A simple and rapid GC/MS method for the simultaneous determination of gaseous metabolites

Nitrous oxide abuse direct measurement for diagnosis and follow-up: update on kinetics and impact on metabolic pathways

Recreational use of nitrous oxide (N2O) has become a major health issue worldwide, with a high number of clinical events, especially in neurology and cardiology. It is essential to be able to detect and monitor N2O abuse to provide effective care and follow-up to these patients. Current recommendations for detecting N2O in cases of recreational misuse and consumption markers are lacking. We aimed to update current knowledge through a review of the literature on N2O measurement and kinetics. We reviewed the outcomes of experiments, whether in preclinical models (in vitro or in vivo), or in humans, with the aim to identify biomarkers of intoxication as well as biomarkers of clinical severity, for laboratory use. Because N2O is eliminated 5 min after inhalation, measuring it in exhaled air is of no value. Many studies have found that urine and blood matrices concentrations are connected to ambient concentrations, but there is no similar data for direct exposure. There have been no studies on N2O measurement in direct consumers. Currently, patients actively abusing N2O are monitored using effect biomarkers (biomarkers related to the effects of N2O on metabolism), such as vitamin B12, homocysteine and methylmalonic acid.

Collaborative metabolisms of urea and cyanate degradation in marine anammox bacterial culture

Anammox process greatly contributes to nitrogen loss occurring in oceanic oxygen minimum zones (OMZs), where the availability of NH4+ is scarce as compared with NO2-. Remineralization of organic nitrogen compounds including urea and cyanate (OCN-) into NH4+ has been believed as an NH4+ source of the anammox process in oxygen minimum zones. However, urea- or OCN-- dependent anammox has not been well examined due to the lack of marine anammox bacterial culture. In the present study, urea and OCN- degradation in a marine anammox bacterial consortium were investigated based on 15N-tracer experiments and metagenomic analysis. Although a marine anammox bacterium, Candidatus Scalindua sp., itself was incapable of urea and OCN- degradation, urea was anoxically decomposed to NH4+ by the coexisting ureolytic bacteria (Rhizobiaceae, Nitrosomonadaceae, and/or Thalassopiraceae bacteria), whereas OCN- was abiotically degraded to NH4+. The produced NH4+ was subsequently utilized in the anammox process. The activity of the urea degradation increased under microaerobic condition (ca. 32-42 μM dissolved O2, DO), and the contribution of the anammox process to the total nitrogen loss also increased up to 33.3% at 32 μM DO. Urea-dependent anammox activities were further examined in a fluid thioglycolate media with a vertical gradient of O2 concentration, and the active collaborative metabolism of the urea degradation and anammox was detected at the lower oxycline (21 μM DO).

Rapid Characterization of Bacterial Lipids with Ambient Ionization Mass Spectrometry for Species Differentiation

Ambient ionization mass spectrometry (AIMS) is both labor and time saving and has been proven to be useful for the rapid delineation of trace organic and biological compounds with minimal sample pretreatment. Herein, an analytical platform of probe sampling combined with a thermal desorption–electrospray ionization/mass spectrometry (TD-ESI/MS) and multivariate statistical analysis was developed to rapidly differentiate bacterial species based on the differences in their lipid profiles. For comparison, protein fingerprinting was also performed with matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) to distinguish these bacterial species. Ten bacterial species, including five Gram-negative and five Gram-positive bacteria, were cultured, and the lipids in the colonies were characterized with TD-ESI/MS. As sample pretreatment was unnecessary, the analysis of the lipids in a bacterial colony growing on a Petri dish was completed within 1 min. The TD-ESI/MS results were further performed by principal component analysis (PCA) and hierarchical cluster analysis (HCA) to assist the classification of the bacteria, and a low relative standard deviation (5.2%) of the total ion current was obtained from repeated analyses of the lipids in a single bacterial colony. The PCA and HCA results indicated that different bacterial species were successfully distinguished by the differences in their lipid profiles as validated by the differences in their protein profiles recorded from the MALDI-TOF analysis. In addition, real-time monitoring of the changes in the specific lipids of a colony with growth time was also achieved with probe sampling and TD-ESI/MS. The developed analytical platform is promising as a useful diagnostic tool by which to rapidly distinguish bacterial species in clinical practice.

