The uptake of permafrost thaw released nitrogen (N) could benefit plant growth and change vegetation community composition in a warming climate in cold regions. However, the capacity of co-existing species to take up different forms of available N beyond the root zone remains largely unknown in permafrost areas with a deep active layer. In situ ¹⁵NH₄Cl, K¹⁵NO₃ and C₂H₅NO₂ (glycine) labelling were conducted up to 70 cm depth for five species. Averaged across the five species, the summed ¹⁵N recovery rate of the three tracers was 10.71% ± 10.69%, 1.69% ± 2.51%, 1.54% ± 4.16% and 0.7% ± 2.23% at 0‒15, 15‒30, 30‒50 and 50‒70 cm, respectively. Kobresia humilis had the largest N uptake diversity. The NO₃^‒-N recovered from 30‒70 cm for K. humilis and Saussurea japonica was much higher than other species, accounting for 23% and 13% of the total N recovered at 0‒70 cm. Root surface area was positively related to the recovery rate of inorganic N at soil below 15 cm whereas a species’ N requirement negatively to the N recovery at 0‒15 cm. The relative cover of a species in a community was negatively related to a species’ N requirement but showed no relationship with the N recovery rate or N uptake diversity. Plant communitycomposition may not be affected by vertical N uptake patterns of co-existing species. Species that can take up N from deep soil layers may gain competitive advantages, thereby altering the plant community structure in a warm climate in the future.

Although grazing and topography jointly regulate grassland ecosystem processes, the interactive influence of their effects on the spatial distribution of soil nitrogen (N) fractions and bioavailability remains unclear. Here, we sampled soils along three topographical positions (i.e., upper, middle, and down slope) in grazing and paired-adjacent enclosed (ungrazed) sites, respectively, in an Inner Mongolia hillslope grassland, and we measured N contents of particulate organic matter (POM-N) and mineral associated organic matter, and potential net N mineralization (Nm). Results showed that POM-N and Nm were, respectively, 174% and 1114% greater in the grazing site than in the enclosed grazing site in the 0–10 cm soil layer at the downslope position. Across the landscape of the grazing sites, POM-N and Nm were 1.79–2.03 and 2.82–6.83 times higher, respectively, in the downslope than in the upper and middle slope positions. Furthermore, POM-N showed a significantly positive correlation with the Nm. The results of this study indicate that grazing and erosion interactively drives the redistribution of POM along the slope by promoting plant residue fragmentation and soil materials movement, thereby reshaping the pattern of soil nitrogen cycling at the landscape scale.

Understanding the effects of phosphorus (P) inputs on soil organic carbon (SOC) sequestration and their links with soil P dynamics is crucial for stabilizing food production and achieving the goal of C neutrality. To explore this, a global meta-analysis and a multi-year field experiment were conducted synchronously. The global dataset encompassing 352 paired observations indicated that P inputs significantly increased soil total P, available P, and SOC contents by 40.6%, 114.7%, and 10.6%, respectively, compared with the control. Increase of SOC was more pronounced in farmlands than in grasslands and forests, with the effects closely tied to P input levels. Meanwhile, field-based study showed that P inputs significantly increased paddy SOC accumulation, while excessive input weakened the benefit. Increased SOC accumulation was accompanied by an increase in most its sub-pools such as particulate organic C and microbial biomass C. These sub-pools notably declined when P input exceeded a critical threshold. The benefits in SOC and its sub-pools were strongly correlated with shifts in soil P availability, microbial biomass P, and phosphatase activity. These findings highlight the significance of P availability and dynamics in SOC accumulation and emphasize the need to define optimal P input thresholds to enhance SOC sequestration.

Loss of soil microbial diversity is accelerating worldwide, yet how this loss alters soil greenhouse gas fluxes remains poorly understood. Here, we provide experimental evidence that diversity loss affects nitrous oxide (N₂O) and methane (CH₄) fluxes through nonlinear, trait-mediated pathways. Using soil microcosm dilution gradients established across three land-use types (forest, grassland, and cropland), we linked shifts in community diversity with key physiological traits: carbon use efficiency (CUE), nitrogen use efficiency (NUE), and turnover rate. Over a 118-day incubation, soil N₂O flux exhibited a pronounced hump-shaped response: moderate diversity loss stimulated emissions, whereas severe loss suppressed them through the breakdown of functional redundancy. Strikingly, even moderate diversity loss reversed soils from CH₄ sinks to net sources. Microbial turnover consistently emerged as the core driver of both N₂O and CH₄ fluxes, with additional contributions from the turnover interactions with CUE and NUE. Variance partitioning further showed that microbial physiological traits explained 62% of CH₄ flux variation and 59% of N₂O flux variation. Together, these findings highlight the pivotal role of microbial traits in mediating soil biodiversity-function relationships. They also emphasize the importance of incorporating trait-based processes into Earth system models to improve predictions of soil climate feedbacks.

