How Moisture Affects the Way Soil Microbes Breathe

Study models soil-pore features that hold or release carbon.

The Science

Researchers recently studied how moisture influences soil heterotrophic respiration, the process by which microbes convert dead organic carbon in soil to carbon dioxide. Their cost-effective modeling strategy is the first to investigate the effect of moisture on these climate-critical respiration rates at the hard-to-simulate pore scale. The study also finds that simulations must acknowledge the diversity of soil-pore spaces, moving beyond the modeling assumption that they are homogeneous.

The Impact

Globally, soils store enormous quantities of organic carbon, some of which is consumed by microbes and exhaled as carbon dioxide. In this way, soils annually produce a major natural carbon dioxide flux into the atmosphere, in an amount roughly six times larger than human emissions of the same greenhouse gas. Understanding what influences this flux has enormous implications for understanding climate change, the carbon cycle, and setting emissions targets.


Moisture conditions in soil affect the respiration rate of heterotrophic microbes. Soils are made of sand, silt, clays, and organic matter. Within all this material, miniature “porospheres” interlock to create microbial habitats made of water and gases. Modeling heterotrophic respiration at this “pore scale” is difficult because of two factors: (1) the computational challenges of modeling fluids at this scale and (2) the microscale differences within soil. In every soil, distribution of organic carbon is highly localized and dependent on physical protection, chemical recalcitrance, pore connectivity, nonuniform microbial colonies, and local moisture content.

This study, led by researchers at Pacific Northwest National Laboratory, is the first to conduct a pore-scale investigation of how moisture-driven respiration rates are affected by soil pore structure heterogeneity, soil organic carbon bioavailability, moisture content distribution, and substrate transport. The work provides insight into the physical processes that control how soil respiration responds to changes in moisture conditions. The study’s numerical analyses represent a cost-effective approach for investigating carbon mineralization in soils.

The simulations in this study generally confirmed that (1) the soil respiration rate is a function of moisture content, (2) such rates increase as moisture (and therefore substrate availability) increases, and (3) soil respiration decreases after some optimum because of oxygen limitation. The model’s results, also replicated by field research, show that respiration rates go up with higher soil porosity and that compacted soils (those with less porosity because they are unplowed and undisturbed) reduce the rate at which carbon dioxide escapes into the atmosphere. The study also warned of a danger to assuming uniform porosity in modeled soils; instead, the researchers found that the structural heterogeneity (diversity) of soils should be modeled as it exists in nature.

Further research is needed to determine how coupled aerobic and anaerobic processes would speed up or slow down the amount of organic carbon sequestered in soil.

Principal Investigator(s)

Vanessa Bailey
Pacific Northwest National Laboratory

Chongxuan Liu
Pacific Northwest National Laboratory


This research was supported by the Terrestrial Ecosystem Science program of the Office of Biological and Environmental Research (BER), within the U.S. Department of Energy (DOE) Office of Science. Part of the research was performed at the Environmental Molecular Science Laboratory (EMSL), a DOE national user facility located at Pacific Northwest National Laboratory.


Yan, Z. et al. “Pore-scale investigation on the response of heterotrophic respiration to moisture conditions in heterogeneous soils.” Biogeochemistry 131(1), 121–34. (2106). [DOI:10.1007/s10533-016-0270-0].