Nitrogen Cycling Processes Research Articles

Metagenomics reveals functional profiles of soil nitrogen and phosphorus cycling under different amendments in saline-alkali soil.

High salinity, low fertility and poor structure in saline-alkali soils led to nutrient cycling slow and microbial activity loss. The application of amendments has proven effective in enhancing soil nutrients, which significantly affects soil nitrogen and phosphorus cycling process. However, the specific impact of different amendments on the microbial functional potential related to nutrient cycling in saline-alkali soils remains unclear. Hence, metagenomics sequencing was used to investigate soil microbial communities and nitrogen and phosphorus cycling genes in response to different amendments, and to examine the influence of soil physicochemical properties on functional genes in the Hetao irrigation district of China. The results showed that amendments application enriched the Proteobacteria abundance, while inhibiting oligotrophic groups such as Chloroflexi. Compared to the control (CK), the combined application of desulfurization gypsum and cattle manure (DC) notably increased nasA (assimilatory nitrate reduction) and nirB (dissimilatory nitrate reduction), as well as phoD and phoA genes (organic P mineralization). Furthermore, soil AK and AP were primary factors affecting microbial communities and N and P cycling genes. Overall, this study offers valuable insights into soil nitrogen and phosphorus cycling genes and their interactions in response to different amendments, where the application of amendments affects nitrogen and phosphorus cycling by altering soil nutrient availability.

Biochar-microplastics interaction modulates soil nitrous oxide emissions and microbial communities

Biochar has been proposed as a soil amendment in vegetable fields, where the widespread use of plastic film leads to significant retention of microplastics (MPs) in the soil. However, the interactive effect of biochar and MPs on plant growth and soil functions remains poorly understood. Here, we conducted a pot experiment to examine the effects of biochar application in the presence of conventional and biodegradable microplastics (0.05% w/w) on the growth of coriander, soil nitrogen (N) cycling processes, and microbial communities. The results showed that biochar application increased aboveground biomass by increasing plant available N of NH4+, regardless of the presence of MPs. Biochar also significantly reduced soil nitrous oxide (N2O) emissions by an average of 16% without MPs. However, when MPs were present, the effect of biochar on N2O emissions was lessened depending on the MP type. Polylactic acid consistently reduced soil N2O emissions and the abundance of N2O production genes, irrespective of biochar application. Conversely, polyethylene without biochar reduced N2O emissions primarily by inhibiting N-related functional genes responsible for nitrification and denitrification. This inhibitory effect was reversed when biochar was applied, leading to a 26% increase in N2O emissions due to increased nifH and nirK gene abundance. Although biochar and MPs did not significantly alter microbial α-diversity, they altered the composition and structure of bacterial and fungal communities, linked to changes in soil N turnover. Our study underscores the critical role of MP type in assessing the effects of biochar on soil N cycling and N2O emissions. Consequently, plastic pollution may complicate the ability of biochar to improve plant growth and soil functions, depending on the characteristics of the MPs.Graphical

Impact of Insect Foliar Herbivory on Soil N₂O Emission and Nitrogen Dynamics in Subtropical Tree Species

Insect foliar herbivory is ubiquitous in terrestrial ecosystems, yet its impacts on soil nitrogen cycling processes remain not yet well known. To examine the impacts of insect foliar herbivory on soil N2O emission flux and available nitrogen (N), we conducted a pot experiment to measure soil available N content and soil N2O emission flux among three treatments (i.e., leaf herbivory, artificial defoliation, and control,) in two broad-leaved trees (Cinnamomum camphora and Liquidambar formosana) and two conifer trees (Pinus massonianna and Cryptomeria fortunei). Our results showed that insect foliar herbivory significantly increased soil inorganic N (i.e., NH4+–N and NO3−–N), dissolved organic nitrogen (DON) and microbial biomass nitrogen (MBN) contents, and urease activity compared to control treatment. However, there were no differences in soil available N contents and urease activity between artificial defoliation and control treatments, implying that insect foliar herbivory had greater impacts on soil available N contents compared to physical damage of leaves. Moreover, soil N2O emission fluxes were increased by insect foliar herbivory in Cinnamomum camphora and Pinus massonianna, but not for the other two tree species, indicating various effect of insect foliar herbivory on soil N2O emission among tree species. Furthermore, our results showed the positive correlations between soil N2O emission flux and soil NO3−–N, DON, MBN, and acid protease activity, and soil inorganic N, pH, and MBN mainly explained soil N2O emission. Our results implied that insect foliar herbivory can speed up soil nitrogen availability in subtropical forests, but the impacts on soil N2O emission are related to tree species.

