Nitric Oxide Reductase Research Articles

Effects of native plants on nitrogen cycling microorganisms in soil

Plants modify the nitrogen (N) cycle in soil through plant N uptake, root exudation, and nitrification inhibition resulting from root exudates and changes to the physicochemical properties of soil. Plants with specific traits can be selected to manage N fluxes in the soil following the land application of N-rich wastes thereby reducing losses of N from these systems into the atmosphere (via nitrous oxide) and waterbodies (via nitrate). Previous work has shown that some New Zealand native myrtaceous species can reduce such losses more than other species, but the underlying mechanisms are unknown. It was hypothesized that lower N losses may result from the inhibition of nitrification and denitrification. We aimed to determine the effect of New Zealand native plant species on the abundance of nitrifying and denitrifying microorganisms in the soil using a pot experiment with five native plant species (Carex secta, Coprosma robusta, Kunzea robusta, Leptospermum scoparium, and Metrosideros umbellata) and exotic pasture (Lolium perenne). Half of the pots received fertilisation with N (urea), phosphorus, potassium, and sulphur, while the remainder were unfertilised controls. We quantified the abundance of bacteria, archaea, and the functional genes encoding nitrite reductase (nirK, nirS), nitrous oxide reductase (nosZ), and bacterial and archaeal ammonia monooxygenase (amoA) in the rhizosphere of these plants. Results indicated that plant species had a significant effect on the abundance of nosZ and bacterial amoA. In fertilised soil, the abundance of bacterial amoA was lower under mono- than dicotyledonous species. Similarly, the chemical properties of the soil differed between these groups. Monocotyledonous species took up more N and had lower concentrations of mineral N in the rhizosphere. This indicates that the increased competition for N likely reduced the abundance of amoA and therefore nitrification and nitrate losses. The results support the utilisation of species selection to reduce N losses. In particular, monocotyledonous species may be planted in high-fertility environments to mitigate N contamination of ground- and surface water. Future work should determine the mechanisms of plant specific interaction with ammonia-oxidising bacteria, although plant uptake can explain some of the observed differences.

Inhibition of nitrous oxide reduction in forest soil microcosms by different forms of methanobactin.

Copper plays a critical role in controlling greenhouse gas emissions as it is a key component of the particulate methane monooxygenase and nitrous oxide reductase. Some methanotrophs excrete methanobactin (MB) that has an extremely high copper affinity. As a result, MB may limit the ability of other microbes to gather copper, thereby decreasing their activity as well as impacting microbial community composition. Here, we show using forest soil microcosms that multiple forms of MB; MB from Methylosinus trichosporium OB3b (MB-OB3b) and MB from Methylocystis sp. strain SB2 (MB-SB2) increased nitrous oxide (N2 O) production as well caused significant shifts in microbial community composition. Such effects, however, were mediated by the amount of copper in the soils, with low-copper soil microcosms showing the strongest response to MB. Furthermore, MB-SB2 had a stronger effect, likely due to its higher affinity for copper. The presence of either form of MB also inhibited nitrite reduction and generally increased the presence of genes encoding for the iron-containing nitrite reductase (nirS) over the copper-dependent nitrite reductase (nirK). These data indicate the methanotrophic-mediated production of MB can significantly impact multiple steps of denitrification, as well as have broad effects on microbial community composition of forest soils.

Nitrogen fertilizer alleviates rice yield loss without increasing global warming potential under elevated temperatures

