The hyporheic zone, where surface water and groundwater mix, is an important microbial habitat where biogeochemical reactions influence water quality. We show that spatial variability in hyporheic flow in the East River near Crested Butte, CO, drives heterogeneity in streambed geochemical conditions and microbial community assemblages, but the diversity of microbial assemblages remains nearly constant throughout the reach. In July 2018, we collected approximately 100 pore water samples at 20-cm depth and analyzed them for anions, cations, dissolved organic carbon, dissolved organic matter (DOM) quality, and basic water quality parameters. Vertical hydraulic head gradients were also measured to assess the potential for upward or downward flow, and heat tracing was used to quantify vertical flux rates at a subset of locations. We found that regions of the streambed that are more groundwater-dominated contain less dissolved oxygen, higher concentrations of reduced metals, and more microbially processed, recalcitrant DOM, while more surface water-dominated locations contain higher dissolved oxygen concentrations and terrestrially derived, labile DOM. 16S rRNA gene sequencing of extracted DNA revealed that microbial community composition varies with geochemical gradients related to hyporheic flow. These findings provide a better understanding of hyporheic controls on streambed biogeochemistry during the baseflow season, which is expected to lengthen with climate change in alpine watersheds due to earlier snowmelt onset and reduced snowpack.Plain Language Summary Groundwater and surface water mixing in streambeds (hyporheic exchange) is important for nutrient and carbon cycling and influences the overall quality of surface water. In this study, we aimed to map relationships between hyporheic exchange, pore water chemistry, and microbial communities in the streambed of an alpine river during low flow conditions. We found that regions of the streambed with greater surface water influence had larger concentrations of dissolved oxygen and microbially available carbon compounds. The composition of streambed microbial communities also shifted with changes in pore water chemistry, though communities were all similarly diverse. As climate change progresses, earlier snowmelt onset and reduced snowpack should alter flow and biogeochemical processes in streambeds. This study provides a baseline for exploring future changes in alpine streambeds.

Terrestrial and aquatic elemental cycles are tightly linked in upland fluvial networks. Biotic and abiotic mineral weathering, microbially mediated degradation of organic matter, and anthropogenic influences all result in the movement of solutes (e.g., carbon, metals, and nutrients) through these catchments, with implications for downstream water quality. Within the river channel, the region of hyporheic mixing represents a hot spot of microbial activity, exerting significant control over solute cycling. To investigate how snowmelt-driven seasonal changes in river discharge affect microbial community assembly and carbon biogeochemistry, depth-resolved pore water samples were recovered from multiple locations around a representative meander on the East River near Crested Butte, CO, USA. Vertical temperature sensor arrays were also installed in the streambed to enable seepage flux estimates. Snowmelt-driven high river discharge led to an expanding zone of vertical hyporheic mixing and introduced dissolved oxygen into the streambed that stimulated aerobic microbial respiration. These physicochemical processes contributed to microbial communities undergoing homogenizing selection, in contrast to other ecosystems where lower permeability may limit the extent of mixing. Conversely, lower river discharge conditions led to a greater influence of upwelling groundwater within the streambed and a decrease in microbial respiration rates. Associated with these processes, microbial communities throughout the streambed exhibited increasing dissimilarity between each other, suggesting that the earlier onset of snowmelt and longer periods of base flow may lead to changes in the composition (and associated function) of streambed microbiomes, with consequent implications for the processing and export of solutes from upland catchments. Plain Language SummarySeasonal changes in river discharge in high-altitude watersheds affect patterns of surface and groundwater mixing in the hyporheic zone (the region in the riverbed where these two water sources interact) that impacts how carbon compounds and dissolved metals are transported.One key constraint with respect to hyporheic mixing concerns the rate of water flow, a process driving the change in oxygen concentration in the riverbed. Oxygen concentration controls rates of carbon degradation and metal inputs from surrounding rocks, which, in turn, affect downstream water quality. In this study, we examined a stream in an alpine watershed, the East River, in the Upper Colorado River Basin, sampling a representative meander at discrete depths throughout the year for microbiological and geochemical analyses. We also installed data loggers to continuously collect temperature information to understand the extent of hyporheic mixing. We found that the movement of dissolved materials was strongly correlated with seasonal changes in flow. Under maximum flow, increased oxygen concentration stimulates microbial degradation of carbon compounds, and conversely, during minimum flow, decreased oxygen c...

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