Oxygen exchange between nitrate molecules during nitrite oxidation by Nitrobacter

Disentangling external loadings, hydrodynamics and biogeochemical controls on the fate of nitrate in a coastal embayment

Nitrogen, as an essential nutrient, largely contributes to the coastal eutrophication. However, the accurate depiction and evaluation of how external loadings, hydrodynamics, and biogeochemical reactions mediate the occurrence, transport, and transformation of nitrate (NO3-) within coastal embayment still pose ongoing challenges to date. In this study, we took advantage of dual isotopes of NO3- to track external NO3- loadings, radium and dual isotopes of H2O to characterize the influences of hydrodynamic on NO3- transport, δ18O-NO3- and δ18O-H2O along with microbial analysis to explore major NO3- biogeochemical reactions in Tolo Harbour, Hong Kong. The multiple isotopic evidence showed that NO3- in surface harbour water was predominantly contributed by precipitation in wet season and its impact was strengthened by stratification. In dry season, NO3- in the surface harbour water became largely influenced by benthic input and biogeochemical reactions due to intensified vertical mixing. Based on NO3- mass balance model, biogeochemical reaction, especially nitrification, was found to be the major process to secure the closure of NO3- budget and increase NO3- inventory from wet to dry season. Hydrodynamics redistributed the external NO3- loadings and mediated nitrogen biogeochemical reactions, both of which further synergistically regulated the fate of NO3- in the embayment.

Bringing Nitric Oxide to the Molybdenum World-A Personal Perspective

Molybdenum-containing enzymes of the xanthine oxidase (XO) family are well known to catalyse oxygen atom transfer reactions, with the great majority of the characterised enzymes catalysing the insertion of an oxygen atom into the substrate. Although some family members are known to catalyse the "reverse" reaction, the capability to abstract an oxygen atom from the substrate molecule is not generally recognised for these enzymes. Hence, it was with surprise and scepticism that the "molybdenum community" noticed the reports on the mammalian XO capability to catalyse the oxygen atom abstraction of nitrite to form nitric oxide (NO). The lack of precedent for a molybdenum- (or tungsten) containing nitrite reductase on the nitrogen biogeochemical cycle contributed also to the scepticism. It took several kinetic, spectroscopic and mechanistic studies on enzymes of the XO family and also of sulfite oxidase and DMSO reductase families to finally have wide recognition of the molybdoenzymes' ability to form NO from nitrite. Herein, integrated in a collection of "personal views" edited by Professor Ralf Mendel, is an overview of my personal journey on the XO and aldehyde oxidase-catalysed nitrite reduction to NO. The main research findings and the path followed to establish XO and AO as competent nitrite reductases are reviewed. The evidence suggesting that these enzymes are probable players of the mammalian NO metabolism is also discussed.

Spatio-temporal analysis of the sources and transformations of anthropogenic nitrogen in a highly degraded coastal basin in Southeast China

Nitrogen transport from terrestrial to aquatic environments could cause water quality deterioration and eutrophication. By sampling in the high- and low-flow periods in a highly disturbed coastal basin of Southeast China, hydrochemical characteristics, nitrate stable isotope composition, estimation of potential nitrogen source input fluxes, and the Bayesian mixing model were combined to determine the sources and transformation of nitrogen. Nitrate was the main form of nitrogen. Nitrification, nitrate assimilation, and NH4+ volatilization were the main nitrogen transformation processes, whereas denitrification was limited due to the high flow rate and unsuitable physicochemical properties. For both sampling periods, non-point source pollution from the upper to the middle reaches was the main source of nitrogen, especially in the high-flow period. In addition to synthetic fertilizer, atmospheric deposition and sewage and manure input were also major nitrate sources in the low-flow period. Hydrological condition was the main factor determining nitrate transformation in this coastal basin, despite the high degree of urbanization and the high volume of sewage discharge in the middle to the lower reaches. The findings of this study highlight that the control of agricultural non-point contamination sources is essential to pollution and eutrophication alleviation, especially for watersheds that receive high amounts of annual precipitation.

Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones

Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially mediated pathway proceeding stepwise from NO3- to N2. This process may be performed entirely by complete denitrifiers capable of all four enzymatic steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas N2O. Metagenomics and marker gene surveys have revealed a diversity of denitrification genes within ODZs, but whether these genes co-occur within complete or partial denitrifiers and the identities of denitrifying taxa remain open questions. We assemble genomes from metagenomes spanning the ETNP and Arabian Sea, and map these metagenome-assembled genomes (MAGs) to 56 metagenomes from all three major ODZs to reveal the predominance of partial denitrifiers, particularly single-step denitrifiers. We find niche differentiation among nitrogen-cycling organisms, with communities performing each nitrogen transformation distinct in taxonomic identity and motility traits. Our collection of 962 MAGs presents the largest collection of pelagic ODZ microorganisms and reveals a clearer picture of the nitrogen cycling community within this environment.

