Organic fertilizers significantly influence soil antibiotic resistance genes (ARGs); however, the impact of manure-free organic amendments on ARG dissemination from bulk soil to the rhizosphere remains unclear. This study investigated dissolved organic matter (DOM) composition and ARG profiles in bulk soil and the radish rhizosphere using three manure-free organic fertilizers with varying hydrochar contents (0%BC, 10%BC, and 30%BC). Under non-fertilized conditions, the rhizosphere harbored lower ARG abundances than bulk soil. Organic fertilization significantly elevated rhizospheric ARG enrichment, driven primarily by rhizosphere bacterial community shifts and antibiotic-resistant bacteria (ARB) accumulation rather than direct exogenous ARG inputs. Notably, the 10%BC treatment effectively mitigated this enrichment, maintaining absolute ARG abundances in the rhizosphere that were 69.5% and 72.5% lower than those in the 0%BC and 30%BC treatments, respectively. Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) revealed that 10%BC selectively enriched low-molecular-weight, highly oxidized lignin-like molecules with higher aromaticity. In contrast, 0%BC and 30%BC accumulated higher-molecular-weight, more bioavailable lignins. Network analysis and structural equation modeling (SEM) demonstrated that these chemically distinct lignins exerted contrasting effects: highly oxidized lignins under 10%BC potentially suppressed horizontal gene transfer (HGT) and ARB accumulation, whereas bioavailable lignins under 30%BC promoted them. Overall, fertilizer-derived lignins serve as crucial molecular mediators steering resistome dynamics across the soil-rhizosphere interface, with their oxidation states and molecular weights exhibiting contrasting roles in modulating HGT and ARG dissemination.

Forest management strategies fundamentally alter above‐ground biodiversity; however, their cascading effects on below‐ground ecological processes, particularly the vertical stratification of biodiversity and its linkage to soil ecosystem multifunctionality (SMF), remain poorly understood. To bridge this gap, we employed a multi‐method framework integrating regional‐scale standardized field experiments, amplicon sequencing and soil profiling to dissect biodiversity–function relationships across multitrophic groups during the conversion of 10 subtropical forests from Cunninghamia lanceolata monocultures to mixed plantations ( Phoebe bournei + C. lanceolata ). Monoculture conversion to mixed plantations significantly increased soil multidiversity (biodiversity across multitrophic levels) and SMF ( p < 0.05). Subsoils demonstrated tighter coupling between multiple biodiversities, especially fungi, and function, particularly for organic matter decomposition, nutrient cycling functional potential and antibiotic resistance gene regulation. Furthermore, we revealed the context dependency of such relationships, which varies markedly with organismal size and rarity, and the importance of biodiversity in maintaining multiple dimensions of functioning in soil ecological networks. More importantly, while plant diversity enhancement in mixed plantations supported SMF compared to monocultures, this effect operated through potential trophic‐level‐specific interactions rather than via multidiversity. Synthesis and applications . Our results indicate that the effect of forest conversion on biodiversity–ecosystem function relationships depends on soil depth. These findings expand our understanding of the conventional topsoil‐centric perspective on biodiversity and ecosystem functioning relationships and highlight the need to integrate soil biota into biodiversity conservation frameworks, particularly in subsoils, to achieve the sustainability of subtropical forest management practices.