NH2OH Disproportionation Mediated by Anaerobic Ammonium-oxidizing (Anammox) Bacteria

Anammox bacteria produce N₂ gas by oxidizing NH₄⁺ with NO₂^–, and hydroxylamine (NH₂OH) is a potential intermediate of the anammox process. N₂ gas production occurs when anammox bacteria are incubated with NH₂OH only, indicating their capacity for NH₂OH disproportionation with NH₂OH serving as both the electron donor and acceptor. Limited information is currently available on NH₂OH disproportionation by anammox bacteria; therefore, the stoichiometry of anammox bacterial NH₂OH disproportionation was examined in the present study using ¹⁵N-tracing techniques. The anammox bacteria, Brocadia sinica, Jettenia caeni, and Scalindua sp. were incubated with the addition of ¹⁵NH₂OH, and the production of ¹⁵N-labeled nitrogenous compounds was assessed. The anammox bacteria tested performed NH₂OH disproportionation and produced ^15-15N₂ gas and NH₄⁺ as reaction products. The addition of acetylene, an inhibitor of the anammox process, reduced the activity of NH₂OH disproportionation, but not completely. The growth of B. sinica by NH₂OH disproportionation (–240.3‍ ‍kJ mol NH₂OH^–1 under standard conditions) was also tested in 3 up-flow column anammox reactors fed with 1) 0.7‍ ‍mM NH₂OH only, 2) 0.7‍ ‍mM NH₂OH and 0.5‍ ‍mM NH₄⁺, and 3) 0.7‍ ‍mM NH₂OH and 0.5‍ ‍mM NO₂^–. NH₂OH consumption activities were markedly reduced after 7‍ ‍d of operation, indicating that B. sinica was unable to maintain its activity or biomass by NH₂OH disproportionation.

N2O Reduction by Gemmatimonas aurantiaca and Potential Involvement of Gemmatimonadetes Bacteria in N2O Reduction in Agricultural Soils

Agricultural soil is the primary N₂O sink limiting the emission of N₂O gas into the atmosphere. Although Gemmatimonadetes bacteria are abundant in agricultural soils, limited information is currently available on N₂O reduction by Gemmatimonadetes bacteria. Therefore, the effects of pH and temperature on N₂O reduction activities and affinity constants for N₂O reduction were examined by performing batch experiments using an isolate of Gemmatimonadetes bacteria, Gemmatimonas aurantiaca (NBRC100505^T). G. aurantiaca reduced N₂O at pH 5–9 and 4–50°C, with the highest activity being observed at pH 7 and 30°C. The affinity constant of G. aurantiaca cells for N₂O was 4.4‍ ‍μM. The abundance and diversity of the Gemmatimonadetes 16S rRNA gene and nosZ encoding nitrous oxide reductase in agricultural soil samples were also investigated by quantitative PCR (qPCR) and amplicon sequencing ana­lyses. Four N₂O-reducing agricultural soil samples were assessed, and the copy numbers of the Gemmatimonadetes 16S rRNA gene (clades G1 and G3), nosZ DNA, and nosZ mRNA were 8.62–9.65×10⁸, 5.35–7.15×10⁸, and 2.23–4.31×10⁹ copies (g dry soil)^–1, respectively. The abundance of the nosZ mRNA of Gemmatimonadetes bacteria and OTU91, OUT332, and OTU122 correlated with the N₂O reduction rates of the soil samples tested, suggesting N₂O reduction by Gemmatimonadetes bacteria. Gemmatimonadetes 16S rRNA gene reads affiliated with OTU4572 and OTU3759 were predominant among the soil samples examined, and these Gemmatimonadetes OTUs have been identified in various types of soil samples.

