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

Nitrous oxide production and consumption by marine ammonia-oxidizing archaea under oxygen depletion

Ammonia-oxidizing archaea (AOA) are key players in the nitrogen cycle and among the most abundant microorganisms in the ocean, thriving even in oxygen-depleted ecosystems. AOA produce the greenhouse gas nitrous oxide (N2O) as a byproduct of ammonia oxidation. Additionally, the recent discovery of a nitric oxide dismutation pathway in the AOA isolate Nitrosopumilus maritimus points toward other N2O production and consumption pathways in AOA. AOA that perform NO dismutation when exposed to oxygen depletion, produce oxygen and dinitrogen as final products. Based on the transient accumulation of N2O coupled with oxygen accumulation, N2O has been proposed as an intermediate in this novel archaeal pathway. In this study, we spiked N2O to oxygen-depleted incubations with pure cultures of two marine AOA isolates that were performing NO dismutation. By using combinations of N compounds with different isotopic signatures (15NO2 - pool +44N2O spike and 14NO2 - pool +46N2O spike), we evaluated the N2O spike effects on the production of oxygen and the isotopic signature of N2 and N2O. The experiments confirmed that N2O is an intermediate in NO dismutation by AOA, distinguishing it from similar pathways in other microbial clades. Furthermore, we showed that AOA rapidly reduce high concentrations of spiked N2O to N2. These findings advance our understanding of microbial N2O production and consumption in oxygen-depleted settings and highlight AOA as potentially important key players in N2O turnover.

Response characteristics of soil microorganisms under strong disturbance conditions in the riparian zone of the three Gorges reservoir Area

The normal operation of the Three Gorges Reservoir, which involves periodic water storage and discharge, has led to strong disturbances in environmental conditions that alter soil microbial habitats in the riparian zones. Riparian zones are an important part of controlling pollution in the Three Gorges Reservoir area, since they act as a final ecological barrier that intercepts pollutants. Meanwhile, monitoring the health of microbial communities in the riparian zone is crucial for maintaining the ecological security of the reservoir area. We specifically investigate the Daning River, which are tributaries of the Three Gorges Reservoir and have typical riparian zones. Soil samples from these areas were subjected to high-throughput sequencing of 16S rRNA genes and 18S rRNA genes, in order to obtain the characteristics of the present microbial communities under strong disturbances in the riparian zones. We studied the characteristics and distribution patterns of microbial communities and their relationship with soil physicochemical properties. The study results indicate that microbial communities exhibit high diversity and evenness, and spatial heterogeneity is present. The ASV dataset contains many sequences not assigned to known genera, suggesting the presence of new fungal genera in the riparian zone. Redundancy analysis (RDA) revealed that pH andNH 4 + -N were the primary environmental factors driving bacterial community variation in the riparian zone, while pH, total carbon (TC) content, andNO 3 - -N were identified as the main drivers of soil archaeal community variation.

Metagenomic analysis insights into the influence of 3,4-dimethylpyrazole phosphate application on nitrous oxide mitigation efficiency across different climate zones in Eastern China

Excessive nitrogen (N) fertilization in agroecological systems increases nitrous oxide (N2O) emissions. 3,4-dimethylpyrazole phosphate (DMPP) is used to mitigate N2O losses. The influence of DMPP efficiency on N2O mitigation was clearly affected by spatiotemporal heterogeneity. Using field and incubation experiments combined with metagenomic sequencing, we aimed to investigate DMPP efficiency and the underlying microbial mechanisms in dark-brown (Siping, SP), fluvo-aquic (Cangzhou, CZ; Xinxiang, XX), and red soil (Wenzhou, WZ) from diverse climatic zones. In the field experiments, the DMPP efficiency in N2O mitigation ranged from 51.6% to 89.9%, in the order of XX, CZ, SP, and WZ. The DMPP efficiency in the incubation experiments ranged from 58.3% to 93.9%, and the order of efficiency from the highest to lowest was the same as that of the field experiments. Soil organic matter, total N, pH, texture, and taxonomic and functional α-diversity were important soil environment and microbial factors for DMPP efficiency. DMPP significantly enriched ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB), which promoted N-cycling with low N2O emissions. Random forest (RF) and regression analyses found that an AOA (Nitrosocosmicus) and NOB (Nitrospina) demonstrated important and positive correlation with DMPP efficiency. Moreover, genes associated with carbohydrate metabolism were important for DMPP efficiency and could influenced N-cycling and DMPP metabolism. The similar DMPP efficiency indicated that the variation in DMPP efficiency was significantly due to soil physicochemical and microbial variations. In conclusion, filling the knowledge gap regarding the response of DMPP efficiency to abiotic and biotic factors could be beneficial in DMPP applications, and in adapting more efficient strategies to improve DMPP efficiency and mitigate N2O emissions in multiple regions.

BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes

BACKGROUND

Exploring metagenomic contigs and "binning" them into metagenome-assembled genomes (MAGs) are essential for the delineation of functional and evolutionary guilds within microbial communities. Despite the advances in automated binning algorithms, their capabilities in recovering MAGs with accuracy and biological relevance are so far limited. Researchers often find that human involvement is necessary to achieve representative binning results. This manual process however is expertise demanding and labor intensive, and it deserves to be supported by software infrastructure.

RESULTS

We present BinaRena, a comprehensive and versatile graphic interface dedicated to aiding human operators to explore metagenome assemblies via customizable visualization and to associate contigs with bins. Contigs are rendered as an interactive scatter plot based on various data types, including sequence metrics, coverage profiles, taxonomic assignments, and functional annotations. Various contig-level operations are permitted, such as selection, masking, highlighting, focusing, and searching. Binning plans can be conveniently edited, inspected, and compared visually or using metrics including silhouette coefficient and adjusted Rand index. Completeness and contamination of user-selected contigs can be calculated in real time. In demonstration of BinaRena's usability, we show that it facilitated biological pattern discovery, hypothesis generation, and bin refinement in a complex tropical peatland metagenome. It enabled isolation of pathogenic genomes within closely related populations from the gut microbiota of diarrheal human subjects. It significantly improved overall binning quality after curating results of automated binners using a simulated marine dataset.

CONCLUSIONS

BinaRena is an installation-free, dependency-free, client-end web application that operates directly in any modern web browser, facilitating ease of deployment and accessibility for researchers of all skill levels. The program is hosted at https://github.com/qiyunlab/binarena , together with documentation, tutorials, example data, and a live demo. It effectively supports human researchers in intuitive interpretation and fine tuning of metagenomic data. Video Abstract.

Nitrification in acidic and alkaline environments

Aerobic nitrification is a key process in the global nitrogen cycle mediated by microorganisms. While nitrification has primarily been studied in near-neutral environments, this process occurs at a wide range of pH values, spanning ecosystems from acidic soils to soda lakes. Aerobic nitrification primarily occurs through the activities of ammonia-oxidising bacteria and archaea, nitrite-oxidising bacteria, and complete ammonia-oxidising (comammox) bacteria adapted to these environments. Here, we review the literature and identify knowledge gaps on the metabolic diversity, ecological distribution, and physiological adaptations of nitrifying microorganisms in acidic and alkaline environments. We emphasise that nitrifying microorganisms depend on a suite of physiological adaptations to maintain pH homeostasis, acquire energy and carbon sources, detoxify reactive nitrogen species, and generate a membrane potential at pH extremes. We also recognize the broader implications of their activities primarily in acidic environments, with a focus on agricultural productivity and nitrous oxide emissions, as well as promising applications in treating municipal wastewater.

