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

Coupling between sediment biogeochemistry and phytoplankton development in a temperate freshwater marsh (Charente-Maritime, France): Evidence of temporal pattern

In freshwater systems, sediment can be an important source for the internal loading of PO₄. The limiting character of this element in such system leads to consider this phenomenon in terms of eutrophication risks and water quality stakes. A four-months follow-up (January, March, April and May 2019) was carried out in a strong phosphate (PO₄) limited secondary channel from an artificial irrigation system of Charente Maritime (France) to link the mobilization of remineralization products in the upper 6 cm layer of sediment (conventional core slicing/centrifugation and DET probes) and the phytoplankton biomass dynamics in the water column. Results showed congruent patterns between the temporal succession of the organic matter mineralization processes in the sediment and the primary biomass dynamics in the water column. In January and March (considered in winter), PO₄ proved to be retained by adsorption onto iron oxides in anoxic sediment since pore water nitrate inhibited for about a month the respiration of metal oxides in the first cm of sediment, thus limiting PO₄ availability and the phytoplankton growth. In April and May (early spring), after exhaustion of pore water nitrate, the dissolutive reduction of iron oxides released PO₄ into pore water generated a significant diffusive outgoing flux from the sediment to the water column with a maximum in April (-1.10E-04±2.81E-05 nmol cm^-2 s^-1). This release coincided with the nanophytoplankton bloom (5.50 µg Chla L^-1) and a potential increase of PO₄ concentration in the water column. This work provides some insight on the importance of benthic-pelagic coupling in anthropogenic systems. This conceptual model has to be deployed on other sites of interest where internal loading of P takes precedence over external inputs and nitrate mitigation drives its benthic recycling and ultimately its bioavailability. This is to be essential to characterize the aquatic environment quality in order to limit eutrophication risks.

Biodegradation of MC252 polycyclic aromatic hydrocarbons and alkanes in two coastal wetlands

Complementary microbial and geochemical assessment techniques investigated the biodegradation of PAHs and alkanes in salt marshes impacted by crude oil following the Macondo spill. Contamination was observed in the top 10 cm of the marsh profile based on PAH analysis and measurement of the δ¹³C signature of impacted marsh soils. Measurement of evolution of ¹³C depleted CO₂ indicated mineralization of crude oil ranging from 2.7-12.1 mg CO₂-C/m²-hr. Changes in weathering ratios of alkylated phenanthrenes and dibenzothiophenes indicated loss of these 3-ring PAHs consistent with biodegradation. A diverse microbial population was observed at both locations dominated by Gammaproteobacteria and including known hydrocarbon degraders such as Marinobacter and Alcanivorax. There was shared richness between sites and across seasons but results suggested substantial turnover of phylotypes in space and time. Biodegradation of alkanes and alkylated PAHs occurred when oxygen was provided in laboratory reactors but not in the absence of oxygen.

Calcium carbonate alters the functional response of coastal sediments to eutrophication-induced acidification

Coastal ocean acidification research is dominated by laboratory-based studies that cannot necessarily predict real-world ecosystem response given its complexity. We enriched coastal sediments with increasing quantities of organic matter in the field to identify the effects of eutrophication-induced acidification on benthic structure and function, and assess whether biogenic calcium carbonate (CaCO₃) would alter the response. Along the eutrophication gradient we observed declines in macrofauna biodiversity and impaired benthic net primary productivity and sediment nutrient cycling. CaCO₃ addition did not alter the macrofauna community response, but significantly dampened negative effects on function (e.g. net autotrophy occurred at higher levels of organic matter enrichment in +CaCO₃ treatments than −CaCO₃ (1400 vs 950 g dw m⁻²)). By identifying the links between eutrophication, sediment biogeochemistry and benthic ecosystem structure and function in situ, our study represents a crucial step forward in understanding the ecological effects of coastal acidification and the role of biogenic CaCO₃ in moderating responses.

