Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrification

N2O recovery from wastewater and flue gas via microbial denitrification: Processes and mechanisms

Nitrous oxide (N2O) is increasingly regarded as a significant greenhouse gas implicated in global warming and the depletion of the ozone layer, yet it is also recognized as a valuable resource. This paper comprehensively reviews innovative microbial denitrification techniques for recovering N2O from nitrogenous wastewater and flue gas. Critical analysis is carried out on cutting-edge processes such as the coupled aerobic-anoxic nitrous decomposition operation (CANDO) process, semi-artificial photosynthesis, and the selective utilization of microbial strains, as well as flue gas absorption coupled with heterotrophic/autotrophic denitrification. These processes are highlighted for their potential to facilitate denitrification and enhance the recovery rate of N2O. The review integrates feasible methods for process control and optimization, and presents the underlying mechanisms for N2O recovery through denitrification, primarily achieved by suppressing nitrous oxide reductase (Nos) activity and intensifying competition for electron donors. The paper concludes by recognizing the shortcomings in existing technologies and proposing future research directions, with an emphasis on prioritizing the collection and utilization of N2O while considering environmental sustainability and economic feasibility. Through this review, we aim to inspire interest in the recovery and utilization of N2O, as well as the development and application of related technologies.

Enhanced nitrogen removal by an isolated aerobic denitrifying strain in a vertical-flow constructed wetland

The addition of bacterial agents is an effective method for improving nitrogen removal from wetlands. Herein, an aerobic denitrifier, RC-15, was added to a vertical-flow constructed wetland (CW), and the presence of functional genes and microbial communities was investigated at different CW depths. For the RC-15-treated CW, the removal of NO3- and TN during the process was significantly greater than in the control. Quantitative PCR revealed that nirS is a dominant denitrifying gene for treating WWTP tailwater. Moreover, the presence of the RC-15 strain significantly enhanced the abundance of the napA gene and nirK gene in the CWs. The napA gene was concentrated in the upper layer of the CWs, and the nirK gene was concentrated in the middle and bottom layers. Compared to the control, the addition of the bacterial agent Trial resulted in a more diverse denitrification pathway, a greater abundance of 16Sr RNA, and a greater number of denitrifying strains. According to the microbial community analysis, Proteobacteria and Chloroflexi dominated denitrification in the CWs. Greater abundances of Thauera, Aeromonas and Ardenticatenales were found at the genus level, indicating that these genera have potential applications in future nitrogen removal projects.

Aquatic nitrous oxide reductase gene (nosZ) phylogeny and environmental distribution

Nitrous oxide (N2O) is a potent greenhouse gas and a major cause of ozone depletion. One-third of atmospheric N2O originates in aquatic environments. Reduction of N2O to dinitrogen gas (N2) requires the nitrous oxide reductase enzyme, which is encoded by the gene nosZ. Organisms that contain nosZ are the only known biological sinks of N2O and are found in diverse genera and a wide range of environments. The two clades of nosZ (Clade I and II) contain great diversity, making it challenging to study the population structure and distribution of nosZ containing organisms in the environment. A database of over 11,000 nosZ sequences was compiled from NCBI (representing diverse aquatic environments) and unpublished sequences and metagenomes (primarily from oxygen minimum zones, OMZs, where N2O levels are often elevated). Sequences were clustered into archetypes based on DNA and amino acid sequence identity and their clade, phylogeny, and environmental source were determined. Further analysis of the source and environmental distribution of the sequences showed strong habitat separation between clades and phylogeny. Although there are more Clade I nosZ genes in the compilation, Clade II is more diverse phylogenetically and has a wider distribution across environmental sources. On the other hand, Clade I nosZ genes are predominately found within marine sediment and are primarily from the phylum Pseudonomonadota. The majority of the sequences analyzed from marine OMZs represented distinct phylotypes between different OMZs showing that the nosZ gene displays regional and environmental separation. This study expands the known diversity of nosZ genes and provides a clearer picture of how the clades and phylogeny of nosZ organisms are distributed across diverse environments.

Genome-Resolved Metagenomics and Denitrifying Strain Isolation Reveal New Insights into Microbial Denitrification in the Deep Vadose Zone

The heavy use of nitrogen fertilizer in intensive agricultural areas often leads to nitrate accumulation in subsurface soil and nitrate contamination in groundwater, which poses a serious risk to public health. Denitrifying microorganisms in the subsoil convert nitrate to gaseous forms of nitrogen, thereby mitigating the leaching of nitrate into groundwater. Here, we investigated denitrifying microorganisms in the deep vadose zone of a typical intensive agricultural area in China through microcosm enrichment, genome-resolved metagenomic analysis, and denitrifying bacteria isolation. A total of 1000 metagenome-assembled genomes (MAGs) were reconstructed, resulting in 98 high-quality, dereplicated MAGs that contained denitrification genes. Among them, 32 MAGs could not be taxonomically classified at the genus or species level, indicating that a broader spectrum of taxonomic groups is involved in subsoil denitrification than previously recognized. A denitrifier isolate library was constructed by using a strategy combining high-throughput and conventional cultivation techniques. Assessment of the denitrification characteristics of both the MAGs and isolates demonstrated the dominance of truncated denitrification. Functional screening revealed the highest denitrification activity in two complete denitrifiers belonging to the genus Pseudomonas. These findings greatly expand the current knowledge of the composition and function of denitrifying microorganisms in subsoils. The constructed isolate library provided the first pool of subsoil-denitrifying microorganisms that could facilitate the development of microbe-based technologies for nitrate attenuation in groundwater.

Response of soil N2O production pathways to biochar amendment and its isotope discrimination methods

Reducing nitrous oxide (N2O) emission from farmland is crucial for alleviating global warming since agriculture is an important contributor of atmospheric N2O. Returning biochar to agricultural fields is an important measure to mitigate soil N2O emissions. Accurately quantifying the effect of biochar on the process of N2O production and its driving factors is critical for achieving N2O emission mitigation. Recently, stable isotope techniques such as isotope labeling, natural abundance, and site preference (SP) value, have been widely used to distinguish N2O production pathways. However, the different isotope methods have certain limitations in distinguishing N2O production in biochar-amended soils where it is difficult to identify the relative contribution of individual pathways for N2O production. This paper systematically reviews the pathways of soil N2O production (nitrification, nitrifier denitrification, bacterial denitrification, fungal denitrification, coupled nitrification-denitrification, dissimilatory nitrate reduction to ammonium and abiotic processes) and their response mechanism to the addition of biochar, as well as the development history and advantages of isotopes in differentiating N2O production pathways in biochar-amended soils. Moreover, the limitations of current research methods and future research directions are proposed. These results will help resolve how biochar affects different processes that lead to soil N2O generation and provide a scientific basis for sustainable agricultural carbon sequestration and the fulfilment of carbon neutrality goals.

Nitrous oxide reduction by two partial denitrifying bacteria requires denitrification intermediates that cannot be respired

Denitrification is a form of anaerobic respiration wherein nitrate (NO3-) is sequentially reduced via nitrite (NO2-), nitric oxide, and nitrous oxide (N2O) to dinitrogen gas (N2) by four reductase enzymes. Partial denitrifying bacteria possess only one or some of these four reductases and use them as independent respiratory modules. However, it is unclear if partial denitrifiers sense and respond to denitrification intermediates outside of their reductase repertoire. Here, we tested the denitrifying capabilities of two purple nonsulfur bacteria, Rhodopseudomonas palustris CGA0092 and Rhodobacter capsulatus SB1003. Each had denitrifying capabilities that matched their genome annotation; CGA0092 reduced NO2- to N2, and SB1003 reduced N2O to N2. For each bacterium, N2O reduction could be used both for electron balance during growth on electron-rich organic compounds in light and for energy transformation via respiration in darkness. However, N2O reduction required supplementation with a denitrification intermediate, including those for which there was no associated denitrification enzyme. For CGA0092, NO3- served as a stable, non-catalyzable molecule that was sufficient to activate N2O reduction. Using a β-galactosidase reporter, we found that NO3- acted, at least in part, by stimulating N2O reductase gene expression. In SB1003, NO2- but not NO3- activated N2O reduction, but NO2- was slowly removed, likely by a promiscuous enzyme activity. Our findings reveal that partial denitrifiers can still be subject to regulation by denitrification intermediates that they cannot use.IMPORTANCEDenitrification is a form of microbial respiration wherein nitrate is converted via several nitrogen oxide intermediates into harmless dinitrogen gas. Partial denitrifying bacteria, which individually have some but not all denitrifying enzymes, can achieve complete denitrification as a community by cross-feeding nitrogen oxide intermediates. However, the last intermediate, nitrous oxide (N2O), is a potent greenhouse gas that often escapes, motivating efforts to understand and improve the efficiency of denitrification. Here, we found that at least some partial denitrifying N2O reducers can sense and respond to nitrogen oxide intermediates that they cannot otherwise use. The regulatory effects of nitrogen oxides on partial denitrifiers are thus an important consideration in understanding and applying denitrifying bacterial communities to combat greenhouse gas emissions.