Isotopic evidence for nitrate sources and controls on denitrification in groundwater beneath an irrigated agricultural district

The application of N fertilisers to enhance crop yield is common throughout the world. Many crops have historically been, or are still, fertilised with N in excess of the crop requirements. A portion of the excess N is transported into underlying aquifers in the form of NO₃^-, which is potentially discharged to surface waters. Denitrification can reduce the severity of NO₃^- export from groundwater. We sought to understand the occurrence and hydrogeochemical controls on denitrification in NO₃^--rich aquifers beneath the Emerald Irrigation Area (EIA), Queensland, Australia, a region of extensive cotton and cereal production. Multiple stable isotope (in H₂O, NO₃^-, DIC, DOC and SO₄^2-) and radioactive isotope (³H and ³⁶Cl) tracers were used to develop a conceptual N process model. Fertiliser-derived N is likely incorporated and retained in the soil organic N pool prior to its mineralisation, nitrification, and migration into aquifers. This process, alongside the near absence of other anthropogenic N sources, results in a homogenised groundwater NO₃^- isotopic signature that allows for denitrification trends to be distinguished. Regional-scale denitrification manifests as groundwater becomes increasingly anaerobic during flow from an upgradient basalt aquifer to a downgradient alluvial aquifer. Dilution and denitrification occurs in localised electron donor-rich suboxic hyporheic zones beneath leaking irrigation channels. Using approximated isotope enrichment factors, estimates of regional-scale NO₃^- removal ranges from 22 to 93% (average: 63%), and from 57 to 91% (average: 79%) beneath leaking irrigation channels. In the predominantly oxic upgradient basalt aquifer, raised groundwater tables create pathways for NO₃^- to be transported to adjacent surface waters. In the alluvial aquifer, the transfer of NO₃^- is limited both physically (through groundwater-surface water disconnection) and chemically (through denitrification). These observations underscore the need to understand regional- and local-scale hydrogeological processes when assessing the impacts of groundwater NO₃^- on adjacent and end of system ecosystems.

Analysis of nitrite oxidation process and nitrification performance by nitrogen and oxygen isotope fractionation effect

The N and O isotope fractionation effects in NO₂^--N oxidation and nitrification performance of an activated sludge system treating municipal wastewater are unknown. The nitrifying sludge was cultured under different temperature (33 ± 1 °C, 25 ± 1 °C,and 18 ± 1 °C) and dissolved oxygen (DO: 0.5-1 mg/L, 3-4 mg/L, and 7-8 mg/L). The inverse kinetic isotope effects of N and O (¹⁵ε_NO2 and ¹⁸ε_NO2) were -0.62‰ to -7.08‰ and -0.87‰ to -1.68‰ in the process of NO₂^--N oxidation, respectively. ¹⁵ε_NO3 gradually increased with increasing of temperature (¹⁵ε_NO3-33°C (14.49‰) > ¹⁵ε_NO3-25°C (10.43‰) > ¹⁵ε_NO3-18°C (7.3‰)), while the ¹⁵ε_NO3:¹⁸ε_NO3 was maintained at 1.02-5.32. The increase of temperature improved the nitrification activity, which promoted the fractionation effect, but the change of DO did not highlight this difference. The exchange of NO₂^--N and H₂O (X_NOB) was 32.5 ± 1.5%, and the kinetic isotope effect of H₂O participating in the reaction (¹⁸ε_{k, H2O, 2}) was 22.57 ± 1.79‰, indicating that H₂O was involved in the NO₂^--N oxidation rather than DO. In summary, the elevated temperature enhanced the fractionation effect of NO₂^--N oxidation. This study provides a new perspective to reveal the mechanism of NO₂^--N oxidation, optimize the process of nitrogen removal from wastewater and further control water eutrophication.

