Complete nitrification by a single microorganism

Comammox and AOA responses to ammonia loading rate in oligotrophic environments

Nitrification is a central process in the global nitrogen cycle, yet the ecological niches and growth strategies of ammonia-oxidizing microorganisms in oligotrophic environments remain poorly understood. To investigate the ecological responses of complete ammonia oxidizers (Comammox) and ammonia-oxidizing archaea (AOA), a membrane bioreactor (MBR) system with two distinct ammonia loading rates (ALRs) was employed in this study. Metagenomic and meta-transcriptomic analyses showed that Comammox species-including Candidatus Nitrospira nitrosa and Candidatus Nitrospira inopinata-underwent a pronounced "bloom" only at high ALR, where their DNA and mRNA relative abundances reached 4.7 % and 5.63 %, respectively. Meanwhile, AOA steadily increased under both high and low ALR in oligotrophic environments. Network analysis further indicated stronger cooperative interactions between Comammox and AOA in higher ALR, highlighting distinct ecological strategies that underpin ammonia oxidation in oligotrophic environments. These findings not only support the development of low-carbon nitrogen removal processes in wastewater treatment but also clarify the impact of nitrogen loading on the distribution of ammonia-oxidizing microorganisms in natural ecosystems and provide insights into the origin and evolutionary pathways of these essential microbes.

Comparative enrichment of complete ammonium oxidation bacteria in floccular sludge reactors: Sequencing batch reactor vs. continuous stirred tank reactor

This study attempted to compare the enrichment of complete ammonium oxidation (comammox) bacteria, which are affiliated with Nitrospira and not able to generate nitrous oxide (N2O, a potent greenhouse gas) through biological pathways, in two commonly-utilized configurations of floccular sludge reactors, i.e., sequencing batch reactor (SBR) and continuous stirred tank reactor (CSTR), under the ammonium condition of mainstream wastewater (i.e., 40.0 g-N/m3). The results in terms of nitrification performance and microbial analyses during 216-d operation showed that compared with SBR offering a fluctuating but generally higher in-situ ammonium concentration (i.e., 1.0-6.0 g-N/m3) which was favorable for the growth of ammonium-oxidizing bacteria (AOB, belonging to Nitrosomonas in this study), CSTR managed to lower the in-situ ammonium level to < 2.0 g-N/m3, thus creating a competitive advantage for comammox bacteria with a highly oligotrophic lifestyle. Such an argument was further supported by dedicated batch tests which revealed that Nitrospira-dominant sludge had a lower maximum ammonium oxidation rate and lower apparent ammonium and oxygen affinity constants than Nitrosomonas-dominant sludge (i.e., 33.5 ± 2.1 mg-N/h/g-MLVSS vs. 139.9 ± 26.7 mg-N/h/g-MLVSS, 1.1 ± 0.1 g-N/m3 vs. 17.6 ± 4.6 g-N/m3, and 0.017 ± 0.002 g-O2/m3 vs. 0.037 ± 0.013 g-O2/m3, respectively), proving the nature of comammox bacteria as a K-strategist. Overall, this study not only provided useful insights into the effective enrichment of comammox bacteria in floccular sludge but also further revealed the interactions between comammox bacteria and AOB, thereby contributing to the future development of comammox-inclusive biological nitrogen removal technologies for sustainable wastewater treatment.

Earth's most needed uncultivated aquatic prokaryotes

Aquatic ecosystems house a significant fraction of Earth's biosphere, yet most prokaryotes inhabiting these environments remain uncultivated. While recently developed genome-resolved metagenomics and single-cell genomics techniques have underscored the immense genetic breadth and metabolic potential residing in uncultivated Bacteria and Archaea, cultivation of these microorganisms is required to study their physiology via genetic systems, confirm predicted biochemical pathways, exploit biotechnological potential, and accurately appraise nutrient turnover. Over the past two decades, the limitations of culture-independent investigations highlighted the importance of cultivation in bridging this vast knowledge gap. Here, we collected more than 80 highly sought-after uncultivated lineages of aquatic Bacteria and Archaea with global ecological impact. In addition to fulfilling critical roles in global carbon, nitrogen, and sulfur cycling, many of these organisms are thought to partake in key symbiotic relationships. This review highlights the vital contributions of uncultured microbes in aquatic ecosystems, from lakes and groundwater to the surfaces and depths of the oceans and will guide current and future initiatives tasked with cultivating our planet's most elusive, yet highly consequential aquatic microflora.

Probe Capture Enrichment Sequencing of amoA Genes Improves the Detection of Diverse Ammonia-Oxidising Archaeal and Bacterial Populations

The ammonia monooxygenase subunit A (amoA) gene has been used to investigate the phylogenetic diversity, spatial distribution and activity of ammonia-oxidising archaeal (AOA) and bacterial (AOB), which contribute significantly to the nitrogen cycle in various ecosystems. Amplicon sequencing of amoA is a widely used method; however, it produces inaccurate results owing to the lack of a 'universal' primer set. Moreover, currently available primer sets suffer from amplification biases, which can lead to severe misinterpretation. Although shotgun metagenomic and metatranscriptomic analyses are alternative approaches without amplification bias, the low abundance of target genes in heterogeneous environmental DNA restricts a comprehensive analysis to a realisable sequencing depth. In this study, we developed a probe set and bioinformatics workflow for amoA enrichment sequencing using a hybridisation capture technique. Using metagenomic mock community samples, our approach effectively enriched amoA genes with low compositional changes, outperforming amplification and meta-omics sequencing analyses. Following the analysis of metatranscriptomic marine samples, we predicted 80 operational taxonomic units (OTUs) assigned to either AOA or AOB, of which 30 OTUs were unidentified using simple metatranscriptomic or amoA gene amplicon sequencing. Mapped read ratios to all the detected OTUs were significantly higher for the capture samples (50.4 ± 27.2%) than for non-capture samples (0.05 ± 0.02%), demonstrating the high enrichment efficiency of the method. The analysis also revealed the spatial diversity of AOA ecotypes with high sensitivity and phylogenetic resolution, which are difficult to examine using conventional approaches.

The functional dominance and metabolic diversity of comammox Nitrospira in recirculating aquaculture systems

As a newly discovered group of ammonia-oxidizing microorganisms, complete ammonia oxidizing (comammox) Nitrospira has been widely found in various oligotrophic ecosystems. However, their activity and ecological niche is still unclear in recirculating aquaculture systems (RAS). This study aimed to compare the abundance and activity of comammox Nitrospira, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), and elucidate metabolic versatility of comammox Nitrospira in RAS. Quantitative PCR (qPCR) results showed that either comammox Nitrospira or AOB numerically predominated, while comammox Nitrospira and AOA shared similar low ammonia niches. Specifically, DNA-based stable isotope probing in conjunction with high-throughput 16S rRNA gene amplicon sequencing revealed that comammox Nitrospira accounted for 79.1 %, 97.5 %, 91.9 % and 97.6 % in the active ammonia-oxidizing community in four selected typical samples representing high abundance of comammox, AOA, and AOB, respectively. Phylogenetic analysis of heavy fraction DNA further identified novel comammox species from Nitrospira nitrificans cluster and clade A.2 acting as active species in different freshwater aquariums. Moreover, metagenome-assembled genome analysis revealed them as novel species with stress resistance and metabolic diversity compared with known comammox Nitrospira. This study underscores the dominant role of comammox Nitrospira as active ammonia-oxidizers in RAS and presents two novel comammox MAGs with metabolic flexibility, enriching our understanding of the nitrification process in oligotrophic artificial ecosystems.

Comammox Nitrospira are the dominant ammonia oxidizers in the Yangtze estuarine biofilms

Biofilms are indispensable ecological habitats for microbes that have garnered global attention and play a potential role in influencing the biogeochemical cycling of nitrogen. However, the biogeochemical significance of biofilms and the mechanisms by which they regulate nitrogen cycling remain elusive. In this study, we utilized DNA-stable isotope probing (DNA-SIP) labelling techniques in conjunction with metagenomics to reveal a nitrifying ecological niche in biofilms taken from the Yangtze Estuary, with those from sediment and water samples for comparison. Quantitative analysis showed that the amoA gene abundance of comammox Nitrospira (2.3 × 103 copies ng-1 DNA) was significantly higher than that of ammonia-oxidizing archaea (AOA-amoA, 62.4 copies ng-1 DNA) and ammonia-oxidizing bacteria (AOB-amoA, 218.1 copies ng-1 DNA) in biofilms, and the average abundance of comammox Nitrospira showed the following order: water > biofilm > sediment. Moreover, the NOB nxrB gene was more abundant than the amoA gene of ammonia oxidizers in all three media. DNA-SIP further revealed that the active comammox Nitrospira clade A mediates the nitrification process in biofilms with peak abundance at a buoyant density of 1.715 g mL-1. Active nitrifying bacteria exhibit metabolic diversity in both biofilms and sediments, and occupy unique nitrifying ecological niches. Additionally, the co-occurrence network showed that chlorophyll a, NO3- and salinity emerged as the predominant physicochemical factors affecting the nitrogen transformation genes in biofilms. Taken together, this study indicates that biofilms constitute an emerging nitrifying ecological niche in estuarine environments and deepens our understanding of the mechanisms by which biofilms function in marine biogeochemistry.

