Inputs of plant carbon (C) may modify the decomposition of soil organic C (SOC) through a phenomenon known as priming effect. Glucose is often used to simulate plant C input in priming effect experiments, but whether adding glucose based on whole soil or as a proportion of SOC result in variations in estimating the magnitude and drivers of priming effects is poorly understood. Here, we collected soil samples from 10 sites along an approximately 2000 km grassland transect inInner Mongolia, China. Subsequently, in a 30-day laboratory incubation experiment, ¹³C-labeled glucose was added to the soil using two methods (i.e., relative to soil C or soil mass): glucose-C=2% SOC and 0.4 mg glucose-C g^‒1 soil. This allowed us to investigate the potential impact of different glucose addition methods on assessing the priming effect. The results showed that different glucose addition methods did not cause significant differences in the overall cumulative priming effect. When glucose was added at a rate of glucose-C=2% SOC, the priming effect mechanism aligned with the co-metabolism hypothesis, with SOM stability (represented by content of soil minerals and (clay+silt) %) being the primary driver. When the glucose was added at a rate of 0.4 mg glucose-C g^‒1 soil, the priming effect mechanism was supported by the nutrient mining hypothesis, and SOM stability was also the main controlling factor of the priming effect. These findings suggest that different glucose addition methods may not cause significant differences in the magnitude of soil priming effect or its primary driving factor, but may lead to variation in understanding the main mechanism behind the priming effect.

Habitat fragmentation poses significant threats to soil biodiversity and ecosystem stability, yet its impacts on multifunctionality resistance under global change remain unclear. Here, we investigated 61 islands in China’s subtropical Zhelin Lake Reservoir, through experiments simulating multiple stressors, to assess how changes in soil biodiversity induced by habitat fragmentation affect the multifunctionality resistance to nitrogen enrichment, warming, and wetting-drying cycles disturbances. Our results revealed that soil moisture, nematode/protist α-diversity, and multifunctionality resistance (quantified through nutrient cycling stability) declined with fragmentation intensity (from the large to small islands). Nematode α-diversity, particularly bacterivorous taxa, emerged as a keystone mediator, directly enhancing resistance to global change stressors via microbial regulation and nutrient cycling. Conversely, protist β-diversity reduced warming resistance through community destabilization. Structural equation modeling demonstrated dual fragmentation effects: direct moisture-driven functional decline versus indirect biodiversity-mediated stabilization. Stressor-specific mechanisms diverged fungal-nematode synergies buffered nitrogen enrichment impacts, while protist community turnover exacerbated thermal vulnerability. These findings challenge microbial-centric paradigms, highlighting the predominate role of microfauna in regulating soil multifunctionality resistance to global change. Our study highlights that conservation strategies should prioritize preserving larger fragments and soil micro-faunal diversity to sustain multifunctionality under global change, emphasizing the conservation of soil microorganisms such as nematodes and protists in fragmented landscapes.

The response of plant−soil−microbial nutrients and stoichiometry to plant−soil feedback (PSF) during secondary succession (SS) is an important driver of plant−community recovery. However, the plant−soil−microbe responses to PSFduring SS are unknown. The effects of PSF on plants at different successionalstages and successional soils regulated by these plants were tested in this study by potting experiments. Results indicated that soils conditioned by Setaria viridis (EarlySoil) and soils conditioned by Artemisia sacrorum (MidSoil) feedback significantly increased the potassium content of Artemisia sacrorum (MidSp) and Bothriochloa ischaemum (LateSp), respectively. MidSp and Setaria viridis (EarlySp) aboveground carbon, nitrogen, and phosphorus contents were promoted by soils conditioned by Bothriochloa ischaemum (LateSoil) and MidSoil, respectively, but provided negative feedbacks on below-ground carbon and phosphorus. The EarlySp and MidSp significantly increased other nutrients in the MidSoil and LateSoil except water-soluble nutrients, the LateSp and MidSp significantly increased the soil nutrients in the MidSoil and EarlySoil, and the MidSp significantly increased their enzyme activity most significantly. Despite the significant impact of PSF on plant stoichiometry, reducing the intensity of phosphorus limitation, plant growth was always phosphorus limited. PSF changed the nitrogen limit of microorganisms, but microorganisms were always limited by phosphorus. Soil physicochemical properties and microbial abundance regulated by MidSp (or EarlySp) were facilitated by LateSp (or MidSp), which ultimately accelerated the SS process. This confirmed the irreversibility of SS and provided new information on plant-soil-microbe dynamics during SS.

Microbial necromass plays a crucial role in soil organic carbon (SOC) formation. However, underlying abiotic and biotic factors on necromass accumulation remain poorly understood. Here, based on a 27-year field fertilization experiment in upland Ultisols, we investigated how changes in fungal and bacterial necromass relate to the abundance, diversity, community structure, and trophic co-occurrence networks of microbial communities, including fungi, bacteria, and protists. Fungal necromass contributed an average of 32.4% to SOC, a greater contribution than the 14.6% from bacterial necromass, regardless of fertilization regimes. Modularity analysis of the protistan-fungal network indicated that Ascomycota fungi were the primary contributors to fungal necromass accumulation in arable soil. The protistan community structure had a significantly negative effect on fungal necromass by directly decomposing fungal residues, rather than altering the fungal community structure. In contrast, soil total nitrogen positively influenced the persistence of bacterial necromass. Bacterial abundance was positively correlated with bacterial necromass. Protists increased bacterial abundance, thereby increasing bacterial necromass in the soil. Overall, protists regulated microbial necromass storage in arable soils either by decomposing fungal necromass or by increasing bacterial abundance.