Sources and behaviour of nitrogen compounds in the shallow groundwater of agricultural areas (Poyang Lake basin, China)

Nitrogen contamination of natural water is a typical problem for various territories throughout the world. One of the regions exposed to nitrogen pollution is located in the Poyang Lake basin. As a result of agricultural activity and dense population, the shallow groundwater of this area is characterised by a high concentration of nitrogen compounds, primarily NO₃^-, with the concentration varying from 0.1mg/L to 206mg/L. Locally, high ammonium content occurs in the shallow groundwater with low reduction potential Eh (<100mV). However, in general, the shallow groundwater of the Poyang Lake basin has Eh>100mV. To identify sources of nitrogen species and the factors that determine their behaviour, the dual stable isotope approach (δ¹⁵N and δ¹⁸О) and physical-chemical modelling were applied. Actual data were collected by sampling shallow groundwater from domestic water supply wells around the lake. The δ¹⁸О values from -4.1‰ to 13.9‰ with an average value of 5.3 permille indicate a significant influence of nitrification on nitrogen balance. The enrichment of nitrate with the ¹⁵N isotope indicates that manure and domestic sewage are the principal sources of nitrogen compounds. Inorganic nitrogen speciation and thermodynamic calculations demonstrate the high stability of nitrate in the studied groundwater. Computer simulation and field observations indicate the reducing conditions formed under joint effects of anthropogenic factors and appropriate natural conditions, such as the low-level topography in which decreased water exchange rate can occur. The simulation also demonstrates the growth in pH of the groundwater as a consequence of fertilisation, which, in turn, conduced to the clay mineral formation at lower concentrations of aqueous clay-forming components than the ones under the natural conditions.

Nitrogen, Sulfur, and Oxygen Isotope Ratios of Animal- and Plant-Based Organic Fertilizers Used in South Korea

Organic fertilizers are increasingly used in agriculture in Asia and elsewhere. Tracer techniques are desirable to distinguish the fate of nutrients added to agroecosystems with organic fertilizers from those contained in synthetic fertilizers. Therefore, we determined the nitrogen, sulfur, and oxygen isotope ratios of nitrogen- and sulfur-bearing compounds in animal- and plant-based organic fertilizers (ABOF and PBOF, respectively) used in South Korea to evaluate whether they are isotopically distinct. The δN values of total and organic nitrogen for ABOF ranged from +7 to +19‰ and were higher than those of PBOF (generally <+6‰). This suggests that ABOFs have distinct δN values suitable for tracing these fertilizer compounds in the plant-soil-water system, whereas PBOFs have similar δN values to synthetic fertilizers. However, δO values for nitrate (δO) from organic fertilizer samples (<+17.0‰) were consistently lower than those of synthetic nitrate-containing fertilizers. The δS values of total sulfur, organic sulfur compounds (e.g., carbon-bonded sulfur and hydriodic acid-reducible sulfur), and sulfate for ABOFs yielded wide and overlapping ranges of +0.3 to +6.3, +0.9 to +7.2, and -2.6 to +14.2‰, whereas those for PBOFs varied from -3.4 to +7.7, +1.4 to +9.4, and -4.1 to +12.5‰, respectively, making it challenging to distinguish the fate of sulfur compounds from ABOF and PBOF in the environment using sulfur isotopes. We conclude that the δN values of ABOFs and the O values of organic fertilizers are distinct from those of synthetic fertilizers and are a promising tool for tracing the fate of nutrients added by organic fertilizers to agroecosystems.

Stable Isotopes Reveal Rapid Cycling of Soil Nitrogen after Manure Application

Understanding the fate of applied nitrogen (N) in agricultural soils is important for agronomic, environmental, and human health reasons, but it is methodologically difficult to study at the field scale. Natural abundance stable isotope measurements (δN) were used in this field study with micrometeorological measurements of nitrous oxide (NO) emissions to identify the biogeochemical processes responsible for rapid N transformations immediately after application of liquid dairy manure. Fifteen samplings occurred between 16 Mar. 2012 and 5 Apr. 2013, with a focus on spring manure application (before and after) and a winter snowmelt period. Concentrations and δN values of ammonium (NH), nitrate (NO), NO, and total N were measured throughout the year. Approximately 56 (±7)% of the NH-N applied in the spring could not be accounted for 3 d after manure application and was presumably lost by ammonia volatilization before it was tilled into the soil and/or removed from the inorganic N pool by microbial assimilation. Almost all of the remaining manure-NH (95 ± 1.1%) was converted within 3 wk to NO and NO by nitrification and nitrifier-denitrification, respectively. The in situ N isotope effect for nitrification (ε) was calculated to be -32.0 (±5.3)‰. Overall, field-scale measurements of δN at natural abundance provided valuable information that was used to distinguish sources of NH (manure vs. soil organic N) and to follow the production and consumption of NO and the pathways of NO production in soil.

