Nitrogen isotopomer site preference of N2O produced by Nitrosomonas europaea and Methylococcus capsulatus Bath

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.

Response of soil N2O production pathways to biochar amendment and its isotope discrimination methods

Reducing nitrous oxide (N2O) emission from farmland is crucial for alleviating global warming since agriculture is an important contributor of atmospheric N2O. Returning biochar to agricultural fields is an important measure to mitigate soil N2O emissions. Accurately quantifying the effect of biochar on the process of N2O production and its driving factors is critical for achieving N2O emission mitigation. Recently, stable isotope techniques such as isotope labeling, natural abundance, and site preference (SP) value, have been widely used to distinguish N2O production pathways. However, the different isotope methods have certain limitations in distinguishing N2O production in biochar-amended soils where it is difficult to identify the relative contribution of individual pathways for N2O production. This paper systematically reviews the pathways of soil N2O production (nitrification, nitrifier denitrification, bacterial denitrification, fungal denitrification, coupled nitrification-denitrification, dissimilatory nitrate reduction to ammonium and abiotic processes) and their response mechanism to the addition of biochar, as well as the development history and advantages of isotopes in differentiating N2O production pathways in biochar-amended soils. Moreover, the limitations of current research methods and future research directions are proposed. These results will help resolve how biochar affects different processes that lead to soil N2O generation and provide a scientific basis for sustainable agricultural carbon sequestration and the fulfilment of carbon neutrality goals.

Pyisotopomer: A Python package for obtaining intramolecular isotope ratio differences from mass spectrometric analysis of nitrous oxide isotopocules

RATIONALE

Obtaining nitrous oxide isotopocule measurements with isotope ratio mass spectrometry (IRMS) involves analyzing the ion current ratios of the nitrous oxide parent ion (N₂ O⁺ ) as well as those of the NO⁺ fragment ion. The data analysis requires correcting for "scrambling" in the ion source, whereby the NO⁺ fragment ion obtains the outer N atom from the N₂ O molecule. While descriptions exist for this correction, and interlaboratory intercalibration efforts have been made, there has yet to be published a package of code for implementing isotopomer calibrations.

METHODS

We developed a user-friendly Python package (pyisotopomer) to determine two coefficients (γ and κ) that describe scrambling in the IRMS ion source, and then used this calibration to obtain intramolecular isotope deltas in N₂ O samples.

RESULTS

With two appropriate reference materials, γ and κ can be determined robustly and accurately for a given IRMS system. An additional third reference material is needed to define the zero-point of the delta scale. We show that IRMS scrambling behavior can vary with time, necessitating regular calibrations. Finally, we present an intercalibration between two IRMS laboratories, using pyisotopomer to calculate γ and κ, and to obtain intramolecular N₂ O isotope deltas in lake water unknowns.

CONCLUSIONS

Given these considerations, we discuss how to use pyisotopomer to obtain high-quality N₂ O isotopocule data from IRMS systems, including the use of appropriate reference materials and frequency of calibration.

Dissolved N2O concentrations in oil palm plantation drainage in a peat swamp of Malaysia

Oil palm plantations in Southeast Asia are the largest supplier of palm oil products and have been rapidly expanding in the last three decades even in peat-swamp areas. Oil palm plantations on peat ecosystems have a unique water management system that lowers the water table and, thus, may yield indirect N₂O emissions from the peat drainage system. We conducted two seasons of spatial monitoring for the dissolved N₂O concentrations in the drainage and adjacent rivers of palm oil plantations on peat swamps in Sarawak, Malaysia, to evaluate the magnitude of indirect N₂O emissions from this ecosystem. In both the dry and wet seasons, the mean and median dissolved N₂O concentrations exhibited over-saturation in the drainage water, i.e., the oil palm plantation drainage may be a source of N₂O to the atmosphere. In the wet season, the spatial distribution of dissolved N₂O showed bimodal peaks in both the unsaturated and over-saturated concentrations. The bulk δ¹⁵N of dissolved N₂O was higher than the source of inorganic N in the oil palm plantation (i.e., N fertilizer and soil organic nitrogen) during both seasons. An isotopocule analysis of the dissolved N₂O suggested that denitrification was a major source of N₂O, followed by N₂O reduction processes that occurred in the drainage water. The δ¹⁵N and site preference mapping analysis in dissolved N₂O revealed that a significant proportion of the N₂O produced in peat and drainage is reduced to N₂ before being released into the atmosphere.

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.

Tracing plant–environment interactions from organismal to planetary scales using stable isotopes: a mini review

Natural isotope variation forms a mosaic of isotopically distinct pools across the biosphere and flows between pools integrate plant ecology with global biogeochemical cycling. Carbon, nitrogen, and water isotopic ratios (among others) can be measured in plant tissues, at root and foliar interfaces, and in adjacent atmospheric, water, and soil environments. Natural abundance isotopes provide ecological insight to complement and enhance biogeochemical research, such as understanding the physiological conditions during photosynthetic assimilation (e.g. water stress) or the contribution of unusual plant water or nutrient sources (e.g. fog, foliar deposition). While foundational concepts and methods have endured through four decades of research, technological improvements that enable measurement at fine spatiotemporal scales, of multiple isotopes, and of isotopomers, are advancing the field of stable isotope ecology. For example, isotope studies now benefit from the maturation of field-portable infrared spectroscopy, which allows the exploration of plant–environment sensitivity at physiological timescales. Isotope ecology is also benefiting from, and contributing to, new understanding of the plant–soil–atmosphere system, such as improving the representation of soil carbon pools and turnover in land surface models. At larger Earth-system scales, a maturing global coverage of isotope data and new data from site networks offer exciting synthesis opportunities to merge the insights of single-or multi-isotope analysis with ecosystem and remote sensing data in a data-driven modeling framework, to create geospatial isotope products essential for studies of global environmental change.

N2O and NOy production by the comammox bacterium Nitrospira inopinata in comparison with canonical ammonia oxidizers

Nitrous oxide (N₂O) and NO_y (nitrous acid (HONO) + nitric oxide (NO) + nitrogen dioxide (NO₂)) are released as byproducts or obligate intermediates during aerobic ammonia oxidation, and further influence global warming and atmospheric chemistry. The ammonia oxidation process is catalyzed by groups of globally distributed ammonia-oxidizing microorganisms, which are playing a major role in atmospheric N₂O and NO_y emissions_. Yet, little is known about HONO and NO₂ production by the recently discovered, widely distributed complete ammonia oxidizers (comammox), able to individually perform the oxidation of ammonia to nitrate via nitrite. Here, we examined the N₂O and NO_y production patterns by comammox bacterium Nitrospira inopinata during aerobic ammonia oxidation, in comparison to its canonical ammonia-converting counterparts, representatives of the ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our findings, i) show low yield NO_y production by the comammox bacterium compared to AOB; ii) highlight the role of the NO reductase in the biological formation of N₂O based on results from NH₂OH inhibition assays and its stimulation during archaeal and bacterial ammonia oxidations; iii) postulate that the lack of hydroxylamine (NH₂OH) and NO transformation enzymatic activities may lead to a buildup of NH₂OH/NO which can abiotically react to N₂O ; iv) collectively confirm restrained N₂O and NO_y emission by comammox bacteria, an unneglectable consortium of microbes in global atmospheric emission of reactive nitrogen gases.

