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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 hydrogenase large subunit sequences to those from Sulfurimonas species. The phylogenetic tree was constructed with the same method as described in Figure 2. The percentage of bootstrap resamplings ≥70 is indicated on the branches. The scale bar represents the expected number of changes per amino acids position. The groups of hydrogenases are classified according to Vignais and Billoud (2007). Isolation sources of Sulfurimonas species are indicated in different colors: blue, marine non-vent water system; purple, marine sediments; red, hydrothermal environments.
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Figure 3: Phylogenetic relationships of hydrogenase large subunit sequences to those from Sulfurimonas species. The phylogenetic tree was constructed with the same method as described in Figure 2. The percentage of bootstrap resamplings ≥70 is indicated on the branches. The scale bar represents the expected number of changes per amino acids position. The groups of hydrogenases are classified according to Vignais and Billoud (2007). Isolation sources of Sulfurimonas species are indicated in different colors: blue, marine non-vent water system; purple, marine sediments; red, hydrothermal environments.

Mentions: Epsilonproteobacteria mostly use the [NiFe]-hydrogenase to catalyze the reaction H2 ↔ 2H+ + 2e- (Vignais and Billoud, 2007). The [NiFe]-hydrogenase is a heterodimer with a small subunit containing three iron–sulfur clusters and a large subunit containing the active site. They are classified in four groups, namely Groups I to IV (Vignais and Billoud, 2007). Except for some of the human and animal pathogens and Thiovolum, most Epsilonproteobacteria have a broad array of different [NiFe]-hydrogenases affiliated with Group I, II, and IV (Supplementary Table S1; Figure 3). Group I hydrogenases are membrane-bound hydrogenases performing respiratory hydrogen oxidation linked to the reduction of electron acceptors (Vignais and Billoud, 2007). They are found in all five Sulfurimonas species (Figure 3, Supplementary Table S1 and references therein), indicating that this group of hydrogenases might be essential for growth. The periplasmic Group I [NiFe]-hydrogenase of S. denitrificans contributes to hydrogen uptake activity in the membrane fractions of the cell extracts (Han and Perner, 2014). In S. paralvinella hydrogen uptake activity was also detected (Takai et al., 2005). However, for S. gotlandica and S. hongkongensis these experiments have not been performed to date. In line with lacking growth on hydrogen, no hydrogen uptake activity was detected in the cell extracts of S. autotrophica (Takai et al., 2005). However, since its genome harbors hydrogenases (Sikorski et al., 2010b), under specific environmental conditions S. autotrophica may well be able to express hydrogenases and consume hydrogen. S. hongkongensis and S. gotlandica even have two and three Group I [NiFe]-hydrogenases, respectively, which may reflect the enzymes’ abilities to function at different hydrogen concentrations, as has been suggested in the Epsilonproteobacteria N. profundicola and S. sp. NBC 37-1 (Nakagawa et al., 2007; Campbell et al., 2009). The Group I Sulfurimonas hydrogenases group into different clusters with phylogenetically diverse Epsilonproteobacteria (Figure 3). This may suggest multiple acquisitions or possibly repeated loss of these hydrogenases among the 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 hydrogenase large subunit sequences to those from Sulfurimonas species. The phylogenetic tree was constructed with the same method as described in Figure 2. The percentage of bootstrap resamplings ≥70 is indicated on the branches. The scale bar represents the expected number of changes per amino acids position. The groups of hydrogenases are classified according to Vignais and Billoud (2007). Isolation sources of Sulfurimonas species are indicated in different colors: blue, marine non-vent water system; purple, marine sediments; red, hydrothermal environments.
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Related In: Results  -  Collection

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

Figure 3: Phylogenetic relationships of hydrogenase large subunit sequences to those from Sulfurimonas species. The phylogenetic tree was constructed with the same method as described in Figure 2. The percentage of bootstrap resamplings ≥70 is indicated on the branches. The scale bar represents the expected number of changes per amino acids position. The groups of hydrogenases are classified according to Vignais and Billoud (2007). Isolation sources of Sulfurimonas species are indicated in different colors: blue, marine non-vent water system; purple, marine sediments; red, hydrothermal environments.
Mentions: Epsilonproteobacteria mostly use the [NiFe]-hydrogenase to catalyze the reaction H2 ↔ 2H+ + 2e- (Vignais and Billoud, 2007). The [NiFe]-hydrogenase is a heterodimer with a small subunit containing three iron–sulfur clusters and a large subunit containing the active site. They are classified in four groups, namely Groups I to IV (Vignais and Billoud, 2007). Except for some of the human and animal pathogens and Thiovolum, most Epsilonproteobacteria have a broad array of different [NiFe]-hydrogenases affiliated with Group I, II, and IV (Supplementary Table S1; Figure 3). Group I hydrogenases are membrane-bound hydrogenases performing respiratory hydrogen oxidation linked to the reduction of electron acceptors (Vignais and Billoud, 2007). They are found in all five Sulfurimonas species (Figure 3, Supplementary Table S1 and references therein), indicating that this group of hydrogenases might be essential for growth. The periplasmic Group I [NiFe]-hydrogenase of S. denitrificans contributes to hydrogen uptake activity in the membrane fractions of the cell extracts (Han and Perner, 2014). In S. paralvinella hydrogen uptake activity was also detected (Takai et al., 2005). However, for S. gotlandica and S. hongkongensis these experiments have not been performed to date. In line with lacking growth on hydrogen, no hydrogen uptake activity was detected in the cell extracts of S. autotrophica (Takai et al., 2005). However, since its genome harbors hydrogenases (Sikorski et al., 2010b), under specific environmental conditions S. autotrophica may well be able to express hydrogenases and consume hydrogen. S. hongkongensis and S. gotlandica even have two and three Group I [NiFe]-hydrogenases, respectively, which may reflect the enzymes’ abilities to function at different hydrogen concentrations, as has been suggested in the Epsilonproteobacteria N. profundicola and S. sp. NBC 37-1 (Nakagawa et al., 2007; Campbell et al., 2009). The Group I Sulfurimonas hydrogenases group into different clusters with phylogenetically diverse Epsilonproteobacteria (Figure 3). This may suggest multiple acquisitions or possibly repeated loss of these hydrogenases among the 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.