Untangling the impacts of bacterial community on carbon dioxide and nitrous oxide across a drinking water reservoir

Reservoirs represent a critical component of greenhouse gas (GHG) emissions, yet the intricacies of how biotic and abiotic factors influence GHG dynamics within reservoirs remain largely unexplored. Herein, we investigated the spatiotemporal patterns of CO2 and N2O emissions and the underlying factors in the Danjiangkou Reservoir, Asia's largest artificial freshwater reservoir. We found that this reservoir was a significant source of GHGs to the atmosphere, with peak CO2 emissions observed in autumn (1544.39 ± 652.53 μatm) and N2O emissions in winter (32.57 ± 8.87 μmol/L). Moreover, we identified crucial bacterial biomarkers that regulate GHG dynamics, and these GHG biomarkers exhibited consistent seasonal patterns with the corresponding GHGs, concerning their abundance and niche breadth. Notably, GHG biomarkers displayed larger effects on the variations of N2O than CO2 emissions, while physiochemical variables were more critical for CO2 dynamics, highlighting the need to consider both biotic and abiotic factors when evaluating GHG emissions from reservoirs. Overall, this study advanced our knowledge of GHG emissions and their driving mechanisms in artificial reservoirs, emphasizing the importance of functional microbes in estimating and managing CO2 and N2O emissions from artificial reservoirs worldwide.

A powerful but frequently overlooked role of thermodynamics in environmental microbiology: inspirations from anammox

Thermodynamics has long been applied in predicting undiscovered microorganisms or analyzing energy flows in microbial metabolism, as well as evaluating microbial impacts on global element distributions. However, further development and refinement in this interdisciplinary field are still needed. This work endeavors to develop a whole-cycle framework integrating thermodynamics with microbiological studies, focusing on representative nitrogen-transforming microorganisms. Three crucial concepts (reaction favorability, energy balance, and reaction directionality) are discussed in relation to nitrogen-transforming reactions. Specifically, reaction favorability, which sheds lights on understanding the diversity of nitrogen-transforming microorganisms, has also provided guidance for novel bioprocess development. Energy balance, enabling the quantitative comparison of microbial energy efficiency, unravels the competitiveness of nitrogen-transforming microorganisms under substrate-limiting conditions. Reaction directionality, revealing the niche-differentiating patterns of nitrogen-transforming microorganisms, provides a foundation for predicting biogeochemical reactions under various environmental conditions. This review highlights the need for a more comprehensive integration of thermodynamics in environmental microbiology, aiming to comprehensively understand microbial impacts on the global environment from micro to macro scales.

Influence of filter backwashing on iron, manganese, and ammonium removal in dual-media rapid sand filters used for drinking water production

Iron (Fe), manganese (Mn), and ammonium (NH4+) removal from groundwater using rapid sand filtration is a widely employed method in drinking water production. Over time, Fe and Mn oxides accumulate in the filter, which necessitates frequent backwashing to avoid clogging. In this study, we investigated the impact of backwashing on the microbial community and filter chemistry in a dual-media filter comprising anthracite and sand layers. Specifically, we focused on the removal of Fe, Mn, and NH4+ over the runtime of the filter. With increasing runtime, depth profiles of dissolved and particulate Fe revealed the buildup of Fe oxide flocs, causing Fe2+ and Mn2+ oxidation and nitrification to occur at greater depths within the filter. Towards the end of the filter runtime, breakthrough of suspended Fe oxides was observed, likely due to preferential flow. Backwashing effectively removed metal oxide flocs and restored the Fe removal efficiency in the top layer of the filter. While the two layers remained separate, the anthracite and sand layers themselves fully mixed during backwashing, leading to a homogenous distribution of the microbial community within each layer. Methyloglobulus and Gallionella were the predominant organisms in the anthracite layer, likely catalyzing methane and Fe2+ oxidation, respectively. The nitrifying community of the anthracite consisted of Nitrosomonas, Candidatus Nitrotoga, and Nitrospira. In contrast, the nitrifying community in the sand layer was dominated by Nitrospira. Backwashing minimally affected the microbial community composition of the filter medium except for Gallionella, which were preferentially washed out. In conclusion, our research offers a molecular and geochemical basis for understanding how backwashing influences the performance of rapid sand filters.

Long-term stability of comammox Nitrospira under weakly acidic conditions and their acid-adaptive mechanisms revealed by genome-centric metatranscriptomics

Despite their widespread presence in acidic environments, the stability and adaptative mechanisms of complete ammonia oxidization (comammox) bacteria remain poorly understood. In this three-year study, comammox Nitrospira consistently dominated both abundance and activity in an acidic nitrifying reactor (pH = 6.3-6.8), as revealed by metagenomic and cDNA-based 16S rRNA sequencing. Batch tests demonstrated their decent nitrification down to pH 4.7, while ceasing at pH 4.2. Genome-centric metatranscriptomics revealed that comammox Nitrospira upregulated a Rh-type ammonium transporter to enhance substrate uptake under acidic conditions. Active proton transport, mediated by NADH dehydrogenases and F-type ATPase, was identified as a primary strategy for maintaining pH homeostasis in comammox Nitrospira. Genes associated with carbon acquisition, chemotaxis, and DNA repair were upregulated at low pH, suggesting these processes play roles in acid adaptation. These findings enhance the understanding of ecological roles and adaptive mechanisms of comammox bacteria in acidic environments.

Path to zero emission of nitrous oxide in sewage treatment: is nitrification controllable or avoidable?

Amid growing concerns over climate change, the need to reduce nitrous oxide (N2O) emissions from sewage treatment is more urgent than ever. Sewage treatment plants are significant sources of N2O due to its production as an intermediate in nitrification and its release into the air during aeration. Effective management of the nitrification process is therefore vital for controlling or eliminating these emissions. Despite substantial efforts to quantify and understand N2O emissions from sewage treatment, success in reducing them has been limited. This review discusses and proposes promising solutions for reducing N2O emissions in sewage treatment, evaluates the potential of various strategies, and identifies ways to accelerate their development and implementation.

Dirammox (direct ammonia oxidation) to nitrogen (N2): discovery, current status, and perspectives

Microbial ammonia oxidation plays an important role in nitrogen (N2) cycling in natural and man-made systems. Heterotrophic microorganisms that oxidize ammonia were observed more than a century ago; however, the underlying molecular mechanism of ammonia oxidation is still mysterious. Dirammox (direct ammonia oxidation to N2) is a newly described heterotrophic ammonia oxidation process in which ammonia or its organic amine is oxidized into hydroxylamine and then directly converted to N2 gas without the involvement of nitrite and nitrate. As demonstrated with Alcaligenes species, the conversion of ammonia to hydroxylamine is mediated by the dnf genes, and hydroxylamine conversion to N2 is considered both a biotic and abiotic process. Dirammox is different from the N2-producing processes of nitrification-denitrification and anaerobic ammonia oxidation (anammox), in which nitrite or nitrate is involved. Here, we review the discovery of dirammox, progress toward understanding its genetics, biochemistry, physiology, and ecology, and future perspectives and directions.

Ecological distribution of ammonia oxidizers in Yellow River sediments and their influencing factors

Ammonia oxidation, the first and rate-limiting step of nitrification, is a crucial step in nitrogen cycling. The distribution patterns of key ammonia oxidizers, including ammonia-oxidizing archaea (AOA) and bacteria (AOB), and comammox (complete ammonia oxidation) Nitrospira, provide vital insights for nitrogen cycling in natural ecosystems. Currently, the distribution and contribution of AOA, AOB and comammox Nitrospira in freshwater ecosystems remain largely underexplored. This study explored the abundances, diversity, phylogenetic characteristics, and community structures of AOA, AOB and comammox Nitrospira in the Yellow River sediments using high-throughput sequencing and qPCR. Comammox Nitrospira displayed the highest amoA gene abundance in sediments from all sampling sites compared to that of AOA and AOB. The diversity of AOA shown no significant correlations with physicochemical properties, while the diversity of AOB negatively correlated with pH (p < 0.05), and the diversity of comammox Nitrospira positively correlated with NH4+ content and TC content (p < 0.05), respectively. Phylogenetic analysis identified Nitrososphaera, Nitrosospira, and cladeA1 as the most dominant clusters of AOA, AOB and comammox Nitrospira, respectively. The community composition of AOA, AOB, and comammox Nitrospira exhibited distinct spatial patterns, varying across the upper, middle and lower reaches. pH was the key factor shaping the community structure of AOB and comammox Nitrospira (p < 0.05), while organic carbon was the key determinant of the AOA community structure (p < 0.05). The results of this study advance our understanding of N cycling in freshwater ecosystems.

Rethinking the effect of salinity on nitrogen removal capacity of aerobic granular sludge from the perspective of size distribution and granular morphology

Granular size induces the operation performance variation of aerobic granular sludge reactor, but the profound reasons are unrevealed. This study investigated the influence of granular size distribution on the reactor operation under salt stress. The effective nitrogen removal was achieved at ≤4% salinity, but declined at 6% salinity. The phenomenon was determined by the granular size fraction. The small granules (d = 200-600 μm) fraction was 77%-81% at ≤4% salinity, while only 57.32% at 6% salinity. That was positively correlated with nitrite reductase (NIR) activity significantly (p < 0.01). Moreover, small granules exhibited smooth surface at ≤4% salinity. The efficient mass transfer area of granules was enlarged by the smooth surface, accelerating substrates mass transfer. Consequently, ammonia monooxygenase (AMO) activity was enhanced significantly (p < 0.05). Ammonia-oxidation bacteria, Nitrosomonas and nitrite-reduction bacteria, Paracoccus were dominated in small granules at 4% salinity, while loss at 6% salinity. Overall, small granules with smooth surface favored the enrichment of nitrogen removal microbes via substrate transfer enhancement, and improved the activity of AMO and NIR. Thus, the favorable nitrogen removal performance of aerobic granular sludge reactor was achieved at ≤4% salinity.