Isotopic overprinting of nitrification on denitrification as a ubiquitous and unifying feature of environmental nitrogen cycling

Natural abundance nitrogen and oxygen isotopes of nitrate (δ¹⁵N_NO3 and δ¹⁸O_NO3) provide an important tool for evaluating sources and transformations of natural and contaminant nitrate (NO₃^-) in the environment. Nevertheless, conventional interpretations of NO₃^- isotope distributions appear at odds with patterns emerging from studies of nitrifying and denitrifying bacterial cultures. To resolve this conundrum, we present results from a numerical model of NO₃^- isotope dynamics, demonstrating that deviations in δ¹⁸O_NO3 vs. δ¹⁵N_NO3 from a trajectory of 1 expected for denitrification are explained by isotopic over-printing from coincident NO₃^- production by nitrification and/or anammox. The analysis highlights two driving parameters: (i) the δ¹⁸O of ambient water and (ii) the relative flux of NO₃^- production under net denitrifying conditions, whether catalyzed aerobically or anaerobically. In agreement with existing analyses, dual isotopic trajectories >1, characteristic of marine denitrifying systems, arise predominantly under elevated rates of NO₂^- reoxidation relative to NO₃^- reduction (>50%) and in association with the elevated δ¹⁸O of seawater. This result specifically implicates aerobic nitrification as the dominant NO₃^- producing term in marine denitrifying systems, as stoichiometric constraints indicate anammox-based NO₃^- production cannot account for trajectories >1. In contrast, trajectories <1 comprise the majority of model solutions, with those representative of aquifer conditions requiring lower NO₂^- reoxidation fluxes (<15%) and the influence of the lower δ¹⁸O of freshwater. Accordingly, we suggest that widely observed δ¹⁸O_NO3 vs. δ¹⁵N_NO3 trends in freshwater systems (<1) must result from concurrent NO₃^- production by anammox in anoxic aquifers, a process that has been largely overlooked.

Assessment of nitrogen and oxygen isotopic fractionation during nitrification and its expression in the marine environment

Nitrification is a microbially-catalyzed process whereby ammonia (NH(3)) is oxidized to nitrite (NO(2)(-)) and subsequently to nitrate (NO(3)(-)). It is also responsible for production of nitrous oxide (N(2)O), a climatically important greenhouse gas. Because the microbes responsible for nitrification are primarily autotrophic, nitrification provides a unique link between the carbon and nitrogen cycles. Nitrogen and oxygen stable isotope ratios have provided insights into where nitrification contributes to the availability of NO(2)(-) and NO(3)(-), and where it constitutes a significant source of N(2)O. This chapter describes methods for determining kinetic isotope effects involved with ammonia oxidation and nitrite oxidation, the two independent steps in the nitrification process, and their expression in the marine environment. It also outlines some remaining questions and issues related to isotopic fractionation during nitrification.

Stable oxygen isotope ratios of nitrate produced from nitrification: (18)O-labeled water incubations of agricultural and temperate forest soils

In many nitrate (NO(3)(-)) source partitioning studies, the delta(18)O value for NO(3)(-) produced from nitrification is often assumed to reflect the isotopic compositions of environmental water (H(2)O) and molecular oxygen (O(2)) in a 2:1 ratio. Most studies that have measured or observed this microbial endmember have found that the delta(18)O-NO(3)(-) was more positive (up to +15 per thousand higher) than the assumed value. Current understanding of the mechanism(s) responsible for this discrepancy is limited. Incubations of one temperate forest soil (organic) and two agricultural soils (mineral) were conducted with (18)O-labeled H(2)O to apportion the sources of oxygen in NO(3)(-) generated from nitrification. The NO(3)(-) produced in all soils had delta(18)O values that could not be explained by a simple endmember mixing ratio of 2:1. A more comprehensive model describing the formation of microbial NO(3)(-) was developed, which accounts for oxygen exchange between H(2)O and NO(2)(-), and includes terms for kinetic and equilibrium isotope effects. Oxygen isotope exchange (i.e., the fraction of NO(3)(-)-oxygen that originates from the abiotic exchange of H(2)O and NO(2)(-)) varied widely between the temperate forest soil (0.37) and the two agricultural soils (0.52 and 0.88). At present, the microbial endmember for nitrification cannot be successfully predicted.

