Soil microbiomes play a pivotal role in supporting plant growth, enhancing nutrient cycling, and mitigating environmental stresses, thereby offering an ecologically sustainable solution for agricultural production. In recent years, multifunctional microbial inoculants—particularly composite formulations comprising multiple beneficial bacteria and fungi—have attracted broad attention for their ability to synergistically promote plant health, suppress pathogens, and remediate degraded soils. This review systematically examines the conceptual basis, formulation technologies, and application strategies of composite microbial inoculants, with special emphases on synthetic microbial communities (SynComs) design, biochar-based carriers, and microbial loading techniques. Furthermore, we highlight the central role of arbuscular mycorrhizal fungi (AMF) as a keystone functional group in enhancing nutrient uptake and stress tolerance. Distinct from existing reviews that primarily focus on microbial community assembly or individual functional traits, this review integrates AMF-centered SynCom design with an engineering-oriented perspective, emphasizing the full workflow from strain selection and community assembly to formulation, carrier optimization, and field application. In recognition of the major challenges in performance consistency, formulation stability, and strain compatibility of composite microbial inoculants under variable agroecological conditions, we propose a roadmap for intelligent formulation design, field-performance optimization, and regulatory standardization. Overall, multifunctional composite microbial inoculants hold transformative potential for green and climate-resilient agriculture, provided that interdisciplinary integration and systems engineering guide their future development.

Harnessing the rhizosphere microbiome to engineer resilient agricultural systems is pivotal for ensuring global food security under accelerating climate change. Achieving this goal, however, demands a unified framework to disentangle the multi-layered drivers of microbial community assembly. Here, we synthesize recent advances into a hierarchical conceptual framework. We delineate how foundational soil physicochemical properties establish a baseline environmental filter. Upon this foundation, the host genotype exerts powerful endogenous control, actively shaping microbial communities through its root architecture, exudate chemistry, and rhizosphere redox dynamics. This co-evolved equilibrium is subsequently modulated by exogenous forces, notably agricultural management practices and climatic perturbations. Moving beyond isolated-factor approaches, we highlight their synergistic interactions as a central yet underexplored frontier. Building on this integrated understanding, we evaluate emerging strategies for microbiome engineering, from soil and host-targeted approaches to the design of sustainable agronomic practices. Finally, we propose future research directions that leverage multi-omics and synthetic communities to shift from descriptive ecology toward predictive design, thereby advancing a sustainable agricultural future. This review synthesizes a novel framework for understanding the assembly and regulation of rhizosphere microbiomes, facilitating their integration into sustainable agroecosystems.

Soil microorganisms are the biological engines of terrestrial ecosystems. The development of molecular technologies has overturned the ‘everything is everywhere’ paradigm, revealing that at the strain-level, soil microbes exhibit distinct biogeographical patterns governed by environmental selection, dispersal, diversification, and drift. In this review, we first summarize the major progresses in soil microbial biogeography. Then, we discuss the potential limitations, including the constraints of space-for-time substitution, the disconnect between statistical correlation and ecological causality, and the inherent challenges in mapping and scaling microbial distributions. Finally, we propose a strategic framework centered on three directions: (1) Enhancing prediction, by integrating microbial traits into Earth System Models to forecast the responses of soil microbes and their associated functions to global change; (2) Deciphering mechanisms, by bridging multi-omics approaches with rigorous experimental validation to establish causality between structure and function; and (3) Achieving manipulation, by leveraging synthetic ecology and core taxa to engineer microbiomes for practical application in One Health initiatives. Moving from pattern description to mechanistic understanding and functional manipulation will enable soil microbial biogeography to provide actionable solutions for sustainability in a rapidly changing world.

Plant–soil feedbacks (PSFs) are fundamental processes linking plant performance to soil biotic and abiotic dynamics, thereby shaping ecosystem structure, productivity, and stability. Root exudates have emerged as central regulators of PSFs, functioning not only as nutrient sources but also as signaling molecules that orchestrate rhizosphere microbial assembly and soil processes. However, a mechanistic synthesis of how diverse exudate classes drive PSFs across ecological contexts remains lacking. Here, we synthesize recent advances in understanding how root exudates mediate PSFs through selective microbial recruitment, nutrient mobilization, and activation of plant defense pathways. We emphasize the dynamic and context-dependent nature of exudation, which varies with plant species, developmental stage, and environmental stress, enabling plants to strategically reprogram their rhizosphere microbiome. Particular attention is given to organic acids, phenolic compounds, and benzoxazinoids as key chemical regulators integrating above- and belowground signaling to suppress soil-borne pathogens and plant-parasitic nematodes. Finally, we discuss ecological and agricultural implications, identify critical knowledge gaps, and propose future research directions for harnessing exudate-mediated PSFs to improve soil health and crop resilience under global environmental change.

