A minimal cross-kingdom SynCom promotes plant growth and suppresses wheat crown rot via coordinated rhizosphere microbiome remodeling

Introduction Wheat crown rot (WCR) caused by Fusarium pseudograminearum threatens wheat productivity, and sustainable control strategies are urgently needed. Methods We constructed a minimal cross-kingdom synthetic community (SynCom) consisting of Trichoderma harzianum T19 and Bacillus rugosus PM16, and evaluated its effects on wheat growth and WCR suppression. Rhizosphere microbiome assembly (full-length 16S rRNA/ITS sequencing) and metabolomic shifts were assessed to elucidate mechanisms. Results The SynCom significantly suppressed WCR and promoted wheat growth under pathogen pressure, improving biomass, chlorophyll content, and yield-related traits. SynCom inoculation remodeled the rhizosphere microbiome by enriching beneficial taxa (e.g., Mortierella) and reducing pathogen-associated fungi, and it enhanced rhizosphere enzyme activities and nutrient availability. Metabolomics revealed accumulation of growth-promoting and defense-related metabolites, supporting coordinated microbiome–metabolome regulation. Discussion A minimal cross-kingdom SynCom can establish a disease-suppressive and growth-promoting rhizosphere through coordinated restructuring of microbial communities and metabolites, highlighting its potential as an eco-friendly strategy for WCR management.