Present limitations and future prospects of stable isotope methods for nitrate source identification in surface- and groundwater

Nitrate (NO3(-)) contamination of surface- and groundwater is an environmental problem in many regions of the world with intensive agriculture and high population densities. Knowledge of the sources of NO3(-) contamination in water is important for better management of water quality. Stable nitrogen (delta15N) and oxygen (delta18O) isotope data of NO3(-) have been frequently used to identify NO3(-) sources in water. This review summarizes typical delta15N- and delta18O-NO3(-) ranges of known NO3(-) sources, interprets constraints and future outlooks to quantify NO3(-) sources, and describes three analytical techniques ("ion-exchange method", "bacterial denitrification method", and "cadmium reduction method") for delta15N- and delta18)O-NO3(-) determination. Isotopic data can provide evidence for the presence of dominant NO3(-) sources. However, quantification, including uncertainty assessment, is lacking when multiple NO3(-) sources are present. Moreover, fractionation processes are often ignored, but may largely constrain the accuracy of NO3(-) source identification. These problems can be overcome if (1) NO3(-) isotopic data are combined with co-migrating discriminators of NO3(-) sources (e.g. (11)B), which are not affected by transformation processes, (2) contributions of different NO3(-) sources can be quantified via linear mixing models (e.g. SIAR), and (3) precise, accurate and high throughput isotope analytical techniques become available.

Oxygen exchange between (de)nitrification intermediates and H2O and its implications for source determination of NO3- and N2O: a review

Stable isotope analysis of oxygen (O) is increasingly used to determine the origin of nitrate (NO(3)-) and nitrous oxide (N(2)O) in the environment. The assumption underlying these studies is that the (18)O signature of NO(3)- and N(2)O provides information on the different O sources (O(2) and H(2)O) during the production of these compounds by various biochemical pathways. However, exchange of O atoms between H(2)O and intermediates of the (de)nitrification pathways may change the isotopic signal and thereby bias its interpretation for source determination. Chemical exchange of O between H(2)O and various nitrogenous oxides has been reported, but the probability and extent of its occurrence in terrestrial ecosystems remain unclear. Biochemical O exchange between H(2)O and nitrogenous oxides, NO(2)- in particular, has been reported for monocultures of many nitrifiers and denitrifiers that are abundant in nature, with exchange rates of up to 100%. Therefore, biochemical O exchange is likely to be important in most soil ecosystems, and should be taken into account in source determination studies. Failing to do so might lead to (i) an overestimation of nitrification as NO(3)- source, and (ii) an overestimation of nitrifier denitrification and nitrification-coupled denitrification as N(2)O production pathways. A method to quantify the rate and controls of biochemical O exchange in ecosystems is needed, and we argue this can only be done reliably with artificially enriched (18)O compounds. We conclude that in N source determination studies, the O isotopic signature of especially N(2)O should only be used with extreme caution.

Respiratory nitrate reductase from Paracoccus denitrificans. Evidence for two b-type haems in the gamma subunit and properties of a water-soluble active enzyme containing alpha and beta subunits

1. The b-type haem centres of the three (alpha, beta and gamma) subunit nitrate reductase from Paracoccus denitrificans have been analysed by redox potentiometry. Two components were identified with mid-point potentials +95 mV and +210 mV. 2. Washing, in the absence of Mg2+ ions, of cytoplasmic membrane vesicles from P. denitrificans promoted selective release of nitrate reductase activity. The released enzyme was purified by chromatography and shown to contain alpha and beta, but not gamma polypeptides. A haem spectrum was absent, consistent with the lack of the gamma subunit. The alpha and beta polypeptides of the water-soluble nitrate reductase had molecular masses that were identical to those of the detergent-purified enzyme and also of the nitrate reductase in cytoplasmic membranes. This observation, together with the failure of protease inhibitors to prevent release from the membrane, indicates that the release is not related to limited proteolysis of the alpha and/or beta polypeptides. The relative molecular mass of the water-soluble alpha beta enzyme was estimated to be approximately 200,000. 3. The water-soluble nitrate reductase was released from intact inverted cytoplasmic membrane vesicles as judged by loss of NADH-NO3- reductase activity and retention by the vesicles after washing of uncoupler-sensitive NADH-oxidase activity. These observations show that alpha and beta polypeptides, and therefore the active site for nitrate reduction, are located on the cytoplasmic side of the membrane. 4. Attempts to reverse the nitrate reductase activity of the enzyme, using nitrate as reductant plus ferricyanide or chlorate as tested oxidants, were unsuccessful. The implications for the mechanism of the enzyme are discussed.