Microbial genetic potential differs among cryospheric habitats of the Damma glacier.

Climate warming has led to glacier retreat worldwide. Studies on the taxonomy and functions of glacier microbiomes help us better predict their response to glacier melting. Here, we used shotgun metagenomic sequencing to study the microbial functional potential in different cryospheric habitats, i.e. surface snow, supraglacial and subglacial sediments, subglacial ice, proglacial stream water and recently deglaciated soils. The functional gene structure varied greatly among habitats, especially for snow, which differed significantly from all other habitats. Differential abundance analysis revealed that genes related to stress responses (e.g. chaperones) were enriched in ice habitat, supporting the fact that glaciers are a harsh environment for microbes. The microbial metabolic capabilities related to carbon and nitrogen cycling vary among cryospheric habitats. Genes related to auxiliary activities were overrepresented in the subglacial sediment, suggesting a higher genetic potential for the degradation of recalcitrant carbon (e.g., lignin). As for nitrogen cycling, genes related to nitrogen fixation were more abundant in barren proglacial soils, possibly due to the presence of Cyanobacteriota in this habitat. Our results deepen our understanding of microbial processes in glacial ecosystems, which are vulnerable to ongoing global warming, and they have implications for downstream ecosystems.

Strip clear-cutting transformations increase soil N2O emissions in abandoned Moso bamboo forests.

Forest transformation can markedly impact soil greenhouse gas emissions and soil environmental factors. Due to increasing labor costs and declining bamboo prices, the abandonment of Moso bamboo forests is sharply escalating in recent years, which weakens the carbon sequestration capacity and decreases the ecological function of forests. To improve the ecological quality of abandoned Moso bamboo forests, transformations of abandoned bamboo forests have occurred. However, the impact of such transformations on N2O emissions remains elusive. To bridge the knowledge gap, we conducted a 23-month field experiment to compare the effects of various forest management practices on soil N2O emissions and soil environmental factors in abandoned Moso bamboo forests in subtropical China. These practices included uncut abandonment as a control, intensive management, three intensities (light, moderate, and heavy) of strip clear-cutting with replanting local tree species, and clear-cutting with replanting transformation. During the experimental period, the mean soil N2O flux in abandoned Moso bamboo forests was 13.2 ± 0.1 µg m-2 h-1, representing a 44% reduction compared to intensive management forests. In comparison to the uncut control, light, moderate, and heavy strip clear-cutting and clear-cutting transformations increased soil N2O emission rates by 20%, 43%, 64%, and 94%, respectively. Soil temperature (69-71%), labile C (2-6%) and N (3-8%) were the main factors that explain N2O emissions following the transformation of abandoned Moso bamboo forests. Additionally, replanting could decrease soil N2O emissions by increasing the contribution of soil moisture. Overall, the light strip clear-cutting transformation is suggested to convert abandoned Moso bamboo forests to mitigate N2O emissions.

Genome-resolved metagenomics reveals the nitrifiers enrichment and species succession in activated sludge under extremely low dissolved oxygen.

Nitrification, a process carried out by aerobic microorganisms that oxidizes ammonia to nitrate via nitrite, is an indispensable step in wastewater nitrogen removal. To facilitate energy and carbon savings, applying low dissolved oxygen (DO) is suggested to shortcut the conventional biological nitrogen removal pathway, however, the impact of low DO on nitrifying communities within activated sludge is not fully understood. This study used genome-resolved metagenomics to compare nitrifying communities under extremely low- and high-DO. Two bioreactors were parallelly operated to perform nitrification and DO was respectively provided by limited gas-liquid mass transfer from the atmosphere (AN reactor, DO < 0.1 mg/L) and by sufficient aeration (AE reactor, DO > 5.0 mg/L). Low DO was thought to limit nitrifiers growth; however, we demonstrated that complete nitrification could still be achieved under the extremely low-DO conditions, but with no nitrite accumulation observed. Kinetic analysis showed that after long-term exposure to low DO, nitrifiers had a higher oxygen affinity constant and could maintain a relatively high nitrification rate, particularly at low levels of DO (<0.2 mg/L). Community-level gene analysis indicated that low DO promoted enrichment of nitrifiers (the genera Nitrosomonas and Nitrospira, increased by 2.3- to 4.3-fold), and also harbored with 2.3 to 5.3 times higher of nitrification functional genes. Moreover, 46 high-quality (>90 % completeness and <5 % contamination) with 3 most abundant medium-quality metagenome-assembled genomes (MAGs) were retrieved using binning methods. Genome-level phylogenetic analysis revealed the species succession within nitrifying populations. Surprisingly, compared to DO-rich conditions, low-DO conditions were found to efficiently suppressed the ordinary heterotrophic microorganisms (e.g., the families Anaerolineales, Phycisphaerales, and Chitinophagales), but selected for the specific candidate denitrifiers (within phylum Bacteroidota). This study provides new microbial insights to demonstrate that low-DO favors the enrichment of autotrophic nitrifiers over heterotrophs with species-level successions, which would facilitate the optimization of energy and carbon management in wastewater treatment.

