Enrichment, Isolation, and Characterization of High-Affinity N2O-Reducing Bacteria in a Gas-Permeable Membrane Reactor

Benthic clade II-type nitrous oxide reducers suppress nitrous oxide emissions in shallow lakes

Shallow lakes, recognized as hotspots for nitrogen cycling, contribute to the emission of the potent greenhouse gas nitrous oxide (N2O), but the current emission estimates for this gas have a high degree of uncertainty. However, the role of N2O-reducing bacteria (N2ORB) as N2O sinks and their contribution to N2O reduction in aquatic ecosystems in response to N2O dynamics have not been determined. Here, we investigated the N2O dynamics and microbial processes in the nitrogen cycle, which included both N2O production and consumption, in five shallow lakes spanning approximately 500 km. The investigated sites exhibited N2O oversaturation, with excess dissolved N2O concentrations (ΔN2O) ranging from 0.55 ± 0.61 to 53.17 ± 15.75 nM. Sediment-bound N2O (sN2O) was significantly positively correlated with the nitrate concentration in the overlying water (p < 0.05), suggesting that nitrate accumulation contributes to benthic N2O generation. High N2O consumption activity (RN2O) corresponded to low ΔN2O. In addition, a significant negative correlation was found between RN2O and nir/nosZ, showing that bacteria encoding nosZ contributed to N2O consumption in the benthic sediments. Redundancy analysis indicated that benthic functional genes effectively reflected the variations in RN2O and ∆N2O. qPCR analysis revealed that the clade II nosZ gene was more sensitive to ΔN2O than the clade I nosZ gene. Furthermore, four novel genera of potential nondenitrifying N2ORB were identified based on metagenome-assembled genome analysis. These genera, which are affiliated with clade II, lack genes responsible for N2O production. Collectively, benthic N2ORB, especially for clade II-type N2ORB, harnesses N2O consumption activity leading to low N2O emissions from shallow lakes. This study advances our knowledge of the role of benthic clade II-type N2ORB in regulating N2O emissions in shallow lakes.

Unlocking bacterial potential to reduce farmland N2O emissions

Farmed soils contribute substantially to global warming by emitting N2O (ref. 1), and mitigation has proved difficult2. Several microbial nitrogen transformations produce N2O, but the only biological sink for N2O is the enzyme NosZ, catalysing the reduction of N2O to N2 (ref. 3). Although strengthening the NosZ activity in soils would reduce N2O emissions, such bioengineering of the soil microbiota is considered challenging4,5. However, we have developed a technology to achieve this, using organic waste as a substrate and vector for N2O-respiring bacteria selected for their capacity to thrive in soil6-8. Here we have analysed the biokinetics of N2O reduction by our most promising N2O-respiring bacterium, Cloacibacterium sp. CB-01, its survival in soil and its effect on N2O emissions in field experiments. Fertilization with waste from biogas production, in which CB-01 had grown aerobically to about 6 × 109 cells per millilitre, reduced N2O emissions by 50-95%, depending on soil type. The strong and long-lasting effect of CB-01 is ascribed to its tenacity in soil, rather than its biokinetic parameters, which were inferior to those of other strains of N2O-respiring bacteria. Scaling our data up to the European level, we find that national anthropogenic N2O emissions could be reduced by 5-20%, and more if including other organic wastes. This opens an avenue for cost-effective reduction of N2O emissions for which other mitigation options are lacking at present.

Looking deeper into the effects of scouring and aeration on membrane aerated biofilms: Analysis of nitrogen conversion, oxygen profiles and nitrous oxide emissions

This study investigated the effects of aeration and scouring strategies on the performance of Membrane Aerated Biofilm Reactors (MABRs) and the distribution of oxygen and nitrous oxide in the biofilm. Four flat sheet MABRs were operated with synthetic feed under different conditions: two with intermittent aeration (iMABR) and two with continuous aeration (cMABR). Scouring was induced by bubbling dinitrogen gas through the reactor bulk at low and high frequencies (LF and HF). In the iMABRs, a partial nitritation biofilm initially developed, but the biofilm adapted to the aeration strategy over time and became nitrifying. The cMABRs directly developed a nitrifying biofilm without a significant phase of partial nitritation. Limiting oxygen availability improved the overall performance with regards to total nitrogen (TN) removal by providing a better environment for anaerobic ammonium oxidation (Anammox) while limiting complete nitrification. Oxygen profiles were measured in the iMABR over time at different biofilms depths, showing that intermittent aeration led to various oxygen concentrations and temporal variations in the oxygen availabilities at different depths of the biofilm. Also, N2O emissions from the MABRs differed greatly between the different systems, but still remained lower compared to other reactor configurations for nitrogen removal, making the MABR technology a worthy alternative. The results showed large differences between the operating strategies of the MABRs and can help to gain more insight into the specific properties of MABRs for nitrogen removal.

