A Minimal Cross-Kingdom SynCom Promotes Plant Growth and Suppresses Wheat Crown Rot via Coordinated Rhizosphere Microbiome Remodeling

Qian Zhou¹Yuzhou Wang¹Tingting Zhou²Kaidiriye Yusupu¹DAN GAO³Huixin Zhao⁴Liufeng Ma^1*

• ¹Kashgar University, Kashgar, China
• ²Xinjiang Uygur Autonomous Region Academy of Animal Science, Urumqi, China
• ³China Academy of Chinese Medical Sciences, Beijing, China
• ⁴Xinjiang Normal University, Urumqi, China

Wheat crown rot (WCR), predominantly caused by Fusarium pseudograminearum, is a destructive fungal disease that severely restricts global wheat production, underscoring the urgent need for sustainable and effective management strategies. Here, we constructed a minimal cross-kingdom synthetic microbial community (SynCom) consisting of Trichoderma harzianum T19 and Bacillus rugosus PM16 and evaluated its biocontrol efficacy and mechanistic basis under non-sterile soil conditions. SynCom inoculation substantially suppressed WCR, reducing disease severity by 70.97%, while concurrently promoting plant performance—doubling shoot and root biomass, elevating chlorophyll content by 38%, and increasing thousand-kernel weight by 12.74%. Multiomics analyses revealed that SynCom treatment reshaped the rhizosphere microbiome by enhancing both bacterial and fungal diversity, enriching beneficial taxa such as Mortierella, and suppressing pathogenic Fusarium. In addition, SynCom application improved soil nutrient availability, boosted soil enzyme activities, strengthened plant antioxidant defenses, and increased the accumulation of defense-related metabolites, including flavonoids. Collectively, these findings demonstrate that a minimal yet rationally designed SynCom can establish a disease-suppressive rhizosphere, enhance plant physiological resilience, and ultimately deliver measurable yield gains. This work provides a promising and environmentally sound biological strategy for managing fungal diseases in economically important crops.