Biokinetic Characterization and Activities of N2O-Reducing Bacteria in Response to Various Oxygen Levels

Evaluating the role of high N2O affinity complete denitrifiers and non-denitrifying N2O reducing bacteria in reducing N2O emissions in river

Freshwater rivers are hotspots of N2O greenhouse gas emissions. Dissolved organic carbon (DOC) is the dominant electron donor for microbial N2O reduction, which can reduce N2O emission through enriching high N2O affinity denitrifiers or enriching non-denitrifying N2O-reducing bacteria (N2ORB), but the primary regulatory pathway remains unclear. Here, field study indicated that high DOC concentration in rivers enhanced denitrification rate but reduced N2O flux by improving nosZ gene abundance. Then, four N2O-fed membrane aeration biofilm reactors inoculated with river sediments from river channel, estuary, adjacent lake, and a mixture were continuously performed for 360 days, including low, high, and mixed DOC stages. During enrichment stages, the (nirS+nirK)/nosZ ratio showed no significant difference, but the community structure of denitrifiers and N2ORB changed significantly (p < 0.05). In addition, N2ORB strains isolated from different enrichment stages positioned in different branches of the phylogenetic tree. N2ORB strains isolated during high DOC stage showed significant higher maximum N2O-reducing capability (Vmax: 0.6 ± 0.4 ×10-4 pmol h-1 cell-1) and N2O affinity (a0: 7.8 ± 7.7 ×10-12 L cell-1 h-1) than strains isolated during low (Vmax: 0.1 ± 0.1 ×10-4 pmol h-1 cell-1, a0: 0.7 ± 0.4 ×10-12 L cell-1 h-1) and mixed DOC stages (Vmax: 0.1 ± 0.1 ×10-4 pmol h-1 cell-1, a0: 0.9 ± 0.9 ×10-12 L cell-1 h-1) (p < 0.05). Hence, under high DOC concentration conditions, the primary factor in reducing N2O emissions in rivers is the enrichment of complete denitrifiers with high N2O affinity, rather than non-denitrifying N2ORB.

Determining how oxygen legacy affects trajectories of soil denitrifier community dynamics and N2O emissions

Denitrification - a key process in the global nitrogen cycle and main source of the greenhouse gas N2O - is intricately controlled by O2. While the transition from aerobic respiration to denitrification is well-studied, our understanding of denitrifier communities' responses to cyclic oxic/anoxic shifts, prevalent in natural and engineered systems, is limited. Here, agricultural soil is exposed to repeated cycles of long or short anoxic spells (LA; SA) or constant oxic conditions (Ox). Surprisingly, denitrification and N2O reduction rates are three times greater in Ox than in LA and SA during a final anoxic incubation, despite comparable bacterial biomass and denitrification gene abundances. Metatranscriptomics indicate that LA favors canonical denitrifiers carrying nosZ clade I. Ox instead favors nosZ clade II-carrying partial- or non-denitrifiers, suggesting efficient partnering of the reduction steps among organisms. SA has the slowest denitrification progression and highest accumulation of intermediates, indicating less functional coordination. The findings demonstrate how adaptations of denitrifier communities to varying O2 conditions are tightly linked to the duration of anoxic episodes, emphasizing the importance of knowing an environment's O2 legacy for accurately predicting N2O emissions originating from denitrification.

Future directions in microbial nitrogen cycling in wastewater treatment

Discoveries in the past decade of novel reactions, processes, and micro-organisms have altered our understanding of microbial nitrogen cycling in wastewater treatment systems. These advancements pave the way for a transition toward more sustainable and energy-efficient wastewater treatment systems that also minimize greenhouse gas emissions. This review highlights these innovative directions in microbial nitrogen cycling within the context of wastewater treatment. Processes such as comammox, Feammox, electro-anammox, and nitrous oxide mitigation offer innovative approaches for sustainable, energy-efficient nitrogen removal. However, while these emerging processes show promise, advancing from laboratory research to practical applications, particularly in decentralized systems, remains a critical next step toward a sustainable and efficient wastewater management.

Respiration and growth of Paracoccus denitrificans R-1 with nitrous oxide as an electron acceptor

In the nitrogen biogeochemical cycle, the reduction of nitrous oxide (N2O) to N2 by N2O reductase, which is encoded by nosZ gene, is the only biological pathway for N2O consumption. In this study, we successfully isolated a strain of denitrifying Paracoccus denitrificans R-1 from sewage treatment plant sludge. This strain has strong N2O reduction capability, and the average N2O reduction rate was 5.10 ± 0.11 × 10-9 µmol·h-1·cell-1 under anaerobic condition in a defined medium. This reduction was accompanied by the stoichiometric consumption of acetate over time when N2O served as the sole electron acceptor and the reduction can yield energy to support microbial growth, suggesting that microbial N2O reduction is related to the energy generation process. Genomic analysis showed that the gene cluster encoding N2O reductase of P. denitrificans R-1 was composed of nosR, nosZ, nosD, nosF, nosY, nosL, and nosZ, which was identified as that in other strains in clade I. Respiratory inhibitors test indicated that the pathway of electron transport for N2O reduction was different from that of the traditional electron transport chain for aerobic respiration. Cu2+, silver nanoparticles, O2, and acidic conditions can strongly inhibit the reduction, whereas NO3- or NH4+ can promote it. These findings suggest that modular N2O reduction of P. denitrificans R-1 is linked to the electron transport and energy conservation, and dissimilatory N2O reduction is a form of microbial anaerobic respiration.

IMPORTANCE

Nitrous oxide (N2O) is a potent greenhouse gas and contributor to ozone layer destruction, and atmospheric N2O has increased steadily over the past century due to human activities. The release of N2O from fixed N is almost entirely controlled by microbial N2O reductase activities. Here, we investigated the ability to obtain energy for the growth of Paracoccus denitrificans R-1 by coupling the oxidation of various electron donors to N2O reduction. The modular N2O reduction process of denitrifying microorganism not only can consume N2O produced by itself but also can consume the external N2O generated from biological or abiotic pathways under suitable condition, which should be critical for controlling the release of N2O from ecosystems into the atmosphere.

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.

