February 01, 2022

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Predicting How Soil Microbes Breathe: Diffusion Limitations Matter

Study reveals importance of accounting for micrometer scale distribution of substrates to predict soil carbon emissions.

Carbon dioxide emissions from the soil profile measured using surface chambers.

[Courtesy Pacific Northwest National Laboratory.]

The Science

Soils act as a vast carbon storehouse that could also be a huge source of greenhouse gas emissions. Microbes within the soil control carbon emissions through cellular respiration, which feeds on surrounding carbon. Oddly, microbes’ metabolic activities are generally substrate (carbon) limited. This contradiction creates significant challenges in the development of models that predict carbon dioxide (CO2) emissions from soil. This project used a spatial modeling analysis to demonstrate how distance among diverse soil components impacts microbial access to substrate—its nourishment—and thus respiration rates at micrometer scales. Findings indicate that contrary to previous predictions, less CO2emissions are present when models account for substrate distribution. 

The Impact

Soil contains twice as much carbon as all vegetation on Earth and far more than is currently in the atmosphere as CO2. Predicting how carbon is stored in soil and released as CO2is a critical calculation in understanding future climate dynamics. This study used novel numerical experiments to examine how microbial respiration in soil should be modeled. Results show that simulations must acknowledge the proximity of microbes and substrates within the soil to accurately predict carbon emissions. 


The distribution of carbon in soil is highly localized due to the arrangement of soil particles, organic carbon, water, and gas. This diverse makeup influences how microbes access substrates for nourishment, which fuels their respiration and how that respiration also depends on soil moisture. Using a simple diffusion-reaction model and numerical experiments, this study demonstrates that moisture interacts with varying substrate distribution at the micrometer scale to control the dynamic transitions between regimes in which either substrate diffusion rate or microbial metabolic activity limits respiration. Such regime shifts are driven by the nonlinearity that emerges from varying distances between microbes and substrates and the varying saturation behaviors of microbial utilization of substrates. As a result, the “real” spatially resolved rates of microbial respiration are always lower than rates calculated based on homogeneous substrate distribution. The novel formulation of diffusion-limited microbial respiration proposed in this study provides biophysical insights about how microscale nonlinearity between substrate distribution and microbial respiration drives prediction biases at a macroscopic level. 

Principal Investigator

Vanessa Bailey
Pacific Northwest National Laboratory

Program Manager

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


This research was supported by the Office of Biological and Environmental Research (BER) Environmental System Science (ESS) program within the U.S. Department of Energy’s (DOE) Office of Science. The Pacific Northwest National Laboratory (PNNL) is operated for DOE by Battelle Memorial Institute under contract DE-AC05-76RL01830. 


Zheng, J., et al. "Revisiting Diffusion-Based Moisture Functions: Why Do They Fail?." Soil Biology and Biochemistry 165 108525  (2022). https://doi.org/10.1016/j.soilbio.2021.108525.