Hyporheic zone denitrification: Controls on effective reaction depth and contribution to whole-stream mass balance
TL;DR: The whole‐stream reaction significance, Rs (dimensionless), was quantified by multiplying Daden‐hz by the proportion of stream discharge passing through the hyporheic zone, and together these two dimensionless metrics, one flow‐path scale and the other reach‐scale, quantify the whole‐ Stream denitrification significance.
Abstract: [1] Stream denitrification is thought to be enhanced by hyporheic transport but there is little direct evidence from the field. To investigate at a field site, we injected 15NO3−, Br (conservative tracer), and SF6 (gas exchange tracer) and compared measured whole-stream denitrification with in situ hyporheic denitrification in shallow and deeper flow paths of contrasting geomorphic units. Hyporheic denitrification accounted for between 1 and 200% of whole-stream denitrification. The reaction rate constant was positively related to hyporheic exchange rate (greater substrate delivery), concentrations of substrates DOC and nitrate, microbial denitrifier abundance (nirS), and measures of granular surface area and presence of anoxic microzones. The dimensionless product of the reaction rate constant and hyporheic residence time, λhzτhz define a Damkohler number, Daden-hz that was optimal in the subset of hyporheic flow paths where Daden-hz ≈ 1. Optimal conditions exclude inefficient deep pathways where substrates are used up and also exclude inefficient shallow pathways that require repeated hyporheic entries and exits to complete the reaction. The whole-stream reaction significance, Rs (dimensionless), was quantified by multiplying Daden-hz by the proportion of stream discharge passing through the hyporheic zone. Together these two dimensionless metrics, one flow-path scale and the other reach-scale, quantify the whole-stream significance of hyporheic denitrification. One consequence is that the effective zone of significant denitrification often differs from the full depth of the hyporheic zone, which is one reason why whole-stream denitrification rates have not previously been explained based on total hyporheic-zone metrics such as hyporheic-zone size or residence time.
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TL;DR: In this paper, a review summarizes results from modeling studies and field observations about flow and transport processes in the hyporheic zone and describes the theories proposed in hydrology and fluid dynamics developed to quantitatively model and predict the hypheic transport of water, heat, and dissolved and suspended compounds from sediment grain scale up to watershed scale.
Abstract: Fifty years of hyporheic zone research have shown the important role played by the hyporheic zone as an interface between groundwater and surface waters. However, it is only in the last two decades that what began as an empirical science has become a mechanistic science devoted to modeling studies of the complex fluid dynamical and biogeochemical mechanisms occurring in the hyporheic zone. These efforts have led to the picture of surface-subsurface water interactions as regulators of the form and function of fluvial ecosystems. Rather than being isolated systems, surface water bodies continuously interact with the subsurface. Exploration of hyporheic zone processes has led to a new appreciation of their wide reaching consequences for water quality and stream ecology. Modern research aims toward a unified approach, in which processes occurring in the hyporheic zone are key elements for the appreciation, management, and restoration of the whole river environment. In this unifying context, this review summarizes results from modeling studies and field observations about flow and transport processes in the hyporheic zone and describes the theories proposed in hydrology and fluid dynamics developed to quantitatively model and predict the hyporheic transport of water, heat, and dissolved and suspended compounds from sediment grain scale up to the watershed scale. The implications of these processes for stream biogeochemistry and ecology are also discussed.
644 citations
TL;DR: In this article, the authors propose river corridor science as a concept that integrates downstream transport with lateral and vertical exchange across interfaces, and include the main channel exchange with recirculating marginal waters, hyporheic exchange, bank storage, and overbank flow onto floodplains under a broad continuum of interactions known as hydrologic exchange flows.
