Cross-kingdom synthetic microbiota supports tomato suppression of Fusarium wilt disease

The role of rhizosphere microbiota in the resistance of tomato plant against soil-borne Fusarium wilt disease (FWD) remains unclear. Here, we showed that the FWD incidence was significantly negatively correlated with the diversity of both rhizosphere bacterial and fungal communities. Using the microbiological culturomic approach, we selected 205 unique strains to construct different synthetic communities (SynComs), which were inoculated into germ-free tomato seedlings, and their roles in suppressing FWD were monitored using omics approach. Cross-kingdom (fungi and bacteria) SynComs were most effective in suppressing FWD than those of Fungal or Bacterial SynComs alone. This effect was underpinned by a combination of molecular mechanisms related to plant immunity and microbial interactions contributed by the bacterial and fungal communities. This study provides new insight into the dynamics of microbiota in pathogen suppression and host immunity interactions. Also, the formulation and manipulation of SynComs for functional complementation constitute a beneficial strategy in controlling soil-borne disease.Published versionFunding for this study has been provided by the National Science Fund for Distinguished Young Scholars (NSFC 31725001) and Biological Resources Programme, Chinese Academy of Sciences (KFJ-BRP-009). X.Z. acknowledges Excellent Young Scholars of State Key Laboratory of Mycology (SKLMQN202101) for supporting his postgraduate research. Clement K.M. Tsui is grateful to CAS President’s International Fellowship Initiative for the award of a visiting scientist fellowship for scientific exchange, grant number 2019VBC0006