Recent Developments and Applications of Biocatalytic and Chemoenzymatic Synthesis for the Generation of Diverse Classes of Drugs

Biocatalytic and chemoenzymatic biosynthesis are powerful methods of organic chemistry that use enzymes to execute selective reactions and allow the efficient production of organic compounds. The advantages of these approaches include high selectivity, mild reaction conditions, and the ability to work with complex substrates. The utilization of chemoenzymatic techniques for the synthesis of complicated compounds has lately increased dramatically in the area of organic chemistry. Biocatalytic technologies and modern synthetic methods are utilized synergistically in a multi-step approach to a target molecule under this paradigm. Chemoenzymatic techniques are promising for simplifying access to essential bioactive compounds because of the remarkable regio- and stereoselectivity of enzymatic transformations and the reaction diversity of modern organic chemistry. Enzyme kits may include ready-to-use, reproducible biocatalysts. Its use opens up new avenues for the synthesis of active therapeutic compounds and aids in drug development by synthesizing active components to construct scaffolds in a targeted and preparative manner. This study summarizes current breakthroughs as well as notable instances of biocatalytic and chemoenzymatic synthesis. To assist organic chemists in the use of enzymes for synthetic applications, it also provides some basic guidelines for selecting the most appropriate enzyme for a targeted reaction while keeping aspects like cofactor requirement, solvent tolerance, use of whole cell or isolated enzymes, and commercial availability in mind.

Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones

Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially mediated pathway proceeding stepwise from NO3- to N2. This process may be performed entirely by complete denitrifiers capable of all four enzymatic steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas N2O. Metagenomics and marker gene surveys have revealed a diversity of denitrification genes within ODZs, but whether these genes co-occur within complete or partial denitrifiers and the identities of denitrifying taxa remain open questions. We assemble genomes from metagenomes spanning the ETNP and Arabian Sea, and map these metagenome-assembled genomes (MAGs) to 56 metagenomes from all three major ODZs to reveal the predominance of partial denitrifiers, particularly single-step denitrifiers. We find niche differentiation among nitrogen-cycling organisms, with communities performing each nitrogen transformation distinct in taxonomic identity and motility traits. Our collection of 962 MAGs presents the largest collection of pelagic ODZ microorganisms and reveals a clearer picture of the nitrogen cycling community within this environment.

Ecological interactions and the underlying mechanism of anammox and denitrification across the anammox enrichment with eutrophic lake sediments

BACKGROUND

Increasing attention has recently been devoted to the anaerobic ammonium oxidation (anammox) in eutrophic lakes due to its potential key functions in nitrogen (N) removal for eutrophication control. However, successful enrichment of anammox bacteria from lake sediments is still challenging, partly due to the ecological interactions between anammox and denitrifying bacteria across such enrichment with lake sediments remain unclear.

RESULTS

This study thus designed to fill such knowledge gaps using bioreactors to enrich anammox bacteria with eutrophic lake sediments for more than 365 days. We continuously monitored the influent and effluent water, measured the anammox and denitrification efficiencies, quantified the anammox and denitrifying bacteria, as well as the related N cycling genes. We found that the maximum removal efficiencies of NH₄⁺ and NO₂^- reached up to 85.92% and 95.34%, respectively. Accordingly, the diversity of anammox and denitrifying bacteria decreased significantly across the enrichment, and the relative dominant anammox (e.g., Candidatus Jettenia) and denitrifying bacteria (e.g., Thauera, Afipia) shifted considerably. The ecological cooperation between anammox and denitrifying bacteria tended to increase the microbial community stability, indicating a potential coupling between anammox and denitrifying bacteria. Moreover, the nirS-type denitrifiers showed stronger coupling with anammox bacteria than that of nirK-type denitrifiers during the enrichment. Functional potentials as depicted by metagenome sequencing confirmed the ecological interactions between anammox and denitrification. Metagenome-assembled genomes-based ecological model indicated that the most dominant denitrifiers could provide various materials such as amino acid, cofactors, and vitamin for anammox bacteria. Cross-feeding in anammox and denitrifying bacteria highlights the importance of microbial interactions for increasing the anammox N removal in eutrophic lakes.

CONCLUSIONS

This study greatly expands our understanding of cooperation mechanisms among anammox and denitrifying bacteria during the anammox enrichment with eutrophic lake sediments, which sheds new insights into N removal for controlling lake eutrophication. Video Abstract.

Genome-resolved metagenomics inferred novel insights into the microbial community, metabolic pathways, and biomining potential of Malanjkhand acidic copper mine tailings

Mine tailing sites provide profound opportunities to elucidate the microbial mechanisms involved in ecosystem functioning. In the present study, metagenomic analysis of dumping soil and adjacent pond around India's largest copper mine at Malanjkhand has been done. Taxonomic analysis deciphered the abundance of phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Chloroflexi. Genomic signatures of viruses were predicted in the soil metagenome, whereas Archaea and Eukaryotes were noticed in water samples. Mesophilic chemolithotrophs, such as Acidobacteria bacterium, Chloroflexi bacterium, and Verrucomicrobia bacterium, were predominant in soil, whereas, in the water sample, the abundance of Methylobacterium mesophilicum, Pedobacter sp., and Thaumarchaeota archaeon was determined. The functional potential analysis highlighted the abundance of genes related to sulfur, nitrogen, methane, ferrous oxidation, carbon fixation, and carbohydrate metabolisms. The genes for copper, iron, arsenic, mercury, chromium, tellurium, hydrogen peroxide, and selenium resistance were found to be predominant in the metagenomes. Metagenome-assembled genomes (MAGs) were constructed from the sequencing data, indicating novel microbial species genetically related to the phylum predicted through whole genome metagenomics. Phylogenetic analysis, genome annotations, functional potential, and resistome analysis showed the resemblance of assembled novel MAGs with traditional organisms used in bioremediation and biomining applications. Microorganisms harboring adaptive mechanisms, such as detoxification, hydroxyl radical scavenging, and heavy metal resistance, could be the potent benefactions for their utility as bioleaching agents. The genetic information produced in the present investigation provides a foundation for pursuing and understanding the molecular aspects of bioleaching and bioremediation applications.

Mycorrhiza-mediated recruitment of complete denitrifying Pseudomonas reduces N2O emissions from soil

BACKGROUND

Arbuscular mycorrhizal fungi (AMF) are key soil organisms and their extensive hyphae create a unique hyphosphere associated with microbes actively involved in N cycling. However, the underlying mechanisms how AMF and hyphae-associated microbes may cooperate to influence N₂O emissions from "hot spot" residue patches remain unclear. Here we explored the key microbes in the hyphosphere involved in N₂O production and consumption using amplicon and shotgun metagenomic sequencing. Chemotaxis, growth and N₂O emissions of isolated N₂O-reducing bacteria in response to hyphal exudates were tested using in vitro cultures and inoculation experiments.

RESULTS

AMF hyphae reduced denitrification-derived N₂O emission (max. 63%) in C- and N-rich residue patches. AMF consistently enhanced the abundance and expression of clade I nosZ gene, and inconsistently increased that of nirS and nirK genes. The reduction of N₂O emissions in the hyphosphere was linked to N₂O-reducing Pseudomonas specifically enriched by AMF, concurring with the increase in the relative abundance of the key genes involved in bacterial citrate cycle. Phenotypic characterization of the isolated complete denitrifying P. fluorescens strain JL1 (possessing clade I nosZ) indicated that the decline of net N₂O emission was a result of upregulated nosZ expression in P. fluorescens following hyphal exudation (e.g. carboxylates). These findings were further validated by re-inoculating sterilized residue patches with P. fluorescens and by an 11-year-long field experiment showing significant positive correlation between hyphal length density with the abundance of clade I nosZ gene.

CONCLUSIONS

The cooperation between AMF and the N₂O-reducing Pseudomonas residing on hyphae significantly reduce N₂O emissions in the microsites. Carboxylates exuded by hyphae act as attractants in recruiting P. fluorescens and also as stimulants triggering nosZ gene expression. Our discovery indicates that reinforcing synergies between AMF and hyphosphere microbiome may provide unexplored opportunities to stimulate N₂O consumption in nutrient-enriched microsites, and consequently reduce N₂O emissions from soils. This knowledge opens novel avenues to exploit cross-kingdom microbial interactions for sustainable agriculture and for climate change mitigation. Video Abstract.

