Intercropping-mediated enrichment of core microbiome enhances suppression of Verticillium wilt in cotton.

BACKGROUND: Verticillium wilt, caused by Verticillium dahliae Kleb., is a devastating soilborne disease threatening global cotton production. Intercropping is a sustainable agricultural practice known to suppress soilborne diseases, yet the microbiome-mediated mechanisms underlying its efficacy against Verticillium wilt remain poorly understood. RESULTS: A three-year field trial (2019-2021) showed that intercropping cotton with mustard significantly reduced Verticillium wilt severity (32.11-39.2%), increased yield (13.88-23.22%), and lowered soil microsclerotia density. Intercropping reshaped soil microbial communities and enriched a core set of beneficial taxa compared to monocropping, generating more complex and cooperative rhizosphere networks during flowering and boll stage. We then constructed an intercropping-enriched synthetic community (IC-SynCom) from the enriched core microbiotas with multiple beneficial traits; this consortium, comprising Bacillus altitudinis strain CRB-021, Lysobacter firmicutimachus strain CRB-253, Rhizobium soli strain CRB-314, Enterobacter hormaechei strain CRB-070, and Pantoea sp. strain CRB-006, achieved the highest control efficacy at 72.83 ± 1.31%, promoted cotton growth, and outperformed single-strain inoculants. qRT-PCR further showed that IC-SynCom activated systemic plant defenses by the upregulation of key defense-related genes, including phenylalanine ammonia-lyase (GhPAL), cinnamate 4-hydroxylase (GhC4H1), pathogenesis-related protein 10 (GhPR10), peroxidase (GhPOD), and β-1,3-glucanase (Ghβ-1,3-glucanase), which are involved in salicylic acid signaling and lignin biosynthesis. CONCLUSIONS: Our findings demonstrate that intercropping enhances soil's capacity to suppress Verticillium wilt by reshaping root-associated microbiomes. A core consortium of intercropping-enriched beneficial microbes (IC-SynCom) effectively suppresses Verticillium wilt through direct antagonism and activation of plant immunity. These results highlight the potential of microbiome-based strategies for sustainable management of soilborne diseases.