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N2O is a powerful greenhouse gas contributing both to global warming and ozone depletion. While fungi have been identified as a putative source of N2O, little is known about their production of this greenhouse gas. Here we investigated the N2O-producing ability of a collection of 207 fungal isolates. Seventy strains producing N2O in pure culture were identified. They were mostly species from the order Hypocreales order—particularly Fusarium oxysporum and Trichoderma spp.—and to a lesser extent species from the orders Eurotiales, Sordariales, and Chaetosphaeriales. The N2O 15N site preference (SP) values of the fungal strains ranged from 15.8‰ to 36.7‰, and we observed a significant taxa effect, with Penicillium strains displaying lower SP values than the other fungal genera. Inoculation of 15 N2O-producing strains into pre-sterilized arable, forest and grassland soils confirmed the ability of the strains to produce N2O in soil with a significant strain-by-soil effect. The copper-containing nitrite reductase gene (nirK) was amplified from 45 N2O-producing strains, and its genetic variability showed a strong congruence with the ITS phylogeny, indicating vertical inheritance of this trait. Taken together, this comprehensive set of findings should enhance our knowledge of fungi as a source of N2O in the environment.

Nitrous oxide (N2O) is a potent greenhouse gas and the predominant ozone depleting substance. The only enzyme known to reduce N2O is the nitrous oxide reductase, encoded by the nosZ gene, which is present among bacteria and archaea capable of either complete denitrification or only N2O reduction to di-nitrogen gas. To determine whether the occurrence of nosZ, being a proxy for the trait N2O reduction, differed among taxonomic groups, preferred habitats or organisms having either NirK or NirS nitrite reductases encoded by the nirK and nirS genes, respectively, 652 microbial genomes across 18 phyla were compared. Furthermore, the association of different co-occurrence patterns with enzymes reducing nitric oxide to N2O encoded by nor genes was examined. We observed that co-occurrence patterns of denitrification genes were not randomly distributed across taxa, as specific patterns were found to be more dominant or absent than expected within different taxonomic groups. The nosZ gene had a significantly higher frequency of co-occurrence with nirS than with nirK and the presence or absence of a nor gene largely explained this pattern, as nirS almost always co-occurred with nor. This suggests that nirS type denitrifiers are more likely to be capable of complete denitrification and thus contribute less to N2O emissions than nirK type denitrifiers under favorable environmental conditions. Comparative phylogenetic analysis indicated a greater degree of shared evolutionary history between nosZ and nirS. However 30% of the organisms with nosZ did not possess either nir gene, with several of these also lacking nor, suggesting a potentially important role in N2O reduction. Co-occurrence patterns were also non-randomly distributed amongst preferred habitat categories, with several habitats showing significant differences in the frequencies of nirS and nirK type denitrifiers. These results demonstrate that the denitrification pathway is highly modular, thus underpinning the importance of community structure for N2O emissions.

Biochar-based controlled release nitrogen fertilizers (BCRNFs) have received increasing attention due to their ability to improve nitrogen-use efficiency (NUE) and increase crop yields. We previously developed a novel BCRNF, but its effects on soil microbes, NUE, and crop yields have not been reported. Therefore, we designed a pot experiment with five randomised treatments: CK (without urea and biochar), B (addition biochar without urea), B + U (biochar mixed urea), Urea (addition urea without biochar), and BCRNF (addition BCRNF), to investigate the effects of BCRNF on nitrifiers and denitrifiers, and how these impact nitrogen supply and NUE. Results of high-throughput sequencing revealed bacterial community groups with higher nutrient metabolic cycling ability under BCRNF treatment during harvest stage. Compared to Urea treatment, BCRNF treatment stimulated nitrification by increasing the copy number of the bacterial amoA gene and reducing nitrous oxide emission by limiting the abundance of nirS and nirK . Eventually, BCRNF successfully enhanced the yield (~ 16.6%) and NUE (~ 58.79%) of rape by slowly releasing N and modulating the abundance of functional microbes through increased soil nitrification and reduced denitrification, as compared with Urea treatment. BCRNF significantly improved soil NO 3 − , leading to an increase in N uptake by rape and NUE, thereby promoting rape growth and increasing grain yield.

