Benthic nitrate removal capacity in marine mangroves of Guadeloupe, Lesser Antilles.

Mangrove sediments are known to be potentially active reducing zones for nitrogen removal. The goal of this work was to investigate the potential for nitrate reduction in marine mangrove sediments along a canal impacted by anthropogenic activity (Guadeloupe, Lesser Antilles). To this end, the effect of nitrate concentration, organic carbon load, and hydraulic retention time was assessed as factors affecting these nitrate reduction rates. Nitrate reduction potential was determined using flow-through reactors in marine mangrove sediments collected along "The Canal des Rotours" in Guadeloupe. Potential nitrate reduction rates, in the presence of indigenous organic carbon, generally increased upon increasing nitrate supply from around 120 nmol cm-3 h-1 (low nitrate) up to 378 nmol cm-3 h-1 (high nitrate). The potential for nitrate reduction increased significantly with the addition of mangrove leaves, whereas the addition of simple, easily degradable carbon (acetate) resulted in an almost fivefold increase in nitrate reduction rates (up to 748 nmol cm-3  h-1 ). The hydraulic retention time also had an impact on the nitrate reducing capacity due to an increased contact time between nitrate and the benthic microbial community. Marine mangrove sediments have a high potential to mitigate nitrogen pollution, mainly governed by the presence of large amounts of degradable carbon in the form of litter. The mangrove sediments from this Caribbean island, currently exposed to a small tidal effect, could increase their nitrate elimination capacities due to prolonged water retention via engineering.

Fate and transport of tetracycline and ciprofloxacin and impact on nitrate reduction activity in coastal sediments from the Seine Estuary, France.

Fluoroquinolones and tetracyclines are frequently detected antibiotics in aquatic sediments. In this study, the transport of ciprofloxacin (CIP) and tetracycline (TET) was investigated in sediments from the Seine Estuary (France), under nitrate reducing conditions. Dynamic flow experiments showed that although TET and CIP strongly interacted with the sediment components through adsorption and (bio)-chemical transformation, they kept their antimicrobial activities. Less nitrate reduction was observed during the first period of breakthrough, while TET and CIP were absent in the column effluent. Batch experiments with freeze-dried vs fresh sediments showed that adsorption and abiotic degradation are the major removal processes, while microbe-driven transformation is of less importance. Whereas TET is to a large extent chemically transformed and little adsorbed in the sediment, CIP was less transformed and more adsorbed, most likely due to the great reactivity of TET with redox-active mineral surfaces. Our findings show the strong capacity of natural sediment to retain and transform antibiotics, while still maintaining their antimicrobial activity or inhibitory effect of nitrate reducing activity.

What do we need to predict groundwater nitrate recovery trajectories?

Nitrate contamination affects many of the Earth's aquifers and surface waters. Large-scale predictions of groundwater nitrate trends normally require the characterization of multiple anthropic and natural factors. To assess different approaches for upscaling estimates of nitrate recovery, we tested the influence of hydrological, historical, and biological factors on predictions of future nitrate concentration in aquifers. We tested the factors with a rich hydrogeological dataset from a fractured bedrock catchment in western France (Brittany). A sensitivity analysis performed on a calibrated model of groundwater flow, denitrification, and nitrogen inputs revealed that trends in nitrate concentration can effectively be approximated with a limited number of key parameters. The total mass of nitrate that entered the aquifer since the beginning of the industrial period needs to be characterized, but the shape of the historical nitrogen input time series can be largely simplified without substantially altering the predictions. Aquifer flow and transport processes can be represented by the mean and standard deviation of the residence time distribution, offering a tractable tool to make reasonable predictions at watershed to regional scales. Apparent sensitivity to denitrification rate was primarily attributable to time lags in oxygen depletion, meaning that denitrification can be simplified to an on/off process, defined only by the time needed for nitrate to reach the hypoxic reactive layer. Obtaining these key parameters at large scales is still challenging with currently available information, but the results are promising regarding our future ability to predict nitrate concentration with integrated monitoring and modeling approaches.

Controls on the Isotopic Composition of Nitrite (δ15N and δ18O) during Denitrification in Freshwater Sediments.