Shifts of soil archaeal nitrification and methanogenesis with elevation in water level fluctuation zone of the three Gorges Reservoir, China

The water level fluctuation zone is a unique ecological zone exposed to long-term drying and flooding and plays a critical role in the transport and transformation of carbon and nitrogen materials in reservoir-river systems. Archaea are a vital component of soil ecosystems in the water level fluctuation zones, however, the distribution and function of archaeal communities in responde to long-term wet and dry alternations are still unclear. The community structure of archaea in the drawdown areas at various elevations of the Three Gorges Reservoir was investigated by selecting surface soils (0-5 cm) of different inundation durations at three sites from upstream to downstream according to the flooding pattern. The results revealed that prolonged flooding and drying increased the community diversity of soil archaea, with ammonia-oxidizing archaea being the dominant species in non-flooded regions, while methanogenic archaea were abundant in soils that had been flooded for an extended period of time. Long-term alternation of wetting and drying increases methanogenesis but decreases nitrification. It was determined that soil pH, NO3--N, TOC and TN are significant environmental factors affecting the composition of soil archaeal communities (P = 0.02). Long-term flooding and drying changed the community composition of soil archaea by altering environmental factors, which in turn influenced nitrification and methanogenesis in soils at different elevations. These findings contribute to our understanding of soil carbon and nitrogen transport transformation processes in the water level fluctuation zone as well as the effects of long-term wet and dry alternation on soil carbon and nitrogen cycles. The results of this study can provide a basis for ecological management, environmental management, and long-term operation of reservoirs in water level fluctuation zones.

Organic substitution stimulates ammonia oxidation-driven N2O emissions by distinctively enriching keystone species of ammonia-oxidizing archaea and bacteria in tropical arable soils

Partial organic substitution (POS) is pivotal in enhancing soil productivity and changing nitrous oxide (N₂O) emissions by profoundly altering soil nitrogen (N) cycling, where ammonia oxidation is a fundamental core process. However, the regulatory mechanisms of N₂O production by ammonia oxidizers at the microbial community level under POS regimes remain unclear. This study explored soil ammonia oxidation and related N₂O production, further building an understanding of the correlations between ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) activity and community structure in tropical arable soils under four-year field management regimes (CK, without fertilizer N; N, with only inorganic N; M1N1, with 1/2 organic N + 1/2 inorganic N; M1N2, with 1/3 organic N + 2/3 inorganic N). AOA contributed more to potential ammonia oxidation (PAO) than AOB across all treatments. In comparison with CK, N treatment had no obvious effects on PAO and lowered related N₂O emissions by decreasing soil pH and downregulating the abundance of AOA- and AOB-amoA. POS regimes significantly enhanced PAO and N₂O emissions relative to N treatment by promoting the abundances and contributions of AOA and AOB. The stimulated AOA-dominated N₂O production under M1N1 was correlated with promoted development of Nitrososphaera. By contrast, the increased AOB-dominated N₂O production under M1N2 was linked to the enhanced development of Nitrosospira multiformis. Our study suggests organic substitutions with different proportions of inorganic and organic N distinctively regulate the development of specific species of ammonia oxidizers to increase associated N₂O emissions. Accordingly, appropriate options should be adopted to reduce environmental risks under POS regimes in tropical croplands.

Pathways of N2O production by marine ammonia-oxidizing archaea determined from dual-isotope labeling

The ocean is a net source of the greenhouse gas and ozone-depleting substance, nitrous oxide (N2O), to the atmosphere. Most of that N2O is produced as a trace side product during ammonia oxidation, primarily by ammonia-oxidizing archaea (AOA), which numerically dominate the ammonia-oxidizing community in most marine environments. The pathways to N2O production and their kinetics, however, are not completely understood. Here, we use 15N and 18O isotopes to determine the kinetics of N2O production and trace the source of nitrogen (N) and oxygen (O) atoms in N2O produced by a model marine AOA species, Nitrosopumilus maritimus. We find that during ammonia oxidation, the apparent half saturation constants of nitrite and N2O production are comparable, suggesting that both processes are enzymatically controlled and tightly coupled at low ammonia concentrations. The constituent atoms in N2O are derived from ammonia, nitrite, O2, and H2O via multiple pathways. Ammonia is the primary source of N atoms in N2O, but its contribution varies with ammonia to nitrite ratio. The ratio of 45N2O to 46N2O (i.e., single or double labeled N) varies with substrate ratio, leading to widely varying isotopic signatures in the N2O pool. O2 is the primary source for O atoms. In addition to the previously demonstrated hybrid formation pathway, we found a substantial contribution by hydroxylamine oxidation, while nitrite reduction is an insignificant source of N2O. Our study highlights the power of dual 15N-18O isotope labeling to disentangle N2O production pathways in microbes, with implications for interpretation of pathways and regulation of marine N2O sources.

