Soil fungi constitute multiple functional communities essential for organic matter decomposition. Cover crops stabilize sustainable crop production by introducing exogenous organic matter to mitigate chemical fertilization-induced soil degradation. But responses of wheat growth to soil characteristics and fungal functionality communities under combined impacts of cover crop and nitrogen fertilization were not obviously elucidated. Herein, the long-term interactive experiments of cover crop and nitrogen fertilization revealed that cover crop increased soil organic carbon by an average of 18% and increased soil mineral-associated organic carbon by 13%, while fertilization increased them by an average of 8% and 7%, respectively. Legume cover crop reduced soil bulk density by 7%-8%, but increased soil water content by 8%-31% among distinct fertilizations. Soil fungal functional communities were mainly composed of the saprotroph communities, their diversity generally had the highest values in the middle fertilization in each cover crop. Meanwhile, cover crop and fertilization singly and interactively had stronger effects on the pathotroph and symbiotroph community compositions, respectively. Stochastic processes governed the saprotroph and pathotroph communities, while deterministic processes intensified along with elevated fertilization. Networks of soil fungal functionality communities were composed of specialized modules consistently containing diversified trophic mode phylotypes. Overall, wheat growth indicated by wheat biomass and grain yield was enhanced by optimal fertilization rate in legume cover crop. Moreover, wheat growth was primarily regulated by the direct effects of pathotroph community composition and the total effects of fertilization and soil characteristics based on partial least squares path modeling. These findings suggest that optimal combinations of cover crop and nitrogen fertilization can benefit crop production through regulating soil characteristics and fungal functionality communities, which likely serves as a valuable reference for cover crop agricultural system to balance the management of cover crop and nitrogen fertilization.

Microbial dormancy is a fundamental ecological strategy that governs soil microbial persistence, functional stability, and the capacity of microbial communities to respond to environmental change. However, how agricultural management practices influence the soil microbial dormancy remains insufficiently understood. To address this knowledge gap, we conducted a long-term field experiment involving three nitrogen fertilization levels and four cover crop treatments to evaluate their effects on soil microbial dormancy. Random forest and variance partitioning analyses were used to identify the key environmental drivers of microbial dormancy. Our results demonstrated that that nitrogen fertilization reduced the soil microbial dormant fraction, with a significant decrease observed under N120 treatment (120 kg N ha−1), where dormancy declined by 7.3

Soil microbial heterotrophic respiration (HR), a crucial carbon flux to the atmosphere, is closely related to microbial community traits. However, community level microbial traits associated with such process remain understudied across forest biomes. Here, we accessed microbial traits influence on HR across a forest climatic gradient in China. We found that microbial HR showed distinct differentiation along an environmental gradient, which were highest in temperate forest Maoer mountain (1067.95 mg C kg−1) and lowest in tropical forest Xishuangbanna (178.83 mg C kg−1). At the community level, microbial HR was tightly related to microbial biomass and composition, and genomic traits. Notably, the HR was positively correlated with guanine-cytosine base pair content, but negatively correlated to the average 16S rRNA copy number and the average genome size of microbes (P < 0.05). Moreover, among the forests, soil organic carbon and alkyl-C/O-alkyl-C ratio were the crucial variables in explaining HR, which attributed to their effects on microbial composition and genomic traits. Overall, microbial genomic traits at the community level play an important role in understanding HR. Our findings elucidate new evidence on the mechanisms driving soil carbon fluxes and enhance predictions of soil carbon responses to future climatic change.

