Revision of N2O-producing pathways in the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC 19718

Long-term addition of organic manure stimulates the growth and activity of comammox in a subtropical Inceptisol

The discovery of complete ammonia oxidizers (comammox) has dramatically altered our perception of nitrogen (N) biogeochemistry. However, their functional importance vs. the canonical ammonia oxidizers (i.e., ammonia oxidizing-archaea (AOA) and bacteria (AOB)) in agroecosystems is still poorly understood. Accordingly, a new assay using acetylene, 3,4-dimethylpyrazole phosphate (DMPP), and 1-octyne was adopted to assess the ammonia (NH3) oxidation and nitrous oxide (N2O) production activity of these functional guilds in a subtropical Inceptisol under long-term different fertilization regimes. These regimes include CK (no fertilizer control), synthetic fertilizer only (NPK), organic manure only (M) and organic manure plus synthetic fertilizer (MNPK). AOA dominated NH3 oxidation in the M treatment, while AOB dominated both NH3 oxidation and N2O production in all treatments except M. Comammox always played a minor role in both NH3 oxidation and N2O production across all treatments. Both M and MNPK treatments significantly increased the activity and growth of comammox. Compared to NPK, comammox exhibited increases of 270 % and 326 % in the NH3 oxidation rates, and increases of 1472 % and 563 % in the N2O production rates in M and MNPK, respectively. Random forest model revealed that copper (Cu), comammox abundance, and dissolved organic nitrogen (DON) were the most important predictors for the NH3 oxidation rates of comammox. Redundancy analyses (RDA) showed that fertilizer treatments significantly altered the community composition of NH3 oxidizers, and pH was the overarching parameter underpinning the community shift of the NH3 oxidizers. Overall, this study provides evidence that comammox play a minor yet unneglectable role in the nitrification of agroecosystems, and the long-term addition of organic manure stimulates the growth and activity of comammox in a subtropical Inceptisol.

Nitrogen input modulates the effects of coastal acidification on nitrification and associated N2O emission

Acidification of coastal waters, synergistically driven by increasing atmospheric carbon dioxide (CO2) and intensive land-derived nutrient inputs, exerts significant stresses on the biogeochemical cycles of coastal ecosystem. However, the combined effects of anthropogenic nitrogen (N) inputs and aquatic acidification on nitrification, a critical process of N cycling, remains unclear in estuarine and coastal ecosystems. Here, we showed that increased loading of ammonium (NH4+) in estuarine and coastal waters alleviated the inhibitory effect of acidification on nitrification rates but intensified the production of the potent greenhouse gas nitrous oxide (N2O), thus accelerating global climate change. Metatranscriptomes and natural N2O isotopic signatures further suggested that the enhanced emission of N2O may mainly source from hydroxylamine (NH2OH) oxidation rather than from nitrite (NO2-) reduction pathway of nitrifying microbes. This study elucidates how anthropogenic N inputs regulate the effects of coastal acidification on nitrification and associated N2O emissions, thereby enhancing our ability to predict the feedbacks of estuarine and coastal ecosystems to climate change and human perturbations.

Dating Ammonia-Oxidizing Bacteria with Abundant Eukaryotic Fossils

Evolution of a complete nitrogen (N) cycle relies on the onset of ammonia oxidation, which aerobically converts ammonia to nitrogen oxides. However, accurate estimation of the antiquity of ammonia-oxidizing bacteria (AOB) remains challenging because AOB-specific fossils are absent and bacterial fossils amenable to calibrate molecular clocks are rare. Leveraging the ancient endosymbiosis of mitochondria and plastid, as well as using state-of-the-art Bayesian sequential dating approach, we obtained a timeline of AOB evolution calibrated largely by eukaryotic fossils. We show that the first AOB evolved in marine Gammaproteobacteria (Gamma-AOB) and emerged between 2.1 and 1.9 billion years ago (Ga), thus postdating the Great Oxidation Event (GOE; 2.4 to 2.32 Ga). To reconcile the sedimentary N isotopic signatures of ammonia oxidation occurring near the GOE, we propose that ammonia oxidation likely occurred at the common ancestor of Gamma-AOB and Gammaproteobacterial methanotrophs, or the actinobacterial/verrucomicrobial methanotrophs which are known to have ammonia oxidation activities. It is also likely that nitrite was transported from the terrestrial habitats where ammonia oxidation by archaea took place. Further, we show that the Gamma-AOB predated the anaerobic ammonia-oxidizing (anammox) bacteria, implying that the emergence of anammox was constrained by the availability of dedicated ammonia oxidizers which produce nitrite to fuel anammox. Our work supports a new hypothesis that N redox cycle involving nitrogen oxides evolved rather late in the ocean.

Nitrous Oxide Emissions from Nitritation Reactors under Hypersaline Conditions

This study focuses on nitrous oxide (N2O) emissions during hypersaline (4 % salinity) nitritation in continuously fed and mixed fixed bed reactors. In the presence of high concentrations of nitrite and ammonium, the percent yield of N2O emissions from ammonium removed decreased with increasing dissolved oxygen (DO). However, N2O production continued even at a high DO of 15 mg/L. Bulk ammonium concentration (not ammonia) was found to be the main controlling factor for N2O emissions under high and low DO during both nitritation and nitrification. Reducing bulk ammonium concentrations below 1 mg N/L in the nitritation reactor under both high and low DO conditions resulted in a reduction of N2O emissions of approximately 90 %. Under full nitrification and low DO, reducing nitrite concentrations below 0.3 mg N/L resulted in a 60 % reduction in N2O emissions. Similar results were observed in a low salinity reactor.

Direct and indirect monitoring methods for nitrous oxide emissions in full-scale wastewater treatment plants: A critical review

Mitigation of nitrous oxide (N2O) emissions in full-scale wastewater treatment plant (WWTP) has become an irreversible trend to adapt the climate change. Monitoring of N2O emissions plays a fundamental role in understanding and mitigating N2O emissions. This paper provides a comprehensive review of direct and indirect N2O monitoring methods. The techniques, strengths, limitations, and applicable scenarios of various methods are discussed. We conclude that the floating chamber technique is suitable for capturing and interpreting the spatiotemporal variability of real-time N2O emissions, due to its long-term in-situ monitoring capability and high data acquisition frequency. The monitoring duration, location, and frequency should be emphasized to guarantee the accuracy and comparability of acquired data. Calculation by default emission factors (EFs) is efficient when there is a need for ambiguous historical N2O emission accounts of national-scale or regional-scale WWTPs. Using process-specific EFs is beneficial in promoting mitigation pathways that are primarily focused on low-emission process upgrades. Machine learning models exhibit exemplary performance in the prediction of N2O emissions. Integrating mechanistic models with machine learning models can improve their explanatory power and sharpen their predictive precision. The implementation of the synergy of nutrient removal and N2O mitigation strategies necessitates the calibration and validation of multi-path mechanistic models, supported by long-term continuous direct monitoring campaigns.

Elucidating the links between N2O dynamics and changes in microbial communities following saltwater intrusions

Saltwater intrusion in estuarine ecosystems alters microbial communities as well as biogeochemical cycling processes and has become a worldwide problem. However, the impact of salinity intrusion on the dynamics of nitrous oxide (N2O) and associated microbial community are understudied. Here, we conducted field microcosms in a tidal estuary during different months (December, April and August) using dialysis bags, and microbes inside the bags encountered a change in salinity in natural setting. We then compared N2O dynamics in the microcosms with that in natural water. Regardless of incubation environment, saltwater intrusion altered the dissolved N2O depending on the initial saturation rates of N2O. While the impact of saltwater intrusion on N2O dynamics was consistent across months, the dissolved N2O was higher in summer than in winter. The N-related microbial communities following saltwater intrusion were dominated by denitrifers, with fewer nitrifiers and bacterial taxa involved in dissimilatory nitrate reduction to ammonium. While denitrification was a significant driver of N2O dynamics in the studied estuary, nitrifier-involved denitrification contributed to the additional production of N2O, evidenced by the strong associations with amoA genes and the abundance of Nitrospira. Higher N2O concentrations in the field microcosms than in natural water limited N2O consumption in the former, given the lack of an association with nosZ gene abundance. The differences in the N2O dynamics observed between the microcosms and natural water could be that the latter comprised not only indigenous microbes but also those accompanied with saltwater intrusion, and that immigrants might be functionally rich individuals and able to perform N transformation in multiple pathways. Our work provides the first quantitative assessment of in situ N2O concentrations in an estuary subjected to a saltwater intrusion. The results highlight the importance of ecosystem size and microbial connectivity in the source-sink dynamics of N2O in changing environments.

