisabeth},
	year = {2011},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1890/110053},
	pages = {503--511},
}

@article{cooke_stream_1998,
	title = {Stream phosphorus and nitrogen export from agricultural and forested watersheds on the {Boreal} {Plain}},
	volume = {55},
	abstract = {We evaluated phosphorus (P) and inorganic nitrogen (IN) export from two agricultural and two forested watersheds on the nutrient-rich but relief-poor Boreal Plain. One agricultural stream was in a watershed that contained cropland, while the second consisted of mixed agricultural activities. Over the 2-year study, total dissolved phosphorus (TDP) concentrations were proportionately high, particularly in the agricultural streams. Flow-weighted TDP averaged 82\% of the total phosphorus (TP) in the agricultural streams and 43\% in the forested streams. In all watersheds, TDP was almost exclusively dissolved reactive phosphorus and most of the annual P export was in summer. The type of agricultural activity in the watershed influenced IN speciation; in the mixed agricultural watershed, 94\% of IN export was ammonium, whereas 98\% of IN load was nitrate from the cropland watershed. Disproportionately high TDP to TP export from agricultural watersheds suggests that, in areas of low relief and relatively high soil water P content, land clearing may influence dissolved more than particulate phosphorus export.},
	language = {en},
	author = {Cooke, Sandra E and Prepas, Ellie E},
	year = {1998},
	pages = {8},
}

@article{vidon_changes_2008,
	title = {Changes in the character of {DOC} in streams during storms in two {Midwestern} watersheds with contrasting land uses},
	volume = {88},
	issn = {1573-515X},
	url = {10.1007/s10533-008-9207-6},
	doi = {10.1007/s10533-008-9207-6},
	abstract = {Dissolved organic carbon (DOC) dynamics in streams is important, yet few studies focus on DOC dynamics in Midwestern streams during storms. In this study, stream DOC dynamics during storms in two Midwestern watersheds with contrasting land uses, the change in character of stream DOC during storms, and the usability of DOC as a hydrologic tracer in artificially drained landscapes of the Midwest are investigated. Major cation/DOC concentrations, and DOC specific UV absorbance (SUVA) and fluorescence index (FI) were monitored at 2–4 h intervals during three spring storms. Although DOC is less aromatic in the mixed land use watershed than in the agricultural watershed, land use has little impact on stream DOC concentration during storms. For both watersheds, DOC concentration follows discharge, and SUVA and FI values indicate an increase in stream DOC aromaticity and lignin content during storms. The comparison of DOC/major cation flushing dynamics indicates that DOC is mainly exported via overland flow/macropore flow. In both watersheds, the increase in DOC concentration in the streams during storms corresponds to a shift in the source of DOC from DOC originating from mineral soil layers of the soil profile at baseflow, to DOC originating from surficial soil layers richer in aromatic substances and lignin during storms. Results also suggest that DOC, SUVA and FI could be used as hydrologic tracers in artificially drained landscapes of the Midwest. These results underscore the importance of sampling streams for DOC during high flow periods in order to understand the fate of DOC in streams.},
	language = {en},
	number = {3},
	urldate = {2020-03-05},
	journal = {Biogeochemistry},
	author = {Vidon, Philippe and Wagner, Laura E. and Soyeux, Emmanuel},
	month = may,
	year = {2008},
	pages = {257--270},
}

@article{hood_changes_2006,
	title = {Changes in the character of stream water dissolved organic carbon during flushing in three small watersheds, {Oregon}},
	volume = {111},
	copyright = {Copyright 2006 by the American Geophysical Union.},
	issn = {2156-2202},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2005JG000082},
	doi = {10.1029/2005JG000082},
	abstract = {The hydrologic and biogeochemical responses of forested watersheds to inputs of rainfall and snowmelt can be an indicator of internal watershed function. In this study, we assess how the quantity and quality, both chemical and spectroscopic, of stream water DOC changes in response to a 6-day storm event during the wet season of 2003 in three small ({\textless}1 km2) basins in the H. J. Andrews Experimental Forest, Oregon. The watersheds included one old-growth watershed (WS02) and two previously logged watersheds (WS01 and WS10). Prestorm concentrations of DOC ranged from 1.5 to 2.2 mg C L−1 in the three watersheds and increased approximately threefold on the ascending limb of the storm hydrograph. Concentrations of DOC were both highest in the unharvested, old-growth watershed. The specific UV absorbance (SUVA, 254 nm) of DOC in the three watersheds increased by 9 to 36\% during the storm, suggesting that DOC mobilized from catchment soils during storms is more aromatic than DOC entering the stream during baseflow. The increase in SUVA was most pronounced in the previously harvested catchments. Chromatographic fractionation of DOC showed that the percentage of DOC composed of non-humic material decreasing by 9 to 22\% during the storm. Shifts in the fluorescence properties of DOC suggest that there was not a pronounced change in the relative proportion of stream water DOC derived from allochthonous versus autochthonous precursor material. Taken together, these results suggest that spectroscopic and chemical characterization of DOC can be used as tools to investigate changing sources of DOC and water within forested watersheds.},
	language = {en},
	number = {G1},
	urldate = {2020-03-05},
	journal = {Journal of Geophysical Research: Biogeosciences},
	author = {Hood, Eran and Gooseff, Michael N. and Johnson, Sherri L.},
	year = {2006},
	note = {\_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2005JG000082},
	keywords = {dissolved organic carbon, flushing, storm response},
}

@article{roley_pore_2016,
	title = {Pore water physicochemical constraints on the endangered clubshell mussel ({Pleurobema} clava)},
	volume = {73},
	issn = {0706-652X},
	url = {https://www.nrcresearchpress.com/doi/abs/10.1139/cjfas-2015-0442},
	doi = {10.1139/cjfas-2015-0442},
	abstract = {Freshwater mussels are in decline worldwide, but it remains challenging to link specific stressors to mussel declines. The clubshell mussel (Pleurobema clava) is a federally endangered species that..., Si les moules d’eau douce sont en déclin à l’échelle mondiale, établir un lien entre des facteurs de stress précis et le déclin des moules demeure difficile. La moule Pleurobema clava, qui figure s...},
	number = {12},
	urldate = {2020-03-04},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Roley, Sarah S. and Tank, Jennifer L.},
	month = may,
	year = {2016},
	note = {Publisher: NRC Research Press},
	pages = {1712--1722},
}

@article{karl_phosphorus_2000,
	title = {Phosphorus, the staff of life},
	volume = {406},
	copyright = {2000 Macmillan Magazines Ltd.},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/35017683},
	doi = {10.1038/35017683},
	abstract = {Studies of lakes in North America reveal that concentrations of phosphate, an essential nutrient for aquatic microorganisms, are 100-1,000 times lower than estimated with conventional techniques. Among the implications are the possible need to rethink nutrient dynamics in both freshwater and marine ecosystems..},
	language = {en},
	number = {6791},
	urldate = {2020-03-04},
	journal = {Nature},
	author = {Karl, David M.},
	month = jul,
	year = {2000},
	note = {Number: 6791
Publisher: Nature Publishing Group},
	pages = {31--33},
}

@article{cembella_utilization_1982,
	title = {The {Utilization} of {Inorganic} and {Organic} {Phosphorous} {Compounds} as {Nutrients} by {Eukaryotic} {Microalgae}: {A} {Multidisciplinary} {Perspective}: {Part} {I}},
	volume = {10},
	issn = {0045-6454},
	shorttitle = {The {Utilization} of {Inorganic} and {Organic} {Phosphorous} {Compounds} as {Nutrients} by {Eukaryotic} {Microalgae}},
	url = {10.3109/10408418209113567},
	doi = {10.3109/10408418209113567},
	number = {4},
	urldate = {2020-03-04},
	journal = {CRC Critical Reviews in Microbiology},
	author = {Cembella, Allan D. and Antia, Naval J. and Harrison, Paul J.},
	month = jan,
	year = {1982},
	note = {Publisher: Taylor \& Francis
\_eprint: 10.3109/10408418209113567},
	pages = {317--391},
}

@article{depinto_algal-available_1981,
	title = {Algal-{Available} {Phosphorus} in {Suspended} {Sediments} from {Lower} {Great} {Lakes} {Tributaries}},
	volume = {7},
	issn = {0380-1330},
	url = {http://www.sciencedirect.com/science/article/pii/S0380133081720598},
	doi = {10.1016/S0380-1330(81)72059-8},
	abstract = {Suspended sediments collected from five tributaries to the lower Great Lakes were chemically analyzed for several forms of phosphorus and bioassayed under aerobic conditions to measure the release of algal-available phosphorus. The bioassay data for all samples, interpreted through a first-order model of available phosphorus release, showed an average of 21.8 percent of the total paniculate phosphorus ultimately was available to Selenastrum capricornutum, and available phosphorus was released at an average rate of 0.154 day−1. Amounts of available phosphorus varied considerably between tributaries with the Ohio tributaries (Maumee, Sandusky, and Cuyahoga Rivers) showing generally greater amounts than those in New York (Cattaraugus and Genesee Rivers). Non-apatite fractions of inorganic phosphorus (base-, and reductant-extractable) correlated well with levels of available phosphorus in the suspended sediment samples; however, the first-order release coefficients showed little dependency on the paniculate phosphorus characteristics. The results indicate that prediction of phosphorus dynamics in the lower Great Lakes may be made with greater accuracy than current models allow by considering available phosphorus to be released from an ultimately-available fraction of the total paniculate phosphorus during residence in the water column.},
	language = {en},
	number = {3},
	urldate = {2020-03-04},
	journal = {Journal of Great Lakes Research},
	author = {DePinto, Joseph V. and Young, Thomas C. and Martin, Scott C.},
	month = jan,
	year = {1981},
	pages = {311--325},
}

@article{pionke_phosphorus_1992,
	title = {{PHOSPHORUS} {STATUS} {AND} {CONTENT} {OF} {SUSPENDED} {SEDIMENT} {IN} {A} {PENNSYLVANIA} {WATERSHED}},
	volume = {153},
	issn = {0038-075X},
	url = {https://journals.lww.com/soilsci/abstract/1992/06000/phosphorus_status_and_content_of_suspended.4.aspx},
	abstract = {The phosphorus (P) concentrations of suspended sediments determined by extraction with Cl resin (resin P), 0.1 N NaOH (NaOH P), and HClO4 (total sediment P), and from P desorption isotherms (intercept P) are presented and compared. The sediment concentrations representing 56 stormflows, sampled from two Pennsylvania agricultural watersheds over 4 years, were low and variable. Resin P and NaOH P constituted 9 and 38\% of the total sediment P, respectively. Intercept P was highly correlated (r = 0.70) and closely estimated resin P, an index of readily desorbable labile and plant-available P. Both resin P (r = 0.75) and intercept P (r = 0.90) were highly correlated with the Equilibrium Phosphorus Concentration (EPC) but were consistently about 100 times more concentrated. NaOH P, an index of algal available P on sediment, was highly correlated with resin P (r = 0.73) and total sediment P (r = 0.87). Export of labile P (resin P plus total soluble P) in stormflow from both watersheds was mostly as soluble P (62–78\%) and thus was controlled more by water than sediment export. Soluble P losses in total stream outflow (storm plus nonstorm) accounted for 50\% of the algal-available P exported and about 30\% of the total P exported from the 7.4 km2 watershed, suggesting that a P loss control strategy based only on erosion control would not be effective in these types of watersheds. About 42\% of total sediment P and 57\% of the total P exported from the 7.4 km2 watershed was estimated to be algal available.
        © Williams \& Wilkins 1992. All Rights Reserved.},
	language = {en-US},
	number = {6},
	urldate = {2020-03-04},
	journal = {Soil Science},
	author = {Pionke, H. B. and Kunishi, H. M.},
	month = jun,
	year = {1992},
	pages = {452--462},
}

@article{yang_qpcr_2018,
	title = {A {qPCR} method to quantify bioavailable phosphorus using indigenous aquatic species},
	volume = {30},
	issn = {2190-4715},
	url = {10.1186/s12302-018-0163-z},
	doi = {10.1186/s12302-018-0163-z},
	abstract = {Bioavailable phosphorus (BAP) represents the sum of phosphorus that is readily available for algae growth and is useful to indicate the severity of eutrophication in aquatic environments.},
	language = {en},
	number = {1},
	urldate = {2020-03-04},
	journal = {Environmental Sciences Europe},
	author = {Yang, Yanan and Yang, Jianghua and Zhang, Xiaowei},
	month = sep,
	year = {2018},
	pages = {32},
}

@article{hudson_phosphate_2000,
	title = {Phosphate concentrations in lakes},
	volume = {406},
	copyright = {2000 Macmillan Magazines Ltd.},
	issn = {1476-4687},
	url = {http://www.nature.com/articles/35017531},
	doi = {10.1038/35017531},
	abstract = {Phosphate is an important nutrient that restricts microbial production in many freshwater1,2,3 and marine environments4,5,6. The actual concentration of phosphate in phosphorus-limited waters is largely unknown because commonly used chemical and radiochemical techniques overestimate the concentration7,8. Here, using a new steady-state radiobioassay to survey a diverse set of lakes, we report phosphate concentrations in lakes that are orders of magnitude lower than estimates made spectrophotometrically or with the frequently used Rigler radiobioassay. Our results, combined with those from the literature, indicate that microbes can achieve rapid turnover rates at picomolar nutrient concentrations. This occurs even though these concentrations are about two orders of magnitude below the level where phosphate uptake is estimated to be half the saturation level for the picoplankton community. Also, while phosphate concentration increased with the concentration of total phosphorus and soluble reactive phosphorus in the lakes we sampled, the proportion of phosphate in the total phosphorus pool decreased from oligotrophic to eutrophic lakes. Such information, as revealed by the phosphate assay that we use here, should allow us to address hypotheses concerning the concentration of phosphate available to planktonic microorganisms in aquatic systems.},
	language = {en},
	number = {6791},
	urldate = {2020-03-04},
	journal = {Nature},
	author = {Hudson, Jeff J. and Taylor, William D. and Schindler, David W.},
	month = jul,
	year = {2000},
	note = {Number: 6791
Publisher: Nature Publishing Group},
	pages = {54--56},
}

@article{smith_assessing_2010-1,
	title = {Assessing {Nutrient} {Transport} {Following} {Dredging} of {Agricultural} {Drainage} {Ditches}},
	volume = {53},
	issn = {2151-0040},
	url = {http://elibrary.asabe.org/abstract.asp??JID=3&AID=29583&CID=t2010&v=53&i=2&T=1},
	doi = {10.13031/2013.29583},
	language = {en},
	number = {2},
	urldate = {2020-03-04},
	journal = {Transactions of the ASABE},
	author = {Smith, D.R. and Huang, C.},
	year = {2010},
	pages = {429--436},
}

@article{smith_sediment_2005,
	title = {Sediment phosphorus dynamics for three tile fed drainage ditches in {Northeast} {Indiana}},
	volume = {71},
	issn = {0378-3774},
	url = {http://www.sciencedirect.com/science/article/pii/S0378377404001842},
	doi = {10.1016/j.agwat.2004.07.006},
	abstract = {Phosphorus (P) losses from agricultural lands degrade surface waters due to anthropogenic eutrophication. Previous studies focused on plot-to-field scale P loss and reductions from best management practices (BMP's), little information in intense agricultural catchments has been gathered on the dynamics influencing P beyond the edge of the field. This study was conducted to examine the phosphorus equilibrium between the water column and sediments in three tile fed drainage ditches in Northeast Indiana. Surface water and sediment samples were collected and analyzed for organic carbon (C), particle size and P from sites along three ditches with similar soils and land use at sites within each watershed draining approximately 300 and 1500ha on each ditch. Organic C, silt and clay fractions of the bottom sediments decreased with increasing drainage area. Soluble P concentrations were low in Ditch A, but increased with increasing drainage area (0.02–0.05mg PL−1). Overall, the P concentrations were higher in the Ditches B and C (0.06–0.09mg PL−1). Exchangeable P, P partitioning index and equilibrium P concentrations (EPCo) decreased with increasing drainage area by as much as 95, 93 and 100\%, respectively, except in one catchment area with a confined animal feeding operation between sampling points, where ExP and EPCo increased by 4 and 116\%, respectively. Aluminum sulfate and calcium carbonate treatment of ditch sediments reduced exchangeable P and sediment EPCo in this study. Results from this study indicated some watershed characteristics, as well as sediment physiochemical properties, affect ditch sediment and water P equilibrium and buffering capacity. Furthermore, this study demonstrated that managers could potentially use chemical treatment of the ditches to increase the temporary retention of P in ditches and maybe reducing sediment P availability.},
	language = {en},
	number = {1},
	urldate = {2020-03-04},
	journal = {Agricultural Water Management},
	author = {Smith, D. R. and Haggard, B. E. and Warnemuende, E. A. and Huang, C.},
	month = jan,
	year = {2005},
	keywords = {Alum, Ditch sediments, EPC, Land use, Phosphorus},
	pages = {19--32},
}

@article{smith_sediment_2005-1,
	title = {Sediment phosphorus dynamics for three tile fed drainage ditches in {Northeast} {Indiana}},
	volume = {71},
	issn = {0378-3774},
	url = {http://www.sciencedirect.com/science/article/pii/S0378377404001842},
	doi = {10.1016/j.agwat.2004.07.006},
	abstract = {Phosphorus (P) losses from agricultural lands degrade surface waters due to anthropogenic eutrophication. Previous studies focused on plot-to-field scale P loss and reductions from best management practices (BMP's), little information in intense agricultural catchments has been gathered on the dynamics influencing P beyond the edge of the field. This study was conducted to examine the phosphorus equilibrium between the water column and sediments in three tile fed drainage ditches in Northeast Indiana. Surface water and sediment samples were collected and analyzed for organic carbon (C), particle size and P from sites along three ditches with similar soils and land use at sites within each watershed draining approximately 300 and 1500ha on each ditch. Organic C, silt and clay fractions of the bottom sediments decreased with increasing drainage area. Soluble P concentrations were low in Ditch A, but increased with increasing drainage area (0.02–0.05mg PL−1). Overall, the P concentrations were higher in the Ditches B and C (0.06–0.09mg PL−1). Exchangeable P, P partitioning index and equilibrium P concentrations (EPCo) decreased with increasing drainage area by as much as 95, 93 and 100\%, respectively, except in one catchment area with a confined animal feeding operation between sampling points, where ExP and EPCo increased by 4 and 116\%, respectively. Aluminum sulfate and calcium carbonate treatment of ditch sediments reduced exchangeable P and sediment EPCo in this study. Results from this study indicated some watershed characteristics, as well as sediment physiochemical properties, affect ditch sediment and water P equilibrium and buffering capacity. Furthermore, this study demonstrated that managers could potentially use chemical treatment of the ditches to increase the temporary retention of P in ditches and maybe reducing sediment P availability.},
	language = {en},
	number = {1},
	urldate = {2020-03-04},
	journal = {Agricultural Water Management},
	author = {Smith, D. R. and Haggard, B. E. and Warnemuende, E. A. and Huang, C.},
	month = jan,
	year = {2005},
	keywords = {Alum, Ditch sediments, EPC, Land use, Phosphorus},
	pages = {19--32},
}

@article{royer_timing_2006,
	title = {Timing of {Riverine} {Export} of {Nitrate} and {Phosphorus} from {Agricultural} {Watersheds} in {Illinois}:  {Implications} for {Reducing} {Nutrient} {Loading} to the {Mississippi} {River}},
	volume = {40},
	issn = {0013-936X},
	shorttitle = {Timing of {Riverine} {Export} of {Nitrate} and {Phosphorus} from {Agricultural} {Watersheds} in {Illinois}},
	url = {10.1021/es052573n},
	doi = {10.1021/es052573n},
	abstract = {Agricultural watersheds in the upper Midwest are the major source of nutrients to the Mississippi River and Gulf of Mexico, but temporal patterns in nutrient export and the role of hydrology in controlling export remain unclear. Here we report on NO3-−N, dissolved reactive phosphorus (DRP), and total P export from three watersheds in Illinois during the past 8−12 years. Our program of intensive, long-term monitoring allowed us to assess how nutrient export was distributed across the range of discharge that occurred at each site and to examine mechanistic differences between NO3-−N and DRP export from the watersheds. Last, we used simple simulations to evaluate how nutrient load reductions might affect NO3-−N and P export to the Mississippi River from the Illinois watersheds. Artificial drainage through under-field tiles was the primary mechanism for NO3-−N export from the watersheds. Tile drainage and overland flow contributed to DRP export, whereas export of particulate P was almost exclusively from overland flow. The analyses revealed that nearly all nutrient export occurred when discharge was ≥ median discharge, and extreme discharges (≥ 90th percentile) were responsible for {\textgreater}50\% of the NO3-−N export and {\textgreater}80\% of the P export. Additionally, the export occurred annually during a period beginning in mid-January and continuing through June. These patterns characterized all sites, which spanned a 4-fold range in watershed area. The simulations showed that reducing in-stream nutrient loads by as much as 50\% during periods of low discharge would not affect annual nutrient export from the watersheds.},
	number = {13},
	urldate = {2020-03-04},
	journal = {Environmental Science \& Technology},
	author = {Royer, Todd V. and David, Mark B. and Gentry, Lowell E.},
	month = jul,
	year = {2006},
	note = {Publisher: American Chemical Society},
	pages = {4126--4131},
}

@article{ren_algal_2017,
	title = {Algal growth and utilization of phosphorus studied by combined mono-culture and co-culture experiments},
	volume = {220},
	issn = {0269-7491},
	url = {http://www.sciencedirect.com/science/article/pii/S0269749116313744},
	doi = {10.1016/j.envpol.2016.09.061},
	abstract = {Phosphorus (P) plays a critical role in algal growth; therefore, a better understanding of P availability is essential to control harmful algal blooms. Three algae species, Microcystis aeruginosa, Chlorella pyrenoidosa, and Pseudokirchneriella subcapitata, were mono-cultured and co-cultured on three types of P substrates, dissolved inorganic P (DIP), phosphomonoesters glucose-6-phosphate (G-6-P) and β-glycerol phosphate (β-glycerol-P), and phosphonate (glyphosate), to explore their growth and P utilization. All three species could utilize dissolved organic P (DOP) to sustain their growth, whereas DIP was their preferred P substrate in both culture types. Algae could regulate the P uptake capacity under different P conditions, and the added P could be rapidly accumulated at the beginning of the culture and slowly utilized during the subsequent life cycle. M. aeruginosa exhibited wider P selectivity and could utilize all three P substrates, whereas the other two species could only use phosphomonoester (G-6-P and β-glycerol-P) in the mono-cultures. However, in the co-cultures, the relative bioavailability of DOP for M. aeruginosa and C. pyrenoidosa was enhanced, and M. aeruginosa might contribute to the growth of C. pyrenoidosa and P. subcapitata when fed with glyphosate. The three species showed an intrinsic ability to produce alkaline phosphatase (AP), and AP activity (APA) was regulated by Pi stress. However, high APA did not necessarily lead to high Pi release and algal growth on unfavorable substrates. Although M. aeruginosa was not superior in growth rate in the mono-cultures, it showed a better P accumulation ability and maintained stable growth on different P substrates. Moreover, it was a good competitor, suppressing the thriving growth of the other species in co-cultures. Overall, the findings indicated the strategic flexibility of P utilization by algae and the strong competitive ability of M. aeruginosa in Pi-limited and DOP-enriched natural waters.},
	language = {en},
	urldate = {2020-03-04},
	journal = {Environmental Pollution},
	author = {Ren, Lingxiao and Wang, Peifang and Wang, Chao and Chen, Juan and Hou, Jun and Qian, Jin},
	month = jan,
	year = {2017},
	keywords = {Alkaline phosphatase activity, Dissolved organic phosphorus, Phosphonates, Phosphorus, Phosphorus cycling},
	pages = {274--285},
}

@article{depinto_experimental_1982,
	title = {An experimental apparatus for evaluating kinetics of available phosphorus release from aquatic particulates},
	volume = {16},
	issn = {0043-1354},
	url = {http://www.sciencedirect.com/science/article/pii/0043135482900434},
	doi = {10.1016/0043-1354(82)90043-4},
	abstract = {An experimental apparatus, referred to herein as a Dual Culture Diffusion Apparatus (DCDA), has been developed and operated to permit the extraction of process kinetic data for several types of particle-water interactions. The DCDA is constructed of two culture vessels separated only by a thin membrane filter, thus facilitating the separation of two particulate suspensions while at the same time permitting their interaction by diffusion of dissolved substances through the membrane. This manuscript describes how the apparatus has been calibrated and applied to measure the rate at which available phosphorus is released from various types of particulates suspended in lake water media.},
	language = {en},
	number = {6},
	urldate = {2020-03-04},
	journal = {Water Research},
	author = {DePinto, Joseph V.},
	month = jan,
	year = {1982},
	pages = {1065--1070},
}

@article{shinohara_composition_2018,
	title = {The composition of particulate phosphorus: {A} case study of the {Grand} {River}, {Canada}},
	volume = {44},
	issn = {0380-1330},
	shorttitle = {The composition of particulate phosphorus},
	url = {http://www.sciencedirect.com/science/article/pii/S0380133018300418},
	doi = {10.1016/j.jglr.2018.03.006},
	abstract = {We examined the fractions of particulate phosphorus (PP) in the lower reaches of the Grand River, Canada, to test the hypothesis that the river is a source of both particulate-bound orthophosphate and labile species of PP. At the mouth of the Grand River, the proportion of particulate organic P (POP) was, on average, 57.7\% of total PP, which was significantly higher than the proportion of particulate inorganic P (PIP) in PP. Analysis with 31P nuclear magnetic resonance (NMR) spectroscopy showed that the proportion of P species other than orthophosphate in the NaOH- EDTA extract was 1.75 times greater than that of orthophosphate. Labile P species (e.g. nucleotides and pyrophosphate) were present in the NMR spectrum; whereas, refractory organic P (myo-inositol hexakisphosphate) was absent. These results suggest that during winter and spring, the Grand River supplies primarily bioavailable phosphorus species in organic forms to Lake Erie, rather than inorganic orthophosphate. These results suggest that labile organic P is contained in PP rather than alkaline extractable inorganic P. Future studies should examine POP species in other rivers of the Lake Erie watershed.},
	language = {en},
	number = {3},
	urldate = {2020-03-04},
	journal = {Journal of Great Lakes Research},
	author = {Shinohara, Ryuichiro and Ouellette, Lance and Nowell, Peter and Parsons, Chris T. and Matsuzaki, Shin-ichiro S. and Paul Voroney, R.},
	month = jun,
	year = {2018},
	keywords = {Labile phosphorus, Organic phosphorus, P nuclear magnetic resonance (NMR), Suspended particles},
	pages = {527--534},
}

@article{mohamed_understanding_2019,
	title = {Understanding and managing the re-eutrophication of {Lake} {Erie}: {Knowledge} gaps and research priorities},
	volume = {38},
	issn = {2161-9549},
	shorttitle = {Understanding and managing the re-eutrophication of {Lake} {Erie}},
	url = {http://www.journals.uchicago.edu/doi/abs/10.1086/705915},
	doi = {10.1086/705915},
	abstract = {Eutrophication of freshwaters is already a problem in many regions globally and will probably worsen as human populations grow and consume more resources. The ability of researchers and governments to anticipate, mitigate, and restore eutrophic freshwaters in a cohesive, integrated manner suffers from key uncertainties in our understanding of the watershed-to-lake continuum. Here, we use Lake Erie and its watershed as an example of a system in which there is a pressing need to resolve these uncertainties. In recent history, Lake Erie both suffered and recovered from serious eutrophication and related issues. More recently, however, there has been a resurgence of eutrophication and associated harmful algal blooms in Lake Erie, with symptoms reminiscent of prior eutrophication. This resurgence has led the USA and Canadian governments to commit to substantially reducing P inputs into Lake Erie in an effort to control eutrophication. We illustrate how key uncertainties about Lake Erie and its watershed contribute to challenges we face in restoring this ecosystem and propose avenues for their resolution. To this end, we contend that an ecosystem approach will be required for managing the eutrophication of freshwaters.},
	number = {4},
	urldate = {2020-03-04},
	journal = {Freshwater Science},
	author = {Mohamed, Mohamed N. and Wellen, Christopher and Parsons, Chris T. and Taylor, William D. and Arhonditsis, George and Chomicki, Krista M. and Boyd, Duncan and Weidman, Paul and Mundle, Scott O. C. and Cappellen, Philippe Van and Sharpley, Andrew N. and Haffner, Douglas G.},
	month = dec,
	year = {2019},
	note = {Publisher: The University of Chicago Press},
	pages = {675--691},
}

@inproceedings{bostrom_bioavailability_1988,
	address = {Dordrecht},
	series = {Developments in {Hydrobiology}},
	title = {Bioavailability of {Different} {Phosphorus} {Forms} in {Freshwater} {Systems}},
	isbn = {978-94-009-3109-1},
	doi = {10.1007/978-94-009-3109-1_9},
	abstract = {The recent literature on the bioavailability of different forms of P in freshwater systems is reviewed. Bioavailable P is defined as the sum of immediately available P and the P that can be transformed into an available form by naturally occurring processes. Methods used to estimate the bioavailable P pool, which vary between studies largely depending on the time perspective applied, are critically evaluated. Most studies on particulate P aim to determine the potentially available P pool. Potential bioavailability of particulate P is normally analysed in bioassays with algal yield determinations and the available P fraction is characterized from interpretations of results of sequential chemical extractions. NaOH-extractable P is in most studies the most algal-available P fraction. For soil samples and tributary water particulate matter, NaOH-P has often been found to be equal to algal extractable P. In other studies depletions of NaOH-P have accounted for the algal P uptake, but only a minor proportion of the fraction has been utilized. Organic P in lake water particulate matter and bed sediments of eutrophic lakes can also be algal-available to a significant extent.Studies on the bioavailability of dissolved P have often been concerned with immediate availability, or the minimum amount of available P. Such studies need other types of experimental design and normally assays with radiotracers are used. Immediately available P is frequently found to be less than P chemically assessed as dissolved reactive P (DRP) at low ({\textless} 10 µg DRP • 1- 1) concentrations. However, immediate availability may also approach or exceed DRP concentrations, especially at higher concentrations. Potential bioavailability, assayed as for particulate P, may generally render higher bioavailability than P assayed as immediately available. Large fractions of dissolved P remain unutilized and are primarily found in the high molecular weight fraction of dissolved P.},
	language = {en},
	booktitle = {Phosphorus in {Freshwater} {Ecosystems}},
	publisher = {Springer Netherlands},
	author = {Boström, Bengt and Persson, Gunnar and Broberg, Brita},
	editor = {Persson, Gunnar and Jansson, Mats},
	year = {1988},
	keywords = {32P, bioassay, bioavailability, dissolved, particulate, phosphorus},
	pages = {133--155},
}

@article{li_influence_2013,
	title = {The influence of dissolved phosphorus molecular form on recalcitrance and bioavailability},
	volume = {182},
	issn = {0269-7491},
	url = {http://www.sciencedirect.com/science/article/pii/S0269749113003485},
	doi = {10.1016/j.envpol.2013.06.024},
	abstract = {Several studies have shown Soluble Reactive Phosphorus (SRP) analyses provide a poor index of dissolved phosphorus (P) bioavailability in natural systems. We tested 21 inorganic and organic P containing compounds with series of nutrient uptake and bioavailability bioassay experiments and chemical characterizations. Our results show that in 81\% of cases, these compounds did not fit the classic assumption that SRP approximately equals Bioavailable P (BAP). Many organic compounds were classified as non-reactive, but had very rapid uptake kinetics and were nearly entirely bioavailable (e.g., several nucleic acids, ATP, RNA, DNA and phosphatidylcholine). Several inorganic compounds also classified as non-reactive but had high bioavailability (i.e., sodium tripolyphosphate and phosphorus pentoxide). Conversely, apatite was operationally classified as reactive, but had low bioavailability. Due to their tendency to alias as SRP, but recalcitrance and very low bioavailability, humic-(Al/Fe)-phosphorus complexes may play an especially important role in the dissolved phosphorus dynamics of natural systems.},
	language = {en},
	urldate = {2020-03-04},
	journal = {Environmental Pollution},
	author = {Li, Bo and Brett, Michael T.},
	month = nov,
	year = {2013},
	keywords = {Bioassay, Bioavailability of phosphorus, Humic substances, Phosphorus},
	pages = {37--44},
}

@article{hensley_evaluating_nodate,
	title = {Evaluating spatiotemporal variation in water chemistry of the upper {Colorado} {River} using longitudinal profiling},
	volume = {n/a},
	copyright = {© 2019 John Wiley \& Sons Ltd},
	issn = {1099-1085},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/hyp.13690},
	doi = {10.1002/hyp.13690},
	abstract = {Stream water chemistry is traditionally measured as variation over time at fixed sites, with sparse sites providing a crude understanding of spatial heterogeneity. An alternative Lagrangian reference frame measures changes with respect to both space and time as water travels through a network. Here, we collected sensor-based measurements of water chemistry at high spatial resolution along nearly 500 km of the Upper Colorado River. Our objective was to understand sources of spatiotemporal heterogeneity across different solutes and determine whether longitudinal change manifests as smooth gradients as suggested by the River Continuum Concept (RCC) or as abrupt changes as suggested by the Serial Discontinuity Concept (SDC). Our results demonstrate that Lagrangian sampling integrates spatiotemporal variation, and profiles reflect processes that vary in both space and time and over different scales. Over each day of sampling, water temperature (T) and dissolved oxygen (DO) varied strongly in response to diel solar cycles, with most of the variation driven by sampling time rather than sampling location. Equilibration of T and DO with the atmosphere limited small scale spatial heterogeneity, with variation at the entire profile scale driven by regional climate gradients. As such, T and DO profiles more closely approximated the smooth gradients of the RCC (though including temporal sampling artefacts). Conversely, variation in specific conductance and nitrate (NO3-N) was largely driven by spatial patterns of lateral inflows such as tributaries and groundwater. This resulted in discrete shifts in the profiles at or downstream of discontinuities, appearing as the profiles expected with the SDC. The concatenation of spatiotemporal variation that produces observed Lagrangian profiles presents interpretive challenges but also augments our understanding of where, how, and critically why water chemistry changes in time and space as it moves through river networks.},
	language = {en},
	number = {n/a},
	urldate = {2020-03-03},
	journal = {Hydrological Processes},
	author = {Hensley, Robert T. and Spangler, Margaret J. and DeVito, Lauren F. and Decker, Paul H. and Cohen, Matthew J. and Gooseff, Michael N.},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/hyp.13690},
	keywords = {Colorado River, Lagrangian profiling, continuum, discontinuity, spatiotemporal variation},
}

@article{schilling_orthophosphorus_2017,
	title = {Orthophosphorus {Contributions} to {Total} {Phosphorus} {Concentrations} and {Loads} in {Iowa} {Agricultural} {Watersheds}},
	volume = {46},
	issn = {0047-2425},
	url = {http://dl.sciencesocieties.org/publications/jeq/articles/46/4/828},
	doi = {10.2134/jeq2017.01.0015},
	language = {en},
	number = {4},
	urldate = {2020-03-03},
	journal = {Journal of Environmental Quality},
	author = {Schilling, Keith E. and Kim, Sea-Won and Jones, Christopher S. and Wolter, Calvin F.},
	year = {2017},
	note = {Publisher: The American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.},
	pages = {828--835},
}

@article{dijkstra_determination_2020,
	title = {Determination of bioavailable phosphorus in water samples using bioassay methods},
	issn = {2215-0161},
	url = {http://www.sciencedirect.com/science/article/pii/S2215016120300273},
	doi = {10.1016/j.mex.2020.100807},
	abstract = {The total phosphorus analyte (TP) has a long history of use in monitoring and regulatory applications relating to management of cultural eutrophication in freshwaters. It has become apparent, however, that the fraction of the TP analyte ultimately available to support algal growth varies significantly spatially (within a system), seasonally, and among systems. The algal bioassay methods described here provide an approach for determining the bioavailable fraction of the three operationally-defined components of TP: soluble reactive phosphorus (SRP), dissolved organic phosphorus (DOP), and particulate phosphorus (PP) in effluents and tributaries discharging to lakes and reservoirs. Application of the technique facilitates a quantitative ranking and targeting of bioavailable phosphorus sources for management.•One congruent method to fractionate particulate and soluble phosphorus (found in aquatic samples) into bioavailable and unavailable fractions was developed based on compilation, adaptation and expansion of two methods from the late 70’s and early 80’s.•Detailed description of steps are laid out including the development of phosphorus starved algal cultures, sub-sampling schedules, kinetics determination and data presentation.•Reproducibility is successfully demonstrated by replication and closure of a mass balance on phosphorus},
	language = {en},
	urldate = {2020-03-03},
	journal = {MethodsX},
	author = {Dijkstra, Marcel L. and Auer, Martin T. and Kuczynski, Anika and Lambert, Renn},
	month = feb,
	year = {2020},
	keywords = {Bioassay, Bioavailable phosphorus, Limiting nutrient},
	pages = {100807},
}

@article{li_relationship_2015,
	title = {The relationship between operational and bioavailable phosphorus fractions in effluents from advanced nutrient removal systems},
	volume = {12},
	issn = {1735-1472, 1735-2630},
	url = {http://link.springer.com/10.1007/s13762-015-0760-y},
	doi = {10.1007/s13762-015-0760-y},
	language = {en},
	number = {10},
	urldate = {2020-03-02},
	journal = {International Journal of Environmental Science and Technology},
	author = {Li, B. and Brett, M. T.},
	month = oct,
	year = {2015},
	pages = {3317--3328},
}

@article{paerl_it_2016,
	title = {It {Takes} {Two} to {Tango}: {When} and {Where} {Dual} {Nutrient} ({N} \& {P}) {Reductions} {Are} {Needed} to {Protect} {Lakes} and {Downstream} {Ecosystems}},
	volume = {50},
	issn = {0013-936X},
	shorttitle = {It {Takes} {Two} to {Tango}},
	url = {10.1021/acs.est.6b02575},
	doi = {10.1021/acs.est.6b02575},
	abstract = {Preventing harmful algal blooms (HABs) is needed to protect lakes and downstream ecosystems. Traditionally, reducing phosphorus (P) inputs was the prescribed solution for lakes, based on the assumption that P universally limits HAB formation. Reduction of P inputs has decreased HABs in many lakes, but was not successful in others. Thus, the “P-only” paradigm is overgeneralized. Whole-lake experiments indicate that HABs are often stimulated more by combined P and nitrogen (N) enrichment rather than N or P alone, indicating that the dynamics of both nutrients are important for HAB control. The changing paradigm from P-only to consideration of dual nutrient control is supported by studies indicating that (1) biological N fixation cannot always meet lake ecosystem N needs, and (2) that anthropogenic N and P loading has increased dramatically in recent decades. Sediment P accumulation supports long-term internal loading, while N may escape via denitrification, leading to perpetual N deficits. Hence, controlling both N and P inputs will help control HABs in some lakes and also reduce N export to downstream N-sensitive ecosystems. Managers should consider whether balanced control of N and P will most effectively reduce HABs along the freshwater-marine continuum.},
	number = {20},
	urldate = {2020-03-02},
	journal = {Environmental Science \& Technology},
	author = {Paerl, Hans W. and Scott, J. Thad and McCarthy, Mark J. and Newell, Silvia E. and Gardner, Wayne S. and Havens, Karl E. and Hoffman, Daniel K. and Wilhelm, Steven W. and Wurtsbaugh, Wayne A.},
	month = oct,
	year = {2016},
	note = {Publisher: American Chemical Society},
	pages = {10805--10813},
}

@article{mulholland_effect_1985,
	title = {Effect of a {Leaf}-{Shredding} {Invertebrate} on {Organic} {Matter} {Dynamics} and {Phosphorus} {Spiralling} in {Heterotrophic} {Laboratory} {Streams}},
	volume = {66},
	issn = {0029-8549},
	url = {https://www.jstor.org/stable/4217613},
	abstract = {The effect of invertebrate shredders on organic matter dynamics and phosphorus spiralling was studied over a 30-week period in laboratory streams. The streams were fed by groundwater, layered with cobble and gravel from a natural stream, covered with opaque material to eliminate algal growth, and initially contained 195 g/m2 of autumn-shed leaves. Four weeks after leaf addition, leaf-shredding snails (Goniobasis clavaeformis) were added to each of three streams in densities of 75, 220, and 800/m2. A fourth stream contained no snails and served as a control. Presence of snails increased the loss rates of coarse particulate organic matter (CPOM) and total organic matter (TOM), primarily by increasing leaf fragmentation and seston export. Although snail feeding increased specific metabolism of microbes associated with CPOM and cobble surfaces, it was not enough to compensate for reduction in bacterial cell numbers per unit surface area and in stream TOM. Consequently mineralization of detritus and wholestream phosphorus utilization rate were maximum in the stream with no snails and decreased with increasing snail density. From previous simulations of a stream model based on the nutrient spiralling concept, we predicted that there should be an intermediate shredder density which would minimize phosphorus spiralling length (maximize phosphorus utilization) in a natural stream nearby. Our current results conflict with the model-based predictions primarily because the increase in microbial metabolism was less important than reduction in bacterial cell numbers and total benthic organic matter resulting from snail feeding. Although our results indicate macroinvertebrate shredders reduce phosphorus utilization in headwater streams, shredders may increase nutrient utilization downstream where riparian inputs are lower, thus linking low- and high-order streams.},
	number = {2},
	urldate = {2020-03-01},
	journal = {Oecologia},
	author = {Mulholland, P. J. and Elwood, J. W. and Newbold, J. D. and Ferren, Leigh Ann},
	year = {1985},
	note = {Publisher: Springer},
	pages = {199--206},
}

@article{meyer_dynamics_1980,
	title = {Dynamics of {Phosphorus} and {Organic} {Matter} during {Leaf} {Decomposition} in a {Forest} {Stream}},
	volume = {34},
	issn = {0030-1299},
	url = {https://www.jstor.org/stable/3544548},
	doi = {10.2307/3544548},
	abstract = {Leaf decomposition rates and changes in leaf phosphorus content during decomposition were followed for one year at six sites in Bear Brook, a forest stream in New Hampshire. Experimental leaf packs consisted of 3 g each of sugar maple, yellow birch, and beech leaves enclosed in 1 mm mesh bags. Leaf decay was slowest in sites where sediment deposition was high and most rapid in sites where sediment deposition was low. There was no correlation between decay rate and numbers or biomass of invertebrates. Leaf phosphorus content increased during decomposition, and the increase was greatest where sediment deposition was greatest. Organic matter losses from a stream can be partitioned into losses due to export downstream and losses due to biological processes. Estimates of biological loss rates obtained using a mass balance approach were slightly lower than estimates obtained using experimental leaf packs. /// Скоростъ разложения листвы и изменения содержания фосфора в листве в ходе разложения измеряли в течение года в 6 местообитаниях в Бир Брук, лесной реке Нъю-Хэмпшира. Пробы листъев составляли по 3 г листвы клена, березы и бука, заключенной в мешочки из сетки с ячеей 1 мм диаметром. Разложение листвы было наиболее медленным в местах с высокой скоростъю осаждения и наиболее быстрым - в мествх с низкой скоростъю осаждения. Корреляции между скоростъю разложения и численностъю либо биомассой беспозвоночных не установлена. Содержание фосфора в листве повышалосъ в ходе разложения. Наиболышее повышение уствновлено в местах с максималъной скоростъю осаждения. Потери органического вещества из реки подразделяются на потери в резулътате выноса по течению и в резулътате биологических процессов. Резулътаты определений скорости биологических потеръ по расчету баланса массы были несколъко ниже, чем резулътаты измерений в пробах листвы в опытах.},
	number = {1},
	urldate = {2020-03-01},
	journal = {Oikos},
	author = {Meyer, Judy L.},
	year = {1980},
	note = {Publisher: [Nordic Society Oikos, Wiley]},
	pages = {44--53},
}

@article{baker_basin_2018,
	title = {Basin risk explains patterns of macroinvertebrate community differences across small streams in the {Fayetteville} {Shale}, {AR}},
	volume = {91},
	issn = {1470-160X},
	url = {http://www.sciencedirect.com/science/article/pii/S1470160X1830205X},
	doi = {10.1016/j.ecolind.2018.03.049},
	abstract = {Understanding the relationship between natural landscape characteristics and human activities is crucial to predicting conditions under which loss of freshwater biodiversity occurs. For example, region-specific human activities, like unconventional natural gas (UNG) development, are often absent from models because of their limited spatial extent, yet their effects may alter stream ecosystems. Unconventional natural gas development is an expanding human activity that requires land-clearing, water withdrawal, and chemicals for hydraulic fracturing that could alter stream habitat and water quality, yet the degree of alteration may depend on basin natural landscape characteristics. We modified a basin-specific multi-metric risk model and used it to predict differences in macroinvertebrate communities in small stream basins (range 5.71–90.96 km2) in the Fayetteville Shale, Arkansas. We modeled basin risk as the interaction between basin natural sensitivity to alterations and basin exposure to human activities. We predicted that macroinvertebrate communities in 18 basins exposed to a gradient of unconventional natural gas (UNG) in a pasture-dominated landscape would experience greater differences in macroinvertebrate metrics across a risk gradient than 22 basins with a similar gradient of pasture land. Macroinvertebrate metrics of diversity declined by as much as 88\% across the basin risk gradient. In contrast, macroinvertebrate metrics of biomass and density increased by 28\% across the same basin risk gradient. Basin risk explained more variation in macroinvertebrate communities than sensitivity or exposure alone, suggesting an interaction between basin natural landscape characteristics and human activities. In contrast to our prediction, all macroinvertebrate metrics responded similarly in basins with and without UNG, which suggests either there was no added stressor-effect of UNG or UNG alterations resulted in the same biological effects as pasture. However, macroinvertebrate metrics in basins with and without UNG responded differently across a sediment-specific risk model where dams were modeled as sediment traps instead of structures that alter flow and temperature. As land alterations continue in the Fayetteville Shale, our basin-specific risk model can be used as a tool to identify at-risk stream communities.},
	language = {en},
	urldate = {2020-03-01},
	journal = {Ecological Indicators},
	author = {Baker, Lucy and Evans-White, Michelle A. and Entrekin, Sally},
	month = aug,
	year = {2018},
	keywords = {Human activities, Landscape natural characteristics, Landscape risk, Macroinvertebrate communities, Multiple stressors, Unconventional natural gas},
	pages = {478--489},
}

@article{baker_basin_2018-1,
	title = {Basin risk explains patterns of macroinvertebrate community differences across small streams in the {Fayetteville} {Shale}, {AR}},
	volume = {91},
	issn = {1470-160X},
	url = {http://www.sciencedirect.com/science/article/pii/S1470160X1830205X},
	doi = {10.1016/j.ecolind.2018.03.049},
	abstract = {Understanding the relationship between natural landscape characteristics and human activities is crucial to predicting conditions under which loss of freshwater biodiversity occurs. For example, region-specific human activities, like unconventional natural gas (UNG) development, are often absent from models because of their limited spatial extent, yet their effects may alter stream ecosystems. Unconventional natural gas development is an expanding human activity that requires land-clearing, water withdrawal, and chemicals for hydraulic fracturing that could alter stream habitat and water quality, yet the degree of alteration may depend on basin natural landscape characteristics. We modified a basin-specific multi-metric risk model and used it to predict differences in macroinvertebrate communities in small stream basins (range 5.71–90.96 km2) in the Fayetteville Shale, Arkansas. We modeled basin risk as the interaction between basin natural sensitivity to alterations and basin exposure to human activities. We predicted that macroinvertebrate communities in 18 basins exposed to a gradient of unconventional natural gas (UNG) in a pasture-dominated landscape would experience greater differences in macroinvertebrate metrics across a risk gradient than 22 basins with a similar gradient of pasture land. Macroinvertebrate metrics of diversity declined by as much as 88\% across the basin risk gradient. In contrast, macroinvertebrate metrics of biomass and density increased by 28\% across the same basin risk gradient. Basin risk explained more variation in macroinvertebrate communities than sensitivity or exposure alone, suggesting an interaction between basin natural landscape characteristics and human activities. In contrast to our prediction, all macroinvertebrate metrics responded similarly in basins with and without UNG, which suggests either there was no added stressor-effect of UNG or UNG alterations resulted in the same biological effects as pasture. However, macroinvertebrate metrics in basins with and without UNG responded differently across a sediment-specific risk model where dams were modeled as sediment traps instead of structures that alter flow and temperature. As land alterations continue in the Fayetteville Shale, our basin-specific risk model can be used as a tool to identify at-risk stream communities.},
	language = {en},
	urldate = {2020-03-01},
	journal = {Ecological Indicators},
	author = {Baker, Lucy and Evans-White, Michelle A. and Entrekin, Sally},
	month = aug,
	year = {2018},
	keywords = {Human activities, Landscape natural characteristics, Landscape risk, Macroinvertebrate communities, Multiple stressors, Unconventional natural gas},
	pages = {478--489},
}

@article{crouse_monitoring_2002,
	title = {Monitoring phosphorus mineralization from poultry manure using phosphatase assays and phosphorus-31 nuclear magnetic resonance spectroscopy},
	volume = {33},
	issn = {0010-3624},
	url = {10.1081/CSS-120003882},
	doi = {10.1081/CSS-120003882},
	abstract = {Phosphatase enzymes are responsible for mineralization of organic-phosphorus (P) compounds in soil where they hydrolyze the organic phosphate esters to inorganic phosphate. One way to monitor the mineralization process in soils receiving poultry manure is by assessing the activity of phosphatase in a soil amended with poultry manure relative to a soil that is not amended. In a laboratory incubation, soil phosphomonoesterase activity and soil phosphodiesterase activity were measured 0, 1, 2, 4, 8, 12, 16, and 20 weeks after soil incorporation of poultry litter. Two soils, both Fine-loamy siliceous, thermic Typic Kandiudults, were used in the study. Both soils differed in their previous management. The first soil was from a conventionally tilled field that received annual poultry litter applications for 18 consecutive years. The second soil was from an adjacent recently cleared woodland that had no history of manure application. In the previously non-manured soil, soil phosphodiesterase activity following poultry litter addition increased from 4 to 66 μg p-nitrophenol g soil−1 hour−1 by the second week. However, in the same soil, after 8 weeks, phosphodiesterase activity resulting from poultry litter applications was not evident. There was a net increase in phosphomonoesterase activity from week 0 to 20 in the previously manured and previously non-manured soils that were amended with poultry litter. A simultaneous study was conducted to measure the relative concentration of organic P forms during the mineralization process using 31P nuclear magnetic resonance. Subsamples from the poultry manure-amended soil were extracted with 0.25 M NaOH+0.05 M EDTA following 0, 1, 2, 4, 8, 12, 16, and 20 weeks after manure addition and incorporation. The concentration of organic P compounds decreased from the time of poultry litter incorporation until week 20 whereas orthophosphate concentration increased during this period.},
	number = {7-8},
	urldate = {2020-03-01},
	journal = {Communications in Soil Science and Plant Analysis},
	author = {Crouse, D. A. and Sierzputowska-Gracz, H. and Mikkelsen, R. L. and Wollum, A. G.},
	month = may,
	year = {2002},
	note = {Publisher: Taylor \& Francis
\_eprint: 10.1081/CSS-120003882},
	pages = {1205--1217},
}

@article{wang_enzymatic_2010,
	title = {Enzymatic hydrolysis of organic phosphorus in river bed sediments},
	volume = {36},
	issn = {0925-8574},
	url = {http://www.sciencedirect.com/science/article/pii/S0925857410000662},
	doi = {10.1016/j.ecoleng.2010.03.006},
	abstract = {Enzymatic hydrolysis of phosphorus (P) in bed sediments is an important process that maintains bioavailable P in the river systems. The P bioavailability is the criterion for assessing the eutrophication potential in rivers and streams. The objective of this research was to determine potential bioavailability of organic P (OP) in the Bronx River bed sediments using native phosphatases (NPase) and phosphodiesterase (PDEase) hydrolysis. The bed sediments collected in summer 2006 and 2007 were incubated at 37°C for 6h at pH 7.5 with NPase. The results showed that NPase hydrolyzed a substantial amount of OP (up to 76\%) under favorable temperature and pH, indicating OP could be hydrolyzed under increased temperature, and in turn increase in P availability in the river. Similarly, the resulting form sediments incubated with PDEase at 37°C and pH 8.8 showed that up to 82\% of OP could be hydrolyzed. Strong correlations between percentage of OP hydrolyzed by PDEase and organic matter (OM) were observed for sediments collected in 2006 (r=0.745; p≤0.01) and 2007 (r=0.724; p≤0.01), indicating PDEase hydrolysable P is mainly associated with OM. It is indicative that local hydro-climatic changes such as temperature increase and pH variations could hydrolyze a substantial amount of OP and increase bioavailable P in the water column, resulting in a potential threat to the river ecosystems.},
	language = {en},
	number = {7},
	urldate = {2020-03-01},
	journal = {Ecological Engineering},
	author = {Wang, Jingyu and Pant, Hari K.},
	month = jul,
	year = {2010},
	keywords = {Bioavailable P, Native phosphatases, P hydrolysis, Phosphodiesterase},
	pages = {963--968},
}

@article{wang_enzymatic_2010-1,
	title = {Enzymatic hydrolysis of organic phosphorus in river bed sediments},
	volume = {36},
	issn = {0925-8574},
	url = {http://www.sciencedirect.com/science/article/pii/S0925857410000662},
	doi = {10.1016/j.ecoleng.2010.03.006},
	abstract = {Enzymatic hydrolysis of phosphorus (P) in bed sediments is an important process that maintains bioavailable P in the river systems. The P bioavailability is the criterion for assessing the eutrophication potential in rivers and streams. The objective of this research was to determine potential bioavailability of organic P (OP) in the Bronx River bed sediments using native phosphatases (NPase) and phosphodiesterase (PDEase) hydrolysis. The bed sediments collected in summer 2006 and 2007 were incubated at 37°C for 6h at pH 7.5 with NPase. The results showed that NPase hydrolyzed a substantial amount of OP (up to 76\%) under favorable temperature and pH, indicating OP could be hydrolyzed under increased temperature, and in turn increase in P availability in the river. Similarly, the resulting form sediments incubated with PDEase at 37°C and pH 8.8 showed that up to 82\% of OP could be hydrolyzed. Strong correlations between percentage of OP hydrolyzed by PDEase and organic matter (OM) were observed for sediments collected in 2006 (r=0.745; p≤0.01) and 2007 (r=0.724; p≤0.01), indicating PDEase hydrolysable P is mainly associated with OM. It is indicative that local hydro-climatic changes such as temperature increase and pH variations could hydrolyze a substantial amount of OP and increase bioavailable P in the water column, resulting in a potential threat to the river ecosystems.},
	language = {en},
	number = {7},
	urldate = {2020-03-01},
	journal = {Ecological Engineering},
	author = {Wang, Jingyu and Pant, Hari K.},
	month = jul,
	year = {2010},
	keywords = {Bioavailable P, Native phosphatases, P hydrolysis, Phosphodiesterase},
	pages = {963--968},
}

@article{liu_spatio-temporal_2017,
	title = {Spatio-temporal patterns of enzyme activities after manure application reflect mechanisms of niche differentiation between plants and microorganisms},
	volume = {112},
	issn = {0038-0717},
	url = {http://www.sciencedirect.com/science/article/pii/S0038071717300081},
	doi = {10.1016/j.soilbio.2017.05.006},
	abstract = {Manure is an important source of nutrients for plants and stimulates a wide range of enzyme-mediated microbial processes. Such stimulation, however, depends on manure distribution and the duration of its decomposition in soil. For the first time, we investigated the spatio-temporal patterns of enzyme activities as affected by manure application strategies: 1) Localized manure: manure application as a layer in the upper soil; 2) Homogenized manure: mixing manure throughout the soil; and 3) Control without manure. Tibetan barley was planted on soil managed with yak manure from the Tibetan Plateau. Soil zymography was used to visualize the two-dimensional distribution and dynamics of the activities of three enzymes responsible for cycling of carbon (β-glucosidase), nitrogen (N-acetylglucosaminidase) and phosphorus (phosphomonoesterase) over 45 days. The manure detritusphere increased enzyme activities relative to the control (which had only the rhizosphere effect of barley) and this stimulation lasted less than 45 days. Enzyme activities in the manure-induced hotspots were higher than on the barley rhizoplane, indicating that the detritusphere stimulated microbial activities more strongly than roots. Homogenized manure led to 3–29\% higher enzyme activities than localized manure, but shoot and root biomass was respectively 3.1 and 6.7 times higher with localized manure application. Nutrients released by high enzyme activities within the whole soil volume will be efficiently trapped by microorganisms. In contrast, nutrients released from manure locally are in excess for microbial uptake and remain available for roots. Consequently, microorganisms were successful competitors for nutrients from homogeneous manure application, while plants benefited more from localized manure application. We conclude that localized manure application decreases competition for nutrients between the microbial community of manure and the roots, and thereby increases plant performance.},
	language = {en},
	urldate = {2020-03-01},
	journal = {Soil Biology and Biochemistry},
	author = {Liu, Shibin and Razavi, Bahar S. and Su, Xu and Maharjan, Menuka and Zarebanadkouki, Mohsen and Blagodatskaya, Evgenia and Kuzyakov, Yakov},
	month = sep,
	year = {2017},
	keywords = {Barley roots, Direct zymography, Enzyme activity visualization, Manure application strategies, Tibetan Plateau},
	pages = {100--109},
}

@article{waldrip_legacy_2015,
	title = {Legacy {Phosphorus} in {Calcareous} {Soils}: {Effects} of {Long}-{Term} {Poultry} {Litter} {Application}},
	volume = {79},
	copyright = {Copyright © by the Soil Science Society of America, Inc.},
	issn = {1435-0661},
	shorttitle = {Legacy {Phosphorus} in {Calcareous} {Soils}},
	url = {http://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaj2015.03.0090},
	doi = {10.2136/sssaj2015.03.0090},
	abstract = {Sequential fractionation coupled with phosphatase hydrolysis allows a greater understanding of the effects of animal manure on the chemical distribution of soil P. Concentrations of specific soil P fractions were determined after long-term ({\textgreater}10 yr) poultry litter application at rates of 4.5, 6.7, 9.0, 11.2, and 13.4 Mg manure ha−1 yr−1 to watershed-scale plots (cultivated and grazed–ungrazed pasture) on a calcareous Texas Blackland Vertisol. Soil total extractable P (Pt) and inorganic P (Pi) were quantified following sequential extraction with H2O, NaHCO3, NaOH, and HCl. Hydrolyzable organic P (Pe) and non-hydrolyzable organic P (Pne) were determined in the extracted fractions following enzymatic hydrolysis. Litter application increased Pt regardless of land-use type compared with the control. Concentrations of H2O-extractable Pi in litter-amended plots increased by 9 to 34\% (cultivated) and 7 to 30\% (pasture) over the control, indicating substantial risk of soluble P runoff. Labile organic P (Po) extracted with H2O and NaHCO3 decreased in the order monoester {\textgreater} nucleic acid {\textgreater} phytate {\textgreater} Pne. An average of 68\% of Pt was extractable with HCl. Organic P comprised the majority (95\%) of HCl-Pt; however, only trace levels of HCl-Po were hydrolyzable, and litter application increased HCl-Pne up to 217\%. Thus, litter application increased levels of both soluble Pi and stable Pne, but the specific response varied with application rate and land management. This study increased understanding of P chemical distribution with time in litter-amended soil with high clay and CaCO3 contents under differing land-use scenarios.},
	language = {en},
	number = {6},
	urldate = {2020-03-01},
	journal = {Soil Science Society of America Journal},
	author = {Waldrip, Heidi M. and Pagliari, Paulo H. and He, Zhongqi and Harmel, R. Daren and Cole, N. Andy and Zhang, Mingchu},
	year = {2015},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.2136/sssaj2015.03.0090},
	pages = {1601--1614},
}

@article{cabrera_soil_2009,
	title = {Soil and runoff response to dairy manure application on {New} {Mexico} rangeland},
	volume = {131},
	issn = {0167-8809},
	url = {http://www.sciencedirect.com/science/article/pii/S0167880909000462},
	doi = {10.1016/j.agee.2009.01.022},
	abstract = {Manure disposal is a major challenge for the fast-growing dairy industry in New Mexico. There are currently over 355,000 milking cows in the state and limited cropland on which to use the manure generated by these cows. On the other hand, 80\% of the state lands classified as rangelands are suffering from a lack of organic matter and nutrients. Application of dairy manure to rangelands could serve a dual purpose: (1) manure disposal from dairies and (2) soil amendment to improve soil characteristics and promote herbaceous production. Manure was applied at two rates according to phosphorus (P) content: (1) a recommended (light) rate (54kgPha−1) to enhance blue grama growth and (2) a gross over-application (heavy) rate (493kgPha−1) to determine the effects on runoff and soil properties. Light applications enhanced soil properties including decreased sediment runoff, increased soil organic matter, increased extractable P, and increased soil moisture, whereas heavy applications increased soil salinity, sodium adsorption ratio, and runoff water. Dairy manure can be safely applied at light rates to conserve and enhance rangeland soil properties and their herbaceous productivity. Manure disposal at heavy rates are unsafe. Further study is required to find out if other safe disposal exists between the light and heavy treatments.},
	language = {en},
	number = {3},
	urldate = {2020-03-01},
	journal = {Agriculture, Ecosystems \& Environment},
	author = {Cabrera, V. E. and Stavast, L. J. and Baker, T. T. and Wood, M. K. and Cram, D. S. and Flynn, R. P. and Ulery, A. L.},
	month = jun,
	year = {2009},
	keywords = {Dairy nutrient utilization, Environmental stewardship, Organic amendment, Soil fertility},
	pages = {255--262},
}

@article{centner_evolving_2001,
	title = {Evolving {Policies} to {Regulate} {Pollution} from {Animal} {Feeding} {Operations}},
	volume = {28},
	issn = {1432-1009},
	url = {10.1007/s002670010246},
	doi = {10.1007/s002670010246},
	language = {en},
	number = {5},
	urldate = {2020-03-01},
	journal = {Environmental Management},
	author = {Centner, TERENCE J.},
	month = nov,
	year = {2001},
	pages = {599--609},
}

@article{mallin_industrialized_2003,
	title = {Industrialized {Animal} {Production}—{A} {Major} {Source} of {Nutrient} and {Microbial} {Pollution} to {Aquatic} {Ecosystems}},
	volume = {24},
	issn = {1573-7810},
	url = {10.1023/A:1023690824045},
	doi = {10.1023/A:1023690824045},
	abstract = {Livestock production has undergone massive industrialization in recent decades. Nationwide, millions of swine, poultry, and cattle are raised and fed in concentrated animal feeding operations (CAFOs) owned by large, vertically integrated producer corporations. The amount of nutrients (nitrogen and phosphorus) in animal manure produced by CAFOs is enormous. For example, on the North Carolina Coastal Plain alone an estimated 124,000 metric tons of nitrogen and 29,000 metric tons of phosphorus are generated annually by livestock. CAFO wastes are largely either spread on fields as dry litter or pumped into waste lagoons and sprayed as liquid onto fields. Large amounts of nitrogen and phosphorus enter the environment through runoff, percolation into groundwater, and volatilization of ammonia. Many CAFOs are located in nutrient-sensitive watersheds where the wastes contribute to the eutrophication of streams, rivers, and estuaries. There is as yet no comprehensive Federal policy in place to protect the environment and human health from CAFO generated pollutants.},
	language = {en},
	number = {5},
	urldate = {2020-03-01},
	journal = {Population and Environment},
	author = {Mallin, Michael A. and Cahoon, Lawrence B.},
	month = may,
	year = {2003},
	pages = {369--385},
}

@article{edwards_effects_1993,
	title = {Effects of {Poultry} {Litter} {Application} {Rate} and {Rainfall} {Intensity} on {Quality} of {Runoff} from {Fescuegrass} {Plots}},
	volume = {22},
	copyright = {© 1993 American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America},
	issn = {1537-2537},
	url = {http://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/jeq1993.00472425002200020017x},
	doi = {10.2134/jeq1993.00472425002200020017x},
	abstract = {A 4 × 2 factorial experiment with three replications was conducted to determine how quality of runoff from grassed areas treated with poultry (Gallus gallus domesticus) litter is impacted by litter application rate and rainfall intensity for storms occurring 1 d after application. Poultry litter was applied at 0, 218, 435, and 870 kg N ha−1 to plots established with fescuegrass (Festuca arundinacea Schreb.) on a Captina silt loam soil (fine-silty, mixed, mesic Typic Fragiudult). Simulated rainfall was applied 24 h after litter application at 5 and 10 cm h−1 until runoff had occurred for a duration of 0.5 h. Flow-weighed composite samples were collected and analyzed for total Kjeldahl nitrogen (TKN), ammonia nitrogen (NH3-N), nitrate nitrogen (NO3-N), total phosphorus (TP), dissolved reactive phosphorus (DP), chemical oxygen demand (COD), total suspended solids, and electrical conductivity. Increasing the litter application rate significantly increased runoff concentrations of all litter constituents investigated. Concentrations of TKN, TP, DP, and COD significantly decreased with increasing rainfall intensity because of more runoff and the associated dilution. Masses of litter constituents transported off the plots via runoff significantly increased with both litter application rate and rainfall intensity. For a given rainfall intensity, the proportions of applied litter constituents lost in runoff were generally indendent of application rate with the exception of total N at the high rainfall intensity.},
	language = {en},
	number = {2},
	urldate = {2020-03-01},
	journal = {Journal of Environmental Quality},
	author = {Edwards, D. R. and Daniel, T. C.},
	year = {1993},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.2134/jeq1993.00472425002200020017x},
	pages = {361--365},
}

@article{ciparis_effects_2012,
	title = {Effects of watershed densities of animal feeding operations on nutrient concentrations and estrogenic activity in agricultural streams},
	volume = {414},
	issn = {0048-9697},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969711011764},
	doi = {10.1016/j.scitotenv.2011.10.017},
	abstract = {Application of manures from animal feeding operations (AFOs) as fertilizer on agricultural land can introduce nutrients and hormones (e.g. estrogens) to streams. A landscape-scale study was conducted in the Shenandoah River watershed (Virginia, USA) in order to assess the relationship between densities of AFOs in watersheds of agricultural streams and in-stream nutrient concentrations and estrogenic activity. The effect of wastewater treatment plants (WWTPs) on nutrients and estrogenic activity was also evaluated. During periods of high and low flow, dissolved inorganic nitrogen (DIN) and orthophosphate (PO4-P) concentrations were analyzed and estrogens/estrogenic compounds were extracted and quantified as17β-estradiol equivalents (E2Eq) using a bioluminescent yeast estrogen screen. Estrogenic activity was measurable in the majority of collected samples, and 20\% had E2Eq concentrations {\textgreater}1ng/L. Relatively high concentrations of DIN ({\textgreater}1000μg/L) were also frequently detected. During all sampling periods, there were strong relationships between watershed densities of AFOs and in-stream concentrations of DIN (R2=0.56–0.81) and E2Eq (R2=0.39–0.75). Relationships between watershed densities of AFOs and PO4-P were weaker, but were also significant (R2=0.27–0.57). When combined with the effect of watershed AFO density, streams receiving WWTP effluent had higher concentrations of PO4-P than streams without WWTP discharges, and PO4-P was the only analyte with a consistent relationship to WWTPs. The results of this study suggest that as the watershed density of AFOs increases, there is a proportional increase in the potential for nonpoint source pollution of agricultural streams and their receiving waters by nutrients, particularly DIN, and compounds that can cause endocrine disruption in aquatic organisms.},
	language = {en},
	urldate = {2020-03-01},
	journal = {Science of The Total Environment},
	author = {Ciparis, Serena and Iwanowicz, Luke R. and Voshell, J. Reese},
	month = jan,
	year = {2012},
	keywords = {Agriculture, Estrogens, Nutrients, Watershed},
	pages = {268--276},
}

@article{daniels_soil_2001,
	title = {Soil {Phosphorus} {Variability} in {Pastures}: {Implications} for {Sampling} and {Environmental} {Management} {Strategies}},
	volume = {30},
	copyright = {© Published in J. Environ. Qual.30:2157–2165.},
	issn = {1537-2537},
	shorttitle = {Soil {Phosphorus} {Variability} in {Pastures}},
	url = {http://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/jeq2001.2157},
	doi = {10.2134/jeq2001.2157},
	abstract = {Soil phosphorus (P) is an increasingly important consideration in the development of P-based nutrient management strategies. The objectives of this study were to (i) obtain baseline information on soil P variability in pastures amended with animal waste, (ii) examine if current sampling recommendations related to the number of subsamples adequately reduce uncertainty to acceptable limits, and (iii) examine the implications of uncertainty in soil P estimates on implementing a soil P threshold of 150 mg kg−1 Grid soil samples were collected from 12 pastures. Soil P was determined using Mehlich 3 extractant and an inductively coupled argon plasma spectrometer. The arithmetic mean of soil P ranged from 7 mg kg−1 in a pasture never amended with animal manure to 437 mg kg−1 in a pasture that had been annually treated long term with poultry litter. Variance of soil P generally increased with mean soil P. The mean standard deviation of all pastures was one-third of the 150 mg kg−1 threshold. This study points out that smaller variances associated with mean soil P values that approach, but do not exceed, the threshold can influence estimates of soil P. In turn, management decisions could inappropriately change. When a uniform acceptance criteria (within 15 mg kg−1) with respect to measured means was used, the required minimum number of subsamples increased with measured standard deviation. The results of this study imply that following soil-sampling recommendations is critical to obtaining trustworthy measures of central tendency, especially in pastures approaching but not exceeding the 150 mg kg−1 threshold.},
	language = {en},
	number = {6},
	urldate = {2020-03-01},
	journal = {Journal of Environmental Quality},
	author = {Daniels, Michael B. and Delaune, Paul and Moore, Phillip A. and Mauromoustakos, Andy and Chapman, Stan L. and Langston, John M.},
	year = {2001},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.2134/jeq2001.2157},
	pages = {2157--2165},
}

@article{michaud_cropping_2004,
	title = {Cropping, soil type and manure application effects on phosphorus export and bioavailability},
	volume = {84},
	issn = {0008-4271, 1918-1841},
	url = {http://www.nrcresearchpress.com/doi/10.4141/S03-014},
	doi = {10.4141/S03-014},
	abstract = {Michaud, A. R. and Laverdière, M. R. 2004. Cropping, soil type and manure application effects on phosphorus export and bioavailability. Can. J. Soil Sci. 84: 295–305. A simulated rainfall study was conducted on an array of 36 runoff plots (6 m2 each) deployed on three benchmark soil series of the Missisquoi region in southwestern Québec. The split-plot experimental design tested the effects and interactions of pig slurry treatment as main plots (check vs. 59 kg P ha–1) and cropping (tilled vs. hay) as subplots, on runoff volume and concentrations in total suspended sediment (TSS), total phosphorus (TP), dissolved reactive soluble P (DRP), particulate P (PP) and bioavailable P (BioP). TP concentration in runoff ranged from a low of 1.17 mg L–1 average on non-amended Bedford hay, to a peak concentration average of 9.55 mg L–1 on manured and tilled Saint-Sébastien plots. Variance analysis indicated significant contributions of treatments in explaining TP concentration in runoff as follows: Soil type effect {\textgreater} Cropping effect {\textgreater} Soil × Cropping interaction {\textgreater} Manure effect. Erosion and sediment transport processes were identified as prime vectors of TP export. Manure effect alone accounted for 35\% of overall DRP variability, while soil type alone accounted for 70\% of variability in particulate P bioavaibility (BioP/PP). Among practical implications of this study is the importance of assessing PP bioavaibility to adequately predict the adverse impact of runoff on aquatic ecosystems. The high level of interaction among cropping and manure treatment and the site-specific influence of soil physical and chemical properties also calls for a holistic approach to nonpoint P risk assessment and management, that focusses on timely manure P management, control of soil P build-up and agricultural practices minimizing surface runoff.},
	language = {en},
	number = {3},
	urldate = {2020-03-01},
	journal = {Canadian Journal of Soil Science},
	author = {Michaud, A. R. and Laverdière, M. R.},
	month = aug,
	year = {2004},
	pages = {295--305},
}

@article{prygiel_biogeochemistry_2015,
	title = {On biogeochemistry and water quality of river canals in {Northern} {France} subject to daily sediment resuspension due to intense boating activities},
	volume = {197},
	issn = {0269-7491},
	url = {http://www.sciencedirect.com/science/article/pii/S0269749114004898},
	doi = {10.1016/j.envpol.2014.11.022},
	abstract = {In Northern France, channelized rivers facilitate greatly the waterway transport that should still increase in the coming years to replace as much as possible the road traffic, considered as a heavier source of pollution. These rivers are now subjected to the good potential status objectives required by the Water Framework Directive. The impact of the recurrent resuspension by the current boat traffic of polluted sediments (due to strong historical pollution) on the water quality is the main concern of this work. Our study reveals that the navigation seems to play a limited role on the enrichment of the water columns by dissolved metals and phosphorus, as well as on the oxygenation of surface waters. Conversely, the cycling of the phytoplankton over the year appears to partly control the physico-chemical and chemical evolutions of the overlying waters.},
	language = {en},
	urldate = {2020-03-01},
	journal = {Environmental Pollution},
	author = {Prygiel, E. and Superville, P. -J. and Dumoulin, D. and Lizon, F. and Prygiel, J. and Billon, G.},
	month = feb,
	year = {2015},
	keywords = {Boat traffic, Phosphorus, Resuspension, River canal, Sediment, Trace metal, Water framework directive},
	pages = {295--308},
}

@article{palmer-felgate_phosphorus_2011,
	title = {Phosphorus release from sediments in a treatment wetland: {Contrast} between {DET} and {EPC0} methodologies},
	volume = {37},
	issn = {0925-8574},
	shorttitle = {Phosphorus release from sediments in a treatment wetland},
	url = {http://www.sciencedirect.com/science/article/pii/S0925857411000061},
	doi = {10.1016/j.ecoleng.2010.12.024},
	abstract = {Wetlands are capable of reducing nutrient loadings to receiving water bodies, and hence many artificial wetlands have been constructed for wastewater nutrient removal. In this study, diffusive equilibrium in thin films (DETs) and equilibrium phosphorus concentration (EPC0) analysis were used to examine the role of sediment as a nutrient source or sink in a constructed treatment wetland in summer. The effect of dredging on sediment-water nutrient exchange was also studied. Soluble reactive phosphorus (SRP), ammonium (NH4+) and sulphate (SO42−) concentration profiles were measured by DET across the sediment-water interface (SWI) in both a settling pond and iris reed bed within the wetland. The SRP concentrations in the sediment pore-waters of the settling pond were extremely high (up to 29,500μg l−1) near the SWI. This is over an order of magnitude higher than the levels found in the water column, which in turn are over an order of magnitude higher than environmental levels proposed to limit eutrophication in rivers. The profiles demonstrated an average net release of SRP and NH4+ from the settling pond sediment to the overlying water of 58mgm−2d−1 (±32mgm−2d−1 (1sd)) and 16mgm−2d−1 (±25mgm−2d−1 (1sd)), respectively. The DET SO42− concentration profiles revealed that the sediment was anoxic within 2cm of the SWI. Dredging of the reed bed made no significant difference to the P release characteristics across the SWI. The EPC0s were much lower than the SRP concentration of the overlying water, indicating that the sediment had the potential to act as a phosphate sink. The apparent contradiction of the DET and EPC0 results is attributed to the fact that DET measurements are made in situ, where as EPC0 measurements are ex situ. These results show that substantial releases of P can occur from wetland sediments, and also highlight the need for caution when interpreting ex situ EPC0 analytical results.},
	language = {en},
	number = {6},
	urldate = {2020-03-01},
	journal = {Ecological Engineering},
	author = {Palmer-Felgate, Elizabeth J. and Bowes, Michael J. and Stratford, Charlie and Neal, Colin and MacKenzie, Sally},
	month = jun,
	year = {2011},
	keywords = {Ammonium, Constructed Wetland, DET, EPC0, Phosphorus, Sediment},
	pages = {826--832},
}

@article{burns_determining_2015,
	title = {Determining riverine sediment storage mechanisms of biologically reactive phosphorus in situ using {DGT}},
	volume = {22},
	issn = {1614-7499},
	url = {10.1007/s11356-015-4109-3},
	doi = {10.1007/s11356-015-4109-3},
	abstract = {Phosphorus (P) is the main reason many surficial water bodies in the UK are currently failing to meet the chemical standards set by the Water Framework Directive (WFD). This work focuses on the role of sediments in the upper reaches of the River Taw in the South West of the UK. Point and diffuse sources of P have been identified as well as a number of mitigation measures applied or planned to address the issues. However, it is unknown what effect these sources have had on the river’s sediments and how they will react to diminishing inputs of P into the water column in the future. The diffusive gradient in thin-films (DGT) method is utilised in situ to quantify and identify labile, potentially bioavailable P fluxes and potential storage mechanisms at sites of known diffuse and point P inputs. In the vicinity of a heavily contaminated point source, data present here shows that sediments are still acting as a sink. The proposed mechanism for this is the formation of a ‘calcium cap’ which provides a geochemical barrier between the sediment and overlying water to prevent loss of labile P. The strong correlation between calcium and total P under most circumstances supports this hypothesis. This conclusion provides some confidence that even though P concentrations in some sediments are significantly elevated, mobility between the sediment and overlying water is restricted. In the context of routine monitoring against WFD targets, the molybdenum blue method generally employed to determine soluble reactive phosphorus was shown to not be equivalent to the DGT labile P pool, especially at pristine or moderately point/diffuse influenced sites. This is likely due to desorption of weakly bound P from colloids, which is unavailable to DGT devices. These results have the potential to be scaled up to the full catchment or other catchments which exhibit similar physical and chemical sediment composition and provide a stronger foundation for management and target setting than current monitoring approaches.},
	language = {en},
	number = {13},
	urldate = {2020-03-01},
	journal = {Environmental Science and Pollution Research},
	author = {Burns, Emily E. and Comber, Sean and Blake, William and Goddard, Rupert and Couldrick, Laurence},
	month = jul,
	year = {2015},
	pages = {9816--9828},
}

@article{van_der_grift_forms_2018,
	title = {Forms of phosphorus in suspended particulate matter in agriculture-dominated lowland catchments: {Iron} as phosphorus carrier},
	volume = {631-632},
	issn = {0048-9697},
	shorttitle = {Forms of phosphorus in suspended particulate matter in agriculture-dominated lowland catchments},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969718306661},
	doi = {10.1016/j.scitotenv.2018.02.266},
	abstract = {The fate and environmental effects of phosphorus (P) in natural waters depend on its chemical forms. The particulate P (PP) concentration is dominant over the dissolved P concentration in agriculture-dominated headwaters in the Netherlands. Routine water quality monitoring programmes do not include the chemical fractionation of PP. To quantify the chemical forms of PP under various conditions in six agriculture-dominated lowland catchments in the Netherlands, a sequential chemical extraction method was applied to suspended particulate matter (SPM) samples collected by centrifugation or filtration. Centrifuge samples had lower values for the sum of the PP fractions compared with the filtration samples due to lower contents from PP fractions other than the Fe-P pool. With an average value of 8.8mgg−1, internationally high P contents of the SPM were found. Ferric iron-bound P was the most important PP fraction in SPM samples (38–95\%; median 74\%), followed by organic P (2–38\%; median 15\%). Exchangeable P ranged from 0.2 to 27\%, with a median of 4.4\%, Ca-P ranged from 0.1 to 11\% with a median of 3.9\% and detrital P was present in only a small fraction (0–6\%; median 1.1\%). Ferric iron-bound P was the dominant PP pool throughout the entire range of watercourses (from headwater ditches to catchment outlets) and in samples taken during winter months as well as those taken during summer months. Furthermore, the PP fraction distribution did not change markedly when flow conditions were altered from low to high discharge. The dominance of the Fe-P pool denotes the presence of Fe(III) precipitates in SPM that originate from exfiltration of anoxic Fe-bearing groundwater. These Fe(III) precipitates are a major fraction of the total SPM concentration (4 to 67\% as Fe(OH)3; median 18\%). Although not measured directly, our results suggest that formation of authigenic Fe(III) precipitates causes a rapid transformation of dissolved P in groundwater to PP in surface water. We advise including sequential chemical extraction of SPM monitoring programmes because the composition of particles is critical for P bioavailability, which is a key driving factor for eutrophication.},
	language = {en},
	urldate = {2020-03-01},
	journal = {Science of The Total Environment},
	author = {van der Grift, Bas and Osté, Leonard and Schot, Paul and Kratz, Arjen and van Popta, Emma and Wassen, Martin and Griffioen, Jasper},
	month = aug,
	year = {2018},
	keywords = {Filtration, Iron hydroxides, Natural water, Phosphate binding, Sequential chemical extraction, Suspended particulate matter},
	pages = {115--129},
}

@article{stutter_interactions_2008,
	title = {Interactions of land use and dynamic river conditions on sorption equilibria between benthic sediments and river soluble reactive phosphorus concentrations},
	volume = {42},
	issn = {0043-1354},
	url = {http://www.sciencedirect.com/science/article/pii/S0043135408002649},
	doi = {10.1016/j.watres.2008.06.017},
	abstract = {Within-river cycling of P is a crucial link between catchment pollution sources and the resulting ecological impacts and integrates the biogeochemistry and hydrodynamics of river systems. This study investigates benthic sediment P sorption in relation to river soluble reactive phosphorus (SRP) concentrations during high- to low-flow changes in a major mixed land use river system in NE Scotland. We hypothesised that sediments comprised P sinks during moderate to higher flows but became P saturated with loss of buffering function during prolonged baseflow. Sediment characteristics were evaluated and equilibrium P concentrations (EPC0) calculated using a standardised batch adsorption method (EPC0 values 0.04–1.75μmolPl−1). Pollution-impacted tributaries (32–69\% catchment agricultural land cover) had increased SRP concentrations (0.19–2.62μmolPl−1) and maintained EPC0{\textless}SRP values during changing flow conditions. Moorland-dominated tributaries and main stem sites had small SRP concentrations (0.03–0.19μmolPl−1) but showed EPC0{\textgreater}SRP values during summer baseflow so that sediments were indicated as P sources. This deviation from a geochemical sediment–water P equilibrium was attributed to biological accumulation of P from the water column into the sediments. In particular, large stores of sediment P accumulated in main stem reaches below agricultural tributaries and this may be consequential for sensitive downstream ecosystems. Hence, biogeochemical processes at the river bed may strongly influence river SRP cycling between geochemical and biotic pools. The nature of this internal reservoir of river P and its ecosystem interactions needs better understanding to enable best results to be attained from catchment mitigation actions designed to maintain/improve ecological status under the Water Framework Directive.},
	language = {en},
	number = {16},
	urldate = {2020-03-01},
	journal = {Water Research},
	author = {Stutter, M. I. and Lumsdon, D. G.},
	month = oct,
	year = {2008},
	keywords = {Biogeochemical-cycling, Buffering, Equilibrium P concentration, Phosphorus, Sediments},
	pages = {4249--4260},
}

@article{smith_dredging_2006,
	title = {Dredging of {Drainage} {Ditches} {Increases} {Short}-{Term} {Transport} of {Soluble} {Phosphorus}},
	volume = {35},
	copyright = {© ASA, CSSA, SSSA},
	issn = {1537-2537},
	url = {http://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/jeq2005.0301},
	doi = {10.2134/jeq2005.0301},
	abstract = {Managed drainage ditches are common in the midwestern United States. These ditches are designed to remove water from fields as quickly as possible, and sediment buildup necessitates dredging, to ensure adequate water removal. This laboratory study was conducted to determine the impact of ditch dredging on soluble phosphorus (P) transport. Ditch sediments were collected from a drainage ditch in northeastern Indiana immediately before and after dredging. The sediments were placed in a stream simulator, and stream water was loaded with 0.55 mM P for 5 d (adsorption experiment). Water was then removed, and “clean” water (no P added) was used for a desorption experiment, lasting 1 d. During the adsorption experiment, pre-dredged sediments were able to remove P from the water column quicker, and P concentrations 120 h after introduction of high P water were lower for the pre-dredged sediments (0.075 mM P) than the dredged sediments (0.111 mM P). During the desorption experiment, P was released to the water column slower in the pre-dredged treatment than the dredged treatment (instantaneous flux at t = 0 was 0.205 μM P h−1 for pre-dredged and 0.488 μM P h−1 for dredged). This occurred despite higher Mehlich 3–extractable P in the pre-dredged sediments than the dredged sediments. Equilibrium phosphorus concentrations (EPCo) were lower in the pre-dredged sediments during both adsorption and desorption experiments. Transport of soluble P immediately after dredging will likely increase in drainage ditches; however, dredging is a necessary management tool to ensure adequate discharge of water from surrounding fields.},
	language = {en},
	number = {2},
	urldate = {2020-03-01},
	journal = {Journal of Environmental Quality},
	author = {Smith, Douglas R. and Warnemuende, E. A. and Haggard, B. E. and Huang, C.},
	year = {2006},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.2134/jeq2005.0301},
	pages = {611--616},
}

@article{munn_habitat-specific_1990,
	title = {Habitat-{Specific} {Solute} {Retention} in {Two} {Small} {Streams}: {An} {Intersite} {Comparison}},
	volume = {71},
	issn = {1939-9170},
	shorttitle = {Habitat-{Specific} {Solute} {Retention} in {Two} {Small} {Streams}},
	url = {http://esajournals.onlinelibrary.wiley.com/doi/abs/10.2307/1938621},
	doi = {10.2307/1938621},
	abstract = {We measured uptake rates of phosphorus, nitrate, calcium, and dissolved organic carbon within two headwater streams, one in the Appalachian mountains of North Carolina and the other in the Cascade range of Oregon. The major physical differences between these two streams are parent geology and local geomorphic structure. Uptake rates were measured following low—level nutrient releases during summer 1987 in 20—m reaches with different geomorphology. The relative importance of biotic vs. abiotic sorption of nitrogen and phosphorus by sediments from the two streams was assessed by laboratory experiments. Nitrate—N uptake rates were high for the western stream (11.9 mg°m—2°min—1) and low for the eastern stream (3.9 mg°m—2°min—1) during the summer. The debris dam reaches in Oregon were the most retentive of N (shortest uptake length of 17 m). Conversely, soluble reactive phosphorus (SRP) uptake rates were higher for the eastern stream (18.6 mg°m—2°min—1), primarily through biotic processes. SRP uptake lengths were short for the cobble (32 m), debris dam (35 m), and rock outcrop (40 m) reaches in the eastern stream. Uptake of SRP in either stream was not related to sediment size fraction but rather to a combination of sediment infiltration rates and quality of organic material. Calcium (Ca) uptake lengths were long in the Oregon stream (1278 m) but short in the Appalachian stream (106 m). Surprisingly, the eastern stream was more retentive of Ca than nitrate (shorter uptake lengths for Ca) during this time period. Debris dams greatly enhanced retention of dissolved organic carbon in both streams (60\% of all uptake in the eastern stream and 81\% in the western stream), although retention was greater in the eastern stream. The lower uptake rate of phosphorus and higher uptake rate of nitrate in the Oregon stream were expected based on geographic location and parent geology; streams in this area drain catchments of volcanic origin and tend to have low N:P (atomic; 1.8 for the western stream) ratios, indicating potential N limitation. Streams flowing over granitic bedrock, such as the eastern stream, tend to have lower P availability (N:P = 15.5). The combined results of laboratory and field measurements indicate that in the eastern stream, strong biotic control of P uptake coupled with high P demand result in relatively short P uptake lengths and a strong impact of P spiraling on ecosystem dynamics. In the western stream, strong biotic control of N uptake combined with strong N demand result in short N uptake lengths. This is especially true at sites of downed timber that retain both FPOM and CPOM, creating a high N demand (shortening N spirals).},
	language = {en},
	number = {6},
	urldate = {2020-03-01},
	journal = {Ecology},
	author = {Munn, Nancy L. and Meyer, Judy L.},
	year = {1990},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.2307/1938621},
	keywords = {calcium, dissolved organic carbon, geology, geomorphology, nitrate, phosphorus, retention, spiraling, uptake lengths, uptake rates},
	pages = {2069--2082},
}

@article{jarvie_measurement_2008,
	series = {Characterization and apportionment of nutrient and sediment sources in catchments},
	title = {Measurement of soluble reactive phosphorus concentration profiles and fluxes in river-bed sediments using {DET} gel probes},
	volume = {350},
	issn = {0022-1694},
	url = {http://www.sciencedirect.com/science/article/pii/S0022169407006294},
	doi = {10.1016/j.jhydrol.2007.10.041},
	abstract = {DET (diffusive equilibrium in thin films) gel probes were used for sampling river-bed sediment porewaters, to characterise in situ soluble reactive phosphorus (SRP) concentration profiles and fluxes. DET probes were deployed in three contrasting rural streams: (1) a headwater ‘pristine’ stream, with minimal P inputs from low intensity grassland and no point sources, (2) an intensively cultivated arable catchment, and (3) a stream subject to high P loadings from sewage effluent and intensive arable farming. The DET results showed highly enriched porewater SRP concentrations of between ca. 400 and 5000μg-Pl−1 in the sewage-impacted stream. In contrast, the arable and pristine streams had porewater SRP concentrations {\textless}70μg-Pl−1 and {\textless}20μg-Pl−1, respectively. Porewater SRP concentration profiles in both the sewage-impacted and arable-impacted streams showed well-defined vertical structure, indicating internal sources and sinks of SRP within the sediment. However, there was little variability in porewater SRP concentrations in the pristine stream. The DET porewater profiles indicated net diffusion of SRP (a) from the overlying river water into the surface sediment and (b) from subsurface sediment upwards towards the sediment–water interface. A mass balance for the sewage-impacted site showed that the influx of SRP into the surface sediments from the overlying river water was small (ca. 1\% of the daily river SRP load). The DET results indicated that, in the arable and sewage-impacted streams, the surface ‘cap’ of fine sediment may play an important role in inhibiting upward movement of SRP from subsurface porewaters into the overlying river water, under steady-state, low-flow conditions.},
	language = {en},
	number = {3},
	urldate = {2020-03-01},
	journal = {Journal of Hydrology},
	author = {Jarvie, Helen P. and Mortimer, Robert J. G. and Palmer-Felgate, Elizabeth J. and Quinton, Katherine St. and Harman, Sarah A. and Carbo, Patricia},
	month = feb,
	year = {2008},
	keywords = {DET, Flux, Gel probe, River, Sediment, Soluble reactive phosphorus (SRP)},
	pages = {261--273},
}

@article{klotz_factors_1985,
	title = {Factors controlling phosphorus limitation in stream sediments},
	volume = {30},
	issn = {1939-5590},
	url = {http://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.1985.30.3.0543},
	doi = {10.4319/lo.1985.30.3.0543},
	abstract = {Factors influencing the phosphorus limitation of benthic microorganisms were determined for four streams (two agricultural and two forested) in central New York State over an annual cycle. Phosphorus limitation was measured biweekly as specific alkaline phosphatase activity (APA) of sediment samples. Analysis of variance showed the forested streams (sites 2 and 4) to have significantly different sediment APA from the agricultural streams (sites 1 and 3), the higher APA for the forested sites indicating greater phosphorus limitation. Stream total reactive phosphorus concentrations showed no relationship with watershed type, with mean annual values of 10.5 and 6.0 µg liter−1 for agricultural sites 1 and 3 and 4.1 and 9.6 for forested sites 2 and 4. With all sites grouped together, sediment APA had a low correlation with stream water phosphate (r = 0.184, n = 73). Phosphorus sorption isotherms showed sediments from agricultural streams to have higher phosphate sorption indices than forested sites and to sorb rapidly large amounts of phosphorus. This resulted in higher available phosphorus content for the agricultural sediments and lower sediment APA.},
	language = {en},
	number = {3},
	urldate = {2020-02-25},
	journal = {Limnology and Oceanography},
	author = {Klotz, R. L.},
	year = {1985},
	pages = {543--553},
}

@article{olander_regulation_2000,
	title = {Regulation of soil phosphatase and chitinase activityby {N} and {P} availability},
	volume = {49},
	issn = {1573-515X},
	url = {10.1023/A:1006316117817},
	doi = {10.1023/A:1006316117817},
	abstract = {Soil microorganisms and plants produce enzymes thatmineralize organically bound nutrients. When nutrientavailability is low, the biota may be able to increase production ofthese enzymes to enhance the supply of inorganicnitrogen (N) and phosphorus (P). Regulation of enzyme productionmay be a point where N and P cyclesinteract. We measured acid phosphatase and chitinase(N-acetyl ß-D-glucosaminide) activity in soilacross a chronosequence in Hawaii where N and Pavailability varies substantially among sites and longterm fertilizer plots had been maintained for over 4years.},
	language = {en},
	number = {2},
	urldate = {2020-02-29},
	journal = {Biogeochemistry},
	author = {Olander, Lydia P. and Vitousek, Peter M.},
	month = may,
	year = {2000},
	pages = {175--191},
}


@article{wang_enzymatic_2010-2,
	title = {Enzymatic hydrolysis of organic phosphorus in river bed sediments},
	volume = {36},
	issn = {0925-8574},
	url = {http://www.sciencedirect.com/science/article/pii/S0925857410000662},
	doi = {10.1016/j.ecoleng.2010.03.006},
	abstract = {Enzymatic hydrolysis of phosphorus (P) in bed sediments is an important process that maintains bioavailable P in the river systems. The P bioavailability is the criterion for assessing the eutrophication potential in rivers and streams. The objective of this research was to determine potential bioavailability of organic P (OP) in the Bronx River bed sediments using native phosphatases (NPase) and phosphodiesterase (PDEase) hydrolysis. The bed sediments collected in summer 2006 and 2007 were incubated at 37°C for 6h at pH 7.5 with NPase. The results showed that NPase hydrolyzed a substantial amount of OP (up to 76\%) under favorable temperature and pH, indicating OP could be hydrolyzed under increased temperature, and in turn increase in P availability in the river. Similarly, the resulting form sediments incubated with PDEase at 37°C and pH 8.8 showed that up to 82\% of OP could be hydrolyzed. Strong correlations between percentage of OP hydrolyzed by PDEase and organic matter (OM) were observed for sediments collected in 2006 (r=0.745; p≤0.01) and 2007 (r=0.724; p≤0.01), indicating PDEase hydrolysable P is mainly associated with OM. It is indicative that local hydro-climatic changes such as temperature increase and pH variations could hydrolyze a substantial amount of OP and increase bioavailable P in the water column, resulting in a potential threat to the river ecosystems.},
	language = {en},
	number = {7},
	urldate = {2020-02-29},
	journal = {Ecological Engineering},
	author = {Wang, Jingyu and Pant, Hari K.},
	month = jul,
	year = {2010},
	keywords = {Bioavailable P, Native phosphatases, P hydrolysis, Phosphodiesterase},
	pages = {963--968},
}

