Effects of carbon substrates on nitrite accumulation in freshwater sediments

High N2O reduction potential by denitrification in the nearshore site of a riparian zone

As a potent atmospheric greenhouse gas and a major source of ozone depletion, nitrous oxide (N₂O) emission has been given increasing attention in aquatic systems, particularly at the aquatic-terrestrial interfaces, such as riparian zones. However, the microbial mechanisms regulating N₂O emission in riparian zones remain unknown. Here, we measured the contributions of denitrification and ammonium oxidation to N₂O emission along with the abundance and community structure of nirK-, nirS-, nosZ I- and nosZ II-harbouring bacteria in both surface sediments (0-10 cm) and overlying water along a lake riparian zone (including nearshore sites and offshore sites). Overall, the nearshore sites of the riparian zones emitted less N₂O than the offshore sites. Nearshore N₂O emission was dominated by denitrification with a high N₂O reduction rate, whereas offshore N₂O emission was driven by ammonium oxidation. Furthermore, N₂O derived from ammonium oxidation was influenced by the NH₄⁺-N content, and denitrification N₂O was modulated by denitrifier communities. The N₂O-producing community was dominated by nirS-harbouring bacteria, while the N₂O-reducing community was dominated by nosZ I-harbouring bacteria. The relative abundance of Hydrogenophilales from nirS-denitrifiers and Chloroflexi unclassified from nosZ II-type communities influenced the N₂O produced by denitrification, according to high-throughput sequencing analysis. Additionally, we also found lower levels of N₂O production per unit volume in overlying water, which were 3-4 orders of magnitude less than in the surface sediment. Overall, we propose that using riparian zones can be an effective management tool for N₂O mitigation by enhancing the N₂O reduction process of denitrification and decreasing ammonium oxidation.

Synergistic Effects of Aquatic Plants and Cyanobacterial Blooms on the Nitrous Oxide Emission from Wetlands

Wetlands provide a habitat for the symbiosis of multiple plants and play a significant role in global N₂O emissions. The metabolic traits and effects on microorganisms, which regulate the conversion of nitrogen to N₂O, varies with plant species. The frequent occurrences of cyanobacterial blooms in wetlands can also have a positive or negative effect on denitrification, entangling N₂O emissions. In situ observations of the Dongting Lake reveal that the fluxes in N₂O emissions vary with the vegetation. Maximum emissions occurred in the mud flat, while the zone with the minimum emissions was populated with carex. In 210-day batch cultures, the addition of cyanobacteria synergistically enhanced N₂O production during the degredation of phalaris and reed. The abundance of the nirS and nirK genes decreased over time except in the phalaris-algae group. To mitigate the N₂O emissions from wetlands, the macrophyte communities need to be protected, and the cyanobacterial blooms need to be avoided by reducing the nitrogen pollution.

Degradation of High-Concentration Nitrate Nitrogen in Groundwater: A Laboratory Study

To investigate effective and reasonable methods for the remediation of nitrate nitrogen pollution in groundwater, two groups of laboratory denitrification experiments were conducted: one on the effect of native denitrifying microbes in groundwater and another on the effect of artificially added denitrifying microbes. The water used in the experiment was typical groundwater with a high concentration of nitrate nitrogen. The temperature was controlled at 15°C. Both groups of experiments established four types of culture environments: anaerobic, anaerobic with an added carbon source (glucose), aerobic, and aerobic with an added carbon source (glucose). The results indicated that native denitrifying microbes in the groundwater have almost no ability to remove high concentrations of nitrate nitrogen. However, artificially added denitrifying microbes can effectively promote denitrification. Artificially added denitrifying microbes had the highest activity in an anaerobic environment in which a carbon source had been added, and the rate removal of a high concentration of nitrate nitrogen in groundwater was the highest and reached as high as 89.52%.

Availability of Nitrite and Nitrate as Electron Acceptors Modulates Anaerobic Toluene-Degrading Communities in Aquifer Sediments

Microorganisms are essential in the degradation of environmental pollutants. Aromatic hydrocarbons, e.g., benzene, toluene, ethylbenzene, and xylene (BTEX), are common aquifer contaminants, whose degradation in situ is often limited by the availability of electron acceptors. It is clear that different electron acceptors such as nitrate, iron, or sulfate support the activity of distinct degraders. However, this has not been demonstrated for the availability of nitrate vs. nitrite, both of which can be respired in reductive nitrogen cycling. Here via DNA-stable isotope probing, we report that nitrate and nitrite provided as electron acceptors in different concentrations and ratios not only modulated the microbial communities responsible for toluene degradation but also influenced how nitrate reduction proceeded. Zoogloeaceae members, mainly Azoarcus spp., were the key toluene degraders with nitrate-only, or both nitrate and nitrite as electron acceptors. In addition, a shift within Azoarcus degrader populations was observed on the amplicon sequence variant (ASV) level depending on electron acceptor ratios. In contrast, members of the Sphingomonadales were likely the most active toluene degraders when only nitrite was provided. Nitrate reduction did not proceed beyond nitrite in the nitrate-only treatment, while it continued when nitrite was initially also present in the microcosms. Likely, this was attributed to the fact that different microbial communities were stimulated and active in different microcosms. Together, these findings demonstrate that the availability of nitrate and nitrite can define degrader community selection and N-reduction outcomes. It also implies that nitrate usage efficiency in bioremediation could possibly be enhanced by an initial co-supply of nitrite, via modulating the active degrader communities.