Perturbation-free measurement of in situ di-nitrogen emissions from denitrification in nitrate-rich aquatic ecosystems

Increased production of reactive nitrogen (Nr) from atmospheric di-nitrogen (N₂) has greatly contributed to increased food production. However, enriching the biosphere with Nr has also caused a series of negative effects on global ecosystems, especially aquatic ecosystems. The main pathway converting Nr back into the atmospheric N₂ pool is the last step in the denitrification process. Despite several attempts, there is still a need for perturbation-free methods for measuring in situ N₂ fluxes from denitrification in aquatic ecosystems at the field scale. Such a method is needed to comprehensively quantify the N₂ fluxes from aquatic ecosystems. Here we observed linear relationships between the δ¹⁵N-N₂O signatures and the logarithmically transformed N₂O/(N₂+N₂O) emission ratios. Through independent measurements, we verified that the perturbation-free N₂ flux from denitrification in nitrate-rich aquatic ecosystems can be inferred from these linear relationships. Our method allowed the determination of field-scale in situ N₂ fluxes from nitrate-rich aquatic ecosystems both with and without overlaying water. The perturbation-free in situ N₂ fluxes observed by the new method were almost one order of magnitude higher than those by the sediment core method. The ability of aquatic ecosystems to remove Nr may previously have been severely underestimated.

High spatial resolution analysis of the distribution of sulfate reduction and sulfide oxidation in hypoxic sediment in a eutrophic estuary

Bottom hypoxia and consequential hydrogen sulfide (H₂S) release from sediment in eutrophic estuaries is a major global environmental issue. We investigated dissolved oxygen, pH and H₂S concentration profiles with microsensors and by sectioning sediment cores followed by colorimetric analysis. The results of these analyses were then compared with the physicochemical properties of the bottom water and sediment samples to determine their relationships with H₂S production in sediment. High organic matter and fine particle composition of the sediment reduced the oxidation-reduction potential, stimulating H₂S production. Use of a microsensor enabled measurement of H₂S concentration profiles with submillimetre resolution, whereas the conventional sediment-sectioning method gave H₂S measurements with a spatial resolution of 10 mm. Furthermore, microsensor measurements revealed H₂S consumption occurring at the sediment surface in both the microbial mat and the sediment anoxic layer, which were not observed with sectioning. This H₂S consumption prevented H₂S release into the overlying water. However, the microsensor measurements had the potential to underestimate H₂S concentrations. We propose that a combination of several techniques to measure microbial activity and determine its relationships with physicochemical properties of the sediment is essential to understanding the sulfur cycle under hypoxic conditions in eutrophic sediments.

Groundwater contamination in coastal urban areas: Anthropogenic pressure and natural attenuation processes. Example of Recife (PE State, NE Brazil)

In a context of increasing land use pressure (over-exploitation, surface-water contamination) and repeated droughts, identifying the processes affecting groundwater quality in coastal megacities of the tropical and arid countries will condition their long-term social and environmental sustainability. The present study focuses on the Brazilian Recife Metropolitan Region (RMR), which is a highly urbanized area (3,743,854 inhabitants in 2010) on the Atlantic coast located next to an estuarial zone and overlying a multi-layered sedimentary system featured by a variable sediment texture and organic content. It investigates the contamination and redox status patterns conditioning potential attenuation within the shallow aquifers that constitute the interface between the city and the strategic deeper semi-confined aquifers. These latter are increasingly exploited, leading to high drawdown in potenciometric levels of 20-30m and up to 70m in some high well density places, and potentially connected to the surface through leakage. From a multi-tracer approach (major ions, major gases, δ(11)B, δ(18)O-SO4, δ(34)S-SO4) carried out during two field campaigns in September 2012 and March 2013 (sampling of 19 wells and 3 surface waters), it has been possible to assess the contamination sources and the redox processes. The increasing trend for mineralization from inland to coastal and estuarial wells (from 119 to around 10,000μS/cm) is at first attributed to water-rock interactions combined with natural and human-induced potentiometric gradients. Secondly, along with this trend, one finds an environmental pressure gradient related to sewage and/or surface-channel network impacts (typically depleted δ(11)B within the range of 10-15‰) that are purveyors of chloride, nitrate, ammonium and sulfate. Nitrate, ammonium and sulfate (ranging from 0 to 1.70mmol/L, from 0 to 0,65mmol/L, from 0.03 to 3.91mmol/L respectively are also potentially produced or consumed through various redox processes (pyrite oxidation, denitrification, dissimilatory nitrate reduction to ammonium) within the system, as is apparent within a patchwork of biogeochemical reactors. Furthermore, intensive pumping in the coastal area with its high well density punctually leads to temporary well salinization ([Cl] reaching temporarily 79mmol/L). Our results, summarized as a conceptual scheme based on environmental conditions, is a suitable basis for implementing sustainable management in coastal sedimentary hydrosystems influenced by highly urbanized conditions.