Biodiesel Co-Product enhances microbial stability and beneficial microbial communities along a gradient of soil water content

Biodiesel Co-Product (BCP) is a complex carbonaceous liquid formed during the commercial production of biodiesel. Previously, BCP was shown to decrease nitrogen (N) leaching from the soil, but the effects of BCP on the diversity, composition, and structure of soil microbial communities are not well understood. Here, we applied 1.5 mg BCP-C to acidic soil (pH 3.5) at a range of different water contents (from 40 % to 100 % water holding capacity) to investigate the interactions between BCP and increasing water holding capacity on the diversity, composition, and interactions of soil microbial communities. Distance-based multivariate linear model (DistLM) and non-metric multidimensional scaling (NMDS) analyses showed that BCP caused larger changes in fungal than bacterial communities, while soil water content had a greater effect on bacterial communities relative to fungal communities. Co-occurrence network analyses indicated that BCP amendment produced more robust and complex bacterial networks and more stable fungal ones. BCP significantly increased the OTU numbers of beneficial microbes (e.g., Trichoderma spp.) in all water contents, with fewer OTU numbers of putative pathogenetic species (Fusarium spp. and Aspergillus spp.). These findings indicate that BCP addition may be conducive to the health and stability of soil ecosystems.

On the hidden diversity and niche specialization of the microbial realm of subterranean estuaries

Subterranean estuaries (STEs) modulate the chemical composition of continental groundwater before it reaches the coast, but their microbial community is poorly known. Here, we explored the microbial ecology of two neighbouring, yet contrasting STEs (Panxón and Ladeira STEs; Ría de Vigo, NW Iberian Peninsula). We investigated microbial composition (16S rRNA gene sequencing), abundance, heterotrophic production and their geochemical drivers. A total of 10,150 OTUs and 59 phyla were retrieved from porewater sampled during four surveys covering each STE seepage face. In both STEs, we find a very diverse microbial community composed by abundant cosmopolitans and locally restricted rare taxa. Porewater oxygen and dissolved organic matter are the main environmental predictors of microbial community composition. More importantly, the high variety of benthic microbiota links to biogeochemical processes of different elements in STEs. The oxygen-rich Panxón beach showed strong associations of the ammonium oxidizing archaea Nitrosopumilales with the heterotrophic community, thus acting as a net source of nitrogen to the coast. On the other hand, the prevailing anoxic conditions of Ladeira beach promoted the dominance of anaerobic heterotrophs related to the degradation of complex and aromatic compounds, such as Dehalococcoidia and Desulfatiglans, and the co-occurrence of methane oxidizers and methanogens.

Different responses of representative denitrifying bacterial strains to gatifloxacin exposure in simulated groundwater denitrification environment

The impact of antibiotics on denitrification in the ecological environment has attracted widespread attention. However, the concentration threshold and inhibitory effect of the same antibiotic on denitrification mediated by mixed denitrifying microbes were conflicting in some studies. In this study, Paracoccus denitrificans, Acidovorax sp., and Pseudomonas aeruginosa were selected as representative denitrifying bacterial strains to explore the response of a single strain to gatifloxacin (GAT) exposure in groundwater denitrification. The results showed that the nitrate and nitrite removal efficiencies of Pseudomonas aeruginosa decreased by 34.87-36.25 % and 18.27-23.31 %, respectively, with exposure to 10 μg/L GAT, accompanied by a significant decline in denitrifying enzyme activity and gene expression. In contrast, the elevated denitrifying enzyme activity and gene expression of Paracoccus denitrificans promoted its nitrate and nitrite reduction by 2.09-10.00 % and 0-8.44 %, respectively. Additionally, there were no obvious effects on the removal of nitrate and nitrite by Acidovorax sp. in the presence of 10 μg/L GAT, which was consistent with the variation in denitrifying enzyme activity and total gene expression levels. The fit results of the Monod equation and its modification further elucidated the nitrate degradation characteristics from the perspective of denitrification kinetics. Furthermore, antibiotic resistance gene (ARG) analysis showed that the addition of 10 μg/L GAT (approximately 30 days) did not observably increase the relative abundance of ARGs. This study provides some preliminary understanding of the response differences of representative denitrifying bacterial strains to antibiotic exposure in groundwater denitrification.

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.

NosZI microbial community determined the potential of denitrification and nitrous oxide emission in river sediments of Qinghai-Tibetan Plateau

Denitrification in river sediments is the hotspot of nitrogen removal and nosZI gene is essential for reducing nitrous oxide (N₂O) emissions. However, few studies tried to link nosZI communities with variations of denitrification rates in sediments along the high-elevation rivers. Here, we investigated the spatial variation of potential denitrification rates of sediments along a section (hereafter YJ) of the middle reaches of the Yarlung Zangbo River in the Qinghai-Tibetan Plateau. We also used the real-time quantitative PCR (qPCR) and high-throughput sequencing techniques to evaluate the abundance and composition of nosZI-containing microbial groups. The influences of physicochemical factors and denitrifier communities on potential denitrification rates were further revealed through structural equation modeling. The obtained results indicated that potential denitrification rates and N₂O/(N₂O + N₂) ratio in the sediments along YJ section were greatly different. Moreover, the alpha diversity and composition of nosZI-containing microbial community in river sediments differed remarkably, mainly driven by the ammonia nitrogen (NH₄⁺-N), organic matter (OM) and pH in sediments. The relative abundances of Zoogloeaceae, Oxalobacteraceae, Rhodospirillaceae and Bradyrhizobiaceae significantly differed among five groups (P < 0.05). Structural equation modeling further suggested that nitrogen nutrients directly influenced the potential denitrification rates, while total phosphorus (TP) showed indirect effects on potential denitrification rates through modulating denitrifier abundances and nosZI community. The abundance and composition of nosZI community were powerful predictors in regulating denitrification rates and N₂O/(N₂O + N₂) ratio. Our findings highlight that the nosZI-containing microbial groups play a non-negligible role in nitrogen removal and N₂O mitigation in high-elevation river sediments.

Organic and inorganic nitrogen removals by an ureolytic heterotrophic nitrification and aerobic denitrification strain Acinetobacter sp. Z1: Elucidating its physiological characteristics and metabolic mechanisms

Although heterotrophic nitrification-aerobic denitrification (HN-AD) is promising in nitrogen removal, it remains unclear for most HN-AD strains in physiological characteristics and metabolic mechanisms. In this study, a newly isolated strain Acinetobacter sp. Z1 converted not only inorganic nitrogen, but also organic nitrogen to N₂. Among them, urea was the preferential nitrogen substrate. Single-factor experiments showed that efficient HN-AD process occurred with acetate as carbon source, C/N ratios of 12 for NH₄⁺-N and 15 for NO₃^--N, pH 8, 30 °C, DO of ∼5.8 mg/L and salinity less than 1.5 %. Subsequently, response surface analysis was applied to predict the optimal growth conditions. Its complete genome annotation in combination with enzymatic activity assay and nitrogen balance calculation showed that at least four pathways involved in nitrogen metabolism. This work indicates that ureolytic strain Z1 could be prepared as bacterial agents with other HN-AD strains to treat urea-containing wastewater like urine from urban community.

Enhanced denitrification of sewage via bio-microcapsules embedding heterotrophic nitrification-aerobic denitrification bacteria Acinetobacter pittii SY9 and corn cob

In this work, bio-microcapsules were prepared by embedding heterotrophic nitrification and aerobic denitrification (HN-AD) bacteria (Acinetobacter Pittii SY9) and corn cob. Bio-microcapsules (20 g/L of corn cob and 30% v/v suspension of strain SY9) were porous (pore size 2579.74-3725.44 nm; porosity 53.6%-79.9%). Under the appropriate conditions (C/N > 2, temperature of 20-35 ℃, rotation speed of 100-120 rpm, pH of 7-9), TN removal efficiency of bio-microcapsules reached 94.4%, and 74.0% of nitrogen was converted into N₂. The results of kinetics fitting indicated that aerobic denitrification was the limiting step during HN-AD process. Bio-microcapsules could slow the carbon release of corn cob for 120 days, which ensuring high HN-AD performance even at low C/N of 2.8. Bio-microcapsule SBR could stably run for 88 days with TN removal efficiency > 90% for synthetic sewage. Bio-microcapsules embedding strain SY9 and corn cob have prospective applications for enhancing denitrification of sewage.

Ubiquity and Diversity of Cold Adapted Denitrifying Bacteria Isolated From Diverse Antarctic Ecosystems

Nitrogen cycle has been poorly investigated in Antarctic ecosystems. In particular, how extreme conditions of low temperature, dryness, and high radiation select the microorganisms involved in the cycle is not yet understood. Denitrification is an important step in the nitrogen cycle in which nitrate is reduced stepwise to the gases NO, N2O, and N2. Denitrification is carried out by a wide group of microorganisms spread in the phylogenetic tree. The aim of this work was to isolate and characterize denitrifying bacteria present in different cold environments from Antarctica. Bacterial isolates were obtained from lake, meltwater, sea, glacier ice, ornithogenic soil, and penguin feces samples from King George Island, Fildes peninsula in the Antarctic. Samples were taken during the deicing season in five sampling campaigns. From all the samples we were able to isolate denitrifying strains. A total of 199 bacterial isolates with the capacity to grow in anaerobic mineral media reducing nitrate at 4°C were obtained. The characterization of the isolates by 16S rRNA gene sequence analysis showed a high predominance of the genus Pseudomonas, followed by Janthinobacterium, Flavobacterium, Psychrobacter, and Yersinia. Other minor genera detected were Cryobacterium, Iodobacter, Kaistella, and Carnobacterium. The capacity to denitrify was not previously described for most of the bacteria related to our isolates and in many of them denitrifying genes were not present suggesting the presence of new genes in this extreme environment. Our work demonstrates the ubiquity of denitrification in the Maritime Antarctica and gives important information linking denitrification at cold temperature with taxa in an unequivocal way.