Comammox Nitrospira act as key bacteria in weakly acidic soil via potential cobalamin sharing

The discovery of comammox Nitrospira in low pH environments has reshaped the ammonia oxidation process in acidic settings, providing a plausible explanation for the higher nitrification rates observed in weakly acidic soils. However, the response of comammox Nitrospira to varying pH levels and its ecological role in these environments remains unclear. Here, a survey across soils with varying pH values (ranging from 4.4 to 9.7) was conducted to assess how comammox Nitrospira perform under different pH conditions. Results showed that comammox Nitrospira dominate ammonia oxidation in weakly acidic soils, functioning as a K-strategy species characterized by slow growth and stress tolerance. As a key species in this environment, comammox Nitrospira may promote bacterial cooperation under low pH conditions. Genomic evidence suggested that cobalamin sharing is a potential mechanism, as comammox Nitrospira uniquely encode a metabolic pathway that compensates for cobalamin imbalance in weakly acidic soils, where 86.8% of metagenome-assembled genomes (MAGs) encode cobalamin-dependent genes. Additionally, we used DNA stable-isotope probing (DNA-SIP) to demonstrate its response to pH fluctuations to reflect how it responds to the decrease in pH. Results confirmed that comammox Nitrospira became dominant ammonia oxidizers in the soil after the decrease in pH. We suggested that comammox Nitrospira will become increasingly important in global soils, under the trend of soil acidification. Overall, our work provides insights that how comammox Nitrospira perform in weakly acidic soil and its response to pH changes.

Relationship assessment of microbial community and cometabolic consumption of 2-chlorophenol

The relationship of microbial community and cometabolic consumption of 2-chlorophenol (2-CP) in a nitrifying sequencing batch reactor (SBR) was studied. The assessment of the population dynamics of the nitrifying sludge during the cometabolic 2-CP consumption with increasing ammonium (NH4+) concentrations in the SBR showed the presence of 39 different species of which 10 were always present in all cycles. Fifty-five percent of the species found were grouped as Proteobacteria (45% as β-proteobacteria and 10% as γ-proteobacteria class), 30% as Acidobacteria, and 15% as Deinococcus-Thermus phyla. NH4+ and cometabolic 2-CP consumption could be related to the presence and permanence of ammonium-oxidizing bacteria (AOB) species and heterotrophic bacteria, while the complete nitrification to the presence of nitrite-oxidizing bacteria (NOB) species. A correlation analysis showed that the complete and stable nitrifying performance (NH4+ consumption efficiencies (ENH4+-N) > 99% and nitrate production yields (YNO3--N) between 0.93 and 0.99), as well as the increase in specific rates (ammonium (qNH4+-N) and 2-CP (q2-CP-C) consumption and nitrate production (qNO3--N)), was associated with the homogeneity of the bacterial community (J index = 0.99). The increase in the proportion of individuals of AOB species such as Nitrosomonas oligotropha and Nitrosomonas marina was associated with the increase in qNH4+-N (r ≥ 0.69) and q2-CP-C (r ≥ 0.64) and, therefore, with the 2-CP cometabolic consumption in the SBR. Finally, the increase in the proportion of individuals of heterotrophic species such as Dokdonella ginsengisoli, Deinococcus peraridilitoris, Truepera radiovictrix, and Stenotrophobacter terrae was associated with the increase in q2-CP-C (r ≥ 0.59). KEY POINTS: • Thirty-nine bacterial species were identified in the nitrifying sludge population of the SBR. • β-Proteobacteria and Acidobacteria were the prevalent (85%) bacterial groups. • AOB and heterotrophic bacteria participate in NH4+ and cometabolic 2-CP consumption.

Side-On Bound Beryllium Dinitrogen Complex: A Precursor for Complete Conversion of Dinitrogen to Ammonia Mediated by N-Heterocyclic Carbene

The complete conversion of dinitrogen to ammonia mediated by a side-on N2-bound carbene-beryllium complex, [NHC-Be(η2-N2)] has been studied considering both the symmetric and unsymmetric pathways. N-heterocyclic carbenes complexed with Be(η2-N2) moieties were considered substrates in our study. We found that two mechanistic pathways were possible for the reduction of dinitrogen to form ammonia. Our calculations revealed that the symmetric pathway is more favorable compared to the unsymmetric one. The interconversion of the complex from the symmetric product to the unsymmetric one involves a large activation energy barrier for the proton transfer pathway. Both of these pathways were associated with high exergonicity, and the N-N bond is observed to be elongated, which indicates that the NHC-Be(η2-N2) complex is a promising candidate for dinitrogen activation and subsequent reduction, resulting in the formation of ammonia. The bonding scenario of the NHC-Be(η2-N2) complex can be explained well by the famous Dewar-Chatt-Duncanson (DCD) model. Our calculations reveal that the symmetric pathway is found to be more suitable due to more negative values of change in Gibbs free energy. Solvent phase calculations have identified the viability of the NHC-Be(η2-N2) complex, indicating that the complex is sustainable in low-polar organic solvents, such as toluene and diethyl ether.

Distribution and key influential factors of comammox in drained and waterlogged soils of zoige plateau peatland

Peatlands are important carbon and nitrogen reservoirs, playing crucial roles in nitrogen cycling. During microbially-driven nitrogen cycling, nitrous oxide (N2O, 298 times global warming potential of CO2) can be emitted, exacerbating global warming. Complete ammonia-oxidizing bacteria (comammox), a newly discovered group of prokaryotes, can independently oxidize ammonia directly to nitrate, bypassing the nitrite stage, and thereby reducing N2O production associated with the traditional two-step nitrification process. However, information on comammox distribution and its key influential factors in plateau peatlands remains scarce. Thus, this study chose Zoige plateau peatland in China to collect soil samples from different soil types (drained and waterlogged), across different seasons (non-growing and growing), and at various depth (0-100 cm) to assess comammox abundance and community composition. Additionally, soil properties were analyzed and correlated with comammox abundance and community composition to identify the key factors affecting comammox distribution. Comammox abundance varied significantly across soil types, depth, and sampling seasons. Waterlogged soils demonstrated higher comammox abundance than drained soils. In waterlogged soils, comammox abundance showed higher during growing season than non-growing season, while the opposite trend was observed in drained soils. Regardless of soil types, comammox abundance decreased with increasing soil depth. In soils of Zoige plateau peatland, comammox clades A.1, A.2, A.3 and B.1 were identified, with clade B.1 dominating the comammox community. Both Nitrospira sp. CG24A (clade B.1) and Candidatus Nitrospira nitrificans (clade A.1) showed great seasonal variations. Soil properties, including moisture, pH, carbon, and nutrients, collectively influenced comammox abundance and diversity. Among these factors, NH4+-N was the main factor affecting comammox abundance, while moisture primarily drove community distribution. These findings provide valuable insights into comammox distribution, enhancing our understanding of its potential role in mitigating N2O emissions and thus nitrogen cycling in plateau peatland soils.

Dredging and sediment discharge in a river with floodplain. Physicochemical and microbiological effects in Paraná river

Alterations caused by human activities in the environment, such as dredging, modify the physicochemical conditions and affect the habitat. Maintenance dredging that allows large vessels access to inland ports is a recurring disruptive action. The study aimed to evaluate, during a maintenance dredging operation in a port area of the Paraná River, the modifications in the structure of the river, the presence of contaminants and bacterial organisms. The effects caused during the operation of a suction dredge in a South America river under two temporal conditions were analyzed: i) the short and medium-term effects on the physicochemical variables, and ii) the immediate effects on the physicochemical variables and the abundance of bacterioplankton. The variables measured in sediment and water samples were limnological parameters (e.g. conductivity, pH, dissolved oxygen, among others), heavy metal concentration, presence of biocides, hydrocarbon molecules, nutrients, sediment granulometry, Escherichia coli, Enterococcus, total coliforms, and heterotrophic bacteria. Some physicochemical variables increased in the water column immediately after the water mass passed through the operating dredge, including sediment resuspension. The parameter changes were transient, as there were no significant increases in the variables downstream of the dredge during dredging and discharge operations or after dredging work. Some metal concentrations increased in the sediment and water column. Bacteria increased during dredging and more after rainfall events. Then, at the end of the dredging, the bacteria concentrations decreased to previous values. The possible effects of dredging disturbance were of the same order or less than those of natural ones, i.e. rainfall. Sixty days after the dredging work was completed, the system was back to normal both in the dredged and discharge areas.