The Response of Rhizosphere Microbial C and N-Cycling Gene Abundance of Sand-Fixing Shrub to Stand Age Following Desert Restoration.

Rhizosphere microorganisms play a pivotal role in biogeochemical cycles, particularly in relation to carbon (C) and nitrogen (N) cycles. However, the impact of stand age on the composition of rhizosphere microbial communities and the abundance involved in C and N cycling remains largely unexplored in restoration ecosystems dominated by shrubs of temperate deserts. This study focuses on revealing changes in microbial composition and functional genes in the rhizosphere soil of Caragana korshinskii after revegetation, as well as their response mechanisms to changes in environmental factors. The alpha diversity of bacteria tended to increase with stand age, whereas that of fungi decreased. The abundance of denitrification; dissimilatory nitrate reduction to ammonium, nitrification, and ammonium assimilation; and C fixation-related gene levels increased with stand age, whereas those related to the degradation of starch, pectin, hemicellulose, cellulose, and aromatics decreased. The parameters MBC, MBN, and TC were the key factors affecting the bacterial community, whereas the fungal community was regulated by TN, EC, pH, and MBC. Stand age indirectly regulated C and N cycling functions of genes through altered soil properties and microbial community structures. This study presents a novel approach to accurately evaluate the C and N cycling dynamics within ecosystems at various stages of restoration.

Green manuring combined with zeolite reduced nitrous oxide emissions in maize field by targeting microbial nitrogen transformations.

Green manure is a crucial strategy for increasing cereal yield and mitigating environmental burden while reducing chemical N fertilizer. To effectively tackle climate change, finding ways to reduce nitrous oxide (N2O) emissions from green manuring systems is vital. Herein, field and 15N labeled microcosm experiments were arranged to investigate the effect and mechanisms of green manuring and zeolite application on N2O emission. Both experiments comprised four treatments: conventional chemical N (N100), 70 % chemical N (N70), N70 with green manure (N70 + CV), and N70 + CV combined with zeolite (N70 + CV + Z). Compared with N100, both N70 + CV and N70 + CV + Z maintained maize yield, cumulative N2O emissions decreased by 37.7 % and 34.9 % in N70 + CV + Z in 2022-yr and 2023-yr, and by 12.8 % in N70 + CV in 2022-yr. Moreover, the reduction of N2O emission primarily occurred after incorporating green manure. The N100 and N70 + CV demonstrated a similar transformed proportion of chemical N to N2O (i.e., 4.9 % and 4.7 %) while reducing it to 2.7 % in N70 + CV + Z. Additionally, a mere 0.7 % of green manure N was transformed to N2O in both N70 + CV and N70 + CV + Z treatments. Compared with N100, both N70 + CV and N70 + CV + Z decreased the relative abundances of ammonia oxidation microbes, increased denitrifier and the ratios of (nirK + nirS)/nosZ and norBC/nosZ. Furthermore, compared with N70 + CV, N70 + CV + Z decreased the relative abundances of N2O-producer and the ratios of (nirK + nirS)/nosZ and norBC/nosZ in denitrification. These findings revealed that the reduction of N2O emissions resulting from green manure replaced chemical N was mainly due to weakened nitrification, while zeolite reduced N2O emissions attributed to enhanced conversion of N2O to N2. Moreover, certain key N-cycling functional bacteria, such as Phycisphaerae, Rubrobacteria, and Thermoflexia, were positively correlated with N2O emission. In contrast, Dehalococcoidia, Gammaproteobacteria, and Betaproteobacteria were negatively correlated with N2O emission. This investigation uncovered the underlying mechanisms for effectively reducing N2O emissions through green manuring combined with zeolite.