China's anthropogenic N2O emissions with analysis of economic costs and social benefits from reductions in 2022

We assess China's overall anthropogenic N2O emissions via the official guidebook published by Chinese government. Results show that China's overall anthropogenic N2O emissions in 2022 were around 1593.1 (1508.7-1680.7) GgN, about 47.0 %, 27.0 %, 13.4 %, 4.9 %, and 7.7 % of which were caused by agriculture, industry, energy utilization, wastewater, and indirect sources, respectively. Maximum reduction rate for N2O emissions from agriculture, industry, energy utilization, wastewater, and indirect sources can achieve 69 %, 99 %, 79 %, 86 %, and 48 %, respectively, in 2022. However, given current global scenarios with a rapidly changing population and geopolitical and energy tension, the emission reduction may not be fully fulfilled. Without compromising yields, China's theoretical minimum anthropogenic N2O emissions would be 600.6 (568.8-633.6) GgN. In terms of the economic costs for reducing one kg of N2O-N emissions, the price ranged from €12.9 to €81.1 for agriculture, from €0.08 to €0.16 for industry, and from €104.8 to €1571.5 for energy utilization. We acknowledge the emission reduction rates may not be completely realistic for large-scale application in China. The social benefits gained from reducing one kg of N2O-N emissions in China was about €5.2, indicating anthropogenic N2O emissions caused a loss 0.03 % of China's GDP, but only justifying reduction in industrial N2O emissions from the economic perspective. We perceive that the present monetized values will be trustworthy for at least three to five years, but later the numerical monetized values need to be considered in inflation and other currency-dependent conditions.

Dual Regulatory Role of Penicillium oxalicum SL2 in Soil: Phosphorus Solubilization and Pb Stabilization

The mechanisms of the P. oxalicum SL2-mediated microbial community on phosphorus solubilization and Pb stabilization were investigated through a 90-day soil experiment. In the treatments inoculated with P. oxalicum SL2, the amount of P. oxalicum SL2-GFP remained at 77.8%-138.6% of the initial inoculation amount after 90 days, and the available phosphorus (AP) content increased 21.7%-40.8% while EDTA-Pb decreased 29.9%-43.2% compared with CK treatment. SEM-EDS results showed that P. oxalicum SL2 changed the agglomeration degree of microaggregates and promoted the combination of Pb with C and O elements. These phenomena were enhanced when applied with Ca3(PO4)2. Microbial community analysis showed that P. oxalicum SL2 improved soil microbial activity, in which the fungi absolute abundance increased about 15 times within 90 days. Correlation analyses and a partial least-squares path model showed that the activation of Penicillium, Ascobolus, Humicola, and Spizellomyces in a fungal community increased the content of oxalate and AP, which directly decreased EDTA-Pb content, while the change of Bacillus, Ramlibacter, Gemmatimonas, and Candidatus Solibacter in the bacterial community regulated Fe/Mn/S/N cycle-related functions, thus promoting the conversion of Pb to oxidizable state. Our findings highlight that P. oxalicum SL2 enhanced the microbial-induced phosphate precipitation process by activating soil microbial communities and regulating their ecological functions.

Quest for Nitrous Oxide-reducing Bacteria Present in an Anammox Biofilm Fed with Nitrous Oxide

N2O-reducing bacteria have been examined and harnessed to develop technologies that reduce the emission of N2O, a greenhouse gas produced by biological nitrogen removal. Recent investigations using omics and physiological activity approaches have revealed the ecophysiologies of these bacteria during nitrogen removal. Nevertheless, their involvement in‍ ‍anammox processes remain unclear. Therefore, the present study investigated the identity, genetic potential, and activity‍ ‍of N2O reducers in an anammox reactor. We hypothesized that N2O is limiting for N2O-reducing bacteria‍ ‍and an‍ ‍exogeneous N2O supply enriches as-yet-uncultured N2O-reducing bacteria. We conducted a 1200-day incubation of N2O-reducing bacteria in an anammox consortium using gas-permeable membrane biofilm reactors (MBfRs), which efficiently supply N2O in a bubbleless form directly to a biofilm grown on a gas-permeable membrane. A 15N tracer test indicated that the supply of N2O resulted in an enriched biomass with a higher N2O sink potential. Quantitative PCR and 16S rRNA amplicon sequencing revealed Clade II nosZ type-carrying N2O-reducing bacteria as protagonists of N2O sinks. Shotgun metagenomics showed the genetic potentials of the predominant Clade II nosZ-carrying bacteria, Anaerolineae and Ignavibacteria in MBfRs. Gemmatimonadota and non-anammox Planctomycetota increased their abundance in MBfRs despite their overall lower abundance. The implication of N2O as an inhibitory compound scavenging vitamin B12, which is essential for the synthesis of methionine, suggested its limited suppressive effect on the growth of B12-dependent bacteria, including N2O reducers. We identified Dehalococcoidia and Clostridia as predominant N2O sinks in an anammox consortium fed exogenous N2O because of the higher metabolic potential of vitamin B12-dependent biosynthesis.

