The diversity of the N2O reducers matters for the N2O:N2 denitrification end-product ratio across an annual and a perennial cropping system

Mineral and organic fertilisation influence ammonia oxidisers and denitrifiers and nitrous oxide emissions in a long-term tillage experiment

Nitrous oxide (N2O) emissions from different agricultural systems have been studied extensively to understand the mechanisms underlying their formation. While a number of long-term field experiments have focused on individual agricultural practices in relation to N2O emissions, studies on the combined effects of multiple practices are lacking. This study evaluated the effect of different tillage [no-till (NT) vs. conventional plough tillage (CT)] in combination with fertilisation [mineral (MIN), compost (ORG), and unfertilised control (CON)] on seasonal N2O emissions and the underlying N-cycling microbial community in one maize growing season. Rainfall events after fertilisation, which resulted in increased soil water content, were the main triggers of the observed N2O emission peaks. The highest cumulative emissions were measured in MIN fertilisation, followed by ORG and CON fertilisation. In the period after the first fertilisation CT resulted in higher cumulative emissions than NT, while no significant effect of tillage was observed cumulatively across the entire season. A higher genetic potential for N2O emissions was observed under NT than CT, as indicated by an increased (nirK + nirS)/(nosZI + nosZII) ratio. The mentioned ratio under NT decreased in the order CON > MIN > ORG, indicating a higher N2O consumption potential in the NT-ORG treatment, which was confirmed in terms of cumulative emissions. The AOB/16S ratio was strongly affected by fertilisation and was higher in the MIN than in the ORG and CON treatments, regardless of the tillage system. Multiple regression has revealed that this ratio is one of the most important variables explaining cumulative N2O emissions, possibly reflecting the role of bacterial ammonia oxidisers in minerally fertilised soil. Although the AOB/16S ratio aligned well with the measured N2O emissions in our experimental field, the higher genetic potential for denitrification expressed by the (nirK + nirS)/(nosZI + nosZII) ratio in NT than CT was not realized in the form of increased emissions. Our results suggest that organic fertilisation in combination with NT shows a promising combination for mitigating N2O emissions; however, addressing the yield gap is necessary before incorporating it in recommendations for farmers.

Nitrification inhibitor chlorate and nitrogen substrates differentially affect comammox Nitrospira in a grassland soil

Introduction

Through the combined use of two nitrification inhibitors, Dicyandiamide (DCD) and chlorate with nitrogen amendment, this study aimed to investigate the contribution of comammox Nitrospira clade B, ammonia oxidizing bacteria (AOB) and archaea (AOA) to nitrification in a high fertility grassland soil, in a 90-day incubation study.

Methods

The soil was treated with nitrogen (N) at three levels: 0 mg-N kg-1 soil, 50 mg-N kg-1 soil, and 700 mg-N kg-1 soil, with or without the two nitrification inhibitors. The abundance of comammox Nitrospira, AOA, AOB, and nitrite oxidising bacteria (NOB) was measured using qPCR. The comammox Nitrospira community structure was assessed using Illumina sequencing.

Results and Discussion

The results showed that the application of chlorate inhibited the oxidation of both NH4+ and NO2- in all three nitrogen treatments. The application of chlorate significantly reduced the abundance of comammox Nitrospira amoA and nxrB genes across the 90-day experimental period. Chlorate also had a significant effect on the beta diversity (Bray-Curtis dissimilarity) of the comammox Nitrospira clade B community. Whilst AOB grew in response to the N substrate additions and were inhibited by both inhibitors, AOA showed litle or no response to either the N substrate or inhibitor treatments. In contrast, comammox Nitrospira clade B were inhibited by the high ammonium concentrations released from the urine substrates. These results demonstrate the differential and niche responses of the three ammonia oxidising communities to N substrate additions and nitrification inhibitor treatments. Further research is needed to investigate the specificity of the two inhibitors on the different ammonia oxidising communities.

Effect of tillage state of paddy soils with heavy metal pollution on the nosZ gene of N2O reductase

Paddy soils are an important source of atmospheric nitrous oxide (N2O). However, numerous studies have focused on N2O production during the soil tillage period, neglecting the N2O production during the dry fallow period. In this study, we conducted an incubation experiment using the acetylene inhibition technique to investigate N2O emission and reduction rates of paddy soil profiles (0-1 m) from Guangdong Province and Jinlin Province in China, with different heavy-metal pollution levels. The abundance and community structures of denitrifying bacteria were determined via quantitative-PCR and Illumina MiSeq sequencing of nosZ, nirK, and nirS genes. Our results showed that the potential N2O emission rate, N2O production rate, and denitrification rate have decreased with increasing soil vertical depth and heavy-metal pollution. More importantly, we found that the functional gene type of N2O reductase switched with the tillage state of paddy soils, which clade Ⅱ nosZ genes were the dominant gene during the tillage period, while clade Ⅰ nosZ genes were the dominant gene during the dry fallow period. The heavy-metal pollution has less effect on the niche differentiation of the nosZ gene. The N2O emission rate was significantly regulated by the genus Bradyhizobium, which contains both N2O reductase and nitrite reductase genes. Our findings suggests that the nosZ gene of N2O reductase can significantly impact the N2O emission from paddy soils.

Substitution of organic and bio-organic fertilizers for mineral fertilizers to suppress nitrous oxide emissions from intensive vegetable fields

To gain insight into the microbial mechanisms associated with the replacement of chemical fertilizers with organic or bio-organic fertilizers to mitigate soil nitrous oxide (N2O) emissions, we measured N2O emissions from greenhouse vegetable soils through field observations and pot experiments. Results showed that organic substitution suppressed N2O emissions by reducing soil mineral N content and stimulating the abundance of the nosZII gene. The trade-off effect of bio-organic substitution on N2O emissions may be due to the stimulated activity of the AOA-amoA gene, resulting in unfavorable conditions for N2O production and thus reduced N2O loss. We also linked the inhibitory effect of organic and bio-organic substitution on N2O emissions to the increased abundance of key species in bacterial co-occurrence networks represented by Patescibacteria as they were significantly and negatively correlated with N2O emissions. However, the mitigation effect of bio-organic substitution on N2O emissions was conteracted by an increase in Bacillus abundance due to the direct negative effect of Bacillus on the nosZII gene abundance. These findings suggest that conventional or bio-organic substitution is a promising strategy for alleviating the environmental costs of crop production.

Denitrification contributes to N2O emission in paddy soils

Denitrification is vital to nitrogen removal and N₂O release in ecosystems; in this regard, paddy soils exhibit strong denitrifying ability. However, the underlying mechanism of N₂O emission from denitrification in paddy soils is yet to be elucidated. In this study, the potential N₂O emission rate, enzymatic activity for N₂O production and reduction, gene abundance, and community composition during denitrification were investigated using the ¹⁵N isotope tracer technique combined with slurry incubation, enzymatic activity detection, quantitative polymerase chain reaction (qPCR), and metagenomic sequencing. Results of incubation experiments showed that the average potential N₂O emission rates were 0.51 ± 0.20 μmol⋅N⋅kg^-1⋅h^-1, which constituted 2.16 ± 0.85% of the denitrification end-products. The enzymatic activity for N₂O production was 2.77-8.94 times than that for N₂O reduction, indicating an imbalance between N₂O production and reduction. The gene abundance ratio of nir to nosZ from qPCR results further supported the imbalance. Results of metagenomic analysis showed that, although Proteobacteria was the common phylum for denitrification genes, other dominant community compositions varied for different denitrification genes. Gammaproteobacteria and other phyla containing the norB gene without nosZ genes, including Actinobacteria, Planctomycetes, Desulfobacterota, Cyanobacteria, Acidobacteria, Bacteroidetes, and Myxococcus, may contribute to N₂O emission from paddy soils. Our results suggest that denitrification is highly modular, with different microbial communities collaborating to complete the denitrification process, thus resulting in an emission estimation of 13.67 ± 5.44 g N₂O⋅m^-2⋅yr^-1 in surface paddy soils.

