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Soil moisture is one of the critical factors affecting N2O emissions. The water regime affects the physical and chemical properties of paddy soil in different soil layers, which, in turn, affects N2O emissions and microbial growth. However, there are few reports on the effects of different soil layers and soil moisture conditions on N2O emission characteristics and microbial mechanisms. A 21-day microcosm experiment was performed to research the effects of soil moisture levels (60%, 100%, and 200% water holding capacity, WHC) and different soil layers (0–10, 10–20, and 20–40 cm) on N2O emissions in hydromorphic and gleyed paddy soils. Function microbes involved in nitrification and denitrification were determined by quantitative PCR. Moreover, the abiotic variables pH, Eh, and exchangeable Fe2+, Fe3+, NH4+-N, and NO3−-N were also analyzed. Results showed that N2O emissions of gleyed paddy soil were significantly higher than that of hydromorphic paddy soil, which was consistent with the result of the abundance of nitrifier and denitrifier in the two paddy soils. Soil depth, water content, and their interaction significantly affected N2O emission (p < 0.05). Cumulative emissions of N2O from each layer of the two paddy soils at 100% and 200% WHC were significantly higher than that under 60% WHC (p < 0.05). N2O emissions decreased significantly with the increase of soil depth (p < 0.05), which was consistent with the change in the abundance of soil nitrifier (AOB and AOA) and denitrifier (nirK and nosZ) function genes with soil depth. The abundance of AOB, AOA, and nirK and nosZ genes decreased significantly with soil depth (p < 0.05), but did not respond significantly to the water regime. Based on the results of redundancy analysis, the contents of Fe2+ and Fe3+ were positively correlated with N2O emissions and the abundance of AOB, AOA, and nirK and nosZ genes. These results indicate that N2O emissions and the abundance of associated microbes are selectively affected by soil moisture and soil layers in the two paddy soils.

Agricultural and industrial practices more than doubled the intrinsic rate of terrestrial N fixation over the past century with drastic consequences, including increased atmospheric nitrous oxide (N ₂O) concentrations. N ₂O is a potent greenhouse gas and contributor to ozone layer destruction, and its release from fixed N is almost entirely controlled by microbial activities. Mitigation of N ₂O emissions to the atmosphere has been attributed exclusively to denitrifiers possessing NosZ, the enzyme system catalyzing N ₂O to N ₂ reduction. We demonstrate that diverse microbial taxa possess divergent nos clusters with genes that are related yet evolutionarily distinct from the typical nos genes of denitirifers. nos clusters with atypical nosZ occur in Bacteria and Archaea that denitrify (44% of genomes), do not possess other denitrification genes (56%), or perform dissimilatory nitrate reduction to ammonium (DNRA; (31%). Experiments with the DNRA soil bacterium Anaeromyxobacter dehalogenans demonstrated that the atypical NosZ is an effective N ₂O reductase, and PCR-based surveys suggested that atypical nosZ are abundant in terrestrial environments. Bioinformatic analyses revealed that atypical nos clusters possess distinctive regulatory and functional components (e.g., Sec vs. Tat secretion pathway in typical nos), and that previous nosZ -targeted PCR primers do not capture the atypical nosZ diversity. Collectively, our results suggest that nondenitrifying populations with a broad range of metabolisms and habitats are potentially significant contributors to N ₂O consumption. Apparently, a large, previously unrecognized group of environmental nosZ has not been accounted for, and characterizing their contributions to N ₂O consumption will advance understanding of the ecological controls on N ₂O emissions and lead to refined greenhouse gas flux models.

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.

Background and Aims Nitrogenous fertilizers provide a short-lived benefit to crops in agroecosystems, but stimulate nitrification and denitrification, processes that result in nitrate pollution, N 2 O production, and reduced soil fertility. Recent advances in plant microbiome science suggest that genetic variation in plants can modulate the composition and activity of rhizosphere N-cycling microorganisms. Here we attempted to determine whether genetic variation exists in Zea mays for the ability to influence the rhizosphere nitrifier and denitrifier microbiome under “real-world” conventional agricultural conditions. Methods To capture an extensive amount of genetic diversity within maize we grew and sampled the rhizosphere microbiome of a diversity panel of germplasm that included ex-PVP inbreds ( Z. mays ssp. mays ), ex-PVP hybrids ( Z. mays ssp. mays ), and teosinte ( Z. mays ssp . mexicana and Z. mays ssp. parviglumis ). From these samples, we characterized the microbiome, a suite of microbial genes involved in nitrification and denitrification and carried out N-cycling potential assays. Results Here we are showing that populations/genotypes of a single species can vary in their ecological interaction with denitrifers and nitrifers. Some hybrid and teosinte genotypes supported microbial communities with lower potential nitrification and potential denitrification activity in the rhizosphere, while inbred genotypes stimulated/did not inhibit these N-cycling activities. These potential differences translated to functional differences in N 2 O fluxes, with teosinte plots producing less GHG than maize plots. Conclusion Taken together, these results suggest that Zea genetic variation can lead to changes in N-cycling processes that result in N leaching and N 2 O production, and thereby are selectable targets for crop improvement. Understanding the underlying genetic variation contributing to belowground microbiome N-cycling into our conventional agricultural system could be useful for sustainability.