Using adaptive and aggressive N2O-reducing bacteria to augment digestate fertilizer for mitigating N2O emissions from agricultural soils

Nitrous oxide (N2O) emitted from agricultural soils destroys stratospheric ozone and contributes to global warming. A promising approach to reduce emissions is fertilizing the soil using organic wastes augmented by non-denitrifying N2O-reducing bacteria (NNRB). To realize this potential, we need a suite of NNRB strains that fulfill several criteria: efficient reduction of N2O, ability to grow in organic waste, and ability to survive in farmland soil. In this study, we enriched such organisms by sequential anaerobic batch incubations with N2O and reciprocating inoculation between the sterilized substrates of anaerobic manure digestate and soils. 16S rDNA amplicon sequencing and metagenomics analysis showed that a cluster of bacteria containing nosZ genes encoding N2O-reductase, was enriched during the incubation process. Strains of several dominant members were then isolated and characterized, and three of them were found to harbor the nosZ gene but none of the other denitrifying genes, thus qualifying as NNRB. The selected isolates were tested for their capacities to reduce N2O emissions from three different typical Chinese farmland soils. The results indicated the significant mitigation effect of these isolates, even in very acidic red soil. In conclusion, this study demonstrated a strategy to engineer the soil microbiome with promising NNRB with high adaptability to livestock manure digestate as well as different agricultural soils, which would be suitable for developing novel fertilizer for farmland application to efficiently mitigate the N2O emissions from agricultural soils.

Enrichment and characterization of a nitric oxide-reducing microbial community in a continuous bioreactor

Nitric oxide (NO) is a highly reactive and climate-active molecule and a key intermediate in the microbial nitrogen cycle. Despite its role in the evolution of denitrification and aerobic respiration, high redox potential and capacity to sustain microbial growth, our understanding of NO-reducing microorganisms remains limited due to the absence of NO-reducing microbial cultures obtained directly from the environment using NO as a substrate. Here, using a continuous bioreactor and a constant supply of NO as the sole electron acceptor, we enriched and characterized a microbial community dominated by two previously unknown microorganisms that grow at nanomolar NO concentrations and survive high amounts (>6 µM) of this toxic gas, reducing it to N2 with little to non-detectable production of the greenhouse gas nitrous oxide. These results provide insight into the physiology of NO-reducing microorganisms, which have pivotal roles in the control of climate-active gases, waste removal, and evolution of nitrate and oxygen respiration.

High nitrous oxide (N2O) greenhouse gas reduction potential of Pseudomonas sp. YR02 under aerobic condition

Aerobic environments exist widely in wastewater treatment plants (WWTP) and are unfavorable for greenhouse gas nitrous oxide (N₂O) reduction. Here, a novel strain Pseudomonas sp. YR02, which can perform N₂O reduction under aerobic conditions, was isolated. The successful amplification of four denitrifying genes proved its complete denitrifying ability. The inorganic nitrogen (IN) removal efficiencies (NRE) were >98.0% and intracellular nitrogen and gaseous nitrogen account for 52.6-58.4% and 41.6-47.4% of input nitrogen, respectively. The priority of IN utilization was TAN > NO₃^--N > NO₂^--N. The optimal conditions for IN and N₂O removal were consistent, except for the C/N ratio, which is 15 and 5 for IN and N₂O removal, respectively. The biokinetic constants analysis indicated strain YR02 had high potential to treat high ammonia and dissolved N₂O wastewater. Strain YR02 bioaugmentation mitigated 98.7% of N₂O emission and improved 32% NRE in WWTP, proving its application potential for N₂O mitigation.

Clarifying Microbial Nitrous Oxide Reduction under Aerobic Conditions: Tolerant, Intolerant, and Sensitive

One of the major challenges for the bioremediation application of microbial nitrous oxide (N2O) reduction is its oxygen sensitivity. While a few strains were reported capable of reducing N2O under aerobic conditions, the N2O reduction kinetics of phylogenetically diverse N2O reducers are not well understood. Here, we analyzed and compared the kinetics of clade I and clade II N2O-reducing bacteria in the presence or absence of oxygen (O2) by using a whole-cell assay with N2O and O2 microsensors. Among the seven strains tested, N2O reduction of Stutzerimonas stutzeri TR2 and ZoBell was not inhibited by oxygen (i.e., oxygen tolerant). Paracoccus denitrificans, Azospirillum brasilense, and Gemmatimonas aurantiaca reduced N2O in the presence of O2 but slower than in the absence of O2 (i.e., oxygen sensitive). N2O reduction of Pseudomonas aeruginosa and Dechloromonas aromatica did not occur when O2 was present (i.e., oxygen intolerant). Amino acid sequences and predicted structures of NosZ were highly similar among these strains, whereas oxygen-tolerant N2O reducers had higher oxygen consumption rates. The results suggest that the mechanism of O2 tolerance is not directly related to NosZ structure but is rather related to the scavenging of O2 in the cells and/or accessory proteins encoded by the nos cluster. IMPORTANCE Some bacteria can reduce N2O in the presence of O2, whereas others cannot. It is unclear whether this trait of aerobic N2O reduction is related to the phylogeny and structure of N2O reductase. The understanding of aerobic N2O reduction is critical for guiding emission control, due to the common concurrence of N2O and O2 in natural and engineered systems. This study provided the N2O reduction kinetics of various bacteria under aerobic and anaerobic conditions and classified the bacteria into oxygen-tolerant, -sensitive, and -intolerant N2O reducers. Oxygen-tolerant N2O reducers rapidly consumed O2, which could help maintain the low O2 concentration in the cells and keep their N2O reductase active. These findings are important and useful when selecting N2O reducers for bioremediation applications.