Abstract: Previously regarded as the passive drains of watersheds, over the past 50 years, rivers have progressively been recognized as being actively connected with off-channel environments. These connections prolong physical storage and enhance reactive processing to alter water chemistry and downstream transport of materials and energy. Here we propose river corridor science as a concept that integrates downstream transport with lateral and vertical exchange across interfaces. Thus, the river corridor, rather than the wetted river channel itself, is an increasingly common unit of study. Main channel exchange with recirculating marginal waters, hyporheic exchange, bank storage, and overbank flow onto floodplains are all included under a broad continuum of interactions known as “hydrologic exchange flows.” Hydrologists, geomorphologists, geochemists, and aquatic and terrestrial ecologists are cooperating in studies that reveal the dynamic interactions among hydrologic exchange flows and consequences for water quality improvement, modulation of river metabolism, habitat provision for vegetation, fish, and wildlife, and other valued ecosystem services. The need for better integration of science and management is keenly felt, from testing effectiveness of stream restoration and riparian buffers all the way to reevaluating the definition of the waters of the United States to clarify the regulatory authority under the Clean Water Act. A major challenge for scientists is linking the small-scale physical drivers with their larger-scale fluvial and geomorphic context and ecological consequences. Although the fine scales of field and laboratory studies are best suited to identifying the fundamental physical and biological processes, that understanding must be successfully linked to cumulative effects at watershed to regional and continental scales.
272 citations
Cites background from "Hyporheic zone denitrification: Con..."
...…hydrologic storage are more broadly distributed than exponential, exhibiting lognormal or power law distributions [W€orman et al., 2002; Haggerty et al., 2002], which has been confirmed by measuring residence time distributions directly in storage zones [Gooseff et al., 2008; Harvey et al., 2013]....
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...…reactions have been detected in streambed algal mats [Gooseff et al., 2004], shallow streambed hyporheic zones [Argerich et al., 2011; Harvey et al., 2013; Briggs et al., 2013a], gravel bars [Pinay et al., 2009; Zarnetske et al., 2011], bank storage exchange zones in river banks…...
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...In fact, these exchanges can explain the downstream influence of chemical reactions on the quality of receiving waters [Findlay, 1995; Marzadri et al., 2014; Harvey et al., 2013]....
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...Nitrogen removal, for example, has been compared within surface water exchange zones in side cavities and hyporheic zones [O’Connor et al., 2010], thalweg and bank margin hyporheic zones [Harvey et al., 2013], and near levee and backwater floodplain environments [Richardson et al., 2004]....
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...…dominant removal of nutrients and contaminants from rivers, enough to explain basin-scale outcomes for downstream water quality, may be isolated within the shallowest part of the hyporheic zone and not through its entire depth [Harvey and Fuller, 1998; Harvey et al., 2013; Briggs et al., 2013a]....
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TL;DR: This article showed that denitrification due to flow through small-scale river bed-forms exceeds that along channel banks in the Mississippi River network, which is the largest river in the US.
Abstract: Microbe-mediated reactions remove nitrogen from river water as it flows through sediments. Simulations of the Mississippi River network suggest that denitrification due to flow through small-scale river bedforms exceeds that along channel banks.
254 citations
TL;DR: In this paper, the coupling among groundwater-surface water mixing, microbial communities and biogeochemistry was investigated using DNA sequencing and ultra-high-resolution organic carbon profiling to investigate the coupling between groundwater and surface water mixing in the hyporheic zone.
Abstract: 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. Groundwater-surface water mixing zones link critical ecosystem domains, but attendant microbe-biogeochemistry-hydrology interactions are poorly known. Here, the authors show that groundwater-surface water mixing stimulates respiration, alters carbon composition, and shifts the ecology from stochastic to deterministic.