Effects of functional-membrane covering technique on nitrogen succession during aerobic composting: Metabolic pathways, functional enzymes, and functional genes

This study investigated and assessed the effect of the functional-membrane covering technique (FMCT) on nitrogen succession during aerobic composting. By comparative experiments involving high-throughput sequencing and qPCR, nitrogen metabolism (including the ko00910 pathway and functional enzyme and gene abundances) was analyzed, and the nitrogen succession mechanism was identified. The FMCT created a micro-positive pressure, improved the aerobic conditions, and increased the oxygen utilization rate and temperature. This strongly affected the nitrogen metabolism pathway and down-regulated the nitrifying and denitrifying bacteria abundances. The FMCT up-regulated the relative abundance of glutamate dehydrogenase and down-regulated the absolute abundances of AOB and nxrA. This and the high temperature increased NH₃ emissions by 13.78%-73.37%. The FMCT down-regulated the abundances of denitrifying gene groups (nirS + nirK)/nosZ and nitric oxide reductase associated with N₂O emissions and decreased N₂O emissions by 16.44%-41.15%. The results improve the understanding of the mechanism involved in nitrogen succession using the FMCT.

Simultaneous removal of aromatic pollutants and nitrate at high concentrations by hypersaline denitrification:Long-term continuous experiments investigation

If we can use toxic aromatic compounds as supplementary carbon source, the simultaneous removal of nitrate (NO₃^-) and aromatic compounds may be achieved at much lower chemical costs. This study uses the expanded granular sludge bed (EGSB) reactors to investigate the hypersaline (> 3%) denitrification performance, the removal of aromatic compounds, i.e., aniline, phenol, and their mixture, and the mechanisms involved in. The four reactors exhibit high removal efficiency of NO₃^- (> 92.8%) and aromatic compounds (> 73.9%) at 0-1200 mg/L of aromatic compounds. The formation of toxic intermediates such as catechol and azo dyes is revealed by gas chromatography mass spectrometry (GC-MS) with and without N,O-Bis(trimethylsilyl) trifluoroacetamide (BSTFA) derivation, and their toxic effects lead to the lower cell survival ratios after exposing to phenol (64.2% ∼ 68.9%) than to aniline and mixture (72.7% ∼ 78.0%). The stable performance is associated with the more secretion of extracellular polymeric substances (EPS) and the adsorption of pollutants on EPS, and this was indicated from the higher fluorescence intensity in three-dimensional excitation-emission matrix (3D-EEM). Moreover, the Halomonas and Azoarcus show high abundance and play important roles in the removal of both NO₃^- and aromatic compounds. Besides, quantitative real time PCR (RT-qPCR) results demonstrate the key role of highly abundant nosZ and nirS genes in denitrification. The toxic organics in industrial wastewaters are potentially feasible carbon sources for denitrification even under high-salinity stress.

Reactive nitrogen restructures and weakens microbial controls of soil N2O emissions

The global surplus of reactive nitrogen (Nr) in agricultural soils is accelerating nitrous oxide (N2O) emission rates, and may also strongly influence the microbial controls of this greenhouse gas resulting in positive feedbacks that further exacerbate N2O emissions. Yet, the link between legacy effects of Nr on microbial communities and altered regulation of N2O emissions is unclear. By examining soils with legacies of Nr-addition from 14 field experiments with different edaphic backgrounds, we show that increased potential N2O production is associated with specific phylogenetic shifts in communities of frequently occurring soil microbes. Inputs of Nr increased the complexity of microbial co-association networks, and altered the relative importance of biotic and abiotic predictors of potential N2O emissions. Our results provide a link between the microbial legacy of Nr addition and increased N2O emissions by demonstrating that biological controls of N2O emissions were more important in unfertilized soils and that these controls are weakened by increasing resource levels in soil.

Global Patterns and Drivers of Soil Dissimilatory Nitrate Reduction to Ammonium

Dissimilatory nitrate reduction to ammonium (DNRA), the nearly forgotten process in the terrestrial nitrogen (N) cycle, can conserve N by converting the mobile nitrate into non-mobile ammonium avoiding nitrate losses via denitrification, leaching, and runoff. However, global patterns and controlling factors of soil DNRA are still only rudimentarily known. By a meta-analysis of 231 observations from 85 published studies across terrestrial ecosystems, we find a global mean DNRA rate of 0.31 ± 0.05 mg N kg^-1 day^-1, being significantly greater in paddy soils (1.30 ± 0.59) than in forests (0.24 ± 0.03), grasslands (0.52 ± 0.15), and unfertilized croplands (0.18 ± 0.04). Soil DNRA was significantly enhanced at higher altitude and lower latitude. Soil DNRA was positively correlated with precipitation, temperature, pH, soil total carbon, and soil total N. Precipitation was the main stimulator for soil DNRA. Total carbon and pH were also important factors, but their effects were ecosystem-specific as total carbon stimulates DNRA in forest soils, whereas pH stimulates DNRA in unfertilized croplands and paddy soils. Higher temperatures inhibit soil DNRA via decreasing total carbon. Moreover, nitrous oxide (N₂O) emissions were negatively related to soil DNRA. Thus, future changes in climate and land-use may interact with management practices that alter soil substrate availability and/or soil pH to enhance soil DNRA with positive effects on N conservation and lower N₂O emissions.

Re-evaluation of the environmental hazards of nZnO to denitrification: Performance and mechanism

Numerous studies have shown that zinc oxide nanoparticles (nZnO) have an inhibitory effect on wastewater biotreatment, where doses exceeding ambient concentrations are used. However, the effect of ambient concentrations of ZnO (<1 mg/L) on anaerobic digestion processes is not clear. Herein, this study comprehensively explored the impact of nZnO on the denitrification performance and core microbial community of activated sludge under ambient concentrations. Results showed that only 0.075 mg/L nZnO had shown a beneficial effect on nitrogen removal by activated sludge. When nZnO concentration reached 0.75 mg/L, significant enhancement of nitrate reduction and mitigation of nitrite accumulation were observed, indicating a remarkable stimulatory effect on nitrogen removal. Simultaneously, nZnO could weaken the sludge surface charge and improve the secretion of extracellular polymeric substances, thus enhancing sludge flocculation for denitrification. Microbial community analysis revealed that nZnO exposure increased the relative abundance of denitrifying bacteria, which could contribute to the reinforcement of traditional denitrification. Furthermore, exogenous addition of NH₄⁺ significantly inhibited the accumulation of nitrite, implying that nZnO had a potential to improve the denitrification process via a partial denitrification-anammox pathway. Considering current ambient concentration, the stimulatory effect shown in our work may better represent the actual behavior of ZnO in wastewater biotreatment.

WIDESPREAD CAPACITY FOR DENITRIFICATION ACROSS A BOREAL FOREST LANDSCAPE

A warming climate combined with frequent and severe fires cause permafrost to thaw, especially in the region of discontinuous permafrost, where soil temperatures may only be a few degrees below 0 °C. Soil thaw releases carbon (C) and nitrogen (N) into the actively cycling pools, and whereas C emissions following permafrost thaw are well documented, the fates of N remain unclear. Denitrification could release N from ecosystems as nitrous oxide (N₂O) or nitrogen gas (N₂), but the contributions of these processes to the high-latitude N cycle remain uncertain. We quantified microbial capacity for denitrification and N₂O production in boreal soils, lakes, and streams using anoxic C- and N-amended assays, and assessed correlates of denitrifying enzyme activity (DEA) in Interior Alaska. Riparian soils and stream sediments supported the highest potential rates of denitrification, upland soils were intermediate, and lakes supported lower rates, whereas deep permafrost soils supported little denitrification. Time since fire had no effect on denitrification potential in upland soils. Across all landscape positions, DEA was negatively correlated with ammonium pools. Within each landscape position, potential rate of denitrification increased with soil or sediment organic matter content. Widespread N loss to denitrification in boreal forests could constrain the capacity for N-limited primary producers to maintain C stocks in soils following permafrost thaw.

Genomic structure predicts metabolite dynamics in microbial communities

The metabolic activities of microbial communities play a defining role in the evolution and persistence of life on Earth, driving redox reactions that give rise to global biogeochemical cycles. Community metabolism emerges from a hierarchy of processes, including gene expression, ecological interactions, and environmental factors. In wild communities, gene content is correlated with environmental context, but predicting metabolite dynamics from genomes remains elusive. Here, we show, for the process of denitrification, that metabolite dynamics of a community are predictable from the genes each member of the community possesses. A simple linear regression reveals a sparse and generalizable mapping from gene content to metabolite dynamics for genomically diverse bacteria. A consumer-resource model correctly predicts community metabolite dynamics from single-strain phenotypes. Our results demonstrate that the conserved impacts of metabolic genes can predict community metabolite dynamics, enabling the prediction of metabolite dynamics from metagenomes, designing denitrifying communities, and discovering how genome evolution impacts metabolism.