Nitrous oxide respiration in acidophilic methanotrophs

Aerobic methanotrophic bacteria are considered strict aerobes but are often highly abundant in hypoxic and even anoxic environments. Despite possessing denitrification genes, it remains to be verified whether denitrification contributes to their growth. Here, we show that acidophilic methanotrophs can respire nitrous oxide (N2O) and grow anaerobically on diverse non-methane substrates, including methanol, C-C substrates, and hydrogen. We study two strains that possess N2O reductase genes: Methylocella tundrae T4 and Methylacidiphilum caldifontis IT6. We show that N2O respiration supports growth of Methylacidiphilum caldifontis at an extremely acidic pH of 2.0, exceeding the known physiological pH limits for microbial N2O consumption. Methylocella tundrae simultaneously consumes N2O and CH4 in suboxic conditions, indicating robustness of its N2O reductase activity in the presence of O2. Furthermore, in O2-limiting conditions, the amount of CH4 oxidized per O2 reduced increases when N2O is added, indicating that Methylocella tundrae can direct more O2 towards methane monooxygenase. Thus, our results demonstrate that some methanotrophs can respire N2O independently or simultaneously with O2, which may facilitate their growth and survival in dynamic environments. Such metabolic capability enables these bacteria to simultaneously reduce the release of the key greenhouse gases CO2, CH4, and N2O.

Biogeography and impact of nitrous oxide reducers in rivers across a broad environmental gradient on emission rates

Microbial communities that reduce nitrous oxide (N2O) are divided into two clades, nosZI and nosZII. These clades significantly differ in their ecological niches and their implications for N2O emissions in terrestrial environments. However, our understanding of N2O reducers in aquatic systems is currently limited. This study investigated the relative abundance and diversity of nosZI- and nosZII-type N2O reducers in rivers and their impact on N2O emissions. Our findings revealed that stream sediments possess a high capacity for N2O reduction, surpassing N2O production under high N2O/NO3- ratio conditions. This study, along with others in freshwater systems, demonstrated that nosZI marginally dominates more often in rivers. While microbes containing either nosZI and nosZII were crucial in reducing N2O emissions, the net contribution of nosZII-containing microbes was more significant. This can be attributed to the nir gene co-occurring more frequently with the nosZI gene than with the nosZII gene. The diversity within each clade also played a role, with nosZII species being more likely to function as N2O sinks in streams with higher N2O concentrations. Overall, our findings provide a foundation for a better understanding of the biogeography of stream N2O reducers and their effects on N2O emissions.

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.

Contribution of Microorganisms with the Clade II Nitrous Oxide Reductase to Suppression of Surface Emissions of Nitrous Oxide

The sources and sinks of nitrous oxide, as control emissions to the atmosphere, are generally poorly constrained for most environmental systems. Initial depth-resolved analysis of nitrous oxide flux from observation wells and the proximal surface within a nitrate contaminated aquifer system revealed high subsurface production but little escape from the surface. To better understand the environmental controls of production and emission at this site, we used a combination of isotopic, geochemical, and molecular analyses to show that chemodenitrification and bacterial denitrification are major sources of nitrous oxide in this subsurface, where low DO, low pH, and high nitrate are correlated with significant nitrous oxide production. Depth-resolved metagenomes showed that consumption of nitrous oxide near the surface was correlated with an enrichment of Clade II nitrous oxide reducers, consistent with a growing appreciation of their importance in controlling release of nitrous oxide to the atmosphere. Our work also provides evidence for the reduction of nitrous oxide at a pH of 4, well below the generally accepted limit of pH 5.

Aerobic denitrification as an N2O source from microbial communities

Nitrous oxide (N2O) is a potent greenhouse gas of primarily microbial origin. Oxic and anoxic emissions are commonly ascribed to autotrophic nitrification and heterotrophic denitrification, respectively. Beyond this established dichotomy, we quantitatively show that heterotrophic denitrification can significantly contribute to aerobic nitrogen turnover and N2O emissions in complex microbiomes exposed to frequent oxic/anoxic transitions. Two planktonic, nitrification-inhibited enrichment cultures were established under continuous organic carbon and nitrate feeding, and cyclic oxygen availability. Over a third of the influent organic substrate was respired with nitrate as electron acceptor at high oxygen concentrations (>6.5 mg/L). N2O accounted for up to one-quarter of the nitrate reduced under oxic conditions. The enriched microorganisms maintained a constitutive abundance of denitrifying enzymes due to the oxic/anoxic frequencies exceeding their protein turnover-a common scenario in natural and engineered ecosystems. The aerobic denitrification rates are ascribed primarily to the residual activity of anaerobically synthesised enzymes. From an ecological perspective, the selection of organisms capable of sustaining significant denitrifying activity during aeration shows their competitive advantage over other heterotrophs under varying oxygen availabilities. Ultimately, we propose that the contribution of heterotrophic denitrification to aerobic nitrogen turnover and N2O emissions is currently underestimated in dynamic environments.

pH selects for distinct N2O-reducing microbiomes in tropical soil microcosms

Nitrous oxide (N2O), a greenhouse gas with ozone destruction potential, is mitigated by the microbial reduction to dinitrogen catalyzed by N2O reductase (NosZ). Bacteria with NosZ activity have been studied at circumneutral pH but the microbiology of low pH N2O reduction has remained elusive. Acidic (pH < 5) tropical forest soils were collected in the Luquillo Experimental Forest in Puerto Rico, and microcosms maintained with low (0.02 mM) and high (2 mM) N2O assessed N2O reduction at pH 4.5 and 7.3. All microcosms consumed N2O, with lag times of up to 7 months observed in microcosms with 2 mM N2O. Comparative metagenome analysis revealed that Rhodocyclaceae dominated in circumneutral microcosms under both N2O feeding regimes. At pH 4.5, Peptococcaceae dominated in high-N2O, and Hyphomicrobiaceae in low-N2O microcosms. Seventeen high-quality metagenome-assembled genomes (MAGs) recovered from the N2O-reducing microcosms harbored nos operons, with all eight MAGs derived from acidic microcosms carrying the Clade II type nosZ and lacking nitrite reductase genes (nirS/K). Five of the eight MAGs recovered from pH 4.5 microcosms represent novel taxa indicating an unexplored N2O-reducing diversity exists in acidic tropical soils. A survey of pH 3.5-5.7 soil metagenome datasets revealed that nosZ genes commonly occur, suggesting broad distribution of N2O reduction potential in acidic soils.