Impact of Biochar on Nitrogen-Cycling Functional Genes: A Comparative Study in Mollisol and Alkaline Soils.

Biochar has gained considerable attention as a sustainable soil amendment due to its potential to enhance soil fertility and mitigate nitrogen (N) losses. This study aimed to investigate the effects of biochar application on the abundance of key N-cycling genes in Mollisol and alkaline soils, focusing on nitrification (AOA, AOB, and nxrB) and denitrification (narG, norB, and nosZ) processes. The experiment was conducted using soybean rhizosphere soil. The results demonstrated that biochar significantly altered the microbial community structure by modulating the abundance of these functional genes. Specifically, biochar reduced narG and nosZ abundance in both soil types, indicating a potential reduction in N2O emissions. In contrast, it promoted the abundance of nxrB, particularly in alkaline soils, suggesting enhanced nitrite oxidation. The study also revealed strong correlations between N-cycling gene abundances and soil properties such as pH, EC (electrical conductivity. Biochar improved soil pH and nutrient availability, creating favorable conditions for AOB and Nitrospira populations, which play key roles in ammonia and nitrite oxidation. Additionally, the reduction in norB/nosZ ratios in biochar-treated soils suggests a shift towards more efficient N2O reduction. These findings highlight biochar's dual role in enhancing soil fertility and mitigating greenhouse gas emissions in Mollisol and alkaline soils. The results provide valuable insights into the sustainable management of agricultural soils through biochar application, emphasizing its potential to optimize nitrogen-cycling processes and improve soil health. Further research is needed to explore the long-term impacts of biochar on microbial communities and nitrogen-cycling under field conditions.

Microplastic effects on soil nitrogen cycling enzymes: A global meta-analysis of environmental and edaphic factors

Microplastic accumulation in soil ecosystems poses significant environmental concerns, potentially impacting nitrogen cycling processes and ecosystem health. This meta-analysis of 147 studies (1138 data points) assessed the impact of microplastics (MPs) on soil nitrogen-acquisition enzymes. We found that MPs exposure significantly increased soil urease (UE) and leucine aminopeptidase activities by 7.6 % and 8.0 %, respectively, while N-acetyl-β-D-glucosaminidase activity was not significantly affected. Biodegradable MPs showed more pronounced effects compared to conventional MPs. Enzyme activities were influenced by MPs properties (e.g., polymer type, size, concentration), experimental conditions (e.g., field or laboratory setting, temperature, nitrogen fertilization), and soil properties (e.g., clay content, pH, organic carbon, total nitrogen). For instance, acidic soils enhanced UE activity, while neutral soils reduced it. These findings emphasize the complex interactions between MPs and soil ecosystems, highlighting the need for context-specific environmental management strategies and policy-making approaches to mitigate the impacts of MPs pollution on soil health.

Integrated impacts of mariculture on nitrogen cycling processes in the coastal groundwater of Beihai, southern China

Groundwater nitrogen (N) contamination in coastal zones is becoming an increasingly serious global issue. Mariculture, as a major anthropogenic activity, has profound impacts on coastal groundwater and constitutes an important source of coastal N contamination. However, a comprehensive understanding of the impact of mariculture on N cycling (especially N removal) is still lacking. Taking the Daguansha mariculture region in southern China as the study area, we aimed to investigate the environmental impact of mariculture on coastal groundwater and identify N cycling processes influenced by mariculture using hydrogeochemistry, multiple isotopes, coupled with 16S rRNA gene sequencing, and the quantitative polymerase chain reaction (qPCR) experiments. The results showed that the combined effects of seawater intrusion and seepage from land-based mariculture ponds have led to localized groundwater salinization in the region. Meanwhile, mariculture promotes nitrification and anammox processes in groundwater. The dominance of ammonia-oxidizing and anammox bacteria in the upper aquifer is attributable to local salinization, N and organic carbon input, as well as anoxic to suboxic conditions induced by seepage from aquaculture ponds. In addition, the gene abundances of ammonia oxidation (dominated by AOA) and denitrification were positively correlated, indicating their cooperative interaction. This study provides deeper insight into N cycling in coastal groundwater systems affected by extensive mariculture.

