Seminars

Plants in nature live in intimate association with diverse microorganisms, collectively called the plant microbiota. Taxonomic compositions of bacterial communities associated with the roots of a wide range of land plant species are largely overlapped, and the common bacterial lineages, including the order Rhizobiales, constitute the “core root microbiota”. Rhizobiales contains a group of bacteria, known as rhizobia, that are characterized by their symbiotic engagements with leguminous plants. However, the genetic and phenotypic nature of interaction between non-leguminous plants and non-symbiotic Rhizobiales is not understood. Our recent genome analysis of 1,314 Rhizobiales isolates originating from both leguminous and non-leguminous plant hosts showed that key symbiosis genes were acquired multiple times and that the most recent Rhizobiales common ancestor had the capacity to colonize the roots of a broad range of hosts. By conducting a large-scale gnotobiotic binary interaction survey, we identified root growth promoting (RGP) activity as a common trait of Rhizoabiales commensals. We also found that the Rhizobiales RGP is strongly inhibited by activation of host immune responses, and some root-associated bacteria, including some Rhizobiales commensals, suppressed host immune responses. We therefore tested a tripartite co-inoculation experiment and revealed that the Rhizobiales RGP under immune-eliciting conditions was rescued by co-inoculation with an immune-suppressing strain. These findings indicate that these traits synergistically operate in a modular fashion, suggesting interactions between these two traits that enable emergent properties of A. thaliana core root microbiota.