How does management legacy, nitrogen addition, and nitrification inhibition affect soil organic matter priming and nitrous oxide production?

Long-term management of croplands influences the fluxes and sources of nitrous oxide (N₂ O). We examined this premise in a greenhouse study by using soils collected from a 38-yr-old field experiment. The sampled treatments were continuous barley (Hordeum vulgare L.; CB), continuous fescue (Festuca rubra L., F. arundinacea Schreb; CF), and two phases of an 8-yr rotation: faba bean (Vicia faba L.; FB) and alfalfa (Medicago sativa L.)-bromegrass (Bromus inermis Leyss) hay. Barley was grown as a test crop in the greenhouse in each soil. The ranking of N₂ O emissions was hay > FB > CB > CF (P < .001). We quantified the ¹⁵ N-site preference to assess the N₂ O-producing processes. Denitrification was the predominant source, contributing 77.4% of the N₂ O production. We also evaluated nitrogen (N) additions: urea alone or urea with a nitrification inhibitor (nitrapyrin or DMPSA). Compared with urea alone, nitrapyrin and DMPSA reduced N₂ O emissions by 16 and 25%, respectively. We used urea labeled with ¹⁵ N to trace N to N₂ O emissions, aboveground plant N uptake, and N retention by soils. Total ¹⁵ N-recovery (N₂ O + plant + soil) was highest under FB (86%) and lowest under CB (29%). We further separated the N₂ O derived from urea versus N₂ O from soil organic matter (SOM). The inhibitor DMPSA reduced the N₂ O derived specifically from added urea-N by more than half (P < .001). With the addition of urea, N₂ O production from mineralization of SOM-N accelerated over the control (without urea), termed the priming effect. This priming of SOM-N contributed with 13% of the total N₂ O production when averaged across the four management legacies. The CB soil had the highest proportion of priming-derived N₂ O (24%). Management legacies clearly differed in soil carbon and N, which governed N₂ O production from denitrification and SOM priming.

Nitrogen isotopic signatures and fluxes of N2O in response to land-use change on naturally occurring saline-alkaline soil

The conversion of natural grassland to semi-natural or artificial ecosystems is a large-scale land-use change (LUC) commonly occurring to saline–alkaline land. Conversion of natural to artificial ecosystems, with addition of anthropogenic nitrogen (N) fertilizer, influences N availability in the soil that may result in higher N₂O emission along with depletion of ¹⁵N, while converting from natural to semi-natural the influence may be small. So, this study assesses the impact of LUC on N₂O emission and ¹⁵N in N₂O emitted from naturally occurring saline–alkaline soil when changing from natural grassland (Phragmites australis) to semi-natural [Tamarix chinensis (Tamarix)] and to cropland (Gossypium spp.). The grassland and Tamarix ecosystems were not subject to any management practice, while the cropland received fertilizer and irrigation. Overall, median N₂O flux was significantly different among the ecosystems with the highest from the cropland (25.3 N₂O-N µg m⁻² h⁻¹), intermediate (8.2 N₂O-N µg m⁻² h⁻¹) from the Tamarix and the lowest (4.0 N₂O-N µg m⁻² h⁻¹) from the grassland ecosystem. The ¹⁵N isotopic signatures in N₂O emitted from the soil were also significantly affected by the LUC with more depleted from cropland (− 25.3 ‰) and less depleted from grassland (− 0.18 ‰). Our results suggested that the conversion of native saline–alkaline grassland with low N to Tamarix or cropland is likely to result in increased soil N₂O emission and also contributes significantly to the depletion of the ¹⁵N in atmospheric N₂O, and the contribution of anthropogenic N addition was found more significant than any other processes.

Mechanisms responsible for N2O emissions from intertidal soils of the Yangtze Estuary

Estuarine and coastal wetland ecosystems are important sources of atmospheric nitrous oxide (N₂O). However, the underlying driver of emitted N₂O from estuarine and coastal wetlands remains poorly understood. Here, natural-abundance isotope technique was applied to characterize the processes responsible for N₂O emission from the intertidal soils of the Yangtze Estuary. Measured N₂O emission rates ranged from 0.70 to 2.15 μmol m^-2 h^-1, with relatively high values at the upper estuarine sites. The δ¹⁵N, δ¹⁸O and SP (intramolecular ¹⁵N site preference) of emitted N₂O varied from -4.5 to 6.7‰, 42.4 to 53.2‰, and 6.7 to 15.4‰, respectively. Gross N₂O production and consumption rates were within the ranges of 3.16-14.34 μmol m^-2 h^-1 and 2.22-12.54 μmol m^-2 h^-1, respectively, showing a similar spatial pattern to N₂O emission. N₂O consumption proportion varied from 69.56 to 90.31%, which was generally lower at the upper estuarine sites. The gross production rates and consumption degree of N₂O simultaneously controlled the variations in N₂O emission. Bacterial denitrification was the dominant production pathway (78.22-97.36%), while hydroxylamine (NH₂OH) oxidation contributed 2.64-21.78% to N₂O production. Soil pH, Fe²⁺/Fe³⁺, sulfide and substrate availability were probably the main factors governing the N₂O emission dynamics. Overall, these results highlight the substantial role of NH₂OH oxidation and N₂O consumption in N₂O release in redox-dynamic soils of estuarine intertidal wetlands.

Optimisation of bioscrubber systems to simultaneously remove methane and purify wastewater from intensive pig farms

The use of bioscrubber is attracting increasing attention for exhaust gas treatment in intensive pig farming. However, the challenge is to improve the methane (CH₄) removal efficiency as well as the possibility of pig house wastewater treatment. Three laboratory-scale bioscrubbers, each equipped with different recirculation water types, livestock wastewater (10-times-diluted pig house wastewater supernatant), a methanotroph growth medium (10-times-diluted), and tap water, were established to evaluate the performance of CH₄ removal and wastewater treatment. The results showed that enhanced CH₄ removal efficiency (25%) can be rapidly achieved with improved methanotrophic activity due to extra nutrient support from the wastewater. The majority of the CH₄ was removed in the middle to end part of the bioscrubbers, which indicated that CH₄ removal could be potentially optimised by extending the length of the reactor. Moreover, 52-86% of the ammonium (NH₄⁺-N), total organic carbon (TOC), and phosphate (PO₄^3--P) removal were simultaneously achieved with CH₄ removal in the present study. Based on these results, this study introduces a low-cost and simple-to-operate method to improve CH₄ removal and simultaneously treat pig farm wastewater in bioscrubbers.

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.