The adverse impacts of climate warming on rice production have become increasingly evident. In this regard, although our previous field studies enabled us to establish the positive impacts of nitrogen fertilizer on rice grain yield during warming, it remains necessary to clarify whether nitrogen fertilizer under elevated temperatures has any adverse effects on the environment during the grain-filling stage. To further investigate the impacts of nitrogen fertilizer on rice yield and the associated emissions of methane (CH4) and nitrous oxide (N2O) under elevated temperatures, we conducted a 2-year paddy field study using a free-air temperature enhancement (FATE) system. FATE system had a favorable warming effect on the canopy and soil, and greatly decreased grain yield by 23 % on average. In two trial years, elevated temperatures significantly increased in CH4 emissions by 17.7 kg ha−1and 18.9 kg ha−1, but did not affect N2O emissions. Consequently, we detected significant increases in global warming potential (GWP) by 52 % and 19 % and greenhouse gas intensity (GHGI) by 94 % and 56 % under elevated temperatures in 2019 and 2020, respectively. Although nitrogen fertilizer had no significant influence on CH4 emissions under elevated temperatures, N2O emissions significantly increased by 1.5 kg ha−1 and 1.4 kg ha−1 in 2019 and 2020. Nevertheless, nitrogen fertilizer did not affect GWP and significantly decreased GHGI by 10 % under elevated temperatures in 2020. Additionally, elevated temperatures significantly increased the abundance of methanogens (mcrA), ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and nitrous oxide reductase (nosZ) genes. Whereas, nitrogen fertilizer significantly increased nitrite reductase (nirS) gene abundance under elevated temperatures. In conclusion, our findings indicated that 60 kg N ha−1 at the heading stage could effectively alleviate the reduction in grain yield attributable to elevated temperatures, without increasing GWP, thereby enhancing the economic and environmental sustainability of paddy field system.

The long-term effect of glutaraldehyde on the bacterial community in anaerobic ammonium oxidation reactor

A 160-day incubation was performed with two anammox reactors (GA and CK) to investigate the effect of glutaraldehyde. The results indicated that anammox bacteria were very sensitive when glutaraldehyde in GA reactor increased to 40 mg/L, the nitrogen removal efficiency sharply decreased to 11%, only one-quarter of CK. Glutaraldehyde changed spatial distribution of exopolysaccharides, caused anammox bacteria (Brocadia CK_gra75) to disassociate from granules (24.70% of the reads in CK but only 14.09% in GA granules). Metagenome analysis indicated glutaraldehyde led to the denitrifier community succession from strains without nir (nitrite reductase) and nor (nitric oxide reductases) genes to those with them, and the rapid growth of denitrifiers with NodT (an outer membrane factor)-related efflux pumps replacing those with another TolC -related ones. Meanwhile, Brocadia CK_gra75 lacks the NodT proteins. This study provides important insight into community adaptation and potential resistance mechanism in an active anammox community after exposure to disinfectant.

The response of C/N/S cycling functional microbial communities to redox conditions in shallow aquifers using in-situ sediment as bio-trap matrix

ABSTRACT Microbial communities are fundamental components driving critical biogeochemical carbon (C), nitrogen (N) and sulfur (S) cycles in groundwater ecosystems. The reduction–oxidation (redox) potential is one important environmental factor influencing the microbial community composition. Here, we developed a bio-trap method using in-situ sediment as a matrix to collect aquifer sediment samples and evaluate the response of microbial composition and C/N/S cycling functions to redox variations created by providing sole O2, joint O2 and H2, and sole H2 to three wells. Illumina sequencing analyses showed that the microbial communities in the bio-trap sediment could respond quickly to redox changes in the wells, demonstrating that this bio-trap method is promising for detecting microbial variation in the aquifer sediment. The microbial metabolic functions related to C, N and S cyclings and organic pollutants degradation were predicted by the Kyoto Encyclopedia of Genes and Genomes (KEGG) approach. It was found that the joint O2 and H2 injection produced medium oxidation–reduction potential (ORP −346 and −614 mV) and enhanced more microbial functions than sole O2 or H2, which mainly include oxidative phosphorylation, most carbon source metabolism, various pollutants degradation, and nitrogen and sulfur metabolism. Moreover, the functional genes encoding phenol monooxygenase, dioxygenase, nitrogen fixation, nitrification, aerobic and anaerobic nitrate reductase, nitrite reductase, nitric oxide reductase, and sulfur oxidation increased. These findings tell us the contaminant bioremediation and N, S metabolism can be promoted by adjusting ORP realised by injecting joint O2 and H2.

