Abundance Of nosZ Genes Research Articles

Rice planting reduced N2O emissions from rice-growing seasons due to increased nosZ gene abundance under a rice-wheat rotation system

Paddy fields experience more frequent events because of redox-induced changes during their growth period, which further govern the processes that influence soil N2O emissions. However, studies on the effects of rice planting on soil N2O emissions and the relevant mechanisms are scarce. Thus, a field employing rice-wheat rotation (RW) in central China, including treatments with rice planting (RW-CC) and without rice planting (RW-NC), was selected to investigate the effects of rice planting on N2O emissions. Several key soil variables and functional genes (nirS, nirK, and nosZ) related to N2O-production and consumption were selected to determine the mechanisms underlying the effects of rice planting on N2O emissions. The results showed that seasonal N2O emissions from RW-NC treatment were 0.88 ± 0.08 and 1.69 ± 0.24 kg N ha−1 for the first and subsequent rice cultivation seasons, respectively, and were significantly higher than those from RW-CC treatment (0.51 ± 0.10 and 1.04 ± 0.18 kg N ha−1, respectively). This indicated the mitigation effect of rice planting on field N2O emissions. For both the RW-CC and RW-NC treatments, N2O fluxes were positively correlated with soil ammonium (NH4+), microbial biomass carbon (MBC), and nirK genes, and negatively correlated with the nosZ gene, indicating that the production- and consumption-related functional genes of soil available C, N, and N2O are the key factors controlling N2O emissions. Compared to RW-NC treatment, a higher abundance of the nosZ gene and lower (nirS+nirK)/nosZ ratios for RW-CC treatment may contribute to a greater reduction of N2O to N2, thus resulting in decreased N2O emissions. Structural equation model (SEM) analysis showed that soil moisture (flood depth), NH4+, MBC, and functional genes together accounted for more than 85 % of the explanatory effects on N2O emissions for both treatments. In general, our research indicates that promoting rice planting could reduce soil N2O emissions during the rice-growing season, thereby reducing the exposure of soil to N fertilization when adopting field agronomic practices; our results also suggest that crop rotation and intercropping should be encouraged.

Cropping rotation improved the bacterial diversity and N-cycling genes in tobacco fields through a 19-year long-term experiment

Soil microorganisms play crucial roles in various processes within the soil ecosystem, such as nutrient cycling, organic matter decomposition, and maintenance of soil structure. However, their responses to fertilization and different cropping systems in tobacco soils remain poorly understood. In this study, we conducted a 19-year-long field experiment on rice-tobacco rotation cropping (R) and continuous tobacco cropping (C), with three fertilization treatments: no fertilizer (NF), chemical NPK fertilizer (NPK), and composted pig manure (OM). The composition, co-occurrence patterns, N-cycling genes (nifH, AOA-amoA, AOB-amoA, nirS, nirK, and nosZ) of the bacterial communities as well as the soil properties were analyzed in the soils after tobacco was harvested. The pH and available potassium (AK) in the rotation cropping soil were significantly lower than those in continuous cropping soil, while the α-diversity index, and the abundance of nifH, nirS, nirK, and nosZ genes were opposite. The phyla Chloroflexi, Desulfobacterota, MBNT15, and Nitrospinota, as well as number of low-abundance genera, were significantly enriched in rice-tobacco rotation cropping. Partial least squares path model (PLSPM) indicated that cropping systems had a greater influence on the variations in bacterial communities compared to fertilization practices. These findings enhance our understanding of the significance of land management and fertilization in shaping the soil bacteria of tobacco. The rice-tobacco rotation cropping system demonstrated greater benefits to soil microorganisms and N-cycling genes compared to continuous cropping system.