Nitrate ammonification is important for soil nitrogen retention. However, the ecology of ammonifiers and their prevalence compared with denitrifiers, being competitors for nitrate, are overlooked. Here, we screen 1 million genomes for nrfA and onr , encoding ammonifier nitrite reductases. About 40% of ammonifier assemblies carry at least one denitrification gene and show higher potential for nitrous oxide production than consumption. We then use a phylogeny-based approach to recruit gene fragments of nrfA, onr and denitrification nitrite reductase genes ( nirK , nirS ) in 1861 global terrestrial metagenomes. nrfA outnumbers the nearly negligible onr counts in all biomes, but denitrification genes dominate, except in tundra. Random forest modelling teases apart the influence of the soil C/N on nrfA -ammonifier vs denitrifier abundance, showing an effect of nitrate rather than carbon content. This study demonstrates the multiple roles nitrate ammonifiers play in nitrogen cycling and identifies factors ultimately controlling the fate of soil nitrate. Nitrate ammonifiers are poorly known despite their importance for soil nitrogen retention. This study shows that they are phylogenetically diverse and globally distributed across terrestrial biomes and that the outcome of the competition with denitrifiers is controlled by soil nitrate.

Aims Biological soil crusts (BSCs) are widely considered critical for soil fertility in arid ecosystems. However, how microbial communities regulate the C and N cycles during BSC succession is not well understood. Methods We utilized GeoChip 5.0 to analyze the functional potential of bacteria and fungi involved in the C and N cycles of BSCs along a 61-year revegetation chronosequence. Results The normalized average signal intensities of different functional genes involved in C and N metabolism in 61-year-old BSCs were significantly different from those in younger BSCs and most functional gene subcategories and the corresponding dominant functional populations were derived from bacterial rather than fungal communities. Most C degradation genes (dominated by the starch-degrading gene amyA ) were derived from Actinobacteria (mainly Streptomyces ) in bacteria, but Ascomycota (mainly Aspergillus ) was the key population for lignin degradation (dominated by the phenol oxidase gene) during BSC succession. N cycle genes involved in denitrification (such as narG , nirK/S , and nosZ ) and N fixation ( nifH ) were mainly derived from Unclassified Bacteria , whereas genes involved in ammonification ( ureC ) were mainly derived from Streptomyces . Moreover, redundancy analysis showed that soil biogeochemical properties were closely related to bacterial and fungal functional gene structures during BSC succession. Conclusions These findings indicate that bacteria play a crucial role in the regulation of C and N cycles during BSC succession in arid ecosystems, while fungi perform supplementary degradation of lignin, and these communities can successfully stimulate an increase in C and N metabolism in soil during the later successional stages of BSCs.

Soils are facing new environmental stressors, such as titanium dioxide nanoparticles (TiO2-NPs). While these emerging pollutants are increasingly released into most ecosystems, including agricultural fields, their potential impacts on soil and its function remain to be investigated. Here we report the response of the microbial community of an agricultural soil exposed over 90 days to TiO2-NPs (1 and 500 mg kg(-1) dry soil). To assess their impact on soil function, we focused on the nitrogen cycle and measured nitrification and denitrification enzymatic activities and by quantifying specific representative genes (amoA for ammonia-oxidizers, nirK and nirS for denitrifiers). Additionally, diversity shifts were examined in bacteria, archaea, and the ammonia-oxidizing clades of each domain. With strong negative impacts on nitrification enzyme activities and the abundances of ammonia-oxidizing microorganism, TiO2-NPs triggered cascading negative effects on denitrification enzyme activity and a deep modification of the bacterial community structure after just 90 days of exposure to even the lowest, realistic concentration of NPs. These results appeal further research to assess how these emerging pollutants modify the soil health and broader ecosystem function.

Denitrification is a key process responsible for the majority of soil nitrous oxide (N2O) emissions but the influences of pH and cultivation on the soil denitrifier community remain poorly understood. We hypothesised that the abundance and community structure of the total bacterial community and bacterial denitrifiers would be pH sensitive and that nirK and nirS containing denitrifiers would differ in their responses to change in pH and cultivation. We investigated the effect of long-term pH-adjusted soils (ranging from pH 4.2 to 6.6) under different lengths of grass cultivation (one, two and three years of ley grass) on the general bacterial and denitrifier functional communities using 16S rRNA, nirK and nirS genes as markers. Denitrifier abundance increased with pH, and at pH below 4.7 there was a greater loss in nirS abundance per unit drop in pH than soils above this threshold pH. All community structures responded to changes in soil pH, while cultivation only influenced the community structure of nirK. These differences in denitrifier responses highlight the importance of considering both nirK and nirS gene markers for estimating denitrifier activity. Identifying such thresholds in response of the microbial community to changes in pH is essential to understanding impacts of management or environmental change.

