The impact of flash floods on microbial distribution and biogeochemistry in the parafluvial zone of a desert stream

1. The impact of flash flooding on microbial distribution and biogeochemistry was investigated in the parafluvial zone (the part of the active channel lateral to the surface stream) of Sycamore Creek, a Sonoran Desert stream in central Arizona. 2. It was hypothesized that subsurface bacteria were dependent on the import of algal-derived organic matter from the surface stream, and it was therefore predicted that microbial numbers and rates of microbially mediated processes would be highest at locations of surface to subsurface hydrologic exchange and at times when algal biomass was high. 3. Prior to a flash flood on 19 July 1994, chlorophyll a was high (≈ 400 mg m^–2) in the surface stream and microbial numbers were highest at the stream–parafluvial interface and declined along parafluvial flowpaths, supporting the hypothesized algal–bacterial linkage. Immediately following the flash flood, chlorophyll a was low (≈ 7 mg m^–2), and microbial numbers were reduced at the stream–parafluvial interface. 4. Counter to expectations, parafluvial functioning (in terms of nitrate production and dissolved oxygen decline along flowpaths) re-established immediately after the flood receded. Therefore, material other than algal exudates supported parafluvial metabolism immediately postflood, and terrestrially derived dissolved organic matter is the likely source. 5. Algae in the surface stream recovered quickly following flooding, but recovery of parafluvial bacteria lagged somewhat behind. These results highlight the importance of surface–subsurface interaction to stream ecosystem functioning and show that the nature of these interactions changes substantially in successional time.     

Methanogenesis in Arizona,USA dryland streams

Methanogenesis was studied in five streams of central and southern Arizona by examining the distribution of methane in interstitial water and evasion of methane in three subsystems (hyporheic, parafluvial and bank sediments). In Sycamore Creek, the primary study site (studied during summer and early autumn), methane content of interstitial water exhibited a distinct spatial pattern. In hyporheic (sediments beneath the wetted channel) and parfluvial zones (active channel sediments lateral to the wetted channel), which were well oxygenated due to high hydrologic exchange with the surface stream and had little particulate organic matter (POM), interstitial methane concentration averaged only 0.03 mgCH₄-C/L. Bank sediments (interface between the active channel and riparian zone), in contrast, which were typically vegetated, had high POM, low hydrologic exchange and concomitantly low dissolved oxygen levels, had interstitial concentration averaging 1.5 mgCH4-C/L. Methane emission from Sycamore Creek, similar to methane concentration, averaged only 3.7 mgCH₄-C·m⁻²·d⁻¹ from hyporheic and parafluvial zones as opposed to 170 mgCH₄-C·m⁻²·d⁻¹ from anoxic bank sediments. Methane in four additional streams sampled (one sampling date during late winter) was low and exhibited little spatial variation most likely due to cooler stream temperatures. Interstitial methane in parafluvial and bank sediments of all four streams ranged from only 0.005 to 0.1 mgCH₄-C/L. Similarly methane evasion was also low from these streams varying from 0 to 5.7 mgCH₄-C·m⁻²·d⁻¹. The effects of organic matter and temperature on methanogenesis were further examined by experimentally manipulating POM and temperature in stoppered flasks filled with hyporheic sediments and stream water. Methane production significantly increased with all independent variables. Methane production is greatest in bank sediments that are relatively isolated hydrologically and lowest in hyporheic and parafluvial sediments that are interactive with the surface stream.     

