ABSTRACTSclerotinia sclerotiorum, a widespread pathogen of dicotyledons, can grow endophytically in wheat, providing protection againstFusariumhead blight and stripe rust and enhancing wheat yield. In this study, we found that wheat seed treatment with strain DT-8, infected withS. sclerotiorumhypovirulence-associated DNA virus 1 (SsHADV-1) and used as a “plant vaccine” for brassica protection, could significantly increase the diversity of the fungal and bacterial community in rhizosphere soil, while the diversity of the fungal community was obviously decreased in the wheat root. Interestingly, the relative abundance of potential plant growth-promoting rhizobacteria (PGPR) and biocontrol agents increased significantly in the DT-8-treated wheat rhizosphere soil. These data might be responsible for wheat growth promotion and disease resistance. These results may provide novel insights for understanding the interaction between the schizotrophic microorganism and the microbiota of plant roots and rhizosphere, screening and utilizing beneficial microorganisms, and further reducing chemical pesticide utilization and increasing crop productivity.IMPORTANCEFungal pathogens are seriously threatening food security and natural ecosystems; efficient and environmentally friendly control methods are essential to increase world crop production.S. sclerotiorum, a widespread pathogen of dicotyledons, can grow endophytically in wheat, providing protection againstFusariumhead blight and stripe rust and enhancing wheat yield. In this study, we discovered thatS. sclerotiorumtreatment increased the diversity of the soil fungal and bacterial community in rhizosphere soil, while the diversity of the fungal community was obviously decreased in the wheat root. More importantly, the relative abundance of potential PGPR and bio-control agents increased significantly in theS. sclerotiorum-treated wheat rhizosphere soil. The importance of this work is that schizotrophicS. sclerotiorumpromotes wheat growth and enhances resistance against fungal diseases via changes in the structure of the root and rhizosphere microbiome.