Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities

Significance Legumes are known as pioneer plants colonizing marginal soils, and as enhancers of the nutritional status in cultivated soils. This beneficial activity has been explained by their capacity to engage in symbiotic relationship with nitrogen-fixing rhizobia. We performed a community profiling analysis of Lotus japonicus wild type and mutants to investigate the role of the nodulation pathway on the structure of the root-associated bacterial microbiota. We found that several bacterial orders were almost entirely depleted from the mutant roots, and that an intact symbiosis is needed for the establishment of taxonomically diverse and distinctive bacterial communities in the root and rhizosphere. Our findings imply that a symbiosis-linked bacterial community, rather than dinitrogen-fixing rhizobia alone, contributes to legume growth and ecological performance.