Factors controlling hyporheic respiration in a desert stream

1. Experimental manipulations were performed to determine the biological, chemical and physical attributes that govern sediment respiration in the hyporheic zone of Sycamore Creek, a Sonoran Desert stream. 2. Hyporheic respiration per unit volume of sediment was inversely related to diameter of sediment particles, indicating that respiration is affected by availability of substrate for microbial colonization (i.e. sediment surfaces). Respiration rate per unit surface area on sediments was positively correlated with particle diameter, indicating greater metabolic activity of microbes on larger sediments. 3. Hyporheic respiration was more than twice as high in water collected from the surface flow than from subsurface flow. Further, hyporheic respiration was highest immediately following exposure of sediments to surface water and declined over time, presumably due to exhaustion of labile organic matter. 4. Microbial activity was stimulated by addition of algal leachate; however, amendments of leaf leachate had little effect. Respiration was also elevated with dextrose and leucine amendments, but not with inorganic nitrogen additions, indicating hyporheic respiration is carbon limited. 5. Water from the stream surface is probably enriched in labile organic matter derived from algae and stimulates respiration at points of hydrologic downwelling where surface water enters hyporheic sediments. The physical structure of sediments further affects metabolism by affecting the area available for microbial attachment.     

Hierarchy,spatial configuration,and nutrient cycling in a desert stream

Abstract Recent studies of nutrient cycling in Sycamore Creek in Arizona, USA, suggest that a thorough understanding requires a spatially explicit, hierarchical approach. Physical configuration determines the path that water follows as it moves downstream. Water follows flowpaths through surface stream components, the hyporheic zone beneath the surface stream, and the parafluvial (sand bar) zone. Characteristic biogeochemical processes in these subsystems alter nitrogen (N) species in transport, in part as a function of available concentrations of N species. At several hierarchical levels, substrate materials are an important determinant of nitrogen dynamics in desert streams. Sand is present in bars of variable size and shape, each of which can be considered a unit, interacting with the surface stream. Groups of these stream-sandbar units form a higher level, the reach. At the next higher scale, sandy reaches (runs) alternate with riffles. Where flowpaths converge, rates of N transformation are high and, as a result, change in concentration is a non-linear function of flowpath length. Disturbance by flash floods alters sandbar configuration. Between floods, the interaction of subsurface and surface flowpaths shapes configuration in each, thus a self-organizing element of spatial structure exists. Sandy runs are dominated by subsurface processes and are likely to be net nitrifiers while riffles are dominated by surface flow and are nitrogen fixers. Whether a stream ecosystem retains nitrogen, or transports it to downstream recipient systems, or is a net emitter of gaseous forms of N, depends upon the dynamics of a spatial mosaic of interacting elements. An understanding of the net effect of this mosaic requires a spatially explicit, hierarchical, multi-scale approach.     

Consequences of a biogeomorphic regime shift for the hyporheic zone of a Sonoran Desert stream

1. Feedbacks between vegetation and geomorphic processes can generate alternative stable states and other nonlinear behaviours in ecological systems, but the consequences of these biogeomorphic interactions for other ecosystem processes are poorly understood. In this study, we describe the changes in the hydrological, geomorphic and biogeochemical characteristics of the hyporheic zone of a Sonoran desert stream (Sycamore Creek, Arizona, U.S.A.) in response to a transition from an unvegetated gravel‐bed state to densely vegetated wetlands (ciénegas). 2. A survey of the entire length of Sycamore Creek indicated that ciénegas occupied c. 18% of the stream, and were disproportionately represented in constrained canyons rather than wide, unconstrained valleys. 3. Vegetated patches were characterized by low concentrations of dissolved oxygen (DO) and nitrate and high concentrations of carbon dioxide and methane in the hyporheic zone. In contrast to unvegetated areas, hyporheic DO in ciénegas exhibited no relationship with vertical hydraulic gradients. 4. Increases in hyporheic DO following removal of vegetation by floods supports the hypothesis that these reduced conditions were the result of biogeochemical and geomorphic changes associated with vegetation establishment. In locations where vegetation persisted, hyporheic DO exhibited no response to flooding; in sections where vegetation was removed hyporheic DO closely tracked post‐flood increases in surface stream DO. 5. Shallow sediments in vegetated patches were finer and more organic‐rich than in unvegetated patches, due to increased deposition during floods. Conservative tracer additions indicated that hydrological exchange between the surface stream and hyporheic zone was much lower in ciénegas than in gravel‐bed reaches. 6. Vegetation establishment in desert streams not only alters the physical and chemical characteristics of the hyporheic zone, but also the nature of interactions between surface and hyporheic subsystems.     

