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

Víctor J. Carrión, Juan Perez-Jaramillo, Viviane Cordovez, Vittorio Tracanna, Mattias De Hollander, Daniel Ruiz-Buck, Lucas W. Mendes, Wilfred F.J. van Ijcken, Ruth Gomez-Exposito, Somayah S. Elsayed, Prarthana Mohanraju, Adini Arifah, John van der Oost, Joseph N. Paulson, Rodrigo Mendes, Gilles P. van Wezel, Marnix H. Medema*, Jos M. Raaijmakers

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

227 Citations (Scopus)


Microorganisms living inside plants can promote plant growth and health, but their genomic and functional diversity remain largely elusive. Here, metagenomics and network inference show that fungal infection of plant roots enriched for Chitinophagaceae and Flavobacteriaceae in the root endosphere and for chitinase genes and various unknown biosynthetic gene clusters encoding the production of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). After strain-level genome reconstruction, a consortium of Chitinophaga and Flavobacterium was designed that consistently suppressed fungal root disease. Site-directed mutagenesis then revealed that a previously unidentified NRPS-PKS gene cluster from Flavobacterium was essential for disease suppression by the endophytic consortium. Our results highlight that endophytic root microbiomes harbor a wealth of as yet unknown functional traits that, in concert, can protect the plant inside out.

Original languageEnglish
Pages (from-to)606-612
Number of pages7
Issue number6465
Publication statusPublished - 1 Nov 2019


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