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

By V. Carrión, J. Pérez-Jaramillo, Viviane Cordovez, Vittorio Tracanna, M. de Hollander, Daniel Ruiz-Buck, L. Mendes, W. V. van Ijcken, Ruth Gomez-Exposito, S. Elsayed and 8 more. Science, 2019

914 citations recorded by the source corpus.

Protecting plants from the inside out Some soils show a remarkable ability to suppress disease caused by plant pathogens, an ability that is attributed to plant-associated microbiota. Carrión et al. investigated the role of endophytes, the intimate microbial community found within roots, in fungal disease suppression (see the Perspective by Tringe). The wilt fungus Rhizoctonia solani infects sugar beets, whereupon transcriptional analysis shows that several bacterial endophyte species activate biosynthetic gene clusters to cause disease suppression. These organisms produce antifungal effectors, including enzymes that can digest fungal cell walls, and secondary metabolites, including phenazines, polyketides, and siderophores, which may contribute to the antifungal phenotype. Science, this issue p. 606; see also p. 568 Bacteria living between and within the roots of plants exposed to a fungal pathogen can help generate a disease-suppressing phenotype. 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.

Subfields: Ecology, Plant Science

View Paper: https://www.semanticscholar.org/paper/5d92742bf3c2eba7f07790834f11354838312287

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Citations in the corpus

A practical guide to amplicon and metagenomic analysis of microbiome data (2020, methodology): “For example, the development and use of methods to remove the host DNA can effectively increase the proportion of the micro-biome in plant endophytes (Carrión et al., 2019) and human respiratory infection samples (Charalampous et al., 2019).”
Pseudomonas simiae WCS417: star track of a model beneficial rhizobacterium (2020, methodology): “Detailed protocols for carrying out Arabidopsis WCS417-ISR bioassays in a soil system and a high throughput system are described by Van Wees et al. (2013) and Cecchini et al. (2019), respectively.”
Climate change impacts on plant pathogens, food security and paths forward (2023, background): “The most well-studied example of microbiota-mediated disease protection is disease-suppressive soil, where active microbiota contribute to disease reduction, even in the presence of the pathogen, susceptible host and favourable environmental conditions 80,86,87 .”