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

Abstract

Ministq of Agriculture, Forestry and Fisheries, Akitsu, and Faculty of To clarify the taxonomic relationships of the genera Rhizomonas and Sphingomonas, the 16s rFWA sequence of Rhizornonas suberifaciens I F 0 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 Porphyrobucter neustonensis and, therefore, belong in the alpha-4 subclass of the Proteobacteria. Within this subclass, Sphingomonus 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. Yabuuchi et al. (42). Sphingomonas macrogoltabidus and Sphingomonas terrae are polyethylene glycolutilizing bacteria (11, 12) which were previously classified as Flavobacterium species. Polyethylene glycol 4000 is utilized by a single bacterium, Sphingomonas terrae, but polyethylene glycol 6000 is utilized by symbiotic mixed cultures of two strains (13), and the dominant bacterium in the mixed cultures is Sphingomonas macrogoltabidus.Recently, we compared the 16s rRNA sequences of the eight previously described and newly proposed species of the genus Sphingomonas with the 16s rRNA sequences of 15 representative species belonging to the alpha subclass of the Proteobacteria (29), and we found that the eight Sphingomonas species form a large and heterogeneous cluster which is clearly separate from all other representatives of the alpha subclass of the Proteobacteria (26,38) except Erythrobacter longus (23,24).On the other hand, the genus Rhizomonas and the single species Rhizomonas suberifaciens were proposed by van Bruggen et al. (32) for the gram-negative, motile, rod-shaped bacteria that cause corky root of lettuce. Most strains of Rhizomonas suberifaciens are oligotrophic (31), but the morphological, physiological, and chemotaxonomic characteristics * Corresponding author. Mailing address: Institute for Fermentation, Osaka, 17-85, Juso-honmachi 2-chome7 Yodogawa-ku, Osaka 532, Japan. Phone: 06-300-6555. Fax: 06-300-6814. of these organisms are similar to those reported for Sphingomonas paucimobilis (33,42). Neither Rhizomonas suberifaciens nor Sphingomonas paucimobilis produces acid on peptone-glucose medium, but both organisms produce acid on ammonium or nitrate-glucose medium (6). Strains of these two species have the same isoprenoid quinone (ubiquinone 10) and similar fatty acid compositions (8, 17,33), and the results of grouping based on these two characteristics have been shown to coincide with the results of grouping based on rRNA-DNA homology data (33).On the basis of these findings, we suggested previously that species belonging to the genera Sphingomonas and Rhizomonus are closely related to each other (29).Recently, on the basis of sequencing data for 270 bases of 16s rRNA genes from eight strains of Rhizomonas species and eight strains of Sphing...

The hierarchical system of the ‘Alphaproteobacteria’: description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov.

“…The topology of this cluster differed from that in the ARB and BMSB trees, both of which showed this cluster to be included in the lineage of the genus Sphingomonas. The members of this cluster produce pigment (yellow, orange or pink) and mainly contain bacteriochlorophyll a, whereas members of the genus Sphingomonas do not (Shiba & Simidu, 1982;Fuerst et al, 1993;Takeuchi et al, 1994;Yurkov et al, 1994;Denner et al, 2002). Takeuchi et al (2001) also showed that the genus Sphingomonas was related only distantly to the genera Erythrobacter, Erythromicrobium and Porphyrobacter based on 16S rRNA gene sequence similarity, which was 92?9-94?8 %, and the genus Sphingomonas had the presence of one or more oligosaccharide-type glycosphingolipid(s) (GSL) as one of its most characteristic features, whereas the genera Erythrobacter, Porphyrobacter and Erythromicrobium contained monosaccharide-type GSLs only.…”

Reassessment of the Phylogenetic Position of Caulobacter subvibrioides

“…Subsequently, it was found that the genera Sphingomonas and Rhizomonas were also members of the expanding alpha-4 subgroup (21,22). Strain CB81 was designated the type strain of the species by Poindexter (12) and was deposited in the American Type Culture Collection as strain ATCC 15264.…”

Superchannel of Bacteria: Biological Significance and New Horizons

“…Three linker loops (loops [1][2][3] connect the N-and C-domains, and the cleft formed between the two domains is the alginate-binding region, which is larger than that observed in other substratebinding proteins, such as maltose-binding proteins. 25,26) The calcium ion in the C-domain has no function in alginate binding, since the location of the ion is far (about 40 Å ) from the cleft.…”

“…1) Due to the presence of GSLs, the genus Sphingomonas is classified independently from pseudomonades and is grouped phylogenetically into the -4 subclass of Proteobacteria. 2) Some sphingomonades are characterized by the fact that their cells are covered with many large pleat-like substances 3) and show extraordinary metabolic abilities to degrade various refractory environmental pollutants. 4) These characteristics, inherent to bacteria of this genus, call attention to an unexpected structure and function of the cell surface.…”