Evaluation of gaseous substrates for microbial immobilization of contaminant mixtures in unsaturated subsurface sediments

Extensive vadose zone metals and organic contamination remains at many former industrial and defense manufacturing sites, and effective remedial solutions are needed to slow or prevent its migration to groundwater. In this study, the application of gaseous substrates to stimulate microbial respiratory reduction of comingled radioisotopes and nitrate under unsaturated conditions was examined for possible application at the Hanford Site, a former nuclear production facility in southeastern WA, USA. First, screening studies were performed to qualitatively measure the sediment respiratory response to 14 gaseous or volatile organic substrates at two moisture contents, 4% and 8%. Volatile substrates produced the strongest respiratory response, among them were butyrate, pentane, butyl acetate. Ethane and butane were the most effective gaseous substrates but only at 8% water content. Hanford sediment from two waste sites with distinctive chemistries were wetted to 7% moisture content, packed into columns, and treated with ethane or butane. After 4 weeks, columns were then leached to quantify retardation in the mobility of aqueous contaminant concentrations compared to no gas control columns. Treatment with both gases resulted in >80% removal of Cr from the aqueous phase. However, NO₃ concentration and a waste sites exposure history to NO₃ had a major effect on U and Tc reduction. Incomplete nitrate reduction outcompeted U and Tc in waste site sediments having limited prior exposure to NO₃. Conversely, waste site sediments co-contaminated with NO₃ were able to achieve highly reduced conditions resulting in complete denitrification of NO₃, and delayed leaching of U and Tc. This implied effective reduction of both contaminants to less mobile species. This study demonstrates that unsaturated vadose sediments at Hanford waste sites have the capacity for a sustained respiratory response to gaseous substrate injection, which could potentially be deployed as part of an overall strategy to reduce the flux of long-lived radionuclides to groundwater at Hanford and other legacy waste sites.

Denitrification is the main microbial N loss pathway on the Qinghai-Tibet Plateau above an elevation of 5000 m

Soil nitrogen (N) deficiency is the major factor contributing to low primary productivity on the Qinghai-Tibet Plateau. However, most of our understanding of N cycling is still based on human disturbed environments, and the microbial mechanisms governing N loss in low primary productivity environment remain unclear. This study explores three microbial N loss pathways in eight wetland and dryland soil profiles from the Qinghai-Tibet Plateau, at an elevation of above 5000 m with little human activity, using ¹⁵N isotopic tracing slurry technology, quantitative PCR, and high-throughput sequencing. No denitrifying anaerobic methane oxidation was detected. Anammox occurred in two of the wetland (n = 4) and dryland (n = 4) soil profiles, while denitrification widely occurred and was the dominant N loss pathway in all samples. Where denitrification and anammox co-occurred, both abundance and activity were higher in wetland than in dryland soils and higher in surface than in subsurface soils. In comparison with non-anammox sites, nitrate levels initiate anammox-related N cycling. High-throughput sequencing and network analysis of nirK, nirS, nosZ, and hzsB gene communities showed that Bradyrhizobiaceae (a family of rhizobia) may play a dominant role in N loss pathways in this region. Given the geological evolution and relatively undisturbed habitat, these findings strongly suggest that denitrification is the dominant N loss pathway in terrestrial habitats of the Qing-Tibet Plateau with minimal anthropogenic activity.

Assessment of Indirect N2O Emission Factors from Agricultural River Networks Based on Long-Term Study at High Temporal Resolution

Assessment of indirect emission factors (EF_5r) of nitrous oxide (N₂O) from agricultural river networks remains challenging, and results are uncertain due to limited data availability. This study compared two methods of assessing EF_5r using data from long-term observations at high temporal resolution in a typical agricultural catchment in subtropical central China. The concentration method (method 1) and the Intergovernmental Panel on Climate Change (IPCC) 2006 method (method 2) were employed to evaluate the emission factor. EF_5r estimated using method 1 (i.e., EF_5r1) was 0.00077 ± 0.00025 (0.00038-0.00097). EF_5r calculated using method 2 (i.e., EF_5r2) was lower than EF_5r1, with a mean value of 0.00004 (0.000015-0.00012). Both EF_5r1 and EF_5r2 were significantly lower than the IPCC 2006 default value of 0.0025, suggesting that N₂O emissions from China and world river networks may be grossly overestimated. A complex N₂O production pathway and diffusion mechanism were responsible for the transfer of N₂O from the sediment to river water and then to the atmosphere. These findings provide essential data for refining national greenhouse gas inventories and contribute evidence for downward revision of indirect emission factors adopted by the IPCC.