Vermicompost and flue gas desulfurization gypsum addition to saline-alkali soil decreases nitrogen losses and enhances nitrogen storage capacity by lowering sodium concentration and alkalinity.

Saline-alkali soils have poor N storage capacity, high N loss and inadequate nutrient supply potential, which are the main limiting factors for crop yields. Vermicompost can increase organic nutrient content, improve soil structure, and enhance microbial activity and function, and the Ca2+ in flue gas desulfurization (FGD) gypsum can replace Na+ and neutralize alkalinity in saline-alkali soils though chemical improvement. This study aimed to determine if vermicompost and FGD gypsum addition could improve the N storage capacity through decreasing NH3 volatilization and 15N/NO3- leaching from saline-alkali soils. The results indicate that the combined application of vermicompost and FGD gypsum led to the displacement and leaching Na+ in the upper soil layer (0-10 cm), as well as the neutralization of HCO3- by the reaction with Ca2+. This treatment also improved soil organic matter content and macroaggregate structure. Also, these amendments significantly increased the abundance of nifH and amoA genes, while concurrently decreasing the abundance of nirK gene. The structural improvements and the lowering of Na + concentration in and alkalinity decreased cumulative NH3 volatilization, and leaching of 15N and NO3- to the deep soil layer (20-30 cm). FGD gypsum increased the 15N stocks and inorganic N stocks of saline-alkali soil, whereas vermicompost not only increased the 15N and inorganic N stocks, but also increased the total N stocks, the combination of vermicompost and FGD gypsum can not only increase the available N storage capacity, but also enhance the potential for N supply. Therefore, vermicompost and FGD gypsum decrease N loss and increase N storage capacity through structural improvement, and lowering of Na+ concentration and alkalinity, which is crucial for improving the productivity of saline-alkali soil.

Enhancing soil gross nitrogen transformation through regulation of microbial nitrogen-cycling genes by biodegradable microplastics.

Microplastics (MPs) in agricultural plastic film mulching system changes microbial functions and nutrient dynamics in soils. However, how biodegradable MPs impact the soil gross nitrogen (N) transformations and crop N uptake remain significantly unknown. In this study, we conducted a paired labeling 15N tracer experiment and microbial N-cycling gene analysis to investigate the dynamics and mechanisms of soil gross N transformation processes in soils amended with conventional (polyethylene, PE) and biodegradable (polybutylene adipate co-terephthalate, PBAT) MPs at concentrations of 0 %, 0.5 %, and 2 % (w/w). The biodegradable MPs-amended soils showed higher gross N mineralization rates (0.5-16 times) and plant N uptake rates (16-32 %) than soils without MPs (CK) and with conventional MPs. The MPs (both PE and PBAT) with high concentration (2 %) increased gross N mineralization rates compared to low concentration (0.5 %). Compare to CK, MPs decreased the soil gross nitrification rates, except for PBAT with 2 % concentration; while PE with 0.5 % concentration and PBAT with 2 % concentration increased but PBAT with 0.5 % concentration decreased the gross N immobilization rates significantly. The results indicated that there were both a concentration effect and a material effect of MPs on soil gross N transformations. Biodegradable MPs increased N-cycling gene abundance by 60-103 %; while there was no difference in the abundance of total N-cycling genes between soils without MPs and with conventional MPs. In summary, biodegradable MPs increased N cycling gene abundance by providing enriched nutrient substrates and enhancing microbial biomass, thereby promoting gross N transformation processes and maize N uptake in short-term. These findings provide insights into the potential consequences associated with the exposure of biodegradable MPs, particularly their impact on soil N cycling processes.

Pyric herbivory decreases soil denitrification despite increased nitrate availability in a temperate grassland.

