Nitrification and denitrification in lake and estuarine sediments measured by the N dilution technique and isotope pairing

The transformation of nitrogen compounds in lake and estuarine sediments incubated in the dark was analyzed in a continuous-flowthrough system. The inflowing water contained NO(3), and by determination of the isotopic composition of the N(2), NO(3), and NH(4) pools in the outflowing water, it was possible to quantify the following reactions: total NO(3) uptake, denitrification based on NO(3) from the overlying water, nitrification, coupled nitrification-denitrification, and N mineralization. In sediment cores from both lake and estuarine environments, benthic microphytes assimilated NO(3) and NH(4) for a period of 25 to 60 h after darkening. Under steady-state conditions in the dark, denitrification of NO(3) originating from the overlying water accounted for 91 to 171 mumol m h in the lake sediments and for 131 to 182 mumol m h in the estuarine sediments, corresponding to approximately 100% of the total NO(3) uptake for both sediments. It seems that high NO(3) uptake by benthic microphytes in the initial dark period may have been misinterpreted in earlier investigations as dissimilatory reduction to ammonium. The rates of coupled nitrification-denitrification within the sediments contributed to 10% of the total denitrification at steady state in the dark, and total nitrification was only twice as high as the coupled process.     

Estimation of Nitrification and Denitrification from Microprofiles of Oxygen and Nitrate in Model Sediment Systems

The coupling between nitrification and denitrification and the regulation of these processes by oxygen were studied in freshwater sediment microcosms with O₂ and NO₃^- microsensors. Depth profiles of nitrification (indicated as NO₃^- production), denitrification (indicated as NO₃^- consumption), and O₂ consumption activities within the sediment were calculated from the measured concentration profiles. From the concentration profiles, it was furthermore possible to distinguish between the rate of denitrification based on the diffusional supply of NO₃^- from the overlying water and the rate based on NO₃^- supplied by benthic nitrification (D_w and D_n, respectively). An increase in O₂ concentration caused a deeper O₂ penetration while a decrease in D_w and an increase in D_n were observed. The relative importance for total denitrification of NO₃^- produced by nitrification thus increased compared with NO₃^- supplied from the water phase. The decrease in D_w at high oxygen was due to an increase in diffusion path for NO₃^- from the overlying water to the denitrifying layers in the anoxic sediment. At high O₂ concentrations, nitrifying activity was restricted to the lower part of the oxic zone where there was a continuous diffusional supply of NH₄⁺ from deeper mineralization processes, and the long diffusion path from the nitrification zone to the overlying water compared with the path to the denitrifying layers led to a stimulation in D_n.     

Nitrogen transformations in microenvironments of river beds and riparian zones

The soil of flooded riparian zones, the rhizosphere of riparian plants, biofilms at solid surfaces in the river, and the surface layer of sediments all constitute important environments for the oxidative or reductive transformations of inorganic nitrogen compounds. The exact microzonation and coupling of the processes have recently been studied intensively with ¹⁵N enrichment methods and microsensors for NH₄⁺, NO₂⁻, NO₃⁻, and N₂O. Microsensor analyses of gradients in sediments and biofilms have shown that nitrate production takes place in an aerobic surface zone that has a maximum thickness of a few millimeters in most shallow-water sediments and may be as thin as 100 μm in biofilms from very eutrophic environments. In the anoxic zone, denitrification is also concentrated in a zone of maximum a few millimeters, and typically half of the nitrate produced by nitrification is denitrified while the other half escapes to the water. The supply of nitrate from above is primarily controlled by the oxic layer acting as a diffusion barrier, and therefore denitrification is generally a linear function of the nitrate concentration in the water. The overlying water is thus a much more important source of nitrate for denitrification if the concentration is high. The rate and location of denitrification are also affected by bioturbating animals, benthic microphytes, plants, and bacteria performing dissimilatory nitrate reduction to ammonium (DNRA).     