Denitrifying nitrous oxide (N 2 O) emissions in agroecosystems result from variations in microbial composition and soil properties. However, the microbial mechanisms of differential N 2 O emissions in agricultural soils are less understood. In this study, microcosm experiments using two main types of Chinese cropland soil were conducted with different supplements of nitrate and glucose to simulate the varying nitrogen and carbon conditions. The results show that N 2 O accumulation in black soil (BF) was significantly higher than that in fluvo-aquic soil (FF) independent of nitrogen and carbon. The abundance of most denitrifying genes was significantly higher in FF, but the ratios of genes responsible for N 2 O production ( nirS and nirK ) to the gene responsible for N 2 O reduction ( nosZ ) did not significantly differ between the two soils. However, the soils showed obvious discrepancies in denitrifying bacterial communities, with a higher abundance of N 2 O-generating bacteria in BF and a higher abundance of N 2 O-reducing bacteria in FF. High accumulation of N 2 O was verified by the bacterial isolates of Rhodanobacter predominated in BF due to a lack of N 2 O reduction capacity. The dominance of Castellaniella and others in FF led to a rapid reduction in N 2 O and thus less N 2 O accumulation, as demonstrated when the corresponding isolate was inoculated into the studied soils. Therefore, the different phenotypes of N 2 O metabolism of the distinct denitrifiers predominantly colonized the two soils, causing differing N 2 O accumulation. This knowledge would help to develop a strategy for mitigating N 2 O emissions in agricultural soils by regulating the phenotypes of N 2 O metabolism.

Understanding aerobic denitrification has become an important focus of environmental microbiology. Aerobic denitrification can be performed by various genera of microorganisms and describes the use of nitrate (NO ₃ ⁻) as oxidizing agents under an aerobic atmosphere. Isolation of aerobic denitrifiers, enzymes involved in aerobic denitrifiers, phylogenetic distribution of aerobic denitrifiers, factors affecting the performance of aerobic denitrifiers, attempts of applications and possible future trends are depicted. The periplasmic nitrate reductase is vital for aerobic denitrifiers and NapA gene may be the proof of aerobic denitrification. Phylogenetic analysis revealed that aerobic denitrifiers mainly belong to α-, β- and γ-Proteobacteria. Aerobic denitrifiers tend to work efficiently at 25 ~ 37°C and pH 7 ~ 8, when dissolved oxygen concentration is 3 ~ 5 mg/L and C/N load ratio is 5 ~ 10. In addition, recent progresses and applications on aerobic denitrifiers are described, including single aerobic reactors, sequencing batch reactor and biofilm reactors. The review attempts to shed light on the fundamental understanding in aerobic denitrification.

Previous studies have shown that phosphorus addition to P-limited soils increases gaseous N loss. A possible explanation for this phenomenon is element stoichiometry (specifically of C:N:P) modifying linked nutrient cycling, leading to enhanced nitrification and denitrification. In this study, we investigated how P stoichiometry influenced the dynamics of soil N-cycle functional genes. Rice seedlings were planted in P-poor soils and incubated with or without P application. Quantitative PCR was then applied to analyze the abundance of ammonia-oxidizing ( amoA ) and denitrifying ( narG nirK , nirS , nosZ ) genes in soil. P addition reduced bacterial amoA abundance but increased denitrifying gene abundance. We suggest this outcome is due to P-induced shifts in soil C:P and N:P ratios that limited ammonia oxidization while enhancing P availability for denitrification. Under P application, the rhizosphere effect raised ammonia-oxidizing bacterial abundance ( amoA gene) and reduced nirK , nirS , and nosZ in rhizosphere soils. The change likely occurred through greater C input and O 2 release from roots, thus altering C availability and redox conditions for microbes. Our results show that P application enhances gaseous N loss potential in paddy fields mainly through stimulating denitrifier growth. We conclude that nutrient availability and elemental stoichiometry are important in regulating microbial gene responses, thereby influencing key ecosystem processes such as denitrification. Graphical abstract ᅟ

