Gene

Phyllosphere

Pseudomonas

Flavobacterium

Bacteria

Biology

Pathogen

Ralstonia solanacearum

Botany

Plant disease resistance

Rhizosphere

Genetics

Microbiome

Bacterial wilt

Microbiology

Nature Biotechnology

Tomato rhizosphere microbiome alterations that contribute to bacterial wilt resistance are detected using metagenomics. Tomato variety Hawaii 7996 is resistant to the soil-borne pathogen Ralstonia solanacearum, whereas the Moneymaker variety is susceptible to the pathogen. To evaluate whether plant-associated microorganisms have a role in disease resistance, we analyzed the rhizosphere microbiomes of both varieties in a mesocosm experiment. Microbiome structures differed between the two cultivars. Transplantation of rhizosphere microbiota from resistant plants suppressed disease symptoms in susceptible plants. Comparative analyses of rhizosphere metagenomes from resistant and susceptible plants enabled the identification and assembly of a flavobacterial genome that was far more abundant in the resistant plant rhizosphere microbiome than in that of the susceptible plant. We cultivated this flavobacterium, named TRM1, and found that it could suppress R. solanacearum-disease development in a susceptible plant in pot experiments. Our findings reveal a role for native microbiota in protecting plants from microbial pathogens, and our approach charts a path toward the development of probiotics to ameliorate plant diseases.

Rhizosphere microbiome structure alters to enable wilt resistance in tomato