The microbial reduction of nitrate, via nitrite into gaseous di-nitrogen (denitrification) plays a major role in nitrogen removal from aquatic ecosystems. Natural abundance stable isotope measurements can reveal insights into the dynamics of production and consumption of nitrite during denitrification. In this study, batch experiments with environmental bacterial communities were used to investigate variations of concentrations and isotope compositions of both nitrite and nitrate under anoxic conditions. To this end, denitrification experiments were carried out with nitrite or nitrate as sole electron acceptors at two substrate levels respectively. For experiments with nitrate as substrate, where the intermediate compound nitrite is both substrate and product of denitrification, calculations of the extent of isotope fractionation were conducted using a non-steady state model capable of tracing chemical and isotope kinetics during denitrification. This study showed that nitrogen isotope fractionation was lower during the use of nitrite as substrate (ε = -4.2 and -4.5‰ for both treatments) as compared to experiments where nitrite was produced as an intermediate during nitrate reduction (ε = -10 and -15‰ for both treatments). This discrepancy might be due to isotopic fractionation within the membrane of denitrifiers. Moreover, our results confirmed previously observed rapid biotic oxygen isotope exchange between nitrite and water.

Stratification of reactivity determines nitrate removal in groundwater.

Biogeochemical reactions occur unevenly in space and time, but this heterogeneity is often simplified as a linear average due to sparse data, especially in subsurface environments where access is limited. For example, little is known about the spatial variability of groundwater denitrification, an important process in removing nitrate originating from agriculture and land use conversion. Information about the rate, arrangement, and extent of denitrification is needed to determine sustainable limits of human activity and to predict recovery time frames. Here, we developed and validated a method for inferring the spatial organization of sequential biogeochemical reactions in an aquifer in France. We applied it to five other aquifers in different geological settings located in the United States and compared results among 44 locations across the six aquifers to assess the generality of reactivity trends. Of the sampling locations, 79% showed pronounced increases of reactivity with depth. This suggests that previous estimates of denitrification have underestimated the capacity of deep aquifers to remove nitrate, while overestimating nitrate removal in shallow flow paths. Oxygen and nitrate reduction likely increases with depth because there is relatively little organic carbon in agricultural soils and because excess nitrate input has depleted solid phase electron donors near the surface. Our findings explain the long-standing conundrum of why apparent reaction rates of oxygen in aquifers are typically smaller than those of nitrate, which is energetically less favorable. This stratified reactivity framework is promising for mapping vertical reactivity trends in aquifers, generating new understanding of subsurface ecosystems and their capacity to remove contaminants.

Benthic nitrite exchanges in the Seine River (France): An early diagenetic modeling analysis.

Nitrite is a toxic intermediate compound in the nitrogen (N) cycle. Elevated concentrations of nitrite have been observed in the Seine River, raising questions about its sources and fate. Here, we assess the role of bottom sediments as potential sources or sinks of nitrite along the river continuum. Sediment cores were collected from two depocenters, one located upstream, the other downstream, from the largest wastewater treatment plant (WWTP) servicing the conurbation of Paris. Pore water profiles of oxygen, nitrate, nitrite and ammonium were measured. Ammonium, nitrate and nitrite fluxes across the sediment-water interface (SWI) were determined in separate core incubation experiments. The data were interpreted with a one-dimensional, multi-component reactive transport model, which accounts for the production and consumption of nitrite through nitrification, denitrification, anammox and dissimilatory nitrate reduction to ammonium (DNRA). In all core incubation experiments, nitrate uptake by the sediments was observed, indicative of high rates of denitrification. In contrast, for both sampling locations, the sediments in cores collected in August 2012 acted as sinks for nitrite, but those collected in October 2013 released nitrite to the overlying water. The model results suggest that the first step of nitrification generated most pore water nitrite at the two locations. While nitrification was also the main pathway consuming nitrite in the sediments upstream of the WWTP, anammox dominated nitrite removal at the downstream site. Sensitivity analyses indicated that the magnitude and direction of the benthic nitrite fluxes most strongly depend on bottom water oxygenation and the deposition flux of labile organic matter.

Do antibiotics have environmental side-effects? Impact of synthetic antibiotics on biogeochemical processes.