Drug discovery-based approach identifies new nitrification inhibitors

Nitrogen (N) fertilization is crucial to sustain global food security, but fertilizer N production is energy-demanding and subsequent environmental N losses contribute to biodiversity loss and climate change. N losses can be mitigated be interfering with microbial nitrification, and therefore the use of nitrification inhibitors in enhanced efficiency fertilizers (EEFs) is an important N management strategy to increase N use efficiency and reduce N pollution. However, currently applied nitrification inhibitors have limitations and do not target all nitrifying microorganisms. Here, to identify broad-spectrum nitrification inhibitors, we adopted a drug discovery-based approach and screened 45,400 small molecules on different groups of nitrifying microorganisms. Although a high number of potential nitrification inhibitors were identified, none of them targeted all nitrifier groups. Moreover, a high number of new nitrification inhibitors were shown to be highly effective in culture but did not reduce ammonia consumption in soil. One archaea-targeting inhibitor was not only effective in soil, but even reduced - when co-applied with a bacteria-targeting inhibitor - ammonium consumption and greenhouse gas emissions beyond what is achieved with currently applied nitrification inhibitors. This advocates for combining different types of nitrification inhibitors in EEFs to optimize N management practices and make agriculture more sustainable.

Role of Nitric Oxide in Hydroxylamine Oxidation by Ammonia-Oxidizing Bacteria

An important role of nitric oxide (NO) as either a free intermediate in the NH3 oxidation pathway or a potential oxidant for NH3 or NH2OH has been proposed for ammonia-oxidizing bacteria (AOB) and archaea (AOA), respectively. However, tracing NO metabolism at low concentrations remains notoriously difficult. Here, we use electrochemical sensors and the mild NO scavenger 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) to trace apparent NO concentration and determine production rates at low micromolar concentrations in the model AOB strain Nitrosomonas europaea. In agreement with previous studies, we found that PTIO does not affect NH3 oxidation instantaneously in both Nitrosospira briensis and Nitrosomonas europaea, unlike inhibitors for ammonia oxidation such as allylthiourea and acetylene, although it effectively scavenged NO from the cell suspensions. Quantitative analysis showed that NO production by N. europaea amounted to 3.15% to 6.23% of NO2- production, whereas N. europaea grown under O2 limitation produced NO equivalent to up to 40% of NO2- production at high substrate concentrations. In addition, we found that PTIO addition to N. europaea grown under O2 limitation abolished N2O production. These results indicate different turnover rates of NO during NH3 oxidation under O2-replete and O2-limited growth conditions in AOB. The results suggest that NO may not be a free intermediate or remain tightly bound to iron centers of enzymes during hydroxylamine oxidation and that only NH3 saturation and adaptation to O2 limitation may lead to significant dissociation of NO from hydroxylamine dehydrogenase. IMPORTANCE Ammonia oxidation by chemolithoautotrophic ammonia-oxidizing bacteria (AOB) is thought to contribute significantly to global nitrous oxide (N2O) emissions and leaching of oxidized nitrogen, particularly through their activity in nitrogen (N)-fertilized agricultural production systems. Although substantial efforts have been made to characterize the N metabolism in AOB, recent findings suggest that nitric oxide (NO) may play an important mechanistic role as a free intermediate of hydroxylamine oxidation in AOB, further implying that besides hydroxylamine dehydrogenase (HAO), additional enzymes may be required to complete the ammonia oxidation pathway. However, the NO spin trap PTIO was found to not inhibit ammonia oxidation in AOB. This study provides a combination of physiological and spectroscopic evidence that PTIO indeed scavenges only free NO in AOB and that significant amounts of free NO are produced only during incomplete hydroxylamine oxidation or nitrifier denitrification under O2-limited growth conditions.

Proterozoic Acquisition of Archaeal Genes for Extracellular Electron Transfer: A Metabolic Adaptation of Aerobic Ammonia-Oxidizing Bacteria to Oxygen Limitation

Many aerobic microbes can utilize alternative electron acceptors under oxygen-limited conditions. In some cases, this is mediated by extracellular electron transfer (or EET), wherein electrons are transferred to extracellular oxidants such as iron oxide and manganese oxide minerals. Here, we show that an ammonia-oxidizer previously known to be strictly aerobic, Nitrosomonas communis, may have been able to utilize a poised electrode to maintain metabolic activity in anoxic conditions. The presence and activity of multiheme cytochromes in N. communis further suggest a capacity for EET. Molecular clock analysis shows that the ancestors of β-proteobacterial ammonia oxidizers appeared after Earth's atmospheric oxygenation when the oxygen levels were >10-4pO2 (present atmospheric level [PAL]), consistent with aerobic origins. Equally important, phylogenetic reconciliations of gene and species trees show that the multiheme c-type EET proteins in Nitrosomonas and Nitrosospira lineages were likely acquired by gene transfer from γ-proteobacteria when the oxygen levels were between 0.1 and 1 pO2 (PAL). These results suggest that β-proteobacterial EET evolved during the Proterozoic when oxygen limitation was widespread, but oxidized minerals were abundant.

Thermodynamic sensitivity of ammonia oxidizers-driven N2O fluxes under oxic-suboxic realms

In terrestrial ecosystems, the nitrogen dynamics, including N₂O production, are majorly regulated by a complex consortium of microbes favored by different substrates and environmental conditions. To better predict the daily, seasonal and annual variation in N₂O fluxes, it is critical to estimate the temperature sensitivity of different ammonia-oxidizing groups under oxic and suboxic conditions prevalent in soils and wetlands. Here, we studied the thermodynamics of N₂O fluxes, via nitrification and nitrifier-denitrification, for two ammonia-oxidizers, archaea (AOA) and bacteria (AOB), across a wide temperature gradient (10-55 °C). Using square root theory (SQRT) and macromolecular rate theory (MMRT) models, we estimated thermodynamic parameters, cardinal temperatures, and maximum temperature sensitivity (T_Smax). The distinction between N₂O pathways was facilitated by microbial-specific inhibitors (PTIO and C₂H₂) and controlled oxygen supply (oxic: ambient; suboxic: ∼4%) environments. We found that nitrification supported by AOA (Nt_A) and AOB (Nt_B) dominated N₂O production in an oxic climate, while only AOB-supported nitrifier-denitrification (ND_B) majorly contributed (>90%) to suboxic N₂O budget. The models predicted significantly higher temperature optima (T_opt) and T_Smax for Nt_A and ND_B compared to Nt_B. Intriguingly, both Nt_B and ND_B exhibited significantly wider temperature ranges than Nt_A. Altogether, our results suggest that temperature and oxygen supply control the dominance of specific AOA- and AOB-supported N₂O pathways in soil and sediments. This emergent understanding can potentially contribute toward novel targeted N₂O inhibitors for GHG mitigation under global warming.

Effects of acidification on nitrification and associated nitrous oxide emission in estuarine and coastal waters

In the context of an increasing atmospheric carbon dioxide (CO₂) level, acidification of estuarine and coastal waters is greatly exacerbated by land-derived nutrient inputs, coastal upwelling, and complex biogeochemical processes. A deeper understanding of how nitrifiers respond to intensifying acidification is thus crucial to predict the response of estuarine and coastal ecosystems and their contribution to global climate change. Here, we show that acidification can significantly decrease nitrification rate but stimulate generation of byproduct nitrous oxide (N₂O) in estuarine and coastal waters. By varying CO₂ concentration and pH independently, an expected beneficial effect of elevated CO₂ on activity of nitrifiers ("CO₂-fertilization" effect) is excluded under acidification. Metatranscriptome data further demonstrate that nitrifiers could significantly up-regulate gene expressions associated with intracellular pH homeostasis to cope with acidification stress. This study highlights the molecular underpinnings of acidification effects on nitrification and associated greenhouse gas N₂O emission, and helps predict the response and evolution of estuarine and coastal ecosystems under climate change and human activities.