Three novel marine species of the genus Reichenbachiella exhibiting degradation of complex polysaccharides

Three novel strains designated ABR2-5T, BKB1-1T, and WSW4-B4T belonging to the genus Reichenbachiella of the phylum Bacteroidota were isolated from algae and mud samples collected in the West Sea, Korea. All three strains were enriched for genes encoding up to 216 carbohydrate-active enzymes (CAZymes), which participate in the degradation of agar, alginate, carrageenan, laminarin, and starch. The 16S rRNA sequence similarities among the three novel isolates were 94.0%-94.7%, and against all three existing species in the genus Reichenbachiella they were 93.6%-97.2%. The genome sizes of the strains ABR2-5T, BKB1-1T, and WSW4-B4T were 5.5, 4.4, and 5.0 Mb, respectively, and the GC content ranged from 41.1%-42.0%. The average nucleotide identity and the digital DNA-DNA hybridization values of each novel strain within the isolates and all existing species in the genus Reichenbachiella were in a range of 69.2%-75.5% and 17.7-18.9%, respectively, supporting the creation of three new species. The three novel strains exhibited a distinctive fatty acid profile characterized by elevated levels of iso-C15:0 (37.7%-47.4%) and C16:1 ω5c (14.4%-22.9%). Specifically, strain ABR2-5T displayed an additional higher proportion of C16:0 (13.0%). The polar lipids were phosphatidylethanolamine, unidentified lipids, aminolipids, and glycolipids. Menaquinone-7 was identified as the respiratory quinone of the isolates. A comparative genome analysis was performed using the KEGG, RAST, antiSMASH, CRISPRCasFinder, dbCAN, and dbCAN-PUL servers and CRISPRcasIdentifier software. The results revealed that the isolates harbored many key genes involved in central metabolism for the synthesis of essential amino acids and vitamins, hydrolytic enzymes, carotenoid pigments, and antimicrobial compounds. The KEGG analysis showed that the three isolates possessed a complete pathway of dissimilatory nitrate reduction to ammonium (DNRA), which is involved in the conservation of bioavailable nitrogen within the ecosystem. Moreover, all the strains possessed genes that participated in the metabolism of heavy metals, including arsenic, copper, cobalt, ferrous, and manganese. All three isolated strains contain the class 2 type II subtype C1 CRISPR-Cas system in their genomes. The distinguished phenotypic, chemotaxonomic, and genomic characteristics led us to propose that the three strains represent three novel species in the genus Reichenbachiella: R. ulvae sp. nov. (ABR2-5T = KCTC 82990T = JCM 35839T), R. agarivorans sp. nov. (BKB1-1T = KCTC 82964T = JCM 35840T), and R. carrageenanivorans sp. nov. (WSW4-B4T = KCTC 82706T = JCM 35841T).

Effect and microbial mechanism of suspended sediments particle size on nitrous oxide emission in eutrophic lakes

Suspended sediment (SPS) is an important environmental factor in eutrophic lakes, where they may play a significant role in the microbial nitrogen cycle and thus affect the N2O source and sink function. This study investigated the correlation and corresponding microbial mechanisms between N2O emission fluxes and SPS particle sizes. N2O emission characteristics were investigated in four parallel operated lab-scale microcosmic systems, in which different sizes of SPS particles were inoculated (i.e., <75, 75-150, 150-300, and >300 μm). The results show that, N2O emission fluxes in the eutrophic lakes were exponentially correlated with the lake trophic level index (TLI) (R2 = 0.94, p < 0.01) and the specific surface area of the SPS (R2 = 0.38, p < 0.05). In the microcosmic systems, SPS with 75-150 μm particles had the highest N2O emission rate of 5.94 ± 0.007 μg N/L/d, which was 2.6 times that of the <75 μm particle size system. The microcosmic system with particle size >300 μm had the highest N2O reduction rate (Vmax) of 6.776 μmol/L/h, which was 16-50 times that of the other three groups. Larger particle size SPS have a smaller specific surface area, which could affect the microenvironment on SPS surface and thus affect the microbe functions. The microbial community structure results indicated that the dominant microorganisms on the SPS surface were denitrifying bacteria. The maximum (nirS + nirK)/nosZ ratio was 30.2 for the 75-150 μm system, which was nearly 2 times higher than the other systems. The >300 μm system had the highest nosZ abundance, indicating a strong ability to reduce N2O. The co-occurrence networks analysis indicated that the cooperation and competition among nitrifiers and denitrifiers determined N2O emissions. These results provide fundamental insights into the influence of SPS size on N2O emissions in eutrophic lakes.

Oxic-anoxic cycling promotes coupling between complex carbon metabolism and denitrification in woodchip bioreactors

Denitrifying woodchip bioreactors (WBRs) are increasingly used to manage the release of non-point source nitrogen (N) by stimulating microbial denitrification. Woodchips serve as a renewable organic carbon (C) source, yet the recalcitrance of organic C in lignocellulosic biomass causes many WBRs to be C-limited. Prior studies have observed that oxic-anoxic cycling increased the mobilization of organic C, increased nitrate (NO3 - ) removal rates, and attenuated production of nitrous oxide (N2 O). Here, we use multi-omics approaches and amplicon sequencing of fungal 5.8S-ITS2 and prokaryotic 16S rRNA genes to elucidate the microbial drivers for enhanced NO3 - removal and attenuated N2 O production under redox-dynamic conditions. Transient oxic periods stimulated the expression of fungal ligninolytic enzymes, increasing the bioavailability of woodchip-derived C and stimulating the expression of denitrification genes. Nitrous oxide reductase (nosZ) genes were primarily clade II, and the ratio of clade II/clade I nosZ transcripts during the oxic-anoxic transition was strongly correlated with the N2 O yield. Analysis of metagenome-assembled genomes revealed that many of the denitrifying microorganisms also have a genotypic ability to degrade complex polysaccharides like cellulose and hemicellulose, highlighting the adaptation of the WBR microbiome to the ecophysiological niche of the woodchip matrix.