Coupled abiotic-biotic cycling of nitrous oxide in tropical peatlands

Atmospheric nitrous oxide (N2O) is a potent greenhouse gas thought to be mainly derived from microbial metabolism as part of the denitrification pathway. Here we report that in unexplored peat soils of Central and South America, N2O production can be driven by abiotic reactions (≤98%) highly competitive to their enzymatic counterparts. Extracted soil iron positively correlated with in situ abiotic N2O production determined by isotopic tracers. Moreover, we found that microbial N2O reduction accompanied abiotic production, essentially closing a coupled abiotic-biotic N2O cycle. Anaerobic N2O consumption occurred ubiquitously (pH 6.4-3.7), with proportions of diverse clade II N2O reducers increasing with consumption rates. Our findings show that denitrification in tropical peat soils is not a purely biological process but rather a 'mosaic' of abiotic and biotic reduction reactions. We predict that hydrological and temperature fluctuations differentially affect abiotic and biotic drivers and further contribute to the high N2O flux variation in the region.

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.

Assembly of root-associated N2O-reducing communities of annual crops is governed by selection for nosZ clade I over clade II

The rhizosphere is a hotspot for denitrification. The nitrous oxide (N₂O) reductase among denitrifiers and nondenitrifying N₂O reducers is the only known N₂O sink in the biosphere. We hypothesized that the composition of root-associated N₂O-reducing communities when establishing on annual crops depend on soil type and plant species, but that assembly processes are independent of these factors and differ between nosZ clades I and II. Using a pot experiment with barley and sunflower and two soils, we analyzed the abundance, composition, and diversity of soil and root-associated N₂O reducing communities by qPCR and amplicon sequencing of nosZ. Clade I was more abundant on roots compared to soil, while clade II showed the opposite. In barley, this pattern coincided with N₂O availability, determined as potential N₂O production rates, but for sunflower no N₂O production was detected in the root compartment. Root and soil nosZ communities differed in composition and phylogeny-based community analyses indicated that assembly of root-associated N₂O reducers was driven by the interaction between plant and soil type, with inferred competition being more influential than habitat selection. Selection between clades I and II in the root/soil interface is suggested, which may have functional consequences since most clade I microorganisms can produce N₂O.

Nitrate Addition Increases the Activity of Microbial Nitrogen Removal in Freshwater Sediment

Denitrification and anammox occur widely in aquatic ecosystems serving vital roles in nitrogen pollution removal. However, small waterbodies are sensitive to external influences; stormwater runoff carrying nutrients and oxygen, flows into waterbodies resulting in a disruption of geochemical and microbial processes. Nonetheless, little is known about how these short-term external inputs affect the microbial processes of nitrogen removal in small waterbodies. To investigate the effects of NO₃⁻, NH₄⁺, dissolved oxygen (DO) and organic C on microbial nitrogen removal in pond sediments, regulation experiments have been conducted using slurry incubation experiments and ¹⁵N tracer techniques in this study. It was demonstrated the addition of NO₃⁻ (50 to 800 μmol L⁻¹) significantly promoted denitrification rates, as expected by Michaelis-Menten kinetics. Ponds with higher NO₃⁻ concentrations in the overlying water responded more greatly to NO₃⁻ additions. Moreover, N₂O production was also promoted by such an addition of NO₃⁻. Denitrification was significantly inhibited by the elevation of DO concentration from 0 to 2 mg L⁻¹, after which no significant increase in inhibition was observed. Denitrification rates increased when organic C was introduced. Due to the abundant NH₄⁺ in pond sediments, the addition demonstrated little influence on nitrogen removal. Moreover, anammox rates showed no significant changes to any amendment.

Using isotope pool dilution to understand how organic carbon additions affect N2 O consumption in diverse soils

Nitrous oxide (N2 O) is a formidable greenhouse gas with a warming potential ~300× greater than CO2 . However, its emissions to the atmosphere have gone largely unchecked because the microbial and environmental controls governing N2 O emissions have proven difficult to manage. The microbial process N2 O consumption is the only know biotic pathway to remove N2 O from soil pores and therefore reduce N2 O emissions. Consequently, manipulating soils to increase N2 O consumption by organic carbon (OC) additions has steadily gained interest. However, the response of N2 O emissions to different OC additions are inconsistent, and it is unclear if lower N2 O emissions are due to increased consumption, decreased production, or both. Simplified and systematic studies are needed to evaluate the efficacy of different OC additions on N2 O consumption. We aimed to manipulate N2 O consumption by amending soils with OC compounds (succinate, acetate, propionate) more directly available to denitrifiers. We hypothesized that N2 O consumption is OC-limited and predicted these denitrifier-targeted additions would lead to enhanced N2 O consumption and increased nosZ gene abundance. We incubated diverse soils in the laboratory and performed a 15 N2 O isotope pool dilution assay to disentangle microbial N2 O emissions from consumption using laser-based spectroscopy. We found that amending soils with OC increased gross N2 O consumption in six of eight soils tested. Furthermore, three of eight soils showed Increased N2 O Consumption and Decreased N2 O Emissions (ICDE), a phenomenon we introduce in this study as an N2 O management ideal. All three ICDE soils had low soil OC content, suggesting ICDE is a response to relaxed C-limitation wherein C additions promote soil anoxia, consequently stimulating the reduction of N2 O via denitrification. We suggest, generally, OC additions to low OC soils will reduce N2 O emissions via ICDE. Future studies should prioritize methodical assessment of different, specific, OC-additions to determine which additions show ICDE in different soils.

Plant biodiversity promotes sustainable agriculture directly and via belowground effects

While the positive relationship between plant biodiversity and ecosystem functioning (BEF) is well established, the extent to which this is mediated via belowground microbial processes is poorly understood. Growing evidence suggests that plant community structure influences soil microbial diversity, which in turn promotes functions desired for sustainable agriculture. Here, we outline the 'plant-directed' and soil microbe-mediated mechanisms expected to promote positive BEF. We identify how this knowledge can be utilized in plant diversification schemes to maximize ecosystem functioning in agroecosystems, which are typically species poor and sensitive to biotic and abiotic stressors. In the face of resource overexploitation and global change, bridging the gaps between biodiversity science and agricultural practices is crucial to meet food security in the Anthropocene.

