[1] The fate of biologically available nitrogen (N) and carbon (C) in stream ecosystems is controlled by the coupling of physical transport and biogeochemical reaction kinetics. However, determining the relative role of physical and biogeochemical controls at different temporal and spatial scales is difficult. The hyporheic zone (HZ), where groundwaterstream water mix, can be an important location controlling N and C transformations because it creates strong gradients in both the physical and biogeochemical conditions that control redox biogeochemistry. We evaluated the coupling of physical transport and biogeochemical redox reactions by linking an advection, dispersion, and residence time model with a multiple Monod kinetics model simulating the concentrations of oxygen (O 2 ), ammonium (NH 4 ), nitrate (NO 3 ), and dissolved organic carbon (DOC). We used global Monte Carlo sensitivity analyses with a nondimensional form of the model to examine coupled nitrification-denitrification dynamics across many scales of transport and reaction conditions. Results demonstrated that the residence time of water in the HZ and the uptake rate of O 2 from either respiration and/or nitrification determined whether the HZ was a source or a sink of NO 3 to the stream. We further show that whether the HZ is a net NO 3 source or net NO 3 sink is determined by the ratio of the characteristic transport time to the characteristic reaction time of O 2 (i.e., the Damköhler number, Da O2 ), where HZs with Da O2 < 1 will be net nitrification environments and HZs with Da O2 ) 1 will be net denitrification environments.Ã Our coupling of the hydrologic and biogeochemical limitations of N transformations across different temporal and spatial scales within the HZ allows us to explain the widely contrasting results of previous investigations of HZ N dynamics which variously identify the HZ as either a net source or sink of NO 3 . Our model results suggest that only estimates of residence times and O 2 uptake rates are necessary to predict this nitrification-denitrification threshold and, ultimately, whether a HZ will be either a net source or sink of NO 3 .Citation: Zarnetske, J. P., R. Haggerty, S. M. Wondzell, V. A. Bokil, and R. González-Pinzón (2012), Coupled transport and reaction kinetics control the nitrate source-sink function of hyporheic zones, Water Resour. Res., 48, W11508,

The use of smart tracers to study hydrologic systems is becoming more widespread. Smart tracers are compounds that irreversibly react in the presence of a process or condition under investigation. Resazurin (Raz) is a smart tracer that undergoes an irreversible reduction to resorufin (Rru) in the presence of cellular metabolic activity. We quantified the relationship between the transformation of Raz and aerobic bacterial respiration in pure culture experiments using two obligate aerobes and two facultative anaerobes, and in colonized surface and shallow (<10 cm) hyporheic sediments using reach‐scale experiments. We found that the transformation of Raz to Rru was nearly perfectly (minr2 = 0.986), positively correlated with aerobic microbial respiration in all experiments. These results suggest that Raz can be used as a surrogate to measure respiration in situ and in vivoat different spatial scales, thus providing an alternative to investigate mechanistic controls of solute transport and stream metabolism on nutrient processing. Lastly, a comparison of respiration and mass‐transfer rates in streams suggests that field‐scale respiration is controlled by the slower of respiration and mass transfer, highlighting the need to understand both biogeochemistry and physics in stream ecosystems.

Shallow benthic biolayers at the top of the streambed are believed to be places of enhanced biogeochemical turnover within the hyporheic zone. They can be investigated by reactive stream tracer tests with tracer recordings in the streambed and in the stream channel. Common in‐stream measurements of such reactive tracers cannot localize where the processing primarily takes place, whereas isolated vertical depth profiles of solutes within the hyporheic zone are usually not representative of the entire stream. We present results of a tracer test where we injected the conservative tracer bromide together with the reactive tracer resazurin into a third‐order stream and combined the recording of in‐stream breakthrough curves with multidepth sampling of the hyporheic zone at several locations. The transformation of resazurin was used as an indicator of metabolism, and high‐reactivity zones were identified from depth profiles. The results from our subsurface analysis indicate that the potential for tracer transformation (i.e., the reaction rate constant) varied with depth in the hyporheic zone. This highlights the importance of the benthic biolayer, which we found to be on average 2 cm thick in this study, ranging from one third to one half of the full depth of the hyporheic zone. The reach‐scale approach integrated the effects of processes along the reach length, isolating hyporheic processes relevant for whole‐stream chemistry and estimating effective reaction rates.