Biotrickling Filtration for the Reduction of N2O Emitted during Wastewater Treatment: Results from a Long-Term In Situ Pilot-Scale Testing

Wastewater treatment plants (WWTPs) are a major source of N₂O, a potent greenhouse gas with 300 times higher global warming potential than CO₂. Several approaches have been proposed for mitigation of N₂O emissions from WWTPs and have shown promising yet only site-specific results. Here, self-sustaining biotrickling filtration, an end-of-the-pipe treatment technology, was tested in situ at a full-scale WWTP under realistic operational conditions. Temporally varying untreated wastewater was used as trickling medium, and no temperature control was applied. The off-gas from the covered WWTP aerated section was conveyed through the pilot-scale reactor, and an average removal efficiency of 57.9 ± 29.1% was achieved during 165 days of operation despite the generally low and largely fluctuating influent N₂O concentrations (ranging between 4.8 and 96.4 ppmv). For the following 60-day period, the continuously operated reactor system removed 43.0 ± 21.2% of the periodically augmented N₂O, exhibiting elimination capacities as high as 5.25 g N₂O m^-3·h^-1. Additionally, the bench-scale experiments performed abreast corroborated the resilience of the system to short-term N₂O starvations. Our results corroborate the feasibility of biotrickling filtration for mitigating N₂O emitted from WWTPs and demonstrate its robustness toward suboptimal field operating conditions and N₂O starvation, as also supported by analyses of the microbial compositions and nosZ gene profiles.

Consumption of N2O by Flavobacterium azooxidireducens sp. nov. Isolated from Decomposing Leaf Litter of Phragmites australis (Cav.)

Microorganisms acting as sinks for the greenhouse gas nitrous oxide (N₂O) are gaining increasing attention in the development of strategies to control N₂O emissions. Non-denitrifying N₂O reducers are of particular interest because they can provide a real sink without contributing to N₂O release. The bacterial strain under investigation (IGB 4-14^T), isolated in a mesocosm experiment to study the litter decomposition of Phragmites australis (Cav.), is such an organism. It carries only a nos gene cluster with the sec-dependent Clade II nosZ and is able to consume significant amounts of N₂O under anoxic conditions. However, consumption activity is considerably affected by the O₂ level. The reduction of N₂O was not associated with cell growth, suggesting that no energy is conserved by anaerobic respiration. Therefore, the N₂O consumption of strain IGB 4-14^T rather serves as an electron sink for metabolism to sustain viability during transient anoxia and/or to detoxify high N₂O concentrations. Phylogenetic analysis of 16S rRNA gene similarity revealed that the strain belongs to the genus Flavobacterium. It shares a high similarity in the nos gene cluster composition and the amino acid similarity of the nosZ gene with various type strains of the genus. However, phylogenomic analysis and comparison of overall genome relatedness indices clearly demonstrated a novel species status of strain IGB 4-14^T, with Flavobacterium lacus being the most closely related species. Various phenotypic differences supported a demarcation from this species. Based on these results, we proposed a novel species Flavobacterium azooxidireducens sp. nov. (type strain IGB 4-14^T = LMG 29709^T = DSM 103580^T).

Effect of nitrous oxide (N2O) on the structure and function of nitrogen-oxide reducing microbial communities

Nitrous oxide (N₂O) is a potent greenhouse gas that can be produced by nitrifying and denitrifying bacteria. Yet the effects of N₂O on microbial communities is not well understood. We used batch tests to explore the effects of N₂O on mixed denitrifying communities. Batch tests were carried out with acetate as the electron donor and with the following electron acceptors: nitrate (NO₃^-), nitrite (NO₂^-), N₂O, NO₃^- + N₂O, and NO₂^- + N₂O. Activated sludge from a municipal wastewater treatment plant was used as the inoculum. The bacteria grew readily with N₂O as the sole acceptor. When N₂O was provided along with NO₃^- or NO₂^-, it was used concurrently and resulted in higher growth rates than the same acceptors without added N₂O. The microbial communities resulting from N₂O addition were significantly different at the genus level from those with just NO₃^- or NO₂^-. Tests with N₂O as the sole added acceptor revealed a reduced diversity. Analysis of inferred gene content using PICRUSt2 indicated a greater abundance of genera with a complete denitrification pathway when growing on N₂O or NO₂^-, relative to all other tests. This suggests that specific N₂O reduction rates are high, and that N₂O alone selects for a low-diversity, fully denitrifying community. When N₂O is present with NO₂^- or NO₃^-, the microbial communities were more diverse and did not select exclusively for full denitrifiers. N₂O alone appears to select for a "generalist" community with full denitrification pathways and lower diversity. In terms of denitrification genes, the combination of acceptors with N₂O appeared to increase the number of microbes carrying nirK, while fully denitrifying bacteria appear more likely to carry nirS. Lastly, all the taxa in NO₂^- and N₂O samples were predicted to harbor nosZ. This suggests the potential for reduced N₂O emissions in denitrifying systems.

