Correlating phylogenetic and functional diversity of the nod-free but nodulating Bradyrhizobium phylogroup

Bradyrhizobium is a main rhizobial lineage of which most members nodulate legume plants using Nod factors synthetized by the nod genes. However, members of the Photosynthetic supergroup (phylogroup) within Bradyrhizobium are nod-free, but still capable of establishing nitrogen-fixing nodules with some tropical legumes of the Aeschynomene genus. These unusual findings are based on the genomic sequences of only 13 Photosynthetic Bradyrhizobium strains, and almost all were isolated from Aeschynomene nodules. Here, we report that Photosynthetic Bradyrhizobium supergroup members are more abundantly associated with rice root (endosphere and rhizosphere) compared to grassland, forest, and maize samples based on rpoB amplicon sequence analyses. We sequenced 263 new isolates of this supergroup mostly from two main subspecies of cultivated rice (Oryza sativa L. spp. indica and japonica). The extended supergroup comprises three major clades with their diversity broadly covering the natural community of this supergroup: a basal clade with significant expansion of its diversity, a clade composed by two phylogenetically diverse strains including one newly isolated, and a new clade exclusively represented by our new strains. Although this supergroup members universally lack the canonical nod genes, all 28 assayed strains covering the broad diversity induced nodules on Aeschynomene indica. The three clades displayed important differences in the efficiency of symbiosis, aligning well with their phylogenetic divergence. With this expanded ecological, phylogenetic, and functional diversity, we conclude that the nod factor-independent nodulation of Aeschynomene is a common trait of this supergroup, in contrast to the photosynthetic trait originally thought of as its unifying feature.