The mitigation effect of free ammonia and free nitrous acid on nitrous oxide production from the full-nitrification and partial-nitritation systems

The potentials of using endogenous free ammonia (FA) and free nitrous acid (FNA) as nitrous oxide (N₂O) mitigators were investigated in treatment of both mainstream and sidestream wastewater. Although the N₂O emission factor of a sidestream partial-nitritation (PN) reactor (averaged 1.70 % ± 0.39 %, n = 30) was about 2.4 times higher than a mainstream full-nitrification (FN) reactor (averaged 0.72 % ± 0.24 %, n = 30) (P < 0.01), one-hour exposure of PN sludge to 1.5 mg HNO₂-N/L FNA could virtually abolish N₂O emission. As for FN sludge, both 45 mg NH₃-N/L FA and 0.015 mg HNO₂-N/L FNA successfully mitigated N₂O production at varying dissolved oxygen (DO) levels (50 % vs 61 %), while 1.5 mg HNO₂-N/L FNA not only reduced more N₂O (92 %) but also altered the N₂O dependency on DO. Both FNA and FA sludge treatment were effective N₂O mitigation strategies with FNA toward the end of carbon neutrality and FA being more economically appealing (2 % cost saving).

Ammonia-Oxidizing Bacteria Maintain Abundance but Lower amoA-Gene Expression during Cold Temperature Nitrification Failure in a Full-Scale Municipal Wastewater Treatment Plant

In this study, we explore the relationship between community structure and transcriptional activity of ammonia-oxidizing bacteria during cold temperature nitrification failure in three parallel full-scale sequencing batch reactors (SBRs) treating municipal wastewater. In the three reactors, ammonia concentrations increased with declines in wastewater temperature below 15°C. We quantified and sequenced 16S rRNA and ammonia monooxygenase (amoA) gene fragments in DNA and RNA extracts from activated sludge samples collected from the SBRs during the warmer seasons (summer and fall) and when water temperatures were below 15°C (winter and spring). Taxonomic community composition of amoA genes and transcripts did not vary much between the warmer and colder seasons. However, we observed significant differences in amoA transcript copy numbers between fall (highest) and spring (lowest). Ammonia-oxidizing bacteria of the genus Nitrosomonas sp. could maintain their population abundance despite lowering their amoA gene expression during winter and spring. In spite of relatively low population abundance, an amoA amplicon sequence variant (ASV) cluster identified as most similar to the amoA gene of Nitrosospira briensis showed the highest amoA transcript-to-gene ratio throughout all four seasons, indicating that some nitrifiers remain active at wastewater temperatures below 15°C. Our results show that 16S rRNA and amoA gene copy numbers are limited predictors of cell activity. To optimize function and performance of mixed community bioprocesses, we need to collect high-resolution quantitative transcriptomic and potentially proteomic data to resolve the response of individual species to changes in environmental parameters in engineered systems. IMPORTANCE The diverse microbial community of activated sludge used in biological treatment systems exhibits dynamic seasonal shifts in community composition and activity. Many wastewater treatment plants in temperate/continental climates experience seasonal cold temperature nitrification failure. "Seasonal nitrification failure" is the discharge of elevated concentrations of ammonia (greater than 4 mg/liter) with treated wastewater during the winter (influent wastewater temperatures below 13°C). This study aims at expanding our understanding of how ammonia-oxidizing bacteria in activated sludge change in activity and growth across seasons. We quantified the ammonia monooxygenase (amoA) gene and transcript copy numbers using real-time PCR and sequenced the amoA amplicons to reveal community structure and activity changes of nitrifying microbial populations during seasonal nitrification failure in three full-scale sequencing batch reactors (SRBs) treating municipal wastewater. Relevant findings presented in this study contribute to explain seasonal nitrification performance variability in SRBs.

Effect of low temperature on contributions of ammonia oxidizing archaea and bacteria to nitrous oxide in constructed wetlands

Constructed wetlands (CWs) have been widely used for ecological remediation of micro-polluted source water. Nitrous oxide (N₂O) from CWs has caused great concern as a greenhouse gas. However, the contribution of ammonia oxidation driven by ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) to N₂O emission, especially at low temperature, was unknown. This study aimed to quantify the contributions of AOA and AOB to N₂O through lab-scale subsurface CWs. The N₂O emission flux of CW at 8 °C was 1.23 mg m^-2·h^-1, significantly lower than that at 25 °C (1.92 mg m^-2·h^-1). The contribution of ammonia oxidation to N₂O at 8 °C (33.04%) was significantly higher than that at 25 °C (24.17%). The N₂O production from AOA increased from 1.91 ng N·g^-1 at 25 °C to 4.11 ng N·g^-1 soil at 8 °C and its contribution increased from 23.38% to 30.18% (P < 0.05). Low temperature impaired functional gene groups and inhibited the activity of AOB, resulting in its declined contribution. Based on the transcriptional analysis, AOA was less affected by low temperature, thus stably contributing to N₂O. Moreover, community diversity and relationships of AOA were enhanced at 8 °C, while AOB declined. The results confirmed the significant contribution of AOA and demonstrated molecular mechanisms (higher activity and community stability) of the increased contribution of AOA to N₂O at low temperature.

Nitrifiers Cooperate to Produce Nitrous Oxide in Plateau Wetland Sediments

The thawing of dormant plateau permafrost emits nitrous oxide (N₂O) through wetlands; however, the N₂O production mechanism in plateau wetlands is still unclear. Here, we used the ¹⁵N-¹⁸O double tracer technique and metagenomic sequencing to analyze the N₂O production mechanism in the Yunnan-Kweichow and Qinghai-Tibet plateau wetlands during the summer of 2020. N₂O production activity was detected in all 16 sediment samples (elevation 1020-4601 m: 2.55 ± 0.42-26.38 ± 3.25 ng N g^-1 d^-1) and was promoted by nitrifier denitrification (ND). The key functional genes of ND (amoA, hao, and nirK) belonged to complete ammonia oxidizing (comammox) bacteria, and the key ND species was the comammox bacterium Nitrospira nitrificans. We found that the comammox bacterial species N. nitrificans and the ammonia oxidizing bacterial (AOB) species Nitrosomonas europaea cooperate to produce N₂O in the plateau wetland sediments. Furthermore, we inferred that environmental factors (elevation and total organic matter (TOM)) influence the cooperation pattern via N. nitrificans, thus affecting the N₂O production activity in the plateau wetland sediments. Our findings advance the mechanistic understanding of nitrifiers in biogeochemical cycles and global climate change.

Temperature dependence of nitrification in a membrane-aerated biofilm reactor

The membrane-aerated biofilm reactor (MABR) is a novel method for the biological treatment of wastewaters and has been successfully applied for nitrification. To improve the design and adaptation of MABR processes for colder climates and varying temperatures, the temperature dependence of a counter-diffusional biofilm's nitrification performance was investigated. A lab-scale MABR system with silicone hollow fibre membranes was operated at various temperatures between 8 and 30°C, and batch tests were performed to determine the ammonia oxidation kinetics. Biofilm samples were taken at 8 and 24°C and analysed with 16S rRNA sequencing to monitor changes in the microbial community composition, and a mathematical model was used to study the temperature dependence of mass transfer. A high nitrification rate (3.08 g N m^-2 d^-1) was achieved at 8°C, and temperature dependence was found to be low (θ = 1.024-1.026) compared to suspended growth processes. Changes in the community composition were moderate, Nitrospira defluvii remaining the most dominant species. Mass transfer limitations were shown to be largely responsible for the observed trends, consistent with other biofilm processes. The results show that the MABR is a promising technology for low temperature nitrification, and appropriate management of the mass transfer resistance can optimise the process for both low and high temperature operation.