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

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

High N2O reduction potential by denitrification in the nearshore site of a riparian zone

As a potent atmospheric greenhouse gas and a major source of ozone depletion, nitrous oxide (N₂O) emission has been given increasing attention in aquatic systems, particularly at the aquatic-terrestrial interfaces, such as riparian zones. However, the microbial mechanisms regulating N₂O emission in riparian zones remain unknown. Here, we measured the contributions of denitrification and ammonium oxidation to N₂O emission along with the abundance and community structure of nirK-, nirS-, nosZ I- and nosZ II-harbouring bacteria in both surface sediments (0-10 cm) and overlying water along a lake riparian zone (including nearshore sites and offshore sites). Overall, the nearshore sites of the riparian zones emitted less N₂O than the offshore sites. Nearshore N₂O emission was dominated by denitrification with a high N₂O reduction rate, whereas offshore N₂O emission was driven by ammonium oxidation. Furthermore, N₂O derived from ammonium oxidation was influenced by the NH₄⁺-N content, and denitrification N₂O was modulated by denitrifier communities. The N₂O-producing community was dominated by nirS-harbouring bacteria, while the N₂O-reducing community was dominated by nosZ I-harbouring bacteria. The relative abundance of Hydrogenophilales from nirS-denitrifiers and Chloroflexi unclassified from nosZ II-type communities influenced the N₂O produced by denitrification, according to high-throughput sequencing analysis. Additionally, we also found lower levels of N₂O production per unit volume in overlying water, which were 3-4 orders of magnitude less than in the surface sediment. Overall, we propose that using riparian zones can be an effective management tool for N₂O mitigation by enhancing the N₂O reduction process of denitrification and decreasing ammonium oxidation.

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

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

How does partial substitution of chemical fertiliser with organic forms increase sustainability of agricultural production?

To ensure global food security, agriculture must increase productivity while reducing environmental impacts associated with chemical nitrogen (N) fertilisation. This necessitates towards more sustainable practices such as recycling organic waste to substitute chemical fertiliser N inputs. However, hitherto how such strategy controls the succession of microbial communities and their relationship with crop yields and environmental impacts have not been comprehensively investigated. We conducted a field experiment with vegetable production in China examining partial substitution (25-50%) of chemical fertiliser with organic forms (pig manure or municipal sludge compost) considering key sustainability metrics: productivity, soil health, environmental impacts and microbial communities. We demonstrate that partial organic substitution improved crop yields, prevented soil acidification and improved soil fertility. Treatments also reduced detrimental environmental impacts with lower N₂O emission, N leaching and runoff, likely due to reduced inorganic nitrogen surplus. Microbial communities, including key genes involved in the N cycle, were dynamic and time-dependent in response to partial organic substitution, and were also important in regulating crop yields and environmental impacts. Partial organic substitution increased bacterial diversity and the relative abundance of several specific microbial groups (e.g. Sphingomonadales, Myxococcales, Planctomycetes, and Rhizobiales) involved in N cycling. Additionally, partial organic substitution reduced the number of bacterial ammonia oxidizers and increased the number of denitrifiers, with the proportion of N₂O-reducers being more pronounced, suggesting a mechanism for reducing N₂O emissions. Comprehensive economic cost-benefit evaluation showed that partial organic substitution increased economic benefit per unit area by 37-46%, and reduced agricultural inputs and environmental impacts per unit product by 22-44%. Among them, 50% substitution of pig manure was the most profitable strategy. The study is crucial to policy-making as it highlights the potential advantages of shifting towards systems balancing chemical and organic fertilisers with economic benefits for farmers, reduced environmental damage and an efficient way for organic waste disposal.

Direct evidence for the role of microbial community composition in the formation of soil organic matter composition and persistence

The largest terrestrial carbon sink on earth is soil carbon stocks. As the climate changes, the rate at which the Earth's climate warms depends in part on the persistence of soil organic carbon. Microbial turnover forms the backbone of soil organic matter (SOM) formation and it has been recently proposed that SOM molecular complexity is a key driver of stability. Despite this, the links between microbial diversity, chemical complexity and biogeochemical nature of SOM remain missing. Here we tested the hypotheses that distinct microbial communities shape the composition of SOM, and microbial-derived SOM has distinct decomposition potential depending on its community of origin. We inoculated microbial communities of varying diversities into a model soil matrix amended with simple carbon (cellobiose) and measured the thermal stability of the resultant SOM. Using a Rock-Eval® ramped thermal analysis, we found that microbial community composition drives the chemical fingerprint of soil carbon. While diversity was not a driver of SOM composition, bacteria-only communities lead to more thermally labile soil C pools than communities with bacteria and fungi. Our results provide direct evidence for a link between microbial community structure, SOM composition, and thermal stability. This evidence demonstrates the relevance of soil microorganisms in building persistent SOM stocks.

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.

Biochar amendment mitigated N2O emissions from paddy field during the wheat growing season

Biochar may variably impact nitrogen (N) transformation and N-cycle-related microbial activities. Yet the mechanism of biochar amendment on nitrous oxide (N₂O) emissions from agricultural ecosystems remains unclear. Based on a 6-year long-term biochar amendment experiment, we applied a dual isotope (¹⁵N-¹⁸O) labeling technique with tracing transcriptional genes to differentiate the contribution of nitrifier nitrification (NN), nitrifier denitrification (ND), nitrification-coupled denitrification (NCD) and heterotrophic denitrification (HD) pathway to N₂O production. Then the field experiment provided quantitative data on dynamic N₂O emissions, soil mineral N and key functional marker gene abundances during the wheat growing season. By using ¹⁵N-¹⁸O isotope, biochar decreased N₂O emission derived from ND (by 45-94%), HD (by 35-46%) and NCD (by 30-64%) compared to the values under N application. Biochar increased the relative contribution of NN to total N₂O production as evidenced by the increase in ammonia-oxidizing bacteria, but did not influence the cumulative NN-derived N₂O. The field experiment found that the majority of the N₂O emissions peaked following fertilization, in parallel with soil NH₄⁺ and nitrite dynamics. Soil N₂O emissions during the wheat growing stage were effectively decreased (by 38-48%) by biochar amendment. Based on the correlation analyses and random forest analysis in both microcosm and field experiments, the decrease in nitrite concentration (by 62-65%) and increase in N₂O consumption were mainly responsible for net N₂O mitigation, as evidenced by the decrease in the ratios of nitrite reductase genes/transcripts (nirS, nirK and fungal nirK) and N₂O reductase gene/transcripts (nosZI and nosZII). Based on the extrapolation from microcosm to field, biochar significantly mitigated N₂O emissions by weakening the ND processes, since NCD and HD contributed little during the N₂O emission "peaks" following urea fertilization. Therefore, emphasis should be put on the ND process and nitrite accumulation during N₂O emission peaks and extrapolated to all agroecosystems.

