Data for "Which plant traits increase soil carbon sequestration? Empirical evidence from a long-term poplar genetic diversity trial"
Authors/Creators
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1.
Oak Ridge National Laboratory
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2.
Colorado State University
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3.
University of Tennessee System
Description
This archive contains all data and code used by the following publication:
Field, J. L., Sloan, B. P., Craig, M. E., Calloway, P., Ottinger, S. L., Mead, T., Abramoff, R. Z., Venegas, M. P., Chhetri, H. B., Haiby, K., Kalluri, U. C., Muchero, W., Schadt, C. W., & Mayes, M. A. (2025). Which plant traits increase soil carbon sequestration? Empirical evidence from a long-term poplar genetic diversity trial (p. 2025.02.17.638464). bioRxiv. https://doi.org/10.1101/2025.02.17.638464
Our analysis combined several soil and root data sets collected by Oak Ridge National Laboratory (ORNL) researchers/collaborators from the Clatskanie Poplar Common Garden in Clatskanie, OR by from 2009-2024. The raw data data files are located */02-data/01-raw/* which we harmonized using the codes in */01-codes/01-harmonize-clatskanie-data-pub.qmd*. The final processed data set used in the paper is found at */02-data/02-processed/clatskanie-c-fit-data.csv* and its columns are described in the table below.
| Variable | Description | Units |
|---|---|---|
| ord | Order of gentoypes used for manuscript plotting | |
| tree | Unique ID for all poplar trees across these data sets (max of 66 trees) | |
| genotype | ID for genotypes contained across these data sets (max of 23 genotypes) | |
| block | ID for replicate blocks (max of 3 replicates) | |
| Depth | Soil core depth at each tree. Primarily use 15 cm for manuscript, see raw data for deeper samples (max 60 cm for select trees) | cm |
| latitude | Latitude of tree | degrees |
| longitude | Longitude of tree | degrees |
| cop_id | Flag to indicate if a given year is before or after coppicing. | |
| height | Tree height | cm |
| dbh | Tree diameter at breast height | cm |
| agb | Estimated aboveground biomass growth rate from @truax2014 based on dbh | kg/yr |
| root_CN | Root carbon to nitrogen ratio | |
| Lig | Root lignin percentage | % |
| BD | Soil bulk density | g/cm$^3$ |
| pH_soil | Soil acidity taken from LDRD soil chemistry data. | |
| CEC | Cation exchange capacity | milliequivalents per 100 grams |
| base_sat | Soil base saturation of CEC | % |
| Sand, Silt, Clay | Percent sand, silt or clay | % |
| POMC, MAOMC, TotC | Particulate (POM), mineral-associated (MAOM), and Total soil organic matter C concentrations | mg C/g soil |
| POMC_st, MAOMC_st, TotC_st | Particulate (POM), mineral-associated (MAOM), and Total soil organic matter C stocks | tonnes C/ha |
| POMC_CN, MAOMC_CN, soil_CN | Particulate (POM), mineral-associated (MAOM), and Total soil organic matter carbon to nitrogen ratios | % |
| TotC_30, TotC_st_30 | Total SOC concentration and stock from 0-30 cm rather than 0-15 cm as the other observations. | mg C/g soil or tonnes C/ha |
| C_chk_rel, C_chk_id | Percentage mass balance error in POMC + MAOMC versus TotC, with less than 30% error being acceptable. | % |
| Al_ppm, B_ppm, Cu_ppm, Fe_ppm, Mn_ppm, Mo_ppm, Na_ppm, Ni_ppm, Zn_ppm | Aluminum, Boron, Copper, Iron, Manganese, Molibdinum, Sodium, Nickel, and Zinc concentrations. | parts per million (ppm) |
| pCa, pK, pMg, pP, pS | Calcium, Potassium, Magnesium, Phosphorus, Sulfur percentages | % |
| _root, _soil, _diff | Suffix indicating either the root or soil elemental or nutrient quantity or the difference in root and soil quantity. |
Finally, the analysis and figure generation codes for the manuscript are located in the */01-codes/01-gcb-pub-analysis.qmd* file, while the figure files are located in */03-figs/*. These *Quarto* notebooks have corresponding rendered markdown files (*.md*) stored in the same location. *R* version 4.4.1 was used for all analysis.
Full Changelog: https://github.com/sloan091/gcb-clatskanie-soil-c/commits/initial-release-gcb
Files
sloan091/gcb-clatskanie-soil-c-initial-release-gcb.zip
Files
(11.2 MB)
| Name | Size | Download all |
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Additional details
Related works
- Is supplement to
- Software: https://github.com/sloan091/gcb-clatskanie-soil-c/tree/initial-release-gcb (URL)
Software
- Repository URL
- https://github.com/sloan091/gcb-clatskanie-soil-c