Enhancing organic matter in arable soils supports soil productivity and offers potential as a greenhouse gas sink. However, the benefit of increasing soil organic matter (SOM) could be offset by stimulation of N₂O emissions. How and to what extent the changes of native SOM affect N₂O emissions remains unclear. Here, we conducted experiments with soils from a 15-year field trial with different fertili-zation managements, resulting in contrasting soil organic carbon (SOC) content (7.4−10.7 g C kg⁻¹). We characterized the SOM molecular composition combining biomarkers approach and found that long-term fertilization decreased the nominal oxidation state of carbon and increased SOM molecular complexity, suggesting a declined chemical reactivity and bioavailability. We further investigated how native SOM differences affect N₂O and N₂ emissions using a fully robotized continuous flow system under changing oxygen conditions. Under simulated oxic-anoxic transition-induced N₂O “hot moment” events, soil with the lowest SOC emitted up to 187% more N₂O and 13% less N₂ than higher-SOC soils, with N₂O+N₂ losses 12% higher. Isotopomer analysis revealed a higher contribution of nitrifier denitrification in low-SOC soil during the anaerobic stage, accounting for 30.5%. Further investigation showed that the low-SOC soil had the highest N₂O/(N₂O+N₂) ratio, the lowest (nirK+nirS)/(nosZI+nosZII) ratio, and the lowest SOM molecular Shannon index and Evenness. Our study suggested that long-term fertilization increased native SOM content, which mitigated N₂O emission by promoting N₂O reduction to N₂ and reducing carbon bioavailability. These findings highlight the potential to achieve simultaneous SOC sequestration and N₂O mitigation through optimized field management practices.

Forest plantations play a critical role in restoring ecosystems and mitigating environmental change. While soil fauna communities represent a key driver of belowground ecosystem dynamics, we know little about the structure and functioning of soil macro-food webs in plantation systems and their responses to changes in environmental conditions. In this study, we used data from a 14-year nitrogen addition experiment in larch plantations to investigate how nitrogen addition influenced the diversity and energetic processes of soil macro-food webs in young and mature plantations. We found that low and high nitrogen addition treatments promoted biodiversity (by 23% and 19%), total biomass (56% and 31%), and energy fluxes (42.5% and 39.5%) of soil macro-food webs in young plantations, but they had no significant impacts on soil macro-food webs in mature plantations. The increase in total energy fluxes was partially mediated by nitrogen-induced changes in consumer biomass. Specifically, total energy fluxes increased with the biomass of secondary consumers (e.g., Carabidae), although the biomass of primary consumers (e.g., Lumbricidae) showed a weaker correlation. The age-specific responses may be understood from the varying nitrogen demands between young and mature plantations. Our findings highlight the need to integrate soil food web dynamics into forest management and underscore the necessity of adopting age-specific strategies in nitrogen management in plantations.

Soil susceptibility to acids is commonly assessed by soil pH buffering capacity (pHBC), which is often estimated in an acid buffer curve and considered to be mainly regulated by abiotic factors. This study was conducted to evaluate the sensitivity of soil pH thresholds and range to exogenous acids and examine the effects of biotic and abiotic factors on the acid buffering capacity of the lateritic red soil in a 90-day-period incubation, with addition of biochar or earthworms in either of sterilized or unsterilized soils as three treatment factors. The results showed that soil pH thresholds and range were highly sensitive indicators of soil susceptibility to pH change, compared with pHBC,and that soil microorganisms significantly regulated soil acid buffering capacity (p<0.05). Earthworm activities lowered soil pH by regulating soil microbial communities, while biochar application significantly increased soil pH. However, neither earthworm nor biochar additions substantially change soil acid buffering capacity. Content and fractions of soil dissolved organic carbon were significantly related to soil acid buffering capacity indices. Our results evidence the feasibility of soil pH thresholds and range to indicate soil susceptibility to external acids and assess soil acidification trends and dissolved organic carbon is of high importance in regulating acid buffering capacity.