Shifts in composition and function of bacterial communities reveal the effect of small barriers on nitrous oxide and methane accumulation in fragmented rivers

Rivers are often blocked by barriers to form different habitats, but it is not clear whether this change will affect the accumulation of N₂O and CH₄ in rivers. Here, low barriers (less than 2 m, LB) increased N₂O concentration by 1.13 times and CH₄ decreased by 0.118 times, while high barriers (higher than 2 m, less than 5 m high, HB) increased N₂O concentration by 1.19 times and CH₄ by 2.76 times. Co-occurrence network analysis indicated LB and HB can promote the enrichment of Cyanobium and Chloroflexi, further limiting complete denitrification and increasing N₂O accumulation. The LB promotes methanotrophs (Methylocystis, Methylophilus, and Methylotenera) to compete with denitrifiers (Pseudomonas) in water, and reduce CH₄ accumulation. While the HB can promote the methanotrophs to compete with nitrifiers (Nitrosospira) in sediment, thus reducing the consumption of CH₄. LB and HB reduce river velocity, increase water depth, and reduce dissolved oxygen (DO), leading to enrichment of nirS-type denitrifiers and the increase of N₂O concentration in water. Moreover, the HB reduces DO concentration and pmoA gene abundance in water, which can increase the accumulation of CH₄. In light of the changes in the microbial community and variation in N₂O and CH₄ accumulation, the impact of fragmented rivers on global greenhouse gas emissions merits further study.

Microplastics distribution characteristics in typical inflow rivers of Taihu lake: Linking to nitrous oxide emission and microbial analysis

The microplastics in nature water are important for the environmental fate of nitrous oxide (N₂O). This study investigated the influence and microbial mechanism of microplastic abundance to the N₂O flux in typical inflow rivers of Taihu lake. The microplastic abundance were in a range of 160-700 particles/m³ surface water, and 514-3018 particles/kg dry sediment. The highest percentage of microplastic color was transparent, significantly higher than other color (p<0.0001) in both surface water and sediment. The dominant microplastic size was 500-5000 μm in surface water, while size lower than 1000 μm was dominant in sediment. The microplastic abundance in sediment was negatively correlated with the concentration of suspended sediments (SPS) (p<0.05), Chl-a (p<0.05), NH₄⁺-N (p<0.05) and TP (p<0.01) in inflow river surface water. The dissolved N₂O concentration were 45.71-132.42 nmol/L, and the N₂O fluxes were 29.85-276.60 μmol/m²/d. The dissolved N₂O concentration was significantly correlated with the nirK abundance and nirK/nosZI ratio negatively (p<0.05), revealed that sediment nirK-type denitrification was the main driver of dissolved N₂O. Meanwhile, the N₂O flux (water-air interface) was significantly correlated with nosZI, napA, narG and nirS negatively, implied that nitrification and denitrification interaction in sediment is the main influence factor. The denitrification process in sediment was the main driven factor of N₂O releasing. Mantel-test shows that microplastic abundance in surface water was significantly correlated with nitrification (p = 0.001∼0.01) and denitrification (p = 0.01∼0.05) genera in water. The dominant denitrification microorganism was Dechloromonas in sediment and Flavobacterium in surface water. These results provided new insight into the fact that plastisphere which comprises microbial community on microplastic could affect the N₂O emission in aquatic system.