Particulate organic carbon (POC) and mineral-associated organic carbon (MAOC) are two operationally defined fractions frequently used in studies related to soil organic carbon (SOC) dynamics. However, the changes and governing mechanisms of these fractions, particularly along a restoration chronosequence, remain poorly understood. Here, we investigated changes in SOC fractions, soil properties, and microbial communities across a restoration chronosequence (1, 5, 7, 13, and 20 years) of alpine meadows using a space-for-time substitution approach on the Qinghai-Tibet Plateau. We quantified the contributions of biotic and abiotic drivers using Spearman correlation analysis, linear regression and random forest analysis. The results revealed a unimodal pattern in SOC, POC, and MAOC contents, peaking at 7, 5, and 7 years, respectively, with no further increase thereafter. Restoration duration strongly shaped microbial community structure and observed species richness, but had no significant effect on Shannon index and Pielou index. Random forest analysis identified soil water content (SWC) and total nitrogen (TN) as the primary predictors of SOC. The microbial community composition dominated the variation in POC while enzyme activity was the key driver of MAOC. Our findings highlight that soil carbon accumulation during alpine meadow restoration is a nonlinear process with a temporal threshold, and POC and MAOC are regulated by distinct biotic and abiotic mechanisms. This study provides a theoretical basis for understanding carbon sequestration mechanisms during alpine meadow restoration and developing sustainable grassland management strategies.

Dormancy, as a microbial survival strategy, plays a crucial role in sustaining microbial diversity. However, the large-scale distribution patterns of microbial dormancy and drivers remain poorly understood. Here, we analyzed 591 soil samples from 197 field sites across China, spanning deserts, croplands, grasslands, and forests, to quantify the proportion of dormant microbial cells (Dormancy%). On average, 95.48% of soil microbial cells were dormant, with the lowest Dormancy% in forests (93.84%) and the highest in deserts (96.81%). This regulation followed a regular mechanism: soil water-holding capacity and beta-1,4-glucosidase activity acted as immediate triggers, while mineral-associated organic carbon, dissolved organic carbon and microbial biomass carbon indirectly governed the process. Overall, this study provides evidence at the China scale for the dominance of dormant microorganisms in terrestrial ecosystems and reveals the environmental regulatory mechanism of dormancy, highlighting its ecological importance for maintaining microbial diversity and ecosystem stability.

Abstract Microbial necromass carbon (MNC) is an important component of the soil carbon sink in alpine meadows on the Qinghai-Tibet Plateau. However, we still know little about how soil properties and the microbial community regulate MNC during ecosystem restoration. This study examined the temporal dynamics of MNC components (bacterial and fungal) and microbial network stability across a 20-year restoration chronosequence (1, 5, 7, 13, and 20 years). The contents of bacterial necromass carbon (BNC), fungal (FNC), and total MNC increased rapidly during the early restoration phase, peaking at 7 years, followed by a decline in later stages. At this peak stage, bacterial network stability reached a relatively high level, in contrast to significantly lower fungal network stability. Random Forest modeling identified soil water content, particulate organic carbon, soil organic carbon, and total nitrogen as dominant abiotic predictors of MNC. Biotically, fungal network stability was a key determinant, showing a significant negative correlation with MNC accumulation. This pattern was linked to the dynamics of ectomycorrhizal fungi. Collectively, these results reveal that MNC sequestration is jointly regulated by soil resource availability and fungal community stability, providing new insights into the microbial mechanisms underlying soil carbon recovery in restored alpine ecosystems.

Management practices, including cover cropping and nitrogen fertilization, are widely recognized to influence agricultural soil multifunctionality (SMF). However, how their effects vary across different management durations, and the underlying mechanisms, remain poorly understood. To address this, we conducted a seven-year field experiment on the Loess Plateau, comparing the effects of cover cropping and nitrogen fertilization on SMF under short-term (4-year) and long-term (7-year) management. Our results show that long-term management significantly enhanced SMF by 57.5% compared to short-term management (p < 0.05). This increase in SMF was associated with a significant reduction in both bacterial and fungal diversity under long-term management (p < 0.05). At the same time, shifts in microbial community composition were observed, including increased relative abundances of keystone taxa such as Ascomycota and Actinobacteria. Collectively, our results suggest that long-term management enhances SMF relative to short-term management despite reduced microbial diversity, indicating that factors beyond diversity, such as shifts in community composition, may contribute to the maintenance of multifunctionality. This insight provides a practical foundation for designing sustainable agricultural soil management strategies aimed at optimizing soil health and ecosystem functioning.