Pyric herbivory, the combination of controlled burning and targeted grazing, is an effective strategy for restoring abandoned, shrub-encroached rangelands to open ecosystems. This practice may impact soil nitrogen pools by altering soil nitrification and denitrification rates, and may lead to an increase of nitrogen losses through nitrate leaching and N-gas emissions. This research, located in the south-western Pyrenees, investigated the effects of pyric herbivory on soil nitrification and denitrification potentials and mineral nitrogen content in a gorse-encroached temperate rangeland six months after the burning was implemented. The study included three treatments: high-severity burning plus grazing, low-severity burning plus grazing, and unburned and ungrazed areas (control). We measured soil nitrification and denitrification potentials (net and gross), the limitation of denitrifiers by nitrogen or organic carbon, and the abundance of nitrite- and nitrous oxide-reducing bacteria. Additional soil and vegetation data complemented these measurements. Results showed that pyric herbivory did not significantly affect nitrification potential, which was low and highly variable. However, it decreased gross denitrification potential and nitrous oxide reduction to dinitrogen in high-severely burned areas compared to the control. Denitrification rates directly correlated with microbial biomass nitrogen, soil organic carbon, soil water content and abundance of nirS-harbouring bacteria. Contrary to the expected, soil nitrate availability did not directly influence denitrification despite being highest in burned areas. Overall, the study suggests that pyric herbivory does not significantly affect mid-term nitrification rates in temperate open ecosystems, but may decrease denitrification rates in intensely burned areas. These findings highlight the importance of assessing the potential impacts of land management practices, such as pyric herbivory, on soil nutrient cycling and ecosystem functioning.

Quest for the Nitrogen-Metabolic Versatility of Microorganisms in Soil and Marine Ecosystems.

Whether nitrogen (N)-metabolic versatility is a common trait of N-transforming microbes or if it only occurs in a few species is still unknown. We collected 83 soil samples from six soil types across China, retrieved 19 publicly available metagenomic marine sample data, and analyzed the functional traits of N-transforming microorganisms using metagenomic sequencing. More than 38% and 35% of N-transforming species in soil and marine ecosystems, respectively, encoded two or more N-pathways, although N-transforming species differed greatly between them. Furthermore, in both soil and marine ecosystems, more than 80% of nitrifying and N-fixing microorganisms at the species level were N-metabolic versatile. This study reveals that N-metabolic versatility is a common trait of N-transforming microbes, which could expand our understanding of the functional traits of drivers of nitrogen biogeochemistry.

Groundwater flow regime shapes nitrogen functional traits by affecting microbial community assembly processes in the subsurface.

The complex nitrogen (N) cycle in groundwater systems is affected by both biological and environmental factors. The interactions between hydrogeological conditions and the microbial community assembly processes that impact N-cycling processes remain poorly understood. We explored the assembly patterns of N-cycling microbial communities along the groundwater flow path. The environmental heterogeneity in different hydrological phases increased along the flow path (mean Ed: 0.16-0.49), accompanied by different microbial community assembly patterns. The assembly patterns that engaged in dissimilatory nitrate reduction to ammonium (DNRA) and denitrification changed across the water-sediment phases. Nitrifying microorganisms in the discharge area were mainly influenced by heterogeneous selection (41-69 %), and were closely correlated with dissolved oxygen (DO) concentrations. Homogeneity along flow-through increased stochastic assemblies, such as downstream drift of anammox bacterial (AnAOB) communities. Thus, the N removal pathway changed from "nitrification-denitrification" in the recharge area to "partial nitrification-anammox" in the discharge area. The increasing environmental heterogeneity brought more deterministic assembly patterns of N-cycling communities, linked to higher community turnover along the groundwater flow path. This study indicated that groundwater flow regime determined microbial community assembly patterns, providing valuable insight into the response of N transitions to environmental variations in groundwater systems.

[Spatial Patterns of Soil Bacterial Communities and N-cycling Functional Groups Along an Altitude Gradient in Datong River Basin].