N2O emissions and source partitioning using stable isotopes under furrow and drip irrigation in vegetable field of North China

N₂O emissions have increased significantly over the last decades, with much of the increase being ascribed to the expansion in agricultural land. Agricultural water management has significant influence on N₂O emissions, hence the investigation of N₂O emissions and the underlying production mechanisms under different irrigation managements would provide insights for N₂O emission reduction and rational water usage. Here, we used the stable isotope method to evaluate the N₂O isotopic signatures and the site preference, to clarify the N₂O emission dynamics and the N₂O source partitioning under different irrigation managements. We applied a furrow irrigation system and a drip irrigation system to maintain two different soil water conditions, allowance of dry-wet cycles and relatively stable water conditions, respectively. We found that the N₂O emission was significantly decreased under drip irrigation compared to furrow irrigation with cumulated N₂O flux of 526.3 mg m^-2 and 571.0 mg m^-2, respectively. In general, furrow irrigation with its dry-wet alternations promoted N₂O emissions, while drip irrigation created a relatively stable environment that reduced N₂O emissions. The intramolecular ¹⁵N isotopic composition of N₂O was used to partition the relative contribution of denitrification and nitrification. Nitrification dominated the processes driving N₂O production under both treatments, nearly accounting for 76% up to 100% during the initial N₂O peaks. Effective measure for mitigating N₂O emissions from the investigated vegetable field could be obtained by replacing the traditional furrow irrigation with drip irrigation.

Low yield and abiotic origin of N2O formed by the complete nitrifier Nitrospira inopinata

Nitrous oxide (N2O) and nitric oxide (NO) are atmospheric trace gases that contribute to climate change and affect stratospheric and ground-level ozone concentrations. Ammonia oxidizing bacteria (AOB) and archaea (AOA) are key players in the nitrogen cycle and major producers of N2O and NO globally. However, nothing is known about N2O and NO production by the recently discovered and widely distributed complete ammonia oxidizers (comammox). Here, we show that the comammox bacterium Nitrospira inopinata is sensitive to inhibition by an NO scavenger, cannot denitrify to N2O, and emits N2O at levels that are comparable to AOA but much lower than AOB. Furthermore, we demonstrate that N2O formed by N. inopinata formed under varying oxygen regimes originates from abiotic conversion of hydroxylamine. Our findings indicate that comammox microbes may produce less N2O during nitrification than AOB.

Constraining N cycling in the ecosystem model LandscapeDNDC with the stable isotope model SIMONE

The isotopic composition (ic) of soil nitrogen (N) and, more recently, the intramolecular distribution of ¹⁵ N in the N₂ O molecule (site preference, SP) are powerful instruments to identify dominant N turnover processes, and to attribute N₂ O emissions to their source processes. Despite the process information contained in the ic of N species and the associated potential for model validation, the implementation of isotopes in ecosystem models has lagged behind. To foster the validation of ecosystem models based on the ic of N species, we developed the stable isotope model for nutrient cycles (SIMONE). SIMONE uses fluxes between ecosystem N pools (soil organic N, mineral N, plants, microbes) calculated by biogeochemical models, and literature isotope effects for these processes to calculate the ic of N species. Here, we present the concept of SIMONE, apply it to simulations of the biogeochemical model LandscapeDNDC, and assess the capability of ¹⁵ N-N₂ O and, to our knowledge for the first time, SP, to constrain simulated N fluxes by LandscapeDNDC. LandscapeDNDC successfully simulated N₂ O emission, soil nitrate, and ammonium, as well as soil environmental conditions of an intensively managed grassland site in Switzerland. Accordingly, the dynamics of ¹⁵ N-N₂ O and SP of soil N₂ O fluxes as simulated by SIMONE agreed well with measurements, though ¹⁵ N-N₂ O was on average underestimated and SP overestimated (root-mean-square error [RMSE] of 8.4‰ and 7.3‰, respectively). Although ¹⁵ N-N₂ O could not constrain the N cycling process descriptions of LandscapeDNDC, the overestimation of SP indicated an overestimation of simulated nitrification rates by 10-59% at low water content, suggesting the revision of the corresponding model parameterization. Our findings show that N isotope modeling in combination with only recently available high- frequency measurements of the N₂ O ic are promising tools to identify and address weaknesses in N cycling of ecosystem models. This will finally contribute to augmenting the development of model-based strategies for mitigating N pollution.

Optimization, purification, and characterization of hydroxylamine oxidoreductase from Acinetobacter sp. Y1

Hydroxylamine oxidoreductase (HAO) is a key enzyme involved in ammonium removal pathway. To further study the enzyme, HAO was purified from heterotrophic nitrifier Acinetobacter sp. Y1 and its property was investigated. Results of single-factor experiments showed that the optimal carbon source, nitrogen source, and C/N ratio were trisodium citrate, ammonium sulfate, and 14, respectively, with incubation time of 16 H. DEAE Sefinose^TM FF anion-exchange chromatography was used to purify HAO, followed by Sefinose^TM CL-6B gel filtration chromatography. SDS-PAGE revealed that a 47 kDa enzyme was purified successfully, with a purification fold of 7.32 and a recovery rate of 19.40%. The optimized enzyme activity of purified HAO was tested at pH 8.0 and 30 °C. The results showed that the activity was increased by 43.78% and 25.64% in the presence of 1 mM Fe²⁺ and Fe³⁺ , respectively. HAO activity was increased with the increase of Na⁺ and K⁺ , Mn²⁺ , Zn²⁺ , Cu²⁺ , Ca²⁺ , Ba²⁺ inhibited the HAO activity at three concentrations. In addition, HAO activity was activated by ethylenediaminetetraacetic acid at 0.4 mM, and a negative effect arose as the dose increased. The purified enzyme from Y1 is different from other reported HAOs. Further study should be conducted to investigate the enzyme.

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.

Methane and nitrous oxide emission from different treatment units of municipal wastewater treatment plants in Southwest Germany

We measured the atmospheric emission rates of methane (CH₄) and nitrous oxide (N₂O) in two wastewater treatment plants in Southwest Germany, which apply different treatment technologies. Dissolved gas concentrations and fluxes were measured during all processing steps as well as in the discharge receiving streams. N₂O isotopocule analysis revealed that NH₂OH oxidation during nitrification contributed 86–96% of the N₂O production in the nitrification tank, whereas microbial denitrification was the main production pathway in the denitrification tank in a conventional activated sludge (CAS) system. During wastewater treatment using a modified Ludzack-Ettinger system (MLE) with energy recovery, N₂O was predominantly produced by the NO₂^- reduction by nitrifier-denitrification process. For both systems, N₂O emissions were low, with emission factors of 0.008% and 0.001% for the MLE and the CAS system, respectively. In the effluent-receiving streams, bacterial denitrification and nitrification contributed nearly equally to N₂O production. The CH₄ emission from the MLE system was estimated as 118.1 g-C d^-1, which corresponds to an emission factor of 0.004%, and was three times lower than the emission from the CAS system with 0.01%.

Estimating N2 O processes during grassland renewal and grassland conversion to maize cropping using N2 O isotopocules

RATIONALE

Enhanced nitrous oxide (N₂ O) emissions can occur following grassland break-up for renewal or conversion to maize cropping, but knowledge about N₂ O production pathways and N₂ O reduction to N₂ is very limited. A promising tool to address this is the combination of mass spectrometric analysis of N₂ O isotopocules and an enhanced approach for data interpretation.