Despite the widely recognized importance of grassland restoration for soil multifunctionality (SMF), its temporal dynamics along the restoration chronosequence and the relative contributions of bacterial and fungal diversity to SMF remain poorly understood, particularly in alpine grasslands. Here, we examined SMF along an alpine grassland restoration chronosequence (1, 5, 7, 13, and 20 years) on the Qinghai-Tibet Plateau. We found that SMF exhibited a pronounced non-linear trajectory, increasing by 39.13% from year 1 to year 7, subsequently declining by 50% and 46.88% at years 13 and 20, respectively, relative to the peak at year 7. Fungal richness varied markedly across the restoration chronosequence, peaking in year 5 with a 16.03% increase relative to year 1, and was positively associated with SMF, whereas bacterial richness showed no significant relationship. Structural equation modeling further confirmed that, along with soil moisture, fungal richness was significantly associated with SMF. Together, our findings highlight fungal diversity as a key driver of SMF during alpine grassland restoration and improve process-based predictions of alpine grassland functioning under ongoing climate change.

Long-term diversified crop rotations alter the soil organic carbon (SOC) content. However, the mechanisms underlying C fraction regulation by soil functional genes and associated microbial communities remain poorly understood. The present study explored the effects of long-term crop rotation on soil C fraction content, soil microbial C-degradation genes, and associated microbial communities in the Loess Plateau. Compared to continuous winter wheat, corn-wheat-millet and alfalfa-potato-wheat rotations significantly increased SOC content by 31.1 % and 47.8 %, respectively. Moreover, these crop rotation regimes led to different degrees of enhancement in soil C fractions, including particulate organic C, potential C mineralization and microbial biomass C. Compared to bare land, continuous winter wheat increased the abundance of C-degradation functional genes by 11.4 %, whereas corn-wheat-millet rotation enhanced it by 15.7 %, pea-wheat-millet rotation by 18.2 %, and alfalfa-potato-wheat rotation by 19.1 %. Bulk density and soil total nitrogen were significantly correlated with soil microbial C-degradation genes and associated microbial communities. The abundance of soil C-degradation genes and microbial diversity was positively correlated with soil C fractions. Moreover, functional genes responsible for lignin and cellulose degradation, including ligB and bglX, were significantly positively correlated with the soil C fraction content. Our findings indicate that long-term diversified crop rotations, such as corn-wheat-millet or alfalfa-potato-wheat, enhance soil C sequestration and soil quality, and provide practical guidance for sustainable agricultural management.

Balancing food security and climate change mitigation has been a global priority, yet viable pathways to achieve both simultaneously remain elusive. The dual potential of cover crops (CCs) to increase soil organic carbon (SOC) and succeeding crop yield was evaluated by meta-analysis of 1396 paired observations globally. Outcomes were Win-Win (+, +), Trade-off 1 (+, -) Trade-off 2 (-, +), and Lose-Lose (-, -) in 68.9%, 16.4%, 9.0%, and 5.7% of the observations, respectively. The synthetic intensity for the responses of SOC and crop yield to CCs was controlled by CC biomass, tillage practice, establishment years, and nitrogen rate. Global optimal window to maximize co-benefits included CC biomass < 7.65 t ha -1 , duration > 4 years, adoption of legume CCs and conservation tillage, and reduced N input. Specifically, CCs had a large Win-Win potential in rice systems and arid regions with low inherent SOC content. Emphasizing context-specific CC management strategies that promote Win-Win and minimize Trade-off or Lose-Lose conditions can reconcile historical contradictions over yield–SOC trade-offs and support the dual goal of enhancing climate mitigation and food security.