Fencing to exclude livestock is one of the effective strategies to passively reshape grassland ecosystem function, yet the dynamics of microbial community construction and their functional traits during restoration remain poorly understood. This study systematically sampled from various microhabitats (phyllosphere, litter, soil) within long-term fenced restoration areas, as well as areas with persistent animal grazing in the Songnen Meadow, to investigate the responses of microbial communities and their potential functional genes. Based on a core-satellite taxa framework, we revealed shared changes in microbial community assembly and functional gene regulation. During grassland restoration, the composition of microbial communities in different microhabitats underwent significant divergence, with the relative abundance of rare satellite taxa increasing, while the relative abundance of core microbial taxa decreased. Although environmental pressure effects on assembly diminished after fencing, deterministic selection processes still dominated the assembly of microbial communities, with stronger deterministic effects observed in the phyllosphere and litter than in the soil. Fencing and associated salinization enhanced the abundance of nutrient cycling functional genes (e.g., genes related to C/N/P hydrolysis, immobilization, and mineralization) by reducing microhabitat specificity. Furthermore, the assembly between core and satellite taxa mediated the distribution patterns of microbial potential functional genes through niche competition-balance mechanisms. This study systematically elucidates the response mechanisms of microbial communities and their functional potential following grazing exclusion in grassland ecosystems, providing theoretical support for developing microbial function-based grassland restoration management strategies.

Soil organic phosphorus (P) represents a critical component of terrestrial ecosystems, yet its mineralization dynamics in biologically-active zones like earthworm drilosphere remain poorly understood. This study combined microcosm experiments with in situ imaging to elucidate the mechanisms of phytate mineralization in earthworm drilosphere, 2-mm soil layer surrounding the burrows. Under phytate application, endogeic earthworms increased the available P content by 6.3 % in the drilosphere and elevated phytase activity by 38%. In situ imaging using diffusive gradients in thin-films and soil zymography revealed that phytate application increased the maximum labile P flux by 54% and maximum acid phosphatase activity by 67%. Hotspot analysis showed phytate application expanded labile P hotspots from 3.1 to 4.2% in soil while reducing acid phosphatase hotspots from 4.8 to 4.6%, indicating elevated baseline enzyme activity in the drilosphere. Microbial community analysis revealed that earthworms restructured drilosphere communities, with Gammaproteobacteria and Sordariomycetes emerging as dominant functional taxa. Functional gene expression analysis showed selective upregulation of phytase genes phoD and phyA and downregulation of P-starvation response genes phoU and phoR, boosting microbial P acquisition capacity. These findings demonstrate that earthworms drive phytate mineralization through integrated mechanisms: enzymatic effects, gene regulations, and microbial community restructure. This work helps to understand the spatially-heterogeneous P dynamics, highlighting soil fauna as ecosystem engineers by creating self-reinforcing systems to maximize organic P utilization.

Antimicrobial resistance (AMR) disseminates throughout the soil-plant continuum via complex microbial interactions. Plants shape root- and leaf-associated microbiomes that sustain plant health; however, soil-borne legacies-enriched with antibiotic-producing microbes and resistance genes-govern AMR dynamics across agroecosystems. Using 16S rRNA gene sequencing, shotgun metagenomics, and high-throughput quantitative PCR, we profiled antibiotic resistance genes (ARGs), mobile genetic elements, and virulence factor genes across bulk soil, rhizosphere, phyllosphere, and root endosphere within soil-tomato and soil-strawberry continua. Recurrent bacterial wilt amplified the resistome, particularly polypeptide resistance genes, thereby establishing the rhizosphere as a major hotspot of ARG accumulation. Multidrug-resistant Ralstonia solanacearum (R. solanacearum) strains acted as major ARG reservoirs, harboring resistance determinants on both chromosomes and megaplasmids. Collectively, these findings demonstrate that pathogen-driven restructuring of the plant microbiome accelerates ARG dissemination, establishing soil-borne diseases as critical amplifiers of AMR across agricultural ecosystems.