Key drivers of heavy metal bioavailability in river sediments and microbial community responses under long-term high-concentration pollution

Given the urgent need for effective environmental management of metal-polluted ecosystems, understanding the drivers of heavy metal bioavailability and microbial adaptation is crucial. The Dongdagou River, a major pollution source to the upper Yellow River, presents significant risks to regional water quality and biodiversity. This study investigates heavy metal bioavailability and its drivers, alongside microbial community responses, in 39 surface sediment samples from the river. The results revealed severe contamination, particularly with cadmium (Cd). Statistical analysis revealed that effective sulfur (ES) plays a crucial role in driving bioavailability. High-throughput sequencing indicated that bacterial communities were primarily dominated by Proteobacteria, with increased microbial diversity observed downstream. Functional predictions highlighted the prevalence of chemoheterotrophy and nitrogen cycling processes, alongside a significant presence of metal-resistance genes and enzymes, such as Cu-Zn superoxide dismutase and metal-efflux transporters. These adaptations imply that microbial communities are developing mechanisms of resilience in response to prolonged heavy metal exposure. These findings offer valuable insights for formulating targeted remediation strategies in environments affected by heavy metal pollution.

Diversity and Function Patterns of Soil Microbial Communities in Native and Invasive Plants Along an Altitudinal Gradient in the Qinling Mountains

Soil microbial communities are essential drivers of ecosystem functions, yet the factors shaping their structure and function, particularly at different altitudes and between invasive and native plants, remain insufficiently understood. Using high-throughput Illumina sequencing, we assessed the composition, diversity, impact factors, and functional potential of the microbial communities associated with Galinsoga quadriradiata (an invasive species) and Artemisia lavandulifolia (a native species) across an altitudinal gradient ranging from 896 m to 1889 m in the Qinling Mountains. The results revealed that both plant species and altitude significantly influenced soil bacterial diversity and community structure. Actinobacteriota, Proteobacteria, and Acidobacteriota accounted for higher proportions in the soils of G. quadriradiata and A. lavandulifolia. A linear discriminant analysis showed that the two species hosted distinct microbial communities, with variations driven by species-specific traits and environmental factors. Compared with plant parameters, environmental factors had a greater impact on plant soil bacterial abundance. Functional analysis indicated that A. lavandulifolia soils were more associated with nitrogen cycling processes, while G. quadriradiata soils contributed more to organic matter decomposition. Therefore, invasive and native plants harbored microbial flora with different nutritional preferences and metabolic characteristics. These findings advance our understanding of plant–microbe interactions along altitudinal gradients, and they have practical implications for managing invasive species and supporting ecosystem resilience.

Freeze–Thaw Events Change Soil Greenhouse Gas Fluxes Through Modifying Soil Carbon and Nitrogen Cycling Processes in a Temperate Forest in Northeastern China

