Phylogeny and distribution of extra-slow-growing Bradyrhizobium japonicum harboring high copy numbers of RSα, RSβ and IS1631

Abstract

We previously reported that extra-slow-growing Bradyrhizobium japonicum isolates obtained from three field sites in Japan, designated as HRS (highly reiterated sequence-possessing) strains, have high copy numbers of the insertion sequences RSalpha and RSbeta. When strain collections in the USA, Japan, Korea, Thailand and China were examined by Southern hybridization using RSalpha, RSbeta and IS1631 as probes, HRS strains were found in the Japanese, Chinese, and American collections, but not in the Korean and Thai ones. Copy number analyses of RSalpha and RSbeta, calibrated with the copy number of rrs (16S rRNA gene), indicated that the HRS stains can be divided into two major groups. Group A is comprised of members with a high copy number of RSalpha (mean+/-S.D., 139+/-27), a low number of RSbeta (mean+/-S.D., 30+/-13) sequences, and extremely slow growth rates (mean doubling time+/-S.D., 27+/-9 h). In contrast, group B is comprised of strains with a high copy number of RSbeta (mean+/-S.D., 93+/-6) and a lower number of RSalpha. These groupings of HRS strains were well correlated with phylogenetic clusters based on rrs, gyrB and serogroups (110/122 and 123/135). Growth rate of B. japonicum strains was also correlated exclusively with RSalpha copy number. The ecological, evolutionary and biotechnological implications of the findings are discussed.

Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members

“…The tree based on the 16S rRNA gene divided the B. japonicum strains into two main clusters, BJ1 and BJ2, as described earlier (Sameshima et al, 2003;Sameshima-Saito et al, 2006) (Figure 3a). B. japonicum strains belonging to the two genome types 110 and 122, as defined by the CGH profile (Figures 1 and 2), still formed a single clade, BJ1 (Figure 3a).…”

Bradyrhizobium iriomotensesp. nov., Isolated from a Tumor-Like Root of the LegumeEntada koshunensisfrom Iriomote Island in Japan

“…Previously, these core house-keeping loci were used in comparative analysis in the taxonomic characterization of rhizobia. 23,[47][48][49][50][51] It has been reported that these protein coding-loci are unlinked in the genome and that they provide independent genealogies for the inference of a reliable phylogenetic tree. 52,53) Sequences of our target house-keeping genes for all the strains were not available in the Genbank, which is why we could not use the same set of strains to construct all the phylogenetic trees.…”

New Method of Denitrification Analysis of Bradyrhizobium Field Isolates by Gas Chromatographic Determination of 15 N-Labeled N 2

“…This polymorphism is probably due to truncation of the processes of anaerobic nitrate respiration (31). It has been shown that indigenous populations of soybean bradyrhizobia show significant field site variation in terms of DNA fingerprints according to insertion sequences, species level, and hydrogen uptake phenotype and genotype (7,16,17,21). Similarly, we wanted to determine whether the denitrification patterns of indigenous populations of soybean bradyrhizobia differed in accordance with their field sites.…”

“…Ϫ, the isolate evolved no 30 c Genotype and phenotype of uptake hydrogenase (16,18). d HRS, highly reiterated sequence-possessing strains carrying high copy numbers of insertion sequences (9,15,18,21).…”