The pollution of microplastics (MPs) in terrestrial ecosystems has drawn growing concern. Nevertheless, the influence of MPs on the fractions of soil organic carbon (SOC), particularly in urban soils, is still not well understood. Particulate organic carbon (POC) as a key component of urban soil organic carbon, is a core element for maintaining the functions of urban soil ecosystems. The effect of MPs on soil carbon dynamics was investigated by exposing soils planted with three common green plants to polypropylene microplastics (MPs) at concentrations of 0%, 0.5%, 1%, and 2% (w/w). The addition of MPs resulted in an 18.6% to 48.2% increase in SOC content. MPs notably boosted POC content by 44.2% to 101.7%, while they only increased mineral-associated organic carbon (MAOC) in soil without plants, with a range of 41.8% to 54.7%. There was a significant negative correlation between SOC and bacterial necromass carbon (BNC) in the absence of MPs, but this negative correlation disappeared with the addition of MPs. Compared with the BNC, the fungal necromass carbon (FNC) mainly contributed to the microbial necromass carbon (MNC) (about 74.6%). Bacterial communities were more sensitive to the addition of MPs than fungal communities. Structural equation model confirmed that MPs addition increases SOC content by promoting the accumulation of POC and BNC contribute to MAOC. Overall, the findings highlight the sensitive response of POC to MPs pollution, which could have a potential effect on soil carbon components in urban soil.

Body size is a master functional trait of soil fauna, reflecting interactions among developmental, life-history, physiological, and ecological processes. Though recognized as a critical parameter, traditional manual measurement remains a major bottleneck due to its low efficiency and subjective error from different labors, hindering progress in large-scale, trait-based soil ecology. To address this gap, we developed FaunaAIM, a novel automated tool for high-throughput extraction of key morphological characteristics of soil fauna from images using machine learning. The workflow introduces an attention-based U-Net model integrated with Convolutional Block Attention Modules (CBAM) for individual segmentation, followed by morphological feature calculation using a series of morphological methods. The model achieved high segmentation accuracy (97.3% precision and a mean Intersection over Union (mIoU) of 0.951) on the test set (n=6000). Automated measurements of body length, body width, and area showed strong agreement with manual assessments, with concordance correlation coefficients (CCC) exceeding 0.97 and no significant systematic bias. Notably, the model was trained exclusively on Collembola data, while accurately segmenting mites, demonstrating strong cross-taxon transferability suitable for community-wide analyses. Overall, FaunaAIM substantially improves measurement efficiency and demonstrates excellent transferability, enabling high-throughput morphological characterization of soil fauna and potentially other biological organisms.

Rice (Oryza sativa L.) is a staple food for more than half of the population worldwide. In addition to its role in food security, rice cultivation systems, particularly flooded paddy fields, are the largest anthropogenic wetlands on Earth, and receive critical concerns as the major sources of methane (CH₄) emissions and hotspots for arsenic (As) mobilization. Thermodynamically, both As mobilization and CH₄ production are driven by similar environmental factors in paddy soils. Growing evidence suggests that these processes share common origins, microbial drivers, and key influencing factors, including soil redox potential and dissolved orgamic matter availability. By regulating the shared facors, simultaneous mitigation of As mobilization and CH₄ emissions may be achievable in paddy soils. However, research in this area remains limited. The perspective proposed in this study could guide the development of integrated strategies to concurrently address As and CH₄ challenges in paddy ecosystems, and increase the sustainability of rice production.

