Steady-state nitrogen isotope effects of N2 and N2O production in Paracoccus denitrificans

Microbial nitrogen transformations tracked by natural abundance isotope studies and microbiological methods: A review

Nitrogen is an essential nutrient in the environment that exists in multiple oxidation states in nature. Numerous microbial processes are involved in its transformation. Knowledge about very complex N cycling has been growing rapidly in recent years, with new information about associated isotope effects and about the microbes involved in particular processes. Furthermore, molecular methods that are able to detect and quantify particular processes are being developed, applied and combined with other analytical approaches, which opens up new opportunities to enhance understanding of nitrogen transformation pathways. This review presents a summary of the microbial nitrogen transformation, including the respective isotope effects of nitrogen and oxygen on different nitrogen-bearing compounds (including nitrates, nitrites, ammonia and nitrous oxide), and the microbiological characteristics of these processes. It is supplemented by an overview of molecular methods applied for detecting and quantifying the activity of particular enzymes involved in N transformation pathways. This summary should help in the planning and interpretation of complex research studies applying isotope analyses of different N compounds and combining microbiological and isotopic methods in tracking complex N cycling, and in the integration of these results in modelling approaches.

Insights into nitrate-reducing Fe(II) oxidation by Diaphorobacter caeni LI3T through kinetic, nitrogen isotope fractionation, and genome analyses

Nitrate (NO3-)-reducing Fe(II) oxidation (NRFO) is prevalent in anoxic environments. However, it is uncertain in which step(s) the biological Fe(II) oxidation is coupled with denitrification during NRFO. In this study, a heterotrophic NRFO bacterium, Diaphorobacter caeni LI3T, was isolated from paddy soil and used to investigate the transformation of Fe(II) and nitrogen as well as nitrogen isotopic fractionation (δ15N-N2O) during NRFO. Fe(II) oxidation was observed in the Cell+NO3- +Fe(II), Cell+NO2- + Fe(II), and NO2- + Fe(II) treatments, resulting in precipitation of amorphous Fe(III) minerals and lepidocrocite on the surface and in the periplasm of cells. The presence of Fe(II) slightly accelerated microbial NO3- reduction in the Cell+NO3- + Fe(II) treatment relative to the Cell+NO3- treatment, but slowed down the NO2- reduction in the Cell+NO2- + Fe(II) treatment relative to the Cell+NO2- treatment likely due to cell encrustation that blocking microbial NO2- reduction in the periplasm. The δ15N-N2O results in the Cell+NO3- + Fe(II) treatment were close to those in the Cell+NO3- and Cell+NO2- treatments, indicating that the accumulative N2O is primarily of biological origin during NRFO. The genome analysis found a complete set of denitrification and oxidative phosphorylation genes in strain LI3T, the metabolic pathways of which were closely related with cyc2 and cytc as indicated by protein-protein interactions network analysis. It is proposed that Fe(II) oxidation is catalyzed by the outer membrane protein Cyc2, with the resulting electrons being transferred to the nitrite reductase NirS via CytC in the periplasm, and the CytC can also accept electrons from the oxidative phosphorylation in the cytoplasmic membrane. Overall, our findings provide new insights into the potential pathways of biological Fe(II) oxidation coupled with nitrate reduction in heterotrophic NRFO bacteria.

Sources of nitrous oxide emissions from hydroponic tomato cultivation: Evidence from stable isotope analyses

Introduction

Hydroponic vegetable cultivation is characterized by high intensity and frequent nitrogen fertilizer application, which is related to greenhouse gas emissions, especially in the form of nitrous oxide (N₂O). So far, there is little knowledge about the sources of N₂O emissions from hydroponic systems, with the few studies indicating that denitrification could play a major role.

Methods

Here, we use evidence from an experiment with tomato plants (Solanum lycopersicum) grown in a hydroponic greenhouse setup to further shed light into the process of N₂O production based on the N₂O isotopocule method and the ¹⁵N tracing approach. Gas samples from the headspace of rock wool substrate were collected prior to and after ¹⁵N labeling at two occasions using the closed chamber method and analyzed by gas chromatography and stable isotope ratio mass spectrometry.

Results

The isotopocule analyses revealed that either heterotrophic bacterial denitrification (bD) or nitrifier denitrification (nD) was the major source of N₂O emissions, when a typical nutrient solution with a low ammonium concentration (1-6 mg L^-1) was applied. Furthermore, the isotopic shift in ¹⁵N site preference and in δ¹⁸O values indicated that approximately 80-90% of the N₂O produced were already reduced to N₂ by denitrifiers inside the rock wool substrate. Despite higher concentrations of ammonium present during the ¹⁵N labeling (30-60 mg L^-1), results from the ¹⁵N tracing approach showed that N₂O mainly originated from bD. Both, ¹⁵N label supplied in the form of ammonium and ¹⁵N label supplied in the form of nitrate, increased the ¹⁵N enrichment of N₂O. This pointed to the contribution of other processes than bD. Nitrification activity was indicated by the conversion of small amounts of ¹⁵N-labeled ammonium into nitrate.

Discussion/Conclusion

Comparing the results from N₂O isotopocule analyses and the ¹⁵N tracing approach, likely a combination of bD, nD, and coupled nitrification and denitrification (cND) was responsible for the vast part of N₂O emissions observed in this study. Overall, our findings help to better understand the processes underlying N₂O and N₂ emissions from hydroponic tomato cultivation, and thereby facilitate the development of targeted N₂O mitigation measures.

Effect of S2O32--S addition on Anammox coupling sulfur autotrophic denitrification and mechanism analysis using N and O dual isotope effects

Anaerobic ammonia oxidation (Anammox) coupling sulfur autotrophic denitrification is an effective method for the advanced nitrogen removal from the wastewater with limited carbon source. The influence of S₂O₃^2--S addition on Anammox coupling sulfur autotrophic denitrification was investigated by adding different concentrations of S₂O₃^2--S (0, 39, 78, 156 and 312 mg/L) to the Anammox system. The contribution of sulfur autotrophic denitrification and Anammox to nitrogen removal at S₂O₃^2--S concentrations of 156 mg/L was 75% ∼83% and 17%∼25%, respectively, and the mixed system achieved completely nitrogen removal. However, Anammox bioactivity was completely inhibited at S₂O₃^2--S concentrations up to 312 mg/L, and only sulfur autotrophic denitrification occurred. The isotopic effects of NO₂^--N (δ¹⁵N_NO2 and δ¹⁸O_NO2) and NO₃^--N (δ¹⁵N_NO3 and δ¹⁸O_NO3) during Anammox coupling sulfur autotrophic denitrification showed a gradual decrease trend with the increase of S₂O₃^2--S addition. The ratios of δ¹⁵N_NO2:δ¹⁸O_NO2 and δ¹⁵N_NO3:δ¹⁸O_NO3 was maintained at 1.30-2.41 and 1.36-2.52, respectively, which revealed that Anammox was dominant nitrogen removal pathway at S₂O₃^2--S concentrations less than 156 mg/L. Microbial diversity gradually decreased with the increase of S₂O₃^2--S. The S₂O₃^2--S addition enhanced the S₂O₃^2--driven autotrophic denitrification and weakened the Anammox, leading to a gradually decreasing trend of the proportion of Candidatus Brocadia as Anammox bacteria from the initial 27% to 4% (S₂O₃^2--S of 156 mg/L). Yet Norank-f-Hydrogenophilaceae (more than 50%) and Thiobacillus (54%) as functional bacteria of autotrophic denitrification obviously increased. The appropriate amount of S₂O₃^2--S addition promoted the performance of Anammox coupling sulfur autotrophic denitrification achieved completely nitrogen removal.

