Native soils with their microbiotas elicit a state of alert in tomato plants

Several studies have investigated soil microbial biodiversity, but understanding of the mech-anisms underlying plant responses to soil microbiota remains in its infancy. Here, we focusedon tomato (Solanum lycopersicum), testing the hypothesis that plants grown on native soilsdisplay different responses to soil microbiotas.Using transcriptomics, proteomics, and biochemistry, we describe the responses of twotomato genotypes (susceptible or resistant to Fusarium oxysporum f. sp. lycopersici) grownon an artificial growth substrate and two native soils (conducive and suppressive toFusarium).Native soils affected tomato responses by modulating pathways involved in responses tooxidative stress, phenol biosynthesis, lignin deposition, and innate immunity, particularly inthe suppressive soil. In tomato plants grown on steam-disinfected soils, total phenols andlignin decreased significantly. The inoculation of a mycorrhizal fungus partly rescued thisresponse locally and systemically. Plants inoculated with the fungal pathogen showed reduceddisease symptoms in the resistant genotype in both soils, but the susceptible genotype waspartially protected from the pathogen only when grown on the suppressive soil. The ‘state of alert’ detected in tomatoes reveals novel mechanisms operating in plants innative soils and the soil microbiota appears to be one of the drivers of these plant responses.