Freeze–thaw events are predicted to be more frequent in temperate forest ecosystems. Whether and how freeze–thaw cycles change soil greenhouse gas fluxes remains elusive. Here, we compared the fluxes of three soil greenhouse gases (CO2, CH4, and N2O) across the spring freeze–thaw (SFT) period, the growing season (GS), and the annual (ALL) period in a temperate broad-leaved Korean pine mixed forest in the Changbai Mountains in Jilin Province, Northeastern China from 2019 to 2020. To assess the mechanisms driving the temporal variation of soil fluxes, we measured eleven soil physicochemical factors, including temperature, volumetric water content, electrical conductivity, gravimetric water content, pH, total carbon, total nitrogen, total-carbon-to-total-nitrogen ratio, nitrate (NO3−), ammonium (NH4+), and dissolved organic carbon, all of which play crucial roles in soil carbon (C) and nitrogen (N) cycling. Our findings indicate that the soil in this forest functioned as a source of CO2 and N2O and as a sink for CH4, with significant differences in greenhouse gas (GHG) fluxes among the SFT, GS, and ALL periods. Our results suggest freeze–thaw events significantly but distinctly impact soil C and N cycling processes compared to normal growing seasons in temperate forests. The soil N2O flux during the SFT (0.65 nmol m−2 s−1) was 4.6 times greater than during the GS (0.14 nmol m−2 s−1), likely due to the decreased NO3− concentrations that affect nitrification and denitrification processes throughout the ALL period, especially at a 5 cm depth. In contrast, soil CO2 and CH4 fluxes during the SFT (0.69 μmol m−2 s−1; −0.61 nmol m−2 s−1) were significantly lower than those during the GS (5.06 μmol m−2 s−1; −2.34 nmol m−2 s−1), which were positively influenced by soil temperature at both 5 cm and 10 cm depths. Soil CO2 fluxes increased with substrate availability, suggesting that the total nitrogen content at 10 cm depth and NH4+ concentration at both depths were significant positive factors. NO3− and NH4+ at both depths exhibited opposing effects on soil CH4 fluxes. Furthermore, the soil volumetric water content suppressed N2O emissions and CH4 oxidation, while the soil gravimetric water content, mainly at a 5 cm depth, was identified as a negative predictor of CO2 fluxes. The soil pH influenced CO2 and N2O emissions by regulating nutrient availability, particularly during the SFT period. These findings collectively contribute to a more comprehensive understanding of the factors driving GHG fluxes in temperate forest ecosystems and provide valuable insights for developing strategies to mitigate climate change impacts.

Effects of reclamation on the distribution and diversity of comammox along the coastal wetlands of China

Reclamation of estuarine wetlands for paddy fields (PF) and aquaculture ponds (AP) used to be a common practice in China, which has changed land types and significantly affected microbial nitrogen transformations. However, its impacts on nitrification process especially complete ammonia oxidizers (comammox) remain poorly understood. Our study investigated the distribution and diversity of comammox across the major estuarine wetland systems along the coast of China by comparing different land types, including paddy fields (PF), aquaculture ponds (AP), and wetlands. The results showed that reclamation for PF and AP (1.94 × 106 copies g−1 soil) significantly reduced the gene abundance of comammox compared with wetlands (3.19 × 106 copies g−1 soil), with higher ammonia-oxidizing archaea (AOA) and bacteria (AOB) abundances and the rates of nitrification in PF than in AP. Phylogenetic analysis revealed different community structures in the two reclamation types. The distribution pattern of comammox genes in PF was similar to that in estuarine wetlands, with clade A1 and clade A2.1 being the dominant branches. Water content, iron, sulfide, and salinity were identified as the key factors affecting the distribution of comammox. This study highlights the impact of reclamation on comammox in estuarine wetlands and expands our understanding of nitrogen cycling processes in estuarine systems.

Methane seepage leads to a specific microplastic aging process in the simulated cold seep environment

Marine microplastics pose a significant threat to ecosystems, and deep-sea regions serve as critical sinks for these pollutants. Among these regions, cold seeps harbor relatively high concentrations of microplastics. However, research on the aging of microplastics under low-temperature, dark, methane-abundant, and high-pressure conditions remains limited. Seawater and sediment were collected from various Haima cold seepage sites to simulate seepage environments in 200-mL high-pressure reactors. Four types of microplastics at high concentrations (approximately 10 %) were cultured and monitored over two months to explore how they aged. The key findings are as follows: (1) Compared to areas of weak seepage, methane seepage accelerated microplastic aging, as evidenced by increased surface roughness, enhanced C-O and (CO)-O bond formation, increased microbial colonization, and reduced contact angles. (2) Microplastic aging is more pronounced in sediments than in seawater, with biodegradable polylactic acid (PLA) exhibiting the most significant aging characteristics and carbon contribution. (3) Aged microplastics induce greater disturbances in inorganic nutrient levels than in organic matter, impacting nitrogen cycle processes involving nitrate, nitrite, and ammonium. This study results reveal the fundamental aging characteristics of microplastics in extremely deep seas and highlight their potential ecological effects.

Revealing the metabolic potential and environmental adaptation of nematophagous fungus, Purpureocillium lilacinum, derived from hadal sediment.