Nitrate removal from drinking water with a focus on biological methods: a review

This article summarizes several developed and industrial technologies for nitrate removal from drinking water, including physicochemical and biological techniques, with a focus on autotrophic nitrate removal. Approaches are primarily classified into separation-based and elimination-based methods according to the fate of the nitrate in water treatment. Biological denitrification as a cost-effective and promising method of biological nitrate elimination is reviewed in terms of its removal process, applicability, efficiency, and associated disadvantages. The various pathways during biological nitrate removal, including assimilatory and dissimilatory nitrate reduction, are also explained. A comparative study was carried out to provide a better understanding of the advantages and disadvantages of autotrophic and heterotrophic denitrification. Sulfur-based and hydrogen-based denitrifications, which are the most common autotrophic processes of nitrate removal, are reviewed with the aim of presenting the salient features of hydrogenotrophic denitrification along with some drawbacks of the technology and research areas in which it could be used but currently is not. The application of algae-based water treatment is also introduced as a nature-inspired approach that may broaden future horizons of nitrate removal technology.

Linking abundance and community of microbial N2O-producers and N2O-reducers with enzymatic N2O production potential in a riparian zone

As aquatic-terrestrial ecotones, riparian zones are hotspots not only for denitrification but also for nitrous oxide (N₂O) emission. Due to the potential role of nosZ II in N₂O mitigation, emerging studies in terrestrial ecosystems have taken this newly reported N₂O-reducer into account. However, our knowledge about the interactions between denitrification activities and both N₂O-producers and reducers (especially for nosZ II) in aquatic ecosystems remains limited. In this study, we investigated spatiotemporal distributions of in situ N₂O flux, potential N₂O production rate, and potential denitrification rate, as well as of the related genes in a riparian zone of Baiyangdian Lake. Real-time quantitative PCR (qPCR) and high-throughput sequencing targeted functional genes were used to analyze the denitrifier communities. Results showed that great differences in microbial activities and abundances were observed between sites and seasons. Waterward sediments (constantly flooded area) had the lowest N₂O production potential in both seasons. Not only the environmental factors (moisture content, NH₄⁺ content and TOM) but also the community structure of N₂O-producers and N₂O-reducers (nirK/nirS and nosZ II/nosZ I ratios) could affect the potential N₂O production rate. The abundance of the four functional genes in the winter was higher than in the summer, and the values all peaked at the occasionally flooded area in the winter. The dissimilarity in community composition was mainly driven by moisture content. Altogether, we propose that the N₂O production potential was largely regulated by the community structure of N₂O-producers and N₂O-reducers in riparian zones. Increasing the constantly flooded area and reducing the occasionally flooded area of lake ecosystems may help reduce the level of denitrifier-produced N₂O.

Anaerobic nitrate reduction divergently governs population expansion of the enteropathogen Vibrio cholerae

To survive and proliferate in the absence of oxygen, many enteric pathogens can undergo anaerobic respiration within the host by using nitrate (NO₃^-) as electron acceptor ^1,2. In these bacteria, NO₃^- is typically reduced by a nitrate reductase to nitrite (NO₂^-), a toxic intermediate that is further reduced by a nitrite reductase³. However, Vibrio cholerae, the intestinal pathogen that causes cholera, lacks a nitrite reductase, leading to NO₂^- accumulation during nitrate reduction⁴. Thus, V. cholerae is thought to be unable to undergo NO₃^--dependent anaerobic respiration⁴. Here, we show that during hypoxic growth, NO₃^- reduction in V. cholerae divergently impacts bacterial fitness in a manner dependent on environmental pH. Remarkably, in alkaline conditions, V. cholerae can reduce NO₃^- to support population growth. Conversely, in acidic conditions, accumulation of NO₂^- from NO₃^- reduction simultaneously limits population expansion and preserves cell viability by lowering fermentative acid production. Interestingly, other bacterial species such as Salmonella typhimurium, enterohemorrhagic Escherichia coli (EHEC) and Citrobacter rodentium also reproduced this pH-dependent response suggesting that this mechanism might be conserved within enteric pathogens. Our findings explain how a bacterial pathogen can use a single redox reaction to divergently regulate population expansion depending on fluctuating environmental pH.

The cycle of nitrogen in river systems: sources, transformation, and flux

Nitrogen is a requisite and highly demanded element for living organisms on Earth. However, increasing human activities have greatly altered the global nitrogen cycle, especially in rivers and streams, resulting in eutrophication, formation of hypoxic zones, and increased production of N2O, a powerful greenhouse gas. This review focuses on three aspects of the nitrogen cycle in streams and rivers. We firstly introduce the distributions and concentrations of nitrogen compounds in streams and rivers as well as the techniques for tracing the sources of nitrogen pollution. Secondly, the overall picture of nitrogen transformations in rivers and streams conducted by organisms is described, especially focusing on the roles of suspended particle-water surfaces in overlying water, sediment-water interfaces, and riparian zones in the nitrogen cycle of streams and rivers. The coupling of nitrogen and other element (C, S, and Fe) cycles in streams and rivers is also briefly covered. Finally, we analyze the nitrogen budget of river systems as well as nitrogen loss as N2O and N2 through the fluvial network and give a summary of the effects and consequences of human activities and climate change on the riverine nitrogen cycle. In addition, future directions for the research on the nitrogen cycle in river systems are outlined.