The management of phosphorus (P) is challenged by the disruption of the soil natural phosphorus cycle, primarily due to over-fertilization. However, less research has been done on how fertilization affects organic acids secreted by roots, which in turn affects bacteria harboring the pqqC and phoD genes. Employing high-throughput sequencing and quantitative PCR, we analyzed the impact of various fertilizer treatments on these bacterial communities. Our research reveals that both organic and inorganic fertilizers alter soil pH, a change that is closely linked to changes in oxalic, gluconic, and succinic acids in the soil. These secretions subsequently modify the composition of pqqC and phoD-harboring bacterial communities, thereby enhancing P solubilization. Our findings suggest that while inorganic fertilizers can increase P-solubilizing bacterial populations by elevating soil pH, organic fertilizers not only boost these bacterial communities but also maintain the P content in the soil, thereby directly supporting P utilization. After the application of organic fertilizers, the content of lactic acid and gluconic acid can not only indirectly affect the abundance of P solubilizing bacteria by increasing soil pH, but also directly increase the effective P content of the soil. Additionally, the introduction of nitrogen (N) and potassium (K) alongside P fertilization appears to fine-tune this microbial-plant interaction, paving the way for more efficient P use in agriculture. Consequently, our research provides sustainable strategies for enhancing agricultural productivity amid P management challenges.

Mixed-species plantations are proven to enhance phosphorus (P) availability in subtropical forest ecosystems. However, the effect of coniferous-broadleaf mixed plantations on soil P cycling dynamics remains poorly understood. Through a long-term field experiment, the study investigated how mixed plantations influence soil P fractions, phoD and pqqC genes, and associated bacterial communities in bulk and rhizosphere soils. Results showed that compared to monocultures, the introduction of broad-leaved trees significantly increased labile P pools, particularly in the rhizosphere. Amplicon-based community profiling of phoD/pqqC genes demonstrated distinct compositional shifts in P-solubilizing bacterial communities across forest types and soil compartments. The pqqC-harboring bacterial communities were more closely related to the P fractions. More importantly, plant properties were important in explaining bulk soil labile P responses, while in rhizosphere soil, labile P was more strongly associated with soil properties, positively affecting labile P. These findings elucidate the complex interplay between tree diversity, microbial functional traits, and soil P transformations. This study underscores the critical role of mixed plantations in promoting microbial-mediated P mobilization and provides valuable insights for designing sustainable forest management strategies to optimize P utilization in subtropical ecosystems.

Municipal solid waste landfills have been recognized as significant reservoirs of antibiotic resistance genes (ARGs). However, the contributions of heavy metals, mobile genetic elements (MGEs), virulence factor genes (VFGs), and bacterial communities to ARG dissemination in surrounding soils remain underexplored. We investigated the spatial distribution of ARGs, MGEs, VFGs, and heavy metals in surface soils within 1 km of a 20-year-old municipal landfill. Cu (32.3 mg/kg) and Cr (70.5 mg/kg) levels were below regulatory thresholds but significantly correlated with ARG abundance (P < 0.05). The relative abundances of ARGs and MGEs fluctuated across sampling points, with no clear decline as distance increased. Structural equation modeling and variation partitioning identified MGEs as the dominant predictors of ARG profiles (standardized coefficient = 0.70, P < 0.001), explaining 26.6 % of the total variance. VFGs contributed 6.4 % and were significantly associated with specific ARG subtypes, suggesting possible co-selection or shared mobility. Bacterial communities indirectly influenced ARG through their association with MGEs. The relative abundance of ARGs peaked at 150 m and 650 m, with quinolone resistance genes being the most abundant. These findings highlight the complex interplay among heavy metals, MGEs, VFGs, and bacterial communities in shaping the dynamics of ARGs, emphasizing the need for integrated monitoring and mitigation strategies in landfill-affected environments.

