Phylogenetic And Whole Genomic Analysis Of Bradyrhizobium In Guangdong And Guangxi Provinces Of Sourthern China

This paper discussed rhizobia collected from the southern subtropical region of China, including Guangdong and Guangxi provinces. The research included diversity and evolutionary analysis of Erythrophleum fordii rhizobia, as well as whole genome analysis about the peanut rhizobia which have new type of nodulation genes.Erythrophleum fordii is also called "ironwood". To investigate the diversity and biogeography of rhizobia associated with this leguminous evergreen tree, root nodules were collected from four sites of the southern subtropical region of China. A total of166isolates were obtained from the nodules and characterized. In a PCR-based restriction fragment length polymorphism (RFLP) analysis of ribosomal intergenic sequences, the isolates were classified into22types within the genus Bradyrhizobium. Sequence analysis of16S rRNA, ribosomal intergenic spacer (IGS), and the housekeeping genes recA and glnll classified the isolates into four groups:the Bradyrhizobium elkanii and Bradyrhizobium pachyrhizi groups comprising the dominant symbionts, Bradyrhizobium yuanmingense, and two unclassified groups comprising the minor symbionts. The phylogenetic results and evolutionary analysis demonstrated that mutation and vertical transmission of genes were the principal processes for the divergent evolution of Bradyrhizobium species associated with E. fordii, while lateral transfer and recombination of housekeeping and symbiotic genes were rare. The nodC and nifH phylogenetic trees defined five or six lineages, which was largely consistent with the definition of genomic species and suggested the co-evolution relationship between housekeeping and nodulation genes.Correlation analyses between rhizobial species and soil factors indicated B. elkanii strains like growing in the acidic soil, and pH (4.24-5.39) of soil had a positive correlation with B. elkanii but did not have effect on B. pachyrhizi. However, the quantities of effective phosphorus (14.0-75.5) had a negative correlation with B. pachyrhizi strains.By polyphasic taxonomy methods, we have identified two novel species of Bradyrhizobium. They were named as Bradyrhizobium erythrophlei sp. nov. and Bradyrhizobium ferriligni sp. nov. represented by CCBAU53325T and CCBAU51502T respectively.According to the genome analysis of two peanut Bradyrhizobium strains with new type of nodulation genes obtained from Guangdong and Guangxi provinces in the south of China, we located16important genes in their genomes respectively and demonstrated they truly had new divergent nod genes which had very low similarities with other known Bradyrhizobium strains’. In addition, the fixation genes of these two peanut strains had higher similarities with photosynthetic Bradyrhizobium strains.