Nitrous oxide fluxes in estuarine environments: response to global change

Nitrous oxide is a powerful, long-lived greenhouse gas, but we know little about the role of estuarine areas in the global N2 O budget. This review summarizes 56 studies of N2 O fluxes and associated biogeochemical controlling factors in estuarine open waters, salt marshes, mangroves, and intertidal sediments. The majority of in situ N2 O production occurs as a result of sediment denitrification, although the water column contributes N2 O through nitrification in suspended particles. The most important factors controlling N2 O fluxes seem to be dissolved inorganic nitrogen (DIN) and oxygen availability, which in turn are affected by tidal cycles, groundwater inputs, and macrophyte density. The heterogeneity of coastal environments leads to a high variability in observations, but on average estuarine open water, intertidal and vegetated environments are sites of a small positive N2 O flux to the atmosphere (range 0.15-0.91; median 0.31; Tg N2 O-N yr(-1) ). Global changes in macrophyte distribution and anthropogenic nitrogen loading are expected to increase N2 O emissions from estuaries. We estimate that a doubling of current median NO3 (-) concentrations would increase the global estuary water-air N2 O flux by about 0.45 Tg N2 O-N yr(-1) or about 190%. A loss of 50% of mangrove habitat, being converted to unvegetated intertidal area, would result in a net decrease in N2 O emissions of 0.002 Tg N2 O-N yr(-1) . In contrast, conversion of 50% of salt marsh to unvegetated area would result in a net increase of 0.001 Tg N2 O-N yr(-1) . Decreased oxygen concentrations may inhibit production of N2 O by nitrification; however, sediment denitrification and the associated ratio of N2 O:N2 is expected to increase.

Interactions between benthic copepods, bacteria and diatoms promote nitrogen retention in intertidal marine sediments

The present study aims at evaluating the impact of diatoms and copepods on microbial processes mediating nitrate removal in fine-grained intertidal sediments. More specifically, we studied the interactions between copepods, diatoms and bacteria in relation to their effects on nitrate reduction and denitrification. Microcosms containing defaunated marine sediments were subjected to different treatments: an excess of nitrate, copepods, diatoms (Navicula sp.), a combination of copepods and diatoms, and spent medium from copepods. The microcosms were incubated for seven and a half days, after which nutrient concentrations and denitrification potential were measured. Ammonium concentrations were highest in the treatments with copepods or their spent medium, whilst denitrification potential was lowest in these treatments, suggesting that copepods enhance dissimilatory nitrate reduction to ammonium over denitrification. We hypothesize that this is an indirect effect, by providing extra carbon for the bacterial community through the copepods' excretion products, thus changing the C/N ratio in favour of dissimilatory nitrate reduction. Diatoms alone had no effect on the nitrogen fluxes, but they did enhance the effect of copepods, possibly by influencing the quantity and quality of the copepods' excretion products. Our results show that small-scale biological interactions between bacteria, copepods and diatoms can have an important impact on denitrification and hence sediment nitrogen fluxes.

The relationship between anammox and denitrification in the sediment of an inland river

This study measured the microbial processes of anaerobic ammonium oxidation (anammox) and denitrification in sediment sampled from two sites in the estuary of an inland river (Koisegawa River, Ibaragi prefecture, Japan) using a nitrogen isotope pairing technique (IPT). The responses of anammox and denitrification activities to temperature and nitrate concentration were also evaluated. Further, to elucidate the correlation between anammox and denitrification processes, an inhibition experiment was conducted, using chlorate to inhibit the first step of denitrification. Denitrification activity was much higher than anammox activity, and it reached a maximum at the surface layer in February 2012. Denitrification activity decreased as sediment depth increased, and a similar phenomenon was observed for anammox activity in the sediment of site A, where aquatic plants were absent from the surroundings. The activities of both denitrification and anammox were temperature-dependent, but they responded differently to changes in incubation temperature. Compared to a linear increase in denitrification as temperature rose to 35 °C, the optimal temperature for anammox was 25 °C, after which the activity decreased sharply. At the same time, both anammox and denitrification activities increased with NO3(-) concentration. The Michaelis-Menten kinetic constants (Vmax and Km) of denitrification were significantly higher than those of the anammox process. Furthermore, anammox activity decreased accordingly when the first step of denitrification was inhibited, which probably reduced the amount of the intermediate NO2(-). Our study provides the first direct exploration of the denitrification-dependent correlation of anammox activity in the sediment of inland river.

