Drivers and modulation strategies of crop rhizosphere microbiome

Abstract

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.

Graphical abstract

Keywords

plant microbiome / plant-soil-microbe interactions / agricultural management practice / abiotic stressors / global climate change / synthetic microbial communities / sustainable agriculture

Highlight

	● Soil properties and host genotypes are core factors shaping rhizosphere microbiome.
	● Climate change and human activity markedly affect rhizosphere microbial community.
	● Optimizing rhizosphere microbiome contributes to sustainable agriculture.
	● Multi-omics and SynComs are future research hotspots of rhizosphere microbiome.

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