Hiroyuki Sawada

Proposal for rejection of Agrobacterium tumefaciens and revised descriptions for the genus Agrobacterium and for Agrobacterium radiobacter and Agrobacterium rhizogenes.

The 16S rRNA sequences of seven representative Agrobacterium strains, eight representative Rhizobium strains, and the type strains of Azorhizobium caulinodans and Bradyrhizobium japonicum were determined. These strains included the type strains of Agrobacterium tumefaciens, Agrobacterium rhizogenes, Agrobacterium radiobacter, Agrobacterium vitis, Agrobacterium rubi, Rhizobium fredii, Rhizobium galegae, Rhizobium huakuii, Rhizobium leguminosarum, Rhizobium loti, Rhizobium meliloti, and Rhizobium tropici. A phylogenetic analysis showed that the 15 strains of Agrobacterium and Rhizobium species formed a compact phylogenetic cluster clearly separated from the other members of the alpha subclass of the Proteobacteria. However, Agrobacterium species and Rhizobium species are phylogenetically entwined with one another, and the two genera cannot be separated. In the Agrobacterium species, the strains of biovar 1, biovar 2, Agrobacterium rubi, and Agrobacterium vitis were clearly separated. The two biovars exhibited homogeneity in their phenotypic, chemotaxonomic, and phylogenetic characteristics, and two species should be established for the two biovars. We considered the nomenclature of the two biovars, and revised descriptions of Agrobacterium radiobacter (for the biovar 1 strains) and Agrobacterium rhizogenes (for the biovar 2 strains) are proposed. The name Agrobacterium tumefaciens is rejected because the type strain of this species was assigned to Agrobacterium radiobacter, and consequently the description of the genus Agrobacterium is revised.

Phylogenetic analysis of Streptomyces spp. causing potato scab based on 16S rRNA sequences.

The complete 16S rRNA sequences of 12 strains of Streptomyces spp., including potato scab pathogens, were determined. Among the strains of Streptomyces scabies that were isolated from diverse geographical areas and differed in melanoid pigment production, either no difference or one difference in sequence was observed. The sequence of S. scabies was most similar to the sequences of Streptomyces diastatochromogenes, Streptomyces bottropensis, and Streptomyces neyagawaensis, which belong to the Diastatochromogenes group. The levels of similarity of the 16S rRNA sequences of Streptomyces acidiscabies and S. scabies were almost the same as the levels of similarity between S. acidiscabies and other Streptomyces strains. Streptomyces sp. strain 91-Sy-13, which was isolated in Japan from potato scab and belongs to a distinct species on the basis of phenotypic characteristics and DNA relatedness, exhibited lower levels of 16S rRNA sequence similarity with other potato scab pathogens, as well as other Streptomyces species. The phylogenetic tree constructed on the basis of 16S rRNA sequence data showed that the Streptomyces spp. that cause potato scab composed unique branches. The results of our phylogenetic analysis based on complete 16S rRNA sequences confirmed the lack of close relationships among Streptomyces spp. that cause potato scab. Our findings suggest that potato scab is caused by phylogenetically diverse Streptomyces species and that the pathogenicities of these organisms developed independently.

Phylogenetic Evidence for Sphingomonas and Rhizomonas as Nonphotosynthetic Members of the Alpha-4 Subclass of the Proteobacteria

To clarify the taxonomic relationships of the genera Rhizomonas and Sphingomonas, the 16S rRNA sequence of Rhizomonas suberifaciens IFO 15211T (T = type strain) was determined. A phylogenetic analysis of aligned 16S rRNA gene sequences revealed that eight species of the genus Sphingomonas and R. suberifaciens are closely related to Erythrobacter longus and Porphyrobacter neustonensis and, therefore, belong in the alpha-4 subclass of the Proteobacteria. Within this subclass, Sphingomonas species and R. suberifaciens are phylogenetically interrelated and comprise several subgroups. Our findings show that the genus and species definitions of these organisms are in need of revision.