Presence of Nitrate-Accumulating Sulfur Bacteria and Their Influence on Nitrogen Cycling in a Shallow Coastal Marine Sediment

Nitrate flux between sediment and water, nitrate concentration profile at the sediment-water interface, and in situ sediment denitrification activity were measured seasonally at the innermost part of Tokyo Bay, Japan. For the determination of sediment nitrate concentration, undisturbed sediment cores were sectioned into 5-mm depth intervals and each segment was stored frozen at −30°C. The nitrate concentration was determined for the supernatants after centrifuging the frozen and thawed sediments. Nitrate in the uppermost sediment showed a remarkable seasonal change, and its seasonal maximum of up to 400 μM was found in October. The directions of the diffusive nitrate fluxes predicted from the interfacial concentration gradients were out of the sediment throughout the year. In contrast, the directions of the total nitrate fluxes measured by the whole-core incubation were into the sediment at all seasons. This contradiction between directions indicates that a large part of the nitrate pool extracted from the frozen surface sediments is not a pore water constituent, and preliminary examinations demonstrated that the nitrate was contained in the intracellular vacuoles of filamentous sulfur bacteria dwelling on or in the surface sediment. Based on the comparison between in situ sediment denitrification activity and total nitrate flux, it is suggested that intracellular nitrate cannot be directly utilized by sediment denitrification, and the probable fate of the intracellular nitrate is hypothesized to be dissimilatory reduction to ammonium. The presence of nitrate-accumulating sulfur bacteria therefore may lower nature's self-purification capacity (denitrification) and exacerbate eutrophication in shallow coastal marine environments.     

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.     

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.     

Niche Differentiation of Ammonia-Oxidising Archaea (AOA) and Bacteria (AOB) in Response to Paper and Pulp Mill Effluent

Sediment organic loading has been shown to affect estuarine nitrification and denitrification, resulting in changes to sediment biogeochemistry and nutrient fluxes detrimental to estuarine health. This study examined the effects of organic loading on nutrient fluxes and microbial communities in sediments receiving effluent from a paper and pulp mill (PPM) by applying microcosm studies and molecular microbial ecology techniques. Three sites near the PPM outfall were compared to three control sites, one upstream and two downstream of the outfall. The control sites showed coupled nitrification–denitrification with minimal ammonia release from the sediment. In contrast, the impacted sites were characterised by nitrate uptake and substantial ammonia efflux from the sediments, consistent with a decoupling of nitrification and denitrification. Analysis of gene diversity demonstrated that the composition of nitrifier communities was not significantly different at the impacted sites compared to the control sites; however, analysis of gene abundance indicated that whilst there was no difference in total bacteria, total archaea or ammonia-oxidising archaea (AOA) abundance between the control and impacted sites, there was a significant reduction in ammonia-oxidising bacteria (AOB) at the impacted sites. The results of this study demonstrate an effect of organic loading on estuarine sediment biogeochemistry and highlight an apparent niche differentiation between AOA and AOB.     

Short-term influence of recolonisation by the polycheate worm [2pt] Nereis succinea on oxygen and nitrogen fluxes and [2pt] denitrification: a microcosm simulation

The short-term effects of sediment recolonisation by Nereis succinea on sediment-water column fluxes of oxygen and dissolved inorganic nitrogen, and rates of denitrification, were studied in microcosms of homogenised, sieved sediments. The added worms enhanced oxygen uptake by the sediments, due to the increased surface area provided by the burrow walls and the degree of stimulation was stable with time. Similarly, ammonium fluxes to the water column were stimulated by N. succinea, but declined over the 3 day incubation in all microcosms including the controls. Nitrate fluxes were generally greater in the faunated microcosms, but highly variable with time. Denitrification rates were positively stimulated by N. succinea populations, denitrification of water column nitrate was stimulated 10-fold in comparison to denitrification coupled to nitrification in the sediments. Rates of denitrification of water column nitrate were not significantly different from rates in undisturbed sediment cores with similar densities of N. succinea, whereas rates of coupled nitrification–denitrification were 3-fold lower in the experimental set-up. These results may reflect the relative growth rates of nitrifying and denitrifying bacteria, which allow more rapid colonisation of new burrow surfaces by denitrifier compared to nitrifier populations. The data indicate that recolonisation by burrowing macrofauna of the highly reduced sediments of the Sacca di Goro, Lagoon, Italy, following the annual dystrophic crisis, may play a significant role in the reoxidation and detoxification of the sediments. The increased rates of denitrification associated with the worm burrows, may promote nitrogen losses, but due to the low capacity of nitrifying bacteria to colonise the new burrow structures, these losses would be highly dependent upon water column nitrate concentrations.     

