https://github.com/bpbond/cpcrw_incubation

PNNL TES incubation of CPCRW soil cores #openexperiment

https://github.com/bpbond/cpcrw_incubation

Repository

PNNL TES incubation of CPCRW soil cores #openexperiment

https://github.com/bpbond/cpcrw_incubation/blob/master/

**August 29, 2017 reproducibility note:** See [this issue](https://github.com/bpbond/cpcrw_incubation/issues/49) for fixing some issues that may crop up when re-running these scripts.

Hurray! The main manuscript for this work is now [published](http://dx.doi.org/10.5194/bg-13-6669-2016) in Biogeosciences. Discussion version is [here](http://www.biogeosciences-discuss.net/bg-2016-234/). Many thanks to the Copernicus publications staff, editor Mike Weintraub, and three anonymous reviewers for their criticisms, insight, and help with this manuscript.

The accompanying 'open experiment' manuscript, describing the repository and scripts used, has been [published in ERL](http://dx.doi.org/10.1088/1748-9326/11/8/084004).


# **DISCLAIMER**
**All the data and results in this repository are provisional and subject to normal scientific fair use expectations.** In particular, the diagnostics below present data that may not have been fully QC'd, checked, or interpreted. We do our best, but make no guarantees as to its correctness.

# cpcrw_incubation
PNNL TES incubation of 2015 CPCRW cores. This is an **#openexperiment** with all raw data, code, diagnostics, etc. posted in this repository; all results can be generated by running the scripts here. See below for details and experimental protocol; more information and photos can be found [here](http://bpbond.github.io/cpcrw_incubation).

This work is funded by DOE's [Terrestrial Ecosystem Science Program](http://tes.science.energy.gov). 

## Current diagnostics

Latest data: 2015-12-09 (incubation day 101)

Script run: 2016-03-31 08:14:03

### Missing/problematic data

![](https://github.com/bpbond/cpcrw_incubation/blob/master/qc_plots/samples_by_date.png)

![](https://github.com/bpbond/cpcrw_incubation/blob/master/qc_plots/orphan_samples.png)

![](https://github.com/bpbond/cpcrw_incubation/blob/master/qc_plots/missing_mass.png)

### Observations over time

![](https://github.com/bpbond/cpcrw_incubation/blob/master/qc_plots/masses.png)

![](https://github.com/bpbond/cpcrw_incubation/blob/master/qc_plots/masses_relative.png)

![](https://github.com/bpbond/cpcrw_incubation/blob/master/qc_plots/CO2_time.png)

![](https://github.com/bpbond/cpcrw_incubation/blob/master/qc_plots/CH4_time.png)

### Variability and outliers

![](https://github.com/bpbond/cpcrw_incubation/blob/master/qc_plots/CO2_CV.png)

![](https://github.com/bpbond/cpcrw_incubation/blob/master/qc_plots/CH4_CV.png)

![](https://github.com/bpbond/cpcrw_incubation/blob/master/qc_plots/coreCV_combined.png)

![](https://github.com/bpbond/cpcrw_incubation/blob/master/qc_plots/coreCV_distribution.png)

![](https://github.com/bpbond/cpcrw_incubation/blob/master/qc_plots/CO2_outliers.png)

![](https://github.com/bpbond/cpcrw_incubation/blob/master/qc_plots/CH4_outliers.png)

### Cumulative fluxes

![](https://github.com/bpbond/cpcrw_incubation/blob/master/qc_plots/cumulative_gas.png)

## Study objectives and approach

**Objective:**

Examine how mineral boreal soils, sampled from the active layer just above permafrost at [CPCRW](http://www.lter.uaf.edu/bnz_cpcrw.cfm), produce GHGs: how production varies with soil moisture, temperature, and other factors.

**Rationale:**

The balance between CO2 and CH4 emissions from soils allows for particularly interesting manipulative experiments and modeling tests, as CH4 is formed under specific conditions and can be readily oxidized back to CO2. This balance thus serves as a particularly interesting mechanistic probe, and stringent test of our understanding and models.

**Approach:**

Sample CPCRW soils just above August frozen soil leveli.e., the base of the active layer using the large augur (7.5 cm w by 30 cm h). Cores should be kept cold, though dont have to stay frozen, and shipped to PNNL.

Sampling will, as much as possible, take place within the open call transects This will allow the two projects to compare spatial similarities in active layer and permafrost soil respiration and conditions.  We anticipate sampling will take place in the black spruce-to-birch hillslope transition zone with an average separation of 2-3 m.

Split cores into six groups:

1. Immediate destructive analyses
2. Maintain at constant (field conditions) water content at 4 C
3. Drydown (no water added) at 4 C
4. Maintain at constant (field conditions) water content at 22 C
5. Maintain at the higher 4 C group water content (as closely as possible to the corresponding point in time) but at 22 C
6. Drydown (no water added) at 22 C

This is designed to give us two control groups that maintain field moisture and different temperatures; two drydown groups; and a drydown group at 22 C that (hopefully) follows the 4 C moisture tracks, allowing us to unambiguously separate temperature and moisture effects.

Groups (ii)-(vi) will be incubated for ~100 days at constant temperatures. Measure mass, adjust water contentfor groups (ii), (iv), (v)and measure CO2/CH4 evolution periodically. Destructive analyses at end of incubation.

This will require 6 groups x 6 reps = 36 cores.

The 4 and 22 C incubation temperatures are driven by logistics (the PNNL growth chambers that can accommodate the samples and Picarro setup), but follow the incubation design of [Treat et al. (2013)](http://dx.doi.org/10.1038/nclimate2010).

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