Soil ecological research in China has accelerated rapidly over the past two decades, with the historically understudied field of soil animal ecology making particularly notable progress. Through a comprehensive bibliometric analysis and literature review, we synthesize these advancements. We document a remarkable increase from 725 to 1094 in global annual publications, driven by national monitoring networks and a shift from taxonomic inventories to functional ecology. Notably, China’s share of global publications in soil fauna research surged from less than 5% in 2006 to 27% in 2025, emerging as a driving force in advancing the field. Key advancements include elucidating the role of soil fauna as bioindicators of climate change and land-use intensification, quantifying their engineering effects on carbon sequestration and nutrient cycling at continental scales, and uncovering the mechanisms by which multi-trophic interactions regulate ecosystem multifunctionality. Despite these gains, critical gaps remain in scaling mechanistic understanding from microcosms to fields and in predicting responses under interacting global changes. We propose a future research agenda emphasizing technological innovation, coordinated networks, and theory integration to position China at the forefront of developing soil biodiversity-based solutions for global sustainability challenges.

Microbial dehalogenation governs the fate of persistent pollutants frequently detected globally-organohalides (OHs) in soils, and is a critical process for mitigating threats to ecosystem health. However, conventional research focused on rare specialist bacteria cannot account for the widespread, low-level OH turnover observed globally. This review applies a potential evolutionary ecology framework, reframing dehalogenation as a community-wide trait that originated from versatile ancestral enzymes and disseminated via horizontal gene transfer (HGT). This evolutionary history highlights the important ecological role of abundant non-specialists, such as methanogens, which capable of perform dehalogenation at certain condition as a secondary metabolic function. These organisms face metabolic trade-offs, allocating resources between primary growth and secondary dehalogenation. This resource partitioning links OH fate to major biogeochemical cycles, challenging traditional remediation approaches for complex environmental media such as soil. To advance the field, future research must quantify in situ fluxes using multi-omics and stable isotope techniques, and develop predictive models to elucidate these trade-offs. Ultimately, we advocate a shift from simple bioaugmentation to predictive ecological engineering—managing soils by manipulating environmental conditions and designing synthetic microbial consortia. This strategy aims to enhance polluted soil resilience and multifunctionality, aligning remediation with the broader goals of sustainable soil health.

Organic-mineral fertilizer combination is a core sustainable agricultural strategy, but its regulatory mechanisms on soil quality and ecosystem multifunctionality (EMF) remain unclear. This study examined 20% nitrogen reduction (RF) and 20% mineral fertilizer substitution with chicken (FF) or cow manure (MF) in north China plain croplands (2022−2023). Compared to conventional fertilization (CF), RF maintained baseline levels of most soilbiochemical characteristics; however, it reduced C-acquisition enzyme activity and EMF in the topsoil (0−20 cm). In contrast, FF and MF increased the soil quality index (SQI, 19%−26%) and EMF (43%−62%) in the topsoil, with positive effects extending to the subsoil (20−40 cm). This was driven by the stimulation of C-, N-, and P-acquisition enzyme activities, alleviated microbial phosphorus limitation, enhanced bacterial diversity, and improved wheat yield by up to 15% relative to CF (p < 0.05). Partial least squares path modeling revealed that soil enzyme activities had a direct, positive effect on both EMF and yield. Soil properties had a direct positive effect on yield (p < 0.001) and directly and indirectly affected EMF by influencing enzyme activities (p < 0.001). This study demonstrates organic substitution enhances soil quality, bacterial diversity, boosts EMF, and increases wheat yield, providing an effective approach for sustainable agriculture production.