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

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

Land use in urban areas impacts the composition of soil bacterial communities involved in nitrogen cycling. A case study from Lefkosia (Nicosia) Cyprus

The different types of land-use and soil lithology in urban and peri-urban areas of modern cities compose a complex mosaic of soil ecosystems. It is largely unknown how these differences result in changes in bacterial community composition and structure as well as in functional guilds involved in N cycling. To investigate the bacterial composition and the proportion of denitrifiers in agricultural, forested, schoolyard and industrial areas, 24 samples were collected from urban and peri-urban sites of Lefkosia. Bacterial diversity and the proportion of denitrifiers were assessed by NGS and qPCR, respectively. Proteobacteria, Actinobacteria, Bacteriodetes, Chloroflexi, Acidobacteria and Planctomycetes were identified as the most dominant phyla across all sites, while agricultural sites exhibited the highest bacterial diversity. Heavy metals such as Co, Pb, V and Al were identified as key factors shaping bacterial composition in industrial and schoolyard sites, while the bacterial assemblages in agricultural and forested sites were associated with Ca. Variance partitioning analysis showed that 10.2% of the bacterial community variation was explained by land use management, 5.1% by chemical elements due to soil lithology, and 1.4% by sampling location. The proportion of denitrifiers varied with land use management. In industrial and schoolyard sites, the abundance of the nosZII bacterial community increased while nirK abundance declined. Our data showed that land use and lithology have a moderate impact on the bacterial assemblages in urban and peri-urban areas of Lefkosia. As the nosZII bacterial community is important to the N₂O sink capacity of soils, it would be interesting to elucidate the factors contributing to the proliferation of the nosZII clade in these soils.

Effects of biochar on nitrification and denitrification-mediated N2O emissions and the associated microbial community in an agricultural soil

Nitrous oxide (N₂O) is a strong greenhouse gas, and it is of great significance for N₂O reduction to study the effects of biochar on its production pathway. In this research, the contributions and mechanisms of biochar on autotrophic nitrification (ANF), heterotrophic nitrification (HNF), and denitrification (DF) to N₂O emissions were studied by using ¹⁵N stable isotopes and high-throughput sequencing after laboratory incubation. The results showed that biochar addition at 2% (B2) significantly reduced the N₂O emissions from the ANF by an average of 20.6%, while adding 5% biochar (B5) had no significant effect on the ANF. Both B2 and B5 significantly reduced the N₂O emissions from the HNF by 15.7% and 13.2%, respectively, and reduced the N₂O emissions from the DF by 40.9% and 11.7%, respectively. B2 enhanced the relative contribution rate of the ANF to N₂O emissions by 6.3%, while B5 had little effect on it. Biochar addition significantly changed the copy numbers of the AOA and AOB, as well as the nirK, nirS, and nosZ genes, but it had no significant effect on the community composition of the AOA and had minimal effect on the AOB community. B2 significantly increased the abundance of the genus Rhodococcus of nirK type denitrifiers and had a significant effect on the relative abundance of Cupriavidus and Pseudomonas of the nosZ type denitrifiers. These results revealed that the inhibitory effects of biochar on N₂O emissions from nitrification might be attributed to the direct immobilization and adsorption of inorganic N by biochar and to its promotion of the genus Rhodococcus of nirK-type denitrifiers and the genera Cupriavidus and Pseudomonas of the nosZ-type denitrifiers. The soil exchangeable NH₄⁺-N and NO₃^--N concentrations were the primary factors affecting the N₂O emission rates. These results help to elucidate the effects and mechanisms of biochar on N₂O production pathways in agricultural soil.

Enhancement of nitrous oxide emissions in soil microbial consortia via copper competition between proteobacterial methanotrophs and denitrifiers

Unique means of copper scavenging have been identified in proteobacterial methanotrophs, particularly the use of methanobactin, a novel ribosomally synthesized post-translationally modified polypeptide that binds copper with very high affinity. The possibility that copper sequestration strategies of methanotrophs may interfere with copper uptake of denitrifiers in situ and thereby enhance N₂O emissions was examined using a suite of laboratory experiments performed with rice paddy microbial consortia. Addition of purified methanobactin from Methylosinus trichosporium OB3b to denitrifying rice paddy soil microbial consortia resulted in substantially increased N₂O production, with more pronounced responses observed for soils with lower copper content. The N₂O emission-enhancing effect of the soil's native mbnA-expressing Methylocystaceae methanotrophs on the native denitrifiers was then experimentally verified with a Methylocystaceae-dominant chemostat culture prepared from a rice paddy microbial consortium as the inoculum. Lastly, with microcosms amended with varying cell numbers of methanobactin-producing Methylosinus trichosporium OB3b before CH₄ enrichment, microbiomes with different ratios of methanobactin-producing Methylocystaceae to gammaproteobacterial methanotrophs incapable of methanobactin production were simulated. Significant enhancement of N₂O production from denitrification was evident in both Methylocystaceae-dominant and Methylococcaceae-dominant enrichments, albeit to a greater extent in the former, signifying the comparative potency of methanobactin-mediated copper sequestration while implying the presence of alternative copper abstraction mechanisms for Methylococcaceae These observations support that copper-mediated methanotrophic enhancement of N₂O production from denitrification is plausible where methanotrophs and denitrifiers cohabit.IMPORTANCE Proteobacterial methanotrophs, groups of microorganisms that utilize methane as source of energy and carbon, have been known to utilize unique mechanisms to scavenge copper, namely utilization of methanobactin, a polypeptide that binds copper with high affinity and specificity. Previously the possibility that copper sequestration by methanotrophs may lead to alteration of cuproenzyme-mediated reactions in denitrifiers and consequently increase emission of potent greenhouse gas N₂O has been suggested in axenic and co-culture experiments. Here, a suite of experiments with rice paddy soil slurry cultures with complex microbial compositions were performed to corroborate that such copper-mediated interplay may actually take place in environments co-habited by diverse methanotrophs and denitrifiers. As spatial and temporal heterogeneity allow for spatial coexistence of methanotrophy (aerobic) and denitrification (anaerobic) in soils, the results from this study suggest that this previously unidentified mechanism of N₂O production may account for significant proportion of N₂O efflux from agricultural soils.

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

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

Nitrate assimilation, dissimilatory nitrate reduction to ammonium, and denitrification coexist in Pseudomonas putida Y-9 under aerobic conditions

The specific nitrate reduction pathway in Pseudomonas putida Y-9 under aerobic conditions was studied. Strain Y-9 removed 82% of the nitrate accompanied by an accumulation of ammonium and a decrease of total nitrogen. Ammonium inhibited nitrate transformation (removal efficiency was 22.65%), illustrating that nitrate assimilation exists in strain Y-9. The detectable ammonium in the supernatant during the nitrate reduction process came from intracellular locations in strain Y-9. The nirBD that encodes nitrite reductase had an important role in strain growth and ammonium production. A ¹⁵N isotope experiment demonstrated that strain Y-9 can conduct dissimilatory nitrate reduction to ammonium (DNRA) and nirBD controls this process. This further indicated that the loss of total nitrogen is due to denitrification. All results highlighted that strain Y-9 performs simultaneous nitrate assimilation, DNRA, and denitrification under aerobic conditions, and nirBD controls the assimilation and DNRA process. Thereinto, nitrate assimilation dominates the removal of nitrate.

Microbial diversity drives carbon use efficiency in a model soil

Empirical evidence for the response of soil carbon cycling to the combined effects of warming, drought and diversity loss is scarce. Microbial carbon use efficiency (CUE) plays a central role in regulating the flow of carbon through soil, yet how biotic and abiotic factors interact to drive it remains unclear. Here, we combine distinct community inocula (a biotic factor) with different temperature and moisture conditions (abiotic factors) to manipulate microbial diversity and community structure within a model soil. While community composition and diversity are the strongest predictors of CUE, abiotic factors modulated the relationship between diversity and CUE, with CUE being positively correlated with bacterial diversity only under high moisture. Altogether these results indicate that the diversity × ecosystem-function relationship can be impaired under non-favorable conditions in soils, and that to understand changes in soil C cycling we need to account for the multiple facets of global changes.