Exploring the Functions of Efficient Canonical Denitrifying Bacteria as N2O Sinks: Implications from 15N Tracer and Transcriptome Analyses

In denitrifying reactors, canonical complete denitrifying bacteria reduce nitrate (NO₃^-) to nitrogen via N₂O. However, they can also produce N₂O under certain conditions. We used a ¹⁵N tracer method, in which ¹⁵N-labeled NO₃^-/nitrite (NO₂^-) and nonlabeled N₂O were simultaneously supplied with organic electron donors to five canonical complete denitrifying bacteria affiliated with either Clade I or Clade II nosZ. We calculated their NO₃^-, NO₂^-, and N₂O consumption rates. The Clade II nosZ bacterium Azospira sp. strain I13 had the highest N₂O consumption rate (3.47 ± 0.07 fmol/cell/h) and the second lowest NO₃^- consumption rate (0.20 ± 0.03 fmol/cell/h); hence, it is a N₂O sink. A change from peptone- to acetate/citrate-based organic electron donors increased the NO₃^- consumption rate by 4.8 fold but barely affected the N₂O consumption rate. Electron flow was directed to N₂O rather than NO₃^- in Azospira sp. strain I13 and Az. oryzae strain PS only exerting a N₂O sink but to NO₃^- in the Clade I nosZ N₂O-reducing bacteria Pseudomonas stutzeri strain JCM 5965 and Alicycliphilus denitrificans strain I51. Transcriptome analyses revealed that the genotype could not fully describe the phenotype. The results show that N₂O production and consumption differ among canonical denitrifying bacteria and will be useful for developing N₂O mitigation strategies.

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

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

Identification of nosZ-expressing microorganisms consuming trace N2O in microaerobic chemostat consortia dominated by an uncultured Burkholderiales

Microorganisms possessing N₂O reductases (NosZ) are the only known environmental sink of N₂O. While oxygen inhibition of NosZ activity is widely known, environments where N₂O reduction occurs are often not devoid of O₂. However, little is known regarding N₂O reduction in microoxic systems. Here, 1.6-L chemostat cultures inoculated with activated sludge samples were sustained for ca. 100 days with low concentration (<2 ppmv) and feed rate (<1.44 µmoles h⁻¹) of N₂O, and the resulting microbial consortia were analyzed via quantitative PCR (qPCR) and metagenomic/metatranscriptomic analyses. Unintended but quantified intrusion of O₂ sustained dissolved oxygen concentration above 4 µM; however, complete N₂O reduction of influent N₂O persisted throughout incubation. Metagenomic investigations indicated that the microbiomes were dominated by an uncultured taxon affiliated to Burkholderiales, and, along with the qPCR results, suggested coexistence of clade I and II N₂O reducers. Contrastingly, metatranscriptomic nosZ pools were dominated by the Dechloromonas-like nosZ subclade, suggesting the importance of the microorganisms possessing this nosZ subclade in reduction of trace N₂O. Further, co-expression of nosZ and ccoNO/cydAB genes found in the metagenome-assembled genomes representing these putative N₂O-reducers implies a survival strategy to maximize utilization of scarcely available electron acceptors in microoxic environmental niches.

Variable Inhibition of Nitrous Oxide Reduction in Denitrifying Bacteria by Different Forms of Methanobactin

Aerobic methanotrophic activity is highly dependent on copper availability, and methanotrophs have developed multiple strategies to collect copper. Specifically, when copper is limiting (ambient concentrations less than 1 μM), some methanotrophs produce and secret a small modified peptide (less than 1,300 Da) termed methanobactin (MB) that binds copper with high affinity. As MB is secreted into the environment, other microbes that require copper for their metabolism may be inhibited as MB may make copper unavailable; e.g., inhibition of denitrifiers as complete conversion nitrate to dinitrogen involves multiple enzymes, some of which are copper-dependent. Of key concern is inhibition of the copper-dependent nitrous oxide reductase (NosZ), the only known enzyme capable of converting nitrous oxide (N₂O) to dinitrogen. Herein, we show that different forms of MB differentially affect copper uptake and N₂O reduction by Pseudomonas stutzeri strain DCP-Ps1 (that expresses clade I NosZ) and Dechloromonas aromatica strain RCB (that expresses clade II NosZ). Specifically, in the presence of MB from Methylocystis sp. strain SB2 (SB2-MB), copper uptake and nosZ expression were more significantly reduced than in the presence of MB from Methylosinus trichosporium OB3b (OB3b-MB). Further, N₂O accumulation increased more significantly for both P. stutzeri strain DCP-Ps1 and D. aromatica strain RCB in the presence of SB2-MB versus OB3b-MB. These data illustrate that copper competition between methanotrophs and denitrifying bacteria can be significant and that the extent of such competition is dependent on the form of MB that methanotrophs produce. IMPORTANCE Herein, it was demonstrated that the different forms of methanobactin differentially enhance N₂O emissions from Pseudomonas stutzeri strain DCP-Ps1 (harboring clade I nitrous oxide reductase) and Dechloromonas aromatica strain RCB (harboring clade II nitrous oxide reductase). This work contributes to our understanding of how aerobic methanotrophs compete with denitrifiers for the copper uptake and also suggests how MBs prevent copper collection by denitrifiers, thus downregulating expression of nitrous oxide reductase. This study provides critical information for enhanced understanding of microbe-microbe interactions that are important for the development of better predictive models of net greenhouse gas emissions (i.e., methane and nitrous oxide) that are significantly controlled by microbial activity.