Fully Reduced and Mixed-Valent Multi-Copper Aggregates Supported by Tetradentate Diamino Bis(thiolate) Ligands.

Tetradentate diamino bis(thiolate) ligands (l-N2S2(2-)) with saturated linkages between heteroatoms support fully reduced [(Cu(l-N2S2))2Cu2] complexes that bear relevance as an entry point toward molecules featuring the Cu2ICu2II(μ4-S) core composition of nitrous oxide reductase (N2OR). Tetracopper [(Cu(l-N2(SMe2)2))2Cu2] (l-N2(SMe2H)2 = N1,N2-bis(2-methyl-2-mercaptopropane)-N1,N2-dimethylethane-1,2-diamine) does not support clean S atom oxidative addition but undergoes Cl atom transfer from PhICl2 or Ph3CCl to afford [(Cu(l-N2(SMe2)2))3(CuCl)5], 14. When introduced to Cu(I) sources, the l-N2(SArH)2 ligand (l-N2(SArH)2 = N1,N2-bis(2-mercaptophenyl)-N1,N2-dimethylethane-1,2-diamine), made by a newly devised route from N1,N2-bis(2-fluorophenyl)-N1,N2-dimethylethane-1,2-diamine, ultimately yields the mixed-valent pentacopper [(Cu(l-N2SAr2))3Cu2] (19), which has 3-fold rotational symmetry (D3) around a Cu2 axis. The single CuII ion of 19 is ensconced within an equatorial l-N2(SAr)2(2-) ligand, as shown by 14N coupling in its EPR spectrum. Formation of 19 proceeds from an initial, fully reduced product, [(Cu(l-N2SAr2))3Cu2(Cu(MeCN))] (17), which is C2 symmetric and exceedingly air-sensitive. While unreactive toward chalcogen donors, 19 supports reversible reduction to the all-cuprous state; generation of [19]1- and treatment with S atom donors only return 19 because structural adjustments necessary for oxidative addition are noncompetitive with outer-sphere electron transfer. Oxidation of 19 is marked by intense darkening, consistent with greater mixed valency, and by dimerization in the crystalline state to a decacopper species ([20]2+) of S4 symmetry.

A 2.2 Å cryoEM structure of a quinol-dependent NO Reductase shows close similarity to respiratory oxidases

Quinol-dependent nitric oxide reductases (qNORs) are considered members of the respiratory heme-copper oxidase superfamily, are unique to bacteria, and are commonly found in pathogenic bacteria where they play a role in combating the host immune response. qNORs are also essential enzymes in the denitrification pathway, catalysing the reduction of nitric oxide to nitrous oxide. Here, we determine a 2.2 Å cryoEM structure of qNOR from Alcaligenes xylosoxidans, an opportunistic pathogen and a denitrifying bacterium of importance in the nitrogen cycle. This high-resolution structure provides insight into electron, substrate, and proton pathways, and provides evidence that the quinol binding site not only contains the conserved His and Asp residues but also possesses a critical Arg (Arg720) observed in cytochrome bo3, a respiratory quinol oxidase.

Bacterial nitric oxide reductase (NorBC) models employing click chemistry

Bacterial NO Reductase (NorBC or cNOR) is a membrane-bound enzyme found in denitrifying bacteria that catalyzes the two-electron reduction of NO to N2O and water. The mechanism by which NorBC operates is highly debated, due to the fact that this enzyme is difficult to work with, and no intermediates of the NO reduction reaction could have been identified so far. The unique active site of NorBC consists of a heme b3/non-heme FeB diiron center. Synthetic model complexes provide the opportunity to obtain insight into possible mechanistic alternatives for this enzyme. In this paper, we present three new synthetic model systems for NorBC, consisting of a tetraphenylporphyrin-derivative clicked to modified BMPA-based ligands (BMPA = bis(methylpyridyl)amine) that model the non-heme site in the enzyme. These complexes have been characterized by EPR, IR and UV–Vis spectroscopy. The reactivity with NO was then investigated, and it was found that the complex with the BMPA-carboxylate ligand as the non-heme component has a very low affinity for NO at the non-heme iron site. If the carboxylate functional group is replaced with a phenolate or pyridine group, reactivity is restored and formation of a diiron dinitrosyl complex was observed. Upon one-electron reduction of the nitrosylated complexes, following the semireduced pathway for NO reduction, formation of dinitrosyl iron complexes (DNICs) was observed in all three cases, but no N2O could be detected.