The widespread cultivation of Cunninghamia lanceolata in China has led to soil degradation and decline in microbial diversity, which have a significant impact on supporting forest ecological services. However, little is known about the long-term consequences from forest management practices on the bacterial functional genes associated with soil nutrient cycling. Here, metagenomic sequencing was used to investigate the soil bacterial functional genes involved in carbon (C), nitrogen (N), and phosphorus (P) cycling in a 16-year pair experiment of pure (C. lanceolata) and mixed plantations (C. lanceolata + Betula luminifera). The results showed that the mixed plantations had much higher soil nutrient content as well as enzyme activity, thereby improving soil multifunctionality (SMF). Forest management practices resulted in differences in the structural and functional composition of soil bacterial communities, such as Chloroflexi, Firmicutes and acid metabolism were enriched in pure plantations, while Acidobacteria, Planctomycetes and amino acid metabolism were enriched in mixed plantations. Compared with monocultures, mixed plantations had higher abundance of genes participated in C degradation, C fixation, methanogenesis, N cycling and P solubilization. The CNP cycling genes also varied with taxon-specific responses to forest management. Forty-seven nearly entire bacterial metagenome-assembled genomes (MAGs) were obtained, in which MAGs enriched in mixed plantations had more functional genes involved in CNP cycling. Notably, acidophilic Acidobacteria played important roles in reduction of Fe(III) and the subsequent release of organic P. In all, our results demonstrated that the use of mixed plantations enhances a number of soil functions via its influence on the abundances of keystone taxa and functional genes, providing a foundation for developing forest management strategies in subtropical regions. In future researches, attention should be paid to the effects of mixed plantations on soil microbial diversity and nutrient cycling across various seasons.

Antibiotic resistance genes (ARGs) are ancient but have become a modern critical threat to health. Gut microbiota, a dynamic reservoir for ARGs, transfer resistance between individuals. Surveillance of the antibiotic resistome in the gut during different host growth phases is critical to understanding the dynamics of the resistome in this ecosystem. Herein, we disentangled the ARG profiles and the dynamic mechanism of ARGs in the egg and adult phases of Tetramorium caespitum. Experimental results showed a remarkable difference in both gut microbiota and gut resistome with the development of T. caespitum. Meta-based metagenomic results of gut microbiota indicated the generalizability of gut antibiotic resistome dynamics during host development. By using Raman spectroscopy and metabolomics, the metabolic phenotype and metabolites indicated that the biotic phase significantly changed lipid metabolism as T. caespitum aged. Lipid metabolites were demonstrated as the main factor driving the enrichment of ARGs in T. caespitum. Cuminaldehyde, the antibacterial lipid metabolite that displayed a remarkable increase in the adult phase, was demonstrated to strongly induce ARG abundance. Our findings show that the gut resistome is host developmental stage-dependent and likely modulated by metabolites, offering novel insights into possible steps to reduce ARG dissemination in the soil food chain.

Cover crops are an increasingly important component of sustainable agriculture, as they can improve soil quality and productivity. However, how cover crops affect soil health and multi-nutrient cycling is not well understood. To address these issues, here, we established a long-term (15-year) field experiment to evaluate the influence of several cover crop treatments (legumes vs. non-legumes vs. mixture crop (legumes + non-legumes)) in a Carya cathayensis plantation on soils. We found that cover crops greatly increased both the soil health index and multi- nutrient cycling in both surface soil (0-20 cm) and subsurface soil (20-40 cm), especially in the mixed cover crop treatment, by enhancing several soil biochemical properties. In addition, cover crops lead to higher carbon (C), nitrogen (N), and phosphorus (P) acquisition enzyme activities. Enzyme stoichiometry analyses showed that microbial activity in the surface soil was mainly P-limited, whereas C-limitation was more pronounced in the subsurface soil. The reduction of C limitation in the cover crops subsurface soil contributes to microbial C turnover, potentially increasing soil C sequestration. Importantly, we found that soil health index was positively correlated with multi-nutrient cycling regardless of soil depth. However, increased microbial metabolic limitation in the subsurface soil detrimental to the maintenance of soil health and multi-nutrient cycling. Furthermore, soil nutrients regulate soil health index and multi-nutrient cycling by influencing microbial resource limitation. Overall, our study illustrates that the use of cover crops, especially cover crop mixtures in the long term can foster soil health and contribute to improved soil multi-nutrient cycling, and can be used as an effective sustainable agricultural management practices.