Large Variations in N2O Fluxes from Bioenergy Crops According to Management Practices and Crop Type

Field N2O emissions are a key point in the evaluation of the greenhouse gas benefits of bioenergy crops. The aim of this study was to investigate N2O fluxes from perennial (miscanthus and switchgrass), semi-perennial (fescue and alfalfa) and annual (sorghum and triticale) bioenergy crops and to analyze the effect of the management of perennials (nitrogen fertilization and/or harvest date). Daily N2O emissions were measured quasi-continuously during at least two years in a long-term experiment, using automated chambers, with 2–5 treatments monitored simultaneously. Cumulative N2O emissions from perennials were strongly affected by management practices: fertilized miscanthus harvested early and unfertilized miscanthus harvested late had systematically much lower emissions than fertilized miscanthus harvested late (50, 160 and 1470 g N2O-N ha−1 year−1, respectively). Fertilized perennials often had similar or higher cumulative emissions than semi-perennial or annual crops. Fluxes from perennial and semi-perennial crops were characterized by long periods with low emissions interspersed with short periods with high emissions. Temperature, water-filled pore space and soil nitrates affected daily emissions but their influence varied between crop types. This study shows the complex interaction between crop type, crop management and climate, which results in large variations in N2O fluxes for a given site.

The distribution of functional N-cycle related genes and ammonia and nitrate nitrogen in soil profiles fertilized with mineral and organic N fertilizer

Nitrogen transformation in soil is a complex process and the soil microbial population can regulate the potential for N mineralization, nitrification and denitrification. Here we show that agricultural soils under standard agricultural N-management are consistently characterized by a high presence of gene copies for some of the key biological activities related to the N-cycle. This led to a strong NO₃^- reduction (75%) passing from the soil surface (15.38 ± 11.36 g N-NO₃ kg^-1 on average) to the 1 m deep layer (3.92 ± 4.42 g N-NO₃ kg^-1 on average), and ensured low nitrate presence in the deepest layer. Under these circumstances the other soil properties play a minor role in reducing soil nitrate presence in soil. However, with excessive N fertilization, the abundance of bacterial gene copies is not sufficient to explain N leaching in soil and other factors, i.e. soil texture and rainfall, become more important in controlling these aspects.

Gross N2O Production Process, Not Consumption, Determines the Temperature Sensitivity of Net N2O Emission in Arable Soil Subject to Different Long-Term Fertilization Practices

Chronic amendment of agricultural soil with synthetic nitrogen fertilization and/or livestock manure has been demonstrated to enhance the feedback intensity of net N₂O emission to temperature variation (i.e., temperature sensitivity, TS). Yet few studies have explored the relevance of changes in underlying gross N₂O production and consumption processes toward explaining this phenomenon, in particular for the latter. Furthermore, the microbe-based mechanisms associated with the variation of N₂O consumption process remain largely unexplored. To address this knowledge gap, a temperature- (15, 25, and 35°C) and moisture-controlled (50% water holding capacity) microcosm incubation experiment was established using an arable soil subject to long-term addition of synthetic fertilizer (NPK), a mixture of synthetic fertilizer with livestock manure (MNPK), or with no fertilizer treatment (CT). Over the incubation time period, the C₂H₂ inhibition method was adopted to monitor reaction rates of gross N₂O production and consumption; the population sizes and community structures of nosZI- and nosZII-N₂O reducers were analyzed using quantitative PCR (Q-PCR) and terminal restriction fragment length polymorphism (T-RFLP). The results indicated that only NPK significantly increased the TS of net N₂O emission, and gross N₂O consumption process consistently occurred under all treatment combinations (temperature and fertilization) at each sampling time point. The responses of gross N₂O production and consumption processes to temperature elevation exhibited fertilization- and sampling time-dependent pattern, and the higher net N₂O production TS in the NPK treatment was underlain by its higher TS of gross production process and insensitivity of gross consumption process to temperature. The size and structure of nosZII-N₂O reducers, as well as the community structure of nosZI-N₂O reducers, were positively correlated with variation of gross N₂O production and consumption rates across all fertilization regimes. NosZII-N₂O reducer abundance was less responsive to temperature change, and its community structure less susceptible to fertilization, as compared with nosZI-N₂O reducers. Overall, our results demonstrate that the TS of the gross N₂O production process, not gross consumption, is the key step regulating the TS of net N₂O production, and both nosZI- and nosZII-N₂O clades are likely active N₂O reducers in the tested soil.

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

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

Quantification of denitrifier genes population size and its relationship with environmental factors

The objectives of this study were to use real-time PCR for culture-independent quantification of the copy numbers of 16S rRNA and denitrification functional genes, and also the relationships between gene copy numbers and soil physicochemical properties. In this study, qPCR analysis of the soil samples showed 16S rRNA, nirS, nirK, nosZI and nosZII average densities of 3.0 × 10⁸, 2.25 × 10⁷, 2.9 × 10⁵, 4.0 × 10⁶ and 1.75 × 10⁷ copies per gram of dry soil, respectively. In addition, the abundances of (nirS + nirK), nosZI and nosZII relative to 16S rRNA genes were 1.4-34.1%, 0.06-3.95% and 1.3-39%, respectively, confirming the low proportion of denitrifiers to total bacteria in soil. This showed that the non-denitrifying nosZII-type bacteria may contribute significantly to N₂O consumption in the soil. Furthermore, the shifts in abundance and diversity of the total bacteria and denitrification functional gene copy numbers correlated significantly with the various soil factors. It is the first study in Turkey about the population size of denitrification functional genes in different soil samples. It also aims to draw attention to nitrous oxide-associated global warming.

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

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

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

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

An evaluation of primers for detecting denitrifiers via their functional genes

Microbial populations provide nitrogen cycling ecosystem services at the nexus of agriculture, environmental quality and climate change. Denitrification, in particular, impacts socio-environmental systems in both positive and negative ways, through reduction of aquatic and atmospheric nitrogen pollution, but also reduction of soil fertility and production of greenhouse gases. However, denitrification rates are quite variable in time and space, and therefore difficult to model. Microbial ecology is working to improve the predictive ecology of denitrifiers by quantifying and describing the diversity of microbial functional groups. However, metagenomic sequencing has revealed previously undescribed diversity within these functional groups, and highlighted a need to reevaluate coverage of existing DNA primers for denitrification functional genes. We provide here a comprehensive in silico evaluation of primer sets that target diagnostic genes in the denitrification pathway. This analysis makes use of current DNA sequence data available for each functional gene. It contributes a comparative analysis of the strengths and limitations of each primer set for describing denitrifier functional groups. This analysis identifies genes for which development of new tools is needed, and aids in interpretation of existing datasets, both of which will facilitate application of molecular methods to further develop the predictive ecology of denitrifiers.

