Biochar has emerged as a nature-based solution to restore degraded drylands; however, its effects on soil microbiomes in semiarid and desertification-prone environments remain less understood. Here, we evaluated how biochar origin and application influence the structure of bacterial communities in a highly degraded Planosol from the Brazilian Caatinga biome. A controlled experiment was conducted using two biochar types, cashew bagasse-derived biochar (CB) and sewage-sludge biochar (SSB), applied at four doses (5, 10, 20, and 40 Mg ha⁻¹), plus an unamended control (0 Mg ha⁻¹), followed by 90 days of maize cultivation. Biochar changed bacterial community composition, with the emergence of distinct microbial assemblages depending on biochar type and dose. A single low dose (5 Mg ha⁻¹) of biochar was sufficient to enhance bacterial richness and Shannon diversity, while SSB promoted the dominance of stress-tolerant taxa (e.g., Bacillus). Functional prediction and co-occurrence networks revealed that CB promoted functions related to nitrogen cycling and chemoheterotrophy, whereas SSB favored metal-tolerant and hydrocarbon-degrading taxa. Network complexity increased with biochar addition, especially at intermediate SSB doses. Overall, CB promoted more stable ecological responses, while sewage-sludge biochar caused stronger shifts. Our results demonstrate that biochar origin and application rate are critical to microbial restoration, i.e., moderate doses stimulate diversity, ecological specialization, and soil multifunctionality, whereas higher inputs, especially of nutrient- and metal-rich biochars, may compress functional traits. Plant-derived biochars, particularly CB, demonstrated potential for restoring soil bacterial structure and resilience in degraded semiarid landscapes when applied at appropriate rates.

Ecosystem degradation restructures soil microbial interaction networks, yet the mechanistic pathways linking network topology to functional decline remain poorly understood. Here, we investigate how grasslandification, that is, “the conversion of alpine wetland meadows into degraded meadows,” alters cross-domain microbial networks across soil depths and plant root compartments on the Tibetan Plateau. Using integrated network analysis, multivariate modeling, and structural equation models (SEMs), we demonstrate that grasslandification drives a systematic restructuring of network architecture through declining connectivity and environmental filtering via soil chemistry and microbial biomass. These networks progressively lost connectivity and became more modular, indicating fragmentation into isolated functional modules with reduced synergistic interactions. Network robustness declined substantially, rendering degraded communities more susceptible to perturbations. Cross-domain ana-lyses revealed that vertical connectivity between soil layers remained intact despite surface degradation, while plant-associated networks became more sensitive, with disrupted rhizosphere-rhizoplane interactions. Keystone taxa shifted from fungal connectors in pristine meadows to bacterial module hubs in degraded meadows, signifying fundamental changes in community assembly. The SEMs highlighted that grasslandification affected soil multifunctionality mainly through indirect pathways mediated by soil chemistry and microbial biomass, while the direct effects of network topology were comparatively weak. This suggested that network changes represent emergent indicators of ecosystem state transitions rather than principal direct drivers of functional loss. We conclude that microbial network restructuring co-occurs with multifunctionality loss during grasslandification, and that network metrics provide early-warning indicators for ecosystem degradation in alpine regions under environmental stress.

Balancing timber production with biodiversity conservation is challenging. Collembola, a key soil mesofauna group, contribute significantly to forest ecosystem functioning and bioindication. We examined long-term, seasonal effects of four management treatments, gap-cutting (G), clear-cutting (CC), retention tree group (R), and preparation cutting (P), in an 80-year-old oak forest, with untreated controls (C), after five and eight years. Collembola responses differed by ecomorphological group and season. Epigeic densities were lowest in G plots after five years but recovered in the eighth year. Hemiedaphic forms were most abundant in C plots, while G and CC plots remained reduced. Euedaphic Collembola responded in the fifth year, particularly in R during spring, but differences largely disappeared by the eighth year. By year eight, G supported the most diverse and even communities, whereas diversity declined in C and R plots. Seasonal differences were strongest in spring but weakened over time. Our findings highlight Collembola’s capacity to recover after disturbance, supporting their use as indicators of ecological recovery. Treatments with limited canopy opening: G and P maintained community structure and enhanced diversity. As succession advanced, vegetation structure became a stronger driver than soil or seasonal factors. Collembola inform monitoring of forest regeneration and guiding sustainable management.