The role of highly sratified nutrient-rich small estuaries as a source of dissolved inorganic nitrogen to coastal seawater, the Qishon (SE Mediterranean) case

We studied the role of small, highly stratified, sulfate and nutrient enriched estuaries, as a source or sink of inorganic nitrogen species, using the Qishon estuary at the Mediterranean coast of Israel, as a case study. Measurements of nutrient concentrations, δ(15)N and δ(18)O of nitrate+nitrite, δ(13)CDIC and δ(18)OH2O were performed during 2008-2009 along the upper-fresh and lower-saline water masses, as well as sediment porewater depth-profiles. Such estuaries are characterized by relatively low removal flux of NO3(-) (via sedimentary denitrification) and enhanced (×3) upward flux of NH4(+) (via sulfate reduction), attributed to the penetration of seawater of low NO3(-) and high dissolved oxygen and sulfate concentrations. The role of such small estuaries in releasing dissolved inorganic nitrogen, especially in sensitive oligotrophic areas as the Levantine basin and in the long-term, as a result of enhanced seawater penetration due to the expected sea level rise, has important environmental policy implications.

Metal-macrofauna interactions determine microbial community structure and function in copper contaminated sediments

Copper is essential for healthy cellular functioning, but this heavy metal quickly becomes toxic when supply exceeds demand. Marine sediments receive widespread and increasing levels of copper contamination from antifouling paints owing to the 2008 global ban of organotin-based products. The toxicity of copper will increase in the coming years as seawater pH decreases and temperature increases. We used a factorial mesocosm experiment to investigate how increasing sediment copper concentrations and the presence of a cosmopolitan bioturbating amphipod, Corophium volutator, affected a range of ecosystem functions in a soft sediment microbial community. The effects of copper on benthic nutrient release, bacterial biomass, microbial community structure and the isotopic composition of individual microbial membrane [phospholipid] fatty acids (PLFAs) all differed in the presence of C. volutator. Our data consistently demonstrate that copper contamination of global waterways will have pervasive effects on the metabolic functioning of benthic communities that cannot be predicted from copper concentrations alone; impacts will depend upon the resident macrofauna and their capacity for bioturbation. This finding poses a major challenge for those attempting to manage the impacts of copper contamination on ecosystem services, e.g. carbon and nutrient cycling, across different habitats. Our work also highlights the paucity of information on the processes that result in isotopic fractionation in natural marine microbial communities. We conclude that the assimilative capacity of benthic microbes will become progressively impaired as copper concentrations increase. These effects will, to an extent, be mitigated by the presence of bioturbating animals and possibly other processes that increase the influx of oxygenated seawater into the sediments. Our findings support the move towards an ecosystem approach for environmental management.

Influence of a burrowing, metal-tolerant polychaete on benthic metabolism, denitrification and nitrogen regeneration in contaminated estuarine sediments

We investigated the effects of the burrowing cirratulid polychaete Cirriformia filigera (Delle Chiaje, 1828) on benthic respiration and nitrogen regeneration in metal-contaminated estuarine sediments using laboratory mesocosms. C. filigera is a dominant component of assemblages in the most severely contaminated sediments within the Derwent estuary, southern Australia. In the presence of C. filigera sediment O2 consumption doubled, with approximately 55% of this increase due to their respiration and the remaining 45% attributable to oxidation reactions and increased microbial respiration associated with burrow walls. Combined NO3 and NO2 fluxes were unaffected. The addition of labile organic matter did not affect benthic fluxes, in the presence or absence of C. filigera, presumably due to the short timeframe of the experiment and naturally enriched test sediments. The results suggest that a combination of tolerance and burrowing activity enables this species to provide an ecosystem service in the removal of N from contaminated sites.