Organic carbon determines nitrous oxide consumption activity of clade I and II nosZ bacteria: Genomic and biokinetic insights

Harnessing nitrous oxide (N2O)-reducing bacteria is a promising strategy to reduce the N2O footprint of engineered systems. Applying a preferred organic carbon source as an electron donor accelerates N2O consumption by these bacteria. However, their N2O consumption potential and activity when fed different organic carbon species remain unclear. Here, we systematically compared the effects of various organic carbon sources on the activity of N2O-reducing bacteria via investigation of their biokinetic properties and genomic potentials. Five organic carbon sources-acetate, succinate, glycerol, ethanol, and methanol-were fed to four N2O-reducing bacteria harboring either clade I or clade II nosZ gene. Respirometric analyses were performed with four N2O-reducing bacterial strains, identifying distinct shifts in DO- and N2O-consumption biokinetics in response to the different feeding schemes. Regardless of the N2O-reducing bacteria, higher N2O consumption rates, accompanied by higher biomass yields, were obtained with acetate and succinate. The biomass yield (15.45 ± 1.07 mg-biomass mmol-N2O-1) of Azospira sp. strain I13 (clade II nosZ) observed under acetate-fed condition was significantly higher than those of Paracoccus denitrificans and Pseudomonas stutzeri, exhibiting greater metabolic efficiency. However, the spectrum of the organic carbon species utilizable to Azospira sp. strain I13 was limited, as demonstrated by the highly variable N2O consumption rates observed with different substrates. The potential to metabolize the supplemented carbon sources was investigated by genomic analysis, the results of which corroborated the N2O consumption biokinetics results. Moreover, electron donor selection had a substantial impact on how N2O consumption activities were recovered after oxygen exposure. Collectively, our findings highlight the importance of choosing appropriate electron donor additives for increasing the N2O sink capability of biological nitrogen removal systems.

Nitrogeniibacter mangrovi gen. nov., sp. nov., a novel anaerobic and aerobic denitrifying betaproteobacterium and reclassification of Azoarcus pumilus as Aromatoleum pumilum comb. nov

Denitrification is a vital link in the global bio-nitrogen cycle. Here, we isolated a strain (M9-3-2^T) that is a novel benzo[a]pyrene (BaP)-tolerant, anaerobic and aerobic denitrifying bacterium from a continuous BaP-enrichment cultured mangrove sediment. In silico comparative genomics and taxonomic analysis clearly revealed that strain M9-3-2^T (=MCCC 1K03313^T=JCM 32045^T) represents a novel species of a novel genus named as Nitrogeniibacter mangrovi gen. nov., sp. nov., belonging to family Zoogloeaceae, order Rhodocyclales. In addition, the species Azoarcus pumilus is transferred into genus Aromatoleum and named Aromatoleum pumilum comb. nov. The predominant respiratory quinone of strain M9-3-2^T was ubiquinone-8 and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified phospholipids and three unidentified aminophospholipids. In this study, the capacity of strain M9-3-2^T to eliminate nitrate was detected under anaerobic and aerobic conditions, and the removal rates of nitrate were 6.1×10^-6 µg N/l/h/cell and 3×10^-7 µg N/l/h/cell, respectively. Our results suggested that strain M9-3-2^T could play an important role in the nitrogen removal regardless of the presence of oxygen in natural or/and man-made ecosystems.

Treatment efficiency and greenhouse gas emissions of non-floating and floating bed activated sludge system with acclimatized sludge treating landfill leachate

This research investigates the treatment efficiency and greenhouse gas (GHG) emissions of non-floating and floating bed AS systems with acclimatized sludge treating landfill leachate. The GHGs under study included carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O). The non-floating and floating bed AS systems were operated in parallel with identical landfill leachate influent under different hydraulic retention time (HRT) conditions (24, 18, and 12 h). The experimental results showed that the treatment efficiency of organic compounds under 24 h HRT of both systems (90 - 98%) were insignificantly different, while the nutrient removal efficiency of both systems were between 54 and 98 %. The treatment efficiency of the floating bed AS system, despite shorter HRT, remained relatively unchanged due to an abundance of effective bacteria residing in the floating media. The CO₂ emissions were insignificantly different between both AS systems under all HRT conditions (22 - 26.3 μmol/cm².min). The CO₂ emissions were positively correlated with organic loading but inversely correlated with HRT. The CH₄ emissions were positively correlated with HRT (26.3 μmol/cm².min under 24 h HRT of the floating bed AS system). The N₂O emissions were positively correlated with nitrogen loading, and the N₂O emissions from the floating bed AS system were lower due to an abundance of N₂O-reducing bacteria. The floating media enhanced the biological treatment efficiency while maintaining the bacterial community in the system. However, the floating media promoted CH₄ production under anoxic conditions. The originality of this research lies in the use of floating media in the biological treatment system to mitigate GHG emissions, unlike existing research which focused primarily on enhancement of the treatment efficiency.