High-throughput sequencing of the mitochondrial genomes from archived fish scales: an example of the endangered putative species flock of Sevan trout <Emphasis Type="Italic">Salmo ischchan</Emphasis>

Burrowing benthic animals belonging to the same functional group may produce species-specific effects on microbially mediated nitrogen (N) processes depending upon different ecological traits. We investigated the effects of two tube-dwelling organisms, amphipods (Corophium insidiosum) and chironomid larvae (Chironomus plumosus), on benthic N cycling in bioturbated estuarine sediments. Aims of this work were to analyze the interactions among burrowers and N-related microbial processes in two distinct sedimentary environments colonized by benthic animals with different ecological traits. We hypothesized higher rates of nitrification and higher coupled nitrification–denitrification in sediments with C. insidiosum due to continuous ventilation rates. We expected higher denitrification of water column nitrate in sediments with C. plumosus due to lower and intermittent ventilation activity and lower oxygen levels in burrows. To this purpose, we combined process–specific (nitrification and denitrification) with net N flux measurements in intact and reconstructed sediments. Sediments with C. insidiosum had higher rates of oxygen demand and of potential nitrification and higher concentration of pore water NH₄⁺ as compared to sediments with C. plumosus. Sediments with both species displayed comparable net N₂ fluxes, mostly sustained by respiration of water column NO₃^? in sediments with chironomid larvae and by NO₃^? produced within sediments in sediments with corophiid amphipods. Corophium insidiosum stimulated nitrification nearly 15-fold more as compared to C. plumosus. Overall, our results demonstrate that sediments with burrowing fauna may display similar rates of denitrification, but underlying mechanisms may deeply vary and be species-specific.     

Simulation Model of the Coupling between Nitrification and Denitrification in a Freshwater Sediment

A model was constructed to simulate the results of experiments which investigated nitrification and denitrification in the freshwater sediment of Lake Vilhelmsborg, Denmark (K. Jensen, N. P. Sloth, N. Risgaard-Petersen, S. Rysgaard, and N. P. Revsbech, Appl. Environ. Microbiol. 60:2094-2100, 1994). The model output faithfully represented the profiles of O₂ and NO₃^- and rates of nitrification, denitrification, and O₂ consumption as the O₂ concentration in the overlying water was increased from 10 to 600 μM. The model also accurately predicted the response, to increasing O₂ concentrations, of the integrated (micromoles per square meter per hour) rates of nitrification and denitrification. The simulated rates of denitrification of NO₃^- diffusing from the overlying water (D_w) and of NO₃^- generated by nitrification within the sediment (D_n) corresponded to the experimental rates as the O₂ concentration in the overlying water was altered. The predicted D_w and D_n rates, as NO₃^- concentration in the overlying water was changed, closely resembled those determined experimentally. The model was composed of 41 layers 0.1 mm thick, of which 3 represented the diffusive boundary layer in the water. Large first-order rate constants for nitrification and denitrification were required to completely oxidize all NH₄⁺ diffusing from the lower sediment layers and to remove much of the NO₃^- produced. In addition to the flux of NH₄⁺ from below, the model required a flux of an electron donor, possibly methane. Close coupling between nitrification and denitrification, achieved by allowing denitrification to tolerate some O₂ (~10 μM), was necessary to reproduce the real data. Spatial separation of the two processes (no toleration by denitrification of O₂) resulted in too high NO₃^- concentrations and too low rates of denitrification.     

Denitrification, Dissimilatory Reduction of Nitrate to Ammonium, and Nitrification in a Bioturbated Estuarine Sediment as Measured with 15N and Microsensor Techniques