Denitrification and nitrogen fixation dynamics in the area surrounding an individual ghost shrimp (Neotrypaea californiensis) burrow system

Bioturbated sediments are thought of as areas of increased denitrification or fixed-nitrogen (N) loss; however, recent studies have suggested that not all N may be lost from these environments, with some N returning to the system via microbial dinitrogen (N(2)) fixation. We investigated denitrification and N(2) fixation in an intertidal lagoon (Catalina Harbor, CA), an environment characterized by bioturbation by thalassinidean shrimp (Neotrypaea californiensis). Field studies were combined with detailed measurements of denitrification and N(2) fixation surrounding a single ghost shrimp burrow system in a narrow aquarium (15 cm by 20 cm by 5 cm). Simultaneous measurements of both activities were performed on samples taken within a 1.5-cm grid for a two-dimensional illustration of their intensity and distribution. These findings were then compared with rate measurements performed on bulk environmental sediment samples collected from the lagoon. Results for the aquarium indicated that both denitrification and N(2) fixation have a patchy distribution surrounding the burrow, with no clear correlation to each other, sediment depth, or distance from the burrow. Field denitrification rates were, on average, lower in a bioturbated region than in a seemingly nonbioturbated region; however, replicates showed very high variability. A comparison of denitrification field results with previously reported N(2) fixation rates from the same lagoon showed that in the nonbioturbated region, depth-integrated (10 cm) denitrification rates were higher than integrated N(2) fixation rates (∼9 to 50 times). In contrast, in the bioturbated sediments, depending on the year and bioturbation intensity, some (∼6.2%) to all of the N lost via denitrification might be accounted for via N(2) fixation.

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.

Effect of nitrification on nitrogen flux across sediment-water interface

Most studies related to nitrogen flux across the sediment-water interface were focused on the effects of aquatic environment factors on nitrification rates, while there is no information about the effects of nitrification on other factors. In this research, laboratory experiments have been conducted to investigate nitrogen flux from the sediment cores collected from the Three-Gorge Reservoir of the Yangtze River (China). The effects of the nitrification process on the fluxes of ammonium (NH4+), nitrite (NO2-) + nitrate (NO3-), and total organic nitrogen (TON) across the sediment-water interface have been examined. The release flux of TON accounted for more than 50% of the total nitrogen. The nitrification process stimulated the growth of ammonifying bacteria and accelerated the release of NH4+ and NOx- from the sediment cores during the 40-day incubation and TON during the first 10-day incubation. A 25% increase in the nitrification rate increased the release rates of NH4+ and TON by approximately two times during the first 8-day incubation.

Influences of infaunal burrows on the community structure and activity of ammonia-oxidizing bacteria in intertidal sediments

Influences of infaunal burrows constructed by the polychaete (Tylorrhynchus heterochaetus) on O(2) concentrations and community structures and abundances of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in intertidal sediments were analyzed by the combined use of a 16S rRNA gene-based molecular approach and microelectrodes. The microelectrode measurements performed in an experimental system developed in an aquarium showed direct evidence of O(2) transport down to a depth of 350 mm of the sediment through a burrow. The 16S rRNA gene-cloning analysis revealed that the betaproteobacterial AOB communities in the sediment surface and the burrow walls were dominated by Nitrosomonas sp. strain Nm143-like sequences, and most of the clones in Nitrospira-like NOB clone libraries of the sediment surface and the burrow walls were related to the Nitrospira marina lineage. Furthermore, we investigated vertical distributions of AOB and NOB in the infaunal burrow walls and the bulk sediments by real-time quantitative PCR (Q-PCR) assay. The AOB and Nitrospira-like NOB-specific 16S rRNA gene copy numbers in the burrow walls were comparable with those in the sediment surfaces. These numbers in the burrow wall at a depth of 50 to 55 mm from the surface were, however, higher than those in the bulk sediment at the same depth. The microelectrode measurements showed higher NH(4)(+) consumption activity at the burrow wall than those at the surrounding sediment. This result was consistent with the results of microcosm experiments showing that the consumption rates of NH(4)(+) and total inorganic nitrogen increased with increasing infaunal density in the sediment. These results clearly demonstrated that the infaunal burrows stimulated O(2) transport into the sediment in which otherwise reducing conditions prevailed, resulting in development of high NH(4)(+) consumption capacity. Consequently, the infaunal burrow became an important site for NH(4)(+) consumption in the intertidal sediment.

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.

Nitrogen transformations in stratified aquatic microbial ecosystems

New analytical methods such as advanced molecular techniques and microsensors have resulted in new insights about how nitrogen transformations in stratified microbial systems such as sediments and biofilms are regulated at a microm-mm scale. A large and ever-expanding knowledge base about nitrogen fixation, nitrification, denitrification, and dissimilatory reduction of nitrate to ammonium, and about the microorganisms performing the processes, has been produced by use of these techniques. During the last decade the discovery of anammmox bacteria and migrating, nitrate accumulating bacteria performing dissimilatory reduction of nitrate to ammonium have given new dimensions to the understanding of nitrogen cycling in nature, and the occurrence of these organisms and processes in stratified microbial communities will be described in detail.