Long-Term Continuous Test of H2-Induced Denitrification Catalyzed by Palladium Nanoparticles in a Biofilm Matrix

Pd0 catalysis and microbially catalyzed reduction of nitrate (NO3--N) were combined as a strategy to increase the kinetics of NO3- reduction and control selectivity to N2 gas versus ammonium (NH4+). Two H2-based membrane biofilm reactors (MBfRs) were tested in continuous mode: one with a biofilm alone (H2-MBfR) and the other with biogenic Pd0 nanoparticles (Pd0NPs) deposited in the biofilm (Pd-H2-MBfR). Solid-state characterizations of Pd0NPs in Pd-H2-MBfR documented that the Pd0NPs were uniformly located along the outer surfaces of the bacteria in the biofilm. Pd-H2-MBfR had a higher rate of NO3- reduction compared to H2-MBfR, especially when the influent NO3- concentration was high (28 mg-N/L versus 14 mg-N/L). Pd-H2-MBfR enriched denitrifiers of Dechloromonas, Azospira, Pseudomonas, and Stenotrophomonas in the microbial community and also increased abundances of genes affiliated with NO3--N reductases, which reflected that the denitrifying bacteria could channel their respiratory electron flow to NO3- reduction to NO2-. N2 selectivity in Pd-H2-MBfR was regulated by the H2/NO3- flux ratio: 100% selectivity to N2 was achieved when the ratio was less than 1.3 e- equiv of H2/e- equiv N, while the selectivity toward NH4+ occurred with larger H2/NO3- flux ratios. Thus, the results with Pd-H2-MBfR revealed two advantages of it over the H2-MBfR: faster kinetics for NO3- removal and controllable selectivity toward N2 versus NH4+. By being able to regulate the H2/NO3- flux ratio, Pd-H2-MBfR has significant implications for improving the efficiency and effectiveness of the NO3- reduction processes, ultimately leading to more environmentally benign wastewater treatment.

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.

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.

Nitrate removal rates, isotopic fractionation, and denitrifying bacteria in a woodchip-based permeable reactive barrier system: a long-term column experiment

This study evaluated the effectiveness of using organic carbon materials (i.e., woodchips) to remove nitrate from groundwater. The results of our flow-through column experiment, which was conducted over 1.6 years, suggested that denitrifying bacteria reduce nitrate by using it as an electron acceptor and woodchips as an electron donor. The nitrate removal rates were sufficiently high (0.39-1.04 mmol L-1 day-1) during the operation of the column. Denitrification process was supported by fractionation of nitrogen and oxygen isotopes (δ15N and δ18O), with the δ15N and δ18O values enriched from 7.4‰ and 22.3‰ to 21.2‰ and 30.4‰, respectively. Enrichment factors ([Formula: see text]) for 15 N and 18O were calculated using the Rayleigh fractionation model, with values of - 13.2‰ for ε15N and - 7.1‰ for ε18O. The fractionation ratio of 15 N to 18O was 1.9:1, confirming denitrification. The most abundant bacterial genera in the soil used for inoculation were Enterobacter (86.7%), Nitrospira (1.8%), and Arthrobacter (1.5%), while those in the column effluent were Macrococcus (37.1%), Escherichia (14.7%), and Shigella (14.6%), indicating that bacterial communities changed in response to geochemical conditions in the column. This study suggests that nitrate in groundwater can be effectively removed using woodchip-based passive treatment systems and that information on isotopic fractionation and denitrifying bacteria can be key tools to understand denitrification.

Nitrification Regulates the Spatiotemporal Variability of N2O Emissions in a Eutrophic Lake

Nitrous oxide (N₂O) emissions from lakes exhibit significant spatiotemporal heterogeneity, and quantitative identification of the different N₂O production processes is greatly limited, causing the role of nitrification to be undervalued or ignored in models of a lake's N₂O emissions. Here, the contributions of nitrification and denitrification to N₂O production were quantitatively assessed in the eutrophic Lake Taihu using molecular biology and isotope mapping techniques. The N₂O fluxes ranged from -41.48 to 28.84 μmol m^-2 d^-1 in the lake, with lower N₂O concentrations being observed in spring and summer and significantly higher N₂O emissions being observed in autumn and winter. The ¹⁵N site preference and relevant isotopic evidence demonstrated that denitrification contributed approximately 90% of the lake's gross N₂O production during summer and autumn, 27-83% of which was simultaneously eliminated via N₂O reduction. Surprisingly, nitrification seemed to act as a key process promoting N₂O production and contributing to the lake as a source of N₂O emissions. A combination of N₂O isotopocule-based approaches and molecular techniques can be used to determine the precise characteristics of microbial N₂O production and consumption in eutrophic lakes. The results of this study provide a basis for accurately assessing N₂O emissions from lakes at the regional and global scales.

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.

Influences of carbon sources on N2O production during denitrification in freshwaters: Activity, isotopes and functional microbes

Denitrification is one of the major sources of N₂O in freshwaters. Diverse forms of organic compounds act as the electron donors for microbial denitrification. However, the influences of carbon sources on N₂O production, N₂O reduction, isotope fractionation and functional microbes during denitrification were largely unknown. In this study, five forms of carbon sources (i.e. acetate, citrate, glucose, cellobiose and leucine) were used to enrich denitrifiers in freshwater sediments. N₂O conversion in the enrichments was investigated by a combination of inhibition technique, natural stable isotope method and metagenomics. Acetylene was effective in inhibiting N₂O reduction without influencing the isotopic characteristics during N₂O production. Glucose led to the least N₂O production and reduction, in accordance with the lowest abundance of both NO and N₂O reductases in this enrichment. δ¹⁸O and site preference value (SP, =δ¹⁵N^α-δ¹⁵N^β) of N₂O were sensitive to discriminate the five carbon sources, except when comparing acetate and leucine. Isotopic values of N₂O were not significantly different in these two enrichments due to the similarity of NO reductases - Pseudomonas-type cNorB. Specifically, the enrichment with cellobiose produced N₂O with the lowest δ¹⁸O values (39.4‰±1.1‰), due to Alicycliphilus with both cNorB and qNorB. The enrichment with glucose led to the highest SP values (8.9‰±8.6‰), caused by Thiobacillus-type cNorB. Our results demonstrated the link between carbon sources, N₂O production and reduction, isotopic signatures, microbial populations and enzymes during denitrification in freshwaters.