@article{berhe_erosion_2013,
	title = {Erosion, deposition, and the persistence of soil organic matter: mechanistic considerations and problems with terminology},
	volume = {38},
	copyright = {Copyright © 2013 John Wiley \& Sons, Ltd.},
	issn = {1096-9837},
	shorttitle = {Erosion, deposition, and the persistence of soil organic matter},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/esp.3408},
	doi = {10.1002/esp.3408},
	abstract = {The effect of erosional detachment, transport, and deposition of topsoil on the stock of soil organic matter (SOM) and its association with soil minerals has been a focus of a growing number of studies. A particularly lively debate is currently centered on the questions of whether terrestrial sedimentation of previously eroded SOM may constitute a relevant sink for atmospheric carbon dioxide (CO2), and how ‘stable’ such carbon (C) might be on multidecadal timescales. In this commentary, we illustrate how redistribution of eroded SOM within a landscape can create situations that are not adequately described by the jargon commonly used to characterize C turnover dynamics. We argue that more quantitative and scientifically rigorous categories are needed to describe soil C turnover and to promote the development of innovative, numerical models of C dynamics in landscapes characterized by significant mass movement. Copyright © 2013 John Wiley \& Sons, Ltd.},
	language = {en},
	number = {8},
	urldate = {2020-02-29},
	journal = {Earth Surface Processes and Landforms},
	author = {Berhe, Asmeret Asefaw and Kleber, Markus},
	year = {2013},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/esp.3408},
	keywords = {SOM carbon, soil erosion, soil organic matter persistence},
	pages = {908--912},
}

@article{sinsabaugh_ecoenzymatic_2011,
	title = {Ecoenzymatic stoichiometry of recalcitrant organic matter decomposition: the growth rate hypothesis in reverse},
	volume = {102},
	issn = {1573-515X},
	shorttitle = {Ecoenzymatic stoichiometry of recalcitrant organic matter decomposition},
	url = {10.1007/s10533-010-9482-x},
	doi = {10.1007/s10533-010-9482-x},
	abstract = {The flow of carbon and nutrients from plant production into detrital food webs is mediated by microbial enzymes released into the environment (ecoenzymes). Ecoenzymatic activities are linked to both microbial metabolism and environmental resource availability. In this paper, we extend the theoretical and empirical framework for ecoenzymatic stoichiometry from nutrient availability to carbon composition by relating ratios of β-1,4-glucosidase (BG), acid (alkaline) phosphatase (AP), β-N-acetylglucosaminidase (NAG), leucine aminopeptidase (LAP) and phenol oxidase (POX) activities in soils to measures of organic matter recalcitrance, using data from 28 ecosystems. BG and POX activities are uncorrelated even though both are required for lignocellulose degradation. However, the ratio of BG:POX activity is negatively correlated with the relative abundance of recalcitrant carbon. Unlike BG, POX activity is positively correlated with (NAG + LAP) and AP activities. We propose that the effect of organic matter recalcitrance on microbial C:N and C:P threshold element ratios (TER) can be represented by normalizing BG, AP and (NAG + LAP) activities to POX activity. The scaling relationships among these ratios indicate that the increasing recalcitrance of decomposing organic matter effectively reverses the growth rate hypothesis of stoichiometric theory by decreasing carbon and nutrient availability and slowing growth, which increases TERN:P. This effect is consistent with the narrow difference between the mean elemental C:N ratios of soil organic matter and microbial biomass and with the inhibitory effect of N enrichment on rates of decomposition and microbial metabolism for recalcitrant organic matter. From these findings, we propose a conceptual framework for bottom-up decomposition models that integrate the stoichiometry of ecoenzymatic activities into general theories of ecology.},
	language = {en},
	number = {1},
	urldate = {2020-02-29},
	journal = {Biogeochemistry},
	author = {Sinsabaugh, Robert L. and Follstad Shah, Jennifer J.},
	month = jan,
	year = {2011},
	pages = {31--43},
}

@article{marin-spiotta_paradigm_2014,
	title = {Paradigm shifts in soil organic matter research affect interpretations of aquatic carbon cycling: transcending disciplinary and ecosystem boundaries},
	volume = {117},
	issn = {1573-515X},
	shorttitle = {Paradigm shifts in soil organic matter research affect interpretations of aquatic carbon cycling},
	url = {10.1007/s10533-013-9949-7},
	doi = {10.1007/s10533-013-9949-7},
	abstract = {New conceptual models that highlight the importance of environmental, rather than molecular, controls on soil organic matter affect interpretations of organic matter (OM) persistence across terrestrial and aquatic boundaries. We propose that changing paradigms in our thinking about OM decomposition explain some of the uncertainties surrounding the fate of land-derived carbon (C) in marine environments. Terrestrial OM, which historically has been thought to be chemically recalcitrant to decay in soil and aquatic environments, dominates inputs to rivers yet is found in trace amounts in the ocean. We discuss three major transformations in our understanding of OM persistence that influence interpretations of the fate of aquatic OM: (1) a shift away from an emphasis on chemical recalcitrance as a primary predictor of turnover; (2) new interpretations of radiocarbon ages, which affect predictions of reactivity; and (3) the recognition that most OM leaving soils in dissolved form has been microbially processed. The first two explain rapid turnover for terrigenous OM in aquatic ecosystems once it leaves the soil matrix. The third suggests that the presence of terrestrial OM in aquatic ecosystems may be underestimated by the use of plant biomarkers. Whether these mechanisms occur in isolation of each other or in combination, they provide insight into the missing terrestrial C signature in the ocean. Spatially and temporally varying transformations of OM along land–water networks require that common terrestrial source indicators be interpreted within specific environmental contexts. We identify areas of research where collaborations between aquatic and terrestrial scientists will enhance quantification of C transfer from soils to inland water bodies, the ocean, and the atmosphere. Accurate estimates of OM processing are essential for improving predictions of the response of vulnerable C pools at the interface of soil and water to changes in climate and land use.},
	language = {en},
	number = {2},
	urldate = {2020-02-29},
	journal = {Biogeochemistry},
	author = {Marín-Spiotta, E. and Gruley, K. E. and Crawford, J. and Atkinson, E. E. and Miesel, J. R. and Greene, S. and Cardona-Correa, C. and Spencer, R. G. M.},
	month = mar,
	year = {2014},
	pages = {279--297},
}

@article{ellison_particulate_2006,
	title = {Particulate phosphorus bioavailability as a function of stream flow and land cover},
	volume = {40},
	issn = {0043-1354},
	url = {http://www.sciencedirect.com/science/article/pii/S0043135406000352},
	doi = {10.1016/j.watres.2006.01.016},
	abstract = {Using total phosphorus concentrations to estimate eutrophication risk is problematic for management purposes, as only some forms of phosphorus are biologically available for phytoplankton growth. This study estimated the bioavailability of particulate phosphorus, in forested, urban, agricultural (i.e. dairy farm) and mixed land cover streams. Sixteen stream sites were sampled during base and storm flow conditions and the following parameters were determined: total suspended solids, total phosphorus, total dissolved phosphorus, particulate phosphorus, percent bioavailable particulate phosphorus (\%BAPP), total bioavailable phosphorus and sediment particle size distribution. Algal assays with Pseudokirchneriella subcapitata were used to measure \%BAPP. Percent BAPP averaged 17\%, 26\% and 24\% for streams draining catchments with forested, mixed use and agricultural land cover, respectively, and \%BAPP did not vary significantly between base and storm flow conditions in these stream types. In contrast, \%BAPP averaged 73\% in the urban streams during baseflows but declined to an average of only 19\% during storms. Particle size distributions did not correlate with \%BAPP in these samples. During storm events, particulate phosphorus concentrations increased in all streams by an average of 614\% and total phosphorus increased by 200\%, whereas total BAP (i.e. total dissolved phosphorus+\%BAPP×particulate phosphorus) only increased by 72\% because on average only 20\% of the particulate phosphorus transported during these events was biologically available.},
	language = {en},
	number = {6},
	urldate = {2020-02-29},
	journal = {Water Research},
	author = {Ellison, Micaela E. and Brett, Michael T.},
	month = mar,
	year = {2006},
	keywords = {Baseflow, Bioavailability, Land cover, Particle size, Particulate phosphorus, Storm flow, Total phosphorus},
	pages = {1258--1268},
}

@article{noll_phosphorus_2009,
	series = {Special issue on {Watershed} {Management} and {Nearshore} {Lake} {Water} {Quality}, {The} {Conesus} {Lake} {Watershed} {Study}},
	title = {Phosphorus fractionation in soil and sediments along a continuum from agricultural fields to nearshore lake sediments: {Potential} ecological impacts},
	volume = {35},
	issn = {0380-1330},
	shorttitle = {Phosphorus fractionation in soil and sediments along a continuum from agricultural fields to nearshore lake sediments},
	url = {http://www.sciencedirect.com/science/article/pii/S0380133009000483},
	doi = {10.1016/j.jglr.2008.08.004},
	abstract = {The movement of phosphorus (P) from agricultural fields to streams and deposition in the nearshore of the lake presents a continuum of related physical and chemical properties that act to partition P into different physico-chemical fractions. We investigated changes in soil and sediment P fractionation as material was eroded from predominantly agricultural fields, transported via stream sediments, and deposited in a nearshore lake environment. Total phosphorus content of the soils and sediment decreased from field soils with an average concentration of 553.81 mg P kg−1 to 202.28 mg P kg−1 in stream sediments to 67.47 mg P kg−1 in lake sediments. Significant changes in P fractionation occurred during erosion, transport, and deposition of the particulate or sediment phase. The fractionation of P within the soils and sediments changed significantly from aluminum and organic matter associated P dominant in field soils to calcium associated P dominant in nearshore lake sediments. Various physical and chemical processes appear to be responsible for these transformations which impact the mobility and bioavailability of P. A significant amount of P was lost from field soils as they were transported and deposited. This P has either become available to biota or deposited in deeper portions of the lake system. Ultimately, the impact of P export on the nearshore lake environment may be influenced by the changes in P fractionation that occurred during transport and deposition and by the influence of macrophytes on the biogeochemical cycling of P in the sediment.},
	language = {en},
	urldate = {2020-02-29},
	journal = {Journal of Great Lakes Research},
	author = {Noll, Mark R. and Szatkowski, Aimee E. and Magee, Erin A.},
	month = jan,
	year = {2009},
	keywords = {Fractionation, Macrophytes, Nearshore, Phosphorus, Sediment, Soil},
	pages = {56--63},
}

@article{poirier_bioavailable_2012,
	title = {Bioavailable {Phosphorus} in {Fine}-{Sized} {Sediments} {Transported} from {Agricultural} {Fields}},
	volume = {76},
	issn = {0361-5995},
	url = {http://dl.sciencesocieties.org/publications/sssaj/articles/76/1/258},
	doi = {10.2136/sssaj2010.0441},
	language = {en},
	number = {1},
	urldate = {2020-02-29},
	journal = {Soil Science Society of America Journal},
	author = {Poirier, Simon-C. and Whalen, Joann K. and Michaud, Aubert R.},
	month = jan,
	year = {2012},
	note = {Publisher: The Soil Science Society of America, Inc.},
	pages = {258--267},
}

@article{jansson_bioavailable_2012,
	title = {Bioavailable phosphorus in humic headwater streams in boreal {Sweden}},
	volume = {57},
	copyright = {© 2012, by the Association for the Sciences of Limnology and Oceanography, Inc.},
	issn = {1939-5590},
	url = {http://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.2012.57.4.1161},
	doi = {10.4319/lo.2012.57.4.1161},
	abstract = {Bioavailable phosphorus (BAP) concentrations were determined nine times between April and October 2010 in two humic boreal headwater streams draining forest- and mire-dominated catchments. BAP was analyzed in a bioassay in which natural P-limited bacterioplankton grew with natural P as the sole P source. In both streams, approximately 90\% of the BAP occurred as dissolved species (passing a 0.2-µm filter), consisting partly of low-molecular-weight forms (passing a filter with nominal cutoff at 1 kDa) and partly of high-molecular-weight forms (passing a 0.2-µm filter but not a 1-kDa filter). Concentrations of total dissolved BAP varied between 1 µg L−1 and 14 µg L−1, with the highest values in the middle of the summer. Compared to the forest stream, BAP concentrations were generally higher in the mire stream, where it occasionally amounted to nearly 50\% of total P. Molybdate reactive phosphorus overestimated BAP considerably. Most of the BAP was in forms other than free orthophosphate. Temporal BAP variations showed no relationships with dissolved organic carbon (C) or iron but were positively related to air temperature and negatively related to the absorbance ratio (a254 : a365) of organic compounds in the water, indicating connections between terrestrial export of BAP and temperature-dependent terrestrial C metabolism. Concentrations of BAP can relieve stream bacteria from P limitation, and a significant share of BAP exported to streams can reach and be used in downstream lakes.},
	language = {en},
	number = {4},
	urldate = {2020-02-29},
	journal = {Limnology and Oceanography},
	author = {Jansson, Mats and Berggren, Martin and Laudon, Hjalmar and Jonsson, Anders},
	year = {2012},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.4319/lo.2012.57.4.1161},
	pages = {1161--1170},
}

@article{hanrahan_among-site_2020,
	title = {Among-site variability in environmental and management characteristics: {Effect} on nutrient loss in agricultural tile drainage},
	issn = {0380-1330},
	shorttitle = {Among-site variability in environmental and management characteristics},
	url = {http://www.sciencedirect.com/science/article/pii/S0380133020300393},
	doi = {10.1016/j.jglr.2020.02.004},
	abstract = {Water quality issues, including harmful and nuisance algal blooms (HNABs), related to nitrogen (N) and phosphorus (P) exported from agricultural lands persist in the Great Lakes region. Previous work examining N and P loss from agricultural fields in portions of the United States (US) and Canada (CA) that drain into Lake Erie, consistently indicate significant nutrient loss from fields in Indiana and Ohio, US compared with those in southwestern Ontario, CA. The primary objective of this study was to examine variation in environmental and management characteristics from 30 sites (US: n = 28, CA: n = 2) located within the Lake Erie Basin and subsequently determine the influence of among-site variation on edge-of-field N and P losses. Using principal component analyses (PCA), we found that among-site variation was predominantly controlled by broad-scale patterns in fertilizer management practices and soil properties; however, N and P loss metrics were largely unexplained by these gradients. As such, fine-scale variability and the interaction of environmental and management characteristics at individual sites more strongly influenced N and P loss. Ultimately, these results further emphasize the importance of site- and nutrient-specific management plans that are needed to mitigate N and P losses from agricultural fields.},
	language = {en},
	urldate = {2020-02-28},
	journal = {Journal of Great Lakes Research},
	author = {Hanrahan, Brittany R. and King, Kevin W. and Macrae, Merrin L. and Williams, Mark R. and Stinner, Jedediah H.},
	month = feb,
	year = {2020},
	keywords = {Agricultural land use, Agricultural management, Nitrogen, Phosphorus},
}

@article{mcdowell_comparison_2001,
	title = {A {Comparison} of {Fluvial} {Sediment} {Phosphorus} ({P}) {Chemistry} in {Relation} to {Location} and {Potential} to {Influence} {Stream} {P} {Concentrations}},
	volume = {7},
	issn = {1573-1421},
	url = {10.1023/A:1015274426411},
	doi = {10.1023/A:1015274426411},
	abstract = {Fluvial sediments are subject to cyclic submersion during changes in stream flow, which can affect their phosphorus (P) sorptive capacity. As fluvial sediments play a major role in determining P concentrations in stream flow, we compared the P chemistry of exposed stream bank and submerged bed sediments from an agricultural catchment in central Pennsylvania, USA. Total P concentration was greater in bank (417 mg kg-1) than bed sediments (281 mg kg-1), but because bed sediments contained more sand-sized material, they could release more P and support a higher solution P concentration (0.043 mg l-1) than bank sediments (0.020 mg l-1). Phosphorus release was a function of Mehlich-3 soluble Fe in stream sediments (r {\textgreater} 0.65), reflecting redox processes in the fluvial system. In contrast, P sorption maxima of bank and bed sediments were related to Mehlich-3 soluble Al (r {\textgreater} 0.78) and organic matter concentration (r {\textgreater} 0.79). Overall, our research suggested that erosion of bank sediments should contribute less P and may be a sink for P in the stream system compared with resuspension of bed sediment. However, bank sediments may have the potential to be a large source of P in downstream reservoirs or lakes, where increased microbial activity and reducing conditions may solubilise sediment-bound P.},
	language = {en},
	number = {4},
	urldate = {2020-02-27},
	journal = {Aquatic Geochemistry},
	author = {McDowell, R. W. and Sharpley, A. N.},
	month = dec,
	year = {2001},
	pages = {255--265},
}

@article{haggard_phosphate_2004,
	title = {{PHOSPHATE} {EQUILIBRIUM} {BETWEEN} {STREAM} {SEDIMENTS} {AND} {WATER}: {POTENTIAL} {EFFECT} {OF} {CHEMICAL} {AMENDMENTS}},
	volume = {47},
	issn = {2151-0059},
	shorttitle = {{PHOSPHATE} {EQUILIBRIUM} {BETWEEN} {STREAM} {SEDIMENTS} {AND} {WATER}},
	url = {http://elibrary.asabe.org/abstract.asp??JID=3&AID=16584&CID=t2004&v=47&i=4&T=1},
	doi = {10.13031/2013.16584},
	language = {en},
	number = {4},
	urldate = {2020-02-27},
	journal = {Transactions of the ASAE},
	author = {Haggard, B.E. and Ekka, S. A. and Matlock, M. D. and Chaubey, I.},
	year = {2004},
	pages = {1113--1118},
}

@article{findlay_importance_1995,
	title = {Importance of surface-subsurface exchange in stream ecosystems: {The} hyporheic zone},
	volume = {40},
	copyright = {© 1995, by the Association for the Sciences of Limnology and Oceanography, Inc.},
	issn = {1939-5590},
	shorttitle = {Importance of surface-subsurface exchange in stream ecosystems},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.1995.40.1.0159},
	doi = {10.4319/lo.1995.40.1.0159},
	abstract = {In many streams, significant amounts of water are exchanged between saturated sediments surrounding the open channel (the hyporheic zone) and the channel itself. Such exchanges with the hyporheic zone have the potential to cause large changes in streamwater chemistry because the rates of biogeochemical processes and the actual types of processes (e.g. anaerobic vs. aerobic metabolism) may be fundamentally different. I propose an organizational scheme for grouping stream systems into clusters of minimal, moderate, and maximal contribution of hyporheic metabolism to the overall ecosystem. Lack of information on quantitative hydrology for different stream systems prohibits actual testing of this framework. An alternative scheme is presented that organizes several well-studied streams as a function of subsurface residence time and differences in oxygen content. This second scheme is intended to stimulate discussion of conceptual frameworks for cross-system comparisons of the importance of hyporheic sediments in stream ecosystems.},
	language = {en},
	number = {1},
	urldate = {2020-02-27},
	journal = {Limnology and Oceanography},
	author = {Findlay, Stuart},
	year = {1995},
	note = {\_eprint: https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.4319/lo.1995.40.1.0159},
	pages = {159--164},
}

@article{montgomery_channel-reach_1997,
	title = {Channel-reach morphology in mountain drainage basins},
	volume = {109},
	issn = {0016-7606},
	url = {https://pubs.geoscienceworld.org/gsabulletin/article/109/5/596/183255/Channel-reach-morphology-in-mountain-drainage},
	doi = {10.1130/0016-7606(1997)109<0596:CRMIMD>2.3.CO;2},
	language = {en},
	number = {5},
	urldate = {2020-02-27},
	journal = {GSA Bulletin},
	author = {Montgomery, David R. and Buffington, John M.},
	month = may,
	year = {1997},
	note = {Publisher: GeoScienceWorld},
	pages = {596--611},
}

@article{rohm_evaluation_1987,
	title = {Evaluation of an {Aquatic} {Ecoregion} {Classification} of {Streams} in {Arkansas}},
	volume = {4},
	issn = {0270-5060},
	url = {10.1080/02705060.1987.9665169},
	doi = {10.1080/02705060.1987.9665169},
	abstract = {The efficacy of a regional stream classification system, based on the principle that streams reflect the character of the lands they drain, was evaluated in Arkansas. The classification consisted of six aquatic ecoregions defined by relatively homogeneous types of land-surface form, soil, potential natural vegetation and land use. Fish, physical habitat and water quality were sampled in 22 streams throughout the state. Data subjected to ordination analysis generally showed greater similarity in streams within the same ecoregion than in streams in different ecoregions. The patterns developed separately from fish, physical habitat and water quality data sets were relatively concordant. The null hypothesis that the classification did not reflect fundamental differences among the streams was rejected. We concluded that a regional stream classification is potentially useful for evaluating and managing streams. The identification of regions containing streams with similar character can aid in selecting reference streams for impact assessments or in selecting monitoring sites from which results may be extrapolated regionally.},
	number = {1},
	urldate = {2020-02-27},
	journal = {Journal of Freshwater Ecology},
	author = {Rohm, Christina M. and Giese, John W. and Bennett, Charles C.},
	month = jun,
	year = {1987},
	note = {Publisher: Taylor \& Francis
\_eprint: 10.1080/02705060.1987.9665169},
	pages = {127--140},
}

@article{clarendon_influence_2019,
	title = {The influence of particle size and mineralogy on both phosphorus retention and release by streambed sediments},
	volume = {19},
	issn = {1614-7480},
	url = {10.1007/s11368-019-02267-w},
	doi = {10.1007/s11368-019-02267-w},
	abstract = {In many streams worldwide including those on the south coast of Western Australia (WA), sediments of the {\textgreater} 2-mm fraction often contribute up to 50\% of the streambed. However, most analysis and interpretation of sediment chemistry, including phosphorus (P), is conducted on the {\textless} 2-mm fraction as this fraction is considered the most chemically reactive. This paper aims to identify the contribution of the {\textgreater} 2-mm fraction to P retention and release in sandy-gravely streams.},
	language = {en},
	number = {5},
	urldate = {2020-02-27},
	journal = {Journal of Soils and Sediments},
	author = {Clarendon, Simon D. V. and Weaver, David M. and Davies, Peter M. and Coles, Neil A.},
	month = may,
	year = {2019},
	pages = {2624--2633},
}

@article{brennan_linking_2017,
	title = {Linking {Soil} {Erosion} to {Instream} {Dissolved} {Phosphorus} {Cycling} and {Periphyton} {Growth}},
	volume = {53},
	copyright = {© 2017 American Water Resources Association},
	issn = {1752-1688},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1752-1688.12534},
	doi = {10.1111/1752-1688.12534},
	abstract = {Phosphorus (P) is a limiting nutrient in freshwater systems and when present in runoff from agricultural lands or urban centers may contribute to excessive periphyton growth. In this study, we examined the link between soil erosion and delivery of eroded soil to streams during flow events, and the impact of that freshly deposited soil on dissolved reactive P (DRP) concentrations and periphyton growth under baseflow conditions when the risk of stream eutrophication is greatest. A microcosm experiment was designed to simulate the release of P from soil which had been amended with different amounts of P fertilizer to overlying water during baseflow conditions. Unglazed tiles, inoculated for five days in a second order stream, were incubated for seven days in microcosms containing soil with eight levels of soil Mehlich-3 plant available phosphorus (M3P) ranging from 20 to 679 mg/kg M3P. Microcosm DRP was monitored. Following incubation tiles were scraped and the periphyton analyzed for chlorophyll a. Microcosm DRP concentrations increased with increasing soil M3P and equilibrium phosphorus concentration (EPC0). Relationships between M3P, EPC0, and DRP were nonlinear and increases in soil M3P and/or DRP had a greater impact on biomass accumulation when these parameters were above threshold values of 30 mg/kg M3P and 0.125 mg/L DRP. Significantly, this ecological threshold corresponds to the agronomic thresholds above which increased soil M3P does not increase plant response.},
	language = {en},
	number = {4},
	urldate = {2020-02-27},
	journal = {JAWRA Journal of the American Water Resources Association},
	author = {Brennan, R. B. and Scott, J. T. and Sharpley, A. N. and Lally, H. T. and Jarvie, H. P. and Bowes, M. J. and Haggard, B. E. and Gbur, E.},
	year = {2017},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1752-1688.12534},
	keywords = {agriculture, chlorophyll a, diffuse pollution, ecology, fluvial-sediment, freshwater, phosphorus},
	pages = {809--821},
}

@article{rogers_phosphorus_2012,
	title = {Phosphorus {Uptake} and {Release} from {Submerged} {Sediments} in a {Simulated} {Stream} {Channel} {Inundated} with a {Poultry} {Litter} {Source}},
	volume = {224},
	issn = {1573-2932},
	url = {10.1007/s11270-012-1361-8},
	doi = {10.1007/s11270-012-1361-8},
	abstract = {Northwest Arkansas, similar to many regions around the world, is home to intensive poultry production, which concentrates large amounts of nutrients in localized areas. Concerns over phosphorus (P) continue in these regions despite extensive conservation management efforts. Part of the concerns relates to the legacy effect of P in streams and the role of fluvial sediments in confounding land conservation measures. Sediment substrate was collected from five streams containing a variety of land uses in the Upper Illinois River Watershed (UIRW) to assess the buffering capacity of sediments on water column P. A purpose built fluvarium was used to determine sediment–P relationships during three flow phases: (I) baseflow ({\textless}0.005 mg P L−1), (II) uptake-enriched (1.8 mg P L−1), and (III) re-equilibration ({\textless}0.005 mg P L−1) where water was circulated over the sediment for 48 h at 0.001 m3 s−1 (1 L s−1). During each phase, flow was monitored and water sampled for determination of dissolved reactive P (DRP). In phase I, DRP reached equilibrium concentrations, which closely mimicked stream DRP at the time of sediment collection (R2 = 0.77), and the highest concentration measured was 0.080 mg P L−1 and the lowest 0.016 mg P L−1. Sediments rapidly bound P (40 \% within 1 h) during phase II. During phase II, 84 to 96 \% of added P was removed from solution. Of this bound P, 1 to 7 \% was released during phase III. Results indicate that fluvial sediments in the UIRW act as transient storage sites for P during high P events. Finally, streams that bound the most P during nutrient-rich flow released the least when returned to low P flow, indicating a greater ability to buffer P in streams.},
	language = {en},
	number = {1},
	urldate = {2020-02-27},
	journal = {Water, Air, \& Soil Pollution},
	author = {Rogers, Christopher W. and Sharpley, Andrew N. and Haggard, Brian E. and Scott, J. Thad},
	month = nov,
	year = {2012},
	pages = {1361},
}

@article{rogers_physicochemical_2011,
	title = {Physicochemical {Characterization} of {Sediment} in {Northwest} {Arkansas} {Streams}},
	volume = {02},
	url = {http://www.scirp.org/journal/PaperInformation.aspx?PaperID=5887&#abstract},
	doi = {10.4236/jep.2011.25072},
	abstract = {Eutrophication of surface waters is a critical concern in regions around the world facing nutrient surpluses as a result of confined animal feeding operations (CAFOs) and subsequent land application of manures. While large amounts of research exist on the transport of nutrient enriched runoff from fields to surface waters less information is available on in-stream processes controlling the transport of P in-stream. Thus, information is needed on the role of stream sediments in regulating transient phosphorus (P) to better understand the relationship between nutrient inputs and water quality. Fine-sized sediments ({\textless}2-mm) regulate P via sorption and burial, while algae attached to larger-sediments ({\textgreater} 2-mm) consume and store P. From fine-sized sediment a modified P saturation ratio (PSR$_{\textrm{mod}}$), related to the sediment’s ability to bind P and determined from Mehlich-3 extracted nutrients, has been correlated to in-stream dissolved reactive P (DRP) concentrations. The objectives of this study were to determine the relative size distribution of total- and fine-sized sediment (sand, silt clay) fractions among streams, determine the optimum sample number needed to characterize Mehlich-3 P (M3P) and PSR$_{\textrm{mod}}$, and finally determine the applicability of PSR$_{\textrm{mod}}$, as an indicator of stream water column DRP concentrations. Stream sediments were sampled from the 0- to 3-cm depth from stream reaches ranging from (25 – 75 m) in August, 2008 for characterization along with water samples collected from the thalweg for DRP concentration determination. Additional water column samples were collected along with fine-sized sedi- ment chemical properties in February, May, and June 2009. The distribution of sediment size classes was statistically similar, with 2- to 20- and 20- to 75-mm sized sediment dominating. Fine-sized sediment ({\textless}2 mm) contributed 9 to 18\% of total-sediment and was comprised primarily of sand. Sampled stream M3P and PSR$_{\textrm{mod}}$, were determined to typically be sufficiently characterized by a sample scheme utilizing three samples points. Modified P saturation ratio of {\textless} 2-mm sediment was highly correlated to DRP levels across sampling dates (r = 0.86), suggesting PSR$_{\textrm{mod}}$, has the potential to be used as an indicator of the ability of stream sediments to enrich stream water with P. Thus, fine-sized sediment nutrient concentrations appear to be key regulators of water column P concentrations.},
	language = {en},
	number = {05},
	urldate = {2020-02-27},
	journal = {Journal of Environmental Protection},
	author = {Rogers, Chris W. and Sharpley, Andrew N. and Haggard, Brian E. and Scott, J. Thad and Drake, Bodie M.},
	month = jul,
	year = {2011},
	note = {Number: 05
Publisher: Scientific Research Publishing},
	pages = {629},
}

@article{gellis_combining_2019,
	title = {Combining sediment fingerprinting with age-dating sediment using fallout radionuclides for an agricultural stream, {Walnut} {Creek}, {Iowa}, {USA}},
	volume = {19},
	issn = {1614-7480},
	url = {10.1007/s11368-018-2168-z},
	doi = {10.1007/s11368-018-2168-z},
	abstract = {The main purpose of this study was to demonstrate the utility of the sediment fingerprinting approach to apportion surface-derived sediment, and then age date that portion using short-lived fallout radionuclides. In systems where a large mass of mobile sediment is in channel storage, age dating provides an understanding of the transfer of sediment through the watershed and the time scales over which management actions to reduce sediment loadings may be effective.},
	language = {en},
	number = {9},
	urldate = {2020-02-27},
	journal = {Journal of Soils and Sediments},
	author = {Gellis, Allen C. and Fuller, Christopher C. and Van Metre, Peter and Filstrup, Christopher T. and Tomer, Mark D. and Cole, Kevin J. and Sabitov, Timur Y.},
	month = sep,
	year = {2019},
	pages = {3374--3396},
}

@article{schmidt_linking_2019,
	title = {Linking the {Agricultural} {Landscape} of the {Midwest} to {Stream} {Health} with {Structural} {Equation} {Modeling}},
	volume = {53},
	issn = {0013-936X},
	url = {10.1021/acs.est.8b04381},
	doi = {10.1021/acs.est.8b04381},
	abstract = {Multiple physical and chemical stressors can simultaneously affect the biological condition of streams. To better understand the complex interactions of land-use practices, water quality, and ecological integrity of streams, the U.S. Geological Survey National Water Quality Assessment Project is conducting regional-scale assessments of stream condition across the United States. In the summer of 2013, weekly water samples were collected from 100 streams in the Midwestern United States. Employing watershed theory, we used structural equation modeling (SEM) to represent a general hypothesis for how 16 variables (previously identified to be important to stream condition) might be inter-related. Again, using SEM, we evaluated the ability of this “stressor network” to explain variations in multimetrics of algal, invertebrate, and fish community health, trimming away any environmental variables not contributing to an explanation of the ecological responses. Seven environmental variables—agricultural and urban land use, sand content of soils, basin area, percent riparian area as forest, channel erosion, and relative bed stability—were found to be important for all three-community metrics. The algal and invertebrate models included water-chemistry variables not included in the fish model. Results suggest that ecological integrity of Midwest streams are affected by both agricultural and urban land uses and by the natural geologic setting, as indicated by the sand content of soils. Chemicals related to crops (pesticides and nutrients) and residential uses (pyrethroids) were found to be more strongly related to ecological integrity than were natural factors (riparian forest, watershed soil character).},
	number = {1},
	urldate = {2020-02-27},
	journal = {Environmental Science \& Technology},
	author = {Schmidt, Travis S. and Van Metre, Peter C. and Carlisle, Daren M.},
	month = jan,
	year = {2019},
	note = {Publisher: American Chemical Society},
	pages = {452--462},
}

@article{konrad_factors_2018,
	title = {Factors {Influencing} {Fine} {Sediment} on {Stream} {Beds} in the {Midwestern} {United} {States}},
	volume = {47},
	issn = {0047-2425},
	url = {https://dl.sciencesocieties.org/publications/jeq/abstracts/47/5/1214},
	doi = {10.2134/jeq2018.02.0060},
	language = {en},
	number = {5},
	urldate = {2020-02-27},
	journal = {Journal of Environmental Quality},
	author = {Konrad, Christopher and Gellis, Allen},
	year = {2018},
	note = {Publisher: The American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.},
	pages = {1214--1222},
}

@article{hatfield_convergence_2013,
	title = {Convergence of agricultural intensification and climate change in the {Midwestern} {United} {States}: implications for soil and water conservation},
	volume = {64},
	issn = {1448-6059},
	shorttitle = {Convergence of agricultural intensification and climate change in the {Midwestern} {United} {States}},
	url = {https://www.publish.csiro.au/mf/MF12164},
	doi = {10.1071/MF12164},
	abstract = {Society faces substantial challenges to expand food production while adapting to climatic changes and ensuring ecosystem services are maintained. A convergence of these issues is occurring in the Midwestern United States, i.e. the ‘cornbelt’ region that provides substantial grain supplies to world markets but is also well known for its contribution to hypoxic conditions in the Gulf of Mexico due to agricultural nutrient losses. This review examines anticipated trends in climate and possible consequences for grain production and soil resource management in this region. The historic climate of this region has been ideal for large-scale agriculture, and its soils are among the world’s most productive. Yet under current trends, degradation of the soil resource threatens our capacity to ensure a stable food supply and a clean environment in the face of a changing climate. A set of strategies and practices can be implemented to meet these challenges by maintaining and improving hydrologic and plant-growth functions of soil, which will improve outcomes for aquatic ecosystems and for the agricultural sector. Soil management ensures our long-term capacity to provide a reliable food supply, and mitigates pressures to expand agricultural practices into marginal croplands that would lead to further environmental degradation.},
	language = {en},
	number = {5},
	urldate = {2020-02-27},
	journal = {Marine and Freshwater Research},
	author = {Hatfield, J. L. and Cruse, R. M. and Tomer, M. D.},
	month = may,
	year = {2013},
	note = {Publisher: CSIRO PUBLISHING},
	pages = {423--435},
}

@article{sayler_alkaline_1979,
	title = {Alkaline {Phosphatase} {Assay} for {Freshwater} {Sediments}: {Application} to {Perturbed} {Sediment} {Systems}},
	volume = {38},
	issn = {0099-2240, 1098-5336},
	shorttitle = {Alkaline {Phosphatase} {Assay} for {Freshwater} {Sediments}},
	url = {https://aem.asm.org/content/38/5/922},
	abstract = {The p-nitrophenyl phosphate hydrolysis-phosphatase assay was modified for use in freshwater sediment. Laboratory studies indicated that the recovery of purified alkaline phosphatase activity was 100\% efficient in sterile freshwater sediments when optimized incubation and sonication conditions were used. Field studies of diverse freshwater sediments demonstrated the potential use of this assay for determining stream perturbation. Significant correlations between phosphatase and total viable cell counts, as well as adenosine triphosphate biomass, suggested that alkaline phosphatase activity has utility as an indicator of microbial population density and biomass in freshwater sediments.},
	language = {en},
	number = {5},
	urldate = {2020-02-26},
	journal = {Applied and Environmental Microbiology},
	author = {Sayler, Gary S. and Puziss, Marla and Silver, Martin},
	month = nov,
	year = {1979},
	pmid = {16345464},
	note = {Publisher: American Society for Microbiology
Section: General Microbial Ecology},
	pages = {922--927},
}

@article{sinsabaugh_ecoenzymatic_2012,
	title = {Ecoenzymatic {Stoichiometry} and {Ecological} {Theory}},
	volume = {43},
	issn = {1543-592X},
	url = {https://www.annualreviews.org/doi/10.1146/annurev-ecolsys-071112-124414},
	doi = {10.1146/annurev-ecolsys-071112-124414},
	abstract = {The net primary production of the biosphere is consumed largely by microorganisms, whose metabolism creates the trophic base for detrital foodwebs, drives element cycles, and mediates atmospheric composition. Biogeochemical constraints on microbial catabolism, relative to primary production, create reserves of detrital organic carbon in soils and sediments that exceed the carbon content of the atmosphere and biomass. The production of organic matter is an intracellular process that generates thousands of compounds from a small number of precursors drawn from intermediary metabolism. Osmotrophs generate growth substrates from the products of biosynthesis and diagenesis by enzyme-catalyzed reactions that occur largely outside cells. These enzymes, which we define as ecoenzymes, enter the environment by secretion and lysis. Enzyme expression is regulated by environmental signals, but once released from the cell, ecoenzymatic activity is determined by environmental interactions, represented as a kinetic cascade, that lead to multiphasic kinetics and large spatiotemporal variation. At the ecosystem level, these interactions can be viewed as an energy landscape that directs the availability and flow of resources. Ecoenzymatic activity and microbial metabolism are integrated on the basis of resource demand relative to environmental availability. Macroecological studies show that the most widely measured ecoenzymatic activities have a similar stoichiometry for all microbial communities. Ecoenzymatic stoichiometry connects the elemental stoichiometry of microbial biomass and detrital organic matter to microbial nutrient assimilation and growth. We present a model that combines the kinetics of enzyme activity and community growth under conditions of multiple resource limitation with elements of metabolic and ecological stoichiometry theory. This biogeochemical equilibrium model provides a framework for comparative studies of microbial community metabolism, the principal driver of biogeochemical cycles.},
	number = {1},
	urldate = {2020-02-26},
	journal = {Annual Review of Ecology, Evolution, and Systematics},
	author = {Sinsabaugh, Robert L. and Follstad Shah, Jennifer J.},
	month = nov,
	year = {2012},
	note = {Publisher: Annual Reviews},
	pages = {313--343},
}

@article{blann_effects_2009,
	title = {Effects of agricultural drainage on aquatic ecosystems: {A} review},
	volume = {39},
	issn = {1064-3389},
	shorttitle = {Effects of {Agricultural} {Drainage} on {Aquatic} {Ecosystems}},
	url = {10.1080/10643380801977966},
	doi = {10.1080/10643380801977966},
	abstract = {The extensive development of surface and subsurface drainage systems to facilitate agricultural production throughout North America has significantly altered the hydrology of landscapes compared to historical conditions. Drainage has transformed nutrient and hydrologic dynamics, structure, function, quantity, and configuration of stream and wetland ecosystems. In many agricultural regions, more than 80\% of some catchment basins may be drained by surface ditches and subsurface drain pipes (tiles). Natural channels have been straightened and deepened for surface drainage ditches with significant effects on channel morphology, instream habitats for aquatic organisms, floodplain and riparian connectivity, sediment dynamics, and nutrient cycling. The connection of formerly isolated wetland basins to extensive networks of surface drainage and the construction of main channel ditches through millions of acres of formerly low-lying marsh or wet prairie, where no defined channel may have previously existed, have resulted in large-scale conversion of aquatic habitat types, from wetland mosaics to linear systems. Reduced surface storage, increased conveyance, and increased effective drainage area have altered the dynamics of and generally increased flows in larger streams and rivers. Cumulatively, these changes in hydrology, geomorphology, nutrient cycling, and sediment dynamics have had profound implications for aquatic ecosystems and biodiversity.},
	number = {11},
	urldate = {2020-01-31},
	journal = {Critical Reviews in Environmental Science and Technology},
	author = {Blann, Kristen L. and Anderson, James L. and Sands, Gary R. and Vondracek, Bruce},
	month = nov,
	year = {2009},
	keywords = {fish, hydrology, macroinvertebrates, nutrients, water quality, wetlands},
	pages = {909--1001},
}

@article{oviedo-vargas_dissolved_2013,
	title = {Dissolved organic carbon manipulation reveals coupled cycling of carbon, nitrogen, and phosphorus in a nitrogen-rich stream},
	volume = {58},
	copyright = {© 2013, by the Association for the Sciences of Limnology and Oceanography, Inc.},
	issn = {1939-5590},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.2013.58.4.1196},
	doi = {10.4319/lo.2013.58.4.1196},
	abstract = {To investigate the coupling between carbon (C) and phosphorus (P) cycling in a human-altered stream, we conducted a whole-ecosystem manipulation of the labile dissolved organic carbon (DOC) pool in a nitrate ()-rich stream in the midwestern United States. For 6 d, we increased stream DOC by ∼ 1 mg L−1 through a continuous addition of sodium acetate. On the sixth day of the addition, ammonium () was increased by ∼ 130 µg N L−1 to examine the potential for nitrogen (N) to mediate coupled C and P cycling. Of the added DOC, 85\% was retained within the treatment reach, which increased ecosystem respiration with respect to the reference reach. Alkaline phosphatase activity (APA) increased from day 1 to day 6; however, water column P uptake only increased on day 6 concurrent with the addition. Gross primary production decreased during the DOC addition relative to the reference reach, yet seemed to recover on day 6 ( addition). These results suggest that during the DOC addition, heterotrophs out-competed autotrophs for N and that sediment-sorbed P sustained the heterotrophic community while P uptake from the water column was dominated by autotrophs. Because APA and P uptake were stimulated by the simultaneous DOC and addition, P cycling appeared to be N limited, despite the high ambient concentration; this indicates a strong preferential uptake of over In streams, C and P cycling can be intrinsically coupled through biological mechanisms, and this coupling can be mediated by the availability of different forms of inorganic N.},
	language = {en},
	number = {4},
	urldate = {2020-02-26},
	journal = {Limnology and Oceanography},
	author = {Oviedo-Vargas, Diana and Royer, Todd V. and Johnson, Laura T.},
	year = {2013},
	note = {\_eprint: https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.4319/lo.2013.58.4.1196},
	pages = {1196--1206},
}

@article{nair_soil_2014,
	title = {Soil phosphorus saturation ratio for risk assessment in land use systems},
	volume = {2},
	issn = {2296-665X},
	url = {https://www.frontiersin.org/articles/10.3389/fenvs.2014.00006/full},
	doi = {10.3389/fenvs.2014.00006},
	abstract = {The risk of phosphorus loss from agricultural soils can have serious implications for water quality. This problem has been noted particularly in sandy soils in several parts of the world including Europe (e.g., the Netherlands, Italy, and UK) and the southeastern USA. However, the capacity of a soil to retain P is limited and even non-sandy soils have the potential to eventually release P when inorganic or organic fertilizer is added over a period of time. A threshold phosphorus saturation ratio (PSR), calculated from P, Fe and Al in an oxalate or a soil test solution such as Mehlich 1 or Mehlich 3, has been recognized as a practical means of determining when a soil has reached a level of P loading that constitutes an environmental risk. When soils are below a threshold PSR value, the equilibrium P concentration (EPC0) is minimal. Further, the soil P storage capacity calculated from the same data is directly linked to the strength of P bonding (KL) as determined from Langmuir isotherms, and KD, the distribution coefficient related to the strength of sorption. While the PSR is occasionally used as a predictor of the onset of environmentally significant P loss from a soil, the procedure might be adopted as a routine soil test.},
	language = {English},
	urldate = {2020-02-26},
	journal = {Frontiers in Environmental Science},
	author = {Nair, Vimala D.},
	year = {2014},
	note = {Publisher: Frontiers},
	keywords = {Langmuir, Mehlich 1, Mehlich 3, linear isotherm, oxalate, phosphorus risk assessment, soil P storage capacity, threshold phosphorus saturation ratio},
}

@article{sims_evaluation_2002,
	title = {Evaluation of {Mehlich} 3 as an {Agri}-{Environmental} {Soil} {Phosphorus} {Test} for the {Mid}-{Atlantic} {United} {States} of {America}},
	volume = {66},
	copyright = {Published in Soil Sci. Soc. Am. J.66:2016–2032.},
	issn = {1435-0661},
	url = {https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaj2002.2016},
	doi = {10.2136/sssaj2002.2016},
	abstract = {Laws and guidelines limiting P applications to cropland based on soil P exist in the Mid-Atlantic USA because of water quality concerns. We evaluated Mehlich 3 (M3) as an environmental soil P test using 465 soils typical to the Mid-Atlantic region and found M3-P accurately predicted water soluble P (WSP), desorbable P (Fe oxide strip P [FeO-P]), and total sorbed P (oxalate P). The M3-P saturation ratio (M3 [P/(Al+Fe)]) was linearly related to the well-established oxalate P saturation method (DPSox) and a M3 [P/(Al+Fe)] range of 0.10 to 0.15 corresponded to reported environmental limits for DPSox (25–40\%). Rainfall simulation and column leaching studies showed M3 [P/(Al+Fe)] predicted runoff and leachate P concentrations better than M3-P. We suggest consideration of the following approach now used in Delaware for agri-environmental interpretation of M3-P and M3 [P/(Al+Fe)]: (i) Below optimum (crop response likely; M3-P ≤ 50 mg kg−1; M3 [P/(Al+Fe)] {\textless} 0.06); (ii) Optimum (economic response to P unlikely, recommendations for P rarely made; M3-P = 51–100 mg kg−1; M3 [P/(Al+Fe)] = 0.06–0.11); (iii) Above Optimum (soil P will not limit crop yields, no P recommended; M3-P {\textgreater} 100 mg kg−1; M3 [P/(Al+Fe)] {\textgreater} 0.11); (iv) Environmental (implement improved P management to reduce potential for nonpoint P pollution—in Delaware M3-P {\textgreater} 150 mg kg−1; M3 [P/(Al+Fe)] {\textgreater} 0.15 is now used). (v) Natural Resource Conservation (no P applied even if the potential water quality impact is low to conserve P, a finite natural resource).},
	language = {en},
	number = {6},
	urldate = {2020-02-26},
	journal = {Soil Science Society of America Journal},
	author = {Sims, J. T. and Maguire, R. O. and Leytem, A. B. and Gartley, K. L. and Pautler, M. C.},
	year = {2002},
	note = {\_eprint: https://acsess.onlinelibrary.wiley.com/doi/pdf/10.2136/sssaj2002.2016},
	pages = {2016--2032},
}

@article{johnson_landscape_1997,
	title = {Landscape influences on water chemistry in {Midwestern} stream ecosystems},
	volume = {37},
	issn = {1365-2427},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-2427.1997.d01-539.x},
	doi = {10.1046/j.1365-2427.1997.d01-539.x},
	abstract = {1. Landscape characteristics of sixty-two subcatchments within the Saginaw Bay Catchment of central Michigan were examined to identify relationships with stream water chemistry. Land use, land cover and elevation were quantified for both entire catchments and the upland–river ecotone (100 m stream buffer strip). Catchment and ecotone data were then empirically compared with stream water chemistry using multivariate and regression analyses. Redundancy analysis was used to partition variance among land use, geology, and the shared influence of land use and geology. 2. Major catchments dominated by rowcrop agriculture had the highest alkalinity, total dissolved solids and nitrate + nitrite concentrations. 3. Strong seasonal differences were observed in total nitrogen and nitrite + nitrate, but not in total phosphorus or suspended solids. Land use and landscape structure factors such as slope and patch density (number of land use patches per km2) accounted for most of the observed variance in summer. 4. In both autumn and summer, landscape factors accounted for much of the observed variation in total dissolved solids and alkalinity. During autumn, geological factors and the shared influence of geology/landscape structure plus land use exerted more influence than did land use alone. 5. Total phosphorus and total suspended solids were much better explained by land use within the stream ecotone in summer than in other seasons. However, total nitrogen, nitrate, orthophosphate and alkalinity were equally well explained by land use within the ecotone and throughout the whole catchment. Only total dissolved solids in summer and ammonium in autumn were explained better by the whole catchment than the ecotone. 6. Our results show that relatively coarse spatial databases can provide useful descriptors of regional water quality.},
	language = {en},
	number = {1},
	urldate = {2020-02-25},
	journal = {Freshwater Biology},
	author = {Johnson, Lucinda and Richards, Carl and Host, George and Arthur, John},
	year = {1997},
	pages = {193--208},
}

@article{herlihy_relationship_1998,
	title = {The {Relationship} {Between} {Stream} {Chemistry} and {Watershed} {Land} {Cover} {Data} in the {Mid}-{Atlantic} {Region}, {U}.{S}.},
	volume = {105},
	issn = {1573-2932},
	url = {10.1023/A:1005028803682},
	doi = {10.1023/A:1005028803682},
	abstract = {In order to investigate the relationship between stream chemistry and watershed land cover at the regional scale, we analyzed data from 368 wadeable streams sampled in the mid-Atlantic region of the U.S. during spring 1993-1994. Study sites were selected using a probability sample and the digitized version of the 1:100,000 scale USGS map stream network as the sample population. Both classified Thematic Mapper (TM) and USGS Land Use/Land Cover (LULC) data were used to quantify land cover in the study watersheds. On average, the most common land cover was forest (77\%) followed by agriculture (20\%), and urban (1\%). Multiple regression analysis showed that concentrations of Cl-, nutrients, acid neutralization capacity, and base cations were the analytes most strongly related to watershed land cover. Despite large differences in resolution and age of the TM and LULC data sources, similar results were obtained with the two sources. Using a greater number of land cover subclasses did not greatly improve the land cover-chemistry relationships. Ecoregions with predominantly forested land cover had weaker relationships than ecoregions with more agricultural and/or urban land cover. In studies or databases without land cover information, Cl- concentration is a good surrogate indicator for general human disturbance in the watershed.},
	language = {en},
	number = {1},
	urldate = {2020-02-25},
	journal = {Water, Air, and Soil Pollution},
	author = {Herlihy, Alan T. and Stoddard, John L. and Johnson, Colleen Burch},
	month = jul,
	year = {1998},
	pages = {377--386},
}

@article{allan_influence_1997,
	title = {The influence of catchment land use on stream integrity across multiple spatial scales},
	volume = {37},
	issn = {1365-2427},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-2427.1997.d01-546.x},
	doi = {10.1046/j.1365-2427.1997.d01-546.x},
	abstract = {1. Despite wide recognition of the need for catchment-scale management to ensure the integrity of river ecosystems, the science and policy basis for joint management of land and water remains poorly understood. An interdisciplinary case study of a river basin in south-eastern Michigan is presented. 2. The River Raisin drains an area of 2776 km2, of which some 70\% is agricultural land. The upper basin consists of till and outwash, and both topography and land use/cover are diverse. The lower basin consists of fine textured lake deposits, is of low relief, and land use is primarily agricultural. 3. The River Raisin basin historically was a region of oak-savannah and wetlands. It was deforested, drained and converted to farmland during the mid-nineteenth century. Human population reached a plateau at about 1880, and then underwent a second period of growth after 1950, mainly in small urban areas. More recently, the amount of agricultural land has declined and forested land has increased, in accord with a general decline in farming activity. 4. It could be suggested that the influence of land use on stream integrity is scale-dependent. Instream habitat structure and organic matter inputs are determined primarily by local conditions such as vegetative cover at a site, whereas nutrient supply, sediment delivery, hydrology and channel characteristics are influenced by regional conditions, including landscape features and land use/cover at some distance upstream and lateral to stream sites. 5. Sediment concentrations measured during low flows were higher in areas of greater agriculture. In a comparison of two subcatchments, sediment yields were up to ten times greater in the more agricultural location, in response to similar storm events. A distributed parameter model linked to a geographical information system predicted that an increase in forested land cover would result in dramatic declines in runoff and sediment and nutrient yields. 6. Habitat quality and biotic integrity varied widely among individual stream sites in accord with patterns in land use/cover. Extent of agricultural land at the subcatchment scale was the best single predictor of local stream conditions. Local riparian vegetation was uncorrelated with overall land use and was a weak secondary predictor of habitat quality and biotic integrity. 7. Investigation of the regulatory agencies involved in land and water management in the basin revealed a complex web of overlapping political jurisdictions. Most land-use decision-making occurs at the local level of township, city or village. Unfortunately, local decision-making bodies typically lack the information and jurisdictional authority to influence up- and downstream events.},
	language = {en},
	number = {1},
	urldate = {2020-02-25},
	journal = {Freshwater Biology},
	author = {Allan, David and Erickson, Donna and Fay, John},
	year = {1997},
	pages = {149--161},
}

@article{arheimer_nitrogen_2000,
	title = {Nitrogen and phosphorus concentrations from agricultural catchments—influence of spatial and temporal variables},
	volume = {227},
	issn = {0022-1694},
	url = {http://www.sciencedirect.com/science/article/pii/S0022169499001778},
	doi = {10.1016/S0022-1694(99)00177-8},
	abstract = {The eutrophication problem has drawn attention to nutrient leaching from arable land in southern Sweden, and further understanding of spatial and temporal variability is needed in order to develop decision-making tools. Thus, the influence of spatial and temporal variables was analysed statistically using empirical time series of different nutrient species from 35 well-documented catchments (2–35km2), which have been monitored for an average of 5years. In the spatial analysis several significant correlations between winter median concentrations and catchment characteristics were found. The strongest correlation was found between inorganic nitrogen and land use, while concentrations of different phosphorus species were highly correlated to soil texture. Multiple linear regression models gave satisfactory results for prediction of median winter concentrations in unmeasured catchments, especially for inorganic nitrogen and phosphate. In the analysis of temporal variability within catchments, internal variables from a dynamic hydrological model (HBV) were linked to concentration fluxes. It was found that phosphorus and inorganic nitrogen concentrations were elevated during flow increase at low-flow conditions, while they were diluted as the wetness in the catchment increased. During unmonitored periods regression models were successful in predicting temporal variability of total phosphorus, phosphate and inorganic nitrogen, while organic nitrogen and particulate phosphorus could not be predicted with this approach. Dividing the data into different flow categories did not improve the prediction of nutrient concentration dynamics. The results and literature review presented, confirm parts of the present HBV-N model approach and will be useful for further development of nutrient routines linked to dynamic hydrological models.},
	language = {en},
	number = {1},
	urldate = {2020-02-25},
	journal = {Journal of Hydrology},
	author = {Arheimer, B. and Lidén, R.},
	month = jan,
	year = {2000},
	keywords = {Agricultural streams, Catchment characteristics, Dynamics, Hydrometeorology, Nitrogen, Phosphorus, Sweden},
	pages = {140--159},
}

@article{sharpley_overcoming_2007,
	title = {Overcoming the challenges of phosphorus-based management in poultry farming},
	volume = {62},
	abstract = {Continued economic and use impacts of accelerated eutrophication of fresh waters caused by elevated phosphorus (P) inputs is placing pressure on agriculture to implement Pbased nutrient management strategies, particularly for confined animal feeding operations.As P-based strategies usually have a negative impact on farm operations and economics, current challenges are to define where there is a problem and how big of a problem, to determine how to implement and maintain effective best management practices (BMPs), and to identify the best incentives for farmer adoption. These challenges need to be overcome to develop equitable solutions among those affected (i.e., farming, municipalities, and public).The 1997 US Census showed poultry operations had a higher confined animal unit density (3.23 AU ha-1 [1.31 AU ac-1]) than either dairy (0.89 AU ha-1 [0.36 AU ac-1]) or swine operations (0.77 AU ha-1 [0.31 AU ac-1]). This coupled with the generally greater (two- to four-fold) concentration of P in poultry manure than in other livestock type manure makes P-based management especially challenging for poultry operations. Furthermore, because the N:P ratio in poultry litter or manure (3:1) is much narrower than plants generally need (8:1), there is an inherent long-term increase in soil P and thus, potential for runoff P enrichment when manure or litter is applied to meet crop N needs. Even so, the short-term impacts of land-applying poultry manure or litter can be successfully mitigated with adoption of P-based BMPs. These include feed (enzymes, crop hybrids), manure (chemical and physical treatment, composting, transportation), land (amendments, conservation tillage, critical area targeting, buffers, soil testing), and grazing management (duration and intensity, stream bank fencing). However, developing and planning BMPs at farm and watershed scales is not the single or final solution. Many farmers simply do not have the financial resources to implement and maintain costly remedial measures. Despite many programs to help defray remedial costs, institutional red-tape and conflicting requirements often limit program enrollment and hinder widespread adoption. Obviously, there are still challenges, but if affected parties work together, there is a better chance these challenges can be overcome.},
	language = {en},
	number = {6},
	journal = {journal of soil and water conservation},
	author = {Sharpley, A N and Herron, S and Daniel, T},
	year = {2007},
	pages = {375--389},
}

@article{bell_changes_2006,
	title = {Changes in {Soil} {Properties} and {Enzymatic} {Activities} {Following} {Manure} {Applications} to a {Rangeland}},
	volume = {59},
	issn = {1550-7424, 1551-5028},
	url = {https://bioone.org/journals/Rangeland-Ecology-and-Management/volume-59/issue-3/05-172R1.1/Changes-in-Soil-Properties-and-Enzymatic-Activities-Following-Manure-Applications/10.2111/05-172R1.1.full},
	doi = {10.2111/05-172R1.1},
	abstract = {Manure amendments to rangelands may alter soil functions related to nutrient recycling. We investigated the influence of grazing and cattle manure on soil carbon, nitrogen, Mehlich 3 phosphorus, and activities of alkaline phosphatase and dehydrogenase. Fertilizer treatments (unamended, manure, or urea potassium dihydrogen phosphate [KH2PO4] fertilizer) were imposed under grazed and nongrazed conditions in a short-grass native rangeland. Manure was applied at rates of ∼ 125 kg N ha−1 and ∼ 42 kg P ha−1, and urea KH2PO4 was applied at 75 kg N ha−1 and 20 kg P ha−1, respectively. Total aboveground biomass and soil samples at 4 depths (0–200 mm) were collected throughout 2 growing seasons. A controlled environment study also evaluated fertilizer source effects on enzymatic activities at 5 P rates (0–120 mg·kg−1 P as manure or urea KH2PO4). Amendments significantly (P {\textless} 0.05) increased extractable P following the second application for the 3 uppermost depth increments. Extractable P was greatest on manure-amended plots, increasing 44\% from February 1999 to July 2000 at the surface. However, increases in P extractability as a proportion of total P applied were similar for manure and KH2PO4. Enzymatic activities were significantly (P {\textless} 0.001) influenced by sampling date and soil depth. There were no consistent grazing effects on enzyme activities. Amendments did not influence dehydrogenase activities in the field; however, in the controlled environment, activities averaged 16\% greater across all rates for manure-amended soil as compared with urea KH2PO4–amended soil (P = 0.025). Phosphatase activities increased significantly following manure applications under both field (P = 0.007) and controlled environment (P = 0.003) conditions. Elevated phosphatase activities following manure applications probably led to enhanced P mineralization and similar P extractabilities as a proportion of total P applied for manure- and KH2PO4–amended soils. Therefore, when determining applications rates, total manure P should be considered bioavailable.},
	number = {3},
	urldate = {2020-02-25},
	journal = {Rangeland Ecology and Management},
	author = {Bell, Jourdan M. and Robinson, Clay A. and Schwartz, Robert C.},
	month = may,
	year = {2006},
	pages = {314--320},
}

@article{zhu_interaction_2016,
	title = {Interaction of alkaline phosphatase with minerals and sediments: {Activities}, kinetics and hydrolysis of organic phosphorus},
	volume = {495},
	issn = {0927-7757},
	shorttitle = {Interaction of alkaline phosphatase with minerals and sediments},
	url = {http://www.sciencedirect.com/science/article/pii/S0927775716300656},
	doi = {10.1016/j.colsurfa.2016.01.056},
	abstract = {Alkaline phosphatase (APase) plays an important role in phosphorus (P) cycling in water and sediments of lakes. Interaction of APase with minerals including goethite and montmorillonite, and sediments from Lake Tai (Ch: Taihu) and Lake Dianchi were investigated. Degradation and bioavailability of organic P (Po) in sediments were further investigated by APase hydrolysis and solution 31P-nuclear magnetic resonance (NMR) spectroscopy. Little APase is adsorbed by sediments, but APase could be strongly adsorbed by goethite and montmorillonite. Some adsorptive sites could be occupied by organic matter or ions in sediments from lakes. Activities of APase immobilized by sediments could be reduced to 1.3\% to 5.3\% of that of free APase. However, APase immobilized by goethite and montmorillonite could retain 27.3\% and 21.6\% of the activity of free APase. Thus, the majority of APase is likely dissolved in overlying water or loosely adsorbed by sediments in lakes. Enzymatic hydrolysis and liberation of orthophosphate from suspensions of sediments were 0.26–4.25mgkg−1 that was readily bioavailable to algae or other organisms. After APase hydrolysis, 31P NMR analysis showed that no detectable changes in Po or condensed P in sediments extracted by NaOH–EDTA. Thus, Po immobilized in sediments couldn’t be directly hydrolyzed by APase, but more Po immobilized in the sediments could be hydrolyzed by APase when they were released into the overlying water under appropriate conditions. Treatments, such as additions of Al hydroxides dosing, would not adsorb or immobilized P, but also immobilized phosphatase, thus decreasing activity of phosphatase and bioavailability of Po in a eutrophic lake.},
	language = {en},
	urldate = {2020-02-25},
	journal = {Colloids and Surfaces A: Physicochemical and Engineering Aspects},
	author = {Zhu, Yuanrong and Wu, Fengchang and Feng, Weiying and Liu, Shasha and Giesy, John P.},
	month = apr,
	year = {2016},
	keywords = {Enzymatic hydrolysis, Eutrophication, Goethite, Montmorillonite, Organic phosphorus, P NMR},
	pages = {46--53},
}

@article{mccarty_can_2016,
	title = {Can {We} {Manage} {Nonpoint}-{Source} {Pollution} {Using} {Nutrient} {Concentrations} during {Seasonal} {Baseflow}?},
	volume = {1},
	issn = {2471-9625},
	url = {http://dl.sciencesocieties.org/publications/ael/abstracts/1/1/160015},
	doi = {10.2134/ael2016.03.0015},
	language = {en},
	number = {1},
	urldate = {2020-02-25},
	journal = {Agricultural \& Environmental Letters},
	author = {McCarty, James A. and Haggard, Brian E.},
	month = may,
	year = {2016},
}

@article{cox_relationships_2013,
	title = {Relationships between stream phosphorus concentrations and drainage basin characteristics in a watershed with poultry farming},
	volume = {95},
	issn = {1573-0867},
	url = {10.1007/s10705-013-9569-6},
	doi = {10.1007/s10705-013-9569-6},
	abstract = {In the Illinois River watershed (Arkansas and Oklahoma) poultry litter is routinely applied to pasture lands as fertilizer supplements. The objective of this study was to quantify the impacts of this practice on water quality in small streams in the watershed. Total phosphorus concentrations in small streams were quantified during a 15 month intensive sampling program for small tributaries, un-impacted by point sources, and covering a range of upstream poultry farming intensities throughout the watershed. Base flow samples were also collected from the tributaries during multiple dry weather sampling events. Correlation analysis was performed for various measurable drainage basin characteristics and phosphorus concentrations. Results show significant positive correlations between total phosphorus concentrations and the intensity of poultry farm operations upstream of sample sites. This relationship is supported by a supplemental synoptic sampling event upstream and downstream of a field applied with poultry litter and by a watershed-scale mass balance analysis. The latter identifies poultry as the single largest contributor of phosphorus inputs to the basin, accounting for over 76 \% of the total watershed load. Study results also show significant, but generally weaker, positive correlations between phosphorus and upstream density of septic tanks and soil conservation service curve number of the drainage basin, but these appear likely to be primarily due to cross-correlations with poultry farm presence. This study demonstrates the use of readily-observed basin characteristics in simple water quality predictive tools and has implications for management of poultry-dominated watersheds.},
	language = {en},
	number = {3},
	urldate = {2020-02-25},
	journal = {Nutrient Cycling in Agroecosystems},
	author = {Cox, Timothy J. and Engel, Bernard A. and Olsen, Roger L. and Fisher, J. B. and Santini, Andrew D. and Bennett, Brian J.},
	month = apr,
	year = {2013},
	pages = {353--364},
}

@article{rogers_physicochemical_2011-1,
	title = {Physicochemical {Characterization} of {Sediment} in {Northwest} {Arkansas} {Streams}},
	volume = {02},
	url = {http://www.scirp.org/journal/PaperInformation.aspx?PaperID=5887&#abstract},
	doi = {10.4236/jep.2011.25072},
	abstract = {Eutrophication of surface waters is a critical concern in regions around the world facing nutrient surpluses as a result of confined animal feeding operations (CAFOs) and subsequent land application of manures. While large amounts of research exist on the transport of nutrient enriched runoff from fields to surface waters less information is available on in-stream processes controlling the transport of P in-stream. Thus, information is needed on the role of stream sediments in regulating transient phosphorus (P) to better understand the relationship between nutrient inputs and water quality. Fine-sized sediments ({\textless}2-mm) regulate P via sorption and burial, while algae attached to larger-sediments ({\textgreater} 2-mm) consume and store P. From fine-sized sediment a modified P saturation ratio (PSR$_{\textrm{mod}}$), related to the sediment’s ability to bind P and determined from Mehlich-3 extracted nutrients, has been correlated to in-stream dissolved reactive P (DRP) concentrations. The objectives of this study were to determine the relative size distribution of total- and fine-sized sediment (sand, silt clay) fractions among streams, determine the optimum sample number needed to characterize Mehlich-3 P (M3P) and PSR$_{\textrm{mod}}$, and finally determine the applicability of PSR$_{\textrm{mod}}$, as an indicator of stream water column DRP concentrations. Stream sediments were sampled from the 0- to 3-cm depth from stream reaches ranging from (25 – 75 m) in August, 2008 for characterization along with water samples collected from the thalweg for DRP concentration determination. Additional water column samples were collected along with fine-sized sedi- ment chemical properties in February, May, and June 2009. The distribution of sediment size classes was statistically similar, with 2- to 20- and 20- to 75-mm sized sediment dominating. Fine-sized sediment ({\textless}2 mm) contributed 9 to 18\% of total-sediment and was comprised primarily of sand. Sampled stream M3P and PSR$_{\textrm{mod}}$, were determined to typically be sufficiently characterized by a sample scheme utilizing three samples points. Modified P saturation ratio of {\textless} 2-mm sediment was highly correlated to DRP levels across sampling dates (r = 0.86), suggesting PSR$_{\textrm{mod}}$, has the potential to be used as an indicator of the ability of stream sediments to enrich stream water with P. Thus, fine-sized sediment nutrient concentrations appear to be key regulators of water column P concentrations.},
	language = {en},
	number = {05},
	urldate = {2020-02-25},
	journal = {Journal of Environmental Protection},
	author = {Rogers, Chris W. and Sharpley, Andrew N. and Haggard, Brian E. and Scott, J. Thad and Drake, Bodie M.},
	month = jul,
	year = {2011},
	pages = {629},
}

@article{agudelo_phosphorus_2011,
	title = {Phosphorus {Adsorption} and {Desorption} {Potential} of {Stream} {Sediments} and {Field} {Soils} in {Agricultural} {Watersheds}},
	volume = {40},
	issn = {1537-2537},
	url = {http://dl.sciencesocieties.org/publications/jeq/articles/40/1/144},
	doi = {10.2134/jeq2010.0153},
	language = {en},
	number = {1},
	urldate = {2020-02-25},
	journal = {Journal of Environmental Quality},
	author = {Agudelo, Sandra C. and Nelson, Nathan O. and Barnes, Philip L. and Keane, Timothy D. and Pierzynski, Gary M.},
	month = jan,
	year = {2011},
	pages = {144--152},
}

@article{delaune_evaluation_2004,
	title = {Evaluation of the {Phosphorus} {Source} {Component} in the {Phosphorus} {Index} for {Pastures}},
	volume = {33},
	issn = {1537-2537},
	url = {http://dl.sciencesocieties.org/publications/jeq/articles/33/6/2192},
	doi = {10.2134/jeq2004.2192},
	language = {en},
	number = {6},
	urldate = {2020-02-25},
	journal = {Journal of Environmental Quality},
	author = {DeLaune, P. B. and Moore, P. A. and Carman, D. K. and Sharpley, A. N. and Haggard, B. E. and Daniel, T. C.},
	month = nov,
	year = {2004},
	pages = {2192--2200},
}

@article{haggard_variations_2007,
	title = {Variations in {Stream} {Water} and {Sediment} {Phosphorus} among {Select} {Ozark} {Catchments}},
	volume = {36},
	issn = {1537-2537},
	url = {http://dl.sciencesocieties.org/publications/jeq/articles/36/6/1725},
	doi = {10.2134/jeq2006.0517},
	language = {en},
	number = {6},
	urldate = {2020-02-25},
	journal = {Journal of Environmental Quality},
	author = {Haggard, Brian E. and Smith, Douglas R. and Brye, Kristofor R.},
	month = nov,
	year = {2007},
	pages = {1725--1734},
}

@article{morgan_fine_2019,
	title = {Fine {Sediment} {Removal} {Influences} {Biogeochemical} {Processes} in a {Gravel}-bottomed {Stream}},
	volume = {64},
	issn = {1432-1009},
	url = {10.1007/s00267-019-01187-2},
	doi = {10.1007/s00267-019-01187-2},
	abstract = {The transport and processing of nutrients and organic matter in streams are important functions that influence the condition of watersheds and downstream ecosystems. In this study, we investigated the effects of streambed sediment removal on biogeochemical cycling in Fawn River, a gravel-bottomed river in Indiana, U.S.A. We measured stream metabolism as well as nitrogen (N) and phosphorus (P) retention in both restored and unrestored reaches of Fawn River to examine how sediment removal affected multiple biogeochemical functions at the reach scale. We also assessed the properties of restored and unrestored streambed sediments to elucidate potential mechanisms driving observed reach-scale differences. We found that sediment removal led to lower rates of primary productivity and ecosystem respiration in the restored reach, likely due to macrophyte removal and potentially due to changes to sediment organic matter quality. We found minimal differences in N and P retention, suggesting that these processes are controlled at larger spatial or temporal scales than were examined in this study. Denitrification enzyme activity was lower in sediments from the restored reach compared to the unrestored reach, suggesting that restoration may have decreased N removal. Our results indicate that most near-term changes in biogeochemical function following restoration could be attributed to macrophyte removal, although effects from sediment removal may emerge over longer timescales.},
	language = {en},
	number = {3},
	urldate = {2020-02-22},
	journal = {Environmental Management},
	author = {Morgan, Joseph A. and Royer, Todd V. and White, Jeffrey R.},
	month = sep,
	year = {2019},
	pages = {258--271},
}

@article{brennan_linking_2017-1,
	title = {Linking {Soil} {Erosion} to {Instream} {Dissolved} {Phosphorus} {Cycling} and {Periphyton} {Growth}},
	volume = {53},
	copyright = {© 2017 American Water Resources Association},
	issn = {1752-1688},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/1752-1688.12534},
	doi = {10.1111/1752-1688.12534},
	abstract = {Phosphorus (P) is a limiting nutrient in freshwater systems and when present in runoff from agricultural lands or urban centers may contribute to excessive periphyton growth. In this study, we examined the link between soil erosion and delivery of eroded soil to streams during flow events, and the impact of that freshly deposited soil on dissolved reactive P (DRP) concentrations and periphyton growth under baseflow conditions when the risk of stream eutrophication is greatest. A microcosm experiment was designed to simulate the release of P from soil which had been amended with different amounts of P fertilizer to overlying water during baseflow conditions. Unglazed tiles, inoculated for five days in a second order stream, were incubated for seven days in microcosms containing soil with eight levels of soil Mehlich-3 plant available phosphorus (M3P) ranging from 20 to 679 mg/kg M3P. Microcosm DRP was monitored. Following incubation tiles were scraped and the periphyton analyzed for chlorophyll a. Microcosm DRP concentrations increased with increasing soil M3P and equilibrium phosphorus concentration (EPC0). Relationships between M3P, EPC0, and DRP were nonlinear and increases in soil M3P and/or DRP had a greater impact on biomass accumulation when these parameters were above threshold values of 30 mg/kg M3P and 0.125 mg/L DRP. Significantly, this ecological threshold corresponds to the agronomic thresholds above which increased soil M3P does not increase plant response.},
	language = {en},
	number = {4},
	urldate = {2020-02-19},
	journal = {JAWRA Journal of the American Water Resources Association},
	author = {Brennan, R. B. and Scott, J. T. and Sharpley, A. N. and Lally, H. T. and Jarvie, H. P. and Bowes, M. J. and Haggard, B. E. and Gbur, E.},
	year = {2017},
	keywords = {agriculture, chlorophyll a, diffuse pollution, ecology, fluvial-sediment, freshwater, phosphorus},
	pages = {809--821},
}

@article{mcdowell_influence_2019,
	title = {The influence of a flood event on the potential sediment control of baseflow phosphorus concentrations in an intensive agricultural catchment},
	volume = {19},
	issn = {1614-7480},
	url = {10.1007/s11368-018-2063-7},
	doi = {10.1007/s11368-018-2063-7},
	abstract = {The growth of periphyton in streams is enhanced by phosphorus (P) in baseflow. The likely control of P concentrations in baseflow can be approximated by the equilibrium P concentration (EPC0) of bed sediments. However, sediment composition changes with spatial scale and flood events. It is unknown if this affects EPC0.},
	language = {en},
	number = {1},
	urldate = {2020-02-19},
	journal = {Journal of Soils and Sediments},
	author = {McDowell, Richard W. and Simpson, Zach P. and Stenger, Roland and Depree, Craig},
	month = jan,
	year = {2019},
	pages = {429--438},
}

@article{kreiling_complex_2019,
	title = {Complex {Response} of {Sediment} {Phosphorus} to {Land} {Use} and {Management} {Within} a {River} {Network}},
	volume = {124},
	copyright = {©2019. American Geophysical Union.},
	issn = {2169-8961},
	url = {http://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2019JG005171},
	doi = {10.1029/2019JG005171},
	abstract = {Rivers affected by anthropogenic nutrient inputs can retain some of the phosphorus (P) load through sediment retention and burial. Determining the influence of land use and management on sediment P concentrations and P retention in fluvial ecosystems is challenging because of different stressors operating at multiple spatial and temporal scales. In this study, we sought to determine how land use and management influenced sediment P concentrations and P retention within a river network draining a watershed modified by mixed land use activities, the Fox River, Wisconsin, USA. Results show that current land use had no detectable effect on sediment P concentrations and only a small potential effect on P retention capacity. However, sites draining predominantly forested areas were associated with riverbed sediments less saturated in P, whereas sites draining mainly agricultural areas were more likely to release sediment-bound P. Current management actions, including the implementation of best management practices, had a small positive effect on P retention capacity but had no observed effect on sediment P concentrations. Our results suggest that fine riverbed sediment throughout the Fox River network is saturated with P and has the capability to release P when water column P concentrations are low. These P-saturated riverbed sediments represent a potential legacy effect of past land use disturbances on P dynamics in the Fox River network.},
	language = {en},
	number = {7},
	urldate = {2020-02-19},
	journal = {Journal of Geophysical Research: Biogeosciences},
	author = {Kreiling, R. M. and Thoms, M. C. and Bartsch, L. A. and Richardson, W. B. and Christensen, V. G.},
	year = {2019},
	keywords = {best management practices, land use disturbance, legacy effects, phosphorus retention, resilience},
	pages = {1764--1780},
}

@article{griffiths_influence_2018,
	title = {Influence of dual nitrogen and phosphorus additions on nutrient uptake and saturation kinetics in a forested headwater stream},
	volume = {37},
	issn = {2161-9549, 2161-9565},
	url = {https://www.journals.uchicago.edu/doi/10.1086/700700},
	doi = {10.1086/700700},
	abstract = {Nitrogen (N) and phosphorus (P) can limit autotrophic and heterotrophic metabolism in lotic ecosystems, yet most studies that evaluate biotic responses to colimitation focus on patch-scale (e.g., nutrient diffusing substrata) rather than stream-scale responses. In this study, we evaluated the effects of single and dual N and P additions on ambient nutrient uptake rates and saturation kinetics during two biologically contrasting seasons (spring, autumn) in Walker Branch, a temperate forested headwater stream in Tennessee, USA. In each season, we used separate instantaneous pulse additions to quantify nutrient uptake rates and saturation kinetics of N (nitrate) and P (phosphate). We then used steady-state injections to elevate background stream water concentrations (to low and then high background concentrations) of one nutrient (e.g., N) and released instantaneous pulses of the other nutrient (e.g., P). We predicted that elevating the background concentration of one nutrient would result in a lower ambient uptake length and a higher maximum areal uptake rate of the other nutrient in this colimited stream. Our prediction held true in spring, as maximum areal uptake rate of N increased with elevated P concentrations from 185 lg m22 min21 (no added P) to 354 lg m22 min21 (high P). This pattern was not observed in autumn, as uptake rates of N were not measurable when P was elevated. Further, elevating background N concentration in either season did not significantly increase P uptake rates, likely because adsorption rather than biotic uptake dominated P dynamics. Laboratory P sorption assays demonstrated that Walker Branch sediments had a high adsorption capacity and were likely a sink for P during most pulse nutrient additions. Therefore, it may be difficult to use coupled pulse nutrient additions to evaluate biotic uptake of N and P in streams with strong P adsorption potential. Future efforts should use dual nutrient addition techniques to investigate reach-scale coupled biogeochemical cycles (C–N–P, and other elemental cycles [e.g., Fe, Mo]) across seasons, biomes, and land-use types and over longer time periods.},
	language = {en},
	number = {4},
	urldate = {2020-02-19},
	journal = {Freshwater Science},
	author = {Griffiths, Natalie A. and Johnson, Laura T.},
	month = dec,
	year = {2018},
	pages = {810--825},
}

@article{palmer-felgate_stream-bed_2009,
	title = {Stream-bed phosphorus in paired catchments with different agricultural land use intensity},
	volume = {134},
	issn = {0167-8809},
	url = {http://www.sciencedirect.com/science/article/pii/S0167880909001662},
	doi = {10.1016/j.agee.2009.05.014},
	abstract = {Stream-bed sediments from three paired catchments, each draining a lower agricultural intensity system and a higher agricultural intensity system, were analysed for (a) total P (TP), (b) bioavailable-P (Resin-P), (c) equilibrium phosphorus concentration (EPC0), and (d) degree of phosphorus saturation (DPS). The influence of agriculture on sediment P was explored within the context of other key variables that may control the sediment P concentrations such as particle size, Fe, Ca and organic matter content, and in terms of potential implications of sediment P to in-stream biota. TP concentrations, EPC0, and the proportion of fine sediment were highest at the sites with the greater agricultural impact. Higher concentrations of bioavailable-P were also found in higher intensity agricultural systems. However, the highest concentrations of bioavailable-P were found at sites with point source inputs. Sites with high Fe concentrations had higher TP concentrations relative to agricultural intensity, but also had lower DPS values, illustrating that the sediment still had the capacity to take up P in a strongly bound form. The results from this study show that higher risk agricultural practices (intensive arable production and dairy and beef production) can lead either directly, or indirectly through increased inputs of fine sediment, to increased sediment TP concentrations. The importance of geochemical and physical controls on the bed sediments’ capacity to mitigate high P inputs in headwater lowland streams, especially under low flows and times of eutrophication risk in spring and summer is illustrated.},
	language = {en},
	number = {1},
	urldate = {2020-02-19},
	journal = {Agriculture, Ecosystems \& Environment},
	author = {Palmer-Felgate, Elizabeth J. and Jarvie, Helen P. and Withers, Paul J. A. and Mortimer, Robert J. G. and Krom, Michael D.},
	month = nov,
	year = {2009},
	keywords = {Agriculture, Equilibrium P concentration, Phosphorus, Rivers, Sediment},
	pages = {53--66},
}

@article{richards_identification_1993,
	title = {Identification of predominant environmental factors structuring stream macroinvertebrate communities within a large agricultural catchment},
	volume = {29},
	issn = {1365-2427},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2427.1993.tb00764.x},
	doi = {10.1111/j.1365-2427.1993.tb00764.x},
	abstract = {1 Patterns of macroinvertebrate community composition were examined in streams within a 40000-km2 catchment in central Michigan, U.S.A., to identify the major environmental gradients influencing community variation. Agriculture and associated clay and sandy soils predominated in much of the region. 2 Eighty macroinvertebrate taxa were collected from stream surveys conducted during May and August 1990. Community composition varied primarily by the proportions of Plecoptera and Ephemeroptera. Benthic communities from the heaviest agricultural zones were most different from those at other sites. 3 Chemical composition among the sites varied most in relation to nutrients (NH3, NO3, PO4). Other parameters were relatively similar. Physical characteristics of the sites were scored in six habitat categories: (i) substrate characteristics, (ii) instream cover, (iii) channel morphology, (iv) riparian zone and stream-bank conditions, (v) riffle/run quality, (vi) pool quality. Most physical habitat scores were lowest in the intense agriculture zones. 4 The relative importance of physical and chemical variables in explaining variation in macroinvertebrate communities was quantified using canonical correspondence analysis. Substrate characteristics were most important in both surveys. Significant correlations (P{\textless}0.05 and P{\textless}0.10) were observed between substrate quality and total numbers of Ephemeropteran, Plecopteran, and Trichopteran taxa. These relationships reflected correlations from sites in the clay soil-type region (P{\textless}0.01 and P{\textless}0.10) which contrasted with non-significant results from the less impacted, sandy soil-type region. 5 Effective stream restoration efforts in this region will require the alteration of local land-use activities that influence the physical habitat. Further development of empirical relationships between catchment activities and substrate and channel characteristics within natural geomorphic regions is essential for the evaluation of restoration projects.},
	language = {en},
	number = {2},
	urldate = {2020-02-18},
	journal = {Freshwater Biology},
	author = {Richards, Carl and Host, George E. and Arthur, John W.},
	year = {1993},
	pages = {285--294},
}

@article{richards_identification_1993-1,
	title = {Identification of predominant environmental factors structuring stream macroinvertebrate communities within a large agricultural catchment},
	volume = {29},
	issn = {0046-5070},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2427.1993.tb00764.x},
	doi = {10.1111/j.1365-2427.1993.tb00764.x},
	abstract = {SUMMARY 1 ?Patterns of macroinvertebrate community composition were examined in streams within a 40000-km2 catchment in central Michigan, U.S.A., to identify the major environmental gradients influencing community variation. Agriculture and associated clay and sandy soils predominated in much of the region. 2 ?Eighty macroinvertebrate taxa were collected from stream surveys conducted during May and August 1990. Community composition varied primarily by the proportions of Plecoptera and Ephemeroptera. Benthic communities from the heaviest agricultural zones were most different from those at other sites. 3 ?Chemical composition among the sites varied most in relation to nutrients (NH3, NO3, PO4). Other parameters were relatively similar. Physical characteristics of the sites were scored in six habitat categories: (i) substrate characteristics, (ii) instream cover, (iii) channel morphology, (iv) riparian zone and stream-bank conditions, (v) riffle/run quality, (vi) pool quality. Most physical habitat scores were lowest in the intense agriculture zones. 4 ?The relative importance of physical and chemical variables in explaining variation in macroinvertebrate communities was quantified using canonical correspondence analysis. Substrate characteristics were most important in both surveys. Significant correlations (P{\textless}0.05 and P{\textless}0.10) were observed between substrate quality and total numbers of Ephemeropteran, Plecopteran, and Trichopteran taxa. These relationships reflected correlations from sites in the clay soil-type region (P{\textless}0.01 and P{\textless}0.10) which contrasted with non-significant results from the less impacted, sandy soil-type region. 5 ?Effective stream restoration efforts in this region will require the alteration of local land-use activities that influence the physical habitat. Further development of empirical relationships between catchment activities and substrate and channel characteristics within natural geomorphic regions is essential for the evaluation of restoration projects.},
	number = {2},
	urldate = {2020-02-18},
	journal = {Freshwater Biology},
	author = {Richards, Carl and Host, George E. and Arthur, John W.},
	month = apr,
	year = {1993},
	pages = {285--294},
}

@article{omernik_ecoregions_1987,
	title = {Ecoregions of the {Conterminous} {United} {States}},
	volume = {77},
	issn = {0004-5608},
	url = {10.1111/j.1467-8306.1987.tb00149.x},
	doi = {10.1111/j.1467-8306.1987.tb00149.x},
	abstract = {A map of ecoregions of the conterminous United States has been compiled to assist managers of aquatic and terrestrial resources in understanding the regional patterns of the realistically attainable quality of these resources. The ecoregions are based on perceived patterns of a combination of causal and integrative factors including land use, land surface form, potential natural vegetation, and soils. A synoptic approach similar to that used to define these ecoregions is also useful for applications of the map. Initial efforts to use the framework are at the state level of resource management; they center on aquatic ecosystems — mainly attainable ranges in chemical quality, biotic assemblages, and lake trophic state.},
	number = {1},
	urldate = {2020-02-17},
	journal = {Annals of the Association of American Geographers},
	author = {Omernik, James M.},
	month = mar,
	year = {1987},
	keywords = {Key Words: ecoregions, ecosystems, cartographic analysis, resource management, regional geography},
	pages = {118--125},
}

@article{omernik_stream_1981,
	title = {Stream nutrient levels and proximity of agricultural and forest land to streams: {Some} relationships},
	volume = {36},
	issn = {0022-4561, 1941-3300},
	shorttitle = {Stream nutrient levels and proximity of agricultural and forest land to streams},
	url = {http://www.jswconline.org/content/36/4/227},
	abstract = {ABSTRACT:
The effectiveness of forested buffer strips for controlling nutrient loss from agricultural land to streams is not well documented. To clarify this effectiveness, an attempt was made to determine whether considering the proximity of two land use types (agriculture and forest) to streams improved the ability to predict nutrient levels over simply using the proportion of watersheds occupied by each land use. Results indicated that considering the proximity of these land uses did not improve this predictive ability. One reason may be that the long-term effects of near-stream vegetation in reducing stream nutrient levels is negligible.},
	language = {en},
	number = {4},
	urldate = {2020-02-16},
	journal = {Journal of Soil and Water Conservation},
	author = {Omernik, J. M. and Abernathy, A. R. and Male, L. M.},
	month = jul,
	year = {1981},
	pages = {227--231},
}

@techreport{omernick_aquatic_1987,
	address = {Reston, VA},
	type = {{USGS} {Unnumbered} {Series}},
	title = {Aquatic ecoregions of the conterminous {United} {States}},
	url = {http://pubs.er.usgs.gov/publication/70046266},
	abstract = {Ecoregions are based on perceived patterns of a combination of causal and integrative factors including land use, land surface form, potential natural vegetation, and soils (Omernik, 1987). This is a copy of the ecoregion coverage of Omernik (1987) with some item names modified. This is NOT the most recent version of the ecoregion definitions, which can be obtained from: Environmental Protection Agency, Western Ecology Division, Corvallis, OR at http://www.epa.gov/wed/pages/ecoregions/level\_iii.htm.},
	urldate = {2020-02-16},
	institution = {U.S. Geological Survey},
	author = {Omernick, J.M.},
	year = {1987},
}

@article{robertson_incorporating_2009,
	title = {Incorporating {Uncertainty} {Into} the {Ranking} of {SPARROW} {Model} {Nutrient} {Yields} {From} {Mississippi}/{Atchafalaya} {River} {Basin} {Watersheds1}},
	volume = {45},
	copyright = {© 2009 American Water Resources Association. No claim to original U.S. government works},
	issn = {1752-1688},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1752-1688.2009.00310.x},
	doi = {10.1111/j.1752-1688.2009.00310.x},
	abstract = {Abstract: Excessive loads of nutrients transported by tributary rivers have been linked to hypoxia in the Gulf of Mexico. Management efforts to reduce the hypoxic zone in the Gulf of Mexico and improve the water quality of rivers and streams could benefit from targeting nutrient reductions toward watersheds with the highest nutrient yields delivered to sensitive downstream waters. One challenge is that most conventional watershed modeling approaches (e.g., mechanistic models) used in these management decisions do not consider uncertainties in the predictions of nutrient yields and their downstream delivery. The increasing use of parameter estimation procedures to statistically estimate model coefficients, however, allows uncertainties in these predictions to be reliably estimated. Here, we use a robust bootstrapping procedure applied to the results of a previous application of the hybrid statistical/mechanistic watershed model SPARROW (Spatially Referenced Regression On Watershed attributes) to develop a statistically reliable method for identifying “high priority” areas for management, based on a probabilistic ranking of delivered nutrient yields from watersheds throughout a basin. The method is designed to be used by managers to prioritize watersheds where additional stream monitoring and evaluations of nutrient-reduction strategies could be undertaken. Our ranking procedure incorporates information on the confidence intervals of model predictions and the corresponding watershed rankings of the delivered nutrient yields. From this quantified uncertainty, we estimate the probability that individual watersheds are among a collection of watersheds that have the highest delivered nutrient yields. We illustrate the application of the procedure to 818 eight-digit Hydrologic Unit Code watersheds in the Mississippi/Atchafalaya River basin by identifying 150 watersheds having the highest delivered nutrient yields to the Gulf of Mexico. Highest delivered yields were from watersheds in the Central Mississippi, Ohio, and Lower Mississippi River basins. With 90\% confidence, only a few watersheds can be reliably placed into the highest 150 category; however, many more watersheds can be removed from consideration as not belonging to the highest 150 category. Results from this ranking procedure provide robust information on watershed nutrient yields that can benefit management efforts to reduce nutrient loadings to downstream coastal waters, such as the Gulf of Mexico, or to local receiving streams and reservoirs.},
	language = {en},
	number = {2},
	urldate = {2020-02-15},
	journal = {JAWRA Journal of the American Water Resources Association},
	author = {Robertson, Dale M. and Schwarz, Gregory E. and Saad, David A. and Alexander, Richard B.},
	year = {2009},
	keywords = {Gulf of Mexico, Mississippi, hypoxia, load, nutrients, ranking, statistical methods, yield},
	pages = {534--549},
}

@article{mcdaniel_relationships_2009,
	title = {Relationships between {Benthic} {Sediments} and {Water} {Column} {Phosphorus} in {Illinois} {Streams}},
	volume = {38},
	copyright = {© American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America},
	issn = {1537-2537},
	url = {https://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/jeq2008.0094},
	doi = {10.2134/jeq2008.0094},
	abstract = {Sediments can be important in regulating stream water P concentrations, and this has implications for establishing nutrient standards that have not been fully investigated. We evaluated abiotic and biotic processes to better understand the role of sediments in determining stream water dissolved P concentrations. Sediment and stream water samples were collected during low discharge from 105 streams across Illinois and analyzed for equilibrium P concentration at zero release or retention (EPC0), P sorption characteristics, stream water P concentration, and sediment particle size. In addition, four east-central Illinois streams were repeatedly sampled to examine temporal patterns in sediment P retention and biotic processing of P. Median dissolved reactive P (DRP) and total P concentrations across the state were 0.081 and 0.168 mg L−1, respectively. Sediment EPC0 concentrations were related to stream water DRP concentrations (rs = 0.75). Sediment silt+clay (and co-correlated organic matter) was related to sorbed P (rs = −0.49) and the reactive sediment pool of P (rs = 0.76). However, for most sites this pool was small given the coarse textures present (median silt+clay was 5.7\%). Repeated sampling at the four intensive sites showed little variation in EPC0 values or alkaline phosphatase activity, suggesting overall stream conditions regulated the biotic processing. Biotic retention of P was 32\% of short-term P removal. We conclude that sediments in Illinois streams are a reflection of and partially affected by stream water P concentrations through both abiotic and biotic processes. Sediments seem unlikely to alter annual stream P loads, but may affect concentrations at low discharge.},
	language = {en},
	number = {2},
	urldate = {2020-02-15},
	journal = {Journal of Environmental Quality},
	author = {McDaniel, Marshall D. and David, Mark B. and Royer, Todd V.},
	year = {2009},
	pages = {607--617},
}

@article{house_factors_2000,
	title = {Factors influencing the measurement of equilibrium phosphate concentrations in river sediments},
	volume = {34},
	issn = {0043-1354},
	url = {http://www.sciencedirect.com/science/article/pii/S0043135499002493},
	doi = {10.1016/S0043-1354(99)00249-3},
	abstract = {A river sediment was treated to obtain different oxic conditions, and the phosphorus status investigated by experiments in which KH2PO4 was added to suspensions in calcium chloride. The pH, redox and solution composition of dissolved Ca, Mg, Fe, Na, K, Mn, Cl and SO4 and soluble reactive phosphorus were measured at the end of 24h mixing. The equilibrium phosphate concentration was calculated from these measurements using the linear, Freundlich and dual-site Langmuir isotherm equations. The chemical speciation of the solutions was evaluated using PHREEQC and a model designed specifically for phosphorus speciation. These were used to estimate the solution saturations with respect to various iron and calcium containing minerals. The results show that at least a two-fold increase in the calculated equilibrium phosphate concentration of the sediment occurs with a moderate change in the electron activity from 8 to 4 as the sediments became reducing. Chemical precipitation and dissolution reactions were also found to be important during the experiments, with dissolved iron concentrations in oxic conditions determined by equilibration with amorphous iron hydroxide. Only in the suspensions with the highest soluble reactive phosphorus concentration was the solubility limit of ferric phosphate approached. There was also evidence for the loss of calcium from the solutions and oversaturation with respect to octacalcium phosphate. Vivianite, found in the sediment, was also expected to dissolve in the most oxic conditions. It is proposed that ancillary measurements of pH, redox potential, dissolved Ca, Fe, Mn and alkalinity during equilibrium phosphate concentration determinations will provide a better understanding to the buffering reactions controlling phosphorus in solutions in contact with sediments.},
	language = {en},
	number = {4},
	urldate = {2020-02-15},
	journal = {Water Research},
	author = {House, W. A. and Denison, F. H.},
	month = mar,
	year = {2000},
	keywords = {calcium phosphate, eutrophication, iron phosphate, phosphate, river sediment},
	pages = {1187--1200},
}

@article{mcdaniel_relationships_2009-1,
	title = {Relationships between {Benthic} {Sediments} and {Water} {Column} {Phosphorus} in {Illinois} {Streams}},
	volume = {38},
	issn = {1537-2537},
	url = {https://dl.sciencesocieties.org/publications/jeq/abstracts/38/2/607},
	doi = {10.2134/jeq2008.0094},
	language = {en},
	number = {2},
	urldate = {2020-02-14},
	journal = {Journal of Environmental Quality},
	author = {McDaniel, Marshall D. and David, Mark B. and Royer, Todd V.},
	month = mar,
	year = {2009},
	pages = {607--617},
}

@article{drake_effect_2012,
	title = {The effect of periphyton stoichiometry and light on biological phosphorus immobilization and release in streams},
	volume = {13},
	issn = {1439-863X},
	url = {10.1007/s10201-011-0359-z},
	doi = {10.1007/s10201-011-0359-z},
	abstract = {Periphyton stoichiometry can vary substantially as a result of differences in stream nutrient availability. A decrease in the periphyton carbon to phosphorus (C:P) ratio should decrease the demand for new P to be immobilized from stream water, but no studies to our knowledge have explored the relationship between periphyton stoichiometry and net P immobilization and release by periphyton. We sought to model biological P immobilization and release (flux) in streams by measuring periphyton stoichiometry and light availability. We measured P flux to and from intact periphyton on stream cobbles (20–100 mm diameter) in 1 L microcosms incubated with streamwater under variable light conditions. Net P immobilization occurred in 75\% of microcosms, net P release occurred in only 5\% of microcosms, and 20\% of microcosms had neither net immobilization nor net release. When normalized to stream conditions, net P immobilization was highest when light availability was high ({\textless}60\% canopy attenuation) and the periphyton C:P ratio was also high. In contrast, net P release occurred only when light availability was low ({\textgreater}60\% canopy attenuation) and the periphyton C:P ratio was also low. A multiple regression model that included both periphyton stoichiometry and light availability from the growing season only, and the interaction term of these two variables, explained 99\% of the variation in daily periphyton P flux observed in the study. These results indicate that in order to predict periphyton P immobilization, periphyton stoichiometry and light availability should be considered together. Furthermore, the results indicate that net P immobilization occurs even in very P-rich periphyton, which can act as a P sink when light availability is high.},
	language = {en},
	number = {1},
	urldate = {2020-02-14},
	journal = {Limnology},
	author = {Drake, W. M. and Scott, J. Thad and Evans-White, Michelle and Haggard, Brian and Sharpley, Andrew and Rogers, Chris W. and Grantz, Erin M.},
	month = apr,
	year = {2012},
	keywords = {Element ratios, Phosphorus spiraling, Transient storage},
	pages = {97--106},
}

