title: Phylogenetic relationships amongst the saltwater members of the genus Bacteriovorax using rpoB sequences and reclassification of Bacteriovorax stolpii as Bacteriolyticum stolpii gen. nov., comb. nov.
abstract: Members of the saltwater genus Bacteriovorax, formerly known as the marine Bdellovibrio, are obligate predatory bacteria that prey selectively on other Gram-negative bacteria. Previous phylogenetic analysis based on the 16S rRNA genes of saltwater Bacteriovorax isolates from environmental samples revealed 11 distinct phylogenetic clusters based on > or =96.5 % gene sequence similarity. In other micro-organisms, the gene coding for the beta-subunit of RNA polymerase (rpoB) has been shown to be more discriminating than 16S rRNA genes. In this study, rpoB sequences from Bacteriovorax isolates were analysed to determine whether the results would be consistent with those based on 16S rRNA gene sequences. A 1242 bp region of the rpoB gene from 74 saltwater Bacteriovorax strains and two freshwater isolates, Bacteriovorax stolpii Uki2T and Peredibacter starrii A3.12T, was amplified by PCR and analysed. The sequences were aligned and phylogenetic trees were constructed using a neighbour-joining algorithm. The resulting tree showed that the rpoB sequences produced smaller subdivisions of isolates, but were nevertheless consistent with the clusters determined using 16S rRNA gene sequences. Thus, the highly conserved 16S rRNA gene sequences provided good phylogenetic information and the rpoB gene sequences permitted greater differentiation in order to further subdivide phylogenetically distinct groups within the genus Bacteriovorax. Also, on the basis of the extensive diversity and large distance between the saltwater members of the genus Bacteriovorax and the freshwater/soil Bacteriovorax, a reclassification of Bacteriovorax stolpii as Bacteriolyticum stolpii gen. nov., comb. nov. is proposed. A new family, Peredibacteraceae fam. nov., is also described.
authors.affiliation: Department of Medical and Research Technology, School of Medicine, University of Maryland, Allied Health Building, 100 Penn Street, Baltimore, MD 21201, USA. spineiro@som.umaryland.edu
authors.forename: Silvia A
authors.initials: SA
authors.lastname: Piñeiro
authors.forename: Henry N
authors.initials: HN
authors.lastname: Williams
authors.forename: O Colin
authors.initials: OC
authors.lastname: Stine
mesh_terms: D000465:Algorithms; D015373:Bacterial Typing Techniques; D001483:Base Sequence; D004269:DNA, Bacterial / Q000032:analysis; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000235:genetics*; D020564:Deltaproteobacteria / Q000145:classification* / Q000235:genetics; D020459:Genes, rRNA; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012623:Seawater / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012321:DNA-Directed RNA Polymerases; C105078:RNA polymerase beta subunit