Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome

Microorganisms living inside plant roots can promote plant growth and health, but their genomic and functional diversity remain elusive. Here, metagenomics and network inference of the endophytic root microbiome of plants grown in soil suppressive to the fungal pathogen Rhizoctonia solani, revealed high abundance of Chitinophagaceae and Flavobacteriaceae and a rich metabolic diversity of 730 biosynthetic gene clusters with only 12 known. Chitinase and NRPS genes were expressed in these endophytic bacterial families primarily upon pathogen challenge of the roots. Following de novo genome assembly, a consortium of endophytic Chitinophaga and Flavobacterium was reconstructed that suppressed root disease more consistently than individual members. CRISPR-Cas-based mutagenesis further revealed that a novel NRPS-PKS hybrid gene cluster from Flavobacterium was key to the disease-suppressive activity of the endophytic consortium. Our results highlight that endophytic root microbiomes harbor a wealth of yet unknown functional traits that, in concert, can protect the plant inside out.