Nitrifying Kinetics and the Persistence of Nitrite in the Seine River, France

Although a higher oxidation rate for nitrite than for ammonia generally prevents nitrite accumulation in oxic waters, nitrite concentrations in the Seine River (1-31 μM) exceed European norms. We investigated the kinetics of in situ ammonia- and nitrite-oxidizing communities in river water and wastewater treatment plant (WWTP) effluents to determine the role of pelagic nitrification in the origin and persistence of nitrite downstream of Paris. The main source of nitrite is the major Parisian WWTP, and its persistence, up to tens of kilometers downstream of the plant, is explained by low ammonia and nitrite oxidation rates and high river flow. Furthermore, similar nitrite and ammonia oxidation rates preclude a rapid consumption of both preexisting nitrite and nitrite produced by ammonia oxidation. Maximum ammonia oxidation rates are two to three times higher downstream than upstream of the WWTP, indicating the input of ammonia oxidizers and ammonia from the WWTP. In both river water and WWTP effluents, nitrite oxidizers were unable to oxidize all available nitrite. In the human-impacted Seine River, this phenomenon might be due to mixotrophy. This study highlights the low resilience of the river to nitrite contamination as well as the importance of managing nitrite, nitrifiers, and organic matter concentrations in WWTP effluents to avoid nitrite persistence in rivers.

Tobacco, Microbes, and Carcinogens: Correlation Between Tobacco Cure Conditions, Tobacco-Specific Nitrosamine Content, and Cured Leaf Microbial Community

Tobacco-specific nitrosamines are carcinogenic N-nitrosamine compounds present at very low levels in freshly harvested tobacco leaves that accumulate during leaf curing. Formation of N-nitrosamine compounds is associated with high nitrate levels in the leaf at harvest, and nitrate is presumed to be the source from which the N-nitrosation species originates. More specifically, nitrite is considered to be a direct precursor, and nitrite is linked with N-nitrosation in many environmental matrices where it occurs via microbial nitrate reduction. Here, we initiate work exploring the role of leaf microbial communities in formation of tobacco-specific nitrosamines. Leaves from burley tobacco line TN90H were air cured under various temperature and relative humidity levels, and 22 cured tobacco samples were analyzed for their microbial communities and leaf chemistry. Analysis of nitrate, nitrite, and total tobacco-specific nitrosamine levels revealed a strong positive correlation between the three variables, as well as a strong positive correlation with increasing relative humidity during cure conditions. 16S rRNA gene amplicon sequencing was used to assess microbial communities in each of the samples. In most samples, Proteobacteria predominated at the phylum level, accounting for >90 % of the OTUs. However, a distinct shift was noted among members of the high tobacco-specific nitrosamine group, with increases in Firmicutes and Actinobacteria. Several OTUs were identified that correlate strongly (positive and negative) with tobacco-specific nitrosamine content. Copy number of bacterial nitrate reductase genes, obtained using quantitative PCR, did not correlate strongly with tobacco-specific nitrosamine content. Incomplete denitrification is potentially implicated in tobacco-specific nitrosamine levels.

Effects of pH on nitrite accumulation during wastewater denitrification

The characteristics of nitrite accumulation during denitrification in mixed liquors with different pH values were studied. The mixed liquors were prepared by adding acclimated denitrifying activated sludge to synthetic wastewater with methanol (CH3OH) as the carbon source (chemical oxygen demand = 600 mg/L) and sodium nitrate (NaNO3) as the nitrogen source (NO3(-)-N = 50 mg/L). The results showed that the pH during denitrification could be kept constant using buffer solutions composed of KH2PO4, Na2HPO4 x 12H2O and Na2B4O7 x 10H2O. Nitrite accumulation was more serious at low pH than at high pH, regardless of whether the pH of the mixed liquor was stabilized during denitrification. The specific rates of nitrate and nitrite reduction were both inhibited by increased pH. The specific rate of nitrate reduction was more vulnerable than that of nitrite reduction to higher pH. Nitrite accumulation during these experiments resulted from different reduction rates for nitrate and nitrite. Nitrite reduction rates were inhibited by the presence of nitrate, which stimulated nitrite accumulation during denitrification.

