Reassessment of the Phylogenetic Position of Caulobacter subvibrioides

Abstract

Determination of the 16s rRNA gene sequence of Caulobacter subvibrioides ATCC 15264T (T = type strain) confirmed that this species is a member of the alpha subclass of the Proteobacteria and showed that it is phylogenetically most closely related to the Caulobacter group comprising the species Caulobacter bacteroides, Caulobacter crescentus, and Brevundimonas (Pseudomonas) diminuta, for which 16s rRNA sequences of the type strains are currently available. The closest known relative of strain ATCC 15264T among these species is B. diminuta (level of direct pairwise sequence similarity, 95%). On the basis of its previously determined 16s rRNA sequence (accession number M83797), C. subvibrioides is most closely related to Sphingomonas adhaesiva in the alpha4 subgroup (level of similarity, 97.7%). Analysis of the hydroxy fatty acids of C. subvibrioides ATCC 15264T showed that the 2-hydroxymyristic acid which is characteristic of the genus Sphingomonas was absent.In 1992 Stahl et al. (20) reported on the phylogeny of the genus Caulobacter. These authors noted that most of the caulobacters, which belong to the alpha subclass of the Proteobacteria (20, 23), made up a diverse but coherent phylogenetic assemblage based on a comparison of their 16s rRNA sequences; the only exception was Caulobacter subvibrioides, which was only peripherally related to the main Caulobacter assemblage. However, insufficient outgroup reference sequences were used for accurate phylogenetic positioning of C. subvibrioides, and the relationship of this organism with other members of the alpha subclass of the Proteobacteriu remained unclear.Later, Hugenholtz et al. (4) showed that the published 16s rRNA sequence of C. subvibrioides CB81 (nucleotide sequence accession number M83797) was most closely related to the sequences of members of the alpha-4 subgroup of the Proteobacteria and that C. subvibrioides grouped with Blastobacter natatorius (19), Erythrobacter longus (15), and Porphyrobacter neustonensis (3). 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. The culture used by Stahl et al. (20) also originated as strain CB81 but has had a different history since.In our experience the designated type strain of C. subvibrioides, strain ATCC 15264 (17), is not a typical member of the alpha-4 subgroup and appears to be typical of the caulobacters. Consequently, we decided to examine the hydroxy fatty acid profile of the type strain of C. subvibrioides to see if it contained the signature 2-hydroxymyristic acid characteristic of the fatty acids of other members of the alpha-4 subgroup, including Sphingomonas spp. (24) organisms as strain ACM 2483T. Cells from our original freezedried ampoules were grown in peptone-yeast extract medium (18) with agitation in an environmental incubator at 28"C, harvested by centrifu...

Phylogeny and polyphasic taxonomy of Caulobacter species. Proposal of Maricaulis gen. nov. with Maricaulis maris (Poindexter) comb. nov. as the type species, and emended description of the genera Brevundimonas and Caulobacter

“…M83797 ; Stahl et al, 1992). We also investigated the 16s rDNA sequence of the type strain of C. subvibrioides and found it to fit into the Brevundimonas cluster, as has also been reported by Sly (1997). Another confusion concerns the type strain of C. bacteroides, in that the 16s rDNA sequence determined by Stahl et al (1992) was identical to the 16s rDNA sequence we have determined for C. fusiformis ATCC 15257T, while the type strain of C. bacteroides, LMG 15096T, appears in fact to be a member of the genus Brevundimonas.…”

“…M83797) described as being from C. subvibrioides strain CB81T (Stahl et al, 1992). However, from the data obtained in this study, the 16s rDNA sequence of C. subvibrioides (LMG 14903T = ATCC 15264T = CB81') was clearly different from the sequence reported by Stahl et al (1992) and, in an independent study, Sly et al (1997) also recognized that the 16s rDNA sequence for C. subvibrioides (ATCC 1 5264' = ACM 2483T = CB8 1 ' ) is different from that published by Stahl et al (1992). The sequence determined in this study for C. subvibrioides was identical with that determined by Sly et al (1 997).…”

“…In a pioneering study, Stahl et al (1992) sequenced the 16s rRNA of several Caulobacter isolates. Although sequences of type strains of Caulobacter species were not included in this study and a strain wrongly labelled as Caulobacter subvibrioides was included (Sly et al, 1997), this study revealed, for the first time, that Caulobacter actually forms two different lineages, one comprising the freshwater and brackish water Caulobacter spp. and the other comprising the marine forms.…”

Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence.

“…1). Previously, it was revealed that some species of the genus Caulobacter were closely related to the two species of the genus Brevundimonas based on the 16S rRNA sequence and compositions of phospho-and sulfolipids (Stahl et al, 1992 ;Abraham et al, 1997 ;Sly et al, 1997). However, two species of the genus Brevundimonas were not compared with the genus Caulobacter when the name Brevundimonas was proposed as a new genus (Segers et al, 1994).…”

Use of Dialysis to Prepare Bacterial DNA Suitable as PCR Template

“…A forward primer, 5 ′ -AAC c / t TGAGAGTTTGAT c / t CTG-3 ′ , was designed on the basis of 16S rRNA sequences available for Caulobacter spp. from the GenBank ® database (www.ncbi.nim.nih.gov) (5,6) and used in combination with the reverse primer 5 ′ -GGTTACCTTGTTACGACTT-3 ′ . These primers overlap by 14 and 19 bases, respectively, the universal eubacterial primers designated fD1 and rP1 by Weisburg et al (7).…”