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). To identify novel immunity-activating bacterial strains, we established a screening method from a library of agricultural soil-derived culturable bacteria, using Solanum lycopersicum (tomato) and the fungal pathogen Botrytis cinerea, the causal agent of gray mold disease. Here, we report the establishment of a screening method and the identification of 13 immunity-inducing strains in tomato plants, including a strain of Chitinophaga arvensicola. A detailed characterization of a subset of five strains, belonging to the species Bacillus velezensis, Paenibacillus peoriae, and Pseudomonas parafulva, revealed that only two of them triggered canonical ISR in Arabidopsis, indicating plant host specificity, alternative modes of action, or both. Furthermore, some of the strains displayed direct anti-microbial activity, and two strains became endophytic. We also found the requirement of the lipid-binding protein DIR1, which is an important factor for systemic acquired resistance, for ISR establishment in Arabidopsis, indicating a possible convergence of systemic acquired resistance and ISR signaling. Finally, we found that P. parafulva TP18m promoted root development as well as enhanced immunity. Taken together, we have established a screening system for immunity-inducing bacteria and identified taxonomically diverse bacterial strains that may be useful for agricultural application. Our characterization revealed diverse features for each strain, which highlights the complexity of the bacteria–host interactions in the rhizosphere.