@article{morgan_fine_2019,
	title = {Fine {Sediment} {Removal} {Influences} {Biogeochemical} {Processes} in a {Gravel}-bottomed {Stream}},
	volume = {64},
	issn = {1432-1009},
	url = {10.1007/s00267-019-01187-2},
	doi = {10.1007/s00267-019-01187-2},
	abstract = {The transport and processing of nutrients and organic matter in streams are important functions that influence the condition of watersheds and downstream ecosystems. In this study, we investigated the effects of streambed sediment removal on biogeochemical cycling in Fawn River, a gravel-bottomed river in Indiana, U.S.A. We measured stream metabolism as well as nitrogen (N) and phosphorus (P) retention in both restored and unrestored reaches of Fawn River to examine how sediment removal affected multiple biogeochemical functions at the reach scale. We also assessed the properties of restored and unrestored streambed sediments to elucidate potential mechanisms driving observed reach-scale differences. We found that sediment removal led to lower rates of primary productivity and ecosystem respiration in the restored reach, likely due to macrophyte removal and potentially due to changes to sediment organic matter quality. We found minimal differences in N and P retention, suggesting that these processes are controlled at larger spatial or temporal scales than were examined in this study. Denitrification enzyme activity was lower in sediments from the restored reach compared to the unrestored reach, suggesting that restoration may have decreased N removal. Our results indicate that most near-term changes in biogeochemical function following restoration could be attributed to macrophyte removal, although effects from sediment removal may emerge over longer timescales.},
	language = {en},
	number = {3},
	urldate = {2020-02-14},
	journal = {Environmental Management},
	author = {Morgan, Joseph A. and Royer, Todd V. and White, Jeffrey R.},
	month = sep,
	year = {2019},
	keywords = {Ecosystem metabolism, Fawn River, Fine sediment, Macrophyte removal, Nutrient retention, Stream restoration},
	pages = {258--271},
}

@article{ahiablame_nutrient_2010,
	title = {Nutrient {Content} at the {Sediment}-{Water} {Interface} of {Tile}-{Fed} {Agricultural} {Drainage} {Ditches}},
	volume = {2},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	url = {https://www.mdpi.com/2073-4441/2/3/411},
	doi = {10.3390/w2030411},
	abstract = {Extensive network of tile drains present in the Midwest USA accelerate losses of nutrients to receiving ditches, rivers and eventually to the Gulf of Mexico. Nutrient inputs from agricultural watersheds and their role in affecting water quality have received increased attention recently; however, benthic sediment-nutrient interactions in tile-fed drainage ditches is still a matter of active research in consideration to nutrient discharge from tile drains. In this study, phosphorus (P) and nitrogen (N) contents and variability of nutrient retention ability of benthic sediments upstream and downstream from tile drain outlets were evaluated in managed agricultural drainage ditches in Indiana. Sediment samples were collected every three months upstream and downstream from selected tile drains in three ditches in northwest Indiana. Sediment equilibrium P concentrations (EPC0) were measured to examine P adsorption-desorption and equilibrium characteristics of benthic sediments in the ditches. P sorption index (PSI), exchangeable P (ExP), and exchangeable NH4+-N (ExN) were measured to evaluate nutrient retention ability and readily available nutrient content of benthic sediments. Results indicated a dynamic interaction between benthic sediment and overlying water column where sediments were acting as a sink or a source of P. There were no differences in nutrient retention ability between sediments collected upstream and sediments collected downstream from the selected tile drains. While the data, except for ExN, was comparable to reported values by previous studies in Indiana’s drainage ditches, there was no particular seasonal pattern in the content of exchangeable nutrient content in sediments at all three sites. This study also suggested that nutrient uptake by benthic sediments in these drainage ditches is not always efficient; therefore watershed management should focus on minimizing the delivery of nutrients into ditches while maintaining their drainage functionality.},
	language = {en},
	number = {3},
	urldate = {2020-02-14},
	journal = {Water},
	author = {Ahiablame, Laurent and Chaubey, Indrajeet and Smith, Douglas},
	month = sep,
	year = {2010},
	keywords = {EPC0, drainage ditches, nutrient dynamics, sediment interactions, sediments},
	pages = {411--428},
}

@article{taube_phosphorus_2019,
	title = {Phosphorus and nitrogen storage, partitioning, and export in a large gravel bed river},
	volume = {657},
	issn = {0048-9697},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969718347867},
	doi = {10.1016/j.scitotenv.2018.11.431},
	abstract = {Nutrient dynamics in a 25 km long treated wastewater effluent impacted reach of a large, gravel-bed river were evaluated in five river compartments: surficial sediment, surface water, hyporheic zone water, and aquatic biomass (including epilithic algae and macrophytes). Nutrient storage within, and export from, the river reach, was quantified to assess the impact of WWTP effluent on nutrient dynamics. More than 98\% of N and P storage was found in the surficial river bed sediment, where it is available to support epilithic algal and macrophyte growth. Nutrient export from the river reach by sediment, hyporheic water, and biomass were small compared to water column transport. The N:P ratios for the five different compartments suggested that the water column was severely P limited, whereas sediment, hyporheic water, and aquatic biomass tended towards co-limitation and N limitation. Within the river reach, the majority of P was stored immediately downstream of the WWTP effluent outfall, whereas N was retained at a higher rate relative to P in the remainder of the reach. Correlation analysis of nutrient exchange between different compartments suggested that multiple nutrient compartments should be considered when establishing nutrient loading criteria. Nutrient analysis in multiple compartments in the river can add valuable insight into nutrient dynamics and nutrient limitation.},
	language = {en},
	urldate = {2020-02-14},
	journal = {Science of The Total Environment},
	author = {Taube, Nadine and Ryan, M. Cathryn and He, Jianxun and Valeo, Caterina},
	month = mar,
	year = {2019},
	keywords = {Bow River, Nitrogen, Nutrient compartments, Nutrient limitation, Phosphorus, Wastewater},
	pages = {717--730},
}

@article{weigelhofer_decoupled_2018,
	title = {Decoupled water-sediment interactions restrict the phosphorus buffer mechanism in agricultural streams},
	volume = {628-629},
	issn = {0048-9697},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969718304182},
	doi = {10.1016/j.scitotenv.2018.02.030},
	abstract = {Our study aimed to explore the effects of agriculture on the phosphorus buffer capacity of 11 headwater streams in Austria. We used phosphorus adsorption curves and re-suspension experiments to determine both, the potential of the sediments to act as phosphorus source or sink and the actual phosphorus exchange between water and sediments. Additionally, we determined the alkaline phosphatase activity (APA) in epilithic and epipsammic biofilms as indicator for the phosphorus demand of the benthic and hyporheic community. We hypothesized that highly polluted streams will show decreased phosphorus buffer capacities, which were either due to saturation or restricted water-sediment interactions. Our results support the second hypothesis. Fine sediment accumulations, organic matter content, and phosphorus concentrations in water and sediments increased with percent cropland in the catchment. Below SRP concentrations of 120μgL−1 in the stream water, sediments showed a high potential for phosphorus release, with zero equilibrium phosphorus concentrations (EPC0) being more than twice as high as SRP concentrations. Above 150μgL−1, EPC0 reached only 20–50\% of SRP concentrations, indicating a high potential of the sediments to act as phosphorus sinks. These findings were confirmed by phosphorus uptake of these sediments during re-suspension. While APA in epilithic biofilms decreased with increasing SRP concentrations, APA in epipsammic biofilms showed the reverse pattern, indicating a restricted phosphorus supply of the hyporheic community despite phosphorus surplus in the water column. Our study shows that inputs of fine sediments from agricultural sources may reduce the phosphorus buffering mechanism of stream sediments through restrictions of water-sediment interactions. Consequently, water column and sediment processes are increasingly decoupled and phosphorus-rich stream water will not effectively reach the reactive sites in the sediments responsible for uptake. Therefore, phosphorus mitigation measures in stream ecosystems must comprise sediment management in the catchment as well as in-stream measures for the rehabilitation of the hyporheic zone.},
	language = {en},
	urldate = {2020-02-14},
	journal = {Science of The Total Environment},
	author = {Weigelhofer, Gabriele and Ramião, José Pedro and Pitzl, Beate and Bondar-Kunze, Elisabeth and O'Keeffe, Joanna},
	month = jul,
	year = {2018},
	keywords = {Epilithic biofilm, Epipsammic biofilm, Equilibrium phosphorus concentration, Phosphatase, Sediment clogging, Uptake},
	pages = {44--52},
}

@article{griffiths_influence_2018-1,
	title = {Influence of dual nitrogen and phosphorus additions on nutrient uptake and saturation kinetics in a forested headwater stream},
	volume = {37},
	issn = {2161-9549},
	url = {https://www.journals.uchicago.edu/doi/10.1086/700700},
	doi = {10.1086/700700},
	abstract = {Nitrogen (N) and phosphorus (P) can limit autotrophic and heterotrophic metabolism in lotic ecosystems, yet most studies that evaluate biotic responses to colimitation focus on patch-scale (e.g., nutrient diffusing substrata) rather than stream-scale responses. In this study, we evaluated the effects of single and dual N and P additions on ambient nutrient uptake rates and saturation kinetics during two biologically contrasting seasons (spring, autumn) in Walker Branch, a temperate forested headwater stream in Tennessee, USA. In each season, we used separate instantaneous pulse additions to quantify nutrient uptake rates and saturation kinetics of N (nitrate) and P (phosphate). We then used steady-state injections to elevate background stream water concentrations (to low and then high background concentrations) of one nutrient (e.g., N) and released instantaneous pulses of the other nutrient (e.g., P). We predicted that elevating the background concentration of one nutrient would result in a lower ambient uptake length and a higher maximum areal uptake rate of the other nutrient in this colimited stream. Our prediction held true in spring, as maximum areal uptake rate of N increased with elevated P concentrations from 185 µg m−2 min−1 (no added P) to 354 µg m−2 min−1 (high P). This pattern was not observed in autumn, as uptake rates of N were not measurable when P was elevated. Further, elevating background N concentration in either season did not significantly increase P uptake rates, likely because adsorption rather than biotic uptake dominated P dynamics. Laboratory P sorption assays demonstrated that Walker Branch sediments had a high adsorption capacity and were likely a sink for P during most pulse nutrient additions. Therefore, it may be difficult to use coupled pulse nutrient additions to evaluate biotic uptake of N and P in streams with strong P adsorption potential. Future efforts should use dual nutrient addition techniques to investigate reach-scale coupled biogeochemical cycles (C–N–P, and other elemental cycles [e.g., Fe, Mo]) across seasons, biomes, and land-use types and over longer time periods.},
	number = {4},
	urldate = {2020-02-14},
	journal = {Freshwater Science},
	author = {Griffiths, Natalie A. and Johnson, Laura T.},
	month = dec,
	year = {2018},
	pages = {810--825},
}

@article{cunha_agriculture_nodate,
	title = {Agriculture influences ammonium and soluble reactive phosphorus retention in {South} {American} headwater streams},
	volume = {n/a},
	copyright = {© 2019 John Wiley \& Sons, Ltd.},
	issn = {1936-0592},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/eco.2184},
	doi = {10.1002/eco.2184},
	abstract = {Agricultural activities can affect the delivery of nutrients to streams, riparian canopy cover, and the capacity of aquatic systems to process nutrients and sediments. There are few measures of nutrient uptake and metabolism from tropical or subtropical streams in general, and even fewer from tropical regions of South America. We examined ammonium (NH4+) and soluble reactive phosphorus (SRP) retention in streams in Brazil and Argentina. We selected 12 streams with relatively little or extensive agricultural activity and conducted whole-stream nutrient additions and measurements of gross primary production and ecosystem respiration. We used multiple linear regression to determine potential drivers of nutrient uptake metrics across the streams. Nutrient concentrations and retention differed significantly between land use categories. Both NH4+ and SRP concentrations were higher in the agricultural sites (means of 161 and 495 μg l–1, respectively), whereas metabolic rates were slower and transient storage was smaller. Our analysis indicated that agriculture increased ambient uptake lengths and decreased uptake velocities. The regression models revealed that ambient SRP had a positive effect on NH4+ uptake and vice versa, suggesting strong stoichiometric controls. Drivers for nutrient uptake in streams with low-intensity agriculture also included canopy cover, temperature, and ecosystem respiration rates. Nutrient assimilation in agricultural sites was influenced by a higher number of variables (gross primary production for SRP, discharge, and transient storage for both nutrients). Our results indicate agricultural activity changes both the magnitude of in-stream nutrient uptake and the mechanisms that control its variation, with important implications for South American streams under agricultural intensification.},
	language = {en},
	number = {n/a},
	urldate = {2020-02-14},
	journal = {Ecohydrology},
	author = {Cunha, Davi Gasparini Fernandes and Finkler, Nícolas Reinaldo and Gómez, Nora and Cochero, Joaquín and Donadelli, Jorge Luis and Saltarelli, Wesley Aparecido and Calijuri, Maria do Carmo and Miwa, Adriana Cristina Poli and Tromboni, Flavia and Dodds, Walter K. and Boëchat, Iola Gonçalves and Gücker, Björn and Thomas, Steven A.},
	keywords = {agricultural watersheds, aquatic metabolism, low-order streams, macronutrient assimilation, nitrogen, phosphorus},
	pages = {e2184},
}

@article{casillas-ituarte_internal_2020,
	title = {Internal {Phosphorus} {Storage} in {Two} {Headwater} {Agricultural} {Streams} in the {Lake} {Erie} {Basin}},
	volume = {54},
	issn = {0013-936X},
	url = {10.1021/acs.est.9b04232},
	doi = {10.1021/acs.est.9b04232},
	abstract = {Internal phosphorus (P) in sediments plays an important role in the nutrient dynamics of lakes, sometimes long after external loads have been reduced. Similarly, internal P sources may drive the nutrient dynamics of small agricultural streams that drain to larger rivers and lakes, despite best management practices intended to reduce external P loads from adjacent fields. Here, internal P concentrations were measured with sequential extraction on cores collected in spring and summer from two small agricultural streams in the drainage basin of Lake Erie, a large, eutrophic lake experiencing increasing SRP loads. Average total extractable P concentrations were similar to within 5\% during spring and summer, but mobile P binding fractions nearly doubled in summer, possibly due to accelerated rates of organic matter mineralization or iron reduction beneath suboxic, stagnant surface waters. One site had chronically greater internal P concentrations by 25–75\%, despite the implementation of best management practices such as grass buffers. The site also had more aquatic vegetation that restricted the flow, less dissolved oxygen in surface water, and greater organic matter in sediments during both seasons, suggesting that variations in hydrology, sediment composition, and vegetation influence hot spots of P retention throughout small agricultural streams.},
	number = {1},
	urldate = {2020-02-14},
	journal = {Environmental Science \& Technology},
	author = {Casillas-Ituarte, Nadia N. and Sawyer, Audrey H. and Danner, Kelsey M. and King, Kevin W. and Covault, Alexandra J.},
	month = jan,
	year = {2020},
	pages = {176--183},
}

@article{dalu_river_2019,
	title = {River nutrient water and sediment measurements inform on nutrient retention, with implications for eutrophication},
	volume = {684},
	issn = {0048-9697},
	url = {http://www.sciencedirect.com/science/article/pii/S004896971932193X},
	doi = {10.1016/j.scitotenv.2019.05.167},
	abstract = {The consideration of nutrients in pollution dynamics is important for environmental management and conservation. Developing countries are yet to appreciate the aquatic ecosystem pollution impacts on their economies and as such, information on water pollution dynamics is limited. This study assessed the spatio-temporal dynamics of nutrient loading and retention in stream water and sediments in the Bloukrans River system, Eastern Cape province, South Africa over the course of the wet and dry season. Sediment and water samples were analysed for total phosphorus (TP) and nitrogen (TN) concentrations, and were used in combination with river flow discharge, to determine nutrient loads. The study results highlight that river discharge plays a significant role in temporal differences in sediment and water column nutrient concentrations. The mean sediment nutrient concentration was high for the dry season, with high values being observed for the urban river system. Nutrient loads were high above the sewage treatment works outflow (i.e. urban sites), as such, a decreasing trend was observed with increasing distance from the urban environment. Nutrient loads were generally high for the dry season in comparison to the wet season indicating organic matter retention (i.e. accumulation from burst sewage pipes) most likely due to low flows. While it was evident that the ageing wastewater infrastructure contributed to the observed state of the Bloukrans River, the high natural nutrient retention capacity seemed to mitigate eutrophication of downstream aquatic ecosystems. As such, the nutrient retention capacity and management of the system is central to the entire Bloukrans River catchment management practices. Therefore, the study contributes to our understanding of water and sediment nutrient pollution dynamics in an arid temperate river landscape where vast spatio-temporal differences in base flow characterise the riverscape.},
	language = {en},
	urldate = {2020-02-14},
	journal = {Science of The Total Environment},
	author = {Dalu, Tatenda and Wasserman, Ryan J. and Magoro, Mandla L. and Froneman, P. William and Weyl, Olaf L. F.},
	month = sep,
	year = {2019},
	keywords = {Aquatic ecosystems, Bloukrans River, Eutrophication, Sediment contaminant assessment, Total nitrogen, Total phosphorus},
	pages = {296--302},
}

@article{munn_habitat-specific_1990,
	title = {Habitat-{Specific} {Solute} {Retention} in {Two} {Small} {Streams}: {An} {Intersite} {Comparison}},
	volume = {71},
	copyright = {© 1990 by the Ecological Society of America},
	issn = {1939-9170},
	shorttitle = {Habitat-{Specific} {Solute} {Retention} in {Two} {Small} {Streams}},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.2307/1938621},
	doi = {10.2307/1938621},
	abstract = {We measured uptake rates of phosphorus, nitrate, calcium, and dissolved organic carbon within two headwater streams, one in the Appalachian mountains of North Carolina and the other in the Cascade range of Oregon. The major physical differences between these two streams are parent geology and local geomorphic structure. Uptake rates were measured following low—level nutrient releases during summer 1987 in 20—m reaches with different geomorphology. The relative importance of biotic vs. abiotic sorption of nitrogen and phosphorus by sediments from the two streams was assessed by laboratory experiments. Nitrate—N uptake rates were high for the western stream (11.9 mg°m—2°min—1) and low for the eastern stream (3.9 mg°m—2°min—1) during the summer. The debris dam reaches in Oregon were the most retentive of N (shortest uptake length of 17 m). Conversely, soluble reactive phosphorus (SRP) uptake rates were higher for the eastern stream (18.6 mg°m—2°min—1), primarily through biotic processes. SRP uptake lengths were short for the cobble (32 m), debris dam (35 m), and rock outcrop (40 m) reaches in the eastern stream. Uptake of SRP in either stream was not related to sediment size fraction but rather to a combination of sediment infiltration rates and quality of organic material. Calcium (Ca) uptake lengths were long in the Oregon stream (1278 m) but short in the Appalachian stream (106 m). Surprisingly, the eastern stream was more retentive of Ca than nitrate (shorter uptake lengths for Ca) during this time period. Debris dams greatly enhanced retention of dissolved organic carbon in both streams (60\% of all uptake in the eastern stream and 81\% in the western stream), although retention was greater in the eastern stream. The lower uptake rate of phosphorus and higher uptake rate of nitrate in the Oregon stream were expected based on geographic location and parent geology; streams in this area drain catchments of volcanic origin and tend to have low N:P (atomic; 1.8 for the western stream) ratios, indicating potential N limitation. Streams flowing over granitic bedrock, such as the eastern stream, tend to have lower P availability (N:P = 15.5). The combined results of laboratory and field measurements indicate that in the eastern stream, strong biotic control of P uptake coupled with high P demand result in relatively short P uptake lengths and a strong impact of P spiraling on ecosystem dynamics. In the western stream, strong biotic control of N uptake combined with strong N demand result in short N uptake lengths. This is especially true at sites of downed timber that retain both FPOM and CPOM, creating a high N demand (shortening N spirals).},
	language = {en},
	number = {6},
	urldate = {2020-02-14},
	journal = {Ecology},
	author = {Munn, Nancy L. and Meyer, Judy L.},
	year = {1990},
	keywords = {calcium, dissolved organic carbon, geology, geomorphology, nitrate, phosphorus, retention, spiraling, uptake lengths, uptake rates},
	pages = {2069--2082},
}

@article{weigelhofer_potential_2017,
	title = {The potential of agricultural headwater streams to retain soluble reactive phosphorus},
	volume = {793},
	issn = {1573-5117},
	url = {10.1007/s10750-016-2789-4},
	doi = {10.1007/s10750-016-2789-4},
	abstract = {The study focuses on the capacity of agricultural headwater streams to retain soluble reactive phosphorus (SRP). In-stream phosphorus uptake was determined via short-term SRP additions in 14 reaches differing in channel morphology and riparian vegetation. In addition, zero equilibrium phosphorus concentrations (EPC0) were estimated for 8 reaches based on adsorption experiments. Average SRP uptake lengths amounted to 3.8 km in channelized sections, 1.9 km in forested sections, and 0.5 km in open meanders. Mass transfer coefficients were highest in open meanders (0.1 cm min−1), followed by forested (0.05 cm min−1) and channelized sections (0.04 cm min−1). EPC0 ranged from 20 to 1,600 µg SRP l−1 and correlated positively with inorganic P and reductant-soluble P concentrations of the sediments. In 50\% of the reaches, phosphorus was released from the sediments at initial water concentrations of up to 500 µg SRP l−1, indicating a high release potential. Although EPC0 did not correlate with in-stream SRP uptake, sediments probably play a significant role for the P retention in agricultural headwater streams as they supply the benthic community with phosphorus from the subsurface. Thus, it is crucial that sediment–water interactions are considered in the restoration and management of agricultural headwater streams.},
	language = {en},
	number = {1},
	urldate = {2020-02-14},
	journal = {Hydrobiologia},
	author = {Weigelhofer, Gabriele},
	month = jun,
	year = {2017},
	keywords = {Agriculture, Equilibrium phosphorus concentrations, Headwater streams, Phosphorus release, Phosphorus uptake, Sediments},
	pages = {149--160},
}

@article{kerr_phosphorus_2011,
	title = {Phosphorus sorption in soils and sediments: implications for phosphate supply to a subtropical river in southeast {Queensland}, {Australia}},
	volume = {102},
	issn = {1573-515X},
	shorttitle = {Phosphorus sorption in soils and sediments},
	url = {10.1007/s10533-010-9422-9},
	doi = {10.1007/s10533-010-9422-9},
	abstract = {Phosphorus (P) is often a key limiting nutrient in freshwater systems, and excessive P can result in algal blooms, with flow-on effects to aquatic food webs. P sorption is an important process in aquatic and terrestrial ecosystems whereby phosphate (PO4 3−) is exchanged between liquid and solid phases. This study shows that differences in the concentration of PO4 3− in a subtropical river system during high and low flow can be attributed to differences in P sorption characterises of its catchment soils and sediments. The sediments have lower Equilibrium Phosphate Concentrations (EPC0) and higher binding energy (Kd); the surface soils have higher EPC0 and higher easily desorbed P (NH4Cl–P). A comparison of filterable reactive phosphorus (frP) in water samples collected at high and low flows, with soil and sediment EPC0, suggested that during event flows, the high EPC0 and NH4Cl–P of surface soils is producing a net movement of PO4 3− from the soil/sediment system into runoff and stream flow. At baseflow, there is more likely a net movement of PO4 3− into the riverbed sediments. This has important implications for management actions aimed at reducing P loads to river systems and downstream water storages, namely the need to increase the infiltration of rainfall to decrease the amount of PO4 3− being flushed from the surface soil.},
	language = {en},
	number = {1},
	urldate = {2020-02-14},
	journal = {Biogeochemistry},
	author = {Kerr, Jason G. and Burford, Michele and Olley, Jon and Udy, James},
	month = jan,
	year = {2011},
	keywords = {Equilibrium phosphate concentration, Phosphorus, Rivers, Sediment, Soil},
	pages = {73--85},
}

@article{hoffman_characteristics_2009,
	title = {Characteristics and {Influence} of {Phosphorus} {Accumulated} in the {Bed} {Sediments} of a {Stream} {Located} in an {Agricultural} {Watershed}},
	volume = {15},
	issn = {1573-1421},
	url = {10.1007/s10498-008-9043-2},
	doi = {10.1007/s10498-008-9043-2},
	abstract = {We investigated the accumulation and influence of bioavailable P (BAP) in sediments of a stream located in an agricultural area of the Lake Mendota watershed in Wisconsin, USA. During hydrologic events, the stream carried high concentrations of suspended sediment (up to 250 mg/l) and BAP (up to 2.5 mg/l). Bed sediments were highly enriched in BAP, as inventories of BAP in the top 10 cm of sediment ranged from 143 to 14,500 μg P/cm2. Space variations in BAP inventories were related to site-specific hydrodynamics and geochemical factors, including iron (Fe; r 2 = 0.71) and aluminum (Al; r 2 = 0.54) concentrations. Most sites behaved as potential sinks for dissolved reactive phosphate during hydrologic events and potential sources during base-flow periods. Through the combination of site-specific factors and geochemical controls, Dorn Creek modifies the amount, timing, and composition of P delivered from the watershed to downstream sites and water bodies.},
	language = {en},
	number = {3},
	urldate = {2020-02-14},
	journal = {Aquatic Geochemistry},
	author = {Hoffman, Adam R. and Armstrong, David E. and Lathrop, Richard C. and Penn, Michael R.},
	month = aug,
	year = {2009},
	keywords = {Agricultural watersheds, Bioavailable phosphorus, Equilibrium phosphorus concentrations, Phosphorus, Sediment},
	pages = {371--389},
}

@article{lottig_benthic_2007,
	title = {Benthic sediment influence on dissolved phosphorus concentrations in a headwater stream},
	volume = {84},
	issn = {1573-515X},
	url = {10.1007/s10533-007-9116-0},
	doi = {10.1007/s10533-007-9116-0},
	abstract = {Phosphate interacts with inorganic sediment particles through sorption reactions in streams. Collectively, this phosphorus (P) buffering mechanism can be an important determinant of soluble reactive P (SRP) concentrations. If sorption reactions control SRP concentrations in a stream, then differences in sediment characteristics may cause spatial differences in SRP concentrations. This prediction was tested by examining sediment-buffering characteristics and spatial variation in SRP among reaches with distinct sediment composition (i.e., fine versus coarse particles) in two tributaries of Boulder Creek, a headwater stream in central Wisconsin. SRP concentrations were significantly lower and algal available P and P sorption capacity were significantly higher in the reach dominated by fine sediments. Although fine particles such as sand had the greatest P sorption capacity, no retention could be attributed to biotic processes, whereas over 50\% of P retention in coarse particles such as gravel could be linked to biotic uptake. Equilibrium P concentration (EPC0) assays from different sediment fractions also indicate that biotic uptake is relatively unimportant in sand particles (EPClive 10 μg/L: EPCkilled 10 μg/L) but very important in gravel or larger particles (EPClive 10 μg/L: EPCkilled 80 μg/L). Thus, sediment influence on stream water P concentrations can shift predictably from abiotic sorption in reaches with fine particles to biotic retention in areas dominated by coarse sediments. Consequently, changes in sediment composition due to natural or anthropogenic disturbance have the potential to alter the type and strength of sediment-associated processes determining ambient stream P concentrations.},
	language = {en},
	number = {3},
	urldate = {2020-02-14},
	journal = {Biogeochemistry},
	author = {Lottig, Noah R. and Stanley, Emily H.},
	month = jul,
	year = {2007},
	keywords = {EPC, Equilibrium phosphorus concentration, Extractable phosphorus, Phosphorus retention, Sediments, Streams},
	pages = {297--309},
}

@article{altieri_adaptation_2017,
	title = {The adaptation and mitigation potential of traditional agriculture in a changing climate},
	volume = {140},
	issn = {1573-1480},
	url = {10.1007/s10584-013-0909-y},
	doi = {10.1007/s10584-013-0909-y},
	abstract = {The threat of global climate change has caused concern among scientists because crop production could be severely affected by changes in key climatic variables that could compromise food security both globally and locally. Although it is true that extreme climatic events can severely impact small farmers, available data is just a gross approximation at understanding the heterogeneity of small scale agriculture ignoring the myriad of strategies that thousands of traditional farmers have used and still use to deal with climatic variability. Scientists have now realized that many small farmers cope with and even prepare for climate change, minimizing crop failure through a series of agroecological practices. Observations of agricultural performance after extreme climatic events in the last two decades have revealed that resiliency to climate disasters is closely linked to the high level of on-farm biodiversity, a typical feature of traditional farming systems.Based on this evidence, various experts have suggested that rescuing traditional management systems combined with the use of agroecologically based management strategies may represent the only viable and robust path to increase the productivity, sustainability and resilience of peasant-based agricultural production under predicted climate scenarios. In this paper we explore a number of ways in which three key traditional agroecological strategies (biodiversification, soil management and water harvesting) can be implemented in the design and management of agroecosystems allowing farmers to adopt a strategy that both increases resilience and provides economic benefits, including mitigation of global warming.},
	language = {en},
	number = {1},
	urldate = {2020-02-14},
	journal = {Climatic Change},
	author = {Altieri, Miguel A. and Nicholls, Clara I.},
	month = jan,
	year = {2017},
	keywords = {Agroforestry System, Extreme Climatic Event, Small Farmer, Soil Organic Carbon, Traditional Agriculture},
	pages = {33--45},
}

@article{kaye_using_2017,
	title = {Using cover crops to mitigate and adapt to climate change. {A} review},
	volume = {37},
	issn = {1773-0155},
	url = {10.1007/s13593-016-0410-x},
	doi = {10.1007/s13593-016-0410-x},
	abstract = {Cover crops have long been touted for their ability to reduce erosion, fix atmospheric nitrogen, reduce nitrogen leaching, and improve soil health. In recent decades, there has been resurgence in cover crop adoption that is synchronous with a heightened awareness of climate change. Climate change mitigation and adaptation may be additional, important ecosystem services provided by cover crops, but they lie outside of the traditional list of cover cropping benefits. Here, we review the potential for cover crops to mitigate climate change by tallying all of the positive and negative impacts of cover crops on the net global warming potential of agricultural fields. Then, we use lessons learned from two contrasting regions to evaluate how cover crops affect adaptive management for precipitation and temperature change. Three key outcomes from this synthesis are (1) Cover crop effects on greenhouse gas fluxes typically mitigate warming by {\textasciitilde}100 to 150 g CO2 e/m2/year, which is higher than mitigation from transitioning to no-till. The most important terms in the budget are soil carbon sequestration and reduced fertilizer use after legume cover crops. (2) The surface albedo change due to cover cropping, calculated for the first time here using case study sites in central Spain and Pennsylvania, USA, may mitigate 12 to 46 g CO2 e/m2/year over a 100-year time horizon. And (3) Cover crop management can also enable climate change adaptation at these case study sites, especially through reduced vulnerability to erosion from extreme rain events, increased soil water management options during droughts or periods of soil saturation, and retention of nitrogen mineralized due to warming. Overall, we found very few tradeoffs between cover cropping and climate change mitigation and adaptation, suggesting that ecosystem services that are traditionally expected from cover cropping can be promoted synergistically with services related to climate change.},
	language = {en},
	number = {1},
	urldate = {2020-02-14},
	journal = {Agronomy for Sustainable Development},
	author = {Kaye, Jason P. and Quemada, Miguel},
	month = jan,
	year = {2017},
	keywords = {Adaptive management, Agriculture, Albedo, Climate change, Cover crops, Global warming, Greenhouse gases, Mitigation, Review},
	pages = {4},
}

@article{congreves_how_2016,
	title = {How does climate variability influence nitrogen loss in temperate agroecosystems under contrasting management systems?},
	volume = {227},
	issn = {0167-8809},
	url = {http://www.sciencedirect.com/science/article/pii/S0167880916302286},
	doi = {10.1016/j.agee.2016.04.025},
	abstract = {Many recent studies have focused on how climate variability affects crop production and yields, however, little is known about the effects of climate variability on nitrogen (N) loss despite the necessity of mitigating N loss for sustainable agroecosystems. By using the DeNitrification and DeComposition (DNDC) model and measurements collected from two management systems (conventional (CV) and best management (BM)) from 2000 to 2004), our objective was to evaluate N losses under different climate scenarios. Our modelled results support the conclusions from previous work that reductions in N losses were obtained by implementing BM rather than CV management. Under numerous climate scenarios (n=25), greater variation was observed in the CV system compared to the BM system for total N losses accumulated over the 5-yr period and for N lost during each year of the crop sequence. Regardless of the management system, the most dominant N loss pathway was NO3− leaching, followed by NH3 volatilization, and N2O emissions. The BM system reduced the frequency of total N loss events compared to CV system, yet, the capacity of the BM system to reduce the frequency of major NO3− events ({\textgreater}1kgd−1) was reduced under a high N loss scenario compared to a low N loss scenario. Higher losses were associated with higher daily temperatures, greater total precipitation, more frequent and intense precipitation events. Thus, the effectiveness of BM systems in controlling major N loss events via NO3− leaching may decrease in the future as a more variable climate ensues with intense precipitation events. Overall, the effect of management remained greater than the impact of climate in determining accumulated N loss over long-term periods, which emphasizes the importance of implementing conservation practices to control N losses.},
	language = {en},
	urldate = {2020-02-14},
	journal = {Agriculture, Ecosystems \& Environment},
	author = {Congreves, K. A. and Dutta, B. and Grant, B. B. and Smith, W. N. and Desjardins, R. L. and Wagner-Riddle, C.},
	month = jul,
	year = {2016},
	keywords = {Agriculture, Biogeochemical cycling, Climate change, Crop and soil management, Nitrogen loss, Process-based modelling},
	pages = {33--41},
}

@article{obrien_ammonium_2008,
	title = {Ammonium uptake and mineralization in prairie streams: chamber incubation and short-term nutrient addition experiments},
	volume = {53},
	issn = {1365-2427},
	shorttitle = {Ammonium uptake and mineralization in prairie streams},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2427.2007.01870.x},
	doi = {10.1111/j.1365-2427.2007.01870.x},
	abstract = {1. We used two separate approaches to estimate ambient ammonium cycling in the north and south branches of Kings Creek, a prairie stream. Chamber experiments were conducted to determine ammonium uptake and mineralization rates associated with epilithic biofilms and filamentous algae collected from the streams. A series of short-term whole-stream ammonium addition experiments were also conducted to estimate the rate of uptake at ambient stream concentrations, based on the relationship between ammonium concentrations and uptake rates. 2. Chamber experiments were scaled up to whole-stream levels, resulting in ambient gross uptake estimates of 0.08 μg−2 s−1 for the north branch and 0.16 μg−2 s−1 for the south branch. The substrata-specific estimates of mineralization were higher than uptake in both streams. 3. Substrata-specific measurements indicated that ammonium uptake is higher in riffle habitats than in pools habitats. The results of the short-term ammonium addition experiments support these findings. 4. Short-term ammonium addition experiments show that uptake rates saturate with increasing ammonium concentrations. The observed saturation of uptake rates is consistent with a Michaelis–Menten relationship. 5. Scaled estimates of uptake from the chamber experiments were similar to estimates of ambient ammonium uptake based on the whole-stream experiments, and were comparable with previous estimates of ammonium uptake and mineralization made by using stable isotope tracer methods in Kings Creek.},
	language = {en},
	number = {1},
	urldate = {2020-02-14},
	journal = {Freshwater Biology},
	author = {O'brien, Jonathan M. and Dodds, Walter K.},
	year = {2008},
	keywords = {mineralization, nitrogen, prairie, streams, uptake},
	pages = {102--112},
}

@article{rabalais_gulf_2019,
	title = {Gulf of {Mexico} {Hypoxia}: {Past}, {Present}, and {Future}},
	volume = {28},
	issn = {1539-607X},
	shorttitle = {Gulf of {Mexico} {Hypoxia}},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/full/10.1002/lob.10351},
	doi = {10.1002/lob.10351},
	abstract = {Abstract One of the largest human-caused areas of bottom-water oxygen deficiency in the coastal ocean is on the northern Gulf of Mexico continental shelf adjacent to the Mississippi River, which discharges nitrogen and phosphorus loads into its surface waters. The beginnings of seasonal hypoxia (≤2 mg?l?1 dissolved oxygen) in this area was in the 1950s with an acceleration in the worsening of severity during the 1970s. Currently, the bottom area of hypoxic areas can approach 23,000?km2, and the volume, 140?km3. Ecosystems, people, and economies are now at risk within the Mississippi River watershed and in the northern Gulf of Mexico. Strengthened nitrogen and phosphorus mitigation, altered agriculture practices, and reduction in carbon and nutrient footprints are key to the recovery of these systems. In this article, we review the past, present, and possible future conditions of the northern Gulf of Mexico and provide insight into possible management actions.},
	number = {4},
	urldate = {2020-02-14},
	journal = {Limnology and Oceanography Bulletin},
	author = {Rabalais, Nancy N. and Turner, R. Eugene},
	month = nov,
	year = {2019},
	pages = {117--124},
}

@article{shipitalo_effects_1996,
	title = {Effects of {Initial} {Water} {Content} on {Macropore}/{Matrix} {Flow} and {Transport} of {Surface}-{Applied} {Chemicals}},
	volume = {25},
	copyright = {© 1996 American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America},
	issn = {1537-2537},
	url = {https://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/jeq1996.00472425002500040005x},
	doi = {10.2134/jeq1996.00472425002500040005x},
	abstract = {Pesticides and fertilizers are often broadcast on no-till fields in the spring when soil water content can be quite variable. Soil water content may influence the contribution of macropores and matrix porosity to water movement and chemical transport in subsequent rainfalls. Therefore, we surface-applied SrBr2 6H2O, atrazine (2-chloro-4-ethylamino-6-isopropylamino-s-triazine), and alachlor [2-chloro-2′,6′-diethyl-N-(methoxymethyl) acetanilide] on nine, 30 by 30 by 30 cm, undisturbed soil blocks obtained from a no-till corn (Zea mays L.) field and maintained at three initial moisture levels 1 h before a 30-mm, 0.5-h simulated rain. To distinguish applied water from resident water and assess interaction of the rainwater with the soil matrix, RbCl was added to the simulated rain as a tracer. Sequential percolate samples were collected from the base of the blocks in ≈ 10-mL increments using a 64-cell grid lysimeter. Flow-weighted concentrations of Cl− and Rb+, respectively, were 75 and 836\% higher in percolate from dry (θ = 0.11 kg kg−1) than from wet blocks (θ = 0.21 kg kg−1), indicating that displacement of resident water and interaction of rainwater with the matrix increased with initial soil water content. As a result, percolate concentrations of the reactive, surface-applied, constituents (Sr2+, atrazine, alachlor) decreased with increasing soil water content. High block to block variability precluded detection of significant differences in percolate volume and total chemical transport among moisture levels. The relative contribution of macropores to chemical transport and water movement appears to be greatest when the soil is dry and decreases as the soil becomes wetter.},
	language = {en},
	number = {4},
	urldate = {2020-02-13},
	journal = {Journal of Environmental Quality},
	author = {Shipitalo, M. J. and Edwards, W. M.},
	year = {1996},
	pages = {662--670},
}

@article{granovsky_impacts_1994,
	title = {Impacts of antecedant moisture and soil surface mulch coverage on water and chemical transport through a no-till soil},
	volume = {32},
	issn = {0167-1987},
	url = {http://www.sciencedirect.com/science/article/pii/0167198794900221},
	doi = {10.1016/0167-1987(94)90022-1},
	abstract = {Flow in macropores of no-tillage soils is often implicated as a principal mechanism responsible for accelerated movement of agrochemcials into groundwater. The objective of this study was to assess the impact of a surface mulch coverage and antecedent water content on water and chemical transport characteristics in a Typic Hapludult soil. SrBr2·6H2O and atrazine were surface-applied to four undisturbed 0.3 m × 0.3 m × 0.3 m surface soil blocks. Three simulated 30 mm rains were applied to the block surfaces, and leachate was collected from 64 cells at the bottom of each block. Leachate volume, chemical amounts, and conducting macropore areas were determined for each cell and block. A parameter, m, found by fitting sorted cumulative outflow curves to an exponential function, was used to desctibe the degree of flow preference in a block. The dominant factor producing transport differences betweent the four blocks was pre-rain moisture content, which correlated negatively with degree of flow preference and positively with total leachate volume in each block. In a drier soil only the more rapid flow pathways, marked by high cell leachate volumes, contributed to the flow, while the slower pathways having greater interaction with the bulk soil were mostly truncated. This resulted in a higher degree of flow preference, smaller total leachate volumes and smaller block-averaged concentrations of Br, Sr and atrazine in soil with lower pre-rain moisture content. The peak of chemical transport was observed after the first simulated rain regardless of pre-rain moisture and surface mulch coverage. Following the second and third rains the chemical transport was reduced twofold for the less reactive Br, three-fold for the more reactive atrazine and ten-fold for Sr, apparently due to the by-pass of chemicals by subsequent leaching events. Much had little effect on water movement, but slightly enhanced the Sr and atrazine transport through the block, most likely by prolonging the chemical contact with infiltrating water at the soil surface.},
	language = {en},
	number = {2},
	urldate = {2020-02-13},
	journal = {Soil and Tillage Research},
	author = {Granovsky, A. V. and McCoy, E. L. and Dick, W. A. and Shipitalo, M. J. and Edwards, W. M.},
	month = nov,
	year = {1994},
	keywords = {Atrazine transport, Br transport, Macropore, Preferential flow, Sr transport},
	pages = {223--236},
}

@article{shipitalo_initial_1990,
	title = {Initial {Storm} {Effects} on {Macropore} {Transport} of {Surface}-{Applied} {Chemicals} in {No}-{Till} {Soil}},
	volume = {54},
	copyright = {© 1990 Soil Science Society of America},
	issn = {1435-0661},
	url = {https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaj1990.03615995005400060004x},
	doi = {10.2136/sssaj1990.03615995005400060004x},
	abstract = {Previous research has established that macropores can rapidly transmit water through soil. This observation has raised concern that macropores may also promote rapid movement of agricultural chemicals to groundwater. This is a particular concern for no-till fields where lack of disruption by tillage can lead to the development of extensive macropore systems. In order to investigate the effect of initial rainfall on chemical transport, strontium bromide hexahydrate (SrBr2·6H2O) and atrazine (2-chloro-4-ethylamino-6-isopro-pylamino -s-triazine) were surface-applied to six 30 by 30 by 30 cm blocks of undisturbed soil obtained from a 25-yr-old, no-till corn (Zea mays L.) field with evidence of well-defined macropores attributable to earthworm activity. Half of the blocks then received a 1-h 5-mm simulated rain, which did not produce percolate. Two days later, the blocks received a 0.5-h 30-mm simulated rain, followed by another 0.5-h 30-mm rain 1 wk later. The remaining blocks received only the two 30-mm events. An average of 12\% of the applied water passed through all the blocks during and shortly after the first 30-mm rain. Bromide, Sr, and atrazine losses in this percolate were 7, 10, and 2 times less, respectively, from blocks that received the 5-mm rain than from blocks not receiving this initial, light rain. The second 30-mm rain on the blocks not receiving the initial 5 mm produced 1.6× more percolate than the first 30-mm rain. Yet, transport and flow-weighted average concentrations of Br, Sr, and atrazine were all reduced. These results indicated that the first storm after application can move solutes into the soil matrix, thereby reducing the potential for transport in macropores during subsequent rainfall events.},
	language = {en},
	number = {6},
	urldate = {2020-02-13},
	journal = {Soil Science Society of America Journal},
	author = {Shipitalo, M. J. and Edwards, W. M. and Owens, L. B. and Dick, W. A.},
	year = {1990},
	pages = {1530--1536},
}

@article{heppell_classification_2002,
	title = {A classification of drainage and macropore flow in an agricultural catchment},
	volume = {16},
	copyright = {Copyright © 2002 John Wiley \& Sons, Ltd.},
	issn = {1099-1085},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/hyp.282},
	doi = {10.1002/hyp.282},
	abstract = {This paper uses a variety of multivariate statistical techniques in order to improve current understanding of the antecedent and rainfall controls on drainage characteristics for an agricultural underdrained clay site. Using the dataset obtained from a two-year hillslope study at Wytham (Oxfordshire, UK) a number of patterns in the nature and style of drainage events were explored. First, using principal components analysis, a distinction was drawn between drainflow controlled by antecedent conditions and drainflow controlled by rainfall characteristics. Dimensional analysis then distinguished between two further types of drainflow event: antecedent limited events (ALE) and non-antecedent limited events (NALE). These were drainflow events requiring a minimum antecedent hydraulic head to occur (ALE) and events that occurred in response to rainfall irrespective of the antecedent conditions, because the rainfall was either of high enough intensity or duration to prompt a response in drainflow (NALE). 2. The dataset also made possible a preliminary investigation into the controls on and types of macropore flow at the site. Principal components analysis identified that rainfall characteristics were more important than antecedent conditions in generating high proportions of macropore flow in drainflow. Of the rainfall characteristics studied, rainfall amount and intensity were the dominant controls on the amount of macropore flow, with duration as a secondary control. Two styles of macropore flow were identified: intensity-driven and duration-driven. Intensity-driven events are characterized by rainfall of high intensity and short duration. During such events the amount of macropore flow is proportional to the rainfall intensity and the interaction between macropore and matrix flow is kinetically limited. The second style of macropore flow is characterized by long-duration events. For these events the amount of macropore flow approaches a maximum value whatever the rainfall duration. This suggests that these events are characterized by an equilibrium interaction between macropores and matrix flow. Copyright © 2002 John Wiley \& Sons, Ltd.},
	language = {en},
	number = {1},
	urldate = {2020-02-13},
	journal = {Hydrological Processes},
	author = {Heppell, C. M. and Worrall, F. and Burt, T. P. and Williams, R. J.},
	year = {2002},
	keywords = {clay soil, macropores, multivariate statistics, underdrainage},
	pages = {27--46},
}

@article{kladivko_pesticide_1999,
	title = {Pesticide and {Nitrate} {Transport} into {Subsurface} {Tile} {Drains} of {Different} {Spacings}},
	volume = {28},
	copyright = {© 1999 American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America},
	issn = {1537-2537},
	url = {https://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/jeq1999.00472425002800030033x},
	doi = {10.2134/jeq1999.00472425002800030033x},
	abstract = {Leaching of agrichemicals into subsurface tile drainage water is a concern for water quality. The objective of this 3-yr study was to determine field-scale pesticide and nitrate (NO3) losses to instrumented subsurface drains as affected by drain spacing (5, 10, and 20 m). Small amounts of carbofuran [2,3-dihydro-2,2-dimethyl-7-benzofuranyl-methylcarbamate]; atrazine [2-chloro-4-(ethylamino)-6-(isopropylamino)-s-triazine]; cyanazine [2-chloro-4-(1-cyano-1-methyl-ethyl-amino)-6-ethylamino-s-triazine]; and alachlor [2-chloro-2′,6′-diethyl-N-(methoxymethyl) acetanilide] were detected in subsurface drainflow in the first large rainstorm after chemical application, which occurred between 3 to 14 d after applications and produced 0.2 to 1.0 cm net drainflow. Annual carbofuran losses in subsurface drainflow ranged from 0.6 to 28.1 g ha−1, or 0.04 to 1.9\% of the amount applied to the soil, depending on year and drain spacing. Losses of all other pesticides were ≤0.1\% of the amount applied. Total mass of pesticides, NO3-N, and water removed by subsurface drains on a per-area basis was greatest for the 5-m spacing and least for the 20-m spacing. Annual NO3-N losses to drainflow ranged from 14 to 105 kg ha−1 during the 1988 to 1991 period. The data indicate that preferential flow may be the primary mechanism of pesticide leaching to shallow ground water in silt loam soils, but that total amounts leached are often quite small. Conversely, NO3-N leaching is most significant during the off-season, when most of the drainflow occurs.},
	language = {en},
	number = {3},
	urldate = {2020-02-13},
	journal = {Journal of Environmental Quality},
	author = {Kladivko, E. J. and Grochulska, J. and Turco, R. F. and Scoyoc, G. E. Van and Eigel, J. D.},
	year = {1999},
	pages = {997--1004},
}

@article{yao_effect_2017,
	title = {Effect of {Antecedent} {Soil} {Water} on {Preferential} {Flow} in {Four} {Soybean} {Plots} in {Southwestern} {China}},
	volume = {182},
	issn = {0038-075X},
	url = {https://journals.lww.com/soilsci/Abstract/2017/03000/Effect_of_Antecedent_Soil_Water_on_Preferential.1.aspx},
	doi = {10.1097/SS.0000000000000198},
	abstract = {ABSTRACT Antecedent soil water exerts considerable influence on the infiltration rate and distribution of preferential flow. Effects of antecedent soil water on preferential flow were investigated through dye experiments with Brilliant Blue FCF (C.I. Food Blue 2) in four soybean plots with low (LWC) and high (HWC) antecedent soil water levels. Changes in soil water were measured during the dye experiments. Horizontal and vertical soil slices were exposed every 10 cm approximately 24 h after the dye tracer application, and staining ratios (stained area to total area) were calculated from photographs. This study demonstrated that the dye tracer infiltrated to a mean depth of 56 cm at an average rate of 1,455 mm h−1 in the LWC plots and to a mean depth of 34 cm and at an average rate of 523 mm h−1 in the HWC plots. Finger flow occurred in Layer B of the LWC plots, possibly resulting in their deeper infiltration depth. The staining ratio in each layer of the LWC plots was generally larger than the corresponding one of the HWC plots. In both the LWC and HWC plots, the average staining ratios decreased with soil depth and exhibited a sharp decrease from Horizon A to B. The largest effect of antecedent soil water on dye tracer movement was found in Layer B. The results indicated that preferential flow was substantial under conditions of low antecedent soil water content in the conditions found in southwestern China. These results could be helpful in improving crop yields and reducing pollution of shallow groundwater by leading farmers to irrigate and till the soil surface with the appropriate frequency.},
	language = {en-US},
	number = {3},
	urldate = {2020-02-13},
	journal = {Soil Science},
	author = {Yao, Jingjing and Cheng, Jinhua and Sun, Long and Zhang, Xin and Zhang, Hongjiang},
	month = mar,
	year = {2017},
	pages = {83--93},
}

@article{schwartz_soil_2003,
	series = {Quantifying agricultural management effects on soil properties and processes},
	title = {Soil hydraulic properties of cropland compared with reestablished and native grassland},
	volume = {116},
	issn = {0016-7061},
	url = {http://www.sciencedirect.com/science/article/pii/S0016706103000934},
	doi = {10.1016/S0016-7061(03)00093-4},
	abstract = {Conversion of cropland to perennial grasses will, over time, produce changes in soil hydraulic properties. The objective of this study was to characterize and compare hydraulic properties of fine-textured soils on adjacent native grassland, recently tilled cropland, and reestablished grassland in the Conservation Reserve Program (CRP) at three locations in the Southern Great Plains. A tension infiltrometer was used to measure unconfined, unsaturated infiltration over a range of supply pressure heads (nominally, h=−150, −100, −50, and −5 mm H2O) at the soil surface. Intact soil cores were sampled within the Ap and Bt horizons to determine bulk density and water desorption curves, θ(h), at potentials ranging from −0.15 to −100 kPa. Unsaturated hydraulic conductivity K(h) over the range in supply pressure heads was estimated using Wooding's equation for steady-state flow from a disc source. The van Genuchten water retention model was fitted to θ(h) data to estimate parameter values. Soils in CRP had greater surface bulk densities than their grassland and cropland counterparts. The shape of the soil water retention curve for grassland and CRP land were similar, suggesting that converted croplands had fully reconsolidated. Mean near-saturated hydraulic conductivities of cropland at h=−5 mm were not significantly different from grassland. However, at −150 mm supply pressure head, cropped soils had a mean unsaturated conductivity 2.3 and 4.1 times greater than CRP land and grassland, respectively. Sites in CRP had the lowest (P{\textless}0.05) near-saturated hydraulic conductivities (h=−5 mm), which suggest that after 10 years, grasses had not fully ameliorated changes in pore structure caused by tillage. Comparison of unsaturated conductivities for grassland and CRP land suggest that long-term structural development on native grasslands was principally confined to effective pore radii greater than 300 μm. Land use practices had a greater effect on water movement than did soil series, indicating that the modifying effects of tillage, reconsolidation, and pore structure evolution on hydraulic properties are important processes governing water movement in these fine-textured soils.},
	language = {en},
	number = {1},
	urldate = {2020-02-13},
	journal = {Geoderma},
	author = {Schwartz, Robert C and Evett, Steven R and Unger, Paul W},
	month = sep,
	year = {2003},
	keywords = {Hydraulic conductivity, Hydraulic properties, Infiltrometers, Porosity, Soil management, Tillage},
	pages = {47--60},
}

@article{bachmair_controls_2009,
	series = {Transfer of pollutants in soils, sediments and water systems: {From} small to large scale ({AquaTerra})},
	title = {Controls of land use and soil structure on water movement: {Lessons} for pollutant transfer through the unsaturated zone},
	volume = {369},
	issn = {0022-1694},
	shorttitle = {Controls of land use and soil structure on water movement},
	url = {http://www.sciencedirect.com/science/article/pii/S0022169409001115},
	doi = {10.1016/j.jhydrol.2009.02.031},
	abstract = {To address the effects of land use and land cover (LULC) on soil structure formation and the significance on preferential flow during infiltration, dye tracer experiments were conducted on five sites differing in LULC, yet displaying similar soil textural characteristics and parent material. Two grassland sites, two farmland sites (tilled and untilled) and one site located in a deciduous forest were investigated. At each site, the same sprinkling experiment was carried out with a Brilliant Blue FCF solution of 4gL−1 to visualize flow paths. To explore the effects of different rainfall amounts (20, 40 and 60mm), each 1.2×1.5m experimental plot was subdivided into three smaller subplots, which were irrigated with an intensity of 15mmh−1 for 80, 160 and 240min, respectively. During the tracer application, water content changes were continuously measured with 16 time domain reflectometry probes horizontally installed into the profile at different depths. After the experiments vertical and horizontal soil sections were excavated and photographed. The pictures were processed using digital image analysis and the resulting dye patterns analyzed for volume and surface density, maximum infiltration depth and macropore structure. Additionally, flow processes were classified into distinct flow type categories. The tracer experiments revealed that preferential flow processes significantly differed among sites of differing LULC yet similar soil texture. As primary controlling factors soil structure, surface micro-topography, surface cover and topsoil matrix characteristics were identified. The effects of different rainfall application amounts were complex and strongly varied among sites, stressing the strong control LULC exerts on water flow in soils. Overall this suggests that land use effects on soil properties need to be considered in hydrological models to obtain realistic predictions concerning water quality and quantity.},
	language = {en},
	number = {3},
	urldate = {2020-02-13},
	journal = {Journal of Hydrology},
	author = {Bachmair, Sophie and Weiler, Markus and Nützmann, Gunnar},
	month = may,
	year = {2009},
	keywords = {Dye tracer experiments, Land use and land cover (LULC), Preferential flow, Soil structure formation, Time domain reflectometry},
	pages = {241--252},
}

@article{cober_winter_2019,
	title = {Winter {Phosphorus} {Release} from {Cover} {Crops} and {Linkages} with {Runoff} {Chemistry}},
	volume = {48},
	issn = {0047-2425},
	url = {http://dl.sciencesocieties.org/publications/jeq/abstracts/48/4/907},
	doi = {10.2134/jeq2018.08.0307},
	language = {en},
	number = {4},
	urldate = {2020-02-12},
	journal = {Journal of Environmental Quality},
	author = {Cober, James R. and Macrae, Merrin L. and Van Eerd, Laura L.},
	year = {2019},
	pages = {907--914},
}

@article{liu_potential_2013,
	title = {Potential phosphorus release from catch crop shoots and roots after freezing-thawing},
	volume = {371},
	issn = {1573-5036},
	url = {10.1007/s11104-013-1716-y},
	doi = {10.1007/s11104-013-1716-y},
	abstract = {Background and aimsCatch crops used for mitigating nutrient losses to water can release phosphorus (P) when exposed to repeated freezing-thawing cycles (FTCs). This study sought to evaluate potential P losses from shoots and roots of eight catch crops.MethodsShoots and roots sampled from perennial ryegrass (Lolium perenne L.), cocksfoot (Dactylis glomerata L.), chicory (Cichorium intybus L.), phacelia (Phacelia tanacetifolia L.), red clover (Trifolium pratense L.), white mustard (Sinapis alba L.), oilseed radish (Raphanus sativus var. oleiformis L.) and white radish (R. sativus var. longipinnatus L.) were treated with no freezing, one single FTC, four continuous FTCs and four discontinuous FTCs. All samples were analysed for water-extractable P (WEP), and root samples also for characteristics such as specific root surface area (SSA).ResultsFreezing-thawing significantly increased potential P losses from both shoots and roots compared with no freezing. The two radish species and white mustard contained significantly higher concentrations of WEP than the other species, among which chicory and phacelia had the lowest WEP. On average, shoots had 43 \% higher WEP than roots. Cumulative P release from shoots and roots was strongly correlated with their total-P content (p = 0.006 and p = 0.002, respectively). Cumulative release of P from taproots was correlated with SSA (p = 0.03).ConclusionsChicory, and possibly phacelia, appear to be promising catch crops for P.},
	language = {en},
	number = {1},
	urldate = {2020-02-12},
	journal = {Plant and Soil},
	author = {Liu, Jian and Khalaf, Rafa and Ulén, Barbro and Bergkvist, Göran},
	month = oct,
	year = {2013},
	keywords = {Catch crop, Climate change, Cover crop, Freezing-thawing, Root morphology, Water-extractable phosphorus},
	pages = {543--557},
}

@article{roberson_freezing_2007,
	title = {Freezing and {Drying} {Effects} on {Potential} {Plant} {Contributions} to {Phosphorus} in {Runoff}},
	volume = {36},
	issn = {1537-2537},
	url = {http://dl.sciencesocieties.org/publications/jeq/abstracts/36/2/532},
	doi = {10.2134/jeq2006.0169},
	language = {en},
	number = {2},
	urldate = {2020-02-12},
	journal = {Journal of Environmental Quality},
	author = {Roberson, Tiffany and Bundy, Larry G. and Andraski, Todd W.},
	month = mar,
	year = {2007},
	pages = {532--539},
}

@article{lozier_potential_2017,
	title = {Potential phosphorus mobilization from above-soil winter vegetation assessed from laboratory water extractions following freeze–thaw cycles},
	volume = {42},
	issn = {0701-1784},
	url = {10.1080/07011784.2017.1331140},
	doi = {10.1080/07011784.2017.1331140},
	abstract = {Maintaining crop residue or cover crops on fields during winter is a recommended beneficial management practice (BMP). However, losses of dissolved reactive phosphorus (DRP) to runoff have been attributed to vegetation following freeze–thaw cycles (FTC). Using a factorial design in the laboratory, this study investigated the potential influence of four FTC types at −4 to +4°C (frozen, frozen and thawed 1×, frozen and thawed 5×, frozen and thawed 5× with extraction after each thaw) and one control (never frozen) on DRP loss from the residue of Triticum aestivum (winter wheat) and from two cover crops, Trifolium pretense (red clover) and Avena sativa (oat). DRP losses were measured using three different water extraction techniques: a traditional laboratory determination of water extractable P (WEP), a modified water extraction intended to simulate a rainfall event, and a modified water extraction intended to simulate surface ponding. Both cover crops released more DRP than winter wheat residue did under all treatments, suggesting that winter wheat residues pose little risk for DRP release during the non-growing season (NGS). Of the two cover crops studied, oat was more sensitive to FTC and may therefore pose a greater risk of late autumn/winter DRP loss in comparison to red clover, which is often terminated in early fall. Water extraction technique was also found to be important, as simulated surface ponding extracted more DRP than simulated rainfall did for all three plant types. These results suggest that both cover crop species and placement in the landscape can be optimized to reduce P release from above-ground vegetation in winter. The use of cover crops in sections of fields that are prone to flooding following large events such as snowmelt should be avoided. Field studies are needed to further examine the rates and timing of potential and actual losses of DRP from above-ground vegetation in winter.},
	number = {3},
	urldate = {2020-02-12},
	journal = {Canadian Water Resources Journal / Revue canadienne des ressources hydriques},
	author = {Lozier, Tatianna M. and Macrae, Merrin L.},
	month = jul,
	year = {2017},
	pages = {276--288},
}

@article{willison_freeze-thaw_1994,
	title = {Freeze-thaw injury is enhanced by post-thaw leaching in water},
	volume = {74},
	issn = {0008-4220},
	url = {https://www.nrcresearchpress.com/doi/10.4141/cjps94-069},
	doi = {10.4141/cjps94-069},
	abstract = {Turnip (Brassica rapa L.) root tissue was exposed to freeze-thaw stresses of −7, −9, -−11 and −19 °C. The post-thawed tissues were either subjected to leaching in deionized water for 2 h or left at 100\% humidity. Tissue survival was then assayed by vital staining using modified 2,3,5-triphenyltetrazolium chloride (TTC) staining in 0.2 M phosphate buffer. Tissue survival was significantly lower for leached samples than for non-leached samples. It is concluded that freeze-thaw injury in plant tissues is enhanced by post-thaw leaching in water. The 0.05 M phosphate buffer commonly used for TTC staining also damaged freeze-thaw injured tissue. Key words:Brassica rapa L., 2,3,5-triphenyltetrazolium chloride (TTC), freeze-thaw injury, leaching},
	number = {2},
	urldate = {2020-02-12},
	journal = {Canadian Journal of Plant Science},
	author = {Willison, J. H. M. and Cheung, C. H. and Zhang, M. I. N. and Xiao, X.},
	month = apr,
	year = {1994},
	pages = {357--358},
}

@article{liu_impacts_2019,
	title = {Impacts of {Cover} {Crops} and {Crop} {Residues} on {Phosphorus} {Losses} in {Cold} {Climates}: {A} {Review}},
	volume = {48},
	issn = {0047-2425},
	shorttitle = {Impacts of {Cover} {Crops} and {Crop} {Residues} on {Phosphorus} {Losses} in {Cold} {Climates}},
	url = {http://dl.sciencesocieties.org/publications/jeq/articles/48/4/850},
	doi = {10.2134/jeq2019.03.0119},
	language = {en},
	number = {4},
	urldate = {2020-02-12},
	journal = {Journal of Environmental Quality},
	author = {Liu, Jian and Macrae, Merrin L. and Elliott, Jane A. and Baulch, Helen M. and Wilson, Henry F. and Kleinman, Peter J. A.},
	year = {2019},
	pages = {850--868},
}

@article{geohring_phosphorus_2001,
	title = {{PHOSPHORUS} {TRANSPORT} {INTO} {SUBSURFACE} {DRAINS} {BY} {MACROPORES} {AFTER} {MANURE} {APPLICATIONS}: {IMPLICATIONS} {FOR} {BEST} {MANURE} {MANAGEMENT} {PRACTICES}},
	volume = {166},
	issn = {0038-075X},
	shorttitle = {{PHOSPHORUS} {TRANSPORT} {INTO} {SUBSURFACE} {DRAINS} {BY} {MACROPORES} {AFTER} {MANURE} {APPLICATIONS}},
	url = {https://journals.lww.com/soilsci/Abstract/2001/12000/PHOSPHORUS_TRANSPORT_INTO_SUBSURFACE_DRAINS_BY.4.aspx},
	abstract = {Land application of liquid manure can result in nutrient enrichment of subsurface drainage effluent when conditions promote leaching or macropore flow. This contamination is most likely to occur when precipitation follows manure application closely and may cause environmental impacts to receiving waters. Field and column studies were initiated in New York to investigate the impact of manure applications on phosphorus (P) transport through the soil into subsurface drains. Field studies evaluated tile effluent contamination from liquid manure under wet and dry antecedent soil moisture conditions (year 1) and under disk and plow tillage practices (year 2). In year 1, liquid dairy manure was broadcast on the surface and the field was then irrigated. Though the tile drains in the wet plots flowed much earlier and in greater volume than the drains in the dry plots, both wet and dry plots produced similar average peak total phosphorus (TP) concentrations. Irrigation 6 days later produced similar tile discharges, but the peak TP concentrations were about one-third of the earlier values. Cumulative TP loss was significantly higher from wet than dry plots. In year 2, manure was tilled into the soil via one-pass disking or plowing before irrigation commenced. The disking did not incorporate the manure into the soil as effectively as did plowing and exhibited one order of magnitude higher effluent TP concentrations and cumulative TP loss. The timing of P transport in tile effluent relative to the tile flow is consistent with macropore transport as the primary mechanism moving TP through the soil. Column studies utilizing packed soil and artificial macropores were used to examine further the role of macropore size on P sorption to pore walls. Dissolved P was added directly to the macropore, and the effluent from the macropore showed that soluble P may be transported through macropores 1 mm or greater with negligible P sorption to pore walls. In the absence of macropores, no measurable P was transported through the soil columns. Consequently, high P concentrations observed in the tile drain effluent soon after manure application during the field studies can be attributed to macropore transport processes. Even small continuous macropores are potential pathways. Plowing-in manure apparently disturbs these macropores and promotes matrix flow, resulting in greatly reduced P concentrations in the drainage effluent.},
	language = {en-US},
	number = {12},
	urldate = {2020-02-12},
	journal = {Soil Science},
	author = {Geohring, Larry D. and McHugh, Oloro V. and Walter, M. Todd and Steenhuis, Tammo S. and Akhtar, M. Saleem and Walter, Michael F.},
	month = dec,
	year = {2001},
	pages = {896--909},
}

@article{plach_dominant_2018,
	title = {Dominant glacial landforms of the lower {Great} {Lakes} region exhibit different soil phosphorus chemistry and potential risk for phosphorus loss},
	volume = {44},
	issn = {0380-1330},
	url = {http://www.sciencedirect.com/science/article/pii/S038013301830128X},
	doi = {10.1016/j.jglr.2018.07.005},
	abstract = {Phosphorus (P) losses from agricultural soils are a growing economic and water-quality concern in the Lake Erie watershed. While recent studies have explored edge-of-field and watershed P losses related to land-use and agricultural management, the potential for soils developed from contrasting parent materials to retain or release P to runoff has not been examined. A field-based study comparing eight agricultural fields in contrasting glacial landscapes (hummocky coarse-textured till-plain, lacustrine and fine-textured till-plain) showed distinct physical and geochemical soil properties influencing inorganic P (Pi) partitioning throughout the soil profile between the two regions. Fields located on the coarse-textured till-plain in mid-western Ontario, Canada had alkaline calcareous soils with the highest Total-Pi concentrations and the majority of soil Pi stored in an acid-soluble pool (up to 91\%). In contrast, loosely to moderately soluble Pi concentrations were higher in soils of the lacustrine and fine-textured till-plain in southwestern Ontario, northeast Indiana and northwestern Ohio, US. Overall, soils on the lacustrine and fine-textured till-plain had a greater shrink swell-capacity, likely creating preferential flow to minimize Pi interaction with the more acidic, lower carbonate and lower sorption capacity soils. These differences in soil Pi retention and transport pathways demonstrate that in addition to management, the natural landscape may exert a significant control on how Pi is mobilized throughout the Lake Erie watershed. Further, results indicate that careful consideration of region-specific hydrology and soil biogeochemistry may be required when designing appropriate management strategies to minimize Pi losses across the lower Great Lakes region.},
	language = {en},
	number = {5},
	urldate = {2020-02-12},
	journal = {Journal of Great Lakes Research},
	author = {Plach, Janina M. and Macrae, Merrin L. and Williams, Mark R. and Lee, Brad D. and King, Kevin W.},
	month = oct,
	year = {2018},
	keywords = {Agriculture, Great Lakes, Phosphorus, Soil geochemistry, Water quality},
	pages = {1057--1067},
}

@article{kung_impact_2000,
	title = {Impact of {Preferential} {Flow} on the {Transport} of {Adsorbing} and {Non}-{Adsorbing} {Tracers}},
	volume = {64},
	copyright = {Soil Science Society of America},
	issn = {1435-0661},
	url = {http://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaj2000.6441290x},
	doi = {10.2136/sssaj2000.6441290x},
	abstract = {Field experiments were conducted by using a tile drain monitoring facility to determine the impact of preferential flow on the transport of adsorbing and non-adsorbing tracers. Simulated rainfall with 7.5 mm h−1 intensity and 7.5 h duration was applied to a 18- by 65-m no-till plot. After 72 min of irrigation, a pulse of Br− and rhodamine WT (water tracer) was applied through irrigation, and 4 h later, a second pulse of Cl− and rhodamine WT was applied. The breakthrough curves (BTC) of these tracers were measured by sampling the tile. The same experiments were repeated in an adjacent conventional-till plot, except the rainfall intensity was reduced to 5 mm h−1 The results showed that both the non-adsorbing and the adsorbing tracers applied in the same pulse arrived at the tile line at the same time and their BTC peaked at the same time. This suggested that water dynamics of preferential flow paths dominated the initial phase of the contaminant transport, regardless of the retardation properties of contaminants. The tracers from the second pulse were detected at only 13 min after application. Among the four tracer pulses in two plots, the BTC from the second pulse in the no-till plot had the longest period in which the non-adsorbing and adsorbing tracers had identical patterns. This indicated that the wetter the soil profile, the longer the water dynamics of preferential flow paths dominate the contaminant transport. The BTC from the second pulse applied to the two plots had identical arrival and peak times.},
	language = {en},
	number = {4},
	urldate = {2020-02-12},
	journal = {Soil Science Society of America Journal},
	author = {Kung, K.-J. S. and Steenhuis, T. S. and Kladivko, E. J. and Gish, T. J. and Bubenzer, G. and Helling, C. S.},
	year = {2000},
	pages = {1290--1296},
}

@article{grant_nutrient_2019,
	title = {Nutrient {Leaching} in {Soil} {Affected} by {Fertilizer} {Application} and {Frozen} {Ground}},
	volume = {18},
	copyright = {© 2019 The Authors.},
	issn = {1539-1663},
	url = {http://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/vzj2018.08.0150},
	doi = {10.2136/vzj2018.08.0150},
	abstract = {Core Ideas Preferential flow is prevalent in clay soil under both frozen and thawed conditions. Preferential flow dominates the infiltration regime under frozen soil conditions in silt loam. Subsurface placement of fertilizer can limit subsurface nutrient leaching. Subsurface placement is particularly effective in soil with abundant preferential flow. Subsurface placement is recommended for fall fertilizer application. Agricultural runoff containing P and N from drainage tiles contributes to nutrient loading in waterways, leading to downstream eutrophication. Recent studies suggest that nutrient losses through tile drains can be reduced if nutrients are applied in the subsurface. This study explored interactions between nutrient supply and infiltrating water during a simulated nongrowing season using a laboratory experiment to understand how water and nutrients move through partially frozen and unfrozen soil and if fertilizer placement influences NO3− and dissolved reactive P (DRP) leaching. Intact silt loam and clay soil monoliths (28 by 30 by 30 cm) were fertilized with P and N via subsurface placement or surface broadcast and subjected to simulated rainfall under unfrozen (10°C) and partially frozen (∼0°C) conditions. Conservative tracers (Br−, Cl−, and D2O) applied to characterize subsurface flow paths throughout a subset of events indicated that matrix flow dominated in unfrozen silt loam soil. However, preferential flow paths dominated in unfrozen clay and in both soil types under partially frozen conditions, transporting applied nutrients while minimizing contact with the soil matrix. The subsurface placement of inorganic fertilizer relative to surface broadcast reduced both NO3− (by 26.85 kg ha−1 [23\%] in silt loam and 65.73 kg ha−1 [61\%] in clay) and DRP losses (by 2.33 kg ha−1 [60\%] in silt loam and 4.25 kg ha−1 [64\%] in clay). This study demonstrates the advantage of subsurface placement of fertilizer in the reduction of nutrient leaching by limiting the interaction of the nutrient supply with preferential flow pathways.},
	language = {en},
	number = {1},
	urldate = {2020-02-12},
	journal = {Vadose Zone Journal},
	author = {Grant, Kirsten N. and Macrae, Merrin L. and Rezanezhad, Fereidoun and Lam, W. Vito},
	year = {2019},
	pages = {180150},
}

@article{kung_quantifying_2000,
	title = {Quantifying {Preferential} {Flow} by {Breakthrough} of {Sequentially} {Applied} {Tracers} {Silt} {Loam} {Soil}},
	volume = {64},
	copyright = {Soil Science Society of America},
	issn = {1435-0661},
	url = {https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaj2000.6441296x},
	doi = {10.2136/sssaj2000.6441296x},
	abstract = {Field experiments were conducted on tile-drained plots at the South East Purdue Agricultural Center in Butlerville, Indiana, to quantify contaminant transport via preferential flow paths in a silt loam soil. Breakthrough patterns of three fluorobenzoic acids (pentafluorobenzoic acid [PFBA], o-trifluoromethylbenzoic acid [o-TFMBA], and 2,6-difluorobenzoic acid [2,6-DFBA]) in a preliminary study indicated that they were transported as conservatively as is bromide (Br−). These four tracers were then sequentially applied, in an adjacent plot, during simulated precipitation (3 mm h−1 intensity, 10-h duration). Bromide was sprayed shortly before irrigation started, while PFBA, o-TFMBA, and 2,6-DFBA were applied at 2, 4, and 6 h thereafter, respectively. Tile flow began increasing at around 3 h, and Br− appeared in tile drain flow ≈4 h after irrigation started, yet benzoic acids, PFBA, o-TFMBA, and 2,6-DFBA, were detected in the tile drainage at 102 min, 42 min, and 18 min after their applications, respectively. Tracer mass recovery from tile drainage was Br− (7.04\%), PFBA (13.9\%), o-TFMBA, (18.7\%), and 2,6-DFBA (19.7\%) of applied mass. The faster arrival time and greater recovery of sequentially applied tracers confirmed that water movement and contaminant transport shifts toward increasingly larger pores of the preferential flow paths as soil becomes wet during a precipitation event. The breakthrough patterns of these tracers can be used to quantify the water flux distributions of preferential paths. Because ≈90\% of the chemical leached from this precipitation event occurred during the first day, it was critical to intensively monitor contaminant transport during the first 24 h after a rainfall. A soil sampling protocol based on collecting soil cores at random locations once every several days is unsuitable for determining the deep leaching under field conditions.},
	language = {en},
	number = {4},
	urldate = {2020-02-12},
	journal = {Soil Science Society of America Journal},
	author = {Kung, K.-J. S. and Kladivko, E. J. and Gish, T. J. and Steenhuis, T. S. and Bubenzer, G. and Helling, C. S.},
	year = {2000},
	pages = {1296--1304},
}

@article{stamm_preferential_1998,
	title = {Preferential {Transport} of {Phosphorus} in {Drained} {Grassland} {Soils}},
	volume = {27},
	issn = {0047-2425},
	url = {http://dl.sciencesocieties.org/publications/jeq/abstracts/27/3/JEQ0270030515},
	doi = {10.2134/jeq1998.00472425002700030006x},
	language = {en},
	number = {3},
	urldate = {2020-02-12},
	journal = {Journal of Environmental Quality},
	author = {Stamm, C. and Flühler, H. and Gächter, R. and Leuenberger, J. and Wunderli, H.},
	year = {1998},
	pages = {515--522},
}

@article{simard_potential_2000,
	title = {Potential for {Preferential} {Pathways} of {Phosphorus} {Transport}},
	volume = {29},
	copyright = {© 2000 American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America},
	issn = {1537-2537},
	url = {http://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/jeq2000.00472425002900010012x},
	doi = {10.2134/jeq2000.00472425002900010012x},
	abstract = {This paper briefly reviews the existing literature and uses evidence from three studies to demonstrate the occurrence of preferential pathways of P transport through soil. Studies conducted in the St. Lawrence lowlands, Canada, indicated that particulate P (PP-i.e., {\textgreater}0.45 µm) the main fraction of total P (TP) in tile-drainage water generated by storm events after periods of low rainfall. In the remainder of the year, the concentration of TP and P forms were related to soil texture, primary tillage intensity and frequency, and showed wide seasonal variations. For a study conducted in the UK under grassland, higher TP concentrations were found in near-surface runoff (0–30 cm) compared with concentrations measured in drainflow. Water passing through the artificial drainage system had a higher proportion of PP (43\%) than water passing close to ({\textless}30 cm) or over the soil surface (31\%). Installation of tile drainage in a poorly draining soil reduces P transfer by improving the infiltration capacity, thereby reducing overland flow volume and allowing P to be retained/sorbed by the soil matrix. Because of the absence of tillage, permanent grasslands accumulate P near the surface. We hypothesize that, if the soil P store is coincident with preferential flow pathways (either artificial mole drainage channels or natural macropores), permanent grassland will be vulnerable to transfer large amounts of P through subsurface pathways. Phosphorus transfer through preferential flow pathways may be particularly important after storm events that rapidly follow periods of drought and/or surface P inputs as inorganic fertilizer or manure.},
	language = {en},
	number = {1},
	urldate = {2020-02-12},
	journal = {Journal of Environmental Quality},
	author = {Simard, R. R. and Beauchemin, S. and Haygarth, P. M.},
	year = {2000},
	pages = {97--105},
}

@article{vidon_seasonal_2009,
	title = {Seasonal solute dynamics across land uses during storms in glaciated landscape of the {US} {Midwest}},
	volume = {376},
	issn = {0022-1694},
	url = {http://www.sciencedirect.com/science/article/pii/S0022169409004041},
	doi = {10.1016/j.jhydrol.2009.07.013},
	abstract = {Considering the importance of solute exports during storms in annual nutrient budgets at the watershed scale, it is critical to understand the impact of seasonality and differences in land use on watershed hydrological and biogeochemical response to storm events. This study investigates the hydrological response to storms and chloride, nitrate and dissolved organic carbon (DOC) export dynamics during one spring storm and two summer storms in an agricultural catchment (watershed A) and a mixed agricultural/urban catchment (watershed M). Drier antecedent moisture conditions in summer were associated with lower runoff ratios during summer storms than during the spring storm studied. Watershed M also had a much flashier hydrologic behavior than watershed A, suggesting that moderate differences in land use significantly affected each watershed hydrological response to storm events. DOC concentrations were not significantly different between watersheds A and M; however, nitrate and chloride concentrations and export rates were, respectively, higher and lower in watershed A than M. Regardless of land use, nitrate concentrations were also consistently higher during the spring storm than during the two summer storms studied. Although DOC concentrations varied seasonally, precipitation characteristics appeared to be the primary controls on DOC concentration during storms. Generally, chloride and DOC concentrations, respectively, decreased and increased along with discharge during storms. No clear concentration patterns relative to discharge were observed for nitrate in the agricultural watershed. Nitrate concentrations tended to increase following the peak in discharge in the mixed land use watershed. Analysis of stream DOC specific UV absorbance (SUVA) indicated a sharp increase in stream DOC aromaticity during storms regardless of land use and seasons, suggesting a shift in the source of DOC to the stream during storms from low aromaticity DOC at baseflow to highly aromatic DOC during storms. Overall, although many variables can contribute to differences in solute flushing patterns between the watersheds studied, this study indicates that moderate differences in land use (85\% agriculture in the agricultural watershed, and 33\% agriculture/33\% urban/17\% pasture/13\% forest in the mixed land use watershed), storm characteristics and seasonality (spring vs. summer) can significantly impact watershed response to precipitation and patterns of chloride, nitrate and DOC exports during storms at the watershed scale. Owing to the importance of solute export dynamics in streams during storms in annual solute budgets, we argue that more studies investigating the impact of seasonality and differences in land uses on watersheds’ hydrological and biogeochemical responses to storms should be conducted in a variety of geomorphic settings.},
	language = {en},
	number = {1},
	urldate = {2020-02-12},
	journal = {Journal of Hydrology},
	author = {Vidon, P. and Hubbard, L. E. and Soyeux, E.},
	month = sep,
	year = {2009},
	keywords = {Chloride, Dissolved organic carbon, Land use, Nitrate, Season, Watershed},
	pages = {34--47},
}

@article{ho_phytoplankton_2017,
	title = {Phytoplankton blooms in {Lake} {Erie} impacted by both long-term and springtime phosphorus loading},
	volume = {43},
	issn = {0380-1330},
	url = {http://www.sciencedirect.com/science/article/pii/S0380133017300667},
	doi = {10.1016/j.jglr.2017.04.001},
	abstract = {Harmful algal blooms in Lake Erie have been increasing in severity over the past two decades, prompting new phosphorus loading target recommendations. We explore long-term drivers of phytoplankton blooms by leveraging new estimates of historical bloom extent from Landsat 5 covering 1984–2001 together with existing data covering 2002–2015. We find that a linear combination of springtime and long-term cumulative dissolved reactive phosphorus (DRP) loading explains a high proportion of interannual variability in maximum summertime bloom extent for 1984–2015 (R2=0.75). This finding suggests that the impacts of internal loading are potentially greater than previously understood, and that the hypothesized recent increased susceptibility to blooms may be attributable to high decadal-scale cumulative loading. Based on this combined loading model, achieving mild bloom conditions in Lake Erie (defined in recent studies as bloom areas below 600km2 nine years out of ten) would require DRP loads to be reduced by 58\% relative to the 2001–2015 average (equivalent to annual DRP loading of 240MT and April to July DRP loading of 78MT). Reaping the full benefits of load reductions may therefore take up to a decade due to the effects of historical loading.},
	language = {en},
	number = {3},
	urldate = {2020-02-11},
	journal = {Journal of Great Lakes Research},
	author = {Ho, Jeff C. and Michalak, Anna M.},
	month = jun,
	year = {2017},
	keywords = {Dissolved reactive phosphorus, Eutrophication models, Harmful algal blooms, Internal loading, Lake Erie, Phosphorus load},
	pages = {221--228},
}

@article{tribouillois_cover_2018,
	title = {Cover crops mitigate direct greenhouse gases balance but reduce drainage under climate change scenarios in temperate climate with dry summers},
	volume = {24},
	copyright = {© 2018 John Wiley \& Sons Ltd},
	issn = {1365-2486},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.14091},
	doi = {10.1111/gcb.14091},
	abstract = {Cover crops provide ecosystem services such as storing atmospheric carbon in soils after incorporation of their residues. Cover crops also influence soil water balance, which can be an issue in temperate climates with dry summers as for example in southern France and Europe. As a consequence, it is necessary to understand cover crops' long-term influence on greenhouse gases (GHG) and water balances to assess their potential to mitigate climate change in arable cropping systems. We used the previously calibrated and validated soil–crop model STICS to simulate scenarios of cover crop introduction to assess their influence on rainfed and irrigated cropping systems and crop rotations distributed among five contrasted sites in southern France from 2007 to 2052. Our results showed that cover crops can improve mean direct GHG balance by 315 kg CO2e ha−1 year−1 in the long term compared to that of bare soil. This was due mainly to an increase in carbon storage in the soil despite a slight increase in N2O emissions which can be compensated by adapting fertilization. Cover crops also influence the water balance by reducing mean annual drainage by 20 mm/year but increasing mean annual evapotranspiration by 20 mm/year compared to those of bare soil. Using cover crops to improve the GHG balance may help to mitigate climate change by decreasing CO2e emitted in cropping systems which can represent a decrease from 4.5\% to 9\% of annual GHG emissions of the French agriculture and forestry sector. However, if not well managed, they also could create water management issues in watersheds with shallow groundwater. Relationships between cover crop biomass and its influence on several variables such as drainage, carbon sequestration, and GHG emissions could be used to extend our results to other conditions to assess the cover crops' influence in a wider range of areas.},
	language = {en},
	number = {6},
	urldate = {2020-02-10},
	journal = {Global Change Biology},
	author = {Tribouillois, Hélène and Constantin, Julie and Justes, Eric},
	year = {2018},
	keywords = {N2O, STICS model, carbon, catch crop, evapotranspiration, simulation, water balance},
	pages = {2513--2529},
}

@article{royer_export_2005,
	title = {Export of dissolved organic carbon from agricultural streams in {Illinois}, {USA}},
	volume = {67},
	issn = {1420-9055},
	url = {10.1007/s00027-005-0781-6},
	doi = {10.1007/s00027-005-0781-6},
	abstract = {.In the Midwestern USA, agricultural soils contain a large pool of organic carbon, yet little is known about carbon export in agriculturally-influenced streams. We studied DOC in three streams draining intensively farmed areas in Illinois, all draining Mollisols with large organic matter pools. Water quality samples were collected (weekly to daily) for 3–10 years and discharge was monitored continuously at each site. In-stream DOC concentrations ranged from 1–16 mg L−1, and high concentrations of DOC occurred both during floods and periods of low discharge. Among sites, average flow-weighted DOC concentrations varied from 3.1 to 3.9 mg L−1. DOC in the streams appeared to originate from two sources: allochthonous DOC from drainage of cropland in late winter through early summer, and autochthonous DOC from algal blooms in late summer through autumn. Inputs of allochthonous DOC were under hydrological control, with most of the allochthonous DOC entering streams during floods. Watershed export of DOC ranged from 3–23 kg ha−1 yr−1. The mass of C exported from watersheds as DOC was strongly related to water yield (r = 0.98), and by inference to precipitation. Bioassays indicated that on average 18\% of the native DOC was bioavailable. Stream export of DOC from the agricultural watersheds was a small flux relative to the pool of soil organic C. However, increases in soil organic C could lead to greater inputs of DOC to streams and increased rates of microbial respiration.},
	language = {en},
	number = {4},
	urldate = {2020-02-10},
	journal = {Aquatic Sciences},
	author = {Royer, Todd V. and David, Mark B.},
	month = dec,
	year = {2005},
	keywords = {DOC, DOM, agriculture, organic matter},
	pages = {465--471},
}

@article{royer_export_2005-1,
	title = {Export of dissolved organic carbon from agricultural streams in {Illinois}, {USA}},
	volume = {67},
	issn = {1420-9055},
	url = {10.1007/s00027-005-0781-6},
	doi = {10.1007/s00027-005-0781-6},
	abstract = {.In the Midwestern USA, agricultural soils contain a large pool of organic carbon, yet little is known about carbon export in agriculturally-influenced streams. We studied DOC in three streams draining intensively farmed areas in Illinois, all draining Mollisols with large organic matter pools. Water quality samples were collected (weekly to daily) for 3–10 years and discharge was monitored continuously at each site. In-stream DOC concentrations ranged from 1–16 mg L−1, and high concentrations of DOC occurred both during floods and periods of low discharge. Among sites, average flow-weighted DOC concentrations varied from 3.1 to 3.9 mg L−1. DOC in the streams appeared to originate from two sources: allochthonous DOC from drainage of cropland in late winter through early summer, and autochthonous DOC from algal blooms in late summer through autumn. Inputs of allochthonous DOC were under hydrological control, with most of the allochthonous DOC entering streams during floods. Watershed export of DOC ranged from 3–23 kg ha−1 yr−1. The mass of C exported from watersheds as DOC was strongly related to water yield (r = 0.98), and by inference to precipitation. Bioassays indicated that on average 18\% of the native DOC was bioavailable. Stream export of DOC from the agricultural watersheds was a small flux relative to the pool of soil organic C. However, increases in soil organic C could lead to greater inputs of DOC to streams and increased rates of microbial respiration.},
	language = {en},
	number = {4},
	urldate = {2020-02-09},
	journal = {Aquatic Sciences},
	author = {Royer, Todd V. and David, Mark B.},
	month = dec,
	year = {2005},
	keywords = {DOC, DOM, agriculture, organic matter},
	pages = {465--471},
}

@article{royer_export_2005-2,
	title = {Export of dissolved organic carbon from agricultural streams in {Illinois}, {USA}},
	volume = {67},
	issn = {1420-9055},
	url = {10.1007/s00027-005-0781-6},
	doi = {10.1007/s00027-005-0781-6},
	abstract = {.In the Midwestern USA, agricultural soils contain a large pool of organic carbon, yet little is known about carbon export in agriculturally-influenced streams. We studied DOC in three streams draining intensively farmed areas in Illinois, all draining Mollisols with large organic matter pools. Water quality samples were collected (weekly to daily) for 3–10 years and discharge was monitored continuously at each site. In-stream DOC concentrations ranged from 1–16 mg L−1, and high concentrations of DOC occurred both during floods and periods of low discharge. Among sites, average flow-weighted DOC concentrations varied from 3.1 to 3.9 mg L−1. DOC in the streams appeared to originate from two sources: allochthonous DOC from drainage of cropland in late winter through early summer, and autochthonous DOC from algal blooms in late summer through autumn. Inputs of allochthonous DOC were under hydrological control, with most of the allochthonous DOC entering streams during floods. Watershed export of DOC ranged from 3–23 kg ha−1 yr−1. The mass of C exported from watersheds as DOC was strongly related to water yield (r = 0.98), and by inference to precipitation. Bioassays indicated that on average 18\% of the native DOC was bioavailable. Stream export of DOC from the agricultural watersheds was a small flux relative to the pool of soil organic C. However, increases in soil organic C could lead to greater inputs of DOC to streams and increased rates of microbial respiration.},
	language = {en},
	number = {4},
	urldate = {2020-02-09},
	journal = {Aquatic Sciences},
	author = {Royer, Todd V. and David, Mark B.},
	month = dec,
	year = {2005},
	keywords = {DOC, DOM, agriculture, organic matter},
	pages = {465--471},
}

@article{mallin_factors_2006,
	title = {Factors contributing to hypoxia in rivers, lakes, and streams},
	volume = {51},
	copyright = {© 2006, by the Association for the Sciences of Limnology and Oceanography, Inc.},
	issn = {1939-5590},
	url = {http://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.2006.51.1_part_2.0690},
	doi = {10.4319/lo.2006.51.1_part_2.0690},
	abstract = {We investigated physical, chemical, and biological variables contributing to biochemical oxygen demand (BOD) in 17 North Carolina lotic and lentic water bodies affected by mild to severe hypoxia. Phytoplankton production created the dominant reservoir of labile carbon driving BOD, and subsequent hypoxia, in a Piedmont river subject to algal blooms, three urban streams, a set of anthropogenically affected tidal creeks, and two urban lakes. Autotrophic phytoplankton production contributed to the BOD load in some rural streams. Autochthonous heterotrophic processes, stimulated primarily by phosphorus and secondarily by nitrogen loading, were the major influences on BOD in two large black water rivers and some rural black water streams. Inputs of biochemical oxygen-demanding materials from storm water runoff contribute to BOD in some urban and rural streams and black water rivers. We suggest that reductions of hypoxia can be better achieved by a system-specific approach based on an array of factors that potentially influence BOD, including both autochthonous and allochthonous variables. In some circumstances targeting the nutrient(s) stimulating phytoplankton blooms will suffice to reduce hypoxia, but in other situations targeting nutrient(s) limiting bacterial production will be necessary. Reduction of non—point source inputs of biochemical oxygen-demanding materials derived from urbanization or other land disrupting activities will be critical in some cases.},
	language = {en},
	number = {1part2},
	urldate = {2020-02-09},
	journal = {Limnology and Oceanography},
	author = {Mallin, Michael A. and Johnson, Virginia L. and Ensign, Scott H. and MacPherson, Tara A.},
	year = {2006},
	pages = {690--701},
}

@article{bernot_nutrient_2006,
	title = {Nutrient uptake in streams draining agricultural catchments of the midwestern {United} {States}},
	volume = {51},
	issn = {1365-2427},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2427.2006.01508.x},
	doi = {10.1111/j.1365-2427.2006.01508.x},
	abstract = {1. Agriculture is a major contributor of non-point source pollution to surface waters in the midwestern United States, resulting in eutrophication of freshwater aquatic ecosystems and development of hypoxia in the Gulf of Mexico. Agriculturally influenced streams are diverse in morphology and have variable nutrient concentrations. Understanding how nutrients are transformed and retained within agricultural streams may aid in mitigating increased nutrient export to downstream ecosystems. 2. We studied six agriculturally influenced streams in Indiana and Michigan to develop a more comprehensive understanding of the factors controlling nutrient retention and export in agricultural streams using nutrient addition and isotopic tracer studies. 3. Metrics of nutrient uptake indicated that nitrate uptake was saturated in these streams whereas ammonium and phosphorus uptake increased with higher concentrations. Phosphorus uptake was likely approaching saturation as evidenced by decreasing uptake velocities with concentration; ammonium uptake velocity also declined with concentration, though not significantly. 4. Higher whole-stream uptake rates of phosphorus and ammonium were associated with the observed presence of stream autotrophs (e.g. algae and macrophytes). However, there was no significant relationship between measures of nutrient uptake and stream metabolism. Water-column nutrient concentrations were positively correlated with gross primary production but not community respiration. 5. Overall, nutrient uptake and metabolism were affected by nutrient concentrations in these agriculturally influenced streams. Biological uptake of ammonium and phosphorus was not saturated, although nitrate uptake did appear to be saturated in these ecosystems. Biological activity in agriculturally influenced streams is higher relative to more pristine streams and this increased biological activity likely influences nutrient retention and transport to downstream ecosystems.},
	language = {en},
	number = {3},
	urldate = {2020-02-09},
	journal = {Freshwater Biology},
	author = {Bernot, Melody J. and Tank, Jennifer L. and Royer, Todd V. and David, Mark B.},
	year = {2006},
	keywords = {agriculture, nitrogen, nutrient uptake, phosphorus, stream},
	pages = {499--509},
}

@article{bernot_nutrient_2006-1,
	title = {Nutrient uptake in streams draining agricultural catchments of the midwestern {United} {States}},
	volume = {51},
	issn = {1365-2427},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2427.2006.01508.x},
	doi = {10.1111/j.1365-2427.2006.01508.x},
	abstract = {1. Agriculture is a major contributor of non-point source pollution to surface waters in the midwestern United States, resulting in eutrophication of freshwater aquatic ecosystems and development of hypoxia in the Gulf of Mexico. Agriculturally influenced streams are diverse in morphology and have variable nutrient concentrations. Understanding how nutrients are transformed and retained within agricultural streams may aid in mitigating increased nutrient export to downstream ecosystems. 2. We studied six agriculturally influenced streams in Indiana and Michigan to develop a more comprehensive understanding of the factors controlling nutrient retention and export in agricultural streams using nutrient addition and isotopic tracer studies. 3. Metrics of nutrient uptake indicated that nitrate uptake was saturated in these streams whereas ammonium and phosphorus uptake increased with higher concentrations. Phosphorus uptake was likely approaching saturation as evidenced by decreasing uptake velocities with concentration; ammonium uptake velocity also declined with concentration, though not significantly. 4. Higher whole-stream uptake rates of phosphorus and ammonium were associated with the observed presence of stream autotrophs (e.g. algae and macrophytes). However, there was no significant relationship between measures of nutrient uptake and stream metabolism. Water-column nutrient concentrations were positively correlated with gross primary production but not community respiration. 5. Overall, nutrient uptake and metabolism were affected by nutrient concentrations in these agriculturally influenced streams. Biological uptake of ammonium and phosphorus was not saturated, although nitrate uptake did appear to be saturated in these ecosystems. Biological activity in agriculturally influenced streams is higher relative to more pristine streams and this increased biological activity likely influences nutrient retention and transport to downstream ecosystems.},
	language = {en},
	number = {3},
	urldate = {2020-02-09},
	journal = {Freshwater Biology},
	author = {Bernot, Melody J. and Tank, Jennifer L. and Royer, Todd V. and David, Mark B.},
	year = {2006},
	keywords = {agriculture, nitrogen, nutrient uptake, phosphorus, stream},
	pages = {499--509},
}