Influence of rewetting on microbial communities involved in nitrification and denitrification in a grassland soil after a prolonged drought period

The frequency of extreme drought and heavy rain events during the vegetation period will increase in Central Europe according to future climate change scenarios, which will affect the functioning of terrestrial ecosystems in multiple ways. In this study, we simulated an extreme drought event (40 days) at two different vegetation periods (spring and summer) to investigate season-related effects of drought and subsequent rewetting on nitrifiers and denitrifiers in a grassland soil. Abundance of the microbial groups of interest was assessed by quantification of functional genes (amoA, nirS/nirK and nosZ) via quantitative real-time PCR. Additionally, the diversity of ammonia-oxidizing archaea was determined based on fingerprinting of the archaeal amoA gene. Overall, the different time points of simulated drought and rewetting strongly influenced the obtained response pattern of microbial communities involved in N turnover as well as soil ammonium and nitrate dynamics. In spring, gene abundance of nirS was irreversible reduced after drought whereas nirK and nosZ remained unaffected. Furthermore, community composition of ammonia-oxidizing archaea was altered by subsequent rewetting although amoA gene abundance remained constant. In contrast, no drought/rewetting effects on functional gene abundance or diversity pattern of nitrifying archaea were observed in summer. Our results showed (I) high seasonal dependency of microbial community responses to extreme events, indicating a strong influence of plant-derived factors like vegetation stage and plant community composition and consequently close plant-microbe interactions and (II) remarkable resistance and/or resilience of functional microbial groups involved in nitrogen cycling to extreme weather events what might indicate that microbes in a silty soil are better adapted to stress situations as expected.

Organic Residue Amendments to Modulate Greenhouse Gas Emissions From Agricultural Soils

Organic fertilizers have been shown to stimulate CH₄ uptake from agricultural soils. Managing fertilizer application to maximize this effect and to minimize emission of other greenhouse gasses offers possibilities to increase sustainability of agriculture. To tackle this challenge, we incubated an agricultural soil with different organic amendments (compost, sewage sludge, digestate, cover crop residues mixture), either as single application or in a mixture and subjected it to different soil moisture concentrations using different amounts of organic amendments. GHG fluxes and in vitro CH₄ oxidation rates were measured repeatedly, while changes in organic matter and abundance of GHG relevant microbial groups (nitrifiers, denitrifiers, methanotrophs, methanogens) were measured at the end of the incubation. Overall the dynamics of the analyzed GHGs differed significantly. While CO₂ and N₂O differed considerably between the treatments, CH₄ fluxes remained stable. In contrast, in vitro CH₄ oxidation showed a clear increase for all amendments over time. CO₂ fluxes were mostly dependent on the amount of organic residue that was used, while N₂O fluxes were affected more by soil moisture. Several combinations of amendments led to reductions of CO₂, CH₄, and/or N₂O emissions compared to un-amended soil. Most optimal GHG balance was obtained by compost amendments, which resulted in a similar overall GHG balance as compared to the un-amended soil. However, compost is not very nutrient rich potentially leading to lower crop yield when applied as single fertilizer. Hence, the combination of compost with one of the more nutrient rich organic amendments (sewage sludge, digestate) provides a trade-off between maintaining crop yield and minimizing GHG emissions. Additionally, we could observe a strong increase in microbial communities involved in GHG consumption in all amendments, with the strongest increase associated with cover crop residue mixtures. Future research should focus on the interrelation of plants, soil, and microbes and their impact on the global warming potential in relation to applied organic amendments.

Predominance and high diversity of genes associated to denitrification in metagenomes of subantarctic coastal sediments exposed to urban pollution

The aim of this work was to characterize the microbial nitrogen cycling potential in sediments from Ushuaia Bay, a subantarctic environment that has suffered a recent explosive demographic growth. Subtidal sediment samples were retrieved in triplicate from two urban points in the Bay, and analyzed through metagenomic shotgun sequencing. Sequences assigned to genes related to nitrification, nitrate reduction and denitrification were predominant in this environment with respect to metagenomes from other environments, including other marine sediments. The nosZ gene, responsible for nitrous oxide transformation into di-nitrogen, presented a high diversity. The majority of NosZ sequences were classified as Clade II (atypical) variants affiliated to different bacterial lineages such as Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, Verrucomicrobia, as well as to Archaea. The analysis of a fosmid metagenomic library from the same site showed that the genomic context of atypical variants was variable, and was accompanied by distinct regulatory elements, suggesting the evolution of differential ecophysiological roles. This work increases our understanding of the microbial ecology of nitrogen transformations in cold coastal environments and provides evidence of an enhanced denitrification potential in impacted sediment microbial communities. In addition, it highlights the role of yet overlooked populations in the mitigation of environmentally harmful forms of nitrogen.

Antibiotic Effects on Microbial Communities Responsible for Denitrification and N2O Production in Grassland Soils

Antibiotics in soils may affect the structure and function of microbial communities. In this study, we investigated the acute effects of tetracycline on soil microbial community composition and production of nitrous oxide (N₂O) and dinitrogen (N₂) as the end-products of denitrification. Grassland soils were pre-incubated with and without tetracycline for 1-week prior to measurements of N₂O and N₂ production in soil slurries along with the analysis of prokaryotic and fungal communities by quantitative polymerase chain reaction (qPCR) and next-generation sequencing. Abundance and taxonomic composition of bacteria carrying two genotypes of N₂O reductase genes (nosZ-I and nosZ-II) were evaluated through qPCR and metabolic inference. Soil samples treated with tetracycline generated 12 times more N₂O, but N₂ production was reduced by 84% compared to the control. In parallel with greater N₂O production, we observed an increase in the fungi:bacteria ratio and a significant decrease in the abundance of nosZ-II carrying bacteria; nosZ-I abundance was not affected. NosZ-II-carrying Bacillus spp. (Firmicutes) and Anaeromyxobacter spp. (Deltaproteobacteria) were particularly susceptible to tetracycline and may serve as a crucial N₂O sink in grassland soils. Our study indicates that the introduction of antibiotics to agroecosystems may promote higher N₂O production due to the inhibitory effects on nosZ-II-carrying communities.

Salinity shifts in marine sediment: Importance of number of fluctuation rather than their intensities on bacterial denitrifying community

The sensitivity of denitrifying community to salinity fluctuations was studied in microcosms filled with marine coastal sediments subjected to different salinity disturbances over time (sediment under frequent salinity changes vs sediment with "stable" salinity pattern). Upon short-term salinity shift, denitrification rate and denitrifiers abundance showed high resistance whatever the sediment origin is. Denitrifying community adapted to frequent salinity changes showed high resistance when salinity increases, with a dynamic nosZ relative expression level. Marine sediment denitrifying community, characterized by more stable pattern, was less resistant when salinity decreases. However, after two successive variations of salinity, it shifted toward the characteristic community of fluctuating conditions, with larger proportion of Pseudomonas-nosZ, exhibiting an increase of nosZ relative expression level. The impact of long-term salinity variation upon bacterial community was confirmed at ribosomal level with a higher percentage of Pseudomonas and lower proportion of nosZII clade genera.