Isotopic assessment of soil N2O emission from a sub-tropical agricultural soil under varying N-inputs

Nitrogen fertilizers result in high crop productivity but also enhance the emission of N₂O, an environmentally harmful greenhouse gas. Only approximately a half of the applied nitrogen is utilized by crops and the rest is either vaporized, leached, or lost as NO, N₂O and N₂ via soil microbial activity. Thus, improving the nitrogen use efficiency of cropping systems has become a global concern. Factors such as types and rates of fertilizer application, soil texture, moisture level, pH, and microbial activity/diversity play important roles in N₂O production. Here, we report the results of N₂O production from a set of chamber experiments on an acidic sandy-loam agricultural soil under varying levels of an inorganic N-fertilizer, urea. Stable isotope technique was employed to determine the effect of increasing N-fertilizer levels on N₂O emissions and identify the microbial processes involved in fertilizer N-transformation that give rise to N₂O. We monitored the isotopic changes in both substrate (ammonium and nitrate) and the product N₂O during the entire course of the incubation experiments. Peak N₂O emissions of 122 ± 98 μg N₂O-N m^-2 h^-1, 338 ± 49 μg N₂O-N m^-2 h^-1 and 739 ± 296 μg N₂O-N m^-2 h^-1 were observed for urea application rate of 40, 80, and 120 μg N g^-1. The duration of emissions also increased with urea levels. The concentration and isotopic compositions of the substrates and product showed time-bound variation. Combining the observations of isotopic effects in δ¹⁵N, δ¹⁸O, and ¹⁵N site preference, we inferred co-occurrence of several microbial N₂O production pathways with nitrification and/or fungal denitrification as the dominant processes responsible for N₂O emissions. Besides this, dominant signatures of bacterial denitrification were observed in a second N₂O emission pulse in intermediate urea-N levels. Signature of N₂O consumption by reduction could be traced during declining emissions in treatment with high urea level.

Source partitioning using N2O isotopomers and soil WFPS to establish dominant N2O production pathways from different pasture sward compositions

Nitrous oxide (N₂O) is a potent greenhouse gas (GHG) emitted from agricultural soils and is influenced by nitrogen (N) fertiliser management and weather and soil conditions. Source partitioning N₂O emissions related to management practices and soil conditions could suggest effective mitigation strategies. Multispecies swards can maintain herbage yields at reduced N fertiliser rates compared to grass monocultures and may reduce N losses to the wider environment. A restricted-simplex centroid experiment was used to measure daily N₂O fluxes and associated isotopomers from eight experimental plots (7.8 m²) post a urea-N fertiliser application (40 kg N ha^-1). Experimental pastures consisted of differing proportions of grass, legume and forage herb represented by perennial ryegrass (Lolium perenne), white clover (Trifolium repens) and ribwort plantain (Plantago lanceolata), respectively. N₂O isotopomers were measured using a cavity ring down spectroscopy (CRDS) instrument adapted with a small sample isotope module (SSIM) for the analysis of gas samples ≤20 mL. Site preference (SP = δ¹⁵N^α - δ¹⁵N^β) and δ¹⁵N^bulk ((δ¹⁵N^α + δ¹⁵N^β) / 2) values were used to attribute N₂O production to nitrification, denitrification or a mixture of both nitrification and denitrification over a range of soil WFPS (%). Daily N₂O fluxes ranged from 8.26 to 86.86 g N₂O-N ha^-1 d^-1. Overall, 34.2% of daily N₂O fluxes were attributed to nitrification, 29.0% to denitrification and 36.8% to a mixture of both. A significant diversity effect of white clover and ribwort plantain on predicted SP and δ¹⁵N^bulk indicated that the inclusion of ribwort plantain may decrease N₂O emission through biological nitrification inhibition under drier soil conditions (31%-75% WFPS). Likewise, a sharp decline in predicted SP indicates that increased white clover content could increase N₂O emissions associated with denitrification under elevated soil moisture conditions (43%-77% WFPS). Biological nitrification inhibition from ribwort plantain inclusion in grassland swards and management of N fertiliser source and application timing to match soil moisture conditions could be useful N₂O mitigation strategies.

Enzyme-Specific Coupling of Oxygen and Nitrogen Isotope Fractionation of the Nap and Nar Nitrate Reductases

Dissimilatory nitrate reduction (DNR) to nitrite is the first step in denitrification, the main process through which bioavailable nitrogen is removed from ecosystems. DNR is catalyzed by both cytosolic (Nar) and periplasmic (Nap) nitrate reductases and fractionates the stable isotopes of nitrogen (¹⁴N, ¹⁵N) and oxygen (¹⁶O, ¹⁸O), which is reflected in residual environmental nitrate pools. Data on the relationship between the pattern in oxygen vs nitrogen isotope fractionation (¹⁸ε/¹⁵ε) suggests that systematic differences exist between marine and terrestrial ecosystems that are not fully understood. We examined the ¹⁸ε/¹⁵ε of nitrate-reducing microorganisms that encode Nar, Nap, or both enzymes, as well as gene deletion mutants of Nar and Nap to test the hypothesis that enzymatic differences alone could explain the environmental observations. We find that the distribution of ¹⁸ε/¹⁵ε fractionation ratios of all examined nitrate reductases forms two distinct peaks centered around an ¹⁸ε/¹⁵ε proportionality of 0.55 (Nap) and 0.91 (Nar), with the notable exception of the Bacillus Nar reductases, which cluster isotopically with the Nap reductases. Our findings may explain differences in ¹⁸ε/¹⁵ε fractionation between marine and terrestrial systems and challenge current knowledge about Nar ¹⁸ε/¹⁵ε signatures.

Nitrite isotope characteristics and associated soil N transformations

Nitrite (NO₂⁻) is a crucial compound in the N soil cycle. As an intermediate of nearly all N transformations, its isotopic signature may provide precious information on the active pathways and processes. NO₂⁻ analyses have already been applied in ¹⁵N tracing studies, increasing their interpretation perspectives. Natural abundance NO₂⁻ isotope studies in soils were so far not applied and this study aims at testing if such analyses are useful in tracing the soil N cycle. We conducted laboratory soil incubations with parallel natural abundance and ¹⁵N treatments, accompanied by isotopic analyses of soil N compounds (NO₃⁻, NO₂⁻, NH₄⁺). The double ¹⁵N tracing method was used as a reference method for estimations of N transformation processes based on natural abundance nitrite dynamics. We obtained a very good agreement between the results from nitrite isotope model proposed here and the ¹⁵N tracing approach. Natural abundance nitrite isotope studies are a promising tool to our understanding of soil N cycling.

Dual isotope ratio normalization of nitrous oxide by bacterial denitrification of USGS reference materials

We measured the δ values of N₂O using gas chromatography isotope ratio mass spectrometry with a preconcentrator (precon-GC-IRMS). The instrumental precision of the mass spectrometer was restricted to below the shot noise limit, which agreed with the theoretical and experimental results of 0.02‰ (δ¹⁵N) and 0.04‰ (δ¹⁸O), respectively. The precision of the measured δ values was significantly improved by the temperature regulation protocol of the LN₂ preconcentrator, which was monitored by various temperature sensors placed along the U-trap. The reproducibility of the He-diluted N₂O gas measurements resulted in 0.063‰ (δ¹⁵N) and 0.075‰ (δ¹⁸O) due to additional sources of uncertainty in the vials used for autosampling and in the general preconcentration process. Multipoint normalization of the dual δ values of the measured N₂O samples was conducted using United States Geological Survey reference materials denitrified by Pseudomonas aureofaciens. Kaiser's ion correction method, based on International Atomic Energy Agency parameters, exhibited low bias for the atomic isotope ratio reduction of the nitrate reference material, for which the oxygen anomaly was considerably high. Dedicated corrections for net isotope fractionation and water exchange were important in improving uncertainties in the procedure for normalizing the oxygen isotope ratio. Blank measurements for correcting biases in isotope ratios caused by pre-dissolved nitrate and nitrite ions in the water solvent led to further improvements, i.e. beyond unevenly controlled net isotope fractionation, throughout the bacterial denitrification process. The uncertainty evaluation revealed that three-point normalization can significantly improve the normalization accuracy compared with two-point normalization. In addition, an alternative strategy was suggested for assigning δ¹⁸O using a CO₂ lab tank, allowing its use as a reference material for N₂O gas tanks.

