Nitrosomonas europaea cytochrome P460 is a direct link between nitrification and nitrous oxide emission

Comparative Proteomics of Three Species of Ammonia-Oxidizing Bacteria

Ammonia-oxidizing bacteria (AOB) are important members of terrestrial, marine, and industrial microbial communities and play a fundamental role in the Nitrogen cycle within these systems. They are responsible for the first step of nitrification, ammonia oxidation to nitrite. Although AOB are widespread and essential to environmental and industrial systems, where they regularly experience fluctuations in ammonia availability, no comparative studies of the physiological response of diverse AOB species at the protein level exist. In the present study, we used 1D-LC-MS/MS proteomics to compare the metabolism and physiology of three species of ammonia AOB, Nitrosomonas europaea, Nitrosospira multiformis, and Nitrosomonas ureae, under ammonia replete and ammonia starved conditions. Additionally, we compared the expression of orthologous genes to determine the major differences in the proteome composition of the three species. We found that approximately one-third of the predicted proteome was expressed in each species and that proteins for the key metabolic processes, ammonia oxidation and carbon fixation, were among the most abundant. The red copper protein, nitrosocyanin was highly abundant in all three species hinting toward its possible role as a central metabolic enzyme in AOB. The proteomic data also allowed us to identify pyrophosphate-dependent 6-phosphofructokinase as the potential enzyme replacing the Calvin-Benson-Bassham cycle enzyme Fructose-1,6-bisphosphatase missing in N. multiformis and N. ureae. Additionally, between species, there were statistically significant differences in the expression of many abundant proteins, including those related to nitrogen metabolism (nitrite reductase), motility (flagellin), cell growth and division (FtsH), and stress response (rubrerythrin). The three species did not exhibit a starvation response at the proteome level after 24 h of ammonia starvation, however, the levels of the RuBisCO enzyme were consistently reduced after the starvation period, suggesting a decrease in capacity for biomass accumulation. This study presents the first published proteomes of N. ureae and N. multiformis, and the first comparative proteomics study of ammonia-oxidizing bacteria, which gives new insights into consistent metabolic features and differences between members of this environmentally and industrially important group.

Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis

Diphthamide biosynthesis involves a carbon-carbon bond-forming reaction catalyzed by a radical S-adenosylmethionine (SAM) enzyme that cleaves a carbon-sulfur (C-S) bond in SAM to generate a 3-amino-3-carboxypropyl (ACP) radical. Using rapid freezing, we have captured an organometallic intermediate with an iron-carbon (Fe-C) bond between ACP and the enzyme's [4Fe-4S] cluster. In the presence of the substrate protein, elongation factor 2, this intermediate converts to an organic radical, formed by addition of the ACP radical to a histidine side chain. Crystal structures of archaeal diphthamide biosynthetic radical SAM enzymes reveal that the carbon of the SAM C-S bond being cleaved is positioned near the unique cluster Fe, able to react with the cluster. Our results explain how selective C-S bond cleavage is achieved in this radical SAM enzyme.

Nitrosospira sp. Govern Nitrous Oxide Emissions in a Tropical Soil Amended With Residues of Bioenergy Crop

Organic vinasse, a residue produced during bioethanol production, increases nitrous oxide (N₂O) emissions when applied with inorganic nitrogen (N) fertilizer in soil. The present study investigated the role of the ammonia-oxidizing bacteria (AOB) community on the N₂O emissions in soils amended with organic vinasse (CV: concentrated and V: non-concentrated) plus inorganic N fertilizer. Soil samples and N₂O emissions were evaluated at 11, 19, and 45 days after fertilizer application, and the bacterial and archaea gene (amoA) encoding the ammonia monooxygenase enzyme, bacterial denitrifier (nirK, nirS, and nosZ) genes and total bacteria were quantified by real time PCR. We also employed a deep amoA amplicon sequencing approach to evaluate the effect of treatment on the community structure and diversity of the soil AOB community. Both vinasse types applied with inorganic N application increased the total N₂O emissions and the abundance of AOB. Nitrosospira sp. was the dominant AOB in the soil and was correlated with N₂O emissions. However, the diversity and the community structure of AOB did not change with vinasse and inorganic N fertilizer amendment. The results highlight the importance of residues and fertilizer management in sustainable agriculture and can be used as a reference and an input tool to determine good management practices for organic fertilization.

