U.S. Department of Energy

Pacific Northwest National Laboratory

How Moisture Affects the Way Soil Microbes Breathe

X-ray tomography images of soil cores pinpoint the concentrations of solids (left, in grey) and the distribution of solids and pores (right, in color).

The Science                      

Researchers at the Pacific Northwest National Laboratory recently studied how moisture influences soil heterotrophic respiration, the process by which microbes convert dead organic carbon in the 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 paper also argues that simulations need to 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, every year soils 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, 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: the computational challenges of modeling fluids at this scale and the microscale differences within soil. In every soil, the distribution of organic carbon is highly localized and dependent on physical protection, chemical recalcitrance, pore connectivity, non-uniform microbial colonies, and local moisture content.

This study is the first to do 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. It provides insight into the physical processes that control how soil respiration responds to changes in moisture conditions. The paper’s numerical analyses represent a cost-effective approach for investigating carbon mineralization in soils.

The simulations in this study generally confirmed that the soil respiration rate is a function of moisture content; that such rates increase as moisture (and therefore substrate availability) increases; and that 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 there is a danger to assuming uniform porosity in modeled soils. It is better, the researchers say, to model the structural heterogeneity – diversity – of soils as they exist in nature.

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


This research was supported by the US Department of Energy (DOE) Biological and Environmental Research (BER) Division through the Terrestrial Ecosystem Science (TES) program. Part of the research was performed at Environmental Molecular Science Laboratory (EMSL), a DOE National user facility located at Pacific Northwest National Laboratory (PNNL). 


Yan Z, “Pore-scale Investigation on the Response of Heterotrophic Respiration to Moisture Conditions in Heterogeneous Soils.” Biogeochemistry,131(1), 121–134. (2106) [DOI: 10.1007/s10533-016-0270-0]

November 2016
| Pacific Northwest National Laboratory