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

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

Genome Sequence of the Type Strain Azospira restricta SUA2 (DSM 18626)

Azospira restricta SUA2^T (DSM 18626) is a Gram-negative-staining bacterium able to fix nitrogen and accumulate polyhydroxybutyrate storage granules. Here, we report the complete genome sequence (3,975,213 bp with 68.64 mol% G+C content), which may prove useful in future efforts to assess the role of Azospira in nutrient cycling.

Azospira restricta SUA2^T (DSM 18626) is a Gram-negative-staining bacterium able to fix nitrogen and accumulate polyhydroxybutyrate storage granules. Here, we report the complete genome sequence (3,975,213 bp with 68.64 mol% G+C content), which may prove useful in future efforts to assess the role of Azospira in nutrient cycling.

Learning from microorganisms: using new insights in microbial physiology for sustainable nitrogen management

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To reduce nitrate to N₂ distinct nitrogen-oxide-reducing microorganisms function together.

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Detecting nirS, nirK or narG genes cannot be directly linked to NO and N₂O emission.

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Nitrogen-oxide-reducing specialists can be exploited to reduce NO and N₂O emission from wwtp.

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Aerobic methanotrophs and methane stripping must be considered for the application of N-DAMO.

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Ammonium recovery could be a more sustainable alternative to nitrogen removal.

Diverse nitrogen-transforming microorganisms with a wide variety of physiological properties are employed for biological nitrogen removal from wastewater. There are many technologies that achieve the required nitrogen discharge standards; however, greenhouse gas emissions and energy consumption constitute the bulk of the environmental footprint of wastewater treatment plants. In this review, we highlight current and proposed approaches aiming to achieve more energy-efficient and environment-friendly biological nitrogen removal, discuss whether new discoveries in microbial physiology of nitrogen-transforming microorganisms could be used to reduce greenhouse gas emissions, and summarize recent advances in ammonium recovery from wastewater.

Remediation of nitrate contamination by membrane hydrogenotrophic denitrifying biofilm integrated in microbial electrolysis cell

Complete biological denitrification is usually restricted in electron donor lacking waters. Hydrogenotrophic denitrification attracts attention for its clean and cost-efficiency advantages. Therein, the hydrogen could be effectively generated by microbial electrolysis cells (MECs) from organic wastes. In this study, a gas diffusion membrane (GDM) integrated MEC (MMEC) was constructed and provided a novel non-polluting approach for nitrate contaminated water remediation, in which the hydrogen was recovered from substrate degradation in anode and diffused across GDM as electron donor for denitrification. The high overall nitrogen removal of 91 ± 0.1%-95 ± 1.9% and 90 ± 1.6%-94 ± 2.2% were respectively achieved in Ti-MMEC and SS-MMEC with titanium and stainless-steel mesh as cathode at all applied voltages (0.4-0.8 V). Decreasing applied voltage from 0.8 to 0.4 V significantly improved the electron utilization efficiency for denitrification from 26 ± 3.6% to 73 ± 0.1% in Ti-MMEC. Integrating MEC with GDM greatly improved TN removal by 40% under applied voltage of 0.8 V. The hydrogenotrophic denitrifiers of Rhodocyclaceae, Paracoccus, and Dethiobacter, dominated in MMECs facilitating TN removal. Functional denitrification related genes including napAB, nirKS, norBC and nosZ predicted by PICRUSt2 based on 16S rRNA gene data demonstrated higher abundance in MMECs.

Temperature and oxygen level determine N2 O respiration activities of heterotrophic N2 O-reducing bacteria: Biokinetic study

Nitrous oxide (N₂ O), a potent greenhouse gas, is reduced to N₂ gas by N₂ O-reducing bacteria (N₂ ORB), a process which represents an N₂ O sink in natural and engineered ecosystems. The N₂ O sink activity by N₂ ORB depends on temperature and O₂ exposure, yet the specifics are not yet understood. This study explores the effects of temperature and oxygen exposure on biokinetics of pure culture N₂ ORB. Four N₂ ORB, representing either clade I type nosZ (Pseudomonas stutzeri JCM5965 and Paracoccus denitrificans NBRC102528) or clade II type nosZ (Azospira sp. strains I09 and I13), were individually tested. The higher activation energy for N₂ O by Azospira sp. strain I13 (114.0 ± 22.6 kJ mol^-1 ) compared with the other tested N₂ ORB (38.3-60.1 kJ mol^-1 ) indicates that N₂ ORB can adapt to different temperatures. The O₂ inhibition constants (K_I ) of Azospira sp. strain I09 and Ps. stutzeri JCM5965 increased from 0.06 ± 0.05 and 0.05 ± 0.02 μmol L^-1 to 0.92 ± 0.24 and 0.84 ± 0.31 μmol L^-1 , respectively, as the temperature increased from 15°C to 35°C, while that of Azospira sp. strain I13 was temperature-independent (p = 0.106). Within the range of temperatures examined, Azospira sp. strain I13 had a faster recovery after O₂ exposure compared with Azospira sp. strain I09 and Ps. stutzeri JCM5965 (p < 0.05). These results suggest that temperature and O₂ exposure result in the growth of ecophysiologically distinct N₂ ORB as N₂ O sinks. This knowledge can help develop a suitable N₂ O mitigation strategy according to the physiologies of the predominant N₂ ORB.