Nitrogen and oxygen transformations were studied in a bioturbated (reworked by animals) estuarine sediment (Norsminde Fjord, Denmark) by using a combination of ¹⁵N isotope (NO₃^-), specific inhibitor (C₂H₂), and microsensor (N₂O and O₂) techniques in a continuous-flow core system. The estuarine water was NO₃^- rich (125 to 600 μM), and NO₃^- was consistently taken up by the sediment on the four occasions studied. Total NO₃^- uptake (3.6 to 34.0 mmol of N m^-2 day^-1) corresponded closely to N₂ production (denitrification) during the experimental steady state, which indicated that dissimilatory, as well as assimilatory, NO₃^- reduction to NH₄⁺ was insignificant. When C₂H₂ was applied in the flow system, denitrification measured as N₂O production was often less (58 to 100%) than the NO₃^- uptake because of incomplete inhibition of N₂O reduction. The NO₃^- formed by nitrification and not immediately denitrified but released to the overlying water, uncoupled nitrification, was calculated both from ¹⁵NO₃^- dilution and from changes in NO₃^- uptake before and after C₂H₂ addition. These two approaches gave similar results, with rates ranging between 0 and 8.1 mmol of N m^-2 day^-1 on the four occasions. Attempts to measure total nitrification activity by the difference between NH₄⁺ fluxes before and after C₂H₂ addition failed because of non-steady-state NH₄⁺ fluxes. The vertical distribution of denitrification and oxygen consumption was studied by use of N₂O and O₂ microelectrodes. The N₂O profiles measured during the experimental steady state were often irregularly shaped, and the buildup of N₂O after C₂H₂ was added was much too fast to be described by a simple diffusion model. Only bioturbation by a dense population of infauna could explain these observations. This was corroborated by the relationship between diffusive and total fluxes, which showed that only 19 to 36 and 29 to 62% of the total O₂ uptake and denitrification, respectively, were due to diffusion-reaction processes at the regular sediment surface, excluding animal burrows.     

Microscale Distribution of Nitrification Activity in Sediment Determined with a Shielded Microsensor for Nitrate

Microprofiles of O₂ and NO₃^- were measured simultaneously in freshwater sediment with microsensors which were completely free from electrical interference because of coaxial designs. Depth profiles of nitrification (NO₃^- production) and denitrification (NO₃^- consumption) were subsequently determined by computer simulation of the measured microprofiles. The nitrifying bacterial community responded very quickly to changes in environmental conditions, and new steady-state microprofiles of O₂ and NO₃^- were usually approached within a few hours after perturbation. Nitrification started quickly after introduction of O₂ in previously anoxic layers, suggesting prolonged survival of the nitrifiers during anaerobiosis. Changes in the availability of O₂ and NH₄⁺ greatly affected the nitrification profile, and there was a high rate of coupled nitrification-denitrification under conditions in which nitrification occurred right above the oxic-anoxic interface. Addition of C₂H₂ rapidly removed the NO₃^- peaks, indicating that NO₃^- production was due mainly to autotrophic nitrification.     

Nitrogen transformations at the sediment–water interface across redox gradients in the Laurentian Great Lakes

The capacity of a lake to remove reactive nitrogen (N) through denitrification has important implications both for the lake and for downstream ecosystems. In large oligotropic lakes such as Lake Superior, where nitrate (NO₃ ^?) concentrations have increased steadily over the past century, deep oxygen penetration into sediments may limit the denitrification rates. We tested the hypothesis that the position of the redox gradient in lake sediments affects denitrification by measuring net N-fluxes across the sediment–water interface for intact sediment cores collected across a range of sediment oxycline values from nearshore and offshore sites in Lake Superior, as well as sites in Lake Huron and Lake Erie. Across this redox gradient, as the thickness of the oxygenated sediment layer increased from Lake Erie to Lake Superior, fluxes of NH₄ ⁺ and N₂ out of the sediment decreased, and sediments shifted from a net sink to a net source of NO₃ ^?. Denitrification of NO₃ ^? from overlying water decreased with thickness of the oxygenated sediment layer. Our results indicate that, unlike sediments from Lake Erie and Lake Huron, Lake Superior sediments do not remove significant amounts of water column NO₃ ^? through denitrification, likely as a result of the thick oxygenated sediment layer.     

Nitrate Accumulation in Aerobic Hypolimnia: Relative Importance of Benthic and Planktonic Nitrifiers in an Oligotrophic Lake

Both nitrate and nitrous oxide accumulate in the hypolimnion of the oligotrophic Lake Taupo, New Zealand, throughout stratification. The two forms of oxidized nitrogen increase in concentration with increasing depth toward the sediments, where the dissolved concentrations of reduced nitrogen are two orders of magnitude higher than concentrations in the overlying water. Nitrification rates were measured by dark [¹⁴C]CO₂ assays with and without the inhibitor nitrapyrin. The fastest rates were recorded for planktonic nitrifiers in the epilimnion and benthic species in the surficial 2.5 mm of the sediments. Nitrifying bacteria were least active in the deep hypolimnion. Deepwater accumulation of NO₃⁻ in Lake Taupo must therefore be a product of benthic rather than planktonic nitrification.     