Nitrous oxide formation during simultaneous phosphorus and nitrogen removal in aerobic granular sludge treating different carbon substrates

The impact of different substrates on N₂O dynamics and gene expression of marker enzymes (nirS, nirK and nosZ) involved in denitrifying enhanced biological phosphorus removal (d-EBPR) was investigated. Aerobic granular sludge fed with VFAs led to an anoxic P-uptake (27.7 ± 1.2 mg PO₄^3--P.gVSS^-1) and N₂O emissions up to 80.7 ± 3.4% N₂O-N. A decisive role of Accumulibacter in N₂O formation was observed. Dosage of amino acids (12.0 ± 1.2 mg PO₄^3--P.gVSS^-1) and glucose (1.5 ± 0.9 mg PO₄^3--P.gVSS^-1) as sole substrate did not support d-EBPR activity. Presence of NO₂^- resulted in higher N₂O formation in comparison to nitrate and a nosZ/(nirS + nirK) ratio lower than 0.3. A linear correlation (R² > 0.95) between the nosZ/(nirS + nirK) ratio and the N₂O reductase rate was found only when dosing the same type of substrate. This suggests an interplay between the microbial community composition and different polyhydroxyalkanoates derivatives, when dosing different substrates.

Novel nitrite reductase domain structure suggests a chimeric denitrification repertoire in the phylum Chloroflexi

Denitrification plays a central role in the global nitrogen cycle, reducing and removing nitrogen from marine and terrestrial ecosystems. The flux of nitrogen species through this pathway has a widespread impact, affecting ecological carrying capacity, agriculture, and climate. Nitrite reductase (Nir) and nitric oxide reductase (NOR) are the two central enzymes in this pathway. Here we present a previously unreported Nir domain architecture in members of phylum Chloroflexi. Phylogenetic analyses of protein domains within Nir indicate that an ancestral horizontal transfer and fusion event produced this chimeric domain architecture. We also identify an expanded genomic diversity of a rarely reported NOR subtype, eNOR. Together, these results suggest a greater diversity of denitrification enzyme arrangements exist than have been previously reported.

Adaptability of enhanced bioretention cell for nitrogen and phosphorus removal under two antibiotics stress

The overuse of antibiotics in the medical and aquaculture industries has led to the frequent detection of antibiotics in wastewater. Considering antibiotics would have an unknown impact on wastewater treatment in the future, the long-term effects of sulfamethoxazole (SMX) and tetracycline (TC) stress on the performance, functional genes and microbial community in three bioretention cells were investigated. The results showed that during the experiment, 0.8-1.2 mg/L of SMX would not destroy the water treatment capacity of the bioretention cells, and had a promoting effect on total nitrogen and ammonia nitrogen. 1.6 mg/L of SMX would cause the reduction of nitrogen removal efficiency and the phenomenon of phosphorus release, but it could be restored after a period of operation. TC of 0.8-1.2 mg/L did not have a significant impact on the removal of nutrients in AC-BRC (activated carbon-bioretention cell) and ACI-BRC (activated carbon and iron-bioretention cell), but TC of 1.2 mg/L caused the phenomenon of phosphorus release in BRC and the decrease of total nitrogen removal rate, 1.6 mg/L TC could make the bioretention cell lose its water treatment capacity. qPCR analysis of denitrification genes showed that the abundance of nirS, nirK, nosZ, and hzo had varying degrees of decrease before and after antibiotic stress, which meant the two antibiotics significantly inhibited the reduction of nitrite and nitrous oxide. But for the total number of bacteria, the relative abundance of the four genes has increased. The results of microbial community analysis also found that Proteobacteria, Bacteroidetes, Chloroflexi, and BIrii41, Denitratisoma, Ferritrophicum, Thiobacillus occupied the dominant species at the phylum level and the genus level respectively, which included most of the denitrifying bacteria. During the experiment, the nitrogen and phosphorus removal efficiency of AC-BRC and ACI-BRC were enhanced obviously, but ammonia nitrogen accumulated in ACI-BRC in the early stage of the reaction.

Dissimilatory nitrate reduction by a freshwater cable bacterium

Cable bacteria (CB) are filamentous Desulfobulbaceae that split the energy-conserving reaction of sulfide oxidation into two half reactions occurring in distinct cells. CB can use nitrate, but the reduction pathway is unknown, making it difficult to assess their direct impact on the N-cycle. Here we show that the freshwater cable bacterium Ca. Electronema sp. GS performs dissimilatory nitrate reduction to ammonium (DNRA). ¹⁵NO₃^--amended sediment with Ca. Electronema sp. GS showed higher rates of DNRA and nitrite production than sediment without Ca. Electronema sp. GS. Electron flux from sulfide oxidation, inferred from electric potential (EP) measurements, matched the electron flux needed to drive CB-mediated nitrate reduction to nitrite and ammonium. Ca. Electronema sp. GS expressed a complete nap operon for periplasmic nitrate reduction to nitrite, and a putative octaheme cytochrome c (pOCC), whose involvement in nitrite reduction to ammonium remains to be verified. Phylogenetic analysis suggests that the capacity for DNRA was acquired in multiple events through horizontal gene transfer from different organisms, before CB split into different salinity niches. The architecture of the nitrate reduction system suggests absence of energy conservation through oxidative phosphorylation, indicating that CB primarily conserve energy through the half reaction of sulfide oxidation.

Patterns and Drivers of nirK-Type and nirS-Type Denitrifier Community Assembly along an Elevation Gradient

nirK-type and nirS-type denitrifier communities mediate the conversion of nitrite to nitric oxide, which is the key step in denitrification. Results of previous studies have indicated that nirK-type and nirS-type denitrifiers may occupy different niches; however, the mechanisms and drivers of their responses to environmental changes within community assembly are poorly understood. In this study, we evaluated the distribution and assembly of nirK-type and nirS-type denitrifier communities along an elevation gradient from 1,800 to 4,100 m at Mount Gongga, China. Results showed that elevational patterns of alpha diversity in nirK-type and nirS-type denitrifier communities followed hump-backed patterns along the elevation gradient. However, nirK-type denitrifier communities formed two distinct clusters that were primarily separated by elevation, whereas nirS-type denitrifier communities formed three distinct clusters that were primarily separated by forest type along the elevation gradient. Moreover, deterministic processes were dominant in governing the assemblages of nirK-type and nirS-type denitrifiers. Soil pH was a key factor influencing the alpha and beta diversity of the nirK-type denitrifier communities, whereas plant richness was a primary variable influencing nirS-type denitrifiers. Additionally, our work revealed that soil denitrification potential was mainly explained by the variation in the beta diversity of denitrifier communities rather than the alpha diversity of denitrifier communities or denitrifier abundances over a large elevation gradient, and nirK-type denitrifiers played more important roles in soil denitrification. These results may contribute to predicting the consequences of global changes on denitrifier communities and their ecological services. IMPORTANCE Mount Gongga is the highest peak in the Hengduan Mountain region and is located at the southeastern fringe of the Tibetan Plateau, Sichuan Province, southwest China. As a transitional zone between the Tibetan Plateau and Sichuan Basin, Gongga Mountain features particularly diverse topography, geology, climate, and biodiversity and is a globally significant hot spot of biodiversity. In this contribution, we comprehensively describe the diversity and assembly of denitrifier communities along an elevation gradient on Gongga Mountain. Our findings established for the first time that the distribution patterns of beta diversity and driving factors differed between nirK-type and nirS-type denitrifier communities, and deterministic processes were dominant in shaping communities of denitrifiers. Moreover, the beta diversity of denitrifier communities rather than alpha diversity or denitrifier abundance played an important role in explaining denitrification potential, and the beta diversity of nirK-type denitrifier communities was more important than nirS-type denitrifier communities in soil denitrification. This work provides crucial insights into the spatial distribution of denitrifier communities and their ecological function and increases our understanding of the mechanisms underlying spatial distribution of community assembly along large elevation gradients.