The altitude distribution patterns of soil microorganisms and their driving mechanisms are crucial for understanding the consequences of climate change on terrestrial ecosystems. There is an obvious altitude difference in Datong River Basin in the Qilian Mountains. Two spatial scale transections were set up along the mountain slope (with altitude spanning 1 000 m) and the mainstream direction (with altitude spanning 300-500 m), respectively. The distribution characteristics of the soil bacterial community structure and diversity along the altitude gradients were examined using high-throughput sequencing technology. Based on the FAPROTAX database, the altitude distribution patterns of nitrogen cycling functional groups were analyzed to investigate the major environmental factors influencing the altitude distribution patterns of soil bacterial communities. The findings revealed that:① Soil physicochemical characteristics varied significantly with altitude. The content of total nitrogen (TN) and nitrate nitrogen (NO3-) were positively correlated with the altitude (P < 0.01), whereas the soil bulk density and pH were negatively connected (P < 0.001). ② The abundance of OTU increased significantly along the altitude (P < 0.01), and the richness and diversity indices increased along the altitude, although the trend was not statistically significant (P > 0.05). ③ The predominant bacterial communities were Acidobacteria, Proteobacteria, and Bacteroidetes, and as altitude climbed, their relative abundances varied between increasing, decreasing, and slightly decreasing, respectively. ④ The nitrogen cycling processes involved 13 functional groups, primarily nitrification, aerobic ammonia oxidation, aerobic nitrite oxidation, etc. As the altitude increased, the response law changed, with an increase in the abundance of nitrobacteria (P < 0.01), a slight increase in the abundance of aerobic ammonia-oxidizing bacteria and nitrite-oxidizing bacteria, and a hump-back tendency in bacteria abundance for nitrogen respiration. ⑤ Redundancy analysis revealed that the key determinants influencing soil bacterial populations at the phylum level were altitude, pH, and the content of NH4+. Mantel analysis showed that the dominant groups of soil bacterial nitrogen cycling were all statistically and significantly driven by altitude (P < 0.01). ⑥ The α-diversity of the bacterial community with increasing altitude were both increased along the mountain slope and the mainstream direction, but the soil properties, the abundance of N-cycling functional groups, and the main environmental factors differed. Therefore, it is of great significance to explore the altitude distribution pattern of soil microorganisms at different spatial scales.

Strategies of soil microbial N-cycling in different cadmium contaminated soil with wheat straw return.

Cadmium contamination inevitably affects the microbially mediated transformation of nitrogen in soils with wheat straw return. The responses of nitrogen functional microorganisms to cadmium in acidic and alkaline soils under wheat straw returned are still unclear. In this study, quantitative polymerase chain reaction (qPCR) and sequencing of nitrifying and denitrifying bacteria were performed to investigate the effects of wheat straw application on nitrogen conversion in different Cd-contaminated soils during an incubation experiment. Results showed that the presence of Cd decreased the abundance of hao gene catalyzing nitrification and norB gene catalyzing denitrification process, resulting the accumulation of NH4+-N and reduction of NO3--N in the acidic soils. Additionally, Cd-contamination stimulates the nitrification catalyzed by bacterial amoA gene and thus reduced the NH4+-N content in the alkaline soils. Meanwhile, Cd dominated the decrease of NO3--N content by promoting denitrification process catalyzed by nirS gene. Among all nitrifying and denitrifying microorganisms, Nitrosospira are tolerant to Cd stress under alkaline condition but sensitive to acidic condition, which dominantly harbored hao gene in the acidic soils and bacterial amoA gene in the alkaline soils. This study aimed to provide reasonable information for the rational adoption of wheat straw returning strategies to realize nitrogen regulation in Cd-contaminated farmland soil.

Biodegradable film mulching increases soil microbial network complexity and decreases nitrogen-cycling gene abundance.

Biodegradable plastic films have emerged as a substitute for conventional plastic films. Nevertheless, responses of plant-associated microbiomes to the application of biodegradable film mulching at field scale have received little attention. A field experiment was conducted to assess the influence of different film mulching treatments on various microbial attributes and nitrogen (N) cycling functional genes in bulk and rhizosphere soils. Biodegradable film mulching raised the bacterial Shannon index in bulk soils but not in rhizosphere soils. Biodegradable film mulching has led to an increase in the complexity and connectivity of microbial networks, as well as an enhancement in the positive association among microorganisms owing to raised soil nutrients and increased crop biomass. In biodegradable film-treated soils, both bacterial and fungal communities were primarily influenced by stochastic processes associated with dispersal limitation. Moreover, conventional plastic film mulching increased denitrification, anammox, N fixation, and dissimilatory nitrate-reduction (DNRA) gene abundance in bulk soils. In rhizosphere soils, biodegradable film mulching reduced nitrification, denitrification, anammox, N fixation, and DNRA gene abundance. Furthermore, keystone genera (e.g., Nitrosospira, Truepera, Adhaeribacter, Opitutus, and Fusarium) were affected by edaphic variables, contributing to decreased N-cycling gene abundance in biodegradable film-treated soils. Collectively, biodegradable film mulching transformed soil microbiome assembly and functional adaptation, and soil nutrient availability and plant biomass were the critical factors influencing the microbial community. These findings present a novel perspective on the diverse impacts of biodegradable and conventional film mulching on soil microbiome and N-cycling processes.

