Genome-Resolved Metagenomic Analysis of Nitrogen-Cycling Microbial Communities in Hydrologically Variable Floodplain Sediments from Riverton, Wyoming


Christopher A. Francis1* (, Katie Langenfeld1, Anna Rasmussen1, Bradley B. Tolar1,5, Linta Reji1,6, Emily Cardarelli1,7, Zach Perzan1, Kristin Boye2, John R. Bargar3, Nicholas Bouskill4


1Stanford University, Stanford, CA; 2SLAC National Accelerator Laboratory, Menlo Park, CA; 3Pacific Northwest National Laboratory, Richland, WA; 4Lawrence Berkeley National Laboratory, Berkeley, CA; 5University of North Carolina–Wilmington, NC; 6Princeton University, Princeton, NJ; 7NASA Jet Propulsion Laboratory, Pasadena, CA


Despite the tremendous biogeochemical importance of nitrification, denitrification, and dissimilatory nitrate reduction to ammonia (DNRA) in floodplain soils and sediments, remarkably little is known regarding the microbial communities responsible for mediating these processes. To address this knowledge gap, researchers have employed genome-resolved metagenomics to examine the phylogenetic diversity and metabolic potential of subsurface nitrogen (N)-cycling microbial communities within sediment cores collected from hydrologically variable floodplain sediments in the Wind River Basin near Riverton, WY. The metagenomic analysis encompasses over 70 samples collected across multiple sites, depths, and time points within the Riverton floodplain, allowing for both spatial and temporal investigations at different scales. For example, researchers have carried out a highly depth-resolved analysis of 13 depths along a 234 cm profile collected from Riverton site KB1 in 2015. At nearby site Pit2, the team collected 40 samples over both time (April to September 2017) and depth (seven distinct subsurface layers within ~170 cm cores) across a full seasonal hydrologic cycle of water table rise, flooding, and summer drought. Finally, in 2019 the team collected depth profiles (down to 180 cm) from site PTT1 in June (several days post inundation), August (peak evapotranspiration), and October (plant senescence). Along with extensive geochemical and 16S rRNA amplicon sequencing data for the wide array of 70+ samples mentioned above, researchers have generated 1000s of metagenome-assembled genomes (MAGs; 50 to 100% complete), many of which correspond to N-cycling taxa. The most in-depth work has focused on MAGs corresponding to ammonia-oxidizing archaea (AOA), which are incredibly diverse (including numerous Nitrososphaeria and Nitrosopumilales lineages) and whose community composition shifts dramatically with depth and relative to the water table. Researchers have also examined the phylogenomic diversity of nitrite-oxidizing bacteria (NOB)—capable of oxidizing the nitrite produced by AOA to nitrate in these sediments—which include diverse members of the Nitrospinaceae and Nitrospiraceae. Currently, researchers are exploring the distribution and extensive diversity of MAGs containing genes encoding one or more enzymatic steps of the denitrification or DNRA pathways (e.g., nar/nap, nir, nor, nos, nrf, etc.), allowing researchers to assess the potential for metabolic handoffs within both the aerobic and anaerobic N-cycling microbial communities at Riverton. Overall, this project is yielding critical genomic and ecophysiological insights into the microbial communities responsible for N-cycling in a terrestrial subsurface ecosystem directly influenced by hydrological fluctuations.