Nitrogen (N) deposition alters the composition and release of plant root exudates, thereby influencing the dynamics of soil organic carbon (SOC). However, the effects of specific root exudate compounds on SOC fractions under different N levels remain unclear. In this study, we conducted an incubation experiment to investigate how oxalic acid, citric acid, D-tryptophan, D(+) maltose, and p-hydroxybenzoic acid interact with different N addition levels (0, 90, 180, and 270 kg N ha⁻¹) in affecting SOC fractions. The results revealed that N addition altered SOC through changes in soil physicochemical properties and microbial activity, reduced soil microbial biomass C, and increased CO₂ emissions. The addition of root exudates resulted in an average 2.5% reduction in SOC. The interaction with N addition significantly (p < 0.05) increased soil microbial biomass C and dissolved organic C by 60% and 9.1%, respectively. Oxalic acid, citric acid, and p-hydroxybenzoic acid significantly (p < 0.05) stimulated greater CO₂ release than D-tryptophan and D(+) maltose. Under N enrichment, root exudates influenced SOC dynamics primarily by regulating soil microbial biomass N. These findings highlight the interactive effects of N deposition and root exudate composition on soil C stability in agricultural ecosystems.

The application of livestock manure increases soil microbial biomass phosphorus (MBP), a highly bioavailable P pool, thereby enhancing soil P fertility and helping address global P challenges. However, it remains unclear how microbial communities adapt their P-acquisition strategies to sustain the elevated MBP, limiting a comprehensive understanding of the microbial mechanisms underlying this sustainable P management practice. This study investigated the relationship between soil MBP and microbial functional profiles of P transformation through metagenomic analysis at a long-term experimental site with repeated applications of swine manure. Manure fertilization significantly increased soil MBP by 153% and reshaped the composition of microbial P-transformation genes, with a significant increase in the normalized abundances of 85 out of the 135 detected genes. MBP was signifi-cantly and positively correlated with the metabolic potential for P-acquisition processes including orthophosphate uptake, phosphoglycerol uptake, phytate hydrolysis, 2-aminoethylphosphonic acid degradation, and phosphite oxidation. Distinct dominant genera were significantly enriched under manure fertilization among the bacterial communities involved in these critical P-acquisition processes. Solirubrobacter and Nocardioides were the shared enriched taxa and crucial for the stability of their corresponding communities. The considerable variation in copy numbers of the corresponding genes among the 56 reconstructed bacterial metagenome-assembled genomes was indicative of potential shifts in the functional capacity for the critical P-acquisition processes of the enriched taxa. Collectively, the findings of this study suggest the detailed adaptive P-acquisition strategies employed by soil microbial communities to maintain the elevated MBP under swine manure fertilization and the microbial taxa contributing to this adaptation.

The excessive use of chemical fertilizers in agriculture has led to a decline in soil biodiversity. Organic fertilizer substitution has been proposed as a sustainable alternative toward the mitigation of these adverse effects, yet its impacts on the diversity of soil microbiota across varying environmental contexts remain poorly quantified. Here, we conducted a meta-analysis of 82 published studies from large-scale agricultural ecosystems. We revealed that organic fertilizer substitution significantly increased the abundances of bacteria, fungi, and nematodes, while enhancing the alpha diversity of bacterial and fungal communities. Specifically, the positive impacts on microbial abundance and alpha diversity became stronger over prolonged experimental timelines. The most potent effects on nematode abundance, arbuscular mycorrhizal fungi (AMF) richness, as well as bacterial Shannon and fungal Chao1 indices were observed under moderate substitution proportions (20%–50%). The stimulatory effects on the abundance and alpha diversity of bacteria and fungi were more pronounced in warm and humid climates, whereas the AMF Shannon index increased in colder regions. Moreover, the nematode Shannon index responded more strongly in drylands than in paddy fields. Collectively, our findings demonstrated that organic fertilizer substitution effectively rebuilt the complexity of the soil micro-food web. Consequently, we recommend a moderate substitution proportion of 20%–50% to maximize biodiversity gains in agricultural soils.