The contributions of ammonia oxidizing bacteria and archaea to nitrification-dependent N2O emission in alkaline and neutral purple soils

Nitrification is believed to be one of the primary processes of N₂O emission in the agroecological system, which is controlled by soil microbes and mainly regulated by soil pH, oxygen content and NH₄⁺ availability. Previous studies have proved that the relative contributions of ammonia oxidizing bacteria (AOB) and archaea (AOA) to N₂O production were varied with soil pH, however, there is still no consensus on the regulating mechanism of nitrification-derived N₂O production by soil pH. In this study, 1-octyne (a selective inhibitor of AOB) and acetylene (an inhibitor of AOB and AOA) were used in a microcosm incubation experiment to differentiate the relative contribution of AOA and AOB to N₂O emissions in a neutral (pH = 6.75) and an alkaline (pH = 8.35) soils. We found that the amendment of ammonium (NH₄⁺) observably stimulated the production of both AOA and AOB-related N₂O and increased the ammonia monooxygenase (AMO) gene abundances of AOA and AOB in the two test soils. Among which, AOB dominated the process of ammonia oxidation in the alkaline soil, contributing 70.8% of N₂O production derived from nitrification. By contrast, the contribution of AOA and AOB accounted for about one-third of nitrification-related N₂O in acidic soil, respectively. The results indicated that pH was a key factor to change abundance and activity of AOA and AOB, which led to the differentiation of derivation of N₂O production in purple soils. We speculate that both NH₄⁺ content and soil pH mediated specialization of ammonia-oxidizing microorganisms together; and both specialization results and N₂O yield led to the different N₂O emission characteristics in purple soils. These results may help inform the development of N₂O reduction strategies in the future.

Effects of hydroxylamine on treatment of anaerobic digestate of pig manure in partial nitrification-anaerobic ammonium oxidation

Partial nitrification-anaerobic ammonium oxidation (PN-anammox) was started up within 40 days by bioaugmentation and aeration control, and its performance in the treatment of anaerobic digestate of pig manure (ADPM) was evaluated. Inhibitors in ADPM decreased the nitrogen removal rate (NRR) by 0.24 g N/L/d. The effect and mechanism of hydroxylamine (NH₂OH) alleviation of PN-anammox inhibition during ADPM treatment were investigated. As an intermediate product of anammox and ammonia-oxidizing bacteria, NH₂OH strengthened energy metabolism, improved the activity and abundance of functional bacteria, and eliminated miscellaneous bacteria, increasing the average NRR by 31%. However, the average nitrous oxide emission was increased by 10.1% via hydroxylamine oxidation. The results showed that synergy and competition among nitrogen-transforming microorganisms were crucial for NRR and that NH₂OH played an essential role in maintaining efficient operation. This study lays a foundation for restoring PN-anammox for treating livestock wastewater.

The Effects of N Enrichment on Microbial Cycling of Non-CO2 Greenhouse Gases in Soils-a Review and a Meta-analysis

Terrestrial ecosystems are typically nitrogen (N) limited, but recent years have witnessed N enrichment in various soil ecosystems caused by human activities such as fossil fuel combustion and fertilizer application. This enrichment may alter microbial processes in soils in a way that would increase the emissions of methane (CH₄) and nitrous oxide (N₂O), thereby aggravating global climate change. This review focuses on the effects of N enrichment on methanogens and methanotrophs, which play a central role in the dynamics of CH₄ at the global scale. We also address the effects of N enrichment on N₂O, which is produced in soils mainly by nitrification and denitrification. Overall, N enrichment inhibits methanogenesis in pure culture experiments, while its effects on CH₄ oxidation are more complicated. The majority of previous studies reported that N enrichment, especially NH₄⁺ enrichment, inhibits CH₄ oxidation, resulting in higher CH₄ emissions from soils. However, both activation and neutral responses have also been reported, particularly in rice paddies and landfill sites, which is well reflected in our meta-analysis. In contrast, N enrichment substantially increases N₂O emission by both nitrification and denitrification, which increases proportionally to the amount of N amended. Future studies should address the effects of N enrichment on the active microbes of those functional groups at multiple scales along with parameterization of microbial communities for the application to climate models at the global scale.

Thermodynamic Analysis of Intermediary Metabolic Steps and Nitrous Oxide Production by Ammonium-Oxidizing Bacteria

Nitrous oxide (N₂O) is a greenhouse gas emitted from wastewater treatment, soils, and agriculture largely by ammonium-oxidizing bacteria (AOB). While AOB are characterized by being aerobes that oxidize ammonium (NH₄⁺) to nitrite (NO₂^-), fundamental studies in microbiology are revealing the importance of metabolic intermediates and reactions that can lead to the production of N₂O. These findings about the metabolic pathways for AOB were integrated with thermodynamic electron-equivalents modeling (TEEM) to estimate kinetic and stoichiometric parameters for each of the AOB's nitrogen (N)-oxidation and -reduction reactions. The TEEM analysis shows that hydroxylamine (NH₂OH) oxidation to nitroxyl (HNO) is the most energetically efficient means for the AOB to provide electrons for ammonium monooxygenation, while oxidations of HNO to nitric oxide (NO) and NO to NO₂^- are energetically favorable for respiration and biomass synthesis. The respiratory electron acceptor can be O₂ or NO, and both have similar energetics. The TEEM-predicted value for biomass yield, maximum-specific rate of NH₄⁺ utilization, and maximum specific growth rate are consistent with empirical observations. NO reduction to N₂O is thermodynamically favorable for respiration and biomass synthesis, but the need for O₂ as a reactant in ammonium monooxygenation likely precludes NO reduction to N₂O from becoming the major pathway for respiration.

Exploring the microbial influence on seasonal nitrous oxide concentration in a full-scale wastewater treatment plant using metagenome assembled genomes

Nitrous oxide is a highly potent greenhouse gas and one of the main contributors to the greenhouse gas footprint of wastewater treatment plants (WWTP). Although nitrous oxide can be produced by abiotic reactions in these systems, biological N₂O production resulting from the imbalance of nitrous oxide production and reduction by microbial populations is the dominant cause. The microbial populations responsible for the imbalance have not been clearly identified, yet they are likely responsible for strong seasonal nitrous oxide patterns. Here, we examined the seasonal nitrous oxide concentration pattern in Avedøre WWTP alongside abiotic parameters, the microbial community composition based on 16S rRNA gene sequencing and already available metagenome-assembled genomes (MAGs). We found that the WWTP parameters could not explain the observed pattern. While no distinct community changes between periods of high and low dissolved nitrous oxide concentrations were determined, we found 26 and 28 species with positive and negative correlations to the seasonal N₂O concentrations, respectively. MAGs were identified for 124 species (approximately 31% mean relative abundance of the community), and analysis of their genomic nitrogen transformation potential could explain this correlation for four of the negatively correlated species. Other abundant species were also analysed for their nitrogen transformation potential. Interestingly, only one full-denitrifier (Candidatus Dechloromonas phosphorivorans) was identified. 59 species had a nosZ gene predicted, with the majority identified as a clade II nosZ gene, mainly from the phylum Bacteroidota. A correlation of MAG-derived functional guilds with the N₂O concentration pattern showed that there was a small but significant negative correlation with nitrite oxidizing bacteria and species with a nosZ gene (N₂O reducers (DEN)). More research is required, specifically long-term activity measurements in relation to the N₂O concentration to increase the resolution of these findings.