Genome-Scale, Constraint-Based Modeling of Nitrogen Oxide Fluxes during Coculture of Nitrosomonas europaea and Nitrobacter winogradskyi

Modern agriculture is sustained by application of inorganic nitrogen (N) fertilizer in the form of ammonium (NH₄⁺). Up to 60% of NH₄⁺-based fertilizer can be lost through leaching of nitrifier-derived nitrate (NO₃⁻), and through the emission of N oxide gases (i.e., nitric oxide [NO], N dioxide [NO₂], and nitrous oxide [N₂O] gases), the latter being a potent greenhouse gas. Our approach to modeling of nitrification suggests that both biotic and abiotic mechanisms function as important sources and sinks of N oxides during microaerobic conditions and that previous models might have underestimated gross NO production during nitrification.

Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, emits nitrogen (N) oxide gases (NO, NO₂, and N₂O), which are potentially hazardous compounds that contribute to global warming. To better understand the dynamics of nitrification-derived N oxide production, we conducted culturing experiments and used an integrative genome-scale, constraint-based approach to model N oxide gas sources and sinks during complete nitrification in an aerobic coculture of two model nitrifying bacteria, the ammonia-oxidizing bacterium Nitrosomonas europaea and the nitrite-oxidizing bacterium Nitrobacter winogradskyi. The model includes biotic genome-scale metabolic models (iFC578 and iFC579) for each nitrifier and abiotic N oxide reactions. Modeling suggested both biotic and abiotic reactions are important sources and sinks of N oxides, particularly under microaerobic conditions predicted to occur in coculture. In particular, integrative modeling suggested that previous models might have underestimated gross NO production during nitrification due to not taking into account its rapid oxidation in both aqueous and gas phases. The integrative model may be found at https://github.com/chaplenf/microBiome-v2.1.

IMPORTANCE Modern agriculture is sustained by application of inorganic nitrogen (N) fertilizer in the form of ammonium (NH₄⁺). Up to 60% of NH₄⁺-based fertilizer can be lost through leaching of nitrifier-derived nitrate (NO₃⁻), and through the emission of N oxide gases (i.e., nitric oxide [NO], N dioxide [NO₂], and nitrous oxide [N₂O] gases), the latter being a potent greenhouse gas. Our approach to modeling of nitrification suggests that both biotic and abiotic mechanisms function as important sources and sinks of N oxides during microaerobic conditions and that previous models might have underestimated gross NO production during nitrification.

Formation of Cys-heme cross-link in K42C myoglobin under reductive conditions with molecular oxygen

The structure and function of heme proteins are regulated by diverse post-translational modifications including heme-protein cross-links, with the underlying mechanisms not well understood. In this study, we introduced a Cys (K42C) close to the heme 4-vinyl group in sperm whale myoglobin (Mb) and solved its X-ray crystal structure. Interestingly, we found that K42C Mb can partially form a Cys-heme cross-link (termed K42C Mb-X) under dithiothreitol-induced reductive conditions in presence of O₂, as suggested by guanidine hydrochloride-induced unfolding and heme extraction studies. Mass spectrometry (MS) studies, together with trypsin digestion studies, further indicated that a thioether bond is formed between Cys42 and the heme 4-vinyl group with an additional mass of 16 Da, likely due to hydroxylation of the α‑carbon. We then proposed a plausible mechanism for the formation of the novel Cys-heme cross-link based on MS, kinetic UV-vis and electron paramagnetic resonance (EPR) studies. Moreover, the Cys-heme cross-link was shown to fine-tune the protein reactivity toward activation of H₂O₂. This study provides valuable insights into the post-translational modification of heme proteins, and also suggests that the Cys-heme cross-link can be induced to form in vitro, making it useful for design of new heme proteins with a non-dissociable heme and improved functions.