Effect of Streptomyces JD211 application on soil physicochemical properties and N2O emission characteristics of rice rhizosphere

Biocontrol agent, as a pollution-free and sustainable plant disease control method, can inhibit the spread of soil-borne diseases and promote the growth of crops. However, there are few studies on the effect of biocontrol agent on N2O emission in rice soil. In this study, after the application of the biocontrol agent Streptomyces JD211, N2O emission from rice soil were measured, and the relationship between the agent and soil N2O emissions were studied in soil chemistry and molecular biology. The results showed that the application of Streptomyces JD211 can significantly reduce the rate of N2O emission from rice soil. The NH4+-N and NO3−-N contents in rice soil decreased in a short period of time after the application of Streptomyces JD211, while the mineral N content in the soil remained stable with rice growth. 16S rRNA gene sequencing and metagenomic sequencing revealed Streptomyces JD211 application mainly increased the relative abundance of Burkholderia and Streptomyces in the soil microbial community, reduced the relative abundance of hao, norB, norC genes, and increased the relative abundance of nosZ and hcp genes. Streptomyces JD211 application promoted N2O transformation and weakened N2O production pathways, which ultimately reduced N2O emissions from rice soils. This study provided new insight of biocontrol agents to regulate soil N2O emissions, which is of great significance for the development and application of biocontrol bacteria and farmland environmental protection.

Mechanisms of the effects of the biochar application rate and time on farmland water, heat and gas environments during soil thawing in seasonally frozen soil areas: A two-year field trial

Biochar has shown great potential in improving the soil environment and alleviating greenhouse gas (GHG) emissions. However, the biochar effect in seasonally frozen soil areas remains unclear due to the complexity of the freezethaw cycle processes. To effectively regulate the soil waterheatgas environment, three treatments, a single high-dose application (BL), two low-dose applications (BS), and no biochar application (CK), were established in a two-year field experiment. The characteristics of soil GHG emissions under the different treatments and their response relationships to soil water, heat and air permeability were explored. The results indicated that the average water content under BL and BS treatments increased by 10.78 % and 7.05 %, respectively, relative to the CK treatment in 2021, while the BS treatment exhibited the best performance in 2022. The temperature regulation effect under the different treatments showed similar trends, with the average temperature under the BS treatment in 2022 was 0.62 °C and 1.38 °C higher, respectively, than that under the BL and CK treatments. The two-year cumulative CO2 emission flux under the BL and BS treatments was 9.36 % and 2.98 % higher, respectively, than that under the CK treatment. Biochar increased soil macropores (>75 µm) and promoted soil gas circulation. Resulting in increased pmoA and nosZ gene abundance and inhibited CH4 and N2O fluxes in soil. The two-year global warming potentials (GWPs) under the BL and BS treatments were 65.7 and 113.17 kg CO2 hm-2 lower, respectively, than that under the CK treatment. Overall, multiple low-dose biochar applications could comprise an efficient and sustainable application mode.

Ascription of nosZ gene, pH and copper for mitigating N2O emissions in acidic soils

Soil nitrous oxide (N2O) emissions are alarming for global warming and climate change. N2O reduction is carried out only by nosZ gene encoded N2O-reductase, which is highly sensitive to acidic pH and copper (Cu) contents. Therefore, a microcosm study was conducted to examine the attribution of soil pH management, Cu supply and nosZ gene abundance for N2O emission mitigation. Cu was applied at the dose of 0, 10, 25 and 50 mg kg−1 to three acidic soils (Soil 1, 2 and 3) without and with dolomite (0 and 5 g kg−1). Cu application and soil pH increment substantially enlarged the abundance of nosZ gene, and consequently mitigated soil N2O emissions; highest reduction with 25 Cu mg kg−1. Decline in NH4+ and subsequently accumulation of NO3−, and large contents of MBC and DOC in dolomite treated soils led to a substantial N2O reduction. The cumulative N2O emissions were lowest in the treatment of 25 Cu mg kg−1 with dolomite application for each soil. Results suggest that soil pH increment, an adequate Cu supply, and nosZ gene abundance can potentially lower soil N2O emissions in acidic soils.

Bacillus paralicheniformis 2R5 and its impact on canola growth and N-cycle genes in the rhizosphere.

