Phylogenetic and DNA-DNA hybridization analyses of Bradyrhizobium species.

Abstract

The 16S rDNA sequence of Bradyrhizobium liaoningense was determined and analysed together with sequences of other Bradyrhizobium species and related taxa. In addition, DNA-DNA hybridizations were performed between representative strains of the three Bradyrhizobium species. Bradyrhizobium liaoningense is genotypically highly related to Bradyrhizobium japonicum, whereas Bradyrhizobium elkanii is more distantly related to these two species. The fact that Afipia, Agromonas, Blastobacter, Nitrobacter and Rhodopseudomonas are phylogenetically more closely related to Bradyrhizobium japonicum than to Bradyrhizobium elkanii is discussed.Keywords : Bradyrhizobium, 16S rDNA phylogeny, DNA-DNA hybridizationsThe genus Bradyrhizobium was created for the slowgrowing members of the genus Rhizobium (Jordan, 1982) and initially contained one species, Bradyrhizobium japonicum, for isolates from Glycine. Other isolates and groups were included in the genus, but not given a formal species status. They were referred to as Bradyrhizobium sp., with the host plant usually listed in parentheses. Using DNA-DNA hybridizations, Hollis et al. (1981) described three homology groups among Rhizobium japonicum strains. Groups I and Ia correspond to the current species Bradyrhizobium japonicum. For group II, a separate species, Bradyrhizobium elkanii, was later proposed on the basis of genotypic and phenotypic results (Kuykendall et al., 1992). Finally, a third species, Bradyrhizobium liaoningense, was proposed for a group of extra-slowgrowing Glycine isolates which were both phenotypically and genotypically distinct from the other two species (Xu et al., 1995). This report included the partial 16S rDNA sequence (260 bp, positions 44-337) of Bradyrhizobium liaoningense strain 2062, which was identical to the sequence of Bradyrhizobium japonicum USDA 110. In view of these findings, assessment of the phylogenetic position of Bradyrhizobium liaoningense requires at least the determination of its complete 16S rDNA sequence. Phylogenetic relationships

Phylogenetic analysis of the genera Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium on the basis of 16S rRNA gene and internally transcribed spacer region sequences

“…Although, according to Willems et al (2001b), LMG 8293 was supposed to be related to genospecies II, which was represented by B. elkanii LMG 6134 T , our results showed that this strain formed an independent cluster with Vga-1 and Mes-1. Furthermore, the ITS region sequences of two strains (LMG 15404-c4 and LMG 10300), which were classified as genospecies VI of Willems et al (2001a), formed a distinct cluster separable from known species and the Korean isolates. The close relationship between the type strains of B. japonicum and B. liaoningense was confirmed by high sequence similarities (16S rRNA gene sequence similarity of 99?8 % and ITS region sequence similarity of 88?2 %) and a high DNA-DNA hybridization value (56 %) (Willems et al, 2001a, b).…”

Description of Afipia birgiae sp. nov. and Afipia massiliensis sp. nov. and recognition of Afipia felis genospecies A.

“…classification of bacteria of the Bradyrhizobium group were highlighted soon after the official description of the genus Afipia (Willems & Collins, 1992) and later by others working on the phylogeny of this group of bacteria (Anzai et al, 2000 ;Teske et al, 1994 ;Lafay & Burdon, 1998 ;Wong et al, 1994 ;Willems et al, 2001 ;Hougardy et al, 2000). The key question raised by several authors is the validity of including these species in a single genus on the basis of 16S rDNA sequences (as members of this group exhibit levels of sequence similarity of 97 % or greater).…”

“…The key question raised by several authors is the validity of including these species in a single genus on the basis of 16S rDNA sequences (as members of this group exhibit levels of sequence similarity of 97 % or greater). It should be noted that genomic data are increasingly available for these species (up to 40 16S rDNA sequences for the Bradyrhizobium species) (Willems et al, 2001), but phenotypic data that could help in the polyphasic taxonomy of these bacteria are still lacking. As observed among Bradyrhizobium species and for the species described in this study or as described previously for Bacillus species (Ash et al, 1991 ;Fox et al, 1992), over-reliance on 16S rDNA sequence comparisons may be foolhardy and should therefore be associated with DNA-DNA hybridization data .…”

Bradyrhizobium manausense sp. nov., isolated from effective nodules of Vigna unguiculata grown in Brazilian Amazonian rainforest soils

“…Although high percentages of 16S rRNA gene sequence similarity were obtained, previous reports have suggested that closely related species of the genus Bradyrhizobium are difficult to distinguish using 16S rRNA gene sequence analysis (Willems et al, 2001;Menna et al, 2009). Therefore, multi locus sequence analysis (MLSA) was performed with glnII (537 bp), recA (415 bp) and rpoB (429 bp) following previous reports (Vinuesa et al, 2005;Martens et al, 2008, Menna et al, 2009.…”