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The globally widespread genus Sulfurimonas: versatile energy metabolisms and adaptations to redox clines.

Han Y, Perner M - Front Microbiol (2015)

Bottom Line: Multiple copies of one type of enzyme (e.g., sulfide:quinone reductases and hydrogenases) may play a pivotal role in Sulfurimonas' flexibility to colonize disparate environments.Many of these genes appear to have been acquired through horizontal gene transfer which has promoted adaptations to the distinct habitats.Here we summarize Sulfurimonas' versatile energy metabolisms and link their physiological properties to their global distribution.

View Article: PubMed Central - PubMed

Affiliation: Molecular Biology of Microbial Consortia, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany.

ABSTRACT
Sulfurimonas species are commonly isolated from sulfidic habitats and numerous 16S rRNA sequences related to Sulfurimonas species have been identified in chemically distinct environments, such as hydrothermal deep-sea vents, marine sediments, the ocean's water column, and terrestrial habitats. In some of these habitats, Sulfurimonas have been demonstrated to play an important role in chemoautotrophic processes. Sulfurimonas species can grow with a variety of electron donors and acceptors, which may contribute to their widespread distribution. Multiple copies of one type of enzyme (e.g., sulfide:quinone reductases and hydrogenases) may play a pivotal role in Sulfurimonas' flexibility to colonize disparate environments. Many of these genes appear to have been acquired through horizontal gene transfer which has promoted adaptations to the distinct habitats. Here we summarize Sulfurimonas' versatile energy metabolisms and link their physiological properties to their global distribution.

No MeSH data available.


Phylogenetic relationships of 16S rRNA gene sequences of Sulfurimonas species and closest relatives. The 16S rRNA gene sequences were compiled by using the ARB software (www.arb-home.de) (Ludwig et al., 2004) and the alignments manually verified against known secondary structure regions. Maximum-Likelihood based trees with 1000 bootstrap replicates were constructed using PhyML (Guindon and Gascuel, 2003). Phylogenetic trees for 16S rRNA gene sequences were calculated considering only related sequences with lengths of at least 1400 bp. Trees were imported into ARB and shorter sequences were added subsequently to the trees without changing its topology. The number in the clade indicates the amount of sequences identified from the distinct environments. Only Bootstrap values ≥70 are shown. The scale bar represents the expected number of changes per nucleotide position.
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Figure 1: Phylogenetic relationships of 16S rRNA gene sequences of Sulfurimonas species and closest relatives. The 16S rRNA gene sequences were compiled by using the ARB software (www.arb-home.de) (Ludwig et al., 2004) and the alignments manually verified against known secondary structure regions. Maximum-Likelihood based trees with 1000 bootstrap replicates were constructed using PhyML (Guindon and Gascuel, 2003). Phylogenetic trees for 16S rRNA gene sequences were calculated considering only related sequences with lengths of at least 1400 bp. Trees were imported into ARB and shorter sequences were added subsequently to the trees without changing its topology. The number in the clade indicates the amount of sequences identified from the distinct environments. Only Bootstrap values ≥70 are shown. The scale bar represents the expected number of changes per nucleotide position.

Mentions: Among the genus Sulfurimonas five species have been isolated and described: Sulfurimonas denitrificans (DSM 1251), previously named Thiomicrospira denitrificans, and S. hongkongensis strain AST-10T (DSM 22096) were isolated from coastal marine sediments (Timmer-Ten Hoor, 1975; Takai et al., 2006; Cai et al., 2014), S. autotrophica strain OK10T (DSM 16294) and S. paralvinellae strain GO25T (DSM 17229) were isolated from sediments and polychaete nests in deep-sea hydrothermal vent fields (Inagaki et al., 2003; Takai et al., 2006), and S. gotlandica strain GD1T (DSM 19862) was isolated from the pelagic redox cline in the central Baltic Sea (Grote et al., 2012; Labrenz et al., 2013). The genomes of S. denitrificans, S. autotrophica, and S. gotlandica have already been sequenced and genome sequencing of S. hongkongensis is currently in progress (Sievert et al., 2008b; Sikorski et al., 2010b; Grote et al., 2012; Cai et al., 2014). Based on 16S rRNA genes, a further species is phylogenetically placed within the Sulfurimonas group, namely Thiomicrospira sp. CVO (Figure 1). When Thiomicrospira sp. CVO was isolated from an oil field in Canada (Voordouw et al., 1996), the highest 16S rRNA gene similarity to an isolated strain was to that of Thiomicrospira denitrificans (96.1% similarity) and thus it was classified into the Thiomicrospira genus (Gevertz et al., 2000). However, Thiomicrospira denitrificans had been wrongly classified into the Thiomicrospira genus (Gammaproteobacteria) and was soon after reclassified into the Sulfurimonas genus (Epsilonproteobacteria) (Takai et al., 2006). Consequently, since Thiomicrospira sp. CVO phylogenetically groups among Sulfurimonas species (Figure 1), a reclassification of this strain into the Sulfurimonas genus needs to be discussed and we here incorporate it into our discussion on Sulfurimonas species.


