Soil-borne diseases pose a severe threat to global agricultural production and food security. Traditional chemical control methods face significant challenges, including environmental pressure, pathogen resistance, and food safety concerns. The rhizosphere microbial community, often termed the plant’s ‘second genome’, plays a pivotal role in maintaining plant health and defending against pathogen invasion. Recent advances in multi-omics technologies, synthetic microbial communities (SynComs) construction, and rhizosphere metabolomics have significantly advanced our understanding of the mechanisms by which rhizosphere microbiomes suppress soil-borne diseases. This review systematically summarizes the following: 1. key drivers of rhizosphere microbial community assembly, particularly plant “cry for help” signaling; 2. core beneficial microbial taxa and their disease-suppressive mechanisms; 3. the critical role of microbial interaction networks; 4. microbiome-based management strategies and their application progress; and 5. current challenges and future research directions. Compared with previous reviews that separately discussed rhizosphere microbiota, disease-suppressive soils, synthetic microbial communities (SynComs), or prebiotics, this review uniquely integrates multiple levels of regulation, from plant genetic determinants (‘M genes’) and root exudate-mediated ‘crying for help’ to microbiome engineering (SynComs and prebiotics) and cross-kingdom interactions (bacteria–fungi–protists–phages). A central conceptual axis of ‘M genes → microbiome engineering → breeding’ is proposed, bridging plant genetics, microbial ecology, and crop improvement for durable disease suppression. Ultimately, this work aims to provide a theoretical foundation for developing efficient and sustainable green control technologies against soil-borne diseases.
Liu et al. (2026) studied this question.