@article{bernot_nutrient_2006-2,
	title = {Nutrient uptake in streams draining agricultural catchments of the midwestern {United} {States}},
	volume = {51},
	issn = {1365-2427},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2427.2006.01508.x},
	doi = {10.1111/j.1365-2427.2006.01508.x},
	abstract = {1. Agriculture is a major contributor of non-point source pollution to surface waters in the midwestern United States, resulting in eutrophication of freshwater aquatic ecosystems and development of hypoxia in the Gulf of Mexico. Agriculturally influenced streams are diverse in morphology and have variable nutrient concentrations. Understanding how nutrients are transformed and retained within agricultural streams may aid in mitigating increased nutrient export to downstream ecosystems. 2. We studied six agriculturally influenced streams in Indiana and Michigan to develop a more comprehensive understanding of the factors controlling nutrient retention and export in agricultural streams using nutrient addition and isotopic tracer studies. 3. Metrics of nutrient uptake indicated that nitrate uptake was saturated in these streams whereas ammonium and phosphorus uptake increased with higher concentrations. Phosphorus uptake was likely approaching saturation as evidenced by decreasing uptake velocities with concentration; ammonium uptake velocity also declined with concentration, though not significantly. 4. Higher whole-stream uptake rates of phosphorus and ammonium were associated with the observed presence of stream autotrophs (e.g. algae and macrophytes). However, there was no significant relationship between measures of nutrient uptake and stream metabolism. Water-column nutrient concentrations were positively correlated with gross primary production but not community respiration. 5. Overall, nutrient uptake and metabolism were affected by nutrient concentrations in these agriculturally influenced streams. Biological uptake of ammonium and phosphorus was not saturated, although nitrate uptake did appear to be saturated in these ecosystems. Biological activity in agriculturally influenced streams is higher relative to more pristine streams and this increased biological activity likely influences nutrient retention and transport to downstream ecosystems.},
	language = {en},
	number = {3},
	urldate = {2020-02-09},
	journal = {Freshwater Biology},
	author = {Bernot, Melody J. and Tank, Jennifer L. and Royer, Todd V. and David, Mark B.},
	year = {2006},
	keywords = {agriculture, nitrogen, nutrient uptake, phosphorus, stream},
	pages = {499--509},
}

@article{bernot_nutrient_2006-3,
	title = {Nutrient uptake in streams draining agricultural catchments of the midwestern {United} {States}},
	volume = {51},
	issn = {1365-2427},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2427.2006.01508.x},
	doi = {10.1111/j.1365-2427.2006.01508.x},
	abstract = {1. Agriculture is a major contributor of non-point source pollution to surface waters in the midwestern United States, resulting in eutrophication of freshwater aquatic ecosystems and development of hypoxia in the Gulf of Mexico. Agriculturally influenced streams are diverse in morphology and have variable nutrient concentrations. Understanding how nutrients are transformed and retained within agricultural streams may aid in mitigating increased nutrient export to downstream ecosystems. 2. We studied six agriculturally influenced streams in Indiana and Michigan to develop a more comprehensive understanding of the factors controlling nutrient retention and export in agricultural streams using nutrient addition and isotopic tracer studies. 3. Metrics of nutrient uptake indicated that nitrate uptake was saturated in these streams whereas ammonium and phosphorus uptake increased with higher concentrations. Phosphorus uptake was likely approaching saturation as evidenced by decreasing uptake velocities with concentration; ammonium uptake velocity also declined with concentration, though not significantly. 4. Higher whole-stream uptake rates of phosphorus and ammonium were associated with the observed presence of stream autotrophs (e.g. algae and macrophytes). However, there was no significant relationship between measures of nutrient uptake and stream metabolism. Water-column nutrient concentrations were positively correlated with gross primary production but not community respiration. 5. Overall, nutrient uptake and metabolism were affected by nutrient concentrations in these agriculturally influenced streams. Biological uptake of ammonium and phosphorus was not saturated, although nitrate uptake did appear to be saturated in these ecosystems. Biological activity in agriculturally influenced streams is higher relative to more pristine streams and this increased biological activity likely influences nutrient retention and transport to downstream ecosystems.},
	language = {en},
	number = {3},
	urldate = {2020-02-09},
	journal = {Freshwater Biology},
	author = {Bernot, Melody J. and Tank, Jennifer L. and Royer, Todd V. and David, Mark B.},
	year = {2006},
	keywords = {agriculture, nitrogen, nutrient uptake, phosphorus, stream},
	pages = {499--509},
}

@article{bernot_nutrient_2006-4,
	title = {Nutrient uptake in streams draining agricultural catchments of the midwestern {United} {States}},
	volume = {51},
	issn = {1365-2427},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2427.2006.01508.x},
	doi = {10.1111/j.1365-2427.2006.01508.x},
	abstract = {1. Agriculture is a major contributor of non-point source pollution to surface waters in the midwestern United States, resulting in eutrophication of freshwater aquatic ecosystems and development of hypoxia in the Gulf of Mexico. Agriculturally influenced streams are diverse in morphology and have variable nutrient concentrations. Understanding how nutrients are transformed and retained within agricultural streams may aid in mitigating increased nutrient export to downstream ecosystems. 2. We studied six agriculturally influenced streams in Indiana and Michigan to develop a more comprehensive understanding of the factors controlling nutrient retention and export in agricultural streams using nutrient addition and isotopic tracer studies. 3. Metrics of nutrient uptake indicated that nitrate uptake was saturated in these streams whereas ammonium and phosphorus uptake increased with higher concentrations. Phosphorus uptake was likely approaching saturation as evidenced by decreasing uptake velocities with concentration; ammonium uptake velocity also declined with concentration, though not significantly. 4. Higher whole-stream uptake rates of phosphorus and ammonium were associated with the observed presence of stream autotrophs (e.g. algae and macrophytes). However, there was no significant relationship between measures of nutrient uptake and stream metabolism. Water-column nutrient concentrations were positively correlated with gross primary production but not community respiration. 5. Overall, nutrient uptake and metabolism were affected by nutrient concentrations in these agriculturally influenced streams. Biological uptake of ammonium and phosphorus was not saturated, although nitrate uptake did appear to be saturated in these ecosystems. Biological activity in agriculturally influenced streams is higher relative to more pristine streams and this increased biological activity likely influences nutrient retention and transport to downstream ecosystems.},
	language = {en},
	number = {3},
	urldate = {2020-02-09},
	journal = {Freshwater Biology},
	author = {Bernot, Melody J. and Tank, Jennifer L. and Royer, Todd V. and David, Mark B.},
	year = {2006},
	keywords = {agriculture, nitrogen, nutrient uptake, phosphorus, stream},
	pages = {499--509},
}

@article{bothwell_phosphoruslimited_1989,
	title = {Phosphorus–{Limited} {Growth} {Dynamics} of {Lotic} {Periphytic} {Diatom} {Communities}: {Areal} {Biomass} and {Cellular} {Growth} {Rate} {Responses}},
	volume = {46},
	issn = {0706-652X},
	shorttitle = {Phosphorus–{Limited} {Growth} {Dynamics} of {Lotic} {Periphytic} {Diatom} {Communities}},
	url = {https://www.nrcresearchpress.com/doi/abs/10.1139/f89-166},
	doi = {10.1139/f89-166},
	abstract = {Three long-term phosphate enrichment experiments were conducted at the Experimental Troughs Apparatus (EXTRA), South Thompson River British Columbia to determine the relationship between external o..., Trois expériences d'enrichssement à long terme par le phosphate ont été effectuées dans des bacs expérimentaux de la station EXTRA(Experimental Troughs Apparatus) dans la rivière Thompson Sud, en C...},
	number = {8},
	urldate = {2020-02-09},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Bothwell, Max L.},
	month = aug,
	year = {1989},
	pages = {1293--1301},
}

@article{mcdowell_approximating_2001,
	title = {Approximating {Phosphorus} {Release} from {Soils} to {Surface} {Runoff} and {Subsurface} {Drainage}},
	volume = {30},
	issn = {1537-2537},
	url = {https://dl.sciencesocieties.org/publications/jeq/articles/30/2/508},
	doi = {10.2134/jeq2001.302508x},
	language = {en},
	number = {2},
	urldate = {2020-02-05},
	journal = {Journal of Environmental Quality},
	author = {McDowell, R. W. and Sharpley, A. N.},
	month = mar,
	year = {2001},
	pages = {508--520},
}

@article{kladivko_pesticide_1991,
	title = {Pesticide and {Nutrient} {Movement} into {Subsurface} {Tile} {Drains} on a {Silt} {Loam} {Soil} in {Indiana}},
	volume = {20},
	issn = {0047-2425},
	url = {https://dl.sciencesocieties.org/publications/jeq/abstracts/20/1/JEQ0200010264},
	doi = {10.2134/jeq1991.00472425002000010043x},
	language = {en},
	number = {1},
	urldate = {2020-02-05},
	journal = {Journal of Environmental Quality},
	author = {Kladivko, E. J. and Van Scoyoc, G. E. and Monke, E. J. and Oates, K. M. and Pask, W.},
	year = {1991},
	pages = {264--270},
}

@article{najm_new_2010,
	title = {New method for the characterization of three-dimensional preferential flow paths in the field},
	volume = {46},
	copyright = {Copyright 2010 by the American Geophysical Union.},
	issn = {1944-7973},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2009WR008594},
	doi = {10.1029/2009WR008594},
	abstract = {Preferential flow path development in the field is the result of the complex interaction of multiple processes relating to the soil's structure, moisture condition, stress level, and biological activity. Visualizing and characterizing the cracking behavior and preferential paths evolution with soil depth has always been a key challenge and a major barrier against scaling up existing hydrologic concepts and models to account for preferential flows. This paper presents a new methodology to quantify soil preferential paths in the field using liquid latex. The evolution of the preferential flow paths at different soil depths and moisture conditions is assessed. Results from different soil series (Savage clay loam soil versus Chalmers clay loam) and different vegetation covers and soil managements (corn/tilled field versus soybean no-till field in the Chalmers soil series) are presented.},
	language = {en},
	number = {2},
	urldate = {2020-02-05},
	journal = {Water Resources Research},
	author = {Najm, Majdi R. Abou and Jabro, Jalal D. and Iversen, William M. and Mohtar, Rabi H. and Evans, Robert G.},
	year = {2010},
	keywords = {multiscale hydrology, preferential flow, soil characterization},
}

@article{gish_impact_1998,
	title = {Impact of roots on ground water quality},
	volume = {200},
	issn = {1573-5036},
	url = {10.1023/A:1004202013082},
	doi = {10.1023/A:1004202013082},
	abstract = {Preferential flow is perhaps the major chemical transport process influencing the rapid and typically unexpected movement of agricultural chemicals to ground water. Plant roots are a major contributor to preferential flow mechanics as they form spatial voids which can be used as preferential flow pathways. Chemical transport of atrazine, deethylatrazine, and bromide solutions concentrations under tilled and no-tilled corn fields was evaluated below the active root zone. Additionally, the impact of roots on flow pathways was visualized using a soluble dye (Brilliant Blue FCF). Pictures of the dye-stained pattern were subsequently digitized to determine the cross-sectional area used for transport as a function of depth. Bromide transit times through the field soils were not influenced by tillage practice, whereas atrazine transport was strongly influenced by tillage practice. Under no-till field conditions, atrazine was rarely detected but deethylatrazine concentrations were greater than those observed under tilled field conditions. Visual observation indicated that the dye under no-tillage was more predominant in the corn row, indicative of transport through void root channels. No-tillage practices may decrease the likelihood of ground water contamination through leaching due to the formation of stable root channels where an organic carbon source and microbial population are preferentially located to degrade pesticides.},
	language = {en},
	number = {1},
	urldate = {2020-02-05},
	journal = {Plant and Soil},
	author = {Gish, Timothy J. and Gimenez, Daniel and Rawls, Walter J.},
	month = mar,
	year = {1998},
	keywords = {chemical transport, pesticide behavior, preferential flow},
	pages = {47--54},
}

@article{ghestem_influence_2011,
	title = {The {Influence} of {Plant} {Root} {Systems} on {Subsurface} {Flow}: {Implications} for {Slope} {Stability}},
	volume = {61},
	issn = {0006-3568},
	shorttitle = {The {Influence} of {Plant} {Root} {Systems} on {Subsurface} {Flow}},
	url = {https://academic.oup.com/bioscience/article/61/11/869/223555},
	doi = {10.1525/bio.2011.61.11.6},
	abstract = {Abstract.  Although research has explained how plant roots mechanically stabilize soils, in this article we explore how root systems create networks of preferen},
	language = {en},
	number = {11},
	urldate = {2020-02-05},
	journal = {BioScience},
	author = {Ghestem, Murielle and Sidle, Roy C. and Stokes, Alexia},
	month = nov,
	year = {2011},
	pages = {869--879},
}

@article{schaik_linking_2014,
	title = {Linking spatial earthworm distribution to macropore numbers and hydrological effectiveness},
	volume = {7},
	copyright = {Copyright © 2013 John Wiley \& Sons, Ltd.},
	issn = {1936-0592},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/eco.1358},
	doi = {10.1002/eco.1358},
	abstract = {Due to its high spatial and temporal variability, preferential flow is difficult to measure and quantify. Earthworms create macropores that provide common pathways for preferential flow. Therefore in this article, we link earthworm abundance to macropore numbers and hydrological effectiveness, with the future aim to use species distribution models of earthworms for the spatial parameterization of preferential flow. Earthworms are generally categorized into three ecological types with varying burrowing behaviour, resulting in a different impact on soil hydrological processes. Therefore, we studied the relationships between the abundance of the earthworm ecological types and macropores of different size classes and in different soil depths. The abundance and biomass of earthworms were well correlated to different sizes of macropores in different soil depths. This is mainly the case for the larger, vertically oriented macropores ({\textgreater}6 mm diameter), which are generally connected to the soil surface and hydrologically most effective. The correlation of total earthworm biomass and macropores ranges from 0·72 to 0·89 for different soil depths. Although there is quite some variation in infiltration patterns, infiltration from macropores into the matrix is profile-specific, as it varies strongly between profiles, but not within one profile. Macropore coating seems to have a larger effect on this macropore matrix interaction than the soil physical properties of the matrix. Although the amount of macropores and their effectiveness are clearly related to the earthworm distribution, the variation in infiltration from macropores to soil matrix should be further studied. Copyright © 2013 John Wiley \& Sons, Ltd.},
	language = {en},
	number = {2},
	urldate = {2020-02-05},
	journal = {Ecohydrology},
	author = {Schaik, Loes van and Palm, Juliane and Klaus, Julian and Zehe, Erwin and Schröder, Boris},
	year = {2014},
	keywords = {earthworm ecological types, infiltration patterns, macropores, preferential flow, spatial parameterization},
	pages = {401--408},
}

@article{clothier_roots_1997,
	title = {{ROOTS}: {THE} {BIG} {MOVERS} {OF} {WATER} {AND} {CHEMICAL} {IN} {SOIL}},
	volume = {162},
	issn = {0038-075X},
	shorttitle = {{ROOTS}},
	url = {https://journals.lww.com/soilsci/Abstract/1997/08000/ROOTS__THE_BIG_MOVERS_OF_WATER_AND_CHEMICAL_IN.2.aspx},
	abstract = {Root water uptake and the dynamic availability of water  to plants is a phenomenon that tends to be overlooked by soil scientists, despite  the often dominant role of roots as a sink for water in the soil. Water taken up  by roots is vital for plant growth and the productive management of soils. In addition,  trapping and consuming water in the rootzone means there is less remaining to act  as a vehicle to carry chemicals beyond the grasp of roots and consign them to either  receiving groundwater bodies or surface reserves. Here we review landmark developments  in the theoretical description of the availability of water to roots. By the 1960s,  thanks to Wilford Gardner and others, we had achieved a good theoretical understanding  of the interplay between soil characteristics and water availability for a single,  isolated, semiinfinite root embedded in a cylinder of soil. We discuss the incorporation  of these simple theoretical notions into the multitude of comprehensive simulation  models of rootzone functioning that followed the democratic spread of computers throughout  the 1970s. Much still remains to be done in linking rootzone form to root functioning,  but technology is coming to the rescue. New techniques are providing improved means  by which we can better observe both the changing spatial form of roots and the temporal  pattern of their functioning. Time Domain Reflectometry for measuring soil water  content close to roots and near the soil surface, in tandem with instantaneous monitoring  of sap flow directly within roots, is providing a sharper view of root functioning.  Mean while improved rhizotrons, along with new techniques of image analysis and topological  description, are providing better descriptions of root system form. We feel that  progress in understanding the role of roots as the big movers of water and chemical  in soil will, in the near future, remain driven by improvements in our ability to  observe the link between rootzone form and function.},
	language = {en-US},
	number = {8},
	urldate = {2020-02-05},
	journal = {Soil Science},
	author = {Clothier, Brent E. and Green, Steve R.},
	month = aug,
	year = {1997},
	pages = {534--543},
}

@article{clothier_preferential_2008,
	title = {Preferential flow and transport in soil: progress and prognosis},
	volume = {59},
	copyright = {2007 British Society of Soil Science},
	issn = {1365-2389},
	shorttitle = {Preferential flow and transport in soil},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2389.2007.00991.x},
	doi = {10.1111/j.1365-2389.2007.00991.x},
	abstract = {Soil is the first filter of the world’s water; its buffering and filtering determine the quality and quantity of our reserves of subterranean and surface water. Preferential flow can either enhance, or curtail, the capacity of the soil to buffer and filter, and it can compromise, or boost, other ecosystem services. We ask ‘when do preferential flow and transport matter?’ We identify 12 of 17 ecosystem services that benefit from preferential flow and three that are affected detrimentally. We estimate by simple arithmetic the value of preferential flow to ecosystem services to be globally some US\$304 billion (109) per year. We review the 1989 Monte Verità meeting on preferential flow processes and summarize the 2006 presentations, some of which are published in this issue of the Journal. New technologies and innovative experiments have increased our understanding of the conditions that initiate and sustain preferential flows. We identify contemporary exigencies, and suggest avenues for their resolution. We are progressing through observation-led discovery. Our prognosis is that new data will enable us to develop better models, and more aptly to parameterize existing models, and thereby predict the impact, benefits and detriments of preferential flow in soil.},
	language = {en},
	number = {1},
	urldate = {2020-02-05},
	journal = {European Journal of Soil Science},
	author = {Clothier, B. E. and Green, S. R. and Deurer, M.},
	year = {2008},
	pages = {2--13},
}

@article{beven_macropores_1982,
	title = {Macropores and water flow in soils},
	volume = {18},
	copyright = {Copyright 1982 by the American Geophysical Union.},
	issn = {1944-7973},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/WR018i005p01311},
	doi = {10.1029/WR018i005p01311},
	abstract = {This paper reviews the importance of large continuous openings (macropores) on water flow in soils. The presence of macropores may lead to spatial concentrations of water flow through unsaturated soil that will not be described well by a Darcy approach to flow through porous media. This has important implications for the rapid movement of solutes and pollutants through soils. Difficulties in defining what constitutes a macropore and the limitations of current nomenclature are reviewed. The influence of macropores on infiltration and subsurface storm flow is discussed on the basis of both experimental evidence and theoretical studies. The limitations of models that treat macropores and matrix porosity as separate flow domains is stressed. Little-understood areas are discussed as promising lines for future research. In particular, there is a need for a coherent theory of flow through structured soils that would make the macropore domain concept redundant.},
	language = {en},
	number = {5},
	urldate = {2020-02-05},
	journal = {Water Resources Research},
	author = {Beven, Keith and Germann, Peter},
	year = {1982},
	pages = {1311--1325},
}

@article{germann_rapid_1986,
	title = {Rapid drainage response to precipitation},
	volume = {1},
	copyright = {Copyright © 1986 John Wiley \& Sons, Ltd},
	issn = {1099-1085},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/hyp.3360010103},
	doi = {10.1002/hyp.3360010103},
	abstract = {Rapid drainage flow increases at the 2·4 m depth in the Coshocton lysimeters were related to the storms that most likely initiated them. The time lapsed between the onset of the storm and rapid drainage response was less than 2 days in 98 per cent of the 389 cases observed in five lysimeters between 1976 and 1982. A pronounced seasonal variation in the frequency of rapid responses was found, with the first quarter of the year comprising the highest number of events. During winter, when soil moisture is generally high, a storm yielding 6 mm/d was already sufficient to initiate this response while summer storms producing more than 50 mm/d did not always initiate a drainage response. Average drainage yield per event was found to be more closely related to the type and usage of a soil than to seasonal effects.},
	language = {en},
	number = {1},
	urldate = {2020-02-05},
	journal = {Hydrological Processes},
	author = {Germann, Peter F.},
	year = {1986},
	keywords = {Antecedent soilmoisture, Critical daily precipitation, Macropore flow, Weighing monolith lysimeters},
	pages = {3--13},
}

@article{ho_challenges_2015,
	title = {Challenges in tracking harmful algal blooms: {A} synthesis of evidence from {Lake} {Erie}},
	volume = {41},
	issn = {0380-1330},
	shorttitle = {Challenges in tracking harmful algal blooms},
	url = {http://www.sciencedirect.com/science/article/pii/S0380133015000027},
	doi = {10.1016/j.jglr.2015.01.001},
	abstract = {Harmful algal blooms (HABs) are becoming increasingly common in freshwater ecosystems globally, raising complex questions about the factors that influence their initiation and growth. These questions have increasingly been answered through mechanistic and stochastic modeling efforts that rely on historical information about HABs in a given system for development, validation, and calibration. Therefore, understanding processes that control HABs is predicated on the ability to answer much more basic questions about what has actually occurred in a given system, namely questions of HAB occurrence, extent, intensity, and timing. Here we explore the state of the science in answering these basic questions; we use Lake Erie as a case study, where nearly two decades after the resurgence of HABs, a summer 2014 event caused a mandatory three day tap water ban for Toledo, Ohio. We find that, even for well-studied systems, unambiguous answers to basic questions about HAB occurrence are lacking, raising concerns about their use as a basis for addressing mechanistic questions about controlling factors. This ambiguity is found to be caused by differences in the methods used to track HABs, the specific harm being considered, the linkage to that harm (direct or indirect), the threshold defining harm, and spatiotemporal variability in sampling. Further work is therefore needed to integrate heterogeneous types of observations in order to better leverage existing and future monitoring programs, and to guide modeling efforts toward deeper understanding of HAB causes and consequences.},
	language = {en},
	number = {2},
	urldate = {2020-02-05},
	journal = {Journal of Great Lakes Research},
	author = {Ho, Jeff C. and Michalak, Anna M.},
	month = jun,
	year = {2015},
	keywords = {Aquatic ecology, Ecosystem indicators, Freshwater eutrophication, Harmful algal blooms, Lake Erie},
	pages = {317--325},
}

@article{shaughnessy_sediments_2019,
	title = {Sediments in {Agricultural} {Reservoirs} {Act} as {Sinks} and {Sources} for {Nutrients} over {Various} {Timescales}},
	volume = {55},
	copyright = {©2019. American Geophysical Union. All Rights Reserved.},
	issn = {1944-7973},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018WR024004},
	doi = {10.1029/2018WR024004},
	abstract = {Reservoirs along rivers have the potential to act as nutrient sinks (e.g., denitrification and sedimentation) or sources (e.g., decomposition and redox changes), potentially reducing or enhancing nutrient loads downstream. This study investigated the spatial and temporal variability of water and lakebed sediment chemistry for an agricultural reservoir, Carlyle Lake (Illinois, U.S.), to assess the role of sediments as nutrient sinks or sources. Samples were collected across the reservoir over a 2-year period. We measured N- and P-species in water at the sediment-water interface, in sediment porewaters, and loosely bound to sediment exchange sites. Total N, total P, total C, organic matter, Fe, Mn, and grain size were measured in bulk sediments. We observed a strong gradient in sedimentary total N, total P, total C, organic matter, and metals along the reservoir, with the lowest concentrations at the river mouth and the highest concentrations near the dam. Additionally, we did a long-term nutrient mass balance using historical water quality data for streams entering and exiting the reservoir and the reservoir itself. Mass balance calculations showed that Carlyle Lake, on average, removed 2,738 Mg N/year and released 121 Mg P/year over the multidecadal observation period. While N was consistently removed from the system over time, P was initially stored in, but later released from, the reservoir. The subsequent release of legacy P from the reservoir led to higher outgoing, compared with incoming, P loads. Thus, reservoirs in intensively managed landscapes can act as sinks for N but sources for P over decadal timescales.},
	language = {en},
	number = {7},
	urldate = {2020-02-05},
	journal = {Water Resources Research},
	author = {Shaughnessy, A. R. and Sloan, J. J. and Corcoran, M. J. and Hasenmueller, E. A.},
	year = {2019},
	keywords = {intensively managed landscapes, nutrients, reservoirs, water quality},
	pages = {5985--6000},
}

@article{jones_relating_2019,
	title = {Relating carbon and nitrogen transport from constructed farm drainage},
	volume = {213},
	issn = {0378-3774},
	url = {http://www.sciencedirect.com/science/article/pii/S0378377418308515},
	doi = {10.1016/j.agwat.2018.10.004},
	abstract = {Fertility and crop production in soils of the recently-glaciated agricultural Midwestern U.S. link to soil inorganic and organic carbon, soil nitrogen and nitrogen inputs. Research relating transport of each to the others through the constructed drainage network to receiving streams is sparse. The main objective of this work was to quantify and characterize concentrations and yields of inorganic and organic carbon (IC and OC) along with nitrate-nitrogen (NO3-N) using a four-year dataset that included discharge from two managed drainage districts in the Cornbelt state of Iowa. Our analysis shows loss of carbon through these constructed drainage networks averages 124 kg ha−1 yr−1 with more than 90\% of this total in carbonate form and only 7\% in organic forms, a small amount relative to soil organic stores. Transport of NO3-N can total as much as 97 kg ha−1 yr−1. Although loads of IC, OC and NO3-N all vary similarly with discharge, NO3-N is especially transport-limited. Elevated OC concentrations in March are likely linked to recent manure application to soil surfaces, with concentrations returning to a consistent baseline thereafter. Concentrations of IC are lowest at high flows, indicating dilution by fresh water from recent hydrologic events into the drainage system which disproportionately mobilize NO3-N compared to IC. Although yields of IC and OC to the drainage system indicate tile drainage does not threaten to deplete soil organic matter stores, returning the system to a condition where carbon and nitrogen cycle together could improve stream water quality.},
	language = {en},
	urldate = {2020-02-05},
	journal = {Agricultural Water Management},
	author = {Jones, Christopher S. and Schilling, Keith E. and Seeman, Anthony},
	month = mar,
	year = {2019},
	keywords = {Alkalinity, Inorganic carbon, Nitrate-nitrogen, Organic carbon, Soil drainage, Tile, Water quality},
	pages = {12--23},
}

@article{stelzer_influence_2003,
	title = {The influence of dissolved nutrients and particulate organic matter quality on microbial respiration and biomass in a forest stream},
	volume = {48},
	issn = {1365-2427},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-2427.2003.01141.x},
	doi = {10.1046/j.1365-2427.2003.01141.x},
	abstract = {1. Although dissolved nutrients and the quality of particulate organic matter (POM) influence microbial processes in aquatic systems, these factors have rarely been considered simultaneously. We manipulated dissolved nutrient concentrations and POM type in three contiguous reaches (reference, nitrogen, nitrogen + phosphorus) of a low nutrient, third-order stream at Hubbard Brook Experimental Forest (U.S.A). In each reach we placed species of leaves (mean C : N of 68 and C : P of 2284) and wood (mean C : N of 721 and C : P of 60 654) that differed in elemental composition. We measured the respiration and biomass of microbes associated with this POM before and after nutrient addition. 2. Before nutrient addition, microbial respiration rates and biomass were higher for leaves than for wood. Respiration rates of microbes associated with wood showed a larger response to increased dissolved nutrient concentrations than respiration rates of microbes associated with leaves, suggesting that the response of microbes to increased dissolved nutrients was influenced by the quality of their substrate. 3. Overall, dissolved nutrients had strong positive effects on microbial respiration and fungal, but not bacterial, biomass, indicating that microbial respiration and fungi were nutrient limited. The concentration of nitrate in the enriched reaches was within the range of natural variation in forest streams, suggesting that natural variation in nitrate among forest streams influences carbon mineralisation and fungal biomass.},
	language = {en},
	number = {11},
	urldate = {2020-02-05},
	journal = {Freshwater Biology},
	author = {Stelzer, Robert S. and Heffernan, James and Likens, Gene E.},
	year = {2003},
	keywords = {fungi, microbial respiration, nitrogen, organic matter, phosphorus},
	pages = {1925--1937},
}

@article{kaplan_microbial_1983,
	title = {Microbial heterotrophic utilization of dissolved organic matter in a piedmont stream},
	volume = {13},
	issn = {1365-2427},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2427.1983.tb00686.x},
	doi = {10.1111/j.1365-2427.1983.tb00686.x},
	abstract = {SUMMARY. 1 The microbial heterotrophic utilization of dissolved organic matter (DOM) was determined experimentally in microcosms using stream water and stream-bed sediments from a third order reach of White Clay Creek (Pennsylvania, U.S.A.). 2 Sources of DOM for the experiments included White Clay Creek water at baseflow and stormflow and cold water extracts of jewel weed (Impatiens capensis L.) and spicebush (Linderu henzoin (L.) Blume). 3 The heterotrophic activity of the sediments was measured as uptake of the following: dissolved organic carbon (DOC), molecular weight fractions within the DOC pool, carbohydrates, amino acids and peptides, phenolics, and dissolved oxygen (DO), all in the overlying water. 4 Concentrations of adenosine triphosphate (ATP), and direct microscopic counts of bacteria were used to estimate bacterial biomass in the surface sediments. 5 The microcosm experiments showed that specific DOC molecular size classes and DOM functional groups were selectively removed from solution, exposure to one DOM source affected responses to a different DOM source and certain DOM sources were more readily utilized than others. 6 Continued exposure to a DOM source increased microbial heterotrophic activity (a condition which persisted even after removal of the DOM source for several days). 7 Rates of biotic DOC uptake ranged from 3.6 to 242.8 mg Cm-2h-1. 8 Indirect estimates of biosynthesis calculated from DOC and DO data ranged from 1.6 at baseflow and 2.6–61.2 at stormflow to as high as 192.6 mg C m-2 h-1 when the community was repeatedly exposed to enriched DOM sources. 9 The mean generation times of bacteria in sediments, determined from direct microscopy data, ranged from 12.5 to 46.2 h at 15°C.},
	language = {en},
	number = {4},
	urldate = {2020-02-05},
	journal = {Freshwater Biology},
	author = {Kaplan, Louisa and Bott, Thomas L.},
	year = {1983},
	pages = {363--377},
}

@misc{noauthor_microbial_nodate,
	title = {Microbial heterotrophic utilization of dissolved organic matter in a piedmont stream - {KAPLAN} - 1983 - {Freshwater} {Biology} - {Wiley} {Online} {Library}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2427.1983.tb00686.x},
	urldate = {2020-02-05},
}

@misc{noauthor_microbial_nodate-1,
	title = {Microbial heterotrophic utilization of dissolved organic matter in a piedmont stream - {KAPLAN} - 1983 - {Freshwater} {Biology} - {Wiley} {Online} {Library}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2427.1983.tb00686.x},
	urldate = {2020-02-05},
}

@article{singh_cover_2018,
	title = {Cover {Crops} for {Managing} {Stream} {Water} {Quantity} and {Improving} {Stream} {Water} {Quality} of {Non}-{Tile} {Drained} {Paired} {Watersheds}},
	volume = {10},
	issn = {2073-4441},
	doi = {10.3390/w10040521},
	abstract = {In the Midwestern United States, cover crops are being promoted as a best management practice for managing nutrient and sediment losses from agricultural fields through surface and subsurface water movement. To date, the water quality benefits of cover crops have been inferred primarily from plot scale studies. This project is one of the first to analyze the impacts of cover crops on stream water quality at the watershed scale. The objective of this research was to evaluate nitrogen, phosphorus, and sediment loss in stream water from a no-till corn-soybean rotation planted with winter cover crops cereal rye (Secale cereale) and hairy vetch (Vicia villosa) in non-tile drained paired watersheds in Illinois, USA. The paired watersheds are under mixed land use (agriculture, forest, and pasture). The control watershed had 27 ha of row-crop agriculture, and the treatment watershed had 42 ha of row crop agriculture with cover crop treatment (CC-treatment). During a 4-year calibration period, 42 storm events were collected and Event Mean Concentrations (EMCs) for each storm event were calculated for total suspended solids (TSS), nitrate-N (NO3-N), ammonia-N (NH4-N), dissolved reactive phosphorus (DRP), and total discharge. Predictive regression equations developed from the calibration period were used for calculating TSS, NO3-N, NH4-N, and DRP losses of surface runoff for the CC-treatment watershed. The treatment period consisted of total 18 storm events, seven of which were collected during the cereal rye, eight in the hairy vetch cover crop season and three during cash crop season. Cover crops reduced TSS and discharge by 33\% and 34\%, respectively in the CC-treatment watershed during the treatment period. However, surprisingly, EMCs for NO3-N, NH4-N, and DRP did not decrease. Stream discharge from the paired-watersheds will continue to be monitored to determine if the current water quality results hold or new patterns emerge.},
	language = {English},
	number = {4},
	journal = {Water},
	author = {Singh, Gurbir and Schoonover, Jon E. and Williard, Karl W. J.},
	month = apr,
	year = {2018},
	note = {WOS:000434954900175},
	keywords = {agricultural watersheds, cereal   rye, cereal rye, conservation practices, hairy vetch, headwater streams, management, nitrogen, nutrient losses, phosphorus losses, residual nutrient management, sediment export, soil properties, surface   runoff, united-states},
	pages = {521},
}

@article{bechmann_freezethaw_2005,
	title = {Freeze–{Thaw} {Effects} on {Phosphorus} {Loss} in {Runoff} from {Manured} and {Catch}-{Cropped} {Soils}},
	volume = {34},
	issn = {1537-2537},
	url = {https://dl.sciencesocieties.org/publications/jeq/articles/34/6/2301},
	doi = {10.2134/jeq2004.0415},
	language = {en},
	number = {6},
	urldate = {2020-02-04},
	journal = {Journal of Environmental Quality},
	author = {Bechmann, Marianne E. and Kleinman, Peter J. A. and Sharpley, Andrew N. and Saporito, Lou S.},
	month = nov,
	year = {2005},
	pages = {2301--2309},
}

@article{van_esbroeck_annual_2016,
	title = {Annual and seasonal phosphorus export in surface runoff and tile drainage from agricultural fields with cold temperate climates},
	volume = {42},
	issn = {0380-1330},
	url = {http://www.sciencedirect.com/science/article/pii/S038013301600006X},
	doi = {10.1016/j.jglr.2015.12.014},
	abstract = {Phosphorus (P) export from agriculture fields is contributing to algal blooms within Lake Erie. Field data quantifying the magnitude, timing and pathways of P loss are required to develop and test solutions. This study quantifies annual and seasonal losses of dissolved (DRP) and total (TP) phosphorus in surface runoff and tile drainage from three reduced tillage fields (October 2011 to April 2013). The non-growing season (NGS, October to April) was a critical period, with 83 to 97\% of annual combined [surface + tile] runoff; 84 to 100\% of DRP loss; 67 to 98\% of TP loss occurring in this time. Annual export (May 2012 to April 2013) ranged from 0.332 to 0.419kg TP/ha/yr and 0.034 to 0.096kg DRP/ha/yr. Tile drainage contributed the majority of annual water export from fields (78 to 90\%) whereas surface runoff contributed little (10 to 22\%). Tiles exported 0.169 to 0.255kg TP/ha/yr (40 to 77\% of total TP load) and 0.017 to 0.023kg DRP/ha/yr (19 to 67\% of total DRP load). Thus, surface runoff, which primarily occurred during winter thaws, exported disproportionately more P relative to its contribution to flow. Phosphorus losses in tile drain effluent monitored over an additional NGS (October 2011 to April 2012) were elevated at two sites following the fall application of P. This study provides an improved understanding of edge-of-field P losses in humid, cold temperate regions that experience significant winter periods, and provides estimates of P loads from fields in which P conservation strategies are employed.},
	language = {en},
	number = {6},
	urldate = {2020-02-04},
	journal = {Journal of Great Lakes Research},
	author = {Van Esbroeck, Chris J. and Macrae, Merrin L. and Brunke, Richard I. and McKague, Kevin},
	month = dec,
	year = {2016},
	keywords = {Agriculture, Eutrophication, Lake Erie, Reduced tillage, Seasonality, Water quality},
	pages = {1271--1280},
}

@article{stenberg_tile_2012,
	series = {Climate {Change} and {Macronutrient} {Cycling} along the {Atmospheric}, {Terrestrial}, {Freshwater} and {Estuarine} {Continuum} - {A} {Special} {Issue} dedicated to {Professor} {Colin} {Neal}},
	title = {Tile drain losses of nitrogen and phosphorus from fields under integrated and organic crop rotations. {A} four-year study on a clay soil in southwest {Sweden}},
	volume = {434},
	issn = {0048-9697},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969711015051},
	doi = {10.1016/j.scitotenv.2011.12.039},
	abstract = {In order to explore the influence of site-specific soil properties on nitrogen (N) and phosphorus (P) losses between individual fields and crop sequences, 16 drained fields with clay soils were investigated in a four-year study. Mean total N (TN) loss was 6.6–11.1 from a conventional, 14.3–21.5 from an organic and 13.1–23.9kgha−1year−1 from an integrated cropping system across a 4year period, with 75\% in nitrate form (NO3–N). Mean total P (TP) loss was 0.96–3.03, 0.99–4.63 and 0.76–2.67kgha−1year−1, from the three systems respectively during the same period, with 25\% in dissolved reactive form (DRP). Median N efficiency was calculated to be 70\% including gains from estimated N fixation. According to principal component factor (PCA) analysis, field characteristics and cropping system were generally more important for losses of N and P than year. Accumulation of soil mineral N in the autumn and (estimated) N fixation was important for N leaching. No P fertilisers were used at the site in either cropping system. Total P concentration in drainage water from each of the fields was marginally significantly (p{\textless}0.05) correlated to TP concentration in the topsoil (r=0.52), measured in hydrochloric acid extract (P-HCl). Mean DRP concentrations were significantly (p{\textless}0.01) correlated to degree of P saturation (DPS-AL) and soil carbon (C) content in the topsoil (r=0.63). Good establishment of a crop with efficient nutrient uptake and good soil structure was general preconditions for low nutrient leaching. Incorporation of ley by tillage operations in the summer before autumn crop establishment and repeated operations in autumn as well, increased N leaching. Crop management in sequences with leguminous crops needs to be considered carefully when designing cropping systems high efficiency in N utilisation and low environmental impact.},
	language = {en},
	urldate = {2020-02-04},
	journal = {Science of The Total Environment},
	author = {Stenberg, Maria and Ulén, Barbro and Söderström, Mats and Roland, Björn and Delin, Karl and Helander, Carl-Anders},
	month = sep,
	year = {2012},
	keywords = {Cropping system, Degree of phosphorus saturation, Leaching, Nitrogen fixation, Soil mineral nitrogen, Water nutrient balance},
	pages = {79--89},
}

@article{yang_impact_nodate,
	title = {Impact of cover crop on {Corn}-{Soybean} productivity and {Soil} {Water} dynamics under different seasonal rainfall patterns},
	volume = {n/a},
	copyright = {This article is protected by copyright. All rights reserved},
	issn = {1435-0645},
	url = {https://acsess.onlinelibrary.wiley.com/doi/abs/10.1002/agj2.20110},
	doi = {10.1002/agj2.20110},
	abstract = {The impact of cover crop (CC) on soil water balance and agricultural production is closely related to rainfall amount, duration, and distribution in rainfed cropping systems. This study used the RZWQM2 model calibrated and validated with 4-yr field measurements to predict the impact of planting a winter wheat (Triticum aestivum L.) CC in a no-till rainfed corn (Zea mays L.)-soybean (Glycine max L.) rotation on soil water balance, crop yield, and grain water-use efficiency (WUE) in northeast Mississippi, USA. Seasonal rainfall for 80 consecutive years (1938 to 2017) was classified as ‘wet’, ‘normal’, and ‘dry’ years using frequency analysis and the data sets matched chronologically to wheat, corn, and soybean growth periods were used as an input parameter in RZWQM2 simulations. During autumn and spring (early October to early April), the CC reduced deep drainage by 69 mm (11\%), 53 mm (15\%), and 51 mm (21\%) mm and increased evapotranspiration by 79 mm (55\%), 81 mm (57\%), and 73 mm (56\%) mm in wet, normal, and dry years, respectively. Averaged across 40 years, the CC decreased surface evaporation by 64 mm (32\%) and 38 mm (24\%) mm for corn and soybean growth periods, respectively. Wheat CC also improved soil water storage in early crop growth period during April-June in any of the three rainfall patterns. Regardless of rainfall patterns, the increase in WUE can be attributed to a decrease in evapotranspiration during cash crop period without sacrificing cash crop yield in the CC system. Introducing CC into cropping systems is beneficial to reduce annual deep drainage and evaporation while maintaining higher crop yields under different rainfall patterns. This article is protected by copyright. All rights reserved},
	language = {en},
	number = {n/a},
	urldate = {2020-02-04},
	journal = {Agronomy Journal},
	author = {Yang, Wei and Feng, Gary and Read, John J. and Ouyang, Ying and Han, Jianjun and Li, Pinfang},
	keywords = {Climate variability, agricultural system models, crop rotation, deep drainage, evapotranspiration, rainfall},
}

@article{kladivko_nitrate_2004,
	title = {Nitrate {Leaching} to {Subsurface} {Drains} as {Affected} by {Drain} {Spacing} and {Changes} in {Crop} {Production} {System}},
	volume = {33},
	copyright = {© ASA, CSSA, SSSA},
	issn = {1537-2537},
	url = {https://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/jeq2004.1803},
	doi = {10.2134/jeq2004.1803},
	abstract = {Subsurface drainage is a beneficial water management practice in poorly drained soils but may also contribute substantial nitrate N loads to surface waters. This paper summarizes results from a 15-yr drainage study in Indiana that includes three drain spacings (5, 10, and 20 m) managed for 10 yr with chisel tillage in monoculture corn (Zea mays L.) and currently managed under a no-till corn–soybean [Glycine max (L.) Merr.] rotation. In general, drainflow and nitrate N losses per unit area were greater for narrower drain spacings. Drainflow removed between 8 and 26\% of annual rainfall, depending on year and drain spacing. Nitrate N concentrations in drainflow did not vary with spacing, but concentrations have significantly decreased from the beginning to the end of the experiment. Flow-weighted mean concentrations decreased from 28 mg L−1 in the 1986–1988 period to 8 mg L−1 in the 1997–1999 period. The reduction in concentration was due to both a reduction in fertilizer N rates over the study period and to the addition of a winter cover crop as a “trap crop” after corn in the corn–soybean rotation. Annual nitrate N loads decreased from 38 kg ha−1 in the 1986–1988 period to 15 kg ha−1 in the 1997–1999 period. Most of the nitrate N losses occurred during the fallow season, when most of the drainage occurred. Results of this study underscore the necessity of long-term research on different soil types and in different climatic zones, to develop appropriate management strategies for both economic crop production and protection of environmental quality.},
	language = {en},
	number = {5},
	urldate = {2020-02-04},
	journal = {Journal of Environmental Quality},
	author = {Kladivko, E. J. and Frankenberger, J. R. and Jaynes, D. B. and Meek, D. W. and Jenkinson, B. J. and Fausey, N. R.},
	year = {2004},
	pages = {1803--1813},
}

@article{kaspar_effectiveness_2012,
	title = {Effectiveness of oat and rye cover crops in reducing nitrate losses in drainage water},
	volume = {110},
	issn = {0378-3774},
	url = {http://www.sciencedirect.com/science/article/pii/S0378377412000960},
	doi = {10.1016/j.agwat.2012.03.010},
	abstract = {Much of the NO3 in the riverine waters of the upper Mississippi River basin in the United States originates from agricultural land used for corn (Zea mays L.) and soybean (Glycine max [L.] Merr.) production. Cover crops grown between maturity and planting of these crops are one approach for reducing losses of NO3. In this experiment, we evaluated the effectiveness of oat (Avena sativa L.) and rye (Secale cereale L.) cover crops in reducing NO3 concentrations and loads in subsurface drainage water. The oat fall cover crop was broadcast seeded into living corn and soybean crops before harvest in late August or early September and was killed by cold temperatures in late November or early December The rye winter cover crop, which had already been used annually for four years, was planted with a grain drill after corn and soybean harvest, overwintered, grew again in the spring, and was killed with herbicides before main crop planting. These treatments were evaluated in subsurface-drained field plots with an automated system for measuring drainage flow and collecting proportional samples for analysis of NO3 concentrations from each plot. The rye winter cover crop significantly reduced drainage water NO3 concentrations by 48\% over five years, but this was less than the 58\% reduction observed in its first four years of use. The oat fall cover crop reduced NO3 concentrations by 26\% or about half of the reduction of the rye cover crop. Neither cover crop significantly reduced cumulative drainage or nitrate loads because of variability in cumulative annual drainage among plots. Both oat and rye cover crops are viable management options for significantly reducing NO3 losses to surface waters from agricultural drainage systems used for corn and soybean production.},
	language = {en},
	urldate = {2020-02-04},
	journal = {Agricultural Water Management},
	author = {Kaspar, T. C. and Jaynes, D. B. and Parkin, T. B. and Moorman, T. B. and Singer, J. W.},
	month = jul,
	year = {2012},
	keywords = {Corn–soybean rotation, Cover crops, Nitrate leaching, Nitrate uptake, Subsurface drainage, Water quality},
	pages = {25--33},
}

@article{kaspar_rye_2007,
	title = {Rye {Cover} {Crop} and {Gamagrass} {Strip} {Effects} on {NO3} {Concentration} and {Load} in {Tile} {Drainage}},
	volume = {36},
	copyright = {© American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America},
	issn = {1537-2537},
	url = {https://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/jeq2006.0468},
	doi = {10.2134/jeq2006.0468},
	abstract = {A significant portion of the NO3 from agricultural fields that contaminates surface waters in the Midwest Corn Belt is transported to streams or rivers by subsurface drainage systems or “tiles.” Previous research has shown that N fertilizer management alone is not sufficient for reducing NO3 concentrations in subsurface drainage to acceptable levels; therefore, additional approaches need to be devised. We compared two cropping system modifications for NO3 concentration and load in subsurface drainage water for a no-till corn (Zea mays L.)-soybean (Glycine max [L.] Merr.) management system. In one treatment, eastern gamagrass (Tripsacum dactyloides L.) was grown in permanent 3.05-m-wide strips above the tiles. For the second treatment, a rye (Secale cereale L.) winter cover crop was seeded over the entire plot area each year near harvest and chemically killed before planting the following spring. Twelve 30.5 × 42.7-m subsurface-drained field plots were established in 1999 with an automated system for measuring tile flow and collecting flow-weighted samples. Both treatments and a control were initiated in 2000 and replicated four times. Full establishment of both treatments did not occur until fall 2001 because of dry conditions. Treatment comparisons were conducted from 2002 through 2005. The rye cover crop treatment significantly reduced subsurface drainage water flow-weighted NO3 concentrations and NO3 loads in all 4 yr. The rye cover crop treatment did not significantly reduce cumulative annual drainage. Averaged over 4 yr, the rye cover crop reduced flow-weighted NO3 concentrations by 59\% and loads by 61\%. The gamagrass strips did not significantly reduce cumulative drainage, the average annual flow-weighted NO3 concentrations, or cumulative NO3 loads averaged over the 4 yr. Rye winter cover crops grown after corn and soybean have the potential to reduce the NO3 concentrations and loads delivered to surface waters by subsurface drainage systems.},
	language = {en},
	number = {5},
	urldate = {2020-02-04},
	journal = {Journal of Environmental Quality},
	author = {Kaspar, T. C. and Jaynes, D. B. and Parkin, T. B. and Moorman, T. B.},
	year = {2007},
	pages = {1503--1511},
}

@article{strock_cover_2004,
	title = {Cover {Cropping} to {Reduce} {Nitrate} {Loss} through {Subsurface} {Drainage} in the {Northern} {U}.{S}. {Corn} {Belt}},
	volume = {33},
	issn = {1537-2537},
	url = {https://dl.sciencesocieties.org/publications/jeq/articles/33/3/1010},
	doi = {10.2134/jeq2004.1010},
	language = {en},
	number = {3},
	urldate = {2020-02-04},
	journal = {Journal of Environmental Quality},
	author = {Strock, J. S. and Porter, P. M. and Russelle, M. P.},
	month = may,
	year = {2004},
	pages = {1010--1016},
}

@article{brendel_catchment-scale_2019,
	title = {Catchment-scale {Phosphorus} {Export} through {Surface} and {Drainage} {Pathways}},
	volume = {48},
	copyright = {© 2019 The Authors.},
	issn = {1537-2537},
	url = {http://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/jeq2018.07.0265},
	doi = {10.2134/jeq2018.07.0265},
	abstract = {The site-specific nature of P fate and transport in drained areas exemplifies the need for additional data to guide implementation of conservation practices at the catchment scale. Total P (TP), dissolved reactive P (DRP), and total suspended solids (TSS) were monitored at five sites—two streams, two tile outlets, and a grassed waterway—in three agricultural subwatersheds (221.2–822.5 ha) draining to Black Hawk Lake in western Iowa. Median TP concentrations ranged from 0.034 to 1.490 and 0.008 to 0.055 mg P L−1 for event and baseflow samples, respectively. The majority of P and TSS export occurred during precipitation events and high-flow conditions with greater than 75\% of DRP, 66\% of TP, and 59\% of TSS export occurring during the top 25\% of flows from all sites. In one subwatershed, a single event (annual recurrence interval {\textless} 1 yr) was responsible for 46.6, 84.0, and 81.0\% of the annual export of TP, DRP, and TSS, respectively, indicating that frequent, small storms have the potential to result in extreme losses. Isolated monitoring of surface and drainage transport pathways indicated significant P and TSS losses occurring through drainage; over the 2-yr study period, the drainage pathway was responsible for 69.8, 59.2, and 82.6\% of the cumulative TP, DRP, and TSS export, respectively. Finally, the results provided evidence that particulate P losses in drainage were greater than dissolved P losses. Understanding relationships between flow, precipitation, transport pathway, and P fraction at the catchment scale is needed for effective conservation practice implementation. Core Ideas Single events accounted for the vast majority of annual P and total suspended solids export. Frequent, low-depth events resulted in extreme P and total suspended solids losses. Particulate P losses in drainage waters can exceed dissolved P losses.},
	language = {en},
	number = {1},
	urldate = {2020-02-01},
	journal = {Journal of Environmental Quality},
	author = {Brendel, Conrad E. and Soupir, Michelle L. and Long, Leigh Ann M. and Helmers, Matthew J. and Ikenberry, Charles D. and Kaleita, Amy L.},
	year = {2019},
	pages = {117--126},
}

@article{vidon_phosphorus_2011,
	title = {Phosphorus dynamics in tile-drain flow during storms in the {US} {Midwest}},
	volume = {98},
	issn = {0378-3774},
	url = {http://www.sciencedirect.com/science/article/pii/S037837741000315X},
	doi = {10.1016/j.agwat.2010.09.010},
	abstract = {Excess phosphorus (P) in freshwater systems has been associated with eutrophication in agro-ecosystems of the US Midwest and elsewhere. A better understanding of processes regulating both soluble reactive phosphorus (SRP) and total phosphorus (TP) exports to tile-drains is therefore critical to minimize P losses to streams while maintaining crop yield. This paper investigates SRP and TP dynamics at a high temporal resolution during four spring storms in two tile-drains in the US Midwest. Depending on the storm, median concentrations varied between 0.006–0.025mg/L for SRP and 0.057–0.176mg/L for TP. For large storms ({\textgreater}6cm bulk precipitation), for which macropore flow represented between 43 and 50\% of total tile-drain flow, SRP transport to tile-drains was primarily regulated by macropore flow. For smaller tile-flow generating events ({\textless}3cm bulk precipitation), for which macropore flow only accounted for 11–17\% of total tile-drain flow, SRP transport was primarily regulated by matrix flow. Total P transport to tile-drains was primarily regulated by macropore flow regardless of the storm. Soluble reactive P (0.01–1.83mgm−2/storm) and TP (0.10–8.64mgm−2/storm) export rates were extremely variable and positively significantly correlated to both mean discharge and bulk precipitation. Soluble reactive P accounted for 9.9–15.5\% of TP fluxes for small tile-flow generating events ({\textless}3cm bulk precipitation) and for 16.2–22.0\% of TP fluxes for large precipitation events ({\textgreater}6cm bulk precipitation). Although significant variations in tile-flow response to precipitation were observed, no significant differences in SRP and TP concentrations were observed between adjacent tile-drains. Results stress the dominance of particulate P and the importance of macropore flow in P transport to tile-drains in the US Midwest. Although only spring storms are investigated, this study brings critical insight into P dynamics in tile-drains at a critical time of the year for water quality management.},
	language = {en},
	number = {4},
	urldate = {2020-02-01},
	journal = {Agricultural Water Management},
	author = {Vidon, P. and Cuadra, P. E.},
	month = feb,
	year = {2011},
	keywords = {Drainage, Macropore flow, Matrix flow, Non-point source pollution, Particulate phosphorus, Rainfall events, Soluble reactive phosphorus},
	pages = {532--540},
}

@article{lozier_release_2017,
	title = {Release of phosphorus from crop residue and cover crops over the non-growing season in a cool temperate region},
	volume = {189},
	issn = {0378-3774},
	url = {http://www.sciencedirect.com/science/article/pii/S0378377417301579},
	doi = {10.1016/j.agwat.2017.04.015},
	abstract = {In northern climates, crop residue and cover crops are potential sources of dissolved reactive phosphorus (DRP) to runoff; yet, there are few field studies to quantify this. The objectives of this study were (1) to quantify changes in water extractable phosphorus (WEP) concentrations in the residues of Triticum aestivum L. (winter wheat), Trifolium pretense L. (red clover) and Avena sativa L. (oat) cover crops and surface soil in two agricultural fields (ILD and LON) over the non-growing season (NGS); and (2) to determine if changes in WEP in vegetation residue or soil were reflected in loads of DRP or total P (TP) in surface runoff and/or tile drain effluent. Concentrations of WEP in cover crops were larger than those in wheat residue and soil. Water extractable P concentrations in vegetation increased with plant decomposition and decreased following runoff events indicating that the plant WEP was mobilized in runoff. Differences in WEP concentrations were not observed with topography, with the exception of the period following snowmelt when low-lying areas prone to surface inundation were depleted relative to upland locations. Although WEP appeared to have been mobilized from vegetation and soil pools, loads of DRP (0.165–0.245kgha−1) and TP (0.295kgha−1–0.360kgha−1) leaving the fields were small in comparison to P pools in cover crops (7.70kgha−1 oat, 1.70kgha−1 red clover), wheat residues (0.03–0.06kgha−1) and soils (1.39–5.87kgha−1), suggesting that much of the P released from vegetation was retained within the field. This study provides insight into the timing and magnitude of P release from vegetation throughout the non-growing season in regions with cool temperate climates, and provides an improved understanding of the contribution of cover crops to winter P losses.},
	language = {en},
	urldate = {2020-02-01},
	journal = {Agricultural Water Management},
	author = {Lozier, T. M. and Macrae, M. L. and Brunke, R. and Van Eerd, L. L.},
	month = jul,
	year = {2017},
	keywords = {Best management practices, Nutrient losses, Peak flow events, Surface runoff, Tile drainage, Winter cover crops},
	pages = {39--51},
}

@misc{noauthor_commentary_nodate,
	title = {Commentary: {Achieving} phosphorus reduction targets for {Lake} {Erie} - {ScienceDirect}},
	url = {https://www.sciencedirect.com/science/article/pii/S0380133018302016},
	urldate = {2020-01-31},
}

@misc{noauthor_agronomy_nodate,
	title = {Agronomy {Journal} - {Agronomy}, {Soils} \& {Environmental} {Quality} {Phosphorus} {Leaching} from {Two} {Soils} with {Catch} {Crops} {Exposed} to {Freeze}–{Thaw} {Cycles} {\textbar} {Digital} {Library}},
	url = {https://dl.sciencesocieties.org/publications/aj/articles/105/3/803},
	urldate = {2020-01-31},
}

@misc{noauthor_drainage_nodate,
	title = {Drainage water management combined with cover crop enhances reduction of soil phosphorus loss - {ScienceDirect}},
	url = {https://www.sciencedirect.com/science/article/pii/S0048969717302668},
	urldate = {2020-01-31},
}

@article{six_history_2004,
	series = {Advances in {Soil} {Structure} {Research}},
	title = {A history of research on the link between (micro)aggregates, soil biota, and soil organic matter dynamics},
	volume = {79},
	issn = {0167-1987},
	url = {http://www.sciencedirect.com/science/article/pii/S0167198704000881},
	doi = {10.1016/j.still.2004.03.008},
	abstract = {Since the 1900s, the link between soil biotic activity, soil organic matter (SOM) decomposition and stabilization, and soil aggregate dynamics has been recognized and intensively been studied. By 1950, many studies had, mostly qualitatively, investigated the influence of the five major factors (i.e. soil fauna, microorganisms, roots, inorganics and physical processes) on this link. After 1950, four theoretical mile-stones related to this subject were realized. The first one was when Emerson [Nature 183 (1959) 538] proposed a model of a soil crumb consisting of domains of oriented clay and quartz particles. Next, Edwards and Bremner [J. Soil Sci. 18 (1967) 64] formulated a theory in which the solid-phase reaction between clay minerals, polyvalent cations and SOM is the main process leading to microaggregate formation. Based on this concept, Tisdall and Oades [J. Soil Sci. 62 (1982) 141] coined the aggregate hierarchy concept describing a spatial scale dependence of mechanisms involved in micro- and macroaggregate formation. Oades [Plant Soil 76 (1984) 319] suggested a small, but very important, modification to the aggregate hierarchy concept by theorizing the formation of microaggregates within macroaggregates. Recent research on aggregate formation and SOM stabilization extensively corroborate this modification and use it as the base for furthering the understanding of SOM dynamics. The major outcomes of adopting this modification are: (1) microaggregates, rather than macroaggregates protect SOM in the long term; and (2) macroaggregate turnover is a crucial process influencing the stabilization of SOM. Reviewing the progress made over the last 50 years in this area of research reveals that still very few studies are quantitative and/or consider interactive effects between the five factors. The quantification of these relationships is clearly needed to improve our ability to predict changes in soil ecosystems due to management and global change. This quantification can greatly benefit from viewing aggregates as dynamic rather than static entities and relating aggregate measurements with 2D and 3D quantitative spatial information.},
	language = {en},
	number = {1},
	urldate = {2020-01-31},
	journal = {Soil and Tillage Research},
	author = {Six, J and Bossuyt, H and Degryze, S and Denef, K},
	month = sep,
	year = {2004},
	keywords = {Aggregate, Dry–wet cycle, Earthworm, Freeze–thaw cycle, History, Root, Soil biota, Soil organic matter},
	pages = {7--31},
}

@article{stone_preferential_2006,
	title = {Preferential {Flow} {Estimates} to an {Agricultural} {Tile} {Drain} with {Implications} for {Glyphosate} {Transport}},
	volume = {35},
	copyright = {© ASA, CSSA, SSSA},
	issn = {1537-2537},
	url = {https://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/jeq2006.0068},
	doi = {10.2134/jeq2006.0068},
	abstract = {Agricultural subsurface drains, commonly referred to as tile drains, are potentially significant pathways for the movement of fertilizers and pesticides to streams and ditches in much of the Midwest. Preferential flow in the unsaturated zone provides a route for water and solutes to bypass the soil matrix and reach tile drains faster than predicted by traditional displacement theory. This paper uses chloride concentrations to estimate preferential flow contributions to a tile drain during two storms in May 2004. Chloride, a conservative anion, was selected as the tracer because of differences in chloride concentrations between the two sources of water to the tile drain, preferential and matrix flow. A strong correlation between specific conductance and chloride concentration provided a mechanism to estimate chloride concentrations in the tile drain throughout the storm hydrographs. A simple mixing analysis was used to identify the preferential flow component of the storm hydrograph. During two storms, preferential flow contributed 11 and 51\% of total storm tile drain flow; the peak contributions, 40 and 81\%, coincided with the peak tile drain flow. Positive relations between glyphosate [N-(phosphonomethyl)glycine] concentrations and preferential flow for the two storms suggest that preferential flow is an important transport pathway to the tile drain.},
	language = {en},
	number = {5},
	urldate = {2020-01-31},
	journal = {Journal of Environmental Quality},
	author = {Stone, Wesley W. and Wilson, John T.},
	year = {2006},
	pages = {1825--1835},
}

@article{king_phosphorus_2015,
	title = {Phosphorus transport in agricultural subsurface drainage: a review.},
	volume = {44},
	shorttitle = {Phosphorus transport in agricultural subsurface drainage},
	doi = {10.2134/jeq2014.04.0163},
	abstract = {Phosphorus (P) loss from agricultural fields and watersheds has been an important water quality issue for decades because of the critical role P plays in eutrophication. Historically, most research has focused on P losses by surface runoff and erosion because subsurface P losses were often deemed to be negligible. Perceptions of subsurface P transport, however, have evolved, and considerable work has been conducted to better understand the magnitude and importance of subsurface P transport and to identify practices and treatments that decrease subsurface P loads to surface waters. The objectives of this paper were (i) to critically review research on P transport in subsurface drainage, (ii) to determine factors that control P losses, and (iii) to identify gaps in the current scientific understanding of the role of subsurface drainage in P transport. Factors that affect subsurface P transport are discussed within the framework of intensively drained agricultural settings. These factors include soil characteristics (e.g., preferential flow, P sorption capacity, and redox conditions), drainage design (e.g., tile spacing, tile depth, and the installation of surface inlets), prevailing conditions and management (e.g., soil-test P levels, tillage, cropping system, and the source, rate, placement, and timing of P application), and hydrologic and climatic variables (e.g., baseflow, event flow, and seasonal differences). Structural, treatment, and management approaches to mitigate subsurface P transport-such as practices that disconnect flow pathways between surface soils and tile drains, drainage water management, in-stream or end-of-tile treatments, and ditch design and management-are also discussed. The review concludes by identifying gaps in the current understanding of P transport in subsurface drains and suggesting areas where future research is needed.},
	number = {2},
	journal = {Journal of environmental quality},
	author = {King, K. W. and Williams, Mark R. and Macrae, Merrin L. and Fausey, Norman R. and Frankenberger, Jane R. and Smith, Douglas R. and Kleinman, Peter J. A. and Brown, Larry Curtis},
	year = {2015},
	keywords = {Phosphorus, Sensorineural Hearing Loss (disorder), Soil, Water},
	pages = {467--485},
}

@article{kerr_phosphorus_2011,
	title = {Phosphorus sorption in soils and sediments: implications for phosphate supply to a subtropical river in southeast {Queensland}, {Australia}},
	volume = {102},
	issn = {1573-515X},
	shorttitle = {Phosphorus sorption in soils and sediments},
	url = {10.1007/s10533-010-9422-9},
	doi = {10.1007/s10533-010-9422-9},
	abstract = {Phosphorus (P) is often a key limiting nutrient in freshwater systems, and excessive P can result in algal blooms, with flow-on effects to aquatic food webs. P sorption is an important process in aquatic and terrestrial ecosystems whereby phosphate (PO4 3−) is exchanged between liquid and solid phases. This study shows that differences in the concentration of PO4 3− in a subtropical river system during high and low flow can be attributed to differences in P sorption characterises of its catchment soils and sediments. The sediments have lower Equilibrium Phosphate Concentrations (EPC0) and higher binding energy (Kd); the surface soils have higher EPC0 and higher easily desorbed P (NH4Cl–P). A comparison of filterable reactive phosphorus (frP) in water samples collected at high and low flows, with soil and sediment EPC0, suggested that during event flows, the high EPC0 and NH4Cl–P of surface soils is producing a net movement of PO4 3− from the soil/sediment system into runoff and stream flow. At baseflow, there is more likely a net movement of PO4 3− into the riverbed sediments. This has important implications for management actions aimed at reducing P loads to river systems and downstream water storages, namely the need to increase the infiltration of rainfall to decrease the amount of PO4 3− being flushed from the surface soil.},
	language = {en},
	number = {1},
	urldate = {2020-01-29},
	journal = {Biogeochemistry},
	author = {Kerr, Jason G. and Burford, Michele and Olley, Jon and Udy, James},
	month = jan,
	year = {2011},
	keywords = {Equilibrium phosphate concentration, Phosphorus, Rivers, Sediment, Soil},
	pages = {73--85},
}

@article{hoffman_characteristics_2009,
	title = {Characteristics and {Influence} of {Phosphorus} {Accumulated} in the {Bed} {Sediments} of a {Stream} {Located} in an {Agricultural} {Watershed}},
	volume = {15},
	issn = {1573-1421},
	url = {10.1007/s10498-008-9043-2},
	doi = {10.1007/s10498-008-9043-2},
	abstract = {We investigated the accumulation and influence of bioavailable P (BAP) in sediments of a stream located in an agricultural area of the Lake Mendota watershed in Wisconsin, USA. During hydrologic events, the stream carried high concentrations of suspended sediment (up to 250 mg/l) and BAP (up to 2.5 mg/l). Bed sediments were highly enriched in BAP, as inventories of BAP in the top 10 cm of sediment ranged from 143 to 14,500 μg P/cm2. Space variations in BAP inventories were related to site-specific hydrodynamics and geochemical factors, including iron (Fe; r 2 = 0.71) and aluminum (Al; r 2 = 0.54) concentrations. Most sites behaved as potential sinks for dissolved reactive phosphate during hydrologic events and potential sources during base-flow periods. Through the combination of site-specific factors and geochemical controls, Dorn Creek modifies the amount, timing, and composition of P delivered from the watershed to downstream sites and water bodies.},
	language = {en},
	number = {3},
	urldate = {2020-01-29},
	journal = {Aquatic Geochemistry},
	author = {Hoffman, Adam R. and Armstrong, David E. and Lathrop, Richard C. and Penn, Michael R.},
	month = aug,
	year = {2009},
	keywords = {Agricultural watersheds, Bioavailable phosphorus, Equilibrium phosphorus concentrations, Phosphorus, Sediment},
	pages = {371--389},
}

@article{taube_phosphorus_2019,
	title = {Phosphorus and nitrogen storage, partitioning, and export in a large gravel bed river},
	volume = {657},
	issn = {0048-9697},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969718347867},
	doi = {10.1016/j.scitotenv.2018.11.431},
	abstract = {Nutrient dynamics in a 25 km long treated wastewater effluent impacted reach of a large, gravel-bed river were evaluated in five river compartments: surficial sediment, surface water, hyporheic zone water, and aquatic biomass (including epilithic algae and macrophytes). Nutrient storage within, and export from, the river reach, was quantified to assess the impact of WWTP effluent on nutrient dynamics. More than 98\% of N and P storage was found in the surficial river bed sediment, where it is available to support epilithic algal and macrophyte growth. Nutrient export from the river reach by sediment, hyporheic water, and biomass were small compared to water column transport. The N:P ratios for the five different compartments suggested that the water column was severely P limited, whereas sediment, hyporheic water, and aquatic biomass tended towards co-limitation and N limitation. Within the river reach, the majority of P was stored immediately downstream of the WWTP effluent outfall, whereas N was retained at a higher rate relative to P in the remainder of the reach. Correlation analysis of nutrient exchange between different compartments suggested that multiple nutrient compartments should be considered when establishing nutrient loading criteria. Nutrient analysis in multiple compartments in the river can add valuable insight into nutrient dynamics and nutrient limitation.},
	language = {en},
	urldate = {2020-01-29},
	journal = {Science of The Total Environment},
	author = {Taube, Nadine and Ryan, M. Cathryn and He, Jianxun and Valeo, Caterina},
	month = mar,
	year = {2019},
	keywords = {Bow River, Nitrogen, Nutrient compartments, Nutrient limitation, Phosphorus, Wastewater},
	pages = {717--730},
}

@article{parker_effect_2018,
	title = {Effect of particle size and heterogeneity on sediment biofilm metabolism and nutrient uptake scaled using two approaches},
	volume = {9},
	copyright = {© 2018 The Authors.},
	issn = {2150-8925},
	url = {http://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecs2.2137},
	doi = {10.1002/ecs2.2137},
	abstract = {Numerous studies have examined the effect of sediment particle size and distribution on community structure, but few have focused explicitly on how physical habitat characteristics influence biogeochemical functions of freshwater biofilms. In this study, we evaluated the effect of particle size and heterogeneity on rates of biofilm metabolism and nutrient uptake in colonized and native sediments normalized using two different scaling approaches. Coarse, pebble- to cobble-sized sediments were sorted into four homogeneous particle size treatments plus one heterogeneous treatment. Each treatment was deployed, in replicate, within one riffle and one run habitat feature in three different high-latitude stream reaches with contrasting hydrological and physicochemical characteristics. A treatment of native, homogeneous sediment was also evaluated at each deployment location. After incubating for approximately five weeks, metabolism and nutrient uptake of biofilms in all treatments (n = 69) were measured in recirculating microcosm chambers. For each treatment, functional rates were normalized by projected surface area and sediment surface area scaling approaches, which account for the surface area in plan view (looking top-down) and the total surface area of all sediment particles, respectively. This comparison was designed to determine whether treatment effects were independent of increased surface area associated with smaller particle sizes or heterogeneous sediments. Community respiration and uptake of ammonium-nitrogen and phosphate-phosphorus by biofilms decreased significantly as the particle size of homogeneous treatments increased when normalized by projected surface area, but significantly increased with increasing particle size when normalized by sediment surface area. Sediment particle size had a limited influence on production rates evaluated across treatments. Heterogeneous and homogeneous treatments with similar median particle sizes did not differ significantly from one another for most biogeochemical functions measured. Our findings indicate that rates of biogeochemical function in heterogeneous habitats were directly related to the total sediment surface area available for biofilm colonization. The significant interactions between sediment surface area and rates of respiration and nutrient uptake suggest that information about the size and distribution of sediment particles could substantially improve our ability to predict and scale measurements of important biogeochemical functions in streams.},
	language = {en},
	number = {3},
	urldate = {2020-01-29},
	journal = {Ecosphere},
	author = {Parker, Samuel P. and Bowden, William B. and Flinn, Michael B. and Giles, Courtney D. and Arndt, Kyle A. and Beneš, Joshua P. and Jent, Derrick G.},
	year = {2018},
	keywords = {biofilm, function, habitat, metabolism, nutrient, scale, sediment, stream, uptake},
	pages = {e02137},
}

@article{drake_effect_2012,
	title = {The effect of periphyton stoichiometry and light on biological phosphorus immobilization and release in streams},
	volume = {13},
	issn = {1439-863X},
	url = {10.1007/s10201-011-0359-z},
	doi = {10.1007/s10201-011-0359-z},
	abstract = {Periphyton stoichiometry can vary substantially as a result of differences in stream nutrient availability. A decrease in the periphyton carbon to phosphorus (C:P) ratio should decrease the demand for new P to be immobilized from stream water, but no studies to our knowledge have explored the relationship between periphyton stoichiometry and net P immobilization and release by periphyton. We sought to model biological P immobilization and release (flux) in streams by measuring periphyton stoichiometry and light availability. We measured P flux to and from intact periphyton on stream cobbles (20–100 mm diameter) in 1 L microcosms incubated with streamwater under variable light conditions. Net P immobilization occurred in 75\% of microcosms, net P release occurred in only 5\% of microcosms, and 20\% of microcosms had neither net immobilization nor net release. When normalized to stream conditions, net P immobilization was highest when light availability was high ({\textless}60\% canopy attenuation) and the periphyton C:P ratio was also high. In contrast, net P release occurred only when light availability was low ({\textgreater}60\% canopy attenuation) and the periphyton C:P ratio was also low. A multiple regression model that included both periphyton stoichiometry and light availability from the growing season only, and the interaction term of these two variables, explained 99\% of the variation in daily periphyton P flux observed in the study. These results indicate that in order to predict periphyton P immobilization, periphyton stoichiometry and light availability should be considered together. Furthermore, the results indicate that net P immobilization occurs even in very P-rich periphyton, which can act as a P sink when light availability is high.},
	language = {en},
	number = {1},
	urldate = {2020-01-29},
	journal = {Limnology},
	author = {Drake, W. M. and Scott, J. Thad and Evans-White, Michelle and Haggard, Brian and Sharpley, Andrew and Rogers, Chris W. and Grantz, Erin M.},
	month = apr,
	year = {2012},
	keywords = {Element ratios, Phosphorus spiraling, Transient storage},
	pages = {97--106},
}

@article{mcdowell_relationship_2015,
	title = {Relationship between {Sediment} {Chemistry}, {Equilibrium} {Phosphorus} {Concentrations}, and {Phosphorus} {Concentrations} at {Baseflow} in {Rivers} of the {New} {Zealand} {National} {River} {Water} {Quality} {Network}},
	volume = {44},
	copyright = {Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.},
	issn = {1537-2537},
	url = {http://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/jeq2014.08.0362},
	doi = {10.2134/jeq2014.08.0362},
	abstract = {Stream sediments can act as a source or a sink of dissolved (filtered) phosphorus (P) via abiotic and biotic processes. The cumulative action and magnitude of abiotic processes has been quantified by the equilibrium P concentration at zero net sorption or desorption (EPC0). The EPC0 was determined in 76 large rivers of contrasting climate, topography, and geology across New Zealand. Measurements of EPC0 (0.004–0.065 mg L−1) indicated sediments were acting as a source of filtered reactive P (FRP) to the water column. The EPC0 was related to the proportion of intensive agriculture in the catchment, the concentration of readily available P in the sediment, sediment size, and catchment slope and elevation. Determination of EPC0 will yield a relative assessment of the sediment's ability to supply P to the water column especially at baseflow. Furthermore, the EPC0 may be less prone to short-term variation (e.g., diurnal patterns) compared with grab samples. This information will help target efforts to mitigate FRP concentrations in rivers by managing sediment inputs. Additional work is required to determine, for instance, how long an EPC0 measurement remains valid before new sediment is deposited or existing sediment is scoured.},
	language = {en},
	number = {3},
	urldate = {2020-01-29},
	journal = {Journal of Environmental Quality},
	author = {McDowell, R. W.},
	year = {2015},
	pages = {921--929},
}

@article{baker_phosphorus_2014,
	title = {Phosphorus loading to {Lake} {Erie} from the {Maumee}, {Sandusky} and {Cuyahoga} rivers: {The} importance of bioavailability},
	volume = {40},
	issn = {0380-1330},
	shorttitle = {Phosphorus loading to {Lake} {Erie} from the {Maumee}, {Sandusky} and {Cuyahoga} rivers},
	url = {http://www.sciencedirect.com/science/article/pii/S0380133014001178},
	doi = {10.1016/j.jglr.2014.05.001},
	abstract = {Lake Erie has undergone re-eutrophication beginning in the 1990s, even though total phosphorus (TP) loads to the lake continued to slowly decline. Using our 1982 and 2007–10 studies of the bioavailability of dissolved and particulate phosphorus export from major Ohio tributaries, together with our long-term TP and dissolved reactive phosphorus (DRP) loading data, we estimated long-term annual export of dissolved and particulate bioavailable phosphorus. DRP was found to adequately represent dissolved bioavailable export while 26–30\% of the particulate phosphorus (PP) was extractable by 0.1N NaOH, a frequently used indicator of PP bioavailability. During the period of re-eutrophication (1991–2012), DRP export from nonpoint sources in the Maumee and Sandusky rivers increased dramatically while NaOH-PP export had a slight decline for the Maumee and a small increase in the Sandusky. For the Cuyahoga River, both DRP and NaOH-PP increased, but these changes were small in relation to those of the Maumee and Sandusky. During this period, whole lake loading of both non-point and point sources of phosphorus declined. This study indicates that increased nonpoint loading of DRP is an important contributing factor to re-eutrophication. Although nonpoint control programs in the Maumee and Sandusky have been effective in reducing erosion and PP export, these programs have been accompanied by increased DRP export. Future target loads for Lake Erie should focus on reducing bioavailable phosphorus, especially DRP from nonpoint sources. Agricultural P load reduction programs should address both DRP and PP, and take into account the lower bioavailability of PP.},
	language = {en},
	number = {3},
	urldate = {2020-01-29},
	journal = {Journal of Great Lakes Research},
	author = {Baker, D. B. and Confesor, R. and Ewing, D. E. and Johnson, L. T. and Kramer, J. W. and Merryfield, B. J.},
	month = sep,
	year = {2014},
	keywords = {Bioavailable phosphorus, Dissolved phosphorus, Lake Erie re-eutrophication, Nonpoint sources, Particulate phosphorus, Point sources},
	pages = {502--517},
}

@article{lottig_benthic_2007,
	title = {Benthic sediment influence on dissolved phosphorus concentrations in a headwater stream},
	volume = {84},
	issn = {1573-515X},
	url = {10.1007/s10533-007-9116-0},
	doi = {10.1007/s10533-007-9116-0},
	abstract = {Phosphate interacts with inorganic sediment particles through sorption reactions in streams. Collectively, this phosphorus (P) buffering mechanism can be an important determinant of soluble reactive P (SRP) concentrations. If sorption reactions control SRP concentrations in a stream, then differences in sediment characteristics may cause spatial differences in SRP concentrations. This prediction was tested by examining sediment-buffering characteristics and spatial variation in SRP among reaches with distinct sediment composition (i.e., fine versus coarse particles) in two tributaries of Boulder Creek, a headwater stream in central Wisconsin. SRP concentrations were significantly lower and algal available P and P sorption capacity were significantly higher in the reach dominated by fine sediments. Although fine particles such as sand had the greatest P sorption capacity, no retention could be attributed to biotic processes, whereas over 50\% of P retention in coarse particles such as gravel could be linked to biotic uptake. Equilibrium P concentration (EPC0) assays from different sediment fractions also indicate that biotic uptake is relatively unimportant in sand particles (EPClive 10 μg/L: EPCkilled 10 μg/L) but very important in gravel or larger particles (EPClive 10 μg/L: EPCkilled 80 μg/L). Thus, sediment influence on stream water P concentrations can shift predictably from abiotic sorption in reaches with fine particles to biotic retention in areas dominated by coarse sediments. Consequently, changes in sediment composition due to natural or anthropogenic disturbance have the potential to alter the type and strength of sediment-associated processes determining ambient stream P concentrations.},
	language = {en},
	number = {3},
	urldate = {2020-01-29},
	journal = {Biogeochemistry},
	author = {Lottig, Noah R. and Stanley, Emily H.},
	month = jul,
	year = {2007},
	keywords = {EPC, Equilibrium phosphorus concentration, Extractable phosphorus, Phosphorus retention, Sediments, Streams},
	pages = {297--309},
}

@article{casillas-ituarte_internal_2020,
	title = {Internal {Phosphorus} {Storage} in {Two} {Headwater} {Agricultural} {Streams} in the {Lake} {Erie} {Basin}},
	volume = {54},
	issn = {0013-936X},
	url = {10.1021/acs.est.9b04232},
	doi = {10.1021/acs.est.9b04232},
	abstract = {Internal phosphorus (P) in sediments plays an important role in the nutrient dynamics of lakes, sometimes long after external loads have been reduced. Similarly, internal P sources may drive the nutrient dynamics of small agricultural streams that drain to larger rivers and lakes, despite best management practices intended to reduce external P loads from adjacent fields. Here, internal P concentrations were measured with sequential extraction on cores collected in spring and summer from two small agricultural streams in the drainage basin of Lake Erie, a large, eutrophic lake experiencing increasing SRP loads. Average total extractable P concentrations were similar to within 5\% during spring and summer, but mobile P binding fractions nearly doubled in summer, possibly due to accelerated rates of organic matter mineralization or iron reduction beneath suboxic, stagnant surface waters. One site had chronically greater internal P concentrations by 25–75\%, despite the implementation of best management practices such as grass buffers. The site also had more aquatic vegetation that restricted the flow, less dissolved oxygen in surface water, and greater organic matter in sediments during both seasons, suggesting that variations in hydrology, sediment composition, and vegetation influence hot spots of P retention throughout small agricultural streams.},
	number = {1},
	urldate = {2020-01-29},
	journal = {Environmental Science \& Technology},
	author = {Casillas-Ituarte, Nadia N. and Sawyer, Audrey H. and Danner, Kelsey M. and King, Kevin W. and Covault, Alexandra J.},
	month = jan,
	year = {2020},
	pages = {176--183},
}

@article{dalu_river_2019,
	title = {River nutrient water and sediment measurements inform on nutrient retention, with implications for eutrophication},
	volume = {684},
	issn = {0048-9697},
	url = {http://www.sciencedirect.com/science/article/pii/S004896971932193X},
	doi = {10.1016/j.scitotenv.2019.05.167},
	abstract = {The consideration of nutrients in pollution dynamics is important for environmental management and conservation. Developing countries are yet to appreciate the aquatic ecosystem pollution impacts on their economies and as such, information on water pollution dynamics is limited. This study assessed the spatio-temporal dynamics of nutrient loading and retention in stream water and sediments in the Bloukrans River system, Eastern Cape province, South Africa over the course of the wet and dry season. Sediment and water samples were analysed for total phosphorus (TP) and nitrogen (TN) concentrations, and were used in combination with river flow discharge, to determine nutrient loads. The study results highlight that river discharge plays a significant role in temporal differences in sediment and water column nutrient concentrations. The mean sediment nutrient concentration was high for the dry season, with high values being observed for the urban river system. Nutrient loads were high above the sewage treatment works outflow (i.e. urban sites), as such, a decreasing trend was observed with increasing distance from the urban environment. Nutrient loads were generally high for the dry season in comparison to the wet season indicating organic matter retention (i.e. accumulation from burst sewage pipes) most likely due to low flows. While it was evident that the ageing wastewater infrastructure contributed to the observed state of the Bloukrans River, the high natural nutrient retention capacity seemed to mitigate eutrophication of downstream aquatic ecosystems. As such, the nutrient retention capacity and management of the system is central to the entire Bloukrans River catchment management practices. Therefore, the study contributes to our understanding of water and sediment nutrient pollution dynamics in an arid temperate river landscape where vast spatio-temporal differences in base flow characterise the riverscape.},
	language = {en},
	urldate = {2020-01-29},
	journal = {Science of The Total Environment},
	author = {Dalu, Tatenda and Wasserman, Ryan J. and Magoro, Mandla L. and Froneman, P. William and Weyl, Olaf L. F.},
	month = sep,
	year = {2019},
	keywords = {Aquatic ecosystems, Bloukrans River, Eutrophication, Sediment contaminant assessment, Total nitrogen, Total phosphorus},
	pages = {296--302},
}

@article{cunha_agriculture_nodate,
	title = {Agriculture influences ammonium and soluble reactive phosphorus retention in {South} {American} headwater streams},
	volume = {n/a},
	copyright = {© 2019 John Wiley \& Sons, Ltd.},
	issn = {1936-0592},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1002/eco.2184},
	doi = {10.1002/eco.2184},
	abstract = {Agricultural activities can affect the delivery of nutrients to streams, riparian canopy cover, and the capacity of aquatic systems to process nutrients and sediments. There are few measures of nutrient uptake and metabolism from tropical or subtropical streams in general, and even fewer from tropical regions of South America. We examined ammonium (NH4+) and soluble reactive phosphorus (SRP) retention in streams in Brazil and Argentina. We selected 12 streams with relatively little or extensive agricultural activity and conducted whole-stream nutrient additions and measurements of gross primary production and ecosystem respiration. We used multiple linear regression to determine potential drivers of nutrient uptake metrics across the streams. Nutrient concentrations and retention differed significantly between land use categories. Both NH4+ and SRP concentrations were higher in the agricultural sites (means of 161 and 495 μg l–1, respectively), whereas metabolic rates were slower and transient storage was smaller. Our analysis indicated that agriculture increased ambient uptake lengths and decreased uptake velocities. The regression models revealed that ambient SRP had a positive effect on NH4+ uptake and vice versa, suggesting strong stoichiometric controls. Drivers for nutrient uptake in streams with low-intensity agriculture also included canopy cover, temperature, and ecosystem respiration rates. Nutrient assimilation in agricultural sites was influenced by a higher number of variables (gross primary production for SRP, discharge, and transient storage for both nutrients). Our results indicate agricultural activity changes both the magnitude of in-stream nutrient uptake and the mechanisms that control its variation, with important implications for South American streams under agricultural intensification.},
	language = {en},
	number = {n/a},
	urldate = {2020-01-29},
	journal = {Ecohydrology},
	author = {Cunha, Davi Gasparini Fernandes and Finkler, Nícolas Reinaldo and Gómez, Nora and Cochero, Joaquín and Donadelli, Jorge Luis and Saltarelli, Wesley Aparecido and Calijuri, Maria do Carmo and Miwa, Adriana Cristina Poli and Tromboni, Flavia and Dodds, Walter K. and Boëchat, Iola Gonçalves and Gücker, Björn and Thomas, Steven A.},
	keywords = {agricultural watersheds, aquatic metabolism, low-order streams, macronutrient assimilation, nitrogen, phosphorus},
	pages = {e2184},
}

@article{weigelhofer_potential_2017,
	title = {The potential of agricultural headwater streams to retain soluble reactive phosphorus},
	volume = {793},
	issn = {1573-5117},
	url = {10.1007/s10750-016-2789-4},
	doi = {10.1007/s10750-016-2789-4},
	abstract = {The study focuses on the capacity of agricultural headwater streams to retain soluble reactive phosphorus (SRP). In-stream phosphorus uptake was determined via short-term SRP additions in 14 reaches differing in channel morphology and riparian vegetation. In addition, zero equilibrium phosphorus concentrations (EPC0) were estimated for 8 reaches based on adsorption experiments. Average SRP uptake lengths amounted to 3.8 km in channelized sections, 1.9 km in forested sections, and 0.5 km in open meanders. Mass transfer coefficients were highest in open meanders (0.1 cm min−1), followed by forested (0.05 cm min−1) and channelized sections (0.04 cm min−1). EPC0 ranged from 20 to 1,600 µg SRP l−1 and correlated positively with inorganic P and reductant-soluble P concentrations of the sediments. In 50\% of the reaches, phosphorus was released from the sediments at initial water concentrations of up to 500 µg SRP l−1, indicating a high release potential. Although EPC0 did not correlate with in-stream SRP uptake, sediments probably play a significant role for the P retention in agricultural headwater streams as they supply the benthic community with phosphorus from the subsurface. Thus, it is crucial that sediment–water interactions are considered in the restoration and management of agricultural headwater streams.},
	language = {en},
	number = {1},
	urldate = {2020-01-29},
	journal = {Hydrobiologia},
	author = {Weigelhofer, Gabriele},
	month = jun,
	year = {2017},
	keywords = {Agriculture, Equilibrium phosphorus concentrations, Headwater streams, Phosphorus release, Phosphorus uptake, Sediments},
	pages = {149--160},
}

@article{weigelhofer_decoupled_2018,
	title = {Decoupled water-sediment interactions restrict the phosphorus buffer mechanism in agricultural streams},
	volume = {628-629},
	issn = {0048-9697},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969718304182},
	doi = {10.1016/j.scitotenv.2018.02.030},
	abstract = {Our study aimed to explore the effects of agriculture on the phosphorus buffer capacity of 11 headwater streams in Austria. We used phosphorus adsorption curves and re-suspension experiments to determine both, the potential of the sediments to act as phosphorus source or sink and the actual phosphorus exchange between water and sediments. Additionally, we determined the alkaline phosphatase activity (APA) in epilithic and epipsammic biofilms as indicator for the phosphorus demand of the benthic and hyporheic community. We hypothesized that highly polluted streams will show decreased phosphorus buffer capacities, which were either due to saturation or restricted water-sediment interactions. Our results support the second hypothesis. Fine sediment accumulations, organic matter content, and phosphorus concentrations in water and sediments increased with percent cropland in the catchment. Below SRP concentrations of 120μgL−1 in the stream water, sediments showed a high potential for phosphorus release, with zero equilibrium phosphorus concentrations (EPC0) being more than twice as high as SRP concentrations. Above 150μgL−1, EPC0 reached only 20–50\% of SRP concentrations, indicating a high potential of the sediments to act as phosphorus sinks. These findings were confirmed by phosphorus uptake of these sediments during re-suspension. While APA in epilithic biofilms decreased with increasing SRP concentrations, APA in epipsammic biofilms showed the reverse pattern, indicating a restricted phosphorus supply of the hyporheic community despite phosphorus surplus in the water column. Our study shows that inputs of fine sediments from agricultural sources may reduce the phosphorus buffering mechanism of stream sediments through restrictions of water-sediment interactions. Consequently, water column and sediment processes are increasingly decoupled and phosphorus-rich stream water will not effectively reach the reactive sites in the sediments responsible for uptake. Therefore, phosphorus mitigation measures in stream ecosystems must comprise sediment management in the catchment as well as in-stream measures for the rehabilitation of the hyporheic zone.},
	language = {en},
	urldate = {2020-01-29},
	journal = {Science of The Total Environment},
	author = {Weigelhofer, Gabriele and Ramião, José Pedro and Pitzl, Beate and Bondar-Kunze, Elisabeth and O'Keeffe, Joanna},
	month = jul,
	year = {2018},
	keywords = {Epilithic biofilm, Epipsammic biofilm, Equilibrium phosphorus concentration, Phosphatase, Sediment clogging, Uptake},
	pages = {44--52},
}

@article{plach_supply_2018,
	title = {Supply and {Transport} {Limitations} on {Phosphorus} {Losses} from {Agricultural} {Fields} in the {Lower} {Great} {Lakes} {Region}, {Canada}},
	volume = {47},
	issn = {0047-2425},
	url = {http://dl.sciencesocieties.org/publications/jeq/articles/47/1/96#ref-2},
	doi = {10.2134/jeq2017.06.0234},
	language = {en},
	number = {1},
	urldate = {2020-01-28},
	journal = {Journal of Environmental Quality},
	author = {Plach, Janina M. and Macrae, Merrin L. and Ali, Genevieve A. and Brunke, Richard R. and English, Michael C. and Ferguson, Gabrielle and Lam, W. Vito and Lozier, Tatianna M. and McKague, Kevin and O’Halloran, Ivan P. and Opolko, Gilian and Van Esbroeck, Christopher J.},
	year = {2018},
	pages = {96--105},
}

@article{hess_rainfall_2018,
	title = {Rainfall {Intensification} {Enhances} {Deep} {Percolation} and {Soil} {Water} {Content} in {Tilled} and {No}-{Till} {Cropping} {Systems} of the {US} {Midwest}},
	volume = {17},
	copyright = {© 2018 The Authors.},
	issn = {1539-1663},
	url = {https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/vzj2018.07.0128},
	doi = {10.2136/vzj2018.07.0128},
	abstract = {Core Ideas Rainfall intensification increased deep percolation in tilled and no-till systems. Rainfall intensification increased deep soil water content in both cropping systems. A bromide tracer was detected at 1.2-m depth sooner in no-till than tilled systems. The effect of rainfall intensification on surface soil moisture varied seasonally. Globally, the proportion of total rainfall occurring as extreme events is increasing, which may have consequences for agriculture. In the US Midwest, we conducted a 234-d manipulative experiment in 16 paired plots where we increased the proportion of rain falling in extreme events on tilled and no-till cropping systems. We compared the effects of larger, less frequent rain events (“intensified” rainfall) vs. smaller, more frequent rain events (“normal” rainfall) on soil water content and deep percolation. The effect of intensified rainfall on the volumetric water content (VWC) of soil at the 10-cm depth during the experiment varied seasonally: in spring, intensified rainfall decreased the average VWC at the 10-cm depth by 0.05 ± 0.01 cm3 cm−3 compared with normal rainfall, but in summer and fall, it had no effect. In soil at the 100-cm depth, VWC declined during the summer in normal but not intensified plots. A surface-added Br− tracer was detected and peaked earlier in soil water at 120 cm under intensified rainfall vs. normal rainfall (by 6 ± 3 and 74 ± 33 d, respectively) regardless of tillage, although it was detected sooner in no-till than tilled systems (by 9 ± 3 d). Also, less Br− was recovered in soil under intensified (8 ± 8\% of total Br− added) vs. normal rainfall (21 ± 3\%). Our results suggest that rainfall intensification will increase deep percolation and deep soil water content in cropping systems regardless of tillage. Such changes to soil water dynamics may alter plant water and nutrient availability.},
	language = {en},
	number = {1},
	urldate = {2020-01-28},
	journal = {Vadose Zone Journal},
	author = {Hess, Laura J. T. and Hinckley, Eve-Lyn S. and Robertson, G. Philip and Hamilton, Stephen K. and Matson, Pamela A.},
	year = {2018},
	pages = {180128},
}

@article{hess_rainfall_2020,
	title = {Rainfall intensification increases nitrate leaching from tilled but not no-till cropping systems in the {U}.{S}. {Midwest}},
	volume = {290},
	issn = {0167-8809},
	url = {http://www.sciencedirect.com/science/article/pii/S0167880919303639},
	doi = {10.1016/j.agee.2019.106747},
	abstract = {As global surface temperatures rise, the percentage of total precipitation that falls in extreme events is increasing in many areas (“rainfall intensification”), including the U.S. Midwest, a major agricultural region. While it is well known that losses of nitrogen (N) fertilizers applied in excess of crop N demand have consequences for non-agricultural ecosystems, the effects of rainfall intensification on N losses from agricultural fields are uncertain. We conducted a 234-day field experiment in which we evaluated the effects of rainfall intensification on N leaching, soil inorganic N pools, soil N transformations, and crop N content in replicated tilled and no-till row crop systems of the upper Midwest. Under rainfall exclusion shelters we exposed 5 × 5 m plots to a control rainfall treatment with relatively small, frequent rainfall events historically typical of the region, and an intensified rainfall treatment with the same total rainfall added in larger, less frequent events. Although rainfall intensification increased modeled water percolation to 1.2 m in both tilled and no-till systems, as reported previously, it increased nitrate leaching only in tilled systems. Extractable soil nitrate concentrations throughout the experiment were on average 32 \% higher in surface soils exposed to intensified rainfall compared to control rainfall regardless of tillage management. In-situ net N mineralization and nitrification rates measured during a two-week period in summer showed no significant differences between rainfall or tillage treatments. Inorganic N pools (0–1.2 m depth) were 43 \% greater in no-till soils compared to tilled soils and were unaffected by rainfall intensification; crop N concentrations and total N were likewise unaffected. Our results suggest that rainfall intensification in tilled cropping systems will increase N leaching to groundwater, with consequent economic and environmental harm. No-till management, however, may buffer systems against the effects of intensification on nitrate loss.},
	language = {en},
	urldate = {2020-01-28},
	journal = {Agriculture, Ecosystems \& Environment},
	author = {Hess, Laura J. T. and Hinckley, Eve-Lyn S. and Robertson, G. Philip and Matson, Pamela A.},
	month = mar,
	year = {2020},
	keywords = {Agriculture, Climate change, Nitrate leaching, Nitrogen, Precipitation, Tillage},
	pages = {106747},
}