Soil N2O emissions and functional genes in response to grazing grassland with livestock: A meta-analysis

Livestock grazing affects nitrous oxide (N2O) emissions from grassland ecosystems by altering soil physical, chemical and biological properties. However, how soil N2O emissions related to nitrogen process rates and functional genes are unexplored. We compiled 83 published studies of soil N2O emissions, potential nitrification and denitrification rates, and the abundance of nitrogen functional genes to uncover their associations with varying intensities of livestock grazing. Compared to ungrazed condition, heavy and moderate grazing reduced N2O emissions by 22–25%, nitrification rate by 23–37%, and denitrification rate by 44–48%, respectively, while light grazing had no effect. Furthermore, moderate to heavy grazing intensities decreased the abundances of ammonia-oxidizing bacteria ammonia monooxygenase (AOB amoA) by 40–47%. Heavy grazing also simultaneously decreased ammonia-oxidizing archaea (AOA amoA) by 43%. Additionally, grazing significantly decreased the abundance of nitrate reductase (narG) and nitrite reductase (nirS) and by 28% and 35%, respectively, but did not affect the abundance of nitrous oxide reductase (nosZ). Overall, potential nitrification rate was positively correlated with AOB amoA and AOA amoA abundances. This global-scale assessment demonstrates that moderate to heavy livestock grazing can reduce grassland N2O emissions, and such reductions were linked to decreased abundances of amoA genes with decreasing soil moisture and inorganic N (NO3– and NH4+) availabilities. Considering that heavy grazing may increase the risk of grassland degradation, we recommend that livestock grazing at an appropriately moderate intensity is important for sustaining livestock production while contributing to greenhouse gas mitigation.

Antibiotics Resistance and Adhesive Properties of Clinical Staphylococcus aureus Isolated from Wound Infections.

Staphylococcus aureus (S. aureus) is a ubiquitous pathogen responsible for several severe infections. This study aimed to investigate the adhesive properties and antibiotic resistance among clinical S. aureus isolated from Hail Hospital Province, Kingdom of Saudi Arabia (KSA), using molecular approaches. This study was conducted according to the ethical committee at Hail's guidelines on twenty-four S. aureus isolates. A polymerase chain reaction (PCR) was performed to identify genes encoding the β-lactamase resistance (blaZ), methicillin resistance (mecA), fluoroquinolone resistance (norA), nitric oxide reductase (norB), fibronectin (fnbA and fnbB), clumping factor (clfA) and intracellular adhesion factors (icaA and icaD). This qualitative study tested adhesion based on exopolysaccharide production on Congo red agar (CRA) medium and biofilm formation on polystyrene by S. aureus strains. Among 24 isolates, the cna and blaz were the most prevalent (70.8%), followed by norB (54.1%), clfA (50.0%), norA (41.6%), mecA and fnbB (37.5%) and fnbA (33.3%). The presence of icaA/icaD genes was demonstrated in almost all tested strains in comparison to the reference strain, S. aureus ATCC 43300. The phenotypic study of adhesion showed that all tested strains had moderate biofilm-forming capacity on polystyrene and represented different morphotypes on a CRA medium. Five strains among the twenty-four harbored the four genes of resistance to antibiotics (mecA, norA, norB and blaz). Considering the genes of adhesion (cna, clfA, fnbA and fnbB), these genes were present in 25% of the tested isolates. Regarding the adhesive properties, the clinical isolates of S. aureus formed biofilm on polystyrene, and only one strain (S17) produced exopolysaccharides on Congo red agar. All these results contribute to an understanding that the pathogenesis of clinical S. aureus isolates is due to their antibiotic resistance and adhesion to medical material.

