October 04, 2023

New R Package Makes Disentangling the Components of Biogeochemical Fluxes Easier

A stable isotope technique called pool dilution is crucial for obtaining essential Earth system data.

Conceptual depiction of initial and final incubation conditions under two different development pathways for a soil methane pool dilution experiment.

In soil, microbes produce and consume methane. Using pool dilution, researchers can separate the rate of methane production and consumption from the net rate using stable isotope tracers (¹³CH₄) and optimization equations.

[Reprinted under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND 4.0) from Morris, K. A., et al. "PoolDilutionR: An R Package for Easy Optimization of Isotope Pool Dilution Calculations." Methods in Ecology and Evolution 14 (11), 2728–37 (2023). DOI:10.1111/2041-210X.14223.]

The Science

Biogeochemical processes, often called fluxes, recycle materials through the Earth system. Underlying productive and consumptive processes control the flux magnitude. Typically, these two components cannot be separated, and only the net flux is measured. Using stable isotope tracers, chemically identical, microscopically “tagged” molecules allow researchers to calculate the two gross components, but the equations are difficult to navigate. This study presents a new R package to address complicated equations in this system.

The Impact

Earth system models answer questions about current and future environmental conditions. Despite the urgent need for gross biogeochemical flux data to improve model performance, such data is rarely collected. A key technique for collecting gross flux data is stable isotope pool dilution, which first gained prominence in the 1990s but remains underutilized in part due to the calculations’ relative inaccessibility. PoolDilutionR is a user-friendly software package that brings the theory of pool dilution into the 21st century by allowing researchers to process their pool dilution data easily in one of the most popular software languages in the field. This open-source tool will allow wider application of pool dilution and easier generation of critical Earth system data.

Summary

Despite being a powerful method for quantifying gross biogeochemical transformation rates, isotopic pool dilution is seldom employed. Pacific Northwest National Laboratory offers a user-friendly R package that optimizes rates and fractionation constants using standard pool dilution time series data, featuring comprehensive documentation and examples for seamless integration. The package is easily integrated into analytical pipelines to facilitate broader implementation of pool dilution methods.

Principal Investigator

Vanessa Bailey
Pacific Northwest National Laboratory
[email protected]

Program Manager

Daniel Stover
U.S. Department of Energy, Biological and Environmental Research (SC-33)
Environmental System Science
[email protected]

Funding

This research is based on work supported by Coastal Observations, Mechanisms, and Predictions Across Systems and Scales—Field, Measurements, and Experiments, a multi-institutional project supported by the U.S. Department of Energy, Office of Science, Biological and Environmental Research program as part of the Environmental System Science program.

References

Morris, K. A. et al. "PoolDilutionR: An R Package for Easy Optimization of Isotope Pool Dilution Calculations." Methods in Ecology and Evolution 14 (11), 2728–37 (2023). https://doi.org/10.1111/2041-210X.14223.