Priming of soil organic carbon (SOC) mineralization by fresh carbon inputs plays an important role in terrestrial carbon cycling. Despite the attempts to elucidate the mechanisms of soil priming and its response to nitrogen addition, findings remain discordant or even contradictory. We conducted a 30-day incubation experiment using ¹³C-labeled glucose and nitrogen addition on 51 soils (belonging to 15 soil profiles along a temperate forest elevation gradient). Results showed that positive priming peaked in the first four days of incubation, and then declined and remained relatively stable. Early-stage priming was positively correlated with the response of soil microbial biomass and SOC-derived dissolved organic carbon. In the late stage, extracellular enzyme activities increased, and their responses were positively correlated with priming intensity. These results suggested that early-stage priming was mainly driven by the adjustment in soil microbial biomass and the abiotic mediation of mineral-protected organic compounds, and late-stage priming was caused by the increased enzyme activities. Considering the pre-increased copiotrophic bacterial taxa and the minimal nitrogen demand in the late stage, the “stoichiometric decomposition” theory might be responsible for late-stage priming. Nitrogen addition decreased MBC content and soil extracellular enzyme activities, leading to lower SOC mineralization. However, the suppression effects were comparable between the treatments without and with glucose addition. Thus, nitrogen addition had negligible effect on carbon-induced priming intensity. Knowledge about the temporal pattern of soil priming and how its response to nitrogen addition could improve the predictions of global carbon distribution and dynamics.

Soil acidification and magnesium (Mg) deficiency are common problems in tea plantations. The application of biochar and Mg fertilizer has been believed to alleviate soil acidification and improve soil Mg nutrient. However, it is unclear how co-application of biochar and Mg fertilizer improve soil pH, nutrients, and microbial communities, and then enhance tea quality and yield. A 2-year field experiment was conducted to determine the effects of co-application of biochar and Mg on soil properties, microbial community, tea quality and yield in a strongly acidic tea plantation. The results showed that Mg fertilizer with biochar was conducive to alleviate soil acidification, with pH increased from 4.25 to 4.72. Soil total carbon, total nitrogen, available potassium and exchangeable magnesium contents and bacterial community diversity significantly enhanced. In addition, the relative abundance of some potential beneficial bacteria, including Devosia, Bacillariophyta, Gaiella increased. The contents of amino acid and caffeine in tea were significantly increased, and the yield was increased by 39.40% with biochar and Mg fertilizer co-application. In general, biochar and Mg fertilizer co-application is beneficial to soil acidification and the promotion of tea quality and yield, which may be a visionary fertilizer management strategy for strongly acidic tea plantations.

Iron (Fe) binding was an important mechanism for the stabilisation of organic carbon (C) in soils. Slipping of the mattic layer exposes soils and changes the microbial Fe cycling and iron-bound organic carbon (Fe-OC) distribution. The coupled relationships were investigated among Fe, C, and key Fe redox cycling functional genes in the alpine meadows with and without mattic layer in the Qinghai-Tibet Plateau. Compared with the meadow layer and eluvial horizon, SOC content decreased by 17.7 g kg⁻¹ from 39.7−90.3 g kg⁻¹ after the mattic layer slipped, while the Fe-OC% increased from 2.7% and 5.7% to 12.7%. The proportion of the residual Fe fraction (RES-Fe) increased by 5.2% to 7.9%, and the organic matter-bound Fe fraction (OM-Fe) was decreased by 6%, the shift in Fe fractions caused an increase of Fe-OC%. Furthermore, the total average signal intensity of the genes for Fe cycling and redox was increased. The proportion of RES-Fe increased with CirA, feoB, fhuE and ahpC, fnr, narJ, perR, and soxR. The proportion of RED-Fe decreased with the fhuE and narI genes. In conclusion, the shift in Fe redox genes can be expected to increase the RES-Fe fractions, which promoted the accumulation of Fe-OC after the mattic layer slipped.

Microbial food web organisms’ responses to fertilization are influenced by their r/K-strategies. The roles of r/K-strategist microbes and their associated microbivorous nematodes in regulating herbivorous nematodes abundances remain unexplored, especially under different fertilization regimes. Filling this knowledge gap is critical for enhancing agricultural sustainability through optimization of microbial food web. Here, the microbial food web community structure was analyzed in two soil compartments (bulk/rhizosphere soil) from oilseed rape (Brassica napus L.) season to investigate interactions between r/K-strategist microbes and nematodes under organic and inorganic fertilization regimes. Fertilization regimes, rather than soil compartments, predominantly controlled the microbial food web community structure. Under organic fertilization, the relative abundances of r-strategist bacteria and bacterivores of cp-3 guild were greater in the rhizosphere than in the bulk soil. In contrast, under inorganic fertilization regimes, K-strategist bacteria and bacterivores of cp-2 guild were enriched in the rhizosphere versus the bulk soil. Differential r/K-strategist bacteria controlled the microbial food web network, with r- and K-strategist bacteria predominating under organic and inorganic fertilization, respectively. Soil organic carbon from organic fertilization stimulated the growth of r-strategist bacteria, which interacted with bacterivores of cp-3 guild to reduce the relative abundance of herbivores in the rhizosphere soil. Acidification from inorganic fertilization enriched K-strategist bacteria, which interacted with bacterivores cp-2 or cp-3 guilds to suppress herbivores abundances in the rhizosphere soil. Overall, our findings highlight the importance of cross-kingdom interactions among r/K-strategist organisms for the biocontrol of herbivores, providing guidance for harnessing microbial food web to create a healthy plant rhizosphere.