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

Nitrous oxide (N₂O)-reducing bacteria, which reduce N₂O to nitrogen in the absence of oxygen, are phylogenetically spread throughout various taxa and have a potential role as N₂O sinks in the environment. However, research on their physiological traits has been limited. In particular, their activities under microaerophilic and aerobic conditions, which severely inhibit N₂O reduction, remain poorly understood. We used an O₂ and N₂O micro-respirometric system to compare the N₂O reduction kinetics of four strains, i.e., two strains of an Azospira sp., harboring clade II type nosZ, and Pseudomonas stutzeri and Paracoccus denitrificans, harboring clade I type nosZ, in the presence and absence of oxygen. In the absence of oxygen, the highest N₂O-reducing activity, V_m,N2O, was 5.80 ± 1.78 × 10^-3 pmol/h/cell of Azospira sp. I13, and the highest and lowest half-saturation constants were 34.8 ± 10.2 μM for Pa. denitirificans and 0.866 ± 0.29 μM for Azospira sp. I09. Only Azospira sp. I09 showed N₂O-reducing activity under microaerophilic conditions at oxygen concentrations below 110 μM, although the activity was low (10% of V_m,N2O). This trait is represented by the higher O₂ inhibition coefficient than those of the other strains. The activation rates of N₂O reductase, which describe the resilience of the N₂O reduction activity after O₂ exposure, differ for the two strains of Azospira sp. (0.319 ± 0.028 h^-1 for strain I09 and 0.397 ± 0.064 h^-1 for strain I13) and Ps. stutzeri (0.200 ± 0.013 h^-1), suggesting that Azospira sp. has a potential for rapid recovery of N₂O reduction and tolerance against O₂ inhibition. These physiological characteristics of Azospira sp. can be of promise for mitigation of N₂O emission in industrial applications.

Long-term effects of contrasting tillage on soil organic carbon, nitrous oxide and ammonia emissions in a Mediterranean Vertisol under different crop sequences

This 2-year study aimed to verify whether the continuous application of no tillage (NT) for over 20years, in comparison with conventional tillage (CT), affects nitrous oxide (N₂O) and ammonia (NH₃) emissions from a Vertisol and, if so, whether such an effect varies with crop sequence (continuous wheat, WW and wheat after faba bean, FW). To shed light on the mechanisms involved in determining N-gas emissions, soil bulk density, water filled pore space (WFPS), some carbon (C) and nitrogen (N) pools, denitrifying enzyme activity (DEA), and nitrous oxide reductase gene abundance (nosZ gene) were also assessed at 0-15 and 15-30cm soil depth. Tillage system had no significant effect on total NH₃ emissions. On average, total N₂O emissions were higher under NT (2.45kgN₂O-Nha^-1) than CT (1.72kgN₂O-Nha^-1), being the differences between the two tillage systems greater in FW than WW. The higher N₂O emissions in NT treatments were ascribed to the increased bulk density, WFPS, and extractable organic C under NT compared to CT, all factors that generally promote the production of N₂O. Moreover, compared to CT, NT enhanced the potential DEA (114 vs 16μgNkg^-1h^-1) and nosZ gene abundance (116 vs 69 copy number mg^-1 dry soil) in the topsoil. Finally, NT compared to CT led to an average annual increase in C stock of 0.70MgCha^-1year^-1. Though NT can increase the amount os soil organic matter so storing CO₂ into soil, some criticisms related to the increase of N₂O emission arise, thereby suggesting the need for defining management strategies to mitigate such a negative effect.

Sediment denitrification in Yangtze lakes is mainly influenced by environmental conditions but not biological communities

Globally, shallow lakes have suffered from excessive nitrogen (N) loading due to increased human activities in catchments, resulting in water quality degradation and aquatic biodiversity loss. Sediment denitrification, which reduces nitrate (NO₃^-) to N gaseous products, is the most important mechanism for permanent N removal in freshwater lakes. However, the relative contribution of abiotic and biotic factors to the sediment denitrification is highly variable. Here, we determined the unamended denitrification rate and nitrous oxide (N₂O) production rate of 74 sediment samples from 22 eutrophic lakes in the Yangtze River basin. We also quantified the diversity and abundance of denitrifying communities using nirK and nirS genes. The results of variance partitioning analyses showed that water physicochemical properties (e.g., dissolved oxygen) and nutrients (e.g., NO₃^- concentration) but not denitrifier communities and submerged vegetation were the major factor groups predicting denitrification and N₂O production rates. Path analyses further revealed that water physicochemical properties and nutrients could affect denitrification and N₂O production rates both directly and indirectly, and the direct effects were considerably higher than the indirect effects mediated through changes in sediment characteristics, denitrifier communities and submerged vegetation. These findings suggest that the dominant N removal process in Yangtze lakes is largely regulated by abiotic factors rather than diversity and abundance of denitrifiers and submerged macrophytes. Additionally, the findings in this study are helpful in developing a targeted strategy to assess and enhance the N removal capability of eutrophic lakes in China.

Methanobactin from Methylosinus trichosporium OB3b inhibits N2O reduction in denitrifiers

Methanotrophs synthesize methanobactin, a secondary metabolite that binds copper with an unprecedentedly high affinity. Such a strategy may provide methanotrophs a "copper monopoly" that can inhibit the activity of copper-containing enzymes of other microbes, e.g., copper-dependent N₂O reductases. Here, we show that methanobactin from Methylosinus trichosporium OB3b inhibited N₂O reduction in denitrifiers. When Pseudomonas stutzeri DCP-Ps1 was incubated in cocultures with M. trichosporium OB3b or with purified methanobactin from M. trichosporium OB3b, stoichiometric N₂O production was observed from NO₃^- reduction, whereas no significant N₂O accumulation was observed in cocultures with a mutant defective in methanobactin production. Copper uptake by P. stutzeri DCP-Ps1 was inhibited by the presence of purified methanobactin, leading to a significant downregulation of nosZ transcription. Similar findings were observed with three other denitrifier strains. These results suggest that in situ stimulation of methanotrophs can inadvertently increase N₂O emissions, with the potential for increasing net greenhouse gas emissions.

Peaks of in situ N2 O emissions are influenced by N2 O-producing and reducing microbial communities across arable soils

Agriculture is the main source of terrestrial N₂ O emissions, a potent greenhouse gas and the main cause of ozone depletion. The reduction of N₂ O into N₂ by microorganisms carrying the nitrous oxide reductase gene (nosZ) is the only known biological process eliminating this greenhouse gas. Recent studies showed that a previously unknown clade of N₂ O-reducers (nosZII) was related to the potential capacity of the soil to act as a N₂ O sink. However, little is known about how this group responds to different agricultural practices. Here, we investigated how N₂ O-producers and N₂ O-reducers were affected by agricultural practices across a range of cropping systems in order to evaluate the consequences for N₂ O emissions. The abundance of both ammonia-oxidizers and denitrifiers was quantified by real-time qPCR, and the diversity of nosZ clades was determined by 454 pyrosequencing. Denitrification and nitrification potential activities as well as in situ N₂ O emissions were also assessed. Overall, greatest differences in microbial activity, diversity, and abundance were observed between sites rather than between agricultural practices at each site. To better understand the contribution of abiotic and biotic factors to the in situ N₂ O emissions, we subdivided more than 59,000 field measurements into fractions from low to high rates. We found that the low N₂ O emission rates were mainly explained by variation in soil properties (up to 59%), while the high rates were explained by variation in abundance and diversity of microbial communities (up to 68%). Notably, the diversity of the nosZII clade but not of the nosZI clade was important to explain the variation of in situ N₂ O emissions. Altogether, these results lay the foundation for a better understanding of the response of N₂ O-reducing bacteria to agricultural practices and how it may ultimately affect N₂ O emissions.