Chemical fertilization has a negative impact on natural environment. Plant growth-promoting (PGP) rhizobacterial biofertilizers can be a safer alternative to synthetic agrochemicals. In this research, a culture-based method was used to assess the population size of rhizobacteria at the vegetative, flowering, and maturity stages of canola. Rhizobacteria were then isolated from each of the canola growth stages, and their seven PGP traits were determined. The highest abundance of culturable bacteria was found at vegetative stage of the plants. Furthermore, four out of seven PGP traits were produced by the highest % of isolates at vegetative stage. In the greenhouse experiment that included six rhizobacterial strains with best PGP traits, the greatest canola growth promotion ability under sterile conditions was observed after the introduction of Bacillus paralicheniformis 2R5. Moreover, under non-sterile conditions, 2R5 significantly increased canola growth. The presence of trpA, B, C, D, E, F and pstA, S genes in the 2R5 genome could be associated with canola growth promotion abilities. chiA and mbtH genes could contribute to 2R5 antifungal activity against fungal pathogens. Moreover, the introduction of 2R5 significantly increased the abundance of narG, nosZ, nifH, and nirS genes, which can prove that 2R5 strain may be an important member of soil bacterial community.

Irrigation rather than fertilization drives the abundance, community structure and assembly process of soil denitrifiers

Fertilization and irrigation have significant impacts on soil nitrogen cycling and associated microbes, yet we have limited understanding on community structure and assembly process of soil denitrifiers. Here, we examined the abundance, diversity, composition, and assembly process of soil denitrifier communities harboring the nirS, nirK, and nosZ genes in soils under long-term (11 years) fertilization and irrigation managements. Our results indicated that irrigation significantly increased the abundance of nirS, nirK, and nosZ genes by 6.10–18.85, 2.36–2.85, and 4.85–6.16 times in the chemical fertilizer (NPK) treatments and by 1.02–13.68, 0.95–1.45, and 1.49–2.28 times in the manure (M) treatments compared to the corresponding control without irrigation (I0), respectively. Principal co-ordinates analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA) showed that fertilization had a more important role in altering the nosZ-type denitrifier community structure, while irrigation dominated in influencing the nirS- and nirK-type. Regardless of fertilization, irrigation shifted community assembly of the nirS-type denitrifier from deterministic process to stochastic process, while driving the nosZ-type from stochastic process to deterministic process. The nirK-type denitrifier was determined by stochastic process and was neither affected by fertilization nor irrigation. Network co-occurrence analysis showed that irrigation differently affected the community network complexity under NPK and M. One irrigation (I1) and two irrigations (I2) increased and decreased the network complexity, respectively, in the NPK treatments, while opposite results were found in M. Additionally, soil moisture and pH significantly (p < 0.05) correlated with the gene abundance, community structure, and assembly process of the denitrifiers. Overall, irrigation rather than fertilization greatly induced the changes in abundance, community structure, network structure, and assembly process of the denitrifiers via soil moisture and pH, highlighting the importance of irrigation in regulating soil denitrification associated microbes.

Climatic effect from oyster reef restoration in Spartina alterniflora invaded intertidal mudflat: From the perspective of CH4 and N2O production

Spartina alterniflora is a dominant invasive species along the coast of China. A surprising phenomenon that the oyster reef formation is substituting the S. alterniflora invasion, was recently observed in the west coast of Bohai Bay, North China. As the intertidal mudflat ecosystem is critical for coastal blue carbon, this paper aims to evaluate the climatic effect of the alternation from the perspective of potential CH4 and N2O production. The sediment geochemical properties and potential CH4 and N2O productions were therefore measured in sediments dominated by Spartina alterniflora (SA), oyster reef (OR), mixture of S. alterniflora and oyster reef (SA-OR) and bare mudflat (BM) at an intertidal mudflat. Meanwhile, sediment microbial community structure and function genes were also determined utilizing metagenome high-throughput sequencing technology. Our results indicated that the formation of oyster reef in S. alterniflora invaded intertidal mudflat might slightly reduce the sediment potential CH4 production and enhance the sediment potential N2O production. The oyster reef formation could alter the community composition of methanogens and the abundance of functional genes in methanogenesis, and transform the main pathway from methylotrophic to hydrogenotrophic methanogenesis in surface sediments. Metagenome sequencing revealed that the oyster reef formation may promote nitrification, inhibit dissimilatory nitrate reduction (DNRA) and nitrate assimilation functions, and reduce the abundance of nosZ genes. Mantel analysis showed that pH, soluble salt and dissolved carbon (DC) were the most important factors influencing the composition of microbial community. In general, our results imply that the growth of oyster reef in the S. alterniflora invaded area has opposing effects from the prospective of the potential CH4 and N2O production.