Determination of 15N/14N of Ammonium, Nitrite, Nitrate, Hydroxylamine, and Hydrazine Using Colorimetric Reagents and Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS)

In the nitrogen (N) cycle, nitrogenous compounds are chemically and biologically converted to various aqueous and gaseous N species. The ¹⁵N-labeling approach is a powerful culture-dependent technique to obtain insights into the complex nitrogen transformation reactions that occur in cultures. In the ¹⁵N-labeling approach, the fates of supplemented ¹⁵N- and/or unlabeled gaseous and aqueous compounds are tracked by mass spectrometry (MS) analysis, whereas MS analysis of aqueous N species requires laborious sample preparation steps and is performed using isotope-ratio mass spectrometry, which requires an expensive mass spectrometer. We developed a simple and high-throughput MS method for determining the ¹⁵N atoms percent of NH₄⁺, NO₂^-, NO₃^-, NH₂OH, and N₂H₄, where liquid samples (<0.5 mL) were mixed with colorimetric reagents (naphthylethylenediamine for NO₂^-, indophenol for NH₄⁺, and p-aminobenzaldehyde for N₂H₄), and the mass spectra of the formed N complex dyes were obtained by matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) MS. NH₂OH and NO₃^- were chemically converted to NO₂^- by iodine oxidation and copper/hydrazine reduction reaction, respectively, prior to the above colorimetric reaction. The intensity of the isotope peak (M + 1 or M + 2) increased when the N complex dye was formed by coupling with a ¹⁵N-labeled compound, and a linear relationship was found between the determined ¹⁵N/¹⁴N peak ratio and ¹⁵N atom% for the tested N species. The developed method was applied to bacterial cultures to examine their N-transformation reactions, enabling us to observe the occurrence of NO₂^- oxidation and NO₃^- reduction in a hypoxic Nitrobacter winogradskyi culture. IMPORTANCE ¹⁵N/¹⁴N analysis for aqueous N species is a powerful tool for obtaining insights into the global N cycle, but the procedure is cumbersome and laborious. The combined use of colorimetric reagents and MALDI-TOF MS, designated color MALDI-TOF MS, enabled us to determine the ¹⁵N atom% of common aqueous N species without laborious sample preparation and chromatographic separation steps; for instance, the ¹⁵N atom% of NO₂^- can be determined from >1,000 liquid samples daily at <$1 (U.S.) per 384 samples for routine analysis. This convenient MS method is a powerful tool that will advance our ability to explore the N-transformation reactions that occur in various environments and biological samples.

Cell Density-dependent Anammox Activity of Candidatus Brocadia sinica Regulated by N-acyl Homoserine Lactone-mediated Quorum Sensing

The activity of anaerobic ammonia-oxidizing (anammox) bacteria is considered to depend on cell density; however, this has not yet been confirmed due to the fastidious nature of anammox bacteria (e.g., slow growth, oxygen sensitivity, and rigid aggregate formation). In the present study, the cell density-dependent occurrence of anammox activity (^14-15N₂ gas production rate) was investigated using planktonic enrichment cultures of Candidatus Brocadia sinica. This activity was detectable when the density of cells was higher than 10⁷‍ ‍cells‍ ‍mL^–1 and became stronger with increases in cell density. At the cell densities, the transcription of the BROSI_A1042 and BROSI_A3652 genes, which are potentially involved in the biosynthesis and reception of N-acyl homoserine lactone (AHL), was detectable in Brocadia sinica cells. The presence of AHL molecules in the MBR culture of B. sinica was confirmed by an AHL reporter assay and gas chromatography mass spectrometry analysis. The exogenous addition of the MBR culture extract and AHL molecules (a cocktail of C₆, C₈, C₁₀, and C₁₂-homoserine lactones) increased the specific ^14-15N₂ production rate of B. sinica. These results suggest that the specific anammox activity of B. sinica is regulated by AHL-mediated quorum sensing.