METHODS

The isotopocule mapping approach was applied to field data using a δ¹⁵ N^sp_N2O and δ¹⁸ O_N2O map to simultaneously determine N₂ O production pathways contribution and N₂ O reduction for the first time. Based on the isotopic composition of N₂ O produced and literature values for specific N₂ O pathways, it was possible to distinguish: (i) heterotrophic bacterial denitrification and/or nitrifier denitrification and (ii) nitrification and/or fungal denitrification and the contribution of N₂ O reduction.

RESULTS

The isotopic composition of soil-emitted N₂ O largely resembled the known end-member values for bacterial denitrification. The isotopocule mapping approach indicated different effects of N₂ O reduction on the isotopic composition of soil-emitted N₂ O for the two soils under study. Differing N₂ O production pathways in different seasons were not observed, but management events and soil conditions had a significant impact on pathway contribution and N₂ O reduction. N₂ O reduction data were compared with a parallel ¹⁵ N-labelling experiment.

CONCLUSIONS

The field application of the isotopocule mapping approach opens up new prospects for studying N₂ O production and consumption of N₂ O in soil simultaneously based on mass spectrometric analysis of natural abundance N₂ O. However, further studies are needed in order to properly validate the isotopocule mapping approach.

Quantifying nitrous oxide production pathways in wastewater treatment systems using isotope technology - A critical review

Nitrous oxide (N₂O) is an important greenhouse gas and an ozone-depleting substance which can be emitted from wastewater treatment systems (WWTS) causing significant environmental impacts. Understanding the N₂O production pathways and their contribution to total emissions is the key to effective mitigation. Isotope technology is a promising method that has been applied to WWTS for quantifying the N₂O production pathways. Within the scope of WWTS, this article reviews the current status of different isotope approaches, including both natural abundance and labelled isotope approaches, to N₂O production pathways quantification. It identifies the limitations and potential problems with these approaches, as well as improvement opportunities. We conclude that, while the capabilities of isotope technology have been largely recognized, the quantification of N₂O production pathways with isotope technology in WWTS require further improvement, particularly in relation to its accuracy and reliability.

Large variability in CO2 and N2 O emissions and in 15 N site preference of N2 O from reactions of nitrite with lignin and its derivatives at different pH

RATIONALE

Chemodenitrification is an important N₂ O source in soil; however, knowledge about the production of CO₂ and N₂ O from abiotic nitrite-SOM reactions, especially the N₂ O isotopic signatures (intramolecular ¹⁵ N site preference (SP), and δ¹⁵ N^bulk and δ¹⁸ O values), is quite limited at present.

METHODS

N₂ O and CO₂ emissions from chemical reactions of nitrite with lignin products were determined with gas chromatography, and their response surfaces as a function of pH from 3 to 6 and nitrite concentration from 0.1 to 0.5 mM were explored with polynomial regression. The intramolecular ¹⁵ N distribution of N₂ O, as well as δ¹⁵ N^bulk and δ¹⁸ O values, were measured with an isotope ratio mass spectrometer coupled to an online pre-concentration unit. The variability in N₂ O SP values was tested from pH 3 to 5, and for nitrite concentrations from 0.3 to 0.5 mM.

RESULTS

Both CO₂ and N₂ O emissions varied largely with pH and the structure of lignin products. The highest N₂ O emission occurred at pH 4-5 in 4-hydroxy-3,5-dimethoxybenzaldehyde and 4-hydroxy-3,5-dimethoxybenzoic acid treatments, and at pH 3 in the treatments with lignin, 4-hydroxy-3-methoxybenzaldehyde, 4-hydroxy-3-methoxybenzoic acid, 4-hydroxybenzaldehyde, and 4-hydroxybenzoic acid. A wide range of N₂ O SP values (11.9-37.4‰), which was pH dependent and not distinguishable from microbial pathways, was observed at pH 3-5. The δ¹⁵ N^bulk and δ¹⁸ O values of N₂ O were both in a similar range to that reported for fungal denitrification and bacterial denitrification.

CONCLUSIONS

These results present the first characterization of the isotopic composition of N₂ O from chemodenitrification in pure chemical assays. Chemical reactions of nitrite with lignin are pH-dependent and associated with substantial CO₂ and N₂ O emissions. The SP values of N₂ O derived from chemodenitrification were neither distinguishable from the biotic pathways nor remained stable with varying pH. Therefore, the use of N₂ O isotopic signatures for source partitioning is restricted when chemodenitrification is contributing significantly to N₂ O emission.

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.

Chemodenitrification in the cryoecosystem of Lake Vida, Victoria Valley, Antarctica

Lake Vida, in the Victoria Valley of East Antarctica, is frozen, yet harbors liquid brine (~20% salt, >6 times seawater) intercalated in the ice below 16 m. The brine has been isolated from the surface for several thousand years. The brine conditions (permanently dark, -13.4 °C, lack of O₂ , and pH of 6.2) and geochemistry are highly unusual. For example, nitrous oxide (N₂ O) is present at a concentration among the highest reported for an aquatic environment. Only a minor ¹⁷ O anomaly was observed in N₂ O, indicating that this gas was predominantly formed in the lake. In contrast, the ¹⁷ O anomaly in nitrate (NO3-) in Lake Vida brine indicates that approximately half or more of the NO3- present is derived from atmospheric deposition. Lake Vida brine was incubated in the presence of ¹⁵ N-enriched substrates for 40 days. We did not detect microbial nitrification, dissimilatory reduction of NO3- to ammonium (NH4+), anaerobic ammonium oxidation, or denitrification of N₂ O under the conditions tested. In the presence of ¹⁵ N-enriched nitrite (NO2-), both N₂ and N₂ O exhibited substantial ¹⁵ N enrichments; however, isotopic enrichment declined with time, which is unexpected. Additions of ¹⁵ N-NO2- alone and in the presence of HgCl₂ and ZnCl₂ to aged brine at -13 °C resulted in linear increases in the δ¹⁵ N of N₂ O with time. As HgCl₂ and ZnCl₂ are effective biocides, we interpret N₂ O production in the aged brine to be the result of chemodenitrification. With this understanding, we interpret our results from the field incubations as the result of chemodenitrification stimulated by the addition of ¹⁵ N-enriched NO2- and ZnCl₂ and determined rates of N₂ O and N₂ production of 4.11-41.18 and 0.55-1.75 nmol L^-1  day^-1 , respectively. If these rates are representative of natural production, the current concentration of N₂ O in Lake Vida could have been reached between 6 and 465 years. Thus, chemodenitrification alone is sufficient to explain the high levels of N₂ O present in Lake Vida.

Measurement of rare isotopologues of nitrous oxide by high-resolution multi-collector mass spectrometry

RATIONALE

Bulk and position-specific stable isotope characterization of nitrous oxide represents one of the most powerful tools for identifying its environmental sources and sinks. Constraining (14) N(15) N(18) O and (15) N(14) N(18) O will add two new dimensions to our ability to uniquely fingerprint N2 O sources.

METHODS

We describe a technique to measure six singly and doubly substituted isotopic variants of N2 O, constraining the values of δ(15) N, δ(18) O, ∆(17) O, (15) N site preference, and the clumped isotopomers (14) N(15) N(18) O and (15) N(14) N(18) O. The technique uses a Thermo MAT 253 Ultra, a high-resolution multi-collector gas source isotope ratio mass spectrometer. It requires 8-10 hours per sample and ~10 micromoles or more of pure N2 O.