Rock fragments occur commonly in the pedosphere, but the total soil carbon stocks (STC) and total soil nitrogen stocks (STN) they comprise are generally overlooked in soil studies. To accurately eva-luate the impact of erroneous calculation of STC and STN in rock fragments in soil research, we calculated errors in STC and STN by assuming the content of C and N in rock fragments are the same as those in fine soil or assuming them to be zero in a boreal forest watershed ecosystem of northeast China. Generally, the overestimation of STC and STN is 34% and 48% in the surface soil layer of 0−40 cm, respectively, assuming the same values for rock fragments as for fine soil. The underestimation of STC and STN is 16% and 12%, respectively, assuming the values to be zero. We also found that these errors may cause misinterpretations of the effects of slope position and forest type on surface soil STC and STN. Our results highlight the importance of including rock fragments in the material cycle of the pedosphere.

Soil is crucial in the global carbon cycle, while modeling the spatiotemporal changes of soil organic carbon (SOC) is challenging. This study integrates an ensemble model and the spatiotemporal substitution method to predict and map SOC reserves in the surface layer of the Yangtze River Basin under future climate change and land use patterns. We identified total nitrogen, precipitation, altitude, fertilization amount, and land use as the main factors affecting the spatial variability of SOC reserves. Under the scenario of moderate greenhouse gas emissions with some climate mitigation efforts (SSP245), the soil will act as a carbon sink, increasing by 20 Tg C in the 2030s and by 70 Tg C in the 2050s compared to 2010. In contrast, under the scenario of high greenhouse gas emissions with minimal climate mitigation efforts (SSP585), the soil will act as a carbon source, decreasing by 50 Tg C in the 2030s and by 20 Tg C in the 2050s. In the future, SOC reserves will be mainly concentrated in cultivated land and forests, accounting for 70.23% and 72.07%, respectively. These findings provide insights for ecological restoration and land use planning, guiding future carbon sequestration policies in the Yangtze River Basin.

Soil microbes are crucial for agricultural sustainability, yet the genomic evidence of their interactions with soil abiotic and biotic factors remains unclear. Herein, we evaluated the contribution of soil bacteria to soil functions and soybean yields by analyzing 4281 bacterial metagenomic assembled genomes (MAGs) recovered from 113 natural fields across China, integrated 12 enzymic activities and 58 quantified nutrient-cycling genes. Genome-resolved metagenomics revealed the diverse genic traits of keystone bacteria, and their roles in nutrient accumulation, fungal pathogen suppression, and herbicide biodegradation, thereby promoting soybean yields. Soil pH and C/N content were important abiotic factors that determined the dominant life history strategy of keystone communities, thus affecting nutrient-cycling genes abundance. We proposed agricultural management suggestions based on diversified planting aligned with the soil environmental preferences of keystone bacteria, verified in two long-term cropping fields. By recovering 7803 vMAGs, we found the lysogenic virus-host dynamics could promote keystone bacteria adaptation by providing P-acquisition auxiliary metabolic genes (AMGs), leading to ecological advantages. We reported a novel P-acquisition strategy involving phnA-associated phosphonate hydrolysis employed by viruses, significantly influencing keystone-host phosphorus cycling. Overall, our study significantly advances the understanding of keystone bacteria in supporting crop production, with implications for precision microbiome management in agroecosystems.

Tea (Camellia sinensis L.) is a globally cultivated beverage crop, but long-term cultivation may degrade soil health by altering biological properties. We used high-throughput sequencing, phospholipid fatty acid (PLFA) analysis, and the Quantitative Microbial Ecology Chip (QMEC) to compare soil microbial structure and function in tea gardens and adjacent natural forests. Soil pH was significantly lower in tea gardens across all depths compared to natural forests. PLFA analysis showed reduced Gram-positive and Gram-negative bacterial, fungal, and total microbial biomass in tea gardens. High-throughput sequencing revealed distinct bacterial and fungal communities, with tea gardens exhibiting lower alpha-diversity than natural forests. Unique bacterial operational taxonomic units (OTUs) in tea gardens were negatively correlated with key functional genes (e.g., carbon and nitrogen cycling), whereas natural forest OTUs showed positive correlations. Soil pH decline, driven by long-term tea cultivation, was the primary factor shaping these microbial shifts. These findings indicate that extended tea planting impairs soil functions, compromising soil health. The observed deterioration underscores the need for targeted management to address the interplay between land use, soil health, and microbial dynamics, highlighting avenues for future research to enhance soil resilience in tea gardens.

Understanding the dynamics of soil microbial communities and their responses to seasonal fluctuations is crucial for maintaining soil health and predicting the effects of climate change. We investigated seasonal impacts on soil microorganisms in tropical dry forests, Andean forests, and páramos. We characterized bacterial and fungal communities using 16S rRNA and ITS gene metabarcoding, complemented by soil chemical analysis. Proteobacteria, Actinobacteriota, Acidobacteriota, and Chloroflexi dominated bacterial communities. Fungi primarily comprised Ascomycota, Basidiomycota, and Mortierellomycota across all ecosystems. Bacterial Shannon diversity was significantly higher during the dry season at all sites, irrespective of ecosystem type. While fungal communities also showed higher species richness in the dry season, these differences were not statistically significant. Correlations between microbial communities and soil properties were generally stronger in the dry season, particularly in tropical dry forests. These findings suggest bacterial communities are more responsive to seasonal environmental shifts, whereas fungal communities exhibit greater structural stability. The páramo notably exhibited the greatest seasonal variability and highest proportion of unclassified reads, underscoring its ecological sensitivity and need for further research and conservation. This study provides valuable insights into the temporal dynamics of microbes in underexplored ecosystems, which are particularly vulnerable to the effects of climate change.