249 citations
Pennsylvania State University1, Stanford University2, Colorado School of Mines3, University of Illinois at Urbana–Champaign4, University of Georgia5, United States Geological Survey6, Towson University7, University of Vermont8, University of Kansas9, University of Texas at El Paso10, Yale University11, University of California, Berkeley12, University of British Columbia13, Lawrence Berkeley National Laboratory14, Pacific Northwest National Laboratory15, Massachusetts Institute of Technology16, University of Arizona17, University of Oxford18, Duke University19
TL;DR: A review of multi-component Reactive Transport Models (RTMs) can be found in this article, where the authors present seven testable hypotheses that emphasize the unique capabilities of process-based RTMs for elucidating chemical weathering and its physical and biogeochemical drivers; understanding the interactions among roots, micro-organisms, carbon, water, and minerals in the rhizosphere; assessing the effects of heterogeneity across spatial and temporal scales; and integrating the vast quantity of novel data (genomics, transcriptomics, proteomics, metabolomics), elemental concentration and speciation
207 citations
Cites background from "Hyporheic zone denitrification: Con..."
...Nitrate removal in the shallowest hyporheic zone ( 4 cm) can be substantial enough to account for total nitrate removal of the whole stream (Harvey et al., 2013)....
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...Nitrate removal in the shallowest hyporheic zone (<4 cm) can be substantial enough to account for total nitrate removal of the whole stream (Harvey et al., 2013)....
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References
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Florida International University1, State University of New York System2, University of Wisconsin-Madison3, University of California, Santa Barbara4, Arizona State University5, Northern Arizona University6, United States Geological Survey7, University of Minnesota8, University of Washington9, University of New Hampshire10
TL;DR: In this paper, the authors define biogeochemical hot spots as patches that show disproportionately high reaction rates relative to the surrounding matrix, whereas hot moments occur when episodic hydrological flowpaths reactivate and/or mobilize accumulated reactants.
Abstract: Rates and reactions of biogeochemical processes vary in space and time to produce both hot spots and hot moments of elemental cycling. We define biogeochemical hot spots as patches that show disproportionately high reaction rates relative to the surrounding matrix, whereas hot moments are defined as short periods of time that exhibit disproportionately high reaction rates relative to longer intervening time periods. As has been appreciated by ecologists for decades, hot spot and hot moment activity is often enhanced at terrestrial-aquatic interfaces. Using examples from the carbon (C) and nitrogen (N) cycles, we show that hot spots occur where hydrological flowpaths converge with substrates or other flowpaths containing complementary or missing reactants. Hot moments occur when episodic hydrological flowpaths reactivate and/or mobilize accumulated reactants. By focusing on the delivery of specific missing reactants via hydrologic flowpaths, we can forge a better mechanistic understanding of the factors that create hot spots and hot moments. Such a mechanistic understanding is necessary so that biogeochemical hot spots can be identified at broader spatiotemporal scales and factored into quantitative models. We specifically recommend that resource managers incorporate both natural and artificially created biogeochemical hot spots into their plans for water quality management. Finally, we emphasize the needs for further research to assess the potential importance of hot spot and hot moment phenomena in the cycling of different bioactive elements, improve our ability to predict their occurrence, assess their importance in landscape biogeochemistry, and evaluate their utility as tools for resource management.
2,096 citations
TL;DR: Denitrification occurs in essentially all river, lake, and coastal marine ecosystems that have been studied as discussed by the authors, and the major source of nitrate for denitrification in most river and lake sediments underlying an aerobic water column is nitrate produced in the sediments, not nitrate diffusing into the overlying water.
Abstract: Denitrification occurs in essentially all river, lake, and coastal marine ecosystems that have been studied. In general, the range of denitrification rates measured in coastal marine sediments is greater than that measured in lake or river sediments. In various estuarine and coastal marine sediments, rates commonly range between 50 and 250 µmol N m−2 h−1, with extremes from 0 to 1,067. Rates of denitrification in lake sediments measured at near-ambient conditions range from 2 to 171 µmol N m−2 h−1. Denitrification rates in river and stream sediments range from 0 to 345 µmol N m−2 h−1. The higher rates are from systems that receive substantial amounts of anthropogenic nutrient input. In lakes, denitrification also occurs in low oxygen hypolimnetic waters, where rates generally range from 0.2 to 1.9 µmol N liter−1 d−1. In lakes where denitrification rates in both the water and sediments have been measured, denitrification is greater in the sediments.