Community Level Analysis: Genetic and Biogeochemical Approaches to Investigate Community Composition and Function in Aerobic Ammonia Oxidation

Aerobic ammonia oxidation is the process that converts ammonium to nitrate and thus links the regeneration of organic nitrogen to fixed nitrogen loss by denitrification. It is performed by a phylogenetically restricted group of Proteobacteria (ammonia-oxidizing bacteria, AOB) that are autotrophic and obligately aerobic. This chapter describes methods for the measurement of ammonia oxidation in the environment, with a focus on seawater systems and stable isotopic tracer methods. It also summarizes the current state of molecular ecological approaches for detection of AOB in the environment and characterization of the composition of AOB assemblages.

Simultaneous assessment of nitrification and denitrification on freshwater epilithic biofilms by acetylene block method

Acetylene (C2H2) inhibits key enzymes involved in nitrification (Ammonium monooxygenase) and denitrification (N2O reductases). Thus an injection of C2H2 at mid time of a batch type incubation make it possible to assess denitrification by measurement of the N2O accumulation as well as nitrification, calculated from the variations of the ammonium flux. As estimated by the "acetylene block technique", denitrification is known to be only a measure of the denitrification rate supported by nitrate diffusing from the water column (Dw). This paper presents a first application on river epilithic biofilms which proved that the simultaneous measurement of Dw and nitrification allows the estimation of the order of magnitude of total denitrification (Dt) when nitrification is detected in the tested sample. This approach appears to be an easy tool for determination of nitrification and denitrification in natural samples and as thus presents an alternative to isotopic 15N methods.

Ecology of Thioploca spp.: nitrate and sulfur storage in relation to chemical microgradients and influence of Thioploca spp. on the sedimentary nitrogen cycle

Microsensors, including a recently developed NO3(-) biosensor, were applied to measure O(2) and NO3(-) profiles in marine sediments from the upwelling area off central Chile and to investigate the influence of Thioploca spp. on the sedimentary nitrogen metabolism. The studies were performed in undisturbed sediment cores incubated in a small laboratory flume to simulate the environmental conditions of low O(2), high NO3(-), and bottom water current. On addition of NO3(-) and NO2(-), Thioploca spp. exhibited positive chemotaxis and stretched out of the sediment into the flume water. In a core densely populated with Thioploca, the penetration depth of NO3(-) was only 0.5 mm and a sharp maximum of NO3(-) uptake was observed 0.5 mm above the sediment surface. In sediments with only few Thioploca spp., NO3(-) was detectable down to a depth of 2 mm and the maximum consumption rates were observed within the sediment. No chemotaxis toward nitrous oxide (N2O) was observed, which is consistent with the observation that Thioploca does not denitrify but reduces intracellular NO3(-) to NH(4)(+). Measurements of the intracellular NO3(-) and S(0) pools in Thioploca filaments from various depths in the sediment gave insights into possible differences in the migration behavior between the different species. Living filaments containing significant amounts of intracellular NO3(-) were found to a depth of at least 13 cm, providing final proof for the vertical shuttling of Thioploca spp. and nitrate transport into the sediment.

Evaluation of the denitrifying microbiota of anoxic reactors

Removal of inorganic nitrogen compounds from wastewaters can be accomplished by a combination of the biological processes of nitrification and denitrification. The information on the microbiota present in denitrifying reactors is still scarce. In the present work the evaluation of the denitrifying microbiota of different reactor sludges was performed by specific activity measurements and MPN count of denitrifiers. We also present the isolation and physiological and phylogenetic characterisation of denitrifying bacteria from the anoxic reactor of a combined system treating landfill leachate. Specific denitrifying activity measurements were faster to perform and more reliable than MPN enumerations. 16S rDNA characterisation of the isolates showed that they belonged to the genera Thauera, Acidovorax and Alcaligenes and were closely related to microorganisms retrieved from ecosystems rich in recalcitrant compounds. Two of the isolates could grow on aromatic compounds as sole carbon source.