Transcriptional activity of ammonia oxidisers in response to soil temperature, moisture and nitrogen amendment

The contrasting response of AOA, AOB, and comammox Nitrospira amoA transcript abundance to temperature, moisture, and nitrogen was investigated using soil microcosms. The moisture, temperature, and nitrogen treatments were selected to represent conditions typically found in a New Zealand (NZ) dairy farm. AOB dominated all synthetic urine treated soils. Peak AOB amoA transcript abundance was positively correlated with estimated soil ammonia availability. While AOB gDNA abundance and nitrification rate trends were similar. AOA were strongly influenced by soil temperature. At 20°C, AOA amoA peak transcript abundance averaged over 1 order of magnitude higher than at 8°C. Within the AOA community a member of the Nitrosocosmicus clade was positively correlated with ammonium and estimated ammonia concentrations. The presence and relative increase of an AOA community member in a high nitrogen environment poses an interesting contrast to current scientific opinion in NZ. Comammox Nitrospira abundance showed no correlation with soil moisture. This suggests that previously found associations are more complex than originally thought. Further research is required to determine the drivers of comammox Nitrospira abundance in a high moisture environment. Overall, these results indicate that AOB are the main drivers of nitrification in New Zealand dairy farm soils.

Optimization of Compost and Peat Mixture Ratios for Production of Pepper Seedlings

Substituting peat moss with compost derived from organic waste in plant nurseries presents a promising solution for reducing environmental impact, improving waste management, and enhancing soil health while promoting sustainable agricultural practices. However, selecting the appropriate proportions of both materials is crucial for each plant species. This study investigates the effects of different ratios of compost and peat mixtures on the growth and development of pepper seedlings. The compost mixtures used in the study included the following combinations: sewage sludge with sawdust (A), sewage sludge with sawdust and biodegradable garden/park waste (B), and biodegradable garden/park waste with sawdust (C). The final substrates used for seedling production were composed of composts (A, B, C) and peat (O) as a structural additive, mixed in different proportions by mass: I-O 25%, II-O 50%, and III-O 75%. Seedlings grown in these substrates were assessed using biometric and physiological measurements. Nematode species present in substrates were identified by metabarcoding analysis. The results revealed that substrate productivity depended not only on nutrient content but also on structural properties, which were significantly influenced by the peat proportion. Among the tested compost mixtures, variant A I emerged as the most effective substrate, promoting optimal seedling growth. Molecular nematode analysis revealed significant nematode contamination in substrates with higher peat proportions (C II and C III), including Meloidogyne sp. Lichtenburg (26%), Meloidogyne hispanica (5%), Meloidogyne sp. Mi_c1 (3%), Meloidogyne ethiopica (2%), and Meloidogyne thailandica (1%). The findings underscore the critical importance of achieving an optimal balance between nutrient content and structural properties in substrates to support the healthy growth and development of pepper seedlings. To further enhance crop performance and reduce the risk of pest-related damage, it is essential to prioritize the improvement of substrate selection strategies. Monitoring for nematode contamination is crucial to prevent potential compromises in seedling quality and overall productivity.

Application of the nitrogen-to-argon ratio to understand nitrogen transformation pathways in landfills under in-situ stabilization

The ratio of nitrogen (N2) to argon (Ar) in landfill gas was compared to the atmospheric gas ratio to quantify the balance between N2 generating (anaerobic ammonium oxidation, denitrification) and N2 consuming (nitrogen fixation) processes on three landfills undergoing in-situ stabilization. In the aerated landfills, as much as 22% of the extracted N2 could be explained by net denitrification, with coexisting aerobic and anaerobic domains fostering nitrification-dependent denitrification. Nitrogen fixation was also occasionally observed. Removal of nitrogen via the gas phase exceeded nitrogen removed via the leachate by up to a factor of 33. Contrastingly, the anaerobic landfill under leachate recirculation showed a net reduction of N2 in relation to Ar, indicating nitrogen fixation as the dominant mechanism, equivalent up to 28% of the nitrogen in the extracted landfill gas. The balance between denitrification and nitrogen fixation in the aerated sites varied seasonally, likely caused by increased evapotranspiration in the summer, allowing greater air intrusion through the cover soil, resulting in higher NO3- and NO2- availability for denitrification and anammox. No such variability was observed for the landfill under liquid recirculation. The nitrogen transforming microbial community comprised of species responsible for nitrification, ammonification, denitrification, and anammox, indicating all processes may coexist. The findings show aeration supports nitrogen removal through the gas phase, but also suggest that nitrogen fixation adds nitrogen to the waste body in anaerobic domains. This could delay reaching environmental compliance criteria for leachate nitrogen, both for in-situ treatment by aeration and by leachate recirculation.

Metabolic labour division trade-offs in denitrifying microbiomes

Division of metabolic labour is a defining trait of natural and engineered microbiomes. Denitrification-the stepwise reduction of nitrate and nitrite to nitrogenous gases-is inherently modular, catalysed either by a single microorganism (termed complete denitrifier) or by consortia of partial denitrifiers. Despite the pivotal role of denitrification in biogeochemical cycles and environmental biotechnologies, the ecological factors selecting for complete versus partial denitrifiers remain poorly understood. In this perspective, we critically review over 1500 published metagenome-assembled genomes of denitrifiers from diverse and globally relevant ecosystems. Our findings highlight the widespread occurrence of labour division and the dominance of partial denitrifiers in complex ecosystems, contrasting with the prevalence of complete denitrifiers only in simple laboratory cultures. We challenge current labour division theories centred around catabolic pathways, and discuss their limits in explaining the observed niche partitioning. Instead, we propose that labour division benefits partial denitrifiers by minimising resource allocation to denitrification, enabling broader metabolic adaptability to oligotrophic and dynamic environments. Conversely, stable, nutrient-rich laboratory cultures seem to favour complete denitrifiers, which maximise energy generation through denitrification. To resolve the ecological significance of metabolic trade-offs in denitrifying microbiomes, we advocate for mechanistic studies that integrate mixed-culture enrichments mimicking natural environments, multi-meta-omics, and targeted physiological characterisations. These undertakings will greatly advance our understanding of global nitrogen turnover and nitrogenous greenhouse gases emissions.

Microbial community and functional shifts across agricultural and urban landscapes within a Lake Erie watershed

The role of sediment microbial communities in regulating the loss and retention of nutrients in aquatic ecosystems has been increasingly recognised. However, in the Great Lakes, where nutrient mitigation focuses on harmful algal blooms, there are limited studies examining the fundamental role of water/sediment microbes in nutrient biogeochemical cycling. Little is understood in this regard considering the increase in anthropogenic pressure on in-stream biological processes impacting nutrient flux to lakes. In this study, metagenomic and metatranscriptomic approaches were used to investigate the microbial community and gene regulation. The study focused on nitrogen (N) metabolism in a nutrient-polluted watershed of Lake Erie in southwestern Ontario, Canada. Nutrients and microbial analyses of water and sediments were collected in 2020 and 2021 from Sturgeon Creek headwaters to the nearshore of Lake Erie. Results showed no significant shifts in community structure with nutrient concentrations or land use. Metabolically, active genes involved in denitrification (consisting of 32-53% of N metabolic transcripts) showed the highest expression within agricultural and wetland dominant locations. Based on active gene expression patterns, the urbanised location coinciding with peak nitrate (NO3-) concentrations showed the greatest potential for nitrous oxide (N2O) emission and nitrogen loss along this transect. In contrast to denitrification, direct nitrification (5-21% of N metabolic transcripts) increased two-fold approaching downstream and nearshore lake locations. Across this river-lake corridor, expression of key functional genes associated with N transformation showed strong correlation with the change in concentrations of aqueous NO3- and nitrite (NO2-) and the ratio of NO2-/NO3-. Our findings demonstrated a clear link between sediment microbial metabolism and overlying water chemistry in this lotic system. We suggest that future studies assessing nutrient mitigation consider sediment biogeochemical processes and N-metabolising bacteria, and their fundamental role and cooperative relationship with nutrient and hydrological dynamics of overlying waters.

Both AOA and AOB contribute to nitrification and show linear correlation with nitrate leaching in purple soils with a wide nitrogen gradient

Ammonia oxidizers play an important role in nitrification that forms nitrate, the main form of leaching nitrogen (N). However, little is known about how ammonia oxidizers bridge long-term N fertilization levels and soil nitrate leaching. We conducted a field experiment in purple soil, investigating the interactions among soil physico-chemical parameters, ammonia-oxidizing microbial communities, and N leaching under 0, 90, 180, 270, and 360 kg N ha-1 yr-1 fertilization levels. We found that soil inorganic N leaching increased exponentially with increasing N application rate. N fertilization enhanced the abundances of the amoA gene in ammonia-oxidizing archaea (AOA) and bacteria (AOB), while partial least squares regression analysis revealed that AOA and AOB abundances were correlated with pH and soil organic carbon (SOC). Compared with no N fertilization, N application reduced AOA alpha diversity and increased AOB alpha diversity. AOA alpha diversity was associated with pH and bulk density, whereas soil SOC and inorganic N content were more important in predicting changes in AOB alpha diversity. A linear relationship was established between soil NO3--N leaching, the potential nitrification rate (PNR), and the abundances of AOA and AOB. The association of soil NO3--N leaching and PNR with both AOA and AOB abundances were further corroborated by Mantel test, random forest regression, and partial least squares path modelling. Furthermore, alterations in the AOB alpha diversity, soil pH and NH4+-N content also contribute to the increasing soil NO3--N leaching along the N application rate. Our results suggest that AOA, which previous studies have found to be active only under low N conditions, can also contribute to nitrification and support soil NO3--N leaching at a wide range of N gradients. Overall, this finding advances the current understanding of the relationship between soil N leaching and microbial functional properties to some extent.