The dark side of the hyporheic zone: depth profiles of nitrogen and its processing in stream sediments

1. Although it is well known that sediments can be hot spots for nitrogen transformation in streams, many previous studies have confined measurements of denitrification and nitrate retention to shallow sediments (<5 cm deep). We determined the extent of nitrate processing in deeper sediments of a sand plains stream (Emmons Creek) by measuring denitrification in core sections to a depth of 25 cm and by assessing vertical nitrate profiles, with peepers and piezometers, to a depth of 70 cm. 2. Denitrification rates of sediment slurries based on acetylene block were higher in shallower core sections. However, core sections deeper than 5 cm accounted for 68% of the mean depth‐integrated denitrification rate. 3. Vertical hydraulic gradient and vertical profiles of pore water chloride concentration suggested that deep ground water upwelled through shallow sediments before discharging to the stream channel. The results of a two‐source mixing model based on chloride concentrations suggested that the hyporheic zone was very shallow (<5 cm) in Emmons Creek. 4. Vertical profiles showed that nitrate concentration in shallow ground water was about 10–60% of the nitrate concentration of deep ground water. The mean nitrate concentrations of deep and shallow ground water were 2.17 and 0.73 mg NO₃‐N L^?1, respectively. 5. Deep ground water tended to be oxic (6.9 mg O₂ L^?1) but approached anoxia (0.8 mg O₂ L^?1) after passing through shallow, organic carbon‐rich sediments, which suggests that the decline in the nitrate concentrations of upwelling ground water was because of denitrification. 6. Collectively, our results suggest that there is substantial nitrate removal occurring in deep sediments, below the hyporheic zone, in Emmons Creek. Our findings suggest that not accounting for nitrate removal in deep sediments could lead to underestimates of nitrogen processing in streams and catchments.     

Relationships between DOC bioavailability and nitrate removal in an upland stream: An experimental approach

The Catskill Mountains of southeastern New York State have among thehighest rates of atmospheric nitrogen deposition in the United States. Somestreams draining Catskill catchments have shown dramatic increases in nitrateconcentrations while others have maintained low nitrate concentrations. Streamsin which exchange occurs between surface and subsurface (i.e. hyporheic) watersare thought to be conducive to nitrate removal via microbial assimilationand/ordenitrification. Hyporheic exchange was documented in the Neversink River inthesouthern Catskill Mountains, but dissolved organic carbon (DOC) and nitrate(NO₃ ^–) losses along hyporheic flowpaths werenegligible. In this study, Neversink River water was amended with natural,bioavailable dissolved organic carbon (BDOC) (leaf leachate) in a series ofexperimental mesocosms that simulated hyporheic flowpaths. DOC and N dynamicswere examined before and throughout a three week BDOC amendment. In addition,bacterial production, dissolved oxygen demand, denitrification, and sixextracellular enzyme activities were measured to arrive at a mechanisticunderstanding of potential DOC and NO₃ ^– removalalong hyporheic flowpaths. There were marked declines in DOC and completeremoval of nitrate in the BDOC amended mesocosms. Independent approaches wereused to partition NO₃ ^– loss into two fractions:denitrification and assimilation. Microbial assimilation appears to be thepredominant process explaining N loss. These results suggest that variabilityinBDOC may contribute to temporal differences in NO₃ ^–export from streams in the Catskill Mountains.     

