Core microbiota recruited by healthy grapevines enhance resistance against root rot disease

BACKGROUND: Root rot disease caused by fungal pathogens of wine grapevines poses a serious threat to their growth and results in a substantial economic impact on grape industry. The rhizosphere microbiome recruited to plants is critical for mitigating soil-borne pathogens. However, how beneficial microbes influence disease resistance remains unclear. RESULTS: We investigate the composition and gene functions of microorganisms in wine grapevines with root rot disease and healthy controls by amplicon and metagenomic sequencing. We use culturomics and in vivo experiments to verify the pathogen and beneficial strains to improve plant health. We find that root rot disease in grapevines significantly affects rhizosphere microbiome diversity and composition. The microbial interkingdom network indicates that the disease destabilizes the bacteria-fungi co-occurrence network. We find that plants recruit the potentially beneficial bacteria Pseudomonas, Bacillus and Streptomyces in healthy rhizosphere soil. By culturomics, we confirm that Fusarium solani is the main pathogen causing root rot disease. We further observe that these three key beneficial bacteria from the co-occurrence networks enhance the resistance of grapevines to pathogens. Furthermore, metagenomic analysis reveals that beneficial bacterial strains suppress pathogens by enriching potential functional genes in pathways involved in disease resistance. CONCLUSIONS: Our findings highlight the critical role of disease resistance pathways of potentially beneficial microorganisms in fighting disease and supporting plant health, offering new insight for the exploration of beneficial microbial resources and providing a basis for the development of biological control of grape root rot disease.