Extreme soil salinity reduces N and P metabolism and related microbial network complexity and community immigration rate

Soil microbiomes are well known to suffer from the effects of rising salinity. There are, however, no current understandings regarding its specific effects on microbial metabolic functions associated with nitrogen (N) and phosphorus (P) cycling, particularly in the Yellow River Delta (YRD), one of the largest estuaries in the world. This research examined soil microbiomes at 50 sites in the YRD region to analyze their co-occurrence networks and their relationship with N (nitrification, denitrification, dissimilatory, assimilatory, fixation, and mineralization) and P (solubilization, mineralization, transportation, and regulation) metabolism processes. Our findings indicate a notable reduction in soil multifunctionality as salinity levels increase, with Halofilum-ochraceum playing a significant role in nitrification, whereas Bacteroidetes-SB0662-bin-6 helps solubilize inorganic P in highly saline areas. High soil salinity negatively affected the amoA gene involved in nitrification and increased the nosZ gene involved in denitrification in extreme salinity soil with 8.2 g/kg salt content. Extreme salinity significantly reduced the expression of genes involved in inorganic P solubilization, such as ppa and ppx. Additionally, the alkaline P gene phoD exhibited significant decreases in extremely saline soils, thereby impeding the mineralization of organic P. The neutral community models indicated that microbial community immigration rate showed a linear negative relationship with soil EC in the six N and four P processes. Salinization, however, displayed a nonlinear pattern with clearly defined thresholds on the community of microbes involved in N and P cycling. Reduced microbial diversity and interactions are causing a decline in soil multifunctionality, and the soil multifunctionality and network edges jointly limited the microbial community immigration rate involved in N and P cycling. It is crucial to preserve soil microbial functions to support nutrient cycling and predict the ecological effects of soil salinization.

Ecological dynamics explain modular denitrification in the ocean

Microorganisms in marine oxygen minimum zones (OMZs) drive globally impactful biogeochemical processes. One such process is multistep denitrification (NO3-→NO2-→NO→N2O→N2), which dominates OMZ bioavailable nitrogen (N) loss and nitrous oxide (N2O) production. Denitrification-derived N loss is typically measured and modeled as a single step, but observations reveal that most denitrifiers in OMZs contain subsets ("modules") of the complete pathway. Here, we identify the ecological mechanisms sustaining diverse denitrifiers, explain the prevalence of certain modules, and examine the implications for N loss. We describe microbial functional types carrying out diverse denitrification modules by their underlying redox chemistry, constraining their traits with thermodynamics and pathway length penalties, in an idealized OMZ ecosystem model. Biomass yields of single-step modules increase along the denitrification pathway when organic matter (OM) limits growth, which explains the viability of populations respiring NO2- and N2O in a NO3--filled ocean. Results predict denitrifier community succession along environmental gradients: Pathway length increases as the limiting substrate shifts from OM to N, suggesting a niche for the short NO3-→NO2- module in free-living, OM-limited communities, and for the complete pathway in organic particle-associated communities, consistent with observations. The model captures and mechanistically explains the observed dominance and higher oxygen tolerance of the NO3-→NO2- module. Results also capture observations that NO3- is the dominant source of N2O. Our framework advances the mechanistic understanding of the relationship between microbial ecology and N loss in the ocean and can be extended to other processes and environments.

Dynamic changes, cycling and downward fate of dissolved carbon and nitrogen photosynthetically-derived from glaciers in upper Indus river basin

Glaciers play key roles in capturing, storing, and transforming global carbon and nitrogen, thereby contributing markedly to their cycles. However, an integrated mechanistic approach is still lacking regarding glacier's primary producers (PP), in terms of stable dissolved inorganic carbon isotope (δ13C-DIC) and its relationship with dissolved carbon and nitrogen transformation d ynamic changes/cycling. Here, we sampled waters from glaciers, streams, tributaries, and the Indus River (IR) mainstream in the Upper IR Basin, Western Himalaya. Dissolved organic matter (DOM) appears to increase, on average, by ∼2.5-23.4% with fluctuations when passing from glaciers to streams-tributaries-IR mainstream (the upper and lower parts, respectively) continuum, implying that DOM originates from glaciers PP and is subsequently degraded. The corresponding fluctuations are observed for fluorescent DOM (FDOM), dissolved organic nitrogen (8.0-106.8%), NO3--N (-13.5/+16.6%), NH4+-N (-8.8/+13.0%), and NO2--N (70.7-217.5%). These variations are associated with overall DOM/FDOM transformations, with the production of ending byproducts (e.g. CO2/DIC). The δ13C-DIC values fluctuated from glaciers (-5.3 ± 2.5‰) to streams (-4.4 ± 2.1‰), tributaries (-4.3 ± 1.6‰), and IR mainstream (-4.2 ± 1.3‰). The δ13C-DIC data are consistent with C transformations that involve lighter CO2 emission into the atmosphere, whereas highly depleted DIC/CO2 is the signature of DOM degradation after its fresh production from glaciers PP which originated by photosynthetic activities (e.g. uptake/sink of atmospheric CO2: -8.4‰). Finally, glacier-fed meltwaters would simultaneously contribute to the biogeochemical characteristics of downward margins and specific ecosystems (lake/pond/groundwater/hot springs) via transformation dynamics/cycling of dissolved C and N with high photo/microbial lability. Our results highlight the substantial contribution of western Himalayan glaciers-derived DOM to the global C and N cycles.

Promoting Electrochemical Nitrate Reduction to Ammonia on Silver Nanocrystals Doped with Iron Series Elements

Electrochemical nitrate reduction to ammonia (NRA) is a promising approach to remove environmental pollutants while producing green NH3 under ambient conditions. Ag-based nanomaterials have been used in NRA but their iron series elements (Fe, Co, Ni) doping has not been explored yet. Herein, an effective and versatile doping strategy of Ag nanocrystals by iron series elements for efficient NRA is presented. Experimental results show that doping with Fe, Co or Ni can improve the NRA activity. Among the catalysts, AgCo delivers the best performance with a Faraday efficiency (FE) of 88.3 % and ammonia selectivity of 97.4 % at-0.23 V vs RHE, which is 1.9 and 6.2 times higher than that of plain Ag (46.4 % FE and 15.8 % selectivity), respectively. A highest NO3 - conversion rate of AgCo (91.8 %) is achieved, which maintains 16.4 ppm NO3 --N in 4 hours, meeting the drinking water level (~15 ppm NO3 --N). Moreover, the FE, selectivity, conversion rate of AgCo do not decay after the four consecutive cycles. It is found that Co doping can effectively induce the change of Ag d-band center for optimized NRA. This work reveals doping effects of iron series elements on Ag-based catalysts, and shows potential practical application in NRA.

Temperature differentially regulates estuarine microbial N2O production along a salinity gradient

Nitrous oxide (N2O) is atmospheric trace gas that contributes to climate change and affects stratospheric and ground-level ozone concentrations. Ammonia oxidizers and denitrifiers contribute to N2O emissions in estuarine waters. However, as an important climate factor, how temperature regulates microbial N2O production in estuarine water remains unclear. Here, we have employed stable isotope labeling techniques to demonstrate that the N2O production in estuarine waters exhibited differential thermal response patterns between nearshore and offshore regions. The optimal temperatures (Topt) for N2O production rates (N2OR) were higher at nearshore than offshore sites. 15N-labeled nitrite (15NO2-) experiments revealed that at the nearshore sites dominated by ammonia-oxidizing bacteria (AOB), the thermal tolerance of 15N-N2OR increases with increasing salinity, suggesting that N2O production by AOB-driven nitrifier denitrification may be co-regulated by temperature and salinity. Metatranscriptomic and metagenomic analyses of enriched water samples revealed that the denitrification pathway of AOB is the primary source of N2O, while clade II N2O-reducers dominated N2O consumption. Temperature regulated the expression patterns of nitrite reductase (nirK) and nitrous oxide reductase (nosZ) genes from different sources, thereby influencing N2O emissions in the system. Our findings contribute to understanding the sources of N2O in estuarine waters and their response to global warming.

Simulation of rapid sand filters to understand and design sequential iron and manganese removal using reactive transport modelling

Iron (Fe2+), manganese (Mn2+), and ammonium (NH4+) oxidation processes were studied in three single media and three dual media full-scale rapid sand filters (RSFs) using reactive transport modelling (RTM) in PHREEQC and parameter estimation using PEST. Here, we present the insights gained into the spatial distribution of Fe and Mn mineral coatings in RSFs and its influence on the oxidation sequence and rates. Fe2+ and Mn2+ oxidation predominantly occurred simultaneously in the RSFs, contrary to the expected sequential oxidation based on Gibbs free energy calculations. During backwashing, RSF grains become fully mixed, which initiates heterogeneous Mn2+ oxidation on Mn-coated grains that end up in the top layer. The resulting grains have a mixed Fe/Mn mineral coating, which is limiting heterogeneous Mn2+ oxidation due to the limited Mn mineral surface available. Mixed coatings did not seem to affect Fe2+ oxidation rates, instead oxidation rates were increasing at lower pH. We found that RSFs can be designed to spatially separate Fe2+ and Mn2+ oxidation, which results in optimal conditions for Mn2+ oxidation. The RSF needs to consist of two layers with varying density to inhibit mixing and complete Fe2+ oxidation should occur in the top layer. The developed RTM can be used to estimate the depth at which Fe2+ oxidation is complete, and thus the ideal intersection depth of the two layers. A novel perspective is provided on how mineral coating distribution in single and dual media filters influence removal rates and the sequence of oxidation, which contributes to the design of more efficient groundwater filters.