Treatment of high ethanol concentration wastewater by biological sand filters: enhanced COD removal and bacterial community dynamics

Winery wastewater is characterized by its high chemical oxygen demand (COD), seasonal occurrence and variable composition, including periodic high ethanol concentrations. In addition, winery wastewater may contain insufficient inorganic nutrients for optimal biodegradation of organic constituents. Two pilot-scale biological sand filters (BSFs) were used to treat artificial wastewater: the first was amended with ethanol and the second with ethanol, inorganic nitrogen (N) and phosphorus (P). A number of biochemical parameters involved in the removal of pollutants through BSF systems were monitored, including effluent chemistry and bacterial community structures. The nutrient supplemented BSF showed efficient COD, N and P removal. Comparison of the COD removal efficiencies of the two BSFs showed that N and P addition enhanced COD removal efficiency by up to 16%. Molecular fingerprinting of BSF sediment samples using denaturing gradient gel electrophoresis (DGGE) showed that amendment with high concentrations of ethanol destabilized the microbial community structure, but that nutrient supplementation countered this effect.

River bed carbon and nitrogen cycling: state of play and some new directions

The significance of freshwaters as key players in the global budget of both carbon dioxide and methane has recently been highlighted. In particular, rivers clearly do not act simply as inert conduits merely piping carbon from catchment to coast, but, on the whole, their metabolic activity transforms a considerable fraction of the carbon that they convey. In addition, nitrogen is cycled, sometimes in tight unison with carbon, with appreciable amounts being 'denitrified' between catchment and coast. However, shortfalls in our knowledge about the significance of exchange and interaction between rivers and their catchments, particularly the significance of interactions mediated through hyporheic sediments, are still apparent. From humble beginnings of quantifying the consumption of oxygen by small samples of gravel, to an integrated measurement of reach scale transformations of carbon and nitrogen, our understanding of the cycling of these two macro elements in rivers has improved markedly in the past few decades. However, recent discoveries of novel metabolic pathways in both the nitrogen and carbon cycle across a spectrum of aquatic ecosystems, highlights the need for new directions and a truly multidisciplinary approach to quantifying the flux of carbon and nitrogen through rivers.

Carbon sources influence the nitrate removal activity, community structure and biofilm architecture

Influence of the frequently used carbon sources in nitrate removal processes were evaluated in a lab-scale biofilm reactor. The NO3-N removal efficiency was in the order acetate>glucose>methanol>ethanol. Acetate-fed biofilm reduced nearly 100% NO3-N with negligible amount of NO2-N accumulation. Although 99% NO3-N was reduced in the glucose-fed biofilm, substantial NH3-N and NO2-N accumulated. Methanol-fed biofilm reduced 72% of NO3-N with accumulation of 2.2 mg L(-1) of NO2-N, while biofilm formed in presence of ethanol showed 61% reduction in NO3-N although relatively higher ratio of denitrifiers were observed. Acetate and ethanol-fed biofilm displayed characteristic biofilm architecture with voids, but the former had relatively higher thickness and diffusion distance. In presence of glucose and methanol, a confluent biofilm without characteristic voids was formed. Pseudomonas sp. numerically dominated the acetate and ethanol-fed biofilm, while Enterobacter sp. and Methylobacillus sp., were abundant in glucose and methanol biofilms respectively.

Inhibition of nitrate reduction by chromium (VI) in anaerobic soil microcosms

Chromium is often found as a cocontaminant at sites polluted with organic compounds. For nitrate-respiring microbes, Cr(VI) may be not only directly toxic but may also specifically interfere with N reduction. In soil microcosms amended with organic electron donors, Cr(VI), and nitrate, bacteria oxidized added carbon, but relatively low doses of Cr(VI) caused a lag and then lower rates of CO(2) accumulation. Cr(VI) strongly inhibited nitrate reduction; it occurred only after soluble Cr(VI) could not be detected. However, Cr(VI) additions did not eliminate Cr-sensitive populations; after a second dose of Cr(VI), bacterial activity was strongly inhibited. Differences in microbial community composition (assayed by PCR-denaturing gradient gel electrophoresis) driven by different organic substrates (glucose and protein) were smaller than when other electron acceptors had been used. However, the selection of bacterial phylotypes was modified by Cr(VI). Nine isolated clades of facultatively anaerobic Cr(VI)-resistant bacteria were closely related to cultivated members of the phylum Actinobacteria or Firmicutes. In Bacillus cereus GNCR-4, the nature of the electron donor (fermentable or nonfermentable) affected Cr(VI) resistance level and anaerobic nitrate metabolism. Our results indicate that carbon utilization and nitrate reduction in these soils were contingent upon the reduction of added Cr(VI). The amount of Cr(VI) required to inhibit nitrate reduction was 10-fold less than for aerobic catabolism of the same organic substrate. We speculate that the resistance level of a microbial process is directly related to the diversity of microbes capable of conducting it.