RESULTS

We demonstrate the precision and accuracy of these measurements by analyzing N2 O brought to equilibrium in its position-specific and clumped isotopic composition by heating in the presence of a catalyst. Finally, an illustrative analysis of biogenic N2 O from a denitrifying bacterium suggests that its clumped isotopic composition is controlled by kinetic isotope effects in N2 O production.

CONCLUSIONS

We developed a method for measuring six isotopic variants of N2 O and tested it with analyses of biogenic N2 O. The added isotopic constraints provided by these measurements will enhance our ability to apportion N2 O sources.

Isotope signatures of N2O emitted from vegetable soil: Ammonia oxidation drives N2O production in NH4(+)-fertilized soil of North China

Nitrous oxide (N₂O) is a potent greenhouse gas. In North China, vegetable fields are amended with high levels of N fertilizer and irrigation water, which causes massive N₂O flux. The aim of this study was to determine the contribution of microbial processes to N₂O production and characterize isotopic signature effects on N₂O source partitioning. We conducted a microcosm study that combined naturally abundant isotopologues and gas inhibitor techniques to analyze N₂O flux and its isotopomer signatures [δ¹⁵N^bulk, δ¹⁸O, and SP (intramolecular ¹⁵N site preference)] that emitted from vegetable soil after the addition of NH₄⁺ fertilizers. The results show that ammonia oxidation is the predominant process under high water content (70% water-filled pore space), and nitrifier denitrification contribution increases with increasing N content. δ¹⁵N^bulk and δ¹⁸O of N₂O may not provide information about microbial processes due to great shifts in precursor signatures and atom exchange, especially for soil treated with NH₄⁺ fertilizer. SP and associated two end-member mixing model are useful to distinguish N₂O source and contribution. Further work is needed to explore isotopomer signature stability to improve N₂O microbial process identification.

Multi-species measurements of nitrogen isotopic composition reveal the spatial constraints and biological drivers of ammonium attenuation across a highly contaminated groundwater system

Groundwater under industrial sites is characterised by heterogeneous chemical mixtures, making it difficult to assess the fate and transport of individual contaminants. Quantifying the in-situ biological removal (attenuation) of nitrogen (N) is particularly difficult due to its reactivity and ubiquity. Here a multi-isotope approach is developed to distinguish N sources and sinks within groundwater affected by complex industrial pollution. Samples were collected from 70 wells across the two aquifers underlying a historic industrial area in Belgium. Below the industrial site the groundwater contained up to 1000 mg N l(-1) ammonium (NH4(+)) and 300 mg N l(-1) nitrate (NO3(-)), while downgradient concentrations decreased to ∼1 mg l(-1) DIN ([DIN] = [NH4(+)N] + [NO3(-)N] + [NO2(-)N]). Mean δ(15)N-DIN increased from ∼2‰ to +20‰ over this flow path, broadly confirming that biological N attenuation drove the measured concentration decrease. Multi-variate analysis of water chemistry identified two distinct NH4(+) sources (δ(15)NNH4(+) from -14‰ and +5‰) within the contaminated zone of both aquifers. Nitrate dual isotopes co-varied (δ(15)N: -3‰ - +60‰; δ(18)O: 0‰ - +50‰) within the range expected for coupled nitrification and denitrification of the identified sources. The fact that δ(15)NNO2(-) values were 50‰-20‰ less than δ(15)NNH4(+) values in the majority of wells confirmed that nitrification controlled N turnover across the site. However, the fact that δ(15)NNO2(-) was greater than δ(15)NNH4(+) in wells with the highest [NH4(+)] shows that an autotrophic NO2(-) reduction pathway (anaerobic NH4(+) oxidation or nitrifier-denitrification) drove N attenuation closest to the contaminant plume. This direct empirical evidence that both autotrophic and heterotrophic biogeochemical processes drive N attenuation in contaminated aquifers demonstrates the power of multiple N isotopes to untangle N cycling in highly complex systems.

Isotopic evidence for nitrous oxide production pathways in a partial nitritation-anammox reactor

Nitrous oxide (N2O) production pathways in a single stage, continuously fed partial nitritation-anammox reactor were investigated using online isotopic analysis of offgas N2O with quantum cascade laser absorption spectroscopy (QCLAS). N2O emissions increased when reactor operating conditions were not optimal, for example, high dissolved oxygen concentration. SP measurements indicated that the increase in N2O was due to enhanced nitrifier denitrification, generally related to nitrite build-up in the reactor. The results of this study confirm that process control via online N2O monitoring is an ideal method to detect imbalances in reactor operation and regulate aeration, to ensure optimal reactor conditions and minimise N2O emissions. Under normal operating conditions, the N2O isotopic site preference (SP) was much higher than expected - up to 40‰ - which could not be explained within the current understanding of N2O production pathways. Various targeted experiments were conducted to investigate the characteristics of N2O formation in the reactor. The high SP measurements during both normal operating and experimental conditions could potentially be explained by a number of hypotheses: i) unexpectedly strong heterotrophic N2O reduction, ii) unknown inorganic or anammox-associated N2O production pathway, iii) previous underestimation of SP fractionation during N2O production from NH2OH, or strong variations in SP from this pathway depending on reactor conditions. The second hypothesis - an unknown or incompletely characterised production pathway - was most consistent with results, however the other possibilities cannot be discounted. Further experiments are needed to distinguish between these hypotheses and fully resolve N2O production pathways in PN-anammox systems.

Diverse electron sources support denitrification under hypoxia in the obligate methanotroph Methylomicrobium album strain BG8

Aerobic methane-oxidizing bacteria (MOB) are a diverse group of microorganisms that are ubiquitous in natural environments. Along with anaerobic MOB and archaea, aerobic methanotrophs are critical for attenuating emission of methane to the atmosphere. Clearly, nitrogen availability in the form of ammonium and nitrite have strong effects on methanotrophic activity and their natural community structures. Previous findings show that nitrite amendment inhibits the activity of some cultivated methanotrophs; however, the physiological pathways that allow some strains to transform nitrite, expression of gene inventories, as well as the electron sources that support this activity remain largely uncharacterized. Here we show that Methylomicrobium album strain BG8 utilizes methane, methanol, formaldehyde, formate, ethane, ethanol, and ammonia to support denitrification activity under hypoxia only in the presence of nitrite. We also demonstrate that transcript abundance of putative denitrification genes, nirS and one of two norB genes, increased in response to nitrite. Furthermore, we found that transcript abundance of pxmA, encoding the alpha subunit of a putative copper-containing monooxygenase, increased in response to both nitrite and hypoxia. Our results suggest that expression of denitrification genes, found widely within genomes of aerobic methanotrophs, allow the coupling of substrate oxidation to the reduction of nitrogen oxide terminal electron acceptors under oxygen limitation. The present study expands current knowledge of the metabolic flexibility of methanotrophs by revealing that a diverse array of electron donors support nitrite reduction to nitrous oxide under hypoxia.