Black Truffles Affect Quercus aliena Physiology and Root-Associated nirK- and nirS-Type Denitrifying Bacterial Communities in the Initial Stage of Inoculation

Truffles (Tuber spp.) are edible ectomycorrhizal fungi with high economic value. Bacteria in ectomycorrhizosphere soils are considered to be associated with the nutrient uptake of truffles and hosts. Whether Tuber spp. inoculation can affect the growth of Quercus aliena, the ectomycorrhizosphere soil, and the rhizosphere nirK and nirS-denitrifier communities at the ectomycorrhizae formation stage is still unclear. Therefore, we inoculated Q. aliena with the black truffles Tuber melanosporum and Tuber indicum, determined the physiological activity and morphological indices of Q. aliena seedlings, analyzed the physicochemical properties of ectomycorrhizosphere soils, and applied DNA sequencing to assess the nirK and nirS- denitrifier community structure in ectomycorrhizosphere soils. Peroxidase activity was higher in the seedlings inoculated with T. melanosporum than in the T. indicum inoculation and uninoculated control treatments. The available phosphorus contents were lower and nitrate contents were higher in those with truffle inoculation, and T. melanosporum treatment differed more from the control than the T. indicum treatment. The richness of the nirK-community was highest in the T. indicum treatment and lowest in the uninoculated treatment. The differences in nirK-community composition across treatments were not statistically significant, but the nirS communities were different. The nirS-type bacteria correlated with three environmental factors (pH, available phosphorus, and nitrate contents), whereas the nirK-type bacteria were only associated with the nitrate contents. Generally, this work revealed that inoculation with Tuber spp. would change a few nutrient contents and richness of nirK-type bacteria and had little effects on growth of Q. aliena seedlings in the initial stage of inoculation. The results of this study may provide in-depth insights into the relationships between Tuber spp. and hosts, which should be taken into account when developing truffle production methods.

Cryptic Sulfur and Oxygen Cycling Potentially Reduces N2O-Driven Greenhouse Warming: Underlying Revision Need of the Nitrogen Cycle

Increasing global deoxygenation has widely formed oxygen-limited biotopes, altering the metabolic pathways of numerous microbes and causing a large greenhouse effect of nitrous oxide (N₂O). Although there are many sources of N₂O, denitrification is the sole sink that removes N₂O from the biosphere, and the low-level oxygen in waters has been classically thought to be the key factor regulating N₂O emissions from incomplete denitrification. However, through microcosm incubations with sandy sediment, we demonstrate here for the first time that the stress from oxygenated environments does not suppress, but rather boosts the complete denitrification process when the sulfur cycle is actively ongoing. This study highlights the potential of reducing N₂O-driven greenhouse warming and fills a gap in pre-cognitions on the nitrogen cycle, which may impact our current understanding of greenhouse gas sinks. Combining molecular techniques and kinetic verification, we reveal that dominant inhibitions in oxygen-limited environments can interestingly undergo triple detoxification by cryptic sulfur and oxygen cycling, which may extensively occur in nature but have been long neglected by researchers. Furthermore, reviewing the present data and observations from natural and artificial ecosystems leads to the necessary revision needs of the global nitrogen cycle.

Metaproteomics, Heterotrophic Growth, and Distribution of Nitrosomonas europaea and Nitrobacter winogradskyi after Long-Term Operation of an Autotrophic Nitrifying Biofilm Reactor

Bioregenerative life support systems (BLSS) are currently in development to tackle low recovery efficiencies, high energy demands, as well as food, water, and oxygen production challenges through the regeneration of nutrients from waste streams. The MELiSSA pilot plant has been developed as a testbed for regenerative life support system bioreactor operation and characterization. As nitrogen is a vital resource in such systems, we studied the functional composition of a new packed-bed nitrifying bioreactor inoculated with a co-culture of Nitrosomonas europaea (ATCC 25978) and Nitrobacter winogradskyi (ATCC 25391). After 840 days of autotrophic continuous cultivation, the packed-bed was sampled at five vertical positions, each with three horizontal positions, and the biomass at each position was characterized via qPCR, 16S amplicon sequencing, and liquid chromatography tandem mass spectrometry. The total number of cells within the different sections fluctuated around 8.95 ± 5.10 × 107 cells/mL of beads. Based on 16S amplicons and protein content, N. europaea and N. winogradskyi constituted overall 44.07 ± 11.75% and 57.53 ± 12.04% of the nitrifying bioreactor, respectively, indicating the presence of a heterotrophic population that, even after such a long operation time, did not affect the nitrification function of the bioreactor. In addition, DNA-based abundance estimates showed that N. europaea was slightly more abundant than N. winogradskyi, whereas protein-based abundance estimates indicated a much higher abundance of N. europaea. This highlights that single-method approaches need to be carefully interpreted in terms of overall cell abundance and metabolic activity.

Differential response of soil CO2 , CH4 , and N2 O emissions to edaphic properties and microbial attributes following afforestation in central China

Land use change specially affects greenhouse gas (GHG) emissions, and it can act as a sink/source of GHGs. Alterations in edaphic properties and microbial attributes induced by land use change can individually/interactively contribute to GHG emissions, but how they predictably affect soil CO₂ , CH₄ , and N₂ O emissions remain unclear. Here, we investigated the direct and indirect controls of edaphic properties (i.e., dissolved organic carbon [DOC], soil organic C, total nitrogen, C:N ratio, NH4+ -N, NO3- -N, soil temperature [ST], soil moisture [SM], pH, and bulk density [BD]) and microbial attributes (i.e., total phospholipid fatty acids [PLFAs], 18:1ω7c, nitrifying genes [ammonia-oxidizing archaea, ammonia-oxidizing bacteria], and denitrifying genes [nirS, nirK, and nosZ]) over the annual soil CO₂ , CH₄ , and N₂ O emissions from the woodland, shrubland, and abandoned land in subtropical China. Soil CO₂ and N₂ O emissions were higher in the afforested lands (woodland and shrubland) than in the abandoned land, but the annual cumulative CH₄ uptake did not significantly differ among all land use types. The CO₂ emission was positively associated with microbial activities (e.g., total PLFAs), while the CH₄ uptake was tightly correlated with soil environments (i.e., ST and SM) and chemical properties (i.e., DOC, C:N ratio, and NH4+ -N concentration), but not significantly related to the methanotrophic bacteria (i.e., 18:1ω7c). Whereas, soil N₂ O emission was positively associated with nitrifying genes, but negatively correlated with denitrifying genes especially nosZ. Overall, our results suggested that soil CO₂ and N₂ O emissions were directly dependent on microbial attributes, and soil CH₄ uptake was more directly related to edaphic properties rather than microbial attributes. Thus, different patterns of soil CO₂ , CH₄ , and N₂ O emissions and associated controls following land use change provided novel insights into predicting the effects of afforestation on climate change mitigation outcomes.

Envisioning role of ammonia oxidizing bacteria in bioenergy production and its challenges: a review

Ammonia oxidizing bacteria (AOB) play a key role in the biological oxidation of ammonia to nitrite and mark their significance in the biogeochemical nitrogen cycle. There has been significant development in harnessing the ammonia oxidizing potential of AOB in the past few decades. However, very little is known about the potential applications of AOB in the bioenergy sector. As alternate sources of energy represent a thrust area for environmental sustainability, the role of AOB in bioenergy production becomes a significant area of exploration. This review highlights the role of AOB in bioenergy production and emphasizes the understanding of the genetic make-up and key cellular biochemical reactions occurring in AOB, thereby leading to the exploration of its various functional aspects. Recent outcomes in novel ammonia/nitrite oxidation steps occurring in a model AOB - Nitrosomonas europaea propel us to explore several areas of environmental implementation. Here we present the significant role of AOB in microbial fuel cells (MFC) where Nitrosomonas sp. play both anodic and cathodic functions in the generation of bioelectricity. This review also presents the potential role of AOB in curbing fuel demand by producing alternative liquid fuel such as methanol and biodiesel. Herein, the multiple roles of AOB in bioenergy production namely: bioelectricity generation, bio-methanol, and biodiesel production have been presented.