@article{daryanto_meta-analysis_2017,
	title = {Meta-{Analysis} of {Phosphorus} {Loss} from {No}-{Till} {Soils}},
	volume = {46},
	issn = {1537-2537},
	url = {https://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/jeq2017.03.0121},
	doi = {10.2134/jeq2017.03.0121},
	abstract = {Agriculture is a significant contributor to phosphorus (P) enrichment in aquatic ecosystems. No-till (NT) farming has been proposed as an alternative approach to conventional tillage (CT) in reducing soil P export, but published data have shown contrasting impacts, likely due to the interacting effects of different physical (climate region, rainfall variability, transport pathway, slope gradient) and management variables (NT duration, crop species). We conducted a meta-analysis to understand the extent to which each of these variables controls the concentration and load of different P fractions (dissolved P, particulate P) in agricultural runoff and leaching. In comparison with CT, particulate P loss was significantly lower with NT adoption (45 and 55\% reduction in concentration and load, respectively), but an increase in dissolved P loss was observed. The extent of the reduction or increase, however, varied with different physical and management variables. In comparison with CT, for example, NT was not effective in reducing particulate P concentration during wet years and particulate P load on steep slopes (4–9\%). Total P concentration was also similar with CT at sites under prolonged NT duration (∼10 yr) and at NT fields planted with soybean [Glycine max (L.) Merr.]. Our results underscore the need to consider the covarying physical and management factors when assessing the potential of NT farming in controlling P loss in the environment. The limited impact of NT on dissolved P loss remains a serious impediment toward harnessing the water quality benefits of this management practice. Core Ideas No-till was effective in reducing particulate P loss but increased dissolved P loss. NT covaried with several physical and management variables in affecting P loss. NT must be combined with other land management strategies to reduce dissolved P loss.},
	language = {en},
	number = {5},
	urldate = {2020-01-28},
	journal = {Journal of Environmental Quality},
	author = {Daryanto, Stefani and Wang, Lixin and Jacinthe, Pierre André},
	year = {2017},
	pages = {1028--1037},
}

@article{young_effects_1999,
	title = {Effects of land use on stream metabolism and organic matter turnover},
	volume = {9},
	copyright = {© 1999 by the Ecological Society of America},
	issn = {1939-5582},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/1051-0761%281999%29009%5B1359%3AEOLUOS%5D2.0.CO%3B2},
	doi = {10.1890/1051-0761(1999)009[1359:EOLUOS]2.0.CO;2},
	abstract = {We measured ecosystem metabolism and organic matter transport seasonally in five streams draining catchments dominated by native forest, exotic pine plantation, grazed tussock grassland, or developed pasture. All streams are tributaries of the Taieri River in southeastern New Zealand. Whole-stream metabolism was estimated by both two-station and single-station open-channel methods, allowing comparison between these techniques. Transfer of oxygen across the stream surface was estimated using reaeration coefficients determined from three different procedures: tracer gas injections (propane), analysis of the oxygen record, and empirical velocity–depth equations. Measurements of gross primary production (GPP) and community respiration (CR) showed differences among streams that reflected method rather than ecosystem process. The ratio of GPP:CR and net ecosystem metabolism, however, showed strong concordance among methods, suggesting that bias involved in standardizing estimates to areal units may be more important than differences among methods. The two-station approach appeared to cope more adequately with steep slope, high bed roughness, and low GPP than did the single-station method. However, in tranquil and productive streams, both methods worked well. When differences between methods were accounted for, results emphasized how differences in terrestrial landscapes may markedly affect ecosystem processes within streams. Shading by the heavy canopy at the native forest site, turbidity at the pasture site, and the valley walls at one of the tussock grassland sites appeared to limit GPP. CR was high in the native forest site, due to a large supply of organic material from the riparian zone. Concentrations of seston were highest at the developed pasture site, apparently a result of intensive grazing and associated bank failure. The organic content of seston was highest in the native forest site and lowest in the pasture site. Organic carbon spiraling length in the pasture site was longer than average for a stream of its size, whereas spiraling length in the native forest site was short when compared to similar-sized streams elsewhere. Changes in catchment land use and riparian vegetation, as well as reach-specific geomorphic factors, alter light availability and organic matter supply, which are fundamental factors controlling organic matter production, respiration, and transport in streams.},
	language = {en},
	number = {4},
	urldate = {2019-10-15},
	journal = {Ecological Applications},
	author = {Young, Roger G. and Huryn, Alexander D.},
	year = {1999},
	keywords = {New Zealand, autotrophy, ecosystem metabolism, heterotrophy, land use, light availability, open-system methods, organic matter, oxygen, reaeration, seston transport, stream},
	pages = {1359--1376},
}

@article{wiley_longitudinal_1990,
	title = {Longitudinal structure of an agricultural prairie river system and its relationship to current stream ecosystem theory},
	volume = {47},
	issn = {0706-652X, 1205-7533},
	url = {http://www.nrcresearchpress.com/doi/10.1139/f90-039},
	doi = {10.1139/f90-039},
	language = {en},
	number = {2},
	urldate = {2019-10-15},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Wiley, M. J. and Osborne, L. L. and Larimore, R. W.},
	month = feb,
	year = {1990},
	pages = {373--384},
}

@article{ryder_evaluating_2008,
	title = {Evaluating cover crops ({Sudex}, {Sunn} {Hemp}, {Oats}) for use as vegetative filters to control sediment and nutrient loading from agricultural runoff in a {Hawaiian} watershed},
	volume = {44},
	copyright = {© 2008 American Water Resources Association},
	issn = {1752-1688},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1752-1688.2008.00189.x},
	doi = {10.1111/j.1752-1688.2008.00189.x},
	abstract = {Abstract: A study was conducted to determine the effects of three land covers (sunn hemp –Crotalaria juncea, sudex, a sorghum-sudangrass hybrid –Sorghum bicolor x S. bicolor var. sudanese, and common oats –Avena sativa) planted as vegetative filter strips on the reduction of sediment and nutrient loading of surface runoff within the Kaika-Waialua watershed on the island of Oahu, Hawaii. Runoff samples were collected and analyzed for total suspended solids (TSS), total dissolved solids (TDS), phosphorous, and three forms of nitrogen (nitrate, ammonium, total nitrogen). Study results show that during seven out of 10 runoff events, the three cover crop treatments significantly reduced TSS as compared to the fallow treatment. Average removal efficiencies were 85, 77, and 73\% for oats, sunn hemp, and sudex, respectively, as compared to the fallow treatment. Nutrient concentrations were low with phosphorous concentrations, lower than 1 (μg/ml) for all treatments, and total nitrogen (TN) concentrations below 7 (μg/ml) except in the sunn hemp treatment, where TN concentrations were less than 10 (μg/ml). Results of analysis of TDS showed that the cover crop treatments did not decrease dissolved solids concentrations in comparison with the fallow treatment. Analysis of nutrient concentrations in runoff samples did not detect any significant decreases in phosphorous, nitrogen, ammonium, or TN concentrations in comparison to the fallow treatment. However, a significant increase in TN concentrations in the sunn hemp treatment was detected and showed the nitrogen fixing capacity of sunn hemp. No treatment effects on runoff volume were detected, and runoff volumes were directly correlated with rainfall amounts showing no crops significantly impacted soil infiltration rates. These results were attributed to extremely low soil hydraulic conductivities (0.0001-7 cm/day at the soil surface, 15 and 30 cm below the soil surface). This study showed that cover crops planted as vegetative filters can effectively reduce sediment loads coming from idle and fallow fields on moderately steep volcanically derived highly weathered soils.},
	language = {en},
	number = {3},
	urldate = {2019-10-15},
	journal = {JAWRA Journal of the American Water Resources Association},
	author = {Ryder, M. H. and Fares, A.},
	year = {2008},
	keywords = {buffer strips, erosion, land covers, total dissolved solids, total suspended solids, watershed management},
	pages = {640--653},
}

@article{qi_soil_2010,
	title = {Soil water dynamics under {Winter} {Rye} cover crop in central {Iowa}},
	volume = {9},
	issn = {1539-1663},
	url = {http://pubs.geoscienceworld.org/vzj/article/9/1/53/144338/Soil-Water-Dynamics-under-Winter-Rye-Cover-Crop-in},
	doi = {10.2136/vzj2008.0163},
	language = {en},
	number = {1},
	urldate = {2020-01-22},
	journal = {Vadose Zone Journal},
	author = {Qi, Zhiming and Helmers, Matthew J.},
	month = feb,
	year = {2010},
	pages = {53--60},
}

@article{odum_trophic_1957,
	title = {Trophic structure and productivity of {Silver} {Springs}, {Florida}},
	volume = {27},
	issn = {0012-9615},
	url = {http://www.jstor.org/stable/1948571},
	doi = {10.2307/1948571},
	number = {1},
	urldate = {2019-08-24},
	journal = {Ecological Monographs},
	author = {Odum, Howard T.},
	year = {1957},
	pages = {55--112},
}

@article{fisher_temporal_1982,
	title = {Temporal succession in a desert stream ecosystem following flash flooding},
	volume = {52},
	copyright = {© 1982 by the Ecological Society of America},
	issn = {1557-7015},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.2307/2937346},
	doi = {10.2307/2937346},
	abstract = {Recovery of a desert stream after an intense flash flooding event is described as a model of temporal succession in lotic ecosystems. A late summer flood in Sycamore Creek, Arizona, virtually eliminated algae and reduced invertebrate standing crop by 98\%. Physical and morphometric conditions typical of the preflood period were restored in 2 d and the biota recovered in 2—3 wk. Algal communities responded rapidly and achieved a standing crop of nearly 100 g/m2 in 2 wk. Community composition was dominated by diatoms early in succession and by filamentous greens and blue—greens later. Macroinvertebrates also recolonized denuded substrates rapidly, largely by immigration of aerial adults and subsequent oviposition. Growth and development were rapid and several generations of the dominant mayfly and dipteran taxa were completed during the 1st mo of recovery. Invertebrate dry biomass reached 7.3 g/m2 in 1 mo. Gross primary production (Pg) measured as O2 increased in a similar asymptotic fashion and reached 6.6 g°m—2°d—1 in 30 d. Pg exceeded community respiration (R) after day 5 and Pg/R averaged 1.46 for the remainder of the 2—mo sequence. This ecosystem is thus autotrophic and exports organic matter downstream and by drying, laterally. Uptake of nitrate and phosphorus were proportional to net primary production and exhibited a marked downstream decline in concentration during both light and dark periods. Temporal trajectories of various community and ecosystem attributes are compared with those suggested by Odum (1969) to be diagnostic of successional status. Agreement was poor in attributes which are especially modified in open, frequently disturbed ecosystems such as streams.},
	language = {en},
	number = {1},
	urldate = {2020-01-23},
	journal = {Ecological Monographs},
	author = {Fisher, Stuart G. and Gray, Lawrence J. and Grimm, Nancy B. and Busch, David E.},
	year = {1982},
	pages = {93--110},
}

@article{cardinale_influence_2002,
	title = {The influence of substrate heterogeneity on biofilm metabolism in a stream ecosystem},
	volume = {83},
	copyright = {© 2002 by the Ecological Society of America},
	issn = {1939-9170},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/0012-9658%282002%29083%5B0412%3ATIOSHO%5D2.0.CO%3B2},
	doi = {10.1890/0012-9658(2002)083[0412:TIOSHO]2.0.CO;2},
	abstract = {Simplification of natural habitats is a growing global concern demanding that ecologists better understand how habitat heterogeneity influences the structure and functioning of ecosystems. While there is extensive evidence that physical habitat heterogeneity affects the structure of biotic communities (i.e., organismal abundance, distribution, diversity, etc.), ecologists know little about how variability in physical conditions within habitats regulates ecological processes that are important for the functioning of an ecosystem. We performed a field experiment to assess the effects of geomorphic heterogeneity (i.e., variation in substrate size) on rates of benthic productivity and respiration at the scale of whole riffle habitats in a stream ecosystem. While holding median sizes constant, we manipulated variation in the size of stream bed sediments in replicate riffles to create two treatments representing increased and decreased levels of physical habitat heterogeneity relative to natural conditions in the stream. Physical habitat heterogeneity had an immediate and significant impact on the primary productivity of stream algae and on the respiration of the benthic biofilm. The rates of both ecological processes were elevated in the high-heterogeneity riffles, probably as a result of quantified alterations to near-bed flow velocity and turbulence intensity. Results presented here provide support for the widely held, but largely untested, assumption that physical habitat heterogeneity exhibits control over ecosystem-level processes, and it suggests that human-induced simplification of habitats may indeed be altering the functioning of ecosystems.},
	language = {en},
	number = {2},
	urldate = {2019-10-15},
	journal = {Ecology},
	author = {Cardinale, Bradley J. and Palmer, Margaret A. and Swan, Christopher M. and Brooks, Shane and Poff, N. LeRoy},
	year = {2002},
	keywords = {abiotic variation, biofilm metabolism, ecological processes, ecosystem functioning, physical habitat simplification, stream algae, stream riffles},
	pages = {412--422},
}

@article{appling_overcoming_2018,
	title = {Overcoming equifinality: {Leveraging} long time series for stream metabolism estimation},
	volume = {123},
	copyright = {©2018. The Authors.},
	issn = {2169-8961},
	shorttitle = {Overcoming {Equifinality}},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2017JG004140},
	doi = {10.1002/2017JG004140},
	abstract = {The foundational ecosystem processes of gross primary production (GPP) and ecosystem respiration (ER) cannot be measured directly but can be modeled in aquatic ecosystems from subdaily patterns of oxygen (O2) concentrations. Because rivers and streams constantly exchange O2 with the atmosphere, models must either use empirical estimates of the gas exchange rate coefficient (K600) or solve for all three parameters (GPP, ER, and K600) simultaneously. Empirical measurements of K600 require substantial field work and can still be inaccurate. Three-parameter models have suffered from equifinality, where good fits to O2 data are achieved by many different parameter values, some unrealistic. We developed a new three-parameter, multiday model that ensures similar values for K600 among days with similar physical conditions (e.g., discharge). Our new model overcomes the equifinality problem by (1) flexibly relating K600 to discharge while permitting moderate daily deviations and (2) avoiding the oft-violated assumption that residuals in O2 predictions are uncorrelated. We implemented this hierarchical state-space model and several competitor models in an open-source R package, streamMetabolizer. We then tested the models against both simulated and field data. Our new model reduces error by as much as 70\% in daily estimates of K600, GPP, and ER. Further, accuracy benefits of multiday data sets require as few as 3 days of data. This approach facilitates more accurate metabolism estimates for more streams and days, enabling researchers to better quantify carbon fluxes, compare streams by their metabolic regimes, and investigate controls on aquatic activity.},
	language = {en},
	number = {2},
	urldate = {2019-08-24},
	journal = {Journal of Geophysical Research: Biogeosciences},
	author = {Appling, Alison P. and Hall, Robert O. and Yackulic, Charles B. and Arroita, Maite},
	year = {2018},
	keywords = {aquatic, carbon, metabolism, oxygen, photosynthesis, respiration},
	pages = {624--645},
}

@article{allan_landscapes_2004,
	title = {Landscapes and riverscapes: {The} influence of land use on stream ecosystems},
	volume = {35},
	issn = {1543-592X},
	shorttitle = {Landscapes and {Riverscapes}},
	url = {https://www-annualreviews-org.proxy.library.nd.edu/doi/10.1146/annurev.ecolsys.35.120202.110122},
	doi = {10.1146/annurev.ecolsys.35.120202.110122},
	abstract = {Local habitat and biological diversity of streams and rivers are strongly influenced by landform and land use within the surrounding valley at multiple scales. However, empirical associations between land use and stream response only varyingly succeed in implicating pathways of influence. This is the case for a number of reasons, including (a) covariation of anthropogenic and natural gradients in the landscape; (b) the existence of multiple, scale-dependent mechanisms; (c) nonlinear responses; and (d) the difficulties of separating present-day from historical influences. Further research is needed that examines responses to land use under different management strategies and that employs response variables that have greater diagnostic value than many of the aggregated measures in current use. In every respect, the valley rules the stream.      H.B.N. Hynes (1975)},
	number = {1},
	urldate = {2019-08-10},
	journal = {Annual Review of Ecology, Evolution, and Systematics},
	author = {Allan, J. David},
	month = nov,
	year = {2004},
	pages = {257--284},
}

@article{hall_ecosystem_2003,
	title = {Ecosystem metabolism controls nitrogen uptake in streams in {Grand} {Teton} {National} {Park}, {Wyoming}},
	volume = {48},
	copyright = {© 2003, by the Association for the Sciences of Limnology and Oceanography, Inc.},
	issn = {1939-5590},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.2003.48.3.1120},
	doi = {10.4319/lo.2003.48.3.1120},
	abstract = {Streams and rivers regulate nitrogen transport (N) to downstream ecosystems. Rates of N uptake can be high in streams, but controls on the variation in uptake rates of N among streams are not known. We measured ammonium (NH+4) and nitrate (NO−3 ) uptake velocities (Vf) and compared these with whole-reach estimates of gross primary production (GPP) and community respiration (CR) in 11 low-nitrogen streams in Grand Teton National Park, Wyoming. We predicted that increased metabolism would positively relate to higher N demand because of stoichiometric N requirements associated with carbon fixation. Rates of GPP and CR explained 82\% of variation in NH+4 Vf. Nitrate Vf was controlled by GPP, not CR, with GPP explaining 75\% of variation in NO−3 Vf. Nitrate concentrations did not increase downstream during NH+4 addition in all streams, including streams with zero NO−3 uptake, suggesting low nitrification rates relative to NH+4 uptake. Using a stoichiometric model, we show that areal N uptake estimated from microbial and algal production was similar to measured areal N uptake. High primary production could be a prerequisite for streams exhibiting high NO−3 uptake rates.},
	language = {en},
	number = {3},
	urldate = {2020-01-24},
	journal = {Limnology and Oceanography},
	author = {Hall, Robert Jr O. and Tank, Jennifer L.},
	year = {2003},
	pages = {1120--1128},
}

@misc{noauthor_modeling_nodate,
	title = {Modeling the coupled dynamics of stream metabolism and microbial biomass - {Segatto} - - {Limnology} and {Oceanography} - {Wiley} {Online} {Library}},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/full/10.1002/lno.11407},
	urldate = {2020-01-24},
}

@article{qasem_effect_2019,
	title = {The effect of floods on ecosystem metabolism in suburban streams},
	volume = {38},
	issn = {2161-9549},
	url = {https://www.journals.uchicago.edu/doi/10.1086/703459},
	doi = {10.1086/703459},
	abstract = {Urban and suburban streams experience rapid changes in flow during flood events, which can affect ecosystem function and stream metabolism (i.e., gross primary production [GPP], ecosystem respiration [ER], and net ecosystem production [NEP]). To assess these effects, we calculated stream metabolism from hourly measurements of dissolved oxygen (DO), temperature, and flow at seven sites around the Chicago region during summer and fall of 2009 to 2013. We examined the biophysical effect of flood events by calculating metrics that characterized GPP and ER’s resistance (magnitude of change) and resilience (speed of recovery) to flooding as well as flood flashiness. Diel patterns in DO and GPP were observed during base flow conditions and flood events. Streams showed net heterotrophy at most of the sites, as GPP ranged from 0.98 – 6.61 g O2 m−2 d−1, ER ranged from −3.62 to −19.53 g O2 m−2 d−1, and NEP ranged from −16.84 to 1.06 g O2 m−2 d−1. Following floods, both GPP and ER decreased but ER exhibited a significantly higher resistance (i.e., changed less) than GPP. ER and GPP recovered to preflood levels within approximately 1 to 10 days, and there was no significant difference between ER and GPP resilience. Overall, our study indicates that large flow events sustain heterotrophic conditions more than autotrophic conditions. We concluded that flood events significantly affected stream metabolism and flood flashiness was a primary controlling factor on reducing metabolism rates.},
	number = {2},
	urldate = {2020-01-24},
	journal = {Freshwater Science},
	author = {Qasem, Karoline and Vitousek, Sean and O’Connor, Ben and Hoellein, Timothy},
	month = jun,
	year = {2019},
	pages = {412--424},
}

@article{strock_cover_2004,
	title = {Cover {Cropping} to {Reduce} {Nitrate} {Loss} through {Subsurface} {Drainage} in the {Northern} {U}.{S}. {Corn} {Belt}},
	volume = {33},
	issn = {1537-2537},
	url = {https://dl.sciencesocieties.org/publications/jeq/articles/33/3/1010},
	doi = {10.2134/jeq2004.1010},
	language = {en},
	number = {3},
	urldate = {2020-01-23},
	journal = {Journal of Environmental Quality},
	author = {Strock, J. S. and Porter, P. M. and Russelle, M. P.},
	month = may,
	year = {2004},
	pages = {1010--1016},
}

@article{michaud_tile_2019,
	title = {Tile {Drainage} as a {Hydrologic} {Pathway} for {Phosphorus} {Export} from an {Agricultural} {Subwatershed}},
	volume = {48},
	copyright = {Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.},
	issn = {1537-2537},
	url = {https://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/jeq2018.03.0104},
	doi = {10.2134/jeq2018.03.0104},
	abstract = {Cyanobacteria growth in Missisquoi Bay of Lake Champlain is triggered by the P load carried by tributaries in surrounding watersheds where agriculture is a dominant land use. The objective of this study was to apportion the total P (TP) load in streamflow from an agricultural subwatershed into distinct hydrologic pathways: groundwater resurgence, surface runoff, and tile drainage components (matrix flow and preferential flow). Stream discharge during peak flow was separated into these four components using electrical conductivity (EC)–discharge relationships developed from the stream water EC at the subwatershed outlet and from EC values of surface runoff and tile drain water in 10 fields within the subwatershed. The four-component hydrograph model revealed that 46 to 67\% of the TP load at the outlet originated from surface runoff during peak flow. Preferential flow was responsible for most of the particulate P and dissolved reactive P loads lost through tile drainage. Groundwater resurgence was a minor source of TP, whereas other sources such as streambank erosion and resuspended sediments contributed up to 21\% of the TP load and from 36 to 41\% of the particulate P load at the subwatershed outlet. This work confirms that tile drainage contributes to the TP load in agricultural subwatersheds in the Missisquoi Bay region. Core Ideas Field water sources affected electrolytes and electrical conductivity in streamflow. Water yield from field hydrologic pathways was deduced from the stream hydrograph. Matrix and preferential flows to tile drainage, and surface runoff, were quantified. Preferential flow was an important source of sediment and P loads in streamflow. Stream water quality may be negatively affected by tile drainage outflows.},
	language = {en},
	number = {1},
	urldate = {2020-01-23},
	journal = {Journal of Environmental Quality},
	author = {Michaud, Aubert R. and Poirier, Simon-Claude and Whalen, Joann K.},
	year = {2019},
	pages = {64--72},
}

@article{bou_lahdou_hydrologic_2019,
	title = {Hydrologic controls of controlled and free draining subsurface drainage systems},
	volume = {213},
	issn = {0378-3774},
	url = {http://www.sciencedirect.com/science/article/pii/S037837741831672X},
	doi = {10.1016/j.agwat.2018.10.038},
	abstract = {One of the strategies proposed for reducing nitrate losses from subsurface tile drain systems in Midwestern agricultural lands, controlled drainage, is known to reduce drain flow on an annual basis, but is not well understood for individual events. Understanding hydrologic controls that regulate outflow from free and controlled drainage systems during drainage events can offer improved insight on the overall functioning of these systems so that they can be better managed or retrofitted to increase their environmental benefits. This study used data from a monitoring site in east central Indiana to investigate the hydrology of 22 drainage events in free and controlled subsurface drainage systems. Relationships between event drainage volume, drain flow hydrograph metrics, column soil moisture, water table depth, and precipitation time series for each event were explored to determine the effect of precipitation characteristics and antecedent conditions on these metrics. Controlled drainage reduced event drainage volume and peak flows by 22\% ± 12\% and 29\% ± 16\% respectively, and increased the time to peak of drainage by 98\% ± 52\%. Higher total precipitation and precipitation time spread increased infiltration, while the average precipitation intensity did not correlate with drainage volumes in either system. Peak flow rate in free draining quadrants were positively affected by higher precipitation and average precipitation intensity, while in managed quadrants, the antecedent soil moisture appeared to be more influential in affecting peak flow rate than precipitation characteristics. Surface runoff potential increased with the increase in average precipitation intensity in all quadrants. Saturation excess ponding or possibly overland flow occurred in events that have a low average precipitation intensity, and a high precipitation time spread. Field observations indicate that saturation excess overland flow was more pronounced in controlled quadrants because water table levels rose higher than the water table levels of their free draining counterpart.},
	language = {en},
	urldate = {2020-01-23},
	journal = {Agricultural Water Management},
	author = {Bou Lahdou, Guy and Bowling, Laura and Frankenberger, Jane and Kladivko, Eileen},
	month = mar,
	year = {2019},
	keywords = {Controlled subsurface drainage, Drainage event, Event based analysis, Hydrologic Controls, Tile drainage},
	pages = {605--615},
}

@article{vidon_impact_2010,
	title = {Impact of precipitation characteristics on soil hydrology in tile-drained landscapes},
	volume = {24},
	issn = {1099-1085},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/hyp.7627},
	doi = {10.1002/hyp.7627},
	abstract = {Understanding the variables regulating tile-flow response to precipitation in the US Midwest is critical for water quality management. This study (1) investigates the relationship between precipitation characteristics, antecedent water table depth and tile-flow response at a high temporal resolution during storms; and (2) determines the relative importance of macropore flow versus matrix flow in tile flow in a tile-drained soya bean field in Indiana. In spring, although variations in antecedent water table depth imparted some variation in tile-flow response to precipitation, bulk precipitation was the best predictor of mean tile flow, maximum tile flow, time to peak, and run-off ratio. The contribution of macropore flow to total flow significantly increased with precipitation amount, and macropore flow represented between 11 and 50\% of total drain flow, with peak contributions between 15 and 74\% of flow. For large storms ({\textgreater}6 cm bulk precipitation), cations data indicated a dilution of groundwater with new water as discharge peaked. Although no clear dilution or concentration patterns for Mg2+ or K+ were observed for smaller tile flow generating events ({\textless}3 cm bulk precipitation), macropore flow still contributed between 11 and 17\% of the total flow for these moderate size storms. Inter-drain comparison stressed the need to use triplicate or duplicate tile drain experiments when investigating tile drainage impact on water and N losses at the plot scale. These results significantly increase our understanding of the hydrological functioning of tile-drained fields in spring, when most N losses to streams occur in the US Midwest. Copyright © 2010 John Wiley \& Sons, Ltd.},
	language = {en},
	number = {13},
	urldate = {2020-01-23},
	journal = {Hydrological Processes},
	author = {Vidon, P. and Cuadra, P. E.},
	year = {2010},
	keywords = {drainage, hydrograph separation, hydrology, macropore flow, precipitation, soil},
	pages = {1821--1833},
}

@article{rhoads_stream_2003,
	title = {Stream geomorphology, bank vegetation, and three-dimensional habitat hydraulics for fish in midwestern agricultural streams},
	volume = {39},
	copyright = {Copyright 2003 by the American Geophysical Union.},
	issn = {1944-7973},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2003WR002294},
	doi = {10.1029/2003WR002294},
	abstract = {Past work on physical habitat in streams has not explicitly considered how differences in channel planform and bank vegetation influence the three-dimensionality of habitat hydraulics. This study statistically compares frequency distributions of bed elevations, a stage-independent index of variability in flow depth, and three-dimensional velocity components for four stream reaches in east central Illinois that have different geomorphological conditions and types of bank vegetation. The analysis shows that bed elevations in a straight channelized reach are significantly less variable than bed elevations in the other three reaches. Distributions of downstream velocities do not differ significantly for two reaches with similar bank vegetation but substantially different channel morphologies, whereas distributions of cross-stream and vertical velocities are sensitive to differences both in channel planform and bank vegetation. Channel curvature enhances the variance of cross-stream and vertical velocity distributions through the production of large-scale helical motion. Conditions that result in net cross-stream flow, such as abrupt changes in curvature or deflection of the flow laterally, systematically influence the mean of cross-stream velocity distributions. Corresponding fish studies indicate that the straight, channelized reach has the lowest biotic integrity of the four sites. A detailed comparison of fish population characteristics between this reach and an unmodified reach immediately upstream reveals that the unmodified reach has significantly greater species richness, species diversity, and total biomass than the channelized reach. Thus geomorphological complexity, through its influence on the three-dimensionality of habitat hydraulics, appears to significantly influence fish community characteristics.},
	language = {en},
	number = {8},
	urldate = {2020-01-23},
	journal = {Water Resources Research},
	author = {Rhoads, Bruce L. and Schwartz, John S. and Porter, Stacey},
	year = {2003},
	keywords = {fish communities, habitat hydraulics, stream geomorphology, stream habitat},
}

@article{murdock_interactions_2004,
	title = {Interactions between flow, periphyton, and nutrients in a heavily impacted urban stream: implications for stream restoration effectiveness},
	volume = {22},
	issn = {0925-8574},
	shorttitle = {Interactions between flow, periphyton, and nutrients in a heavily impacted urban stream},
	url = {http://www.sciencedirect.com/science/article/pii/S0925857404000618},
	doi = {10.1016/j.ecoleng.2004.05.005},
	abstract = {Urban stream restoration is a very complex task due largely to the interactions between the physical, chemical, and biological stream components. Because of these interactions, restoring only a single component to a more natural state could have a negative affect on stream health. We studied pre-restoration interactions between hydrology, nutrients, and periphyton in a stream where wastewater effluent and a highly developed urban watershed dominated stream flow. Floods capable of scouring all visible periphyton from the stream were produced from rainfall events as small as 1.3cm and created 47 periphyton biomass reset events during our 22-month study period. Despite these disturbances, periphyton biomass rapidly accumulated throughout the stream and reached nuisance levels after 5 days of growth during every season. Floods did, however, severely limit the occurrence of steady-state assemblages, which attained biomass levels 30 times the nuisance level. Although the high frequency of floods did not prevent nuisance levels of periphyton, it did allow more edible early stage periphyton assemblages to become far more common than late-stage, less edible assemblages. In the case of the stream studied, a successful restoration strategy must consider coupled processes relating to hydrology, chemistry, and biota.},
	language = {en},
	number = {3},
	urldate = {2020-01-23},
	journal = {Ecological Engineering},
	author = {Murdock, Justin and Roelke, Daniel and Gelwick, Frances},
	month = may,
	year = {2004},
	keywords = {Flood frequency, Periphyton, Scouring, Stream restoration, Urban watershed, Wastewater effluent},
	pages = {197--207},
}

@article{biggs_eutrophication_2000,
	title = {Eutrophication of streams and rivers: dissolved nutrient-chlorophyll relationships for benthic algae},
	volume = {19},
	issn = {0887-3593},
	shorttitle = {Eutrophication of streams and rivers},
	url = {https://www.journals.uchicago.edu/doi/10.2307/1468279},
	doi = {10.2307/1468279},
	abstract = {Statistical models for predicting the effects on algal biomass of eutrophication are much better developed for lentic systems than for lotic systems, partly because of the dynamic physical nature of streams as controlled by flood regimes. I analyzed data from 30 sites in 25 runoff-fed streams and rivers to develop statistical models for mean monthly and maximum chlorophyll a as a function of soluble nutrient concentrations and days of accrual (reflecting the frequency of flood disturbance events). Variation in stream-water nutrients explained 12–22.6\% of the variation in mean monthly chlorophyll a and 29.5–32.5\% of the variation in maximum chlorophyll a among sites. Days of accrual explained 39.7\% and 61.8 \% of the variation in mean monthly and maximum chlorophyll a, respectively. Multiple regression models combining dissolved nutrient data and days of accrual explained 43.7–48.8\% of the variation in mean monthly chlorophyll a and 72.1–74.1\% of the variation in maximum chlorophyll a among sites. In streams with infrequent floods and long accrual periods (e.g., {\textgreater}100 d), a relatively small increase in dissolved nutrients greatly increased the frequency of high biomass events. However, as could be anticipated, this result did not occur in more flood-prone streams. A nomograph to predict oligo-, meso-, and eutrophic conditions as a function of nutrient concentrations and days of accrual is presented based on the regression models for maximum chlorophyll a. The models need further testing, but might be useful for predicting the effects of changes in nutrients on benthic algal biomass in other temperate streams and rivers. I suggest that variable nutrient criteria for the prevention of benthic algal proliferations could be set in streams in relation to regimes of local flood frequency and expected time available for biomass accrual. The present analysis suggests that managing nutrient supply could not only reduce the magnitude of maximum biomass, but also reduce the frequency and duration of benthic algal proliferations in streams.},
	number = {1},
	urldate = {2020-01-23},
	journal = {Journal of the North American Benthological Society},
	author = {Biggs, Barry J. F.},
	month = mar,
	year = {2000},
	pages = {17--31},
}

@article{uehlinger_ecosystem_1998,
	title = {Ecosystem {Metabolism}, {Disturbance}, and {Stability} in a {Prealpine} {Gravel} {Bed} {River}},
	volume = {17},
	issn = {0887-3593},
	url = {https://www.journals.uchicago.edu/doi/10.2307/1467960},
	doi = {10.2307/1467960},
	abstract = {The extent of temporal variation in ecosystem metabolism was determined in a 6th-order, gravel-bottomed, prealpine river (mean discharge 4.6 m$^{\textrm{3}}$/s), which is subject to disturbance by bed-moving spates. Daily integrals of gross primary production and ecosystem respiration were measured for 447 d between May 1992 and November 1994 based on single station diel oxygen curves. In 1993 gross primary production averaged 2.5 g O$_{\textrm{2}}$ m$^{\textrm{-2}}$d$^{\textrm{-1}}$ and ecosystem respiration averaged 3.5 g O$_{\textrm{2}}$ m$^{\textrm{-2}}$d$^{\textrm{-1}}$ (maximum daily rates observed in summer were 12.6 and 11.7 g O$_{\textrm{2}}$ m$^{\textrm{-2}}$d$^{\textrm{-1}}$). During the investigation, 32 bed-moving spates (peak discharge {\textgreater}28 m$^{\textrm{3}}$/s) occurred. Bed-moving spates distinctly depressed primary production and ecosystem respiration. Spates shifted ecosystem metabolism toward heterotrophy (decreased P/R) because gross primary production was more affected than ecosystem respiration. Recovery rates of gross primary production were high in summer and low in winter. Recovery of ecosystem respiration showed less distinct seasonal variation. Energy flow through the system was calculated as the sum of gross primary production and ecosystem respiration. Upper (maximum energy flow) and lower (resistant energy flow) boundaries were estimated, within which energy flow varied. The ratio of maximum to resistant energy flow, which ranged from 6.1 to 9.6, indicated that resistance to spates was small, at least after extended periods free of spates (5-8 wk).},
	number = {2},
	urldate = {2020-01-23},
	journal = {Journal of the North American Benthological Society},
	author = {Uehlinger, Urs and Naegeli, Markus W.},
	month = jun,
	year = {1998},
	pages = {165--178},
}

@article{uehlinger_annual_2006,
	title = {Annual cycle and inter-annual variability of gross primary production and ecosystem respiration in a floodprone river during a 15-year period},
	volume = {51},
	issn = {1365-2427},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2427.2006.01551.x},
	doi = {10.1111/j.1365-2427.2006.01551.x},
	abstract = {1. Temporal variation in ecosystem metabolism over a 15-year period (1986–2000) was evaluated in a seventh order channelised gravel bed river (mean annual discharge 48.7 m3 s−1) of the Swiss Plateau. The river is subject to frequent disturbance by bed-moving spates. Daily integrals of gross primary production (GPP) and ecosystem respiration (ER) were calculated based on single-station diel oxygen curves. 2. Seasonal decomposition of the time series of monthly metabolism rates showed that approximately 50\% of the variation of GPP and ER can be attributed to season. Annual GPP averaged 5.0 ± 0.6 g O2 m−2 day−1 and showed no long-term trend. 3. Ecosystem respiration, averaging 6.2 ± 1.4 g O2 m−2 day−1, declined from 8.8 to 4.1 g O2 m−2 day−1 during the 15-year period. This significant trend paralleled a decline in nitrate and soluble reactive phosphorus concentrations, and the biochemical oxygen demand discharged by sewage treatment facilities upstream of the study reach. The ratio of GPP to ER (P/R) increased from 0.53 to about 1 as consequence of ER reduction. 4. Bed moving spates reduced GPP by 49\% and ER by 19\%. Postspate recovery of GPP was rapid between spring and autumn and slow during winter. Recovery of ER lacked any seasonal pattern. Annual patterns of daily GPP and to a minor extent of daily ER can be described as a sequence of recovery periods frequently truncated by spates. 5. The study showed that disturbance by frequent bed-moving spates resulted in major stochastic variation in GPP and ER but annual patterns were still characterised by a distinct seasonal cycle. It also became evident that stream metabolism is a suitable method to assess effects of gradual changes in water quality.},
	language = {en},
	number = {5},
	urldate = {2020-01-23},
	journal = {Freshwater Biology},
	author = {Uehlinger, Urs},
	year = {2006},
	keywords = {P/R, disturbance, long-term trend, river metabolism, stability},
	pages = {938--950},
}

@article{beaulieu_continuous_2013,
	title = {Continuous monitoring reveals multiple controls on ecosystem metabolism in a suburban stream},
	volume = {58},
	copyright = {Published 2013. This article is a U.S. Government work and is in the public domain in the USA.},
	issn = {1365-2427},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/fwb.12097},
	doi = {10.1111/fwb.12097},
	abstract = {1. Primary production and respiration in streams, collectively referred to as stream ecosystem metabolism, are fundamental processes that determine trophic structure, biomass and nutrient cycling. Few studies have used high-frequency measurements of gross primary production (GPP) and ecosystem respiration (ER) over extended periods to characterise the factors that control stream ecosystem metabolism at hourly, daily, seasonal and annual scales. 2. We measured ecosystem metabolism at 5-min intervals for 23 months in Shepherd Creek, a small suburban stream in Cincinnati, Ohio (U.S.A.). 3. Daily GPP was best predicted by a model containing light and its synergistic interaction with water temperature. Water temperature alone was not significantly related to daily GPP, rather high temperatures enhanced the capacity of autotrophs to use available light. 4. The relationship between GPP and light was further explored using photosynthesis–irradiance curves (P–I curves). Light saturation of GPP was evident throughout the winter and spring and the P–I curve frequently exhibited strong counterclockwise hysteresis. Hysteresis occurred when water temperatures were greater in the afternoon than in the morning, although light was similar, further suggesting that light availability interacts synergistically with water temperature. 5. Storm flows strongly depressed GPP in the spring while desiccation arrested aquatic GPP and ER in late summer and autumn. 6. Ecosystem respiration was best predicted by GPP, water temperature and the rate of water exchange between the surface channel and transient storage zones. We estimate that c. 70\% of newly fixed carbon was immediately respired by autotrophs and closely associated heterotrophs. 7. Interannual, seasonal, daily and hourly variability in ecosystem metabolism was attributable to a combination of light availability, water temperature, storm flow dynamics and desiccation. Human activities affect all these factors in urban and suburban streams, suggesting stream ecosystem processes are likely to respond in complex ways to changing land use and climate.},
	language = {en},
	number = {5},
	urldate = {2020-01-23},
	journal = {Freshwater Biology},
	author = {Beaulieu, Jake J. and Arango, Clay P. and Balz, David A. and Shuster, William D.},
	year = {2013},
	keywords = {autotrophic respiration, desiccation, hysteresis, photosynthesis–irradiance curve},
	pages = {918--937},
}

@article{figueroa-nieves_controls_2006,
	title = {Controls on chlorophyll-a in nutrient-rich agricultural streams in {Illinois}, {USA}},
	volume = {568},
	issn = {1573-5117},
	url = {10.1007/s10750-006-0114-3},
	doi = {10.1007/s10750-006-0114-3},
	abstract = {Nitrogen and phosphorus are the primary nutrients that affect water quality in streams in the midwestern USA and high concentrations of these nutrients tend to increase algal biomass. However, how nutrients interact with physical controls in regulating algal biomass is not well known in agricultural streams. Eighteen streams in east-central Illinois (USA) were sampled during June and September 2003 to analyze factors possibly regulating algal biomass. Additionally, two shaded and two non-shaded sites in the Embarras River in east-central Illinois were sampled intensively from June to December 2003. Both sestonic and periphytic chlorophyll-a (chl-a) were analyzed, and periphytic chl-a was assessed on natural substrata and unglazed ceramic tiles. Although high concentrations of nutrients were found in these streams (mean total P = 0.09–0.122 mg l−1 and mean NO3-N=4.4–8.4 mg l−1), concentrations of sestonic chl-a were low among all sites and both sampling periods ({\textless}18 mg m−3, median values of 5 and 3 in June and September, respectively). Filamentous algae were an important component of the algal communities in streams with stable substrata. Periphytic chl-a was generally not related to the concentration of N or P in the water column, and in non-shaded streams periphyton appeared at times to be light-limited due to turbid water. Turbidity was found to be an important factor controlling chl-a on ceramic tiles across the 18 sites and for the Embarras River sites; chl-a decreased exponentially in concentration (132–0 mg m−2) as turbidity increased from 4 to 39 NTU (r2 = 0.80). In general, the interaction between hydrology and light (turbidity) likely controlled algal biomass in these nutrient-rich, agricultural streams.},
	language = {en},
	number = {1},
	urldate = {2020-01-23},
	journal = {Hydrobiologia},
	author = {Figueroa-Nieves, Débora and Royer, Todd V. and David, Mark B.},
	month = sep,
	year = {2006},
	pages = {287--298},
}

@article{walsh_urban_2005,
	title = {The urban stream syndrome: current knowledge and the search for a cure},
	volume = {24},
	issn = {2161-9549, 2161-9565},
	shorttitle = {The urban stream syndrome},
	url = {https://bioone.org/journals/Freshwater-Science/volume-24/issue-3/04-028.1/The-urban-stream-syndrome--current-knowledge-and-the-search/10.1899/04-028.1.full},
	doi = {10.1899/04-028.1},
	abstract = {The term “urban stream syndrome” describes the consistently observed ecological degradation of streams draining urban land. This paper reviews recent literature to describe symptoms of the syndrome, explores mechanisms driving the syndrome, and identifies appropriate goals and methods for ecological restoration of urban streams. Symptoms of the urban stream syndrome include a flashier hydrograph, elevated concentrations of nutrients and contaminants, altered channel morphology, and reduced biotic richness, with increased dominance of tolerant species. More research is needed before generalizations can be made about urban effects on stream ecosystem processes, but reduced nutrient uptake has been consistently reported. The mechanisms driving the syndrome are complex and interactive, but most impacts can be ascribed to a few major large-scale sources, primarily urban stormwater runoff delivered to streams by hydraulically efficient drainage systems. Other stressors, such as combined or sanitary sewer overflows, wastewater treatment plant effluents, and legacy pollutants (long-lived pollutants from earlier land uses) can obscure the effects of stormwater runoff. Most research on urban impacts to streams has concentrated on correlations between instream ecological metrics and total catchment imperviousness. Recent research shows that some of the variance in such relationships can be explained by the distance between the stream reach and urban land, or by the hydraulic efficiency of stormwater drainage. The mechanisms behind such patterns require experimentation at the catchment scale to identify the best management approaches to conservation and restoration of streams in urban catchments. Remediation of stormwater impacts is most likely to be achieved through widespread application of innovative approaches to drainage design. Because humans dominate urban ecosystems, research on urban stream ecology will require a broadening of stream ecological research to integrate with social, behavioral, and economic research.},
	number = {3},
	urldate = {2020-01-23},
	journal = {Freshwater Science},
	author = {Walsh, Christopher J. and Roy, Allison H. and Feminella, Jack W. and Cottingham, Peter D. and Groffman, Peter M. and Morgan, Raymond P.},
	month = sep,
	year = {2005},
	pages = {706--723},
}

@article{reisinger_recovery_2017,
	title = {Recovery and resilience of urban stream metabolism following {Superstorm} {Sandy} and other floods},
	volume = {8},
	copyright = {© 2017 Reisinger et al.},
	issn = {2150-8925},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecs2.1776},
	doi = {10.1002/ecs2.1776},
	abstract = {Urban streams are exposed to multiple different stressors on a regular basis, with increased hydrological flashiness representing a common urban stream stressor. Stream metabolism, the coupled ecosystem functions of gross primary production (GPP) and ecosystem respiration (ER), controls numerous other ecosystem functions and integrates multiple processes occurring within streams. We examined the effect of one large (Superstorm Sandy) and multiple small and moderately sized flood events in Baltimore, Maryland, to quantify the response and recovery of urban stream GPP and ER before and after floods of different magnitudes. We also compared GPP and ER before and after Superstorm Sandy to literature values. We found that both GPP and ER decreased dramatically immediately following floods of varying magnitudes, but on average GPP was more reduced than ER (80\% and 66\% average reduction in GPP and ER, respectively). Both GPP and ER recovered rapidly following floods within 4–18 d, and recovery intervals did not differ significantly between GPP and ER. During the two-week recovery following Superstorm Sandy, two urban streams exhibited a range of metabolic activity equivalent to 15\% of the entire range of GPP and ER reported in a recent meta-analysis of stream metabolism. Urban streams exhibit a substantial proportion of the natural variation in metabolism found across stream ecosystems over relatively short time scales. Not only does urbanization cause increased hydrological flashiness, it appears that metabolic activity in urban streams may be less resistant, but also more resilient to floods than in other streams draining undeveloped watersheds, which have been more studied. Our results show that antecedent conditions must be accounted for when drawing conclusions about stream metabolism measurements, and the rapid recovery and resilience of urban streams should be considered in watershed management and stream restoration strategies targeting ecosystem functions and services.},
	language = {en},
	number = {4},
	urldate = {2020-01-23},
	journal = {Ecosphere},
	author = {Reisinger, Alexander J. and Rosi, Emma J. and Bechtold, Heather A. and Doody, Thomas R. and Kaushal, Sujay S. and Groffman, Peter M.},
	year = {2017},
	keywords = {Superstorm Sandy, disturbance, ecosystem respiration, flood, gross primary production, recovery, recurrence interval, resilience, resistance},
	pages = {e01776},
}

@article{van_esbroeck_annual_2016,
	title = {Annual and seasonal phosphorus export in surface runoff and tile drainage from agricultural fields with cold temperate climates},
	volume = {42},
	issn = {0380-1330},
	url = {http://www.sciencedirect.com/science/article/pii/S038013301600006X},
	doi = {10.1016/j.jglr.2015.12.014},
	abstract = {Phosphorus (P) export from agriculture fields is contributing to algal blooms within Lake Erie. Field data quantifying the magnitude, timing and pathways of P loss are required to develop and test solutions. This study quantifies annual and seasonal losses of dissolved (DRP) and total (TP) phosphorus in surface runoff and tile drainage from three reduced tillage fields (October 2011 to April 2013). The non-growing season (NGS, October to April) was a critical period, with 83 to 97\% of annual combined [surface + tile] runoff; 84 to 100\% of DRP loss; 67 to 98\% of TP loss occurring in this time. Annual export (May 2012 to April 2013) ranged from 0.332 to 0.419kg TP/ha/yr and 0.034 to 0.096kg DRP/ha/yr. Tile drainage contributed the majority of annual water export from fields (78 to 90\%) whereas surface runoff contributed little (10 to 22\%). Tiles exported 0.169 to 0.255kg TP/ha/yr (40 to 77\% of total TP load) and 0.017 to 0.023kg DRP/ha/yr (19 to 67\% of total DRP load). Thus, surface runoff, which primarily occurred during winter thaws, exported disproportionately more P relative to its contribution to flow. Phosphorus losses in tile drain effluent monitored over an additional NGS (October 2011 to April 2012) were elevated at two sites following the fall application of P. This study provides an improved understanding of edge-of-field P losses in humid, cold temperate regions that experience significant winter periods, and provides estimates of P loads from fields in which P conservation strategies are employed.},
	language = {en},
	number = {6},
	urldate = {2020-01-23},
	journal = {Journal of Great Lakes Research},
	author = {Van Esbroeck, Chris J. and Macrae, Merrin L. and Brunke, Richard I. and McKague, Kevin},
	month = dec,
	year = {2016},
	keywords = {Agriculture, Eutrophication, Lake Erie, Reduced tillage, Seasonality, Water quality},
	pages = {1271--1280},
}

@article{hallama_hidden_2019,
	title = {Hidden miners – the roles of cover crops and soil microorganisms in phosphorus cycling through agroecosystems},
	volume = {434},
	issn = {1573-5036},
	url = {10.1007/s11104-018-3810-7},
	doi = {10.1007/s11104-018-3810-7},
	abstract = {Phosphorus (P) is a limiting nutrient in many agroecosystems and costly fertilizer inputs can cause negative environmental impacts. Cover crops constitute a promising management option for sustainable intensification of agriculture. However, their interactions with the soil microbial community, which is a key driver of P cycling, and their effects on the following crop, have not yet been systematically assessed.},
	language = {en},
	number = {1},
	urldate = {2020-01-23},
	journal = {Plant and Soil},
	author = {Hallama, Moritz and Pekrun, Carola and Lambers, Hans and Kandeler, Ellen},
	month = jan,
	year = {2019},
	pages = {7--45},
}

@article{osmond_increasing_2019,
	title = {Increasing the {Effectiveness} and {Adoption} of {Agricultural} {Phosphorus} {Management} {Strategies} to {Minimize} {Water} {Quality} {Impairment}},
	volume = {48},
	issn = {0047-2425},
	url = {https://dl-sciencesocieties-org.proxy.library.nd.edu/publications/jeq/articles/48/5/1204},
	doi = {10.2134/jeq2019.03.0114},
	language = {en},
	number = {5},
	urldate = {2020-01-23},
	journal = {Journal of Environmental Quality},
	author = {Osmond, D. L. and Shober, A. L. and Sharpley, A. N. and Duncan, E. W. and Hoag, D. L. K.},
	year = {2019},
	pages = {1204--1217},
}

@article{grant_differences_2019,
	title = {Differences in preferential flow with antecedent moisture conditions and soil texture: {Implications} for subsurface {P} transport},
	volume = {33},
	copyright = {© 2019 John Wiley \& Sons, Ltd.},
	issn = {1099-1085},
	shorttitle = {Differences in preferential flow with antecedent moisture conditions and soil texture},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1002/hyp.13454},
	doi = {10.1002/hyp.13454},
	abstract = {Preferential flowpaths transport phosphorus (P) to agricultural tile drains. However, if and to what extent this may vary with soil texture, moisture conditions, and P placement is poorly understood. This study investigated (a) interactions between soil texture, antecedent moisture conditions, and the relative contributions of matrix and preferential flow and (b) associated P distributions through the soil profile when fertilizers were applied to the surface or subsurface. Brilliant blue dye was used to stain subsurface flowpaths in clay and silt loam plots during simulated rainfall events under wet and dry conditions. Fertilizer P was applied to the surface or via subsurface placement to plots of different soil texture and moisture condition. Photographs of dye stains were analysed to classify the flow patterns as matrix dominated or macropore dominated, and soils within plots were analysed for their water-extractable P (WEP) content. Preferential flow occurred under all soil texture and moisture conditions. Dye penetrated deeper into clay soils via macropores and had lower interaction with the soil matrix, compared with silt loam soil. Moisture conditions influenced preferential flowpaths in clay, with dry clay having deeper infiltration (92 ± 7.6 cm) and less dye–matrix interaction than wet clay (77 ± 4.7 cm). Depth of staining did not differ between wet (56 ± 7.2 cm) and dry (50 ± 6.6 cm) silt loam, nor did dominant flowpaths. WEP distribution in the top 10 cm of the soil profile differed with fertilizer placement, but no differences in soil WEP were observed at depth. These results demonstrate that large rainfall events following drought conditions in clay soil may be prone to rapid P transport to tile drains due to increased preferential flow, whereas flow in silt loams is less affected by antecedent moisture. Subsurface placement of fertilizer may minimize the risk of subsurface P transport, particularily in clay.},
	language = {en},
	number = {15},
	urldate = {2020-01-23},
	journal = {Hydrological Processes},
	author = {Grant, Kirsten N. and Macrae, Merrin L. and Ali, Genevieve A.},
	year = {2019},
	keywords = {agriculture, antecedent moisture conditions, dye tracer, fertilizer placement, phosphorus, preferential flow, soil texture, vadose zone},
	pages = {2068--2079},
}

@article{plach_agricultural_2019,
	title = {Agricultural {Edge}-of-{Field} {Phosphorus} {Losses} in {Ontario}, {Canada}: {Importance} of the {Nongrowing} {Season} in {Cold} {Regions}},
	volume = {48},
	copyright = {©2019 The Authors. Re-use requires permission from the publisher.},
	issn = {1537-2537},
	shorttitle = {Agricultural {Edge}-of-{Field} {Phosphorus} {Losses} in {Ontario}, {Canada}},
	url = {http://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/jeq2018.11.0418},
	doi = {10.2134/jeq2018.11.0418},
	abstract = {Agricultural P losses are a global economic and water quality concern. Much of the current understanding of P dynamics in agricultural systems has been obtained from rainfall-driven runoff, and less is known about cold-season processes. An improved understanding of the magnitude, form, and transport flow paths of P losses from agricultural croplands year round, and the climatic drivers of these processes, is needed to prioritize and evaluate appropriate best management practices (BMPs) to protect soil-water quality in cold regions. This study examines multiyear, year-round, high-frequency edge-of-field P losses (soluble reactive P and total P [TP]) in overland flow and tile drainage from three croplands in southern Ontario, Canada. Annual and seasonal budgets for water, P, and estimates of field P budgets (including fertilizer inputs, crop uptake, and runoff) were calculated for each site. Annual edge-of-field TP loads ranged from 0.18 to 1.93 kg ha−1 yr−1 (mean = 0.59 kg ha−1 yr−1) across the region, including years with fertilizer application. Tile drainage dominated runoff across sites, whereas the contribution of tiles and overland flow to P loss differed regionally, likely related to site-specific topography, soil type, and microclimate. The nongrowing season was the dominant period for runoff and P loss across sites, where TP loss during this period was often associated with overland flow during snowmelt. These results indicate that emphasis should be placed on BMPs that are effective during both the growing and nongrowing season in cold regions, but that the suitability of various BMPs may vary for different sites. Core Ideas We conducted a multiyear, field-based study of edge-of-field runoff and P loss. Tile drainage was the dominant pathway for runoff. Contribution of tiles and overland flow to P loss differed regionally. The nongrowing season was critical for edge-of-field runoff and P loss.},
	language = {en},
	number = {4},
	urldate = {2020-01-23},
	journal = {Journal of Environmental Quality},
	author = {Plach, Janina and Pluer, Will and Macrae, Merrin and Kompanizare, Mazda and McKague, Kevin and Carlow, Ryan and Brunke, Richard},
	year = {2019},
	pages = {813--821},
}

@article{macrae_evaluating_2019,
	title = {Evaluating {Hydrologic} {Response} in {Tile}-{Drained} {Landscapes}: {Implications} for {Phosphorus} {Transport}},
	volume = {48},
	issn = {0047-2425},
	shorttitle = {Evaluating {Hydrologic} {Response} in {Tile}-{Drained} {Landscapes}},
	url = {https://dl-sciencesocieties-org.proxy.library.nd.edu/publications/jeq/abstracts/48/5/1347},
	doi = {10.2134/jeq2019.02.0060},
	language = {en},
	number = {5},
	urldate = {2020-01-23},
	journal = {Journal of Environmental Quality},
	author = {Macrae, M. L. and Ali, G. A. and King, K. W. and Plach, J. M. and Pluer, W. T. and Williams, M. and Morison, M. Q. and Tang, W.},
	year = {2019},
	pages = {1347--1355},
}

@article{lam_effects_2016,
	title = {Effects of tillage practices on phosphorus transport in tile drain effluent under sandy loam agricultural soils in {Ontario}, {Canada}},
	volume = {42},
	issn = {0380-1330},
	url = {http://www.sciencedirect.com/science/article/pii/S0380133016000071},
	doi = {10.1016/j.jglr.2015.12.015},
	abstract = {Agricultural watersheds have been identified as a source of nutrients to surface water bodies, contributing to the degradation of water quality. Reduced till (RT) management practices have been employed to reduce the potential for particulate P loss in surface runoff, but may increase the transfer of dissolved reactive phosphorus (DRP) into tile drains. It is unclear if RT increases P losses in tile drainage when nutrient management strategies are used and fertilizers are applied in the subsurface. It is also unclear how these management strategies perform year round, including during the snowmelt period. The objectives of this study are to quantify year round losses of runoff, DRP and total phosphorus (TP) losses from drainage tiles beneath annual disk till (AT) and reduced till (RT) plots, and, to investigate the role of seasonality (particularly winter snowmelt) on runoff and P losses. Results indicate that both runoff and P-export were episodic across all plots and most annual losses occurred during a few key events under heavy precipitation or snowmelt events. Runoff and P losses through drainage tiles were primarily observed between October and May, with most losses occurring in March during snowmelt. Tillage practices did not affect DRP or TP concentrations or loads in tile drainage. This study has highlighted the importance of the non-growing season (particularly winter) in annual P loss, and has demonstrated that the cumulative Best Management Practices (BMPs) used at the study sites may be an effective way to reduce P losses in tile drain effluent.},
	language = {en},
	number = {6},
	urldate = {2020-01-23},
	journal = {Journal of Great Lakes Research},
	author = {Lam, W. V. and Macrae, M. L. and English, M. C. and O'Halloran, I. P. and Wang, Y. T.},
	month = dec,
	year = {2016},
	keywords = {Canada, Lake Simcoe, Phosphorus, Seasonality, Tile drains, Tillage},
	pages = {1260--1270},
}

@article{gentry_phosphorus_2007,
	title = {Phosphorus {Transport} {Pathways} to {Streams} in {Tile}-{Drained} {Agricultural} {Watersheds}},
	volume = {36},
	issn = {1537-2537},
	url = {https://dl.sciencesocieties.org/publications/jeq/abstracts/36/2/408},
	doi = {10.2134/jeq2006.0098},
	language = {en},
	number = {2},
	urldate = {2020-01-23},
	journal = {Journal of Environmental Quality},
	author = {Gentry, L. E. and David, M. B. and Royer, T. V. and Mitchell, C. A. and Starks, K. M.},
	month = mar,
	year = {2007},
	pages = {408--415},
}

@article{daigh_subsurface_2014,
	title = {Subsurface {Drainage} {Flow} and {Soil} {Water} {Dynamics} of {Reconstructed} {Prairies} and {Corn} {Rotations} for {Biofuel} {Production}},
	volume = {13},
	issn = {1539-1663},
	url = {http://pubs.geoscienceworld.org/vzj/article/13/4/vzj2013.10.0177/91319/Subsurface-Drainage-Flow-and-Soil-Water-Dynamics},
	doi = {10.2136/vzj2013.10.0177},
	language = {en},
	number = {4},
	urldate = {2020-01-22},
	journal = {Vadose Zone Journal},
	author = {Daigh, Aaron L. and Zhou, Xiaobo and Helmers, Matthew J. and Pederson, Carl H. and Ewing, Robert and Horton, Robert},
	month = apr,
	year = {2014},
}

@article{blaszczak_scoured_2019,
	title = {Scoured or suffocated: {Urban} stream ecosystems oscillate between hydrologic and dissolved oxygen extremes},
	volume = {64},
	copyright = {© 2018 The Authors. Limnology and Oceanography published by Wiley Periodicals, Inc. on behalf of Association for the Sciences of Limnology and Oceanography.},
	issn = {1939-5590},
	shorttitle = {Scoured or suffocated},
	url = {http://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lno.11081},
	doi = {10.1002/lno.11081},
	abstract = {Headwater streams draining urbanized watersheds are subject to frequent and intense storm flows. These floods can disrupt metabolic processes occurring in benthic biofilms via the removal of biomass (i.e., scouring flows, bed mobilization) or light attenuation due to turbidity. Furthermore, channel incision caused by frequent hydraulic disturbance alters the geomorphology of streams, indirectly changing the flow and light regimes experienced by benthic biofilms. We measured dissolved oxygen (DO) and modeled whole-stream metabolism for 18 months in six urban headwater streams in the North Carolina Piedmont, U.S.A. All streams were heterotrophic and had low rates of productivity despite relatively high streamwater nutrient concentrations. Light availability at the channel surface explained more of the day to day variation in gross primary productivity within each stream than did hydrologic disturbance. Yet among streams, the explanatory power of light declined with increasing hydrologic flashiness. We found a surprisingly wide range in DO regimes, which ranged from frequent hypoxia to near constant saturation. Hypoxia was more common in streams with lower channel gradients where bedrock outcroppings and culverts create rapid slope transitions between pools. We hypothesize this geomorphic change increases the susceptibility of benthic biota to perturbation during storms and the mean water residence time during baseflow. Increased water residence times together with elevated organic matter and nutrient inputs can set up ideal conditions for hypoxia at baseflows punctuated by frequent scouring storm flows. As a result, benthic biota are caught between hydrologic and chemical extremes that constrain their productivity.},
	language = {en},
	number = {3},
	urldate = {2020-01-22},
	journal = {Limnology and Oceanography},
	author = {Blaszczak, Joanna R. and Delesantro, Joseph M. and Urban, Dean L. and Doyle, Martin W. and Bernhardt, Emily S.},
	year = {2019},
	pages = {877--894},
}

@article{li_relative_2018,
	title = {The relative importance of different grass components in controlling runoff and erosion on a hillslope under simulated rainfall},
	volume = {558},
	issn = {0022-1694},
	url = {http://www.sciencedirect.com/science/article/pii/S0022169418300076},
	doi = {10.1016/j.jhydrol.2018.01.007},
	abstract = {The effects of vegetation cover on overland flow and erosion processes on hillslopes vary with vegetation type and spatial distribution and the different vegetation components, including the above- and below-ground biomass. However, few attempts have been made to quantify how these factors affect erosion processes. Field experimental plots (5 m × 2 m) with a slope of approximately 25° were constructed and simulated rainfall (60 mm hr−1) (Rainfall) and simulated rainfall combined with upslope overland flow (20 L min−1) (Rainfall + Flow) were applied. Three grass species were planted, specifically Astragalus adsurgens (A. adsurgens), Medicago sativa (M. sativa) and Cosmos bipinnatus (C. bipinnatus). To isolate and quantify the relative contributions of the above-ground grass parts (stems, litter cover and leaves) and the roots to reducing surface runoff and erosion, each of the three grass species was subjected to three treatments: intact grass control (IG), no litter or leaves (only the grass stems and roots were reserved) (NLL), and only roots remaining (OR). The results showed that planting grass significantly reduced overland flow rate and velocity and sediment yield, and the mean reductions were 21.8\%, 29.1\% and 67.1\%, respectively. M. sativa performed the best in controlling water and soil losses due to its thick canopy and dense, fine roots. Grasses reduced soil erosion mainly during the early stage of overland flow generation. The above-ground grass parts primarily contributed to reducing overland flow rate and velocity, with mean relative contributions of 64\% and 86\%, respectively. The roots played a predominant role in reducing soil erosion, with mean contribution of 84\%. Due to the impact of upslope inflow, overland flow rate and velocity and sediment yield increased under the Rainfall + Flow conditions. The results suggest that grass species on downslope parts of semi-arid hillslopes performed better in reducing water and soil losses. This study is beneficial for forage selection, allocation and management practices, such as forage harvesting, when implementing restoration strategies to control soil and water losses.},
	language = {en},
	urldate = {2020-01-22},
	journal = {Journal of Hydrology},
	author = {Li, Changjia and Pan, Chengzhong},
	month = mar,
	year = {2018},
	keywords = {China, Grass, Loess soil, Overland flow, Rainfall simulation, Roots, Sediment},
	pages = {90--103},
}

@article{loecke_weather_2017,
	title = {Weather whiplash in agricultural regions drives deterioration of water quality},
	volume = {133},
	issn = {1573-515X},
	url = {10.1007/s10533-017-0315-z},
	doi = {10.1007/s10533-017-0315-z},
	abstract = {Excess nitrogen (N) impairs inland water quality and creates hypoxia in coastal ecosystems. Agriculture is the primary source of N; agricultural management and hydrology together control aquatic ecosystem N loading. Future N loading will be determined by how agriculture and hydrology intersect with climate change, yet the interactions between changing climate and water quality remain poorly understood. Here, we show that changing precipitation patterns, resulting from climate change, interact with agricultural land use to deteriorate water quality. We focus on the 2012–2013 Midwestern U.S. drought as a “natural experiment”. The transition from drought conditions in 2012 to a wet spring in 2013 was abrupt; the media dubbed this “weather whiplash”. We use recent (2010–2015) and historical data (1950–2015) to connect weather whiplash (drought-to-flood transitions) to increases in riverine N loads and concentrations. The drought likely created highly N-enriched soils; this excess N mobilized during heavy spring rains (2013), resulting in a 34\% increase (10.5 vs. 7.8 mg N L−1) in the flow-weighted mean annual nitrate concentration compared to recent years. Furthermore, we show that climate change will likely intensify weather whiplash. Increased weather whiplash will, in part, increase the frequency of riverine N exceeding E.P.A. drinking water standards. Thus, our observations suggest increased climatic variation will amplify negative trends in water quality in a region already grappling with severe impairments.},
	language = {en},
	number = {1},
	urldate = {2020-01-21},
	journal = {Biogeochemistry},
	author = {Loecke, Terrance D. and Burgin, Amy J. and Riveros-Iregui, Diego A. and Ward, Adam S. and Thomas, Steven A. and Davis, Caroline A. and Clair, Martin A. St.},
	month = mar,
	year = {2017},
	keywords = {Agriculture, Climate variability, Nitrate, Water quality},
	pages = {7--15},
}

@article{mcmillan_before_2018,
	title = {Before the storm: antecedent conditions as regulators of hydrologic and biogeochemical response to extreme climate events},
	volume = {141},
	issn = {0168-2563, 1573-515X},
	shorttitle = {Before the storm},
	url = {http://link.springer.com/10.1007/s10533-018-0482-6},
	doi = {10.1007/s10533-018-0482-6},
	language = {en},
	number = {3},
	urldate = {2020-01-21},
	journal = {Biogeochemistry},
	author = {McMillan, Sara K. and Wilson, Henry F. and Tague, Christina L. and Hanes, Daniel M. and Inamdar, Shreeram and Karwan, Diana L. and Loecke, Terry and Morrison, Jonathan and Murphy, Sheila F. and Vidon, Philippe},
	month = dec,
	year = {2018},
	pages = {487--501},
}

@article{metre_high_2016,
	title = {High {Nitrate} {Concentrations} in {Some} {Midwest} {United} {States} {Streams} in 2013 after the 2012 {Drought}},
	volume = {45},
	copyright = {© 2016 The Authors.},
	issn = {1537-2537},
	url = {http://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/jeq2015.12.0591},
	doi = {10.2134/jeq2015.12.0591},
	abstract = {Nitrogen sources in the Mississippi River basin have been linked to degradation of stream ecology and to Gulf of Mexico hypoxia. In 2013, the USGS and the USEPA characterized water quality stressors and ecological conditions in 100 wadeable streams across the midwestern United States. Wet conditions in 2013 followed a severe drought in 2012, a weather pattern associated with elevated nitrogen concentrations and loads in streams. Nitrate concentrations during the May to August 2013 sampling period ranged from {\textless}0.04 to 41.8 mg L−1 as N (mean, 5.31 mg L−1). Observed mean May to June nitrate concentrations at the 100 sites were compared with May to June concentrations predicted from a regression model developed using historical nitrate data. Observed concentrations for 17 sites, centered on Iowa and southern Minnesota, were outside the 95\% confidence interval of the regression-predicted mean, indicating that they were anomalously high. The sites with a nitrate anomaly had significantly higher May to June nitrate concentrations than sites without an anomaly (means, 19.8 and 3.6 mg L−1, respectively) and had higher antecedent precipitation indices, a measure of the departure from normal precipitation, in 2012 and 2013. Correlations between nitrate concentrations and watershed characteristics and nitrogen and oxygen isotopes of nitrate indicated that fertilizer and manure used in crop production, principally corn, were the dominant sources of nitrate. The anomalously high nitrate levels in parts of the Midwest in 2013 coincide with reported higher-than-normal nitrate loads in the Mississippi River. Core Ideas Multiyear precipitation patterns can affect nitrate loading to streams. Anomalously high nitrate concentrations in 2013 in some streams followed the 2012 drought. Nitrate correlated to nitrogen fertilizer applications and multiyear precipitation patterns. High nitrate in small Midwest streams in 2013 coincides with high loading in the Mississippi River.},
	language = {en},
	number = {5},
	urldate = {2020-01-21},
	journal = {Journal of Environmental Quality},
	author = {Metre, Peter C. Van and Frey, Jeffrey W. and Musgrove, MaryLynn and Nakagaki, Naomi and Qi, Sharon and Mahler, Barbara J. and Wieczorek, Michael E. and Button, Daniel T.},
	year = {2016},
	pages = {1696--1704},
}

@article{davis_antecedent_2014,
	title = {Antecedent {Moisture} {Controls} on {Stream} {Nitrate} {Flux} in an {Agricultural} {Watershed}},
	volume = {43},
	copyright = {© 2014 The Authors.},
	issn = {1537-2537},
	url = {http://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/jeq2013.11.0438},
	doi = {10.2134/jeq2013.11.0438},
	abstract = {Evaluating nitrate-N fluxes from agricultural landscapes is inherently complex due to the wide range of intrinsic and dynamic controlling variables. In this study, we investigate the influence of contrasting antecedent moisture conditions on nitrate-N flux magnitude and dynamics in a single agricultural watershed on intra-annual and rainfall-event temporal scales. High temporal resolution discharge and nitrate concentration data were collected to evaluate nitrate-N flux magnitude associated with wet (2009) and dry (2012) conditions. Analysis of individual rainfall events revealed a marked and consistent difference in nitrate-N flux response attributed to wet/dry cycles. Large-magnitude dilutions (up to 10 mg N L−1) persisted during the wet antecedent conditions (2009), consistent with a dominant baseflow contribution and excess groundwater release in relation to precipitation volume (discharge {\textgreater} {\textgreater} precipitation). Smaller-magnitude concentrations ({\textless}7 mg N L−1) were observed during the drought conditions of 2012, consistent with a quickflow-dominated response to rain events and infiltration/storage of precipitation resulting in discharge {\textless} precipitation. Nitrate-N loads and yields from the watershed were much higher (up to an order of magnitude) in the wet year vs. the dry year. Our results suggest that the response of nitrate-N loading to rain events is highly dependent on intra-annual antecedent moisture conditions and subsurface hydrologic connectivity, which together dictate the dominant hydrologic pathways for stream recharge. Additionally, the results of our study indicate that continued pronounced wet/dry cycles may become more dominant as the short-term driver of future nitrate-N exports.},
	language = {en},
	number = {4},
	urldate = {2020-01-21},
	journal = {Journal of Environmental Quality},
	author = {Davis, Caroline A. and Ward, Adam S. and Burgin, Amy J. and Loecke, Terrance D. and Riveros‐Iregui, Diego A. and Schnoebelen, Douglas J. and Just, Craig L. and Thomas, Steven A. and Weber, Larry J. and Clair, Martin A. St},
	year = {2014},
	pages = {1494--1503},
}

@article{casillas-ituarte_internal_2019,
	title = {Internal {Phosphorus} {Storage} in {Two} {Headwater} {Agricultural} {Streams} in the {Lake} {Erie} {Basin}},
	issn = {0013-936X, 1520-5851},
	url = {https://pubs.acs.org/doi/10.1021/acs.est.9b04232},
	doi = {10.1021/acs.est.9b04232},
	abstract = {Internal phosphorus (P) in sediments plays an important role in the nutrient dynamics of lakes, sometimes long after external loads have been reduced. Similarly, internal P sources may drive the nutrient dynamics of small agricultural streams that drain to larger rivers and lakes, despite best management practices intended to reduce external P loads from adjacent fields. Here, internal P concentrations were measured with sequential extraction on cores collected in spring and summer from two small agricultural streams in the drainage basin of Lake Erie, a large, eutrophic lake experiencing increasing SRP loads. Average total extractable P concentrations were similar to within 5\% during spring and summer, but mobile P binding fractions nearly doubled in summer, possibly due to accelerated rates of organic matter mineralization or iron reduction beneath suboxic, stagnant surface waters. One site had chronically greater internal P concentrations by 25−75\%, despite the implementation of best management practices such as grass buffers. The site also had more aquatic vegetation that restricted the flow, less dissolved oxygen in surface water, and greater organic matter in sediments during both seasons, suggesting that variations in hydrology, sediment composition, and vegetation influence hot spots of P retention throughout small agricultural streams.},
	language = {en},
	urldate = {2020-01-20},
	journal = {Environmental Science \& Technology},
	author = {Casillas-Ituarte, Nadia N. and Sawyer, Audrey H. and Danner, Kelsey M. and King, Kevin W. and Covault, Alexandra J.},
	month = dec,
	year = {2019},
	pages = {acs.est.9b04232},
}

@article{krstic_effect_2018,
	title = {The {Effect} of {Cover} {Crops} on {Soil} {Water} {Balance} in {Rain}-{Fed} {Conditions}},
	volume = {9},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	url = {https://www.mdpi.com/2073-4433/9/12/492},
	doi = {10.3390/atmos9120492},
	abstract = {Soil and water conservation benefits of cover crops have been hypothesized as a way to mitigate and adapt to changing climatic conditions, but they can also have detrimental effects if rainfall is limited. Our objective was to quantify effects of winter cover crops on soil water storage and yield of silage maize under the agro-ecological conditions within Vojvodina Province in Serbia. The experiment was conducted under rain-fed conditions at three locations and included a control (bare fallow) plus three cover crop and two N rate treatments. The cover crop treatments were common vetch (Vicia sativa L.), triticale (x Triticosecale Wittm. ex A. Camus) and a mixture of the two species. All were managed as green manure and subsequently fertilized with either 120 or 160 kg N ha\&minus;1 before planting silage maize (Zea mays L.). Cover crop effects on soil water storage were calculated for two periods, March\&ndash;May and May\&ndash;September/October. A Standardized Precipitation Index (SPI) used to characterize drought severity for 2011/2012 and 2012/2013, showed values of 3 and 9, respectively, for the two periods. Soil water storage was reduced by all cover crop treatments, with the greatest deficiency occurring during the extremely dry year of 2012. Previous studies have shown cover crop growth reduced by soil water depletion during their growing season and negative effects on early-season growth and development of subsequent cash crops such as silage maize, but if rainfall is extremely low it can also reduce cash crop yield. This detrimental effect of cover crops on soil water balance was confirmed by correlations between soil water storage and maize silage yield.},
	language = {en},
	number = {12},
	urldate = {2020-01-18},
	journal = {Atmosphere},
	author = {Krstić, Đorđe and Vujić, Svetlana and Jaćimović, Goran and D’Ottavio, Paride and Radanović, Zoran and Erić, Pero and Ćupina, Branko},
	month = dec,
	year = {2018},
	keywords = {cover crops, silage maize, soil, water storage},
	pages = {492},
}

@article{qi_soil_2011,
	title = {Soil water dynamics under various agricultural land covers on a subsurface drained field in north-central {Iowa}, {USA}},
	volume = {98},
	issn = {0378-3774},
	url = {http://www.sciencedirect.com/science/article/pii/S0378377410003628},
	doi = {10.1016/j.agwat.2010.11.004},
	abstract = {Modification of land cover systems is being studied in subsurface drained Iowa croplands due to their potential benefits in increasing soil water and nitrogen depletion thus reducing drainage and NO3–N loss in the spring period. The objective of this study was to evaluate the impacts of modified land covers on soil water dynamics. In each individual year, modified land covers including winter rye–corn (rC), winter rye–soybean (rS), kura clover as a living mulch for corn (kC), and perennial forage (PF), as well as conventional corn (C) and soybean (S), were grown in subsurface drained plots in north-central Iowa. Results showed that subsurface drainage was not reduced under modified land covers in comparison to conventional corn and soybean. Soil water storage (SWS) was significantly reduced by PF treatments during the whole growing seasons and by kC during May through July when compared to the cropping system with corn or soybean only (p{\textless}0.05). Treatments of rC and rS typically maintained higher SWS than C and S, respectively, during the 3 years of this study. In the spring during a 10–15-day period when the rainfall was minimal, SWS in plots with rye, kura clover, and forage decreased at a significantly higher rate than the C and S plots which were bare. Estimated evapotranspiration (ET) during this period was significantly higher in rS, kC, and PF treatments than C and S. The results of this study suggested that significantly higher ET and similar drainage for modified land covers may increase water infiltration, which would be expected to reduce surface runoff thus to decrease stream flow. Because subsurface drainage reduction was not seen in this study, impact of modified land covers on NO3–N loss needs further investigation.},
	language = {en},
	number = {4},
	urldate = {2020-01-18},
	journal = {Agricultural Water Management},
	author = {Qi, Zhiming and Helmers, Matthew J. and Kaleita, Amy L.},
	month = feb,
	year = {2011},
	keywords = {Kura clover, Perennial forage, Rye cover crop, Soil water dynamics},
	pages = {665--674},
}

@article{vannote_river_1980,
	title = {The {River} {Continuum} {Concept}},
	volume = {37},
	issn = {0706-652X},
	url = {https://www.nrcresearchpress.com/doi/10.1139/f80-017},
	doi = {10.1139/f80-017},
	abstract = {From headwaters to mouth, the physical variables within a river system present a continuous gradient of physical conditions. This gradient should elicit a series of responses within the constituent populations resulting in a continuum of biotic adjustments and consistent patterns of loading, transport, utilization, and storage of organic matter along the length of a river. Based on the energy equilibrium theory of fluvial geomorphologists, we hypothesize that the structural and functional characteristics of stream communities are adapted to conform to the most probable position or mean state of the physical system. We reason that producer and consumer communities characteristic of a given river reach become established in harmony with the dynamic physical conditions of the channel. In natural stream systems, biological communities can be characterized as forming a temporal continuum of synchronized species replacements. This continuous replacement functions to distribute the utilization of energy inputs over time. Thus, the biological system moves towards a balance between a tendency for efficient use of energy inputs through resource partitioning (food, substrate, etc.) and an opposing tendency for a uniform rate of energy processing throughout the year. We theorize that biological communities developed in natural streams assume processing strategies involving minimum energy loss. Downstream communities are fashioned to capitalize on upstream processing inefficiencies. Both the upstream inefficiency (leakage) and the downstream adjustments seem predictable. We propose that this River Continuum Concept provides a framework for integrating predictable and observable biological features of lotic systems. Implications of the concept in the areas of structure, function, and stability of riverine ecosystems are discussed.Key words: river continuum; stream ecosystems; ecosystem structure, function; resource partitioning; ecosystem stability; community succession; river zonation; stream geomorphology},
	number = {1},
	urldate = {2020-01-18},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Vannote, Robin L. and Minshall, G. Wayne and Cummins, Kenneth W. and Sedell, James R. and Cushing, Colbert E.},
	month = jan,
	year = {1980},
	pages = {130--137},
}

@article{basche_soil_2016,
	title = {Soil water improvements with the long-term use of a winter rye cover crop},
	volume = {172},
	issn = {03783774},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0378377416301214},
	doi = {10.1016/j.agwat.2016.04.006},
	abstract = {The Midwestern United States, a region that produces one-third of maize and one-quarter of soybean grain globally, is projected to experience increasing rainfall variability. One approach to mitigate climate impacts is to utilize crop and soil management practices that enhance soil water storage and reduce the risks of flooding as well as drought-induced crop water stress. While some research indicates that a winter cover crop in maize-soybean rotations increases soil water availability, producers continue to be concerned that water use by cover crops will reduce water for a following cash crop. We analyzed continuous in-field soil water measurements from 2008 to 2014 at a Central Iowa research site that has included a winter rye cover crop in a maize-soybean rotation for thirteen years. This period of study included years in the top third of the wettest on record (2008, 2010, 2014) as well as drier years in the bottom third (2012, 2013). We found the cover crop treatment to have significantly higher soil water storage at the 0–30 cm depth from 2012 to 2014 when compared to the no cover crop treatment and in most years greater soil water content on individual days analyzed during the cash crop growing season. We further found that the cover crop significantly increased the field capacity water content by 10–11\% and plant available water by 21–22\%. Finally, in 2013 and 2014, we measured maize and soybean biomass every 2–3 weeks and did not see treatment differences in crop growth, leaf area or nitrogen uptake. Final crop yields were not statistically different between the cover and no cover crop treatment in any of the seven years of this analysis. This research indicates that the long-term use of a winter rye cover crop can improve soil water dynamics without sacrificing cash crop growth in maize-soybean crop rotations in the Midwestern United States.},
	language = {en},
	urldate = {2020-01-17},
	journal = {Agricultural Water Management},
	author = {Basche, Andrea D. and Kaspar, Thomas C. and Archontoulis, Sotirios V. and Jaynes, Dan B. and Sauer, Thomas J. and Parkin, Timothy B. and Miguez, Fernando E.},
	month = jul,
	year = {2016},
	pages = {40--50},
}

@article{basche_impact_2017,
	title = {The {Impact} of {Continuous} {Living} {Cover} on {Soil} {Hydrologic} {Properties}: {A} {Meta}-{Analysis}},
	volume = {81},
	issn = {0361-5995},
	shorttitle = {The {Impact} of {Continuous} {Living} {Cover} on {Soil} {Hydrologic} {Properties}},
	url = {http://dl.sciencesocieties.org/publications/sssaj/abstracts/81/5/1179},
	doi = {10.2136/sssaj2017.03.0077},
	language = {en},
	number = {5},
	urldate = {2020-01-17},
	journal = {Soil Science Society of America Journal},
	author = {Basche, Andrea and DeLonge, Marcia},
	year = {2017},
	pages = {1179--1190},
}

@article{williams_effect_2016,
	title = {Effect of tillage on macropore flow and phosphorus transport to tile drains},
	volume = {52},
	copyright = {© 2016. American Geophysical Union. All Rights Reserved.},
	issn = {1944-7973},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2015WR017650},
	doi = {10.1002/2015WR017650},
	abstract = {Elevated phosphorus (P) concentrations in subsurface drainage water are thought to be the result of P bypassing the soil matrix via macropore flow. The objectives of this study were to quantify event water delivery to tile drains via macropore flow paths during storm events and to determine the effect of tillage practices on event water and P delivery to tiles. Tile discharge, total dissolved P (DP) and total P (TP) concentrations, and stable oxygen and deuterium isotopic signatures were measured from two adjacent tile-drained fields in Ohio, USA during seven spring storms. Fertilizer was surface-applied to both fields and disk tillage was used to incorporate the fertilizer on one field while the other remained in no-till. Median DP concentration in tile discharge prior to fertilizer application was 0.08 mg L−1 in both fields. Following fertilizer application, median DP concentration was significantly greater in the no-tilled field (1.19 mg L−1) compared to the tilled field (0.66 mg L−1), with concentrations remaining significantly greater in the no-till field for the remainder of the monitored storms. Both DP and TP concentrations in the no-till field were significantly related to event water contributions to tile discharge, while only TP concentration was significantly related to event water in the tilled field. Event water accounted for between 26 and 69\% of total tile discharge from both fields, but tillage substantially reduced maximum contributions of event water. Collectively, these results suggest that incorporating surface-applied fertilizers has the potential to substantially reduce the risk of P transport from tile-drained fields.},
	language = {en},
	number = {4},
	urldate = {2020-01-17},
	journal = {Water Resources Research},
	author = {Williams, Mark R. and King, Kevin W. and Ford, William and Buda, Anthony R. and Kennedy, Casey D.},
	year = {2016},
	keywords = {event water, isotope hydrograph separation, preferential flow, subsurface, water quality},
	pages = {2868--2882},
}

@misc{noauthor_short-term_nodate,
	title = {Short-term response of aquatic ecosystem metabolism to turbidity disturbance in experimental estuarine wetlands - {ScienceDirect}},
	url = {https://www.sciencedirect.com/science/article/pii/S0925857419302034#f0005},
	urldate = {2020-01-16},
}

@article{uehlinger_resistance_2000,
	title = {Resistance and resilience of ecosystem metabolism in a flood-prone river system},
	volume = {45},
	issn = {1365-2427},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2427.2000.00620.x},
	doi = {10.1111/j.1365-2427.2000.00620.x},
	abstract = {1. Gross primary production (GPP) and ecosystem respiration (ER) were analysed for 18 months in two reaches of the River Thur, a prealpine river in Switzerland. The upper reach at 655 m above sea level (a.s.l.) is bedrock constrained, has a high slope (0.60\%) and a catchment area of 126 km2. The lower reach at 370 m a.s.l. has a more extensive hyporheic zone, a lower slope (0.17\%) and a catchment of 1696 km2. 2. In both reaches, temporal patterns of stream metabolism reflected the occurrence of bed-moving spates. Average reductions of GPP and ER by spates were 53 and 24\% in the upper reach, and 37 and 14\% in the lower reach, respectively. The greater resistance of ER than GPP in both reaches shifted the ecosystem metabolism towards heterotrophy (decrease of the ratio of GPP to ER (P/R)) following spates. 3. Recovery of GPP was significantly faster in the lower reach and exhibited distinct seasonal variation (positive correlation with incident light). The differences in stability (both resistance and resilience) between reaches reflected differences in geomorphic settings and disturbance regime. 4. Stepwise regression analysis was used to explore the potential influence of season, disturbance and prevailing environmental conditions on stream metabolism in each reach. Time since spate plus temperature explained 73 and 86\% of variation in ER and GPP, respectively, in the upper reach and 55\% of variation in ER in the lower reach. Season plus prevailing environmental conditions explained 67\% of variation in GPP in the lower reach. 5. To test how the perception of stability may change with increasing scale of observation, the disturbance regimes of 12 sites were compared with the disturbance regime of the entire Thur catchment. The analysis suggests that stream metabolism at the catchment scale is far more resistant to high flow events than at the reach scale.},
	language = {en},
	number = {3},
	urldate = {2020-01-15},
	journal = {Freshwater Biology},
	author = {Uehlinger, Urs},
	year = {2000},
	keywords = {disturbance, ecosystem respiration, longitudinal change, primary production, spates, spatial scaling, stability},
	pages = {319--332},
}

@article{izagirre_environmental_2008,
	title = {Environmental controls of whole-stream metabolism identified from continuous monitoring of {Basque} streams},
	volume = {27},
	issn = {0887-3593},
	url = {https://www.journals.uchicago.edu/doi/10.1899/07-022.1},
	doi = {10.1899/07-022.1},
	abstract = {Most methods for assessing the ecological status of streams focus on structural characteristics (water quality, community composition, riparian vegetation) but neglect functional properties of the ecosystem because routine methods to assess stream function are scarce. Metabolism, one of the most integrative ecosystem functions, can be a good indicator of stream function because it is relevant across all sizes and types of streams, is sensitive to stressors, such as eutrophication or changes in riparian cover, and can be measured continuously. Environmental controls on whole-ecosystem metabolism were measured at 19 contrasting stream reaches in the Basque Country (northern Spain). Discharge, temperature, and O2 were monitored continuously for 15 mo, reaeration rate was calculated with the nighttime regression method, and whole-stream metabolism was calculated by the single-station open-channel method. The effect of discharge on reaeration coefficients was highly site-specific. Average gross primary production (GPP) ranged from 2.7 to 11.0 g O2 m−2 d−1, was highest at eutrophic sites, and showed no relationship with periphyton biomass. Ecosystem respiration (ER) ranged from 6.3 to 42.6 g O2 m−2 d−1 and was highest at polluted sites. Differences among sites increased in summer. All sites were heterotrophic on an annual basis, but 3 were autotrophic during summer. Turbidity was the main controller of primary production during summer and explained 20\% and 39\% of the spatial variation in GPP and net ecosystem production, respectively. Biological O2 demand of water explained 40\% of ER variance. Catchment activities also controlled GPP, which decreased as population density increased. To our knowledge, our study is the first report of continuous monitoring of whole-stream metabolism at many reaches simultaneously, and it shows the potential of this technique for routine monitoring of stream function.},
	number = {2},
	urldate = {2020-01-15},
	journal = {Journal of the North American Benthological Society},
	author = {Izagirre, Oihana and Agirre, Urko and Bermejo, Miren and Pozo, Jesús and Elosegi, Arturo},
	month = jun,
	year = {2008},
	pages = {252--268},
}

@article{basche_comparing_2019,
	title = {Comparing infiltration rates in soils managed with conventional and alternative farming methods: {A} meta-analysis},
	volume = {14},
	issn = {1932-6203},
	shorttitle = {Comparing infiltration rates in soils managed with conventional and alternative farming methods},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215702},
	doi = {10.1371/journal.pone.0215702},
	abstract = {Identifying agricultural practices that enhance water cycling is critical, particularly with increased rainfall variability and greater risks of droughts and floods. Soil infiltration rates offer useful insights to water cycling in farming systems because they affect both yields (through soil water availability) and other ecosystem outcomes (such as pollution and flooding from runoff). For example, conventional agricultural practices that leave soils bare and vulnerable to degradation are believed to limit the capacity of soils to quickly absorb and retain water needed for crop growth. Further, it is widely assumed that farming methods such as no-till and cover crops can improve infiltration rates. Despite interest in the impacts of agricultural practices on infiltration rates, this effect has not been systematically quantified across a range of practices. To evaluate how conventional practices affect infiltration rates relative to select alternative practices (no-till, cover crops, crop rotation, introducing perennials, crop and livestock systems), we performed a meta-analysis that included 89 studies with field trials comparing at least one such alternative practice to conventional management. We found that introducing perennials (grasses, agroforestry, managed forestry) or cover crops led to the largest increases in infiltration rates (mean responses of 59.2 ± 20.9\% and 34.8 ± 7.7\%, respectively). Also, although the overall effect of no-till was non-significant (5.7 ± 9.7\%), the practice led to increases in wetter climates and when combined with residue retention. The effect of crop rotation on infiltration rate was non-significant (18.5 ± 13.2\%), and studies evaluating impacts of grazing on croplands indicated that this practice reduced infiltration rates (-21.3 ± 14.9\%). Findings suggest that practices promoting ground cover and continuous roots, both of which improve soil structure, were most effective at increasing infiltration rates.},
	language = {en},
	number = {9},
	urldate = {2020-01-10},
	journal = {PLOS ONE},
	author = {Basche, Andrea D. and DeLonge, Marcia S.},
	month = sep,
	year = {2019},
	keywords = {Agricultural methods, Agricultural soil science, Crop management, Crops, Grazing, Livestock, Metaanalysis, Water resources},
	pages = {e0215702},
}

@article{meyer_cover_2019,
	title = {Cover crops reduce water drainage in temperate climates: {A} meta-analysis},
	volume = {39},
	issn = {1774-0746, 1773-0155},
	shorttitle = {Cover crops reduce water drainage in temperate climates},
	url = {http://link.springer.com/10.1007/s13593-018-0546-y},
	doi = {10.1007/s13593-018-0546-y},
	abstract = {Cover crops provide many ecosystem services, such as soil protection, nitrate pollution of water mitigation, and green manure effects. However, the impact of cover crops on soil water balance is poorly studied, despite its potential impact on groundwater recharge. Some studies reported a reduction of the water drainage due to an increase of the evapotranspiration by plant cover transpiration. However, there is no real consensus on the intensity of this phenomenon, which highlights the importance to quantify the impact of cover crops on drainage compared to that of bare soil. We performed a meta-analysis of published papers presenting studies on the impact of cover crops on drainage compared to that of bare soil under temperate climates. Of the 436 papers identified, 28 of them were included in the analysis based on criteria required for performing a relevant meta-analysis. The originality of our study lies in two following results: (1) the quantification of drainage reduction with cover crops by a mean effect size of 27 mm compared to that of bare soil and (2) within the large variability of soils, climates, and cropping systems, no main determining factor was found significant to explain the variability of water drainage reduction. The cover crops provide a service of nitrate pollution mitigation, but the drainage reduction could be considered as a disservice, because they can lead to a reduction in groundwater recharge due to a higher evapotranspiration in comparison to bare soil. This highlights the need of research for optimizing trade-offs between services and disservices of cover crops for water balance.},
	language = {en},
	number = {1},
	urldate = {2020-01-10},
	journal = {Agronomy for Sustainable Development},
	author = {Meyer, Nicolas and Bergez, Jacques-Eric and Constantin, Julie and Justes, Eric},
	month = feb,
	year = {2019},
	pages = {3},
}

@article{kemp_eutrophication_2005,
	title = {Eutrophication of {Chesapeake} {Bay}: historical trends and ecological interactions},
	volume = {303},
	issn = {0171-8630, 1616-1599},
	shorttitle = {Eutrophication of {Chesapeake} {Bay}},
	url = {https://www.int-res.com/abstracts/meps/v303/p1-29/},
	doi = {10.3354/meps303001},
	abstract = {This review provides an integrated synthesis with timelines and evaluations of ecological responses to eutrophication in Chesapeake Bay, the largest estuary in the USA. Analyses of dated sediment cores reveal initial evidence of organic enrichment in {\textasciitilde}200 yr old strata, while signs of increased phytoplankton and decreased water clarity first appeared {\textasciitilde}100 yr ago. Severe, recurring deep-water hypoxia and loss of diverse submersed vascular plants were first evident in the 1950s and 1960s, respectively. The degradation of these benthic habitats has contributed to declines in benthic macroinfauna in deep mesohaline regions of the Bay and blue crabs in shallow polyhaline areas. In contrast, copepods, which are heavily consumed in pelagic food chains, are relatively unaffected by nutrient-induced changes in phytoplankton. Intense mortality associated with fisheries and disease have caused a dramatic decline in eastern oyster stocks and associated Bay water filtration, which may have exacerbated eutrophication effects on phytoplankton and water clarity. Extensive tidal marshes, which have served as effective nutrient buffers along the Bay margins, are now being lost with rising sea level. Although the Bay’s overall fisheries production has probably not been affected by eutrophication, decreases in the relative contribution of demersal fish and in the efficiency with which primary production is transferred to harvest suggest fundamental shifts in trophic and habitat structures. Bay ecosystem responses to changes in nutrient loading are complicated by non-linear feedback mechanisms, including particle trapping and binding by benthic plants that increase water clarity, and by oxygen effects on benthic nutrient recycling efficiency. Observations in Bay tributaries undergoing recent reductions in nutrient input indicate relatively rapid recovery of some ecosystem functions but lags in the response of others.},
	language = {en},
	urldate = {2019-12-31},
	journal = {Marine Ecology Progress Series},
	author = {Kemp, W. M. and Boynton, W. R. and Adolf, J. E. and Boesch, D. F. and Boicourt, W. C. and Brush, G. and Cornwell, J. C. and Fisher, T. R. and Glibert, P. M. and Hagy, J. D. and Harding, L. W. and Houde, E. D. and Kimmel, D. G. and Miller, W. D. and Newell, R. I. E. and Roman, M. R. and Smith, E. M. and Stevenson, J. C.},
	month = nov,
	year = {2005},
	keywords = {Chesapeake Bay, Eutrophication, Nutrients},
	pages = {1--29},
}

