Phylogenetic and population structure of thenod-free but nodulatingBradyrhizobiumphylogroup

Abstract

AbstractBradyrhizobiumis a main rhizobial lineage of which the majority of its members nodulate legume plants using Nod factors (NFs) encoded by thenodgenes. However, the “photosynthetic” phylogroup withinBradyrhizobium(PB) does not containnodgenes but are still capable of establishing a nitrogen-fixing symbiosis with some tropical legumes of theAeschynomenegenus. Furthermore, members of this phylogroup colonize rice roots and promote plant growth. Despite this unique combination of ecological features, genomes of only 13 PB members are sequenced, and almost all are isolated fromAeschynomenespp. nodules. Here, we sequenced 208 new PB members predominantly associated with rice. The extended PB phylogroup comprises three main clades: a basal clade with significant expansion of its diversity, followed by the diversification of a singleton clade from a new clade exclusively represented by our strains. Although the PB strains universally lack the canonicalnodgenes, all 27 assayed strains representing the broad diversity of these clades induced nodules onAeschynomene indica. Interestingly, significant differences in the efficiency of symbiosis between the main clades were observed and the singleton clade showed an intermediate symbiotic phenotype aligning well with its intermediate phylogenetic position. Our strain collection expands the phylogenetic and ecological diversity of thenod-free but nodulatingBradyrhizobiumand shows that the NF-independent nodulation ofAeschynomeneis a common trait of this phylogroup, in contrast to the photosynthetic trait originally thought as its unifying feature.