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.

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.