Characterization of immunity-inducing rhizobacteria highlights diversity in plant-microbe interactions

Abstract The narrow region of soil surrounding roots (rhizosphere) contains an astonishing diversity of microorganisms. Some rhizosphere bacteria can improve plant health and immunity, via direct competition with pathogens or by establishing heightened immunity in aboveground tissues, a phenomenon known as Induced Systemic Resistance (ISR). We screened a bacterial library from agricultural soils to identify strains that, after root treatment, induce immunity in Solanum lycopersicum (tomato) against the fungal pathogen Botrytis cinerea. Here, we report the establishment of a screening method and characterization of a subset of five strains, belonging to the species Bacillus velezensis, Paenibacillus peoriae and Pseudomonas parafulva, that induced systemic resistance in tomato. However interestingly, only two of them triggered canonical ISR in Arabidopsis, indicating plant host specificity and/or alternative modes of actions. Furthermore, some of the strains displayed direct anti-microbial activity. We also found the requirement of the lipid-binding protein DIR1 in ISR establishment, indicating a possible convergence of SAR and ISR signaling. Finally, we found that P. parafulva TP18m, also displayed strong effects on root development. Taken together, we have identified taxonomically diverse immunity-inducing bacteria. Our characterization revealed diverse features, highlighting the complexity of bacteria- host interaction in the rhizosphere. HighlightWe identified taxonomically diverse rhizobacteria that induce systemic resistance in tomato plants to Botrytis after application to the root. These bacteria display diverse modes of action to improve plant health.