Nitric oxide reduction by microbial fuel cell with carbon based gas diffusion cathode for power generation and gas purification

Nitric oxide (NO) from anthropogenic emission is one of the main air contaminants and induces many environmental problems. Microbial fuel cells (MFCs) with gas diffusion cathode provide an alternative technology for NO reduction. In this work, pure NO as the sole electron acceptor of MFCs with gas diffusion cathode (NO-MFCs) was verified. The NO-MFCs obtained a maximum power density of 489 ± 50 mW/m². Compared with MFCs using O₂ in air as electron acceptor (Air-MFCs), the columbic efficiency increased from 23.2% ± 4.3% (Air-MFCs) to 55.7% ± 4.6% (NO-MFCs). The NO removal rate was 12.33 ± 0.14 mg/L/h and N₂ was the main reduction product. Cathode reduction was the dominant pathway of NO conversion in NO-MFCs, including abiotic electrochemical reduction and microbial denitrification process. The predominant genera in anodic microbial community changed from exoelectrogenic bacteria in Air-MFCs to denitrifying bacteria in NO-MFCs and effected the power generation.

Quantification of nosZ genes and transcripts in activated sludge microbiomes with novel group-specific qPCR methods validated with metagenomic analyses

Substantial N₂O emission results from activated sludge nitrogen removal processes. N₂O-reducing organisms possessing NosZ-type N₂O reductases have been recognized to play crucial roles in suppressing emission of N₂O produced in anoxic activated sludge via denitrification; however, which of the diverse nosZ-possessing organisms function as the major N₂O sink in situ remains largely unknown. Here, nosZ genes and transcripts in wastewater microbiomes were analyzed with the group-specific qPCR assays designed de novo combining culture-based and computational approaches. A sewage sample was enriched in a batch reactor fed continuous stream of N₂ containing 20-10,000 ppmv N₂O with excess amount (10 mM) of acetate as the source of carbon and electrons, where 14 genera of potential N₂O-reducers were identified. All available amino acid sequences of NosZ affiliated to these taxa were grouped into five subgroups (two clade I and three clade II groups), and primers/probe sets exclusively and comprehensively targeting the subgroups were designed and validated with in silico PCR. Four distinct activated sludge samples from three different wastewater treatment plants in Korea were analyzed with the qPCR assays and the results were validated with the shotgun metagenome analysis results. With these group-specific qPCR assays, the nosZ genes and transcripts of six additional activated sludge samples were analyzed and the results of the analyses clearly indicated the dominance of two clade II nosZ subgroups (Flavobacterium-like and Dechloromonas-like) among both nosZ gene and transcript pools.

Biogeochemical Implications of N2O-Reducing Thermophilic Campylobacteria in Deep-Sea Vent Fields, and the Description of Nitratiruptor labii sp. nov

Nitrous oxide (N2O) is a potent greenhouse gas and has significantly increased in the atmosphere. Deep-sea hydrothermal fields are representative environments dominated by mesophilic to thermophilic members of the class Campylobacteria that possess clade II nosZ encoding nitrous oxide reductase. Here, we report a strain HRV44T representing the first thermophilic campylobacterium capable of growth by H2 oxidation coupled to N2O reduction. On the basis of physiological and genomic properties, it is proposed that strain HRV44T (=JCM 34002 = DSM 111345) represents a novel species of the genus Nitratiruptor, Nitratiruptor labii sp. nov. The comparison of the N2O consumption ability of strain HRV44T with those of additional Nitratiruptor and other campylobacterial strains revealed the highest level in strain HRV44T and suggests the N2O-respiring metabolism might be the common physiological trait for the genus Nitratiruptor. Our findings provide insights into contributions of thermophilic Campylobacteria to the N2O sink in deep-sea hydrothermal environments.

Characterization of nitrous oxide reduction by Azospira sp. HJ23 isolated from advanced wastewater treatment sludge

A new nitrous oxide (N₂O)-reducing bacterium was isolated from a consortium that was enriched using advanced wastewater treatment sludge as an inoculum and N₂O as the sole nitrogen source. The isolated facultative anaerobe was identified as Azospira sp. HJ23. Azospira sp. HJ23 exhibited optimum N₂O-reducing activity with a C/N ratio of 62 at pH 6 in the temperature range of 37 °C to 40 °C. The optimum carbon source for N₂O reduction was a mixture of glucose and acetate. The maximum rate of N₂O reduction by Azospira sp. HJ23 was 4.8 mmol·g-dry cell^-1·h^-1, and its N₂O-reducing activity was higher than other known N₂O reducers. Azospira sp. HJ23 possessed several functional genes for denitrification. These included narG (NO₃^- reductase), nirK (NO₂^- reductase), norB (NO reductase), and nosZ (N₂O reductase) genes. These results suggest that Azospira sp. HJ23 can be applied in the denitrification process to minimalize N₂O emission.