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U.S. Department of Energy Office of Biological and Environmental Research

PI-Submitted Research Highlights for
Subsurface Biogeochemical Research Program

Microbial Communities in Floodplain Soils Remain Unchanged Throughout Seasonal Redox and Water Table Flux

Chris Francis

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August 14, 2020

Fine-grained sediments appear to host distinct microbial groups that are stimulated through water table rise and fall throughout the season.

The Science
Microbial communities play a crucial role in environmental systems, mediating biogeochemical reactions through metabolic processes that can vary depending on environmental conditions. Understanding these metabolic shifts is particularly important in soils closely connected to groundwater and surface water (e.g., those in floodplains), where redox transformations can determine whether contaminants are sequestered or mobilized. This study characterized microbial community diversity at the uranium- and molybdenum-contaminated Riverton, Wyo., site from spring to fall across multiple depths. Results indicate that communities are surprisingly stable over time, despite extreme seasonal geochemical changes (redox inversion) and hydrological changes (flood to drought). This finding suggests that these microorganisms oscillate between “active” and “dormant,” depending on current environmental conditions, and the products of their metabolism play a greater role in contaminant mobility than the organisms themselves. Future studies to investigate metabolic capacity and activity through metagenomic and metatranscriptomic sequencing will support further integration of hydrological, geochemical, and microbial data into models and other knowledge of contaminant transport and mobility.

The Impact
Biogeochemical changes in the subsurface are driven primarily through microbial life and microbes’ metabolic responses to environmental conditions around them. Soil moisture content, which varies throughout the season from spring flooding to summer drought, profoundly influences microbial communities and the availability of molecular oxygen (O2), thus affecting soil redox conditions and water quality. Microbial responses to hydrological changes therefore comprise keystone functionalities within subsurface ecosystems; however, it is not fully understood how large changes in soil moisture and O2 impact subsurface microorganisms themselves or their metabolism. In this study, surprisingly, microbial communities did not change significantly during seasonal flood-to-drought transitions. Rather, the research team found that depth within the soil profile and soil horizon characteristics were the strongest factors determining microbial diversity. These results provide insight into the complexity of coupling (or decoupling) microbial and geochemical trends in floodplain soils over space and time. For example, seasonal changes in soil moisture apparently are not sufficiently prolonged to displace established microbial groups.

Summary
Riparian floodplains are important regions, given the connectivity of groundwater with river water, biodiversity, presence of contaminants, and capacity to generate and recycle nutrients. In a given year, these floodplains experience changes in precipitation, river discharge (including flooding), and water content (including drought), all of which impact water quality. For example, in the western United States, the U.S. Department of Energy (DOE) manages several former uranium ore–processing floodplain sites, where contaminant concentrations change in response to changing sediment moisture and season. There is a need to understand how hydrology, geochemistry, and microbiology interact to drive these changes. In this study, the team collected floodplain soil samples through a full growing season at the uranium-contaminated Riverton, Wyo., DOE legacy site. These samples were analyzed for key geochemical species, water content, and microbial diversity through community DNA analysis. Findings showed that, despite clear seasonal shifts in geochemical and redox conditions corresponding to changes in hydrological conditions (e.g., flood and drought), microbial community diversity remained largely unaffected. The same microbial groups were present at a given depth throughout the year, indicating their ability to persist despite environmental change. The team did, however, observe slight differences in soil surrounding fine-grained, organic-rich layers (referred to as “transiently reduced zones,” or TRZs). This finding agrees with previously observed export of reducing conditions from TRZs but adds information about how these exports may also impact microbial diversity in adjacent soil layers through water table fluctuations. The results suggest that TRZ soil layers are even more important to floodplain functions than presumed by commonly observed redox transformations, because stable microbial communities drive geochemical changes while remaining relatively unchanged themselves.

Contacts
BER Program Manager
Amy Swain
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Earth and Environmental Systems Sciences Division (SC-33.1) and Biological Systems Science Division (SC-33.2)
Environmental System Science and Biomolecular Characterization and Imaging Science
amy.swain@science.doe.gov

Principal Investigator
Chris Francis
Stanford University, Earth System Science Department
Stanford, CA 94305-4216
Caf@stanford.edu

Funding
Funding was provided by the Subsurface Biogeochemical Research (SBR) program of the Office of Biological and Environmental Research, within the U.S. Department of Energy (DOE) Office of Science, to the SLAC National Accelerator Laboratory Science Focus Area project under contract DE-AC02-76SF00515. Use of the Stanford Synchrotron Radiation Laboratory (SSRL) at SLAC is supported by the Office of Basic Energy Sciences, within the DOE Office of Science.

Publications
Tolar, B.B., Boye, K., Bobb, C. et al. “Stability of floodplain subsurface microbial communities through seasonal hydrological and geochemical cycles.” Frontiers in Earth Science – Biogeoscience 8, 338 (2020). [DOI:10.3389/feart.2020.00338]

John Bargar, Kristin Boye (SLAC National Acceleratory Laboratory, Groundwater Quality SFA)

Bradley Tolar, Callum Bobb, Kate Maher, Christopher Francis (Stanford University, SFA collaborators)

The DOE Joint Genome Institute (JGI) was used for sequencing; ESS-DIVE was utilized for data storage.

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