Arbuscular mycorrhizal (AM) fungi, ubiquitous in diverse habitats including salinized environments, play a pivotal role in ecological processes. Despite advances in understanding their physiological interactions with hosts and soil bioremediation potential, knowledge gaps remain regarding the utilization of stress-adapted indigenous AM fungi. This study investigated AM fungi involved in wild vegetation succession and their hydroponic applicability for plant research. Spores from rhizosphere soils of three vegetation stages in Songnen salinized land were morphologically identified, followed by potting and hydroponic experiments to explore mycorrhizal symbiosis under saline-alkali stress. Specifically, Leymus chinensis, the plant in phase III, was selected as the host, with its rhizosphere soil served as inoculum. Results revealed significant compositional variations across three stages (ANOSIM, p = 0.039). Five key species, including Rhizophagus clarus, were recognized as indicators of initial stages, and three Rhizophagus strains positively correlated with pH and carbonate concentration. In cultivation, AM fungi colonized roots (colonization rate 60%−86.67%) and alleviated salinized stress through morphological improvements, osmotic adjustments, enhanced enzymatic activity, and augmented photosynthesis, regulated by mycorrhizal metabolic pathways (e.g., PWY-7111 and LEU- DEG2-PWY). Mycorrhizal dependency varied by system, with the highest value observed in the box hydroponic setup (MD = 2.15), while tube-based cultivation showed intermediate values closer to potting group. However, sequencing indicated Glomus sensitivity in aquatic conditions, and the box system was more susceptible. These findings provide novel insights into vegetation succession from a mycorrhizal perspective and offer frameworks for AM fungal applications in diverse contexts, facilitating future biological utilization.

Microbial residues carbon (MRC) plays a key role in shaping soil organic carbon (SOC) composition, but there is still no consensus on the pattern of elevational contribution of microbial residues to SOC. Utilizing biomarker amino sugars, this study quantified MRC accumulation and its contribution to SOC sequestration along an elevational gradient. Results showed that MRC concentrations increased significantly with increasing elevation, but their proportionate contribution to SOC showed a paradoxical decrease. MRC accounted for 50.47% of the SOC, including fungal residue carbon (FRC; 38.26%) and bacterial residue carbon (BRC; 12.21%). These results suggest that FRC consistently dominates the contribution of MRC to SOC. Although both FRC and BRC demonstrated similar elevational trends in their absolute accumulation, their accumulation mechanisms were distinctly regulated by environmental factors. BRC accumulation was directly dependent on soil total nitrogen (TN) and soil water content (SWC). In contrast, FRC accumulation was predominantly regulated by SWC alone. The overarching influence of elevation was primarily indirect, mediated through its effects on key soil properties, particularly nitrogen (N) availability and moisture conditions (SWC). This indicates that elevational gradients shape the patterns of microbial residue accumulation and their fractional contribution to SOC largely by modulating N and water availability. These finding provide crucial mechanistic insights into microbial-mediated SOC persistence under changing environmental conditions. The differential controls on fungal versus bacterial residue incorporation underscore the need to account for microbial community composition and their distinct environmental sensitivities in biogeochemical models. Incorporating elevational gradients and their influence on N and moisture dynamics is therefore essential for accurately projecting terrestrial carbon cycling responses to global climate change.

Long-term cattle manure application significantly influences soil phosphorus (P) cycling and associated microbial communities in agricultural systems. However, the mechanisms by which P-transforming microbial communities and their ecological networks mediate P cycling and crop productivity under sustained organic amendment remain poorly understood. This study investigated the effects of 15-year cattle manure application on soil P forms, P-solubilizing microbial communities, and lettuce (Lactuca sativa) yields across three treatments: no fertilization (control), manure-only (M), and combined manure and chemical fertilizer (M+CF). The M+CF treatment significantly enhanced lettuce yields by 77% compared to control and 41% compared to M treatment, while increasing P content by 3.9% and 2.1%, respectively. Metagenomic analysis revealed that manure application increased the diversity (Shannon index: +32.5%) and abundance (+260%) of phoD-harboring bacteria in the M treatment, while M+CF enhanced both diversity (+45.3%) and abundance (+290%) of gcd-harboring bacteria. Proteobacteria (54.2%−68.8%), Acidobacteria (24.2%−33.2%), and Gemmatimonadetes dominated the P-solubilizing bacterial communities across treatments. Network analysis demonstrated that M+CF treatment increased positive microbial correlations by 74.6% compared to control, with enhanced connectivity among keystone taxa, particularly for gcd-harboring microorganisms. Soil enzyme activities showed strong correlations with gene abundances (R² = 0.92 for gcd-ACP; R² = 0.86 for phoD-ALP), suggesting functional linkages between microbial community composition and P transformation processes. Overall, these findings demonstrate that appropriate long-term fertilization strategies can optimize soil P use efficiency, enhance microbial-mediated P transformations, and improve vegetable yields, providing insights for sustainable nutrient management in intensive cropping systems.