Since the 19th century, human-induced nitrogen deposition and increased precipitation have become important features of global change. Protists, as consumers, play a crucial role in the microbial food web, yet our understanding of their reactions to nitrogen deposition and increased precipitation remains limited. Through a 13-year field simulation experiment, this study reveals the response patterns of soil protist communities to nitrogen addition and increased precipitation. The results showed that increased precipitation had no significant effect on the α-diversity of the protist community, but significantly influenced the protist community structure. Moreover, soil water content was the key factor driving the protist community structure. In contrast, although the α-diversity and community structure of the protist community remained stable under nitrogen addition, it significantly altered the abundance patterns of key protistan genera, particularly Monocystis and Gonostomum. Notably, increased precipitation alone reduced network complexity and interaction strength, while nitrogen addition effectively alleviated this negative effect. Overall, our findings confirm that the protist community is more sensitive to increased precipitation than to nitrogen addition. Moreover, under the scenarios of nitrogen addition and increased precipitation, species coexistence increased while network stability decreased, highlighting the importance of considering interactive effects in predicting belowground ecosystem functioning.

Empirical data on soil nitrous oxide (N₂O) uptake and gross N₂O emission remain scarce compared to net emission measurements, limiting mechanistic understanding of how land use regulates N₂O source-sink dynamics. Using ¹⁵N₂O pool dilution technology, we quantified gross N₂O emission across five contrasting land uses (upland, vegetable, orchard, grassland, and forest) in the black soil region of northeast China to explore biotic and abiotic drivers of N₂O uptake. Forest and agricultural soils exhibited divergent N₂O uptake: forest soils showed the highest cumulative uptake (17.65 µg N kg^‒1 soil), associated with sandy texture (55.07%), high soil organic carbon (SOC; 29.33 g kg^‒1), and abundant nosZ clade II denitrifiers (4.23×10⁸ copies g^‒1 dry soil). In contrast, long-term cultivated upland soils displayed minimal uptake (8.19 µg N kg^‒1 soil), coinciding with clay-rich texture (25.10%), depleted SOC (8.54 g kg^‒1), and reduced nosZ clade II abundance (0.27×10⁸ copies g^‒1 dry soil). Piecewise structural equation modeling (piecewise SEM) illustrated that the abundance of nosZ clade I and II genes were positively correlated with SOC, with a standardized path coefficient of β = 0.71 (p < 0.001). Both sand content (β = 0.42, p < 0.05) and nosZ gene abundance (β = 0.36, p < 0.05) had positive direct effects on N₂O uptake. Notably, nosZ clade II abundance was 15-fold higher in forest than upland soils and strongly correlated with SOC (R² = 0.68, p<0.05), suggesting this non-denitrifying functional group is associated with N₂O reduction in high-carbon ecosystems. Our results suggest that contrasting land uses mediate divergent N₂O uptake by altering nosZ clade II communities and carbon availability. Specifically, agricultural intensification coincides with SOC depletion and reduced nosZ clade II, potentially weakening N₂O sink function. In contrast, forest preservation maintains high uptake potential. Mitigation strategies could center on restoring SOC and reducing tillage in agricultural soils to boost nosZ clade II-mediated N₂O uptake, and protecting forest ecosystems to maintain their high N₂O sink capacity.

Fire is a recurring disturbance in rotational shifting cultivation (RSC) system, yet the depth-related organization of soil microbial communities in these systems remains poorly understood. This study investigated microbial diversity, functional potential, and antimicrobial resistance (AMR) in relation to soil depth and fire legacy in fire-affected RSC soils of northern Thailand using metagenomic sequencing. Soil samples were collected from three depth layers: the charcoal-mixed surface (CS, 0–2 cm), nutrient-leaching (N, 10–20 cm), and deep (D, 100 cm) horizons. Results revealed significant depth-dependent variation in soil physicochemical properties, microbial diversity, and taxonomic composition. The CS layer exhibited higher nutrient content and metabolic activity but lower Shannon diversity and evenness compared with deeper soils. Actinomycetota and Bacillota dominated surface soils, while Acidobacteriota and Pseudomonadota were enriched in subsoils, indicating a transition from copiotrophic to oligotrophic communities with increasing depth. Functional gene profiles (COG and KEGG) demonstrated strong vertical differentiation: surface soils were enriched in genes for amino acid metabolism, nutrient transport, and energy production, whereas deeper layers showed higher abundances of genes associated with DNA repair, replication, and stress tolerance. Functional genes linked to carbon, nitrogen, sulfur, and phosphorus cycles displayed clear stratification, with surface layers supporting greater biogeochemical activity. AMR genes, particularly those conferring resistance to Rifamycin, Macrolide, and Glycopeptide antibiotics, were most abundant in the D horizon. These patterns were observed in fire-affected RSC soils and are associated with both soil depth and fire legacy, and may reflect microbial responses to environmental stress conditions.

