Phylogenetic analysis of the genera Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium on the basis of 16S rRNA gene and internally transcribed spacer region sequences.
A total of 128 strains was isolated from more than 23 legume hosts in Korea. Phylogenetic relationships between these Korean isolates and reference strains of the genera Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium were analysed using their 16S rRNA gene and internally transcribed spacer (ITS) region sequences. Among the Bradyrhizobium strains, dendrograms based on both the 16S rRNA gene and ITS region sequences produced two main groups. The ITS tree yielded at least two new clusters that were discernable from the seven previously delineated genospecies. Large discrepancies were revealed between phylogenetic dendrograms based on 16S rRNA gene and ITS region sequences for members of the genus Rhizobium, reflecting their taxonomic heterogeneity. The amalgamation of Rhizobium and former members of Agrobacterium was confirmed using the 16S rRNA tree. Phylogenetic analysis of ITS region sequences showed that the Rhizobium giardinii clade (group II) and the Rhizobium radiobacter/Rhizobium rubi clade (group III) could be tentatively recognized as groups that are separable from the core group (group I), which includes Rhizobium leguminosarum. Dendrograms based on the 16S rRNA gene and ITS region sequences of Mesorhizobium strains were highly conflicting due to the poor taxonomic resolution of the 16S rRNA gene sequences and the low confidence in the ITS dendrogram. Several Korean isolates within the genus Mesorhizobium are thought to represent novel taxa when considering their relatively low ITS region sequence similarities (<80 %) to the reference strains.
Kwon
Soon-Wo
SW
Korean Agricultural Culture Collection (KACC), Genetic Resources Division, National Institute of Agricultural Biotechnology, Rural Development Administration (RDA), Suwon 441-707, Korea.
Park
Jin-Young
JY
Korean Agricultural Culture Collection (KACC), Genetic Resources Division, National Institute of Agricultural Biotechnology, Rural Development Administration (RDA), Suwon 441-707, Korea.
Kim
Jong-Shik
JS
Department of Environmental Sciences, University of California, Riverside, CA 92521-0424, USA.
Kang
Jun-Won
JW
Department of Forest Resources, College of Agriculture and Life Sciences, Seoul National University, Suwon 441-744, Korea.
Cho
Yang-Hee
YH
Korean Agricultural Culture Collection (KACC), Genetic Resources Division, National Institute of Agricultural Biotechnology, Rural Development Administration (RDA), Suwon 441-707, Korea.
Lim
Chun-Keun
CK
College of Agriculture and Life Sciences, Kangwon National University, Chunchon 200-701, Korea.
Parker
Matthew A
MA
Department of Biological Sciences, State University of New York, Binghamton, NY 13902-6000, USA.
Lee
Gil-Bok
GB
Korean Agricultural Culture Collection (KACC), Genetic Resources Division, National Institute of Agricultural Biotechnology, Rural Development Administration (RDA), Suwon 441-707, Korea.
D020561:Alphaproteobacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D020369:Bradyrhizobium / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000032:analysis; D021903:DNA, Ribosomal Spacer / Q000032:analysis*; D007887:Fabaceae / Q000145:classification / Q000382:microbiology*; D020459:Genes, rRNA; D007723:Korea; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012231:Rhizobium / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D017422:Sequence Analysis, DNA; D020579:Sinorhizobium / Q000145:classification / Q000235:genetics / Q000302:isolation & purification
D004269:DNA, Bacterial; D021903:DNA, Ribosomal Spacer; D012336:RNA, Ribosomal, 16S