Deep learning methods are increasingly vital for species classification across animal species. However, the arthropod classification and detection of deep learning remain underexplored, especially soil arthropods. In this study, we collected 5020 images of collembolan individual as the origin dataset, spanning 6 families, 10 genera, and 51 species in China. By employing the cut-paste method, we created community image datasets of collembolan with diversity gradient to train and evaluate YOLOv8 and Faster R-CNN models for collembolan identification using deep learning methods. Our classification model achieved 83.05% precision and detection models exceeded 97%. YOLOv8 models were the most effective, with a higher top-1 precision all over 80% at the family level, compared to the Faster R-CNN model, which had a minimum precision of 60%. Using community datasets of genera belonging to Isotomidae or Entomobryidae family to train YOLOv8 models, we observed precision ranging from 18.51% to 99.17%, reflecting the changes of detection performance based on Collembola diversity. The YOLOv8 models excelled in identifying genera within Isotomidae family compared to Entomobryidae family. Our study pioneers the application of the YOLOv8 deep learning model for rapid detection and classification of Collembola, while proposing an adaptive training strategy specifically designed for diversity gradient samples. Our research demonstrates the potential of deep learning for rapid, accurate Collembola identification and extends to broader ecological assessments.

Soil respiration is a pivotal component of the global carbon cycle, yet the regional-scale variations in CO₂ emissions across steppe ecosystems, especially under anthropogenic nitrogen deposition, remain poorly understood. Here, we investigated soil CO₂ emissions from 30 sites spanning three major steppe regions (Inner Mongolia Plateau, Loess Plateau, and Tibetan Plateau) to elucidate regional patterns and underlying drivers. Our results show that desert steppes emitted 50%−90% less CO₂ than meadow steppes, primarily due to differences in soil organic carbon (SOC). Simulated nitrogen deposition via nitrate ({\mathrm{N}\mathrm{O}}_3^{-}) addition significantly enhanced CO₂ emissions in nitrogen-limited regions (Loess and Tibetan Plateaus), while nitrogen-rich soils (Inner Mongolia Plateau) showed saturation effects. Random forest and partial least squares path modeling (PLSPM) analyses showed that nitrogen availability, climate, and elevation jointly regulated CO₂ fluxes, with distinct regional pathways. These findings highlight the importance of spatial heterogeneity in regulating carbon emissions and suggest region-specific strategies. Protecting high-carbon steppes and regulating nitrogen inputs are vital for mitigating climate feedbacks in China grasslands.

The Datathon series is a global initiative designed to foster microbial data reuse through community-driven metadata harmonization. By convening researchers from specific geographic regions, each annual Datathon promotes standardized metadata practices, supports sequence data archiving, and enables collaborative reuse of microbial metabarcoding datasets. Following successful events in Latin America (2022–2023) and Africa (2024), upcoming Datathons are scheduled for China (June 1–5, 2026) and the Polar regions (November 2026). Each three-day event combines inspiration, training, and collaboration, and is followed by a year of virtual courses, a data helpdesk, and the creation of consolidated datasets co-authored by data contributors. These efforts address critical gaps in metadata quality and accessibility, especially from underrepresented regions, enhancing the utility of publicly archived microbiome data. By empowering local researchers and promoting interoperability, the Datathons aim to build lasting, regionally grounded networks that contribute to a more inclusive, global understanding of microbial biodiversity. We invite participation and collaboration in these upcoming events.

One of the most critical studies on microbial ecology is to reveal microbial turnover patterns along spatial, temporal, or environmental gradients. In such studies, it is often necessary to select appropriate statistical methods based on the experimental design, especially when considering random effects. However, there are few tools that can be readily applied to such cases. In this study, we present a mecoturn R package, designed to support various statistical analyses of microbial turnover along gradients. Two R6 classes (betaturn and taxaturn) have been developed to investigate the beta diversity of microbial communities and the shift profiles of taxonomic abundances, respectively. In each category, several fundamental functions and approaches were encapsulated to enable data preparation, data conversion and filtering, model fitting and visualization. Each analytical component can be implemented with the consideration of random effects, such as (generalized) linear mixed-effects model. Especially in the analysis of beta diversity, the application of linear mixed-effects model fills a gap in the field of related methodologies. To demonstrate the efficacy of two classes and their diverse methodologies, we employed microbial community datasets of bulk soil, rhizosphere soil, and root endophytes of wheat from varying regions of China to conduct a comparative analysis for different pipelines. We found that reasonable analysis considering the heterogeneity of plants can strengthen the reliability of statistical hypothesis testing. The mecoturn package can be freely installed from CRAN (The Comprehensive R Archive Network) or GitHub repository (accessible at: github.com/ChiLiubio/mecoturn).