Coastal saline-alkali soils challenges global agricultural through high salinity, structural degradation, microbial dysfunction, and nutrient depletion. While biochar improves these soils’ physicochemical properties, its capacity to modulate soil microbial communities remains constrained. Therefore, we conducted a soil column experiment to investigate whether vermicompost, as a microbial inoculant can enhance biochar’s remediation efficacy in severely saline-alkali soils through biological reinforcement by enriching functional microbes capable of colonizing and interacting with biochar. Our results revealed that biochar incorporation significantly increased soil organic matter (+180.5%) and other nutrients compared to CK, with further enhancement via synergistic interactions with vermicompost. The vermicompost-supplemented biochar amendment treatment increased water-stable macroaggregates by 20.2% (approximately 2.2 times higher than the sole biochar treatment). The addition of biochar significantly reduced Na⁺, Cl⁻, HCO₃⁻ and SO₄²⁻, but resulted in a decrease in Mg²⁺ and Ca²⁺, while the presence of vermicompost could slow down this trend. Notably, the biochar-vermicompost co-application significantly affected soil bacterial communities by enriching microorganisms associated with carbon and nitrogen nutrient cycling, such as Filobacillus and Xanthobacteraceae. Taken together, these findings indicate that the biochar-vermicompost co-application reduced salt leaching and improves nutrient retention via soil aggregation restructuring, and further remediated saline-alkaline soils by boosting functional microbial communities.

Nitrous oxide (N₂O), a potent greenhouse gas, contributes significantly to global warming, with agricultural soils being a major source due to intensified nitrogen fertilizer use. While straw incorporation is widely adopted to enhance soil organic carbon sequestration and nutrient retention, its impact on N₂O emissions remains controversial. This study investigated the effects of various combinations of rice straw and nitrogen fertilizer on N₂O emissions in a paddy soil through a controlled microcosm experiment. We monitored CO₂ and N₂O fluxes, ammonium and nitrate dynamics, the activities of key extracellular enzymes involved in carbon and nitrogen cycling, and the abundances of N₂O-related microbial guilds. Results showed that straw amendment stimulated microbial activity and enhanced CO₂ emissions, whereas nitrogen addition suppressed heterotrophic respiration. Both straw and nitrogen amendments significantly increased N₂O emissions, with a synergistic effect observed under combined applications. N₂O emissions were primarily driven by nitrogen amendment and exhibited significant positive correlations with the abundances of ammonia-oxidizing bacteria (AOB), complete ammonia oxidizers clade A (comammox clade A), nirK-denitrifiers, and fungal denitrifiers; moreover, random forest modeling revealed that the abundances of AOB, comammox clade A, nirK-denitrifiers accounted for a substantial portion of the variation in cumulative N₂O emissions. Additionally, partial least squares path modeling (PLS-PM) identified a hierarchical regulatory cascade involving nitrogen availability, microbial community dynamics, and enzyme activity as the key mechanisms governing N₂O fluxes. Overall, these findings underscore the critical roles of prokaryotic ammonia oxidizers and nirK-denitrifiers in modulating N₂O emissions and provide valuable insights for developing field management strategies to mitigate greenhouse gas emissions from agricultural soils receiving straw amendment.

Plant–herbivore interactions are strongly shaped by plant genotype and soil resource availability, but studies that jointly consider these factors within an integrated aboveground–belowground framework remain limited. This knowledge gap constrains the optimization of cultivar breeding and fertilizer management for sustainable agriculture. We conducted a factorial greenhouse experiment with three factors, brown planthopper (BPH, Nilaparvata lugens Stål) infestation (present/absent), rice cultivar (resistant or susceptible), and fertilizer type (chemical or organic), to test how cultivar and fertilizer affect rice resistance to BPH and, in turn, how BPH alters soil nutrient availability, microbial biomass, and nematode communities through plant-mediated pathways. Both resistant cultivar and organic fertilizer significantly suppressed BPH performance relative to susceptible cultivar and chemical fertilizer. They also mitigated BPH-induced reductions in plant growth, microbial biomass, soil resources, and bacterial- and fungal-feeding nematodes. In contrast, chemical fertilizer exacerbated BPH impacts, particularly on susceptible rice, and promoted root-feeding nematodes. Cultivar and fertilizer independently affected plant and soil responses without showing synergistic interaction. Our findings suggest that combining resistant cultivars with organic fertilizer strengthens resistance to aboveground herbivores and belowground root-feeding nematodes, while enhancing soil resources and food web stability. This integrated strategy provides an effective approach for sustainable pest management and nutrient regulation in rice systems.