Soil organic carbon (SOC) comprises particulate (POC) and mineral-associated organic carbon (MAOC), which differ in formation, stabilization, and loss mechanisms. While the current global distribution of POC and MAOC is characterized, their vulnerability under future climate scenarios remains unclear. Using 3284 topsoil (0-30 cm) observations from six continents, we identify high-latitude soils as global hotspots of SOC vulnerability under shared socioeconomic pathway scenarios (SSP126, SSP245, and SSP585). Under a high-emission scenario (SSP585), high-latitude soils are projected to lose substantial POC by 2100, accounting for about 81 ± 10% of total SOC losses. These declines are driven by the high proportion of SOC stored as POC (fPOC) and its high temperature sensitivity. We show that fPOC is a robust indicator of SOC vulnerability to climate change. Globally, the projected POC decline corresponds to a cumulative carbon dioxide (CO2) release of 81.34 Pg CO2-equivalent by 2100, highlighting the importance of preserving POC to mitigate climate feedbacks.

Cover crops are primarily decomposed and transformed by conservative soil core microbial community and associated functional genes, thereby supplying soil nutrients and subsequent crop utilization. However, dynamics and interactions of soil core microbial community and nitrogen-cycling functional genes in the wheat rhizosphere throughout growth stage under cover crop remain poorly understood. Herein, the extent to which grass and legume cover crops enhanced soil nutrients and microbial necromass varied considerably at distinct wheat growth stages. Alpha diversity of soil core bacterial and fungal communities exhibited contrasting temporal patterns over the wheat growth stage. Wheat growth stage significantly determined the compositions of soil core microbial community and nitrogen-cycling functional genes. The resistance of these communities and functional genes declined initially at the seedling stage but eventually enhanced by the maturity stage under cover crop. Moreover, potential interaction networks between soil core taxa and nitrogen-cycling functional genes were more complicated and stable at the jointing and maturity stages compare to the seedling and heading stages. Specifically, soil water content and total carbon, bacterial and microbial necromass were deemed as dominant factors. Wheat growth was significantly promoted after seedling by cover crops and was collectively influenced by the networks and compositions of soil core microbial community and nitrogen-cycling functional genes under effects of these dominant factors. Overall, it is essential to account for the temporal dynamics and networks of rhizosphere soil core microbial community and nitrogen-cycling functional genes during the decomposition of different cover crops throughout wheat growth stages.

Nitrogen (N) mineralization is a complex microbial-driven process that controls the supply of N for plants and microbes. The relative contribution of different microbial N-cycling species/genes to the variation in N mineralization rate (NMR) across contrasting forest biomes was unclear. Here, we investigate the linkages between soil metagenomes and N mineralization rates across 10 contrasting forest biomes (covering temperate, subtropical, and tropical forests) along a 3425 km north–south forest in China. We found that the NMR was higher in subtropical forests, and the variation in NMR can be explained by climate and soil environments, particularly for soil substrate NH4+. Similar to NMR, microbial N-cycling genes/species were also higher in subtropical forests, suggesting that the higher microbial N-cycling traits in warm regions may drive higher NMR. We also quantified the contribution of microbial N-cycling gene pathways to NMR across forest biomes and found that the microbial N-denitrification pathway (genes like norZ, narG, nirK, and norB) and nitrification pathway (genes like nxr) explained more variation in NMR than other pathways, such as N ammonification. Collectively, our work demonstrates the importance of microbial N-cycling traits to explain soil N mineralization rates across forest biomes and suggests that this information can be used to help improve the management of the N cycle in forests across biomes.