Production of Nitrous Oxide from Nitrite in Stable Type II Methanotrophic Enrichments

The coupled aerobic-anoxic nitrous decomposition operation is a new process for wastewater treatment that removes nitrogen from wastewater and recovers energy from the nitrogen in three steps: (1) NH4(+) oxidation to NO2(-), (2) NO2(-) reduction to N2O, and (3) N2O conversion to N2 with energy production. Here, we demonstrate that type II methanotrophic enrichments can mediate step two by coupling oxidation of poly(3-hydroxybutyrate) (P3HB) to NO2(-) reduction. Enrichments grown with NH4(+) and NO2(-) were subject to alternating 48-h aerobic and anoxic periods, in which CH4 and NO2(-) were added together in a "coupled" mode of operation or separately in a "decoupled mode". Community structure was stable in both modes and dominated by Methylocystis. In the coupled mode, production of P3HB and N2O was low. In the decoupled mode, significant P3HB was produced, and oxidation of P3HB drove reduction of NO2(-) to N2O with ∼ 70% conversion for >30 cycles (120 d). In batch tests of wasted cells from the decoupled mode, N2O production rates increased at low O2 or high NO2(-) levels. The results are significant for the development of engineered processes that remove nitrogen from wastewater and for understanding of conditions that favor environmental production of N2O.

Rainwater, soil water, and soil nitrate effects on oxygen isotope ratios of nitrous oxide produced in a green tea (Camellia sinensis) field in Japan

RATIONALE

The oxygen exchange fraction between soil H(2)O and N(2)O precursors differs in soils depending on the responsible N(2)O-producing process: nitrification or denitrification. This study investigated the O-exchange between soil H(2)O and N(2)O precursors in a green tea field with high N(2)O emissions.

METHODS

The rainwater δ(18)O value was measured using cavity ring-down spectrometry (CRDS) and compared with that of soil water collected under the tea plant canopy and between tea plant rows. The intramolecular (15)N site preference in (β) N(α) NO (SP = δ(15)N(α) - δ(15)N(β)) was determined after measuring the δ(15)N(α) and δ(15)N(bulk) values using gas chromatography/isotope ratio mass spectrometry (GC/IRMS), and the δ(18) O values of N(2)O and NO(3)(-) were also measured using GC/IRMS.

RESULTS

The range of δ(18)O values of rainwater (-11.15‰ to -4.91‰) was wider than that of soil water (-7.94‰ to -5.64‰). The δ(18)O value of soil water at 50 cm depth was not immediately affected by rainwater. At 10 cm and 20 cm depths of soil between tea plant rows, linear regression analyses of δ(18)O-N(2)O (relative to δ(18)O-NO(3)(-)) versus δ(18) O-H(2)O (relative to δ(18)O-NO(3)(-)) yielded slopes of 0.76-0.80 and intercepts of 31-35‰.

CONCLUSIONS

In soil between tea plant rows, the fraction of O-exchange between H(2)O and N(2)O precursors was approximately 80%. Assuming that denitrification dominated N(2)O production, the net (18)O-isotope effect for denitrification (NO(3)(-) reduction to N(2)O) was approximately 31-35‰, reflecting the upland condition of the tea field.

Stable isotopes and iron oxide mineral products as markers of chemodenitrification

When oxygen is limiting in soils and sediments, microorganisms utilize nitrate (NO3-) in respiration--through the process of denitrification--leading to the production of dinitrogen (N2) gas and trace amounts of nitrous (N2O) and nitric (NO) oxides. A chemical pathway involving reaction of ferrous iron (Fe2+) with nitrite (NO2-), an intermediate in the denitrification pathway, can also result in production of N2O. We examine the chemical reduction of NO2- by Fe(II)--chemodenitrification--in anoxic batch incubations at neutral pH. Aqueous Fe2+ and NO2- reacted rapidly, producing N2O and generating Fe(III) (hydr)oxide mineral products. Lepidocrotite and goethite, identified by synchrotron X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) spectroscopy, were produced from initially aqueous reactants, with two-line ferrihydrite increasing in abundance later in the reaction sequence. Based on the similarity of apparent rate constants with different mineral catalysts, we propose that the chemodenitrification rate is insensitive to the type of Fe(III) (hydr)oxide. With stable isotope measurements, we reveal a narrow range of isotopic fractionation during NO2- reduction to N2O. The location of N isotopes in the linear N2O molecule, known as site preference, was also constrained to a signature range. The coexistence of Fe(III) (hydr)oxide, characteristic 15N and 18O fractionation, and N2O site preference may be used in combination to qualitatively distinguish between abiotic and biogenically emitted N2O--a finding important for determining N2O sources in natural systems.

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.

Interlaboratory assessment of nitrous oxide isotopomer analysis by isotope ratio mass spectrometry and laser spectroscopy: current status and perspectives

RATIONALE

In recent years, research and applications of the N2O site-specific nitrogen isotope composition have advanced, reflecting awareness of the contribution of N2O to the anthropogenic greenhouse effect, and leading to significant progress in instrument development. Further dissemination of N2O isotopomer analysis, however, is hampered by a lack of internationally agreed gaseous N2O reference materials and an uncertain compatibility of different laboratories and analytical techniques.

METHODS

In a first comparison approach, eleven laboratories were each provided with N2O at tropospheric mole fractions (target gas T) and two reference gases (REF1 and REF2). The laboratories analysed all gases, applying their specific analytical routines. Compatibility of laboratories was assessed based on N2O isotopocule data for T, REF1 and REF2. Results for T were then standardised using REF1 and REF2 to evaluate the potential of N2O reference materials for improving compatibility between laboratories.

RESULTS

Compatibility between laboratories depended on the analytical technique: isotope ratio mass spectrometry (IRMS) results showed better compatibility for δ(15)N values, while the performance of laser spectroscopy was superior with respect to N2O site preference. This comparison, however, is restricted by the small number of participating laboratories applying laser spectroscopy. Offset and two-point calibration correction of the N2O isotopomer data significantly improved the consistency of position-dependent nitrogen isotope data while the effect on δ(15)N values was only minor.

CONCLUSIONS

The study reveals that for future research on N2O isotopocules, standardisation against N2O reference material is essential to improve interlaboratory compatibility. For atmospheric monitoring activities, we suggest N2O in whole air as a unifying scale anchor.

Isotopic analysis of N2O produced in a conventional wastewater treatment system operated under different aeration conditions

RATIONALE

Dissolved oxygen (DO) concentration is a key parameter of nitrous oxide (N2O), a greenhouse gas, emitted from wastewater treatment systems. No study of stable isotopes has described N2O production during conventional activated sludge (CAS) treatment under different DO concentrations.

METHODS

Concentrations and isotope ratios, including intramolecular site preference of (15)N in NNO (SP), of N2O were measured using gas chromatography/isotope ratio mass spectrometry (GC/IRMS) for samples from seven points in a wastewater treatment plant (WWTP) operated with three aeration conditions. The δ(15)N values of NH4(+) and the δ(15)N and δ(18)O values of NO3(-) were measured using IRMS.

RESULTS

Aeration tank water was supersaturated with N2O. The highest value, 3700 nmol kg(-1), was observed at the aeration tank end and in settled sludge under the lowest aeration condition. About 0.03% of the influent NH4(+) was emitted as gaseous N2O at the lowest aeration condition. The conversion rate was 0.14% under the highest aeration condition. The SP values were significantly higher at the middle and end of the aeration tanks under the highest aeration condition, but were nearly zero or slightly negative under lower aeration conditions.