In drylands, biocrusts function as essential components of the nitrogen cycle and display pronounced sensitivity to external nitrogen inputs. Episodic rainfall events can mobilize dry-deposited nitrogen into short-term pulse that influences nitrogen retention and transformation. However, the effects of short-term nitrogen pulse, commonly encountered in drylands, on biocrust nitrogen dynamics remain poorly understood. This study simulates rainfall-driven short-term nitrogen pulse to examine how varying pulse concentrations impact biocrusts nitrogen fixation, ammonia oxidation, and overall nitrogen balance under conditions of intensified nitrogen deposition after a 13-year nitrogen addition experiment in Gurbantunggut Desert. The nitrogen pulse sharply disrupted biocrusts' nitrogen cycling. Both nitrogen fixation and ammonia oxidation rates declined precipitously immediately after the pulse. However, within 14–21 days, these rates rebounded to or even surpassed pre-pulse levels. This pattern reflects the biocrusts' acute sensitivity to nitrogen perturbations, as well as their ecological resilience. Over 21 days, cumulative nitrogen fixation decreased by 47%–72% relative to the control, indicating suppression by nitrogen addition; in contrast, cumulative ammonia oxidation increased by 39%–91% but stabilized at moderate to high nitrogen inputs (⩾1.0 g N m^–2 yr^–1, N1.0), revealing a saturation threshold. Moreover, the risk of nitrogen loss increased with higher nitrogen concentrations and plateaued at approximately an 88% elevation under ⩾N1.0, indicating that high nitrogen inputs exacerbate biocrusts nitrogen-loss vulnerabi-lity. These findings elucidate the impacts of acute nitrogen pulse on nitrogen dynamics in biocrusts, highlighting that amid escalating global nitrogen deposition, precise evaluation of nitrogen balance in drylands must integrate pulse effects, biocrusts nitrogen-carrying capacity, input modes, concentrations, durations, and interactions with environmental conditions.

Elevated atmospheric nitrogen (N) and phosphorus (P) depositions are progressively modifying the dynamics of soil dissolved organic matter (DOM) in terrestrial ecosystems. However, the long-term effects on DOM quantity and quality remain poorly understood, especially regarding indirect regulation by plant inputs and microbial decomposition. We conducted a 12-year nutrient addition experiment with N and P in an alpine grassland on the Tibetan Plateau to investigate changes in soil organic matter (SOM), DOM quantity, and quality. SOM was derived from soil organic carbon using an elemental analyzer, while the DOM quantity was determined from dissolved organic carbon using a total organic carbon analyzer. DOM quality was assessed using UV-Visible and 3D-EEM fluorescence spectroscopy. Using linear mixed-effects models, we evaluated the effects of N and P additions on SOM, DOM quantity, and qua-lity. We found that P addition reduced SOM by 16.8%, an effect likely mediated by decreases in root biomass and soil moisture. These changes reduced organic matter inputs and likely destabilized soil aggregates, driving the observed SOM decline. Conversely, N addition altered DOM quality by shifting the balance from plant-derived inputs to microbial signatures. Specifically, increased soil electrical conductivity and inhibited cellobiohydrolase activity reduced the availability of plant-derived cellobiose, thereby favoring the accumulation of microbial-derived signatures. This shift toward a microbially-processed DOM pool was supported by increases of 7.4% and 3.1% in the biological and fluorescence indices, respectively. These contrasting pathways highlight that accurate prediction of carbon persistence requires distinguishing between nutrient-specific controls on DOM quantity versus quality.

Soil microbial functional genes play a crucial role in regulating carbon (C) cycling in mountain ecosystems. Elevation gradients integrate concurrent changes in temperature, moisture, vegetation, and soil properties, providing a natural framework to examine how microbial carbon-cycling functions respond to environmental change. However, studies investigating the responses of soil microbial functional genes related to C cycling along elevation gradients remain limited. In this study, we examined the composition, diversity, and assembly mechanisms of carbohydrate-active enzymes (CAZymes) and other C cycle-related functional genes across different elevations in Changbai Mountain. Our results indicate that the relative abundance of CAZymes and C cycle genes increased overall with the elevation gradient. β-diversity analysis revealed that fungal communities were most sensitive to elevation changes. Furthermore, the species replacement of CAZymes and C cycle genes was strongly regulated by elevation. The community assembly of CAZymes and C cycle genes was predominantly driven by stochastic processes. Importantly, microbial diversity emerged as the strongest predictor of CAZymes and C cycle gene diversity. This result highlights the central role of microbial community structure in regulating soil carbon functional potential along elevation gradients. Overall, our findings provide new insights into the biogeographic patterns and assembly mechanisms of soil C functional genes in mountain ecosystems, thereby enhancing our understanding of C dynamics and providing guidance for organic carbon management under climate change.