Insights into Nitrous Oxide Mitigation Strategies in Wastewater Treatment and Challenges for Wider Implementation

Nitrous oxide (N₂O) emissions account for the majority of the carbon footprint of wastewater treatment plants (WWTPs). Many N₂O mitigation strategies have since been developed while a holistic view is still missing. This article reviews the state-of-the-art of N₂O mitigation studies in wastewater treatment. Through analyzing existing studies, this article presents the essential knowledge to guide N₂O mitigations, and the logics behind mitigation strategies. In practice, mitigations are mainly carried out by aeration control, feed scheme optimization, and process optimization. Despite increasingly more studies, real implementation remains rare, which is a combined result of unclear climate change policies/incentives, as well as technical challenges. Five critical technical challenges, as well as opportunities, of N₂O mitigations were identified. It is proposed that (i) quantification methods for overall N₂O emissions and pathway contributions need improvement; (ii) a reliable while straightforward mathematical model is required to quantify benefits and compare mitigation strategies; (iii) tailored risk assessment needs to be conducted for WWTPs, in which more long-term full-scale trials of N₂O mitigation are urgently needed to enable robust assessments of the resulting operational costs and impact on nutrient removal performance; (iv) current mitigation strategies focus on centralized WWTPs, more investigations are warranted for decentralised systems, especially decentralized activated sludge WWTPs; and (v) N₂O may be mitigated by adopting novel strategies promoting N₂O reduction denitrification or microorganisms that emit less N₂O. Overall, we conclude N₂O mitigation research is reaching a maturity while challenges still exist for a wider implementation, especially in relation to the reliability of N₂O mitigation strategies and potential risks to nutrient removal performances of WWTPs.

How nitrification-related N2O is associated with soil ammonia oxidizers in two contrasting soils in China?

As a key process contributing to N₂O emissions, nitrification is regulated by soil microbes and mainly affected by soil pH, NH₃ availability, temperature and O₂ availability. Current knowledge gaps include how nitrification-related N₂O is associated with soil microbes in different pH soils. In the current study, a microcosm incubation experiment was conducted with two contrasting soils of different pH (5.08, 8.30) under controlled conditions. The soils were amended with ammonium sulphate ((NH₄)₂SO₄, 50 mg N kg^-1) combined with or without nitrification inhibitors and incubated under 20 °C, 65% water hold capacity (WHC) for three weeks. N₂O fluxes, mineral nitrogen (N) concentrations and ammonia oxidizers populations were measured during the incubation to investigate the correlations of nitrification-related N₂O with ammonia oxidizers. The nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) was used to inhibit nitrification albeit to various inhibition effects with different soils. Acetylene (0.1% v/v C₂H₂), an inhibitor of AOA and AOB ammonia monooxygenase (AMO), was used to distinguish N₂O emissions by nitrifiers and denitrifiers. 1-octyne (5 μM aqueous), a selective specific AOB inhibitor, was used to assess the relative contributions of AOA and AOB to N₂O emissions. The results showed that N₂O yield for AOA and AOB varied with soil pH. AOB was the key microbial player in alkaline soil, contributing about 85% of nitrification-related N₂O. Conversely, about 78% of nitrification-related N₂O was contributed by AOA in acidic soil. Furthermore, there was a significant and positive relationship between mineral N (NO₂^-, NO₃^-), AOA and AOB populations and nitrification-related N₂O in alkaline soil. However, in acidic soil, NO₃^- concentration and AOA had significantly positive relationships with nitrification-related N₂O. To conclude, soil pH was a key factor affecting the contribution of ammonia oxidizers to nitrification-related N₂O emissions. AOA-related N₂O production dominated at low pH (5.08), while AOB-related N₂O was favored in alkaline soil (pH 8.3).

Hydroxylamine and the nitrogen cycle: A review

Aerobic ammonium oxidizing bacteria were first isolated more than 100 years ago and hydroxylamine is known to be an intermediate. The enzymatic steps involving hydroxylamine conversion to nitrite are still under discussion. For a long time it was assumed that hydroxylamine was directly converted to nitrite by a hydroxylamine oxidoreductase. Recent enzymatic evidences suggest that the actual product of hydroxylamine conversion is NO and a third, yet unknown, enzyme further converts NO to nitrite. More recently, ammonium oxidizing archaea and complete ammonium oxidizing bacteria were isolated and identified. Still the central nitrogen metabolism of these microorganisms presents to researchers the same puzzle: how hydroxylamine is transformed to nitrite. Nitrogen losses in the form of NO and N₂O have been identified in all three types of aerobic ammonium oxidizing microorganisms and hydroxylamine is known to play a significant role in the formation. Yet, the pathways and the factors promoting the greenhouse gas emissions are to be fully characterized. Hydroxylamine also plays a yet poorly understood role on anaerobic ammonium oxidizing bacteria and is known to inhibit nitrite oxidizing bacteria. In this review, the role of this elusive intermediate in the metabolism of different key players of the nitrogen cycle is discussed, as well as the putative importance of hydroxylamine as a key nitrogen metabolite for microbial interactions within microbial communities and engineered systems. Overall, for the first time putting together the acquired knowledge about hydroxylamine and the nitrogen cycle over the years in a review, setting potential hypothesis and highlighting possible next steps for research.

Changes in the nitrification-denitrification capacity of pilot-scale partially saturated vertical flow wetlands (with corncob in the free-drainage zone) after two years of operation

This six-month study aimed to evaluate the removal of total nitrogen (TN) in two duplicated partially saturated (PS) vertical flow (VF) wetlands added with corncob in two different heights of the free-drainage zone (FDZ) after two years in operation. Both PS VF wetlands efficiently removed organic matter measured as biochemical oxygen demand (BOD₅) and chemical oxygen demand (COD) as well as total suspended solids (TSS) achieving average mass removal efficiencies of 95.3%, 83.2% and 92.9%, respectively, in system I (SI) and 96.3%, 84.0% and 94.9%, respectively, in system II (SII); with no significant differences (p > 0.05) between the systems. Measurements of oxidation-reduction potential (ORP), dissolved oxygen (DO), pH and electrical conductivity (EC) showed suitable conditions in the saturated zone (SZ) of the systems for denitrification process. TN removal was similar in both systems (p > 0.05) (51.5% and 52.9% in SI and SII), and decreased in 15% with respect to the first year. This decrease was due to the lower denitrification capacity of the FDZ as a result of the reduction in the supply of biodegradable carbon by corncob. Denitrification occurred in the SZ, but not at a sufficient level to increase TN removal. NoveltyFirst, the use of lignocellulosic residues in partially saturated vertical wetlands to promote total nitrogen removal is very recent. Furthermore, to the best of our knowledge, this is the first study evaluating TN removal after two years of operation in this type of wetland. Therefore, this study allows us to better understand the function of these systems, in a relatively long term. Thanks to this study: it is possible to confirm that the main process of TN elimination is through the simultaneous nitrification-denitrification process in the free drainage zone (denitrification in the saturated zone is irrelevant) and that TN elimination decreases due to the reduction in carbon supply from the corn, in this area.

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.

Transcriptomic Response of Nitrosomonas europaea Transitioned from Ammonia- to Oxygen-Limited Steady-State Growth

Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea, growing under oxygen-limited conditions.

Ammonia-oxidizing microorganisms perform the first step of nitrification, the oxidation of ammonia to nitrite. The bacterium Nitrosomonas europaea is the best-characterized ammonia oxidizer to date. Exposure to hypoxic conditions has a profound effect on the physiology of N. europaea, e.g., by inducing nitrifier denitrification, resulting in increased nitric and nitrous oxide production. This metabolic shift is of major significance in agricultural soils, as it contributes to fertilizer loss and global climate change. Previous studies investigating the effect of oxygen limitation on N. europaea have focused on the transcriptional regulation of genes involved in nitrification and nitrifier denitrification. Here, we combine steady-state cultivation with whole-genome transcriptomics to investigate the overall effect of oxygen limitation on N. europaea. Under oxygen-limited conditions, growth yield was reduced and ammonia-to-nitrite conversion was not stoichiometric, suggesting the production of nitrogenous gases. However, the transcription of the principal nitric oxide reductase (cNOR) did not change significantly during oxygen-limited growth, while the transcription of the nitrite reductase-encoding gene (nirK) was significantly lower. In contrast, both heme-copper-containing cytochrome c oxidases encoded by N. europaea were upregulated during oxygen-limited growth. Particularly striking was the significant increase in transcription of the B-type heme-copper oxidase, proposed to function as a nitric oxide reductase (sNOR) in ammonia-oxidizing bacteria. In the context of previous physiological studies, as well as the evolutionary placement of N. europaea’s sNOR with regard to other heme-copper oxidases, these results suggest sNOR may function as a high-affinity terminal oxidase in N. europaea and other ammonia-oxidizing bacteria.

