Nitrogen source and Nod factor signaling map out the assemblies of Lotus japonicus root bacterial communities

Symbiosis with soil-dwelling bacteria that fix atmospheric nitrogen allows legume plants to grow in nitrogen-depleted soil. Symbiosis impacts the assembly of root microbiota, but it is unknown how this process takes place and whether it is independent of nitrogen nutrition. We use plant and bacterial mutants either grown in complex nature soil environments or gnotobiotic systems applied with SynComs to address the role of Nod factor signaling on Lotus japonicus root microbiota assembly. Coupled with 16S amplicon sequencing and metabolomic analysis, we found that Nod factors are produced by symbionts to activate Nod factor signaling in the host, and this modulates the assembly of a symbiotic root microbiota. Lotus plants grown in symbiosis-permissive or suppressive soils delineated three nitrogen-dependent nutritional states: starved, symbiotic, or inorganic. We found that root and rhizosphere microbiomes associated with these states differ in composition and connectivity, demonstrating that symbiosis and inorganic nitrogen impact the legume root microbiota differently. Finally, we demonstrated that selected bacterial genera delineating state-dependent microbiomes have a high level of accurate prediction.