Nitrosomonas europaea adaptation to anoxic-oxic cycling: Insights from transcription analysis, proteomics and metabolic network modeling

In suboxic or anoxic environments, nitrous oxide (N₂O) can be produced by ammonia oxidizing bacteria (AOB) as a potent greenhouse gas. Although N₂O producing inventory and pathways have been well-characterized using archetypal AOB, there is little known about their adaptive responses to oxic-anoxic cycling, which is a prevalent condition in soil, sediment, and wastewater treatment bioreactors. In this study, cellular responses of Nitrosomonas europaea 19718 to sustained anoxic-oxic cycling in a chemostat bioreactor were evaluated at transcriptomic, proteomic, and fluxomic levels. During a single oxic-anoxic transition, the accumulations of major intermediates were found at the beginning of anoxia (nitric oxide, NO) and post anoxia (hydroxylamine, NH₂OH, and N₂O). Anoxic-oxic cycling over thirteen days led to significantly reduced accumulations of NH₂OH, NO and N₂O. Distinct from short-term responses, which were mostly regulated at the mRNA level, adapted cells seemed to sustain energy generation under repeated anoxia by partially sacrificing the NO detoxification capacities, and such adaptation was mainly regulated at the protein level. The proteomic data also suggested the potential contributions of the newly discovered cytochrome P460-mediated NH₂OH oxidation pathway to N₂O productions. Flux balance analysis was performed based on a metabolic network model consisting of 49 biochemical reactions involved in nitrogen respiration, and changes in metabolic fluxes after the anoxic-oxic cycling were found to be better correlated with intracellular protein concentrations rather than mRNA levels. Previous studies focusing on single anoxic-oxic transition might have overlooked the adaptive responses of nitrifiers to anoxic-oxic cycling, and thus overestimated NO and N₂O emission levels from natural and engineered nitrification systems.

The Eponymous Cofactors in Cytochrome P460s from Ammonia-Oxidizing Bacteria Are Iron Porphyrinoids Whose Macrocycles Are Dibasic

The enzymes hydroxylamine oxidoreductase and cytochrome (cyt) P460 contain related unconventional "heme P460" cofactors. These cofactors are unusual in their inclusion of nonstandard cross-links between amino acid side chains and the heme macrocycle. Mutagenesis studies performed on the Nitrosomonas europaea cyt P460 that remove its lysine-heme cross-link show that the cross-link is key to defining the spectroscopic properties and kinetic competence of the enzyme. However, exactly how this cross-link confers these features remains unclear. Here we report the 1.45 Å crystal structure of cyt P460 from Nitrosomonas sp. AL212 and conclude that the cross-link does not lead to a change in hybridization of the heme carbon participating in the cross-link but rather enforces structural distortions to the macrocycle away from planarity. Time-dependent density functional theory coupled to experimental structural and spectroscopic analysis suggest that this geometric distortion is sufficient to define the spectroscopic properties of the heme P460 cofactor and provide clues toward establishing a relationship between heme P460 electronic structure and function.

Calibration of the comprehensive NDHA-N2O dynamics model for nitrifier-enriched biomass using targeted respirometric assays

The NDHA model comprehensively describes nitrous oxide (N₂O) producing pathways by both autotrophic ammonium oxidizing and heterotrophic bacteria. The model was calibrated via a set of targeted extant respirometric assays using enriched nitrifying biomass from a lab-scale reactor. Biomass response to ammonium, hydroxylamine, nitrite and N₂O additions under aerobic and anaerobic conditions were tracked with continuous measurement of dissolved oxygen (DO) and N₂O. The sequential addition of substrate pulses allowed the isolation of oxygen-consuming processes. The parameters to be estimated were determined by the information content of the datasets using identifiability analysis. Dynamic DO profiles were used to calibrate five parameters corresponding to endogenous, nitrite oxidation and ammonium oxidation processes. The subsequent N₂O calibration was not significantly affected by the uncertainty propagated from the DO calibration because of the high accuracy of the estimates. Five parameters describing the individual contribution of three biological N₂O pathways were estimated accurately (variance/mean < 10% for all estimated parameters). The NDHA model response was evaluated with statistical metrics (F-test, autocorrelation function). The 95% confidence intervals of DO and N₂O predictions based on the uncertainty obtained during calibration are studied for the first time. The measured data fall within the 95% confidence interval of the predictions, indicating a good model description. Overall, accurate parameter estimation and identifiability analysis of ammonium removal significantly decreases the uncertainty propagated to N₂O production, which is expected to benefit N₂O model discrimination studies and reliable full scale applications.