Response of rare and abundant rhizosphere microbial communities to inoculated rhizobium in cadmium-contaminated soil phytoremediation

Soil microorganisms play an important role in maintaining ecosystem balance and exerting ecological functions. The taxonomic and functional changes in rare and abundant communities during in bioremediation of cadmium-contaminated soils and their contributions to the remediation of ecosystem functions remain elusive despite the significance of rare and abundant microbial taxa in maintaining soil ecological function. Mesorhizobiumloti HZ76-inoculated seedlings of the Robinia pseudoacacia were used to create a symbiotic system. The effects of rhizobium inoculation on rare and abundant rhizosphere microbial populations were investigated in pot experiments. Despite having minimal effects on the α-diversity of rare and abundant microbial communities, inoculation altered microbial community composition and functional gene abundance. For example, abundant phyla such as Proteobacteria were enriched following inoculation, whereas rare phyla such as Ascomycota were depleted. After inoculation, the abundance of nifH gene increased, while the abundance of amoA, amoB, nirS, nirK and nosZ gene decreased. Rare bacterial populations were more susceptible to the inoculated rhizobium's environmental alterations. In rare communities compared to abundance communities, the α-diversity was higher. Stochastic processes predominated in the communities of uncommon and abundant microorganisms. Furthermore, keystone taxa, particularly rare bacterial taxa (Gemmatimonadaceae and Saprospiraceae) and rare fungal taxa (Ascomycota), more mediates nitrogen cycle processes and is directly associated to the abundance of nitrogen functional genes. Together, our findings demonstrate the different ways that rare and abundant microbial species react to rhizobia inoculation and their connections to the nitrogen cycle.

Effects of Biochar Amendment on N2O Emission and Its Functional Genes in Pepper Growing Soil in Tropical Areas

Biochar application may mitigate N2O emissions and increase crop yield, yet little is known about microbial dynamics variation. To investigate the potential of increasing yield and reducing emissions of biochar in tropical areas and the dynamic mechanism of related microorganisms, a pot experiment was conducted to investigate the biochar application on pepper yield, N2O emissions, and dynamic variation of related microorganisms. Three treatments were applied:2% biochar amendment (B), conventional fertilization (CON), and no nitrogen (CK). The results showed that the yield of the CON treatment was higher than that of the CK treatment. Compared with that of the CON treatment, biochar amendment significantly increased the yield of pepper by 18.0% (P<0.05), and biochar amendment could increase the content of NH+4-N and NO-3-N in soil in most periods of pepper growth. Compared with that in the CON treatment, the B treatment significantly reduced cumulative N2O emissions by 18.3% (P<0.05). Ammonia oxidizing archaea (AOA)-amoA and ammonia oxidizing bacteria (AOB)-amoA were very significantly negatively correlated with N2O flux (P<0.01). N2O flux was significantly negatively correlated with nosZ gene abundance (P<0.05). This indicated that N2O emission may have mainly resulted from the denitrification process. In the early stage of pepper growth, biochar significantly reduced N2O emissions by reducing the value of (nirK+nirS)/nosZ, whereas in the late stage of pepper growth, the value of (nirK+nirS)/nosZ of the B treatment was higher than that of the CON treatment, resulting in higher N2O flux in the B treatment. Therefore, biochar amendment could not only increase vegetable production in tropical areas but also reduce N2O emissions, which can be used as a new strategy to improve soil fertility in Hainan Province and other tropical areas.