The role of water exchange between a stream channel and its hyporheic zone in nitrogen cycling at the terrestrial-aquatic interface

The subsurface riparian zone was examined as an ecotone with two interfaces. Inland is a terrestrial boundary, where transport of water and dissolved solutes is toward the channel and controlled by watershed hydrology. Streamside is an aquatic boundary, where exchange of surface water and dissolved solutes is bi-directional and flux is strongly influenced by channel hydraulics. Streamside, bi-directional exchange of water was qualitatively defined using biologically conservative tracers in a third order stream. In several experiments, penetration of surface water extended 18 m inland. Travel time of water from the channel to bankside sediments was highly variable. Subsurface chemical gradients were indirectly related to the travel time. Sites with long travel times tended to be low in nitrate and DO (dissolved oxygen) but high in ammonium and DOC (dissolved organic carbon). Sites with short travel times tended to be high in nitrate and DO but low in ammonium and DOC. Ammonium concentration of interstitial water also was influenced by sorption-desorption processes that involved clay minerals in hyporheic sediments. Denitrification potential in subsurface sediments increased with distance from the channel, and was limited by nitrate at inland sites and by DO in the channel sediments. Conversely, nitrification potential decreased with distance from the channel, and was limited by DO at inland sites and by ammonium at channel locations. Advection of water and dissolved oxygen away from the channel resulted in an oxidized subsurface habitat equivalent to that previously defined as the hyporheic zone. The hyporheic zone is viewed as stream habitat because of its high proportion of surface water and the occurrence of channel organisms. Beyond the channel's hydrologic exchange zone, interstitial water is often chemically reduced. Interstitial water that has not previously entered the channel, groundwater, is viewed as a terrestrial component of the riparian ecotone. Thus, surface water habitats may extend under riparian vegetation, and terrestrial groundwater habitats may be found beneath the stream channel.     

Nutrient transfer between parafluvial interstitial water and river water: influence of gravel bar heterogeneity

1. Nutrient concentrations in interstitial water springs at the downstream ends of two gravel bars in the River Rhône were measured in order to estimate the importance of nutrient inputs [nitrate, dissolved organic carbon (DOC), biodegradable and refractory fractions of DOC] from the parafluvial zone (saturated sediments adjacent to the wetted channel, i.e. interstitial habitats of gravel bars) to the river as well as seasonal variations in these inputs.
2. Compared with surface water, parafluvial water had lower concentrations of DOC (especially the refractory fraction) and generally higher concentrations of nitrate. These differences were at their lowest during winter.
3. The influence of gravel bar geomorphological heterogeneity (grain size and spatial distribution of fine sediments) on parafluvial inputs was studied in terms of nutrient content and biofilm characteristics along transects across the gravel bars.
4. A gravel bar located in a stable area of the river had low transversal heterogeneity and acted as a sink for DOC and as a source of nitrate. The low fine sediment content and the high oxygenation of interstitial water must have enabled aerobic processes such as mineralization of organic matter and nitrification to occur.
5. In contrast, gravel bars located in a degradation zone of the river had a spatially variable structure, acting as a sink for DOC and nitrate because localized accumulation of fine sediment and ensuing hypoxic conditions induced anaerobic processes such as denitrification.
6. This study highlights the important influence of geomorphological heterogeneity in gravel bars for nutrient transformations as well as nutrient exchanges between parafluvial interstitial systems and the adjacent river over a seasonal cycle.     

Macrophyte presence is an indicator of enhanced denitrification and nitrification in sediments of a temperate restored agricultural stream

Stream macrophytes are often removed with their sediments to deepen stream channels, stabilize channel banks, or provide habitat for target species. These sediments may support enhanced nitrogen processing. To evaluate sediment nitrogen processing, identify seasonal patterns, and assess sediment processes relative to stream load, we measured denitrification and nitrification rates in a restored third- to fourth-order agricultural stream, Black Earth Creek, Wisconsin, and estimated processing over a 10 km reach. Our results show that sediments with submerged and emergent macrophytes (e.g., Potomageton spp. and Phalaris arudinacea) support greater denitrification rates than bare sediments (1.12 μmol N g⁻¹ h⁻¹ vs. 0.29). Sediments with macrophytes were not carbon limited and organic matter fraction was weakly correlated to denitrification. The highest denitrification potential occurred in macrophyte beds (5.19 μmol N g⁻¹ h⁻¹). Nitrification rates were greater in emergent beds than bare sediments (1.07 μg N ml⁻¹day⁻¹ vs. 0.35) with the greatest nitrification rates during the summer. Total denitrification removal in sediments with macrophytes was equivalent to 43% of the nitrate stream load (463.7 kg N day⁻¹) during spring and nitrification in sediments with macrophytes was equivalent to 247% of summer ammonium load (3.5 kg N day⁻¹). Although the in-channel connectivity to nitrogen rich water was limited, actual stream nitrogen loads could increase with removal of macrophytes. Macrophyte beds and supporting fringing wetted areas are important if nitrogen management is a concern for riparian stream restoration efforts.     