Revisiting the involvement of ammonia oxidizers and denitrifiers in nitrous oxide emission from cropland soils

Nitrous oxide (N₂O), an ozone-depleting greenhouse gas, is generally produced by soil microbes, particularly NH₃ oxidizers and denitrifiers, and emitted in large quantities after N fertilizer application in croplands. N₂O can be produced via multiple processes, and reduced, with the involvement of more diverse microbes with different physiological constraints than previously thought; therefore, there is a lack of consensus on the production processes and microbes involved under different agricultural practices. In this study, multiple approaches were applied, including N₂O isotopocule analyses, microbial gene transcript measurements, and selective inhibition assays, to revisit the involvement of NH₃ oxidizers and denitrifiers, including the previously-overlooked taxa, in N₂O emission from a cropland, and address the biological and environmental factors controlling the N₂O production processes. Then, we synthesized the results from those approaches and revealed that the overlooked denitrifying bacteria and fungi were more involved in N₂O production than the long-studied ones. We also demonstrated that the N₂O production processes and soil microbes involved were different based on fertilization practices (plowing or surface application) and fertilization types (manure or urea). In particular, we identified the following intensified activities: (1) N₂O production by overlooked denitrifying fungi after manure fertilization onto soil surface; (2) N₂O production by overlooked denitrifying bacteria and N₂O reduction by long-studied N₂O-reducing bacteria after manure fertilization into the plowed layer; and (3) N₂O production by NH₃-oxidizing bacteria and overlooked denitrifying bacteria and fungi when urea fertilization was applied into the plowed layer. We finally propose the conceptual scheme of N flow after fertilization based on distinct physiological constraints among the diverse NH₃ oxidizers and denitrifiers, which will help us understand the environmental context-dependent N₂O emission processes.

Distinct Endophytic Bacterial Communities Inhabiting Seagrass Seeds

Seagrasses are marine angiosperms that can live completely or partially submerged in water and perform a variety of significant ecosystem services. Like terrestrial angiosperms, seagrasses can reproduce sexually and, the pollinated female flower develop into fruits and seeds, which represent a critical stage in the life of plants. Seed microbiomes include endophytic microorganisms that in terrestrial plants can affect seed germination and seedling health through phytohormone production, enhanced nutrient availability and defence against pathogens. However, the characteristics and origins of the seagrass seed microbiomes is unknown. Here, we examined the endophytic bacterial community of six microenvironments (flowers, fruits, and seeds, together with leaves, roots, and rhizospheric sediment) of the seagrass Halophila ovalis collected from the Swan Estuary, in southwestern Australia. An amplicon sequencing approach (16S rRNA) was used to characterize the diversity and composition of H. ovalis bacterial microbiomes and identify core microbiome bacteria that were conserved across microenvironments. Distinct communities of bacteria were observed within specific seagrass microenvironments, including the reproductive tissues (flowers, fruits, and seeds). In particular, bacteria previously associated with plant growth promoting characteristics were mainly found within reproductive tissues. Seagrass seed-borne bacteria that exhibit growth promoting traits, the ability to fix nitrogen and anti-pathogenic potential activity, may play a pivotal role in seed survival, as is common for terrestrial plants. We present the endophytic community of the seagrass seeds as foundation for the identification of potential beneficial bacteria and their selection in order to improve seagrass restoration.

Denitrifying bacterial community dominantly drove nitrogen removals in vertical flow constructed wetlands as impacted by macrophyte planting patterns

The study aims to identify relations of denitrifying bacterial and fungal communities to nitrogen removals in vertical flow wetland microcosms (VFWMs) using four macrophyte species (Iris pseudacorus, Canna glauca, Scirpus validus and Cyperus alternifolius) and three species richness levels (unplanted, monocultured and 4-species mixture) as fixed factors. Results showed that among four macrophyte species, only Canna glauca planting significantly decreased nitrate removal by 87.7% in the VFWMs. The 4-species mixture improved TN and nitrate removals by 84.0% and 91.3%, but decreased ammonium removal by 94.5%. Heatmap and nonmetric multidimensional scaling analyses identified a significant difference in denitrifying bacterial community structure across macrophyte richness levels, but did not identify the difference in denitrifying fungal communities. The redundancy analysis revealed that denitrifying bacterial community individually explained 99.4% and 93.0% variance of nitrogen removals among four macrophyte species and across macrophyte richness levels, while the fungal community only explained 30.7% and 21.8% variance of nitrogen removals. Overall, the macrophyte richness and bacterial denitrifiers are the critical factors of nitrogen removals in the VFWMs, thus providing useful data to design a vertical flow constructed wetland at a full scale.

Ratio of Electron Donor to Acceptor Influences Metabolic Specialization and Denitrification Dynamics in Pseudomonas aeruginosa in a Mixed Carbon Medium

Denitrifying microbes sequentially reduce nitrate (NO3 -) to nitrite (NO2 -), NO, N2O, and N2 through enzymes encoded by nar, nir, nor, and nos. Some denitrifiers maintain the whole four-gene pathway, but others possess partial pathways. Partial denitrifiers may evolve through metabolic specialization whereas complete denitrifiers may adapt toward greater metabolic flexibility in nitrogen oxide (NOx -) utilization. Both exist within natural environments, but we lack an understanding of selective pressures driving the evolution toward each lifestyle. Here we investigate differences in growth rate, growth yield, denitrification dynamics, and the extent of intermediate metabolite accumulation under varying nutrient conditions between the model complete denitrifier Pseudomonas aeruginosa and a community of engineered specialists with deletions in the denitrification genes nar or nir. Our results in a mixed carbon medium indicate a growth rate vs. yield tradeoff between complete and partial denitrifiers, which varies with total nutrient availability and ratios of organic carbon to NOx -. We found that the cultures of both complete and partial denitrifiers accumulated nitrite and that the metabolic lifestyle coupled with nutrient conditions are responsible for the extent of nitrite accumulation.

Recent advances in partial denitrification-anaerobic ammonium oxidation process for mainstream municipal wastewater treatment

To solve the bottleneck of the unstable accumulation of nitrite in the partial nitrification (PN)-anammox (AMX) in municipal wastewater treatment, a novel process called partial denitrification (PD)-AMX has been developed. PD-AMX, which is known for cost-efficiency and environmental friendliness, has currently exhibited a promising potential for the removal of biological nitrogen from municipal wastewater and has attracted much research interest regarding its process mechanisms, as well as its practical applications. Here, we review the recent advances in the PD process and its coupling to the anammox process, including the development, basic principles, main characteristics, and critical process parameters of the stable operation of the PD-AMX process. We also explore the microbial community and its characteristics in the system and summarize the knowledge of the dominant bacteria to clarify the key factors affecting PD-AMX. Then, we introduce the engineering feasibility and economic feasibility as well as the potential challenges of the process. The induction and implementation of partial denitrification and maintenance of mainstream anammox are critical issues to be urgently solved. Meanwhile, the implementation of a full mainstream anammox application remains burdensome, while the mechanism of partial denitrification coupled to anammox needs to be further studied. Additionally, stable operation performance and process control¹ methods need to be optimized or developed for the PD-AMX system for better engineering practice. This review can help to accelerate the research and application of the PD-AMX process for municipal wastewater treatment.

Simultaneous nitrification and denitrification in continuous flow MBBR with novel surface-modified carriers

ABSTRACTMoving-Bed Biofilm Reactor (MBBR) process is an ideal preference for simultaneous nitrification and denitrification (SND) attributing to the longer sludge age and aerobic/anoxic microenvironment along biofilm. However, conventional carriers generally exhibit negative charge and surface hydrophobicity, which are unbeneficial for biofilm formation. In this study, novel surface-modified carriers with favourable hydrophilicity (surface contact angle dropped to 60.2 ± 2.3°) and positive surface charge (+11.7 ± 1.1 mV, pH 7.0) were prepared via polymer blending and implemented for SND in continuous flow MBBR system. Results indicated SND started up quickly with more biomass in MBBR filled with surface-modified carriers. At the operation condition of low dissolved oxygen level (0.75 ± 0.25 mg/L), pH of 7.5 ± 0.5, 23 ± 2°C and C/N ratio of 7, COD, NH₄⁺-N and TN removal efficiencies were 90.5%, 88.6% and 76.6% respectively in MBBR filled with surface-modified carriers, which ensured the effluent met the first grade A of the Discharge Standard of China. On the contrary, COD, NH₄⁺-N and TN removal efficiencies were 89.7%, 82.3% and 60.4% respectively in the control reactors filled with conventional polyethylene carriers. The worse performance of the control reactor was mainly attributed to the less biomass and lower functional bacteria abundance developed on conventional carriers. Moreover, novel carriers provided a favourable niche for more types of functional bacteria, of which autotrophic nitrification, anoxic denitrification, heterotrophic nitrification and aerobic denitrification co-existed and participated in nitrogen removal.

Distribution of Denitrification among Haloarchaea: A Comprehensive Study

Microorganisms from the Halobacteria class, also known as haloarchaea, inhabit a wide range of ecosystems of which the main characteristic is the presence of high salt concentration. These environments together with their microbial communities are not well characterized, but some of the common features that they share are high sun radiation and low availability of oxygen. To overcome these stressful conditions, and more particularly to deal with oxygen limitation, some microorganisms drive alternative respiratory pathways such as denitrification. In this paper, denitrification in haloarchaea has been studied from a phylogenetic point of view. It has been demonstrated that the presence of denitrification enzymes is a quite common characteristic in Halobacteria class, being nitrite reductase and nitric oxide reductase the enzymes with higher co-occurrence, maybe due to their possible role not only in denitrification, but also in detoxification. Moreover, copper-nitrite reductase (NirK) is the only class of respiratory nitrite reductase detected in these microorganisms up to date. The distribution of this alternative respiratory pathway and their enzymes among the families of haloarchaea has also been discussed and related with the environment in which they constitute the major populations. Complete denitrification phenotype is more common in some families like Haloarculaceae and Haloferacaceae, whilst less common in families such as Natrialbaceae and Halorubraceae.