Soil microbes are critical to the maintenance of forest ecosystem function and stability. Forest diversification, such as monocultures versus mixed forests stands, can strongly influence microbial community patterns and processes, as well as their role in soil ecosystem multifunctionality, such as in subtropical forest ecosystems. However, less is known about these patterns and processes vary with soil depth. Here, we investigated the results of an eight-year forest diversification field experiment comparing the soil ecosystem multifunctionality, bacterial and fungal community assembly, and network patterns in mixed versus monoculture plantations along vertical profiles (0-80 cm depth) in a subtropical region. We found that the introduction of broadleaf trees in coniferous monocultures led to enhanced synergies between multiple functions, thus improving soil multifunctionality. The effects of mixed plantations on the functional potential in top soils were greater than in deep soils, especially for carbon degradation genes (apu, xylA, cex, and glx). Microbial community assembly in the top layer, particularly in mixed plantations, was dominated by stochastic processes, whereas deterministic were more important in the deep layer. Soil microbial network complexity and stability were higher in the top layer of mixed plantations, but in the deep layer was monoculture. Interestingly, the changes in microbial communities and multifunctionality in the top layer were mainly related to variation in nutrients, whereas those in the deep were more influenced by soil moisture. Overall, we reveal positive effects of mixed forest stands on soil microbial characteristics and functionality compared to that of monocultures. Our findings highlighted the importance of enhancing functional diversity through the promotion of tree species diversity, and managers can better develop forest management strategies to promote soil health under global change scenarios.

Phyllosphere microbes are closely linked to plant health and are important for the maintenance of host community stability. Tea plants (Camellia sinensis) can synthesize abundant secondary metabolites (SMs), however, it is unclear how they affect tea plant phyllosphere homeostasis. We investigated the effects of secondary metabolites of two tea plant cultivars (Longjing43 and Zhongcha108) that have different levels of resistance to anthracnose on the composition, function, assembly and network of phyllosphere fungi. We found that the phyllosphere fungal compositions of Longjing43 and Zhongcha108 were distinct, with certain fungal pathogens significantly enriched in the susceptible cultivar Longjing43 (e.g., Fusarium), which had a higher relative abundance of phytopathogenic functional groups. In addition, the phyllosphere fungal community assembly of the resistant cultivar Zhongcha108 with a higher habitat niche breadth was more influenced by stochastic processes. More importantly, the fungal network of Zhongcha108 exhibited higher complexity and stability, indicating a more resilient network structure. Random forest and partial least squares path models revealed that secondary metabolites, fungal community diversity, composition and function essentially determined network stability. (−)-Epigallocatechin-3-gallate (EGCG) and caffeine (CAF) were the most important predictors of phyllosphere fungal network stability in 2018 and 2019, respectively. Rare fungal taxa were particularly important in maintaining phyllosphere homeostasis. Our study suggests that secondary metabolites may mediate phyllosphere fungal homeostasis in tea plants. These findings highlight the importance of secondary metabolites in shaping the phyllosphere fungal community and provide ideas for regulating plant resistance to pathogenic fungi.

Long-term cover crops are an emerging approach for achieving sustainable agriculture by reducing fertilizer use and enhancing soil quality. However, soil microbial communities, multifunctionality (i.e., the ability of soil ecosystems to simultaneously provide and maintain multiple ecological functions), and their relationships in cover crops remain poorly understood, especially in cover crop mixtures. To address these issues, here, we conducted a 15-year field experiment under different cover crop deployments (one legume and one brassica grown in monoculture or in mixture) in Carya cathayensis plantations. We found that cover crops significantly increased soil microbial diversity and multifunctionality, especially in mixtures. The bacterial and fungal compositions was significantly affected by cover crops. Interestingly, some taxa may serve as potential indicator species for nutrient status (i.e., bacterial Subgroup_2, Subgroup_6 and Subgroup_17). Cover crops significantly increased beneficial microbial functions (e.g., nitrogen fixation) but decreased pathogen-related functions (e.g., pathotroph). Bacterial and fungal community assemblages under cover crops were dominated by stochastic processes. Cover crops, especially mixtures, had a higher habitat niche breadth (Bcom). In addition, cover crops have more complex and stable bacterial and fungal networks. Partial least squares path modeling further confirmed that the variations in soil multifunctionality were largely related to nutrient resources. Importantly, the relative abundance of rare microbial taxa was also highly correlated with soil multifunctionality. Overall, our study illustrates that the use of cover crops in the long term can foster soil microbial specific taxa and contribute to improved soil multifunctionality. Our study provides support for the benefits of a legume-brassica mixture over monocultures of either and a theoretical basis for exploring cover crops as an ecological management model.

