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The DOE Science News Source is a Newswise initiative to promote research news from the Office of Science of the DOE to the public and news media.
  • 2017-03-13 13:05:13
  • Article ID: 671100

How Moisture Affects the Way Soil Microbes Breathe

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

  • Credit: Image courtesy of Pacific Northwest National Laboratory

    Microbes in the soil are central players in converting carbon into greenhouse gases

The Science

Globally, soils store enormous quantities of carbon. Microbes consume some of that carbon and exhale it as carbon dioxide. Thus, soils contribute carbon dioxide to the air. Researchers studied how moisture influences carbon dioxide releases by microbes converting dead carbon in soil to carbon dioxide. The team’s cost-effective modeling strategy is the first to investigate the effect of moisture on these climate-critical respiration rates in hard-to-simulate pores. The pores are tiny gap-like spaces between the soil particles where water and nutrients flow and microbes thrive, making them a microenvironment. The study finds that simulations must acknowledge the diversity of soil-pore spaces. Simulations must move beyond the modeling assumption that they are uniform, or homogeneous.

The Impact

Soils annually produce a major natural carbon dioxide flux into the atmosphere. Soils release 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. A heterotrophic organism obtains its food and energy by taking in plant matter or other substances. 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 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. Respiration rates increase as moisture (and therefore substrate availability) increases, and 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. 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 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.


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


Z. Yan, C. Liu, K.E. Todd-Brown, Y. Liu, B. Bond-Lamberty, and V.L. Bailey, “Pore-scale investigation on the response of heterotrophic respiration to moisture conditions in heterogeneous soils.” Biogeochemistry 131(1), 121-134 (2016). [DOI: 10.1007/s10533-016-0270-0]

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Argonne to Install Comanche System to Explore ARM Technology for High-Performance Computing

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SLAC's Helen Quinn Honored with 2018 Benjamin Franklin Medal in Physics

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PPPL Honors Grierson and Greenough for Distinguished Research and Engineering Achievements

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Former SLAC Director Jonathan Dorfan Awarded Japan's Order of the Rising Sun

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Jefferson Lab Staff Scientist Honored with APS Fellowship

Fulvia Pilat, a staff scientist at the Department of Energy's Thomas Jefferson National Accelerator Facility, has been named a fellow of the American Physical Society. The honor is bestowed by members of APS on their peers for exceptional contributions to their fields.

First Northwest Theoretical Chemistry Conference Is a Hit!

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Argonne Forms New Divisions to Focus on Computation and Data Science Strengths

Argonne has formed two new research divisions to focus its lab-wide foundational expertise on computational science and data science activities.

Hermann Grunder Recognized by IEEE Nuclear and Plasma Sciences Society

Dr. Hermann Grunder, Founding Director of Jefferson Lab, has been selected as one of two recipients of the 2018 IEEE NPSS Particle Accelerator Science and Technology (PAST) Award.

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The Challenge of Estimating Alaska's Soil Carbon Stocks

A geospatial analysis determined the optimal distribution of sites needed to reliably estimate Alaska's vast soil carbon.

Unplugging the Cellulose Biofuel Bottleneck

Molecular-level understanding of cellulose structure reveals why it resists degradation and could lead to cost-effective biofuels.

How Fungal Enzymes Break Down Plant Cell Walls

Lignocellulose-degrading enzyme complexes could improve biofuel production.

Stretching to Perfection of 2-D Semiconductors

Scientists use heat and mismatched surfaces to stretch films that can potentially improve the efficient operation of devices.

Simple is Beautiful in Quantum Computing

Defect spins in diamond were controlled with a simpler, geometric method, leading to faster computing.

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More frequent storms turn forests from carbon source to sink.

A Chemical Thermometer for Tropical Forests

Monoterpene measures how certain forests respond to heat stress.

Where a Leaf Lands and Lies Influences Carbon Levels in Soil for Years to Come

Whether carbon comes from leaves or needles affects how fast it decomposes, but where it ends up determines how long it's available.

Twisting Molecule Wrings More Power from Solar Cells

Readily rotating molecules let electrons last, resulting in higher solar cell efficiency.

Rules Are Only Suggestions in Heavy Elements

The arrangement of electrons in an exotic human-made element shows that certain properties of heavy elements cannot be predicted using lighter ones.


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