Dimethyl pyrazol-based nitrification inhibitors effect on nitrifying and denitrifying bacteria to mitigate N2O emission

Nitrous oxide (N2O) emissions have been increasing as a result of intensive nitrogen (N) fertilisation. Soil nitrification and denitrification are the main sources of N2O, and the use of ammonium-based fertilisers combined with nitrification inhibitors (NIs) could be useful in mitigating N2O emissions from agricultural systems. In this work we looked at the N2O mitigation capacity of two dimethylpyrazol-based NIs, 3,4-dimethylpyrazole phosphate (DMPP) and 2-(N-3,4-dimethyl-1H-pyrazol-1-yl) succinic acid isomeric mixture (DMPSA), on soil nitrifying and denitrifying microbial populations under two contrasting soil water contents (40% and 80% soil water filled pore space; WFPS). Our results show that DMPP and DMPSA are equally efficient at reducing N2O emissions under 40% WFPS conditions by inhibiting bacterial ammonia oxidation. In contrast, at 80% WFPS DMPSA was less efficient than DMPP at reducing N2O emissions. Interestingly, at 80% WFPS, where lowered oxygen availability limits nitrification, both DMPP and DMPSA not only inhibited nitrification but also stimulated N2O reduction to molecular nitrogen (N2) via nitrous oxide reductase activity (Nos activity). Therefore, in this work we observed that DMP-based NIs stimulated the reduction of N2O to N2 by nitrous oxide reductase during the denitrification process.

Denitrification potential of the eastern oyster microbiome using a 16S rRNA gene based metabolic inference approach

The eastern oyster (Crassostrea virginica) is a foundation species providing significant ecosystem services. However, the roles of oyster microbiomes have not been integrated into any of the services, particularly nitrogen removal through denitrification. We investigated the composition and denitrification potential of oyster microbiomes with an approach that combined 16S rRNA gene analysis, metabolic inference, qPCR of the nitrous oxide reductase gene (nosZ), and N₂ flux measurements. Microbiomes of the oyster digestive gland, the oyster shell, and sediments adjacent to the oyster reef were examined based on next generation sequencing (NGS) of 16S rRNA gene amplicons. Denitrification potentials of the microbiomes were determined by metabolic inferences using a customized denitrification gene and genome database with the paprica (PAthway PRediction by phylogenetIC plAcement) bioinformatics pipeline. Denitrification genes examined included nitrite reductase (nirS and nirK) and nitrous oxide reductase (nosZ), which was further subdivided by genotype into clade I (nosZI) or clade II (nosZII). Continuous flow through experiments measuring N₂ fluxes were conducted with the oysters, shells, and sediments to compare denitrification activities. Paprica properly classified the composition of microbiomes, showing similar classification results from Silva, Greengenes and RDP databases. Microbiomes of the oyster digestive glands and shells were quite different from each other and from the sediments. The relative abundance of denitrifying bacteria inferred by paprica was higher in oysters and shells than in sediments suggesting that oysters act as hotspots for denitrification in the marine environment. Similarly, the inferred nosZI gene abundances were also higher in the oyster and shell microbiomes than in the sediment microbiome. Gene abundances for nosZI were verified with qPCR of nosZI genes, which showed a significant positive correlation (F_1,7 = 14.7, p = 6.0x10^-3, R² = 0.68). N₂ flux rates were significantly higher in the oyster (364.4 ± 23.5 μmol N-N₂ m^-2 h^-1) and oyster shell (355.3 ± 6.4 μmol N-N₂ m^-2 h^-1) compared to the sediment (270.5 ± 20.1 μmol N-N₂ m^-2 h^-1). Thus, bacteria carrying nosZI genes were found to be an important denitrifier, facilitating nitrogen removal in oyster reefs. In addition, this is the first study to validate the use of 16S gene based metabolic inference as a method for determining microbiome function, such as denitrification, by comparing inference results with qPCR gene quantification and rate measurements.

Design and Feasibility Analysis of a Self-Sustaining Biofiltration System for Removal of Low Concentration N2O Emitted from Wastewater Treatment Plants

N₂O is a potent greenhouse gas and ozone-depletion agent. In this study, a biofiltration system was designed for removal of N₂O emitted at low concentrations (<200 ppmv) from wastewater treatment plants. The proposed biofiltration system utilizes untreated wastewater from the primary sedimentation basin as the source of electron donor and nutrients and energy requirement is minimized by utilizing gravitational force and pressure differential to direct liquid medium and gas through the biofilter. The experiments performed with laboratory-scale biofilter in two different configurations confirmed the feasibility of the biofiltration system. The biofilter operated with cycling of raw wastewater exhibited up to 94% and 53% removal efficiency with 100 ppmv N₂O in N₂ and air, respectively, as the feed gas, corroborating that untreated wastewater can serve as a robust source of electron donor and nutrients. The laboratory-scale biofilter operated with a continuous flow-through of synthetic wastewater attained >99.9% removal of N₂O from N₂ background at the gas flow rate up to 2,000 mL·min^-1 and >50% N₂O removal from air background at the gas flow rate of 200 mL·min^-1. nosZ-containing bacterial genera including Flavobacterium (5.92%), Pseudomonas (4.26%) and Bosea (2.39%) were identified in the biofilm samples collected from the oxic biofilter, indicating these organisms were responsible for N₂O removal.

Genomics and Ecology of Novel N2O-Reducing Microorganisms

Microorganisms with the capacity to reduce the greenhouse gas nitrous oxide (N₂O) to harmless dinitrogen gas are receiving increased attention due to increasing N₂O emissions (and our need to mitigate climate change) and to recent discoveries of novel N₂O-reducing bacteria and archaea. The diversity of denitrifying and nondenitrifying microorganisms with capacity for N₂O reduction was recently shown to be greater than previously expected. A formerly overlooked group (clade II) in the environment include a large fraction of nondenitrifying N₂O reducers, which could be N₂O sinks without major contribution to N₂O formation. We review the recent advances about fundamental understanding of the genomics, physiology, and ecology of N₂O reducers and the importance of these findings for curbing N₂O emissions.

Phenotypic and genotypic richness of denitrifiers revealed by a novel isolation strategy

Present-day knowledge on the regulatory biology of denitrification is based on studies of selected model organisms. These show large variations in their potential contribution to NO₂^-, NO, and N₂O accumulation, attributed to lack of genes coding for denitrification reductases, but also to variations in their transcriptional regulation, as well as to post-transcriptional phenomena. To validate the relevance of these observations, there is a need to study a wider range of denitrifiers. We designed an isolation protocol that identifies all possible combinations of truncated denitrification chains (NO₃^-/NO₂^-/NO/N₂O/N₂). Of 176 isolates from two soils (pH 3.7 and 7.4), 30 were denitrifiers sensu stricto, reducing NO₂^- to gas, and five capable of N₂O reduction only. Altogether, 70 isolates performed at least one reduction step, including two DNRA isolates. Gas kinetics and electron flow calculations revealed that several features with potential impact on N₂O production, reported from model organisms, also exist in these novel isolates, including denitrification bet-hedging and control of NO₂^-/NO/N₂O accumulation. Whole genome sequencing confirmed most truncations but also showed that phenotypes cannot be predicted solely from genetic potential. Interestingly, and opposed to the commonly observed inability to reduce N₂O under acidic conditions, one isolate identified as Rhodanobacter reduced N₂O only at low pH.