Structural and biochemical elucidation of class I hybrid cluster protein natively extracted from a marine methanogenic archaeon.

Whilst widespread in the microbial world, the hybrid cluster protein (HCP) has been paradoxically a long-time riddle for microbiologists. During three decades, numerous studies on a few model organisms unravelled its structure and dissected its metal-containing catalyst, but the physiological function of the enzyme remained elusive. Recent studies on bacteria point towards a nitric oxide reductase activity involved in resistance during nitrate and nitrite reduction as well as host infection. In this study, we isolated and characterised a naturally highly produced HCP class I from a marine methanogenic archaeon grown on ammonia. The crystal structures of the enzyme in a reduced and partially oxidised state, obtained at a resolution of 1.45 and 1.36-Å, respectively, offered a precise picture of the archaeal enzyme intimacy. There are striking similarities with the well-studied enzymes from Desulfovibrio species regarding sequence, kinetic parameters, structure, catalyst conformations, and internal channelling systems. The close phylogenetic relationship between the enzymes from Methanococcales and many Bacteria corroborates this similarity. Indeed, Methanococcales HCPs are closer to these bacterial homologues than to any other archaeal enzymes. The relatively high constitutive production of HCP in M. thermolithotrophicus, in the absence of a notable nitric oxide source, questions the physiological function of the enzyme in these ancient anaerobes.

A functional metagenomics study of soil carbon and nitrogen degradation networks and limiting factors on the Tibetan plateau.

The Three-River Source Nature Reserve is located in the core area of the Qinghai-Tibetan Plateau, with the alpine swamp, meadow and steppe as the main ecosystem types. However, the microbial communities in these alpine ecosystems, and their carbon and nitrogen degrading metabolic networks and limiting factors remain unclear. We sequenced the diversity of bacteria and fungi in alpine swamps, meadows, steppes, and their degraded and artificially restored ecosystems and analyzed soil environmental conditions. The results indicated that moisture content had a greater influence on soil microbial community structure compared to degradation and restoration. Proteobacteria dominated in high moisture alpine swamps and alpine meadows, while Actinobacteria dominated in low moisture alpine steppes and artificial grasslands. A metabolic network analysis of carbon and nitrogen degradation and transformation using metagenomic sequencing revealed that plateau microorganisms lacked comprehensive and efficient enzyme systems to degrade organic carbon, nitrogen, and other biological macromolecules, so that the short-term degradation of alpine vegetation had no effect on the basic composition of soil microbial community. Correlation analysis found that nitrogen fixation was strong in meadows with high moisture content, and their key nitrogen-fixing enzymes were significantly related to Sphingomonas. Denitrification metabolism was enhanced in water-deficient habitats, and the key enzyme, nitrous oxide reductase, was significantly related to Phycicoccus and accelerated the loss of nitrogen. Furthermore, Bacillus contained a large number of amylases (GH13 and GH15) and proteases (S8, S11, S26, and M24) which may promote the efficient degradation of organic carbon and nitrogen in artificially restored grasslands. This study illustrated the irrecoverability of meadow degradation and offered fundamental information for altering microbial communities to restore alpine ecosystems.

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.

Complementary Biotransformation of Antimicrobial Triclocarban Obviously Mitigates Nitrous Oxide Emission toward Sustainable Microbial Denitrification.