Organic fertilizer significantly mitigates N2O emissions while increase contributed of comammox Nitrospira in paddy soils

Nitrification is the dominant process for nitrous oxide (N2O) production under aerobic conditions, but the relative contribution of the autotrophic nitrifiers (the ammonia-oxidising archaea (AOA), the ammonia-oxidising bacteria (AOB) and the comammox) to this process is still unclear in some soil types. This is particularly the case in paddy soils under different fertilization regimes. We investigated active nitrifiers and their contribution to nitrification and N2O production in a range of unfertilized and fertilized paddy soils, using 13CO2-DNA based stable isotope probing (SIP) technique combined with a series of specific nitrification inhibitors, including acetylene (C2H2), 3, 4-dimethylpyrazole phosphate (DMPP) and 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO). The soils had a long-term history of fertilizer application, including chemical fertilizer only, a mixture of chemical fertilizers (70 %) and chicken manure (30 %) or a mixture of rice straw and chemical fertilizers. 13CO2-DNA-SIP and Illumina MiSeq sequencing demonstrated that comammox clades A.1 and B were active nitrifiers in all fertilized paddy soils. Inhibitor experiment showed that AOB largely contributed to nitrification activity and N2O emission in all paddy soils, while comammox contribution was more significant than AOA. Fertilization considerably altered nitrifiers' relative contribution to nitrification activity and N2O emissions. Applying organic fertilizers significantly decreased the N2O emissions but increased the contribution of comammox to the process. These findings expand the functional ecological niche of comammox, revealing their nitrification role and N2O production in other ecosystems than oligotrophic habitats.

Wastewater-effluent discharge and incomplete denitrification drive riverine CO2, CH4 and N2O emissions

Rivers are well-known sources of the greenhouse gasses (GHG) carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O). These emissions from rivers can increase because of anthropogenic activities, such as agricultural fertilizer input or the discharge of treated wastewater, as these often contain elevated nutrient concentrations. Yet, the specific effects of wastewater effluent discharge on river GHG emissions remain poorly understood. Here, we studied two lowland rivers which both receive municipal wastewater effluent: river Linge and river Kromme Rijn. Dissolved concentrations and fluxes of CH4, N2O and CO2 were measured upstream, downstream and at discharge locations, alongside water column properties and sediment composition. Microbial communities in the sediment and water column were analysed using 16S rRNA gene sequencing. In general, observed GHG emissions from Linge and Kromme Rijn were comparable to eutrophic rivers in urban and agricultural environments. CO2 emissions peaked at most discharge locations, likely resulting from dissolved CO2 present in the effluent. CH4 emission was highest 2 km downstream, suggesting biological production by methanogenic activity stimulated by the effluents' carbon and nutrient supply. Dissolved N2O concentrations were strongly related to NO3- content of the water column which points towards incomplete riverine denitrification. Notably, methanogenic archaea were more abundant downstream of effluent discharge locations. However, overall microbial community composition remained relatively unaffected in both rivers. In conclusion, we demonstrate a clear link between wastewater effluent discharge and enhanced downstream GHG emission of two rivers. Mitigating the impact of wastewater effluent on receiving rivers will be crucial to reduce riverine GHG contributions.

Low-abundant but highly transcriptionally active uncharacterised Nitrosomonas drive ammonia-oxidation in the Brouage mudflat, France

Exploring differences in nitrification within adjacent sedimentary structures of ridges and runnels on the Brouage mudflat, France, we quantified Potential Nitrification Rates (PNR) alongside amoA genes and transcripts. PNR was lower in ridges (≈1.7 fold-lower) than runnels, despite higher (≈1.8 fold-higher) ammonia-oxidizing bacteria (AOB) abundance. However, AOB were more transcriptionally active in runnels (≈1.9 fold-higher). Sequencing of amoA genes and transcripts revealed starkly contrasting profiles with transcripts from ridges and runnels dominated (≈91 % in ridges and ≈98 % in runnels) by low abundant (≈4.6 % of the DNA community in runnels and ≈0.8 % in ridges) but highly active phylotypes. The higher PNR in runnels was explained by higher abundance of this group, an uncharacterised Nitrosomonas sp. cluster. This cluster is phylogenetically similar to other active ammonia-oxidizers with worldwide distribution in coastal environments indicating its potential, but previously overlooked, contribution to ammonia oxidation globally. In contrast DNA profiles were dominated by highly abundant but low-activity clusters phylogenetically distinct from known Nitrosomonas (Nm) and Nitrosospira (Ns). This cluster is also globally distributed in coastal sediments, primarily detected as DNA, and often classified as Nitrosospira or Nitrosomonas. We therefore propose to classify this cluster as Ns/Nm. Our work indicates that low abundant but highly active AOB could be responsible for the nitrification globally, while the abundant AOB Ns/Nm may not be transcriptionally active, and as such account for the lack of correlation between rate processes and gene abundances often reported in the literature. It also raises the question as to what this seemingly inactive group is doing?

Comprehensive evaluation of primer pairs targeting the ammonia monooxygenase subunit A gene of complete ammonia-oxidizing Nitrospira

Since the discovery of complete ammonia oxidizers (comammox) within the genus Nitrospira, their distribution and abundance across habitats have been intensively studied to better understand their ecological significance. Many primers targeting their ammonia monooxygenase subunit A gene (amoA) have been designed to detect and quantify comammox bacteria and to describe their community structure. We identified 38 published primers, but only few had high coverage and specificity for all known comammox Nitrospira or one of the two described subclades. For each target group, we comprehensively evaluated selected primer pairs using in silico analyses, endpoint PCRs, qPCRs, and amplicon sequencing on samples from various environments. Endpoint PCRs and qPCRs showed that the most commonly used primer pairs (comaA-244F/659R, comaB-244F/659R, and Ntsp-amoA162F/359R) produced several bands, which likely inflated quantifications via qPCR. In contrast, the recently published primer combinations CA377F/C576R, CB377F/C576R, and CA-CB377F/C576R resulted mostly in a single band. Furthermore, amplicon sequencing demonstrated that these primer combinations also captured the highest richness of comammox Nitrospira. Taken together, our results indicate that few existing comammox amoA primer combinations have both high specificity and coverage and that the choice of these high-specificity and high-coverage primer pairs substantially impacts the accurate detection, quantification, and community description of comammox bacteria. We, therefore, recommend using the CA377F/C576R, CB377F/C576R, and CA-CB377F/C576R primer pairs.IMPORTANCEBacteria that can fully convert ammonia via nitrite to nitrate, the complete ammonia oxidizers (comammox), were recently discovered and are found in many natural and engineered environments. PCR-based tools to study their abundance and diversity were rapidly developed, resulting in a plethora of primers available, many of which are widely used. The presence of comammox bacteria in an environment can, however, only be correctly determined if the used primers detect all members of this group while not detecting any other guilds. This study assesses the coverage and specificity of existing primers targeting comammox bacteria using both computational and standard molecular techniques, revealing large differences in their performance. The uniform usage of well-performing primers across studies could aid in generating comparable and generalizable data to better understand the importance of comammox bacteria in the environment.

Comammox rather than AOB dominated the efficient autotrophic nitrification-denitrification process in an extremely oxygen-limited environment

The discovery of complete ammonia oxidizer (comammox) has challenged the traditional understanding of the two-step nitrification process. However, their functions in the oxygen-limited autotrophic nitrification-denitrification (OLAND) process remain unclear. In this study, OLAND was achieved using comammox-dominated nitrifying bacteria in an extremely oxygen-limited environment with a dissolved oxygen concentrations of 0.05 mg/L. The ammonia removal efficiency exceeded 97 %, and the total nitrogen removal efficiency reached 71 % when sodium bicarbonate was used as the carbon source. The pseudo-first- and second-order models were found to best fit the ammonia removal processes under low and high loads, respectively, suggesting distinct ammonia removal pathways. Full-length 16S rRNA gene sequencing and metagenomic results revealed that comammox-dominated under different oxygen levels, in conjunction with anammox and heterotrophic denitrifiers. The abundance of enzymes involved in energy metabolism indicates the coexistence of anammox and autotrophic nitrification-heterotrophic denitrification pathways. The binning results showed that comammox bacteria engaged in horizontal gene transfer with nitrifiers, anammox bacteria, and denitrifiers to adapt to an obligate environments. Therefore, this study demonstrated that comammox, anammox, and heterotrophic denitrifiers play important roles in the OLAND process and provide a reference for further reducing aeration energy in the autotrophic nitrogen removal process.

Simulation and optimisation of magnetic and experimental study of magnetic field coupling constructed wetland

This study developed a novel constructed wetland (CW) coupled with a magnetic field for treating domestic wastewater, and the magnetic field distribution was solved and optimised by the finite element method. Herein, we investigated the effects of optimising magnetic field optimisation and studied its impact on CW treatment performance and the responses of a microbial community. The optimisation results showed that the average magnetic field strength of the CW unit increases from 3 to 8 mT, and the proportion of areas with magnetic field strength greater than 5 mT also increases from 30% to 74%. The water quality analysis results showed that the removal of chemical oxygen demand (COD) and NH4+-N (p < 0.01) was significantly increased by the magnetic field (average 3 mT), increasing by 12.2% and 8.49%, respectively. Moreover, the removal of COD and NH4+-N (p < 0.01) was more significantly increased by M-VFCW(O) (average 8 mT), increasing by 15.58% and 49.1%, respectively. The magnetic field application shifted significantly the abundance of dominant bacteria in CWs. Relative abundance of dominant bacteria such as Proteobacteria (63.3%), Firmicutes (4.72%) and Actinobacteria (2.11%) that played an important role in organics removal and nitrification and denitrification-related bacteria such as Nitrospirae (1.48%) and Planctomycetes (9.58%) significantly promoted in M-VFCW(O). These results suggest that introducing a magnetic field into CWs may improve organics and nitrogen removal via the biological process, and the optimisation of the magnetic field was significant in enhancing the performance of VFCWs.