Dynamics of nitrogen genes in intertidal sediments of Darwin Harbour and their connection to N-biogeochemistry.

Microbial mediated nitrogen (N) transformation is subject to multiple controlling factors such as prevailing physical and chemical conditions, and little is known about these processes in sediments of wet-dry tropical macrotidal systems such as Darwin Harbour in North Australia. To understand key transformations, we assessed the association between the relative abundance of nitrogen cycling genes with trophic status, sediment partition and benthic nitrogen fluxes in Darwin Harbour. We analysed nitrogen cycling gene abundance using a functional gene microarray and quantitative PCRs targeting the denitrification gene (nosZ) and archaeal ammonia oxidation (AOA.1). We found a significant negative correlation between archaeal ammonia oxidation and silicate flux (P = 0.004), an indicator for diatom and benthic microalgal activity. It is suggested that the degradation of the diatomaceous organic matter generates localised anoxic conditions and inhibition of nitrification. Abundance of the nosZ gene was negatively correlated with nutrient load. The lowest nosZ gene levels were in hyper-eutrophic tidal creeks with anoxic conditions and increased levels of sulphide limiting the coupling of nitrification-denitrification (P = 0.016). Significantly higher levels of nosZ genes were measured in the surface (top 2 cm) compared to bulk sediment (top 10 cm) and there was a positive association with di-nitrogen flux (N2) in surface (P = 0.024) but not bulk sediment. This suggests that denitrifiers are most active in surficial sediment at the sediment-water interface. Elevated levels of nosZ genes also occurred in the sediments of tidal creek mouths and mudflats with these depositional zones combining the diffuse and seaward supply of nitrogen and carbon supporting denitrifiers. N-cycle molecular assays using surface sediments show promise as a rapid monitoring technique for impact assessment and measuring ecosystem function. This is particularly pertinent for tropical macrotidal systems where systematic monitoring is sparse and in many cases challenged by climatic extremes and remoteness.

Promoting agricultural waste-driven denitrification and nitrogen sequestration with nano-enabled strategy.

Nanotechnology and biotechnology offer promising avenues for bolstering food security through the facilitation of soil nitrogen (N) sequestration and the reduction of nitrate leaching. Nonetheless, a comprehensive and mechanistic evaluation of their effectiveness and safety remains unclear. In this study, a soil remediation strategy employing nano-Fe3O4 and straw in N-contaminated soil was developed to elucidate N retention mechanisms via diverse metagenomics techniques. The findings revealed that subsoil amended with straw, particularly in conjunction with nano-Fe3O4, significantly increased subsoil N content (53.2%) and decreased nitrate concentration (74.6%) in leachate. Furthermore, the enrichment of functional genes associated with N-cycling, sulfate, nitrate, and iron uptake, along with chemotaxis, and responses to environmental stimuli or microbial collaboration, effectively mitigates nitrate leaching while enhancing soil N sequestration. This study introduces a pioneering approach utilizing nanomaterials in soil remediation, thereby offering the potential for the cultivation of safe vegetables in high N input greenhouse agriculture.

Mycorrhizosphere bacteria inhibit greenhouse gas emissions from microplastics contaminated soil by regulating soil enzyme activities and microbial community structure.