The coexistence of virulence factor genes (VFGs) and antibiotic resistance genes (ARGs) in environmental microbial communities poses an escalating threat to public health, particularly under pollutant-induced selective pressures. While non-antibiotic pollutants have been shown to promote ARG dissemination, their effects on VFGs remain poorly understood. Soil pH can simultaneously affect pollutant bioavailability and microbial community composition, thereby altering selective pressures and modulating the dynamics of both ARGs and VFGs. Here, we assessed the influence of arsenic (As) and triclocarban (TCC), alone and in combination, on soil VFG profiles across a pH gradient. Co-contamination significantly increased VFG abundance, with near-neutral pH intensifying this effect through enhanced pollutant bioavailability. VFG enrichment was primarily driven by pollutant-induced shifts in microbial community composition. In particular, neutral pH conditions promoted the proliferation of γ-Proteobacteria, which may serve as dominant VFG hosts. In addition, the co-contamination enhanced the co-occurrence of VFGs and ARGs, suggesting a potential expansion of pathogenic and antibiotic-resistant bacterial populations and elevating the risk of virulence trait dissemination. These findings underscore the need to evaluate microbial risks from the perspective of VFGs, particularly under co-contamination scenarios, to better anticipate emerging public health threats within a One Health framework.

Collembola predominates soil fauna community of subtropical forests, where they play essential roles in the soil detrital network. Diverse tree species can reshape the functional traits of Collembola communities by altering habitat conditions and food availability, yet little is known about this process. In June 2023, we investigated the structural composition and functional traits of Collembola in the litter and soil layers under six tree species in a subtropical forest common garden. A total of 543 Collembola individuals were captured, belonging to six families, with higher abundance observed in forests dominated by phoebe (Michelia macclurei), fir (Cunninghamia lanceolata), and pine (Pinus massoniana) compared to other forests. Among functional traits, sensory and dispersal traits of Collembola were significantly more pronounced in fir and Sapindus saponaria forests than in Castanopsis carlesii forests. The highest functional diversity indices of Collembola were recorded in fir forests relative to other forest types. Statistical analysis revealed that Collembola dispersal and sensory traits are primarily influenced by litter calcium content and soil organic matter, highlighting their adaptive responses to key environmental factors. This study adopted a functional trait-based approach to explore how tree species affect the community structure and functional traits of Collembola.

The widespread use of antibiotics across medicine, agriculture, aquaculture, and industry has driven a significant increase in antimicrobial resistance (AMR), posing a critical threat to both human health and ecosystem stabi-lity. The persistence and distribution of antibiotics and antibiotic resistance genes (ARGs) in the environment are major concerns because they can disseminate through various pathways, including atmospheric transport, biogeochemical cycling, and trophic transfer. This review focuses on the ecological and public health implications of antibiotics and AMR within the framework of “One Health,” emphasizing their occurrence, fate, degradation, and risks in soil ecosystems. We highlight knowledge gaps and advocate for integrated, cross-sectoral research to inform environmental risk assessment and support evidence-based policies for AMR mitigation and ecological sustainability.

In alpine grasslands, nitrogen limitation constrains plant growth, and nitrogen fertilization is a common strategy for rehabilitating degraded lands. However, the effects of different nitrogen types, levels, and durations on plant diversity and ecosystem functionality remain unclear. This study investigates slightly degraded alpine grasslands in the Three Rivers Source Region of the Qinghai-Tibet Plateau. We applied ammonium sulfate, potassium nitrate, and urea at varying concentrations (20 g m^–2, 10 g m^–2, and 0 g m^–2) and assessed plant biodiversity, biomass, and multifunctionality. Under long-term nitrogen addition, different nitrogen types influenced species loss and gain rates, thereby affecting species richness; increasing nitrogen levels elevated species loss rates, while ecosystem multifunctionality remained unaffected by environmental constraints. In contrast, under short-term nitrogen addition, nitrogen type primarily influenced species gain rates, which altered species richness and, in turn, ecosystem multifunctionality; nitrogen levels affected both species loss and gain rates, jointly shaping richness and multifunctionality. Overall, short-term nitrogen addition significantly increased species diversity and biomass, whereas long-term addition reduced diversity without affecting multifunctionality. These findings underscore the contrasting impacts of short- and long-term nitrogen inputs and the combined regulatory roles of nitrogen type, addition level, and application duration in the ecological restoration of degraded alpine grasslands.