Denitrification measurements in aquatic sediments: A comparison of three methods

Measurements of denitrification using the acetylene inhibition,¹⁵N isotope tracer, and N₂ flux methods were carried out concurrently using sediment cores from Vilhelmsborg sø, Denmark, in an attempt to clarify some of the limitations of each technique. Three experimental treatments of overlying water were used: control, nitrate enriched, and ammonia enriched water. The N₂ flux and¹⁵N tracer experiments showed high rates of coupled nitrification/denitrification in the sediments. The acetylene inhibition method did not capture any coupled nitrification/denitrification. This could be explained by acetylene inhibition of nitrification. A combined¹⁵N tracer/acetylene inhibition experiment demonstrated that acetylene inhibition of N₂O reduction was incomplete and the method, therefore, only measured approximately 50% of the denitrification due to nitrate from the overlying water. Similar rates of denitrification due to nitrate in the overlying water were measured by the N₂ flux method and the acetylene inhibition method, after correcting for the 50% efficiency of acetylene inhibition. Rates of denitrification due to nitrate from the overlying water measured by the¹⁵N tracer method, however, were only approximately 35% or less of those measured by the acetylene inhibition or N₂ flux methods.     

Seasonal oxygen,nitrogen and phosphorus benthic cycling along an impacted Baltic Sea estuary: regulation and spatial patterns

The regulatory roles of temperature, eutrophication and oxygen availability on benthic nitrogen (N) cycling and the stoichiometry of regenerated nitrogen and phosphorus (P) were explored along a Baltic Sea estuary affected by treated sewage discharge. Rates of sediment denitrification, anammox, dissimilatory nitrate reduction to ammonium (DNRA), nutrient exchange, oxygen (O₂) uptake and penetration were measured seasonally. Sediments not affected by the nutrient plume released by the sewage treatment plant (STP) showed a strong seasonality in rates of O₂ uptake and coupled nitrification–denitrification, with anammox never accounting for more than 20 % of the total dinitrogen (N₂) production. N cycling in sediments close to the STP was highly dependent on oxygen availability, which masked temperature-related effects. These sediments switched from low N loss and high ammonium (NH₄ ⁺) efflux under hypoxic conditions in the fall, to a major N loss system in the winter when the sediment surface was oxidized. In the fall DNRA outcompeted denitrification as the main nitrate (NO₃ ^?) reduction pathway, resulting in N recycling and potential spreading of eutrophication. A comparison with historical records of nutrient discharge and denitrification indicated that the total N loss in the estuary has been tightly coupled to the total amount of nutrient discharge from the STP. Changes in dissolved inorganic nitrogen (DIN) released from the STP agreed well with variations in sedimentary N₂ removal. This indicates that denitrification and anammox efficiently counterbalance N loading in the estuary across the range of historical and present-day anthropogenic nutrient discharge. Overall low N/P ratios of the regenerated nutrient fluxes impose strong N limitation for the pelagic system and generate a high potential for nuisance cyanobacterial blooms.     

Microelectrode Measurements of Nitrate Gradients in the Littoral and Profundal Sediments of a Meso-Eutrophic Lake (Lake Vechten, The Netherlands)

NO₃⁻ concentration profiles were measured in the sediments of a meso-eutrophic lake with a newly developed microelectrode. The depth of penetration of NO₃⁻ varied from only 1.3 mm in organic-rich profundal silty sediments to 5 mm in organic-poor littoral sandy sediments. The thickness of the zone of denitrification in the organic-rich sediments was <500 μm. Oxygen profiles measured simultaneously revealed that the zone of denitrification was directly adjacent to the aerobic zone. The results demonstrate high denitrification rates (0.26 to 1.31 mmol m⁻² day⁻¹) at in situ nitrate concentrations in the overlying water (0.030 mmol liter⁻¹) and limitation of denitrification by nitrate availability.     