@article{rabalais_gulf_2002,
	title = {Gulf of {Mexico} hypoxia, {A}.{K}.{A}. “{The} {Dead} {Zone}”},
	volume = {33},
	url = {10.1146/annurev.ecolsys.33.010802.150513},
	doi = {10.1146/annurev.ecolsys.33.010802.150513},
	abstract = {Abstract The second largest zone of coastal hypoxia (oxygen-depleted waters) in the world is found on the northern Gulf of Mexico continental shelf adjacent to the outflows of the Mississippi and Atchafalaya Rivers. The combination of high freshwater discharge, wind mixing, regional circulation, and summer warming controls the strength of stratification that goes through a well-defined seasonal cycle. The physical structure of the water column and high nutrient loads that enhance primary production lead to an annual formation of the hypoxic water mass that is dominant from spring through late summer. Paleoindicators in dated sediment cores indicate that hypoxic conditions likely began to appear around the turn of the last century and became more severe since the 1950s as the nitrate flux from the Mississippi River to the Gulf of Mexico tripled. Whereas increased nutrients enhance the production of some organisms, others are eliminated from water masses (they either emigrate from the area or die) where the oxygen level falls below 2 mg l−1 or lower for a prolonged period. A hypoxia-stressed benthos is typified by short-lived, smaller surface deposit-feeding polychaetes and the absence of marine invertebrates such as pericaridean crustaceans, bivalves, gastropods, and ophiuroids. The changes in benthic communities, along with the low dissolved oxygen, result in altered sediment structure and sediment biogeochemical cycles. Important fisheries are variably affected by increased or decreased food supplies, mortality, forced migration, reduction in suitable habitat, increased susceptibility to predation, and disruption of life cycles.},
	number = {1},
	urldate = {2019-12-31},
	journal = {Annual Review of Ecology and Systematics},
	author = {Rabalais, Nancy N. and Turner, R. Eugene and Wiseman, William J.},
	year = {2002},
	pages = {235--263},
}

@article{diaz_spreading_2008,
	title = {Spreading dead zones and consequences for marine ecosystems},
	volume = {321},
	copyright = {American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	url = {http://science.sciencemag.org/content/321/5891/926},
	doi = {10.1126/science.1156401},
	abstract = {Dead zones in the coastal oceans have spread exponentially since the 1960s and have serious consequences for ecosystem functioning. The formation of dead zones has been exacerbated by the increase in primary production and consequent worldwide coastal eutrophication fueled by riverine runoff of fertilizers and the burning of fossil fuels. Enhanced primary production results in an accumulation of particulate organic matter, which encourages microbial activity and the consumption of dissolved oxygen in bottom waters. Dead zones have now been reported from more than 400 systems, affecting a total area of more than 245,000 square kilometers, and are probably a key stressor on marine ecosystems.},
	language = {en},
	number = {5891},
	urldate = {2019-12-31},
	journal = {Science},
	author = {Diaz, Robert J. and Rosenberg, Rutger},
	month = aug,
	year = {2008},
	pmid = {18703733},
	pages = {926--929},
}

@misc{noauthor_spreading_nodate,
	title = {Spreading {Dead} {Zones} and {Consequences} for {Marine} {Ecosystems} {\textbar} {Science}},
	url = {https://science-sciencemag-org.proxy.library.nd.edu/content/321/5891/926.full},
	urldate = {2019-12-31},
}

@article{reavis_are_2016,
	title = {Are floodplain soils a potential phosphorus source when inundated that can be effectively managed?},
	volume = {1},
	issn = {2471-9625},
	url = {http://dl.sciencesocieties.org/publications/ael/abstracts/1/1/160036},
	doi = {10.2134/ael2016.09.0036},
	language = {en},
	number = {1},
	urldate = {2019-12-02},
	journal = {Agricultural \& Environmental Letters},
	author = {Reavis, Megan A. and Haggard, Brian E.},
	month = dec,
	year = {2016},
}

@article{withers_delivery_2008,
	title = {Delivery and cycling of phosphorus in rivers: {A} review},
	volume = {400},
	issn = {0048-9697},
	shorttitle = {Delivery and cycling of phosphorus in rivers},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969708008139},
	doi = {10.1016/j.scitotenv.2008.08.002},
	abstract = {Phosphorus (P) supply (concentration and flux) is an important driver for biological activity in flowing waters and needs to be managed to avoid eutrophication impacts associated with urbanisation and agricultural intensification. This paper examines the role of in-stream retention and cycling in regulating river P concentrations in order to better understand the links between P sources and their ecological impacts. In terms of their composition (solubility and concentration), patterns of delivery (mode and timing) and therefore ecological relevance, P sources entering rivers are best grouped into wastewater discharges {\textgreater} runoff from impervious surfaces (roads, farmyards) {\textgreater} runoff from pervious surfaces (forestry, cultivated land and pasture). The localized impacts of soluble P discharges during ecologically sensitive periods can be distinguished from the downstream impacts associated with particulate P discharges under high flows due to the different processes by which these sources are retained, transformed and assimilated within the river channel. The range of physico-chemical processes involved in P cycling and the variable importance of these processes in different river environments according to stream size, stream geomorphology and anthropogenic pressures are summarised. It is concluded that the capacity to retain (process) P within the river channel, and hence regulate the downstream delivery of P without stressing the aquatic communities present, is considerable, especially in headwaters. To help achieve good water quality, there is scope to better manage this ecosystem service through regulation of P supply whilst optimising in-stream P retention according to subsidy-stress theory. Further research is needed to develop in-stream management options for maximising P subsidies and to demonstrate that regulation of downstream P delivery will reduce the incidence of eutrophication in connected waterbodies.},
	language = {en},
	number = {1},
	urldate = {2019-12-30},
	journal = {Science of The Total Environment},
	author = {Withers, P. J. A. and Jarvie, H. P.},
	month = aug,
	year = {2008},
	keywords = {Cycling, In-stream processes, Phosphorus, Retention, Rivers, Subsidy-stress theory},
	pages = {379--395},
}

@article{mulholland_phosphorus_1985,
	title = {Phosphorus {Spiralling} in a {Woodland} {Stream}: {Seasonal} {Variations}},
	volume = {66},
	issn = {1939-9170},
	shorttitle = {Phosphorus {Spiralling} in a {Woodland} {Stream}},
	url = {http://esajournals.onlinelibrary.wiley.com/doi/10.2307/1940562},
	doi = {10.2307/1940562},
	abstract = {Four radiotracer releases were performed over an annual period in 1981—1982 to determine seasonal variation in indices and pathways of phosphorus spiralling in Walker Branch, a small woodland stream ...},
	language = {en},
	number = {3},
	urldate = {2019-12-30},
	journal = {Ecology},
	author = {Mulholland, Patrick J. and Newbold, J. Denis and Elwood, Jerry W. and Ferren, Leigh Ann and Webster, Jackson R.},
	month = jun,
	year = {1985},
	pages = {1012--1023},
}

@inproceedings{lijklema_considerations_1993,
	address = {Dordrecht},
	series = {Developments in {Hydrobiology}},
	title = {Considerations in modeling the sediment—water exchange of phosphorus},
	isbn = {978-94-011-1598-8},
	doi = {10.1007/978-94-011-1598-8_27},
	abstract = {The potential to release accumulated phosphorus from sediments has been the major motive to study and to model the fate of this nutrient in sediments.For the dynamics of the sediment-water interaction the sizes of the pools involved and the rates of conversion/transport from one pool to another are of primary interest. As the sediment pools for phosphate are generally much larger than the pools in the water column, a rather slow adjustment of the sediment to management measures will occur. For the analysis of management measures it is obvious that the gradual change in sediment composition must be taken into account. Only for rather short periods the sediment composition can be assumed to be constant; this may be appropriate for studies of e.g. the annual cycle.The sediment-water interaction is a complex resultant of physical, chemical and biological processes, including: physical processes: advection due to seepage or consolidation, pore-water diffusion, transport and mixing of solids by resuspension, sedimentation and bioturbation. chemical processes: adsorption and desorption, dissolution and (co)precipitation, inclusion. biological processes: mineralization of a wide range of organic compounds by various (micro)organisms, each with their own nutrient requirements and electron acceptors. Aspects which are discussed and need to be considered in application of a model in research or management are the level of aggregation and detail that is required and may still be practical, the spatial and temporal scales which are applicable for the processes mentioned and their influence upon the numerical dispersion and model stability, the availability of data for calibration/validation and the resolution of the analytical techniques. These aspects are not independent however.Frequently models are not functional because they contain details which are either unnecessary or suggest a feigned accuracy which is not justified by analytical and experimental resolution of system characteristics.},
	language = {en},
	booktitle = {Proceedings of the {Third} {International} {Workshop} on {Phosphorus} in {Sediments}},
	publisher = {Springer Netherlands},
	author = {Lijklema, Lambertus},
	editor = {Boers, P. C. M. and Cappenberg, Th. E. and van Raaphorst, W.},
	year = {1993},
	keywords = {models, phosphorus, sediment, spatial scales, temporal scales, water},
	pages = {219--231},
}

@article{asli_colloidal_2009,
	title = {Colloidal suspensions of clay or titanium dioxide nanoparticles can inhibit leaf growth and transpiration via physical effects on root water transport},
	volume = {32},
	copyright = {© 2009 Blackwell Publishing Ltd},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-3040.2009.01952.x},
	doi = {10.1111/j.1365-3040.2009.01952.x},
	abstract = {A laboratory investigation was conducted to determine whether colloidal suspensions of inorganic nanoparticulate materials of natural or industrial origin in the external water supplied to the primary root of maize seedlings (Zea mays L.) could interfere with water transport and induce associated leaf responses. Water flow through excised roots was reduced, together with root hydraulic conductivity, within minutes of exposure to colloidal suspensions of naturally derived bentonite clay or industrially produced TiO2 nanoparticles. Similar nanoparticle additions to the hydroponic solution surrounding the primary root of intact seedlings rapidly inhibited leaf growth and transpiration. The reduced water availability caused by external nanoparticles and the associated leaf responses appeared to involve a rapid physical inhibition of apoplastic flow through nanosized root cell wall pores rather than toxic effects. Thus: (1) bentonite and TiO2 treatments also reduced the hydraulic conductivity of cell wall ghosts of killed roots left after hot alcohol disruption of the cell membranes; and (2) the average particle exclusion diameter of root cell wall pores was reduced from 6.6 to 3.0 nm by prior nanoparticle treatments. Irrigation of soil-grown plants with nanoparticle suspensions had mostly insignificant inhibitory effects on long-term shoot production, and a possible developmental adaptation is suggested.},
	language = {en},
	number = {5},
	urldate = {2019-12-30},
	journal = {Plant, Cell \& Environment},
	author = {Asli, Sare and Neumann, Peter M.},
	year = {2009},
	keywords = {TiO2, bentonite, cell walls, hydraulic conductivity, pore size, root clogging},
	pages = {577--584},
}

@article{scott_floodplain_2019,
	title = {Floodplain inundation spectrum across the {United} {States}},
	volume = {10},
	copyright = {2019 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-019-13184-4},
	doi = {10.1038/s41467-019-13184-4},
	abstract = {The variations in overbank flow from rivers onto floodplains from regional to continental scales are understudied. Here, the authors investigate this variation as a function of hydroclimatic parameters and channel size in the conterminous U.S. and find that the timing of floodplain inundation is largely controlled by regional factors, while the frequency, duration and magnitude of these inundations vary consistently with channel size.},
	language = {en},
	number = {1},
	urldate = {2019-12-30},
	journal = {Nature Communications},
	author = {Scott, Durelle T. and Gomez-Velez, Jesus D. and Jones, C. Nathan and Harvey, Judson W.},
	month = nov,
	year = {2019},
	pages = {1--8},
}

@article{dambrosio_evaluating_2015,
	title = {Evaluating {Geomorphic} {Change} in {Constructed} {Two}-{Stage} {Ditches}},
	volume = {51},
	copyright = {© 2015 American Water Resources Association},
	issn = {1752-1688},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1752-1688.12334},
	doi = {10.1111/1752-1688.12334},
	abstract = {Straight, trapezoidal-shaped surface drainage channels efficiently drain the soil profile, but their deviations from natural fluvial conditions drive the need for frequent maintenance. Ecological and socioeconomic impacts of drainage ditch maintenance activities can be significant, leading to harmful algal blooms and increased sedimentation. We developed a two-stage ditch design that is more consistent with fluvial form and process. The approach has potential to enhance ecological services while meeting drainage needs essential for agricultural production. We studied geomorphic change of the inset channel, benches and banks of seven two-stage ditches in Ohio, Indiana, and Michigan. Three to 10 years after construction, inset channel changes reflected natural adjustments, but not all ditches had reached their quasi-equilibrium state. Ditches had experienced both degradation and aggradation on the benches at a rate of 0.5-13 mm/yr. Aggradation on the benches was not likely to threaten tile drain outlets. Localized scour was observed on the banks at some sites, but at all but one site changes were not statistically significant. Except for the removal of woody vegetation, none of the ditches required routine maintenance since construction. Two-stage ditches can be a stable, viable option for drainage ditch management if designed and installed properly on the landscape.},
	language = {en},
	number = {4},
	urldate = {2019-12-30},
	journal = {JAWRA Journal of the American Water Resources Association},
	author = {D'Ambrosio, Jessica L. and Ward, Andrew D. and Witter, Jonathan D.},
	year = {2015},
	keywords = {agricultural engineering, best management practices, drainage ditch, geomorphology, nonpoint source pollution monitoring, watershed management},
	pages = {910--922},
}

@article{roley_how_2016,
	title = {How cost-effective are cover crops, wetlands, and two-stage ditches for nitrogen removal in the {Mississippi} {River} {Basin}?},
	volume = {15},
	issn = {2212-4284},
	url = {http://www.sciencedirect.com/science/article/pii/S2212428416300445},
	doi = {10.1016/j.wre.2016.06.003},
	abstract = {Excess nitrogen (N) causes numerous water quality problems, and in the upper Mississippi River Basin, much of the excess N results from landscape modifications necessary for row crop agriculture. Several conservation practices reduce N export, but cost estimates for these practices are often lacking, which can inhibit decisions by farmers and policy-makers. Many practices are eligible for cost-share funds from the United States Department of Agriculture (USDA), but these programs do not usually cover the full cost, and so farmers need to be able to approximate their share of costs. In addition, cost estimates may help the USDA to set priorities and make programmatic decisions. We address lack of cost information by estimating the direct implementation costs and USDA program costs for three agricultural conservation practices: wetlands, cover crops, and two-stage ditches, over 10 and 50 year time horizons. We then compare these costs to the N removal effectiveness of each practice, in \$kgN−1 removed. Wetlands were the most cost-effective practice (in \$kgN−1 removed) over both time horizons. Over 50 years, the two-stage ditch ranked second in cost-effectiveness and cover crops were least cost-effective, while over 10 years, cover crops were second and two-stage ditches were least cost-effective. Finally, we note that these practices need not be used in isolation, but can be implemented simultaneously to maximize N removal. Overall, our analysis suggests that careful implementation can cost-effectively mitigate N pollution.},
	language = {en},
	urldate = {2019-12-30},
	journal = {Water Resources and Economics},
	author = {Roley, Sarah S. and Tank, Jennifer L. and Tyndall, John C. and Witter, Jonathan D.},
	month = jul,
	year = {2016},
	keywords = {Conservation practices, Cover crops, Eutrophication, Nutrients, Two-stage ditch, Water quality economics, Wetlands},
	pages = {43--56},
}

@article{vymazal_removal_2018,
	title = {Removal of nutrients, organics and suspended solids in vegetated agricultural drainage ditch},
	volume = {118},
	issn = {0925-8574},
	url = {http://www.sciencedirect.com/science/article/pii/S0925857418301174},
	doi = {10.1016/j.ecoleng.2018.04.013},
	abstract = {Agricultural drainage is significant source of nutrients, which contributes to eutrophication of reservoirs and coastal areas. Constructed wetlands and vegetated ditches are promising techniques used for elimination of nutrients and suspended solids from agricultural drainage. While constructed wetlands have been successfully used for several decades vegetated drainage ditches have been used only recently. The current study presents the results from a two-year monitoring (2015–2016) of a naturally vegetated drainage ditch in the Czech Republic. The drainage ditch was 200 m long with Phragmites australis, Typha latifolia and Glyceria maxima being the dominant macrophytes growing in the ditch. Removal of nitrogen averaged 1070 kg ha−1 yr−1 with 804 kg ha−1 yr−1 being removed through denitrification of nitrate nitrogen. Plant uptake was responsible for 26.3\% of the removed nitrogen. The removal of TP averaged 142 kg ha−1 yr−1 with plant uptake being responsible for 14\% of the removed load. Mean removal of suspended solids amounted 20437 kg TSS ha−1 yr−1. Removal of BOD5 and COD averaged 1500 kg ha−1 yr−1 and 7000 kg ha−1 yr−1, respectively. The removal of nitrogen and organics was strongly dependent on water temperature while removal of phosphorus and suspended solids were temperature-independent. The results of this study revealed that the naturally vegetated drainage ditch has comparable treatment efficiency with constructed wetlands in terms of nutrients, suspended solids and organics.},
	language = {en},
	urldate = {2019-12-30},
	journal = {Ecological Engineering},
	author = {Vymazal, Jan and Březinová, Tereza Dvořáková},
	month = aug,
	year = {2018},
	keywords = {Agricultural drainage, Macrophytes, Nutrients, Suspended solids, Vegetated ditch},
	pages = {97--103},
}

@article{taylor_phosphate_1971,
	title = {Phosphate equilibria on stream sediment and {Soil} in a watershed draining an agricultural region},
	volume = {19},
	url = {https://pubs.acs.org/doi/pdf/10.1021/jf60177a061},
	doi = {10.1021/jf60177a061},
	language = {en},
	number = {5},
	urldate = {2019-12-30},
	journal = {Journal of Agricultural and Food Chemistry},
	author = {Taylor, Alan W. and Kunishi, Harry M.},
	year = {1971},
	pages = {827--831},
}

@article{oliveira_land_2019,
	title = {Land use affects lowland stream ecosystems through dissolved oxygen regimes},
	volume = {9},
	copyright = {2019 The Author(s)},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-019-56046-1},
	doi = {10.1038/s41598-019-56046-1},
	abstract = {The aim of the present study was to assess the impact of surrounding land use on the structure and functioning of lowland stream ecosystems. To this end, five different land use types were selected (forest, extensive grassland, intensive grassland, cropland and wastewater treatment plant) each represented by four replicate streams, in which diel dissolved oxygen concentrations were recorded, sediment and water quality parameters were measured and macroinvertebrate community composition was determined. Chironomus sp., Oligochaeta and Gastropoda dominated the cropland and wastewater treatment plant (WWTP) streams, while Plecoptera and most Trichoptera only occurred in forest and extensive grassland streams. Forest streams communities were related to a high oxygen saturation, a high C/N ratio in the sediment and woody debris and coarse particulate organic matter (CPOM) substrate cover. Macroinvertebrate communities in cropland and WWTP streams were related to a low oxygen saturation in water and sediment and high concentrations of dissolved nitrogen, phosphorus and carbon. It is concluded that land use specific impacts on lowland streams are likely exerted via fine sediment accumulation in deposition zones, affecting oxygen regimes, sediment oxygen demand and stream metabolism, ultimately changing macroinvertebrate community composition. This study supports therefore the importance of including the catchment scale in ecological stream quality assessments, combining structural and functional endpoints.},
	language = {en},
	number = {1},
	urldate = {2019-12-27},
	journal = {Scientific Reports},
	author = {Oliveira, Paula C. dos Reis and Geest, Harm G. van der and Kraak, Michiel H. S. and Verdonschot, Piet F. M.},
	month = dec,
	year = {2019},
	pages = {1--10},
}

@article{michaud_tile_2019-1,
	title = {Tile {Drainage} as a {Hydrologic} {Pathway} for {Phosphorus} {Export} from an {Agricultural} {Subwatershed}},
	volume = {48},
	issn = {0047-2425},
	url = {http://dl.sciencesocieties.org/publications/jeq/articles/48/1/64},
	doi = {10.2134/jeq2018.03.0104},
	language = {en},
	number = {1},
	urldate = {2019-12-27},
	journal = {Journal of Environmental Quality},
	author = {Michaud, Aubert R. and Poirier, Simon-Claude and Whalen, Joann K.},
	year = {2019},
	pages = {64--72},
}

@article{zak_phosphorus_2004,
	title = {Phosphorus retention at the redox interface of peatlands adjacent to surface waters in northeast {Germany}},
	volume = {70},
	issn = {1573-515X},
	url = {10.1007/s10533-003-0895-7},
	doi = {10.1007/s10533-003-0895-7},
	abstract = {It is demanded currently in public discussions to rewet peatlands and re-establish their function as nutrient sinks. But due to high phosphorus (P) concentrations in the pore water of rewetted peatlands (40–420 μM) it is hypothesized that they can act as a surplus P source for adjacent surface waters and consequently support the eutrophication of such waters. Our detailed investigations of processes at the redox interface in four fens with different geochemical character show the dependence of P retention from the chemistry of the pore water. The precipitation of Fe(III) oxyhydroxide led to high retention of phosphorus and other substances such as DOC and sulphate in the eutrophic fens. When molar Fe/P ratios were larger than about 3 the initially high P concentrations in the anaerobic pore water (20–210 μM) decreased to concentrations below 1 μM under aerobic conditions. Thus, after rewetting high pore water concentrations of P do not automatically result in an increased P load to adjacent surface waters compared to pre-rewetting conditions. An enhanced P export to adjacent surface waters from eutrophic fens can be expected when the Fe/P ratio is smaller than 3 in the anaerobic pore water. In our investigations of natural, oligotrophic to mesotrophic fens the precipitation of Fe(III) oxyhydroxide was inhibited by the formation of stable dissolved Fe ∼ humic complexes. P retention in these fens was only related to the DOC concentrations at the redox interface, so that lower DOC concentrations concurred with higher P retention. The P equilibrium concentrations in an aerobic environment can be higher than that of eutrophic fens with Fe/P ratios larger than about 3 in the anaerobic pore water.},
	language = {en},
	number = {3},
	urldate = {2019-08-11},
	journal = {Biogeochemistry},
	author = {Zak, D. and Gelbrecht, J. and Steinberg, C. E. W.},
	month = sep,
	year = {2004},
	keywords = {Fen, Humic substances, Iron, Phosphorus retention, Pore water, Redox interface},
	pages = {357--368},
}

@article{sheaffer_reed_2008,
	title = {Reed {Canarygrass} forage yield and nutrient uptake on a year-round wastewater application site},
	volume = {194},
	copyright = {© 2008 The Authors. Journal compilation © 2008 Blackwell Verlag},
	issn = {1439-037X},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/j.1439-037X.2008.00327.x},
	doi = {10.1111/j.1439-037X.2008.00327.x},
	abstract = {Reed canarygrass (Phalaris arundinacea L.) is often planted at wastewater treatment sites to provide ground cover and remove nutrients. Our overall objective was to determine the forage yield and nutrient uptake under year-round potato wastewater application in northern latitudes. Specifically, we determined the effect of N fertilization rate on forage dry matter yield and N and P uptake by reed canarygrass, and compared the forage yield, persistence and nutrient uptake of reed canarygrass relative to those of orchardgrass (Dactylis glomerata L.), smooth bromegrass (Bromis inermis Leyss), timothy (Phleum pratense L.) and quackgrass [Elytrigia repens (L.) Nevski]. With only wastewater application, reed canarygrass had a forage yield of 5.8 Mg ha−1, with N and P uptake of 113 and 30 kg ha−1, respectively. Forage dry matter yield, N uptake and P uptake increased to 14.5 Mg ha−1, 383 kg ha−1 and 64 kg ha−1, respectively, with an N fertilization rate of 224 kg ha−1. Forage yield and N uptake of reed canarygrass, orchardgrass, timothy and smooth bromegrass were similar and exceeded those of quackgrass. Reed canarygrass P uptake exceeded that of the other grasses. Reed canarygrass was less persistent than quackgrass or smooth bromegrass.},
	language = {en},
	number = {6},
	urldate = {2019-08-11},
	journal = {Journal of Agronomy and Crop Science},
	author = {Sheaffer, C. C. and Rosen, C. J. and Gupta, S. C.},
	year = {2008},
	keywords = {Phalaris arundinaceae, bioremediation, perennial grasses, wastewater application, winter survival},
	pages = {465--469},
}

@article{reddy_phosphorus_1999,
	title = {Phosphorus retention in streams and wetlands: {A} review},
	volume = {29},
	issn = {1064-3389},
	shorttitle = {Phosphorus {Retention} in {Streams} and {Wetlands}},
	url = {10.1080/10643389991259182},
	doi = {10.1080/10643389991259182},
	abstract = {Wetlands and streams buffer the interactions among uplands and adjacent aquatic systems. Phosphorus (P) is often the key nutrient found to be limiting in both estuarine and freshwater ecosystems. As such, the ability of wetlands and streams to retain P is key to determining downstream water quality. This article reviews the processes and factors regulating P retention in streams and wetlands and evaluates selected methodologies used to estimate P retention in these systems. Phosphorus retention mechanisms reviewed include uptake and release by vegetation, periphyton and microorganisms; sorption and exchange reactions with soils and sediments; chemical precipitation in the water column; and sedimentation and entrainment. These mechanisms exemplify the combined biological, physical, and chemical nature of P retention in wetlands and streams. Methodologies used to estimate P retention include empirical input-output analysis and mass balances, and process kinetics applied at various scales, including micro- and mesocosms to full-scale systems. Although complex numerical models are available to estimate P retention and transport, a simple understanding of P retention at the process level is important, but the overall picture provided by mass balance and kinetic evaluations are often more useful in estimating long-term P retention.},
	number = {1},
	urldate = {2019-08-10},
	journal = {Critical Reviews in Environmental Science and Technology},
	author = {Reddy, K. R. and Kadlec, R. H. and Flaig, E. and Gale, P. M.},
	month = jan,
	year = {1999},
	pages = {83--146},
}

@article{schindler_experimental_1974,
	title = {Experimental {Lakes} {Area}: {Whole}-lake experiments in eutrophication},
	volume = {31},
	issn = {0015-296X},
	shorttitle = {Experimental {Lakes} {Area}},
	url = {https://www.nrcresearchpress.com/doi/10.1139/f74-110},
	doi = {10.1139/f74-110},
	abstract = {The following whole-lake experiments are described:Lake 227, fertilized for 5 yr with phosphate and nitrate, has shown an enormous increase in phytoplankton, in spite of low carbon concentrations. The carbon necessary for production of algal blooms was found to invade from the atmosphere.Lake 304, eutrophied by fertilization with phosphorus, nitrogen, and carbon in 1971 and 1972, recovered rapidly when phosphorus fertilization was terminated.Lake 226 was split in half with a curtain. One half was fertilized with carbon and nitrogen and the other was fertilized with phosphorus, carbon, and nitrogen. The half of the lake receiving phosphorus developed an algal bloom and the other half did not.Lake 302, which had carbon, nitrogen, and phosphorus added to the hypolimnion, did not develop algal blooms in summer. Small phytoplankton blooms were found under ice in early December, but all nutrients were efficiently sedimented and unavailable the following year.The above studies illustrate clearly that phosphorus control is an efficient primary step in preventing or checking eutrophication problems.A review of other published and ongoing studies in the Experimental Lakes Area is given, illustrating the role which large-scale experiments can play in interpreting environmental problems.},
	number = {5},
	urldate = {2019-08-10},
	journal = {Journal of the Fisheries Research Board of Canada},
	author = {Schindler, D. W. and Fee, E. J.},
	month = may,
	year = {1974},
	pages = {937--953},
}

@article{richardson_processes_1986,
	title = {Processes controlling movement, storage, and export of phosphorus in a fen peatland},
	volume = {56},
	copyright = {© 1986 by the Ecological Society of America},
	issn = {1557-7015},
	url = {http://esajournals.onlinelibrary.wiley.com/doi/abs/10.2307/1942548},
	doi = {10.2307/1942548},
	abstract = {Field and laboratory studies were conducted to determine the mechanisms controlling P movement, storage, and export from a minerotrophic peatland (fen) in central Michigan that had demonstrated high P removal from nutrient additions. An annual P budget completed for the fen ecosystem revealed that plant uptake requirements were 7—9 kg · ha—1 · yr—1, but 35\% of aboveground P uptake by plants was returned to the peatland surface via litterfall. Permanent storage of organic P in peat ranged between 2 and 5 kg · ha—1 · yr—1 under natural levels of P input. Both microbial uptake and soil exchange capacity controlled the amount of P made available for plant growth. Fertilizer additions of 5.5 kg · ha—1 · yr—1 of P and 17 kg · ha—1 · yr—1 of N in the fen resulted in no significant (P {\textless} .05) increase in growth or nutrient uptake by emergent macrophytes as the litter—microorganism compartment (LMC) retained up to 84\% of the added P in year 1. A doubling of the P fertilization level resulted in an LMC retention of only 57\%. In year 2 the retention of P by the LMC dropped to 67 and 31\% for the two fertilizer levels, respectively. Concurrent with decreases in LMC phosphorus retention were increased peat sorption of P, but plant growth responses and P uptake were negligible. Higher level fertilizer additions of 22 and 55 kg · ha—1 · yr—1 of P and 68 and 170 kg · ha—1 · yr—1 of N applied with minimal water additions resulted in significant (P {\textless} .05) increases in net primary productivity and P storage by Carex spp. Narrow—leaved sedge (Carex lasiocarpa, C. oligosperma, and C. aquatilis) removed as much as 61\% of the P additions in year 1, with the LMC sorbing an additional 22\%. Roots and rhizomes accounted for 81\% of plant P storage in the higher fertilizer treatment, when surface water flow rates were reduced and fertilizer additions were sequestered in the root zone. However, seasonal dieback and leaching of P from aboveground standing plant material on the high fertilizer plots resulted in a fivefold increase of P flux to the water compartment. Microcosm 32P studies indicated that most of the P added to the fen ecosystem was removed from the water column within the 1st h by microorganisms and fine sediments, and that sedge uptake was extremely low even 45 d after addition. Thus plant uptake of P is not a major factor in the rapid removal of low levels of newly added PO4 in the fen. Selective biocide treatments used to separate the P uptake by bacteria and actinomycetes from that of fungi and yeasts in the fen surface water revealed that the latter group of microorganisms was the dominant group responsible for initial P removal. Biological uptake and abiotic sorption of P by the fine sediments in the surface waters were also shown to be of the same order of magnitude, but immobilization of P in the peat soil zone was mainly controlled by chemical sorption. Freezing of peat resulted in P release to the water column upon thawing, but concentrations returned to control levels within 24 h, suggesting minimal ecosystem losses of P in spring runoff. A Freundlich P adsorption maximum of 15 and 38 kg/ha was calculated for a 2 cm and 5 cm depth of peat adsorption, respectively. These soil P adsorption maxima are only 23\% (2 cm) and 60\% (5 cm) of annual wastewater P additions of 64 ± 14 kg · ha—1 · yr—1 and may account for the 26 and 42 kg/ha of P exported from the 19.5—ha test area in the fen during the 4th and 5th yr, respectively, of nutrient additions. Collectively, our field research and microcosm studies on the Houghton Lake fen suggest that soil adsorption and peat accumulation (i.e., phosphorus stored in organic matter) control long—term phosphate sequestration. But microorganisms and small sediments control initial uptake rates, especially during periods of low nutrient concentration and standing surface water. Carex P uptake increases later in the growing season during field fertilization, but algal populations in the fen water respond quickly and absorb significant amounts of P in areas where sewage effluent has been added. Both biotic and abiotic control mechanisms are thus functional in the peatland, and the proportional effect of each on P transfers is dependent on water levels, the amount of available P, fluctuating microorganism populations, seasonal changes in P absorption by macrophytes, and P soil adsorption capacity.},
	language = {en},
	number = {4},
	urldate = {2019-12-03},
	journal = {Ecological Monographs},
	author = {Richardson, Curtis J. and Marshall, Paul E.},
	year = {1986},
	pages = {279--302},
}

@article{richardson_mechanisms_1985,
	title = {Mechanisms controlling phosphorus retention capacity in freshwater wetlands},
	volume = {228},
	issn = {0036-8075, 1095-9203},
	url = {http://www.sciencemag.org/cgi/doi/10.1126/science.228.4706.1424},
	doi = {10.1126/science.228.4706.1424},
	abstract = {Freshwater wetland ecosystems do not effectively conserve phosphorus in the way that terrestrial ecosystems do. The phosphorus retention capacity varies greatly among bogs, fens, and swamps and is concomitant with the amorphous acid oxalate-extractable aluminum and iron content in the soil. However, the phosphorus adsorption potential in wetland ecosystems may be predicted solely from the extractable aluminum content of the soil. Wetlands tested as wastewater filtration systems became phosphorus-saturated in a few years, with the export' of excessive quantities ofphosphate.},
	language = {en},
	number = {4706},
	urldate = {2019-12-04},
	journal = {Science},
	author = {Richardson, C. J.},
	month = jun,
	year = {1985},
	pages = {1424--1427},
}

@article{peiffer_interaction_1999,
	title = {The interaction of natural organic matter with iron in a wetland ({Tennessee} {Park}, {Colorado}) receiving acid mine drainage},
	volume = {5},
	issn = {1573-1421},
	url = {10.1023/A:1009617925959},
	doi = {10.1023/A:1009617925959},
	abstract = {Pore water from a wetland receiving acid mine drainage was studied for its iron and natural organic matter (NOM) geochemistry on three different sampling dates during summer 1994. Samples were obtained using a new sampling technique that is based on screened pipes of varying length (several centimeters), into which dialysis vessels can be placed and that can be screwed together to allow for vertical pore-water sampling. The iron concentration increased with time (through the summer) and had distinct peaks in the subsurface. Iron was mainly in the ferrous form; however, close to the surface, significant amounts of ferric iron (up to 40\% of 2 mmol L-1 total iron concentration) were observed. In all samples studied, iron was strongly associated with NOM. Results from laboratory experiments indicate that the NOM stabilizes the ferric iron as small iron oxide colloids (able to pass a 0.45μm dialysis membrane). We hypothesize that, in the pore water of the wetland, the high NOM concentrations ({\textgreater}100 mg C L-1) allow formation of such colloids at the redoxcline close to the surface and at the contact zone to the adjacent oxic aquifer. Therefore, particle transport along flow paths and resultant export of ferric iron from the wetland into ground water might be possible.},
	language = {en},
	number = {2},
	urldate = {2019-08-11},
	journal = {Aquatic Geochemistry},
	author = {Peiffer, Stefan and Walton-Day, Katherine and Macalady, Donald L.},
	month = sep,
	year = {1999},
	keywords = {acid mine drainage, colloidal iron, ferric iron, ferrous iron, natural organic matter, pore water, wetland},
	pages = {207--223},
}

@article{noe_carbon_2005,
	title = {Carbon, nitrogen, and phosphorus accumulation in floodplains of {Atlantic} {Coastal} {Plain} {Rivers}, {USA}},
	volume = {15},
	copyright = {© 2005 by the Ecological Society of America},
	issn = {1939-5582},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/04-1677},
	doi = {10.1890/04-1677},
	abstract = {Net nutrient accumulation rates were measured in riverine floodplains of the Atlantic Coastal Plain in Virginia, Maryland, and Delaware, USA. The floodplains were located in watersheds with different land use and included two sites on the Chickahominy River (urban), one site on the Mattaponi River (forested), and five sites on the Pocomoke River (agricultural). The Pocomoke River floodplains lie along reaches with natural hydrogeomorphology and on reaches with restricted flooding due to channelization and levees. A network of feldspar clay marker horizons was placed on the sediment surface of each floodplain site 3–6 years prior to sampling. Sediment cores were collected from the material deposited over the feldspar clay pads. This overlying sediment was separated from the clay layer and then dried, weighed, and analyzed for its total carbon (C), nitrogen (N), and phosphorus (P) content. Mean C accumulation rates ranged from 61 to 212 g·m−2·yr−1, N accumulation rates ranged from 3.5 to 13.4 g·m−2·yr−1, and P accumulation rates ranged from 0.2 to 4.1 g·m−2·yr−1 among the eight floodplains. Patterns of intersite variation in mineral sediment and P accumulation rates were similar to each other, as was variation in organic sediment and C and N accumulation rates. The greatest sediment and C, N, and P accumulation rates were observed on Chickahominy River floodplains downstream from the growing metropolitan area of Richmond, Virginia. Nutrient accumulation rates were lowest on Pocomoke River floodplains that have been hydraulically disconnected from the main channel by channelization and levees. Sediment P concentrations and P accumulation rates were much greater on the hydraulically connected floodplain immediately downstream of the limit of channelization and dense chicken agriculture of the upper Pocomoke River watershed. These findings indicate that (1) watershed land use has a large effect on sediment and nutrient retention in floodplains, and (2) limiting the hydraulic connectivity between river channels and floodplains minimizes material retention by floodplains in fluvial hydroscapes.},
	language = {en},
	number = {4},
	urldate = {2019-10-08},
	journal = {Ecological Applications},
	author = {Noe, Gregory B. and Hupp, Cliff R.},
	year = {2005},
	keywords = {carbon, coastal plain, connectivity, floodplain, geomorphology, land use, nitrogen, phosphorus, sediment},
	pages = {1178--1190},
}

@article{noe_retention_2009,
	title = {Retention of riverine sediment and nutrient loads by coastal plain floodplains},
	volume = {12},
	issn = {1435-0629},
	url = {10.1007/s10021-009-9253-5},
	doi = {10.1007/s10021-009-9253-5},
	abstract = {Despite the frequent citation of wetlands as effective regulators of water quality, few quantitative estimates exist for their cumulative retention of the annual river loads of nutrients or sediments. Here we report measurements of sediment accretion and associated carbon, nitrogen, and phosphorus accumulation as sedimentation over feldspar marker horizons placed on floodplains of the non-tidal, freshwater Coastal Plain reaches of seven rivers in the Chesapeake Bay watershed, USA. We then scale these accumulation rates to the entire extent of non-tidal floodplain in the Coastal Plain of each river, defined as riparian area extending from the Fall Line to the upper limit of tidal influence, and compare them to annual river loads. Floodplains accumulated a very large amount of material compared to their annual river loads of sediment (median among rivers = 119\%), nitrogen (24\%), and phosphorus (59\%). Systems with larger floodplain areas and longer floodplain inundation retained greater proportions of riverine loads of nitrogen and phosphorus, but systems with larger riverine loads retained a smaller proportion of that load on floodplains. Although the source and long-term fate of deposited sediment and associated nutrients are uncertain, these fluxes represent the interception of large amounts of material that otherwise could have been exported downstream. Coastal Plain floodplain ecosystems are important regulators of sediment, carbon, and nutrient transport in watersheds of the Chesapeake Bay.},
	language = {en},
	number = {5},
	urldate = {2019-10-08},
	journal = {Ecosystems},
	author = {Noe, Gregory B. and Hupp, Cliff R.},
	month = aug,
	year = {2009},
	keywords = {floodplain, nitrogen, phosphorus, retention, river, sediment, wetland},
	pages = {728--746},
}

@article{noe_hydrogeomorphology_2013,
	title = {Hydrogeomorphology influences soil nitrogen and phosphorus mineralization in floodplain wetlands},
	volume = {16},
	issn = {1435-0629},
	url = {10.1007/s10021-012-9597-0},
	doi = {10.1007/s10021-012-9597-0},
	abstract = {Conceptual models of river–floodplain systems and biogeochemical theory predict that floodplain soil nitrogen (N) and phosphorus (P) mineralization should increase with hydrologic connectivity to the river and thus increase with distance downstream (longitudinal dimension) and in lower geomorphic units within the floodplain (lateral dimension). We measured rates of in situ soil net ammonification, nitrification, N, and P mineralization using monthly incubations of modified resin cores for a year in the forested floodplain wetlands of Difficult Run, a fifth order urban Piedmont river in Virginia, USA. Mineralization rates were then related to potentially controlling ecosystem attributes associated with hydrologic connectivity, soil characteristics, and vegetative inputs. Ammonification and P mineralization were greatest in the wet backswamps, nitrification was greatest in the dry levees, and net N mineralization was greatest in the intermediately wet toe-slopes. Nitrification also was greater in the headwater sites than downstream sites, whereas ammonification was greater in downstream sites. Annual net N mineralization increased with spatial gradients of greater ammonium loading to the soil surface associated with flooding, soil organic and nutrient content, and herbaceous nutrient inputs. Annual net P mineralization was associated negatively with soil pH and coarser soil texture, and positively with ammonium and phosphate loading to the soil surface associated with flooding. Within an intensively sampled low elevation flowpath at one site, sediment deposition during individual incubations stimulated mineralization of N and P. However, the amount of N and P mineralized in soil was substantially less than the amount deposited with sedimentation. In summary, greater inputs of nutrients and water and storage of soil nutrients along gradients of river–floodplain hydrologic connectivity increased floodplain soil nutrient mineralization rates.},
	language = {en},
	number = {1},
	urldate = {2019-10-08},
	journal = {Ecosystems},
	author = {Noe, Gregory B. and Hupp, Cliff R. and Rybicki, Nancy B.},
	month = jan,
	year = {2013},
	keywords = {biogeochemistry, geomorphology, hydrologic connectivity, nutrient, riparian, river},
	pages = {75--94},
}

@article{mahl_two-stage_2015,
	title = {Two-stage ditch floodplains enhance {N}-removal capacity and reduce turbidity and dissolved {P} in agricultural streams},
	volume = {51},
	copyright = {© 2015 American Water Resources Association},
	issn = {1752-1688},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/1752-1688.12340},
	doi = {10.1111/1752-1688.12340},
	abstract = {Two-stage ditches represent an emerging management strategy in artificially drained agricultural landscapes that mimics natural floodplains and has the potential to improve water quality. We assessed the potential for the two-stage ditch to reduce sediment and nutrient export by measuring water column turbidity, nitrate (NO3−), ammonium (NH4+), and soluble reactive phosphorus (SRP) concentrations, and denitrification rates. During 2009-2010, we compared reaches with two-stage floodplains to upstream reaches with conventional trapezoid design in six agricultural streams. At base flow, these short two-stage reaches ({\textless}600 m) reduced SRP concentrations by 3-53\%, but did not significantly reduce NO3− concentrations due to very high NO3− loads. The two-stage also decreased turbidity by 15-82\%, suggesting reduced suspended sediment export during floodplain inundation. Reach-scale N-removal increased 3-24 fold during inundation due to increased bioreactive surface area with high floodplain denitrification rates. Inundation frequency varied with bench height, with lower benches being flooded more frequently, resulting in higher annual N-removal. We also found both soil organic matter and denitrification rates were higher on older floodplains. Finally, influence of the two-stage varied among streams and years due to variation in stream discharge, nutrient loads, and denitrification rates, which should be considered during implementation to optimize potential water quality benefits.},
	language = {en},
	number = {4},
	urldate = {2019-08-10},
	journal = {JAWRA Journal of the American Water Resources Association},
	author = {Mahl, Ursula H. and Tank, Jennifer L. and Roley, Sarah S. and Davis, Robert T.},
	year = {2015},
	keywords = {agricultural stream, best management practices, biogeochemistry, denitrification, nutrients, restoration, turbidity, two-stage ditch},
	pages = {923--940},
}

@article{kinsman-costello_re-flooding_2014,
	title = {Re-flooding a historically drained wetland leads to rapid sediment phosphorus release},
	volume = {17},
	issn = {1435-0629},
	url = {10.1007/s10021-014-9748-6},
	doi = {10.1007/s10021-014-9748-6},
	abstract = {Wetland restoration provides many benefits, but re-flooding historically drained land can have unintended negative consequences, including phosphorus (P) release from sediments. To investigate the effects of re-flooding on P cycling, this study monitored a restoration in Michigan that back-flooded old drainage ditches and re-flooded former wetland soils. Immediately after re-flooding, previously exposed sediments released substantial amounts of P to the water column. Soluble reactive phosphorus (SRP) concentrations in re-flooded areas were as high as 750 μg P l−1. At peak P concentrations, there were about 20 times more SRP and 14 times more total P in the surface water than in the much smaller flooded area that existed before re-flooding. Prolific growth of filamentous algae and duckweed was observed in subsequent summers. Sedimental analyses suggest that most of the P released originated from iron-bound fractions. The highest SRP concentrations occurred during the first year when surface water dissolved oxygen was low ({\textless}5.5 mg l−1). Similarly low oxygen in the second year after flooding was not associated with such high P concentrations. After 1 year postflooding, SRP concentrations remained below 50 μg P l−1 (but still high enough to produce eutrophic conditions) until the end of sampling about 15 months after re-flooding. When re-flooding historically drained soils, managers should consider the potential for sediment P release to jeopardize restoration goals and therefore should incorporate longer term monitoring of water quality into restoration plans. Knowledge of sediment P amounts and forms can indicate the potential for P release to overlying water.},
	language = {en},
	number = {4},
	urldate = {2019-08-10},
	journal = {Ecosystems},
	author = {Kinsman-Costello, Lauren E. and O’Brien, Jonathan and Hamilton, Stephen K.},
	month = jun,
	year = {2014},
	keywords = {internal eutrophication, iron, phosphorus, restoration, sediment, wetland},
	pages = {641--656},
}

@article{kindervater_two-stage_2019,
	title = {Two-stage agricultural ditch sediments act as phosphorus sinks in west {Michigan}},
	copyright = {© 2019 American Water Resources Association},
	issn = {1752-1688},
	url = {http://www.onlinelibrary.wiley.com/doi/abs/10.1111/1752-1688.12763},
	doi = {10.1111/1752-1688.12763},
	abstract = {Phosphorus (P) and sediment inputs from agricultural drainage contribute to the development of hypereutrophic conditions in lakes across the world. Two-stage (2-S) ditches, an agricultural best management practice gaining acceptance in the Midwestern United States, increase floodplain area within drainage ditches to help capture nutrients and sediment. While denitrification has been shown to increase on 2-S benches, less is known about their P retention ability. This study assessed the abiotic and biotic P retention of two separate 2-S ditches compared to their corresponding traditional reaches directly upstream within the Macatawa watershed, located in West Michigan. Soluble reactive P export was significantly reduced in 2-S baseflow of both ditch systems. Equilibrium P concentration values suggest retention of P within the 2-S sediment. P was bound within stable fractions in both 2-S and traditional reaches. An analysis of P stock within the ditches revealed sediment held over 96\% of total P (TP) within each reach compared to {\textless}4\% in bench vegetation and periphyton combined. Turbidity, but not TP, was reduced in one study ditch, whereas TP, but not turbidity, was reduced in the other study ditch. Geomorphic stability may have been responsible for differing P retention between ditches. Ability to retain P appears to be impacted by physical as well as biogeochemical characteristics; hence, structure and age of 2-S reaches influence P retention.},
	language = {en},
	urldate = {2019-08-10},
	journal = {JAWRA Journal of the American Water Resources Association},
	author = {Kindervater, Emily and Steinman, Alan D.},
	year = {2019},
	keywords = {West Michigan, best management practices (BMPs), nonpoint source pollution, phosphorus, sediment, soils, two-stage ditch},
	pages = {1--13},
}

@article{jones_seasonal_2015,
	title = {Seasonal variation in floodplain biogeochemical processing in a restored headwater stream},
	volume = {49},
	issn = {0013-936X},
	url = {10.1021/acs.est.5b02426},
	doi = {10.1021/acs.est.5b02426},
	abstract = {Stream and river restoration activities have recently begun to emphasize the enhancement of biogeochemical processing within river networks through the restoration of river-floodplain connectivity. It is generally accepted that this practice removes pollutants such as nitrogen and phosphorus because the increased contact time of nutrient-rich floodwaters with reactive floodplain sediments. Our study examines this assumption in the floodplain of a recently restored, low-order stream through five seasonal experiments. During each experiment, a floodplain slough was artificially inundated for 3 h. Both the net flux of dissolved nutrients and nitrogen uptake rate were measured during each experiment. The slough was typically a source of dissolved phosphorus and dissolved organic matter, a sink of NO3–, and variable source/sink of ammonium. NO3– uptake rates were relatively high when compared to riverine uptake, especially during the spring and summer experiments. However, when scaled up to the entire 1 km restoration reach with a simple inundation model, less than 0.5–1.5\% of the annual NO3– load would be removed because of the short duration of river-floodplain connectivity. These results suggest that restoring river-floodplain connectivity is not necessarily an appropriate best management practice for nutrient removal in low-order streams with legacy soil nutrients from past agricultural landuse.},
	number = {22},
	urldate = {2019-08-23},
	journal = {Environmental Science \& Technology},
	author = {Jones, C. Nathan and Scott, Durelle T. and Guth, Christopher and Hester, Erich T. and Hession, W. Cully},
	month = nov,
	year = {2015},
	pages = {13190--13198},
}

@article{jarvie_increased_2017,
	title = {Increased soluble phosphorus loads to {Lake} {Erie}: {Unintended} consequences of conservation practices?},
	volume = {46},
	issn = {0047-2425},
	shorttitle = {Increased {Soluble} {Phosphorus} {Loads} to {Lake} {Erie}},
	url = {https://dl.sciencesocieties.org/publications/jeq/abstracts/46/1/123},
	doi = {10.2134/jeq2016.07.0248},
	language = {en},
	number = {1},
	urldate = {2019-08-10},
	journal = {Journal of Environmental Quality},
	author = {Jarvie, Helen P. and Johnson, Laura T. and Sharpley, Andrew N. and Smith, Douglas R. and Baker, David B. and Bruulsema, Tom W. and Confesor, Remegio},
	year = {2017},
	pages = {123--132},
}

@article{hoffmann_phosphorus_2009,
	title = {Phosphorus retention in riparian buffers: {Review} of their efficiency},
	volume = {38},
	issn = {1537-2537},
	shorttitle = {Phosphorus {Retention} in {Riparian} {Buffers}},
	url = {http://dl.sciencesocieties.org/publications/jeq/articles/38/5/1942},
	doi = {10.2134/jeq2008.0087},
	language = {en},
	number = {5},
	urldate = {2019-12-03},
	journal = {Journal of Environmental Quality},
	author = {Hoffmann, Carl Christian and Kjaergaard, Charlotte and Uusi-Kämppä, Jaana and Hansen, Hans Christian Bruun and Kronvang, Brian},
	month = sep,
	year = {2009},
	pages = {1942--1955},
}

@article{gerke_adsorption_1992,
	title = {Adsorption of orthophosphate to humic-{Fe}-complexes and to amorphous {Fe}-oxide},
	volume = {155},
	copyright = {Copyright © 1992 WILEY‐VCH Verlag GmbH \& Co. KGaA, Weinheim},
	issn = {1522-2624},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jpln.19921550313},
	doi = {10.1002/jpln.19921550313},
	abstract = {The adsorption of orthophosphate to humic surfaces was studied in a model experiment. The adsorption maximum of humic substances greatly increased with higher concentrations of organically complexed Fe (III), indicating that orthophosphate was bound to humic surfaces via metal bridges. The molar ratio Padsorbed/Fe was nearly 1 for Fe freshly complexed to humic substances, whereas the ratio for amorphous Fe-oxide was a tenfold lower. An increase in pH from 5.2 to 6.2 lead to an increase of P-adsorption of about 30\% in the case of humic-Fe-surfaces, which could be explained by an increased accessibility of adsorption sites at pH 6.2. The addition of a 0.01 M CaCl2-matrix increased orthophosphate adsorption at pH 6.2 but not at pH 5.2. This could be explained by electrostatic interactions caused by the Ca++ ion.},
	language = {en},
	number = {3},
	urldate = {2019-12-04},
	journal = {Zeitschrift für Pflanzenernährung und Bodenkunde},
	author = {Gerke, Jörg and Hermann, Reinhold},
	year = {1992},
	pages = {233--236},
}

@article{davis_influence_2015,
	title = {The influence of two-stage ditches with constructed floodplains on water column nutrients and sediments in agricultural streams},
	volume = {51},
	copyright = {© 2015 American Water Resources Association},
	issn = {1752-1688},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/1752-1688.12341},
	doi = {10.1111/1752-1688.12341},
	abstract = {The two-stage ditch is a novel management practice originally implemented to increase bank stability through floodplain restoration in channelized agricultural streams. To determine the effects of two-stage construction on sediment and nutrient loads, we monitored turbidity, and also measured total suspended solids (TSS), dissolved inorganic nitrogen (N) species, and phosphorus (P) after two-stage ditch construction in reference and manipulated reaches of four streams. Turbidity decreased during floodplain inundation at all sites, but TSS and P, soluble reactive phosphorus (SRP) and total phosphorus (TP) decreased only in the two-stage ditches with longer duration of inundation. Both TSS and TP were positively correlated within individual streams, but neither were correlated with turbidity. Phosphorus was elevated in the stream to which manure was applied adjacent to the two-stage reach, but not the reference reach, suggesting that landscape nutrient management plans could restrict nutrient transport to the stream, ultimately determining the efficacy of instream management practices. In addition, ammonium and nitrate decreased in two-stage reaches with lower initial N concentrations. Overall, results suggest that turbidity, TSS, and TP were reduced during floodplain inundation, but the two-stage alone may not be effective for managing high inorganic N loads.},
	language = {en},
	number = {4},
	urldate = {2019-08-10},
	journal = {JAWRA Journal of the American Water Resources Association},
	author = {Davis, Robert T. and Tank, Jennifer L. and Mahl, Ursula H. and Winikoff, Sarah G. and Roley, Sarah S.},
	year = {2015},
	keywords = {agriculture, nutrients, sediment, streams, turbidity, two-stage ditch, water quality},
	pages = {941--955},
}

@article{aldous_hydrologic_2005,
	title = {Hydrologic regime controls soil phosphorus fluxes in restoration and undisturbed wetlands},
	volume = {13},
	issn = {1526-100X},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/j.1526-100X.2005.00043.x},
	doi = {10.1111/j.1526-100X.2005.00043.x},
	abstract = {Many wetland restoration projects occur on former agricultural soils that have a history of disturbance and fertilization, making them prone to phosphorus (P) release upon flooding. To study the relationship between P release and hydrologic regime, we collected soil cores from three restoration wetlands and three undisturbed wetlands around Upper Klamath Lake in southern Oregon, U.S.A. Soil cores were subjected to one of three hydrologic regimes—flooded, moist, and dry—for 7.5 weeks, and P fluxes were measured upon reflooding. Soils from restoration wetlands released P upon reflooding regardless of the hydrologic regime, with the greatest releases coming from soils that had been flooded or dried. Undisturbed wetland soils released P only after drying. Patterns in P release can be explained by a combination of physical and biological processes, including the release of iron-bound P due to anoxia in the flooded treatment and the mineralization of organic P under aerobic conditions in the dry treatment. Higher rates of soil P release from restoration wetland soils, particularly under flooded conditions, were associated with higher total P concentrations compared with undisturbed wetland soils. We conclude that maintaining moist soil is the means to minimize P release from recently flooded wetland soils. Alternatively, prolonged flooding provides a means of liberating excess labile P from former agricultural soils while minimizing continued organic P mineralization and soil subsidence.},
	language = {en},
	number = {2},
	urldate = {2019-12-04},
	journal = {Restoration Ecology},
	author = {Aldous, Allison and McCormick, Paul and Ferguson, Chad and Graham, Sean and Craft, Chris},
	year = {2005},
	keywords = {Oregon, Upper Klamath Basin, hydrologic regime, lake eutrophication, phosphorus, soils, wetland restoration},
	pages = {341--347},
}

@article{appling_reducing_2015,
	title = {Reducing bias and quantifying uncertainty in watershed flux estimates: the {R} package loadflex},
	volume = {6},
	copyright = {Copyright: © 2015 Appling et al.},
	issn = {2150-8925},
	shorttitle = {Reducing bias and quantifying uncertainty in watershed flux estimates},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/ES14-00517.1},
	doi = {10.1890/ES14-00517.1},
	abstract = {Many ecological insights into the function of rivers and watersheds emerge from quantifying the flux of solutes or suspended materials in rivers. Numerous methods for flux estimation have been described, and each has its strengths and weaknesses. Currently, the largest practical challenges in flux estimation are to select among these methods and to implement or apply whichever method is chosen. To ease this process of method selection and application, we have written an R software package called loadflex that implements several of the most popular methods for flux estimation, including regressions, interpolations, and the special case of interpolation known as the period-weighted approach. Our package also implements a lesser-known and empirically promising approach called the “composite method,” to which we have added an algorithm for estimating prediction uncertainty. Here we describe the structure and key features of loadflex, with a special emphasis on the rationale and details of our composite method implementation. We then demonstrate the use of loadflex by fitting four different models to nitrate data from the Lamprey River in southeastern New Hampshire, where two large floods in 2006–2007 are hypothesized to have driven a long-term shift in nitrate concentrations and fluxes from the watershed. The models each give believable estimates, and yet they yield different answers for whether and how the floods altered nitrate loads. In general, the best modeling approach for each new dataset will depend on the specific site and solute of interest, and researchers need to make an informed choice among the many possible models. Our package addresses this need by making it simple to apply and compare multiple load estimation models, ultimately allowing researchers to estimate riverine concentrations and fluxes with greater ease and accuracy.},
	language = {en},
	number = {12},
	urldate = {2019-12-12},
	journal = {Ecosphere},
	author = {Appling, Alison P. and Leon, Miguel C. and McDowell, William H.},
	year = {2015},
	keywords = {R, composite method, concentration, constituent, flux, nutrient, software, solute load models, uncertainty, watershed},
	pages = {1--25},
}

@article{choquette_tracking_2019,
	title = {Tracking changes in nutrient delivery to western {Lake} {Erie}: {Approaches} to compensate for variability and trends in streamflow},
	volume = {45},
	issn = {0380-1330},
	shorttitle = {Tracking changes in nutrient delivery to western {Lake} {Erie}},
	url = {http://www.sciencedirect.com/science/article/pii/S0380133018302235},
	doi = {10.1016/j.jglr.2018.11.012},
	abstract = {Tracking changes in stream nutrient inputs to Lake Erie over multidecadal time scales depends on the use of statistical methods that can remove the influence of year-to-year variability of streamflow but also explicitly consider the influence of long-term trends in streamflow. The methods introduced in this paper include an extended version of Weighted Regressions on Time, Discharge, and Season (WRTDS) modeling that explicitly considers nonstationary streamflow by incorporating information on changes in the frequency distribution of daily measured streamflow (discharge) over time. Soluble reactive phosphorus (SRP) trends in annual flow-normalized fluxes (loads) at five long-term monitoring sites in the western Lake Erie drainage basin show increases of 109 to 322\% over the period 1995 to 2015. About one-third of the increase appears attributable to increasing discharge trends, while the remaining two-thirds appears to be driven by changes in concentration versus discharge relationships reflecting higher concentrations for any given discharge during recent years. Trends in total phosphorus and three nitrogen parameters (total nitrogen, nitrate-nitrite, and total Kjeldahl nitrogen) at the 10 sites analyzed were much less pronounced, and commonly show decreases in concentration-discharge relationships accompanied by increases in discharge, resulting in little net change in total flux. Trends in monthly SRP fluxes and discharge, dissolved versus particulate fractions of nutrients, and N:P flux ratios were also evaluated. The methods described here provide tools to more clearly discern the effectiveness of nutrient-control strategies and can serve as ongoing measures of progress, or lack of progress, towards nutrient-reduction goals.},
	language = {en},
	number = {1},
	urldate = {2019-12-11},
	journal = {Journal of Great Lakes Research},
	author = {Choquette, A. F. and Hirsch, R. M. and Murphy, J. C. and Johnson, L. T. and Confesor, R. B.},
	month = feb,
	year = {2019},
	keywords = {Lake Erie, Nitrogen, Nutrient, Phosphorus, Streamflow, Trend},
	pages = {21--39},
}

@article{cunha_agriculture_nodate,
	title = {Agriculture influences ammonium and soluble reactive phosphorus retention in {South}-{American} headwater streams},
	volume = {n/a},
	copyright = {This article is protected by copyright. All rights reserved.},
	issn = {1936-0592},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/eco.2184},
	doi = {10.1002/eco.2184},
	abstract = {Agricultural activities can affect the delivery of nutrients to streams, riparian canopy cover, and the capacity of aquatic systems to process nutrients and sediments. There are few measures of nutrient uptake and metabolism from tropical or sub-tropical streams in general, and even fewer from tropical regions of South America. We examined ammonium (NH4+) and soluble reactive phosphorus (SRP) retention in streams in Brazil and Argentina. We selected twelve streams with relatively little or extensive agricultural activity and conducted whole-stream nutrient additions and measurements of Gross Primary Production (GPP) and Ecosystem Respiration (ER). We used multiple linear regression to determine potential drivers of nutrient uptake metrics across the streams. Nutrient concentrations and retention differed significantly between land use categories. Both NH4+ and SRP concentrations were higher in the agricultural sites (means of 161 and 495 μg L-1, respectively), whereas metabolic rates were slower and transient storage smaller. Our analysis indicated that agriculture increased ambient uptake lengths and decreased uptake velocities. The regression models revealed that ambient SRP had a positive effect on NH4+ uptake and vice-versa, suggesting strong stoichiometric controls. Drivers for nutrient uptake in streams with low-intensity agriculture also included canopy cover, temperature, and ER rates. Nutrient assimilation in agricultural sites was influenced by a higher number of variables (GPP for SRP, and discharge, and transient storage for both nutrients). Our results indicate agricultural activity changes both the magnitude of in-stream nutrient uptake and the mechanisms that control its variation, with important implications for South American streams under agricultural intensification.},
	language = {en},
	number = {n/a},
	urldate = {2019-12-10},
	journal = {Ecohydrology},
	author = {Cunha, Davi Gasparini Fernandes and Finkler, Nícolas Reinaldo and Gómez, Nora and Cochero, Joaquín and Donadelli, Jorge Luis and Saltarelli, Wesley Aparecido and Calijuri, Maria do Carmo and Miwa, Adriana Cristina Poli and Tromboni, Flavia and Dodds, Walter K. and Boëchat, Iola Gonçalves and Gücker, Björn and Thomas, Steven A.},
	keywords = {Agricultural watersheds, Aquatic metabolism, Low-order streams, Macronutrient assimilation, Nitrogen, Phosphorus},
	pages = {e2184},
}

@article{kaspar_small_2001,
	title = {Small grain cover crops and wheel traffic effects on infiltration, runoff, and erosion},
	volume = {56},
	issn = {0022-4561, 1941-3300},
	url = {http://www.jswconline.org/content/56/2/160},
	abstract = {ABSTRACT:
Oat and rye cover crops have the potential to reduce erosion when following soybean crops in Iowa. Oat and rye cover crops were overseeded into no-till soybeans in August of 1995, 1996 and 1997 on a sloping site. Infiltration, runoff, and interrill erosion were measured in April of 1996, 1997, and 1998 using an oscillating sprinkler bead rainfall simulator that applied water at approximately 125 mm hr−1. Rill erosion was measured by making flow additions to the upslope end of plots. All measurements were made concurrently on tracked and untracked interrows. Cover crops had no effect on infiltration and erosion in 1996 In 1997, both oat and rye cover crops reduced interrill erosion, but in 1998 only rye increased infiltration and reduced interrill erosion and runoff Untracked interrows had less interrill erosion and runoff, and more infiltration than tracked interrows. In 1997 and 1998, both oat and rye cover crops reduced rill erosion, but wheel traffic had no measurable effect on rill erosion.},
	language = {en},
	number = {2},
	urldate = {2019-12-07},
	journal = {Journal of Soil and Water Conservation},
	author = {Kaspar, T. C. and Radke, J. K. and Laflen, J. M.},
	month = apr,
	year = {2001},
	pages = {160--164},
}

@article{dodds_role_2003,
	title = {The role of periphyton in phosphorus retention in shallow freshwater aquatic systems},
	volume = {39},
	issn = {0022-3646},
	url = {http://onlinelibrary.wiley.com/doi/full/10.1046/j.1529-8817.2003.02081.x},
	doi = {10.1046/j.1529-8817.2003.02081.x},
	abstract = {Eutrophication caused by phosphorus (P) leads to water quality problems in aquatic systems, particularly freshwaters, worldwide. Processing of nutrients in shallow habitats removes P from water naturally and periphyton influences P removal from the water column in flowing waters and wetlands. Periphyton plays several roles in removing P from the water column, including P uptake and deposition, filtering particulate P from the water, and attenuating flow, which decreases advective transport of particulate and dissolved P from sediments. Furthermore, periphyton photosynthesis locally increases pH by up to 1 unit, which can lead to increased precipitation of calcium phosphate, concurrent deposition of carbonate-phosphate complexes, and long-term burial of P. Actively photosynthesizing periphyton can cause super-saturated O2 concentrations near the sediment surface encouraging deposition of metal phosphates. However, anoxia associated with periphyton respiration at night may offset this effect. Linking the small-scale functional role of periphyton to ecosystem-level P retention will require more detailed studies in a variety of ecosystems or large mesocosms. A case study from the Everglades illustrates the importance of considering the role of periphyton in P removal from wetlands. In general, periphyton tends to increase P retention and deposition. In pilot-scale constructed periphyton-dominated wetlands in South Florida, about half of the inflowing total P was removed.},
	number = {5},
	urldate = {2019-12-06},
	journal = {Journal of Phycology},
	author = {Dodds, Walter K.},
	month = oct,
	year = {2003},
	keywords = {eutrophication, microalgae, microphytobenthos, periphyton, phosphate, phosphorus, tertiary treatment, water quality},
	pages = {840--849},
}

@article{cohen_diel_2013,
	title = {Diel phosphorus variation and the stoichiometry of ecosystem metabolism in a large spring-fed river},
	volume = {83},
	copyright = {© 2013 by the Ecological Society of America},
	issn = {1557-7015},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/12-1497.1},
	doi = {10.1890/12-1497.1},
	abstract = {Elemental cycles are coupled directly and indirectly to ecosystem metabolism at multiple time scales. Understanding coupling in lotic ecosystems has recently advanced through simultaneous high-frequency measurements of multiple solutes. Using hourly in situ measurements of soluble reactive phosphorus (SRP), specific conductance (SpC), and dissolved oxygen (DO), we estimated phosphorus (P) retention pathways and dynamics in a large (discharge, Q ≈ 7.5 m3/s) spring-fed river (Ichetucknee River, Florida, USA). Across eight multi-day deployments, highly regular diel SRP variation of 3–9 μg P/L (mean ∼50 μg P/L) was strongly correlated with DO variation, suggesting photosynthetic control directly via assimilation, and/or indirectly via geochemical reactions. Consistent afternoon SRP maxima and midnight minima suggest peak removal lags gross primary production (GPP) by ∼8 hours. Two overlapping processes were evident, one dominant with maximum removal near midnight, the other smaller with maximum removal near midday. Hourly [Ca] measurements during three 24-hour deployments showed consistent afternoon minima, suggesting that calcite precipitates as GPP increases pH and mineral saturation state. Resulting P co-precipitation was modeled using SpC as a [Ca] proxy, yielding a diel P signal adjusted for the primary geochemical retention pathway. P assimilation, the dominant diel signal, was computed by interpolating between daily concentration maxima, both with and without geochemical adjustment, and converting concentration deficits to fluxes using discharge and benthic area. Adjusting for calcite co-precipitation yielded assimilation rates (13.7 ± 5.8 mg P·m−2·d−1) strongly correlated with GPP, accounting for 72\% ± 9\% of gross removal, and ecosystem C:P stoichiometry (466 [± 12]:1) consistent with dominant vascular autotrophs (478 [± 24]:1). Without adjusting for co-precipitation, covariance with GPP was weaker, and C:P implausibly high. Consistent downstream P accumulation, likely from P-rich porewater seepage, varied across deployments (3–22\% of total flux) and co-varied with discharge and respiration. Asynchronous N and P assimilation may arise from differential timing of protein and ribosome production, with the latter requiring maximal carbohydrate stores and minimal photolytic interference. This study demonstrates direct and indirect coupling of biological, hydrological, and geochemical processes and the utility of high-resolution time series of multiple solutes for understanding these linkages.},
	language = {en},
	number = {2},
	urldate = {2019-12-06},
	journal = {Ecological Monographs},
	author = {Cohen, Matthew J. and Kurz, Marie J. and Heffernan, James B. and Martin, Jonathan B. and Douglass, Rachel L. and Foster, Chad R. and Thomas, Ray G.},
	year = {2013},
	keywords = {coupled elemental cycles, ecosystem stoichiometry, metabolism, nutrient assimilation, sensors, springs},
	pages = {155--176},
}

@article{trentman_quantifying_2015,
	title = {Quantifying ambient nitrogen uptake and functional relationships of uptake versus concentration in streams: a comparison of stable isotope, pulse, and plateau approaches},
	volume = {125},
	issn = {1573-515X},
	shorttitle = {Quantifying ambient nitrogen uptake and functional relationships of uptake versus concentration in streams},
	url = {10.1007/s10533-015-0112-5},
	doi = {10.1007/s10533-015-0112-5},
	abstract = {Nutrient releases and spiraling metrics are frequently used to quantify the downstream transport of nutrients and to better understand the effects of anthropogenic inputs to downstream waters. Ambient uptake rates in streams can be measured through stable isotope enrichments, while pulse and plateau additions can estimate such rates via extrapolation and modeling techniques, respectively. Data from these releases can be used to estimate ambient uptake rates from nutrient additions and possibly determine the functional relationships between nutrient concentrations and uptake rates. Here, we compared estimated ambient rates calculated from established pulse and plateau approaches, results obtained from new modeling approaches, and rates at ambient concentrations from stable isotope enrichments. Comparative releases of NH4Cl and 15NH4Cl were conducted in four experimental reaches across the grassland Kings Creek and urban Campus Creek, KS. Nutrient uptake was predominantly linear with increasing ammonium. Estimated ambient uptake rates varied among sites, release methods, and data analysis approaches. However, plateau ambient rates from new modeling approaches matched closely with measured ambient rates from isotope enrichments at three sites, suggesting that modeled plateau data may be best for a first look at determining nutrient uptake rates at an individual site. Limitations and benefits of each approach vary; however, baseflow discharge may be a key driver when choosing a method. If possible, multiple methods should be attempted at each location and under each novel set of conditions to determine the best approach prior to designing and implementing a more extensive series of measurements.},
	language = {en},
	number = {1},
	urldate = {2019-12-06},
	journal = {Biogeochemistry},
	author = {Trentman, Matt T. and Dodds, Walter K. and Fencl, Jane S. and Gerber, Kayla and Guarneri, Jay and Hitchman, Sean M. and Peterson, Zach and Rüegg, Janine},
	month = aug,
	year = {2015},
	keywords = {Ammonium uptake, Nutrient spiraling, TASCC, Uptake length},
	pages = {65--79},
}

@article{haggard_nutrient_2005,
	title = {Nutrient retention in a point-source-enriched stream},
	volume = {24},
	issn = {0887-3593},
	url = {http://www.journals.uchicago.edu/doi/abs/10.1899/0887-3593(2005)024%3C0029%3ANRIAPS%3E2.0.CO%3B2},
	doi = {10.1899/0887-3593(2005)024<0029:NRIAPS>2.0.CO;2},
	abstract = {The capacity of a 3rd-order Ozark Plateau stream (Arkansas, USA) to take up (or remove) nutrient inputs from a rural wastewater treatment plant (WWTP) was examined using nutrient spiraling methods. Short-term nutrient additions often are used to assess nutrient uptake length, where an exponential decline in the concentration of the added nutrient reflects gross nutrient uptake. We applied this quantitative framework using WWTP effluent as a stream nutrient addition, and estimated net nutrient uptake length (Snet), mass transfer coefficient (vf-net), and uptake rate (Unet) in Columbia Hollow, Arkansas. Water samples were collected at a reference site upstream of the WWTP input and at 6 sites downstream of the WWTP (0.3–2.7 km). Input from the WWTP significantly increased discharge, temperature, conductivity, soluble reactive P (SRP), and NH4-N, and decreased pH and NO3-N 0.3 km downstream from the point source. When P additions from the WWTP were low, stored SRP was released from the stream reach to maintain high water-column concentrations. Dissolved inorganic N was not retained in Columbia Hollow. Most or all of the NH4-N added from the point source was converted to NO3-N, resulting in net nitrification rates of 7 to 31 g NO3-N m−2 d−1. The relationship between dilution-corrected concentrations and distance from the WWTP input indicated no significant nutrient retention, or that several stream kilometers were required before N and P were taken up. Unet typically was {\textgreater}7- to 10-fold higher and vf-net estimates were 10- to 100-fold lower than values reported for undisturbed streams, indicating low relative nutrient demand. Rather than acting as a nutrient sink, Columbia Hollow appeared to be acting as a short-term storage zone for P and a transformer of N. Thus, the effect of this rural WWTP on the stream was profound, distorting N and P cycling in Columbia Hollow.},
	number = {1},
	urldate = {2019-12-06},
	journal = {Journal of the North American Benthological Society},
	author = {Haggard, Brian E. and Stanley, Emily H. and Storm, Daniel E.},
	month = mar,
	year = {2005},
	pages = {29--47},
}

@article{reddy_phosphorus_1998,
	title = {Phosphorus {Sorption} {Capacities} of {Wetland} {Soils} and {Stream} {Sediments} {Impacted} by {Dairy} {Effluent}},
	volume = {27},
	issn = {0047-2425},
	url = {http://dl.sciencesocieties.org/publications/jeq/abstracts/27/2/JEQ0270020438},
	doi = {10.2134/jeq1998.00472425002700020027x},
	language = {en},
	number = {2},
	urldate = {2019-12-06},
	journal = {Journal of Environmental Quality},
	author = {Reddy, K. R. and O Connor, G. A. and Gale, P. M.},
	year = {1998},
	pages = {438--4473},
}

@article{dunne_biogeochemical_2006,
	title = {Biogeochemical indices of phosphorus retention and release by wetland soils and adjacent stream sediments},
	volume = {26},
	issn = {0277-5212, 1943-6246},
	url = {http://link.springer.com/article/10.1672/0277-5212(2006)26[1026:BIOPRA]2.0.CO;2},
	doi = {10.1672/0277-5212(2006)26[1026:BIOPRA]2.0.CO;2},
	abstract = {Eutrophication is still a water quality problem within many watersheds. The Lake Okeechobee Basin, Florida, USA, like many watersheds is impacted by eutrophication caused by excess phosphorus (P). To...},
	language = {en},
	number = {4},
	urldate = {2019-12-06},
	journal = {Wetlands},
	author = {Dunne, Ed J. and Reddy, Ramesh and Clark, Mark W.},
	month = dec,
	year = {2006},
	pages = {1026--1041},
}

@article{gerard_clay_2016,
	title = {Clay minerals, iron/aluminum oxides, and their contribution to phosphate sorption in soils — {A} myth revisited},
	volume = {262},
	issn = {0016-7061},
	url = {http://www.sciencedirect.com/science/article/pii/S0016706115300653},
	doi = {10.1016/j.geoderma.2015.08.036},
	abstract = {There is a general consensus that adsorption/desorption (i.e. sorption) is the major process controlling dissolved PO4. However, many uncertainties exist with respect to PO4 sorption capacity and properties of clay minerals as compared to Fe/Al oxides. I reviewed experimental studies performed over a time period of 70years in an attempt to rationalize this knowledge. I found that the binding capacity of clay minerals may be close to or even higher than that of Fe/Al oxides, depending on the specific surface area of these soil constituents. I also found that the pH-dependency of PO4 sorption on clay minerals can differ greatly from that on Fe/Al oxides depending on PO4 loading. Surface reactions occurring at structural Al sites of clay minerals appeared to consistently control sorption at low PO4 concentrations. The analysis indicates that different sorption sites such as structural Fe sites and/or other processes such as the penetration of PO4 into amorphous regions of the mineral are more effective at controlling PO4 sorption at high concentrations. The implications of these findings in soil and rhizosphere are discussed. The possible contributions of kaolinite and goethite to PO4 sorption in a clayed ferralitic soil were estimated. Results suggest that in most soils clay minerals should be considered per se as important PO4-binding constituents, possibly outcompeting Fe/Al oxides.},
	language = {en},
	urldate = {2019-12-05},
	journal = {Geoderma},
	author = {Gérard, Frédéric},
	month = jan,
	year = {2016},
	keywords = {Gibbsite, Goethite, Illite, Kaolinite, Montmorillonite, Phosphorus},
	pages = {213--226},
}

@article{edzwald_phosphate_1976,
	title = {Phosphate adsorption reactions with clay minerals},
	volume = {10},
	issn = {0013-936X},
	url = {10.1021/es60116a001},
	doi = {10.1021/es60116a001},
	number = {5},
	urldate = {2019-12-05},
	journal = {Environmental Science \& Technology},
	author = {Edzwald, James K. and Toensing, Donald C. and Leung, Michael Chi-Yew.},
	month = may,
	year = {1976},
	pages = {485--490},
}

@article{sunohara_long-term_2015,
	title = {Long-{Term} {Observations} of {Nitrogen} and {Phosphorus} {Export} in {Paired}-{Agricultural} {Watersheds} under {Controlled} and {Conventional} {Tile} {Drainage}},
	volume = {44},
	issn = {0047-2425},
	url = {http://dl.sciencesocieties.org/publications/jeq/abstracts/44/5/1589},
	doi = {10.2134/jeq2015.01.0008},
	language = {en},
	number = {5},
	urldate = {2019-12-05},
	journal = {Journal of Environmental Quality},
	author = {Sunohara, M. D. and Gottschall, N. and Wilkes, G. and Craiovan, E. and Topp, E. and Que, Z. and Seidou, O. and Frey, S. K. and Lapen, D. R.},
	year = {2015},
	pages = {1589--1604},
}

@article{davis_uptake_1983,
	title = {Uptake and release of nutrients by living and decomposing {Typha} glauca godr. tissues at {Eagle} {Lake}, {Iowa}},
	volume = {16},
	issn = {0304-3770},
	url = {http://www.sciencedirect.com/science/article/pii/0304377083900530},
	doi = {10.1016/0304-3770(83)90053-0},
	abstract = {Uptake and release of nitrogen, phosphorus, potassium, calcium, and sodium from living above-ground and below-ground tissues and from decomposing litter of Typha glauca Godr. were studied at Eagle Lake, IA, during 1976. All nutrients were accumulated rapidly by shoots in the spring. Some of the nitrogen and phosphorus came from belowground storage; but potassium, calcium, and sodium were extracted entirely from the soil. Nutrients were immobilized in shoot tissues for different periods of time. Potassium content declined as rapidly as it had accumulated, and there was no evidence of belowground storage. Nitrogen and phosphorus content also declined, though not as rapidly. Approximately 45\% of the nitrogen and phosphorus lost from the shoots was translocated to the rhizomes and stored. Calcium and sodium were conserved in shoot tissues until the shoots died. In the decomposing litter, potassium and sodium content declined, phosphorus and calcium content remained relatively constant, but nitrogen content increased. Over the full year of production and decomposition, this Typha glauca stand accumulated calcium and nitrogen, maintained phosphorus levels, and lost potassium and sodium.},
	language = {en},
	number = {1},
	urldate = {2019-12-05},
	journal = {Aquatic Botany},
	author = {Davis, Craig B. and van der Valk, A. G.},
	month = may,
	year = {1983},
	pages = {75--89},
}

@article{scalenghe_effect_2002,
	title = {The effect of reducing conditions on the solubility of phosphorus in a diverse range of {European} agricultural soils},
	volume = {53},
	issn = {1365-2389},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-2389.2002.00462.x},
	doi = {10.1046/j.1365-2389.2002.00462.x},
	abstract = {The effects of reducing conditions on solubility of phosphorus (P) can directly influence water quality. The release of P is enhanced although the P is not directly involved in reduction processes. We here compare the responses to flooding of 12 overfertilized agricultural soils in widely varying pedological and management regimes, belonging to seven World Reference Base groups. The redox potential initially ranged from 305 to 515 mV and decreased to −157 to −195 mV within 32 days. The onset of reducing conditions led to an increase in the concentration of soluble P. The maximum rate of solubilization occurred within 1–3 weeks under reducing conditions, and the steady-state concentrations of P never exceeded 200 μmol dm−3. Four stages in the development of the reduction process are identified, and a simple empirical model describes the change in concentrations of soluble P. The potential of P release under reduction is positively correlated with the soil saturation with P. Flooding over a few weeks triggered the release of large amounts of P. Constant pe + pH is related to constant concentration of molybdate-reactive P, suggesting that soluble P is effectively buffered so that P will be immobilized. In general the solubilization of P under reducing conditions is likely to be aggravated by the increased soil P status that has resulted from overfertilization of agricultural land with P. These findings bear on the establishment and long-term effectiveness of riparian buffer zones where phosphorus is likely to accumulate by the interception of drainage.},
	language = {en},
	number = {3},
	urldate = {2019-12-04},
	journal = {European Journal of Soil Science},
	author = {Scalenghe, R. and Edwards, A. C. and Marsan, F. Ajmone and Barberis, E.},
	year = {2002},
	pages = {439--447},
}

@article{kronvang_sediment_2009,
	title = {Sediment deposition and net phosphorus retention in a hydraulically restored lowland river floodplain in {Denmark}: combining field and laboratory experiments},
	volume = {60},
	issn = {1448-6059},
	shorttitle = {Sediment deposition and net phosphorus retention in a hydraulically restored lowland river floodplain in {Denmark}},
	url = {http://www.publish.csiro.au/mf/MF08066},
	doi = {10.1071/MF08066},
	abstract = {Restoration of river systems allowing the transformation of former drained and dry riparian areas into riparian wetlands will increase the overbank storage of sediment and sediment-associated phosphorus (P). Wetland restoration is therefore a cost-effective mitigation measure to reduce the sediment and nutrient transport to river systems. The studied floodplain of the River Odense was restored in 2003 by remeandering the river channel along a 6-km reach. The restoration project involved 78 ha of riparian areas that were transformed from mainly arable land to extensive grassland and wetlands. The aim of the study was to quantify and model sediment and particulate P deposition on restored river floodplains. The present study suggests that during a 47-day flooding period, the river floodplain is able to retain 9–14.8\% of the sediment and 1.1–3.7\% of the particulate P transported in the river. Incubation experiments further showed that a maximum of 11–25\% of the deposited phosphorus can be released as dissolved inorganic phosphorus following deposition. The results from the best deposition model (R2 = 0.42 for sediment and R2 = 0.44 for particulate P) show that work should be done to further improve the performance of these models.},
	language = {en},
	number = {7},
	urldate = {2019-12-04},
	journal = {Marine and Freshwater Research},
	author = {Kronvang, Brian and Hoffmann, Carl C. and Dröge, Rianne},
	month = aug,
	year = {2009},
	pages = {638--646},
}

@article{dolan_phosphorus_1981,
	title = {Phosphorus {Dynamics} of a {Florida} {Freshwater} {Marsh} {Receiving} {Treated} {Wastewater}},
	volume = {18},
	issn = {0021-8901},
	url = {www.jstor.org/stable/2402490},
	doi = {10.2307/2402490},
	abstract = {(1) A study was made of the effect of secondarily treated effluent on the phosphorus budget of a central Florida freshwater marsh. The marsh was chiefly composed of Sagittaria lancifolia. Pontederia cordata. Panicum spp. and Hibiscus sp. Three 2000 m\${\textasciicircum}2\$ plots received effluent at the rates of 1 3. 3.8 and 10.2 cm wk\${\textasciicircum}\{-1\}\$, while a fourth 2000 m\${\textasciicircum}2\$ plot was a control plot which received 3.8 cm wk\${\textasciicircum}\{-1\}\$ of freshwater. (2) In the first year the plot receiving the high rate of effluent showed increased net production of plant shoots, increased litter production, increased root and rhizome production and higher phosphorus concentrations in living and dead plant tissue compared with the control plot. (3) Effluent treatments did not significantly increase the phosphorus concentrations measured in the groundwater draining from the experimental plots. All the wells within the effluent plots had phosphorus concentrations c. 97\% less than the phosphorus concentration of the applied effluent. (4) Phosphorus budgets were constructed for the control plot and the plot receiving the high effluent treatment. Over the course of the study 38.03 g P m\${\textasciicircum}\{-2\}\$ were applied to the high effluent plot. Of the total input 26.31, 8.81 and 1.97 g P m\${\textasciicircum}\{-2\}\$ were stored in the soil, roots and rhizomes, and litter respectively. Outflow of phosphorus from the plot amounted to only 0.94 g P m\${\textasciicircum}\{-2\}\$ The freshwater control plot received a total of 0.38 g P m\${\textasciicircum}\{-2\}\$ Storage in the litter accounted for 0.21 g P m\${\textasciicircum}\{-2\}\$ and outflow accounted for the remaining 0.17 g P m\${\textasciicircum}\{-2\}\$ There was no evidence of a spring flush of phosphorus from either the control or effluent plot. (5) The marsh successfully removed phosphorus from the effluent during the first year of application. It was concluded that long-term use of the marsh for phosphorus removal may be contingent upon the phosphorus adsorption capacity of the soil and the rate of peat production.},
	number = {1},
	urldate = {2019-12-04},
	journal = {Journal of Applied Ecology},
	author = {Dolan, Thomas J. and Bayley, Suzanne E. and Zoltek, John and Hermann, Albert J.},
	year = {1981},
	pages = {205--219},
}

@article{turner_carbon_1993,
	title = {Carbon, nitrogen, and phosphorus leaching rates from {Spartina} alterniflora salt marshes},
	volume = {92},
	issn = {0171-8630, 1616-1599},
	url = {http://www.int-res.com/articles/meps/92/m092p135.pdf},
	doi = {10.3354/meps092135},
	abstract = {Annual carbon, nitrogen, and phosphorus leachate rates from live Spartina alterniflora Loisel in a Louisiana (USA) salt marsh were estimated to be 200, 14, and 3 g m-2, respectively, and to peak in summer and higher salinit{\textasciitilde}esL. eachate losses of P, N and C are equivalent to a turnover of live plant tissues of 10, 17 and 49 d, respectively, when submerged, and 148, 250 and 721 d, respectively, when unsubmerged. Plant leachate losses during marsh submergence and non-submergence are nearly equal because release rates are 15x greater during submergence. Nitrogen and carbon concentrations relative to phosphorus are proportionately 4 x higher in leachates than in live plant tissues. The amounts released are high enough to account for measured seasonal changes in the heterotrophic rates of the estuarine plankton community. Leachates appear to be an underappreciated yet significant nutrient and carbon source for salt marsh food webs, and of potential widespread significance for many other estuarine communities.},
	language = {en},
	urldate = {2019-12-03},
	journal = {Marine Ecology Progress Series},
	author = {Turner, Re},
	year = {1993},
	pages = {135--140},
}

@article{kiedrzynska_quantification_2008,
	title = {Quantification of phosphorus retention efficiency by floodplain vegetation and a management strategy for a eutrophic reservoir restoration},
	volume = {33},
	issn = {0925-8574},
	url = {http://www.sciencedirect.com/science/article/pii/S0925857407002078},
	doi = {10.1016/j.ecoleng.2007.10.010},
	abstract = {This paper presents an ecohydrological approach to the reduction in the phosphorus load transported by the Pilica River into a lowland reservoir in the central region of Poland. The research was carried out on a 26.6ha section of the river floodplain where vegetation was the important component accumulating phosphorus (P) in plant tissues. Quantification of P accumulation in plant tissues and retention efficiency by plant communities in the floodplain were analyzed in order to develop a vegetation management strategy that would enhance river self-purification. A Digital Terrain Model (DTM), a location–altitude map, an inundation model of the floodplain, and a map of the distribution of plant communities were used to evaluate the capacity of the floodplain to retain P. In summer, the biological potential for phosphorus retention in the floodplain was estimated to be as high as 255kg P. However, this potential can be increased by planting fast-growing patches of willow. Therefore, covering 24\% or 48\% of the entire floodplain (identified by DTM analysis) where are suitable hydrological conditions for growth and cultivation of willows may increase this accumulation to 332 or 399kg P, respectively. In the long run, an appropriate management strategy (cutting and removing the biomass from the floodplain) should favor a decrease in nutrient transport downstream.},
	language = {en},
	number = {1},
	urldate = {2019-12-03},
	journal = {Ecological Engineering},
	author = {Kiedrzyńska, Edyta and Wagner, Iwona and Zalewski, Maciej},
	month = may,
	year = {2008},
	keywords = {Ecohydrology, Floodplain wetlands, Groundwater, Inundation model, Pilica River, Plants phosphorus accumulation, Wetland plant management},
	pages = {15--25},
}

@article{oorschot_influence_1998,
	title = {The influence of soil desiccation on plant production, nutrient uptake and plant nutrient availability in two {French} floodplain grasslands},
	volume = {14},
	copyright = {Copyright © 1998 John Wiley \& Sons, Ltd.},
	issn = {1099-1646},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1646%28199807/08%2914%3A4%3C313%3A%3AAID-RRR506%3E3.0.CO%3B2-U},
	doi = {10.1002/(SICI)1099-1646(199807/08)14:4<313::AID-RRR506>3.0.CO;2-U},
	abstract = {The effects of summer soil desiccation on plant production and plant nutrient availability (determined by wet chemical extraction) in floodplain grasslands along the rivers Allier and Loire in France were investigated. Soil desiccation in these river floodplains is the result of human interference with the natural flooding regime of rivers, such as dam construction and gravel mining. Flooding periods along the Allier have a longer duration (maximum of 202 days as opposed to 38 days for the Loire). The main comparison was between floodplain grasslands along the two rivers. Additional comparisons were made between relatively high lying, wetter areas (‘ridges’) and low lying, drier areas (‘swales’) within both floodplains. Thus, areas with different soil moisture content were examined, independent of river influences. The availability of P was higher in the Allier floodplain than in the Loire floodplain, but it was similar between ridges and swales. It was concluded that P-availability was not related to soil wetness, but to river sedimentation. Plant production, plant nutrient uptake, and biologically mediated soil processes, such as N-mineralization and nitrification, were all higher on the wetter Allier floodplain and in the wetter swales. These higher process rates were noted where higher amounts of soil bound carbon and nutrients were found as well. Plant production, N-mineralization and nitrification were moisture limited at the dry ridge on the Loire floodplain, as moisture levels were below the wilting point here (pF{\textgreater}4.2). On the wetter parts of the floodplain, plant production was N-limited. This was concluded from low tissue N/P ratios (about 10) and a positive relation between plant production and N-mineralization. On the wetter parts, the rate of N-mineralization depended on the size of soil organic-N pools. The size of these pools was positively related to soil wetness, which can be interpreted as a positive effect of river flooding. Reduced flooding lowers the nutrient input to floodplains and contributes to the occurrence of soil desiccation in summer, which results in lower nutrient cycling and reduced accumulation of soil organic matter. These effects have negative consequences for important floodplain functions, such as nutrient retention and biomass production. © 1998 John Wiley \& Sons, Ltd.},
	language = {en},
	number = {4},
	urldate = {2019-12-03},
	journal = {Regulated Rivers: Research \& Management},
	author = {Oorschot, Mark van and Hayes, Chris and Strien, Iwan van},
	year = {1998},
	keywords = {floodplain grasslands, hydrological changes, plant nutrient availability, plant production, river flooding},
	pages = {313--327},
}

@article{gehrels_transformation_1989,
	title = {The transformation and export of phosphorus from {Wetlands}},
	volume = {3},
	copyright = {Copyright © 1989 John Wiley \& Sons, Ltd},
	issn = {1099-1085},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1002/hyp.3360030407},
	doi = {10.1002/hyp.3360030407},
	abstract = {There is widespread acceptance of the phosphorus retention capability of wetlands even though research findings are often inconclusive and contradictory. The results of a one year phosphorus budget study indicate that internal wetland processes may transform sediment bound phosphorus to plant available orthophosphorus. While total phosphorus imports were nearly double the total phosphorus exports for the study wetland, orthophosphorus exports were 22 per cent greater than imports. This study supports the recent finding that wetlands have limited capability to retain orthophosphorus and indicates that wetlands may even increase the export of orthophosphorus. The generally accepted nutrient retention function of wetlands and their possible role in eutrophication is thus questionable.},
	language = {en},
	number = {4},
	urldate = {2019-12-03},
	journal = {Hydrological Processes},
	author = {Gehrels, Jim and Mulamoottil, George},
	year = {1989},
	keywords = {Eutrophication, Hydrology Mass Balance, Wetlands Phosphorus},
	pages = {365--370},
}

@article{kroger_plant_2007,
	title = {Plant senescence: {A} mechanism for nutrient release in temperate agricultural wetlands},
	volume = {146},
	issn = {0269-7491},
	shorttitle = {Plant senescence},
	url = {http://www.sciencedirect.com/science/article/pii/S0269749106003800},
	doi = {10.1016/j.envpol.2006.06.005},
	abstract = {The beneficial uptake of nutrients by wetland plants is countered to some extent by nutrient release back into the aquatic environment due to vegetative die-back. This current study examined whether Leersia oryzoides, a common wetland plant, exhibits luxury uptake of nutrients from simulated farm runoff. The study also tested whether with subsequent decomposition, these nutrients are released back into the water column. When exposed to elevated ({\textgreater}2mg/L N and P) runoff, L. oryzoides assimilated significantly higher concentrations of nitrogen (p{\textless}0.001) and phosphorus (p{\textless}0.001) in above-ground biomass as compared to non-enriched treatments ({\textless}0.05mg/L N and P). Subsequently, senescence of enriched above-ground biomass yielded significantly higher concentrations of phosphorus (2.19±0.84mg P/L). Using L. oryzoides as our model, this study demonstrates nitrogen and phosphorus sequestration during the growing season and release of phosphorus in the winter.},
	language = {en},
	number = {1},
	urldate = {2019-12-03},
	journal = {Environmental Pollution},
	author = {Kröger, R. and Holland, M. M. and Moore, M. T. and Cooper, C. M.},
	month = mar,
	year = {2007},
	keywords = {Assimilation, Drainage ditch, Nutrients, Wetlands},
	pages = {114--119},
}