The major source of nitrate for denitrification in most river, lake, and coastal marine sediments underlying an aerobic water column is nitrate produced in the sediments, not nitrate diffusing into the sediments from the overlying water. During the mineralization of organic matter in sediments, a major portion of the mineralized nitrogen is lost from the ecosystem via denitrification. In freshwater sediments, denitrification appears to remove a larger percentage of the mineralized nitrogen. N2 fluxes accounted for 76–100% of the sediment-water nitrogen flux in rivers and lakes, but only 15–70% in estuarine and coastal marine sediments. Benthic N2O fluxes were always small compared to N, fluxes.
The loss of nitrogen via denitrification exceeds the input of nitrogen via N2 fixation in almost all river, lake, and coastal marine ecosystems in which both processes have been measured.
Denitrification is also important relative to other inputs of fixed N in both freshwater and coastal marine ecosystems. In the two rivers where both denitrification measurements and N input data were available, denitrification removed an amount of nitrogen equivalent to 7 and 35% of the external nitrogen loading. In six lakes and six estuaries where data are available, denitrification is estimated to remove an amount of nitrogen equivalent to between 1 and 36% of the input to the lakes and between 20 and 50% of the input to the estuaries.
1,571 citations
"Hyporheic zone denitrification: Con..." refers background in this paper
...Thus, even though denitrification has been investigated across the nation and around the world [Seitzinger, 1988; Mulholland et al., 2008; Seitzinger et al., 2006] it remains difficult to predict why one stream may have greater denitrification than another [Ensign and Doyle, 2006]....
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TL;DR: The precision of the method is better than 0.2/1000 (1 SD) at concentrations of nitrate down to 1 microM, and the nitrogen isotopic differences among various standards and samples are accurately reproduced.
Abstract: We report a new method for measurement of the isotopic composition of nitrate (NO3-) at the natural-abundance level in both seawater and freshwater. The method is based on the isotopic analysis of nitrous oxide (N2O) generated from nitrate by denitrifying bacteria that lack N2O-reductase activity. The isotopic composition of both nitrogen and oxygen from nitrate are accessible in this way. In this first of two companion manuscripts, we describe the basic protocol and results for the nitrogen isotopes. The precision of the method is better than 0.2‰ (1 SD) at concentrations of nitrate down to 1 μM, and the nitrogen isotopic differences among various standards and samples are accurately reproduced. For samples with 1 μM nitrate or more, the blank of the method is less than 10% of the signal size, and various approaches may reduce it further.
1,562 citations
"Hyporheic zone denitrification: Con..." refers methods in this paper
...Dissolved N2 was extracted from headspace samples, trapped in a closed loop, and then released in a He carrier stream through a mole sieve capillary gas chromatograph for isotopic analysis of the N2 peak by CFIRMS [Smith et al., 2006]....
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...…on a spectrophotometer at 562 nm. [21] For isotopic analysis, NO3 (þ NO2 ) was converted to N2O by the denitrifier method (using Pseudomonas aureofaciens) and analyzed by continuous-flow isotope-ratio mass spectrometry (CFIRMS) [Sigman et al., 2001; Casciotti et al., 2002; Coplen et al., 2004]....
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...Ferrous iron was measured in the lab by the ferrozine method with absorbance measured on a spectrophotometer at 562 nm. [21] For isotopic analysis, NO3 (þ NO2 ) was converted to N2O by the denitrifier method (using Pseudomonas aureofaciens) and analyzed by continuous-flow isotope-ratio mass spectrometry (CFIRMS) [Sigman et al., 2001; Casciotti et al., 2002; Coplen et al., 2004]....