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 N₂O 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 N₂O 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.     

Temporal variations in microbenthic metabolism and inorganic nitrogen fluxes in sandy and muddy sediments of a tidally dominated bay in the northern Wadden Sea

Factors controlling seasonal variations in benthic metabolism (O₂ flux) and dissolved inorganic nitrogen (DIN) fluxes were examined during a 12–14 month period at three intertidal Wadden Sea stations. Since the flux measurements were made as small-scale laboratory core incubations, the results are primarily related to the microbenthic community (microalgae, bacteria, micro-, meio- and small macrofauna) and cannot be considered representative of the total benthic community in the Wadden Sea. Furthermore, it has to be emphasized that light intensity during day-time simulations were constant and saturating at all times. Benthic primary production and oxygen uptake appeared to be temperature dependent with a ‘seasonal Q₁₀’ of 1.7–1.8 and 2.7–4.3, respectively. Inundation had no effect on oxygen fluxes as evidenced by similar sediment respiration with and without water cover. A stronger temperature dependence of primary production in muddy than in sandy sediment indicated that the overall control in the latter may be complex due to factors like macrofaunal grazing and nutrient availability. Benthic respiration may not be controlled by temperature alone, as sedimentary organic matter content correlated significantly with both temperature and benthic respiration. Annual gross primary production in high intertidal sandy sediment was 10 and 50% higher than in low intertidal sandy and muddy sediments, respectively. Since annual benthic community respiration was 2 times higher in muddy than sandy sediments, the annual net primary production was about 0 in the former and 17–19 mol C m^?2 yr^?1 in the latter. However, heterotrophic contribution by larger faunal components as well as removal of organic carbon by waves and tidal currents, which are not included here, may balance the budget at the sandy stations. There was no or only weak relationships between (light and dark) DIN exchange and factors like temperature, sedimentary organic content, and oxygen fluxes. Factors related to nutrient fluxes, such as denitrification and nutrient concentration in the overlying water, may have hampered any such relationships. In fact, DIN fluxes at all three stations appeared to be strongly controlled by DIN concentrations in the overlying water. On an annual basis, the sediment appeared to be a net sink for DIN.     

Benthic fluxes of nutrients and some trace metals in the Tamar estuary,SW England

Pore water concentration gradients and fluxes of chemical components have been studied in sediments from six intertidal sites in the Tamar Estuary, SW England over the course of a year. Fluxes of nutrients (ammonia, nitrate, nitrite, phosphate and silicate) and trace metals (iron, manganese, zinc, copper and cadmium) were determined using a laboratory microcosm incorporatingin situ pore water samplers. Nutrients (except nitrate) were transported out of the sediment throughout the year, but nitrate fluxes were directed into the sediment in the summer (denitrification) and out of the sediment in the winter (nitrification). The activities of benthic macrofauna resulted in enhanced fluxes but these differed between sites depending on population structure and density and whether irrigation or sediment reworking predominated. Fluxes of trace metals were seasonally and spatially variable and specific differences were observed that could be attributed to both chemical and biological activity.     

Nitrous oxide formation in the Colne estuary, England: the central role of nitrite

