Comparative genomic analysis of North American Bradyrhizobium symbionts of Chamaecrista fasciculata (Caesalpinioideae) with related bradyrhizobia

The symbionts of Chamaecrista fasciculata , a caesalpinioid legume, were isolated from plants growing in native soil or by host trapping. To these, we added strains from the United States Department of Agriculture and strains isolated earlier from nodules of C. fasciculata and Chamaecrista nictitans . The phylogeny of 16 strains was determined by examining and comparing sequences of their rrs (16S rRNA) genes, the intergenic transcribed spacer region, two “core” housekeeping genes ( recA and dnaK ), and two symbiotic ( nodA and nifH ) genes. Seven strains were whole-genome sequenced and compared phylogenomically to related strains isolated from Caesalpinioideae nodules. All the symbionts belonged to Bradyrhizobium spp. dispersed in both Mega Clades-I and II, with some forming novel clusters and others sharing similarities with previously reported Chamaecrista symbionts. All strains nodulated and enhanced C. fasciculata growth in nitrogen-free axenic conditions. The draft genomes of seven Chamaecrista strains were sequenced, including four isolated from C. fasciculata in the United States (CFUW1, CFUSD1, CFUMN1, and USDA3010) and three from Brazil (JHI2701, JHI2711, and Cens1A). Comparative genomic analysis based on average nucleotide identity and digital DNA-DNA hybridization suggested that six strains were closely related to Bradyrhizobium frederickii , Bradyrhizobium ferriligni , Bradyrhizobium elkanii , Bradyrhizobium australafricanum , “ Bradyrhizobium brasilense, ” and Bradyrhizobium yuanmingense . Meanwhile, the C. fasciculata strain USDA3010 and the non-mimosoid Caesalpinioideae Dimorphandra wilsonii strain DW12.5 are potential new species.