@article{Novel,
	title = {A novel denitrifying methanotroph of the {NC10} phylum and its microcolony},
	volume = {6},
	copyright = {2016 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/srep32241},
	doi = {10.1038/srep32241},
	abstract = {The NC10 phylum is a candidate phylum of prokaryotes and is considered important in biogeochemical cycles and evolutionary history. NC10 members are as-yet-uncultured and are difficult to enrich and our knowledge regarding this phylum is largely limited to the first species ‘Candidatus Methylomirabilis oxyfera’ (M. oxyfera). Here, we enriched NC10 members from paddy soil and obtained a novel species of the NC10 phylum that mediates the anaerobic oxidation of methane (AOM) coupled to nitrite reduction. By comparing the new 16S rRNA gene sequences with those already in the database, this new species was found to be widely distributed in various habitats in China. Therefore, we tentatively named it ‘Candidatus Methylomirabilis sinica’ (M. sinica). Cells of M. sinica are roughly coccus-shaped (0.7–1.2 μm), distinct from M. oxyfera (rod-shaped; 0.25–0.5 × 0.8–1.1 μm). Notably, microscopic inspections revealed that M. sinica grew in honeycomb-shaped microcolonies, which was the first discovery of microcolony of the NC10 phylum. This finding opens the possibility to isolate NC10 members using microcolony-dependent isolation strategies.},
	language = {en},
	number = {1},
	urldate = {2024-05-08},
	journal = {Scientific Reports},
	author = {He, Zhanfei and Cai, Chaoyang and Wang, Jiaqi and Xu, Xinhua and Zheng, Ping and Jetten, Mike S. M. and Hu, Baolan},
	month = sep,
	year = {2016},
	note = {Publisher: Nature Publishing Group},
	keywords = {Carbon cycle, Environmental microbiology, Microbial ecology},
	pages = {32241},
}

@misc{NEON,
	title = {Onaqui {NEON} {\textbar} {NSF} {NEON} {\textbar} {Open} {Data} to {Understand} our {Ecosystems}},
	url = {https://www.neonscience.org/field-sites/onaq},
	urldate = {2024-05-08},
}

@misc{DOE,
	title = {{DOE} {Joint} {Genome} {Institute}: {A} {DOE} {Office} of {Science} {User} {Facility} of {Lawrence} {Berkeley} {National} {Laboratory}},
	shorttitle = {{DOE} {Joint} {Genome} {Institute}},
	url = {https://jgi.doe.gov/},
	language = {en-US},
	urldate = {2024-05-08},
	journal = {DOE Joint Genome Institute},
}

@article{Metagenome,
	title = {{DOE} {JGI} {Metagenome} {Workflow}},
	volume = {6},
	issn = {2379-5077},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8269246/},
	doi = {10.1128/mSystems.00804-20},
	abstract = {The DOE Joint Genome Institute (JGI) Metagenome Workflow performs metagenome data processing, including assembly; structural, functional, and taxonomic annotation; and binning of metagenomic data sets that are subsequently included into the Integrated Microbial Genomes and Microbiomes (IMG/M) (I.-M. A. Chen, K. Chu, K. Palaniappan, A. Ratner, et al., Nucleic Acids Res, 49:D751–D763, 2021, https://doi.org/10.1093/nar/gkaa939) comparative analysis system and provided for download via the JGI data portal (https://genome.jgi.doe.gov/portal/). This workflow scales to run on thousands of metagenome samples per year, which can vary by the complexity of microbial communities and sequencing depth. Here, we describe the different tools, databases, and parameters used at different steps of the workflow to help with the interpretation of metagenome data available in IMG and to enable researchers to apply this workflow to their own data. We use 20 publicly available sediment metagenomes to illustrate the computing requirements for the different steps and highlight the typical results of data processing. The workflow modules for read filtering and metagenome assembly are available as a workflow description language (WDL) file (https://code.jgi.doe.gov/BFoster/jgi\_meta\_wdl). The workflow modules for annotation and binning are provided as a service to the user community at https://img.jgi.doe.gov/submit and require filling out the project and associated metadata descriptions in the Genomes OnLine Database (GOLD) (S. Mukherjee, D. Stamatis, J. Bertsch, G. Ovchinnikova, et al., Nucleic Acids Res, 49:D723–D733, 2021, https://doi.org/10.1093/nar/gkaa983)., IMPORTANCE The DOE JGI Metagenome Workflow is designed for processing metagenomic data sets starting from Illumina fastq files. It performs data preprocessing, error correction, assembly, structural and functional annotation, and binning. The results of processing are provided in several standard formats, such as fasta and gff, and can be used for subsequent integration into the Integrated Microbial Genomes and Microbiomes (IMG/M) system where they can be compared to a comprehensive set of publicly available metagenomes. As of 30 July 2020, 7,155 JGI metagenomes have been processed by the DOE JGI Metagenome Workflow. Here, we present a metagenome workflow developed at the JGI that generates rich data in standard formats and has been optimized for downstream analyses ranging from assessment of the functional and taxonomic composition of microbial communities to genome-resolved metagenomics and the identification and characterization of novel taxa. This workflow is currently being used to analyze thousands of metagenomic data sets in a consistent and standardized manner.},
	number = {3},
	urldate = {2024-05-08},
	journal = {mSystems},
	author = {Clum, Alicia and Huntemann, Marcel and Bushnell, Brian and Foster, Brian and Foster, Bryce and Roux, Simon and Hajek, Patrick P. and Varghese, Neha and Mukherjee, Supratim and Reddy, T. B. K. and Daum, Chris and Yoshinaga, Yuko and O’Malley, Ronan and Seshadri, Rekha and Kyrpides, Nikos C. and Eloe-Fadrosh, Emiley A. and Chen, I-Min A. and Copeland, Alex and Ivanova, Natalia N.},
	pmid = {34006627},
	pmcid = {PMC8269246},
	pages = {e00804--20},
}