Dissimilatory Nitrate Reduction to Ammonium and Responsible Microbes in Japanese Rice Paddy Soil

Nitrification–denitrification processes in the nitrogen cycle have been extensively examined in rice paddy soils. Nitrate is generally depleted in the reduced soil layer below the thin oxidized layer at the surface, and this may be attributed to high denitrification activity. In the present study, we investigated dissimilatory nitrate reduction to ammonium (DNRA), which competes with denitrification for nitrate, in order to challenge the conventional view of nitrogen cycling in paddy soils. We performed paddy soil microcosm experiments using ¹⁵N tracer analyses to assess DNRA and denitrification rates and conducted clone library analyses of transcripts of nitrite reductase genes (nrfA, nirS, and nirK) in order to identify the microbial populations carrying out these processes. The results obtained showed that DNRA occurred to a similar extent to denitrification and appeared to be enhanced by a nitrate limitation relative to organic carbon. We also demonstrated that different microbial taxa were responsible for these distinct processes. Based on these results and previous field observations, nitrate produced by nitrification within the surface oxidized layer may be reduced not only to gaseous N₂ via denitrification, but also to NH₄⁺ via DNRA, within the reduced layer. The present results also indicate that DNRA reduces N loss through denitrification and nitrate leaching and provides ammonium to rice roots in rice paddy fields.

Multivariate calibration method for mass spectrometry of interfering gases such as mixtures of CO, N2 , and CO2

A multivariate calibration method for mass spectrometry is presented that enables a quantitative analysis of gas mixtures containing interfering gases that contribute to the same mass-to-charge ratios at nominal resolution. Multiple calibration gas mixtures with linearly independent compositions are used in order to obtain the calibration constants for the contribution of each gas to each of the mass-to-charge ratio peaks. The method was successfully applied to the quantitative detection of CO in a mixture with CO₂ and N₂ , which represents a difficulty commonly encountered in heterogeneous catalysis and electrocatalysis research.

Synergistic inhibition of anaerobic ammonium oxidation (anammox) activity by phenol and thiocyanate

Coke-oven wastewater discharged from the steel-manufacturing process is phenol and thiocyanate (SCN)-rich wastewater, which inhibits microbial activities in biological wastewater treatment processes. In the present study, synergistic inhibition of anaerobic ammonium oxidation (anammox) activity by phenol and SCN was examined by batch incubation and continuous operation of an anammox reactor. The comparison of anammox activities determined in the batch incubation, in which the anammox biomass was anoxically incubated with 10-250 mg L^-1 of i) phenol, ii) SCN, or iii) both phenol and SCN, showed that synergistic inhibition by phenol and SCN was greater than the inhibitions by phenol or SCN alone. The synergistic inhibition by phenol and SCN was further investigated by operating an up-flow column anammox reactor for 262 d. The removal efficiencies of NH₄⁺ and NO₂^- deteriorated when phenol and SCN concentrations in the influent increased to 16 and 32 mg L^-1, respectively, and the inhibition of anammox activity was further investigated by a¹⁵NO₂^- tracer experiment. Addition of phenol and SCN resulted in a population shift of anammox bacteria, and the dominant species changed from "Candidatus Kuenenia stuttgartiensis" to "Ca. Brocadia sinica". The relative abundance of Azoarcus and Thiobacillus 16S rRNA gene reads increased during the operation, suggesting that they were responsible for the anaerobic phenol and SCN degradation. The present study is the first to document the synergistic inhibition of anammox activity by phenol and SCN and the microbial consortia involved in the nitrogen removal as well as the phenol and SCN degradations.

Mitigation of nitrous oxide emissions from acidic soils by Bacillus amyloliquefaciens, a plant growth-promoting bacterium