Sedimentary dissolved organic matter (DOM) plays a critical role in carbon cycling in arid inland river systems, yet its spatial variability and associated environmental factors remain poorly understood. Herein, we investigated the spatial heterogeneity of sedimentary DOM along the Niya River Basin (northwestern China) using optical spectroscopy coupled with PARAFAC modeling and multivariate statistical analyses. Results showed that DOM exhibited weak vertical differentiation but pronounced longitudinal heterogeneity along the upstream to downstream gradient. Six fluorescence components were identified, including humic-like and protein-like substances derived from terrestrial inputs and microbial processing. Upstream sediments were dominated by terrestrially derived DOM, whereas midstream and downstream regions reflected combined influences of hydrological transport and microbial transformation. Statistical analyses showed that grain-size parameters, including sand content and mean grain size, together with sediment physicochemical indicators such as TOC, TN, NH₄⁺, pH, and electrical conductivity, were strongly associated with variations in DOM composition. Hydrological conditions may also be indirectly linked to DOM variability through their covariance with sediment properties. Overall, our findings highlight that hydrological conditions and multi-factor associations are closely related to sedimentary DOM variability in arid inland rivers, providing new insights into carbon cycling and ecosystem functioning in water-limited environments.

Labile carbon availability can greatly affect the soil organic carbon (SOC) decomposition through priming effect (PE). However, the effects of temperature on CO₂ emissions, PE, and the underlying mechanisms in forest soils along urban-rural gradient are still unclear, which will induce uncertainties in the prediction of terrestrial-climate feedbacks during urbanization. In this study, we thus performed a 35-day incubation experiment using ¹³C-labeled glucose, with soils collected from urban, suburban, and rural forests to test effects of labile C addition on priming and the temperature sensitivity (Q₁₀ values) of SOC decomposition. Results showed that the cumulative CO₂ emissions were significantly increased with increasing glucose addition and rising temperature, which exhibited a decreasing trend from urban to rural forest soil. CO₂ emissions from native rural soil were obviously lower than that of urban and suburban soils at the end of the incubation regardless of temperature. Cumulative primed C increased with the amount of glucose added, and the values at 25 °C (suburban soil with low glucose addition excepted) were significantly higher than that at 15 °C. The magnitude of the positive priming declined along the urban-rural gradient soils incubated at 15 °C. There were no significant differences in the Q₁₀ values of SOC decomposition during incubation, which were significantly decreased after glucose addition. Redundancy analysis indicated that Gm‒ (18.97%), Gm+/Gm‒ (18.02%), and bacteria (11.28%) accounted for most of the variation in CO₂ emissions at 15 °C. Whereas at 25 °C, the ratios of F/B (23.27%), Actinomycetes (21.07%), and Gm‒ (17.51%) had higher explanatory power, suggesting the different roles of microbial group in SOC decomposition at varied temperature. Our results provide novel insights into forest soil carbon cycling mechanisms that mediating soil-climate feedbacks in the context of rapid urbanization and global warming.