Nitrous Oxide Emission from Full-Scale Anammox-Driven Wastewater Treatment Systems

Wastewater treatment plants (WWTPs) are important contributors to global greenhouse gas (GHG) emissions, partly due to their huge emission of nitrous oxide (N₂O), which has a global warming potential of 298 CO₂ equivalents. Anaerobic ammonium-oxidizing (anammox) bacteria provide a shortcut in the nitrogen removal pathway by directly transforming ammonium and nitrite to nitrogen gas (N₂). Due to its energy efficiency, the anammox-driven treatment has been applied worldwide for the removal of inorganic nitrogen from ammonium-rich wastewater. Although direct evidence of the metabolic production of N₂O by anammox bacteria is lacking, the microorganisms coexisting in anammox-driven WWTPs could produce a considerable amount of N₂O and hence affect the sustainability of wastewater treatment. Thus, N₂O emission is still one of the downsides of anammox-driven wastewater treatment, and efforts are required to understand the mechanisms of N₂O emission from anammox-driven WWTPs using different nitrogen removal strategies and develop effective mitigation strategies. Here, three main N₂O production processes, namely, hydroxylamine oxidation, nitrifier denitrification, and heterotrophic denitrification, and the unique N₂O consumption process termed nosZ-dominated N₂O degradation, occurring in anammox-driven wastewater treatment systems, are summarized and discussed. The key factors influencing N₂O emission and mitigation strategies are discussed in detail, and areas in which further research is urgently required are identified.

Di(2-ethylhexyl) phthalate and dibutyl phthalate have a negative competitive effect on the nitrification of black soil

Di (2-ethylhexyl) phthalate (DEHP) and dibutyl phthalate (DBP) are the most widely used plasticizers for agricultural mulching films and one of the most common organic pollutants in black soil. However, little is known about the effect of these two contaminants on nitrification in black soil. This study investigated the changes of 20 mg/kg DEHP and DBP on the diversity of nitrification microbial communities, the abundance of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) related genes, and the activities of key enzymes involved in nitrification. During ammonia oxidation, DEHP and DBP had uncompetitive inhibition of urease, reducing the copy number of amoA gene, and microorganisms (Azoarcus, Streptomyces and Caulobacter) would use inorganic nitrogen as a nitrogen source for physiological growth. During nitrite oxidation, the copy number of nxrA gene also reduced, and the relative abundance of chemoautotrophic nitrifying bacteria (Nitrosomonas and Nitrobacter) decreased. Moreover, the path analysis results showed that DEHP and DBP mainly directly or indirectly affect AOB and NOB through three ways. These results help better understand the ecotoxicological effects of DEHP and DBP on AOB and NOB in black soil.

Structure and function of the soil microbiome underlying N2O emissions from global wetlands

Wetland soils are the greatest source of nitrous oxide (N₂O), a critical greenhouse gas and ozone depleter released by microbes. Yet, microbial players and processes underlying the N₂O emissions from wetland soils are poorly understood. Using in situ N₂O measurements and by determining the structure and potential functional of microbial communities in 645 wetland soil samples globally, we examined the potential role of archaea, bacteria, and fungi in nitrogen (N) cycling and N₂O emissions. We show that N₂O emissions are higher in drained and warm wetland soils, and are correlated with functional diversity of microbes. We further provide evidence that despite their much lower abundance compared to bacteria, nitrifying archaeal abundance is a key factor explaining N₂O emissions from wetland soils globally. Our data suggest that ongoing global warming and intensifying environmental change may boost archaeal nitrifiers, collectively transforming wetland soils to a greater source of N₂O.

Current and future threats to human health in the Anthropocene

It has been widely recognised that the threats to human health from global environmental changes (GECs) are increasing in the Anthropocene epoch, and urgent actions are required to tackle these pressing challenges. A scoping review was conducted to provide an overview of the nine planetary boundaries and the threats to population health posed by human activities that are exceeding these boundaries in the Anthropocene. The research progress and key knowledge gaps were identified in this emerging field. Over the past three decades, there has been a great deal of research progress on health risks from climate change, land-use change and urbanisation, biodiversity loss and other GECs. However, several significant challenges remain, including the misperception of the relationship between human and nature; assessment of the compounding risks of GECs; strategies to reduce and prevent the potential health impacts of GECs; and uncertainties in fulfilling the commitments to the Paris Agreement. Confronting these challenges will require rigorous scientific research that is well-coordinated across different disciplines and various sectors. It is imperative for the international community to work together to develop informed policies to avert crises and ensure a safe and sustainable planet for the present and future generations.