Nitrogen and phosphorus interchange between sediments and overlying water of a wastewater retention pond

Nitrogen and P interchange between the sediments and the overlying water of a simulated retention pond used for wastewater treatment were evaluated under conditions of seasonal temperature fluctuations and varying physico-chemical conditions (exposing floodwater surface to daylight vs. dark and turbulent vs. quiscent floodwater). Natural sediment columns obtained from two types of field retention ponds were used. One type of retention pond consisted of calcareous clay loam sediment while the sediment of second retention pond contained organic soil. Nutrient interchange between sediments and the overlying water was measured once a month over a period of one year. Nitrogen removal rates from floodwater were controlled by the initial floodwater NH ₄ ⁺ and NO ₃ ^? concentration, rate of NH ₄ ⁺ diffusion from the sediments to the overlying water, ammonification in the sediments, NH₃ volatilization and nitrification at the sediment-water interface, and denitrification in the sediments. Under the conditions studied, NH ₄ ⁺ concentrations of the floodwater were in the range of 0.01 to 0.05 µg/ml, while NO ₃ ^? concentrations were in the range of 0.27 to 0.78 µg/ml. Sediments with organic soil were found to be less effective in the removal of floodwater organic N, organic C and P, compared to the sediments with calcareous clay loam. Phosphorus exchange rates were dependent on the capacity of the sediment to adsorb or desorb P. Total P exchange rates were in the range of ?1.04 to 0.34 mg P/m² day. Seasonal temperature fluctuations, turbulent vs. quiscent water conditions or exposing the floodwater surface to daylight or dark had very little effect on N and P exchange rates.     

Ammonium, nitrate, and total nitrogen in the soil water of feedlot and field soil profiles

A level feedlot, located in an area consisting of Wann silt loam changing with depth to sand, appears to contribute no more NO₃^- nitrogen, NH₄⁺ nitrogen, and total nitrogen to the shallow water table beneath it than an adjacent cropped field. Soil water samples collected at 46, 76, and 107 cm beneath the feedlot surface generally showed NO₃^- nitrogen concentrations of less than 1 μg/ml. During the summer months, soil water NO₃^- nitrogen increased at the 15-cm depth, indicating that nitrification took place at the feedlot surface. However, the low soil water NO₃^- nitrogen values below 15 cm indicate that denitrification takes place beneath the surface.     

Pore water nutrient profiles and dynamics in soft bottoms of the northern Baltic Sea

Chemical profiles of nutrients at the sediment–water interface were measured in the northern Baltic Sea. A whole core squeezer technique capable of mm-scale resolution was used to obtain the vertical profiles of NO₃ ^–, NO₂ ^–, o-P, NH₄ ⁺ and Si in the soft bottom sediments. The profiles were compared with nutrient flux and denitrification measurements. In the Gulf of Finland, the profiles revealed a marked chemical zonation in NO₃ ^– and NO₂ ^– distribution indicating strong potential of nitrification just under the sediment surface followed by a layer of denitrification down to a depth of 30 mm. Below the depth of 20 mm NO₃ ^– was usually absent, whereas other nutrients were increasing steadily in concentration. A distinct minimum of NO₃ ^– was observed at the sediment–water interface, suggesting NO₃ ^– uptake by a microbial biofilm and/or active denitrification at the suboxic microniches usually present in organic-rich sediments. At the deep stations in the Baltic Proper, the NO₃ ^– concentration in pore water, as well as denitrification, were very low. The concentrations of NH₄ ⁺, o-P and Si were usually increasing steadily with depth.     

Nutrient cycling in shallow,oligotrophic Lake Kvie,Denmark

The importance of isoetids for the exchange of dissolved inorganic nitrogen (DIN) between sediment and water was studied in shallow Lake Kvie, Denmark. Vegetated sediments from the littoral zone (55% of lake area) were compared to unvegetated sediments from the littoral and profundal zone. Clear effects of the isoetids were found on DIN in the porewater. At the vegetated station, NH₄ ⁺ showed the highest concentrations just below the surface (< 40 µM) whereas NO₃ ^- was dominating below 5 cm depth with concentrations up to 100 µM during the spring. The unvegetated littoral sediment showed a distinct change between winter where NH₄ ⁺ dominated and summer where NO₃ ^- was most abundant. NH₄ ⁺ dominated in the profundal sediment and showed increasing concentration with depth. The E_h was high (> 400 mV) in the vegetated sediment, indicating isoetid release of O₂ in the rhizosphere. A low DIN uptake was observed at the vegetated station while, based on porewater data, a diffusive release from the sediment was expected. This difference was due to plant assimilation. In general a release of NH₄ ⁺ and an uptake of NO₃ ^- was seen in all sediments. The denitrification rate calculated from the mass balance for the entire lake was 0.4 mmol m - 2 d^-1 and accounted for removal of 77% of the annual N-input to Lake Kvie.     