CONCLUSIONS

Under the highest aeration condition, NH2OH oxidation (nitrification) was the main contributor to N2O production at about 90% and 57%, respectively, at the aeration tank middle and end. At other sampling points, 55-63% of the N2O was produced by bacterial NO2(-) reduction (nitrifier-denitrification) with a lower nitrification contribution. For all sampling points in the lower aeration experiments, NO2(-) reduction was a major N2O production pathway.

Identification of key nitrous oxide production pathways in aerobic partial nitrifying granules

The identification of the key nitrous oxide (N2O) production pathways is important to establish a strategy to mitigate N2O emission. In this study, we combined real-time gas-monitoring analysis, (15)N stable isotope analysis, denitrification functional gene transcriptome analysis and microscale N2O concentration measurements to identify the main N2O producers in a partial nitrification (PN) aerobic granule reactor, which was fed with ammonium and acetate. Our results suggest that heterotrophic denitrification was the main contributor to N2O production in our PN aerobic granule reactor. The heterotrophic denitrifiers were probably related to Rhodocyclales bacteria, although different types of bacteria were active in the initial and latter stages of the PN reaction cycles, most likely in response to the presence of acetate. Hydroxylamine oxidation and nitrifier denitrification occurred, but their contribution to N2O emission was relatively small (20-30%) compared with heterotrophic denitrification. Our approach can be useful to quantitatively examine the relative contributions of the three pathways (hydroxylamine oxidation, nitrifier denitrification and heterotrophic denitrification) to N2O emission in mixed microbial populations.

Isotopic signatures of N2O produced by ammonia-oxidizing archaea from soils

N2O gas is involved in global warming and ozone depletion. The major sources of N2O are soil microbial processes. Anthropogenic inputs into the nitrogen cycle have exacerbated these microbial processes, including nitrification. Ammonia-oxidizing archaea (AOA) are major members of the pool of soil ammonia-oxidizing microorganisms. This study investigated the isotopic signatures of N2O produced by soil AOA and associated N2O production processes. All five AOA strains (I.1a, I.1a-associated and I.1b clades of Thaumarchaeota) from soil produced N2O and their yields were comparable to those of ammonia-oxidizing bacteria (AOB). The levels of site preference (SP), δ(15)N(bulk) and δ(18)O -N2O of soil AOA strains were 13-30%, -13 to -35% and 22-36%, respectively, and strains MY1-3 and other soil AOA strains had distinct isotopic signatures. A (15)N-NH4(+)-labeling experiment indicated that N2O originated from two different production pathways (that is, ammonia oxidation and nitrifier denitrification), which suggests that the isotopic signatures of N2O from AOA may be attributable to the relative contributions of these two processes. The highest N2O production yield and lowest site preference of acidophilic strain CS may be related to enhanced nitrifier denitrification for detoxifying nitrite. Previously, it was not possible to detect N2O from soil AOA because of similarities between its isotopic signatures and those from AOB. Given the predominance of AOA over AOB in most soils, a significant proportion of the total N2O emissions from soil nitrification may be attributable to AOA.

Genome analysis coupled with physiological studies reveals a diverse nitrogen metabolism in Methylocystis sp. strain SC2

BACKGROUND

Methylocystis sp. strain SC2 can adapt to a wide range of methane concentrations. This is due to the presence of two isozymes of particulate methane monooxygenase exhibiting different methane oxidation kinetics. To gain insight into the underlying genetic information, its genome was sequenced and found to comprise a 3.77 Mb chromosome and two large plasmids.

PRINCIPAL FINDINGS

We report important features of the strain SC2 genome. Its sequence is compared with those of seven other methanotroph genomes, comprising members of the Alphaproteobacteria, Gammaproteobacteria, and Verrucomicrobia. While the pan-genome of all eight methanotroph genomes totals 19,358 CDS, only 154 CDS are shared. The number of core genes increased with phylogenetic relatedness: 328 CDS for proteobacterial methanotrophs and 1,853 CDS for the three alphaproteobacterial Methylocystaceae members, Methylocystis sp. strain SC2 and strain Rockwell, and Methylosinus trichosporium OB3b. The comparative study was coupled with physiological experiments to verify that strain SC2 has diverse nitrogen metabolism capabilities. In correspondence to a full complement of 34 genes involved in N2 fixation, strain SC2 was found to grow with atmospheric N2 as the sole nitrogen source, preferably at low oxygen concentrations. Denitrification-mediated accumulation of 0.7 nmol (30)N2/hr/mg dry weight of cells under anoxic conditions was detected by tracer analysis. N2 production is related to the activities of plasmid-borne nitric oxide and nitrous oxide reductases.

CONCLUSIONS/PERSPECTIVES

Presence of a complete denitrification pathway in strain SC2, including the plasmid-encoded nosRZDFYX operon, is unique among known methanotrophs. However, the exact ecophysiological role of this pathway still needs to be elucidated. Detoxification of toxic nitrogen compounds and energy conservation under oxygen-limiting conditions are among the possible roles. Relevant features that may stimulate further research are, for example, absence of CRISPR/Cas systems in strain SC2, high number of iron acquisition systems in strain OB3b, and large number of transposases in strain Rockwell.

Isotopomer and isotopologue signatures of N2O produced in alpine ecosystems on the Qinghai-Tibetan Plateau

RATIONALE

Static-chamber flux measurements have suggested that one of the world's largest grasslands, the Qinghai-Tibetan Plateau (QTP), is a potential source of nitrous oxide (N2O), a major greenhouse gas. However, production and consumption pathways of N2O have not been identified by in situ field measurements.

METHODS

Ratios of N2O isotopomers ((14)N(15)N(16)O and (15)N(14)N(16)O) and an isotopologue ((14)N(14)N(18)O) with respect to (14)N(14)N(16)O in the atmosphere, static chambers, and soils were measured by gas chromatography and mass spectrometry in the summer of 2005 and the following winter of 2006 at three typical alpine ecosystems: alpine meadow, alpine shrub, and alpine wetland, on the QTP, China.

RESULTS

Site preference (SP) values of soil-emitted N2 O were estimated as 33.7‰ and 30.1‰ for alpine meadow and shrub, respectively, suggesting larger contributions by fungal denitrification, than by bacterial denitrification and nitrifier-denitrification, to N2 O production. Statistical analysis of the relationship between SP and δ(15)N(bulk) values indicated that in alpine meadow, shrub, and wetland sites fungal denitrification contributed 40.7%, 40.0%, and 23.2% to gross N2O production and the produced N2O was reduced by 87.6%, 82.9%, and 92.7%, respectively.

CONCLUSIONS

The combined measurements of N2O concentration, flux, and isotopomeric signatures provide a robust estimation of N2O circulation dynamics in alpine ecosystems on the QTP, which would contribute to the development of ecosystem nitrogen cycle model.

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.