Cover cropping is an effective agricultural management strategy for enhancing soil organic carbon (SOC) sequestration and mitigating climate change. However, the contribution of different cover crop species to individual carbon (C) fractions in soil remains unclear. An in-situ decomposition experiment using C-13-labeled residues of soybean (SB) or sudangrass (SG), along with a control with no residue (CK), was designed to explore the dynamics of residue decomposition, distribution of cover crop-derived C into aggregate-protected and -unprotected C, and the sequestration mechanisms of these fractions. The aggregate-protected C included intra-aggregate particulate organic C (iPOC) and mineral-associated organic C (MAOC), and aggregate-unprotected C included coarse particulate organic C (cPOC) and free fine particulate organic C (fPOC). The amount and rate of cover crop residue C mineralization were greater in SB than in SG across all wheat-growing stages. The SB increased large macroaggregate (>2 mm) compared to SG during the early wheat growth stages. The aggregate-protected C fractions were greater in SB and SG than CK at the pre-sowing, tillering, and heading stages. The C-13 labeling indicated that C sequestration occurred primarily as aggregate-protected C, predominantly as MAOC. The recovery efficiencies of cover crop-derived C into soil C fractions fell below 0 % at green-up and jointing stages. At maturity stage, the cumulative C recovery rate of cover crop-derived C into SOC was greater in SB (16.3 %) than in SG (8.76 %). Correlation analysis indicated that cover cropping promoted SOC sequestration primarily and directly by increasing the aggregate-protected C. Structural equation model analysis suggested that SG sequestered C into soils primarily by increasing cPOC and iPOC, In contrast, SB sequestered C by increasing cPOC, iPOC, and MAOC. This study elucidates the dynamic effects of cover cropping on soil C during wheat growth and the distinct C sequestration mechanisms in legume and non-legume systems.

Soil microbes are the planet's most abundant, diverse, and functionally vital organisms, yet only a small portion of these microbes actively drive soil processes. While resource availability is known to influence microbial physiological traits under multiple soil processes, how aboveground resource input structures the spatial distribution of the soil active microbiome remains virtually unknown. Here, we report the results from a continental standardized soil sampling at 601 sites across major biomes in China. We measured the proportion of the active microbiome (SAM%) using 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) staining by flow cytometry and simultaneously evaluated their main environmental drivers. On average, < 2% of all microbes constitute the active soil microbiome. Forests supported the most active soil microbiomes (> 2%), while cropland harbored the lowest (< 1%). Aboveground productivity, peaking in tropical warmer and wetter regions, was the major environmental factor explaining variation in the active soil microbiome. Our study suggests that a less productive planet may result in drastic reductions in the active soil microbiome with consequences for supporting ecosystem function and biogeochemical cycles under climate change.

Soil viruses control the dynamics and metabolism of their hosts, strongly modifying carbon and nutrient cycling as well as soil biochemistry. Warming specifically affects viruses and their hosts, but the consequences of climate warming on the virus-host interactions, and for soil functions, remain unknown. We investigated the viral communities and the virus-host interactions under warming in situ based on a forest soil column translocation experiment. The abundance of the Petitvirales (DNA viruses) decreased by 25%, but that of the Durnavirales and Martellivirales (RNA viruses) strongly increased. The DNA viral lysogenic signals and RNA viral lytic proteins increased in soil, indicating the opposite lifestyles of DNA and RNA viruses. Correspondingly, the DNA abundance of viral hosts increased, whereas RNA viral hosts remained stable. The high DNA viruses/host ratios reflect very intensive interactions between the virus and host, leading to the drop in the host functions (such as carbon metabolism processes and nitrogen and phosphorus cycles) up to 43%. In contrast, the functions of the hosts for RNA viruses increased by up to 48%. The fundamental difference in behaviour of DNA and RNA viruses is that the former use mainly lysogenic, whereas the latter lytic, lifestyles and thus control the responses of host communities to warming. Conclusively, the opposite response of DNA and RNA viruses to warming in abundance, lifestyle, and interactions with hosts leads to divergent changes in nutrient fluxes in soil. These new perspectives on viral regulations of microbial communities and their function under soil warming reveal the undeniable role of viruses in microbial ecology.