Changes in the dissolved nitrogen pool across land cover gradients in Wisconsin streams

Increases in anthropogenic nitrogen fixation have resulted in wide-scale enrichment of aquatic ecosystems. Existing biogeochemical theory suggests that N enrichment is associated with increasing concentrations of nitrate; however, dissolved organic nitrogen (DON) is often a major component of the total dissolved nitrogen (TDN) pool in streams and rivers, and its concentration can be significantly elevated in human-influenced basins. We examined N concentrations during summer base flow conditions in 324 Wisconsin streams to determine whether DON was a significant component of TDN and how its relative contribution changed across a gradient of increasing human (agriculture and urban) land use for 84 of these sites. Total dissolved nitrogen varied from 0.09 to 20.74 mg/L, and although DON was significantly higher in human-dominated basins relative to forested and mixed-cover basins, its concentration increased relatively slowly in response to increasing human land cover. This limited response reflected a replacement of wetland-derived DON in low-N streams by anthropogenic sources in human-dominated sites, such that net changes in DON were small across the land use gradient. Nitrate-N increased exponentially in response to greater human land cover, and NH4-N and NO2-N were present at low levels. Nitrite-N exceeded NH4-N at 20% of sites and reached a maximum concentration of 0.10 mg/L. This examination suggests that basic mechanisms driving N losses from old-growth forests subject to N saturation also shape the summertime N pool in Wisconsin streams, in addition to other processes dictated by landscape context. The overwhelming role of human land use in determining the relative and absolute composition of the summertime N pool included (1) rapid increases in NO3-N, (2) limited changes in DON, and (3) the unexpected occurrence of NO2-N. High (>3 mg/L) TDN conditions dominated by NO3-N, regardless of landscape context or forms of N inputs, indicate a state of "N hypersaturation", which appears to be increasingly common in human-influenced streams and rivers. Many sites in agriculturally rich areas had NO2-N and NO3-N concentrations that, if sustained, are at chronically toxic levels for sensitive aquatic biota, suggesting that N enrichment now has local consequences for resident stream biota in addition to contributing to coastal eutrophication.

Nitrate attenuation in groundwater: a review of biogeochemical controlling processes

Biogeochemical processes controlling nitrate attenuation in aquifers are critically reviewed. An understanding of the fate of nitrate in groundwater is vital for managing risks associated with nitrate pollution, and to safeguard groundwater supplies and groundwater-dependent surface waters. Denitrification is focused upon as the dominant nitrate attenuation process in groundwater. As denitrifying bacteria are essentially ubiquitous in the subsurface, the critical limiting factors are oxygen and electron donor concentration and availability. Variability in other environmental conditions such as nitrate concentration, nutrient availability, pH, temperature, presence of toxins and microbial acclimation appears to be less important, exerting only secondary influences on denitrification rates. Other nitrate depletion mechanisms such as dissimilatory nitrate reduction to ammonium and assimilation of nitrate into microbial biomass are unlikely to be important in most subsurface settings relative to denitrification. Further research is recommended to improve current understanding on the influence of organic carbon, sulphur and iron electron donors, physical restrictions on microbial activity in dual porosity aquifers, influences of environmental condition (e.g. pH in poorly buffered environments and salinity in coastal or salinized soil settings), co-contaminant influences (particularly the contrasting inhibitory and electron donor influences of pesticides) and improved quantification of denitrification rates in the laboratory and field.

Transport and fate of nitrate at the ground-water/surface-water interface

Although numerous studies of hyporheic exchange and denitrification have been conducted in pristine, high-gradient streams, few studies of this type have been conducted in nutrient-rich, low-gradient streams. This is a particularly important subject given the interest in nitrogen (N) inputs to the Gulf of Mexico and other eutrophic aquatic systems. A combination of hydrologic, mineralogical, chemical, dissolved gas, and isotopic data were used to determine the processes controlling transport and fate of NO(3)(-) in streambeds at five sites across the USA. Water samples were collected from streambeds at depths ranging from 0.3 to 3 m at three to five points across the stream and in two to five separate transects. Residence times of water ranging from 0.28 to 34.7 d m(-1) in the streambeds of N-rich watersheds played an important role in allowing denitrification to decrease NO(3)(-) concentrations. Where potential electron donors were limited and residence times were short, denitrification was limited. Consequently, in spite of reducing conditions at some sites, NO(3)(-) was transported into the stream. At two of the five study sites, NO(3)(-) in surface water infiltrated the streambeds and concentrations decreased, supporting current models that NO(3)(-) would be retained in N-rich streams. At the other three study sites, hydrogeologic controls limited or prevented infiltration of surface water into the streambed, and ground-water discharge contributed to NO(3)(-) loads. Our results also show that in these low hydrologic-gradient systems, storm and other high-flow events can be important factors for increasing surface-water movement into streambeds.