The extreme environment shapes fungi in deep-sea sediments with novel metabolic capabilities. The ubiquity of fungi in deep-sea habitats supports their significant roles in these ecosystems. However, there is limited research on the metabolic activities and adaptive mechanisms of filamentous fungi in deep-sea ecosystems. In this study, we investigated the biological activities, including antibacterial, antitumor and nematicidal activity of Purpureocillium lilacinum FDZ8Y1, isolated from sediments of the Mariana Trench. A key feature of P. lilacinum FDZ8Y1 was its tolerance to high hydrostatic pressure (HHP), up to 110 MPa. We showed that HHP affected its vegetative growth, development, and production of secondary metabolites, indicating the potential for discovering novel natural products from hadal fungi. Whole-genome sequencing of P. lilacinum FDZ8Y1 revealed the metabolic potential of this piezotolerant fungus in carbon (carbohydrate metabolism), nitrogen (assimilatory nitrate reduction and protein degradation) and sulfur cycling processes (assimilatory sulfate reduction). Transcriptomic analysis under elevated HHP showed that P. lilacinum FDZ8Y1 may activate several metabolic pathways and stress proteins to cope with HHP, including fatty acid metabolism, the antioxidant defense system, the biosynthetic pathway for secondary metabolites, extracellular enzymes and membrane transporters. This study provides valuable insights into the metabolic potential and adaptation mechanisms of hadal fungi to the challenging conditions of the hadal environment.

Physicochemical perturbation increases nitrous oxide production from denitrification in soils and sediments

Abstract. Atmospheric concentrations of nitrous oxide (N2O), a potent greenhouse gas that is also responsible for significant stratospheric ozone depletion, have increased in response to the intensified use of agricultural fertilizers and other human activities that have accelerated nitrogen cycling processes. Microbial denitrification in soils and sediments is a major source of N2O, produced as an intermediate during the reduction of oxidized forms of nitrogen to dinitrogen gas (N2). Substrate availability (nitrate and organic matter) and environmental factors such as oxygen levels, temperature, moisture, and pH influence rates of denitrification and N2O production. Here we describe the role of physicochemical perturbation (defined here as a change from the ambient environmental conditions) in influencing rates of denitrification and N2O production. Changes in salinity, temperature, moisture, pH, and zinc in agricultural soils induced a short-term perturbation response characterized by lower rates of total denitrification and higher rates of net N2O production. The ratio of N2O to total denitrification (N2O : DNF) increased strongly with physicochemical perturbation. A salinity press experiment on tidal freshwater marsh soils revealed that increased N2O production was likely driven by transcriptional inhibition of the nitrous oxide reductase (nos) gene and that the microbial community adapted to altered salinity over a relatively short time frame (within 1 month). Perturbation appeared to confer resilience to subsequent disturbance, and denitrifiers from an environment without salinity fluctuations (tidal freshwater estuarine sediments) demonstrated a stronger N2O perturbation response than denitrifiers from environments with more variable salinity (oligohaline and mesohaline estuarine sediments), suggesting that the denitrifying community from physicochemically stable environments may have a stronger perturbation response. These findings provide a framework for improving our understanding of the dynamic nature of N2O production in soils and sediments, in which changes in physical and/or chemical conditions initiate a short-term perturbation response that promotes N2O production that moderates over time and with subsequent physicochemical perturbation.

Metagenomic study of the microbiome and key geochemical potentials associated with architectural heritage sites: a case study of the Song Dynasty city wall in Shou County, China.