The globally widespread genus Sulfurimonas: versatile energy metabolisms and adaptations to redox clines.

Han Y, Perner M - Front Microbiol (2015)

Phylogenetic relationships of 16S rRNA gene sequences of Sulfurimonas species and closest relatives. The 16S rRNA gene sequences were compiled by using the ARB software (www.arb-home.de) (Ludwig et al., 2004) and the alignments manually verified against known secondary structure regions. Maximum-Likelihood based trees with 1000 bootstrap replicates were constructed using PhyML (Guindon and Gascuel, 2003). Phylogenetic trees for 16S rRNA gene sequences were calculated considering only related sequences with lengths of at least 1400 bp. Trees were imported into ARB and shorter sequences were added subsequently to the trees without changing its topology. The number in the clade indicates the amount of sequences identified from the distinct environments. Only Bootstrap values ≥70 are shown. The scale bar represents the expected number of changes per nucleotide position.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4584964&req=5

Figure 1: Phylogenetic relationships of 16S rRNA gene sequences of Sulfurimonas species and closest relatives. The 16S rRNA gene sequences were compiled by using the ARB software (www.arb-home.de) (Ludwig et al., 2004) and the alignments manually verified against known secondary structure regions. Maximum-Likelihood based trees with 1000 bootstrap replicates were constructed using PhyML (Guindon and Gascuel, 2003). Phylogenetic trees for 16S rRNA gene sequences were calculated considering only related sequences with lengths of at least 1400 bp. Trees were imported into ARB and shorter sequences were added subsequently to the trees without changing its topology. The number in the clade indicates the amount of sequences identified from the distinct environments. Only Bootstrap values ≥70 are shown. The scale bar represents the expected number of changes per nucleotide position.
Mentions: Among the genus Sulfurimonas five species have been isolated and described: Sulfurimonas denitrificans (DSM 1251), previously named Thiomicrospira denitrificans, and S. hongkongensis strain AST-10T (DSM 22096) were isolated from coastal marine sediments (Timmer-Ten Hoor, 1975; Takai et al., 2006; Cai et al., 2014), S. autotrophica strain OK10T (DSM 16294) and S. paralvinellae strain GO25T (DSM 17229) were isolated from sediments and polychaete nests in deep-sea hydrothermal vent fields (Inagaki et al., 2003; Takai et al., 2006), and S. gotlandica strain GD1T (DSM 19862) was isolated from the pelagic redox cline in the central Baltic Sea (Grote et al., 2012; Labrenz et al., 2013). The genomes of S. denitrificans, S. autotrophica, and S. gotlandica have already been sequenced and genome sequencing of S. hongkongensis is currently in progress (Sievert et al., 2008b; Sikorski et al., 2010b; Grote et al., 2012; Cai et al., 2014). Based on 16S rRNA genes, a further species is phylogenetically placed within the Sulfurimonas group, namely Thiomicrospira sp. CVO (Figure 1). When Thiomicrospira sp. CVO was isolated from an oil field in Canada (Voordouw et al., 1996), the highest 16S rRNA gene similarity to an isolated strain was to that of Thiomicrospira denitrificans (96.1% similarity) and thus it was classified into the Thiomicrospira genus (Gevertz et al., 2000). However, Thiomicrospira denitrificans had been wrongly classified into the Thiomicrospira genus (Gammaproteobacteria) and was soon after reclassified into the Sulfurimonas genus (Epsilonproteobacteria) (Takai et al., 2006). Consequently, since Thiomicrospira sp. CVO phylogenetically groups among Sulfurimonas species (Figure 1), a reclassification of this strain into the Sulfurimonas genus needs to be discussed and we here incorporate it into our discussion on Sulfurimonas species.

Bottom Line: Multiple copies of one type of enzyme (e.g., sulfide:quinone reductases and hydrogenases) may play a pivotal role in Sulfurimonas' flexibility to colonize disparate environments.Many of these genes appear to have been acquired through horizontal gene transfer which has promoted adaptations to the distinct habitats.Here we summarize Sulfurimonas' versatile energy metabolisms and link their physiological properties to their global distribution.

View Article: PubMed Central - PubMed

Affiliation: Molecular Biology of Microbial Consortia, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany.

ABSTRACT
Sulfurimonas species are commonly isolated from sulfidic habitats and numerous 16S rRNA sequences related to Sulfurimonas species have been identified in chemically distinct environments, such as hydrothermal deep-sea vents, marine sediments, the ocean's water column, and terrestrial habitats. In some of these habitats, Sulfurimonas have been demonstrated to play an important role in chemoautotrophic processes. Sulfurimonas species can grow with a variety of electron donors and acceptors, which may contribute to their widespread distribution. Multiple copies of one type of enzyme (e.g., sulfide:quinone reductases and hydrogenases) may play a pivotal role in Sulfurimonas' flexibility to colonize disparate environments. Many of these genes appear to have been acquired through horizontal gene transfer which has promoted adaptations to the distinct habitats. Here we summarize Sulfurimonas' versatile energy metabolisms and link their physiological properties to their global distribution.

No MeSH data available.