Forest soil carbon (C) accumulates predominantly from the decomposition of plant litter, with most plant-derived C being processed by soil microbes. However, the microbial mechanisms associated with C decomposition in forests across biomes remain elusive. Using metagenomic sequencing, we explored the topsoil microbial functional group of decomposer microbial carbohydrate-active enzymes (CAZyme) and studied the C decomposition of plant- and microbial-derived components in forests across biomes from tropical to temperate regions. The results showed that the composition of soil microbial CAZyme families, which degrade plant- and microbial-derived components, significantly varied from warmer to colder forest biomes. Soils with higher annual temperatures and lower organic matter (OM) recalcitrance (indicated by Alky-C/O-alkyl-C: A/O) in subtropical/tropical forests supported higher proportions of CAZyme genes fundamental for the decomposition of complex plant and fungal derived biomass. In contrast, soils with lower annual temperatures and higher OM recalcitrance (e.g., A/O, organic carbon, microbial biomass) in cold temperate forests exhibited higher proportions of CAZyme genes for the degradation of bacterial-derived peptidoglycan. Such trends of microbial CAZyme families were largely explained by the relative abundance of bacterial dominant phylum members (i.e., Proteobacteria, Actinobacteria, Acidobacteria, and Bacteroidetes). Collectively, our study demonstrated the importance of functional microbiome responsible for the decomposition of plant and microbial inputs, providing a solid mechanism to understand the often-reported responses of soil organic matter decomposition and C sequestration to warming. These results are integral to understanding the contribution of soil microbiome to C fluxes under on-going climate change.

Surface mulching with crop straw or plastic film has a great potential in soil carbon (C) sequestration. A 10-yr field experiment on spring maize was conducted in the Loess Plateau of China to compare the impacts of crop straw (SM) and plastic film (FM) mulching on soil microbial C-degradation genes using a metagenomic approach. Compared to those with no mulching (CK), soil C fractions significantly increased under SM while decreased under FM. However, the relative abundance of total microbial C-degradation genes did not change under SM, but was significantly lower by 3.9 % under FM. Specifically, the relative abundance of genes involved in stable C degradation did not vary with mulching, while those in labile C degradation decreased by 14.0 % (p < 0.05) under FM compared to CK. At the gene group level, FM decreased the relative abundances of genes involved in the degradation of monosaccharides, disaccharides, polysaccharides, hemicellulose, cellulose, and chitin by 5.9 %, 9.2 %, 3.3 %, 8.6 %, 8.1 %, and 25.4 % (p < 0.05), respectively, compared to CK. The random forest analysis indicated that the PYG was the predominant gene affecting microbial biomass C, followed by araB, K07046, E3.1.1.11; pectinesterase, and bglB. Genes involved in soil C-degradation were more abundant in Proteobacteria and Actinobacteria than in other phyla. Mantel test showed that soil pH and C:P ratio emerged as the key factors influencing microbial C-degradation genes. Therefore, soil C-degradation potential would be inhibited by long-term mulching practices, especially with plastic film. The combined application of crop straw and plastic film mulching may accomplish the dual objectives of enhancing soil C storage and lowering Cdegradation potential in dryland cropping systems.

Soil potential pathogenic microbiota exacerbate the environment and human health through invading normal tissues of the human body, but their distributions and interactions across functional domains in urban greenspaces are poorly understood. Herein, we collected soil samples from parkland and residential land to explore the relationships between soil health and the dynamics of soil potential pathogenic microbiota. Soil organic matter-associated properties, soil multifunctionality and health were significantly about 30 % higher in parkland, but soil stoichiometry including C/N, C/P, and C/N/P were lower in parkland. Alpha diversity of soil pathogenic bacterial communities was higher than for fungal communities in residential land. The relative abundances of the dominant genera Mycobacterium, Metarhizium, and Cladosporium that may cause chronic lung and gastrointestinal diseases in humans were greater for residential land. Potential connected networks including soil pathogenic bacterial and fungal phylotypes were more complicated and stable in residential land, based on higher total and positive connections and higher robustness. Meanwhile, bacterial phylotypes belonging to the genus Shigella were identified as keystone species in parkland network, all of which were chronic pathogens. Soil total nitrogen and phosphorus as dominant properties had greater total effects on soil health in parkland and residential land, respectively. In general, soil health was mostly affected by soil multifunctionality in parkland, but was subject to higher explanation in residential land. These findings underscore intimate relationships between soil health and the dynamics of soil potential pathogenic microbiota in urban greenspaces, which has implications for human daily outdoor routines and urban habitability.

Soil microbes, particularly active microbes, play a crucial role in conserving soil carbon under climate change, especially in forest ecosystems, constituting over 50