Isotope signatures of N₂O in a mixed microbial population system: constraints on N₂O producing pathways in wastewater treatment

We present measurements of site preference (SP) and bulk (15)N/(14)N ratios (δ(15)N(bulk)(N2O)) of nitrous oxide (N(2)O) by quantum cascade laser absorption spectroscopy (QCLAS) as a powerful tool to investigate N(2)O production pathways in biological wastewater treatment. QCLAS enables high-precision N(2)O isotopomer analysis in real time. This allowed us to trace short-term fluctuations in SP and δ(15)N(bulk)(N2O) and, hence, microbial transformation pathways during individual batch experiments with activated sludge from a pilot-scale facility treating municipal wastewater. On the basis of previous work with microbial pure cultures, we demonstrate that N(2)O emitted during ammonia (NH(4)(+)) oxidation with a SP of -5.8 to 5.6 ‰ derives mostly from nitrite (NO(2)(-)) reduction (e.g., nitrifier denitrification), with a minor contribution from hydroxylamine (NH(2)OH) oxidation at the beginning of the experiments. SP of N(2)O produced under anoxic conditions was always positive (1.2 to 26.1 ‰), and SP values at the high end of this spectrum (24.9 to 26.1 ‰) are indicative of N(2)O reductase activity. The measured δ(15)N(bulk)(N2O) at the initiation of the NH(4)(+) oxidation experiments ranged between -42.3 and -57.6 ‰ (corresponding to a nitrogen isotope effect Δδ(15)N = δ(15)N(substrate) - δ(15)N(bulk)(N2O) of 43.5 to 58.8 ‰), which is considerably higher than under denitrifying conditions (δ(15)N(bulk)(N2O) 2.4 to -17 ‰; Δδ(15)N = 0.1 to 19.5 ‰). During the course of all NH(4)(+) oxidation and nitrate (NO(3)(-)) reduction experiments, δ(15)N(bulk)(N2O) increased significantly, indicating net (15)N enrichment in the dissolved inorganic nitrogen substrates (NH(4)(+), NO(3)(-)) and transfer into the N(2)O pool. The decrease in δ(15)N(bulk)(N2O) during NO(2)(-) and NH(2)OH oxidation experiments is best explained by inverse fractionation during the oxidation of NO(2)(-) to NO(3)(-).

Novel laser spectroscopic technique for continuous analysis of N2O isotopomers--application and intercomparison with isotope ratio mass spectrometry

RATIONALE

Nitrous oxide (N(2)O), a highly climate-relevant trace gas, is mainly derived from microbial denitrification and nitrification processes in soils. Apportioning N(2)O to these source processes is a challenging task, but better understanding of the processes is required to improve mitigation strategies. The N(2)O site-specific (15)N signatures from denitrification and nitrification have been shown to be clearly different, making this signature a potential tool for N(2)O source identification. We have applied for the first time quantum cascade laser absorption spectroscopy (QCLAS) for the continuous analysis of the intramolecular (15)N distribution of soil-derived N(2)O and compared this with state-of-the-art isotope ratio mass spectrometry (IRMS).

METHODS

Soil was amended with nitrate and sucrose and incubated in a laboratory setup. The N(2)O release was quantified by FTIR spectroscopy, while the N(2)O intramolecular (15)N distribution was continuously analyzed by online QCLAS at 1 Hz resolution. The QCLAS results on time-integrating flask samples were compared with those from the IRMS analysis.

RESULTS

The analytical precision (2σ) of QCLAS was around 0.3‰ for the δ(15)N(bulk) and the (15)N site preference (SP) for 1-min average values. Comparing the two techniques on flask samples, excellent agreement (R(2)= 0.99; offset of 1.2‰) was observed for the δ(15)N(bulk) values while for the SP values the correlation was less good (R(2 )= 0.76; offset of 0.9‰), presumably due to the lower precision of the IRMS SP measurements.

CONCLUSIONS

These findings validate QCLAS as a viable alternative technique with even higher precision than state-of-the-art IRMS. Thus, laser spectroscopy has the potential to contribute significantly to a better understanding of N turnover in soils, which is crucial for advancing strategies to mitigate emissions of this efficient greenhouse gas.

N(2)O emissions and source processes in snow-covered soils in the Swiss Alps

Nitrous oxide (N2O) emissions from snow-covered soils represent a significant fraction of the annual flux from alpine, subalpine or cold-temperate regions. In winter 2010-2011, we investigated the temporal variability of N2O emissions and source processes from a subalpine valley in the Swiss Alps. The study included regular measurements of N2O snow profiles at a fixed location and an intensive sampling campaign along a transversal cut through the valley with grassland at the bottom and coniferous forest at the slopes. During the intensive campaign, recently developed laser spectroscopy was employed for high-precision N2O isotopomer analysis. Maximum N2O fluxes (0.77±0.64 nmol m(-2) h(-1)) were found for periods with elevated air temperature and, in contrast to our expectations, were higher from forest than from grassland in mid-February. At maximum snow height (63 cm) the main N2O source processes were heterotrophic denitrification and nitrifier denitrification. The reduction of N2O by heterotrophic denitrifiers was much more pronounced for the grassland compared with the forest soil, as indicated by the (15)N site preferences of 16.4±11.5 ‰ (grassland) and-1.6±2.1 ‰ (forest). This illustrates the potential of laser spectroscopic N2O isotopomer analysis for the identification of source processes even at low emission rates in nutrient poor ecosystems.

Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies

Nitrous oxide (N(2)O) is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO) production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N(2)O is formed biologically from the oxidation of hydroxylamine (NH(2)OH) or the reduction of nitrite (NO(-) (2)) to NO and further to N(2)O. Our review of the biological pathways for N(2)O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO(-) (2) to NO and the further reduction of NO to N(2)O, while N(2)O formation from NH(2)OH is only performed by ammonia oxidizing bacteria (AOB). In addition to biological pathways, we review important chemical reactions that can lead to NO and N(2)O formation due to the reactivity of NO(-) (2), NH(2)OH, and nitroxyl (HNO). Moreover, biological N(2)O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N(2)O build-up are key to understand mechanisms of N(2)O release. Here, we discuss novel technologies that allow experiments on NO and N(2)O formation at high temporal resolution, namely NO and N(2)O microelectrodes and the dynamic analysis of the isotopic signature of N(2)O with quantum cascade laser absorption spectroscopy (QCLAS). In addition, we introduce other techniques that use the isotopic composition of N(2)O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N(2)O build-up.

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.

Isotopic signature of N(2)O produced by marine ammonia-oxidizing archaea

The ocean is an important global source of nitrous oxide (N(2)O), a greenhouse gas that contributes to stratospheric ozone destruction. Bacterial nitrification and denitrification are thought to be the primary sources of marine N(2)O, but the isotopic signatures of N(2)O produced by these processes are not consistent with the marine contribution to the global N(2)O budget. Based on enrichment cultures, we report that archaeal ammonia oxidation also produces N(2)O. Natural-abundance stable isotope measurements indicate that the produced N(2)O had bulk δ(15)N and δ(18)O values higher than observed for ammonia-oxidizing bacteria but similar to the δ(15)N and δ(18)O values attributed to the oceanic N(2)O source to the atmosphere. Our results suggest that ammonia-oxidizing archaea may be largely responsible for the oceanic N(2)O source.