Inferring the Evolutionary History of Vibrios by Means of Multilocus Sequence Analysis

Abstract

We performed the first broad study aiming at the reconstruction of the evolutionary history of vibrios by means of multilocus sequence analysis of nine genes. Overall, 14 distinct clades were recognized using the SplitsTree decomposition method. Some of these clades may correspond to families, e.g., the clades Salinivibrio and Photobacteria, while other clades, e.g., Splendidus and Harveyi, correspond to genera. The common ancestor of all vibrios was estimated to have been present 600 million years ago. We can define species of vibrios as groups of strains that share >95% gene sequence similarity and >99.4% amino acid identity based on the eight protein-coding housekeeping genes. The gene sequence data were used to refine the standard online electronic taxonomic scheme for vibrios (http://www.taxvibrio.lncc.br).Vibrios are widespread in the aquatic environment, occupying a variety of ecological niches, such as the human and animal gut, the surface of chitinous organisms, most notably copepods, and the coral mucus layer. A better understanding of the ecology and the patterns of distribution of vibrios relies on the online electronic taxonomy. Polyphasic taxonomic studies of vibrios performed in recent years have underpinned this new paradigm in studies of the biodiversity and systematics of this group (16,17,19). Currently, we recognize 78 species of vibrios distributed into five phylogenetic robust clades corresponding to the genera Vibrio, Photobacterium, Salinivibrio, Enterovibrio, and Grimontia based on 16S rRNA gene sequences (16,17,19). Both genome content and architecture indicate that these genera share a common ancestor (12). In addition, the genera within vibrios are defined on the basis of their shared sequence similarities in different loci. Species within the genus Vibrio share at least 85% gene sequence similarity in recA, rpoA, and pyrH (18).Species of vibrios are defined as clusters of strains with high phenotypic and genotypic similarities. Clusters comprise strains with highly similar genomes as determined by multilocus sequence analysis (MLSA), amplified fragment length polymorphism analysis, and DNA-DNA hybridization (DDH) (16,17,19). Formal delineation of bacterial species still relies on DDH, with a cutoff level of Ͼ70% DDH similarity, but this technique is time-consuming and can be performed in relatively few laboratories and, more importantly, the DDH data are not cumulative in online databases. Clearly, a reliable and straightforward alternative is the use of MLSA. The usefulness of MLSA in the taxonomy of vibrios was described in previous papers (e.g., references 15 and 18). Overall, species form discrete clusters on the basis of recA, rpoA, and pyrH, with a species cutoff level of Ͼ94% gene sequence similarity (18). However, some groups of species, e.g., the Vibrio splendidus and Vibrio harveyi species groups, were somewhat fuzzy on the basis of recA, gyrB, and gapA (15, 18). Thus, it is very important to evaluate additional genetic markers that can distinguish closely related species o...

Vibrio inhibens sp. nov., a novel bacterium with inhibitory activity against Vibrio species

“…Genomic DNA extraction, PCR amplification and sequencing of the 16S rRNA, DNA gyrase B subunit (gyrB), urydilate kinase (pyrH), recombination repair protein (recA) and topoisomerase I (topA), were carried out as described previously by Sawabe et al 17 and Balcázar et al 18 The sequences obtained were compared against the sequences available in the GenBank, EMBL and DDBJ databases obtained from the National Center for Biotechnology Information using the BLASTN. 19 Phylogenetic analysis was performed using the software MEGA version 4.0 (Center for Evolutionary Medicine and Informatics, Tempe, AZ, USA) after multiple alignments of data by CLUSTAL X.…”

“…Multilocus sequencing analysis of housekeeping genes has been used previously for inferring evolutionary relationships among members of the genus Vibrio. 17,26 In the present study, we used four housekeeping genes, gyrB, pyrH, recA and topA, in order to establish the taxonomic position of strain BFLP-10 T . The phylogenetic trees based on gyrB, pyrH, recA and topA gene sequences revealed low levels of similarity (o91.2%) between strain BFLP-10 T and the most closely related species (Figure 2).…”

Description of Enterovibrio nigricans sp. nov., reclassification of Vibrio calviensis as Enterovibrio calviensis comb. nov. and emended description of the genus Enterovibrio Thompson et al. 2002

“…Three years later, a second Enterovibrio species was described, Enterovibrio coralii, isolated from diseased corals (Thompson et al, 2005b). It is also recognized, although no formal proposal has been made, that Vibrio calviensis (Denner et al, 2002) shares greater phylogenetic relatedness with members of Enterovibrio than with Vibrio species, according to recent phylogenetic analyses (Thompson et al, 2005b;Sawabe et al, 2007). In fact, the generic assignment of V. calviensis was already considered somewhat provisional at the time of its description (Denner et al, 2002).…”

Vibrio porteresiae sp. nov., a diazotrophic bacterium isolated from a mangrove-associated wild rice (Porteresia coarctata Tateoka)

“…Strains MSSRF30 T and MSSRF31 may belong to the V. cholerae clade (Fig. 2), as defined by Sawabe et al (2007b), which is strong evidence to propose these two new isolates as a novel taxon in the genus Vibrio.…”

“…In order to overcome the effects of gene conversion and recombination, multigene phylogenetic trees were constructed for strains MSSRF30 T and MSSRF31 using the four genes. The sequences of the pyrH (445 bp), recA (652 bp), rpoA (834 bp) and 16S rRNA genes (1272 bp) of 62 representative type strains (Thompson et al, 2005;Sawabe et al, 2007b), including strain MSSRF30 T , of the family Vibrionaceae were retained and used to reconstruct a concatenated network tree based on SPLITSTREE version 4.6 (Huson & Bryant, 2005). In the SPLITS decomposition analysis using nine gene loci, at least 14 distinctive clades were recognized for vibrios (Sawabe et al, 2007b).…”