Antibiotic use in the early 1900 vastly improved human health but at the same time started an arms race of antibiotic resistance. The widespread use of antibiotics has resulted in ubiquitous trace concentrations of many antibiotics in most environments. Little is known about the impact of these antibiotics on microbial processes or "non-target" organisms. This mini-review summarizes our knowledge of the effect of synthetically produced antibiotics on microorganisms involved in biogeochemical cycling. We found only 31 articles that dealt with the effects of antibiotics on such processes in soil, sediment, or freshwater. We compare the processes, antibiotics, concentration range, source, environment, and experimental approach of these studies. Examining the effects of antibiotics on biogeochemical processes should involve environmentally relevant concentrations (instead of therapeutic), chronic exposure (versus acute), and monitoring of the administered antibiotics. Furthermore, the lack of standardized tests hinders generalizations regarding the effects of antibiotics on biogeochemical processes. We investigated the effects of antibiotics on biogeochemical N cycling, specifically nitrification, denitrification, and anammox. We found that environmentally relevant concentrations of fluoroquinolones and sulfonamides could partially inhibit denitrification. So far, the only documented effects of antibiotic inhibitions were at therapeutic doses on anammox activities. The most studied and inhibited was nitrification (25-100 %) mainly at therapeutic doses and rarely environmentally relevant. We recommend that firm conclusions regarding inhibition of antibiotics at environmentally relevant concentrations remain difficult due to the lack of studies testing low concentrations at chronic exposure. There is thus a need to test the effects of these environmental concentrations on biogeochemical processes to further establish the possible effects on ecosystem functioning.

Nitrate ammonification in mangrove soils: a hidden source of nitrite?

Nitrate reduction is considered to be a minor microbial pathway in the oxidation of mangrove-derived organic matter due to a limited supply of nitrate in mangrove soils. At a limited availability of this electron acceptor compared to the supply of degradable carbon, nitrate ammonification is thought to be the preferential pathway of nitrate reduction. Mangrove forest mutually differ in their productivity, which may lead to different available carbon to nitrate ratios in their soil. Hence, nitrate ammonification is expected to be of more importance in high- compared to low-productive forests. The hypothesis was tested in flow-through reactors that contain undisturbed mangrove soils from high-productive Avicennia germinans and Rhizophora mangle forests in Florida and low-productive Avicennia marina forests in Saudi Arabia. Nitrate was undetectable in the soils from both regions. It was assumed that a legacy of nitrate ammonification would be reflected by a higher ammonium production from these soils upon the addition of nitrate. Unexpectedly, the soils from the low-productive forests in Saudi Arabia produced considerably more ammonium than the soils from the high-productive forests in Florida. Hence, other environmental factors than productivity must govern the selection of nitrate ammonification or denitrification. A rather intriguing observation was the 1:1 production of nitrite and ammonium during the consumption of nitrate, more or less independent from sampling region, location, sampling depth, mangrove species and from the absence or presence of additional degradable carbon. This 1:1 ratio points to a coupled production of ammonium and nitrite by one group of nitrate-reducing microorganisms. Such a production of nitrite will be hidden by the presence of active nitrite-reducing microorganisms under the nitrate-limited conditions of most mangrove forest soils.

Modelling the fate of nitrite in an urbanized river using experimentally obtained nitrifier growth parameters.

Maintaining low nitrite concentrations in aquatic systems is a major issue for stakeholders due to nitrite's high toxicity for living species. This study reports on a cost-effective and realistic approach to study nitrite dynamics and improve its modelling in human-impacted river systems. The implementation of different nitrifying biomasses to model riverine communities and waste water treatment plant (WWTP)-related communities enabled us to assess the impact of a major WWTP effluent on in-river nitrification dynamics. The optimal kinetic parameters and biomasses of the different nitrifying communities were determined and validated by coupling laboratory experiments and modelling. This approach was carried out in the Seine River, as an example of a large human-impacted river with high nitrite concentrations. The simulation of nitrite fate was performed at a high spatial and temporal resolution (Δt = 10 min, dx¯ = 500 m) including water and sediment layers along a 220 km stretch of the Seine River for a 6-year period (2007-2012). The model outputs were in good agreement with the peak of nitrite downstream the WWTP as well as its slow decrease towards the estuary. Nitrite persistence between the WWTP and the estuary was mostly explained by similar production and consumption rates of nitrite in both water and sediment layers. The sediment layer constituted a significant source of nitrite, especially during high river discharges (0.1-0.4 mgN h(-1) m(-2)). This points out how essential it is to represent the benthic layer in river water quality models, since it can constitute a source of nitrite to the water-column. As a consequence of anthropogenic emissions and in-river processes, nitrite fluxes to the estuary were significant and varied from 4.1 to 5.5 TN d(-1) in low and high water discharge conditions, respectively, over the 2007-2012 period. This study provides a methodology that can be applied to any anthropized river to realistically parametrize autochthonous and WWTP-related nitrifier communities and simulate nitrite dynamics. Based on simulation analysis, it is shown that high spatio-temporal resolution hydro-ecological models are efficient to 1) estimate water quality criteria and 2) forecast the effect of future management strategies. Process-based simulations constitute essential tools to complete our understanding of nutrient cycling, and to decrease monitoring costs in the context of water quality and eutrophication management in river ecosystems.