Despite its potentially high relevance for nitrate removal in freshwater environments limited in organic carbon, chemolithoautotrophic denitrification has rarely been studied in oligotrophic groundwater. Using thiosulfate and H2 as electron donors, we established a chemolithoautotrophic enrichment culture from groundwater of a carbonate-rock aquifer to get more insight into the metabolic repertoire, substrate turnover, and transcriptional activity of subsurface denitrifying consortia. The enriched consortium was dominated by representatives of the genus Thiobacillus along with denitrifiers related to Sulfuritalea hydrogenivorans, Sulfuricella denitrificans, Dechloromonas sp. and Hydrogenophaga sp., representing the consortium's capacity to use multiple inorganic electron donors. Microcosm experiments coupled with Raman gas spectroscopy demonstrated complete denitrification driven by reduced sulfur compounds and hydrogen without formation of N2O. The initial nitrate/thiosulfate ratio had a strong effect on nosZ transcriptional activity and on N2 formation, suggesting similar patterns of the regulation of gene expression as in heterotrophic denitrifiers. Sequence analysis targeting nirS and nosZ transcripts identified Thiobacillus denitrificans-related organisms as the dominant active nirS-type denitrifiers in the consortium. An additional assessment of the nirS-type denitrifier community in the groundwaterclearly confirmed the potential for sulfur- and hydrogen-dependent chemolithoautotrophic denitrification as important metabolic feature widely spread among subsurface denitrifiers at the Hainich Critical Zone Exploratory.

Environmental changes can alter the interactions between biotic and abiotic ecosystem components in tidal wetlands and therefore impact important ecosystem functions. The objective of this study was to determine how saltwater intrusion affects wetland nutrient biogeochemistry, with a specific focus on the soil microbial communities and physicochemical parameters that control nitrate removal. Our work took place in a tidal freshwater marsh in South Carolina, USA, where a 3.5-year saltwater intrusion experiment increased porewater salinities from freshwater to oligohaline levels. We measured rates of denitrification, soil oxygen demand, and dissimilatory nitrate reduction to ammonium (DNRA) and used molecular genetic techniques to assess the abundance and community structure of soil microbes. In soils exposed to elevated salinities, rates of denitrification were reduced by about 70% due to changes in the soil physicochemical environment (higher salinity, higher carbon: nitrogen ratio) and shifts in the community composition of denitrifiers. Saltwater intrusion also affected the microbial community responsible for DNRA, increasing the abundance of genes associated with this process and shifting microbial community composition. Though rates of DNRA were below detection, the microbial community response may be a precursor to increased rates of DNRA with continued saltwater intrusion. Overall, saltwater intrusion reduces the ability of tidal freshwater marshes to convert reactive nitrogen to dinitrogen gas and therefore negatively affects their water quality functions. Continued study of the interrelationships between biotic communities, the abiotic environment, and biogeochemical transformations will lead to a better understanding of how the progressive replacement of tidal freshwater marshes with brackish analogues will affect the overall functioning of the coastal landscape.

The heterotrophic denitrification requires the participation of electrons which are derived from direct electron donor (usually nicotinamide adenine dinucleotide (NADH)), and the electrons are transferred via electron transport system in denitrifiers and then consumed by denitrifying enzymes. Despite the reported electron transfer ability of humic substances (HS), the influences of fulvic acid (FA), an ubiquitous major component of HS, on promoting NADH generation, electron transfer, and consumption in denitrification process have never been reported. The presence of FA, compared with the control, was found not only significantly improved the total nitrogen (TN) removal efficiency (99.9 % versus 74.8 %) but remarkably reduced the nitrite accumulation (0.2 against 43.8 mg/L) and N 2 O emission (0.003 against 0.240 mg nitrogen/mg TN removed). The mechanisms study showed that FA increased the metabolism of carbon source via glycolysis and tricarboxylic acid (TCA) cycle pathways to produce more available NADH. FA also facilitated the electron transfer activities from NADH to denitrifying enzymes via complex I and complex III in electron transport system, which improved the reduction of nitrate and accelerated the transformations of nitrite and N 2 O, and lower nitrite and N 2 O accumulations were therefore observed. In addition, the consumption of electrons in denitrification was enhanced due to FA stimulating the synthesis and the catalytic activity of key denitrifying enzymes, especially nitrite reductase and N 2 O reductase. It will provide an important new insight into the potential effect of FA on microbial denitrification metabolism process and even nitrogen cycle in nature niches.