Environmental transitions often result in resource mixtures that overcome limitations to microbial metabolism, resulting in biogeochemical hotspots and moments. Riverine systems, where groundwater mixes with surface water (the hyporheic zone), are spatially complex and temporally dynamic, making development of predictive models challenging. Spatial and temporal variations in hyporheic zone microbial communities are a key, but understudied, component of riverine biogeochemical function. Here, to investigate the coupling among groundwater–surface water mixing, microbial communities and biogeochemistry, we apply ecological theory, aqueous biogeochemistry, DNA sequencing and ultra-high-resolution organic carbon profiling to field samples collected across times and locations representing a broad range of mixing conditions. Our results indicate that groundwater–surface water mixing in the hyporheic zone stimulates heterotrophic respiration, alters organic carbon composition, causes ecological processes to shift from stochastic to deterministic and is associated with elevated abundances of microbial taxa that may degrade a broad suite of organic compounds.

Physicochemical relationships in the boundary zone between groundwater and surface water (i.e. the hyporheic zone) are controlled by surface water hydrology and the hydrogeologic properties of the riverbed. We studied how sediment permeability and river discharge altered the vertical hydraulic gradient (VHG) and water quality of the hyporheic zone within the Hanford Reach of the Columbia River. The Columbia River at Hanford is a large, cobble-bed river where water level fluctuates up to 2 m daily because of hydropower generation. Concomitant with river stage recordings, continuous readings were made of water temperature, specific conductance, dissolved oxygen and water level of the hyporheic zone. The water level data were used to calculate VHG between the river and hyporheic zone. Sediment permeability was estimated using slug tests conducted in piezometers installed into the river bed. The response of water quality measurements and VHG to surface water fluctuations varied widely among study sites, ranging from no apparent response to covariance with river discharge. At some sites, a hysteretic relationship between river discharge and VHG was indicated by a time lag in the response of VHG to changes in river stage. The magnitude, rate of change and hysteresis of the VHG response varied the most at the least permeable location (hydraulic conductivity (K) ¼ 2.9 Â 10 À4 cms À1 ) and the least at the most permeable location (K ¼ 8.8 Â 10 À3 cms À1 ). Our study provides empirical evidence that sediment properties and river discharge both control the water quality of the hyporheic zone. Regulated rivers, like the Columbia River at Hanford, that undergo large, frequent discharge fluctuations represent an ideal environment in which to study hydrogeologic processes over relatively short time periods (i.e. days to weeks) that would require much longer periods (i.e. months to years) to evaluate in unregulated systems.

The hyporheic corridor (HC) encompasses the river–groundwater continuum, where the mixing of groundwater (GW) with river water (RW) in the HC can stimulate biogeochemical activity. Here we propose a novel thermodynamic mechanism underlying this phenomenon and reveal broader impacts on dissolved organic carbon (DOC) and microbial ecology. We show that thermodynamically favorable DOC accumulates in GW despite lower DOC concentration, and that RW contains thermodynamically less-favorable DOC, but at higher concentrations. This indicates that GW DOC is protected from microbial oxidation by low total energy within the DOC pool, whereas RW DOC is protected by lower thermodynamic favorability of carbon species. We propose that GW–RW mixing overcomes these protections and stimulates respiration. Mixing models coupled with geophysical and molecular analyses further reveal tipping points in spatiotemporal dynamics of DOC and indicate important hydrology–biochemistry–microbial feedbacks. Previously unrecognized thermodynamic mechanisms regulated by GW–RW mixing may therefore strongly influence biogeochemical and microbial dynamics in riverine ecosystems.

Understanding how microorganisms alter their physical and chemical environment