Sustainable nitrogen cycle is an essential biogeochemical process that ensures ecosystem safety and byproduct greenhouse gas nitrous oxide reduction. Antimicrobials are always co-occurring with anthropogenic reactive nitrogen sources. However, their impacts on the ecological safety of microbial nitrogen cycle remain poorly understood. Here, a denitrifying bacterial strain Paracoccus denitrificans PD1222 was exposed to a widespread broad-spectrum antimicrobial triclocarban (TCC) at environmental concentrations. The denitrification was hindered by TCC at 25 μg L-1 and was completely inhibited once the TCC concentration exceeded 50 μg L-1. Importantly, the accumulation of N2O at 25 μg L-1 of TCC was 813 times as much as the control group without TCC, which attributed to the significantly downregulated expression of nitrous oxide reductase and the genes related to electron transfer, iron, and sulfur metabolism under TCC stress. Interestingly, combining TCC-degrading denitrifying Ochrobactrum sp. TCC-2 with strain PD1222 promoted the denitrification process and mitigated N2O emission by 2 orders of magnitude. We further consolidated the importance of complementary detoxification by introducing a TCC-hydrolyzing amidase gene tccA from strain TCC-2 into strain PD1222, which successfully protected strain PD1222 against the TCC stress. This study highlights an important link between TCC detoxification and sustainable denitrification and suggests a necessity to assess the ecological risks of antimicrobials in the context of climate change and ecosystem safety.

Vertically stratified methane, nitrogen and sulphur cycling and coupling mechanisms in mangrove sediment microbiomes

BackgroundMangrove ecosystems are considered as hot spots of biogeochemical cycling, yet the diversity, function and coupling mechanism of microbially driven biogeochemical cycling along the sediment depth of mangrove wetlands remain elusive. Here we investigated the vertical profile of methane (CH4), nitrogen (N) and sulphur (S) cycling genes/pathways and their potential coupling mechanisms using metagenome sequencing approaches.ResultsOur results showed that the metabolic pathways involved in CH4, N and S cycling were mainly shaped by pH and acid volatile sulphide (AVS) along a sediment depth, and AVS was a critical electron donor impacting mangrove sediment S oxidation and denitrification. Gene families involved in S oxidation and denitrification significantly (P < 0.05) decreased along the sediment depth and could be coupled by S-driven denitrifiers, such as Burkholderiaceae and Sulfurifustis in the surface sediment (0–15 cm). Interestingly, all S-driven denitrifier metagenome-assembled genomes (MAGs) appeared to be incomplete denitrifiers with nitrate/nitrite/nitric oxide reductases (Nar/Nir/Nor) but without nitrous oxide reductase (Nos), suggesting such sulphide-utilizing groups might be an important contributor to N2O production in the surface mangrove sediment. Gene families involved in methanogenesis and S reduction significantly (P < 0.05) increased along the sediment depth. Based on both network and MAG analyses, sulphate-reducing bacteria (SRB) might develop syntrophic relationships with anaerobic CH4 oxidizers (ANMEs) by direct electron transfer or zero-valent sulphur, which would pull forward the co-existence of methanogens and SRB in the middle and deep layer sediments.ConclusionsIn addition to offering a perspective on the vertical distribution of microbially driven CH4, N and S cycling genes/pathways, this study emphasizes the important role of S-driven denitrifiers on N2O emissions and various possible coupling mechanisms of ANMEs and SRB along the mangrove sediment depth. The exploration of potential coupling mechanisms provides novel insights into future synthetic microbial community construction and analysis. This study also has important implications for predicting ecosystem functions within the context of environmental and global change.8kPXxAybXxhPRn3YMgQLJxVideo

Reconnaissance of Oxygenic Denitrifiers in Agriculturally Impacted Soils.

