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

• Published in: Science (American Association for the Advancement of Science) Vol. 366; no. 6465; pp. 606 - 612
• Main Authors: Carrión, Víctor J, Perez-Jaramillo, Juan, Cordovez, Viviane, Tracanna, Vittorio, de Hollander, Mattias, Ruiz-Buck, Daniel, Mendes, Lucas W, van Ijcken, Wilfred F J, Gomez-Exposito, Ruth, Elsayed, Somayah S, Mohanraju, Prarthana, Arifah, Adini, van der Oost, John, Paulson, Joseph N, Mendes, Rodrigo, van Wezel, Gilles P, Medema, Marnix H, Raaijmakers, Jos M
• Format: Journal Article
• Language: English
• Published: United States The American Association for the Advancement of Science 01-11-2019
• Subjects: Antifungal activity; Bacteria - classification; Bacterial Physiological Phenomena; Bacteroidetes - physiology; Beta vulgaris - microbiology; Biodiversity; Cell walls; Chitinase; Chitinases - genetics; Chitinophagaceae; Consortia; Disease Resistance; Endophytes; Endophytes - physiology; Flavobacterium; Flavobacterium - physiology; Fungal diseases; Fungi; Fungicides; Gene clusters; Genes, Bacterial; Genome, Bacterial; Genomes; Metabolites; Metagenome; Microbiomes; Microbiota; Microorganisms; Mutagenesis, Site-Directed; Pathogens; Peptide Synthases - genetics; Phenotypes; Plant diseases; Plant Diseases - microbiology; Plant growth; Plant protection; Plant roots; Plant Roots - microbiology; Polyketide Synthases - genetics; Polyketides; Rhizoctonia - pathogenicity; Rhizoctonia solani; Roots; Secondary metabolites; Siderophores; Site-directed mutagenesis; Soil Microbiology; Sugar beets; Transcription; Wilt
• ISSN: 0036-8075; 1095-9203
• DOI: 10.1126/science.aaw9285

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
and
was designed that consistently suppressed fungal root disease. Site-directed mutagenesis then revealed that a previously unidentified NRPS-PKS gene cluster from
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.