Rhizomicrobiome of terra preta soil manipulates grapevine chemotype, resistance against trunk diseases, and endophytic community structure

Similar to human gut enterotypes, soil microbiota might harbour beneficial microorganisms maintaining plant health and resilience against environmental challenges. We searched for soil microorganisms promoting the grapevines resilience against trunk disease (GTD) which is one of the most destructive diseases for viticulture worldwide. We found that mixing the soil of the vineyard with compost and biochar promoted the plant defence mechanisms and controlled the disease development. Rhizomicrobiome and plant responses were studied using multi-omics techniques, e.g. shotgun metagenome sequencing as well as targeted and untargeted metabolomics. By reconstructing the bacterial genomes, mixed soil showed higher abundance of many bacterial taxa, e.g. g_Niastella, g_Chryseolinea of p_Bacteroidota with remarkable pathways, e.g. ubiquinone, iso-chorismate and chitinase synthesis pathways. Such pathways could promote the defence mechanisms in grapevines against biotic stress. Metabolomics analysis further revealed that mixing soil with compost and biochar influenced the chemotype of roots tissues. In grapevine roots grown in standard soil, GTD infection corresponded with higher levels of organic acids and sugar derivatives. On the other hand, compost and biochar significantly reduced sugar and organic acid concentrations in roots while increasing the abundance of twenty aromatic and phenolic compounds with antioxidant properties, such as stilbenes and flavonoids. Some bioactive stilbenes members such as resveratrol, piceatannol, and 2-Hydroxyiminostilbenes, which were significantly prevalent in plants of mixed soil, were classified as grapevine resistance factors against trunk diseases.