Identifying the origin of nitrous oxide dissolved in deep ocean by concentration and isotopocule analyses

Nitrous oxide (N₂O) contributes to global warming and stratospheric ozone depletion. Although its major sources are regarded as bacterial or archaeal nitrification and denitrification in soil and water, the origins of ubiquitous marine N₂O maximum at depths of 100–800 m and N₂O dissolved in deeper seawater have not been identified. We examined N₂O production processes in the middle and deep sea by analyzing vertical profiles of N₂O concentration and isotopocule ratios, abundance ratios of molecules substituted with rare stable isotopes ¹⁵N or ¹⁸O to common molecules ¹⁴N¹⁴N¹⁶O, in the Atlantic, Pacific, Indian, and Southern oceans. Isotopocule ratios suggest that the N₂O concentration maxima is generated by in situ microbial processes rather than lateral advection or diffusion from biologically active sea areas such as the eastern tropical North Pacific. Major production process is nitrification by ammonia-oxidizing archaea (AOA) in the North Pacific although other processes such as bacterial nitrification/denitrification and nitrifier-denitrification also significantly contribute in the equatorial Pacific, eastern South Pacific, Southern Ocean/southeastern Indian Ocean, and tropical South Atlantic. Concentrations of N₂O below 2000 m show significant correlation with the water mass age, which supports an earlier report suggesting production of N₂O during deep water circulation. Furthermore, the isotopocule ratios suggest that AOA produce N₂O in deep waters. These facts indicate that AOA have a more important role in marine N₂O production than bacteria and that change in global deep water circulation could affect concentration and isotopocule ratios of atmospheric N₂O in a millennium time scale.

Altering N2O emissions by manipulating wheat root bacterial community

Nitrous oxide (N₂O) is a greenhouse gas and a potent ozone-depleting substance in the stratosphere. Agricultural soils are one of the main global sources of N₂O emissions, particularly from cereal fields due to their high areal coverage. The aim of this study was to isolate N₂O-reducing bacteria able to mitigate N₂O emissions from the soil after inoculation. We isolated several bacteria from wheat roots that were capable of N₂O reduction in vitro and studied their genetic potential and activity under different environmental conditions. Three of these isolates- all carrying the nitrous oxide reductase-encoding clade I nosZ, able to reduce N₂O in vitro, and efficient colonizers of wheat roots- presented different N₂O-reduction strategies when growing in the root zone, possibly due to the different conditions in situ and their metabolic preferences. Each isolate seemed to prefer to operate at different altered oxygen levels. Isolate AU243 (related to Agrobacterium/Rhizobium) could reduce both nitrate and N₂O and operated better at lower oxygen levels. Isolate AU14 (related to Alcaligenes faecalis), lacking nitrate reductases, operated better under less anoxic conditions. Isolate NT128 (related to Pseudomonas stutzeri) caused slightly increased N₂O emissions under both anoxic and ambient conditions. These results therefore emphasize the importance of a deep understanding of soil–plant–microbe interactions when environmental application is being considered.

In Situ Quantification of Biological N2 Production Using Naturally Occurring 15N15N

We describe an approach for determining biological N₂ production in soils based on the proportions of naturally occurring ¹⁵N¹⁵N in N₂. Laboratory incubation experiments reveal that biological N₂ production, whether by denitrification or anaerobic ammonia oxidation, yields proportions of ¹⁵N¹⁵N in N₂ that are within 1‰ of that predicted for a random distribution of ¹⁵N and ¹⁴N atoms. This relatively invariant isotopic signature contrasts with that of the atmosphere, which has ¹⁵N¹⁵N proportions in excess of the random distribution by 19.1 ± 0.1‰. Depth profiles of gases in agricultural soils from the Kellogg Biological Station Long-Term Ecological Research site show biological N₂ accumulation that accounts for up to 1.6% of the soil N₂. One-dimensional reaction-diffusion modeling of these soil profiles suggests that subsurface N₂ pulses leading to surface emission rates as low as 0.3 mmol N₂ m^-2 d^-1 can be detected with current analytical precision, decoupled from N₂O production.

Biochar amendment suppresses N2 O emissions but has no impact on 15 N site preference in an anaerobic soil

RATIONALE

Biochar amendments often decrease N₂ O gas production from soil, but the mechanisms and magnitudes are still not well characterized since N₂ O can be produced via several different microbial pathways. We evaluated the influence of biochar amendment on N₂ O emissions and N₂ O isotopic composition, including ¹⁵ N site preference (SP) under anaerobic conditions.

METHODS

An agricultural soil was incubated with differing levels of biochar. Incubations were conducted under anaerobic conditions for 10 days with and without acetylene, which inhibits N₂ O reduction to N₂ . The N₂ O concentrations were measured every 2 days, the SPs were determined after 5 days of incubation, and the inorganic nitrogen concentrations were measured after the incubation.

RESULTS

The SP values with acetylene were consistent with N₂ O production by bacterial denitrification and those without acetylene were consistent with bacterial denitrification that included N₂ O reduction to N₂ . There was no effect of biochar on N₂ O production in the presence of acetylene between day 3 and day 10. However, in the absence of acetylene, soils incubated with 4% biochar produced less N₂ O than soils with no biochar addition. Different amounts of biochar amendment did not change the SP values.

CONCLUSIONS

Our study used N₂ O emission rates and SP values to understand biochar amendment mechanisms and demonstrated that biochar amendment reduces N₂ O emissions by stimulating the last step of denitrification. It also suggested a possible shift in N₂ O-reducing microbial taxa in 4% biochar samples.

High nitrogen isotope fractionation of nitrate during denitrification in four forest soils and its implications for denitrification rate estimates

Denitrification is a major process contributing to the removal of nitrogen (N) from ecosystems, but its rate is difficult to quantify. The natural abundance of isotopes can be used to identify the occurrence of denitrification and has recently been used to quantify denitrification rates at the ecosystem level. However, the technique requires an understanding of the isotopic enrichment factor associated with denitrification, which few studies have investigated in forest soils. Here, soils collected from two tropical and two temperate forests in China were incubated under anaerobic or aerobic laboratory conditions for two weeks to determine the N and oxygen (O) isotope enrichment factors during denitrification. We found that at room temperature (20°C), NO₃^- was reduced at a rate of 0.17 to 0.35μgNg^-1h^-1, accompanied by the isotope fractionation of N (¹⁵ε) and O (¹⁸ε) of 31‰ to 65‰ (48.3±2.0‰ on average) and 11‰ to 39‰ (18.9±1.7‰ on average), respectively. The N isotope effects were, unexpectedly, much higher than reported in the literature for heterotrophic denitrification (typically ranging from 5‰ to 30‰) and in other environmental settings (e.g., groundwater, marine sediments and agricultural soils). In addition, the ratios of Δδ¹⁸O:Δδ¹⁵N ranged from 0.28 to 0.60 (0.38±0.02 on average), which were lower than the canonical ratios of 0.5 to 1 for denitrification reported in other terrestrial and freshwater systems. We suggest that the isotope effects of denitrification for soils may vary greatly among regions and soil types and that gaseous N losses may have been overestimated for terrestrial ecosystems in previous studies in which lower fractionation factors were applied.