Abiotic Conversion of Extracellular NH2OH Contributes to N2O Emission during Ammonia Oxidation

Abiotic processes involving the reactive ammonia-oxidation intermediates nitric oxide (NO) or hydroxylamine (NH₂OH) for N₂O production have been indicated recently. The latter process would require the availability of substantial amounts of free NH₂OH for chemical reactions during ammonia (NH₃) oxidation, but little is known about extracellular NH₂OH formation by the different clades of ammonia-oxidizing microbes. Here we determined extracellular NH₂OH concentrations in culture media of several ammonia-oxidizing bacteria (AOB) and archaea (AOA), as well as one complete ammonia oxidizer (comammox) enrichment (Ca. Nitrospira inopinata) during incubation under standard cultivation conditions. NH₂OH was measurable in the incubation media of Nitrosomonas europaea, Nitrosospira multiformis, Nitrososphaera gargensis, and Ca. Nitrosotenuis uzonensis, but not in media of the other tested AOB and AOA. NH₂OH was also formed by the comammox enrichment during NH₃ oxidation. This enrichment exhibited the largest NH₂OH:final product ratio (1.92%), followed by N. multiformis (0.56%) and N. gargensis (0.46%). The maximum proportions of NH₄⁺ converted to N₂O via extracellular NH₂OH during incubation, estimated on the basis of NH₂OH abiotic conversion rates, were 0.12%, 0.08%, and 0.14% for AOB, AOA, and Ca. Nitrospira inopinata, respectively, and were consistent with published NH₄⁺:N₂O conversion ratios for AOB and AOA.

Influences of the heme-lysine crosslink in cytochrome P460 over redox catalysis and nitric oxide sensitivity

Ammonia (NH₃)-oxidizing bacteria (AOB) derive total energy for life from the multi-electron oxidation of NH₃ to nitrite (NO₂^-). One obligate intermediate of this metabolism is hydroxylamine (NH₂OH), which can be oxidized to the potent greenhouse agent nitrous oxide (N₂O) by the AOB enzyme cytochrome (cyt) P460. We have now spectroscopically characterized a 6-coordinate (6c) {FeNO}⁷ intermediate on the NH₂OH oxidation pathway of cyt P460. This species has two fates: it can either be oxidized to the {FeNO}⁶ that then undergoes attack by NH₂OH to ultimately generate N₂O, or it can lose its axial His ligand, thus generating a stable, off-pathway 5-coordinate (5c) {FeNO}⁷ species. We show that the wild type (WT) cyt P460 exhibits a slow nitric oxide (NO)-independent conversion (k_His-off = 2.90 × 10^-3 s^-1), whereas a cross-link-deficient Lys70Tyr cyt P460 mutant protein underwent His dissociation via both a NO-independent (k_His-off = 3.8 × 10^-4 s^-1) and a NO-dependent pathway [k_His-off(NO) = 790 M^-1 s^-1]. Eyring analyses of the NO-independent pathways for these two proteins revealed a significantly larger (ca. 27 cal mol^-1 K^-1) activation entropy (ΔS^‡) in the cross-link-deficient mutant. Our results suggest that the Lys-heme cross-link confers rigidity to the positioning of the heme P460 cofactor to avoid the fast NO-dependent His dissociation pathway and subsequent formation of the off-pathway 5c {FeNO}⁷ species. The relevance of these findings to NO signaling proteins such as heme-nitric oxide/oxygen binding (H-NOX) is also discussed.

Contributions of nitrification and denitrification to N2O emissions from aged refuse bioreactor at different feeding loads of ammonia substrates

Nitrous oxide (N₂O) is a strong greenhouse gas, and its emissions from microbial nitrification (NF) and denitrification (DNF) are a threat to the environment. In the present study, a combined approach consisting of ¹⁵N stable isotope and molecular biology (qPCR) was used to determine the contributions of autotrophic nitrification (ANF), heterotrophic nitrification (HNF), and DNF to N₂O emissions in laboratory incubations of aged refuse for different ammonia (NH₄⁺-N) loads (200, 400, and 800mg·NH₄⁺-N/kg·aged refuse) and incubation times (2-144h). Experimental results showed that the N₂O emissions increased with the increase in applied amount of NH₄⁺-N substrates. Simultaneous nitrification and denitrification (SND) were demonstrated to be present in the incubations of aged refuse. The results of ¹⁵N stable isotope labelling experiment indicated that NF (54.60%-68.8%) and DNF (83.38%-85.90%) contributed to majority of N₂O emissions in the incubations of 24h and 72h, respectively. The results of functional genes (amoA and nosZ) quantification experiments indicated that the high gene copies of amoA and nosZ were present at 24h and 72h, respectively. The study also demonstrated the utility of a combined stable isotope and molecular biology approach. The approaches not only provide similar inferences about the N₂O emissions, but also enable the determination of relative contributions of ANF, HNF, and DNF to N₂O emissions. The results of the study are important in providing guidance to artificially optimize the operating conditions for alleviating N₂O emissions in aged refuse bioreactors.