@article{wang_detailed_2000,
	title = {A detailed ecosystem model of phosphorus dynamics in created riparian wetlands},
	volume = {126},
	issn = {0304-3800},
	url = {http://www.sciencedirect.com/science/article/pii/S030438000000260X},
	doi = {10.1016/S0304-3800(00)00260-X},
	abstract = {A generalized yet detailed wetland ecosystem model was calibrated and validated with 3 years’s data from four similarly constructed wetlands in northeastern Illinois, USA. The model was used to explore the role of different wetland structure and function in relation to phosphorus retention, to integrate collected data and provide a better understanding at the ecosystem level about constructed wetlands, and to predict the sediment and phosphorus retentions under different hydrologic conditions. Four submodels — hydrology, primary productivity, sediments, and phosphorus — were included in the model. Phosphorus cycling was reasonably simulated with one set of parameters for a total of 10 wetland-years. The model showed that autochthonous organic matter production varies from 300 to 1036 g dw m−2 year−1, with 12 to 103 g dw m−2 year−1 accumulating as bottom detritus. This compares to inflows of sediments from the river (allochthonous) of 192–934 g dw m−2 year−1. Simulated sediment accumulation ranged from 6 to 29 mm year−1 with high inflow wetlands having higher sediment accumulation rates than low flow wetlands. Model estimates are well below the 50–100 mm year−1 rates predicted by sedimentation trap data in previous studies. Total phosphorus retained with sedimentation is simulated at a rate of 1.08–2.47 g P m−2 year−1, in the range of values reported for other wetlands. Simulations showed that macrophytes pumped about 0.31–1.66 g P m−2 year−1 out of deep sediments, and increased total phosphorus in the water column mostly during the non-growing season. Simulated phosphorus retention increased by 5.1\% when macrophytes were removed from the wetland. Simulated phosphorus retention decreased from 90 to 50\% when inflow increases from 8 cm week−1 to 200 cm week−1. Manipulating the hydrologic regime to increase phosphorus removal efficiency may be a desirable strategy for constructed wetlands. Constructed wetlands are dynamic ecosystems for which we generally have poor predictive capabilities; ecological modelling provides us with a useful tool for understanding wetland function and structure, testing hypothesis, and making predictions.},
	language = {en},
	number = {2},
	urldate = {2019-12-03},
	journal = {Ecological Modelling},
	author = {Wang, Naiming and Mitsch, William J},
	month = feb,
	year = {2000},
	keywords = {Des Plaines River Wetland Demonstration Project, Ecosystem modelling, Freshwater marsh, Nutrient cycling, Phosphorus, Wetland},
	pages = {101--130},
}

@article{howardwilliams_cycling_1985,
	title = {Cycling and retention of nitrogen and phosphorus in wetlands: a theoretical and applied perspective},
	volume = {15},
	issn = {1365-2427},
	shorttitle = {Cycling and retention of nitrogen and phosphorus in wetlands},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2427.1985.tb00212.x},
	doi = {10.1111/j.1365-2427.1985.tb00212.x},
	abstract = {SUMMARY. 1 This review considers the internal fluxes and transformations of nitrogen and phosphorus in wetland ecosystems. Emphasis is placed on the dynamic nature of nutrient cycling and the review is slanted towards an applied perspective, namely the possible use of wetlands as sinks for unwanted nutrients. 2 A number of basic concepts pertaining to wetland ecosystems are first explained. These are: successional time scales, exchange equilibria and the concepts of storage and through flow, resource consumption and supply including the ideas of new and regenerated nutrients and the nutrient spiralling concept. Much of the following review material is referenced back to these concepts. 3 Descriptions of the basic pathways of nutrients through different types of wetland systems are given with the emphasis placed on the movement into and out of the major storage compartments of wetland systems. 4 The problems of conversion of qualitative information (or data in concentration units) on nutrient movements and transformations, into data on mass flows are then discussed. The importance of understanding groundwater, evapotranspiration processes and the effects of floods and seasonality on mass flow calculations can be significant. Unidentified groundwater sources can dilute nutrient concentrations, and evapotranspiration can increase concentrations. The pattern of through flow can also alter nutrient levels. Increasing residence time has the effect of decreasing nutrients in the wetland outflow. 5 The review then considers the effects of adding nutrients to wetlands. The concept of the loading capacity is discussed in relation to the length of time a wetland can continue to remove nutrients from through flow. Sediment accumulation and degassing are seen as the major long-term nutrient sinks. Nutrient enrichment results in biological changes to wetlands. These involve both changes in species composition and productivity. Not all are deleterious. 6 The literature indicates that natural wetlands are not particularly effective as nutrient sinks when compared with conventional stripping plants but their value lies in removal of diffuse nutrient runoff at low concentrations. Dealing with this type of runoff by conventional means is not generally feasible. 7 Recent studies show that artificially created wetlands can he effective systems for nutrient (particularly N) removal only if their internal removed mechanisms are understood and if these are optimized by management techniques.},
	language = {en},
	number = {4},
	urldate = {2019-12-03},
	journal = {Freshwater Biology},
	author = {Howard‐Williams, Clive},
	year = {1985},
	pages = {391--431},
}

@misc{noauthor_microbial_nodate,
	title = {Microbial {Biomass} {Responses} to {Soil} {Drying}-{Rewetting} and {Phosphorus} {Leaching}.},
	url = {http://link.galegroup.com/apps/doc/A602498415/EAIM?sid=lms},
	language = {en},
	urldate = {2019-11-22},
}

@article{noe_effects_2019,
	title = {The effects of restored hydrologic connectivity on floodplain trapping vs. release of phosphorus, nitrogen, and sediment along the {Pocomoke} {River}, {Maryland} {USA}},
	volume = {138},
	issn = {0925-8574},
	url = {http://www.sciencedirect.com/science/article/pii/S0925857419302708},
	doi = {10.1016/j.ecoleng.2019.08.002},
	abstract = {River channelization and artificial levees have decreased the hydrologic connectivity of river-floodplain systems around the world. In response, restoration through enhancing connectivity has been advocated to improve the functions of floodplains, but uncertain benefits and the possibility of phosphate release from re-flooded soils has limited implementation. In this study, we measured change in floodplain P, N, and sediment mass balances after restoration along channelized reaches in the lowland Pocomoke River, Maryland USA. Two floodplains (one headwater, one mainstem) restored through partial levee breaches were compared to two additional mainstem floodplains (one natural unchannelized, one unrestored channelized). Potential soluble reactive P (SRP) release from soil cores during experimental laboratory floods; soil P, Fe, and Al fractionation; and deposition and P and N content of sediment were measured before and after the restoration period, as well as in situ inputs and release of SRP and dissolved inorganic N from soils after restorations. Potential SRP release, during both the before and after restoration period, was greatest at the channelized mainstem and restored mainstem sites, lower at the restored headwater site, and small at the natural mainstem site. Both restored sites had smaller potential SRP release after restoration compared to before restoration. In situ SRP release slightly exceeded inputs to soils at connected sites during the post-restoration period, with less net release at the restored sites compared to the natural mainstem site. The magnitude of gross and net SRP release from soils in the field was smaller than, and uncorrelated with, potential SRP release estimated from laboratory experimental floods. Gross soil SRP release rates in the field were predictable using the ratio of soil oxalate-extractable P/Al. Sedimentation inputs of P and N increased at all sites during the post-restoration period, with rates at restored sites intermediate compared to the much higher rates at the natural mainstem site and somewhat lower rates at the channelized mainstem site. These sediment inputs of nutrients were much larger than rates of inorganic P and N release from soils, indicating net trapping of P and N after restoration. Restoring floodplain hydrologic connectivity showed moderate success at increasing the trapping of P, N, and sediment, with relatively little phosphate release, and therefore improving water quality.},
	language = {en},
	urldate = {2019-11-22},
	journal = {Ecological Engineering},
	author = {Noe, Gregory B. and Boomer, Kathy and Gillespie, Jaimie L. and Hupp, Cliff R. and Martin-Alciati, Mario and Floro, Kelly and Schenk, Edward R. and Jacobs, Amy and Strano, Steve},
	month = nov,
	year = {2019},
	keywords = {Connectivity, Floodplain, Nutrient, Restoration, Sediment, Water quality},
	pages = {334--352},
}

@article{schonbrunner_impact_2012,
	title = {Impact of drying and re-flooding of sediment on phosphorus dynamics of river-floodplain systems},
	volume = {432},
	issn = {0048-9697},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969712008406},
	doi = {10.1016/j.scitotenv.2012.06.025},
	abstract = {One of the consequences of human impacts on floodplains is a change in sedimentation leading to enhanced floodplain aggradation. Thus, accumulated sediments rich in nutrients might interfere with floodplain restoration. In this study we investigated the phosphorus release behavior of sediments from shallow backwaters of an isolated floodplain of the Danube River situated east of the city of Vienna with the aim to understand the effects of changes in dry/wet cycles on established floodplain sediments. In the light of restoration plans aiming at increased surface water exchange with the river main channel, the response of sediments to frequent alternations between desiccation and inundation periods is a key issue as changes of sediment properties are expected to affect phosphorus release. In order to determine the effect of changing hydrological conditions on internal phosphorus loading, we exposed sediments to different dry/wet treatments in a laboratory experiment. Total phosphorus (TP) release from sediments into the water column increased with increasing duration of dry periods prior to re-wetting. Partial correlation analysis showed significant positive correlations between ΔTP and ΔNH4+ as well as between ΔTP and ΔFe3+ concentrations (Δ refers to the difference between the final and initial concentration during the wetting period), indicating that enhanced mineralization rates leading to a concomitant release of NH4+ and TP and the reduction of iron hydroxides leading to a concomitant release of Fe3+ and TP are the mechanisms responsible for the rise in TP. Repeated drying and wetting resulted in elevated phosphorus release. This effect was more pronounced when drying periods led to an 80\% reduction in water content, indicating that the degree of drying is a major determinant controlling phosphorus release upon re-wetting. The reconnection of isolated floodplains will favor fluctuating hydrologic conditions and is therefore expected to initially lead to high rates of phosphorus release from sediments.},
	language = {en},
	urldate = {2019-11-22},
	journal = {Science of The Total Environment},
	author = {Schönbrunner, Iris M. and Preiner, Stefan and Hein, Thomas},
	month = aug,
	year = {2012},
	keywords = {Dry/wet cycles, Floodplain, Iron reduction, Mineralization, Phosphorus, Sediment},
	pages = {329--337},
}

@article{mcdaniel_relationships_2009,
	title = {Relationships between {Benthic} {Sediments} and {Water} {Column} {Phosphorus} in {Illinois} {Streams}},
	volume = {38},
	issn = {1537-2537},
	url = {https://dl.sciencesocieties.org/publications/jeq/abstracts/38/2/607},
	doi = {10.2134/jeq2008.0094},
	language = {en},
	number = {2},
	urldate = {2019-11-22},
	journal = {Journal of Environmental Quality},
	author = {McDaniel, Marshall D. and David, Mark B. and Royer, Todd V.},
	month = mar,
	year = {2009},
	pages = {607--617},
}

@article{hall_metabolism_2016,
	title = {Metabolism, {Gas} {Exchange}, and {Carbon} {Spiraling} in {Rivers}},
	volume = {19},
	issn = {1435-0629},
	url = {10.1007/s10021-015-9918-1},
	doi = {10.1007/s10021-015-9918-1},
	abstract = {Ecosystem metabolism, that is, gross primary productivity (GPP) and ecosystem respiration (ER), controls organic carbon (OC) cycling in stream and river networks and is expected to vary predictably with network position. However, estimates of metabolism in small streams outnumber those from rivers such that there are limited empirical data comparing metabolism across a range of stream and river sizes. We measured metabolism in 14 rivers (discharge range 14–84 m3 s−1) in the Western and Midwestern United States (US). We estimated GPP, ER, and gas exchange rates using a Lagrangian, 2-station oxygen model solved in a Bayesian framework. GPP ranged from 0.6–22 g O2 m−2 d−1 and ER tracked GPP, suggesting that autotrophic production supports much of riverine ER in summer. Net ecosystem production, the balance between GPP and ER was 0 or greater in 4 rivers showing autotrophy on that day. River velocity and slope predicted gas exchange estimates from these 14 rivers in agreement with empirical models. Carbon turnover lengths (that is, the distance traveled before OC is mineralized to CO2) ranged from 38 to 1190 km, with the longest turnover lengths in high-sediment, arid-land rivers. We also compared estimated turnover lengths with the relative length of the river segment between major tributaries or lakes; the mean ratio of carbon turnover length to river length was 1.6, demonstrating that rivers can mineralize much of the OC load along their length at baseflow. Carbon mineralization velocities ranged from 0.05 to 0.81 m d−1, and were not different than measurements from small streams. Given high GPP relative to ER, combined with generally short OC spiraling lengths, rivers can be highly reactive with regard to OC cycling.},
	language = {en},
	number = {1},
	urldate = {2019-11-21},
	journal = {Ecosystems},
	author = {Hall, Robert O. and Tank, Jennifer L. and Baker, Michelle A. and Rosi-Marshall, Emma J. and Hotchkiss, Erin R.},
	month = jan,
	year = {2016},
	keywords = {Ecosystem respiration, carbon spiraling, ecosystem metabolism, gas exchange, gross primary production, rivers},
	pages = {73--86},
}
@article{bernhardt2022light,
  title={Light and flow regimes regulate the metabolism of rivers},
  author={Bernhardt, Emily S and Savoy, Phil and Vlah, Michael J and Appling, Alison P and Koenig, Lauren E and Hall Jr, Robert O and Arroita, Maite and Blaszczak, Joanna R and Carter, Alice M and Cohen, Matt and others},
  journal={Proceedings of the National Academy of Sciences},
  volume={119},
  number={8},
  pages={e2121976119},
  year={2022},
  publisher={National Academy of Sciences},
doi={10.1073/pnas.2121976119 j}
}

@article{bernhardt_metabolic_2018,
	title = {The metabolic regimes of flowing waters},
	volume = {63},
	issn = {0024-3590},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/full/10.1002/lno.10726},
	doi = {10.1002/lno.10726},
	abstract = {Abstract The processes and biomass that characterize any ecosystem are fundamentally constrained by the total amount of energy that is either fixed within or delivered across its boundaries. Ultimately, ecosystems may be understood and classified by their rates of total and net productivity and by the seasonal patterns of photosynthesis and respiration. Such understanding is well developed for terrestrial and lentic ecosystems but our understanding of ecosystem phenology has lagged well behind for rivers. The proliferation of reliable and inexpensive sensors for monitoring dissolved oxygen and carbon dioxide is underpinning a revolution in our understanding of the ecosystem energetics of rivers. Here, we synthesize our current understanding of the drivers and constraints on river metabolism, and set out a research agenda aimed at characterizing, classifying and modeling the current and future metabolic regimes of flowing waters.},
	number = {S1},
	urldate = {2019-11-21},
	journal = {Limnology and Oceanography},
	author = {Bernhardt, E. S. and Heffernan, J. B. and Grimm, N. B. and Stanley, E. H. and Harvey, J. W. and Arroita, M. and Appling, A. P. and Cohen, M. J. and McDowell, W. H. and Hall Jr., R. O. and Read, J. S. and Roberts, B. J. and Stets, E. G. and Yackulic, C. B.},
	month = mar,
	year = {2018},
	pages = {S99--S118},
}

@article{madinger_linking_2019,
	title = {Linking denitrification with ecosystem respiration in mountain streams},
	volume = {4},
	issn = {2378-2242},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lol2.10111},
	doi = {10.1002/lol2.10111},
	abstract = {Rivers denitrify a portion of their nitrate () load, but estimates are difficult using microcosm or reach-scale measurements that require specific biogeochemical and hydrologic conditions. Measuring reach-scale oxygen (O2) respiration fluxes is easier than nitrogen (N2) fluxes, thus we paired microcosm estimates of denitrification by N2 production with estimates of aerobic respiration. The median molar ratio of ΔN2:−ΔO2 from 13 streams was 0.011 (95\% credible interval 0.0002–0.027 mol:mol). We then measured diel O2 concentrations from 11 streams and converted to ecosystem respiration (ER) using a multiday oxygen model. Given reach-scale ER of −160 mmol O2 m−2 d−1, the estimated median denitrification was 1.5 mmol N2 m−2 d−1 (credible interval (CI): 0.18–4.21) across our streams. Our estimates of denitrification constituted 19\% of gross uptake (CI: 0–51\%). In streams, ΔN2:−ΔO2 was lower than in estuarine and marine ecosystems. Despite multiple sources of error, this approach estimates reach-scale denitrification and variation with concentrations.},
	language = {en},
	number = {5},
	urldate = {2019-11-21},
	journal = {Limnology and Oceanography Letters},
	author = {Madinger, Hilary L. and Hall, Robert O.},
	year = {2019},
	pages = {145--154},
}

@article{savoy_metabolic_2019,
	title = {Metabolic rhythms in flowing waters: {An} approach for classifying river productivity regimes},
	volume = {64},
	issn = {1939-5590},
	shorttitle = {Metabolic rhythms in flowing waters},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lno.11154},
	doi = {10.1002/lno.11154},
	abstract = {Although seasonal patterns of ecosystem productivity have been extensively described and analyzed with respect to their primary forcings in terrestrial and marine systems, comparatively little is known about these same processes in rivers. However, it is now possible to perform a large-scale synthesis on the patterns and drivers of river productivity regimes because of the recent sensor advances allowing for near-continuous estimates of river productivity. Here, we explore a dataset of 47 U.S. rivers to examine whether there are characteristic river productivity regimes. We use classification approaches to develop a typology of productivity regimes and then use these regimes to examine differences with respect to potential controls of productivity. We identified two distinct metabolic regimes, which we named Summer Peak and Spring Peak Rivers, within our dataset. These regimes meaningfully differed in both the timing and magnitude of productivity and were robust to different approaches to classification. We also found that several variables, including watershed area and characteristics of water temperature or discharge, were able to predict the class membership of these regimes with modest accuracy. Our results support the presence of characteristic metabolic regimes and suggests that these regimes may have common sets of environmental controls. We present classification as one approach to begin exploring the productivity regimes of rivers. The strength of our approach is that it fully leverages these newly available high-frequency productivity estimates to create classes that can be used to draw inferences about how the controls of river productivity differ between or within systems.},
	language = {en},
	number = {5},
	urldate = {2019-11-21},
	journal = {Limnology and Oceanography},
	author = {Savoy, Philip and Appling, Alison P. and Heffernan, James B. and Stets, Edward G. and Read, Jordan S. and Harvey, Judson W. and Bernhardt, Emily S.},
	year = {2019},
	pages = {1835--1851},
}

@article{koenig_emergent_2019,
	title = {Emergent productivity regimes of river networks},
	volume = {4},
	copyright = {© 2019 The Authors. Limnology and Oceanography published by Wiley Periodicals, Inc. on behalf of Association for the Sciences of Limnology and Oceanography.},
	issn = {2378-2242},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lol2.10115},
	doi = {10.1002/lol2.10115},
	abstract = {High-resolution data are improving our ability to resolve temporal patterns and controls on river productivity, but we still know little about the emergent patterns of primary production at river-network scales. Here, we estimate daily and annual river-network gross primary production (GPP) by applying characteristic temporal patterns of GPP (i.e., regimes) representing distinct river functional types to simulated river networks. A defined envelope of possible productivity regimes emerges at the network-scale, but the amount and timing of network GPP can vary widely within this range depending on watershed size, productivity in larger rivers, and reach-scale variation in light within headwater streams. Larger rivers become more influential on network-scale GPP as watershed size increases, but small streams with relatively low productivity disproportionately influence network GPP due to their large collective surface area. Our initial predictions of network-scale productivity provide mechanistic understanding of the factors that shape aquatic ecosystem function at broad scales.},
	language = {en},
	number = {5},
	urldate = {2019-11-21},
	journal = {Limnology and Oceanography Letters},
	author = {Koenig, Lauren E. and Helton, Ashley M. and Savoy, Philip and Bertuzzo, Enrico and Heffernan, James B. and Hall, Robert O. and Bernhardt, Emily S.},
	year = {2019},
	pages = {173--181},
}

@article{battin_contributions_2003,
	title = {Contributions of microbial biofilms to ecosystem processes in stream mesocosms},
	volume = {426},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/articles/nature02152},
	doi = {10.1038/nature02152},
	language = {en},
	number = {6965},
	urldate = {2019-11-19},
	journal = {Nature},
	author = {Battin, Tom J. and Kaplan, Louis A. and Denis Newbold, J. and Hansen, Claude M. E.},
	month = nov,
	year = {2003},
	pages = {439--442},
}

@misc{noauthor_contributions_nodate,
	title = {Contributions of microbial biofilms to ecosystem processes in stream mesocosms {\textbar} {Nature}},
	url = {https://www.nature.com/articles/nature02152},
	urldate = {2019-11-19},
}

@article{lamberti_productive_1989,
	title = {Productive {Capacity} of {Periphyton} as a {Determinant} of {Plant}-{Herbivore} {Interactions} in {Streams}},
	volume = {70},
	copyright = {© 1989 by the Ecological Society of America},
	issn = {1939-9170},
	url = {http://esajournals.onlinelibrary.wiley.com/doi/abs/10.2307/1938117},
	doi = {10.2307/1938117},
	abstract = {To investigate the influence of plant productivity on plant—herbivore interactions in stream ecosystems, we varied the productive capacity of algal assemblages by exposing periphyton to three levels of irradiance and two levels of grazing. We studied interactions between algal assemblages (grown from algae obtained from four Oregon streams) and herbivorous snails (Juga silicula) in 15 laboratory streams containing either 250 snails/m2 or no snails. Biomass, production, export, and taxonomic structure of the algal community were measured at intervals throughout the 75—d study. Ingestion rate and assimilation efficiency of snails also were measured on six different dates using dual—isotope labeling, and snail growth was measured at the end of the experiment. Rates of primary production, algal biomass accumulation, and dominance by chlorophytes generally increased with higher irradiance, although these patterns were modified by herbivores. Ungrazed periphyton at low irradiance (photon flux density: 20μmol°m—2°s—1) accumulated little biomass, which was further reduced by grazing snails. At intemediate (100 μmol°m—2°s—1) and high (400μmol°m—2°s—1) irradiance, snails delayed the accumulation of algal biomass but did not affect the final biomass attained. After 43 d, net primary production (NPP) at high irradiance was unaffected by grazing, whereas grazing increased NPP at both low and intermediate irradiance. Algal export increased with both irradiance and the presence of grazers and constituted a significant loss of plant biomass from the streams. Grazing by Juga delayed algal succession and altered algal taxonomic structure and assemblage physiognomy by reducing the relative abundance of erect and non—attached algae, while increasing the abundance of adnate diatoms. Snails grew slowly at low irradiance, due to scant food resources, but had high growth rates at intermediate and high irradiance, probably because food was not limiting. Assimilation efficiencies for snails generally varied from 40 to 70\% and were highest at low irradiance. At low irradiance, 90\% of benthic production was harvested by grazers, whereas only 10\% accumulated as attached biomass or was exported. At higher irradiances, {\textless}15\% of primary production was harvested by grazers, and {\textgreater}85\% persisted as attached algae or was exported. In these stream ecosystems, the biomass and production of grazers were influenced by abiotic constriants placed on algal productive capacity (i.e., the ability of a plant assemblage to generate biomass). The structure and metabolism of algal assemblages were affected, in turn, by consumptive demand of herbivores. The productive capacity of periphyton modified the nature and outcome of plant—herbivore interactions. This capacity therefore has important implications for the operation of stream ecosystems.},
	language = {en},
	number = {6},
	urldate = {2019-11-19},
	journal = {Ecology},
	author = {Lamberti, Gary A. and Gregory, Stanley V. and Ashkenas, Linda R. and Steinman, Alan D. and McIntire, C. David},
	year = {1989},
	keywords = {Juga, Oregon, algae, benthos, chlorophyll a, feeding, grazing, herbivory, ingestion, periphyton, primary production, streams},
	pages = {1840--1856},
}

@article{stewart_responses_1987,
	title = {Responses of stream algae to grazing minnows and nutrients: a field test for interactions},
	volume = {72},
	issn = {1432-1939},
	shorttitle = {Responses of stream algae to grazing minnows and nutrients},
	url = {10.1007/BF00385036},
	doi = {10.1007/BF00385036},
	abstract = {SummaryPrevious studies have shown that an algivorous grazing minnow (Campostoma anomalum) is the major herbivore in Brier Creek, a hardwater stream in south central Oklahoma. In summer and autumn schools of Campostoma virtually eliminate algae from substrate surfaces in deeper areas of some pools. The pool-to-pool distributions of algae and Campostoma reported for this stream could occur if nutrient limitation permits grazing by Campostoma to “outrun” algal growth. To test this hypothesis, mesh pens were built to exclude Campostoma from substrates in each of four typical Campostoma pools. N+P+K lawn fertilizer was added daily to two of the four pools; the other two, which received no fertilizer additions and which were not visibly affected by fertilizer transported downstream from the pools enriched with nutrients, served as controls. Algae accumulated rapidly on natural substrates and on unglazed ceramic tiles in grazer-exclusion pens in pools receiving N+P+K additions and more slowly in pens in both control pools. Periphyton biomass on grazed substrates in all four pools remained low throughout the experiment. Hence, Campostoma at normal densities were able to outrun algal growth even when nutrients were added. Eleven days after the experiment started, I determined biomass, biomass-specific net primary productivity, and areal net primary productivity of periphyton on substrates exposed to all combinations of grazer (+,0) and nutrient (+,0) treatments. Grazing increased biomass-specific primary productivity, prevented accumulation of biomass, and decreased areal primary productivity of periphyton. Additions of N+P+K increased biomass-specific net primary productivity of grazed and ungrazed periphyton and markedly increased biomass of periphyton on substrates protected from Campostoma. Although food supply for Campostoma appeared to be greater with nutrient additions, condition of Campostoma in pools receiving N+P+K was not significantly different from Campostoma collected from control pools 35 days after the experiment started. I conclude that although nutrient supply limits biomass-specific primary productivity of periphyton in Brier Creek, nutrient limitation in this stream exacerbates, rather than causes, the visually conspicuous pool-to-pool complimentary distribution of algae and Campostoma: in this stream, grazing by Campostoma at natural densities can outrun periphyton growth even when nutrients are added.},
	language = {en},
	number = {1},
	urldate = {2019-11-19},
	journal = {Oecologia},
	author = {Stewart, A. J.},
	month = apr,
	year = {1987},
	keywords = {Aufwuchs algae, Campostoma, Fertilizer, Grazing, Nutrients},
	pages = {1--7},
}

@article{taylor_fish-mediated_2012,
	title = {Fish-mediated nutrient cycling and benthic microbial processes: can consumers influence stream nutrient cycling at multiple spatial scales?},
	volume = {31},
	issn = {2161-9549, 2161-9565},
	shorttitle = {Fish-mediated nutrient cycling and benthic microbial processes},
	url = {https://www.journals.uchicago.edu/doi/10.1899/11-113.1},
	doi = {10.1899/11-113.1},
	abstract = {Fish-mediated nutrient recycling influences nutrient dynamics in stream ecosystems, but its consequences for smaller-scale microbial processes in benthic habitats are not well understood. We quantified the effect of nutrient recycling by the grazing fish, Campostoma anomalum, on downstream periphyton in 12 flow-through stream mesocosms. We compared periphyton nutrient ratios and algal biomass (as chlorophyll a [chl a]) between tiles upstream and downstream of enclosures with and without fish to measure nutrient-cycling effects in streams with low (11) and high (177) surface-water dissolved N:P molar ratios. No upstream–downstream changes in periphyton nutrient ratios were observed in low N:P streams with or without fish. In high N:P streams, periphyton C:N decreased and C:P and N:P increased on tiles downstream of enclosures. In high N:P streams, downstream changes in periphyton nutrient ratios were greater in streams with than without fish, and chl a significantly increased downstream of enclosures with fish. We linked nutrient-recycling effects to downstream microbial processes by comparing bacterial biomass production (BBP), photosynthesis (PS) rates, and the degree of coupling between the 2 processes on tiles downstream of enclosures. We estimated the degree of coupled production between algae and bacteria downstream of enclosures as the covariance between PS and BBP among replicates within each stream (COVPS–BBP). In high N:P streams, areal BBP and PS rates and COVPS–BBP were higher downstream of enclosures with fish. Chl a and COVPS–BBP declined with increasing periphyton C:N content, resulting in a positive relationship between COVPS–BBP and algal biomass across all treatments. Our results indicate that grazing fish alter stream ecosystem N and P dynamics through consumer-mediated recycling pathways, but downstream responses depend on background nutrient regimes. Fish-mediated changes in nutrient dynamics and algal biomass influence reliance of heterotrophs and autotrophs on nutrients recycled within periphyton communities to support benthic production.},
	language = {en},
	number = {3},
	urldate = {2019-11-19},
	journal = {Freshwater Science},
	author = {Taylor, Jason M. and Back, Jeffrey A. and Valenti, Theodore W. and King, Ryan S.},
	month = sep,
	year = {2012},
	pages = {928--944},
}

@article{murdock_dynamic_2011,
	title = {Dynamic influences of nutrients and grazing fish on periphyton during recovery from flood},
	volume = {30},
	issn = {0887-3593},
	url = {http://www.journals.uchicago.edu/doi/abs/10.1899/10-039.1},
	doi = {10.1899/10-039.1},
	abstract = {Nutrients and grazers both can regulate benthic algal structure and function in streams, but the relative strength of each factor depends on stream biotic and abiotic conditions. The abundance of stream organisms and nutrient availability can change rapidly after a flood. Thus, nutrient and grazer influences on algal development and how these drivers interact may vary temporally during recovery. We measured benthic structural and functional development for 35 d after a simulated flood in large outdoor mesocosms under a gradient of 6 nutrient loadings crossed with 6 densities of grazing fish (Southern redbelly dace, Phoxinus erythrogaster). Nutrients influenced algal development more than dace did and were better correlated with algal function (area-specific primary productivity and nutrient uptake) than with structure (biomass). Dace influenced all structural variables and biomass-specific gross primary productivity, but their influence was relatively weak and was observed only early in recovery. Dace influence weakened and nutrient influence strengthened during recovery. Understanding context-dependent relationships in postdisturbance community dynamics is essential for predicting ecosystem responses to future changes in nutrient inputs and biodiversity, particularly in systems, such as headwater streams, with frequent disturbance.},
	number = {2},
	urldate = {2019-11-19},
	journal = {Journal of the North American Benthological Society},
	author = {Murdock, Justin N. and Dodds, Walter K. and Gido, Keith B. and Whiles, Matt R.},
	month = jun,
	year = {2011},
	pages = {331--345},
}

@article{murdock_dynamic_2011-1,
	title = {Dynamic influences of nutrients and grazing fish on periphyton during recovery from flood},
	volume = {30},
	issn = {0887-3593, 1937-237X},
	url = {https://www.journals.uchicago.edu/doi/10.1899/10-039.1},
	doi = {10.1899/10-039.1},
	abstract = {Nutrients and grazers both can regulate benthic algal structure and function in streams, but the relative strength of each factor depends on stream biotic and abiotic conditions. The abundance of stream organisms and nutrient availability can change rapidly after a flood. Thus, nutrient and grazer influences on algal development and how these drivers interact may vary temporally during recovery. We measured benthic structural and functional development for 35 d after a simulated flood in large outdoor mesocosms under a gradient of 6 nutrient loadings crossed with 6 densities of grazing fish (Southern redbelly dace, Phoxinus erythrogaster). Nutrients influenced algal development more than dace did and were better correlated with algal function (area-specific primary productivity and nutrient uptake) than with structure (biomass). Dace influenced all structural variables and biomass-specific gross primary productivity, but their influence was relatively weak and was observed only early in recovery. Dace influence weakened and nutrient influence strengthened during recovery. Understanding context-dependent relationships in postdisturbance community dynamics is essential for predicting ecosystem responses to future changes in nutrient inputs and biodiversity, particularly in systems, such as headwater streams, with frequent disturbance.},
	language = {en},
	number = {2},
	urldate = {2019-11-19},
	journal = {Journal of the North American Benthological Society},
	author = {Murdock, Justin N. and Dodds, Walter K. and Gido, Keith B. and Whiles, Matt R.},
	month = jun,
	year = {2011},
	pages = {331--345},
}

@article{veach_topdown_2018,
	title = {Top–down effects of a grazing, omnivorous minnow ({Campostoma} anomalum) on stream microbial communities},
	volume = {37},
	issn = {2161-9549},
	url = {http://www.journals.uchicago.edu/doi/abs/10.1086/696292},
	doi = {10.1086/696292},
	abstract = {Top–down control exerted by macroconsumers can strongly affect lower trophic levels and ecosystem processes. Studies of effects on primary consumers in streams have been focused on algae, and effects on bacteria are largely unknown. We manipulated the density of an omnivorous, grazing minnow, the central stoneroller (Campostoma anomalum), in experimental stream mesocosms (treatments with 0, 1, 2, 3, 4, 5, 6, or 7 individuals) to understand consumer effects on algal and bacterial abundance (chlorophyll a [Chl a] extraction, bacterial cell counts, biomass measurements) and bacterial diversity and community composition (via Illumina MiSeq sequencing of the V4 region of the 16S ribosomal RNA gene). Increasing C. anomalum density reduced algal biomass until density reached {\textasciitilde}2 fish (5 g fish biomass/m2), and higher fish densities did not affect algal biomass. Fish biomass did not affect bacterial cell counts. Biofilm organic matter decreased with increasing C. anomalum biomass. Bacterial community composition was not affected by fish biomass, but variation in community composition was correlated with shifts in bacterial abundances. Evenness of bacterial operational taxonomic units (OTUs) decreased with increasing C. anomalum biomass, indicating that bacterial communities exhibited a greater degree of OTU dominance when fish biomass was higher. These findings suggest that this grazing fish species reduces algal abundance and organic matter in low-nutrient streams until a threshold of moderate fish abundance is reached and that it reduces evenness of benthic bacterial communities but not bacterial biomass. Given the importance of biofilm bacteria for ecosystem processes and the ubiquity of grazing fishes in streams, future researchers should explore both top–down and bottom–up interactions in alternative environmental contexts and with other grazing fish species.},
	number = {1},
	urldate = {2019-11-18},
	journal = {Freshwater Science},
	author = {Veach, Allison M. and Troia, Matthew J. and Jumpponen, Ari and Dodds, Walter K.},
	month = mar,
	year = {2018},
	pages = {121--133},
}

@article{berga_combined_2015,
	title = {Combined effects of zooplankton grazing and dispersal on the diversity and assembly mechanisms of bacterial metacommunities},
	volume = {17},
	copyright = {© 2014 Society for Applied Microbiology and John Wiley \& Sons Ltd},
	issn = {1462-2920},
	url = {https://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.12688},
	doi = {10.1111/1462-2920.12688},
	abstract = {Effects of dispersal and the presence of predators on diversity, assembly and functioning of bacterial communities are well studied in isolation. In reality, however, dispersal and trophic interactions act simultaneously and can therefore have combined effects, which are poorly investigated. We performed an experiment with aquatic metacommunities consisting of three environmentally different patches and manipulated dispersal rates among them as well as the presence or absence of the keystone species Daphnia magna. Daphnia magna reduced both local and regional diversity, whereas dispersal increased local diversity but decreased beta-diversity having no net effect on regional diversity. Dispersal modified the assembly mechanisms of bacterial communities by increasing the degree of determinism. Additionally, the combination of the D. magna and dispersal increased the importance of deterministic processes, presumably because predator-tolerant taxa were spread in the metacommunity via dispersal. Moreover, the presence of D. magna affected community composition, increased community respiration rates but did not affect bacterial production or abundance, whereas dispersal slightly increased bacterial production. In conclusion, our study suggests that predation by a keystone species such as D. magna and dispersal additively influence bacterial diversity, assembly processes and ecosystem functioning.},
	language = {en},
	number = {7},
	urldate = {2019-11-18},
	journal = {Environmental Microbiology},
	author = {Berga, Mercè and Östman, Örjan and Lindström, Eva S. and Langenheder, Silke},
	year = {2015},
	pages = {2275--2287},
}

@article{birtel_grazers_2016,
	title = {Grazers structure the bacterial and algal diversity of aquatic metacommunities},
	volume = {97},
	copyright = {© 2016 by the Ecological Society of America},
	issn = {1939-9170},
	url = {http://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecy.1612},
	doi = {10.1002/ecy.1612},
	abstract = {Consumers can have strong effects on the biotic and abiotic dynamics of spatially-structured ecosystems. In metacommunities, dispersing consumers can alter local assembly dynamics either directly through trophic interactions or indirectly by modifying local environmental conditions. In aquatic systems, very little is known about how key grazers, such as Daphnia, structure the microbial diversity of metacommunities and influence bacterial-mediated ecosystem functions. In an outdoor mesocosm experiment with replicate metacommunities (two 300 L mesocosms), we tested how the presence and absence of Daphnia and the initial density of the microbial community (manipulated via dilution) influenced the diversity and community structure of algae and bacteria, and several ecosystem properties (e.g., pH, dissolved substances) and functions (e.g., enzyme activity, respiration). We found that Daphnia strongly affected the local and regional diversity of both phytoplankton and bacteria, the taxonomic composition of bacterial communities, the biomass of algae, and ecosystem metabolism (i.e., respiration). Diluting the microbial inoculum (0.2–5 μm size fraction) to the metacommunities increased local phytoplankton diversity, decreased bacteria beta-diversity, and changed the relative abundance of bacterial classes. Changes in the rank abundance of different bacterial groups exhibited phylogenetic signal, implying that closely related bacteria species might share similar responses to the presence of Daphnia.},
	language = {en},
	number = {12},
	urldate = {2019-11-18},
	journal = {Ecology},
	author = {Birtel, Julia and Matthews, Blake},
	year = {2016},
	keywords = {Daphnia, bacteria, community assembly, consumers, metacommunities, phylogenetic diversity, phytoplankton},
	pages = {3472--3484},
}

@article{zwart_cross-scale_2019,
	title = {Cross-{Scale} {Interactions} {Dictate} {Regional} {Lake} {Carbon} {Flux} and {Productivity} {Response} to {Future} {Climate}},
	volume = {46},
	copyright = {©2019. The Authors.},
	issn = {1944-8007},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2019GL083478},
	doi = {10.1029/2019GL083478},
	abstract = {Lakes support globally important food webs through algal productivity and contribute significantly to the global carbon cycle. However, predictions of how broad-scale lake carbon flux and productivity may respond to future climate are extremely limited. Here, we used an integrated modeling framework to project changes in lake-specific and regional primary productivity and carbon fluxes under 21st century climate for thousands of lakes. We observed high uncertainty in whether lakes collectively were to increase or decrease lake CO2 emissions and carbon burial in our modeled region owing to divergence in projected regional water balance among climate models. Variation in projected air temperature influenced projected changes in lake primary productivity (but not CO2 emissions or carbon burial) as warmer air temperatures decreased productivity through reduced lake water volume. Cross-scale interactions between regional drivers and local characteristics dictated the magnitude and direction of lake-specific carbon flux and productivity responses to future climate.},
	language = {en},
	number = {15},
	urldate = {2019-11-13},
	journal = {Geophysical Research Letters},
	author = {Zwart, J. A. and Hanson, Z. J. and Read, J. S. and Fienen, M. N. and Hamlet, A. F. and Bolster, D. and Jones, S. E.},
	year = {2019},
	keywords = {climate change, lake carbon cycling, lake productivity},
	pages = {8840--8851},
}


@article{peipoch_niche_2019,
	title = {Niche partitioning of microbial communities in riverine floodplains},
	volume = {9},
	copyright = {2019 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-019-52865-4},
	doi = {10.1038/s41598-019-52865-4},
	abstract = {Riverine floodplains exhibit high floral and faunal diversity as a consequence of their biophysical complexity. Extension of such niche partitioning processes to microbial communities is far less resolved or supported. Here, we evaluated the responses of aquatic biofilms diversity to environmental gradients across ten riverine floodplains with differing degrees of flow alteration and habitat diversity to assess whether complex floodplains support biofilm communities with greater biodiversity and species interactions. No significant evidence was found to support a central role for habitat diversity in promoting microbial diversity across 116 samples derived from 62 aquatic habitats, as neither α (H’: 2.8–4.1) nor β (Sørensen: 0.3–0.39) diversity were positively related to floodplain complexity across the ten floodplains. In contrast, our results documented the sensitivity of biofilm communities to regional templates manifested as gradients of carbon, nitrogen, and phosphorous availability. Large-scale conditions reflecting nitrogen limitation increased the relative abundance of N-fixing cyanobacteria (up to 0.34 as fraction of total reads), constrained the total number of interactions among bacterial taxa, and reinforced negative over positive interactions, generating unique microbial communities and networks that reflect large-scale species sorting in response to regional geochemical gradients.},
	language = {en},
	number = {1},
	urldate = {2019-11-12},
	journal = {Scientific Reports},
	author = {Peipoch, Marc and Miller, Scott R. and Antao, Tiago R. and Valett, H. Maurice},
	month = nov,
	year = {2019},
	pages = {1--13},
}

@misc{noauthor_implementation_nodate,
	title = {Implementation of ecological modeling as an effective management and investigation tool: {Lake} {Kinneret} as a case study - {ScienceDirect}},
	url = {https://www-sciencedirect-com.proxy.library.nd.edu/science/article/pii/S0304380009002336#fig1},
	urldate = {2019-11-11},
}

@article{mcintyre_fish_2008,
	title = {Fish {Distributions} and {Nutrient} {Cycling} in {Streams}: {Can} {Fish} {Create} {Biogeochemical} {Hotspots}?},
	volume = {89},
	issn = {0012-9658},
	shorttitle = {Fish {Distributions} and {Nutrient} {Cycling} in {Streams}},
	url = {http://www.jstor.org/stable/27650758},
	abstract = {Rates of biogeochemical processes often vary widely in space and time, and characterizing this variation is critical for understanding ecosystem functioning. In streams, spatial hotspots of nutrient transformations are generally attributed to physical and microbial processes. Here we examine the potential for heterogeneous distributions of fish to generate hotspots of nutrient recycling. We measured nitrogen (N) and phosphorus (P) excretion rates of 47 species of fish in an N-limited Neotropical stream, and we combined these data with population densities in each of 49 stream channel units to estimate unit- and reach-scale nutrient recycling. Species varied widely in rates of N and P excretion as well as excreted N:P ratios (6—176 molar). At the reach scale, fish excretion could meet {\textgreater}75\% of ecosystem demand for dissolved inorganic N and turn over the ambient NH₄ pool in {\textless}0.3 km. Areal N excretion estimates varied 47-fold among channel units, suggesting that fish distributions could influence local N availability. P excretion rates varied 14-fold among units but were low relative to ambient concentrations. Spatial variation in aggregate nutrient excretion by fish reflected the effects of habitat characteristics (depth, water velocity) on community structure (body size, denisty, species composition), and the preference of large-bodied species for deep runs was particularly important. We conclude that the spatial distribution of fish could indeed create hotspots of nutrient recycling during the dry season in this species-rich tropical stream. The prevalence of patchy distributions of stream fish and invertebrates suggests that hotspots of consumer nutrient recycling may often occur in stream ecosystems.},
	number = {8},
	urldate = {2019-11-06},
	journal = {Ecology},
	author = {McIntyre, Peter B. and Flecker, Alexander S. and Vanni, Michael J. and Hood, James M. and Taylor, Brad W. and Thomas, Steven A.},
	year = {2008},
	pages = {2335--2346},
}

@article{hanrahan_winter_2018,
	title = {Winter cover crops reduce nitrate loss in an agricultural watershed in the central {U}.{S}.},
	volume = {265},
	issn = {0167-8809},
	url = {http://www.sciencedirect.com/science/article/pii/S0167880918302779},
	doi = {10.1016/j.agee.2018.07.004},
	abstract = {Agricultural land use in the Midwestern U.S. is the major source of nitrogen (N) causing recurring hypoxia in the northern Gulf of Mexico. Despite efforts to reduce losses, N export from tile-drained, agricultural watersheds throughout the Corn Belt persists. The use of effective agricultural conservation practices can reduce N loss from fields, yet little is known about how field-scale implementation will translate into watershed-scale reductions in N export. In this study, we used a sampling approach with high spatial and temporal resolution to quantify changes in tile drain load and watershed export of nitrate (NO3−-N) after planting cover crops on {\textgreater}60\% of croppable acres in a small, agricultural watershed. We found that median NO3−-N losses from tiles draining fields with cover crops were 69–90\% lower than tiles draining fields without cover crops during winter/spring. Measured instantaneous flow was the major driver of NO3−-N losses from tile drains, though results suggest that this relationship differed between tiles with and without cover crops in spring. The signature of cover crops at the field-scale was evident in watershed NO3−-N export, particularly during times of elevated flows; median daily NO3−-N exported in elevated flows was 18–22\% lower during years with watershed-scale planting of cover crops compared to years without. Nevertheless, changes in watershed NO3−-N export were smaller than the observed reductions in tile drain loads. Results indicate that tile drain reductions directly reflected the influence of cover crops at the field-scale while watershed export integrated both past and present management, ultimately complicating attempts to distinguish the effect of conservation efforts at larger spatial scales.},
	language = {en},
	urldate = {2019-10-17},
	journal = {Agriculture, Ecosystems \& Environment},
	author = {Hanrahan, Brittany R. and Tank, Jennifer L. and Christopher, Sheila F. and Mahl, Ursula H. and Trentman, Matt T. and Royer, Todd V.},
	month = oct,
	year = {2018},
	keywords = {Agriculture, Conservation, Land use, Water quality, Watershed-scale},
	pages = {513--523},
}

@article{gokkaya_subsurface_2017,
	series = {Ecological {Engineering} of {Sustainable} {Landscapes}},
	title = {Subsurface tile drained area detection using {GIS} and remote sensing in an agricultural watershed},
	volume = {108},
	issn = {0925-8574},
	url = {http://www.sciencedirect.com/science/article/pii/S0925857417303762},
	doi = {10.1016/j.ecoleng.2017.06.048},
	abstract = {Subsurface tile drainage has been used around the globe to lower the water table and drain soils that are seasonally or perennially wet making them suitable for agriculture and/or increasing productivity. However, tile drainage systems have a negative impact on water quality of adjacent streams and ditches due to the transport of excess fertilizer nutrients like nitrogen (N) and phosphorus (P) from fields. To support nutrient management and conservation practices like drain water management (DWM), accurate delineation of the agricultural area drained by tiles is critical for quantifying nutrient yields (nutrient mass per area per time) to downstream water bodies. In this study, we tested Geographic Information System decision tree classification (GIS DTC) and satellite remote sensing based methods (i.e., image differencing) to determine tile drainage area in an agricultural watershed, Shatto Ditch Watershed (SDW) in Indiana, USA. Using these techniques, we estimated that 79\% of the cultivated area of SDW is tile drained with 94\% accuracy according to the image differencing approach whereas 55\% is classified as tile drained with an accuracy of 75\% based on estimates from the DTC approach with the most relaxed rule thresholds (where tiles exist on ≤4\% slope with poorly and moderately well drained soils). Using satellite imagery to characterize tile drained area at a high resolution over large geographical extent shows promise and will be important for accurately quantifying nutrient yields from tiles which will inform management and conservation efforts to reduce excess nutrient export to downstream water bodies.},
	language = {en},
	urldate = {2019-10-17},
	journal = {Ecological Engineering},
	author = {Gökkaya, Kemal and Budhathoki, Milan and Christopher, Sheila F. and Hanrahan, Brittany R. and Tank, Jennifer L.},
	month = nov,
	year = {2017},
	keywords = {Decision tree classification, Drain water management, GIS, Midwest, Nutrient runoff, Satellite remote sensing, Subsurface tile drainage},
	pages = {370--379},
}

@article{young_organic_2008,
	title = {Organic matter breakdown and ecosystem metabolism: functional indicators for assessing river ecosystem health},
	volume = {27},
	issn = {0887-3593},
	shorttitle = {Organic matter breakdown and ecosystem metabolism},
	url = {http://www.journals.uchicago.edu/doi/abs/10.1899/07-121.1},
	doi = {10.1899/07-121.1},
	abstract = {River health monitoring traditionally has made use of structural measurements (water quality or taxonomic composition of aquatic organisms). We argue that a more complete assessment of river health should include functional metrics, such as rates of organic matter decomposition and ecosystem metabolism. Leaf breakdown links the characteristics of riparian vegetation with the activity of both aquatic invertebrates and microbial organisms and is affected by natural and human-induced variation in a wide range of environmental factors. Measurement of leaf breakdown is relatively simple and has modest equipment requirements. River metabolism (gross primary productivity and ecosystem respiration) measures the rates of production and use of organic C in river ecosystems as a whole, providing a direct estimate of the food base that determines life-supporting capacity. Metabolism measurements require more sophisticated equipment than do measurements of leaf breakdown, but improvements in technology have made metabolism measurements relatively easy. We review the factors that influence leaf breakdown and river metabolism and pay particular attention to the effects of human-induced environmental stressors. We also describe how measurements can be standardized and suggest criteria for interpreting functional measures in terms of river ecosystem health. Last, we consider the strengths and weaknesses of both methods as functional measures and provide recommendations for their use as biomonitoring tools.},
	number = {3},
	urldate = {2019-10-16},
	journal = {Journal of the North American Benthological Society},
	author = {Young, Roger G. and Matthaei, Christoph D. and Townsend, Colin R.},
	month = sep,
	year = {2008},
	pages = {605--625},
}

@article{marcarelli_predicting_2010,
	title = {Predicting effects of hydrologic alteration and climate change on ecosystem metabolism in a western {U}.{S}. river},
	volume = {20},
	copyright = {© 2010 by the Ecological Society of America},
	issn = {1939-5582},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/09-2364.1},
	doi = {10.1890/09-2364.1},
	abstract = {We estimated past and future hydrographs and patterns of ecosystem metabolism in a fifth-order river of the western United States, where water use and climate change are both expected to alter hydrology in the immediate future. We first reconstructed the unregulated hydrograph to estimate how the current hydrograph has been altered. Due to consumptive use, 95\% as irrigation, current discharge during summer (July–September) was 70\% lower than would occur if the river was unregulated. We then predicted a future hydrograph including effects of consumptive use and climate change; the magnitude of flow changes were minor under this regime relative to those already manifested by consumptive uses. We used time-series regression and a six-year continuous record of open-water metabolism to demonstrate that, under the current hydrologic regime, gross primary production (GPP) was dependent on both water temperature and flow and that ecosystem respiration (ER) was most dependent on temperature. Monte Carlo simulations under the three hydrologic regimes and three temperature scenarios (current, +2°C, +4°C) suggested that flow, but not temperature, may have profound effects on the magnitude of metabolism. Linking temporally detailed analyses of ecological function and hydrology may lead to better understanding and management of changes due to basin-scale water use and/or global-scale climate change.},
	language = {en},
	number = {8},
	urldate = {2019-10-16},
	journal = {Ecological Applications},
	author = {Marcarelli, Amy M. and Kirk, Robert W. Van and Baxter, Colden V.},
	year = {2010},
	keywords = {climate change, discharge, ecosystem metabolism, flow reconstruction, hydrologic regime, irrigation, river, western United States},
	pages = {2081--2088},
}

@article{izagirre_environmental_2008,
	title = {Environmental controls of whole-stream metabolism identified from continuous monitoring of {Basque} streams},
	volume = {27},
	issn = {0887-3593},
	url = {http://www.journals.uchicago.edu/doi/abs/10.1899/07-022.1},
	doi = {10.1899/07-022.1},
	abstract = {Most methods for assessing the ecological status of streams focus on structural characteristics (water quality, community composition, riparian vegetation) but neglect functional properties of the ecosystem because routine methods to assess stream function are scarce. Metabolism, one of the most integrative ecosystem functions, can be a good indicator of stream function because it is relevant across all sizes and types of streams, is sensitive to stressors, such as eutrophication or changes in riparian cover, and can be measured continuously. Environmental controls on whole-ecosystem metabolism were measured at 19 contrasting stream reaches in the Basque Country (northern Spain). Discharge, temperature, and O2 were monitored continuously for 15 mo, reaeration rate was calculated with the nighttime regression method, and whole-stream metabolism was calculated by the single-station open-channel method. The effect of discharge on reaeration coefficients was highly site-specific. Average gross primary production (GPP) ranged from 2.7 to 11.0 g O2 m−2 d−1, was highest at eutrophic sites, and showed no relationship with periphyton biomass. Ecosystem respiration (ER) ranged from 6.3 to 42.6 g O2 m−2 d−1 and was highest at polluted sites. Differences among sites increased in summer. All sites were heterotrophic on an annual basis, but 3 were autotrophic during summer. Turbidity was the main controller of primary production during summer and explained 20\% and 39\% of the spatial variation in GPP and net ecosystem production, respectively. Biological O2 demand of water explained 40\% of ER variance. Catchment activities also controlled GPP, which decreased as population density increased. To our knowledge, our study is the first report of continuous monitoring of whole-stream metabolism at many reaches simultaneously, and it shows the potential of this technique for routine monitoring of stream function.},
	number = {2},
	urldate = {2019-10-16},
	journal = {Journal of the North American Benthological Society},
	author = {Izagirre, Oihana and Agirre, Urko and Bermejo, Miren and Pozo, Jesús and Elosegi, Arturo},
	month = jun,
	year = {2008},
	pages = {252--268},
}

@article{schulte_prairie_2017,
	title = {Prairie strips improve biodiversity and the delivery of multiple ecosystem services from corn–soybean croplands},
	volume = {114},
	copyright = {©  . Freely available online through the PNAS open access option.},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/114/42/11247},
	doi = {10.1073/pnas.1620229114},
	abstract = {Loss of biodiversity and degradation of ecosystem services from agricultural lands remain important challenges in the United States despite decades of spending on natural resource management. To date, conservation investment has emphasized engineering practices or vegetative strategies centered on monocultural plantings of nonnative plants, largely excluding native species from cropland. In a catchment-scale experiment, we quantified the multiple effects of integrating strips of native prairie species amid corn and soybean crops, with prairie strips arranged to arrest run-off on slopes. Replacing 10\% of cropland with prairie strips increased biodiversity and ecosystem services with minimal impacts on crop production. Compared with catchments containing only crops, integrating prairie strips into cropland led to greater catchment-level insect taxa richness (2.6-fold), pollinator abundance (3.5-fold), native bird species richness (2.1-fold), and abundance of bird species of greatest conservation need (2.1-fold). Use of prairie strips also reduced total water runoff from catchments by 37\%, resulting in retention of 20 times more soil and 4.3 times more phosphorus. Corn and soybean yields for catchments with prairie strips decreased only by the amount of the area taken out of crop production. Social survey results indicated demand among both farming and nonfarming populations for the environmental outcomes produced by prairie strips. If federal and state policies were aligned to promote prairie strips, the practice would be applicable to 3.9 million ha of cropland in Iowa alone.},
	language = {en},
	number = {42},
	urldate = {2019-10-15},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Schulte, Lisa A. and Niemi, Jarad and Helmers, Matthew J. and Liebman, Matt and Arbuckle, J. Gordon and James, David E. and Kolka, Randall K. and O’Neal, Matthew E. and Tomer, Mark D. and Tyndall, John C. and Asbjornsen, Heidi and Drobney, Pauline and Neal, Jeri and Ryswyk, Gary Van and Witte, Chris},
	month = oct,
	year = {2017},
	pmid = {28973922},
	keywords = {US Corn Belt, agriculture, agroecosystem services, perennials, sustainability},
	pages = {11247--11252},
}

@article{nunes_impacts_2011,
	title = {Impacts of land use and cover type on runoff and soil erosion in a marginal area of {Portugal}},
	volume = {31},
	issn = {0143-6228},
	url = {http://www.sciencedirect.com/science/article/pii/S014362281000175X},
	doi = {10.1016/j.apgeog.2010.12.006},
	abstract = {This paper presents the results of soil hydrological and erosional responses to different land use and cover types in a marginal area of Portugal. The six land uses and vegetation covers studied (cereal crop, fallow land, shrub cover, recovering autochthonous vegetation, land afforested with Pinus pinaster and pastureland) are representative of situations commonly found throughout central and northern Portugal and also in other Mediterranean systems. The specific goals were to evaluate and compare the hydrological and erosional response of soils representing different land uses and vegetation types, to establish the influence of climatic variability and soil surface characteristics, and to assess the efficiency of alternative land uses proposed by the Common Agrarian Policy in terms of hydrogeomorphic behaviour. The results show significant hydrogeomorphic responses among land uses/covers, indicating arable land and coniferous afforestation as the most serious in terms of runoff and soil erosion. With these types of land use, the soil transported by runoff peaks during autumn/winter coincided with the highest and most erosive rainfall in the experiment area. Conversely, shrub cover and recovering oak, resulting from land abandonment and plant succession, and pastureland, as consequence of conversion to arable land, showed the greatest rainfall infiltration capacity and the lowest rate of soil erosion. According to the results, vegetation dynamics emerges as a key factor in quantifying and interpreting the hydrological and erosional response of the land use/covers monitored. Soil erosion can subsequently be controlled by changing land use and increasing the ground cover, which was revealed as one of the basic approaches to controlling soil erosion in all types of land use.},
	number = {2},
	urldate = {2019-10-15},
	journal = {Applied Geography},
	author = {Nunes, Adélia N. and de Almeida, António C. and Coelho, Celeste O. A.},
	month = apr,
	year = {2011},
	keywords = {Hydrological response, Land use/cover, Marginal area, Portugal, Soil erosion},
	pages = {687--699},
}

@article{malik_use_2000,
	title = {Use of cover crops in short rotation hardwood plantations to control erosion},
	volume = {18},
	issn = {0961-9534},
	url = {http://www.sciencedirect.com/science/article/pii/S0961953400000167},
	doi = {10.1016/S0961-9534(00)00016-7},
	abstract = {This study was designed to test whether the cultivation of cover crops between tree rows in short-rotation woody crop (SRWC) plantations could reduce erosion. Sweetgum (Liquidambar styraciflua L.) seedlings were planted as the SRWC at a 1.5×3 m spacing. Four cover crops, annual ryegrass (Lolium multiflorum L. a winter annual grass); tall fescue (Festuca arundinacea L. a cool-season perennial grass); crimson clover (Trifolium incarnatum L. a winter annual legume); and Interstate sericea lespedeza [Lespedeza cuneata (Dumont) G. Don. a summer growing-perennial legume], were tested at two different strip widths (1.22 and 2.44 m) in comparison with complete competition control. Erosion was measured from 1 August, 1995 to 8 March, 1997 (585 days) by sediment accumulation near the fence where 72 PVC pipes were inserted into soil on a 4.65 m2 (50 ft3) grid area of each plot. The total rainfall recorded during this period was 2422.91 mm (95.3 in.). All cover crops reduced erosion over the complete competition free plot (control), although tall fescue performed poorly at the narrow strip width. There were no significant differences between grasses and legumes for erosion control. Winter annual crops provided significantly more erosion protection than summer growing-perennials. With the exception of tall fescue, narrow strip widths performed as well as wider strip widths. The results indicate that cover crops ryegrass, crimson clover, lespedeza and tall fescue controlled about 64, 61, 51 and 37\% soil erosion respectively as compared to the control during the critical early years of stand development in SRWC hardwood plantations.},
	number = {6},
	urldate = {2019-10-15},
	journal = {Biomass and Bioenergy},
	author = {Malik, R. K. and Green, T. H. and Brown, G. F. and Mays, D.},
	month = jun,
	year = {2000},
	keywords = {Cover crops, SRWC, Short rotation hardwood, Soil erosion, Sweetgum},
	pages = {479--487},
}

@article{mctammany_recovery_nodate,
	title = {Recovery of stream ecosystem metabolism from historical agriculture},
	volume = {26},
	abstract = {Agriculture has influenced southern Appalachian streams for centuries, but recent socioeconomic trends in the region have led to extensive reforestation of agricultural land. Stream ecosystem metabolism might recover from agricultural influence as watersheds undergo reforestation, particularly when shade from terrestrial vegetation is restored. We determined historical (1950) and current (1993) forest cover in 2nd- and 3rd-order watersheds in 4 counties of the southern Appalachians using a geographic information system. Streams were placed into landuse categories based on \% forested land cover in watersheds and riparian zones. Categories included forested (FOR; .98\% forested) and 3 levels of agriculture (AG; ranging from 95\% forest to ,60\% forest) with no change in \% forest over the past 50 y, and 2 levels of recovery from agriculture (REC) indicated by reforestation after land abandonment. We selected 3 streams from each category and measured gross primary production (GPP) and 24-h respiration (R24) using a 2-station diurnal O2 change technique and gas releases to determine reaeration rates. We calculated net ecosystem production (NEP) and the ratio of GPP to R24 (P/R) to compare ecosystem energetics among landuse categories. We measured nutrient concentrations, photosynthetically active radiation (PAR), temperature (degree-days), suspended particle concentrations, and benthic algae (chlorophyll a and ash-free dry mass) to determine if these factors were affected by current or historical agriculture and were correlated with metabolism. Concentrations of inorganic nutrients, PAR, degree-days, suspended solids, and benthic algae were significantly higher in AG streams than in FOR streams. Nutrient and suspended solid concentrations also were higher in REC than in FOR streams, but PAR, degree-days, and benthic algae were similar in REC and FOR streams. GPP varied from ,0.1 g O2 mÀ2 dÀ1 in FOR streams to 1.0 g O2 mÀ2 dÀ1 in AG streams. GPP was similar in REC and FOR streams, suggesting that shading caused by reforestation might reduce GPP to pre-agricultural levels. R24 was 4 to 203 greater than GPP in all stream types, resulting in highly negative NEP. NEP was less negative in AG streams than in FOR and REC streams. Negative NEP and P/R consistently ,1 could have been caused by allochthonous organic matter from remnant forested land (up to 75\% forested) in agricultural watersheds. GPP and P/R were strongly correlated with PAR, degree-days, and algal biomass, suggesting that reduced light limited primary production in the streams studied. R24 was positively correlated with nutrient concentrations. Shading caused by reforestation appears to be an important mechanism by which stream metabolism recovers from historical agriculture. Our results provide support for stream restoration efforts focused on developing and maintaining streamside forests.},
	language = {en},
	author = {McTammany, M E and Benfield, E F and Webster, J R},
	pages = {14},
}

@article{mctammany_recovery_2007,
	title = {Recovery of stream ecosystem metabolism from historical agriculture},
	volume = {26},
	issn = {0887-3593},
	url = {http://www.journals.uchicago.edu/doi/abs/10.1899/06-092.1},
	doi = {10.1899/06-092.1},
	abstract = {Agriculture has influenced southern Appalachian streams for centuries, but recent socioeconomic trends in the region have led to extensive reforestation of agricultural land. Stream ecosystem metabolism might recover from agricultural influence as watersheds undergo reforestation, particularly when shade from terrestrial vegetation is restored. We determined historical (1950) and current (1993) forest cover in 2nd- and 3rd-order watersheds in 4 counties of the southern Appalachians using a geographic information system. Streams were placed into landuse categories based on \% forested land cover in watersheds and riparian zones. Categories included forested (FOR; {\textgreater}98\% forested) and 3 levels of agriculture (AG; ranging from 95\% forest to {\textless}60\% forest) with no change in \% forest over the past 50 y, and 2 levels of recovery from agriculture (REC) indicated by reforestation after land abandonment. We selected 3 streams from each category and measured gross primary production (GPP) and 24-h respiration (R24) using a 2-station diurnal O2 change technique and gas releases to determine reaeration rates. We calculated net ecosystem production (NEP) and the ratio of GPP to R24 (P/R) to compare ecosystem energetics among landuse categories. We measured nutrient concentrations, photosynthetically active radiation (PAR), temperature (degree-days), suspended particle concentrations, and benthic algae (chlorophyll a and ash-free dry mass) to determine if these factors were affected by current or historical agriculture and were correlated with metabolism. Concentrations of inorganic nutrients, PAR, degree-days, suspended solids, and benthic algae were significantly higher in AG streams than in FOR streams. Nutrient and suspended solid concentrations also were higher in REC than in FOR streams, but PAR, degree-days, and benthic algae were similar in REC and FOR streams. GPP varied from {\textless}0.1 g O2 m−2 d−1 in FOR streams to 1.0 g O2 m−2 d−1 in AG streams. GPP was similar in REC and FOR streams, suggesting that shading caused by reforestation might reduce GPP to pre-agricultural levels. R24 was 4 to 20× greater than GPP in all stream types, resulting in highly negative NEP. NEP was less negative in AG streams than in FOR and REC streams. Negative NEP and P/R consistently {\textless}1 could have been caused by allochthonous organic matter from remnant forested land (up to 75\% forested) in agricultural watersheds. GPP and P/R were strongly correlated with PAR, degree-days, and algal biomass, suggesting that reduced light limited primary production in the streams studied. R24 was positively correlated with nutrient concentrations. Shading caused by reforestation appears to be an important mechanism by which stream metabolism recovers from historical agriculture. Our results provide support for stream restoration efforts focused on developing and maintaining streamside forests.},
	number = {3},
	urldate = {2019-10-15},
	journal = {Journal of the North American Benthological Society},
	author = {McTammany, M. E. and Benfield, E. F. and Webster, J. R.},
	month = sep,
	year = {2007},
	pages = {532--545},
}

@article{clapcott_land_2016,
	title = {Land use affects temporal variation in stream metabolism},
	volume = {35},
	issn = {2161-9549},
	url = {http://www.journals.uchicago.edu/doi/abs/10.1086/688872},
	doi = {10.1086/688872},
	abstract = {Stream metabolism (gross primary production and ecosystem respiration) is increasingly used to assess waterway health because mean values are responsive to spatial variation in land use, but little is known about how human land use influences the temporal variability of stream metabolism. We investigated daily variation in dissolved O2 (DO) concentrations and calculated mean and within-season variation in gross primary production (GPP) and ecosystem respiration (ER) rates at 13 stream sites across a landuse intensity gradient in the Auckland region, New Zealand, over 9 y. Based on generalized linear mixed models, mean daily GPP (0.1–12.6 g O2 m−2 d−1) and ER (1.8–29.6 g O2 m−2 d−1) and seasonal variation in stream metabolism were significantly related to landuse intensity with higher variability associated with higher values of a landuse stress score. Overall, mean daily rates and day-to-day variation in GPP and ER were greatest in summer and least in winter. We recommend summer monitoring over a minimum 5-d period to assess stream health. Our results show that human land use affects the mean and the temporal variability of DO and stream metabolism. This finding has important consequences for characterizing in-stream processes and the resilience of stream ecosystems. Only long-term temporal monitoring provides the data needed to assess fully how streams function.},
	number = {4},
	urldate = {2019-10-15},
	journal = {Freshwater Science},
	author = {Clapcott, J. E. and Young, R. G. and Neale, M. W. and Doehring, K. and Barmuta, L. A.},
	month = sep,
	year = {2016},
	pages = {1164--1175},
}

@article{fellows_benthic_2009,
	title = {Benthic metabolism in two turbid dryland rivers},
	volume = {54},
	copyright = {© 2008 The Authors, Journal compilation © 2008 Blackwell Publishing Ltd},
	issn = {1365-2427},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2427.2008.02104.x},
	doi = {10.1111/j.1365-2427.2008.02104.x},
	abstract = {1. Australian dryland rivers have among the most variable discharge of any rivers worldwide and are characterized by extended periods of no flow during which aquatic habitat contracts into isolated waterholes. Despite naturally high turbidity, benthic primary production is known to be the main source of carbon to waterhole food webs. The objective of this study was to quantify rates of benthic metabolism and identify factors influencing these rates in two Australian dryland rivers, the Cooper Creek and the Warrego River. 2. Both rivers have similar variable hydrology and high levels of turbidity (photic depths {\textless} 0.4 m), but fish abundance in Cooper Creek is 10 times than that of the Warrego River. Therefore, an additional aim of the study was to determine if fish abundances reflected underlying differences in benthic primary production. 3. Benthic gross primary production (GPP), benthic respiration, nutrient concentrations and light penetration were measured immediately after flow had ceased (‘post-flow’) and after at least 2 months of zero flow (‘no-flow’) in 15 waterholes from each river. A subset of four waterholes from each river was sampled on two additional occasions to determine if patterns were consistent over time. 4. Cooper Creek generally had higher rates of GPP and a more autotrophic benthic zone than the Warrego River. As a result, the expected positive relationship between fish abundance and GPP was generally observed at a broad catchment scale. 4. Light was the major control in benthic GPP in both rivers, as nutrient concentrations were high on all sampling occasions. However, for similar values of photic depth, GPP was greater in Cooper Creek than in the Warrego River. This suggests that more frequent disturbance of the littoral zone may inhibit biofilm development in waterholes of the Warrego River. 5. Although flow variability in dryland rivers is extreme compared with other rivers worldwide, cycles of expansion and contraction of aquatic habitat in these two rivers were associated with a shift in the dominance of regional scale (subcatchments contributing to river flow) versus local scale (waterhole morphology) influences on ecosystem functioning, similar to floodplain rivers in tropical and temperate regions.},
	language = {en},
	number = {2},
	urldate = {2019-10-15},
	journal = {Freshwater Biology},
	author = {Fellows, Christine S. and Bunn, Stuart E. and Sheldon, Fran and Beard, Nerida J.},
	year = {2009},
	keywords = {desert river, gross primary production, light limitation, respiration, waterhole},
	pages = {236--253},
}

@article{elliott_short-term_1983,
	title = {Short-term bacterial growth, nutrient uptake, and {ATP} turnover in sterilized, inoculated and {C}-amended soil: {The} influence of {N} availability},
	volume = {15},
	issn = {0038-0717},
	shorttitle = {Short-term bacterial growth, nutrient uptake, and {ATP} turnover in sterilized, inoculated and {C}-amended soil},
	url = {http://www.sciencedirect.com/science/article/pii/0038071783901232},
	doi = {10.1016/0038-0717(83)90123-2},
	abstract = {Bacteria, Pseudomonas paucimobilis, were inoculated at two concentrations (6.56 × 104 g−1 and 6.56 × 106g−1) into sterilized soil amended with 700 μg glucose-C g−1. Two levels of NH+4-N (11.0μg g−1 and 81.0 μg g−1) were used. The subsequent development was followed for three days by measurement of several biological, chemical and physiological parameters. The amount of bacterial biomass-C (μg g−1 soil) became twice as great in high as in low N treatments, and significantly decreased between 39.5 and 63.5 h for the high inoculum, high N level treatment due to decreasing cell size. By the end of the experiment the cumulative respired carbon was twice as great and more inorganic P was immobilized for high compared to low N treatments and all available NH+4-N was taken up by the final sample time. Soil ATP concentrations were twice as large in high N treatments but the turnover times were twice as long compared to low N systems. The yield coefficient (Y), calculated from respiration and biomass-C values, equalled 0.61 while substrate was plentiful. Nitrogen limitation did not alter the efficiencey with which glucose was transformed into biomass, but rather controlled the total amount of glucose used and biomass produced.},
	number = {1},
	urldate = {2019-10-08},
	journal = {Soil Biology and Biochemistry},
	author = {Elliott, E. T. and Cole, C. V. and Fairbanks, B. C. and Woods, L. E. and Bryant, R. J. and Coleman, D. C.},
	month = jan,
	year = {1983},
	pages = {85--91},
}

@article{lee_bacterial_2014,
	title = {Bacterial growth efficiency varies in soils under different land management practices},
	volume = {69},
	issn = {0038-0717},
	url = {http://www.sciencedirect.com/science/article/pii/S0038071713004197},
	doi = {10.1016/j.soilbio.2013.11.012},
	abstract = {Transformations of plant-derived carbon into soil organic carbon (SOC) influences both local and global carbon cycles. Soil bacteria play a major role in SOC transformations, which are important for maintaining soil fertility and for stabilizing carbon in soil. SOC is consumed by bacteria in soil and transformed into biomass or respired to carbon dioxide. This bacterial-driven partitioning of SOC is defined as Bacterial Growth Efficiency (BGE) and it is an integral component of models that simulate carbon dynamics. We tested the variability of BGE in microbial communities from soil by measuring bacterial production (BP) and respiration (BR), the two components of BGE, in slurries of soils collected from deciduous forests and croplands at the Kellogg Biological Station Long Term Ecological Research site. BP was measured as 3H-leucine incorporation into protein and BR as oxygen consumption. The differences in BP and BR in soil under different land management practices revealed that BGE was not static but varied from 0.23 to 0.63, supporting more recent SOC models. Bacterial communities from soils of soybean monoculture cropland tended to have a higher BGE than those from deciduous forests. BGE of cropland soil microbes exhibited a large seasonal variation not observed in forest soils. Nutrient amendments on rotation cropland soil microcosms showed that BGE is sensitive to substrate availability and nutrient stoichiometry. Using a range of growth efficiency expected of terrestrial ecosystem, simulations of carbon dynamics in a forest using the DAYCENT model revealed the sensitivity of equilibrium soil carbon values to changes in growth efficiency. Decreasing the default growth efficiency of 0.45 to a growth efficiency of 0.35 reduced the active carbon fraction by 22\%. This sensitivity emphasizes the importance of site-specific BGE measurements for improving the predictive capacity of SOC models, especially when investigating the effects of changes in land management practices on labile SOC transformation. The weak correlation of BP and BR in most soil tested also showed that BGE is a more valuable measurement than the common interpretation of bacterial activity based on BR.},
	urldate = {2019-10-08},
	journal = {Soil Biology and Biochemistry},
	author = {Lee, Zarraz M. and Schmidt, Thomas M.},
	month = feb,
	year = {2014},
	keywords = {Bacterial growth efficiency, Bacterial production, Carbon modeling, Carbon use efficiency, Growth efficiency, Soil carbon transformation, Terrestrial ecosystem},
	pages = {282--290},
}

@article{craft_carbon_2018,
	series = {Wetlands and {Carbon} {Revisited}},
	title = {Carbon sequestration and nutrient accumulation in floodplain and depressional wetlands},
	volume = {114},
	issn = {0925-8574},
	url = {http://www.sciencedirect.com/science/article/pii/S0925857417303622},
	doi = {10.1016/j.ecoleng.2017.06.034},
	abstract = {We measured soil organic carbon (C) sequestration and nutrient (nitrogen-N, phosphorus- P) burial in Czech and Midwest U.S. freshwater floodplain and depressional wetlands to evaluate how landscape position and agricultural land use intensity affects C, N, and P retention. Land use in the South Bohemia of the Czech Republic is dominated by forest and pasture, whereas in the Midwest U.S., land use is dominated by row crop agriculture. Cs-137 and 210Pb dating of soil cores revealed comparable rates of soil accretion among wetland types, ranging from 0.5mm/yr in a Czech floodplain wetland to 2.3mm/yr in a U.S. depressional wetland. Carbon sequestration and N \& P burial did not differ among floodplain (47+14gC/m2/yr, 3.7+1gN/m2/yr, 0.47+0.16g P/m2/yr) and depressional wetlands (50+19g/m2/yr, 3.6+1.3gN/m2/yr, 0.51+0.14g P/m2/yr). However, sediment deposition in Czech floodplain and depressional wetlands was only 10–50\% (150–340g/m2/yr) of rates measured in U.S. wetlands (650–1460g/m2/yr). Our results suggest that, in agricultural landscapes, land use intensity rather than landscape position – floodplain versus depression – drives wetland C sequestration and nutrient retention through increased sediment deposition.},
	urldate = {2019-10-08},
	journal = {Ecological Engineering},
	author = {Craft, Christopher and Vymazal, Jan and Kröpfelová, Lenka},
	month = apr,
	year = {2018},
	keywords = {Agriculture, Carbon, Erosion, Geomorphic, Land use, Landscape position, Nitrogen, Nutrients, Phosphorus, Sediment},
	pages = {137--145},
}

@article{cleveland_c:n:p_2007,
	title = {C:{N}:{P} stoichiometry in soil: is there a “{Redfield} ratio” for the microbial biomass?},
	volume = {85},
	issn = {1573-515X},
	shorttitle = {C},
	url = {10.1007/s10533-007-9132-0},
	doi = {10.1007/s10533-007-9132-0},
	abstract = {Well-constrained carbon:nitrogen:phosphorus (C:N:P) ratios in planktonic biomass, and their importance in advancing our understanding of biological processes and nutrient cycling in marine ecosystems, has motivated ecologists to search for similar patterns in terrestrial ecosystems. Recent analyses indicate the existence of “Redfield-like” ratios in plants, and such data may provide insight into the nature of nutrient limitation in terrestrial ecosystems. We searched for analogous patterns in the soil and the soil microbial biomass by conducting a review of the literature. Although soil is characterized by high biological diversity, structural complexity and spatial heterogeneity, we found remarkably consistent C:N:P ratios in both total soil pools and the soil microbial biomass. Our analysis indicates that, similar to marine phytoplankton, element concentrations of individual phylogenetic groups within the soil microbial community may vary, but on average, atomic C:N:P ratios in both the soil (186:13:1) and the soil microbial biomass (60:7:1) are well-constrained at the global scale. We did see significant variation in soil and microbial element ratios between vegetation types (i.e., forest versus grassland), but in most cases, the similarities in soil and microbial element ratios among sites and across large scales were more apparent than the differences. Consistent microbial biomass element ratios, combined with data linking specific patterns of microbial element stoichiometry with direct evidence of microbial nutrient limitation, suggest that measuring the proportions of C, N and P in the microbial biomass may represent another useful tool for assessing nutrient limitation of ecosystem processes in terrestrial ecosystems.},
	language = {en},
	number = {3},
	urldate = {2019-10-08},
	journal = {Biogeochemistry},
	author = {Cleveland, Cory C. and Liptzin, Daniel},
	month = sep,
	year = {2007},
	keywords = {Carbon, Microbial biomass, Nitrogen, Phosphorus, Soil, Stoichiometry},
	pages = {235--252},
}

@article{zhou_dominating_2017,
	title = {Dominating aquatic macrophytes for the removal of nutrients from waterways of the {Indian} {River} {Lagoon} basin, {South} {Florida}, {USA}},
	volume = {101},
	issn = {0925-8574},
	url = {http://www.sciencedirect.com/science/article/pii/S092585741730006X},
	doi = {10.1016/j.ecoleng.2017.01.006},
	abstract = {Aquatic macrophytes have an important role in cleaning eutrophic runoff water from agriculture and urban areas. However, minimal information is available regarding the quantity of nutrients and/or pollutant they can remove each year from the water and sediments in waterways. This study investigated the biomass productivity of eight dominating aquatic plant species, the concentrations of nutrients in plant tissues and their capacity to absorb and store nutrients. Samples of plant, water, and sediment were collected from October 30 to November 19, 2014 at 22 representative sites in the waterways of the Indian River Lagoon basin, South Florida, USA. The biomass yield of the plant species decreased in the order: cattail (Typha orientalis){\textgreater} pickerelweed (Pontederia cordata){\textgreater} water lettuce (Pistia stratiotes){\textgreater} hydrilla (Hydrilla verticillata){\textgreater} maidencane (Panicum hemitomon){\textgreater} spatterdock (Nuphar advena){\textgreater} pondweed (Potamogeton spp.){\textgreater} salvinia (Salvinia spp.). Cattail had the highest biomass productivity, but only a small part (35.8\%) of the total biomass productivity was harvestable, whereas, water lettuce and hydrilla were mostly harvestable and could contribute almost 100\% to harvestable biomass. Concentration of nutrients in plant varied significantly among the eight plant species and with the sampling sites, suggesting that in addition to genetic differences, physicochemical parameters of overlying water and surface sediment influenced uptake of nutrients by the plants. Among the eight plant species, cattail had the highest total nitrogen (N) (23.4gNm−2) and phosphorus (P) (1.59gPm−2) storage but water lettuce and hydrilla exhibited the highest total N (14.6gNm−2) and P (1.04gPm−2) net storage capacity in this survey. In addition, the highest N and P uptake per year occurred with water lettuce and hydrilla, with the peak of 146kgNha−1y−1 and 10.4kgPha−1y−1, respectively. The results also indicate that multiple harvests of biomass are necessary to realize the removal potential of nutrients/pollutant by the aquatic plants, as the harvesting (cutting) practice can enhance plant growth and prevent release of nutrients/pollutant back into water from plant residue decomposition, which are estimated at 1.87×103 to 72.4×103kgN and 0.07×103 to 4.80×103kg P per year in the IRL basin.},
	urldate = {2019-10-08},
	journal = {Ecological Engineering},
	author = {Zhou, Xiaohong and He, Zhenli and Jones, Kimberly D. and Li, Liguang and Stoffella, Peter J.},
	month = apr,
	year = {2017},
	keywords = {Aquatic plants, Harvesting, Nitrogen, Nutrients storage, Phosphorus, Uptake},
	pages = {107--119},
}

@article{noe_seasonal_2007,
	title = {Seasonal variation in nutrient retention during inundation of a short-hydroperiod floodplain},
	volume = {23},
	issn = {1535-1467},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1002/rra.1035},
	doi = {10.1002/rra.1035},
	abstract = {Floodplains are generally considered to be important locations for nutrient retention or inorganic-to-organic nutrient conversions in riverine ecosystems. However, little is known about nutrient processing in short-hydroperiod floodplains or seasonal variation in floodplain nutrient retention. Therefore, we quantified the net uptake, release or transformation of nitrogen (N), phosphorus (P) and suspended sediment species during brief periods (1–2 days) of overbank flooding through a 250-m floodplain flowpath on the fourth-order Mattawoman Creek, Maryland U.S.A. Sampling occurred during a winter, two spring and a summer flood in this largely forested watershed with low nutrient and sediment loading. Concentrations of NO increased significantly in surface water flowing over the floodplain in three of the four floods, suggesting the floodplain was a source of NO. The upper portion of the floodplain flowpath consistently exported NH, most likely due to the hyporheic flushing of floodplain soil NH, which was then likely nitrified to NO in floodwaters. The floodplain was a sink for particulate organic P (POP) during two floods and particulate organic N and inorganic suspended sediment (ISS) during one flood. Large releases of all dissolved inorganic N and P species occurred following a snowmelt and subsequent cold winter flood. Although there was little consistency in most patterns of nutrient processing among the different floods, this floodplain, characterized by brief inundation, low residence time and low nutrient loading, behaved oppositely from the conceptual model for most floodplains in that it generally exported inorganic nutrients and imported organic nutrients. Published in 2007 by John Wiley \& Sons, Ltd.},
	language = {en},
	number = {10},
	urldate = {2019-10-08},
	journal = {River Research and Applications},
	author = {Noe, Gregory B. and Hupp, Cliff R.},
	year = {2007},
	keywords = {flood, floodplain, nitrogen, nutrient, phosphorus, retention, sediment, wetland},
	pages = {1088--1101},
}

@article{blersch_metabolic_2019,
	title = {Metabolic {Variance}: {A} {Metric} to {Detect} {Shifts} in {Stream} {Ecosystem} {Function} as a {Result} of {Stream} {Restoration}},
	volume = {55},
	copyright = {© 2019 American Water Resources Association},
	issn = {1752-1688},
	shorttitle = {Metabolic {Variance}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1752-1688.12753},
	doi = {10.1111/1752-1688.12753},
	abstract = {The restoration of lotic ecosystems as currently practiced is constrained by a limited understanding of the emergence of stream ecosystem functions and their linkages to perceived ecosystem services valued by society. An investigation was made into the connections between ecosystem function and hydraulic structure of a stream impacted by gravel mining operations in western New York. Stream ecosystem metabolic parameters were measured using two-point dissolved oxygen diurnals on multiple reaches of the same stream, and were correlated with geomorphic and hydraulic descriptors of the same reaches. Results showed ecosystem metabolism at the reach scale varied as a function of geomorphic condition, where higher primary production and community respiration (CR) were observed for reaches observed to be unstable vs. those that were stable or restored. The metabolic variance of a stream ecosystem, proposed as a measure of the degree to which a desired ecological functional goal has been achieved post-restoration, is determined as the rate of change of the ratio of primary production to CR. Shifts in the P/R ratio were evident in reaches post-restoration, presumably as a result of changes in hydraulic structure, supporting the utility of the ratio by describing a direct link between instream hydraulic conditions and ecosystem function.},
	language = {en},
	number = {3},
	urldate = {2019-09-25},
	journal = {JAWRA Journal of the American Water Resources Association},
	author = {Blersch, Stacey Sloan and Blersch, David M. and Atkinson, Joseph F.},
	year = {2019},
	keywords = {ecosystem function, ecosystem metabolism, environmental indicators, hydraulics, monitoring, restoration, rivers/streams},
	pages = {608--621},
}

@article{mcdaniel_relationships_2009-1,
	title = {Relationships between {Benthic} {Sediments} and {Water} {Column} {Phosphorus} in {Illinois} {Streams}},
	volume = {38},
	issn = {1537-2537},
	url = {https://www.agronomy.org/publications/jeq/abstracts/38/2/607},
	doi = {10.2134/jeq2008.0094},
	language = {en},
	number = {2},
	urldate = {2019-09-18},
	journal = {Journal of Environment Quality},
	author = {McDaniel, Marshall D. and David, Mark B. and Royer, Todd V.},
	year = {2009},
	pages = {607},
}

@article{schade_stoichiometry_2011,
	title = {The stoichiometry of nitrogen and phosphorus spiralling in heterotrophic and autotrophic streams},
	volume = {56},
	copyright = {© 2010 Blackwell Publishing Ltd},
	issn = {1365-2427},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2427.2010.02509.x},
	doi = {10.1111/j.1365-2427.2010.02509.x},
	abstract = {1. Nutrient spiralling provides a conceptual framework and a whole-system approach to investigate ecosystem responses to environmental changes. We use spiralling metrics to examine how the coupling of nitrogen and phosphorus uptake varies between streams dominated by either heterotrophic (i.e. bacteria-dominated) or autotrophic (algal-dominated) microbial communities. 2. Algae generally exhibit greater capacity to store nutrients than bacteria because of differences in cellular structures. These differences led us to hypothesise that the uptake of N and P in heterotrophic ecosystems should have reduced stoichiometric variation in response to changes in supply N : P compared to autotrophic ecosystems when assimilation dominates nutrient uptake. 3. To test this hypothesis, we used an array of serial nutrient additions in several streams in the South Fork Eel River watershed in Northern California. In one set of experiments, N and P were added alone and simultaneously in separate experiments to two small, heterotrophic streams to assess uptake rates and interactions between nutrient cycles. In a second set of experiments, N and P were added simultaneously at a range of N : P in one heterotrophic and one autotrophic stream to assess differences in uptake responses to changes in supply N : P. 4. Results of these experiments suggest two important conclusions. First, increased N supply significantly shortened P uptake lengths, while P addition had little impact on N uptake in both streams, indicating that uptake of non-limiting nutrients is tightly coupled to the availability of the limiting element. Second, changes in P uptake and uptake ratios (UN : UP) with increased supply N : P supported our hypothesis that heterotrophic streams are more homeostatic in their responses to changes in nutrient supply than autotrophic streams, suggesting that physiological controls on nutrient use scale up to influence ecosystem-scale patterns in nutrient cycling.},
	language = {en},
	number = {3},
	urldate = {2019-09-16},
	journal = {Freshwater Biology},
	author = {Schade, John D. and MacNEILL, Keeley and Thomas, Steve A. and McNEELY, F. Camille and Welter, Jill R. and Hood, James and Goodrich, Maria and Power, Mary E. and Finlay, Jacques C.},
	year = {2011},
	keywords = {autotrophic, ecosystem homeostasis, heterotrophic, nutrient spiralling, stoichiometry},
	pages = {424--436},
}

@article{roberts_multiple_2007,
	title = {Multiple {Scales} of {Temporal} {Variability} in {Ecosystem} {Metabolism} {Rates}: {Results} from 2 {Years} of {Continuous} {Monitoring} in a {Forested} {Headwater} {Stream}},
	volume = {10},
	issn = {1435-0629},
	shorttitle = {Multiple {Scales} of {Temporal} {Variability} in {Ecosystem} {Metabolism} {Rates}},
	url = {10.1007/s10021-007-9059-2},
	doi = {10.1007/s10021-007-9059-2},
	abstract = {Headwater streams are key sites of nutrient and organic matter processing and retention, but little is known about temporal variability in gross primary production (GPP) and ecosystem respiration (ER) rates as a result of the short duration of most metabolism measurements in lotic ecosystems. We examined temporal variability and controls on ecosystem metabolism by measuring daily rates continuously for 2 years in Walker Branch, a first-order deciduous forest stream. Four important scales of temporal variability in ecosystem metabolism rates were identified: (1) seasonal, (2) day-to-day, (3) episodic (storm-related), and (4) inter-annual. Seasonal patterns were largely controlled by the leaf phenology and productivity of the deciduous riparian forest. Walker Branch was strongly net heterotrophic throughout the year with the exception of the open-canopy spring when GPP and ER rates were co-equal. Day-to-day variability in weather conditions influenced light reaching the streambed, resulting in high day-to-day variability in GPP particularly during spring (daily light levels explained 84\% of the variance in daily GPP in April). Episodic storms depressed GPP for several days in spring, but increased GPP in autumn by removing leaves shading the streambed. Storms depressed ER initially, but then stimulated ER to 2–3 times pre-storm levels for several days. Walker Branch was strongly net heterotrophic in both years of the study, with annual GPP being similar (488 and 519 g O2 m−2 y−1 or 183 and 195 g C m−2 y−1) but annual ER being higher in 2004 than 2005 (−1,645 vs. −1,292 g O2 m−2 y−1 or −617 and −485 g C m−2 y−1). Inter-annual variability in ecosystem metabolism (assessed by comparing 2004 and 2005 rates with previous measurements) was the result of the storm frequency and timing and the size of the spring macroalgal bloom. Changes in local climate can have substantial impacts on stream ecosystem metabolism rates and ultimately influence the carbon source and sink properties of these important ecosystems.},
	language = {en},
	number = {4},
	urldate = {2019-09-05},
	journal = {Ecosystems},
	author = {Roberts, Brian J. and Mulholland, Patrick J. and Hill, Walter R.},
	month = jun,
	year = {2007},
	keywords = {Oedogonium, bryophytes, disturbance, ecosystem respiration, inter-annual variability, leaf litter, light, macroalgae, periphyton, primary production, reaeration, seasonal patterns, storms},
	pages = {588--606},
}

@article{ardon_phosphorus_2010,
	title = {Phosphorus export from a restored wetland ecosystem in response to natural and experimental hydrologic fluctuations},
	volume = {115},
	copyright = {Copyright 2010 by the American Geophysical Union.},
	issn = {2156-2202},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2009JG001169},
	doi = {10.1029/2009JG001169},
	abstract = {Wetland restoration is a commonly used approach to reduce nutrient loading to freshwater and coastal ecosystems, with many wetland restoration efforts occurring in former agricultural fields. Restored wetlands are expected to be effective at retaining or removing both nitrogen and phosphorus (P), yet restoring wetland hydrology to former agricultural fields can lead to the release of legacy fertilizer P. Here, we examined P cycling and export following rewetting of the Timberlake Restoration Project, a 440 ha restored riverine wetland complex in the coastal plain of North Carolina. We also compared P cycling within the restored wetland to two minimally disturbed nearby wetlands and an adjacent active agricultural field. In the restored wetland we observed increased soluble reactive phosphorus (SRP) concentrations following initial flooding, consistent with our expectations that P bound to iron would be released under reducing conditions. SRP concentrations in spring were 2.5 times higher leaving the restored wetland than a forested wetland and an agricultural field. During two large-scale drawdown and rewetting experiments we decreased the water depth by 1 m in ∼10 ha of inundated wetland for 2 weeks, followed by reflooding. Rewetting following experimental drainage had no effect on SRP concentrations in winter, but SRP concentrations did increase when the experiment was repeated during summer. Our best estimates suggest that this restored wetland could release legacy fertilizer P for up to a decade following hydrologic restoration. The time lag between restoration and biogeochemical recovery should be incorporated into management strategies of restored wetlands.},
	language = {en},
	number = {G4},
	urldate = {2019-09-02},
	journal = {Journal of Geophysical Research: Biogeosciences},
	author = {Ardón, Marcelo and Montanari, Shaena and Morse, Jennifer L. and Doyle, Martin W. and Bernhardt, Emily S.},
	year = {2010},
	keywords = {phosphorus, restoration, wetland},
}

@misc{noauthor_phosphorus_nodate,
	title = {Phosphorus export from a restored wetland ecosystem in response to natural and experimental hydrologic fluctuations - {Ardón} - 2010 - {Journal} of {Geophysical} {Research}: {Biogeosciences} - {Wiley} {Online} {Library}},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2009JG001169},
	urldate = {2019-09-02},
}

@misc{noauthor_phosphorus_nodate-1,
	title = {Phosphorus export from a restored wetland ecosystem in response to natural and experimental hydrologic fluctuations - {Ardón} - 2010 - {Journal} of {Geophysical} {Research}: {Biogeosciences} - {Wiley} {Online} {Library}},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/epdf/10.1029/2009JG001169},
	urldate = {2019-09-02},
}

@misc{noauthor_biological_nodate,
	title = {Biological stoichiometry of {Daphnia} growth: {An} ecophysiological test of the growth rate hypothesis - {Acharya} - 2004 - {Limnology} and {Oceanography} - {Wiley} {Online} {Library}},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.2004.49.3.0656},
	urldate = {2019-09-02},
}

@article{acharya_biological_2004,
	title = {Biological stoichiometry of {Daphnia} growth: {An} ecophysiological test of the growth rate hypothesis},
	volume = {49},
	copyright = {© 2004, by the Association for the Sciences of Limnology and Oceanography, Inc.},
	issn = {1939-5590},
	shorttitle = {Biological stoichiometry of {Daphnia} growth},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.2004.49.3.0656},
	doi = {10.4319/lo.2004.49.3.0656},
	abstract = {The growth rate hypothesis (GRH) proposes that variation in organism C: P and N: P ratios reflects variation in P content associated with altered allocation to P-rich ribosomal RNA under different growth rates. We tested the GRH by examining the effects of food quantity and stoichiometric quality (differing carbon : nitrogen : phosphorus [C :N: P] ratios) on juvenile growth and chemical composition (C :N: P, RNA, and DNA contents) of two species of Daphnia (D. galeata, D. pulicaria). Daphnia in P-limited experiments were fed saturating and limiting concentrations of food (Scenedesmus acutus) of high P (C: P = 110 ± 7.3), medium P (456 ± 20.7), and low P (934 ± 23.6), and in an N-limited experiment D. pulicaria was fed saturating concentrations of high N (C:N = 6.31 ± 0.35), medium 1 and medium 2 (9.0 ± 0.42; 15.0 ± 0.49, respectively), and low N (18.22 ± 0.56) food. In P-limited experiments, both Daphnia species grew fastest under P-rich, high food conditions and grew slowest under P-deficient, low food conditions, showing effects of both food quality and quantity. Daphnia body percentage P, C: P, N: P, and percentage RNA were tightly correlated with growth rates, and RNA contributed a significant fraction of total body P (48.8\% [62.0\%]). This strong three-way (growth-RNA-P) set of correlations supports the GRH. In the N-limited experiment, food C:N had a moderate effect on Daphnia growth. While there was a good linear correlation between P and RNA, growth rate was uncorrelated with RNA content and P content, suggesting that the three-way coupling of growth, RNA, and P content is broken under N limitation of growth, but more data for these conditions are needed. These data help in delineating the physiological conditions under which the GRH holds and may be useful in interpreting variation in body stoichiometry of zooplankton from field and lab studies.},
	language = {en},
	number = {3},
	urldate = {2019-09-02},
	journal = {Limnology and Oceanography},
	author = {Acharya, Kumud and Kyle, Marcia and Elser, James J.},
	year = {2004},
	pages = {656--665},
}