Historical cultural heritage sites are valuable for all of mankind, as they reflect the material and spiritual wealth of by nations, countries, or specific groups during the development of human civilization. The types and functions of microorganisms that form biofilms on the surfaces of architectural heritage sites influence measures to preserve and protect these sites. These microorganisms contribute to the biocorrosion of architectural heritage structures through the cycling of chemical elements. The ancient city wall of Shou County is a famous architectural and cultural heritage site from China's Song Dynasty, and the protection and study of this site have substantial historical and cultural significance. In this study, we used metagenomics to study the microbial diversity and taxonomic composition of the Song Dynasty city wall in Shou County, a tangible example of Chinese cultural heritage. The study covered three main topics: (1) examining the distribution of bacteria in the biofilm on the surfaces of the Song Dynasty city wall in Shou County; (2) predicting the influence of bacteria involved in the C, N, and S cycles on the corrosion of the city wall via functional gene analysis; and (3) discussing cultural heritage site protection measures for biocorrosion-related bacteria to investigate the impact of biocorrosion on the Song Dynasty city wall in Shou County, a tangible example of Chinese cultural heritage. The study revealed that (1) the biofilm bacteria mainly belonged to Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes, and Firmicutes, which accounted for more than 70% of the total bacteria in the biofilms. The proportion of fungi in the microbial community of the well-preserved city wall was greater than that in the damaged city wall. The proportion of archaea was low-less than 1%. (2) According to the Shannon diversity index, the well-preserved portion of the ancient city wall had the highest diversity of bacteria, fungi, and archaea, and bacterial diversity on the good city wall was greater than that on the corroded city wall. (3) Bray-Curtis distances revealed that the genomes of the two good city walls were similar and that the genomes of the corroded city wall portions were similar. Researchers also detected human intestine-related bacteria in four locations on the city walls, with the proportion of these bacteria in the microbial community being greater on good city walls than on bad city walls. (4) KEGG functional analysis revealed that the energy metabolism and inorganic ion transport activities of the bacterial community on the corroded city wall were greater than those of the good city wall. (5) In the carbon cycle, the absence of active glycolysis, the ED pathway, and the TCA cycle played significant roles in the collapse of the east city wall. (6) The nitrogen cycling processes involved ammonia oxidation and nitrite reduction to nitrate. (7) In the sulfur cycle, researchers discovered a crucial differential functional gene, SoxY, which facilitates the conversion of thiosulfate to sulfate. This study suggests that, in the future, biological approaches can be used to help cultural heritage site protectors achieve targeted and precise protection of cultural relics through the use of microbial growth inhibition technology. The results of this study serve as a guide for the protection of cultural heritage sites in other parts of China and provide a useful supplement to research on the protection of world cultural heritage or architectural heritage sites.

Simulation of spatially distributed sources, transport, and transformation of nitrogen from fertilization and septic systems in a suburban watershed

Abstract. Excess export of reactive nitrogen in the form of nitrate (NO3-) from suburban watersheds is a major source of water quality degradation and threatens the health of downstream and coastal waterbodies. Ecosystem restoration and best management practices (BMPs) can be introduced to reduce in-stream NO3- loads by promoting vegetation uptake and denitrification in the upland and riparian areas. However, accurately evaluating the effectiveness of these practices and setting regulations for nitrogen inputs requires an understanding of how human sources of nitrogen interact with ecohydrological systems. We evaluated how the spatial and temporal distribution of nitrogen sources interacts with ecohydrological transport and transformation processes along surface and subsurface flow paths with respect to nitrogen cycling and export. Embedding distributed household sources of nitrogen and water within hillslope hydrologic systems influences the development of both planned and unplanned “hot spots” of nitrogen flux and retention in suburban ecosystems. We chose a well-monitored low-density suburban watershed, Baisman Run, in Baltimore County, Maryland, USA, to evaluate patterns of in-stream NO3- concentrations and terrestrial nitrogen cycling processes in response to three common activities: irrigation, fertilization, and on-site sanitary wastewater disposal (septic systems). We augmented a distributed ecohydrological model, RHESSys (Regional Hydro-Ecological Simulator System), with estimates of the spatial distribution of these loads at household parcel level to develop a predictive understanding of the factors generating upland and riparian nitrogen cycling, transport, and stream NO3- concentrations. We calibrate subsurface hydraulic parameters only without calibrating ecosystem and biogeochemical processes. The calibrated model predicted mean NO3- concentrations of 1.43 mg NO3--N L−1 compared to the observed 1.6 mg NO3--N L−1 from water year 2013 to 2017. With spatially explicit irrigation, fertilizer, and septic effluent inputs, estimated denitrification rates in grass lawns, a dominant land cover in suburban landscapes, were also in the range of previously measured values. The highest predicted denitrification rates (N retention hot spots) were downslope of lawn and septic locations in a constructed wetland and at a riparian sediment accumulation zone at the base of a gully receiving street drainage. These locations illustrate the development of hot spots for nitrogen cycling and export in both planned and “accidental” retention features. Appropriate siting of suburban nutrient management and BMPs should assess and incorporate spontaneously developed nutrient hot spots to design improved landscape ecosystem N retention and water quality.