Nitrate and nitrite concentrations in the water and nitrous oxide and nitrite fluxes across the sediment-water interface were measured monthly in the River Colne estuary, England, from December 1996 to March 1998. Water column concentrations of N(2)O in the Colne were supersaturated with respect to air, indicating that the estuary was a source of N(2)O for the atmosphere. At the freshwater end of the estuary, nitrous oxide effluxes from the sediment were closely correlated with the nitrite concentrations in the overlying water and with the nitrite influx into the sediment. Increases in N(2)O production from sediments were about 10 times greater with the addition of nitrite than with the addition of nitrate. Rates of denitrification were stimulated to a larger extent by enhanced nitrite than by nitrate concentrations. At 550 microM nitrite or nitrate (the highest concentration used), the rates of denitrification were 600 micromol N.m(-2).h(-1) with nitrite but only 180 micromol N.m(-2).h(-1) with nitrate. The ratios of rates of nitrous oxide production and denitrification (N(2)O/N(2) x 100) were significantly higher with the addition of nitrite (7 to 13% of denitrification) than with nitrate (2 to 4% of denitrification). The results suggested that in addition to anaerobic bacteria, which possess the complete denitrification pathway for N(2) formation in the estuarine sediments, there may be two other groups of bacteria: nitrite denitrifiers, which reduce nitrite to N(2) via N(2)O, and obligate nitrite-denitrifying bacteria, which reduce nitrite to N(2)O as the end product. Consideration of free-energy changes during N(2)O formation led to the conclusion that N(2)O formation using nitrite as the electron acceptor is favored in the Colne estuary and may be a critical factor regulating the formation of N(2)O in high-nutrient-load estuaries.     

The effect of sewage effluent on denitrification in Grasmere (English Lake District)

SUMMARY. Denitrification processes in Grasmere were studied using several techniques. Sediments were analysed for nitrate reductase activity and the accumulation of nitrogenous gases in samples incubated in the laboratory. Changes in the concentrations of inorganic nitrogen species in the water column and the release of gas bubbles into gas traps suspended above the sediment were also measured. Sewage effluent entered the lake via the main inflow and faecal bacteria were used as tracers to map the path of the river (and effluent) across the lake. The main river flow was west of the island in the centre of the lake and across the smaller of the two main basins. A preliminary study indicated that this western basin was the site of most active denitrification and this was confirmed in the following year when a seasonal survey showed that deoxygenation, nitrate reduction and ammonium accumulation was more advanced at this site. In addition, this basin was the only area where consistent discharge of nitrogen and methane from the profundal zone was observed. The nitrate reductase assay demonstrated that the sediment was the major site of denitrification, and that activity in the water column was higher in the anoxic hypolimnion than in the euphotic zone. Gas evolution from incubated sediment samples was analysed by gas liquid chromatography (GLC) and indicated that maximum denitrifying activity occurred below the mud surface in oxidized sediments. There was reasonable agreement between the enzyme assay and the GLC technique but neither predicted events in the field satisfactorily. Viable, most probable number (MPN) counts of denitrifying bacteria had similar limitations. A bimodal seasonal pattern of nitrate reductase activity was observed at four sites during thermal stratification, but this could not be explained fully. The major site of denitrification was identified and it was calculated that the nitrogen gas discharged was equivalent to c. 54% of the nitrate removed from the water column.     

Denitrification in Marl and Peat Sediments in the Florida Everglades

The potential for denitrification in marl and peat sediments in the Shark River Slough in the Everglades National Park was determined by the acetylene blockage assay. The influence of nitrate concentration on denitrification rate and N₂O yield from added nitrate was examined. The effects of added glucose and phosphate and of temperature on the denitrification potential were determined. The sediments readily denitrified added nitrate. N₂O was released from the sediments both with and without added acetylene. The marl sediments had higher rates than the peat on every date sampled. Denitrification was nitrate limited; however, the yields of N₂O amounted to only 10 to 34% of the added nitrate when 100 μM nitrate was added. On the basis of measured increases in ammonium concentration, it appears that the balance of added nitrate may be converted to ammonium in the marl sediment. The sediment temperature at the time of sampling greatly influenced the denitrification potential (15-fold rate change) at the marl site, indicating that either the number or the specific activity of the denitrifiers changed in response to temperature fluctuations (9 to 25°C) in the sediment. It is apparent from this study that denitrification in Everglades sediments is not an effective means of removing excess nitrogen which may be introduced as nitrate into the ecosystem with supply water from the South Florida watershed and that sporadic addition of nitrate-rich water may lead to nitrous oxide release from these wetlands.     