Effects of Cropping Systems on Soil Physicochemical Properties and Abundances and Spatial Distributions of Nitrogen-Cycling Bacteria

Soil nitrogen (N) is a common limiting factor where soil N-cycling is a key component of agroecosystems. Soil N transformation processes are largely mediated by microbes, and understanding bacteria involvement in soil N-cycling in agricultural systems has both agronomic and environmental importance. This 2 yr field-scale study examined the abundances and spatial distributions of the total bacterial community (16S rRNA), bacteria involved in nitrification (amoA) and denitrification (narG, nirK, and nosZ), and soil physicochemical properties of winter wheat (Triticum aestivum L.)–soybean (Glycine max L.) double-crop with 2–3 weeks of spring grazing (WGS) and without grazing (WS) and tall fescue (Festuca arundinacea (L.) Schreb.) pasture (TF) managed to near-natural conditions with similar grazing. The TF soil had a significantly higher abundance of 16S rRNA, amoA, narG, nirK, and nosZ genes than the WS and WGS soils, which had similar levels between themselves. Soil organic matter (OM) and soil pH had stronger effects on the N-cycling bacteria gene abundance. All bacterial gene concentrations and soil pH showed nonrandom distribution patterns with a 141–186 m range autocorrelation. These results indicate that biological N transformation processes are more important in natural agricultural systems and the abundance of N-cycling bacteria can be manipulated by field-scale management strategies.

Effects of biochar in combination with varied N inputs on grain yield, N uptake, NH3 volatilization, and N2O emission in paddy soil.

Biochar application can improve crop yield, reduce ammonia (NH3) volatilization and nitrous oxide (N2O) emission from farmland. We here conducted a pot experiment to compare the effects of biochar application on rice yield, nitrogen (N) uptake, NH3 and N2O losses in paddy soil with low, medium, and high N inputs at 160 kg/ha, 200 kg/ha and 240 kg/ha, respectively. The results showed that: (1) Biochar significantly increased the rice grain yield at medium (200 kg/ha) and high (240 kg/ha) N inputs by 56.4 and 70.5%, respectively. The way to increase yield was to increase the rice N uptake, rice panicle number per pot and 1,000 grain weight by 78.5-96.5%, 6-16% and 4.4-6.1%, respectively; (2) Under low (160 kg/ha) N input, adding biochar effectively reduced the NH3 volatilization by 31.6% in rice season. The decreases of pH value and NH4+-N content in surface water, and the increases of the abundance of NH4+-N oxidizing archaea and bacteria (AOA and AOB) communities contributed to the reduction of NH3 volatilization following the biochar application; (3) Under same N input levels, the total N2O emission in rice season decreased by 43.3-73.9% after biochar addition. The decreases of nirK and nirS gene abundances but the increases of nosZ gene abundance are the main mechanisms for biochar application to reduce N2O emissions. Based on the results of the current study, adding biochar at medium (200 kg/ha) N level (N200 + BC) is the best treatment to synchronically reduce NH3 and N2O losses, improve grain yield, and reduce fertilizer application in rice production system.

Increased simulated precipitation frequency promotes greenhouse gas fluxes from the soils of seasonal fallow croplands

AbstractIntroductionFarmlands are key sources of greenhouse gas (GHG) emissions, which are susceptible to changes in precipitation regimes. The soils of seasonal fallow contribute approximately half of annual GHG emissions from farmlands, but the effect of precipitation frequency on soil GHG emissions from seasonal fallow croplands remains virtually unknown.Materials and MethodsWe conducted a microcosm study to evaluate the response of nitrous oxide (N2O), methane (CH4) and carbon dioxide (CO2) fluxes from typical paddy and upland soils to the changes in watering frequency simulating precipitation scenarios of subtropical regions during seasonal fallow. We also analyzed changes of soil properties and biotic characteristics associated with GHG emissions, including abundances of soil denitrifiers (nirK, nirS, nosZI and nosZII genes), methanotrophs (pmoA gene) and methanogens (mcrA gene) to altered watering frequency.ResultsIncreased watering frequency led to overall increases in soil N2O and CO2 fluxes compared with low frequency. Compared with low frequency, high watering frequency decreased CH4 flux from the paddy soil by 3.5 times, while enhanced CH4 flux from the upland soil by 60%. Furthermore, the increased watering frequency had positive effects on cumulative N2O and CO2 fluxes from the upland soil, whereas no similar trend was observed for the paddy soil. Hierarchical partitioning analyses showed that N2O fluxes from the paddy soil were mostly related to nitrogen availability, and mcrA gene abundance had more than 90% of relative independent effects on CH4 and CO2 fluxes from the paddy soil. For the upland soil, nosZ (60.34%), pmoA (53.18%) and nir (47.07%) gene abundances were important predictors of N2O, CH4 and CO2 fluxes, respectively.ConclusionOur results demonstrate that increased watering frequency facilitates GHG emissions by changing soil properties and functional gene abundances. These findings provide new insights into GHG fluxes from seasonal fallow croplands in response to altered precipitation patterns.