Steady-State Oxygen Isotope Effects of N2O Production in Paracoccus denitrificans

Knowledge of isotopic discrimination, or fractionation, by denitrifying bacteria can benefit agricultural fertilizer management, wastewater treatment, and other applications. However, the complexity of N transformation pathways in the environment and the sensitivity of denitrification to environmental conditions warrant better isotopic distinction between denitrification and other processes, especially for oxygen isotopes. Here, we present a dataset of δ¹⁸O measurements in continuous culture of Paracoccus denitrificans. The authors hope that it will be useful in further studies of N₂O in the environment.

Isotopocule analysis of biologically produced nitrous oxide in various environments

Natural abundance ratios of isotopocules, molecules that have the same chemical constitution and configuration, but that only differ in isotope substitution, retain a record of a compound's origin and reactions. A method to measure isotopocule ratios of nitrous oxide (N₂ O) has been established by using mass analysis of molecular ions and fragment ions. The method has been applied widely to environmental samples from the atmosphere, ocean, fresh water, soils, and laboratory-simulation experiments. Results show that isotopocule ratios, particularly the ¹⁵ N-site preference (difference between isotopocule ratios ¹⁴ N¹⁵ N¹⁶ O/¹⁴ N¹⁴ N¹⁶ O and ¹⁵ N¹⁴ N¹⁶ O/¹⁴ N¹⁴ N¹⁶ O), have a wide range that depends on their production and consumption processes. Observational and laboratory studies of N₂ O related to biological processes are reviewed and discussed to elucidate complex material cycles of this trace gas, which causes global warming and stratospheric ozone depletion. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:135-160, 2017.

Feasibility of two low-cost organic substrates for inducing denitrification in artificial recharge ponds: Batch and flow-through experiments

Anaerobic batch and flow-through experiments were performed to assess the capacity of two organic substrates to promote denitrification of nitrate-contaminated groundwater within managed artificial recharge systems (MAR) in arid or semi-arid regions. Denitrification in MAR systems can be achieved through artificial recharge ponds coupled with a permeable reactive barrier in the form of a reactive organic layer. In arid or semi-arid regions, short-term efficient organic substrates are required due to the short recharge periods. We examined the effectiveness of two low-cost, easily available and easily handled organic substrates, commercial plant-based compost and crushed palm tree leaves, to determine the feasibility of using them in these systems. Chemical and multi-isotopic monitoring (δ¹⁵N_NO3, δ¹⁸O_NO3, δ³⁴S_SO4, δ¹⁸O_SO4) of the laboratory experiments confirmed that both organic substrates induced denitrification. Complete nitrate removal was achieved in all the experiments with a slight transient nitrite accumulation. In the flow-through experiments, ammonium release was observed at the beginning of both experiments and lasted longer for the experiment with palm tree leaves. Isotopic characterisation of the released ammonium suggested ammonium leaching from both organic substrates at the beginning of the experiments and pointed to ammonium production by DNRA for the palm tree leaves experiment, which would only account for a maximum of 15% of the nitrate attenuation. Sulphate reduction was achieved in both column experiments. The amount of organic carbon consumed during denitrification and sulphate reduction was 0.8‰ of the total organic carbon present in commercial compost and 4.4% for the palm tree leaves. The N and O isotopic fractionation values obtained (ε_N and ε_O) were -10.4‰ and -9.0‰ for the commercial compost (combining data from both batch and column experiments), and -9.9‰ and -8.6‰ for the palm tree column, respectively. Both materials showed a satisfactory capacity for denitrification, but the palm tree leaves gave a higher denitrification rate and yield (amount of nitrate consumed per amount of available C) than commercial compost.

Plant δ15 N reflects the high landscape-scale heterogeneity of soil fertility and vegetation productivity in a Mediterranean semiarid ecosystem

We investigated the magnitude and drivers of spatial variability in soil and plant δ¹⁵ N across the landscape in a topographically complex semiarid ecosystem. We hypothesized that large spatial heterogeneity in water availability, soil fertility and vegetation cover would be positively linked to high local-scale variability in δ¹⁵ N. We measured foliar δ¹⁵ N in three dominant plant species representing contrasting plant functional types (tree, shrub, grass) and mycorrhizal association types (ectomycorrhizal or arbuscular mycorrhizal). This allowed us to investigate whether δ¹⁵ N responds to landscape-scale environmental heterogeneity in a consistent way across species. Leaf δ¹⁵ N varied greatly within species across the landscape and was strongly spatially correlated among co-occurring individuals of the three species. Plant δ¹⁵ N correlated tightly with soil δ¹⁵ N and key measures of soil fertility, water availability and vegetation productivity, including soil nitrogen (N), organic carbon (C), plant-available phosphorus (P), water-holding capacity, topographic moisture indices and normalized difference vegetation index. Multiple regression models accounted for 62-83% of within-species variation in δ¹⁵ N across the landscape. The tight spatial coupling and interdependence of the water, N and C cycles in drylands may allow the use of leaf δ¹⁵ N as an integrative measure of variations in moisture availability, biogeochemical activity, soil fertility and vegetation productivity (or 'site quality') across the landscape.

Nitrogen, carbon, and sulfur isotopic change during heterotrophic (Pseudomonas aureofaciens) and autotrophic (Thiobacillus denitrificans) denitrification reactions

In batch culture experiments, we examined the isotopic change of nitrogen in nitrate (δ(15)NNO3), carbon in dissolved inorganic carbon (δ(13)CDIC), and sulfur in sulfate (δ(34)SSO4) during heterotrophic and autotrophic denitrification of two bacterial strains (Pseudomonas aureofaciens and Thiobacillus denitrificans). Heterotrophic denitrification (HD) experiments were conducted with trisodium citrate as electron donor, and autotrophic denitrification (AD) experiments were carried out with iron disulfide (FeS2) as electron donor. For heterotrophic denitrification experiments, a complete nitrate reduction was accomplished, however bacterial denitrification with T. denitrificans is a slow process in which, after seventy days nitrate was reduced to 40% of the initial concentration by denitrification. In the HD experiment, systematic change of δ(13)CDIC (from -7.7‰ to -12.2‰) with increase of DIC was observed during denitrification (enrichment factor εN was -4.7‰), suggesting the contribution of C of trisodium citrate (δ(13)C=-12.4‰). No SO4(2-) and δ(34)SSO4 changes were observed. In the AD experiment, clear fractionation of δ(13)CDIC during DIC consumption (εC=-7.8‰) and δ(34)SSO4 during sulfur use of FeS2-S (around 2‰), were confirmed through denitrification (εN=-12.5‰). Different pattern in isotopic change between HD and AD obtained on laboratory-scale are useful to recognize the type of denitrification occurring in the field.

Isotope fractionation factors controlling isotopocule signatures of soil-emitted N₂O produced by denitrification processes of various rates

RATIONALE

This study aimed (i) to determine the isotopic fractionation factors associated with N2O production and reduction during soil denitrification and (ii) to help specify the factors controlling the magnitude of the isotope effects. For the first time the isotope effects of denitrification were determined in an experiment under oxic atmosphere and using a novel approach where N2O production and reduction occurred simultaneously.

METHODS

Soil incubations were performed under a He/O2 atmosphere and the denitrification product ratio [N2O/(N2 + N2O)] was determined by direct measurement of N2 and N2O fluxes. N2O isotopocules were analyzed by mass spectrometry to determine δ(18)O, δ(15)N and (15)N site preference within the linear N2O molecule (SP). An isotopic model was applied for the simultaneous determination of net isotope effects (η) of both N2O production and reduction, taking into account emissions from two distinct soil pools.

RESULTS

A clear relationship was observed between (15)N and (18)O isotope effects during N2O production and denitrification rates. For N2O reduction, diverse isotope effects were observed for the two distinct soil pools characterized by different product ratios. For moderate product ratios (from 0.1 to 1.0) the range of isotope effects given by previous studies was confirmed and refined, whereas for very low product ratios (below 0.1) the net isotope effects were much smaller.