Nitrous oxide (N2O) is an effective ozone-depleting substance and an important greenhouse gas in the atmosphere. Fertilization is a major factor that dictates agricultural N2O emissions. In this work, as opposed to the commonly-seen highly-soluble nitrogen (N) fertilizers, the feasibility of using struvite as a slow-releasing N-fertilizer and its mechanism for mitigating N2O emissions were investigated. During the 149-d field cultivation of water spinach (Ipomoea Aquatica Forsk), struvite exhibited comparable crop yields, with a 40.8-58.1% N2O reduction compared with commercial fertilizers. In addition, struvite fertilization increased soil bacterial diversity and denitrification genes levels (narG, nirS, nirK, norB and nosZ) effectively, but decreased nitrification genes contents (amoA). By conducting partial least-square path modeling, it was found that the use of struvite would satisfy the soil N control and pH regulation, which altered N-cycling related bacteria and ultimately mitigated N2O emissions. From an economic aspect, using struvite as a N-fertilizer may increase the struvite market price from 50 to 131.7 €/ton. These findings help change the inherent impression that struvite is only suitable as a P-fertilizer, the application of struvite as N-fertilizer could effectively mitigate the agriculture N2O emission and inspire the application of struvite-based P-recovery technologies.

Conversion from pure plantations to mixed plantations can significantly increase forest productivity and provide better ecosystem services, yet there is still a lack effective of assessment methods to determine how this conversion affects belowground biodiversity and ecological functions. We conducted an in-situ experiment to investigate the impacts of forest conversion (Cunninghamia lanceolata pure plantations vs. C. lanceolata-Betula luminifera mixed plantations) on soil multifunctionality, bacterial composition, network patterns and assembly mechanisms in southern subtropical China. The results showed that compared with monoculture plantations, most soil physicochemical properties and enzyme activities were higher in mixed plantations. The mixed plantations increased bacterial α-diversity, and community structure differed between the two forest types. Network analysis showed that the network structure of the mixed plantation was more complex and stable, and contained more keystone taxa. Furthermore, stochastic processes primarily governed the assembly of bacterial communities. Forest conversion increased habitat niche breadth and the importance of stochastic processes. Based on PICRUSt2, the mixed plantations significantly increased soil multifunctionality and bacterial functions (e.g., carbohydrate metabolism and energy metabolism). Moreover, variations in the bacterial community and functionality were highly correlated with soil pH and nutrients. Our study showed that the conversion of monoculture plantations into mixed plantations enhances soil fertility and has more positive benefits. The changes in soil bacterial composition and function were mainly mediated by soil pH and nutrient increases caused by forest conversion, which contributes to assessing the eco-environmental effects of mixed planting in reforestation.

Stimulating compost humification is an important way for carbon sequestration and that in itself is significant, especial under the context of carbon neutrality. However, a longer humification cycle occurs in the traditional composting. Microbial inoculants markedly increase the formation of humus during composting, which attracts extensive attention. Microbial inoculants as a bioaugmentation technology, their perfermances on compost humification are significantly influenced by material nature, microbial species, inoculation dosages, and inoculation methods. So far, the effects of microbial inoculants on compost maturity and microbial diversity are known though previous published reviews, while the overview of their regulatory role in humus formation still be relatively absent. This review innovatively summarized the promotion effects of microbial inoculants on humification process and related biological mechanisms during composting. Lastly, further research on the development of microbial inoculants and the optimization of inoculation methods will promote humification process and produce high quality compost.