The Contribution of Anammox to Nitrogen Removal Is Greater in Bulk Soils Than in Rhizosphere Soils in Riparian Wetlands Along the Yangtze River

AbstractThe importance of denitrification and anaerobic ammonium oxidation (anammox) in removing nitrogen (N) from upland runoff has been well documented in riparian wetlands. However, the relative contributions of denitrification and anammox to N removal in the rhizosphere and non‐rhizosphere soils of riparian zones remain unclear. Here, we explored the denitrification and anammox rates in the rhizosphere and bulk soils (0–5 and 10–15 cm) of 39 riparian wetlands along the Yangtze River using the 15N isotope pairing technique. Additionally, we used a quantitative polymerase chain reaction assay to determine the abundance of soil denitrifying and anammox bacteria using nosZ and hzsB genes, respectively. The results showed that both denitrification and anammox rates were significantly higher in rhizosphere soils than in bulk soils, suggesting that the rhizosphere environment is favorable for N removal. The contribution of anammox constituted over half (62.53% ± 1.49%) of the N loss and was greater in bulk soils (68.57% ± 1.42%) than in rhizosphere soils (55.64% ± 2.42%). Higher nosZ and hzsB gene abundances were also observed in rhizosphere soils than in bulk soils. Denitrification and anammox rates were significantly regulated by edaphic properties, microbial abundance, and plant biomass. The structural equation model further revealed that soil pH and N availability could affect denitrification and anammox rates both directly and indirectly by altering nosZ and hzsB gene abundance. Overall, this study highlights that the rhizosphere is a control point for N removal and harbors more functional microbes than bulk soils. Therefore, revegetation may effectively enhance the N removal function of riparian wetlands along the Yangtze River.

Performance and mechanism of simultaneous nitrification and denitrification in zeolite spheres internal loop airlift reactor

An internal loop airlift reactor was constructed with zeolite spheres as biofilm carriers (ZS-ALR), and the performance and mechanism of nitrogen removal were investigated. The results indicated that the TN, NH4+-N and TOC removal efficiencies of ZS-ALR reached 96.12%, 100% and 94.54% under appropriate conditions (HRT of 6–8 h, aeration rates of 80–120 mL/min, C/N ratios of 4–6), and the highest TN removal rate constant was 0.01156 min−1. Further investigating the influence of ammonia-N concentrations on nitrogen removal and biofilm stability revealed that catabolism was important in TN removal, and the prominent genera for nitrogen removal included Sphaerotilus (42.20%), Flavobacterium (17.47%) and Fusibacter (6.14%). Meanwhile, the abundance of amoA, napA, narG and nosZ genes was markedly influenced by ammonia-N concentrations. The nitrogen removal of ZS-ALR was mainly through ammonia-N adsorption by zeolite spheres and simultaneous nitrification and denitrification by biofilm.

Effects of long-term organic fertilizer substitutions on soil nitrous oxide emissions and nitrogen cycling gene abundance in a greenhouse vegetable field