CONCLUSIONS

The fractionation factors associated with denitrification, determined under oxic incubation, are similar to the factors previously determined under anoxic conditions, hence potentially applicable for field studies. However, it was shown that the η(18)O/η(15)N ratios, previously accepted as typical for N2O reduction processes (i.e., higher than 2), are not valid for all conditions.

Denitrification, anammox, and N₂ production in marine sediments

Fixed nitrogen limits primary productivity in many parts of the global ocean, and it consequently plays a role in controlling the carbon dioxide content of the atmosphere. The concentration of fixed nitrogen is determined by the balance between two processes: the fixation of nitrogen gas into organic forms by diazotrophs, and the reconversion of fixed nitrogen to nitrogen gas by denitrifying organisms. However, current sedimentary denitrification rates are poorly constrained, especially in permeable sediments, which cover the majority of the continental margin. Also, anammox has recently been shown to be an additional pathway for the loss of fixed nitrogen in sediments. This article briefly reviews sedimentary fixed nitrogen loss by sedimentary denitrification and anammox, including in sediments in contact with oxygen-deficient zones. A simple extrapolation of existing rate measurements to the global sedimentary denitrification rate yields a value smaller than many existing measurement-based estimates but still larger than the rate of water column denitrification.

N and O isotope fractionation in nitrate during chemolithoautotrophic denitrification by Sulfurimonas gotlandica

Chemolithoautotrophic denitrification is an important mechanism of nitrogen loss in the water column of euxinic basins, but its isotope fractionation factor is not known. Sulfurimonas gotlandica GD1(T), a recently isolated bacterial key player in Baltic Sea pelagic redoxcline processes, was used to determine the isotope fractionation of nitrogen and oxygen in nitrate during denitrification. Under anoxic conditions, nitrate reduction was accompanied by nitrogen and oxygen isotope fractionation of 23.8 ± 2.5‰ and 11.7 ± 1.1‰, respectively. The isotope effect for nitrogen was in the range determined for heterotrophic denitrification, with only the absence of stirring resulting in a significant decrease of the fractionation factor. The relative increase in δ(18)ONO3 to δ(15)NNO3 did not follow the 1:1 relationship characteristic of heterotrophic, marine denitrification. Instead, δ(18)ONO3 increased slower than δ(15)NNO3, with a conserved ratio of 0.5:1. This result suggests that the periplasmic nitrate reductase (Nap) of S. gotlandica strain GD1(T) fractionates the N and O in nitrate differently than the membrane-bound nitrate reductase (Nar), which is generally prevalent among heterotrophic denitrifiers and is considered as the dominant driver for the observed isotope fractionation. Hence in the Baltic Sea redoxcline, other, as yet-unidentified factors likely explain the low apparent fractionation.

Isotopic fractionation by a fungal P450 nitric oxide reductase during the production of N2O

Nitrous oxide (N2O) is a potent greenhouse gas with a 100-year global warming potential approximately 300 times that of CO2. Because microbes account for over 75% of the N2O released in the U.S., understanding the biochemical processes by which N2O is produced is critical to our efforts to mitigate climate change. In the current study, we used gas chromatography-isotope ratio mass spectrometry (GC-IRMS) to measure the δ(15)N, δ(18)O, δ(15)N(α), and δ(15)N(β) of N2O generated by purified fungal nitric oxide reductase (P450nor) from Histoplasma capsulatum. The isotope values were used to calculate site preference (SP) values (difference in δ(15)N between the central (α) and terminal (β) N atoms in N2O), enrichment factors (ε), and kinetic isotope effects (KIEs). Both oxygen and N(α) displayed normal isotope effects during enzymatic NO reduction with ε values of -25.7‰ (KIE = 1.0264) and -12.6‰ (KIE = 1.0127), respectively. However, bulk nitrogen (average δ(15)N of N(α) and N(β)) and N(β) exhibited inverse isotope effects with ε values of 14.0‰ (KIE = 0.9862) and 36.1‰ (KIE = 0.9651), respectively. The observed inverse isotope effect in δ(15)N(β) is consistent with reversible binding of the first NO in the P450nor reaction mechanism. In contrast to the constant SP observed during NO reduction in microbial cultures, the site preference measured for purified H. capsulatum P450nor was not constant, increasing from ∼ 15‰ to ∼ 29‰ during the course of the reaction. This indicates that SP for microbial cultures can vary depending on the growth conditions, which may complicate source tracing during microbial denitrification.

Soil denitrification potential and its influence on N2O reduction and N2O isotopomer ratios

RATIONALE

N2O isotopomer ratios may provide a useful tool for studying N2O source processes in soils and may also help estimating N2O reduction to N2. However, remaining uncertainties about different processes and their characteristic isotope effects still hamper its application. We conducted two laboratory incubation experiments (i) to compare the denitrification potential and N2O/(N2O+N2) product ratio of denitrification of various soil types from Northern Germany, and (ii) to investigate the effect of N2O reduction on the intramolecular (15)N distribution of emitted N2O.

METHODS

Three contrasting soils (clay, loamy, and sandy soil) were amended with nitrate solution and incubated under N2 -free He atmosphere in a fully automated incubation system over 9 or 28 days in two experiments. N2O, N2, and CO2 release was quantified by online gas chromatography. In addition, the N2O isotopomer ratios were determined by isotope-ratio mass spectrometry (IRMS) and the net enrichment factors of the (15)N site preference (SP) of the N2O-to-N2 reduction step (η(SP)) were estimated using a Rayleigh model.

RESULTS

The total denitrification rate was highest in clay soil and lowest in sandy soil. Surprisingly, the N2O/(N2O+N2) product ratio in clay and loam soil was identical; however, it was significantly lower in sandy soil. The IRMS measurements revealed highest N2O SP values in clay soil and lowest SP values in sandy soil. The η(SP) values of N2O reduction were between -8.2 and -6.1‰, and a significant relationship between δ(18)O and SP values was found.

CONCLUSIONS

Both experiments showed that the N2O/(N2O+N2) product ratio of denitrification is not solely controlled by the available carbon content of the soil or by the denitrification rate. Differences in N2O SP values could not be explained by variations in N2O reduction between soils, but rather originate from other processes involved in denitrification. The linear δ(18)O vs SP relationship may be indicative for N2O reduction; however, it deviates significantly from the findings of previous studies.

Nitrous oxide emissions from soils: how well do we understand the processes and their controls?

Although it is well established that soils are the dominating source for atmospheric nitrous oxide (N₂O), we are still struggling to fully understand the complexity of the underlying microbial production and consumption processes and the links to biotic (e.g. inter- and intraspecies competition, food webs, plant–microbe interaction) and abiotic (e.g. soil climate, physics and chemistry) factors. Recent work shows that a better understanding of the composition and diversity of the microbial community across a variety of soils in different climates and under different land use, as well as plant–microbe interactions in the rhizosphere, may provide a key to better understand the variability of N₂O fluxes at the soil–atmosphere interface. Moreover, recent insights into the regulation of the reduction of N₂O to dinitrogen (N₂) have increased our understanding of N₂O exchange. This improved process understanding, building on the increased use of isotope tracing techniques and metagenomics, needs to go along with improvements in measurement techniques for N₂O (and N₂) emission in order to obtain robust field and laboratory datasets for different ecosystem types. Advances in both fields are currently used to improve process descriptions in biogeochemical models, which may eventually be used not only to test our current process understanding from the microsite to the field level, but also used as tools for up-scaling emissions to landscapes and regions and to explore feedbacks of soil N₂O emissions to changes in environmental conditions, land management and land use.