Bacterial wilt, caused by Ralstonia solanacearum (RS), is a major constraint on tomato production worldwide. This study investigated how multi-trophic rhizosphere communities associated with five tomato cultivars (AM, DF, MF, NP, and ZY) respond to RS invasion using sterile plate and greenhouse pot assays. Rhizosphere bacterial and protistan communities were characterized by 16S and 18S rRNA gene amplicon sequencing under control and RS-inoculated conditions. Results showed that both cultivar identity and RS invasion significantly shaped microbial structures and compositions. RS infection exerted a stronger influence on bacterial communities than protists, whereas cultivar identity was the primary driver for protistan shifts. Random forest classification and differential abundance analysis identified specific microbial taxa that effectively discriminated cultivars and infection status. Community assembly analysis further revealed that bacterial assembly shifted from predominantly deterministic to more stochastic processes under pathogen pressure, while protistan assembly remained largely stochastic. Collectively, these results demonstrate that tomato cultivars harbor distinct multi-trophic rhizosphere microbial configurations under pathogen invasion, and highlight the importance of incorporating protists into rhizosphere community frameworks for understanding and potentially enhancing bacterial wilt suppression.

Agricultural soils are major contributors to atmospheric nitrous oxide (N₂O), yet the microbial and environmental determinants of denitrification-driven N₂O emission potential remain poorly understood across contrasting agroecosystems. We combined a regional field survey of paired upland and paddy soils with anaerobic incubations to disentangle how denitrifier abundance, community composition, and soil properties regulate potential N₂O emissions. Results revealed consistently higher abundances of four key denitrifier genes (nirK, nirS, nosZ I, nosZ II) in upland soils, whereas paddy soils, despite lower gene copy numbers, displayed roughly fourfold greater potential N₂O emissions and elevated capacity for both N₂O production and reduction. Across all sites, variation-partitioning and structural equation modeling identified community composition, rather than gene abundance or alpha diversity, as the strongest predictor of potential emissions. Ecosystem-specific analyses revealed that in upland soils, denitrifier abundance explained up to 88% of the variance in potential N₂O flux, whereas in paddy soils neither microbial abundance nor community traits showed significant predictive power, and soil physicochemical factors exerted only weak indirect effects. These results suggest that robust prediction of soil N₂O emissions therefore requires ecosystem-specific frameworks that integrate microbial abundance, community assembly, and key environmental constraints. Such context-aware approaches can advance mechanistic understanding of N₂O fluxes and guide targeted mitigation strategies for upland and flooded agricultural systems.

The intensification of agriculture to meet global food demand has significantly increased greenhouse gas (GHG) emissions, mainly as a result of overuse of chemical fertilizers (CF). Green manure (GM) has emerged as a promising climate-smart strategy for improving soil fertility and mitigating environmental impact. This review provides current knowledge on the role of GM in regulating GHG emissions, focusing on the interplay between GM decomposition dynamics, biological nitrogen fixation (BNF), and integrated nutrient management. We analyzed how GM characteristics, particularly the carbon-to-nitrogen (C:N) ratio, and environmental factors influence the processes driving GHG fluxes. The review highlights the synergistic application of GM with CF is a central pathway highlighted as a key mechanism for synchronizing N release with crop demand, thereby improving N use efficiency and reducing N₂O emissions by 20%–50% compared to CF alone. Furthermore, we explored the enzymatic mechanism by which BNF influences the soil N cycle and potentially mitigates N₂O flux. However, significant variability in emissions persists owing to regional differences in climate, soil texture and fertility, and management practices. Major research gaps that require attention include the need for long-term field data and refined predictive models that explicitly capture climate–soil–management interactions and multi-gas trade-offs. Tailored GM-CF integration strategies, supported by advanced monitoring and precision agriculture, are essential for achieving climate-resilient agroecosystems that balance productivity and emission reduction.

Invasive earthworms can exacerbate soil N leaching and N₂O emissions, particularly in disturbed habitats with high populations. While earthworms and arbuscular mycorrhizal fungi (AMF) can synergistically influence plant N uptake, it remains unclear whether AMF inoculation can mitigate earthworm-induced N loss. We conducted a two-way factorial microcosm experiment to evaluate the effects of the pantropical earthworm Pontoscolex corethrurus and AMF (Rhizophagus intraradices) on soil N leaching and N₂O fluxes. We further employed ¹⁵NH₄¹⁵NO₃ labeling and qPCR to assess associated changes in nitrification and denitrification processes. P. corethrurus increased both N leaching and N₂O emissions, whereas AMF inoculation significantly reduced N₂O emissions and NH₄⁺ leaching. The ¹⁵N₂O patterns matched total N₂O fluxes, suggesting emissions primarily derived from nitrification and denitrification. Abundance of nitrification- (amoA, amoB,) and denitrification-related genes (nirK, nirS, nosZ) showed positive correlations with soil NH₄⁺ concentration and N₂O emissions, indicating that microbial functional potential is closely linked to inorganic N availability and N₂O emissions. AMF reduced these gene abundances, particularly in the rhizosphere, consistent with decreased NH₄⁺ leaching and N₂O emissions. These findings highlight the ecosystem risks posed by P. corethrurus and suggest AMF inoculation represents a promising strategy to mitigate earthworm-induced N₂O emissions in tropical and subtropical regions.

