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Unravelling the soil immune response

Victor Carrion: Netherlands Institute of Ecology

<div>Soil and plant microbiomes contribute to a range of plant support functions, including nutrient acquisition and disease protection. To date, the molecular mechanisms involved in natural disease suppressive soils have primarily been studied for single microbial strains isolated from the rhizosphere and endosphere. The role of microbial consortia in this soil immune response is much less studied. Here, we conducted a microbiome-wide analysis of the taxonomic diversity and functional potential of the endosphere of plants grown in a soil that is naturally suppressive to damping-off disease caused by the fungal root pathogen<em> Rhizoctonia solani</em>. Metagenomic analyses showed a significant enrichment of Chitinophagaceae, Flavobacteriaceae, Burkholderiaceae, Pseudomonadaceae and Xanthomonadaceae families in the endosphere of plants challenged with the fungal pathogen. Binning of the metagenomic sequences allowed de novo assembly of mulitple high quality genomes of different endophytic bacterial genera. Subsequent trait-based analyses revealed numerous biosynthetic gene clusters (BGCs) overrepresented in the endophytic bacterial families of plants under pathogen attack, including BGCs involved in signal transduction, extracellular enzyme and secondary metabolite production. Network analyses further indicated that the traits enriched in the endophytic microbiome, in particular nonribosomal peptides and polyketides, involve several novel BGCs encoding metabolites with yet unknown structures and activities. Bioassays further showed that consortia of endophytic strains and not single strains conferred disease protection to the host plant. Collectively these results indicate that endophytic microbial consortia with diverse functional traits contribute to the soil immune response.</div>