Desulfurobacterium atlanticum sp nov., Desulfurobacterium pacificum sp nov and Thermovibrio guaymasensis sp nov., three thermophilic members of the Desulfurobacteriaceae fam. nov., a deep branching lineage within the Bacteria

UMR 6197, Centre National de la Recherche Scientifique, IFREMER and Université de Bretagne Occidentale, IFREMER Centre de Brest, BP 70, 29280 Plouzané, France.
International Journal of Systematic and Evolutionary Microbiology (Impact Factor: 2.51). 01/2007; 56(Pt 12):2843-52. DOI: 10.1099/ijs.0.63994-0
Source: PubMed


Three thermophilic, anaerobic, strictly chemolithoautotrophic, sulphur- and/or thiosulphate-reducing bacteria, designated SL17(T), SL19(T) and SL22(T), were isolated from deep-sea hydrothermal samples collected at 13 degrees N (East Pacific Rise), Guaymas Basin (Gulf of California) and 23 degrees N (Mid-Atlantic Ridge), respectively. These strains differed in their morphology, temperature range and optimum for growth, energy substrates and 16S rRNA gene sequences. The G+C content of the genomic DNA was 41 mol% (SL22(T)), 42 mol% (SL17(T)) and 46 mol% (SL19(T)). Comparative analysis of phenotypic and phylogenetic traits indicated that strains SL17(T) and SL22(T) represented two novel species of the genus Desulfurobacterium and that strain SL19(T) should be considered as a novel species of the genus Thermovibrio. The names Desulfurobacterium pacificum sp. nov. (type strain SL17(T)=DSM 15522(T)=JCM 12127(T)), Desulfurobacterium atlanticum sp. nov. (type strain SL22(T)=DSM 15668(T)=JCM 12129(T)) and Thermovibrio guaymasensis sp. nov. (type strain SL19(T)=DSM 15521(T)=JCM 12128(T)) are proposed for these organisms. Furthermore, phylogenetic data based on 16S rRNA gene sequence analyses correlated with the significant phenotypic differences between members of the lineage encompassing the genera Desulfurobacterium, Thermovibrio and Balnearium and that of the families Aquificaceae and Hydrogenothermaceae. It is therefore proposed that this lineage represents a new family, Desulfurobacteriaceae fam. nov., within the order Aquificales.