Nitrite accumulation during denitrification depends on the carbon quality and quantity in wastewater treatment with biofilters.

This study aims to understand the mechanisms of nitrite appearance during wastewater denitrification by biofilters, focusing on the role of the carbon source. Experiments were carried out at lab-scale (batch tests) and full-scale plant (Parisian plant, capacities of 240,000 m(3) day(-1)). Results showed that the nature of the carbon source affects nitrite accumulation rates. This accumulation is low, 0.05 to 0.10 g N-NO2(-) per g N-NO3(-) eliminated, for alcohols such as methanol, ethanol, or glycerol. The utilization of glycerol leads to fungal development causing clogging of the biofilters. This fungal growth and consequent clogging exclude this carbon source, with little nitrite accumulation, as carbon source for denitrification. Whatever the carbon source, the C/N ratio in the biofilter plays a major role in the appearance of residual nitrite; an optimal C/N ratio from 3.0 to 3.2 allows a complete denitrification without any nitrite accumulation.

Exposure to vancomycin causes a shift in the microbial community structure without affecting nitrate reduction rates in river sediments.

Antibiotics and antibiotic resistance genes have shown to be omnipresent in the environment. In this study, we investigated the effect of vancomycin (VA) on denitrifying bacteria in river sediments of a Waste Water Treatment Plant, receiving both domestic and hospital waste. We exposed these sediments continuously in flow-through reactors to different VA concentrations under denitrifying conditions (nitrate addition and anoxia) in order to determine potential nitrate reduction rates and changes in sedimentary microbial community structures. The presence of VA had no effect on sedimentary nitrate reduction rates at environmental concentrations, whereas a change in bacterial (16S rDNA) and denitrifying (nosZ) community structures was observed (determined by polymerase chain reaction-denaturing gradient gel electrophoresis). The bacterial and denitrifying community structure within the sediment changed upon VA exposure indicating a selection of a non-susceptible VA population.

Nitrite reduction by biogenic hydroxycarbonate green rusts: evidence for hydroxy-nitrite green rust formation as an intermediate reaction product.

The present study investigates for the first time the reduction of nitrite by biogenic hydroxycarbonate green rusts, bio-GR(CO3), produced from the bioreduction of ferric oxyhydroxycarbonate (Fohc), a poorly crystalline solid phase, and of lepidocrocite, a well-crystallized Fe(III)-oxyhydroxide mineral. Results show a fast Fe(II) production from Fohc, which leads to the precipitation of bio-GR(CO3) particles that were roughly 2-fold smaller (2.3 ± 0.4 µm) than those obtained from the bioreduction of lepidocrocite (5.0 ± 0.4 µm). The study reveals that both bio-GR(CO3) are capable of reducing nitrite ions into gaseous nitrogen species such as NO, N2O, or N2 without ammonium production at neutral initial pH and that nitrite reduction proceeded to a larger extent with smaller particles than with larger ones. On the basis of the identification of intermediates and end-reaction products using X-ray diffraction and X-ray absorption fine structure (XAFS) spectroscopy at the Fe K-edge, our study shows the formation of hydroxy-nitrite green rust, GR(NO2), a new type of green rust 1, and suggests that the reduction of nitrite by biogenic GR(CO3) involves both external and internal reaction sites and that such a mechanism could explain the higher reactivity of green rust with respect to nitrite, compared to other mineral substrates possessing only external reactive sites.

Chronic exposure of river sediments to environmentally relevant levels of tetracycline affects bacterial communities but not denitrification rates.