Insights on the marine microbial nitrogen cycle from isotopic approaches to nitrification

The microbial nitrogen (N) cycle involves a variety of redox processes that control the availability and speciation of N in the environment and that are involved with the production of nitrous oxide (N₂O), a climatically important greenhouse gas. Isotopic measurements of ammonium (NH⁺₄), nitrite (NO⁻₂), nitrate (NO⁻₃), and N₂O can now be used to track the cycling of these compounds and to infer their sources and sinks, which has lead to new and exciting discoveries. For example, dual isotope measurements of NO⁻₃ and NO⁻₂ have shown that there is NO⁻₃ regeneration in the ocean's euphotic zone, as well as in and around oxygen deficient zones (ODZs), indicating that nitrification may play more roles in the ocean's N cycle than generally thought. Likewise, the inverse isotope effect associated with NO⁻₂ oxidation yields unique information about the role of this process in NO⁻₂ cycling in the primary and secondary NO⁻₂ maxima. Finally, isotopic measurements of N₂O in the ocean are indicative of an important role for nitrification in its production. These interpretations rely on knowledge of the isotope effects for the underlying microbial processes, in particular ammonia oxidation and nitrite oxidation. Here we review the isotope effects involved with the nitrification process and the insights provided by this information, then provide a prospectus for future work in this area.

Effect of different carbon substrates on nitrate stable isotope fractionation during microbial denitrification

In batch experiments, we studied the isotope fractionation in N and O of dissolved nitrate during dentrification. Denitrifying strains Thauera aromatica and "Aromatoleum aromaticum strain EbN1" were grown under strictly anaerobic conditions with acetate, benzoate, and toluene as carbon sources. (18)O-labeled water and (18)O-labeled nitrite were added to the microcosm experiments to study the effect of putative backward reactions of nitrite to nitrate on the stable isotope fractionation. We found no evidence for a reverse reaction. Significant variations of the stable isotope enrichment factor ε were observed depending on the type of carbon source used. For toluene (ε(15)N, -18.1 ± 0.6‰ to -7.3 ± 1.4‰; ε(18)O, -16.5 ± 0.6‰ to -16.1 ± 1.5‰) and benzoate (ε(15)N, -18.9 ± 1.3‰; ε(18)O, -15.9 ± 1.1‰) less negative isotope enrichment factors were calculated compared to those derived from acetate (ε(15)N, -23.5 ± 1.9‰ to -22.1 ± 0.8‰; ε(18)O, -23.7 ± 1.8‰ to -19.9 ± 0.8‰). The observed isotope effects did not depend on the growth kinetics which were similar for the three types of electron donors. We suggest that different carbon sources change the observed isotope enrichment factors by changing the relative kinetics of nitrate transport across the cell wall compared to the kinetics of the intracellular nitrate reduction step of microbial denitrification.

Isotopologue enrichment factors of N(2)O reduction in soils

Isotopic signatures can be used to study sink and source processes of N(2)O, but the success of this approach is limited by insufficient knowledge on the isotope fractionation factors of the various reaction pathways. We investigated isotope enrichment factors of the N(2)O-to-N(2) step of denitrification (epsilon) in two arable soils, a silt-loam Haplic Luvisol and a sandy Gleyic Podzol. In addition to the epsilon of (18)O (epsilon(18O)) and of average (15)N (epsilon(bulk)), the epsilon of the (15)N site preference within the linear N(2)O molecule (epsilon(SP)) was also determined. Soils were anaerobically incubated in gas-tight bottles with N(2)O added to the headspace to induce N(2)O reduction. Pre-treatment included the removal of NO(3) (-) to prevent N(2)O production. Gas samples were collected regularly to determine the dynamics of N(2)O reduction, the time course of the isotopic signatures of residual N(2)O, and the associated isotope enrichment factors. To vary reduction rates and associated fractionation factors, several treatments were established including two levels of initial N(2)O concentration and anaerobic pre-incubation with or without addition of N(2)O. N(2)O reduction rates were affected by the soil type and initial N(2)O concentration. The epsilon(18O) and epsilon(bulk) ranged between -13 and -20 per thousand, and between -5 and -9 per thousand, respectively. Both quantities were more negative in the Gleyic Podzol. The epsilon of the central N position (epsilon(alpha)) was always larger than that of the peripheral N-position (epsilon(beta)), giving epsilon(SP) of -4 to -8 per thousand. The ranges and variation patterns of epsilon were comparable with those from previous static incubation studies with soils. Moreover, we found a relatively constant ratio between epsilon(18O) and epsilon(bulk) which is close to the default ratio of 2.5 that had been previously suggested. The fact that different soils exhibited comparable epsilon under certain conditions suggests that these values could serve to identify N(2)O reduction from the isotopic fingerprints of N(2)O emitted from any soil.

N(2)O concentration and isotope signature along profiles provide deeper insight into the fate of N(2)O in soils

Nitrous oxide is an important greenhouse gas and its origin and fate are thus of broad interest. Most studies on emissions of nitrous oxide from soils focused on fluxes between soil and atmosphere and hence represent an integration of physical and biological processes at different depths of a soil profile. Analysis of N(2)O concentration and isotope signature along soil profiles was suggested to improve the localisation of sources and sinks in soils as well as underlying processes and could therefore extend our knowledge on processes affecting surface N(2)O fluxes. Such a mechanistic understanding would be desirable to improve N(2)O mitigation strategies and global N(2)O budgets. To investigate N(2)O dynamics within soil profiles of two contrasting (semi)natural ecosystem types (a temperate acidic fen and a Norway spruce forest), soil gas samplers were constructed to meet the different requirements of a water-saturated and an unsaturated soil, respectively. The samplers were installed in three replicates and allowed soil gas sampling from six different soil depths. We analysed soil air for N(2)O concentration and isotope composition and calculated N(2)O net turnover using a mass balance approach and considering diffusive fluxes. At the fen site, N(2)O was mainly produced in 30-50 cm soil depth. Diffusion to adjacent layers above and below indicated N(2)O consumption. Values of delta(15)N and delta(18)O of N(2)O in the fen soil were always linearly correlated and their qualitative changes within the profile corresponded with the calculated turnover processes, suggesting further reduction of N(2)O. In the spruce forest, highest N(2)O production occurred in the topsoil, but there was also notable production occurring in the subsoil at a depth of 70 cm. Changes in N(2)O isotope composition as to be expected from local production and consumption processes within the soil profile did hardly occur, though. This was presumably caused by high diffusive fluxes and comparatively low net turnover, as isotope signatures approached values measured for ambient N(2)O towards the topsoil. Our results demonstrate a highly variable influence of diffusive versus production/consumption processes on N(2)O concentration and isotope composition, depending on the type of ecosystem. This finding indicates the necessity of further N(2)O concentration and isotope profile investigations in different types of natural and anthropogenic ecosystems in order to generalise our mechanistic understanding of N(2)O exchange between soil and atmosphere.

Isotopologue fractionation during N(2)O production by fungal denitrification

Identifying the importance of fungi to nitrous oxide (N2O) production requires a non-intrusive method for differentiating between fungal and bacterial N2O production such as natural abundance stable isotopes. We compare the isotopologue composition of N2O produced during nitrite reduction by the fungal denitrifiers Fusarium oxysporum and Cylindrocarpon tonkinense with published data for N2O production during bacterial nitrification and denitrification. The fractionation factors for bulk nitrogen isotope values for fungal denitrification were in the range -74.7 to -6.6 per thousand. There was an inverse relationship between the absolute value of the fractionation factors and the reaction rate constant. We interpret this in terms of variation in the relative importance of the rate constants for diffusion and enzymatic reduction in controlling the net isotope effect for N2O production during fungal denitrification. Over the course of nitrite reduction, the delta(18)O values for N2O remained constant and did not exhibit a relationship with the concentration characteristic of an isotope effect. This probably reflects isotopic exchange with water. Similar to the delta(18)O data, the site preference (SP; the difference in delta(15)N between the central and outer N atoms in N2O) was unrelated to concentration during nitrite reduction and, therefore, has the potential to act as a conservative tracer of production from fungal denitrification. The SP values of N2O produced by F. oxysporum and C. tonkinense were 37.1 +/- 2.5 per thousand and 36.9 +/- 2.8 per thousand, respectively. These SP values are similar to those obtained in pure culture studies of bacterial nitrification but quite distinct from SP values for bacterial denitrification. The large magnitude of the bulk nitrogen isotope fractionation and the delta(18)O values associated with fungal denitrification are distinct from bacterial production pathways; thus multiple isotopologue data holds much promise for resolving bacterial and fungal production. Our work further provides insight into the role that fungal and bacterial nitric oxide reductases have in determining site preference during N2O production.