Row crop production in the agricultural Midwest pollutes waterways with nitrate, and exacerbates climate change through increased emissions of nitrous oxide and methane. Oxygenic denitrification processes in agricultural soils mitigate nitrate and nitrous oxide pollution by short-circuiting the canonical pathway to avoid nitrous oxide formation. Furthermore, many oxygenic denitrifiers employ a nitric oxide dismutase (nod) to create molecular oxygen that is used by methane monooxygenase to oxidize methane in otherwise anoxic soils. The direct investigation of nod genes that could facilitate oxygenic denitrification processes in agricultural sites is limited, with no prior studies investigating nod genes at tile drainage sites. Thus, we performed a reconnaissance of nod genes at variably saturated surface sites, and within a variably to fully saturated soil core in Iowa to expand the known distribution of oxygenic denitrifiers. We identified new nod gene sequences from agricultural soil and freshwater sediments in addition to identifying nitric oxide reductase (qNor) related sequences. Surface and variably saturated core samples displayed a nod to 16S rRNA gene relative abundance of 0.004% to 0.1% and fully saturated core samples had relative nod gene abundance of 1.2%. The relative abundance of the phylum Methylomirabilota increased from 0.6% and 1% in the variably saturated core samples to 3.8% and 5.3% in the fully saturated core samples. The more than 10-fold increase in relative nod abundance and almost 9-fold increase in relative Methylomirabilota abundance in fully saturated soils suggests that potential oxygenic denitrifiers play a greater nitrogen cycling role under these conditions. IMPORTANCE The direct investigation of nod genes in agricultural sites is limited, with no prior studies investigating nod genes at tile drains. An improved understanding of nod gene diversity and distribution is significant to the field of bioremediation and ecosystem services. The expansion of the nod gene database will advance oxygenic denitrification as a potential strategy for sustainable nitrate and nitrous oxide mitigation, specifically for agricultural sites.

Denitrification process of Casuarina root nodule endophyte Frankia.

To examine the characteristic of denitrification in Frankia, a symbiotic nitrogen-fixing microbe associated with non-leguminous plants, and its role as a N2O source or sink, Casuarina root nodule endophyte Frankia was isolated using sectioning method, which was then purely cultured to investigate the denitrification process under NO3- addition. The results showed that after addition of NO3- to the medium under anaerobic condition, the concentration of NO3- decreased with time, while the concentrations of NO2- and N2O initially increased and then decreased over time. Key denitrification genes and nitrogenase gene were detected at 26 h, 54 h and 98 h during incubation. Abundances of these genes significantly differed among each other, and their dynamics were asynchronous. Redundancy analysis of the effect of NO3-, NO2-, N2O concentrations on abundances of denitrification genes and nitrogenase gene indicated that 81.9% of the total variation in gene abundances could be explained by the first two axes. Frankia had a denitrifying activity under anaerobic condition, with denitrification genes, including nitrous oxide reductase gene (nosZ), being identified. Our results suggested that Frankia possessed a complete denitrification pathway and the ability of N2O reduction under anaerobic condition.

Effects of long-term no-tillage on the functional potential of microorganisms involved in the nitrogen, phosphorus and sulfur cycles of black soil.

Understanding the effects of different tillage practices on functional microbial abundance and composition in nitrogen (N), phosphorus (P) and sulfur (S) cycles are essential for the sustainable utilization of black soils. Based on an 8-year field experiment located in Changchun, Jilin Province, we analyzed the abundance and composition of N, P and S cycling microorganisms and their driving factors in different depths of black soil under no til-lage (NT) and conventional tillage (CT). Results showed that compared with CT, NT significantly increased soil water content (WC) and microbial biomass carbon (MBC) at soil depth of 0-20 cm. Compared with CT, NT significantly increased the abundances of functional and encoding genes related to N, P and S cycling, including the nosZ gene encoding N2O reductase, the ureC gene performing organic nitrogen ammoniation, the nifH gene encoding nitrogenase ferritin, the functional genes phnK and phoD driving organic phosphorus mineralization, the encoding pyrroloquinoline quinone synthase ppqC gene and the encoding exopolyphosphate esterase ppX gene, and the soxY and yedZ genes driving sulfur oxidation. The results of variation partitioning analysis and redundancy analysis showed that soil basic properties were the main factors affecting the microbial composition of N, P and S cycle functions (the total interpretation rate was 28.1%), and that MBC and WC were the most important drivers of the functional potential of soil microorganisms in N, P and S cycling. Overall, long-term no tillage could increase the abundance of functional genes of soil microorganisms by affecting soil environment. From the perspective of molecular biology, our results elucidated that no tillage could be used as an effective soil management measure to improve soil health and maintain green agricultural development.

Hysteretic response of N2O reductase activity to soil pH variations after application of lime to an acidic agricultural soil

Hysteretic response of N2O reductase activity to soil pH variations after application of lime to an acidic agricultural soil

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

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