Enzymes catalyze key reactions within Earth’s life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 μm) along a 5,000-km-long, 1-km-deep transect in the central Pacific Ocean. Eighty-five percent of total protein abundance was of bacterial origin, with Archaea contributing 1.6%. Over 2,000 functional KEGG Ontology (KO) groups were identified, yet only 25 KO groups contributed over half of the protein abundance, simultaneously indicating abundant key functions and a long tail of diverse functions. Vertical attenuation of individual proteins displayed stratification of nutrient transport, carbon utilization, and environmental stress. The microbial community also varied along horizontal scales, shaped by environmental features specific to the oligotrophic North Pacific Subtropical Gyre, the oxygen-depleted Eastern Tropical North Pacific, and nutrient-rich equatorial upwelling. Some of the most abundant proteins were associated with nitrification and C1 metabolisms, with observed interactions between these pathways. The oxidoreductases nitrite oxidoreductase (NxrAB), nitrite reductase (NirK), ammonia monooxygenase (AmoABC), manganese oxidase (MnxG), formate dehydrogenase (FdoGH and FDH), and carbon monoxide dehydrogenase (CoxLM) displayed distributions indicative of biogeochemical status such as oxidative or nutritional stress, with the potential to be more sensitive than chemical sensors. Enzymes that mediate transformations of atmospheric gases like CO, CO₂, NO, methanethiol, and methylamines were most abundant in the upwelling region.We identified hot spots of biochemical transformation in the central Pacific Ocean, highlighted previously understudied metabolic pathways in the environment, and provided rich empirical data for biogeochemical models critical for forecasting ecosystem response to climate change.

Although cumulative N2O emissions are greater in the winter fallow season than in the rice-growing period, the mechanisms by which the emissions affect fallow paddy fields remain unclear. We aimed to identify N2O flux characteristics and illustrate how key nirS-, nirK- and nosZ-containing denitrifiers affect N2O emission levels in acidic fallow paddy soil. Five water-filled pore space (WFPS) levels were set at 25%, 50%, 75%, 100% and 125%, respectively. During the 48-h-long, high-flux incubation period, the N2O flux was the highest in soil samples with 75% WFPS, followed by those with 100% WFPS. The size of nirS-containing denitrifier community was more sensitive to the shifts in soil moisture and showed a stronger correlation with N2O flux than that of nirK-containing denitrifiers, whereas higher N2O concentrations induced an increase in the levels of nosZ-containing bacteria. After incubation for 48 h, nirK- and nosZ-denitrifying bacterial composition varied remarkably under 50%, 75%, and 100% WFPS treatments. However, the composition of nirS-containing denitrifying bacterial community gradually varied with an increase in soil moisture from 25% to 100% WFPS. Certain dominant OTUs of nirK- nirS- and nosZ-containing denitrifiers were highly abundant, especially under treatments of 50%, 75% and 100% WFPS, which were closely associated with the N2O flux. Thus, nirK, nirS and nosZ-containing denitrifiers respond to soil moisture differently, and enriched species might mainly be involved in controlling N2O flux in fallow paddy soils via denitrification, while the abundance of nirS-containing denitrifiers might affect N2O emission levels more significantly than that of nirK-containing denitrifiers.

Purpose Reduce the climate cost of plastic mulch is an important issue for the sustainable development of dryland. Previous studies suggest plastic mulch has risk to increase nitrous oxide emission, but how this produced by the complex interaction between soil properties and microbial is still an unsolved problem and need to research to develop targeted practice. Methods To address this question, molecular ecology tools, including real-time quantitative and high-throughput sequencing were employed to explore how plastic mulch induced change on soil environment and then stimulates denitrification. Three mulching treatments were compared, including no mulching, spring and autumn mulching. Results Plastic mulch induced significant increase in the richness and diversity of nir-containing denitrifiers. The nirS and nirK-gene abundance was the greatest under the autumn mulching, and a more conspicuous change in the community structure and abundance was observed for nirK gene than for nirS denitrifiers. The most differentially abundant taxa in the autumn mulching were Anaeromyxobacter , Terriglobus , Edwardsiella , Catenulispora and Acidobacterium for nirK genes and Cupriavidus for nirS genes. Mulching increased the potential denitrification enzyme activity by 58% and 29% for autumn and spring mulching, respectively, and this effect was mirrored by the abundance of nirK, but not by nirS denitrifiers. The nirK gene was significantly correlated to variations in soil moisture, temperature, and nitrate nitrogen. Conclusion Plastic mulch stimulates denitrification by inducing higher moisture, temperature and nitrate nitrogen content and structural change in the community of nirK denitrifying bacteria in dryland agroecosystems.