Implementation of artificial neural networks (ANNs) to analysis of inter-taxa communities of benthic microorganisms and macroinvertebrates in a polluted stream

This study was performed to gain an understanding of the structural and functional relationships between inter-taxa communities (macroinvertebrates as consumers, and microbes as decomposers or preys for the invertebrates) in a polluted stream using artificial neural networks techniques. Sediment samples, carrying microorganisms (eubacteria) and macroinvertebrates, were seasonally collected from similar habitats in streams with different levels of pollution. Microbial community taxa and densities were determined using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and 16S rDNA sequence analysis techniques. The identity and density of macroinvertebrates were concurrently determined. In general, differences were observed on grouping by self-organizing map (SOM) in polluted, clean and recovering sites based on the microbial densities, while the community patterns were partly dependent on the sampling period. A Spearman rank order correlation analysis revealed correlations of several eubacterial species with those of macroinvertebrates: a negative correlation was observed between Acidovorax sp. (from polluted sites) and Gammaridae (mostly from the clean site), while Herbaspirillum sp. and Janthinobacterium sp. appeared to have positive correlations with some macroinvertebrate species. The population dynamics of the tolerant texa, Tubificidae and Chironomidae, appeared to be related with changes in the densities of Acidovorax sp. This study revealed community relationships between macroinvertebrates and microorganisms, reflecting the connectivity between the two communities via the food chain. A further physio-ecological and symbiological study on the invertebrate-microorganism relationships will be required to understand the degradation and utilization of detritus in aquatic ecosystems as well as to elucidate the roles of the inter-taxa in the recovery of polluted aquatic environments.

Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis

Many of the proteins that are candidates for bioenergetic pathways involved with sulfate respiration in Desulfovibrio spp. have been studied, but complete pathways and overall cell physiology remain to be resolved for many environmentally relevant conditions. In order to understand the metabolism of these microorganisms under adverse environmental conditions for improved bioremediation efforts, Desulfovibrio vulgaris Hildenborough was used as a model organism to study stress response to nitrite, an important intermediate in the nitrogen cycle. Previous physiological studies demonstrated that growth was inhibited by nitrite and that nitrite reduction was observed to be the primary mechanism of detoxification. Global transcriptional profiling with whole-genome microarrays revealed coordinated cascades of responses to nitrite in pathways of energy metabolism, nitrogen metabolism, oxidative stress response, and iron homeostasis. In agreement with previous observations, nitrite-stressed cells showed a decrease in the expression of genes encoding sulfate reduction functions in addition to respiratory oxidative phosphorylation and ATP synthase activity. Consequently, the stressed cells had decreased expression of the genes encoding ATP-dependent amino acid transporters and proteins involved in translation. Other genes up-regulated in response to nitrite include the genes in the Fur regulon, which is suggested to be involved in iron homeostasis, and genes in the Per regulon, which is predicted to be responsible for oxidative stress response.

Influence of nutrients, hexadecane, and temporal variations on nitrification and exopolysaccharide composition of river biofilms

Biofilms were cultivated on polycarbonate strips in rotating annular reactors using South Saskatchewan River water during the fall of 1999 and the fall of 2001. The reactors were supplemented with carbon (glucose), nitrogen (NH4Cl), phosphorus (KH2PO4), or combined nutrients (CNP), with or without hexadecane. The impact of these treatments on nitrification and on the exopolysaccharide composition of river biofilms was determined. The results showed that the biofilms had higher NH4+oxidation, NO3–production, and N2O production activities in fall 1999 than fall 2001 when grown with CNP but had higher activities in fall 2001 than fall 1999 when grown with individual nutrients. The exopolysaccharide amounts and proportions were generally higher in fall 1999 than fall 2001, as a consequence of the higher nutrient levels in the river water in the first year of this study. The addition of P and especially CNP stimulated NH4+oxidation by the biofilms, showing a P limitation in this river ecosystem. The presence of hexadecane negatively affected these activities and lowered the amounts of exopolysaccharides in CNP and P biofilms in fall 1999 but increased the biofilm activities and exopolysaccharide amounts in CNP biofilm in fall 2001. Antagonistic, synergistic, and independent effects between nutrients and hexadecane were also observed. This study demonstrated that the biofilm autotrophic nitrification activity in the South Saskatchewan River was limited by P, that this activity and the exopolysaccharide amounts and proportions were dependent on the nutrient concentrations in the river water, and suggested that exopolysaccharides may play a protective role for biofilm microorganisms against toxic pollutants.Key words: river biofilms, nitrification, nutrients, hexadecane, exopolysaccharides.

Influence of nutrient inputs, hexadecane, and temporal variations on denitrification and community composition of river biofilms

