Many studies have investigated the highly complex microbial assemblages that are associated with different plants and specific plant compartments, such as the rhizosphere, phyllosphere and endosphere. Although it is becoming increasingly clear that the plant microbiome has important functions in plant growth, development and health, a clear understanding of the functional role of plant-associated microorganisms and their functional capacity in promoting distinct plant phenotypes is lacking. Some soils were previously shown to protect plants from root pathogens. This effect, referred to as ‘disease-suppressiveness’, is partially conferred by microorganisms found in the rhizosphere, which provide a first line of defence against plant disease. In this study, Carrión et al. investigated how the endophytic root microbiome forms a second line of defence against the fungal root pathogen Rhizoctonia solani and report that Chitinophaga and Flavobacterium species and their functional traits have a role in plant protection from disease.
In the endophytic metagenomes, the authors identified genes that exhibited increased expression following infection, such as genes encoding enzymes associated with fungal cell wall degradation, which suggests a role in protection from fungal pathogens. In addition, several previously unknown secondary metabolite biosynthetic gene clusters (BGCs) were overrepresented in the endophytic microbiomes of pathogen-inoculated suppressive soils. On the basis of metagenomics and network inference combined with de novo assembly of endophyte genomes, the authors reconstructed disease-suppressive synthetic consortia. Following colonization of the rhizosphere and root endosphere of sugar beet seedlings, disease incidence was decreased, an effect that was even observed for a ‘minimal’ consortium comprising one Chitinophaga isolate and one Flavobacterium isolate. Transcriptional analysis showed an increased expression of chitinase and an uncharacterized BGC in the root endosphere-colonizing consortia following pathogen challenge. Site-directed mutagenesis of this BGC in Flavobacterium reduced the disease-suppressive effect of the isolate alone, as well as of the minimal consortium.
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