Effects of the Radicle Sheath on the Rhizosphere Microbial Community Structure of Seedlings in Early Spring Desert Species Leontice incerta

Most research on plant–microbe interactions emphasize the effects of micronutrients on the rhizosphere microbial community structure. However, the influence of seed structures, particularly the radicle sheath, on microbial diversity at the seedling root tips under varying temperatures and humidity has been less explored. This study conducted controlled indoor experiments in the northern desert of Xinjiang to assess the radicle sheath’s impact on microbial community composition, diversity, and function. The results indicated no significant changes in the Chao1 index for bacteria and fungi, but notable differences were observed in the Shannon and Simpson indices (p < 0.05). Under drought conditions, the radicle sheath significantly reduced bacterial infections without affecting fungi. Genus-level analysis showed an increased abundance of specific dominant bacterial groups when the radicle sheath was retained. NMDS analysis confirmed its significant effect on both bacterial and fungal community structures. LEfSe analysis identified 34 bacterial and 15 fungal biomarkers, highlighting the treatment’s impacts on microbial taxonomic composition. Functional predictions using PICRUSt 2 revealed that the radicle sheath facilitated the conversion of CH4 to CH3OH and various nitrogen cycle processes under drought. Overall, the radicle sheath plays a crucial role in maintaining rhizosphere microbial community stability and enhancing the functions of both bacteria and fungi under drought conditions.

Drivers of denitrification and nitrification in a dryland agroecosystem: The role of abiotic and biotic factors

Agricultural practices such as tillage and fertilization impact soil nitrogen (N) cycling processes, but how they alter the coupling between the activity, abundance and diversity of N-cycling microbes remains to be understood. Here, we used a fifteen-year trial in a dryland agroecosystem on the Loess Plateau of China (two tillage regimes crossed with six fertilization treatments) to understand how (de)nitrification potentials are determined by soil abiotic conditions and the abundances and compositions of the (de)nitrifier communities. We measured the abundances of bacterial (AOB) and archaeal (AOA) ammonia oxidizers and nirK- and nirS-nitrite reducers, their community compositions, potential nitrification (PNA) and denitrification (PDA), and soil abiotic conditions. PNA and PDA across the 12 treatments were positively correlated to AOB abundance and nirS abundance, respectively. Co-occurrence network analysis revealed the presence of dominant ecological modules of (de)nitrifiers sensitive to agricultural treatments, and more complex network under no-tilled than tilled conditions as well as under multiple fertilizers than unfertilized conditions. Path analysis and random forest analysis both showed that PNA was explained by AOB abundances and the relative abundance of one module of (de)nitrifiers driven by soil ammonium concentration, while PDA was most related to soil organic carbon concentration, pH and to a lesser extent nirS abundance. These findings demonstrate that, in agricultural soils, the potential of denitrification –a facultative activity for denitrifiers– is mainly predicted by abiotic conditions, while the potential of nitrification –an obligate activity for nitrifiers– is determined by biotic variables, here AOB abundances and a particular cluster of microbial populations.

Activity of novel virus families infecting soil nitrifiers is concomitant with host niche differentiation.