@article{Utah,
	title = {Great {Salt} {Lake} microbiology: a historical perspective},
	volume = {21},
	issn = {1139-6709},
	shorttitle = {Great {Salt} {Lake} microbiology},
	doi = {10.1007/s10123-018-0008-z},
	abstract = {Over geologic time, the water in the Bonneville basin has risen and fallen, most dramatically as freshwater Lake Bonneville lost enormous volume 15,000-13,000 years ago and became the modern day Great Salt Lake. It is likely that paleo-humans lived along the shores of this body of water as it shrunk to the present margins, and native peoples inhabited the surrounding desert and wetlands in recent times. Nineteenth century Euro-American explorers and pioneers described the geology, geography, and flora and fauna of Great Salt Lake, but their work attracted white settlers to Utah, who changed the lake immeasurably. Human intervention in the 1950s created two large sub-ecosystems, bisected by a railroad causeway. The north arm approaches ten times the salinity of sea water, while the south arm salinity is a meager four times that of the oceans. Great Salt Lake was historically referred to as sterile, leading to the nickname "America's Dead Sea." However, the salty brine is teaming with life, even in the hypersaline north arm. In fact, scientists have known that this lake contains a diversity of microscopic lifeforms for more than 100 years. This essay will explore the stories of the people who observed and researched the salty microbiology of Great Salt Lake, whose discoveries demonstrated the presence of bacteria, archaea, algae, and protozoa that thrive in this lake. These scientists documented the lake's microbiology as the lake changed, with input from human waste and the creation of impounded areas. Modern work on the microbiology of Great Salt Lake has added molecular approaches and illuminated the community structures in various regions, and fungi and viruses have now been described. The exploration of Great Salt Lake by scientists describing these tiny inhabitants of the brine illuminate the larger terminal lake with its many facets, anthropomorphic challenges, and ever-changing shorelines.},
	number = {3},
	journal = {International Microbiology: The Official Journal of the Spanish Society for Microbiology},
	author = {Baxter, Bonnie K.},
	month = sep,
	year = {2018},
	pmid = {30810951},
	pmcid = {PMC6133049},
	keywords = {20th Century, 21st Century, Biota, Extremophiles, Great Salt Lake, Halophiles, History, History of science, Humans, Hypersaline, Lakes, Microbiology, Salinity, Utah},
	pages = {79--95},
}

@article{Shrub,
	title = {Grass-{Shrub} {Associations} over a {Precipitation} {Gradient} and {Their} {Implications} for {Restoration} in the {Great} {Basin}, {USA}},
	volume = {10},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0143170},
	abstract = {As environmental stress increases positive (facilitative) plant interactions often predominate. Plant-plant associations (or lack thereof) can indicate whether certain plant species favor particular types of microsites (e.g., shrub canopies or plant-free interspaces) and can provide valuable insights into whether "nurse plants" will contribute to seeding or planting success during ecological restoration. It can be difficult, however, to anticipate how relationships between nurse plants and plants used for restoration may change over large-ranging, regional stress gradients. We investigated associations between the shrub, Wyoming big sagebrush (Artemisia tridentata ssp. wyomingensis), and three common native grasses (Poa secunda, Elymus elymoides, and Pseudoroegneria spicata), representing short-, medium-, and deep-rooted growth forms, respectively, across an annual rainfall gradient (220-350 mm) in the Great Basin, USA. We hypothesized that positive shrub-grass relationships would become more frequent at lower rainfall levels, as indicated by greater cover of grasses in shrub canopies than vegetation-free interspaces. We sampled aerial cover, density, height, basal width, grazing status, and reproductive status of perennial grasses in canopies and interspaces of 25-33 sagebrush individuals at 32 sites along a rainfall gradient. We found that aerial cover of the shallow rooted grass, P. secunda, was higher in sagebrush canopy than interspace microsites at lower levels of rainfall. Cover and density of the medium-rooted grass, E. elymoides were higher in sagebrush canopies than interspaces at all but the highest rainfall levels. Neither annual rainfall nor sagebrush canopy microsite significantly affected P. spicata cover. E. elymoides and P. spicata plants were taller, narrower, and less likely to be grazed in shrub canopy microsites than interspaces. Our results suggest that exploring sagebrush canopy microsites for restoration of native perennial grasses might improve plant establishment, growth, or survival (or some combination thereof), particularly in drier areas. We suggest that land managers consider the nurse plant approach as a way to increase perennial grass abundance in the Great Basin. Controlled experimentation will provide further insights into the life stage-specific effectiveness and practicality of a nurse plant approach for ecological restoration in this region.},
	language = {eng},
	number = {12},
	journal = {PloS One},
	author = {Holthuijzen, Maike F. and Veblen, Kari E.},
	year = {2015},
	pmid = {26625156},
	pmcid = {PMC4666403},
	keywords = {Conservation of Natural Resources, Eating, Poaceae, Rain, United States},
	pages = {e0143170},
}