IMPORTANCE Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea, growing under oxygen-limited conditions.

Nitrous oxide production by ammonia oxidizers: Physiological diversity, niche differentiation and potential mitigation strategies

Oxidation of ammonia to nitrite by bacteria and archaea is responsible for global emissions of nitrous oxide directly and indirectly through provision of nitrite and, after further oxidation, nitrate to denitrifiers. Their contributions to increasing N₂ O emissions are greatest in terrestrial environments, due to the dramatic and continuing increases in use of ammonia-based fertilizers, which have been driven by requirement for increased food production, but which also provide a source of energy for ammonia oxidizers (AO), leading to an imbalance in the terrestrial nitrogen cycle. Direct N₂ O production by AO results from several metabolic processes, sometimes combined with abiotic reactions. Physiological characteristics, including mechanisms for N₂ O production, vary within and between ammonia-oxidizing archaea (AOA) and bacteria (AOB) and comammox bacteria and N₂ O yield of AOB is higher than in the other two groups. There is also strong evidence for niche differentiation between AOA and AOB with respect to environmental conditions in natural and engineered environments. In particular, AOA are favored by low soil pH and AOA and AOB are, respectively, favored by low rates of ammonium supply, equivalent to application of slow-release fertilizer, or high rates of supply, equivalent to addition of high concentrations of inorganic ammonium or urea. These differences between AOA and AOB provide the potential for better fertilization strategies that could both increase fertilizer use efficiency and reduce N₂ O emissions from agricultural soils. This article reviews research on the biochemistry, physiology and ecology of AO and discusses the consequences for AO communities subjected to different agricultural practices and the ways in which this knowledge, coupled with improved methods for characterizing communities, might lead to improved fertilizer use efficiency and mitigation of N₂ O emissions.

A Physiological and Genomic Comparison of Nitrosomonas Cluster 6a and 7 Ammonia-Oxidizing Bacteria

Ammonia-oxidizing bacteria (AOB) within the genus Nitrosomonas perform the first step in nitrification, ammonia oxidation, and are found in diverse aquatic and terrestrial environments. Nitrosomonas AOB were grouped into six defined clusters, which correlate with physiological characteristics that contribute to adaptations to a variety of abiotic environmental factors. A fundamental physiological trait differentiating Nitrosomonas AOB is the adaptation to either low (cluster 6a) or high (cluster 7) ammonium concentrations. Here, we present physiological growth studies and genome analysis of Nitrosomonas cluster 6a and 7 AOB. Cluster 6a AOB displayed maximum growth rates at ≤ 1 mM ammonium, while cluster 7 AOB had maximum growth rates at ≥ 5 mM ammonium. In addition, cluster 7 AOB were more tolerant of high initial ammonium and nitrite concentrations than cluster 6a AOB. Cluster 6a AOB were completely inhibited by an initial nitrite concentration of 5 mM. Genomic comparisons were used to link genomic traits to observed physiological adaptations. Cluster 7 AOB encode a suite of genes related to nitrogen oxide detoxification and multiple terminal oxidases, which are absent in cluster 6a AOB. Cluster 6a AOB possess two distinct forms of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and select species encode genes for hydrogen or urea utilization. Several, but not all, cluster 6a AOB can utilize urea as a source of ammonium. Hence, although Nitrosomonas cluster 6a and 7 AOB have the capacity to fulfill the same functional role in microbial communities, i.e., ammonia oxidation, differentiating species-specific and cluster-conserved adaptations is crucial in understanding how AOB community succession can affect overall ecosystem function.

Niche Differentiation of Aerobic and Anaerobic Ammonia Oxidizers in a High Latitude Deep Oxygen Minimum Zone

To elucidate the potential for nitrification and denitrification processes in a high latitude deep oxygen minimum zone (OMZ) we determined the abundance and community composition of the main microbial players in the aerobic and anaerobic (anammox) ammonium oxidation and denitrification processes in the Gulf of Alaska throughout the water column. Within the dominant bacterial groups, Flavobacterales, Rhodobacterales, Actinomarinales, and SAR86 were more abundant in epipelagic waters and decreased with depth, whereas SAR11, SAR324, Marinimicrobia, and Thiomicrospirales increased their contribution to the bacterial community with depth. Nitrosopumilaceae also increased with depth and dominated the OMZ and bathypelagic archaeal communities. Euryarchaeota Marine Group II exhibited an opposite depth pattern to Nitrosopumilaceae, whereas Marine Group III and Woesearchaeota were more abundant in the bathypelagic realm. Candidatus Brocadia contributed 70-100% of the anammox bacterial community throughout the water column. Archaeal ammonia oxidizers (AOA) dominated the microbial community involved in the nitrogen cycle. Two AOA ecotypes, the high ammonia (HAC) and low ammonia (LAC)-AOA, characterized by distinct genes for aerobic ammonia oxidation (amoA) and for denitrification (nirK), exhibited a distinct distribution pattern related to depth and ammonia concentrations. HAC-AOA dominated in epipelagic (80.5 ± 28.3% of total AOA) oxygenated and ammonia-rich waters, and LAC-AOA dominated in the OMZ (90.9 ± 5.1%) and bathypelagic waters (85.5 ± 13.5%), characterized by lower oxygen and ammonia concentrations. Bacterial denitrifiers (3.7 ± 6.9 bacterial nirK gene mL-1) and anaerobic ammonia oxidizers (78 ± 322 anammox 16S rRNA genes L-1) were low in abundance under the oxygen conditions in the Gulf of Alaska throughout the water column. The widespread distribution of bacterial denitrifiers and anaerobic ammonia oxidizers in low abundances reveals a reservoir of genetic and metabolic potential ready to colonize the environment under the predicted increase of OMZs in the ocean. Taken together, our results reinforce the niche partitioning of archaeal ammonia oxidizers based on their distinct metabolic characteristics resulting in the dominance of LAC-AOA in a high latitude deep OMZ. Considering the different ecological roles and functions of the two archaeal ecotypes, the expansion of the zones dominated by the LAC-ecotype might have implications for the nitrogen cycle in the future ocean.

Ammonia oxidation: Ecology, physiology, biochemistry and why they must all come together

Ammonia oxidation is a fundamental core process in the global biogeochemical nitrogen cycle. Oxidation of ammonia (NH3) to nitrite (NO2 -) is the first and rate-limiting step in nitrification and is carried out by distinct groups of microorganisms. Ammonia oxidation is essential for nutrient turnover in most terrestrial, aquatic and engineered ecosystems and plays a major role, both directly and indirectly, in greenhouse gas production and environmental damage. Although ammonia oxidation has been studied for over a century, this research field has been galvanised in the past decade by the surprising discoveries of novel ammonia oxidising microorganisms. This review reflects on the ammonia oxidation research to date and discusses the major gaps remaining in our knowledge of the biology of ammonia oxidation.

Simultaneous nitrification, denitrification and phosphorus removal in a sequencing batch reactor (SBR) under low temperature

Simultaneous nitrogen and phosphorus removal in winter is one of the great challenges in wastewater treatment processes due to the poor bioactivity of microbial communities. In this study, excellent performance of simultaneous nitrification, denitrification and phosphorus removal (SNDPR) was achieved at low temperature of 10 ^°C and COD/N ratio of 6 in a lab-scale sequencing batch reactor. Total nitrogen (TN) and phosphorus (TP) removal efficiency reached 89.6% and 97.5%, respectively, accompanied with N₂O emission of 7.46% TN due to the primary contribution (70%) of nitrifier denitrification. It was further confirmed that polyphosphate accumulating organisms (PAOs) were dominant in microbial communities revealed by fluorescence in situ hybridization and 16S rRNA amplicon sequencing. Moreover, denitrifying phosphorus removal by PAOs through nitrite pathway was found to be the main reason for the high efficiency of this SNDPR process. Denitrifying PAOs, especially the subgroup PAOII capable of utilizing nitrite to take up phosphorus, played a significant role in highly efficient TN and TP removal at low temperature. Furthermore, genus Propionivibrio was enriched (48.9%) in the bacterial community based on the 16S rRNA analysis, which was proposed to be a crucial member involved in the nitrogen and phosphorus removal simultaneously at low temperature in this system.