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.

Pathways and Controls of N2O Production in Nitritation-Anammox Biomass

Nitrous oxide (N₂O) is an unwanted byproduct during biological nitrogen removal processes in wastewater. To establish strategies for N₂O mitigation, a better understanding of production mechanisms and their controls is required. A novel stable isotope labeling approach using ¹⁵N and ¹⁸O was applied to investigate pathways and controls of N₂O production by biomass taken from a full-scale nitritation-anammox reactor. The experiments showed that heterotrophic denitrification was a negligible source of N₂O under oxic conditions (≥0.2 mg O₂ L^-1). Both hydroxylamine oxidation and nitrifier denitrification contributed substantially to N₂O accumulation across a wide range of conditions with varying concentrations of O₂, NH₄⁺, and NO₂^-. The O₂ concentration exerted the strongest control on net N₂O production with both production pathways stimulated by low O₂, independent of NO₂^- concentrations. The stimulation of N₂O production from hydroxylamine oxidation at low O₂ was unexpected and suggests that more than one enzymatic pathway may be involved in this process. N₂O production by hydroxylamine oxidation was further stimulated by NH₄⁺, whereas nitrifier denitrification at low O₂ levels was stimulated by NO₂^- at levels as low as 0.2 mM. Our study shows that ¹⁵N and ¹⁸O isotope labeling is a useful approach for direct quantification of N₂O production pathways applicable to diverse environments.

Effects of silver nanoparticles on nitrification and associated nitrous oxide production in aquatic environments

Silver nanoparticles (AgNPs) are the most common materials in nanotechnology-based consumer products globally. Because of the wide application of AgNPs, their potential environmental impact is currently a highly topical focus of concern. Nitrification is one of the processes in the nitrogen cycle most susceptible to AgNPs but the specific effects of AgNPs on nitrification in aquatic environments are not well understood. We report the influence of AgNPs on nitrification and associated nitrous oxide (N₂O) production in estuarine sediments. AgNPs inhibited nitrification rates, which decreased exponentially with increasing AgNP concentrations. The response of nitrifier N₂O production to AgNPs exhibited low-dose stimulation (<534, 1476, and 2473 μg liter^-1 for 10-, 30-, and 100-nm AgNPs, respectively) and high-dose inhibition (hormesis effect). Compared with controls, N₂O production could be enhanced by >100% at low doses of AgNPs. This result was confirmed by metatranscriptome studies showing up-regulation of nitric oxide reductase (norQ) gene expression in the low-dose treatment. Isotopomer analysis revealed that hydroxylamine oxidation was the main N₂O production pathway, and its contribution to N₂O emission was enhanced when exposed to low-dose AgNPs. This study highlights the molecular underpinnings of the effects of AgNPs on nitrification activity and demonstrates that the release of AgNPs into the environment should be controlled because they interfere with nitrifying communities and stimulate N₂O emission.

Nitric oxide is an obligate bacterial nitrification intermediate produced by hydroxylamine oxidoreductase

Ammonia (NH₃)-oxidizing bacteria (AOB) emit substantial amounts of nitric oxide (NO) and nitrous oxide (N₂O), both of which contribute to the harmful environmental side effects of large-scale agriculture. The currently accepted model for AOB metabolism involves NH₃ oxidation to nitrite (NO₂^-) via a single obligate intermediate, hydroxylamine (NH₂OH). Within this model, the multiheme enzyme hydroxylamine oxidoreductase (HAO) catalyzes the four-electron oxidation of NH₂OH to NO₂^- We provide evidence that HAO oxidizes NH₂OH by only three electrons to NO under both anaerobic and aerobic conditions. NO₂^- observed in HAO activity assays is a nonenzymatic product resulting from the oxidation of NO by O₂ under aerobic conditions. Our present study implies that aerobic NH₃ oxidation by AOB occurs via two obligate intermediates, NH₂OH and NO, necessitating a mediator of the third enzymatic step.

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.