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Groundwater-surface-water (GW-SW) interactions in streams are difficult to quantify because of heterogeneity in hydraulic and reactive processes across a range of spatial and temporal scales. The challenge of quantifying these interactions has led to the development of several techniques, from centimeter-scale probes to whole-system tracers, including chemical, thermal, and electrical methods. We co-applied conservative and smart reactive solute-tracer tests, measurement of hydraulic heads, distributed temperature sensing, vertical profiles of solute tracer and temperature in the stream bed, and electrical resistivity imaging in a 450-m reach of a 3 rd -order stream. GW-SW interactions were not spatially expansive, but were high in flux through a shallow hyporheic zone surrounding the reach. NaCl and resazurin tracers suggested different surface-subsurface exchange patterns in the upper ⅔ and lower ⅓ of the reach. Subsurface sampling of tracers and vertical thermal profiles quantified relatively high fluxes through a 10-to 20-cm deep hyporheic zone with chemical reactivity of the resazurin tracer indicated at 3-, 6-, and 9-cm sampling depths. Monitoring of hydraulic gradients along transects with MINI-POINT streambed samplers starting ∼40 m from the stream indicated that groundwater discharge prevented development of a larger hyporheic zone, which progressively decreased from the stream thalweg toward the banks. Distributed temperature sensing did not detect extensive inflow of ground water to the stream, and electrical resistivity imaging showed limited large-scale hyporheic exchange. We recommend choosing technique(s) based on: 1) clear definition of the questions to be addressed (physical, biological, or chemical processes), 2) explicit identification of the spatial and temporal scales to be covered and those required to provide an appropriate context for interpretation, and 3) maximizing generation of mechanistic understanding and reducing costs of implementing multiple techniques through collaborative research.

The resazurin‐resorufin tracer system has been used to quantify surface water‐sediment interactions and microbial metabolic activity in stream ecosystems for one decade. This review describes the evolution of the tracer technique and summarizes how it has been used by the hydrologic and stream ecology communities. We highlight major hydrologic applications and milestones in the advancement of the reactive tracer system on scales ranging from cells to river reaches and catchments. We discuss the advantages and limitations of the resazurin‐resorufin system for hydrologic applications and suggest new directions of research, including how to address existing knowledge gaps. Beyond the goal of summarizing information that is specific to the development of the resazurin‐resorufin system, this review seeks to inform on the development of new “smart” tracer techniques as they, very likely, will face the same or similar challenges and opportunities encountered in the development of the resazurin‐resorufin system. The supporting information furthermore contains a detailed manual for the application of the resazurin‐resorufin system as hydrologic tracer and MATLAB codes for the analysis of their reactive transport.

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Fine particles (1–100 µm), including particulate organic carbon (POC) and fine sediment, influence stream ecological functioning because they may contain or have a high affinity to sorb nitrogen and phosphorus. These particles are immobilized within stream storage areas, especially hyporheic sediments and benthic biofilms. However, fine particles are also known to remobilize under all flow conditions. This combination of downstream transport and transient retention, influenced by stream geomorphology, controls the distribution of residence times over which fine particles influence stream ecosystems. The main objective of this study was to quantify immobilization and remobilization rates of fine particles in a third‐order sand‐and‐gravel bed stream (Difficult Run, Virginia, USA) within different geomorphic units of the stream (i.e., pool, lateral cavity, and thalweg). During our field injection experiment, a thunderstorm‐driven spate allowed us to observe fine particle dynamics during both base flow and in response to increased flow. Solute and fine particles were measured within stream surface waters, pore waters, sediment cores, and biofilms on cobbles. Measurements were taken at four different subsurface locations with varying geomorphology and at multiple depths. Approximately 68% of injected fine particles were retained during base flow until the onset of the spate. Retention was evident even after the spate, with 15.4% of the fine particles deposited during base flow still retained within benthic biofilms on cobbles and 14.9% within hyporheic sediment after the spate. Thus, through the combination of short‐term remobilization and long‐term retention, fine particles can serve as sources of carbon and nutrients to downstream ecosystems over a range of time scales.