Indications for enzymatic denitrification to N2O at low pH in an ammonia-oxidizing archaeon

Nitrous oxide (N₂O) is a key climate change gas and nitrifying microbes living in terrestrial ecosystems contribute significantly to its formation. Many soils are acidic and global change will cause acidification of aquatic and terrestrial ecosystems, but the effect of decreasing pH on N₂O formation by nitrifiers is poorly understood. Here, we used isotope-ratio mass spectrometry to investigate the effect of acidification on production of N₂O by pure cultures of two ammonia-oxidizing archaea (AOA; Nitrosocosmicus oleophilus and Nitrosotenuis chungbukensis) and an ammonia-oxidizing bacterium (AOB; Nitrosomonas europaea). For all three strains acidification led to increased emission of N₂O. However, changes of ¹⁵N site preference (SP) values within the N₂O molecule (as indicators of pathways for N₂O formation), caused by decreasing pH, were highly different between the tested AOA and AOB. While acidification decreased the SP value in the AOB strain, SP values increased to a maximum value of 29‰ in N. oleophilus. In addition, ¹⁵N-nitrite tracer experiments showed that acidification boosted nitrite transformation into N₂O in all strains, but the incorporation rate was different for each ammonia oxidizer. Unexpectedly, for N. oleophilus more than 50% of the N₂O produced at pH 5.5 had both nitrogen atoms from nitrite and we demonstrated that under these conditions expression of a putative cytochrome P450 NO reductase is strongly upregulated. Collectively, our results indicate that N. oleophilus might be able to enzymatically denitrify nitrite to N₂O at low pH.

Ecological and physiological implications of nitrogen oxide reduction pathways on greenhouse gas emissions in agroecosystems

Microbial reductive pathways of nitrogen (N) oxides are highly relevant to net emissions of greenhouse gases (GHG) from agroecosystems. Several biotic and abiotic N-oxide reductive pathways influence the N budget and net GHG production in soil. This review summarizes the recent findings of N-oxide reduction pathways and their implications to GHG emissions in agroecosystems and proposes several mitigation strategies. Denitrification is the primary N-oxide reductive pathway that results in direct N2O emissions and fixed N losses, which add to the net carbon footprint. We highlight how dissimilatory nitrate reduction to ammonium (DNRA), an alternative N-oxide reduction pathway, may be used to reduce N2O production and N losses via denitrification. Implications of nosZ abundance and diversity and expressed N2O reductase activity to soil N2O emissions are reviewed with focus on the role of the N2O-reducers as an important N2O sink. Non-prokaryotic N2O sources, e.g. fungal denitrification, codenitrification and chemodenitrification, are also summarized to emphasize their potential significance as modulators of soil N2O emissions. Through the extensive review of these recent scientific advancements, this study posits opportunities for GHG mitigation through manipulation of microbial N-oxide reductive pathways in soil.

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.

Overdose fertilization induced ammonia-oxidizing archaea producing nitrous oxide in intensive vegetable fields

Little is known about the effects of nitrogen (N) fertilization rates on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) and their differential contribution to nitrous oxide (N₂O) production, particularly in greenhouse based high N input vegetable soils. Six N treatments (N1, N2, N3, N4, N5 and N6 representing 0, 293, 587, 880, 1173 and 1760 kg N ha^-1 yr^-1, respectively) were continuously managed for three years in a typically intensified vegetable field in China. The aerobic incubation experiment involving these field-treated soils was designed to evaluate the relative contributions of AOA and AOB to N₂O production by using acetylene or 1-octyne as inhibitors. The results showed that the soil pH and net nitrification rate gradually declined with increasing the fertilizer N application rates. The AOA were responsible for 44-71% of the N₂O production with negligible N₂O from AOB in urea unamended control soils. With urea amendment, the AOA were responsible for 48-53% of the N₂O production in the excessively fertilized soils, namely the N5-N6 soils, while the AOB were responsible for 42-55% in the conventionally fertilized soils, namely the N1-N4 soils. Results indicated that overdose fertilization induced higher AOA-dependent N₂O production than AOB, whereas urea supply led to higher AOB-dependent N₂O production than AOA in conventionally fertilized soils. Additionally, a positive relationship existed between N₂O production and NO₂^- accumulation during the incubation. Further mechanisms for NO₂^--dependent N₂O production in intensive vegetable soils therefore deserve urgent attention.

Genomic profiling of four cultivated Candidatus Nitrotoga spp. predicts broad metabolic potential and environmental distribution

Nitrite-oxidizing bacteria (NOB) play a critical role in the mitigation of nitrogen pollution by metabolizing nitrite to nitrate, which is removed via assimilation, denitrification, or anammox. Recent studies showed that NOB are phylogenetically and metabolically diverse, yet most of our knowledge of NOB comes from only a few cultured representatives. Using cultivation and genomic sequencing, we identified four putative Candidatus Nitrotoga NOB species from freshwater sediments and water column samples in Colorado, USA. Genome analyses indicated highly conserved 16S rRNA gene sequences, but broad metabolic potential including genes for nitrogen, sulfur, hydrogen, and organic carbon metabolism. Genomic predictions suggested that Ca. Nitrotoga can metabolize in low oxygen or anoxic conditions, which may support an expanded environmental niche for Ca. Nitrotoga similar to other NOB. An array of antibiotic and metal resistance genes likely allows Ca. Nitrotoga to withstand environmental pressures in impacted systems. Phylogenetic analyses highlighted a deeply divergent nitrite oxidoreductase alpha subunit (NxrA), suggesting a novel evolutionary trajectory for Ca. Nitrotoga separate from any other NOB and further revealing the complex evolutionary history of nitrite oxidation in the bacterial domain. Ca. Nitrotoga-like 16S rRNA gene sequences were prevalent in globally distributed environments over a range of reported temperatures. This work considerably expands our knowledge of the Ca. Nitrotoga genus and suggests that their contribution to nitrogen cycling should be considered alongside other NOB in wide variety of habitats.

Ammonia Monooxygenase-Mediated Cometabolic Biotransformation and Hydroxylamine-Mediated Abiotic Transformation of Micropollutants in an AOB/NOB Coculture

Biotransformation of various micropollutants (MPs) has been found to be positively correlated with nitrification in activated sludge communities. To further elucidate the roles played by ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), we investigated the biotransformation capabilities of an NOB pure culture ( Nitrobacter sp.) and an AOB ( Nitrosomonas europaea)/NOB ( Nitrobacter sp.) coculture for 15 MPs, whose biotransformation was reported previously to be associated with nitrification. The NOB pure culture did not biotransform any investigated MP, whereas the AOB/NOB coculture was capable of biotransforming six MPs (i.e., asulam, bezafibrate, fenhexamid, furosemide, indomethacin, and rufinamide). Transformation products (TPs) were identified, and tentative structures were proposed. Inhibition studies with octyne, an ammonia monooxygenase (AMO) inhibitor, suggested that AMO was the responsible enzyme for MP transformation that occurred cometabolically. For the first time, hydroxylamine, a key intermediate of all aerobic ammonia oxidizers, was found to react with several MPs at concentrations typically occurring in AOB batch cultures. All of these MPs were also biotransformed by the AOB/NOB coculture. Moreover, the same asulam TPs were detected in both biotransformation and hydroxylamine-treated abiotic transformation experiments, whereas rufinamide TPs formed from biological transformation were not detected during hydroxylamine-mediated abiotic transformation, which was consistent with the inability of rufinamide abiotic transformation by hydroxylamine. Thus, in addition to cometabolism likely carried out by AMO, an abiotic transformation route indirectly mediated by AMO might also contribute to MP biotransformation by AOB.

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.

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.

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.