Distinct rhizosphere microbiomes and metabolomes mediate Fusarium crown rot resistance across wheat cultivars

Soil-borne Fusarium crown rot (FCR) poses a major challenge to wheat production. Plants can recruit beneficial microbes through a "cry-for-help" strategy in response to pathogen attack, yet how different wheat genotypes modulate this response remains unclear. In FCR-affected wheat fields, we systematically investigated the interactions among wheat, pathogens, rhizosphere microbes, and metabolites using a combination of phenotypic assessment, molecular detection, and microbiome and metabolome profiling. Our results showed that wheat genotype and plant health jointly shaped rhizosphere microbial communities and metabolite profiles. Beneficial Bacillus species were key taxa in healthy rhizosphere communities, whereas the susceptible cultivar additionally relied on Pseudomonas to maintain plant health. In vitro assays and a pot experiment confirmed that these microbes antagonize the pathogen and enhance wheat performance, thereby alleviating FCR. Furthermore, the tolerant cultivar exhibited more complex rhizosphere microbial co-occurrence networks and harbored conserved taxa, such as Devosia. Microbe-metabolite interaction networks revealed strong associations between beneficial rhizosphere microbes (e.g., Bacillus and Pseudomonas) and specific metabolites, such as tritrans-heptacis-undecaprenyl phosphate, PE(14:1(9Z)/20:5(5Z,8Z,11Z,14Z,17Z)), and 1,2-Dioleoyl-sn-glycerol-3-phosphate. Collectively, our results provide novel evidence that rhizosphere metabolite-mediated plant-microbe interactions contribute to the suppression of soil-borne diseases.