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TL;DR: It is suggested that terrestrial, freshwater, and marine systems in which denitrification occurs can be organized along a continuum ranging from (1) those in which nitrification and Denitrification are tightly coupled in space and time to (2) thoseIn aquatic ecosystems, N inputs influenceDenitrification rates whereas hydrology and geomorphology influence the proportion of N inputs that are denitrified.
Abstract: Denitrification is a critical process regulating the removal of bioavailable nitrogen (N) from natural and human-altered systems. While it has been extensively studied in terrestrial, freshwater, and marine systems, there has been limited communication among denitrification scientists working in these individual systems. Here, we compare rates of denitrification and controlling factors across a range of ecosystem types. We suggest that terrestrial, freshwater, and marine systems in which denitrification occurs can be organized along a continuum ranging from (1) those in which nitrification and denitrification are tightly coupled in space and time to (2) those in which nitrate production and denitrification are relatively decoupled. In aquatic ecosystems, N inputs influence denitrification rates whereas hydrology and geomorphology influence the proportion of N inputs that are denitrified. Relationships between denitrification and water residence time and N load are remarkably similar across lakes, river reaches, estuaries, and continental shelves. Spatially distributed global models of denitrification suggest that continental shelf sediments account for the largest portion (44%) of total global denitrification, followed by terrestrial soils (22%) and oceanic oxygen minimum zones (OMZs; 14%). Freshwater systems (groundwater, lakes, rivers) account for about 20% and estuaries 1% of total global denitrification. Denitrification of land-based N sources is distributed somewhat differently. Within watersheds, the amount of land-based N denitrified is generally highest in terrestrial soils, with progressively smaller amounts denitrified in groundwater, rivers, lakes and reservoirs, and estuaries. A number of regional exceptions to this general trend of decreasing denitrification in a downstream direction exist, including significant denitrification in continental shelves of N from terrestrial sources. Though terrestrial soils and groundwater are responsible for much denitrification at the watershed scale, per-area denitrification rates in soils and groundwater (kg Nkm � 2 � yr � 1 ) are, on average, approximately one-tenth the per-area rates of denitrification in lakes, rivers, estuaries, continental shelves, or OMZs. A number of potential approaches to increase denitrification on the landscape, and thus decrease N export to sensitive coastal systems exist. However, these have not generally been widely tested for their effectiveness at scales required to significantly reduce N export at the whole watershed scale.
1,487 citations
TL;DR: A novel method for measurement of the oxygen isotopic composition (18O/16O) of nitrate (NO3-) from both seawater and freshwater with higher sensitivity, lack of interference by other solutes, and ease of sample preparation is reported.
Abstract: We report a novel method for measurement of the oxygen isotopic composition (18O/16O) of nitrate (NO3-) from both seawater and freshwater. The denitrifier method, based on the isotope ratio analysis of nitrous oxide generated from sample nitrate by cultured denitrifying bacteria, has been described elsewhere for its use in nitrogen isotope ratio (15N/14N) analysis of nitrate.1 Here, we address the additional issues associated with 18O/16O analysis of nitrate by this approach, which include (1) the oxygen isotopic difference between the nitrate sample and the N2O analyte due to isotopic fractionation associated with the loss of oxygen atoms from nitrate and (2) the exchange of oxygen atoms with water during the conversion of nitrate to N2O. Experiments with 18O-labeled water indicate that water exchange contributes less than 10%, and frequently less than 3%, of the oxygen atoms in the N2O product for Pseudomonas aureofaciens. In addition, both oxygen isotope fractionation and oxygen atom exchange are consi...
1,291 citations
"Hyporheic zone denitrification: Con..." refers methods in this paper
...…on a spectrophotometer at 562 nm. [21] For isotopic analysis, NO3 (þ NO2 ) was converted to N2O by the denitrifier method (using Pseudomonas aureofaciens) and analyzed by continuous-flow isotope-ratio mass spectrometry (CFIRMS) [Sigman et al., 2001; Casciotti et al., 2002; Coplen et al., 2004]....
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