Isotope fractionation factors of N2O diffusion

Isotopic signatures of N2O are increasingly used to constrain the total global flux and the relative contribution of nitrification and denitrification to N2O emissions. Interpretation of isotopic signatures of soil-emitted N2O can be complicated by the isotopic effects of gas diffusion. The aim of our study was to measure the isotopic fractionation factors of diffusion for the isotopologues of N2O and to estimate the potential effect of diffusive fractionation during N2O fluxes from soils using simple simulations. Diffusion experiments were conducted to monitor isotopic signatures of N2O in reservoirs that lost N2O by defined diffusive fluxes. Two different mathematical approaches were used to derive diffusive isotope fractionation factors for 18O (epsilon18O), average 15N (epsilonbulk) and 15N of the central (alpha(-)) and peripheral (beta(-)) position within the linear N2O molecule (epsilon15Nalpha, epsilon15Nbeta). The measured epsilon18O was -7.79 +/- 0.27 per thousand and thus higher than the theoretical value of -8.7 per thousand. Conversely, the measured epsilonbulk (-5.23 +/- 0.27 per thousand) was lower than the theoretical value (-4.4 per thousand). The measured site-specific 15N fractionation factors were not equal, giving a difference between epsilon15Nalpha and epsilon15Nbeta (epsilonSP) of 1.55 +/- 0.28 per thousand. Diffusive fluxes of the N2O isotopologues from the soil pore space to the atmosphere were simulated, showing that isotopic signatures of N2O source pools and emitted N2O can be substantially different during periods of non-steady state fluxes. Our results show that diffusive isotope fractionation should be taken into account when interpreting natural abundance isotopic signatures of N2O fluxes from soils.

A review of stable isotope techniques for N2O source partitioning in soils: recent progress, remaining challenges and future considerations

Nitrous oxide is produced in soil during several processes, which may occur simultaneously within different micro-sites of the same soil. Stable isotope techniques have a crucial role to play in the attribution of N(2)O emissions to different microbial processes, through estimation (natural abundance, site preference) or quantification (enrichment) of processes based on the (15)N and (18)O signatures of N(2)O determined by isotope ratio mass spectrometry. These approaches have the potential to become even more powerful when linked with recent developments in secondary isotope mass spectrometry, with microbial ecology, and with modelling approaches, enabling sources of N(2)O to be considered at a wide range of scales and related to the underlying microbiology. Such source partitioning of N(2)O is inherently challenging, but is vital to close the N(2)O budget and to better understand controls on the different processes, with a view to developing appropriate management practices for mitigation of N(2)O. In this respect, it is essential that as many of the contributing processes as possible are considered in any study aimed at source attribution, as mitigation strategies for one process may not be appropriate for another. To aid such an approach, here the current state of the art is critically examined, remaining challenges are highlighted, and recommendations are made for future direction.

Estimation of nitrogen removal rate in aqueous phase based on delta15N in microorganisms in solid phase

Microbial nitrification and denitrification are important processes for removing nitrogenous compounds in aqueous systems. Nitrogen removal rate estimation is essential for controlling nitrogen removal processes and modeling the nitrogen cycle in ecosystems. The model described the relationship between ammonium removal rate (aqueous phase) and the nitrogen stable isotope ratio (delta15N) of microorganisms (solid phase) when a coupled nitrification-denitrification process occurs and assimilation and advections are maintained in a steady state. An oxidation ditch in a municipal wastewater treatment plant was evaluated for 3 years using the model. The ammonium removal rate was calculated from the data of delta15N of the activated sludge, it correlated significantly with the observed removal rate. The isotope fractionation factor (epsilon) was determined to be -5.5 per thousand by using a nonlinear method. The model and obtained factor value were applicable for standard activated-sludge processes performed in parallel in the oxidation ditch and a river watershed. The model may help illustrate nitrogen behavior in ecosystems.

The intramolecular δ15N of lysine responds to respiratory status in Paracoccus denitrificans

Presented here is the first experimental evidence that natural, intramolecular, isotope ratios are sensitive to physiological status, based on observations of intramolecular delta(15)N of lysine in the mitochondrial mimic Paracoccus denitrificans. Paracoccus denitrificans, a versatile, gram-negative bacterium, was grown either aerobically or anaerobically on isotopically-characterized ammonium as sole cell-nitrogen source. Nitrogen isotope composition of the biomass with respect to source ammonium was Delta(15)N(cell - NH4) = delta(15) - delta(15)N(NH4) = -6.2 +/- 1.2 per thousand for whole cells under aerobic respiration, whereas cells grown anaerobically produced no net fractionation (Delta(15)N(cell - NH4) = -0.3 +/- 0.23 per thousand). Fractionation of (15)N between protein nitrogen and total cell nitrogen increased during anaerobic respiration and suggests that residual nitrogen-containing compounds in bacterial cell membranes are isotopically lighter under anaerobic respiration. In aerobic cells, the lysine intramolecular difference between peptide and sidechain nitrogen is negligible, but in anaerobic cells was a remarkable Delta(15)N(p - s) = delta(15)N(peptide) - delta(15)N(sidechain) = +11.0 per thousand, driven predominantly by enrichment at the peptide N. Consideration of known lysine pathways suggests this to be likely due to enhanced synthesis of peptidoglycans in the anaerobic state. These data indicate that distinct pathway branching ratios associated with microbial respiration can be detected by natural intramolecular Deltadelta(15)N measurements, and are the first in vivo observations of position-specific measurements of nitrogen isotope fractionation.

The calibration of the intramolecular nitrogen isotope distribution in nitrous oxide measured by isotope ratio mass spectrometry

Two alternative approaches for the calibration of the intramolecular nitrogen isotope distribution in nitrous oxide using isotope ratio mass spectrometry have yielded a difference in the 15N site preference (defined as the difference between the delta15N of the central and end position nitrogen in NNO) of tropospheric N2O of almost 30 per thousand. One approach is based on adding small amounts of labeled 15N2O to the N2O reference gas and tracking the subsequent changes in m/z 30, 31, 44, 45 and 46, and this yields a 15N site preference of 46.3 +/- 1.4 per thousand for tropospheric N2O. The other involves the synthesis of N2O by thermal decomposition of isotopically characterized ammonium nitrate and yields a 15N site preference of 18.7 +/- 2.2 per thousand for tropospheric N2O. Both approaches neglect to fully account for isotope effects associated with the formation of NO+ fragment ions from the different isotopic species of N2O in the ion source of a mass spectrometer. These effects vary with conditions in the ion source and make it impossible to reproduce a calibration based on the addition of isotopically enriched N2O on mass spectrometers with different ion source configurations. These effects have a much smaller impact on the comparison of a laboratory reference gas with N2O synthesized from isotopically characterized ammonium nitrate. This second approach was successfully replicated and leads us to advocate the acceptance of the site preference value 18.7 +/- 2.2 per thousand for tropospheric N2O as the provisional community standard until further independent calibrations are developed and validated. We present a technique for evaluating the isotope effects associated with fragment ion formation and revised equations for converting ion signal ratios into isotopomer ratios.