Copper pyrazole addition regulates soil mineral nitrogen turnover by mediating microbial traits

The huge amount of urea applied has necessitated best-developed practices to slow down the release of nitrogen (N) fertilizer while minimizing nitrate loss. However, the impact of nitrification inhibitors on mineral-N turnover and the associated microbial mechanisms at different stages remains unknown. A 60-day incubation experiment was conducted with four treatments: no fertilizer (CK), urea (U), urea with copper pyrazole (UC), and urea coated with copper pyrazole (SUC), to evaluate the changes about soil ammonia N (N H 4 + -N) and nitrate N ( NO 3 - -N) levels as well as in soil microbial community throughout the whole incubation period. The results showed that copper pyrazole exhibited significantly higher inhibition rates on urease compared to other metal-pyrazole coordination compounds. The soilN H 4 + -N content peaked on the 10th day and was significantly greater in UC compared to U, while the NO 3 - -N content was significantly greater in U compared to UC on the 60th day. Copper pyrazole mainly decreased the expression of nitrifying (AOB-amoA) and denitrifying (nirK) genes, impacting the soil microbial community. Co-occurrence network suggested that Mycobacterium and Cronobacter sakazakii-driven Cluster 4 community potentially affected the nitrification process in the initial phase, convertingN H 4 + -N to NO 3 - -N. Fusarium-driven Cluster 3 community likely facilitated the denitrification of NO 3 - -N and caused N loss to the atmosphere in the late stage. The application of copper pyrazole may influence the process of nitrification and denitrification by regulating soil microbial traits (module community and functional genes). Our research indicates that the addition of copper pyrazole alters the community function driven by keystone taxa, altering mineral-N turnover and supporting the use of nitrification inhibitors in sustainable agriculture.

"Metagenomics reveal the potential for geosmin and 2-methylisoborneol production across multiple bacterial phyla in recirculating aquaculture systems"

Geosmin and 2-methylisoborneol (MIB) are known to cause taste-and-odour problems in recirculating aquaculture systems (RAS). Both geosmin and MIB are microbial metabolites belonging to terpenoids. Precursors for terpenoids are biosynthesized via the methylerythritol phosphate (MEP) and the mevalonate (MVA) pathways. We carried out a metagenomic analysis of 50 samples from five RAS to investigate terpenoid biosynthesis and metabolic potential for geosmin and MIB production in RAS microbiomes. A total of 1008 metagenome-assembled genomes (MAGs) representing 26 bacterial and three archaeal phyla were recovered. Although most archaea are thought to use the MVA pathway for terpenoid precursor biosynthesis, an Iainarchaeota archaeal MAG is shown to harbour a complete set of genes encoding the MEP pathway but lacking genes associated with the MVA pathway. In this study, a total of 16 MAGs affiliated with five bacterial phyla (Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexota, and Myxococcota) were identified as possessing potential geosmin or MIB synthases. These putative taste and odour producers were diverse, many were taxonomically unidentified at the genus or species level, and their relative abundance differed between the investigated RAS farms. The metagenomic study of the RAS microbiomes revealed a previously unknown phylogenetic diversity of the potential to produce geosmin and MIB.

Oxygen-to-ammonium-nitrogen ratio as an indicator for oxygen supply management in microoxic bioanodic ammonium oxidation

Microbial electrolysis cells (MECs) have been proven effective for oxidizing ammonium (NH4+), where the anode acts as an electron acceptor, reducing the energy input by substituting oxygen (O2). However, O2 has been proved to be essential for achieving high removal rates MECs. Thus, precise control of oxygen supply is crucial for optimizing treatment performance and minimizing energy consumption. Unlike previous studies focusing on dissolved oxygen (DO) levels, this study introduces the O2/NH4+-N ratio as a novel control parameter for balancing oxidation rates and the selectivity of NH4+ oxidation towards dinitrogen gas (N2) under limited oxygen condition. Our results demonstrated that the O2/NH4+-N ratio is a more relevant oxygen supply indicator compared to DO level. Oxygen served as a more favorable electron acceptor than the electrode, increasing NH4+ oxidation rates but also resulting in more oxidized products such as nitrate (NO3-). Additionally, nitrous oxide (N2O) and N2 production were higher with the electrode as the electron acceptor compared to oxygen alone. An O2/NH4+-N ratio of 0.5 was found to be optimal, achieving a balance between product selectivity for N2 (51.4 % ± 4.5 %) and oxidation rates (344.6 ± 14.7 mg-N/L*d), with the columbic efficiency of 30.7 % ± 2.0 %. Microbial community analysis revealed that nitrifiers and denitrifiers were the primary bacteria involved, with oxygen promoting the growth of nitrite-oxidizing bacteria, thus facilitating complete NH4+ oxidation to NO3-. Our study provides new insights and guidelines on the appropriate oxygen dosage, offering strategies into optimizing operational conditions for NH4+ removal using MECs.

Growth of complete ammonia oxidizers on guanidine

Guanidine is a chemically stable nitrogen compound that is excreted in human urine and is widely used in manufacturing of plastics, as a flame retardant and as a component of propellants, and is well known as a protein denaturant in biochemistry1-3. Guanidine occurs widely in nature and is used by several microorganisms as a nitrogen source, but microorganisms growing on guanidine as the only substrate have not yet been identified. Here we show that the complete ammonia oxidizer (comammox) Nitrospira inopinata and probably most other comammox microorganisms can grow on guanidine as the sole source of energy, reductant and nitrogen. Proteomics, enzyme kinetics and the crystal structure of a N. inopinata guanidinase homologue demonstrated that it is a bona fide guanidinase. Incubation experiments with comammox-containing agricultural soil and wastewater treatment plant microbiomes suggested that guanidine serves as substrate for nitrification in the environment. The identification of guanidine as a growth substrate for comammox shows an unexpected niche of these globally important nitrifiers and offers opportunities for their isolation.

Emerging biotechnological applications of anaerobic ammonium oxidation

Anaerobic ammonium oxidation (anammox) is an energy-efficient method for nitrogen removal that opens the possibility for energy-neutral wastewater treatment. Research on anammox over the past decade has primarily focused on its implementation in domestic wastewater treatment. However, emerging studies are now expanding its use to novel biotechnological applications and wastewater treatment processes. This review highlights recent advances in the anammox field that aim to overcome conventional bottlenecks, and explores novel and niche-specific applications of the anammox process. Despite the promising results and potential of these advances, challenges persist for their real-world implementation. This underscores the need for a transition from laboratory achievements to practical, scalable solutions for wastewater treatment which mark the next crucial phase in the evolution of anammox research.

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.

A positive contribution to nitrogen removal by a novel NOB in a full-scale duck wastewater treatment system

Nitrite-oxidizing bacteria (NOB) are undesirable in the anaerobic ammonium oxidation (anammox)-driven nitrogen removal technologies in the modern wastewater treatment plants (WWTPs). Diverse strategies have been developed to suppress NOB based on their physiological properties that we have understood. But our knowledge of the diversity and mechanisms employed by NOB for survival in the modern WWTPs remains limited. Here, Three NOB species (NOB01-03) were recovered from the metagenomic datasets of a full-scale WWTP treating duck breeding wastewater. Among them, NOB01 and NOB02 were classified as newly identified lineage VII, tentatively named Candidatus (Ca.) Nitrospira NOB01 and Ca. Nitrospira NOB02. Analyses of genomes and in situ transcriptomes revealed that these two novel NOB were active and showed a high metabolic versatility. The transcriptional activity of Ca. Nitrospira could be detected in all tanks with quite different dissolved oxygen (DO) (0.01-5.01 mg/L), illustrating Ca. Nitrospira can survive in fluctuating DO conditions. The much lower Ca. Nitrospira abundance on the anammox bacteria-enriched sponge carrier likely originated from the intensification substrate (NO2 -) competition from anammox and denitrifying bacteria. In particular, a highlight is that Ca. Nitrospira encoded and treanscribed cyanate hydratase (CynS), amine oxidase, urease (UreC), and copper-containing nitrite reductase (NirK) related to ammonium and NO production, driving NOB to interact with the co-existed AOB and anammox bacteria. Ca. Nitrospira strains NOB01 and NOB02 showed quite different niche preference in the same aerobic tank, which dominanted the NOB communities in activated sludge and biofilm, respectively. In addition to the common rTCA cycle for CO2 fixation, a reductive glycine pathway (RGP) was encoded and transcribed by NOB02 likely for CO2 fixation purpose. Additionally, a 3b group hydrogenase and respiratory nitrate reductase were uniquely encoded and transcribed by NOB02, which likely confer a survival advantage to this strain in the fluctuant activated sludge niche. The discovery of this new genus significantly broadens our understanding of the ecophysiology of NOB. Furthermore, the impressive metabolic versatility of the novel NOB revealed in this study advances our understanding of the survival strategy of NOB and provides valuable insight for suppressing NOB in the anammox-based WWTP.