Simultaneous nitrification-denitrification in biofilm systems for wastewater treatment: Key factors, potential routes, and engineered applications

Simultaneous nitrification-denitrification (SND) is an advantageous bioprocess that allows the complete removal of ammonia nitrogen through sequential redox reactions leading to nitrogen gas production. SND can govern nitrogen removal in single-stage biofilm systems, such as the moving bed biofilm reactor and aerobic granular sludge system, as oxygen gradients allow the development of multilayered biofilms including nitrifying and denitrifying bacteria. Environmental and operational conditions can strongly influence SND performance, biofilm development and biochemical pathways. Recent advances have outlined the possibility to reduce the carbon and energy consumption of the process via the "shortcut pathway", and simultaneously remove both N and phosphorus under specific operational conditions, opening new possibilities for wastewater treatment. This work critically reviews the factors influencing SND and its application in biofilm systems from laboratory to full scale. Operational strategies to enhance SND efficiency and hints to reduce nitrous oxide emission and operational costs are provided.

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.

Inoculation effect of Pseudomonas sp. TF716 on N2O emissions during rhizoremediation of diesel-contaminated soil

The demand for rhizoremediation technology that can minimize greenhouse gas emissions while effectively removing pollutants in order to mitigate climate change has increased. The inoculation effect of N₂O-reducing Pseudomonas sp. TF716 on N₂O emissions and on remediation performance during the rhizoremediation of diesel-contaminated soil planted with tall fescue (Festuca arundinacea) or maize (Zea mays) was investigated. Pseudomonas sp. TF716 was isolated from the rhizosphere soil of tall fescue. The maximum N₂O reduction rate of TF716 was 18.9 mmol N₂O g dry cells⁻¹ h⁻¹, which is superior to the rates for previously reported Pseudomonas spp. When Pseudomonas sp. TF716 was added to diesel-contaminated soil planted with tall fescue, the soil N₂O-reduction potential was 2.88 times higher than that of soil with no inoculation during the initial period (0–19 d), and 1.08–1.13 times higher thereafter. However, there was no enhancement in the N₂O-reduction potential for the soil planted with maize following inoculation with strain TF716. In addition, TF716 inoculation did not significantly affect diesel degradation during rhizoremediation, suggesting that the activity of those microorganisms involved in diesel degradation was unaffected by TF716 treatment. Analysis of the dynamics of the bacterial genera associated with N₂O reduction showed that Pseudomonas had the highest relative abundance during the rhizoremediation of diesel-contaminated soil planted with tall fescue and treated with strain TF716. Overall, these results suggest that N₂O emissions during the rhizoremediation of diesel-contaminated soil using tall fescue can be reduced with the addition of Pseudomonas sp. TF716.

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.

Pathways of soil N2O uptake, consumption, and its driving factors: a review

Nitrous oxide (N₂O) is an important greenhouse gas that plays a significant role in atmospheric photochemical reactions and contributes to stratospheric ozone depletion. Soils are the main sources of N₂O emissions. In recent years, it has been demonstrated that soil is not only a source but also a sink of N₂O uptake and consumption. N₂O emissions at the soil surface are the result of gross N₂O production, uptake, and consumption, which are co-occurring processes. Soil N₂O uptake and consumption are complex biological processes, and their mechanisms are still worth an in-depth systematic study. This paper aimed to systematically address the current research progress on soil N₂O uptake and consumption. Based on a bibliometric perspective, this study has highlighted the pathways of soil N₂O uptake and consumption and their driving factors and measurement techniques. This systematic review of N₂O uptake and consumption will help to further understand N transformations and soil N₂O emissions.

N2O Reduction by Gemmatimonas aurantiaca and Potential Involvement of Gemmatimonadetes Bacteria in N2O Reduction in Agricultural Soils

Agricultural soil is the primary N₂O sink limiting the emission of N₂O gas into the atmosphere. Although Gemmatimonadetes bacteria are abundant in agricultural soils, limited information is currently available on N₂O reduction by Gemmatimonadetes bacteria. Therefore, the effects of pH and temperature on N₂O reduction activities and affinity constants for N₂O reduction were examined by performing batch experiments using an isolate of Gemmatimonadetes bacteria, Gemmatimonas aurantiaca (NBRC100505^T). G. aurantiaca reduced N₂O at pH 5–9 and 4–50°C, with the highest activity being observed at pH 7 and 30°C. The affinity constant of G. aurantiaca cells for N₂O was 4.4‍ ‍μM. The abundance and diversity of the Gemmatimonadetes 16S rRNA gene and nosZ encoding nitrous oxide reductase in agricultural soil samples were also investigated by quantitative PCR (qPCR) and amplicon sequencing ana­lyses. Four N₂O-reducing agricultural soil samples were assessed, and the copy numbers of the Gemmatimonadetes 16S rRNA gene (clades G1 and G3), nosZ DNA, and nosZ mRNA were 8.62–9.65×10⁸, 5.35–7.15×10⁸, and 2.23–4.31×10⁹ copies (g dry soil)^–1, respectively. The abundance of the nosZ mRNA of Gemmatimonadetes bacteria and OTU91, OUT332, and OTU122 correlated with the N₂O reduction rates of the soil samples tested, suggesting N₂O reduction by Gemmatimonadetes bacteria. Gemmatimonadetes 16S rRNA gene reads affiliated with OTU4572 and OTU3759 were predominant among the soil samples examined, and these Gemmatimonadetes OTUs have been identified in various types of soil samples.

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.

Temporal triggers of N2O emissions during cyclical and seasonal variations of a full-scale sequencing batch reactor treating municipal wastewater

To investigate the major triggers of nitrous oxide (N₂O) production in a full-scale wastewater treatment plant, N₂O emissions and wastewater characteristics (ammonia, nitrite, nitrate, total nitrogen, dissolved inorganic carbon, dissolved organic carbon, pH, temperature, dissolved oxygen and specific oxygen uptake rate), the results of variations in the cycling of a sequential batch reactor (SBR, where only full nitrification was performed), were monitored seasonally for 16 months. Major triggers of N₂O production were investigated based on a seasonal measured database using a random forest (RF) model and sensitivity analysis, which was applied to identify important input variables. As the result of seasonal monitoring in the full-scale SBR, the N₂O emission factor relative to daily total nitrogen removal ranged from 0.05 to 2.68%, corresponding to a range of N₂O production rate from 0.02 to 0.70 kg-N/day. Results from the RF model and sensitivity analysis revealed that emissions during nitrification were directly or indirectly related to nitrite accumulation, temperature, ammonia loading rate and the specific oxygen uptake rate ratio between ammonia oxidizing bacteria and nitrite oxidizing bacteria (sOUR-ratio). However, changes in the microbial community did not significantly impact N₂O emissions. Based on these results, the sOUR-ratio could represent the major trigger for N₂O emission in a full-scale BNR system: a higher sOUR-ratio value with an average of 3.13 ± 0.23 was linked to a higher N₂O production rate with an average value of 1.27 ± 0.12 kg-N/day (corresponding to 3.96 ± 1.20% of N₂O emission factor relative to daily TN removal), while a lower sOUR-ratio with an average value of 2.39 ± 0.27 was correlated with a lower N₂O production average rate of 0.17 ± 0.11 kg-N/day (corresponding to 0.74 ± 0.69% of N₂O emission factor) (p-value = 0.00001, Mann-Whitney test).

