Phylogenetic position of Salinibacter ruber based on concatenated protein alignments

Soria‐Carrasco, Víctor; Valens-Vadell, Maria; Peña, Arantxa; Antón, Josefa; Amann, Rudolf; Castresana, José; Rosselló‐Móra, Ramon

doi:10.1016/j.syapm.2006.07.001

Cited by 29 publications

(11 citation statements)

References 35 publications

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“…The low resolution of 16S rRNA gene-based phylogeny with respect to closely related species has often been reported [52], [53]. Nevertheless, this approach has been proven to present reliable phylogenetic backbones, which are comparable to MLSA-based approaches [54], [55]. Thus, despite the differences of both Octadecabacter strains on genomic level, the 16S rRNA gene sequences indicate that Arctic and Antarctic strains are phylogenetically closely linked.…”

Section: Resultsmentioning

confidence: 99%

Poles Apart: Arctic and Antarctic Octadecabacter strains Share High Genome Plasticity and a New Type of Xanthorhodopsin

et al. 2013

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The genus Octadecabacter is a member of the ubiquitous marine Roseobacter clade. The two described species of this genus, Octadecabacter arcticus and Octadecabacter antarcticus, are psychrophilic and display a bipolar distribution. Here we provide the manually annotated and finished genome sequences of the type strains O. arcticus 238 and O. antarcticus 307, isolated from sea ice of the Arctic and Antarctic, respectively. Both genomes exhibit a high genome plasticity caused by an unusually high density and diversity of transposable elements. This could explain the discrepancy between the low genome synteny and high 16S rRNA gene sequence similarity between both strains. Numerous characteristic features were identified in the Octadecabacter genomes, which show indications of horizontal gene transfer and may represent specific adaptations to the habitats of the strains. These include a gene cluster encoding the synthesis and degradation of cyanophycin in O. arcticus 238, which is absent in O. antarcticus 307 and unique among the Roseobacter clade. Furthermore, genes representing a new subgroup of xanthorhodopsins as an adaptation to icy environments are present in both Octadecabacter strains. This new xanthorhodopsin subgroup differs from the previously characterized xanthorhodopsins of Salinibacter ruber and Gloeobacter violaceus in phylogeny, biogeography and the potential to bind 4-keto-carotenoids. Biochemical characterization of the Octadecabacter xanthorhodopsins revealed that they function as light-driven proton pumps.

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Section: Resultsmentioning

confidence: 99%

Poles Apart: Arctic and Antarctic Octadecabacter strains Share High Genome Plasticity and a New Type of Xanthorhodopsin

et al. 2013

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“…A phylogenetic analysis was performed for 22 genes from the S. ruber M31 T genome. Although single genes supported different topologies, the topology of the concatenated data sets was found identical to that based on 16S rRNA gene analysis (Soria‐Carrasco et al ., ).…”

Section: Discussionmentioning

confidence: 97%

Salinibacter: an extremely halophilic bacterium with archaeal properties

Oren

2013

FEMS Microbiol Lett

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The existence of large number of a member of the Bacteroidetes in NaCl-saturated brines in saltern crystallizer ponds was first documented in 1999 based on fluorescence in situ hybridization studies. Isolation of the organism and its description as Salinibacter ruber followed soon. It is a rod-shaped, red-orange pigmented, extreme halophile that grows optimally at 20-30% salt. The genus is distributed worldwide in hypersaline environments. Today, the genus Salinibacter includes three species, and a somewhat less halophilic relative, Salisaeta longa, has also been documented. Although belonging to the Bacteria, Salinibacter shares many features with the Archaea of the family Halobacteriaceae that live in the same habitat. Both groups use KCl for osmotic adjustment of their cytoplasm, both mainly possess salt-requiring enzymes with a large excess of acidic amino acids, and both contain different retinal pigments: light-driven proton pumps, chloride pumps, and light sensors. Salinibacter produces an unusual carotenoid, salinixanthin that forms a light antenna and transfers energy to the retinal group of xanthorhodopsin, a light-driven proton pump. Other unusual features of Salinibacter and Salisaeta include the presence of novel sulfonolipids (halocapnine derivatives). Salinibacter has become an excellent model for metagenomic, biogeographic, ecological, and evolutionary studies.

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“…The MLSA approach, based on different gene data sets, does not resolve putative genetic-geographic patterns, as the genetic divergence may be too subtle for the given selection of genes. However, one must take into account that, despite the fact that large sets of concatenated genes tend to reflect the organismal phylogeny (Só ria-Carrasco et al, 2007), perhaps only full genome sequences may reflect geographical isolation in the strain collection of S. ruber, in accordance with taxa segregation that correlates with the average nucleotide or amino-acid identity of shared genes (Konstantinidis and Tiedje, 2005). However, the backlogs in the current state of full genome sequencing make the metabolomic approach a fast and less expensive alternative for revealing prokaryotic biogeography, with the added value of being discriminative at different levels at the geographical scale.…”

Section: Biogeographical Comparisons At the Phenotypic Levelmentioning

confidence: 99%

Metabolic evidence for biogeographic isolation of the extremophilic bacterium Salinibacter ruber

et al. 2008

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The biogeography of prokaryotes and the effect of geographical barriers as evolutionary constraints are currently subjected to great debate. Some clear-cut evidence for geographic isolation has been obtained by genetic methods but, in many cases, the markers used are too coarse to reveal subtle biogeographical trends. Contrary to eukaryotic microorganisms, phenotypic evidence for allopatric segregation in prokaryotes has never been found. Here we present, for the first time, a metabolomic approach based on ultrahigh resolution mass spectrometry to reveal phenotypic biogeographical discrimination. We demonstrate that strains of the cosmopolitan extremophilic bacterium Salinibacter ruber, isolated from different sites in the world, can be distinguished by means of characteristic metabolites, and that these differences can be correlated to their geographical isolation site distances. The approach allows distinct degrees of discrimination for isolates at different geographical scales. In all cases, the discriminative metabolite patterns were quantitative rather than qualitative, which may be an indication of geographically distinct transcriptional or posttranscriptional regulations.

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Phylogenetic position of Salinibacter ruber based on concatenated protein alignments

Cited by 29 publications

References 35 publications

Poles Apart: Arctic and Antarctic Octadecabacter strains Share High Genome Plasticity and a New Type of Xanthorhodopsin

Poles Apart: Arctic and Antarctic Octadecabacter strains Share High Genome Plasticity and a New Type of Xanthorhodopsin

Salinibacter: an extremely halophilic bacterium with archaeal properties

Metabolic evidence for biogeographic isolation of the extremophilic bacterium Salinibacter ruber

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