Experimental measurement of sediment nitrification and denitrification in Hamilton Harbour,Canada

This research examines the role of sediment nitrification and denitrification in the nitrogen cycle of Hamilton Harbour. The Harbour is subject to large ammonia and carbon loadings from a waste-water treatment plant and from steel industries. Spring ammonia concentrations rapidly decrease from 4.5 to 0.5 mg 1⁻¹, while spring nitrate concentrations increase from 1 to 2 mg l⁻¹, by mid-summer. A three-layer sediment model was developed. The first layer is aerobic; in it, oxidation of organics and nitrification occurs. The second layer is for denitrification, and the third layer is for anaerobic processes. Ammonia sources for nitrification include diffusion from the water column, sources associated with the oxidation of organics, sources from denitrification and from anaerobic processes. Diffusion of oxygen, ammonia and nitrate across the sediment-water interface occurs. Temperature effects are modelled using the Arrhenius concept. A combination of zero-order kinetics for nitrate or ammonia consumption with diffusion results in a half-order reaction, with respect to the water column loss rate to sediments. From experimental measurement, the rate of nitrification is 200 mg N 1⁻¹ sediment per day, while that of denitrification is 85 mg N 1–1 sediment per day at 20 °C. The Arrhenius activation energy is estimated as 15 000 cal/ mole-K and 17 000 cal/ mole-K for nitrification and denitrification, respectively, between 10 °C and 20 °C. Calculations of the flux of ammonia with the sediments, using the biofilm model, compare favourably with experimental observations. The ammonia flux from the water column is estimated to account for 20% of the observed decrease in water column stocks of ammonia, while the nitrate flux from the water column is estimated to account for 25% of the total nitrogen produced by the sediments.     

Coupling between anammox and autotrophic denitrification for simultaneous removal of ammonium and sulfide by enriched marine sediments

In the present study, the capacity of enrichments derived from marine sediments collected from different sites of the Mexican littoral to perform anaerobic ammonium oxidation (anammox) coupled to sulfide-dependent denitrification for simultaneous removal of ammonium and sulfide linked to nitrite reduction was evaluated. Sulfide-dependent denitrification out-competed anammox during the simultaneous oxidation of sulfide and ammonium. Significant accumulation of elemental sulfur (ca. 14–30 % of added sulfide) occurred during the coupling between the two respiratory processes, while ammonium was partly oxidized (31–47 %) due to nitrite limitation imposed in sediment incubations. Nevertheless, mass balances revealed up to 38 % more oxidation of the electron donors available (ammonium and sulfide) than that expected from stoichiometry. Recycling of nitrite, from nitrate produced through anammox, is proposed to contribute to extra oxidation of sulfide, while additional ammonium oxidation is suggested by sulfate-reducing anammox (SR-anammox). The complex interaction between nitrogenous and sulfurous compounds occurring through the concomitant presence of autotrophic denitrification, conventional anammox and SR-anammox may significantly drive the nitrogen and sulfur fluxes in marine environments.     

Hypolimnetic phosphorus and nitrogen dynamics in a small,eutrophic lake with a seasonally anoxic hypolimnion

In situ estimates of sediment nutrient flux are necessary to understand seasonal variations in internal loading in lakes. We investigated the sources and sinks of nutrients in the hypolimnion of a small (0.33 km²), relatively shallow (18 m max. depth), eutrophic lake (Lake Okaro, New Zealand) in order to determine changes in sediment nutrient fluxes resulting from a whole lake sediment capping trial using a modified zeolite phosphorus inactivation agent (Z2G1). Sediment nutrient fluxes in the hypolimnion were estimated as the residual term in a nutrient budget model that accounted for mineralisation of organic nutrients, nutrient uptake by phytoplankton and mixing, nitrification, adsorption/desorption and diffusion of dissolved nutrients at the thermocline. Of the total hypolimnetic phosphate and ammonium fluxes during one period of seasonal stratification (2007–08), up to 60 and 50%, respectively, were derived from the bottom sediments, 18 and 24% were due to mineralisation of organic species, 36 and 28% were due to phytoplankton uptake and 9 and 6% were from diffusion across the thermocline. Adsorption/desorption of phosphate to suspended solids and nitrification were of minor (<8%) importance to the total fluxes. Any reduction in sediment nutrient release by Z2G1 was small compared with both the total sediment nutrient flux and the sum of other hypolimnetic fluxes. Uneven sediment coverage of Z2G1 may have been responsible for the limited effect of the sediment capping layer formed by Z2G1.     