Combination of 15N Tracer and Microbial Analyses Discloses N2O Sink Potential of the Anammox Community

Although nitrogen removal by partial nitritation and anammox is more cost-effective than conventional nitrification and denitrification, one downside is the production and accumulation of nitrous oxide (N₂O). The potential exploitation of N₂O-reducing bacteria, which are resident members of anammox microbial communities, for N₂O mitigation would require more knowledge of their ecophysiology. This study investigated the phylogeny of resident N₂O-reducing bacteria in an anammox microbial community and quantified individually the processes of N₂O production and N₂O consumption. An up-flow column-bed anammox reactor, fed with NH₄⁺ and NO₂^- and devoid of oxygen, emitted N₂O at an average conversion ratio (produced N₂O: influent nitrogen) of 0.284%. Transcriptionally active and highly abundant nosZ genes in the reactor biomass belonged to the Burkholderiaceae (clade I type) and Chloroflexus genera (clade II type). Meanwhile, less abundant but actively transcribing nosZ strains were detected in the genera Rhodoferax, Azospirillum, Lautropia, and Bdellovibrio and likely act as an N₂O sink. A novel ¹⁵N tracer method was adapted to individually quantify N₂O production and N₂O consumption rates. The estimated true N₂O production rate and true N₂O consumption rate were 3.98 ± 0.15 and 3.03 ± 0.18 mg_N·g_VSS^-1·day^-1, respectively. The N₂O consumption rate could be increased by 51% (4.57 ± 0.51 mg_N·g_VSS^-1·day^-1) with elevated N₂O concentrations but kept comparable irrespective of the presence or absence of NO₂^-. Collectively, the approach allowed the quantification of N₂O-reducing activity and the identification of transcriptionally active N₂O reducers that may constitute as an N₂O sink in anammox-based processes.

Beyond denitrification: The role of microbial diversity in controlling nitrous oxide reduction and soil nitrous oxide emissions

Many biotic and abiotic processes contribute to nitrous oxide (N₂ O) production in the biosphere, but N₂ O consumption in the environment has heretofore been attributed primarily to canonical denitrifying microorganisms. The nosZ genes encoding the N₂ O reductase enzyme, NosZ, responsible for N₂ O reduction to dinitrogen are now known to include two distinct groups: the well-studied Clade I which denitrifiers typically possess, and the novel Clade II possessed by diverse groups of microorganisms, most of which are non-denitrifiers. Clade II N₂ O reducers could play an important, previously unrecognized role in controlling N₂ O emissions for several reasons, including: (1) the consumption of N₂ O produced by processes other than denitrification, (2) hypothesized non-respiratory functions of NosZ as an electron sink or for N₂ O detoxification, (3) possible differing enzyme kinetics of Clade II NosZ compared to Clade I NosZ, and (4) greater nosZ gene abundance for Clade II compared to Clade I in soils of many ecosystems. Despite the potential ecological significance of Clade II NosZ, a census of 800 peer-reviewed original research articles discussing nosZ and published from 2013 to 2019 showed that the percentage of articles evaluating or mentioning Clade II nosZ increased from 5% in 2013 to only 22% in 2019. The census revealed that the slowly spreading awareness of Clade II nosZ may result in part from disciplinary silos, with the percentage of nosZ articles mentioning Clade II nosZ ranging from 0% in Agriculture and Agronomy journals to 32% in Multidisciplinary Sciences journals. In addition, inconsistent nomenclature for Clade I nosZ and Clade II nosZ, with 17 different terminologies used in the literature, may have created confusion about the two distinct groups of N₂ O reducers. We provide recommendations to accelerate advances in understanding the role of the diversity of N₂ O reducers in regulating soil N₂ O emissions.

Differential expression of clade I and II N2O reductase genes in denitrifying Thauera linaloolentis 47LolT under different nitrogen conditions

Nitrous oxide (N2O) is a potent greenhouse gas and its reduction to dinitrogen gas by the N2O reductase (encoded by the nosZ gene) is the only known biological N2O sink. Within the nosZ phylogeny there are two major clades (I and II), which seem to have different ecological niches. However, physiological differences of nosZI and nosZII expression that may impact emissions of N2O are not well understood. Here, we evaluated the differential expression of nosZI and nosZII, both present in Thauera linaloolentis strain 47LolT, in response to N2O concentration and the presence of the competing electron acceptor nitrate (NO3-). Different N2O levels had a negligible effect on the expression of both nosZ clades. Interestingly, nosZII expression was strongly upregulated in the absence of NO3-, while nosZI expression remained constant across the conditions tested. Thus, NO3- possibly inhibited nosZII expression, which suggests that N2O mitigation mediated by nosZII can be restricted due to the presence of NO3- in the environment. This is the first study demonstrating differential expression of nosZI and nosZII genes under the same physiological conditions and their implications for N2O emission under varying environmental conditions in terms of NO3- availability.

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.