Soil health in rice paddies is a key determinant of sustainable agriculture, as it directly affects both crop productivity and long-term soil quality. This study investigated the effects of different organic amendments on soil health in subtropical rice fields in Zhejiang Province, China, using the Soil Health Index (SHI) as an integrative assessment. Results showed that organic amendments significantly enhanced soil health, particularly in the treatment combining conventional fertilization with biochar-based organic fertilizer (BF), which achieved the highest SHI. Improvements were mainly associated with increases in soil pH, nutrient availability, and microbial biomass. Carbon- and phosphorus-related indicators, along with microbial biomass, contributed most to SHI improvement, suggesting that microbial-mediated C and P cycling play pivotal roles in soil health enhancement. Metagenomic analyses revealed enhanced microbial functions related to carbon fixation and phosphorus mobilization under organic treatments. Organic amendments enhanced microbial carbon and phosphorus cycling by increasing the relative abundance of key genes related to CO₂ fixation such as K14465, methane oxidation such as frmB, and phosphorus mobilization such as aepW, thereby reinforcing carbon and phosphorus transformation processes essential for soil health. Key microbial families, including Nitrosopumilaceae and Xanthobacteraceae, were enriched, indicating greater functional specialization and nutrient transformation capacity. Overall, the synergistic application of biochar- and bio-organic fertilizers improved soil structure, nutrient cycling, and microbial functionality. These findings provide valuable insights for optimizing organic fertilization strategies to sustain soil productivity and ecological stability in paddy ecosystems.

Microbial extracellular enzymes are key indicators of soil biogeochemical functioning, yet their sensitivity to storage conditions remains unclear and limits cross-study comparability. We evaluated how three storage conditions (−20 °C, air-drying, and freeze-drying) affect hydrolytic and oxidative enzyme activities across forest soils spanning an acidic-to-alkaline pH gradient in China (Acrisols, Luvisols, and Calcisols). Storage at −20 °C consistently preserved higher hydrolytic activities, whereas air-drying and freeze-drying caused significant reductions across all soils. Conversely, oxidative enzymes showed soil-specific responses: −20 °C was optimal for Acrisols; both −20 °C and freeze-drying outperformed air-drying in Luvisols; while storage conditions little affected Calcisols. Multivariate analysis revealed that, although both enzyme types were influenced by key soil properties (e.g., pH, carbon, nutrients), their primary drivers differed. Hydrolytic activities were predominantly governed by storage conditions, whereas oxidative activities were mainly regulated by climatic factors (temperature and precipitation). These findings underscore the necessity of tailoring storage protocols to specific soil and enzyme types. Standardizing and explicitly reporting these conditions will improve the reproducibility of enzyme assays, providing a robust methodological foundation for future ecological research.

Fertilization is a widely adopted agricultural practice with profound impacts on soil microbial communities. However, the global response of soil bacteriome to different fertilization strategies remains inadequately characterized. Here, we conducted an integrated analysis on over 2900 raw bacterial amplicon sequencing samples from 82 studies worldwide to assess how microbial communities respond to inorganic (IF), organic (OF), and combined (IFOF) fertilization across environmental gradients. Results demonstrate that the effects of fertilization on community structure and diversity depend strongly on local soil properties, although OF maintained stable alpha-diversity across varying pH and experimental durations. Notably, meta-cooccurrence networks revealed that organic amendments (OF and IFOF) promoted microbial networks with higher complexity, modularity, and stability compared to IF and unfertilized controls, suggesting strengthened ecological resilience. The IFOF network contained several highly connected keystone taxa including Acidothermus, Devosia, and Bradyrhizobium, which exhibited sensitivity to gradients in soil nutrients, pH, and climate variables. Random forest models further confirmed the ecological importance of these taxa, achieving high accuracy (>90%) in classifying fertilization treatments. Moreover, threshold indicator taxon analysis quantified responses of these keystone taxa to environmental gradients, identifying optimal organic fertilization amendment rates to support keystone taxa (e.g., Bradyrhizobium abundance peaked at 15 tons per hectare per year). This study provides the first global-scale integration of sequencing data with meta-network analysis, revealing how long-term fertilization influences soil microbial communities and associations.

