Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes

Subsurface groundwater-surface water mixing zones (hyporheic zones) have enhanced biogeochemical activity, but assembly processes governing subsurface microbiomes remain a critical uncertainty in understanding hyporheic biogeochemistry. To address this obstacle, we investigated (a) biogeographical patterns in attached and waterborne microbiomes across three hydrologically-connected, physicochemically-distinct zones (inland hyporheic, nearshore hyporheic, and river); (b) assembly processes that generated these patterns; (c) groups of organisms that corresponded to deterministic changes in the environment; and (d) correlations between these groups and hyporheic metabolism. All microbiomes remained dissimilar through time, but consistent presence of similar taxa suggested dispersal and/or common selective pressures among zones. Further, we demonstrated a pronounced impact of deterministic assembly in all microbiomes as well as seasonal shifts from heterotrophic to autotrophic microorganisms associated with increases in groundwater discharge. The abundance of one statistical cluster of organisms increased with active biomass and respiration, revealing organisms that may strongly influence hyporheic biogeochemistry. Based on our results, we propose a conceptualization of hyporheic zone metabolism in which increased organic carbon concentrations during surface water intrusion support heterotrophy, which succumbs to autotrophy under groundwater discharge. These results provide new opportunities to enhance microbially-explicit ecosystem models describing hyporheic zone biogeochemistry and its influence over riverine ecosystem function. Originality-Significance Statement Subsurface zones of groundwater and surface water mixing (hyporheic zones) are hotspots of biogeochemical activity and strongly influence carbon, nutrient and contaminant dynamics within riverine ecosystems. Hyporheic zone microbiomes are responsible for up to 95% of riverine ecosystem respiration, yet the ecology of these microbiomes remains poorly understood. While significant progress is being made in the development of microbially-explicit ecosystem models, poor understanding of hyporheic zone microbial ecology impedes development of such models in this critical zone. To fill the knowledge gap, we present a comprehensive analysis of biogeographical patterns in hyporheic microbiomes as well as the ecological processes that govern their composition and function through space and time. Despite pronounced hydrologic connectivity throughout the hyporheic zone—and thus a strong potential for dispersal—we find that ecological selection deterministically governs microbiome composition within local environments, and we identify specific groups of organisms that correspond to seasonal changes in hydrology. Based on our results, we propose a conceptual model for hyporheic zone metabolism in which comparatively high-organic C conditions during surface water intrusion into the hyporheic zone support heterotrophic metabolisms that succumb to autotrophy during time periods of groundwater discharge. These results provide new opportunities to develop microbially-explicit ecosystem models that incorporate the hyporheic zone and its influence over riverine ecosystem function.