Microplastics (MPs) accumulation in terrestrial ecosystems can affect greenhouse gases (GHGs) production by altering microbial and soil structure. Presently, research on the MPs effect on plants is not consistent, and underlying molecular mechanisms associated with GHGs are yet unknown. For the first time, we conducted a microcosm study to explore the impact of MPs addition (Raw vs. aged) and Trichoderma longibrachiatum and Bacillus subtilis inoculation (Sole vs. combination) on GHGs emission, soil community structure, physiochemical properties, and enzyme activities. Our results indicated that the addition of aged MPs considerably enhanced the GHGs emissions (N2O (+16%) and CO2 (+21%), respectively), C and N cycling gene expression, microbial biomass carbon, and soil physiochemical properties than raw MPs. However, the soil microbial community structure and enzyme activities were enhanced in raw MPs added treatments, irrespective of the MPs type added to soil. However, microbial inoculation significantly reduced GHGs emission by altering the expression of C and N cycling genes in both types of MPs added treatments. The soil microbial community structure, enzymes activities, physiochemical properties and microbial biomass carbon were enhanced in the presence of microbial inoculation in both type of MPs. Among sole and combined inoculation of Trichoderma and Bacillus subtilis, the co-applied Trichoderma and Bacillus subtilis considerably reduced the GHGs emission (N2O (-64%) and CO2 (-61%), respectively) by altering the expression of C and N cycling genes regardless of MPs type used. The combined inoculation also enhanced soil enzyme activities, microbial community structure, physiochemical properties and microbial biomass carbon in both types of MPs treatment. Our findings provide evidence that polyethylene MPs likely pose a high risk of GHGs emission while combined application of Trichoderma and Bacillus subtilis significantly reduced GHGs emission by altering C and N cycling gene expression, soil microbial community structure, and enzyme activities under MPs pollution in a terrestrial ecosystem.

The dynamic features and microbial mechanism of nitrogen transformation for hydrothermal aqueous phase as fertilizer in dryland soil.

Hydrothermal aqueous phase (HAP) contains abundant organics and nutrients, which have potential to partially replace chemical fertilizers for enhancing plant growth and soil quality. However, the underlying reasons for low available nitrogen (N) and high N loss in dryland soil remain unclear. A cultivation experiment was conducted using HAP or urea to supply 160 mg N kg-1 in dryland soil. The dynamic changes of soil organic matters (SOMs), pH, N forms, and N cycling genes were investigated. Results showed that SOMs from HAP stimulated urease activity and ureC, which enhanced ammonification in turn. The high-molecular-weight SOMs relatively increased during 5-30 d and then biodegraded during 30-90 d, which SUV254 changed from 0.51 to 1.47 to 0.29 L-1 m-1. This affected ureC that changed from 5.58 to 5.34 to 5.75 lg copies g-1. Relative to urea, addition HAP enhanced ON mineralization by 8.40 times during 30-90 d due to higher ureC. It decreased NO3-N by 65.35%-77.32% but increased AOB and AOA by 0.25 and 0.90 lg copies g-1 at 5 d and 90 d, respectively. It little affected nirK and increased nosZ by 0.41 lg copies g-1 at 90 d. It increased N loss by 4.59 times. The soil pH for HAP was higher than that for urea after 11 d. The comprehensive effects of high SOMs and pH, including ammonification enhancement and nitrification activity inhibition, were the primary causes of high N loss. The core idea for developing high-efficiency HAP fertilizer is to moderately inhibit ammonification and promote nitrification.

Microbial species pool-mediated diazotrophic community assembly in crop microbiomes during plant development.

Plant-associated diazotrophs strongly relate to plant nitrogen (N) supply and growth. However, our knowledge of diazotrophic community assembly and microbial N metabolism in plant microbiomes is largely limited. Here we examined the assembly and temporal dynamics of diazotrophic communities across multiple compartments (soils, epiphytic and endophytic niches of root and leaf, and grain) of three cereal crops (maize, wheat, and barley) and identified the potential N-cycling pathways in phylloplane microbiomes. Our results demonstrated that the microbial species pool, influenced by site-specific environmental factors (e.g., edaphic factors), had a stronger effect than host selection (i.e., plant species and developmental stage) in shaping diazotrophic communities across the soil-plant continuum. Crop diazotrophic communities were dominated by a few taxa (~0.7% of diazotrophic phylotypes) which were mainly affiliated with Methylobacterium, Azospirillum, Bradyrhizobium, and Rhizobium. Furthermore, eight dominant taxa belonging to Azospirillum and Methylobacterium were identified as keystone diazotrophic taxa for three crops and were potentially associated with microbial network stability and crop yields. Metagenomic binning recovered 58 metagenome-assembled genomes (MAGs) from the phylloplane, and the majority of them were identified as novel species (37 MAGs) and harbored genes potentially related to multiple N metabolism processes (e.g., nitrate reduction). Notably, for the first time, a high-quality MAG harboring genes involved in the complete denitrification process was recovered in the phylloplane and showed high identity to Pseudomonas mendocina. Overall, these findings significantly expand our understanding of ecological drivers of crop diazotrophs and provide new insights into the potential microbial N metabolism in the phyllosphere.IMPORTANCEPlants harbor diverse nitrogen-fixing microorganisms (i.e., diazotrophic communities) in both belowground and aboveground tissues, which play a vital role in plant nitrogen supply and growth promotion. Understanding the assembly and temporal dynamics of crop diazotrophic communities is a prerequisite for harnessing them to promote plant growth. In this study, we show that the site-specific microbial species pool largely shapes the structure of diazotrophic communities in the leaves and roots of three cereal crops. We further identify keystone diazotrophic taxa in crop microbiomes and characterize potential microbial N metabolism pathways in the phyllosphere, which provides essential information for developing microbiome-based tools in future sustainable agricultural production.