Hyporheic zone hydrology and nitrogen dynamics in relation to the streambed topography of a N-rich stream

The influence of riffle-pool units on hyporheic zone hydrology and nitrogen dynamics was investigated in Brougham Creek, a N-rich agricultural stream in Ontario, Canada. Subsurface hydraulic gradients, differences in background stream and groundwater concentrations of conservative ions, and the movement of a bromide tracer indicated the downwelling of stream water at the head of riffles and upwelling in riffle-pool transitions under base flow conditions. Channel water also flowed laterally into the floodplain at the upstream end of riffles and followed a subsurface concentric flow path for distances of up to 20 m before returning to the stream at the transition from riffles to pools. Differences in observed vs predicted concentrations based on background chloride patterns indicated that the hyporheic zone was a sink for nitrate and a source for ammonium. The removal of nitrate in the streambed was confirmed by the loss of nitrate in relation to co-injected bromide in areas of downwelling stream water in two riffles. Average stream water nitrate-N concentrations of 1.0 mg/L were often depleted to <0.005 mg/L near the sediment-water interface. Consequently, an extensive volume of the hyporheic zone in the streambed and floodplain had a large unused potential for nitrate removal. Conceptual models based mainly on studies of streams with low nutrient concentrations have emphasized the extent of surface-subsurface exchanges and water residence times in the hyporheic zone as important controls on stream nutrient retention. In contrast, we suggest that nitrate retention in N-rich streams is influenced more by the size of surface water storage zones which increase the residence time of channel water in contact with the major sites of rapid nitrate depletion adjacent to the sediment-water interface.     

Nitrate depletion in the riparian zone and stream channel of a small headwater catchment

A mass balance procedure was used to determine rates of nitrate depletion in the riparian zone and stream channel of a small New Zealand headwater stream. In all 12 surveys the majority of nitrate loss (56–100%) occurred in riparian organic soils, despite these soils occupying only 12% of the stream's border. This disproportionate role of the organic soils in depleting nitrate was due to two factors. Firstly, they were located at the base of hollows and consequently a disproportionately high percentage (37–81%) of the groundwater flowed through them in its passage to the stream. Secondly, they were anoxic and high in both denitrifying enzyme concentration and available carbon. Direct estimates ofin situ denitrification rate for organic soils near the upslope edge (338 mg N m^–2 h^–1) were much higher than average values estimated for the organic soils as a whole (0.3–2.1 mg N m^–2 h^–1) and suggested that areas of these soils were limited in their denitrification activity by the supply of nitrate. The capacity of these soils to regulate nitrate flux was therefore under-utilized. The majority of stream channel nitrate depletion was apparently due to plant uptake, with estimates of thein situ denitrification rate of stream sediments being less than 15% of the stream channel nitrate depletion rate estimated by mass balance.This study has shown that catchment hydrology can interact in a variety of ways with the biological processes responsible for nitrate depletion in riparian and stream ecosystems thereby having a strong influence on nitrate flux. This reinforces the view that those seeking to understand the functioning of these ecosystems need to consider hydrological phenomena.     

