SLAC Floodplain Hydro-Biogeochemistry Science Focus Area: Genome-Based Analysis of Microbial Genetic Potential to Drive Shifts in Subsurface Geochemistry in Floodplain Sediments


Anna Rasmussen1* (, Bradley B. Tolar1,3, Cherie DeVore1, Sam Pierce2, John R. Bargar4, Kristin Boye2, Christopher A. Francis1 (


1Stanford University, Stanford, CA; 2SLAC National Accelerator Laboratory, Menlo Park, CA; 3University of North CarolinaWilmington, Wilmington, NC; 4Pacific Northwest National Laboratory, Richland, WA



The Slate River (SR) floodplain experiences seasonal rise and fall in the water table related to snowmelt-induced flooding, precipitation, and evapotranspiration. These fluctuations in the water table determine the inputs of nutrients and other substances to the subsurface and oxygen penetration depth, thus strongly influencing microbial communities and biogeochemical cycling. This work has used amplicon sequencing to investigate microbial community composition across multiple depths and time points from 2018 to 2021 at two SR floodplain sampling locations (OBJ1 and OBJ2). These spatiotemporal analyses have revealed diverse populations of bacteria and archaea—including methanogens, methanotrophs, sulfur-oxidizing and sulfur-reducing taxa, ammonia-oxidizing archaea (AOA), and iron-cycling bacteria—with striking distributions across oxic-anoxic boundaries. Further examination of the genetic potential at different depths and oxygen conditions was conducted on metagenome-assembled genomes (MAGs) from June 2018 samples from both sampling locations at depths ranging from 50–150 cm below ground surface.

The research team recovered 1233 MAGs (>50% complete) spanning 38 bacterial and archaeal phyla. Of note, many genomes were recovered for putative methane-cycling organisms. While methanogens (Methanomassiliicocales, Methanoregulaceae, Methanotrichaceae) are limited to deeper anoxic depths, diverse and abundant genomes were recovered from putative methanotrophs across the entire depth profile, including Methanoperedens, Methylomirabilis, and Bin18 and Binataceae (Binatota). Methanoperedens can have significant metabolic flexibility, coupling anaerobic methane oxidation to myriad electron acceptors (e.g., nitrate, iron, manganese, and potentially selenate, arsenate, and elemental sulfur) and can display a pleomorphic lifestyle that could allow this group to thrive in a dynamic floodplain. Other putative methanotrophs, Methylomirabilis and Binatota, occur in shallower, unsaturated depths. Methylomirabilis are also known for their ability to oxidize methane using nitrite (n-DAMO) and co-occur with nitrifiers in samples. In oxic depths, genomes were recovered for distinct guilds of nitrifiers, including AOA and putative comammox bacteria within Nitrospiraceae. Careful investigation of the recovered genomes will further elucidate connections between methane and other biogeochemical cycles. Thus far, >3700 MAGs have also been generated from samples collected in 2019 and 2020, allowing for comparison of metabolic potential before and after construction of a beaver dam near OBJ2.