Nitrous oxide (N₂ O) is a long-lived greenhouse gas that can result in the alteration of atmospheric chemistry and cause accompanying changes in global climate. To date, many techniques have been used to mitigate the emissions of N₂ O from agricultural fields, which represent one of the most important sources of N₂ O. In this study, we designed a greenhouse pot experiment and a microcosmic serum bottle incubation experiment using acidic soil from a vegetable farm to study the effects of Bacillus amyloliquefaciens (BA) on plant growth and N₂ O emission rates. The addition of BA to the soil promoted plant growth enhanced the soil pH and increased the total nitrogen (TN) contents in the plants. At the same time, it decreased the concentrations of ammonium (NH₄⁺ ), nitrate (NO₃^- ) and TN in the soil. Overall, the addition of BA resulted in a 50% net reduction of N₂ O emissions compared with the control. Based on quantitative PCR and the network analysis of DNA sequencing, it was demonstrated that BA partially inhibited the nitrification process through the significant reduction of ammonia oxidizing bacteria. Meanwhile, it enhanced the denitrification process, mainly by increasing the abundance of N₂ O-reducing bacteria in the treatment with BA. The results of our microcosm experiment provided evidence that strongly supported the above findings under more strictly controlled laboratory conditions. Taken together, the results of our study evidently demonstrated that BA has dual effects on the promotion of plant growth and the dramatic reduction of greenhouse emissions, thus suggesting the possibility of screening beneficial microbial organisms from the environment that can promote plant growth and mitigate greenhouse trace gases.

Hybrid Nitrous Oxide Production from a Partial Nitrifying Bioreactor: Hydroxylamine Interactions with Nitrite

The goal of this study was to elucidate the mechanisms of nitrous oxide (N₂O) production from a bioreactor for partial nitrification (PN). Ammonia-oxidizing bacteria (AOB) enriched from a sequencing batch reactor (SBR) were subjected to N₂O production pathway tests. The N₂O pathway test was initiated by supplying an inorganic medium to ensure an initial NH₄⁺-N concentration of 160 mg-N/L, followed by ¹⁵NO₂^- (20 mg-N/L) and dual ¹⁵NH₂OH (each 17 mg-N/L) spikings to quantify isotopologs of gaseous N₂O (⁴⁴N₂O, ⁴⁵N₂O, and ⁴⁶N₂O). N₂O production was boosted by ¹⁵NH₂OH spiking, causing exponential increases in mRNA transcription levels of AOB functional genes encoding hydroxylamine oxidoreductase (haoA), nitrite reductase (nirK), and nitric oxide reductase (norB) genes. Predominant production of ⁴⁵N₂O among N₂O isotopologs (46% of total produced N₂O) indicated that coupling of ¹⁵NH₂OH with ¹⁴NO₂^- produced N₂O via N-nitrosation hybrid reaction as a predominant pathway. Abiotic hybrid N₂O production was also observed in the absence of the AOB-enriched biomass, indicating multiple pathways for N₂O production in a PN bioreactor. The additional N₂O pathway test, where ¹⁵NH₄⁺ was spiked into 400 mg-N/L of NO₂^- concentration, confirmed that the hybrid N₂O production was a dominant pathway, accounting for approximately 51% of the total N₂O production.

Higher diversity and abundance of denitrifying microorganisms in environments than considered previously

Denitrification is an important process in the global nitrogen cycle. The genes encoding NirK and NirS (nirK and nirS), which catalyze the reduction of nitrite to nitric oxide, have been used as marker genes to study the ecological behavior of denitrifiers in environments. However, conventional polymerase chain reaction (PCR) primers can only detect a limited range of the phylogenetically diverse nirK and nirS. Thus, we developed new PCR primers covering the diverse nirK and nirS. Clone library and qPCR analysis using the primers showed that nirK and nirS in terrestrial environments are more phylogenetically diverse and 2-6 times more abundant than those revealed with the conventional primers. RNA- and culture-based analyses using a cropland soil also suggested that microorganisms with previously unconsidered nirK or nirS are responsible for denitrification in the soil. PCR techniques still have a greater capacity for the deep analysis of target genes than PCR-independent methods including metagenome analysis, although efforts are needed to minimize the PCR biases. The methodology and the insights obtained here should allow us to achieve a more precise understanding of the ecological behavior of denitrifiers and facilitate more precise estimate of denitrification in environments.