Denitrification in deep subsurface sediments

Dissimilatory nitrate reduction (denitrification) in subsurface sediments by indigenous microflora was investigated in samples obtained over a range of depths from 0 to 289 m. Denitrifying activity in sediment samples retrieved from similar stratigraphic horizons at four different sites was determined by measuring the accumulation of N₂O using the acetylene blockage technique. Denitrification was detected in unamended samples which received only prereduced deionized water at almost all depths in all sediments sampled. The surface sediments showed the highest denitrification activity. In the deeper sediments, denitrifying activity was much higher in saturated sandy samples and lower or absent in drier clay samples. Addition of nitrate enhanced denitrification activity in all samples from below the water table down to the maximum depth sampled (289 m), while addition of a carbon (succinate) source in general had no stimulatory effect. These results show that denitrifying microorganisms were present in all of the deep subsurface sediments tested in this study. Furthermore, these results suggest that adequate supplies of metabolizable organic carbon were available to support denitrifying activity. However, denitrification may be limited by inadequate supplies of nitrate in the sediments.     

Nitrogen processing in the hyporheic zone of a pastoral stream

The distribution of nitrogen-transforming processes, and factors controlling their rates, were determined within the hyporheic zone of a lowland stream draining agricultural land. In the field, physicochemical parameters were measured along a 10m-long hyporheic flow line between downwelling and upwelling zones. Sediment cores were retrieved from the stream bed surface, and from 20, 40 and 60cm deep in each zone, and in the laboratory, water from the corresponding depth was percolated through each core at the natural flow rate. Concentrations of nitrogen species and oxygen were measured before and after flow through each core. Denitrification was measured using a ¹⁵N-nitrate tracer. Shallow and downwelling zone samples were clearly distinct from deeper and upwelling zone samples in terms of physicochemical conditions, microbial processes and factors controlling nitrogen processing. Denitrification was highest in surface and downwelling zone cores, despite high oxygen levels, probably due to high pore-water nitrate concentrations in these cores and isolation of the denitrifying bacteria from oxygen in the bulk water by the hyporheic biofilms. Denitrification was limited by oxygen inhibition in the downwelling group, and by nitrate availability in the upwelling group. Strong evidence indicated that dissimilatory nitrate reduction to ammonium, occurred in almost all cores, and outcompeted denitrification for nitrate. In contrast, nitrification was undetectable in all but two cores, probably because of intense competition for oxygen. Field patterns and lab experiments indicated that the hyporheic zone at this moderately N-rich site is a strong sink for nitrate, fitting current theories that predict where hyporheic zones are nitrate sinks or nitrate sources.     

The Effects of an Environmental Flow Release on Water Quality in the Hyporheic Zone of the Hunter River,Australia

Environmental flow releases have been advocated as a useful rehabilitation strategy for improving river condition but assessments of their success have typically focused on surface water quality and biota. In this study, we investigated the impacts of an environmental flow release on water temperature, conductivity, dissolved oxygen, and nitrate concentrations in surface and subsurface (hyporheic) water at upwelling and downwelling zones in three sites along the Hunter River, New South Wales, Australia. We hypothesised that the flow pulse would ‘flush’ the sediments with oxygenated water, stimulating hyporheic microbial activity and nitrification, enhancing nitrate concentrations over time. Surface and subsurface samples were collected before, 7 days after, and 49 days after an environmental flow release of 5000 Ml for a period of 3 days. No lasting effects on dissolved oxygen or conductivity were evident at most sites although dissolved oxygen declined over time at the downwelling site at Bowmans Crossing. At the downwelling zones at all sites, hyporheic nitrate concentrations declined initially following the release, but then rose or leveled off by Day 49. This initial drop in concentration was attributed to flushing of nitrate from the sediments. At two sites, nitrate concentrations had increased by Day 49 in the upwelling zones while at the third site, it fell significantly, associated with very low dissolved oxygen and likely reductive loss of nitrate. Electrical conductivity data indicate that potential inputs of agriculturally enriched groundwater may contribute to the nitrogen dynamics of the Hunter River. This study highlights the spatial heterogeneity that occurs in the hyporheic zone within and among sites of a regulated river, and emphasises the need for multiple-site surveys and an understanding of groundwater dynamics to assess physicochemical responses of the hyporheic zone to environmental flow releases.     