Chemolithoautotrophic nitrifiers are model groups for linking phylogeny, evolution, and ecophysiology. Ammonia-oxidizing bacteria (AOB) typically dominate the first step of ammonia oxidation at high ammonium supply rates, ammonia-oxidizing archaea (AOA) and complete ammonia-oxidizing Nitrospira (comammox) are often active at lower supply rates or during AOB inactivity, and nitrite-oxidizing bacteria (NOB) complete canonical nitrification. Soil virus communities are dynamic but contributions to functional processes are largely undetermined. In addition, characterizing viruses infecting hosts with low relative abundance, such as nitrifiers, may be constrained by vast viral diversity, partial genome recovery, and difficulties in host linkage. Here, we describe a targeted incubation study that aimed to determine whether growth of different nitrifier groups in soil is associated with active virus populations and if process-focused analyses facilitate characterization of high-quality virus genomes. dsDNA viruses infecting different nitrifier groups were enriched in situ via differential host inhibition. Growth of each nitrifier group was consistent with predicted inhibition profiles and concomitant with the abundance of their viruses. These included 61 high-quality/complete virus genomes 35-173kb in length with minimal similarity to validated families. AOA viruses lacked ammonia monooxygenase sub-unit C (amoC) genes found in marine AOA viruses but some encoded AOA-specific multicopper oxidase type 1 (MCO1), previously implicated in copper acquisition, and suggesting a role in supporting energy metabolism of soil AOA. Findings demonstrate focused incubation studies facilitate characterization of active host-virus interactions associated with specific processes and viruses of soil AOA, AOB, and NOB are dynamic and potentially influence nitrogen cycling processes.

Meta-analysis: Global patterns and drivers of denitrification, anammox and DNRA rates in wetland and marine ecosystems

Nitrogen cycling is one of the most important biogeochemical processes on Earth, and denitrification, anammox and DNRA processes are important nitrogen cycling processes in estuarine ecosystems. However, due to the large input of anthropogenic nitrogen sources, a large number of environmental problems have now occurred in the estuary. But the global patterns and controlling factors of denitrification, anammox and DNRA rates in wetland marine ecosystems are not yet known. We reached our conclusions through a global synthesis of 546 observation sites from 78 peer-reviewed papers: The three rates were generally higher in areas near wetlands than in coastal areas. The rate of denitrification was highest in the subtropical region the seasonal variability was not significant; and TOC was the main factor controlling denitrification. The rate of anammox was significantly higher in the subtropical region than in the tropical and boreal zones, and the seasonal variability was significant; and at the same time, TN was the main driver of the anammox rate of the wetland ocean. DNRA rates were significantly higher in the tropics than in the subtropics and temperate zones; and the main driver of DNRA rates was temperature. Nitrogen cycle functional genes also had an indirect effect on their rates. With NH4 + -N significantly affecting nirK abundance and TN significantly affecting the gene abundance of nirS; TOC and TN had a greater effect on hzo abundance, which indirectly affected anammox rates; for DNRA, C/N significantly affects the gene abundance of nrfA, which indirectly affects the DNRA rate. Therefore, the findings of this study indicate that physicochemical indicators about N and climatic characteristics have a profound effect on the nitrogen cycling process, which provides a good feedback for studying the role of denitrification and provides a positive impact on global climate and environmental governance.

Significance of Urea in Sustaining Nitrite Production by Ammonia Oxidizers in the Oligotrophic Ocean

AbstractNitrification, the stepwise oxidation of ammonia to nitrate via nitrite, is a key process in the marine nitrogen cycle. Reported nitrite oxidation rates frequently exceed ammonia oxidation rates below the euphotic zone, raising the fundamental question of whether the two steps are balanced and if alternative sources contribute to nitrite production in the dark ocean. Here we present vertically resolved profiles of ammonia, urea, and nitrite oxidation rates and their kinetic traits in the oligotrophic Subtropical North Pacific. Our results show active urea‐derived nitrogen oxidation (urea‐N oxidation) in the presence of experimental ammonium amendment, suggesting direct urea utilization. The depth‐integrated rates of urea‐N oxidation and ammonia oxidation are comparable, demonstrating that urea‐N oxidation is a significant source of nitrite. The additional nitrite from urea‐N oxidation helps to balance the two steps of nitrification in our study region. Nitrifiers exhibit high affinity for their substrates, and the apparent half‐saturation constants for ammonia and nitrite oxidation decrease with depth. The apparent half‐saturation constant for urea‐N oxidation is higher than that for ammonia oxidation and shows no clear vertical trend. Such kinetic traits may account for the relatively higher urea concentration than ammonium concentration in the ocean's interior. Moreover, a compilation of our results and reported data shows a trend of increased urea‐N oxidation relative to ammonia oxidation from the eutrophic coastal zone to the oligotrophic open ocean. This trend reveals a substrate‐dependent biogeographic distribution of urea‐N oxidation across marine environments and provides new information on the balance and flux of the marine nitrification process.