Understanding the Role of Microbes in Greenhouse Gas Production in Agricultural Soils

The Science

It is critical to understand the role of agricultural practices on soil greenhouse gas (GHG) emissions as expanded collections of agricultural residues are considered for bioenergy production and shifts are made to farming dedicated bioenergy crops. Production and consumption of carbon dioxide, methane, and other GHGs are predominantly mediated by soil microbes, yet the relationship between functional processes and microbial diversity in these systems is poorly understood. Researchers at the DOE Great Lakes Bioenergy Research Center (GLBRC) have examined agricultural GHG production, linking these processes to microbial community activities. The study included agricultural soils under various management practices, both successional grasslands on abandoned agricultural land and mature forests or grasslands that had never been farmed. GHG production and consumption rates were correlated to soil microbial community composition. Rates of methane consumption were found to be highest in non-agricultural forests and grasslands, which also showed the greatest diversity of methane-consuming microbes (i.e., methanotrophs). Successional sites were intermediate in terms of both methane consumption and methanotroph diversity, suggesting a gradual recovery process following disruption by traditional tillage agriculture. These results have important implications in considering sustainable establishment and long-term management of bioenergy landscapes and predictive modeling of GHG emissions.


Agriculture has marked impacts on the production of carbon dioxide (CO2) and consumption of methane (CH4) by microbial communities in upland soils—Earth’s largest biological sink for atmospheric CH4. To determine whether the diversity of microbes that catalyze the flux of these greenhouse gases is related to the magnitude and stability of these ecosystem-level processes, researchers conducted molecular surveys of CH4-oxidizing bacteria (methanotrophs) and total bacterial diversity across a range of land uses and measured the in situ flux of CH4 and CO2 at a site in the upper United States Midwest. Conversion of native lands to row-crop agriculture led to a sevenfold reduction in CH4 consumption and a proportionate decrease in methanotroph diversity. Sites with the greatest stability in CH4 consumption harbored the most methanotroph diversity. In fields abandoned from agriculture, the rate of CH4 consumption increased with time along with the diversity of methanotrophs. Conversely, estimates of total bacterial diversity in soil were not related to the rate or stability of CO2 emission. These combined results are consistent with the expectation that microbial diversity is a better predictor of the magnitude and stability of processes catalyzed by organisms with highly specialized metabolisms, like CH4 oxidation, as compared with processes driven by widely distributed metabolic processes, like CO2 production in heterotrophs. The data also suggest that managing lands to conserve or restore methanotroph diversity could mitigate the atmospheric concentrations of this potent greenhouse gas.

Principal Investigator

Thomas M. Schmidt
Michigan State University

BER Program Manager

Dawn Adin

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


Levine, U. Y., T. K. Teal, G. P. Robertson, and T. M. Schmidt. 2011. “Agriculture’s Impact on Microbial Diversity and Associated Fluxes of Carbon Dioxide and Methane,” The ISME Journal 5, 1683–91. DOI:10.1038/ismej.2011.40.