State-of-the-Art Biocatalysis

The use of enzyme-mediated reactions has transcended ancient food production to the laboratory synthesis of complex molecules. This evolution has been accelerated by developments in sequencing and DNA synthesis technology, bioinformatic and protein engineering tools, and the increasingly interdisciplinary nature of scientific research. Biocatalysis has become an indispensable tool applied in academic and industrial spheres, enabling synthetic strategies that leverage the exquisite selectivity of enzymes to access target molecules. In this Outlook, we outline the technological advances that have led to the field's current state. Integration of biocatalysis into mainstream synthetic chemistry hinges on increased access to well-characterized enzymes and the permeation of biocatalysis into retrosynthetic logic. Ultimately, we anticipate that biocatalysis is poised to enable the synthesis of increasingly complex molecules at new levels of efficiency and throughput.

In Silico Analysis of the Enzymes Involved in Haloarchaeal Denitrification

During the last century, anthropogenic activities such as fertilization have led to an increase in pollution in many ecosystems by nitrogen compounds. Consequently, researchers aim to reduce nitrogen pollutants following different strategies. Some haloarchaea, owing to their denitrifier metabolism, have been proposed as good model organisms for the removal of not only nitrate, nitrite, and ammonium, but also (per)chlorates and bromate in brines and saline wastewater. Bacterial denitrification has been extensively described at the physiological, biochemical, and genetic levels. However, their haloarchaea counterparts remain poorly described. In previous work the model structure of nitric oxide reductase was analysed. In this study, a bioinformatic analysis of the sequences and the structural models of the nitrate, nitrite and nitrous oxide reductases has been described for the first time in the haloarchaeon model Haloferax mediterranei. The main residues involved in the catalytic mechanism and in the coordination of the metal centres have been explored to shed light on their structural characterization and classification. These results set the basis for understanding the molecular mechanism for haloarchaeal denitrification, necessary for the use and optimization of these microorganisms in bioremediation of saline environments among other potential applications including bioremediation of industrial waters.

Nitrogen transformation and dynamic changes in related functional genes during functional-membrane covered aerobic composting

The effects of functional membrane covering (FMC) on nitrogen transformation and related functional genes during aerobic composting were investigated by performing a comparable experiment. The FMC increased the pile temperature, promoted compost maturity, and decreased nitrogen loss. The FMC reduced NH₃ and N₂O emissions by 7.34% and 26.27%, respectively. The water film and the micro-positive pressure environment under the membrane effectively prevented NH₃ escaping. The FMC up-regulated the amoA gene copy number (promoting NH₃/NH₄⁺ oxidation). The reduction of N₂O emission by the FMC was mainly related to denitrifying genes (nirK, nirS, and nosZ). The FMC down-regulated the nirK and nirS gene copy numbers, but up-regulated the nosZ gene copy number. Pearson correlation analysis indicated that the functional membrane characteristics and differences between the composting pile environments caused by the FMC significantly affected the nitrogen forms and the related functional genes. The FMC strongly decreased nitrogen emissions and therefore conserved nitrogen.

Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N2O emissions and nitrite accumulation in soil

Soil pH is a key controller of denitrification. We analysed the metagenomics/transcriptomics and phenomics of two soils from a long-term liming experiment, SoilN (pH 6.8) and un-limed SoilA (pH 3.8). SoilA had severely delayed N₂O reduction despite early transcription of nosZ (mainly clade I), encoding N₂O reductase, by diverse denitrifiers. This shows that post-transcriptionally hampered maturation of the NosZ apo-protein at low pH is a generic phenomenon. Identification of transcript reads of several accessory genes in the nos cluster indicated that enzymes for NosZ maturation were present across a range of organisms, eliminating their absence as an explanation for the failure to produce a functional enzyme. nir transcript abundances (for NO₂⁻ reductase) in SoilA suggest that low NO₂⁻ concentrations in acidic soils, often ascribed to abiotic degradation, are primarily due to biological activity. The accumulation of NO₂⁻ in neutral soil was ascribed to high nar expression (nitrate reductase). The -omics results revealed dominance of nirK over nirS in both soils while qPCR showed the opposite, demonstrating that standard primer pairs only capture a fraction of the nirK pool. qnor encoding NO reductase was strongly expressed in SoilA, implying an important role in controlling NO. Production of HONO, for which some studies claim higher, others lower, emissions from NO₂⁻ accumulating soil, was estimated to be ten times higher from SoilA than from SoilN. The study extends our understanding of denitrification-driven gas emissions and the diversity of bacteria involved and demonstrates that gene and transcript quantifications cannot always reliably predict community phenotypes.

Nitrogen-cycling gene pool shrunk by species interactions among denser bacterial and archaeal community stimulated by excess organic matter and total nitrogen in a eutrophic bay

Microbial densities, functional genes, and their responses to environment factors have been studied for years, but still a lot remains unknown about their interactions with each other. In this study, the abundances of 7 nitrogen cycling genes in the sediments from Hangzhou Bay were analyzed along with bacterial and archaeal 16S rRNA abundances as the biomarkers of their densities. The amount of organic matter (OM) and total nitrogen (TN) strongly positively correlated with each other and microbial densities, while total phosphate (TP) and ammonia-nitrogen (NH₃-N) did not. Most studied genes were density suppressed, while nirS was density stable, and nosZ and hzo were density irrelevant. This suggests eutrophication could limit inorganic nitrogen cycle pathways and the removal of nitrogen in the sediment and emit more greenhouse gases. This study provides a new insight of microbial community structures, functions and their interactions in the sediments of eutrophic bays.

Warming Shapes nirS- and nosZ-Type Denitrifier Communities and Stimulates N2O Emission in Acidic Paddy Soil

Warming strongly stimulates soil nitrous oxide (N2O) emission, contributing to the global warming trend. Submerged paddy soils exhibit huge N2O emission potential; however, the N2O emission pathway and underlying mechanisms for warming are not clearly understood. We conducted an incubation experiment using 15N to investigate the dynamics of N2O emission at controlled temperatures (5, 15, 25, and 35°C) in 125% water-filled pore space. The community structures of nitrifiers and denitrifiers were determined via high-throughput sequencing of functional genes. Our results showed that elevated temperature sharply enhanced soil N2O emission from submerged paddy soil. Denitrification was the main contributor, accounting for more than 90% of total N2O emission at all treatment temperatures. N2O flux was coordinatively regulated by nirK-, nirS-, and nosZ-containing denitrifiers but not ammonia-oxidizing archaea or ammonia-oxidizing bacteria. The nirS-containing denitrifiers were more sensitive to temperature shifts, especially at a lower temperature range (5 to 25°C), and showed a stronger correlation with N2O flux than that of nirK-containing denitrifiers. In contrast, nosZ-containing denitrifiers exhibited substantial variation at higher temperatures (15 to 35°C), thereby playing an important role in N2O consumption. Certain taxa of nirS- and nosZ-containing denitrifiers regulated N2O flux, including nirS-containing denitrifiers affiliated with Rhodanobacter and Cupriavidus as well as nosZ-containing denitrifiers affiliated with Azoarcus and Azospirillum. Together, these findings suggest that elevated temperature can significantly increase N2O emission from denitrification in submerged paddy soils by shifting the overall community structures and enriching some indigenous taxa of nirS- and nosZ-containing denitrifiers. IMPORTANCE The interdependence between global warming and greenhouse gas N2O has always been the hot spot. However, information on factors contributing to N2O and temperature-dependent community structure changes is scarce. This study demonstrated high-temperature-induced N2O emission from submerged paddy soils, mainly via stimulating denitrification. Further, we speculate that key functional denitrifiers drive N2O emission. This study showed that denitrifiers were more sensitive to temperature rise than nitrifiers, and the temperature sensitivity differed among denitrifier communities. N2O-consuming denitrifiers (nosZ-containing denitrifiers) were more sensitive at a higher temperature range than N2O-producing denitrifiers (nirS-containing denitrifiers). This study's findings help predict N2O fluxes under different degrees of warming and develop strategies to mitigate N2O emissions from paddy fields based on microbial community regulation.

No-Till and Solid Digestate Amendment Selectively Affect the Potential Denitrification Activity in Two Mediterranean Orchard Soils

Improved soil managements that include reduced soil disturbance and organic amendment incorporation represent valuable strategies to counteract soil degradation processes that affect Mediterranean tree cultivations. However, changes induced by these practices can promote soil N loss through denitrification. Our research aimed to investigate the short-term effects of no-tillage and organic amendment with solid anaerobic digestate on the potential denitrification in two Mediterranean orchard soils showing contrasting properties in terms of texture and pH. Denitrifying enzyme activity (DEA) and selected soil variables (available C and N, microbial biomass C, basal respiration) were monitored in olive and orange tree orchard soils over a five-month period. Our results showed that the application of both practices increased soil DEA, with dynamics that varied according to the soil type. Increased bulk density, lowered soil aeration, and a promoting effect on soil microbial community growth were the main DEA triggers under no-tillage. Conversely, addition of digestate promoted DEA by increasing readily available C and N with a shorter effect in the olive grove soil, due to greater sorption and higher microbial efficiency, and a long-lasting consequence in the orange orchard soil related to a larger release of soluble substrates and their lower microbial use efficiency.