A long-term perspective of dissolved organic carbon transport in Sycamore Creek, Arizona, USA

Dissolved organic carbon (DOC) dynamics were examined over five years (1989–1993) in Sycamore Creek, a Sonoran Desert stream, specifically focusing on DOC concentration in surface and hyporheic waters, and rates of export. In 1989 and 1990, the years of lowest stream discharge (0.08 and 0.04 m³ s^–1 annual mean of daily discharge, respectively), DOC was high, averaging 7.37 and 6.22 mgC l^–1 (weighted annual means). In contrast, from 1991 through 1993, a period of increased flow (1.1, 1.2 and 4.3 m³ s^–1), concentration was significantly lower (P<0.001) with annual mean concentrations of 3.54, 3.49 and 3.39 mgC l^–1. Concentration exhibited little spatial variation between two sampling stations located 6 km apart along the mainstem or between surface and hyporheic waters. Annual export of DOC from Sycamore Creek varied 100-fold over the five-year period from a mean rate of only 24 kgC d^–1 in 1990 to 2100 kgC d^–1 in 1993. Ninety percent of DOC was exported by flows greater than 2.8 m³ s^–1, and 50% during flows greater than 27 m³ s^–1; flows of 2.8 and 24 m³ s^–1 occurred only 9 and 1% of the time. The export of organic matter in Sycamore Creek appears to be coupled to El Niño-Southern Oscillation phenomena. The years of highest export, 1991–1993, had El Niño conditions while 1989 and 1990 had medial conditions.     

Effects of augmentation of coarse particulate organic matter on metabolism and nutrient retention in hyporheic sediments

SUMMARY 1. Metabolic and biogeochemical processes in hyporheic zones may depend on inputs of coarse particulate organic matter. Our research focused on how differing quantity and quality of organic matter affects metabolism and nutrient retention in the hyporheic zone of a first-order Appalachian stream.
2. Sixteen plots were established on a tributary of Hugh White Creek, NC, U.S.A. Sediment was extracted and treated with leaves, wood, plastic strips or remained unamended. Following treatment, sediment was returned to the stream and, approximately 3 months later, samples were removed from each plot.
3. Aerobic and anaerobic metabolism were measured as the change in O₂ and CO₂ in recirculating microcosms. At the same time, we monitored other possible terminal electron accepting processes and changes in nutrient concentrations. Aerobic metabolism was low in all treatments and respiratory quotients calculated for all treatments indicated that metabolism was dominated by anaerobic processes.
4. Rates of anaerobic respiration and total (combined aerobic and anaerobic) respiration were significantly greater ( P  < 0.05) in plots treated with leaf organic matter compared to controls.
5. Addition of leaves, which had a low C:N ratio, stimulated respiration in hyporheic sediments. Anaerobic processes dominated metabolism in both control and amended sediments. Enhanced metabolic rates increased retention of many solutes, indicating that energy flow and nutrient dynamics in the subsurface of streams may depend upon the quantity and quality of imported carbon.     

A mixing model analysis of stream solute dynamics and the contribution of a hyporheic zone to ecosystem function*

1. We monitored streamwater and streambed sediment porewaters from White Clay Creek (WCC), SE Pennsylvania, for dissolved organic carbon (DOC), dissolved oxygen (DO) and conductivity to investigate organic matter processing within the hyporheic zone. Dissolved organic carbon and DO concentrations were higher in the streamwater than in the porewaters and, in many cases, concentrations continued to diminish with increasing depth into the streambed. 2. Hydrological exchange data demonstrated that the permeability of the stream bed declines with depth and constrains downwelling, effectively isolating porewaters >30 cm from streamwater. 3. End‐member mixing analysis (EMMA) based on conductivity documented a DOC source and DO sink in the hyporheic zone. We calculated hyporheic streambed DOC fluxes and respiration from the EMMA results and estimates of water flux. Based upon our calculations of biodegradable DOC entering the hyporheic zone, we estimate that DOC supports 39% of the hyporheic zone respiration, with the remaining 61% presumably being supported by entrained particulate organic carbon. Hyporheic respiration averaged 0.38 g C m^?2 d^?1, accounted for 41% of whole ecosystem respiration, and increased baseflow ecosystem efficiency from 46 to 59%. 4. Advective transport of labile organic molecules into the streambed concentrates microbial activity in near‐surface regions of the hyporheic zone. Steep gradients in biogeochemical activity could explain how a shallow and hydrologically constrained hyporheic zone can dramatically influence organic matter processing at the ecosystem scale.     