Identification and characterization of ecologically significant prokaryotes in the sediment of freshwater lakes: molecular and cultivation studies

The aim of this review is to interpret recent studies in which molecular methods were used to identify and characterize prokaryotes in lake sediments and related habitats. In the first part studies based on the phylogenetic diversity of prokaryotes found in lacustrine habitats are summarized. The application of various cultivation-independent methods for the characterization of distinct groups of sediment bacteria is exemplified with morphologically conspicuous, colorless sulfur bacteria in the second part of this review. Finally, traditional and recently developed methods are described which could be used for linking the function of microbial populations with their identification. The potential of these approaches for the study of lake sediments is discussed in order to give a perspective for future studies in this habitat.

Nitrogen cycling in coastal marine ecosystems

It is generally considered that nitrogen availability is one of the major factors regulating primary production in temperate coastal marine environments. Coastal regions often receive large anthropogenic inputs of nitrogen that cause eutrophication. The impact of these nitrogen additions has a profound effect in estuaries and coastal lagoons where water exchange is limited. Such increased nutrient loading promotes the growth of phytoplankton and fast growing pelagic macroalgae while rooted plants (sea-grasses) and benthic are suppressed due to reduced light availability. This shift from benthic to pelagic primary production introduces large diurnal variations in oxygen concentrations in the water column. In addition oxygen consumption in the surface sediments increases due to the deposition of readily degradable biomass. In this review the physico-chemical and biological factors regulating nitrogen cycling in coastal marine ecosystems are considered in relation to developing effective management programmes to rehabilitate seagrass communities in lagoons currently dominated by pelagic macroalgae and/or cyanobacteria.

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 O 2 and NO 3 - microsensors. Depth profiles of nitrification (indicated as NO 3 - production), denitrification (indicated as NO 3 - consumption), and O 2 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 NO 3 - from the overlying water and the rate based on NO 3 - supplied by benthic nitrification ( D w and D n , respectively). An increase in O 2 concentration caused a deeper O 2 penetration while a decrease in D w and an increase in D n were observed. The relative importance for total denitrification of NO 3 - produced by nitrification thus increased compared with NO 3 - supplied from the water phase. The decrease in D w at high oxygen was due to an increase in diffusion path for NO 3 - from the overlying water to the denitrifying layers in the anoxic sediment. At high O 2 concentrations, nitrifying activity was restricted to the lower part of the oxic zone where there was a continuous diffusional supply of NH 4 + 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 .

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

Microprofiles of O 2 and NO 3 - were measured simultaneously in freshwater sediment with microsensors which were completely free from electrical interference because of coaxial designs. Depth profiles of nitrification (NO 3 - production) and denitrification (NO 3 - 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 O 2 and NO 3 - were usually approached within a few hours after perturbation. Nitrification started quickly after introduction of O 2 in previously anoxic layers, suggesting prolonged survival of the nitrifiers during anaerobiosis. Changes in the availability of O 2 and NH 4 + 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 C 2 H 2 rapidly removed the NO 3 - peaks, indicating that NO 3 - production was due mainly to autotrophic nitrification.

Selective Inhibition of Ammonium Oxidation and Nitrification-Linked N 2 O Formation by Methyl Fluoride and Dimethyl Ether

Methyl fluoride (CH 3 F) and dimethyl ether (DME) inhibited nitrification in washed-cell suspensions of Nitrosomonas europaea and in a variety of oxygenated soils and sediments. Headspace additions of CH 3 F (10% [vol/vol]) and DME (25% [vol/vol]) fully inhibited NO 2 - and N 2 O production from NH 4 + in incubations of N. europaea , while lower concentrations of these gases resulted in partial inhibition. Oxidation of hydroxylamine (NH 2 OH) by N. europaea and oxidation of NO 2 - by a Nitrobacter sp. were unaffected by CH 3 F or DME. In nitrifying soils, CH 3 F and DME inhibited N 2 O production. In field experiments with surface flux chambers and intact cores, CH 3 F reduced the release of N 2 O from soils to the atmosphere by 20- to 30-fold. Inhibition by CH 3 F also resulted in decreased NO 3 - + NO 2 - levels and increased NH 4 + levels in soils. CH 3 F did not affect patterns of dissimilatory nitrate reduction to ammonia in cell suspensions of a nitrate-respiring bacterium, nor did it affect N 2 O metabolism in denitrifying soils. CH 3 F and DME will be useful in discriminating N 2 O production via nitrification and denitrification when both processes occur and in decoupling these processes by blocking NO 2 - and NO 3 - production.