The influence of an invasive plant on denitrification in an urban wetland

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Microphytobenthos activity and fluxes at the sediment-water interface: interactions and spatial variability

In this study oxygen and nutrient fluxes and denitrification rates across the sediment-water interface were measured via intact core incubations with a twofold aim: show whether microphytobenthos activity affects these processes and analyse the dispersion of replicate measurements. Eighteen intact sediment cores (i.d. 8 cm) were randomly sampled from a shallow microtidal brackish pond at Tjarno, on the west coast of Sweden, and were incubated in light and in darkness simulating in situ conditions. During incubation O₂, inorganic N and SiO₂ fluxes and denitrification rates (isotope pairing) were measured. Assuming mean values of 18 cores as best estimate of true average (BEA), the accuracy of O₂, NH₄ ⁺, NO₃ ^- and SiO₂ fluxes calculated for an increasing number of subsamples was tested. At the investigated site, microalgae strongly influenced benthic O₂, inorganic N and SiO₂ fluxes and coupled (D_n) and uncoupled (D_w) denitrification through their photosynthetic activity. In the shift between dark and light conditions NH₄ ⁺ and SiO₂ effluxes (60 and 110 µmol m^-2h^-1) and D_n (5 µmol m^-2 h^-1) dropped to zero, NO₃ ^- uptake (70 µmol m^-2 h^-1) showed a 30% increase, while D_w (20 µmol m^-2 h^-1) showed an 80% decrease. For O₂ and NO₃ ^- dark fluxes, 4 core replicates were sufficient to obtain averages within 5-10% of the best estimated mean, while 10-20% accuracy was obtained with 4-12 replicates for SiO₂ and >10 replicates for NH₄ ⁺ dark fluxes. Mean accuracy was considerably lower for all light incubations, probably due to the patchy distribution of the benthic microalgal community.     

Linkages between organic matter mineralization and denitrification in eight riparian wetlands

Denitrification (N₂ production) and oxygen consumption rates were measured at ambient field nitrate concentrations during summer in sediments from eight wetlands (mixed hardwood swamps, cedar swamps, heath dominated shrub wetland, herbaceous peatland, and a wetland lacking live vegetation) and two streams. The study sites included wetlands in undisturbed watersheds and in watersheds with considerable agricultural and/or sewage treatment effluent input. Denitrification rates measured in intact cores of water-saturated sediment ranged from 20 to 260 mol N m^-2 h^-1 among the three undisturbed wetlands and were less variable (180 to 260 mol N M^-2 h^-1) among the four disturbed wetlands. Denitrification rates increased when nitrate concentrations in the overlying water were increased experimentally (1 up to 770 M), indicating that nitrate was an important factor controlling denitrification rates. However, rates of nitrate uptake from the overlying water were not a good predictor of denitrification rates because nitrification in the sediments also supplied nitrate for denitrification. Regardless of the dominant vegetation, pH, or degree of disturbance, denitrification rates were best correlated with sediment oxygen consumption rates (r ² = 0.912) indicating a relationship between denitrification and organic matter mineralization and/or sediment nitrification rates. Rates of denitrification in the wetland sediments were similar to those in adjacent stream sediments. Rates of denitrification in these wetlands were within the range of rates previously reported for water-saturated wetland sediments and flooded soils using whole core¹⁵N techniques that quantify coupled nitrification/denitrification, and were higher than rates reported from aerobic (non-saturated) wetland sediments using acetylene block methods.     

Microphytobenthos and chironomid larvae attenuate nutrient recycling in shallow‐water sediments

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