Kinetics of nitrous oxide mass transfer from porewater into root aerenchyma of wetland plants

The creation and/or restoration of wetlands is an important strategy for controlling the release of reactive nitrogen (N) via denitrification, but there can be tradeoffs between enhanced denitrification and the production of nitrous oxide (N₂ O), a potent greenhouse gas. A knowledge gap in current understanding of belowground wetland N dynamics is the role of gas transfer through the root aerenchyma system of wetland plants as a shortcut emission pathway for N₂ O in denitrifying wetland soils. This investigation evaluates the significance of mass transfer into gas-filled root aerenchyma for the N₂ O budget in wetland mesocosms planted with Sagittaria latifolia Willd. and Schoenoplectus acutus (Muhl. ex Bigelow) Á. Löve & D. Löve. Dissolved gas tracer push-pull tests with N₂ O and the nonreactive gas tracers helium, sulfur hexafluoride, and ethane were used to estimate first-order rate constants for gas transfer into roots and microbial N₂ O reduction and thereby disentangle the effects of root-mediated gas transport from microbial metabolism on N₂ O balances in saturated soils. Root-mediated gas transport was estimated to account for up to 37% of overall N₂ O removal from the wetland soils. Rates of microbial N₂ O reduction varied widely based on the organic matter content of the soil media and served as a key control on the fraction of N₂ O that transferred into roots. This research identifies transport through root aerenchyma as a potential shortcut pathway for N₂ O emission from wetland soils and sediments and indicates that this process should be considered in both measurements and mechanistic modeling of belowground wetland N dynamics.

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.

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.

Hierarchical detection of diverse Clade II (atypical) nosZ genes using new primer sets for classical- and multiplex PCR array applications

The reduction of nitrous oxide (N₂O) to N₂ represents the key terminal step in canonical denitrification. Nitrous oxide reductase (NosZ), the enzyme associated with this biological step, however, is not always affiliated with denitrifying microorganisms. Such organisms were shown recently to possess a Clade II (atypical) nosZ gene, in contrast to Clade I (typical) nosZ harbored in more commonly studied denitrifiers. Subsequent phylogenetic analyses have shown that Clade II NosZ are affiliated with a much broader diversity of microorganisms than those with Clade I NosZ, the former including both non-denitrifiers and denitrifiers. Most studies attempting to characterize the nosZ gene diversity using DNA-based PCR approaches have only focused on Clade I nosZ, despite recent metagenomic sequencing studies that have demonstrated the dominance of Clade II nosZ genes in many ecosystems, particularly soil. As a result, these studies have greatly underestimated the genetic potential for N₂O reduction present in ecosystems. Because the high diversity of Clade II NosZ makes it impossible to design a universal primer set that would effectively amplify all nosZ genes in this clade, we developed a suite of primer sets to specifically target seven of ten designated subclades of Clade II nosZ genes. The new primer sets yield suitable product sizes for paired end amplicon sequencing and qPCR, demonstrated here in their use for both conventional single-reaction and multiplex array platforms. In addition, we show the utility of these primers for detecting nosZ gene transcripts from mRNA extracted from soil.

Consumption of N2O and other N-cycle intermediates by Gemmatimonas aurantiaca strain T-27

Bacteria affiliated with the phylum Gemmatimonadetes are found in high abundance in many terrestrial and aquatic environments, yet little is known about their metabolic capabilities. Difficulty in their cultivation has prompted interest in identifying better growth conditions for metabolic studies, especially related to their ability to reduce N₂O, a potent greenhouse gas. T-27 Gemmatimonas aurantiaca is one of few cultivated strains of Gemmatimonadetes available for physiological studies. Our objective was to test this organism's ability to use nitrite, nitrate, and N₂O, and mineral forms of assimilable NH₄ ⁺ at concentrations not typically used in tests for compound utilization. Cultures incubated under anaerobic conditions with nitrate, nitrite or N₂O failed to grow or show depletion of these substrates. Nitrate and nitrite (1 mM) were not used even when cells were grown aerobically with the O₂ allowed to deplete first. N₂O reduction only commenced in the presence of O₂ and continued to be depleted when refed to the culture under anaerobic, microaerobic and aerobic atmospheres. Carbon mineralization was coupled to the electron-accepting processes, with higher reducing equivalents needed for N₂O utilization under aerobic atmospheres. N₂O was reduced to N₂ in the presence of 20% O₂, however the rate of this reaction is reduced in the presence of high O₂ concentration. This study demonstrated that G. aurantiaca T-27 possesses unique characteristics for assimilative and dissimilative N processes with new implications for cultivation strategies to better assess the metabolic abilities of Gemmatimonadetes.

Nitrous Oxide and Methane Dynamics in Woodchip Bioreactors: Effects of Water Level Fluctuations on Partitioning into Trapped Gas Phases

Woodchip bioreactors (WBRs) are low-cost, passive systems for nonpoint source nitrogen removal at terrestrial-aquatic interfaces. The greenhouse gases nitrous oxide (N₂O) and methane (CH₄) can be produced within WBRs, and efforts to reduce N₂O and CH₄ emissions from WBR systems require improved understanding of the biogeochemical and physical-chemical mechanisms regulating their production, transport, and release. This study evaluates the impact of trapped gas-filled void volumes as sinks of dissolved gases from water and as sources of episodic fluxes when water levels fall. Dissolved gas tracer experiments in a laboratory bioreactor were used to parameterize nonequilibrium advection-dispersion-gas transfer models and quantify trapping of gas-filled voids as a function of antecedent hydrological conditions. Experiments following a water-level rise revealed that up to 24% of the WBR pore volume was occupied by trapped gas phases, which were primarily located in pore spaces inside woodchips. This finding was confirmed with X-ray-computed microtomography. N₂O (3.3-10%) and CH₄ (4.3-14%) injected into the reactor following a water table rise partitioned into gas-filled voids and were released when water tables fell. In the case of N₂O, partitioning into trapped gas phases makes N₂O unavailable for enzymatic reduction, potentially enhancing N₂O fluxes under fluctuating water levels.

Effects of thiosulfate addition on ammonia and nitrogen removal in biofilters packed with Oyaishi (pumice tuff)

Ammonia removal is achieved partly by absorption and nitrification in biofilters, resulting in the accumulation of nitrogen and the necessity of treating the effluent water. We investigated the effects of thiosulfate addition to a biofilter containing pumice tuff for ammonia and nitrogen removal in a laboratory-scale experiment. The addition of thiosulfate to the circulating water led to a decreased nitrate and nitrite along with an increase of sulfate. The inorganic nitrogen in the circulating water decreased by up to 44% with thiosulfate addition compared to without thiosulfate. Batch experiments revealed that denitrification activity decreased exponentially along with increases in dissolved oxygen; however, approximately 30% of denitrification activity was maintained at dissolved oxygen concentration of 3.3 mg/L. Metabarcoding of 16S rRNA genes indicated that the genus Thiobacillus had a relative abundance of 0.002%-0.016% of total bacteria in the biofilter packing material. The circulating water pH was decreased below 5 with sulfur oxidation, and ammonium was accumulated without pH control resulting in a decrease in the relative abundance of the family Nitrosomonadaceae. Its relative abundance increased with control of pH to near neutral, indicating that ammonia-oxidizing activity could be maintained by adjusting pH. Thiosulfate addition could stimulate nitrogen removal by sulfur-dependent denitrification in biofiltration systems.

