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.