Invasive plants pose a major threat to biodiversity and ecosystem stability. However, little is known about the assembly processes and interactions of soil fungal communities under co-invasion of alien plants. This study investigated the assembly processes and co-occurrence networks of different fungal taxa in invaded and non-invaded soils during the co-invasion of four invasive plants. The fungal community was composed of conditionally rare and abundant taxa (CRAT) and conditionally rare taxa (CRT). The alpha diversity of the CRAT was greater than that of the CRT, and plant co-invasion increased the alpha diversity. The network structure of the CRAT was more complex than that of the CRT, and plant co-invasion increased network complexity but decreased stability. Fungal community assembly was driven primarily by deterministic processes, with the relative deterministic effects of the CRAT being stronger than those of the CRT, and plant invasion enhanced the deterministic process. The niche breadth of the CRAT was narrower than that of the CRT, and the niche breadth of fungi was increased by plant co-invasion. The soil pH and the C to P ratio (C/P) were the important driving factors for community construction. The differences between the CRAT and CRT may indicate that they have different filtering mechanisms in response to the external environment. The co-invasion of four Asteraceae plants enhanced nutrient utilization efficiency of the soil microbial community, enabling them to successfully invade even under limited resource conditions.

Straw incorporation and nitrogen amendment in agricultural soils have been shown to increase the diversity of bacterial communities and antibiotic resistance genes (ARGs). However, the effects of straw types and nitrogen amendment levels on ARG dissemination potential lack genetic evidence. Here, we conducted a metagenomic analysis of 24 agricultural soils amended with wheat or maize straw under a nitrogen fertilization gradient (0, 200, 400, and 600 kya). Our results showed that the incorporation of wheat straw in soils significantly increased the abundance of ARGs and mobile genetic elements (MGEs) compared with maize straw. Moreover, genetic evidence of the coexistence of ARGs and MGEs (distance < 5000 bp) demonstrated that the dissemination potential of ARGs was significantly greater in wheat than in maize straw-returning soils. Glycopeptide, fluoroquinolone and diaminopyrimidine resistance were the dominant ARGs and were assigned to Pseudomonadota, Actinobacteria and Firmicutes, which were also the predominant bacteria harboring ARG-MGE. Compared with the absence of nitrogen amendment or at 600 kya, nitrogen amendment at 200 and 400 kya increased the ARG dissemination potential in wheat straw-returning soils. The different correlation patterns between the dominant ARGs and the carbon and nitrogen metabolism genes implied that bacteria involved in degrading organic substrates and nitrogen metabolism may have antibiotic resistance ability. This study suggested that wheat straw incorporation and nitrogen fertilization contribute to the spread of ARGs in agricultural soils and should not be neglected.

Agricultural technologies play a significant role in shaping the landscape of our planet. Their impact will be particularly noticeable in subarctic and Arctic regions, where the consequences are likely to be the most significant. This study examines the functional properties of pristine and agricultural tundra soils (Histosols, Podzols) and ancient borehole sediments (aged 10000 to 35000 years). Using PacBio sequencing, we found that bacterial and fungal diversity varies by soil type and land use. Borehole samples showed bacterial diversity comparable to modern soils but significantly lower fungal diversity. Agricultural activity introduced fungal plant pathogens and reduced bacterial metabolic pathways. Hydrolase activity in tundra soils depended on nutrient availability and microbial diversity. Compared to modern soils, ancient deposits had a 2.3-fold greater diversity of antibiotic resistance genes (ARGs) and resistance mechanisms, despite lower microbial diversity. Environmental factors strongly influenced microbial and resistome diversity in modern forest-tundra soils. In contrast, ancient ARG diversity likely arose from antibiotic-producing species, which enriched ARGs while reducing microbial diversity. In summary, this study advances our understanding of structure-function relationships in cryogenic soil microbiomes, the transformative effects of agropedogenesis on microbial communities and resistomes, and provides critical baseline data for developing sustainable agricultural practices in permafrost-affected regions.

Soil salinity critically restricts plant growth and productivity, especially in degraded arid and semiarid ecosystems. However, the mechanisms by which Achnatherum inebrians adapts to salt stress through modulations of microbial structure and metabolite composition in root exudates remain poorly understood. In this study, we analyzed the effects of salt stress on the diversity and composition of rhizosphere microbial community and root exudates of A. inebrians using high-throughput sequencing and gas chromatography-mass spectrometry (GC-MS). It was found that salt stress significantly reduced plant biomass while increasing total P, available P and NO₃⁻-N contents in the rhizosphere soil. NaCl stress significantly affected the β-diversity and recruited salt-tolerance plant growth promoting rhizosphere bacteria and fungi. GC-MS based metabolomics profiling revealed that salt stress influenced root exudate composition. Key metabolites, such as arbutin, functioned as antioxidants to protect cellular membranes and exhibited strong correlations with microbial community shifts and rhizosphere soil properties. Importantly, exogenous application of 1 mM N-acetyl-D-galactosamine significantly improved A. inebrians fresh weight and K⁺ uptake while reducing Na⁺ accumulation under salt stress. These findings suggest that A. inebrians adapts to salinity stress through root exudate-driven modulation of rhizosphere microbial communities, thereby enhancing soil nutrient availability and salt tolerance of plants. This study provides new insights into plant-microbe interactions in soil salinization and offers potential strategies for enhancing plant resilience in challenging environments.