The effects of tetracycline (TC) at chronic sub-inhibitory exposure concentrations on benthic denitrification rates and bacterial communities were explored. River sediments were continuously exposed to different TC concentrations (0.5, 20 and 10,000 µg L(-1)) for 2 weeks in flow-through reactors allowing denitrification and bacterial growth conditions. Bacterial communities were fingerprinted by Denaturing Gradient Gel Electrophoresis of 16S rRNA gene amplification products. Cultivable denitrifiers enriched from the sediment were tested for TC resistance (2-128 mg L(-1)). Denitrification rates were unaffected by exposure to TC, regardless of concentration. In contrast, the bacterial community composition changed significantly from sub-inhibitory (ng-µg L(-1)) to therapeutic (mg L(-1)) exposure concentrations. Furthermore the cultivable denitrifiers showed a high TC sensitivity (<4 mg L(-1)). Maintenance of efficient benthic denitrification rates, even at the highest level of TC exposure most likely originated from an adaptation of the autochthonous bacterial community where dominant species become those that acquire, or already have resistance to antibiotics.

The effect of environmental and therapeutic concentrations of antibiotics on nitrate reduction rates in river sediment.

The use of antibiotics in both human and veterinary medicine has led to increased presence of these compounds and antibiotic resistance in the environment. In this study, the effect of low, environmentally relevant (mg L(-1)) concentrations of vancomycin (VA), flumequine (FLU), and sulfamethoxazole (SMX) on nitrate reduction rates was studied in river sediments. Nitrate reduction rates were determined by supplying intact sediments for several weeks with both nitrate and antibiotics (ng L(-1), µg L(-1), and mg L(-1) concentrations), including a non-amended control. Furthermore the concentrations of the three investigated antibiotics were measured in the initial (natural) sediments and the sediments supplied with the antibiotics. The antibiotic concentrations in the sediments decreased (on average 62% for FLU and 93% for SMX) during the experiments, indicating loss of antibiotics due to sorption or (bio) degradation. Nitrate reduction rates were not affected by environmental concentrations of VA, FLU and SMX. FLU and SMX only partially inhibited nitrate reduction rates at high, therapeutic concentrations by 41 and 39% respectively. The three tested antibiotics significantly enhanced the production of nitrite, an intermediate in dissimilatory nitrate reduction. Nitrite production increased 1.9 and 1.4 fold for environmental VA concentrations (107 and 187 µg L(-1) respectively), application of 58 mg L(-1) SMX resulted in a 7.5 fold increase and augmented 16 and 8.5 fold in the presence of respectively 13 µg L(-1) and 52 mg L(-1) FLU. Even though inhibition of nitrate reduction rates was observed at therapeutic antibiotic concentrations, nitrate reduction proceeded under all experimental conditions, indicating the presence of resistance toward these antibiotics among the nitrate reducing bacteria. The accumulation of nitrite suggests that the nitrite reduction step was more affected than the overall nitrate reduction process.

Environmental controls on nitrogen and sulfur cycles in surficial aquatic sediments.

Enhanced anthropogenic inputs of nitrogen (N) and sulfur (S) have disturbed their biogeochemical cycling in aquatic and terrestrial ecosystems. The N and S cycles interact with one another through competition for labile forms of organic carbon between nitrate-reducing and sulfate-reducing bacteria. Furthermore, the N and S cycles could interact through nitrate [Formula: see text] reduction coupled to S oxidation, consuming [Formula: see text] and producing sulfate [Formula: see text] The research questions of this study were: (1) what are the environmental factors explaining variability in N and S biogeochemical reaction rates in a wide range of surficial aquatic sediments when [Formula: see text] and [Formula: see text] are present separately or simultaneously, (2) how the N and S cycles could interact through S oxidation coupled to [Formula: see text] reduction, and (3) what is the extent of sulfate reduction inhibition by nitrate, and vice versa. The N and S biogeochemical reaction rates were measured on intact surface sediment slices using flow-through reactors. The two terminal electron acceptors [Formula: see text] and [Formula: see text] were added either separately or simultaneously and [Formula: see text] and [Formula: see text] reduction rates as well as [Formula: see text] reduction linked to S oxidation were determined. We used redundancy analysis, to assess how environmental variables were related to these rates. Our analysis showed that overlying water pH and salinity were two dominant environmental factors that explain 58% of the variance in the N and S biogeochemical reaction rates when [Formula: see text] and [Formula: see text] were both present. When [Formula: see text] and [Formula: see text] were added separately, however, sediment N content in addition to pH and salinity accounted for 62% of total variance of the biogeochemical reaction rates. The [Formula: see text] addition had little effect on [Formula: see text] reduction; neither did the [Formula: see text] addition inhibit [Formula: see text] reduction. The presence of [Formula: see text] led to [Formula: see text] production most likely due to the oxidation of sulfur. Our observations suggest that metal-bound S, instead of free sulfide produced by [Formula: see text] reduction, was responsible for the S oxidation.