Perspectives and predictions on the microbial ecology of the hyporheic zone

1. Studies of hyporheic microbial ecology have suggested an important role for hyporheic microbial processes in stream ecosystem functioning. Using evidence from microbial communities in other aquatic habitats, some predictions are made concerning the diversity of microbial types and microbial processes likely to occur in the hyporheic zone, and the relative importance of these various types to the hyporheic ecosystem. 2. It is predicted that the biofilm growth form of interstitial micro-organisms will create a variety of microniches, allowing coexistence of a great diversity of microbial types, and promoting the activity of some otherwise poor competitors. It is further predicted that the confluence of reduced groundwaters and aerobic surface waters will favour chemolithotrophic processes in the hyporheic zone, but that these will contribute significantly to hyporheic production only if surface water is very low in dissolved organic carbon, or the groundwater is extremely reduced, such as by the influence of riparian wetlands. A variety of anaerobic respiratory pathways, such as nitrate, ferric ion, sulphate and even methanogenic respiration will be employed in the hyporheic zone, with biofilm dynamics permitting these to occur even in aerobic sediments. Anaerobic pathways may account for a significant proportion of total hyporheic organic matter mineralization. 3. The role of fungi in hyporheic dynamics is, as yet, almost completely unstudied. However, it is expected that they will be important in breaking down buried particulate organic matter (POM), which may account for a large proportion of total stream POM. 4. Physicochemical conditions in hyporheic sediments appear to be highly heterogeneous, and this heterogeneity may be very important in the cycling of certain nutrients, especially nitrogen, which involves a series of steps requiring different conditions. 5. Various new techniques are now available by which biofilm dynamics and in situ microbial processes may be measured. Studies are recommended of intact microbial communities both at the microscale of the biofilm and at the scale of the heterogeneities occurring in hyporheic sediments. Studies are needed that measure actual rates of microbial processes under in situ conditions.     

Bacterial community dynamics in the hyporheic zone of an intermittent stream

The dynamics of in situ bacterial communities in the hyporheic zone of an intermittent stream were described in high spatiotemporal detail. We assessed community dynamics in stream sediments and interstitial pore water over a two-year period using terminal-restriction fragment length polymorphism. Here, we show that sediments remained saturated despite months of drought and limited hydrologic connectivity. The intermittency of stream surface water affected interstitial pore water communities more than hyporheic sediment communities. Seasonal changes in bacterial community composition was significantly associated with water intermittency, phosphate concentrations, temperature, nitrate and dissolved organic carbon (DOC) concentrations. During periods of low- to no-surface water, communities changed from being rich in operational taxonomic units (OTUs) in isolated surface pools, to a few OTUs overall, including an overall decline in both common and rare taxa. Individual OTUs were compared between porewater and sediments. A total of 19% of identified OTUs existed in both porewater and sediment samples, suggesting that bacteria use hyporheic sediments as a type of refuge from dessication, transported through hydrologically connected pore spaces. Stream intermittency impacted bacterial diversity on rapid timescales (that is, within days), below-ground and in the hyporheic zone. Owing to the coupling of intermittent streams to the surrounding watershed, we stress the importance of understanding connectivity at the pore scale, consequences for below-ground and above-ground biodiversity and nutrient processing, and across both short- and long-time periods (that is, days to months to years).