Although straw return enhances soil carbon accumulation, its net climatic effect depends on the balance between carbon stabilization and greenhouse gas emissions, which is influenced by the management practice. This study investigated the impact of four straw return methods: straw removal (SR), granulated straw return (GSR), chopped straw return (CSR), and in-situ burning (ISB) on soil organic carbon fraction dynamics and greenhouse gas emissions in a coastal double-season rice paddy. Changes insoil carbon fractions, dissolved organic matter composition andgreenhouse gas fluxes were analyzed. Results showed that GSR progressively increased the stable mineral-associated carbon pool, achieving the lowest global warming potential in the following full growing season and suggesting a favorable trajectory for long-term sequestration. CSR enhanced carbon association with crystalline iron oxides but also stimulated rapid decomposition, leading to sustained higher emissions. ISB minimized short-term emissions but failed to contribute to stable carbon accrual. Multivariate analysis identified soil pH, Fe mineralogy and microbial cellulolytic activity as key regulators of the carbon–climate trade-off. Our findings demonstrate that straw processing determines its environmental fate, and that practices which promote slow substrate release and mineral stabilization are more effective in reconciling soil carbon accumulation with climate change mitigation in paddies.

As early as the 12^th century, Chinese farmers already started to intentionally scoop out river silt as fertilizer for agricultural production and apply river silt in farmland where fruit trees, mulberry trees and lowland rice were planted. After the 17^th century, lan heni 罱河泥 [scooping out river silt for fertilization] gradually became an important farming activity in Jiangnan [the southern part of the lower reaches of the Yangtze River], while river silt also turned into one of the four most essential types of fertilizers in the region. Lanni 罱泥, an alias of lan heni, was often carried out with the help of specialized farm implements, and in late fall, winter and spring or on rainy days so as to be staggered from other farming activities. Only after being sun-dried could the river silt scooped out be available for use. In the 1980s, along with the use of chemical fertilizers, river silt gradually lost its value as fertilizer, while lan heni was included in lists of intangible cultural heritage as an endangered folklore. In recent years, along with the continuous advancement of China’s ecological civilization, the traditional technique lan heni began to rejuvenate in some areas as it brings many co-benefits, such as improving aquatic ecosystem health. However, an important issue worth discussing is still how the role of river silt as fertilizer can be restored so that it can be used to improve the quality of the aquatic ecosystems.

The synergistic mechanisms by which potassium high-efficiency (KHE) vegetable soybeans coordinate root exudation and microbial recruitment to enhance potasium absorption under low-K stress remain unclear. Integrating hydroponic and pot experiments, this study analyzed root organic acid exudation, soil potassium availability, microbiome structure, and isolated K-solubilizing bacteria using KHE and K low-efficiency (KLE) varieties. Results showed that under low-K stress, KHE plants exhibited a resilient exudation profile, notably surging malonic acid secretion. This trait mechanistically explains the effective soil K activation in pot experiments, indicated by significant rhizosphere acidification positively correlating with total K depletion. Concurrently, the KHE variety maintained a stable rhizosphere microbiome, characterized by the selective enrichment of specific bacterial (Paenibacillus, Rhodanobacter) and fungal (Penicillium, Aspergillus, Chaetomium) genera. To validate this, we isolated Paenibacillus strains BK1 and BK2 from the KHE rhizosphere. BK2 demonstrated potash feldspar activation (5.7% solubilization efficiency) via medium acidification, significantly enhancing plant growth and K accumulation. Overall, this research reveals a dual mechanism for efficient K utilization: chemical weathering driven by targeted organic acid exudation and the synergistic enrichment of specific rhizosphere microbes.