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

The recent discovery of nitrous oxide (N₂O)-reducing bacteria suggests a potential biological sink for the potent greenhouse gas N₂O. For an application toward N₂O mitigation, characterization of more isolates will be required. Here, we describe the successful enrichment and isolation of high-affinity N₂O-reducing bacteria using a N₂O-fed reactor (N₂OFR). Two N₂OFRs, where N₂O was continuously and directly supplied as the sole electron acceptor to a biofilm grown on a gas-permeable membrane, were operated with acetate or a mixture of peptone-based organic substrates as an electron donor. In parallel, a NO₃^- -fed reactor (NO₃FR), filled with a nonwoven sheet substratum, was operated using the same inoculum. We hypothesized that supplying N₂O vs NO₃^- would enhance the dominance of distinct N₂O-reducing bacteria. Clade II type nosZ bacteria became rapidly enriched over clade I type nosZ bacteria in the N₂OFRs, whereas the opposite held in the NO₃FR. High-throughput sequencing of 16S rRNA gene amplicons revealed the dominance of Rhodocyclaceae in the N₂OFRs. Strains of the Azospira and Dechloromonas genera, canonical denitrifiers harboring clade II type nosZ, were isolated with high frequency from the N₂OFRs (132 out of 152 isolates). The isolates from the N₂OFR demonstrated higher N₂O uptake rates (V_max: 4.23 × 10^-3-1.80 × 10^-2 pmol/h/cell) and lower N₂O half-saturation coefficients (K_m,N2O: 1.55-2.10 μM) than a clade I type nosZ isolate from the NO₃FR. Furthermore, the clade II type nosZ isolates had higher specific growth rates on N₂O than nitrite as an electron acceptor. Hence, continuously and exclusively supplying N₂O in an N₂OFR allows the enrichment and isolation of high-affinity N₂O-reducing strains, which may be used as N₂O sinks in bioaugmentation efforts.

Bacterial nitrous oxide respiration: electron transport chains and copper transfer reactions

Biologically catalyzed nitrous oxide (N₂O, laughing gas) reduction to dinitrogen gas (N₂) is a desirable process in the light of ever-increasing atmospheric concentrations of this important greenhouse gas and ozone depleting substance. A diverse range of bacterial species produce the copper cluster-containing enzyme N₂O reductase (NosZ), which is the only known enzyme that converts N₂O to N₂. Based on phylogenetic analyses, NosZ enzymes have been classified into clade I or clade II and it has turned out that this differentiation is also applicable to nos gene clusters (NGCs) and some physiological traits of the corresponding microbial cells. The NosZ enzyme is the terminal reductase of anaerobic N₂O respiration, in which electrons derived from a donor substrate are transferred to NosZ by means of an electron transport chain (ETC) that conserves energy through proton motive force generation. This chapter presents models of the ETCs involved in clade I and clade II N₂O respiration as well as of the respective NosZ maturation and maintenance processes. Despite differences in NGCs and growth yields of N₂O-respiring microorganisms, the deduced bioenergetic framework in clade I and clade II N₂O respiration is assumed to be equivalent. In both cases proton motive quinol oxidation by N₂O is thought to be catalyzed by the Q cycle mechanism of a membrane-bound Rieske/cytochrome bc complex. However, clade I and clade II organisms are expected to differ significantly in terms of auxiliary electron transport processes as well as NosZ active site maintenance and repair.

Enhanced Nitrous Oxide Production in Denitrifying Dechloromonas aromatica Strain RCB Under Salt or Alkaline Stress Conditions

Salinity and pH have direct and indirect impacts on the growth and metabolic activities of microorganisms. In this study, the effects of salt and alkaline stresses on the kinetic balance between nitrous oxide (N₂O) production and consumption in the denitrification pathway of Dechloromonas aromatica strain RCB were examined. N₂O accumulated transiently only in insignificant amounts at low salinity (≤0.5% NaCl) and circumneutral pH (7.0 and 7.5). As compared to these control conditions, incubation at 0.7% salinity resulted in substantially longer lag phase and slower growth rate, along with the increase in the amounts of transiently accumulated N₂O (15.8 ± 2.8 μmoles N₂O-N/vessel). Incubation at pH 8.0 severely inhibited growth and resulted in permanent accumulation of 29.9 ± 1.3 μmoles N₂O-N/vessel from reduction of 151 ± 20 μmoles NO₃⁻/vessel. Monitoring of temporal changes in nirS₁, nirS₂, and nosZ transcription suggested that the nosZ/(nirS₁+nirS₂) ratios were indicative of whether N₂O was produced or consumed at the time points where measurements were taken. The salt and alkaline stresses altered the N₂O consumption kinetics of the resting D. aromatica cells with expressed nitrous oxide reductases. The N₂O consumption rates of the cells subjected to the salt and alkaline stress conditions were significantly reduced from 0.84 ± 0.007 μmoles min⁻¹ mg protein⁻¹ of the control to 0.27 ± 0.02 μmoles min⁻¹ mg protein⁻¹ and 0.31 ± 0.03 μmoles min⁻¹ mg protein⁻¹, respectively, when the initial dissolved N₂O concentration was 0.1 mM. As the rates of N₂O production from NO₂⁻ reduction was not significantly affected by the stresses (0.45–0.55 μmoles min⁻¹ mg protein⁻¹), the N₂O consumption rate was lower than the N₂O production rate at the stress conditions, but not at the control condition. These results clearly indicate that the altered kinetics of expressed nitrous oxide reductase and the resultant disruption of kinetic balance between N₂O production and consumption was another cause of enhanced N₂O emission observed under the salt and alkaline stress conditions. These findings suggest that canonical denitrifiers may become a significant N₂O source when faced with abrupt environmental changes.

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

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