Integrated Soil-Crop System Management (ISSM) has emerged as an effective approach to improve nutrient cycling and crop yield in China. However, its pH-dependent impact on the nitrogen (N) cycling capacity of soil microbiome remains largely unexplored, despite the critical role of pH in shaping microbial processes. Here, we employed comprehensive metagenomic analysis across multiple agricultural sites in China to investigate the effects of ISSM on the N-cycling potential along soil pH gradients, with Farmlandʼs Practice (FP) as a reference. Actinobacteria and Proteobacteria dominated microbial communities across all treatments and pH conditions, accounting for 88%–90% of the total abundance. Microbial alpha diversity remained consistent across the pH gradient, but exhibited significant negative correlations with soil organic carbon and total N. Soil pH showed a strong positive correlation with the abundance of genes associated with nitrification, but showed a negative correlation with denitrification gene abundance. Particularly, ISSM significantly increased the total abundance of nitrogen-cycling genes in the two most acidic soils (LS, GZL), but not in the less acidic (HEB), near-neutral (BD), and alkaline (TY) soils. Relative to FP, the normalized gene abundances associated with denitrification and NH₄⁺ to Org-N were enriched in LS_ISSM, while those related to DNRA, NO₃⁻ reduction to ammonia, and nitrification were higher in GZL_ISSM. These results highlight the potential of ISSM to modulate microbial nitrogen cycling and point to the importance of site-specific strategies, particularly in acidic soils, for enhancing nitrogen retention.

Feng tian is a unique land-use practice in Chinese agricultural history. It first appeared in the water-rich regions of southern China. People stabilized floating mats formed by wild rice and enriched them with silt, creating a base for cultivating crops such as rice. From the early 7^th century to the mid-to-late 14^th century, feng tian was widely practiced in southern China. However, as polders expanded and reduced lake areas, wild rice habitats gradually diminished. As a result, feng tian declined and was eventually forgotten by later generations. Since the 1980s, Chinese scientists have conducted several studies on floating cultivation. From growing rice on water to developing floating farms and ecological islands, these efforts have revitalized the ancient tradition. Such innovations increase crop yields but also help reduce problems like water eutrophication. From a global agricultural civilization perspective, China’s feng tian stands out among other forms of floating fields for its early origins and distinctive characteristics in construction methods, soil fertility, and crop types. It reflects the remarkable ecological wisdom of ancient Chinese people.

Rice, feeding billions, accumulates both toxic trace elements (Cd, As, Al) and essential micronutrients (Se, Cu, Zn, Mn, Fe), posing food safety challenges. This study explores the interactions among soil properties, bacterial communities, and trace element dynamics across Chinaʼs major paddy soil types. Our analysis showed that strongly acidic soils (pH ≤ 5.5) had higher total As, Al, and Se, while neutral soils (6.5 < pH ≤ 7.5) exhibited greater Cd and Mn bioavailability. Bacterial diversity (alpha and beta) significantly influenced trace element accumulation in rice. Bacterial diversity, soil nutrients, and pH explained a large part of the variance in trace element content in soil (total: 35.24%, 21.69%, and 13.02%; bioavailable: 23.68%, 29.63%, and 11.81%) and rice grains (23.09%, 10.25%, and 17.42%). Co-occurrence networks identified keystone bacterial ASVs, predominantly uncultured lineages (64%), strongly correlated with specific ASVs (R² = 0.53−0.80, P < 0.001). Structural Equation Modeling revealed soil type, pH, and nutrients collectively explained 32% of bacterial alpha diversity and 75% of community composition variation, driving subsequent trace element distribution in soil and rice. Our findings underscore complex soil-microbe-element interactions, emphasizing managing soil pH and bacterial diversity to optimize rice nutrition of essential elements and mitigate risks from toxic elements.

Root-knot nematodes (RKNs) are major soil-borne pests that cause substantial agricultural losses globally. Biological control using microbial antagonists has emerged as a promising, environmentally sustainable, and cost-effective stra-tegy for RKN management. However, the diversity and mechanisms of nematode-antagonistic microbes in the rhizosphereremain insufficiently explored. Here, we systematically profiled the maize rhizosphere microbiome across developmental stages under Meloidogyne incognita infestation and identified microbial taxa with potential nematode-suppressive activity. RKN infection significantly reshaped the rhizosphere with the strongest effects observed during the seedling and jointing stages. Among the taxa enriched in RKN-infected rhizospheres, Streptomyces and Bradyrhizobium emerged as core candidates. Functional assays revealed that Streptomyces, but not Bradyrhizobium, exhibited strong nematode-antagonistic activity, reducing RKN gall formation from 75% to 31% compared to the control treatment. In particular, the effective Streptomyces strain suppressed RKN infection through dual mechanisms: the production of nematicidal metabolites and the activation of the maize jasmonic acid signaling pathway. These findings identify Streptomyces as a central component of the maize rhizosphere microbiome with dual modes of action against RKN, offering new opportunities for microbiome-informed nematode biocontrol and soil health management in sustainable agriculture.