@article{elser_growth_2003,
	title = {Growth rate–stoichiometry couplings in diverse biota},
	volume = {6},
	issn = {1461-0248},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1461-0248.2003.00518.x},
	doi = {10.1046/j.1461-0248.2003.00518.x},
	abstract = {Biological stoichiometry provides a mechanistic theory linking cellular and biochemical features of co-evolving biota with constraints imposed by ecosystem energy and nutrient inputs. Thus, understanding variation in biomass carbon : nitrogen : phosphorus (C : N : P) stoichiometry is a major priority for integrative biology. Among various factors affecting organism stoichiometry, differences in C : P and N : P stoichiometry have been hypothesized to reflect organismal P-content because of altered allocation to P-rich ribosomal RNA at different growth rates (the growth rate hypothesis, GRH). We tested the GRH using data for microbes, insects, and crustaceans and we show here that growth, RNA content, and biomass P content are tightly coupled across species, during ontogeny, and under physiological P limitation. We also show, however, that this coupling is relaxed when P is not limiting for growth. The close relationship between P and RNA contents indicates that ribosomes themselves represent a biogeochemically significant repository of P in ecosystems and that allocation of P to ribosome generation is a central process in biological production in ecological systems.},
	language = {en},
	number = {10},
	urldate = {2019-09-02},
	journal = {Ecology Letters},
	author = {Elser, J. J. and Acharya, K. and Kyle, M. and Cotner, J. and Makino, W. and Markow, T. and Watts, T. and Hobbie, S. and Fagan, W. and Schade, J. and Hood, J. and Sterner, R. W.},
	year = {2003},
	keywords = {Growth, RNA, phosphorous, stoichiometry},
	pages = {936--943},
}

@article{elser_growth_2003-1,
	title = {Growth rate–stoichiometry couplings in diverse biota},
	volume = {6},
	issn = {1461-0248},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1461-0248.2003.00518.x},
	doi = {10.1046/j.1461-0248.2003.00518.x},
	abstract = {Biological stoichiometry provides a mechanistic theory linking cellular and biochemical features of co-evolving biota with constraints imposed by ecosystem energy and nutrient inputs. Thus, understanding variation in biomass carbon : nitrogen : phosphorus (C : N : P) stoichiometry is a major priority for integrative biology. Among various factors affecting organism stoichiometry, differences in C : P and N : P stoichiometry have been hypothesized to reflect organismal P-content because of altered allocation to P-rich ribosomal RNA at different growth rates (the growth rate hypothesis, GRH). We tested the GRH using data for microbes, insects, and crustaceans and we show here that growth, RNA content, and biomass P content are tightly coupled across species, during ontogeny, and under physiological P limitation. We also show, however, that this coupling is relaxed when P is not limiting for growth. The close relationship between P and RNA contents indicates that ribosomes themselves represent a biogeochemically significant repository of P in ecosystems and that allocation of P to ribosome generation is a central process in biological production in ecological systems.},
	language = {en},
	number = {10},
	urldate = {2019-09-02},
	journal = {Ecology Letters},
	author = {Elser, J. J. and Acharya, K. and Kyle, M. and Cotner, J. and Makino, W. and Markow, T. and Watts, T. and Hobbie, S. and Fagan, W. and Schade, J. and Hood, J. and Sterner, R. W.},
	year = {2003},
	keywords = {Growth, RNA, phosphorous, stoichiometry},
	pages = {936--943},
}

@article{elser_growth_2003-2,
	title = {Growth rate–stoichiometry couplings in diverse biota},
	volume = {6},
	issn = {1461-0248},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1461-0248.2003.00518.x},
	doi = {10.1046/j.1461-0248.2003.00518.x},
	abstract = {Biological stoichiometry provides a mechanistic theory linking cellular and biochemical features of co-evolving biota with constraints imposed by ecosystem energy and nutrient inputs. Thus, understanding variation in biomass carbon : nitrogen : phosphorus (C : N : P) stoichiometry is a major priority for integrative biology. Among various factors affecting organism stoichiometry, differences in C : P and N : P stoichiometry have been hypothesized to reflect organismal P-content because of altered allocation to P-rich ribosomal RNA at different growth rates (the growth rate hypothesis, GRH). We tested the GRH using data for microbes, insects, and crustaceans and we show here that growth, RNA content, and biomass P content are tightly coupled across species, during ontogeny, and under physiological P limitation. We also show, however, that this coupling is relaxed when P is not limiting for growth. The close relationship between P and RNA contents indicates that ribosomes themselves represent a biogeochemically significant repository of P in ecosystems and that allocation of P to ribosome generation is a central process in biological production in ecological systems.},
	language = {en},
	number = {10},
	urldate = {2019-09-02},
	journal = {Ecology Letters},
	author = {Elser, J. J. and Acharya, K. and Kyle, M. and Cotner, J. and Makino, W. and Markow, T. and Watts, T. and Hobbie, S. and Fagan, W. and Schade, J. and Hood, J. and Sterner, R. W.},
	year = {2003},
	keywords = {Growth, RNA, phosphorous, stoichiometry},
	pages = {936--943},
}

@article{elser_organism_1996,
	title = {Organism {Size}, {Life} {History}, and {N}:{P} {Stoichiometry}},
	volume = {46},
	issn = {00063568, 15253244},
	shorttitle = {Organism {Size}, {Life} {History}, and {N}},
	url = {https://academic.oup.com/bioscience/article-lookup/doi/10.2307/1312897},
	doi = {10.2307/1312897},
	language = {en},
	number = {9},
	urldate = {2019-09-02},
	journal = {BioScience},
	author = {Elser, James J. and Dobberfuhl, Dean R. and MacKay, Neil A. and Schampel, John H.},
	month = oct,
	year = {1996},
	pages = {674--684},
}

@article{elser_organism_1996-1,
	title = {Organism {Size}, {Life} {History}, and {N}:{P} {Stoichiometry}},
	volume = {46},
	issn = {00063568, 15253244},
	shorttitle = {Organism {Size}, {Life} {History}, and {N}},
	url = {https://academic.oup.com/bioscience/article-lookup/doi/10.2307/1312897},
	doi = {10.2307/1312897},
	language = {en},
	number = {9},
	urldate = {2019-09-02},
	journal = {BioScience},
	author = {Elser, James J. and Dobberfuhl, Dean R. and MacKay, Neil A. and Schampel, John H.},
	month = oct,
	year = {1996},
	pages = {674--684},
}

@article{shaughnessy_sediments_2019,
	title = {Sediments in {Agricultural} {Reservoirs} {Act} as {Sinks} and {Sources} for {Nutrients} over {Various} {Timescales}},
	volume = {55},
	copyright = {©2019. American Geophysical Union. All Rights Reserved.},
	issn = {1944-7973},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018WR024004},
	doi = {10.1029/2018WR024004},
	abstract = {Reservoirs along rivers have the potential to act as nutrient sinks (e.g., denitrification and sedimentation) or sources (e.g., decomposition and redox changes), potentially reducing or enhancing nutrient loads downstream. This study investigated the spatial and temporal variability of water and lakebed sediment chemistry for an agricultural reservoir, Carlyle Lake (Illinois, U.S.), to assess the role of sediments as nutrient sinks or sources. Samples were collected across the reservoir over a 2-year period. We measured N- and P-species in water at the sediment-water interface, in sediment porewaters, and loosely bound to sediment exchange sites. Total N, total P, total C, organic matter, Fe, Mn, and grain size were measured in bulk sediments. We observed a strong gradient in sedimentary total N, total P, total C, organic matter, and metals along the reservoir, with the lowest concentrations at the river mouth and the highest concentrations near the dam. Additionally, we did a long-term nutrient mass balance using historical water quality data for streams entering and exiting the reservoir and the reservoir itself. Mass balance calculations showed that Carlyle Lake, on average, removed 2,738 Mg N/year and released 121 Mg P/year over the multidecadal observation period. While N was consistently removed from the system over time, P was initially stored in, but later released from, the reservoir. The subsequent release of legacy P from the reservoir led to higher outgoing, compared with incoming, P loads. Thus, reservoirs in intensively managed landscapes can act as sinks for N but sources for P over decadal timescales.},
	language = {en},
	number = {7},
	urldate = {2019-08-29},
	journal = {Water Resources Research},
	author = {Shaughnessy, A. R. and Sloan, J. J. and Corcoran, M. J. and Hasenmueller, E. A.},
	year = {2019},
	keywords = {intensively managed landscapes, nutrients, reservoirs, water quality},
	pages = {5985--6000},
}

@misc{noauthor_flow_nodate,
	title = {Flow {Extremes} as {Spatiotemporal} {Control} {Points} on {River} {Solute} {Fluxes} and {Metabolism} - {Hensley} - 2019 - {Journal} of {Geophysical} {Research}: {Biogeosciences} - {Wiley} {Online} {Library}},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2018JG004738},
	urldate = {2019-08-28},
}

@article{roberts_multiple_2007-1,
	title = {Multiple {Scales} of {Temporal} {Variability} in {Ecosystem} {Metabolism} {Rates}: {Results} from 2 {Years} of {Continuous} {Monitoring} in a {Forested} {Headwater} {Stream}},
	volume = {10},
	issn = {1435-0629},
	shorttitle = {Multiple {Scales} of {Temporal} {Variability} in {Ecosystem} {Metabolism} {Rates}},
	url = {10.1007/s10021-007-9059-2},
	doi = {10.1007/s10021-007-9059-2},
	abstract = {Headwater streams are key sites of nutrient and organic matter processing and retention, but little is known about temporal variability in gross primary production (GPP) and ecosystem respiration (ER) rates as a result of the short duration of most metabolism measurements in lotic ecosystems. We examined temporal variability and controls on ecosystem metabolism by measuring daily rates continuously for 2 years in Walker Branch, a first-order deciduous forest stream. Four important scales of temporal variability in ecosystem metabolism rates were identified: (1) seasonal, (2) day-to-day, (3) episodic (storm-related), and (4) inter-annual. Seasonal patterns were largely controlled by the leaf phenology and productivity of the deciduous riparian forest. Walker Branch was strongly net heterotrophic throughout the year with the exception of the open-canopy spring when GPP and ER rates were co-equal. Day-to-day variability in weather conditions influenced light reaching the streambed, resulting in high day-to-day variability in GPP particularly during spring (daily light levels explained 84\% of the variance in daily GPP in April). Episodic storms depressed GPP for several days in spring, but increased GPP in autumn by removing leaves shading the streambed. Storms depressed ER initially, but then stimulated ER to 2–3 times pre-storm levels for several days. Walker Branch was strongly net heterotrophic in both years of the study, with annual GPP being similar (488 and 519 g O2 m−2 y−1 or 183 and 195 g C m−2 y−1) but annual ER being higher in 2004 than 2005 (−1,645 vs. −1,292 g O2 m−2 y−1 or −617 and −485 g C m−2 y−1). Inter-annual variability in ecosystem metabolism (assessed by comparing 2004 and 2005 rates with previous measurements) was the result of the storm frequency and timing and the size of the spring macroalgal bloom. Changes in local climate can have substantial impacts on stream ecosystem metabolism rates and ultimately influence the carbon source and sink properties of these important ecosystems.},
	language = {en},
	number = {4},
	urldate = {2019-08-24},
	journal = {Ecosystems},
	author = {Roberts, Brian J. and Mulholland, Patrick J. and Hill, Walter R.},
	month = jun,
	year = {2007},
	keywords = {Oedogonium, bryophytes, disturbance, ecosystem respiration, inter-annual variability, leaf litter, light, macroalgae, periphyton, primary production, reaeration, seasonal patterns, storms},
	pages = {588--606},
}

@article{mulholland_inter-biome_2001,
	title = {Inter-biome comparison of factors controlling stream metabolism},
	volume = {46},
	issn = {1365-2427},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-2427.2001.00773.x},
	doi = {10.1046/j.1365-2427.2001.00773.x},
	abstract = {1. We studied whole-ecosystem metabolism in eight streams from several biomes in North America to identify controls on the rate of stream metabolism over a large geographic range. The streams studied had climates ranging from tropical to cool-temperate and from humid to arid and were all relatively uninfluenced by human disturbances. 2. Rates of gross primary production (GPP), ecosystem respiration (R) and net ecosystem production (NEP) were determined using the open-system, two-station diurnal oxygen change method. 3. Three general patterns in metabolism were evident among streams: (1) relatively high GPP with positive NEP (i.e. net oxygen production) in early afternoon, (2) moderate primary production with a distinct peak in GPP during daylight but negative NEP at all times and (3) little or no evidence of GPP during daylight and a relatively constant and negative NEP over the entire day. 4. Gross primary production was most strongly correlated with photosynthetically active radiation (PAR). A multiple regression model that included log PAR and stream water soluble reactive phosphorus (SRP) concentration explained 90\% of the variation in log GPP. 5. Ecosystem respiration was significantly correlated with SRP concentration and size of the transient storage zone and, together, these factors explained 73\% of the variation in R. The rate of R was poorly correlated with the rate of GPP. 6. Net ecosystem production was significantly correlated only with PAR, with 53\% of the variation in log NEP explained by log PAR. Only Sycamore Creek, a desert stream in Arizona, had positive NEP (GPP: R {\textgreater} 1), supporting the idea that streams are generally net sinks rather than net sources of organic matter. 7. Our results suggest that light, phosphorus concentration and channel hydraulics are important controls on the rate of ecosystem metabolism in streams over very extensive geographic areas.},
	language = {en},
	number = {11},
	urldate = {2019-08-24},
	journal = {Freshwater Biology},
	author = {Mulholland, P. J. and Fellows, C. S. and Tank, J. L. and Grimm, N. B. and Webster, J. R. and Hamilton, S. K. and Martí, E. and Ashkenas, L. and Bowden, W. B. and Dodds, W. K. and Mcdowell, W. H. and Paul, M. J. and Peterson, B. J.},
	year = {2001},
	keywords = {inter-biome, metabolism, primary production, respiration, stream},
	pages = {1503--1517},
}

@article{marzolf_improvements_1994,
	title = {Improvements to the {Diurnal} {Upstream}–{Downstream} {Dissolved} {Oxygen} {Change} {Technique} for {Determining} {Whole}-{Stream} {Metabolism} in {Small} {Streams}},
	volume = {51},
	issn = {0706-652X},
	url = {https://www.nrcresearchpress.com/doi/abs/10.1139/f94-158},
	doi = {10.1139/f94-158},
	abstract = {Whole-stream metabolism in a first-order stream was measured using upstream–downstream changes in dissolved oxygen (DO) concentration measured at 1-min intervals over a 40-h period. The measured ch..., Le métabolisme global du cours d'eau dans un cours d'eau de premier ordre a été mesuré en utilisant les changements amont–aval de la concentration d'oxygène dissous (OD) mesurés à des intervalles d...},
	number = {7},
	urldate = {2019-08-24},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Marzolf, Erich R. and Mulholland, Patrick J. and Steinman, Alan D.},
	month = jul,
	year = {1994},
	pages = {1591--1599},
}

@article{johnson_landscape_1997,
	title = {Landscape influences on water chemistry in {Midwestern} stream ecosystems},
	volume = {37},
	copyright = {Blackwell Science Ltd, Oxford},
	issn = {1365-2427},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-2427.1997.d01-539.x},
	doi = {10.1046/j.1365-2427.1997.d01-539.x},
	abstract = {1. Landscape characteristics of sixty-two subcatchments within the Saginaw Bay Catchment of central Michigan were examined to identify relationships with stream water chemistry. Land use, land cover and elevation were quantified for both entire catchments and the upland–river ecotone (100 m stream buffer strip). Catchment and ecotone data were then empirically compared with stream water chemistry using multivariate and regression analyses. Redundancy analysis was used to partition variance among land use, geology, and the shared influence of land use and geology. 2. Major catchments dominated by rowcrop agriculture had the highest alkalinity, total dissolved solids and nitrate + nitrite concentrations. 3. Strong seasonal differences were observed in total nitrogen and nitrite + nitrate, but not in total phosphorus or suspended solids. Land use and landscape structure factors such as slope and patch density (number of land use patches per km2) accounted for most of the observed variance in summer. 4. In both autumn and summer, landscape factors accounted for much of the observed variation in total dissolved solids and alkalinity. During autumn, geological factors and the shared influence of geology/landscape structure plus land use exerted more influence than did land use alone. 5. Total phosphorus and total suspended solids were much better explained by land use within the stream ecotone in summer than in other seasons. However, total nitrogen, nitrate, orthophosphate and alkalinity were equally well explained by land use within the ecotone and throughout the whole catchment. Only total dissolved solids in summer and ammonium in autumn were explained better by the whole catchment than the ecotone. 6. Our results show that relatively coarse spatial databases can provide useful descriptors of regional water quality.},
	language = {en},
	number = {1},
	urldate = {2019-08-24},
	journal = {Freshwater Biology},
	author = {Johnson, Lucinda and Richards, Carl and Host, George and Arthur, John},
	year = {1997},
	pages = {193--208},
}

@article{griffiths_agricultural_2013,
	title = {Agricultural land use alters the seasonality and magnitude of stream metabolism},
	volume = {58},
	copyright = {© 2013, by the Association for the Sciences of Limnology and Oceanography, Inc.},
	issn = {1939-5590},
	url = {http://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.2013.58.4.1513},
	doi = {10.4319/lo.2013.58.4.1513},
	abstract = {We present a comprehensive data set of gross primary production (GPP) and ecosystem respiration (ER) in open-canopy, nutrient-rich streams draining row-crop agriculture in the midwestern United States. We used two approaches to characterize temporal and spatial variation in whole-stream metabolism: continuous measurements in one agricultural stream for 1 yr, and periodic daily measurements in six agricultural streams on six dates spanning summer, autumn, and winter. Continuous measurements revealed high rates of GPP (range: 0.1 to 22.0 g O2 m−2 d−1) and ER (range: −0.9 to −34.8 g O2 m−2 d−1) that varied seasonally with light availability and temperature. GPP and ER were correlated during periods of high autotrophic production, suggesting that autotrophic respiration comprised a large portion of ER; however, the GPP : ER ratio exceeded 1 for only 4\% of the year. While there were distinct temporal patterns in metabolism in one agricultural stream, rates of GPP and ER were similar among six streams when assessed via periodic daily measurements, and 26\% of all periodic daily measurements were autotrophic with GPP : ER {\textgreater} 1. However, these periodic measurements were collected under baseflow conditions and may have overestimated the extent of autotrophy in agricultural streams. Overall, the open canopy and elevated nutrients of agricultural streams resulted in higher rates of GPP and ER compared with more pristine systems. Estimates of metabolism are needed from underrepresented systems to accurately quantify carbon fluxes from fluvial ecosystems.},
	language = {en},
	number = {4},
	urldate = {2019-08-24},
	journal = {Limnology and Oceanography},
	author = {Griffiths, Natalie A. and Tank, Jennifer L. and Royer, Todd V. and Roley, Sarah S. and Rosi-Marshall, Emma J. and Whiles, Matt R. and Beaulieu, Jake J. and Johnson, Laura T.},
	year = {2013},
	pages = {1513--1529},
}

@article{dodds_abiotic_2013,
	title = {Abiotic controls and temporal variability of river metabolism: multiyear analyses of {Mississippi} and {Chattahoochee} {River} data},
	volume = {32},
	issn = {2161-9549},
	shorttitle = {Abiotic controls and temporal variability of river metabolism},
	url = {http://www.journals.uchicago.edu/doi/abs/10.1899/13-018.1},
	doi = {10.1899/13-018.1},
	abstract = {Whole-ecosystem metabolism is an important indicator of the role of organic matter, C cycling, and trophic structure in rivers. Ecosystem metabolism is well studied in small streams, but less is known about metabolism in large rivers. We estimated daily whole-ecosystem metabolism over 2 y for 1 site each at the Mississippi and Chattahoochee Rivers in the USA to understand factors influencing temporal patterns of ecosystem metabolism. We estimated rates of gross primary production (GPP), community respiration (CR), and net ecosystem production (NEP) with a curve-fitting approach with publicly available discharge (Q), dissolved O2, temperature, and photosynthetically active radiation (PAR) data. Models were run for week-long blocks, and power analyses suggested that rates should be established at least once for each 10-wk period throughout the year to characterize annual rates of metabolism accurately in these 2 rivers. We analyzed weekly rates averaged over 10-wk periods with Spearman rank correlation to identify potential drivers and with path analyses to identify interactions among variables driving GPP, CR, and NEP. Both rivers had an overall negative NEP, and the Mississippi River had stronger seasonal trends. In the Mississippi River, CR was strongly positively correlated with Q, which suggests variation in seasonal availability of allochthonous C. In the Chattahoochee, CR was most strongly positively correlated with GPP, whereas GPP was negatively correlated with Q, which suggests that autochthonous processes and water-column light attenuation played important roles in C dynamics. Our results suggest that these large rivers were net heterotrophic at annual time scales but autotrophy can be important seasonally.},
	number = {4},
	urldate = {2019-08-24},
	journal = {Freshwater Science},
	author = {Dodds, Walter K. and Veach, Allison M. and Ruffing, Claire M. and Larson, Danelle M. and Fischer, Jason L. and Costigan, Katie H.},
	month = dec,
	year = {2013},
	pages = {1073--1087},
}

@article{demars_temperature_2011,
	title = {Temperature and the metabolic balance of streams},
	volume = {56},
	copyright = {© 2011 Blackwell Publishing Ltd},
	issn = {1365-2427},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2427.2010.02554.x},
	doi = {10.1111/j.1365-2427.2010.02554.x},
	abstract = {1. It is becoming increasingly clear that fresh waters play a major role in the global C cycle. Stream ecosystem respiration (ER) and gross primary productivity (GPP) exert a significant control on organic carbon fluxes in fluvial networks. However, little is known about how climate change will influence these fluxes. 2. Here, we used a ‘natural experiment’ to demonstrate the role of temperature and nutrient cycling in whole-system metabolism (ER, GPP and net ecosystem production – NEP), in naturally heated geothermal (5–25 °C) Icelandic streams. 3. We calculated ER and GPP with a new, more accurate method, which enabled us to take into account the additional uncertainties owing to stream spatial heterogeneity in oxygen concentrations within a reach. ER ranged 1–25 g C m−2 day−1 and GPP 1–10 g C m−2 day−1. The median uncertainties (based on 1 SD) in ER and GPP were 50\% and 20\%, respectively. 4. Despite extremely low water nutrient concentrations, high metabolic rates in the warm streams were supported by fast cycling rates of nutrients, as revealed from inorganic nutrient (N, P) addition experiments. 5. ER exceeded GPP in all streams (with average GPP/ER = 0.6) and was more strongly related to temperature than GPP, resulting in elevated negative NEP with warming. We show that, as a first approximation based on summer investigations, global stream carbon emission to the atmosphere would nearly double from 0.12 Pg C year−1 at 13 °C to 0.21 (0.15–0.33) Pg C year−1 with a 5 °C warming. 6. Compared to previous studies from natural systems (including terrestrial ecosystems), the temperature dependence of stream metabolism was not confounded by latitude or altitude, seasonality, light and nutrient availability, water chemistry, space availability (water transient storage), and water availability. 7. Consequently, stream nutrient processing is likely to increase with warming, protecting downstream ecosystems (rivers, estuaries, coastal marine systems) during the summer low flows from nutrient enrichment, but at the cost of increased CO2 flux back to the atmosphere.},
	language = {en},
	number = {6},
	urldate = {2019-08-24},
	journal = {Freshwater Biology},
	author = {Demars, Benoît O. L. and Manson, J. Russell and Ólafsson, Jon S. and Gíslason, Gísli M. and Gudmundsdóttir, Rakel and Woodward, Guy and Reiss, Julia and Pichler, Doris E. and Rasmussen, Jes J. and Friberg, Nikolai},
	year = {2011},
	keywords = {fluvial ecosystem, groundwater-fed stream, metabolic theory of ecology, nutrient spiralling, photosynthesis},
	pages = {1106--1121},
}

@misc{noauthor_landscapes_nodate,
	title = {Landscapes and {Riverscapes}: {The} {Influence} of {Land} {Use} on {Stream} {Ecosystems} {\textbar} {Annual} {Review} of {Ecology}, {Evolution}, and {Systematics}},
	url = {https://www-annualreviews-org.proxy.library.nd.edu/doi/10.1146/annurev.ecolsys.35.120202.110122},
	urldate = {2019-08-24},
}

@article{bernot_inter-regional_2010,
	title = {Inter-regional comparison of land-use effects on stream metabolism},
	volume = {55},
	copyright = {© 2010 Blackwell Publishing Ltd},
	issn = {1365-2427},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2427.2010.02422.x},
	doi = {10.1111/j.1365-2427.2010.02422.x},
	abstract = {1. Rates of whole-system metabolism (production and respiration) are fundamental indicators of ecosystem structure and function. Although first-order, proximal controls are well understood, assessments of the interactions between proximal controls and distal controls, such as land use and geographic region, are lacking. Thus, the influence of land use on stream metabolism across geographic regions is unknown. Further, there is limited understanding of how land use may alter variability in ecosystem metabolism across regions. 2. Stream metabolism was measured in nine streams in each of eight regions (n = 72) across the United States and Puerto Rico. In each region, three streams were selected from a range of three land uses: agriculturally influenced, urban-influenced, and reference streams. Stream metabolism was estimated from diel changes in dissolved oxygen concentrations in each stream reach with correction for reaeration and groundwater input. 3. Gross primary production (GPP) was highest in regions with little riparian vegetation (sagebrush steppe in Wyoming, desert shrub in Arizona/New Mexico) and lowest in forested regions (North Carolina, Oregon). In contrast, ecosystem respiration (ER) varied both within and among regions. Reference streams had significantly lower rates of GPP than urban or agriculturally influenced streams. 4. GPP was positively correlated with photosynthetically active radiation and autotrophic biomass. Multiple regression models compared using Akaike’s information criterion (AIC) indicated GPP increased with water column ammonium and the fraction of the catchment in urban and reference land-use categories. Multiple regression models also identified velocity, temperature, nitrate, ammonium, dissolved organic carbon, GPP, coarse benthic organic matter, fine benthic organic matter and the fraction of all land-use categories in the catchment as regulators of ER. 5. Structural equation modelling indicated significant distal as well as proximal control pathways including a direct effect of land-use on GPP as well as SRP, DIN, and PAR effects on GPP; GPP effects on autotrophic biomass, organic matter, and ER; and organic matter effects on ER. 6. Overall, consideration of the data separated by land-use categories showed reduced inter-regional variability in rates of metabolism, indicating that the influence of agricultural and urban land use can obscure regional differences in stream metabolism.},
	language = {en},
	number = {9},
	urldate = {2019-08-24},
	journal = {Freshwater Biology},
	author = {Bernot, Melody J. and Sobota, Daniel J. and Hall, Robert O. and Mulholland, Patrick J. and Dodds, Walter K. and Webster, Jackson R. and Tank, Jennifer L. and Ashkenas, Linda R. and Cooper, Lee W. and Dahm, Clifford N. and Gregory, Stanley V. and Grimm, Nancy B. and Hamilton, Stephen K. and Johnson, Sherri L. and Mcdowell, William H. and Meyer, Judith L. and Peterson, Bruce and Poole, Geoffrey C. and Valett, H. Maurice and Arango, Clay and Beaulieu, Jake J. and Burgin, Amy J. and Crenshaw, Chelsea and Helton, Ashley M. and Johnson, Laura and Merriam, Jeff and Niederlehner, B. R. and O’brien, Jonathan M. and Potter, Jody D. and Sheibley, Richard W. and Thomas, Suzanne M. and Wilson, Kym},
	year = {2010},
	keywords = {ecosystem respiration, land use, metabolism, primary production, stream},
	pages = {1874--1890},
}

@article{arroita_twenty_2019,
	title = {Twenty years of daily metabolism show riverine recovery following sewage abatement: {Long}-term recovery of a polluted river},
	volume = {64},
	issn = {00243590},
	shorttitle = {Twenty years of daily metabolism show riverine recovery following sewage abatement},
	url = {http://doi.wiley.com/10.1002/lno.11053},
	doi = {10.1002/lno.11053},
	abstract = {Human activities have altered the environmental controls on river metabolism, i.e., gross primary production (GPP) and ecosystem respiration (ER). These coupled processes affect water quality, CO2 emissions, and biodiversity. Efforts to mitigate these impacts often lack long-term, high-resolution data needed to assess their success. Here, we estimated a 20-yr time series of daily metabolism from dissolved oxygen (DO) data following pollution abatement (sewage treatment) in the Oria River, Spain. Ammonium concentration declined immediately after sewage abatement, whereas dissolved organic matter absorbance (proxy for concentration) declined slowly. Summer GPP declined with ammonium concentration. ER declined more strongly but more gradually than GPP and was driven by lower rates of autotrophic respiration (AR) and heterotrophic respiration following sewage treatment. Reduced AR reflected a decrease in the fraction of daily GPP being respired by algae themselves. Decline in ER caused net ecosystem production to increase from highly negative to approximately zero. Diel DO swings also declined and episodes of hypoxia nearly disappeared following reduced metabolic rates, and were paralleled by lower benthic chlorophyll a, increased macroinvertebrate indices, and a recovery of fish assemblages. Overall, wastewater treatment plants installation constrained river metabolism, greatly improved water quality, and enabled invertebrates and fish to recolonize the river. However, most variables responded gradually and these changes would not have been evident with short-term DO data. These gradual responses revealed the need of long-term, high-resolution data to gain insight into long-temporal scale responses superimposed on short-temporal scale metabolic variation, especially in the current context of climate and land-use change.},
	language = {en},
	number = {S1},
	urldate = {2019-08-24},
	journal = {Limnology and Oceanography},
	author = {Arroita, Maite and Elosegi, Arturo and Hall, Robert O.},
	month = jan,
	year = {2019},
	pages = {S77--S92},
}

@article{hall_estimating_2013,
	title = {Estimating autotrophic respiration in streams using daily metabolism data},
	volume = {32},
	issn = {2161-9549},
	url = {http://www.journals.uchicago.edu/doi/abs/10.1899/12-147.1},
	doi = {10.1899/12-147.1},
	abstract = {The fraction of gross primary production (GPP) that is immediately respired by autotrophs and their closely associated heterotrophs (ARf) is unknown. This value is necessary to calculate the autotrophic base of food webs, which requires knowing production available for grazers. ARf is also necessary for estimating heterotrophic respiration (HR) which is needed to calculate C spiraling in streams and rivers. We suggest a way to estimate ARf from daily metabolism data using quantile regression between GPP and 90\% quantile of ecosystem respiration (ER). We reasoned that autotrophic respiration represents the lower limit for ER on any one day and used quantile regression to estimate the relationship of the lower quantile of ER with respect to GPP. We examined this approach with simulation modeling and application of quantile regression to estimates of continuous GPP and ER from {\textgreater}20 streams. Simulation modeling showed that low-uncertainty estimates of ARf required large variation in daily GPP. Covariance between HR and GPP, which might be observed if the processes were temperature controlled, biased estimates of ARf. Seasonal estimates of ARf were robust to daily variation in ARf as a function of GPP. ARf calculated from previously published estimates of daily metabolism from streams averaged 0.44 (SD  =  0.19) with high variation among streams. This value is higher than most physiological measurements, probably because of light limitation of algae and from HR closely associated with daily GPP. How much of ARf was from algal respiration vs closely associated heterotrophic respiration is not known, but we suggest that the value (1 – ARf)GPP represents the amount of C available to animals.},
	number = {2},
	urldate = {2019-08-24},
	journal = {Freshwater Science},
	author = {Hall, Robert O. and Beaulieu, Jake J.},
	month = jun,
	year = {2013},
	pages = {507--516},
}

@article{roley_influence_2014,
	title = {The influence of floodplain restoration on whole-stream metabolism in an agricultural stream: insights from a 5-year continuous data set},
	volume = {33},
	issn = {2161-9549},
	shorttitle = {The influence of floodplain restoration on whole-stream metabolism in an agricultural stream},
	url = {http://www.journals.uchicago.edu/doi/abs/10.1086/677767},
	doi = {10.1086/677767},
	abstract = {Channelized streams are common in North American agricultural regions, where they minimize water residence time and biological nutrient processing. Floodplain restoration done via the 2-stage-ditch management strategy can improve channel stability and nutrient retention during storms. We examined the influence of floodplain restoration on whole-stream metabolism by measuring gross primary production (GPP) and ecosystem respiration (ER) for 1 y before and 4 y after restoration of an upstream, unaltered control reach and a downstream, restored reach. Both reaches were biologically active and dynamic. GPP ranged from 0.1 to 22.1 g O2 m−2 d−1, and ecosystem respiration (ER) rates ranged from −0.1 to −38.7 g O2 m−2 d−1. We used time-series analysis and found that GPP increased postrestoration during floodplain inundation when expressed per unit length, but not per unit area, of stream. GPP was more resilient post- than prerestoration and returned to prestorm levels more quickly after than before floodplain construction. In contrast, the floodplain restoration had no effect on ER or on any metric of metabolism during base flow. Overall, we showed that floodplain–stream linkages can be important regulators of metabolism in restored agricultural streams.},
	number = {4},
	urldate = {2019-08-24},
	journal = {Freshwater Science},
	author = {Roley, Sarah S. and Tank, Jennifer L. and Griffiths, Natalie A. and Hall, Robert O. and Davis, Robert T.},
	month = dec,
	year = {2014},
	pages = {1043--1059},
}

@article{hall_turbidity_2015,
	title = {Turbidity, light, temperature, and hydropeaking control primary productivity in the {Colorado} {River}, {Grand} {Canyon}},
	volume = {60},
	copyright = {© 2015 Association for the Sciences of Limnology and Oceanography},
	issn = {1939-5590},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lno.10031},
	doi = {10.1002/lno.10031},
	abstract = {Dams and river regulation greatly alter the downstream environment for gross primary production (GPP) because of changes in water clarity, flow, and temperature regimes. We estimated reach-scale GPP in five locations of the regulated Colorado River in Grand Canyon using an open channel model of dissolved oxygen. Benthic GPP dominates in Grand Canyon due to fast transport times and low pelagic algal biomass. In one location, we used a 738 days time series of GPP to identify the relative contribution of different physical controls of GPP. We developed both linear and semimechanistic time series models that account for unmeasured temporal covariance due to factors such as algal biomass dynamics. GPP varied from 0 g O2 m−2 d−1 to 3.0 g O2 m−2 d−1 with a relatively low annual average of 0.8 g O2 m−2 d−1. Semimechanistic models fit the data better than linear models and demonstrated that variation in turbidity primarily controlled GPP. Lower solar insolation during winter and from cloud cover lowered GPP much further. Hydropeaking lowered GPP but only during turbid conditions. Using the best model and parameter values, the model accurately predicted seasonal estimates of GPP at 3 of 4 upriver sites and outperformed the linear model at all sites; discrepancies were likely from higher algal biomass at upstream sites. This modeling approach can predict how changes in physical controls will affect relative rates of GPP throughout the 385 km segment of the Colorado River in Grand Canyon and can be easily applied to other streams and rivers.},
	language = {en},
	number = {2},
	urldate = {2019-08-24},
	journal = {Limnology and Oceanography},
	author = {Hall, Robert O. and Yackulic, Charles B. and Kennedy, Theodore A. and Yard, Michael D. and Rosi‐Marshall, Emma J. and Voichick, Nicholas and Behn, Kathrine E.},
	year = {2015},
	pages = {512--526},
}



@article{richardson_processes_1986,
	title = {Processes {Controlling} {Movement}, {Storage}, and {Export} of {Phosphorus} in a {Fen} {Peatland}},
	volume = {56},
	issn = {0012-9615},
	url = {https://www.jstor.org/stable/1942548},
	doi = {10.2307/1942548},
	abstract = {Field and laboratory studies were conducted to determine the mechanisms controlling P movement, storage, and export from a minerotrophic peatland (fen) in central Michigan that had demonstrated high P removal from nutrient additions. An annual P budget completed for the fen ecosystem revealed that plant uptake requirements were 7-9 kg@?ha{\textasciicircum}-{\textasciicircum}1@?yr{\textasciicircum}-{\textasciicircum}1, but 35\% of aboveground P uptake by plants was returned to the peatland surface via litterfall. Permanent storage of organic P in peat ranged between 2 and 5 kg@?ha{\textasciicircum}-{\textasciicircum}1@?yr{\textasciicircum}-{\textasciicircum}1 under natural levels of P input. Both microbial uptake and soil exchange capacity controlled the amount of P made available for plant growth. Fertilizer additions of 5.5 kg@?ha{\textasciicircum}-{\textasciicircum}1@?yr{\textasciicircum}-{\textasciicircum}1 of P and 17 kg@?ha{\textasciicircum}-{\textasciicircum}1@?yr{\textasciicircum}-{\textasciicircum}1 of N in the fen resulted in no significant (P {\textless} .05) increase in growth or nutrient uptake by emergent macrophytes as the litter-microorganism compartment (LMC) retained up to 84\% of the added P in year 1. A doubling of the P fertilization level resulted in an LMC retention of only 57\%. In year 2 the retention of P by the LMC dropped to 67 and 31\% for the two fertilizer levels, respectively. Concurrent with decreases in LMC phosphorus retention were increased peat sorption of P, but plant growth responses and P uptake were negligible. Higher level fertilizer additions of 22 and 55 kg@?ha{\textasciicircum}-{\textasciicircum}1@?yr{\textasciicircum}-{\textasciicircum}1 of P and 68 and 170 kg@?ha{\textasciicircum}-{\textasciicircum}1@?yr{\textasciicircum}-{\textasciicircum}1 of N applied with minimal water additions resulted in significant (P {\textless} .05) increases in net primary productivity and P storage by Carex spp. Narrow-leaved sedge (Carex lasiocarpa, C. oligosperma, and C. aquatilis) removed as much as 61\% of the P additions in year 1, with the LMC sorbing an additional 22\%. Roots and rhizomes accounted for 81\% of plant P storage in the higher fertilizer treatment, when surface water flow rates were reduced and fertilizer additions were sequestered in the root zone. However, seasonal dieback and leaching of P from aboveground standing plant material on the high fertilizer plots resulted in a fivefold increase of P flux to the water compartment. Microcosm {\textasciicircum}3{\textasciicircum}2P studies indicated that most of the P added to the fen ecosystem was removed from the water column within the 1st h by microorganisms and fine sediments, and that sedge uptake was extremely low even 45 d after addition. Thus plant uptake of P is not a major factor in the rapid removal of low levels of newly added PO"4 in the fen. Selective biocide treatments used to separate the P uptake by bacteria and actinomycetes from that of fungi and yeasts in the fen surface water revealed that the latter group of microorganisms was the dominant group responsible for initial P removal. Biological uptake and abiotic sorption of P by the fine sediments in the surface waters were also shown to be of the same order of magnitude, but immobilization of P in the peat soil zone was mainly controlled by chemical sorption. Freezing of peat resulted in P release to the water column upon thawing, but concentrations returned to control levels within 24 h, suggesting minimal ecosystem losses of P in spring runoff. A Freundlich P adsorption maximum of 15 and 38 kg/ha was calculated for a 2 cm and 5 cm depth of peat adsorption, respectively. These soil P adsorption maxima are only 23\% (2 cm) and 60\% (5 cm) of annual wastewater P additions of 64 @+ 14 kg@?ha{\textasciicircum}-{\textasciicircum}1@?yr{\textasciicircum}-{\textasciicircum}1 and may account for the 26 and 42 kg/ha of P exported from the 19.5-ha test area in the fen during the 4th and 5th yr, respectively, of nutrient additions. Collectively, our field research and microcosm studies on the Houghton Lake fen suggest that soil adsorption and peat accumulation (i.e., phosphorus stored in organic matter) control long-term phosphate sequestration. But microorganisms and small sediments control initial uptake rates, especially during periods of low nutrient concentration and standing surface water. Carex P uptake increases later in the growing season during field fertilization, but algal populations in the fen water respond quickly and absorb significant amounts of P in areas where sewage effluent has been added. Both biotic and abiotic control mechanisms are thus functional in the peatland, and the proportional effect of each on P transfers is dependent on water levels, the amount of available P, fluctuating microorganism populations, seasonal changes in P absorption by macrophytes, and P soil adsorption capacity.},
	number = {4},
	urldate = {2019-08-23},
	journal = {Ecological Monographs},
	author = {Richardson, Curtis J. and Marshall, Paul E.},
	year = {1986},
	pages = {280--302},
}

@article{kiedrzynska_quantification_2008,
	title = {Quantification of phosphorus retention efficiency by floodplain vegetation and a management strategy for a eutrophic reservoir restoration},
	volume = {33},
	issn = {0925-8574},
	url = {http://www.sciencedirect.com/science/article/pii/S0925857407002078},
	doi = {10.1016/j.ecoleng.2007.10.010},
	abstract = {This paper presents an ecohydrological approach to the reduction in the phosphorus load transported by the Pilica River into a lowland reservoir in the central region of Poland. The research was carried out on a 26.6ha section of the river floodplain where vegetation was the important component accumulating phosphorus (P) in plant tissues. Quantification of P accumulation in plant tissues and retention efficiency by plant communities in the floodplain were analyzed in order to develop a vegetation management strategy that would enhance river self-purification. A Digital Terrain Model (DTM), a location–altitude map, an inundation model of the floodplain, and a map of the distribution of plant communities were used to evaluate the capacity of the floodplain to retain P. In summer, the biological potential for phosphorus retention in the floodplain was estimated to be as high as 255kg P. However, this potential can be increased by planting fast-growing patches of willow. Therefore, covering 24\% or 48\% of the entire floodplain (identified by DTM analysis) where are suitable hydrological conditions for growth and cultivation of willows may increase this accumulation to 332 or 399kg P, respectively. In the long run, an appropriate management strategy (cutting and removing the biomass from the floodplain) should favor a decrease in nutrient transport downstream.},
	number = {1},
	urldate = {2019-08-23},
	journal = {Ecological Engineering},
	author = {Kiedrzyńska, Edyta and Wagner, Iwona and Zalewski, Maciej},
	month = may,
	year = {2008},
	keywords = {Ecohydrology, Floodplain wetlands, Groundwater, Inundation model, Pilica River, Plants phosphorus accumulation, Wetland plant management},
	pages = {15--25},
}

@article{murphy_modified_1962,
	title = {A modified single solution method for the determination of phosphate in natural waters},
	volume = {27},
	issn = {0003-2670},
	url = {http://www.sciencedirect.com/science/article/pii/S0003267000884445},
	doi = {10.1016/S0003-2670(00)88444-5},
	abstract = {A single solution reagent is described for the determination of phosphorus in sea water. It consists of an acidified solution of ammonium molybdate containing ascorbic acid and a small amount of antimony. This reagent reacts rapidly with phosphate ion yielding a blue-purple compound which contains antimony and phosphorus in a 1:1 atomic ratio. The complex is very stable and obeys Beer's law up to a phosphate concentration of at least 2 μg/ml.The sensitivity of the procedure is comparable with that of the stannous chloride method. The salt error is less than 1 \%.
Résumé
Une méthode spectrophotométrique est décrite pour le dosage du phosphate dans l'eau de mer, an moyen de molybdate d'ammonium, en présence d'acide ascorbique et d'antimoinc. Il se forme rapidement un composé violet bleu, renfermant antimoine et phosphore dans un rapport atomique de 1:1.
Zusammenfassung
Beschreibung einer Methode zur Bestimmung von Phosphat in Mecrwasser mit Hilfe von Ammoniummolybdat in Gegenwart von Ascorbinsäure und Antimon. Der gebildete blau-violette Komplex wird spektrophotometrisch gemessen.},
	urldate = {2019-08-22},
	journal = {Analytica Chimica Acta},
	author = {Murphy, J. and Riley, J. P.},
	month = jan,
	year = {1962},
	pages = {31--36},
}

@article{solorzano_determination_1969,
	title = {Determination of {Ammonia} in {Natural} {Waters} by the {Phenolhypochlorite} {Method}},
	volume = {14},
	issn = {0024-3590},
	url = {http://www.jstor.org/stable/2834079},
	number = {5},
	urldate = {2019-08-22},
	journal = {Limnology and Oceanography},
	author = {Solorzano, Lucia},
	year = {1969},
	pages = {799--801},
}

@article{hensley_flow_2019,
	title = {Flow {Extremes} as {Spatiotemporal} {Control} {Points} on {River} {Solute} {Fluxes} and {Metabolism}},
	volume = {124},
	issn = {2169-8961},
	url = {http://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JG004738},
	doi = {10.1029/2018JG004738},
	abstract = {Floods are dominant controls on export of solutes from catchments. In contrast, low-flow periods such as droughts are potentially dominant control points for biogeochemical processing, enhancing spatiotemporal variation in solute concentrations, stream metabolism, and nutrient uptake. Using complementary time series (i.e., an Eulerian reference frame) and longitudinal profiling (i.e., a Lagrangian reference frame), we investigated hydrologic controls on temporal and spatial variation in solute flux and metabolism in the Lower Santa Fe River (FL, USA), where highly colored surface water mixes with exceptionally clear groundwater from springs. Gage measurements suggest groundwater inputs ranged from {\textless}1\% (during extreme floods) to 86\% (during extreme drought) of total discharge (Q). Mass transport of most solutes was dominated by high-Q periods. Most solute C-Q relationships exhibited statistically significant slope breakpoints near the transition between surface and groundwater dominance. In particular, parameters controlling water column light attenuation were chemostatic above median Q but markedly reduced at low Q. As a result, river metabolism and assimilatory nitrate (NO3−) uptake were consistently suppressed at high Q and enhanced at low Q, with greater variability in response to drivers other than water column light transmittance. Spatial variation in solute concentrations was also enhanced at low Q, induced by discrete groundwater inflow and biogeochemical processing along the reach. Contrasting reference frames yielded corroborative evidence for transport dominance at high Q, which damps spatiotemporal heterogeneity. In contrast, low-Q periods enable localized mixing controls on solute concentrations and high rates of metabolism and nutrient processing that increase spatiotemporal variability.},
	language = {en},
	number = {3},
	urldate = {2019-08-21},
	journal = {Journal of Geophysical Research: Biogeosciences},
	author = {Hensley, Robert T. and Kirk, Lily and Spangler, Margaret and Gooseff, Michael N. and Cohen, Matthew J.},
	year = {2019},
	keywords = {Lagrangian, flow, flux, metabolism, solute},
	pages = {537--555},
}

@article{reisinger_varying_2015,
	title = {The varying role of water column nutrient uptake along river continua in contrasting landscapes},
	volume = {125},
	issn = {1573-515X},
	url = {10.1007/s10533-015-0118-z},
	doi = {10.1007/s10533-015-0118-z},
	abstract = {Nutrient transformation processes such as assimilation, dissimilatory transformation, and sorption to sediments are prevalent in benthic zones of headwater streams, but may also occur in the water column. The river continuum concept (RCC) predicts that water column processes become increasingly important with increasing stream size. We predicted that water column nutrient uptake increases with stream size, mirroring carbon/energy dynamics predicted by the RCC. We measured water column uptake of ammonium (NH+4NH4+\{{\textbackslash}text\{NH\}\}\_\{4\}{\textasciicircum}\{ + \}), nitrate (NO−3NO3−\{{\textbackslash}text\{NO\}\}\_\{3\}{\textasciicircum}\{ - \}), and soluble reactive phosphorus (SRP) in 1st through 5th order stream and river reaches (discharge: 50–68,000 L s−1) in three watersheds ranging from {\textless}1 to {\textgreater}70 \% developed lands. We found that water column volumetric uptake (U vol ) of NH+4NH4+\{{\textbackslash}text\{NH\}\}\_\{4\}{\textasciicircum}\{ + \}, NO−3NO3−\{{\textbackslash}text\{NO\}\}\_\{3\}{\textasciicircum}\{ - \}, and SRP did not significantly differ among watersheds and we did not find any longitudinal patterns for U vol . Uptake velocity (v f ) of NH+4NH4+\{{\textbackslash}text\{NH\}\}\_\{4\}{\textasciicircum}\{ + \} increased with stream size, whereas NO−3NO3−\{{\textbackslash}text\{NO\}\}\_\{3\}{\textasciicircum}\{ - \} and SRP v f did not differ with stream size or among watersheds. Both U vol and v f were related to water column metabolism and material suspended in the water column, but specific relationships differed among solutes and uptake metrics. Median water column v f across 15 sites was 4, 9, and 19 \% of median whole-stream NH+4NH4+\{{\textbackslash}text\{NH\}\}\_\{4\}{\textasciicircum}\{ + \}, NO−3NO3−\{{\textbackslash}text\{NO\}\}\_\{3\}{\textasciicircum}\{ - \}, and SRP v f based upon a previous meta-analysis. Thus, although we could not demonstrate a generalized longitudinal pattern in water column nutrient uptake, water column processes can be important. An improved mechanistic understanding of the controls on uptake and the ultimate fate of nutrients will facilitate effective management and restoration for mitigating downstream nutrient export.},
	language = {en},
	number = {1},
	urldate = {2019-08-16},
	journal = {Biogeochemistry},
	author = {Reisinger, Alexander J. and Tank, Jennifer L. and Rosi-Marshall, Emma J. and Hall, Robert O. and Baker, Michelle A.},
	month = aug,
	year = {2015},
	keywords = {Nitrogen, Nutrient uptake, Phosphorus, River continuum, Water column},
	pages = {115--131},
}

@article{hodaj_impact_2017,
	title = {Impact of a two-stage ditch on channel water quality},
	volume = {192},
	issn = {0378-3774},
	url = {http://www.sciencedirect.com/science/article/pii/S0378377417302299},
	doi = {10.1016/j.agwat.2017.07.006},
	abstract = {A two-stage ditch involves modifications of a conventional, trapezoidal drainage ditch to better replicate the features of a natural stream through the addition of adjacent floodplains or benches. Previous research in Indiana and Ohio has shown that two-stage ditches offer the potential to reduce sediment load and extend the interaction time between water, bench vegetation, and bench soil allowing larger uptake of nutrients by the vegetation and increasing the denitrification rates. A two-stage ditch was constructed that drains an area of approximately 267ha of farmland used for corn and soybean production. Discharge, nitrate-N (NO3), total phosphorus (TP), soluble reactive phosphorus (SRP) and total suspended sediment (TSS) were monitored in the two-stage ditch and a control reach immediately upstream. The two-stage ditch was found to significantly decrease TP, SRP and TSS concentrations and loads. Although the two-stage ditch decreased NO3 concentrations significantly, it did not have a significant impact on NO3 loads. More specifically, the two-stage ditch reduced the loads of TP by 40\%, SRP by 11\% and TSS by 22–40\% depending on the stage of vegetation establishment on its floodplain benches, compared to an increase in load of 78\%, 2\% and 1\%, respectively in the control reach.},
	urldate = {2019-08-16},
	journal = {Agricultural Water Management},
	author = {Hodaj, Andi and Bowling, Laura C. and Frankenberger, Jane R. and Chaubey, Indrajeet},
	month = oct,
	year = {2017},
	keywords = {Agricultural, Channel, Ditches, Nitrate, Phosphorus, Suspended sediments, Two-stage ditch, Water quality},
	pages = {126--137},
}

@article{ogaard_freezing_2015,
	title = {Freezing and thawing effects on phosphorus release from grass and cover crop species},
	volume = {65},
	issn = {0906-4710},
	url = {10.1080/09064710.2015.1030444},
	doi = {10.1080/09064710.2015.1030444},
	abstract = {Cover crops, grassed buffer zones along watercourses and grassed waterways are recommended for mitigating erosion and phosphorus (P) losses from fields with arable crop production. There are, however, concerns that plant covers may release dissolved P and contribute to P loss after plant freezing. The objective of this study was to evaluate P release after freezing from different plant species of interest for use either as cover crops or in grassed buffer zones/waterways. In the laboratory, seven plant species (red clover (Trifolium pratense L.), timothy (Phleum pratense L.), annual ryegrass (Lolium multiflorum Lam.), hairy vetch (Vicia villosa Roth.), rye (Secale cereale L.) oil radish (Raphanus sativus L. var. oleiferus) and winter rapeseed (Brassica napus L. var. oleifera f. biennis)) were subjected to daily freeze–thaw cycles (FTCs; −10°C/+5°C) for one week. In a two-year outdoor experiment located under a roof to protect the plants from rain and snow, eight plant species (white clover (Trifolium repens L.), timothy, meadow fescue (Festuca pratensis L.), smooth meadow grass (Poa pratensis L.), annual ryegrass, perennial ryegrass (Lolium perenne L.), rye and hairy vetch) were subjected to winter temperatures. The plants were sampled in winter and spring. The results showed that after seven FTCs in the laboratory, less than 15\% of the total phosphorus (TP) was water-extractable P for all species except oilseed radish for which 32\% of the TP was water extractable. In the outdoor experiment, the plants were exposed to temperatures below −20°C during both winters. Depending on the plant species, 18–42\% and 17–48\% of the TP was water extractable in the spring of the first and second year, respectively. The minimum temperatures and the plant growth conditions were important for the ranking of different plant species with respect to the risk of off-season P leaching.},
	number = {6},
	urldate = {2019-08-11},
	journal = {Acta Agriculturae Scandinavica, Section B — Soil \& Plant Science},
	author = {Øgaard, Anne Falk},
	month = aug,
	year = {2015},
	keywords = {cover crops, grassed buffer zones, grassed waterways, phosphorus mitigation, water-extractable phosphorus},
	pages = {529--536},
}

@article{christen_buffers_2013,
	title = {Buffers for biomass production in temperate {European} agriculture: {A} review and synthesis on function, ecosystem services and implementation},
	volume = {55},
	issn = {0961-9534},
	shorttitle = {Buffers for biomass production in temperate {European} agriculture},
	url = {http://www.sciencedirect.com/science/article/pii/S0961953412003935},
	doi = {10.1016/j.biombioe.2012.09.053},
	abstract = {Buffer strips on agricultural land have been shown to protect surface water quality by reducing erosion and diffuse pollution. They can also play a key role in nature conservation and flood risk mitigation as well as in the design of bioenergy landscapes resilient to changes in climate, environmental pressures from intensive agriculture and policy developments. Use of conservation buffers by farmers outside of designated schemes is limited to date, but the increasing demand for bioenergy and the combination of agricultural production with conservation calls for a much wider implementation. This paper reviews the biophysical knowledge on buffer functioning and associated ecosystem services. It describes how a three-zone buffer design, with arable fields buffered in combination by grassland, short rotation forestry (SRF) or coppice (SRC) and undisturbed vegetation along water courses, can be incorporated into farming landscapes as productive conservation elements and reflects on the potential for successful implementation. Land use plays a much greater role in determining catchment hydrology than soil type: shelterbelts or buffer strips have markedly higher infiltration capacity than arable or pasture land. Root architecture of trees, shrubs and herbaceous plants differs between species and is important for the extent of hydrological changes after establishment. Riparian buffers retain 30–99\% of nitrate N and 20–100\% of phosphorus from runoff and shallow groundwater. Buffers are also highly effective for pesticide removal and farmland biodiversity conservation with a high potential for low-input fuel, feed, or fibre production. Landscape amenities, sporting opportunities, and a display of land stewardship are additional benefits.},
	urldate = {2019-08-11},
	journal = {Biomass and Bioenergy},
	author = {Christen, Benjamin and Dalgaard, Tommy},
	month = aug,
	year = {2013},
	keywords = {Agri-environmental management, Diffuse pollution, Farm diversification, Riparian buffer, Short rotation coppice, Short rotation forestry},
	pages = {53--67},
}

@article{kao_differential_2003,
	title = {Differential nitrogen and phosphorus retention by five wetland plant species},
	volume = {23},
	issn = {0277-5212, 1943-6246},
	url = {http://link.springer.com/article/10.1672/0277-5212(2003)023[0979:DNAPRB]2.0.CO;2},
	doi = {10.1672/0277-5212(2003)023[0979:DNAPRB]2.0.CO;2},
	abstract = {Riparian wetlands have a demonstrated ability to filter and control nitrogen (N) and phosphorus (P) movement into streams and other bodies of water; few studies, however, have examined the roles that...},
	language = {en},
	number = {4},
	urldate = {2019-08-11},
	journal = {Wetlands},
	author = {Kao, Jenny T. and Titus, John E. and Zhu, Wei-Xing},
	month = dec,
	year = {2003},
	pages = {979--987},
}

@article{christen_buffers_2013-1,
	title = {Buffers for biomass production in temperate {European} agriculture: {A} review and synthesis on function, ecosystem services and implementation},
	volume = {55},
	issn = {0961-9534},
	shorttitle = {Buffers for biomass production in temperate {European} agriculture},
	url = {http://www.sciencedirect.com/science/article/pii/S0961953412003935},
	doi = {10.1016/j.biombioe.2012.09.053},
	abstract = {Buffer strips on agricultural land have been shown to protect surface water quality by reducing erosion and diffuse pollution. They can also play a key role in nature conservation and flood risk mitigation as well as in the design of bioenergy landscapes resilient to changes in climate, environmental pressures from intensive agriculture and policy developments. Use of conservation buffers by farmers outside of designated schemes is limited to date, but the increasing demand for bioenergy and the combination of agricultural production with conservation calls for a much wider implementation. This paper reviews the biophysical knowledge on buffer functioning and associated ecosystem services. It describes how a three-zone buffer design, with arable fields buffered in combination by grassland, short rotation forestry (SRF) or coppice (SRC) and undisturbed vegetation along water courses, can be incorporated into farming landscapes as productive conservation elements and reflects on the potential for successful implementation. Land use plays a much greater role in determining catchment hydrology than soil type: shelterbelts or buffer strips have markedly higher infiltration capacity than arable or pasture land. Root architecture of trees, shrubs and herbaceous plants differs between species and is important for the extent of hydrological changes after establishment. Riparian buffers retain 30–99\% of nitrate N and 20–100\% of phosphorus from runoff and shallow groundwater. Buffers are also highly effective for pesticide removal and farmland biodiversity conservation with a high potential for low-input fuel, feed, or fibre production. Landscape amenities, sporting opportunities, and a display of land stewardship are additional benefits.},
	urldate = {2019-08-11},
	journal = {Biomass and Bioenergy},
	author = {Christen, Benjamin and Dalgaard, Tommy},
	month = aug,
	year = {2013},
	keywords = {Agri-environmental management, Diffuse pollution, Farm diversification, Riparian buffer, Short rotation coppice, Short rotation forestry},
	pages = {53--67},
}

@article{kawashima_phosphate_1986,
	title = {Phosphate adsorption onto hydrous manganese({IV}) oxide in the presence of divalent cations},
	volume = {20},
	issn = {0043-1354},
	url = {http://www.sciencedirect.com/science/article/pii/0043135486901958},
	doi = {10.1016/0043-1354(86)90195-8},
	abstract = {Alkaline earth cations, Ba2+, Sr2+, Ca2+, Mg2+ and transition metal ions, Mn2+, Co2+, Ni2+, cause hydrous manganese(IV) oxide (HMO) to strongly adsorb phosphate between pH 6 and 9 depending on the cation. The effectiveness of the alkaline earth cations to cause P adsorption was Ba2+ {\textgreater} Sr2+ {\textgreater} Ca2+ {\textgreater} Mg2+, which is the same order as their affinities for the oxide. Changes with time were found in the abilities of the transition metals to cause P adsorption onto HMO and this may be due to conversion of the adsorbed cation to its oxide. A new potential role for HMO as an adsorbent of phosphate in natural waters was indicated.},
	number = {4},
	urldate = {2019-08-11},
	journal = {Water Research},
	author = {Kawashima, M and Tainaka, Y and Hori, T and Koyama, M and Takamatsu, T},
	month = apr,
	year = {1986},
	keywords = {adsorption, hydrous Mn(IV) oxide, natural waters, phosphate, sediment, surface accumulation},
	pages = {471--475},
}

@article{zak_phosphorus_2010,
	title = {Phosphorus mobilization in rewetted fens: the effect of altered peat properties and implications for their restoration},
	volume = {20},
	copyright = {© 2010 by the Ecological Society of America},
	issn = {1939-5582},
	shorttitle = {Phosphorus mobilization in rewetted fens},
	url = {http://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/08-2053.1},
	doi = {10.1890/08-2053.1},
	abstract = {Rewetting of drained fens is necessary to stop further soil degradation and to reestablish important ecological functions. However, substantial changes of peat characteristics in the upper soil layers, due to drainage and land use, could counteract their recovery as nutrient-poor systems for an unknown period. We assessed the importance of altered peat properties, such as the degree of peat decomposition and the amount of redox-sensitive phosphorus (P) compounds, for P mobilization in different degraded fens. An experimental design involving 63 intact peat cores from fens with varying drainage and land-use histories was developed to quantify the mobilization of P, as well as that of iron (Fe), ammonium, carbon dioxide, and methane, all indicators of organic-matter decomposition and/or P-releasing processes. We found that net P release rates in peat cores with highly decomposed peat (range: 0.1–52.3 mg P·m−2·d−1) were significantly correlated to the amount of P bound to redox-sensitive compounds and the molar Fe:P as well as Al:P ratios of peat. We conclude that the following general rules apply for P mobilization in rewetted fens: (1) elevated levels of P release rates and P concentrations in pore water up to three orders of magnitude larger than under natural reference conditions can only be expected for rewetted fens whose surface soil layers consist of highly decomposed peat; (2) peat characteristics, such as the amount of P bound to redox-sensitive Fe(III) compounds (positive correlation) and molar ratios of Fe:P or Al:P (negative correlations), explain the high range of P release rates; and (3) a critical P export to adjacent lakes or rivers can only be expected if molar Fe:P ratios of highly decomposed peat are less than 10.},
	language = {en},
	number = {5},
	urldate = {2019-08-11},
	journal = {Ecological Applications},
	author = {Zak, Dominik and Wagner, Carola and Payer, Brian and Augustin, Jürgen and Gelbrecht, Jörg},
	year = {2010},
	keywords = {P mobilization, P retention, carbon fluxes, iron precipitation, minerotrophic peatlands, peat characteristics, redox processes, restoration, rewetting of drained fens, top soil removal, wetland},
	pages = {1336--1349},
}

@article{surridge_phosphorus_2012,
	title = {Phosphorus mobilisation and transport within a long-restored floodplain wetland},
	volume = {44},
	issn = {0925-8574},
	url = {http://www.sciencedirect.com/science/article/pii/S0925857412000596},
	doi = {10.1016/j.ecoleng.2012.02.009},
	abstract = {Re-wetting river floodplains as part of hydrological restoration can provide environmental, economic and social benefits. However, labile forms of nutrients have accumulated in many floodplains and enhanced nutrient mobility has been reported after re-wetting of some floodplain sediments. Increases in nutrient mobility could restrict the net benefit of floodplain restoration, although the long-term impacts of restoration on nutrient mobility are largely unknown. We used in situ hydrological and hydrochemical monitoring to examine the mobility of phosphorus (P) during a range of hydrological events within a long-restored (more than 20 years) floodplain in Norfolk, England. Our data suggest that P was released from sediments to porewater and surface water following inundation of the floodplain. The concentration of P exceeded 6.5mgPL−1 in porewater and 0.5mgPL−1 in surface water within six weeks of inundation, significantly higher than the concentration in rainwater ({\textless}0.015mgPL−1) or in floodwater from the adjacent river (x¯=0.11 mg P L−1) that inundated the floodplain. Sediment geochemistry was used to predict changes in the mobility of P following inundation, based on the molar ratio of redox-sensitive P to iron or the molar quantity of redox-sensitive P within the floodplain sediments. We found that short-term hydrological events, both external (tidal pulse) and internal (water-table drawdown) in origin, were associated with increases in the concentration of dissolved forms of P within the floodplain drainage network. These increases coincided with porewater movement to the drainage network, suggesting that advection along shallow sub-surface flowpaths was important for the transport of P. Our research indicates that some restored floodplains could inadvertently represent sources of P to adjacent streams and rivers.},
	urldate = {2019-08-11},
	journal = {Ecological Engineering},
	author = {Surridge, Ben W. J. and Heathwaite, A. Louise and Baird, Andy J.},
	month = jul,
	year = {2012},
	keywords = {Biogeochemistry, Floodplain, Phosphorus, Redox, Restoration, Wetland},
	pages = {348--359},
}

@article{schonbrunner_impact_2012,
	title = {Impact of drying and re-flooding of sediment on phosphorus dynamics of river-floodplain systems},
	volume = {432},
	issn = {0048-9697},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969712008406},
	doi = {10.1016/j.scitotenv.2012.06.025},
	abstract = {One of the consequences of human impacts on floodplains is a change in sedimentation leading to enhanced floodplain aggradation. Thus, accumulated sediments rich in nutrients might interfere with floodplain restoration. In this study we investigated the phosphorus release behavior of sediments from shallow backwaters of an isolated floodplain of the Danube River situated east of the city of Vienna with the aim to understand the effects of changes in dry/wet cycles on established floodplain sediments. In the light of restoration plans aiming at increased surface water exchange with the river main channel, the response of sediments to frequent alternations between desiccation and inundation periods is a key issue as changes of sediment properties are expected to affect phosphorus release. In order to determine the effect of changing hydrological conditions on internal phosphorus loading, we exposed sediments to different dry/wet treatments in a laboratory experiment. Total phosphorus (TP) release from sediments into the water column increased with increasing duration of dry periods prior to re-wetting. Partial correlation analysis showed significant positive correlations between ΔTP and ΔNH4+ as well as between ΔTP and ΔFe3+ concentrations (Δ refers to the difference between the final and initial concentration during the wetting period), indicating that enhanced mineralization rates leading to a concomitant release of NH4+ and TP and the reduction of iron hydroxides leading to a concomitant release of Fe3+ and TP are the mechanisms responsible for the rise in TP. Repeated drying and wetting resulted in elevated phosphorus release. This effect was more pronounced when drying periods led to an 80\% reduction in water content, indicating that the degree of drying is a major determinant controlling phosphorus release upon re-wetting. The reconnection of isolated floodplains will favor fluctuating hydrologic conditions and is therefore expected to initially lead to high rates of phosphorus release from sediments.},
	urldate = {2019-08-10},
	journal = {Science of The Total Environment},
	author = {Schönbrunner, Iris M. and Preiner, Stefan and Hein, Thomas},
	month = aug,
	year = {2012},
	keywords = {Dry/wet cycles, Floodplain, Iron reduction, Mineralization, Phosphorus, Sediment},
	pages = {329--337},
}

@article{kinsman-costello_phosphorus_2016,
	title = {Phosphorus release from the drying and reflooding of diverse shallow sediments},
	volume = {130},
	issn = {1573-515X},
	url = {10.1007/s10533-016-0250-4},
	doi = {10.1007/s10533-016-0250-4},
	abstract = {Phosphorus (P) retention is an important ecosystem service provided by sediments and soils. However, when shallow aquatic sediments and poorly drained soils dry and re-flood, they can be a source, rather than a sink, of P. Using experimental drying and re-flooding in the laboratory, we assessed the resultant sediment–water P exchange in a biogeochemically diverse set of sediments from 16 sites in Michigan. The direction and magnitude of P exchange to pore waters and surface waters upon re-flooding varied among sediments. Different sediment properties were related to P release to pore water than to P release to overlying surface water, suggesting that different processes control two phases of sediment P release: mobilization from solid to dissolved forms in the sediment pore water; and movement of dissolved P from pore water into overlying surface water. We observed especially high P release in dried and re-flooded sediments with high amounts of loosely sorbed phosphate, suggesting that drained sediments with a legacy of high P loads will be most likely to release P and experience internal eutrophication when re-flooded. The differential responses of sediments suggest that aquatic ecosystem restoration and management for nutrient removal must be evaluated with site-specific knowledge of sediment and soil biogeochemistry.},
	language = {en},
	number = {1},
	urldate = {2019-08-10},
	journal = {Biogeochemistry},
	author = {Kinsman-Costello, Lauren E. and Hamilton, Stephen K. and O’Brien, Jonathan M. and Lennon, Jay T.},
	month = oct,
	year = {2016},
	keywords = {Iron, Phosphorus, Sediment, Soil, Water level fluctuations, Wetland restoration},
	pages = {159--176},
}

@article{opperman_sustainable_2009,
	title = {Sustainable {Floodplains} {Through} {Large}-{Scale} {Reconnection} to {Rivers}},
	volume = {326},
	copyright = {Copyright © 2009, American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	url = {http://science.sciencemag.org/content/326/5959/1487},
	doi = {10.1126/science.1178256},
	abstract = {If riverside levees are strategically removed or repositioned, the result can be reduced flood risk and increased goods and services.
If riverside levees are strategically removed or repositioned, the result can be reduced flood risk and increased goods and services.},
	language = {en},
	number = {5959},
	urldate = {2019-08-10},
	journal = {Science},
	author = {Opperman, Jeffrey J. and Galloway, Gerald E. and Fargione, Joseph and Mount, Jeffrey F. and Richter, Brian D. and Secchi, Silvia},
	month = dec,
	year = {2009},
	pmid = {20007887},
	pages = {1487--1488},
}

@misc{noauthor_gale_nodate,
	title = {Gale {Academic} {OneFile} {Select} - {Results} - {Start} {Page} (286) {And} {Issue} {Number} (4) {And} {ISSN} (00224561) {And} {Volume} {Number} (62)},
	url = {http://link.galegroup.com/apps/doc//EAIM?sid=lms},
	language = {en},
	urldate = {2019-08-10},
}

@article{dunn_role_2016,
	title = {The {Role} of {County} {Surveyors} and {County} {Drainage} {Boards} in {Addressing} {Water} {Quality}},
	volume = {57},
	issn = {1432-1009},
	url = {10.1007/s00267-016-0689-z},
	doi = {10.1007/s00267-016-0689-z},
	abstract = {Water quality problems stemming from the Midwestern U.S. agricultural landscape have been widely recognized and documented. The Midwestern state of Indiana contains tens of thousands of miles of regulated drains that represent biotic communities that comprise the headwaters of the state’s many rivers and creeks. Traditional management, however, reduces these waterways to their most basic function as conveyances, ignoring their role in the ecosystem as hosts for biotic and abiotic processes that actively regulate the fate and transport of nutrients and farm chemicals. Novel techniques and practices such as the two-stage ditch, denitrifying bioreactor, and constructed wetlands represent promising alternatives to traditional management approaches, yet many of these tools remain underutilized. To date, conservation efforts and research have focused on increasing the voluntary adoption of practices among agricultural producers. Comparatively little attention has been paid to the roles of the drainage professionals responsible for the management of waterways and regulated drains. To address this gap, we draw on survey responses from 39 county surveyors and 85 drainage board members operating in Indiana. By examining the backgrounds, attitudes, and actions of these individuals, we consider their role in advocating and implementing novel conservation practices.},
	language = {en},
	number = {6},
	urldate = {2019-08-10},
	journal = {Environmental Management},
	author = {Dunn, Mike and Mullendore, Nathan and de Jalon, Silvestre Garcia and Prokopy, Linda Stalker},
	month = jun,
	year = {2016},
	keywords = {Best management practices, Conservation agriculture, County surveyors, Drainage, Indiana},
	pages = {1217--1229},
}

@article{needelman_improved_nodate,
	title = {Improved management of agricultural drainage ditches for water quality protection: {An} overview},
	abstract = {Agricultural drainage ditches are essential for the removal of surface and ground water to allow for crop production in poorly drained agricultural landscapes. Ditches also mediate the flow of pollutants from agroecosystems to downstream water bodies. This paper provides an overview of the science, management, and policy of ditches. Ditches provide a unique opportunity to address nonpoint source pollution problems from agriculture due to the concentration of the contaminants and the engineered nature of ditch systems. A better understanding of the nature of these complex system and the technologies available and under development to improve their management will assist in the design and implementation of water quality protection programs.},
	language = {en},
	journal = {JOURNAL OF SOIL AND WATER CONSERVATION},
	author = {Needelman, B A},
	pages = {8},
}

@article{needelman_drainage_2007,
	title = {Drainage {Ditches} {Improved} management of agricultural drainage ditches for water quality protection: {An} overview},
	volume = {62},
	issn = {0022-4561, 1941-3300},
	shorttitle = {Drainage {Ditches} {Improved} management of agricultural drainage ditches for water quality protection},
	url = {http://www.jswconline.org/content/62/4/171},
	abstract = {Abstract:
Agricultural drainage ditches are essential for the removal of surface and ground water to allow for crop production in poorly drained agricultural landscapes. Ditches also mediate the flow of pollutants from agroecosystems to downstream water bodies. This paper provides an overview of the science, management, and policy of ditches. Ditches provide a unique opportunity to address nonpoint source pollution problems from agriculture due to the concentration of the contaminants and the engineered nature of ditch systems. A better understanding of the nature of these complex system and the technologies available and under development to improve their management will assist in the design and implementation of water quality protection programs.},
	language = {en},
	number = {4},
	urldate = {2019-08-10},
	journal = {Journal of Soil and Water Conservation},
	author = {Needelman, Brian A. and Kleinman, Peter J. A. and Strock, Jeffrey S. and Allen, Arthur L.},
	month = jul,
	year = {2007},
	pages = {171--178},
}

@article{norman_r._fausey_drainage_1995,
	title = {Drainage and {Water} {Quality} in {Great} {Lakes} and {Cornbelt} {States}},
	volume = {121},
	url = {https://ascelibrary.org/doi/abs/10.1061/(ASCE)0733-9437(1995)121:4(283)},
	doi = {10.1061/(ASCE)0733-9437(1995)121:4(283)},
	number = {4},
	urldate = {2019-08-10},
	journal = {Journal of Irrigation and Drainage Engineering},
	author = {Norman R. Fausey and {Larry C. Brown} and {Harold W. Belcher} and {Rameshwar S. Kanwar}},
	month = jul,
	year = {1995},
	pages = {283--288},
}

@article{roley_floodplain_2012,
	title = {Floodplain restoration enhances denitrification and reach-scale nitrogen removal in an agricultural stream},
	volume = {22},
	copyright = {© 2012 by the Ecological Society of America},
	issn = {1939-5582},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/11-0381.1},
	doi = {10.1890/11-0381.1},
	abstract = {Streams of the agricultural Midwest, USA, export large quantities of nitrogen, which impairs downstream water quality, most notably in the Gulf of Mexico. The two-stage ditch is a novel restoration practice, in which floodplains are constructed alongside channelized ditches. During high flows, water flows across the floodplains, increasing benthic surface area and stream water residence time, as well as the potential for nitrogen removal via denitrification. To determine two-stage ditch nitrogen removal efficacy, we measured denitrification rates in the channel and on the floodplains of a two-stage ditch in north-central Indiana for one year before and two years after restoration. We found that instream rates were similar before and after the restoration, and they were influenced by surface water NO3− concentration and sediment organic matter content. Denitrification rates were lower on the constructed floodplains and were predicted by soil exchangeable NO3− concentration. Using storm flow simulations, we found that two-stage ditch restoration contributed significantly to NO3− removal during storm events, but because of the high NO3− loads at our study site, {\textless}10\% of the NO3− load was removed under all storm flow scenarios. The highest percentage of NO3− removal occurred at the lowest loads; therefore, the two-stage ditch's effectiveness at reducing downstream N loading will be maximized when the practice is coupled with efforts to reduce N inputs from adjacent fields.},
	language = {en},
	number = {1},
	urldate = {2019-08-10},
	journal = {Ecological Applications},
	author = {Roley, Sarah S. and Tank, Jennifer L. and Stephen, Mia L. and Johnson, Laura T. and Beaulieu, Jake J. and Witter, Jonathan D.},
	year = {2012},
	keywords = {Tippecanoe River, USA, agriculture, denitrification, floodplain, north-central Indiana, stream restoration, two-stage ditch},
	pages = {281--297},
}

@article{hanrahan_restored_2018,
	title = {Restored floodplains enhance denitrification compared to naturalized floodplains in agricultural streams},
	volume = {141},
	issn = {1573-515X},
	url = {10.1007/s10533-018-0431-4},
	doi = {10.1007/s10533-018-0431-4},
	abstract = {Predicted changes in the timing and magnitude of storms have the potential to amplify water quality challenges associated with agricultural runoff. In agricultural streams of the Midwestern US, floodplain restoration has the potential to enhance inorganic nitrogen (N) removal by increasing the bioreactive surface area for microbially-mediated denitrification. The restoration of inset floodplains via construction of the two-stage ditch increases denitrification compared to channelized systems, however, little is known about how denitrification on restored floodplains compares to those formed naturally when stream channel management lapses. We used sacrificial microcosm incubations and membrane-inlet mass spectrometry (MIMS) to compare denitrification rates in floodplain soils collected along transects in both naturalized and restored floodplains; longitudinal transects spanned two zones in the active floodplain (near-stream, NS vs. middle, MID) and a third zone that reflected upland conditions in the riparian buffer strip (UP). Denitrification rates were 35–49\% higher in the restored, inset floodplains compared to naturalized floodplains. Variation in denitrification rates were primarily explained by soil organic matter (OM) and OM was {\textgreater} 20\% higher in restored floodplains than naturalized, highlighting the contrasts between stable, constructed floodplains with heterogeneous, depositional bars typical of naturalizing channels. Consequently, restored inset floodplains could remove {\textgreater} 70\% more N than the naturalized floodplains during similar storm inundation events.},
	language = {en},
	number = {3},
	urldate = {2019-08-10},
	journal = {Biogeochemistry},
	author = {Hanrahan, Brittany R. and Tank, Jennifer L. and Dee, Martha M. and Trentman, Matt T. and Berg, Elizabeth M. and McMillan, Sara K.},
	month = dec,
	year = {2018},
	keywords = {Agricultural streams, Denitrification, Inset floodplains, Restoration, Two-stage ditch},
	pages = {419--437},
}

@article{michalak_record-setting_2013,
	title = {Record-setting algal bloom in {Lake} {Erie} caused by agricultural and meteorological trends consistent with expected future conditions},
	volume = {110},
	copyright = {©  . Freely available online through the PNAS open access option.},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/110/16/6448},
	doi = {10.1073/pnas.1216006110},
	abstract = {In 2011, Lake Erie experienced the largest harmful algal bloom in its recorded history, with a peak intensity over three times greater than any previously observed bloom. Here we show that long-term trends in agricultural practices are consistent with increasing phosphorus loading to the western basin of the lake, and that these trends, coupled with meteorological conditions in spring 2011, produced record-breaking nutrient loads. An extended period of weak lake circulation then led to abnormally long residence times that incubated the bloom, and warm and quiescent conditions after bloom onset allowed algae to remain near the top of the water column and prevented flushing of nutrients from the system. We further find that all of these factors are consistent with expected future conditions. If a scientifically guided management plan to mitigate these impacts is not implemented, we can therefore expect this bloom to be a harbinger of future blooms in Lake Erie.},
	language = {en},
	number = {16},
	urldate = {2019-08-10},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Michalak, Anna M. and Anderson, Eric J. and Beletsky, Dmitry and Boland, Steven and Bosch, Nathan S. and Bridgeman, Thomas B. and Chaffin, Justin D. and Cho, Kyunghwa and Confesor, Rem and Daloğlu, Irem and DePinto, Joseph V. and Evans, Mary Anne and Fahnenstiel, Gary L. and He, Lingli and Ho, Jeff C. and Jenkins, Liza and Johengen, Thomas H. and Kuo, Kevin C. and LaPorte, Elizabeth and Liu, Xiaojian and McWilliams, Michael R. and Moore, Michael R. and Posselt, Derek J. and Richards, R. Peter and Scavia, Donald and Steiner, Allison L. and Verhamme, Ed and Wright, David M. and Zagorski, Melissa A.},
	month = apr,
	year = {2013},
	pmid = {23576718},
	keywords = {Anabaena sp., Microcystis sp., aquatic ecology, climate change, extreme precipitation events},
	pages = {6448--6452},
}

@article{de_pinto_great_1986,
	title = {Great lakes water quality improvement},
	volume = {20},
	issn = {0013-936X},
	url = {10.1021/es00150a001},
	doi = {10.1021/es00150a001},
	number = {8},
	urldate = {2019-08-10},
	journal = {Environmental Science \& Technology},
	author = {De Pinto, Joseph V. and Young, Thomas C. and McIlroy, Lyn M.},
	month = aug,
	year = {1986},
	pages = {752--759},
}

@article{scavia_assessing_2014,
	title = {Assessing and addressing the re-eutrophication of {Lake} {Erie}: {Central} basin hypoxia},
	volume = {40},
	issn = {0380-1330},
	shorttitle = {Assessing and addressing the re-eutrophication of {Lake} {Erie}},
	url = {http://www.sciencedirect.com/science/article/pii/S0380133014000252},
	doi = {10.1016/j.jglr.2014.02.004},
	abstract = {Relieving phosphorus loading is a key management tool for controlling Lake Erie eutrophication. During the 1960s and 1970s, increased phosphorus inputs degraded water quality and reduced central basin hypolimnetic oxygen levels which, in turn, eliminated thermal habitat vital to cold-water organisms and contributed to the extirpation of important benthic macroinvertebrate prey species for fishes. In response to load reductions initiated in 1972, Lake Erie responded quickly with reduced water-column phosphorus concentrations, phytoplankton biomass, and bottom-water hypoxia (dissolved oxygen {\textless}2mg/l). Since the mid-1990s, cyanobacteria blooms increased and extensive hypoxia and benthic algae returned. We synthesize recent research leading to guidance for addressing this re-eutrophication, with particular emphasis on central basin hypoxia. We document recent trends in key eutrophication-related properties, assess their likely ecological impacts, and develop load response curves to guide revised hypoxia-based loading targets called for in the 2012 Great Lakes Water Quality Agreement. Reducing central basin hypoxic area to levels observed in the early 1990s (ca. 2000km2) requires cutting total phosphorus loads by 46\% from the 2003–2011 average or reducing dissolved reactive phosphorus loads by 78\% from the 2005–2011 average. Reductions to these levels are also protective of fish habitat. We provide potential approaches for achieving those new loading targets, and suggest that recent load reduction recommendations focused on western basin cyanobacteria blooms may not be sufficient to reduce central basin hypoxia to 2000km2.},
	number = {2},
	urldate = {2019-08-10},
	journal = {Journal of Great Lakes Research},
	author = {Scavia, Donald and David Allan, J. and Arend, Kristin K. and Bartell, Steven and Beletsky, Dmitry and Bosch, Nate S. and Brandt, Stephen B. and Briland, Ruth D. and Daloğlu, Irem and DePinto, Joseph V. and Dolan, David M. and Evans, Mary Anne and Farmer, Troy M. and Goto, Daisuke and Han, Haejin and Höök, Tomas O. and Knight, Roger and Ludsin, Stuart A. and Mason, Doran and Michalak, Anna M. and Peter Richards, R. and Roberts, James J. and Rucinski, Daniel K. and Rutherford, Edward and Schwab, David J. and Sesterhenn, Timothy M. and Zhang, Hongyan and Zhou, Yuntao},
	month = jun,
	year = {2014},
	keywords = {Best management practices, Hypoxia, Lake Erie, Phosphorus load targets},
	pages = {226--246},
}

@article{beeton_eutrophication_1965,
	title = {Eutrophication of the {St}. {Lawrence} {Great} {Lakes}},
	volume = {10},
	issn = {1939-5590},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.1965.10.2.0240},
	doi = {10.4319/lo.1965.10.2.0240},
	abstract = {Lakes Huron, Michigan, and Superior are classified as oligotrophic lakes on the basis of their biological, chemical, and physical characteristics. Lake Ontario, although rich in nutrients, is morphometrically oligotrophic or mesotrophic because of its large area of deep water. Lake Erie, the most productive of the lakes and the shallowest, is eutrophic. Several changes commonly associated with eutrophication in small lakes have been observed in the Great Lakes. These changes apparently reflect accelerated eutrophication in the Great Lakes due to man’s activity. Chemical data compiled from a number of sources, dating as early as 1854, indicate a progressive increase in the concentrations of various major ions and total dissolved solids in all of the lakes except Lake Superior. The plankton has changed somewhat in Lake Michigan and the plankton, benthos, and fish populations of Lake Erie are greatly different today from those of the past. An extensive area of hypolimnetic water of Lake Erie has developed low dissolved oxygen concentrations in late summer within recent years.},
	language = {en},
	number = {2},
	urldate = {2019-08-10},
	journal = {Limnology and Oceanography},
	author = {Beeton, Alfred M.},
	year = {1965},
	pages = {240--254},
}


@article{zhang_changes_2013,
	title = {Changes of tannin and nutrients during decomposition of branchlets of {Casuarina} equisetifolia plantation in subtropical coastal areas of {China}},
	volume = {59},
	issn = {12141178, 18059368},
	url = {http://pse.agriculturejournals.cz/doi/10.17221/598/2012-PSE.html},
	doi = {10.17221/598/2012-PSE},
	abstract = {A litterbag experiment was conducted to investigate the changes of tannins and nutrients in branchlets at different decomposition stages of Casuarina equisetifolia in southern subtropical coastal zone, China, using the colorimetric assays. The time required for the loss of half of the initial dry weight (t50) was 9.13 months. Total phenolics (TP), extractable condensed tannins (ECT), protein-bound condensed tannins (PBCT), total condensed tannins (TCT) and protein precipitation capacity (PPC) of branchlets litter decreased rapidly, while fibre-bound condensed tannins (FBCT) increased during decomposition. Nitrogen and phosphorus concentration of the branchlet litter both increased gradually during decay. Negative correlations between TP and nitrogen or phosphorus, as well as TCT and nitrogen or phosphorus were found. These chemical changes enhanced the current knowledge on the potential ecological role of nutrient transformation in tannins in C. equisetifolia plantations.},
	language = {en},
	number = {2},
	urldate = {2023-03-26},
	journal = {Plant, Soil and Environment},
	author = {Zhang, L.H. and Zhang, S.J. and Ye, G.F. and Shao, H.B. and Lin, G.H. and Brestic, M.},
	month = feb,
	year = {2013},
	pages = {74--79},
	file = {Zhang et al. - 2013 - Changes of tannin and nutrients during decompositi.pdf:C\:\\Users\\Saheed Jimoh\\Zotero\\storage\\7AWKZMYY\\Zhang et al. - 2013 - Changes of tannin and nutrients during decompositi.pdf:application/pdf},
}

@Manual{r_2021,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2021},
    url = {https://www.R-project.org/},
  }

@article{kang2013prevention,
  title={The prevention and handling of the missing data},
  author={Kang, Hyun},
  journal={Korean journal of anesthesiology},
  volume={64},
  number={5},
  pages={402--406},
  year={2013},
  publisher={The Korean Society of Anesthesiologists},
doi={10.4097/kjae.2013.64.5.402}
}

@article{Gharib2014,
   abstract = {The Markov-Bernoulli geometric distribution is obtained when a generalization, as a Markov process, of the independent Bernoulli sequence of random variables is introduced by considering the success probability changes with respect to the Markov chain. The resulting model is called the Markov-Bernoulli model and it has a wide variety of application fields. In this study, some characterizations are given concerning the Markov-Bernoulli geometric distribution as the distribution of the summation index of independent randomly truncated non-negative integer valued random variables. The achieved results generalize the corresponding characterizations concerning the usual geometric distribution. © 2014 Science Publications.},
   author = {Mohamed Gharib and Mahmoud M. Ramadan and Khaled A.H. Al-Ajmi},
   doi = {10.3844/jmssp.2014.186.191},
   issn = {15493644},
   issue = {2},
   journal = {Journal of Mathematics and Statistics},
   keywords = {Characterization,Markov-Bernoulli geometric distribution,Random sum,Random truncation},
   pages = {186-191},
   publisher = {Science Publications},
   title = {Characterization of Markov-Bernoulli geometric distribution related to random sums},
   volume = {10},
   year = {2014},
}

@article{Edwards1960,
    author = {A. W. F. Edwards},
    title = {The Meaning of Binomial Distribution},
    journal = {Nature},
    year = {1960},
    volume = {186},
    issue = {1074},
    doi = {10.1038/1861074a0}
}

@article{sammaknejad2019review,
  title={A review of the expectation maximization algorithm in data-driven process identification},
  author={Sammaknejad, Nima and Zhao, Yujia and Huang, Biao},
  journal={Journal of process control},
  volume={73},
  pages={123--136},
  year={2019},
  publisher={Elsevier}
}

@article{dempster1977maximum,
  title={Maximum likelihood from incomplete data via the EM algorithm},
  author={Dempster, Arthur P and Laird, Nan M and Rubin, Donald B},
  journal={Journal of the royal statistical society: series B (methodological)},
  volume={39},
  number={1},
  pages={1--22},
  year={1977},
  publisher={Wiley Online Library}
}

@article{vamanu2019altered,
  title={Altered in vitro metabolomic response of the human microbiota to sweeteners},
  author={Vamanu, Emanuel and Pelinescu, Diana and Gatea, Florentina and S{\^a}rbu, Ionela},
  journal={Genes},
  volume={10},
  number={7},
  pages={535},
  year={2019},
  publisher={MDPI}
}

@article{lopucki2022handling,
  title={Handling missing data in ecological studies: Ignoring gaps in the dataset can distort the inference},
  author={{\L}opucki, Rafa{\l} and Kiersztyn, Adam and Pitucha, Grzegorz and Kitowski, Ignacy},
  journal={Ecological Modelling},
  volume={468},
  pages={109964},
  year={2022},
  publisher={Elsevier},
doi={10.1016/j.ecolmodel.2022.109964}
}

@inproceedings{aleryani2018dealing,
  title={Dealing with missing data and uncertainty in the context of data mining},
  author={Aleryani, Aliya and Wang, Wenjia and De La Iglesia, Beatriz},
  booktitle={Hybrid Artificial Intelligent Systems: 13th International Conference, HAIS 2018, Oviedo, Spain, June 20-22, 2018, Proceedings 13},
  pages={289--301},
  year={2018},
  organization={Springer},
doi={10.1007/978-3-319-92639-1_24}
}

@article{luengo2010study,
  title={A study on the use of imputation methods for experimentation with radial basis function network classifiers handling missing attribute values: The good synergy between rbfns and eventcovering method},
  author={Luengo, Juli{\'a}n and Garc{\'\i}a, Salvador and Herrera, Francisco},
  journal={Neural Networks},
  volume={23},
  number={3},
  pages={406--418},
  year={2010},
  publisher={Elsevier}
}

@article{newman_missing_2014,
	title = {Missing Data: {Five} Practical Guidelines},
	volume = {17},
	issn = {1094-4281},
	shorttitle = {Missing {Data}},
	doi = {10.1177/1094428114548590},
	abstract = {Missing data (a) reside at three missing data levels of analysis (item-, construct-, and person-level), (b) arise from three missing data mechanisms (missing completely at random, missing at random, and missing not at random) that range from completely random to systematic missingness, (c) can engender two missing data problems (biased parameter estimates and inaccurate hypothesis tests/inaccurate standard errors/low power), and (d) mandate a choice from among several missing data treatments (listwise deletion, pairwise deletion, single imputation, maximum likelihood, and multiple imputation). Whereas all missing data treatments are imperfect and are rooted in particular statistical assumptions, some missing data treatments are worse than others, on average (i.e., they lead to more bias in parameter estimates and less accurate hypothesis tests). Social scientists still routinely choose the more biased and error-prone techniques (listwise and pairwise deletion), likely due to poor familiarity with and misconceptions about the less biased/less error-prone techniques (maximum likelihood and multiple imputation). The current user-friendly review provides five easy-to-understand practical guidelines, with the goal of reducing missing data bias and error in the reporting of research results. Syntax is provided for correlation, multiple regression, and structural equation modeling with missing data.},
	number = {4},
	urldate = {2023-04-15},
	journal = {Organizational Research Methods},
	author = {Newman, Daniel A.},
	year = {2014},
	note = {Publisher: SAGE Publications Inc},
	pages = {372--411}
}

@article{dong2013principled,
  title={Principled missing data methods for researchers},
  author={Dong, Yiran and Peng, Chao-Ying Joanne},
  journal={SpringerPlus},
  volume={2},
  pages={1--17},
  year={2013},
  publisher={Springer}
}

@article{van2006imputation,
  title={Imputation of missing values is superior to complete case analysis and the missing-indicator method in multivariable diagnostic research: a clinical example},
  author={Van der Heijden, Geert JMG and Donders, A Rogier T and Stijnen, Theo and Moons, Karel GM},
  journal={Journal of clinical epidemiology},
  volume={59},
  number={10},
  pages={1102--1109},
  year={2006},
  publisher={Elsevier}
}

@inproceedings{tran2017missing,
  title={Missing modalities imputation via cascaded residual autoencoder},
  author={Tran, Luan and Liu, Xiaoming and Zhou, Jiayu and Jin, Rong},
  booktitle={Proceedings of the IEEE conference on computer vision and pattern recognition},
  pages={1405--1414},
  year={2017}
}

@book{van2018flexible,
  title={Flexible imputation of missing data},
  author={Van Buuren, Stef},
  year={2018},
  publisher={CRC press}
}

@article{horton2007much,
  title={Much ado about nothing: A comparison of missing data methods and software to fit incomplete data regression models},
  author={Horton, Nicholas J and Kleinman, Ken P},
  journal={The American Statistician},
  volume={61},
  number={1},
  pages={79--90},
  year={2007},
  publisher={Taylor \& Francis},
doi={10.1198/000313007X172556}
}

@article{fichman2003multiple,
  title={Multiple imputation for missing data: Making the most of what you know},
  author={Fichman, Mark and Cummings, Jonathon N},
  journal={Organizational Research Methods},
  volume={6},
  number={3},
  pages={282--308},
  year={2003},
  publisher={Sage Publications}
}

@inproceedings{rubin1988overview,
  title={An overview of multiple imputation},
  author={Rubin, Donald B},
  booktitle={Proceedings of the survey research methods section of the American statistical association},
  volume={79},
  pages={84},
  year={1988},
  organization={Citeseer}
}

@article{rubin1996multiple,
  title={Multiple imputation after 18+ years},
  author={Rubin, Donald B},
  journal={Journal of the American statistical Association},
  volume={91},
  number={434},
  pages={473--489},
  year={1996},
  publisher={Taylor \& Francis}
}

@article{nadjafi2022expectation,
  title={Expectation-maximization algorithm to develop a normal distribution NHPP reliability growth model},
  author={Nadjafi, Mohammad and Gholami, Peyman},
  journal={Engineering Failure Analysis},
  volume={140},
  pages={106575},
  year={2022},
  publisher={Elsevier},
doi={10.1016/j.engfailanal.2022.106575}
}

@article{li2019expectation,
  title={An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data},
  author={Li, Chenhao and Chng, Kern Rei and Kwah, Junmei Samantha and Av-Shalom, Tamar V and Tucker-Kellogg, Lisa and Nagarajan, Niranjan},
  journal={Microbiome},
  volume={7},
  number={1},
  pages={1--14},
  year={2019},
  publisher={BioMed Central},
doi={10.1186/s40168-019-0729-z}
}

@article{velicer2005comparison,
  title={A comparison of missing-data procedures for ARIMA time-series analysis},
  author={Velicer, Wayne F and Colby, Suzanne M},
  journal={Educational and Psychological Measurement},
  volume={65},
  number={4},
  pages={596--615},
  year={2005},
  publisher={Sage Publications Sage CA: Thousand Oaks, CA}
}

@article{honaker2011,
  title={Amelia II: A program for missing data},
  author={Honaker, James and King, Gary and Blackwell, Matthew},
  journal={Journal of Statistical Software},
  volume={45},
  pages={1--47},
  year={2011}
}