Contribution of sediment fluxes and transformations to the summer nitrogen budget of an Upper Mississippi River backwater system

Routing nitrate through backwaters of regulated floodplain rivers to increase retention could decrease loading to nitrogen (N)-sensitive coastal regions. Sediment core determinations of N flux were combined with inflow–outflow fluxes to develop mass balance approximations of N uptake and transformations in a flow-controlled backwater of the Upper Mississippi River (USA). Inflow was the dominant nitrate source (>95%) versus nitrification and varied as a function of source water concentration since flow was constant. Nitrate uptake length increased linearly, while uptake velocity decreased linearly, with increasing inflow concentration to 2 mg l⁻¹, indicating limitation of N uptake by loading. N saturation at higher inflow concentration coincided with maximum uptake capacity, 40% uptake efficiency, and an uptake length 2 times greater than the length of the backwater. Nitrate diffusion and denitrification in sediment accounted for 27% of the backwater nitrate retention, indicating that assimilation by other biota or denitrification on other substrates were the dominant uptake mechanisms. Ammonium export from the backwater was driven by diffusive efflux from the sediment. Ammonium increased from near zero at the inflow to a maximum mid-lake, then declined slightly toward the outflow due to uptake during transport. Ammonium export was small compared to nitrate retention. Handling editor: J. Padisak     

The functional group approach to bioturbation: II. The effects of the Macoma balthica community on fluxes of nutrients and dissolved organic carbon across the sediment-water interface

We have examined the effects of individual members of the two dominant functional groups of the Macoma balthica community on fluxes of nutrients and dissolved organic carbon between sediment and overlying water. The biodiffusers M. balthica and Mya arenaria and the gallery-diffuser Nereis virens were added to microcosms containing sieved tidal flat sediment, using identical biovolume for each treatment to facilitate comparison. Both functional groups enhanced fluxes over a control without macrofauna. The gallery-diffuser had the greatest effect. The two biodiffusers had opposite effects on the flux of nitrate. M. balthica, which lives near the sediment surface, caused nitrate release whereas M. arenaria caused nitrate uptake. Both organisms increased the release of ammonia, but M. arenaria had the greater effect. We attribute this intra-functional difference not so much to different functionality as to interactions between organisms and the depth distribution of pore water constituents. Because the burrow of M. balthica is located within the nitrification zone of the sediment, the depth averaged concentration of nitrate in its burrow is higher than in the overlying water, and burrow flushing leads to net release of nitrate. In contrast, the burrow of M. arenaria includes both nitrification and denitrification zones, which lower the depth averaged concentration of nitrate below the concentration in the overlying water. The functional group approach needs to take the processes that control sediment chemistry into account in order to predict fluxes sucessfully.     

The effects of sediment desiccation on the potential for nitrification, denitrification, and methanogenesis in an Australian reservoir

Sediments from an Australian reservoir were selected for varying degrees of in situ desiccation (i.e. non-desiccated, partially desiccated and desiccated). Sediment samples were then chemically amended with appropriate electron donors and acceptors to ascertain the effect of sediment desiccation on the potential for nitrification, denitrification, methanogenesis, and the interaction of these processes. There was no detectable nitrification in these sediments yet up to 75% of added nitrate was converted to dinitrogen. Denitrification was predominantly limited by nitrate although there was evidence of carbon co-limitation. None of the nitrogen cycle processes were notably affected by sediment desiccation. There was no flush of mineral nitrogen from desiccated sediments upon rewetting. Methanogenesis did not begin in these sediments until nitrate concentrations fell below 2.25 * 10^-5 M. Methanogenesis was always carbon limited. Methanogens were affected by sediment desiccation but were capable of recovery over time upon rewetting of sediments.     