Stimulation of N2 O emission via bacterial denitrification driven by acidification in estuarine sediments

Ocean acidification in nitrogen-enriched estuaries has raised global concerns. For decades, biotic and abiotic denitrification in estuarine sediments has been regarded as the major ways to remove reactive nitrogen, but they occur at the expense of releasing greenhouse gas nitrous oxide (N₂ O). However, how these pathways respond to acidification remains poorly understood. Here we performed a N₂ O isotopocules analysis coupled with respiration inhibition and molecular approaches to investigate the impacts of acidification on bacterial, fungal, and chemo-denitrification, as well as N₂ O emission, in estuarine sediments through a series of anoxic incubations. Results showed that acidification stimulated N₂ O release from sediments, which was mainly mediated by the activity of bacterial denitrifiers, whereas in neutral environments, N₂ O production was dominated by fungi. We also found that the contribution of chemo-denitrification to N₂ O production cannot be ignored, but was not significantly affected by acidification. The mechanistic investigation further demonstrated that acidification changed the keystone taxa of sedimentary denitrifiers from N₂ O-reducing to N₂ O-producing ones and reduced microbial electron-transfer efficiency during denitrification. These findings provide novel insights into how acidification stimulates N₂ O emission and modulates its pathways in estuarine sediments, and how it may contribute to the acceleration of global climate change in the Anthropocene.

Metagenomic insights into nitrogen and phosphorus cycling at the soil aggregate scale driven by organic material amendments

The soil microbiome, existing as interconnected communities closely associated with soil aggregates, is the key driver in nutrient cycling. However, the underlying genomic information encoding the machinery of the soil microbiome involved in nutrient cycling at the soil aggregate scale is barely known. Here comparative metagenomics and genome binning were applied to investigate microbial functional profiles at the soil aggregate scale under different organic material amendments in a long-term field experiment. Soil samples were sieved into large macroaggregates (>2 mm), macroaggregates (0.25-2 mm) and microaggregates (<0.25 mm). Microbial taxonomic and functional alpha diversity were significantly correlated to soil NO₃^- and SOC. The highest abundance of nasB, nirK, and amoA genes, which are responsible for denitrification and ammonia oxidizers driving nitrification, was observed in microaggregates. Both manure and peat treatments significantly decreased the abundance of napA and nrfA that encode enzymes involved in dissimilatory nitrate reduction to ammonium (DNRA). As a biomarker for soil inorganic P solubilization, the relative abundance of gcd was significantly increased in macroaggregates and large macroaggregates. Three nearly complete genomes of Nitrososphaeraceae (AOA) and seven bacterial genomes were shown to harbor a series of genes involved in nitrification and P solubilization, respectively. Our study provides comprehensive insights into the microbial genetic potential for DNRA and P-solubilizing activity across different soil aggregate fractions and fertilization regimes.

Nutrient-Limited Enrichments of Nitrifiers From Soil Yield Consortia of Nitrosocosmicus-Affiliated AOA and Nitrospira-Affiliated NOB

The discovery of ammonia-oxidizing archaea (AOA) and complete ammonia-oxidizing (comammox) bacteria widespread in terrestrial ecosystems indicates an important role of these organisms in terrestrial nitrification. Recent evidence indicated a higher ammonia affinity of comammox bacteria than of terrestrial AOA and ammonia-oxidizing bacteria (AOB), suggesting that comammox bacteria could potentially represent the most low-nutrient adapted nitrifiers in terrestrial systems. We hypothesized that a nutrient-limited enrichment strategy could exploit the differences in cellular kinetic properties and yield enrichments dominated by high affinity and high yield comammox bacteria. Using soil with a mixed community of AOA, AOB, and comammox Nitrospira, we compared performance of nutrient-limited chemostat enrichment with or without batch culture pre-enrichment in two different growth media without inhibitors or antibiotics. Monitoring of microbial community composition via 16S rRNA and amoA gene sequencing showed that batch enrichments were dominated by AOB, accompanied by low numbers of AOA and comammox Nitrospira. In contrast, nutrient-limited enrichment directly from soil, and nutrient-limited sub-cultivation of batch enrichments consistently yielded high enrichments of Nitrosocosmicus-affiliated AOA associated with multiple canonical nitrite-oxidizing Nitrospira strains, whereas AOB numbers dropped below 0.1% and comammox Nitrospira were lost completely. Our results reveal competitiveness of Nitrosocosmicus sp. under nutrient limitation, and a likely more complex or demanding ecological niche of soil comammox Nitrospira than simulated in our nutrient-limited chemostat experiments.