Real time monitoring of gases emitted from soils using a multi-turn time-of-flight mass spectrometer "MULTUM-S II"

Many miniaturized mass spectrometers used for on-site analysis have been designed and developed recently utilizing a broad range of analyzer platforms. These instruments are expected to have widespread applications covering many fields of interest. In our laboratory, a miniaturized multi-turn time-of-flight (TOF) mass spectrometer "MULTUM-S II" was designed and constructed. The size and weight of the developed "MULTUM-S II" are 45 cm × 23 cm × 64 cm and 36 kg. Irrespective of this small platform, it still boasts a high mass resolution capability of more than 30,000. In this study, we attempted to carry out real-time monitoring of gaseous compounds such as N2, O2, CO2, N2O and CH4. Using conventional miniaturized mass spectrometers, CO2 and N2O cannot be detected simultaneously due to the low mass resolution inherent to these established analyzer designs. Using a new method, "GC/high resolution mass spectrometry" described in this paper, real time monitoring of gases emitted from soils can be achieved. In a soil incubation experiment, CO2 and N2O started to increase just after water supplement and these gases varied similarly during the experiment, thus showing that this improved gas analyzing system could monitor the short time response of gaseous production in soil.

N(2)O emission from degraded soybean nodules depends on denitrification by Bradyrhizobium japonicum and other microbes in the rhizosphere

A model system developed to produce N(2)O emissions from degrading soybean nodules in the laboratory was used to clarify the mechanism of N(2)O emission from soybean fields. Soybean plants inoculated with nosZ-defective strains of Bradyrhizobium japonicum USDA110 (ΔnosZ, lacking N(2)O reductase) were grown in aseptic jars. After 30 days, shoot decapitation (D, to promote nodule degradation), soil addition (S, to supply soil microbes), or both (DS) were applied. N(2)O was emitted only with DS treatment. Thus, both soil microbes and nodule degradation are required for the emission of N(2)O from the soybean rhizosphere. The N(2)O flux peaked 15 days after DS treatment. Nitrate addition markedly enhanced N(2)O emission. A (15)N tracer experiment indicated that N(2)O was derived from N fixed in the nodules. To evaluate the contribution of bradyrhizobia, N(2)O emission was compared between a nirK mutant (ΔnirKΔnosZ, lacking nitrite reductase) and ΔnosZ. The N(2)O flux from the ΔnirKΔnosZ rhizosphere was significantly lower than that from ΔnosZ, but was still 40% to 60% of that of ΔnosZ, suggesting that N(2)O emission is due to both B. japonicum and other soil microorganisms. Only nosZ-competent B. japonicum (nosZ+ strain) could take up N(2)O. Therefore, during nodule degradation, both B. japonicum and other soil microorganisms release N(2)O from nodule N via their denitrification processes (N(2)O source), whereas nosZ-competent B. japonicum exclusively takes up N(2)O (N(2)O sink). Net N(2)O flux from soybean rhizosphere is likely determined by the balance of N(2)O source and sink.

High abundance of ammonia-oxidizing archaea in acidified subtropical forest soils in southern China after long-term N deposition

Nitrification has been believed to be performed only by autotrophic ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) until the recent discovery of ammonia-oxidizing archaea (AOA). Meanwhile, it has been questioned whether AOB are significantly responsible for NH(3) oxidation in acidic forest soils. Here, we investigated nitrifying communities and their activity in highly acidified soils of three subtropical forests in southern China that had received chronic high atmospheric N deposition. Nitrifying communities were analyzed using PCR- and culture (most probable number)-based approaches. Nitrification activity was analyzed by measuring gross soil nitrification rates using a (15) N isotope dilution technique. AOB were not detected in the three forest soils: neither via PCR of 16S rRNA and ammonia monooxygenase (amoA) genes nor via culture-based approaches. In contrast, an extraordinary abundance of the putative archaeal amoA was detected (3.2 × 10(8) -1.2 × 10(9)  g soil(-1) ). Moreover, this abundance was correlated with gross soil nitrification rates. This indicates that amoA-possessing archaea rather than bacteria were predominantly responsible for nitrification of the soils. Furthermore, sequences of the genus Nitrospira, a dominant group of soil NOB, were detected. Thus, nitrification of acidified subtropical forest soils in southern China could be performed by a combination of AOA and NOB.