Diversity of nitrogen cycling genes at a Midwest long-term ecological research site with different management practices

Nitrogen fertilizer results in the release of nitrous oxide (N₂O), a concern because N₂O is an ozone-depleting substance and a greenhouse gas. Although the reduction of N₂O to nitrogen gas can control emissions, the factors impacting the enzymes involved have not been fully explored. The current study investigated the abundance and diversity of genes involved in nitrogen cycling (primarily denitrification) under four agricultural management practices (no tillage [NT], conventional tillage [CT], reduced input, biologically-based). The work involved examining soil shotgun sequencing data for nine genes (napA, narG, nirK, nirS, norB, nosZ, nirA, nirB, nifH). For each gene, relative abundance values, diversity and richness indices, and taxonomic classification were determined. Additionally, the genes associated with nitrogen metabolism (defined by the KEGG hierarchy) were examined. The data generated were statistically compared between the four management practices. The relative abundance of four genes (nifH, nirK, nirS, and norB) were significantly lower in the NT treatment compared to one or more of the other soils. The abundance values of napA, narG, nifH, nirA, and nirB were not significantly different between NT and CT. The relative abundance of nirS was significantly higher in the CT treatment compared to the others. Diversity and richness values were higher for four of the nine genes (napA, narG, nirA, nirB). Based on nirS/nirK ratios, CT represents the highest N₂O consumption potential in four soils. In conclusion, the microbial communities involved in nitrogen metabolism were sensitive to different agricultural practices, which in turn, likely has implications for N₂O emissions. KEY POINTS: • Four genes were less abundant in NT compared to one or more of the others soils (nifH, nirK, nirS, norB). • The most abundant sequences for many of the genes classified within the Proteobacteria. • Higher diversity and richness indices were observed for four genes (napA, narG, nirA, nirB). • Based on nirS/nirK ratios, CT represents the highest N₂O consumption potential.

Dechloromonas and close relatives prevail during hydrogenotrophic denitrification in stimulated microcosms with oxic aquifer material

Globally occurring nitrate pollution in groundwater is harming the environment and human health. In situ hydrogen addition to stimulate denitrification has been proposed as a remediation strategy. However, observed nitrite accumulation and incomplete denitrification are severe drawbacks that possibly stem from the specific microbial community composition. We set up a microcosm experiment comprising sediment and groundwater from a nitrate polluted oxic oligotrophic aquifer. After the microcosms were sparged with hydrogen gas, samples were taken regularly within 122 h for nitrate and nitrite measurements, community composition analysis via 16S rRNA gene amplicon sequencing and gene and transcript quantification via qPCR of reductase genes essential for complete denitrification. The highest nitrate reduction rates and greatest increase in bacterial abundance coincided with a 15.3-fold increase in relative abundance of Rhodocyclaceae, specifically six ASVs that are closely related to the genus Dechloromonas. The denitrification reductase genes napA, nirS and clade I nosZ also increased significantly over the observation period. We conclude that taxa of the genus Dechloromonas are the prevailing hydrogenotrophic denitrifiers in this nitrate polluted aquifer and the ability of hydrogenotrophic denitrification under the given conditions is species-specific.

Aerobic Denitrification and Heterotrophic Sulfur Oxidation in the Genus Halomonas Revealed by Six Novel Species Characterizations and Genome-Based Analysis

Bacteria of Halomonas are widely distributed in various environments and play a substantial role in the nutrient cycle. In this report, 14 strains capable of aerobic denitrification and heterotrophic sulfur oxidation were isolated from different habitats. Based on the phenotypic, genotypic, and chemotaxonomic analyses, these strains were considered to represent six novel species of the genus Halomonas, for which the names Halomonas zhangzhouensis sp. nov. type strain CXT3-11T ( = MCCC 1A11036T = KCTC 72087T), Halomonas aerodenitrificans sp. nov. CYD-9T ( = MCCC 1A11058T = KCTC 72088T), Halomonas sulfidoxydans sp. nov. CYN-1-2T ( = MCCC 1A11059T = KCTC 72089T), Halomonas ethanolica sp. nov. CYT3-1-1T ( = MCCC 1A11081T = KCTC 72090T), Halomonas sulfidivorans sp. nov. NLG_F1ET ( = MCCC 1A13718T = KCTC 72091T), and Halomonas tianxiuensis sp. nov. BC-M4-5T ( = MCCC 1A14433T = KCTC 72092T) are proposed. Intriguingly, they formed a unique group with 11 other species designated as the "H. desiderata group." To better understand their featured metabolisms, genes involved in denitrification and sulfur oxidation were analyzed, along with 193 other available genomes of the whole genus. Consistently, complete denitrification pathways were confirmed in the "H. desiderata group," in which napA, narG, nirS, norB, and nosZ genes coexist. Their nitrite reductase NirS formed a unique evolutionary lineage, distinguished from other denitrifiers in Halomonas. In addition, diverse occurrence patterns of denitrification genes were also observed in different phylogenetic clades of Halomonas. With respect to sulfur oxidation, fccAB genes involved in sulfide oxidation commonly exist in the "H. desiderata group," while sqr genes are diverse and can be found in more species; sqr genes co-occurred with fccAB in eight strains of this study, contributing to more active sulfide oxidation. Besides, the tsdA gene, which encodes an enzyme that oxidizes thiosulfate to tetrathionate, is ubiquitous in the genus Halomonas. The widespread presence of sqr/fccAB, pdo, and tsdA in Halomonas suggests that many Halomonas spp. can act as heterotrophic sulfur oxidizers. These results provide comprehensive insights into the potential of denitrification and sulfur oxidation in the whole genus of Halomonas. With regard to the global distribution of Halomonas, this report implies their unneglectable role in the biogeochemical cycle.

Community Composition and Spatial Distribution of N-Removing Microorganisms Optimized by Fe-Modified Biochar in a Constructed Wetland

Microbial nitrogen (N) removal capability can be significantly enhanced in a horizontal subsurface flow constructed wetland (HSCW) amended by Fe-modified biochar (FeB). To further explore the microbiological mechanism of FeB enhancing N removal, nirS- and nirK-denitrifier community diversities, as well as spatial distributions of denitrifiers and anaerobic ammonium oxidation (anammox) bacteria, were investigated in HSCWs (C-HSCW: without biochar and FeB; B-HSCW: amended by biochar; FeB-HSCW: amended by FeB) treating tailwater from a wastewater treatment plant, with C-HSCW without biochar and FeB and B-HSCW amended by biochar as control. The community structures of nirS- and nirK-denitrifiers in FeB-HSCW were significantly optimized for improved N removal compared with the two other HSCWs, although no significant differences in their richness and diversity were detected among the HSCWs. The spatial distributions of the relative abundance of genes involved in denitrification and anammox were more heterogeneous and complex in FeB-HSCW than those in other HSCWs. More and larger high-value patches were observed in FeB-HSCW. These revealed that FeB provides more appropriate habitats for N-removing microorganisms, which can prompt the bacteria to use the habitats more differentially, without competitive exclusion. Overall, the Fe-modified biochar enhancement of the microbial N-removal capability of HSCWs was a result of optimized microbial community structures, higher functional gene abundance, and improved spatial distribution of N-removing microorganisms.

Strategies to Overcome Intermediate Accumulation During in situ Nitrate Remediation in Groundwater by Hydrogenotrophic Denitrification

Bioremediation of polluted groundwater is one of the most difficult actions in environmental science. Nonetheless, the clean-up of nitrate polluted groundwater may become increasingly important as nitrate concentrations frequently exceed the EU drinking water limit of 50 mg L-1, largely due to intensification of agriculture and food production. Denitrifiers are natural catalysts that can reduce increasing nitrogen loading of aquatic ecosystems. Porous aquifers with high nitrate loading are largely electron donor limited and additionally, high dissolved oxygen concentrations are known to reduce the efficiency of denitrification. Therefore, denitrification lag times (time prior to commencement of microbial nitrate reduction) up to decades were determined for such groundwater systems. The stimulation of autotrophic denitrifiers by the injection of hydrogen into nitrate polluted regional groundwater systems may represent a promising remediation strategy for such environments. However, besides high costs other drawbacks, such as the transient or lasting accumulation of the cytotoxic intermediate nitrite or the formation of the potent greenhouse gas nitrous oxide, have been described. In this article, we detect causes of incomplete denitrification, which include environmental factors and physiological characteristics of the underlying bacteria and provide possible mitigation approaches.