Long-Term Low Dissolved Oxygen Operation Decreases N2O Emissions in the Activated Sludge Process

Nitrous oxide (N₂O) is an important greenhouse gas and a dominant ozone-depleting substance. Nitrification in the activated sludge process (ASP) is an important N₂O emission source. This study demonstrated that a short-term low dissolved oxygen (DO) increased the N₂O emissions by six times, while long-term low DO operation decreased the N₂O emissions by 54% (P < 0.01). Under long-term low DO, the ammonia oxidizer abundance in the ASP increased significantly, and thus, complete nitrification was recovered and no NH₃ or nitrite accumulated. Moreover, long-term low DO decreased the abundance of ammonia-oxidizing bacteria (AOB) by 28%, while increased the abundance of ammonia-oxidizing archaea (AOA) by 507%, mainly due to their higher oxygen affinity. As a result, AOA outnumbered AOB with the AOA/AOB amoA gene ratio increasing to 19.5 under long-term low DO. The efficient nitrification and decreased AOB abundance might not increase N₂O production via AOB under long-term low DO conditions. The enriched AOA could decrease the N₂O emissions because they were reported to lack canonical nitric oxide (NO) reductase genes that convert NO to N₂O. Probably because of AOA enrichment, the positive and significant (P = 0.02) correlation of N₂O emission and nitrite concentration became insignificant (P = 0.332) after 80 days of low DO operation. Therefore, ASPs can be operated with low DO and extended sludge age to synchronously reduce N₂O production and carbon dioxide emissions owing to lower aeration energy without compromising the nitrification efficiency.

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

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

A Critical Review on Nitrous Oxide Production by Ammonia-Oxidizing Archaea

The continuous increase of nitrous oxide (N₂O) in the atmosphere has become a global concern because of its property as a potent greenhouse gas. Given the important role of ammonia-oxidizing archaea (AOA) in ammonia oxidation and their involvement in N₂O production, a clear understanding of the knowledge on archaeal N₂O production is necessary for global N₂O mitigation. Compared to bacterial N₂O production by ammonia-oxidizing bacteria (AOB), AOA-driven N₂O production pathways are less-well elucidated. In this Critical Review, we synthesized the currently proposed AOA-driven N₂O production pathways in combination with enzymology distinction, analyzed the role of AOA species involved in N₂O production pathways, discussed the relative contribution of AOA to N₂O production in both natural and anthropogenic environments, summarized the factors affecting archaeal N₂O yield, and compared the distinctions among approaches used to differentiate ammonia oxidizer-associated N₂O production. We, then, put forward perspectives for archaeal N₂O production and future challenges to further improve our understanding of the production pathways, putative enzymes involved and potential approaches for identification in order to potentially achieve effective N₂O mitigations.

Micro-graphite particles accelerate denitrification in biological treatment systems

Accelerated denitrification is an essential problem in the biological treatment of nitrogenous wastewater. In this study, we report that denitrification is accelerated by micro-graphite particles (MGPs). The denitrification rate was increased by 83.4% or 11.1% in synthetic (with 0.16 g/L MGPs) or industrial nitrogenous wastewater (with 0.12 g/L MGP), respectively. The mechanism was revealed via a quantitative polymerase chain reaction (q-PCR), high-throughput sequencing, and scanning electron microscopy (SEM). The abundance of denitrifying bacteria Paracoccus in the sludge was increased by micro-graphite particles. The number of denitrifying bacteria with the nirS gene was increased significantly (75.6%). To the best of our knowledge, this is the first report that MGP could enhance denitrification via the sludge. MGP can denitrify in industrial applications.

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.