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Available from: Stephane L'haridon
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    • "The phylum Aquificae is composed of a single order, Aquificales, and three families, Aquificaceae, Hydrogenothermaceae, and Desulfurobacteriaceae (Reysenbach et al., 2005; L'Haridon et al., 2006). Aquificales are present in many terrestrial and marine geothermal systems where they often form multicellular " streamer " assemblages (Huber et al., 1998; Reysenbach et al., 2000, 2005; Takacs et al., 2001; Eder and Huber, 2002; Spear et al., 2005; Hou et al., 2013; Takacs-Vesbach et al., 2013) but can also be prominent members of planktonic microbial communities (Cole et al., 2013; Hou et al., 2013; Murphy et al., 2013). "
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    ABSTRACT: The order Aquificales (phylum Aquificae) consists of thermophilic and hyperthermophilic bacteria that are prominent in many geothermal systems, including those in Tengchong, Yunnan Province, China. However, Aquificales have not previously been isolated from Tengchong. We isolated five strains of Aquificales from diverse springs (temperature 45.2-83.3°C and pH 2.6-9.1) in the Rehai Geothermal Field from sites in which Aquificales were abundant. Phylogenetic analysis showed that four of the strains belong to the genera Hydrogenobacter, Hydrogenobaculum, and Sulfurihydrogenibium, including strains distant enough to likely justify new species of Hydrogenobacter and Hydrogenobaculum. The additional strain may represent a new genus in the Hydrogenothermaceae. All strains were capable of aerobic respiration under microaerophilic conditions; however, they had variable capacity for chemolithotrophic oxidation of hydrogen and sulfur compounds and nitrate reduction.
    Full-text · Article · Feb 2015 · Frontiers in Microbiology
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    • "Members of the genus Aquifex, such as Aquifex aeolicus VF5, are among the most extreme thermophilic bacteria known, occupying a habitat originally thought to be exclusively occupied by members of the archaeal domain. Aquifex lends its name to the order Aquificales and phylum Aquificae, a group based on 16S ribosomal DNA (rDNA) phylogeny (Huber et al. 1992; Cole et al. 2009) with considerable phylogenetic, ecological, morphological , and metabolic diversity, including the freshwater, filamentous Thermocrinis ruber (Huber et al. 1998); the acidophile Hydrogenobaculum acidophilum (Stohr et al. 2001); and obligate anaerobes in the family Desulfurobacteraceae (L'Haridon et al. 2006). Attempts to determine the evolutionary position of the enigmatic Aquificae phylum have usually supported one of two conflicting hypotheses (Huber and Hannig, 2006) (fig.1): "
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    ABSTRACT: Lateral gene transfer (LGT) is an important factor contributing to the evolution of prokaryotic genomes. The Aquificae are a hyperthermophilic bacterial group whose genes show affiliations to many other lineages, including the hyperthermophilic Thermotogae, the Proteobacteria, and the Archaea. Previous phylogenomic analyses focused on Aquifex aeolicus identified Thermotogae and Aquificae either as successive early branches or sisters in a rooted bacterial phylogeny, but many phylogenies and cellular traits have suggested a stronger affiliation with the Epsilonproteobacteria. Different scenarios for the evolution of the Aquificae yield different phylogenetic predictions. Here we outline these scenarios and consider the fit of the available data, including three sequenced Aquificae genomes, to different sets of predictions. Evidence from phylogenetic profiles and trees suggests that the Epsilonproteobacteria have the strongest affinities with the three Aquificae analyzed. However, this pattern is shown by only a minority of encoded proteins, and the Archaea, many lineages of thermophilic bacteria, and members of genus Clostridium and class Deltaproteobacteria also show strong connections to the Aquificae. The phylogenetic affiliations of different functional subsystems showed strong biases: most but not all genes implicated in the core translational apparatus tended to group Aquificae with Thermotogae, while a wide range of metabolic and cellular processes strongly supported the link between Aquificae and Epsilonproteobacteria. Depending on which sets of genes are privileged, either Thermotogae or Epsilonproteobacteria is the most plausible adjacent lineage to the Aquificae. Both scenarios require massive sharing of genes to explain the history of this enigmatic group, whose history is further complicated by specific affinities of different members of Aquificae to different partner lineages.
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    • "Two out of three families of the Aquificae, Aquificaceae , and Hydrogenothermaceae contain the viral-type PolA; however, the more deeply branching third family, Desulfurobacteriaceae , has a prototypical bacterial PolA. This suggests that a viral-type polA gene replaced its xenolog and became fixed in the genome of a common ancestor of two of three families of Aquificae following their divergence from the Desulfurobacteriaceae (L'Haridon et al. 2006; Hugler et al. 2007). Once fixed in the Aquificae, this polA gene probably descended vertically, because it mirrors the 16S rRNA gene phylogeny. "
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    ABSTRACT: Bioinformatics and functional screens identified a group of Family A-type DNA Polymerase (polA) genes encoded by viruses inhabiting circumneutral and alkaline hot springs in Yellowstone National Park and the U.S. Great Basin. The proteins encoded by these viral polA genes (PolAs) shared no significant sequence similarity with any known viral proteins, but were remarkably similar to PolAs encoded by two of three families of the bacterial phylum Aquificae and by several apicoplast-targeted PolA-like proteins found in the eukaryotic phylum Apicomplexa, which includes the obligate parasites Plasmodium, Babesia, and Toxoplasma. The viral gene products share signature elements previously associated only with Aquificae and Apicomplexa PolA-like proteins and were similar to proteins encoded by prophage elements of a variety of otherwise unrelated Bacteria, each of which additionally encoded a prototypical bacterial PolA. Unique among known viral DNA polymerases, the viral PolA proteins of this study share with the Apicomplexa proteins large amino-terminal domains with putative helicase/primase elements but low primary sequence similarity. The genomic context and distribution, phylogeny, and biochemistry of these PolA proteins suggest that thermophilic viruses transferred polA genes to the Apicomplexa, likely through secondary endosymbiosis of a virus-infected proto-apicoplast, and to the common ancestor of two of three Aquificae families, where they displaced the orthologous cellular polA gene. Based on biochemical activity, gene structure, and sequence similarity we speculate that the xenologous viral-type polA genes may have functions associated with diversity-generating recombination in both Bacteria and Apicomplexa.
    Full-text · Article · Apr 2013 · Molecular Biology and Evolution
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