Intensive vegetable fields, characterized by extremely high nitrogen (N) application rates, emit a large amount of the potent greenhouse gas nitrous oxide (N2O). Short-term substitution of organic fertilizers for chemical fertilizers may mitigate N2O emissions from vegetable fields. However, the long-term impacts, particularly on soil background N2O emissions (excluding effects caused by newly applied fertilizers) in vegetable fields, remain poorly elucidated. Thus, we conducted an 11-year experiment to investigate the long-term fertilization effects on soil background N2O emissions and the abundance of N-cycling genes in a greenhouse vegetable field. The soil capacity for potential denitrification activity (PDA) was further measured to evaluate denitrification potential. The field experiment comprised of four treatments: no fertilization (control, CK), only chemical N fertilizers (CF), 50 % of chemical N fertilizers substituted by organic fertilizers (OL), and 87.5 % of chemical fertilizers substituted by organic fertilizers (OH). The long-term application of chemical fertilizers alone (CF) and organic fertilizer substitutions (OL and OH) increased soil background N2O emissions 30-fold and 10-fold, respectively, with average N2O fluxes of 1.2 ± 3.8, 33.8 ± 5.1, 9.4 ± 2.3 and 10.2 ± 2.7 μg N2O-N m−2 h−1 in the CK, CF, OL and OH treatment, respectively. The CF treatment significantly decreased the abundance of AOA amoA, nirS and nosZ genes, while both the OL and OH treatments increased the abundance of AOB amoA, and the OH treatment also increased nosZ gene abundance. Soil pH was a key determinant of the contrasting responses of N-cycling genes to different fertilizer types. Compared with low fertilizer substitutions (OL), high organic fertilizer substitutions (OH) did not result in more soil background N2O emissions, despite higher potential denitrification activities and soil total N contents. This was due to increased abundance of nosZ gene and likely enhanced N2O consumption activities. Soil NO3−-N concentrations, soil pH, and the abundance of nosZ gene were three main factors in controlling the responses of soil background N2O emissions to long-term fertilization. Overall, this study suggests that in the long-term perspective organic fertilizer substitution is a beneficial practice to mitigate N2O emissions from intensive greenhouse vegetable cropping systems.

Stimulating effects of snow cover on gaseous nitrogen emissions are intensified by biological soil crusts

Winter weather patterns are changing due to global climate change, which impacts the soil nitrogen cycle and greenhouse gas flux in these ecosystems, particularly the snow cover in temperate deserts. Biological soil crusts are important soil communities of the desert ecosystem and are sensitive to environmental changes. However, knowledge of the responses of gaseous nitrogen emissions from biological soil crusts to changes in snow cover is limited. In this study, the effects of snow cover on gaseous nitrogen emissions and the abundance of nitrifier (amoA) and denitrifier (narG, nirS, nirK, nosZ) genes were investigated in three snow cover treatments (snow removal, ambient snow, and increased snow depth). Snow cover significantly affected N2O and NO emissions from bare sand and biological soil crusts in winter. The abundance of denitrifier genes in bare sand and biological soil crusts and the abundance of nitrifier genes in moss crust increased with the depths of snow addition. N2O emissions increased with the successional stages of biological soil crusts during the winter. Both N2O and NO emissions from bare sand and biological soil crusts peaked in the freeze–thaw period (March) and were lowest in mid-winter (January). The emissions of N2O increased with increasing the abundance of amoA, nirK and nosZ genes. Our findings show that N2O emissions generally increased with increasing snow cover through their effects on nitrogen cycle related functional microbial groups. These effects were regulated by the types of biological soil crust, which can increase the effect of snow cover in winter.

Response of gene abundance of ammonia-oxidizing microorganisms and denitrifying microorganisms to nitrogen and phosphorus addition in subtropical forest.