Influence of 15N enrichment on the net isotopic fractionation factor during the reduction of nitrate to nitrous oxide in soil

Nitrous oxide, a greenhouse gas, is mainly emitted from soils during the denitrification process. Nitrogen stable-isotope investigations can help to characterise the N(2)O source and N(2)O production mechanisms. The stable-isotope approach is increasingly used with (15)N natural abundance or relatively low (15)N enrichment levels and requires a good knowledge of the isotopic fractionation effect inherent to this biological mechanism. This paper reports the measurement of the net and instantaneous isotopic fractionation factor (alpha(s/p) (i)) during the denitrification of NO(3) (-) to N(2)O over a range of (15)N substrate enrichments (0.37 to 1.00 atom% (15)N). At natural abundance level, the isotopic fractionation effect reported falls well within the range of data previously observed. For (15)N-enriched substrate, the value of alpha(s/p) (i) was not constant and decreased from 1.024 to 1.013, as a direct function of the isotopic enrichment of the labelled nitrate added. However, for enrichment greater than 0.6 atom% (15)N, the value of alpha(s/p) (i) seems to be independent of substrate isotopic enrichment. These results suggest that for isotopic experiments applied to N(2)O emissions, the use of low (15)N-enriched tracers around 1.00 atom% (15)N is valid. At this enrichment level, the isotopic effect appears negligible in comparison with the enrichment of the substrate.

Fractionation factors for stable isotopes of N and O during N2O reduction in soil depend on reaction rate constant

Nitrous oxide (N(2)O) is a major greenhouse gas that is mainly produced but also reduced by microorganisms in soils. We determined factors for N and O isotope fractionation during the reduction of N(2)O to N(2) in soil in a flow-through incubation experiment. The absolute value of the fractionation factors decreased with increasing reaction rate constant. Reaction rates constants ranged from 1.7 10(-4) s(-1) to 4.5 10(-3) s(-1). The minimum, maximum and median of the observed fractionation factors were for N -36.0 per thousand, -1.0 per thousand and -9.3 per thousand and for O -74.0 per thousand, -6.9 per thousand and -26.3 per thousand, respectively. The ratio of O isotope fractionation to N isotope fractionation was 2.4 +/- 0.3 and it was independent from the reaction rate constants. This leads us to conclude that fractionation factors are variables while their ratio in this particular reaction might be a constant.

Distinguishing nitrous oxide production from nitrification and denitrification on the basis of isotopomer abundances

The intramolecular distribution of nitrogen isotopes in N2O is an emerging tool for defining the relative importance of microbial sources of this greenhouse gas. The application of intramolecular isotopic distributions to evaluate the origins of N2O, however, requires a foundation in laboratory experiments in which individual production pathways can be isolated. Here we evaluate the site preferences of N2O produced during hydroxylamine oxidation by ammonia oxidizers and by a methanotroph, ammonia oxidation by a nitrifier, nitrite reduction during nitrifier denitrification, and nitrate and nitrite reduction by denitrifiers. The site preferences produced during hydroxylamine oxidation were 33.5 +/- 1.2 per thousand, 32.5 +/- 0.6 per thousand, and 35.6 +/- 1.4 per thousand for Nitrosomonas europaea, Nitrosospira multiformis, and Methylosinus trichosporium, respectively, indicating similar site preferences for methane and ammonia oxidizers. The site preference of N2O from ammonia oxidation by N. europaea (31.4 +/- 4.2 per thousand) was similar to that produced during hydroxylamine oxidation (33.5 +/- 1.2 per thousand) and distinct from that produced during nitrifier denitrification by N. multiformis (0.1 +/- 1.7 per thousand), indicating that isotopomers differentiate between nitrification and nitrifier denitrification. The site preferences of N2O produced during nitrite reduction by the denitrifiers Pseudomonas chlororaphis and Pseudomonas aureofaciens (-0.6 +/- 1.9 per thousand and -0.5 +/- 1.9 per thousand, respectively) were similar to those during nitrate reduction (-0.5 +/- 1.9 per thousand and -0.5 +/- 0.6 per thousand, respectively), indicating no influence of either substrate on site preference. Site preferences of approximately 33 per thousand and approximately 0 per thousand are characteristic of nitrification and denitrification, respectively, and provide a basis to quantitatively apportion N2O.

Distinguishing nitrous oxide production from nitrification and denitrification on the basis of isotopomer abundances

The intramolecular distribution of nitrogen isotopes in N2O is an emerging tool for defining the relative importance of microbial sources of this greenhouse gas. The application of intramolecular isotopic distributions to evaluate the origins of N2O, however, requires a foundation in laboratory experiments in which individual production pathways can be isolated. Here we evaluate the site preferences of N2O produced during hydroxylamine oxidation by ammonia oxidizers and by a methanotroph, ammonia oxidation by a nitrifier, nitrite reduction during nitrifier denitrification, and nitrate and nitrite reduction by denitrifiers. The site preferences produced during hydroxylamine oxidation were 33.5 +/- 1.2 per thousand, 32.5 +/- 0.6 per thousand, and 35.6 +/- 1.4 per thousand for Nitrosomonas europaea, Nitrosospira multiformis, and Methylosinus trichosporium, respectively, indicating similar site preferences for methane and ammonia oxidizers. The site preference of N2O from ammonia oxidation by N. europaea (31.4 +/- 4.2 per thousand) was similar to that produced during hydroxylamine oxidation (33.5 +/- 1.2 per thousand) and distinct from that produced during nitrifier denitrification by N. multiformis (0.1 +/- 1.7 per thousand), indicating that isotopomers differentiate between nitrification and nitrifier denitrification. The site preferences of N2O produced during nitrite reduction by the denitrifiers Pseudomonas chlororaphis and Pseudomonas aureofaciens (-0.6 +/- 1.9 per thousand and -0.5 +/- 1.9 per thousand, respectively) were similar to those during nitrate reduction (-0.5 +/- 1.9 per thousand and -0.5 +/- 0.6 per thousand, respectively), indicating no influence of either substrate on site preference. Site preferences of approximately 33 per thousand and approximately 0 per thousand are characteristic of nitrification and denitrification, respectively, and provide a basis to quantitatively apportion N2O.

Distinguishing nitrous oxide production from nitrification and denitrification on the basis of isotopomer abundances

The intramolecular distribution of nitrogen isotopes in N2O is an emerging tool for defining the relative importance of microbial sources of this greenhouse gas. The application of intramolecular isotopic distributions to evaluate the origins of N2O, however, requires a foundation in laboratory experiments in which individual production pathways can be isolated. Here we evaluate the site preferences of N2O produced during hydroxylamine oxidation by ammonia oxidizers and by a methanotroph, ammonia oxidation by a nitrifier, nitrite reduction during nitrifier denitrification, and nitrate and nitrite reduction by denitrifiers. The site preferences produced during hydroxylamine oxidation were 33.5 +/- 1.2 per thousand, 32.5 +/- 0.6 per thousand, and 35.6 +/- 1.4 per thousand for Nitrosomonas europaea, Nitrosospira multiformis, and Methylosinus trichosporium, respectively, indicating similar site preferences for methane and ammonia oxidizers. The site preference of N2O from ammonia oxidation by N. europaea (31.4 +/- 4.2 per thousand) was similar to that produced during hydroxylamine oxidation (33.5 +/- 1.2 per thousand) and distinct from that produced during nitrifier denitrification by N. multiformis (0.1 +/- 1.7 per thousand), indicating that isotopomers differentiate between nitrification and nitrifier denitrification. The site preferences of N2O produced during nitrite reduction by the denitrifiers Pseudomonas chlororaphis and Pseudomonas aureofaciens (-0.6 +/- 1.9 per thousand and -0.5 +/- 1.9 per thousand, respectively) were similar to those during nitrate reduction (-0.5 +/- 1.9 per thousand and -0.5 +/- 0.6 per thousand, respectively), indicating no influence of either substrate on site preference. Site preferences of approximately 33 per thousand and approximately 0 per thousand are characteristic of nitrification and denitrification, respectively, and provide a basis to quantitatively apportion N2O.