Potential denitrification and nitrous oxide production in the sediments of the Seine River Drainage Network (France).

To investigate bottom sediment denitrification at the scale of the Seine drainage network, a semi-potential denitrification assay was used in which river sediments (and riparian soils) were incubated for a few hours under anaerobic conditions with non limiting nitrate concentrations. This method allowed the nitrous oxide (N(2)O) concentration in the headspace, as well as the nitrate, nitrite, and ammonium concentrations to be determined during incubation. The rates at which nitrate decreased and N(2)O increased were then used to assess the potential denitrification activity and associated N(2)O production in the Seine River Basin. We observed a longitudinal pattern characterized by a significant increase of the potential rate of denitrification from upstream sectors to large downstream rivers (orders 7-8), from approximately 3.3 to 9.1 microg NO(3)(-)-N g(-1) h(-1), respectively, while the N(2)O production rates was the highest both in headwaters and in large order rivers (0.14 and 0.09 N(2)O-N g(-1) h(-1), respectively) and significantly lower in the intermediate sectors (0.01 and 0.03 N(2)O-N g(-1) h(-1)). Consequently, the ratio N(2)O production:NO(3) reduction was found to reach 5% in headstreams, whereas it averaged 1.2% in the rest of the drainage network, an intermediate percentage being found for the riparian soils. Finally, the ignition loss of sediments, together with other redundant variables (particulate organic carbon content: g C 100 g(-1) dry weight [dw], moisture: g water 100 g(-1) dw, sediment size <50 mum: g material size <50 mum 100 g(-1) dw) were found to control these activities. However, the biodegradability of organic matter must be measured to better understand the factor controlling denitrification and its associated N(2)O production.

Nitrous oxide production kinetics during nitrate reduction in river sediments.

A significant amount of nitrogen entering river basins is denitrified in riparian zones. The aim of this study was to evaluate the influence of nitrate and carbon concentrations on the kinetic parameters of nitrate reduction as well as nitrous oxide emissions in river sediments in a tributary of the Marne (the Seine basin, France). In order to determine these rates, we used flow-through reactors (FTRs) and slurry incubations; flow-through reactors allow determination of rates on intact sediment slices under controlled conditions compared to sediment homogenization in the often used slurry technique. Maximum nitrate reduction rates (R(m)) ranged between 3.0 and 7.1microg Ng(-1)h(-1), and affinity constant (K(m)) ranged from 7.4 to 30.7mg N-NO(3)(-)L(-1). These values were higher in slurry incubations with an R(m) of 37.9microg Ng(-1)h(-1) and a K(m) of 104mg N-NO(3)(-)L(-1). Nitrous oxide production rates did not follow Michaelis-Menten kinetics, and we deduced a rate constant with an average of 0.7 and 5.4ng Ng(-1)h(-1) for FTR and slurry experiments respectively. The addition of carbon (as acetate) showed that carbon was not limiting nitrate reduction rates in these sediments. Similar rates were obtained for FTR and slurries with carbon addition, confirming the hypothesis that homogenization increases rates due to release of and increasing access to carbon in slurries. Nitrous oxide production rates in FTR with carbon additions were low and represented less than 0.01% of the nitrate reduction rates and were even negligible in slurries. Maximum nitrate reduction rates revealed seasonality with high potential rates in fall and winter and low rates in late spring and summer. Under optimal conditions (anoxia, non-limiting nitrate and carbon), nitrous oxide emission rates were low, but significant (0.01% of the nitrate reduction rates).

Comparison of deep-sea sediment microbial communities in the Eastern Mediterranean.