We conducted a nitrogen (N) and phosphorus (P) addition experiment in Qianjiangyuan National Park in 2015, to investigate the response of ammonia-oxidizing microorganisms and denitrifying microorganisms. There were four treatments, including N addition (N), P addition (P), NP, and control (CK). Soil samples were collected in April (wet season) and November (dry season) of 2021. The abundance of amoA gene of ammonia-oxidizing microorganisms (i.e., ammonia-oxidizing archaea, AOA; ammonia-oxidizing bacteria, AOB; comammox) and denitrifying microbial genes (i.e., nirS, nirK, and nosZ) were determined using quantitative PCR approach. The results showed that soil pH was significantly decreased by long-term N addition, while soil ammonium and nitrate contents were significantly increased. Soil available P and total P contents were significantly increased with the long-term P addition. The addition of N (N and NP treatments) significantly increased the abundance of AOB-amoA gene in both seasons, and reached the highest in the N treatment around 8.30×107 copies·g-1 dry soil. The abundance of AOA-amoA gene was significantly higher in the NP treatment than that in CK, with the highest value around 1.17×109 copies·g-1 dry soil. There was no significant difference in N-related gene abundances between two seasons except for the abundance of comammox-amoA. Nitrogen addition exerted significant effect on the abundance of AOB-amoA, nirK and nosZ genes, especially in wet season. Phosphorus addition exerted significant effect on the abundance of AOA-amoA and AOB-amoA genes in both seasons, but did not affect denitrifying gene abundances. Soil pH, ammonium, nitrate, available P, and soil water contents were the main factors affecting the abundance of soil N-related functional genes. In summary, the response of soil ammonia-oxidizing microorganisms and denitrifying microorganisms was more sensitive to N addition than to P addition. These findings shed new light for evaluating soil nutrient availability as well as their response mechanism to global change in subtropical forests.

Network analysis of 16S rRNA sequences suggests microbial keystone taxa contribute to marine N2O cycling

The mechanisms by which large-scale microbial community function emerges from complex ecological interactions between individual taxa and functional groups remain obscure. We leveraged network analyses of 16S rRNA amplicon sequences obtained over a seven-month timeseries in seasonally anoxic Saanich Inlet (Vancouver Island, Canada) to investigate relationships between microbial community structure and water column N2O cycling. Taxa separately broadly into three discrete subnetworks with contrasting environmental distributions. Oxycline subnetworks were structured around keystone aerobic heterotrophs that correlated with nitrification rates and N2O supersaturations, linking N2O production and accumulation to taxa involved in organic matter remineralization. Keystone taxa implicated in anaerobic carbon, nitrogen, and sulfur cycling in anoxic environments clustered together in a low-oxygen subnetwork that correlated positively with nitrification N2O yields and N2O production from denitrification. Close coupling between N2O producers and consumers in the anoxic basin is indicated by strong correlations between the low-oxygen subnetwork, PICRUSt2-predicted nitrous oxide reductase (nosZ) gene abundances, and N2O undersaturation. This study implicates keystone taxa affiliated with common ODZ groups as a potential control on water column N2O cycling and provides a theoretical basis for further investigations into marine microbial interaction networks.

Soil pH management for mitigating N2O emissions through nosZ (Clade I and II) gene abundance in rice paddy system

Soil nitrous oxide (N2O) is produced by abiotic and biotic processes, but it is solely consumed by denitrifying microbes-encoded by nosZ genes. The nosZ gene includes two groups i.e. Clade I and Clade II, which are highly sensitive to pH. Managing pH of acidic soils can substantially influence soil N2O production or consumption through nosZ gene abundance. Nevertheless, the response of nosZ (Clade I and Clade II) to pH management needs elucidation in acidic soils. To clarify this research question, a pot experiment growing rice crop was conducted with three treatments: control (only soil), low dose of dolomite (LDD), and high dose of dolomite (HDD). The soil pH increased from 5.41 to 6.23 in the control, 6.5 in LDD and 6.8 in HDD treatment under flooded condition. The NH4+ and NO3− contents increased and reached the maximum at 30.4 and 21.5 mg kg−1, respectively, in HDD treatment under flooding condition. The contents of dissolved organic carbon and microbial biomass carbon showed a swift rise at midseason aeration and reached maximum at 30.7 and 101 mg kg−1 in the HDD treatment. Clade I, Clade II and 16S rRNA genes abundance increased with the onset of flooding, and occurred maximum in the HDD treatment. A peak in N2O emissions (5.96 μg kg−1 h−1) occurred at midseason events in the control when no dolomite was added. Dolomite application significantly (p ≤ 0.001) suppressed N2O emissions, and HDD treatment was more effective in reducing emissions. Pearson correlation, linear regressions and principal component analysis displayed that increased soil pH and Clade I and Clade II were the main controlling factors for N2O emission mitigation in acidic soil. This research demonstrates that ameliorating soil acidity with dolomite application is a potential option for the mitigation of N2O emissions.