Seasonal changes in N-cycling functional genes in sediments and their influencing factors in a typical eutrophic shallow lake, China.

N-cycling processes mediated by microorganisms are directly linked to the eutrophication of lakes and ecosystem health. Exploring the variation and influencing factors of N-cycling-related genes is of great significance for controlling the eutrophication of lakes. However, seasonal dynamics of genomic information encoding nitrogen (N) cycling in sediments of eutrophic lakes have not yet been clearly addressed. We collected sediments in the Baiyangdian (BYD) Lake in four seasons to explore the dynamic variation of N-cycling functional genes based on a shotgun metagenome sequencing approach and to reveal their key influencing factors. Our results showed that dissimilatory nitrate reduction (DNRA), assimilatory nitrate reduction (ANRA), and denitrification were the dominant N-cycling processes, and the abundance of nirS and amoC were higher than other functional genes by at least one order of magnitude. Functional genes, such as nirS, nirK and amoC, generally showed a consistent decreasing trend from the warming season (i.e., spring, summer, fall) to the cold season (i.e., winter). Furthermore, a significantly higher abundance of nitrification functional genes (e.g., amoB, amoC and hao) in spring and denitrification functional genes (e.g., nirS, norC and nosZ) in fall were observed. N-cycling processes in four seasons were influenced by different dominant environmental factors. Generally, dissolved organic carbon (DOC) or sediment organic matter (SOM), water temperature (T) and antibiotics (e.g., Norfloxacin and ofloxacin) were significantly correlated with N-cycling processes. The findings imply that sediment organic carbon and antibiotics may be potentially key factors influencing N-cycling processes in lake ecosystems, which will provide a reference for nitrogen management in eutrophic lakes.

Structure and Functions of Endophytic Bacterial Communities Associated with Sphagnum Mosses and Their Drivers in Two Different Nutrient Types of Peatlands.

Sphagnum mosses are keystone plant species in the peatland ecosystems that play a crucial role in the formation of peat, which shelters a broad diversity of endophytic bacteria with important ecological functions. In particular, methanotrophic and nitrogen-fixing endophytic bacteria benefit Sphagnum moss hosts by providing both carbon and nitrogen. However, the composition and abundance of endophytic bacteria from different species of Sphagnum moss in peatlands of different nutrient statuses and their drivers remain unclear. This study used 16S rRNA gene amplicon sequencing to examine endophytic bacterial communities in Sphagnum mosses and measured the activity of methanotrophic microbial by the 13C-CH4 oxidation rate. According to the results, the endophytic bacterial community structure varied among Sphagnum moss species and Sphagnum capillifolium had the highest endophytic bacterial alpha diversity. Moreover, chlorophyll, phenol oxidase, carbon contents, and water retention capacity strongly shaped the communities of endophytic bacteria. Finally, Sphagnum palustre in Hani (SP) had a higher methane oxidation rate than S. palustre in Taishanmiao. This result is associated with the higher average relative abundance of Methyloferula an obligate methanotroph in SP. In summary, this work highlights the effects of Sphagnum moss characteristics on the endophytic bacteriome. The endophytic bacteriome is important for Sphagnum moss productivity, as well as for carbon and nitrogen cycles in Sphagnum moss peatlands.