Bacterial and archaeal communities in sediments obtained from three geographically-distant mud volcanoes, a control site and a microbial mat in the Eastern Mediterranean deep-sea were characterized using direct 16S rRNA gene analyses. The data were thus in relation to the chemical characteristics of the (stratified) habitats to infer community structure-habitat relationships. The bacterial sequences in the different habitats were related to those of Actinobacteria, Bacilli, Chloroflexi, Alpha-, Beta-, Gamma-, Delta- and Epsilonproteobacteria and unclassified bacteria, including the JS1 group. The archaeal sequences found were affiliated with those of the Methanosarcinales, Thermoplasmales, Halobacteriales and Crenarchaea belonging to marine benthic group I and B, as well as MCG group archaea. In each sample, the communities were diverse and unique at the phylotype level. However, at higher taxonomic levels, similar groups were found in different sediments, and similar depth layers tended to contain similar communities. The sequences that dominated in all top layers (as well as in the mat) probably represented organisms involved in aerobic heterotrophy, sulfide-based chemoautotrophy and methanotrophy and/or methylotrophy. Sequences of organisms most likely involved in anaerobic methane oxidation, sulfate reduction and anaerobic heterotrophy were predominantly found in deeper layers. The data supported the notion of (1) uniqueness of each habitat at fine taxonomic levels, (2) stratification in depth and (3) conservation of function in the sediments.

Potential nitrate removal in a coastal freshwater sediment (Haringvliet Lake, The Netherlands) and response to salinization.

Nitrogen transformations and their response to salinization were studied in bottom sediment of a coastal freshwater lake (Haringvliet Lake, The Netherlands). The lake was formed as the result of a river impoundment along the south-western coast of the Netherlands, and is currently targeted for restoration of estuarine conditions. Nitrate porewater profiles indicate complete removal of NO(3)(-) within the upper few millimeters of sediment. Rapid NO(3)(-) consumption is consistent with the high potential rates of nitrate reduction (up to 200 nmol N cm(-3) h(-1)) measured with flow-through reactors (FTRs) on intact sediment slices. Acetylene-block FTR experiments indicate that complete denitrification accounts for approximately half of the nitrate reducing activity. The remaining NO(3)(-) reduction is due to incomplete denitrification and alternative reaction pathways, most likely dissimilatory nitrate reduction to NH(4)(+) (DNRA). Results of FTR experiments further indicate that increasing bottom water salinity may lead to a transient release of NH(4)(+) and dissolved organic carbon from the sediment, and enhance the rates of nitrate reduction and nitrite production. Increased salinity may thus, at least temporarily, increase the efflux of NH(4)(+) from the sediment to the surface water. This work shows that salinity affects the relative importance of denitrification compared to alternative nitrate reduction pathways, limiting the ability of denitrification to remove bioavailable nitrogen from aquatic ecosystems.

Vertical distribution of denitrification in an estuarine sediment: integrating sediment flowthrough reactor experiments and microprofiling via reactive transport modeling.

Denitrifying activity in a sediment from the freshwater part of a polluted estuary in northwest Europe was quantified using two independent approaches. High-resolution N(2)O microprofiles were recorded in sediment cores to which acetylene was added to the overlying water and injected laterally into the sediment. The vertical distribution of the rate of denitrification supported by nitrate uptake from the overlying water was then derived from the time series N(2)O concentration profiles. The rates obtained for the core incubations were compared to the rates predicted by a forward reactive transport model, which included rate expression for denitrification calibrated with potential rate measurements obtained in flowthrough reactors containing undisturbed, 1-cm-thick sediment slices. The two approaches yielded comparable rate profiles, with a near-surface, 2- to 3-mm narrow zone of denitrification and maximum in situ rates on the order of 200 to 300 nmol cm(-3) h(-1). The maximum in situ rates were about twofold lower than the maximum potential rate for the 0- to 1-cm depth interval of the sediment, indicating that in situ denitrification was nitrate limited. The experimentally and model-derived rates of denitrification implied that there was nitrate uptake by the sediment at a rate that was on the order of 50 (+/- 10) nmol cm(-2) h(-1), which agreed well with direct nitrate flux measurements for core incubations. Reactive transport model calculations showed that benthic uptake of nitrate at the site is particularly sensitive to the nitrate concentration in the overlying water and the maximum potential rate of denitrification in the sediment.