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Biodiversity is thought to prevent decline in community function in response to changing environmental conditions through replacement of organisms with similar functional capacity but different optimal growth characteristics. We examined how this concept translates to the within-gene level by exploring seasonal dynamics of within-gene diversity for genes involved in nitrogen cycling in hyporheic zone communities. Nitrification genes displayed low richness-defined as the number of unique within-gene phylotypes-across seasons. Conversely, denitrification genes varied in both richness and the degree to which phylotypes were recruited or lost. These results demonstrate that there is not a universal mechanism for maintaining community functional potential for nitrogen cycling activities, even across seasonal environmental shifts to which communities would be expected to be well adapted. As such, extreme environmental changes could have very different effects on the stability of the different nitrogen cycle activities. These outcomes suggest a need to modify existing conceptual models that link biodiversity to microbiome function to incorporate within-gene diversity. Specifically, we suggest an expanded conceptualization that 1) recognizes component steps (genes) with low diversity as potential bottlenecks influencing pathway-level function, and 2) includes variation in both the number of entities (e.g. species, phylotypes) that can contribute to a given process and the turnover of those entities in response to shifting conditions. Building these concepts into process-based ecosystem models represents an exciting opportunity to connect within-gene-scale ecological dynamics to ecosystem-scale services., Competing Interests: The authors have declared that no competing interests exist.

The original version of this Article contained an error in Fig. 6e, in which the text in the legend was omitted. This has been corrected in both the PDF and HTML versions of the article.

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.

The United States is home to 2198 dams actively used for hydropower production. With the December 2015 consensus adoption of the United Nations Framework Convention on Climate Change Paris Agreement, it is important to accurately quantify anthropogenic greenhouse gas emissions. Methane ebullition, or methane bubbles originating from river or lake sediments, has been shown to account for nearly all methane emissions from tropical hydropower reservoirs to the atmosphere. However, distinct ebullitive methane fluxes have been studied in comparatively few temperate hydropower reservoirs globally. This study measures ebullitive and diffusive methane fluxes from two eastern Washington reservoirs, and synthesizes existing studies of methane ebullition in temperate, boreal, and tropical hydropower reservoirs. Ebullition comprises nearly all methane emissions (>97%) from this study's two eastern Washington hydropower reservoirs to the atmosphere. Summer methane ebullition from these reservoirs was higher than ebullition in six southeastern U.S. hydropower reservoirs, however it was similar to temperate reservoirs in other parts of the world. Our literature synthesis suggests that methane ebullition from temperate hydropower reservoirs can be seasonally elevated compared to tropical climates, however annual emissions are likely to be higher within tropical climates, emphasizing the possible range of methane ebullition fluxes and the need for the further study of temperate reservoirs. Possible future changes to the Intergovernmental Panel on Climate Change and UNFCCC guidelines for national greenhouse gas inventories highlights the need for accurate assessment of reservoir emissions.

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.

Slug tests performed using mini-piezometers with internal diameters as small as 0.43 cm can provide a cost effective tool for hydraulic characterization. We evaluated the hydraulic properties of the apparatus in a laboratory environment and compared those results with field tests of mini-piezometers installed into locations with varying hydraulic properties. Based on our evaluation, slug tests conducted in mini-piezometers using the fabrication and installation approach described here are effective within formations where the hydraulic conductivity is less than 1 × 10(-3) cm/s. While these constraints limit the potential application of this method, the benefits to this approach are that the installation, measurement, and analysis is cost effective, and the installation can be completed in areas where other (larger diameter) methods might not be possible. Additionally, this methodology could be applied to existing mini-piezometers previously installed for other purposes. Such analysis of existing installations could be beneficial in interpreting previously collected data (e.g., water-quality data or hydraulic head data)., (© 2015, National Ground Water Association.)

Measurement of ground water/surface water interaction within the hyporheic zone is increasingly recognized as an important aspect of subsurface contaminant fate and transport. Understanding the interaction between ground water and surface water is critical in developing a complete conceptual model of contaminant transport through the hyporheic zone. At the Hanford Site near Richland, Washington, ground water contaminated with uranium discharges to the Columbia River through the hyporheic zone. Ground water flux varies according to changes in hydraulic gradient caused by fluctuating river stage, which changes in response to operation of dams on the Columbia River. Piezometers and continuous water quality monitoring probes were installed in the hyporheic zone to provide long-term, high-frequency measurement of hydraulic gradient and estimated uranium concentrations. Subsequently, the flux of water and uranium was calculated for each half-hour time period over a 15-month study period. In addition, measurement of water levels in the near-shore unconfined aquifer enhanced the understanding of the relationship between river stage, aquifer elevation, and uranium flux. Changing river stage resulted in fluctuating hydraulic gradient within the hyporheic zone. Further, influx of river water caused lower uranium concentrations as a result of dilution. The methods employed in this study provide a better understanding of the interaction between surface and ground water in a situation with a dynamically varying vertical hydraulic gradient and illustrate how the combination of relatively standard methods can be used to derive an accurate estimation of water and contaminant flux through the hyporheic zone.

Biogeochemical processes within riverbed hyporheic zones (HZ) can potentially impact the fate and transport of contaminants. We evaluated a modified freeze core technique for the collection of intact cobble-bed samples from the Columbia River HZ along a stretch of the Hanford Reach in Washington State and investigated microbiological and geochemical parameters of corresponding frozen and unfrozen samples. During three sampling periods (March, May, and November 2000), relatively high numbers of viable aerobic heterotrophic bacteria were recovered from both unfrozen (10(6)-10(7) cfu/g) and frozen samples (10(5)-10(6) cfu/g). Relatively large populations of sulfate-, nitrate-, and iron-reducing bacteria were present, and significant concentrations of acid-volatile sulfide were measured in some samples, indicating that anoxic regions exist within this zone. Cr(VI), a priority groundwater pollutant on adjacent U.S. Department of Energy lands, was probably removed from solution in HZ samples by a combination of microbial activity and chemical reduction, presumably via products of anaerobic microbial metabolism. These results suggest that biogeochemical processes in the Columbia River HZ may contribute to the natural attenuation of Cr(VI). Although freezing modestly diminished recovery of viable bacteria, freeze core techniques proved reliable for the collection of intact hyporheic sediments.