The Science

In rice paddies and other frequently flooded areas, groups of bacteria and other microbes adapt to repeated wet-dry cycles. These microbes exert a lot of influence. They alter the availability of nutrients to help nearby plants grow. Also, they influence carbon dioxide and other emissions. A team examined frequently flooded soils from rice paddies to see how microbial communities function during floods. Their work yielded surprising results. They found that analyzing the carbon that microbes extract from water might be enough to understand and model these important communities.

The Impact

How microbes function in frequently flooded soils has profound impacts on crops. Why? In part, because microbes can deliver nutrients to plants and stabilize or release atmospheric emissions from soils. Knowing how microbial communities work in soils—before, during, and after flooding—can help scientists improve models and promote beneficial changes in those communities.


To know how microbial activity varied in response to flooding, the team studied three types of organic matter that are commonly found in three types of rice paddy soils: dried rice straw, charred rice straw, and cattle manure. Team members came from the SLAC National Accelerator Laboratory; Stanford University; Swedish University of Agricultural Sciences; University of California, Riverside; and EMSL, the Environmental Molecular Sciences Laboratory, a Department of Energy Office of Science user facility. While other studies used a similar approach to look at well-aerated, upland soil and simple carbon compounds, or single microorganisms, none examined the full complexity of natural soil and carbon substrates during the transition from dry to flooded conditions. The team used EMSL’s Fourier-transform ion cyclotron resonance mass spectrometer to analyze dissolved carbon and then observed how microbial functioning changed. These pioneering experiments produced surprising results. Not only were researchers able to better understand how microbes breathed and obtained energy during flooded conditions, but they discovered that a focus on water-extractable carbon was sufficient to predict microbial respiration rates from diverse metabolic strategies. Though more in-depth studies will be important to reveal underlying functions, the insights gained from this study give scientists a proxy to begin modeling these complex interactions.


This work was supported by the Department of Energy’s (DOE’s) Office of Science, Office of Biological and Environmental Research (BER), including support of the Environmental Molecular Sciences Laboratory (EMSL), a DOE Office of Science user facility; SLAC National Accelerator Laboratory and the BER Subsurface Biogeochemical Research program through the SLAC Groundwater Quality Science Focus Area; Swedish Foundation for International Cooperation in Research and Higher Education; Swedish Research Council for Environment, Agricultural Sciences, and Spatial Planning; and U.S. National Science Foundation Graduate Research Fellowship Program.


K. Boye, A.H. Hermann, M.V. Schaefer, M.M. Tfaily, and S. Fendorf, “Discerning microbially mediated processes during redox transitions in flooded soils using carbon and energy balances.” Frontiers in Environmental Science (2018). [DOI: 10.3389/fenvs.2018.00015]