Denitrification in Marine Sediment: Measurement of Capacity and Estimate of In Situ Rate

The acetylene block technique was used to assay denitrification in undisturbed sediment cores of an intertidal mud flat. Nitrogen loss due to this process was estimated at 1 to 41 kg of N/hectare (ha) per year. Anaerobic nitrate-saturated slurry of the same sediment had a denitrification capacity of 1,026 kg of N/ha per year. The acetylene block technique failed at low nitrate concentrations, so that denitrification at average in situ nitrate concentrations could not be determined. Denitrification followed zero-order kinetics at nitrate concentrations high enough to allow successful blockage of N₂O reduction. Thus, an estimate of in situ rates based on kinetic parameters and in situ nitrate concentrations was impossible. No denitrification was observed in a slurry of the top 1.5 cm under aerated conditions and nitrate saturation. In undisturbed sediment, significant denitrification occurred in few discrete sites within a matrix of undetectable or low activity. Despite numerous errors contributing to the uncertainty of the estimate of in situ rates, the result obtained by this method was considered more valuable than the determination of denitrification capacities. Methods which include severe changes of physical and chemical parameters may frequently lead to overestimates of denitrification rates.     

Nitrate Reduction Functional Genes and Nitrate Reduction Potentials Persist in Deeper Estuarine Sediments. Why?

Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are processes occurring simultaneously under oxygen-limited or anaerobic conditions, where both compete for nitrate and organic carbon. Despite their ecological importance, there has been little investigation of how denitrification and DNRA potentials and related functional genes vary vertically with sediment depth. Nitrate reduction potentials measured in sediment depth profiles along the Colne estuary were in the upper range of nitrate reduction rates reported from other sediments and showed the existence of strong decreasing trends both with increasing depth and along the estuary. Denitrification potential decreased along the estuary, decreasing more rapidly with depth towards the estuary mouth. In contrast, DNRA potential increased along the estuary. Significant decreases in copy numbers of 16S rRNA and nitrate reducing genes were observed along the estuary and from surface to deeper sediments. Both metabolic potentials and functional genes persisted at sediment depths where porewater nitrate was absent. Transport of nitrate by bioturbation, based on macrofauna distributions, could only account for the upper 10 cm depth of sediment. A several fold higher combined freeze-lysable KCl-extractable nitrate pool compared to porewater nitrate was detected. We hypothesised that his could be attributed to intracellular nitrate pools from nitrate accumulating microorganisms like Thioploca or Beggiatoa. However, pyrosequencing analysis did not detect any such organisms, leaving other bacteria, microbenthic algae, or foraminiferans which have also been shown to accumulate nitrate, as possible candidates. The importance and bioavailability of a KCl-extractable nitrate sediment pool remains to be tested. The significant variation in the vertical pattern and abundance of the various nitrate reducing genes phylotypes reasonably suggests differences in their activity throughout the sediment column. This raises interesting questions as to what the alternative metabolic roles for the various nitrate reductases could be, analogous to the alternative metabolic roles found for nitrite reductases.     

Pelagic-benthic coupling of nucleic acids in an abyssal location of the northeastern Atlantic Ocean.

Spatial and temporal changes in sedimentary nucleic acid concentrations in an abyssal locality of the northeastern Atlantic Ocean were investigated in relation to fluxes of nucleic acids produced in the photic layer. Sediment trap material, collected between 1996 and 1998 at depths of 1,000, 3,000, and 4,700 m, and sediment samples were analyzed for DNA and RNA content. Nucleic acid concentrations in the sediments were very high and displayed significant temporal changes, whereas mesoscale variability was low. DNA and RNA concentrations generally displayed opposite temporal patterns, which are likely to be dependent on the nature and characteristics of DNA and RNA molecules. Nucleic acid fluxes were high and displayed clear seasonal changes apparently coupled with seasonal pulses of primary production. However, while median values of DNA fluxes were relatively similar in all sediment traps, median values of RNA fluxes almost doubled from the 1,000- to the 4,700-m depth, suggesting differences in the metabolic activity of microbes associated with sinking particles. Significant relationships between DNA concentrations in the sediments and DNA fluxes and between RNA concentrations and RNA fluxes, indicating the presence of a clear pelagic-benthic coupling of particulate nucleic acids, were observed. The benthic system investigated was not steady state since we estimated that, from September 1996 to October 1998, nucleic acid concentration in the sediments decreased by about 165 mg of DNA m(-2). Vertical profiles revealed a significant decrease in DNA concentration with depth in the sediments, reaching an asymptotic value of about 5 microg g(-1). This DNA fraction constitutes a pool of potentially refractory DNA (accounting for 16 to 40% of the total DNA pool) that might be buried in the sediments.