Watersheds are important for supplying fresh water, the quality of which depends on complex interplay involving physical, chemical and biological processes. As water percolates through the soil and underlying weathering rock en route to the river corridor, microorganisms mediate key geochemical transformations, yet the distribution and functional capacities of subsurface microbial communities remain little understood. Here, we used genome resolved metagenomics to study microbial communities during late summer along a 230 m hillslope meadow to floodplain transect within the mountainous East-River watershed, Colorado. We found very limited strain/species overlap at different depths below the ground surface and at different distances along the hillslope, possibly due to restricted hydraulic connectivity after early stages of snowmelt, and show that communities are largely distinct in their metabolic capacities. Both proximity to the river and to the underlying Mancos shale apparently control species distribution and metabolic potential. Functions such as carbon fixation and selenate reduction were prevalent at multiple sites, although the lineages of organisms responsible tend to be location-specific. For example, selenate reduction within the hillslope is linked to Candidate phyla Rokubacteria and Methylomirabillis, but only Deltaproteobacteria are predicted to have this capacity at the floodplain. Based on the abundance of genomically-encoded functions that utilize it as an electron donor or acceptor, sulfur is significantly more important for microbial metabolism at the floodplain compared to on the hillslope. Nitrification and methylamine oxidation are likely only occurring within the floodplain, with nitrification capacity in shallow soil and methylamine oxidation in deeper unsaturated sediment. The capacity for nitrogen fixation was mostly associated with Geobacteraceae and Myxococcales (phylum Deltaproteobacteria) at the floodplain. Thus, we conclude that metabolic potential and microbial community composition vary as a function of depth and distance along a mountainous watershed hillslope to floodplain transect, and that the microbiome of the floodplain compartment plays a significant role in nitrogen fixation and sulfur cycling at this site.

Taxonomically and metabolically distinct microbial communities with depth and across a hillslope to riparian zone transect