Nitrogen metabolism network in the biotreatment combination of coking wastewater: Take the OHO process as a case

As steel production increases, large volumes of highly toxic and nitrogen-rich coking wastewater (CWW) are produced, prompting the development of a novel oxic-hydrolytic-oxic (OHO) biological treatment combination designed for highly efficient removal of nitrogen-contained contaminants. However, previous studies have not comprehensively explored the CWW biotreatment from the perspective of nitrogen metabolism functional genes and pathways. Based on the investigation of taking the full-scale OHO biotreatment combination as a case, it was found that the O1 and O2 bioreactors remove nitrogen through the ammonia assimilation accounting for 33.87% of the total nitrogen (TN) removal rate, while the H bioreactor removes nitrogen through the simultaneous nitrification-denitrification accounting for 61.11% of the TN removal rate. The major ammonia assimilation taxa include Thauera, Immundisolibacter and Thiobacillus; the major nitrifying taxa include Nitrospira and Nitrosomonas; and the major denitrifying taxa include Thiobacillus, Lautropia and Mesorhizobium. Additionally, the H bioreactor exhibits the potential to be optimized for simultaneous nitrification-denitrification coupled with anaerobic ammonium oxidation (Anammox). These understandings will guide the optimization of engineering design and operational practices, contributing to more effective and sustainable wastewater treatment strategies.

Response of comammox Nitrospira clades A and B communities to long-term fertilization and rhizosphere effects and their relative contribution to nitrification in a subtropical paddy field of China

The recently discovered complete ammonia oxidation (comammox Nitrospira) containing clade A and clade B has further complemented our understanding of nitrification process. Nevertheless, understanding the community feature of comammox Nitrospira clades A and B and their relative contribution to nitrification in paddy rhizosphere are still in its infancy. In this study, we assessed the community diversity and structure of comammox Nitrospira clades A and B in paddy rhizosphere and bulk soils under thirty years of different fertilization strategies, i.e., non-fertilization control (CK), chemical fertilizers application (NPK), and NPK plus swine manure (NPKM), respectively. NPKM significantly increased the a-diversity (Chao1 and Shannon indices) of comammox Nitrospira clade A and altered the community structure (P < 0.05) but had little effect on clade B. A two-way analysis of variance (ANOVA) showed that the effect of long-term fertilization on soil comammox Nitrospira community and nitrification potential rate (PNR) was much greater than that of rhizosphere. Compared with NPK, soil PNR was greatly increased by 51.0% under the NPKM treatment in the rhizosphere (P < 0.05). Phylogenetic analysis showed that NPKM improved the relative abundances of sub-clade A.2.1 and sub-clade A.3.2 of the comammox clade A community, with an average increase of 212.2 and 210.4% in both rhizosphere and bulk soils relative to the NPK treatment. Soil organic matter, NH4+-N, and pH were significant soil drivers of comammox Nitrospira clades A and B community. Furthermore, linear regression and structural equation modeling clearly showed that comammox Nitrospira clade A a-diversity were significantly associated with soil PNR (P < 0.05). Our results suggest (i) that comammox Nitrospira clade A are sensitive to the organic fertilization; and (ii) that comammox Nitrospira clade A contribute more to nitrification than clade B under the long-term organic fertilized paddy soil.

The evolution of autonomy from two cooperative specialists in fluctuating environments

From microbes to humans, organisms perform numerous tasks for their survival, including food acquisition, migration, and reproduction. A complex biological task can be performed by either an autonomous organism or by cooperation among several specialized organisms. However, it remains unclear how autonomy and cooperation evolutionarily switch. Specifically, it remains unclear whether and how cooperative specialists can repair deleted genes through direct genetic exchange, thereby regaining metabolic autonomy. Here, we address this question by experimentally evolving a mutualistic microbial consortium composed of two specialists that cooperatively degrade naphthalene. We observed that autonomous genotypes capable of performing the entire naphthalene degradation pathway evolved from two cooperative specialists and dominated the community. This evolutionary transition was driven by the horizontal gene transfer (HGT) between the two specialists. However, this evolution was exclusively observed in the fluctuating environment alternately supplied with naphthalene and pyruvate, where mutualism and competition between the two specialists alternated. The naphthalene-supplied environment exerted selective pressure that favors the expansion of autonomous genotypes. The pyruvate-supplied environment promoted the coexistence and cell density of the cooperative specialists, thereby increasing the likelihood of HGT. Using a mathematical model, we quantitatively demonstrate that environmental fluctuations facilitate the evolution of autonomy through HGT when the relative growth rate and carrying capacity of the cooperative specialists allow enhanced coexistence and higher cell density in the competitive environment. Together, our results demonstrate that cooperative specialists can repair deleted genes through a direct genetic exchange under specific conditions, thereby regaining metabolic autonomy.

Optimizing the Lattice Nitrogen Coordination to Break the Performance Limitation of Metal Nitrides for Electrocatalytic Nitrogen Reduction

Metal nitrides (MNs) are attracting enormous attention in the electrocatalytic nitrogen reduction reaction (NRR) because of their rich lattice nitrogen (Nlat) and the unique ability of Nlat vacancies to activate N2. However, continuing controversy exists on whether MNs are catalytically active for NRR or produce NH3 via the reductive decomposition of Nlat without N2 activation in the in situ electrochemical conditions, let alone the rational design of high-performance MN catalysts. Herein, we focus on the common rocksalt-type MN(100) catalysts and establish a quantitative theoretical framework based on the first-principles microkinetic simulations to resolve these puzzles. The results show that the Mars-van Krevelen mechanism is kinetically more favorable to drive the NRR on a majority of MNs, in which Nlat plays a pivotal role in achieving the Volmer process and N2 activation. In terms of stability, activity, and selectivity, we find that MN(100) with moderate formation energy of Nlat vacancy (E vac) can achieve maximum activity and maintain electrochemical stability, while low- or high-E vac ones are either unstable or catalytically less active. Unfortunately, owing to the five-coordinate structural feature of Nlat on rocksalt-type MN(100), this maximum activity is limited to a yield of NH3 of only ∼10-15 mol s-1 cm-2. Intriguingly, we identify a volcano-type activity-regulating role of the local structural features of Nlat and show that the four-coordinate Nlat can exhibit optimal activity and overcome the performance limitation, while less coordinated Nlat fails. This work provides, arguably for the first time, an in-depth theoretical insight into the activity and stability paradox of MNs for NRR and underlines the importance of reaction kinetic assessment in comparison with the prevailing simple thermodynamic analysis.

A difficult coexistence: Resolving the iron-induced nitrification delay in groundwater filters

Rapid sand filters (RSF) are an established and widely applied technology for the removal of dissolved iron (Fe2+) and ammonium (NH4+) among other contaminants in groundwater treatment. Most often, biological NH4+oxidation is spatially delayed and starts only upon complete Fe2+ depletion. However, the mechanism(s) responsible for the inhibition of NH4+oxidation by Fe2+ or its oxidation (by)products remains elusive, hindering further process control and optimization. We used batch assays, lab-scale columns, and full-scale filter characterizations to resolve the individual impact of the main Fe2+ oxidizing mechanisms and the resulting products on biological NH4+ oxidation. modeling of the obtained datasets allowed to quantitatively assess the hydraulic implications of Fe2+ oxidation. Dissolved Fe2+ and the reactive oxygen species formed as byproducts during Fe2+ oxidation had no direct effect on ammonia oxidation. The Fe3+ oxides on the sand grain coating, commonly assumed to be the main cause for inhibited ammonia oxidation, seemed instead to enhance it. modeling allowed to exclude mass transfer limitations induced by accumulation of iron flocs and consequent filter clogging as the cause for delayed ammonia oxidation. We unequivocally identify the inhibition of NH4+oxidizing organisms by the Fe3+ flocs generated during Fe2+ oxidation as the main cause for the commonly observed spatial delay in ammonia oxidation. The addition of Fe3+ flocs inhibited NH4+oxidation both in batch and column tests, and the removal of Fe3+ flocs by backwashing completely re-established the NH4+removal capacity, suggesting that the inhibition is reversible. In conclusion, our findings not only identify the iron form that causes the inhibition, albeit the biological mechanism remains to be identified, but also highlight the ecological importance of iron cycling in nitrifying environments.

Role of comammox bacteria in granular bioreactor for nitrogen removal via partial nitritation/anammox

In this study, two bioprocess models were first constructed with the newly-discovered comammox process described as one-step and two-step nitrification and evaluated against relevant experimental data. The validated models were then applied to reveal the potential effect of comammox bacteria on the granular bioreactor particularly suitable for undertaking partial nitritation/anammox (PN/A) under different operating conditions of bulk dissolved oxygen (DO) and influent NH4+. The results showed although comammox bacteria-based PN/A could achieve > 80.0 % total nitrogen (TN) removal over a relatively wider range of bulk DO and influent NH4+ (i.e., 0.25-0.40 g-O2/m3 and 470-870 g-N/m3, respectively) without significant nitrous oxide (N2O) production (< 0.1 %), the bulk DO should be finely controlled based on the influent NH4+ to avoid the undesired full nitrification by comammox bacteria. Comparatively, conventional ammonium-oxidizing bacteria (AOB)-based PN/A not only required higher bulk DO to achieve > 80.0 % TN removal but also suffered from 1.7 %∼2.8 % N2O production.