Biofilms were cultivated on polycarbonate strips in rotating annular reactors using South Saskatchewan River water during the fall of 1999 and the fall of 2001, supplemented with carbon (glucose), nitrogen (NH4Cl), phosphorus (KH2PO4), or combined nutrients (CNP), with or without hexadecane, a model compound representing aliphatic hydrocarbons used to simulate a pollutant. In fall 1999 and fall 2001, comparable denitrification activities and catabolic potentials were observed in the biofilms, implying that denitrifying populations showed similar activity patterns and catabolic potentials during the fall from year to year in this river ecosystem, when environmental conditions were similar. Both nirS and nirK denitrification genes were detected by PCR amplification, suggesting that both denitrifying bacterial subpopulations can potentially contribute to total denitrification. Between 91.7 and 99.8% of the consumed N was emitted in the form of N2, suggesting that emission of N2O, a major potent greenhouse gas, by South Saskatchewan River biofilms is low. Denitrification was markedly stimulated by the addition of CNP, and nirS and nirK genes were predominant only in the presence of CNP. In contrast, individual nutrients had no impact on denitrification and on the occurrence of nirS and nirK genes detected by PCR amplification. Similarly, only CNP resulted in significant increases in algal and bacterial biomass relative to control biofilms. Biomass measurements indicated a linkage between autotrophic and heterotrophic populations in the fall 1999 biofilms. Correlation analyses demonstrated a significant relationship (P < or = 0.05) between the denitrification rate and the biomass of algae and heterotrophic bacteria but not cyanobacteria. At the concentration assessed (1 ppb), hexadecane partially inhibited denitrification in both years, slightly more in the fall of 2001. This study suggested that the response of the anaerobic heterotrophic biofilm community may be cyclic and predictable from year to year and that there are interactive effects between nutrients and the contaminant hexadecane.

Microscale and molecular assessment of impacts of nickel, nutrients, and oxygen level on structure and function of river biofilm communities

Studies were carried out to assess the influence of nutrients, dissolved oxygen (DO) concentration, and nickel (Ni) on river biofilm development, structure, function, and community composition. Biofilms were cultivated in rotating annular reactors with river water at a DO concentration of 0.5 or 7.5 mg liter(-1), with or without a combination of carbon, nitrogen, and phosphorus (CNP) and with or without Ni at 0.5 mg liter(-1). The effects of Ni were apparent in the elimination of cyanobacterial populations and reduced photosynthetic biomass in the biofilm. Application of lectin-binding analyses indicated changes in exopolymer abundance and a shift in the glycoconjugate makeup of the biofilms, as well as in the response to all treatments. Application of the fluorescent live-dead staining (BacLight Live-Dead staining kit; Molecular Probes, Eugene, Oreg.) indicated an increase in the ratio of live to dead cells under low-oxygen conditions. Nickel treatments had 50 to 75% fewer 'live' cells than their corresponding controls. Nickel at 0.5 mg liter(-1) corresponding to the industrial release rate concentration for nickel resulted in reductions in carbon utilization spectra relative to control and CNP treatments without nickel. In these cases, the presence of nickel eliminated the positive influence of nutrients on the biofilm. Other culture-dependent analyses (plate counts and most probable number) revealed no significant treatment effect on the biofilm communities. In the presence of CNP and at both DO levels, Ni negatively affected denitrification but had no effect on hexadecane mineralization or sulfate reduction. Analysis of total community DNA indicated abundant eubacterial 16S ribosomal DNA (rDNA), whereas Archaea were not detected. Amplification of the alkB gene indicated a positive effect of CNP and a negative effect of Ni. The nirS gene was not detected in samples treated with Ni at 0.5 mg liter(-1), indicating a negative effect on specific populations of bacteria, such as denitrifiers, resulting in a reduction in diversity. Denaturing gradient gel electrophoresis revealed that CNP had a beneficial impact on biofilm bacterial diversity at high DO concentrations, but none at low DO concentrations, and that the negative effect of Ni on diversity was similar at both DO concentrations. Notably, Ni resulted in the appearance of unique bands in 16S rDNA from Ni, DO, and CNP treatments. Sequencing results confirmed that the bands belonged to bacteria originating from freshwater and marine environments or from agricultural soils and industrial effluents. The observations indicate that significant interactions occur between Ni, oxygen, and nutrients and that Ni at 0.5 mg liter(-1) may have significant impacts on river microbial community diversity and function.

Impact of seasonal variations and nutrient inputs on nitrogen cycling and degradation of hexadecane by replicated river biofilms

Biofilm communities cultivated in rotating annular bioreactors using water from the South Saskatchewan River were assessed for the effects of seasonal variations and nutrient (C, N, and P) additions. Confocal laser microscopy revealed that while control biofilms were consistently dominated by bacterial biomass, the addition of nutrients shifted biofilms of summer and fall water samples to phototrophic-dominated communities. In nutrient-amended biofilms, similar patterns of nitrification, denitrification, and hexadecane mineralization rates were observed for winter and spring biofilms; fall biofilms had the highest rates of nitrification and hexadecane mineralization, and summer biofilms had the highest rates of denitrification. Very low rates of all measured activities were detected in control biofilms (without nutrient addition) regardless of season. Nutrient addition caused large increases in hexadecane mineralization and denitrification rates but only modest increases, if any, in nitrification rates, depending upon the season. Generally, both alkB and nirK were more readily PCR amplified from nutrient-amended biofilms. Both genes were amplified from all samples except for nirK from the fall control biofilm. It appears that bacterial production in the South Saskatchewan River water is limited by the availability of nutrients and that biofilm activities and composition vary with nutrient availability and time of year.

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.