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Permanent draft genome of Thermithiobaclillus tepidarius DSM 3134 T , a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia

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ABSTRACT

Thermithiobacillus tepidarius DSM 3134T was originally isolated (1983) from the waters of a sulfidic spring entering the Roman Baths (Temple of Sulis-Minerva) at Bath, United Kingdom and is an obligate chemolithoautotroph growing at the expense of reduced sulfur species. This strain has a genome size of 2,958,498 bp. Here we report the genome sequence, annotation and characteristics. The genome comprises 2,902 protein coding and 66 RNA coding genes. Genes responsible for the transaldolase variant of the Calvin-Benson-Bassham cycle were identified along with a biosynthetic horseshoe in lieu of Krebs’ cycle sensu stricto. Terminal oxidases were identified, viz. cytochrome c oxidase (cbb3, EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). Metalloresistance genes involved in pathways of arsenic and cadmium resistance were found. Evidence of horizontal gene transfer accounting for 5.9 % of the protein-coding genes was found, including transfer from Thiobacillus spp. and Methylococcus capsulatus Bath, isolated from the same spring. A sox gene cluster was found, similar in structure to those from other Acidithiobacillia – by comparison with Thiobacillus thioparus and Paracoccus denitrificans, an additional gene between soxA and soxB was found, annotated as a DUF302-family protein of unknown function. As the Kelly-Friedrich pathway of thiosulfate oxidation (encoded by sox) is not used in Thermithiobacillus spp., the role of the operon (if any) in this species remains unknown. We speculate that DUF302 and sox genes may have a role in periplasmic trithionate oxidation.

No MeSH data available.


Related in: MedlinePlus

Transmission electron micrograph of T. tepidarius from a thiosulfate-limited chemostat (20 mM, 0.15 h-1). Cells were obtained from a chemostat-culture at steady-state by centrifugation and were washed and suspended in sterile 150 mM sodium chloride solution and applied to Formvar® and carbon coated copper grid before washing with further saline and staining in 50 mM uranyl acetate for 5 mins and washing again. Stained grids were visualized in a JEOL JEM-1400Plus transmission electron microscope, operating at 120 kV
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Fig2: Transmission electron micrograph of T. tepidarius from a thiosulfate-limited chemostat (20 mM, 0.15 h-1). Cells were obtained from a chemostat-culture at steady-state by centrifugation and were washed and suspended in sterile 150 mM sodium chloride solution and applied to Formvar® and carbon coated copper grid before washing with further saline and staining in 50 mM uranyl acetate for 5 mins and washing again. Stained grids were visualized in a JEOL JEM-1400Plus transmission electron microscope, operating at 120 kV

Mentions: Cells are 0.6 – 1.0 by 0.2 to 0.4 μm and stain Gram negative. They are rapidly motile by means of a single polar flagellum up to 4 μm in length, as shown in Fig. 2. Ubiquinone-8 is the dominant respiratory quinone and cells fix carbon dioxide via the Calvin-Benson-Bassham cycle at the expense of inorganic sulfur oxidation. Cells accumulate polyphosphate (‘volutin’) granules when grown in batch culture but are typically free from storage granules when grown in energy-source-limited chemostats. Anaerobic growth is not observed with tetrathionate as the electron donor and nitrate, nitrite, nitrous oxide, elementary sulfur, sulfate, tetrathionate or pyruvate as terminal electron acceptors, but cultures can reduce nitrate to nitrite. Experimental estimations of G + C content of genomic DNA are 66.6 ± 0.5 mol% by buoyant density [1] or 65.9 ± 0.8 mol% by acid denaturation [9] in our hands. Dry biomass is 47 % (w/w) C regardless of the energy source used. T. tepidariusDSM 3134T does not grow on any organic carbon compound tested, including sugars (glucose, ribose, fructose, sucrose), intermediates of Krebs cycle (citrate, succinate, fumarate, malate, oxaloacetate), carboxylates (glycolate, formate, acetate, propionate, pyruvate), C1 compounds (monomethylamine, dimethylamine, trimethylamine, methanol, methane), structural amino acids (all 20), substituted thiophenes (thiophene-2-carboxylate, thiophene-3-carboxylate) or complex media (yeast extract, nutrient broth, brain-heart infusion, Columbia sheep blood agar, chocolate agar). Energy sources that support autotrophic growth are elementary sulfur, sulfide, trithionate, tetrathionate, hexathionate, heptathionate and thiosulfate. Fe(II), Mn(II), Cu(I), U(IV), pentathionate, dithionate, thiocyanate, sulfite, carbon disulfide, carbonyl sulfide, dimethylsulfide, dimethylsulfoxide, dimethylsulfone and formate do not support autotrophic growth as energy sources. The high growth yields and tetrathionate-accumulation in the early phases of growth make this strain a very interesting model organism for elucidation of sulfur oxidation pathways and their evolution.Fig. 2


Permanent draft genome of Thermithiobaclillus tepidarius DSM 3134 T , a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia
Transmission electron micrograph of T. tepidarius from a thiosulfate-limited chemostat (20 mM, 0.15 h-1). Cells were obtained from a chemostat-culture at steady-state by centrifugation and were washed and suspended in sterile 150 mM sodium chloride solution and applied to Formvar® and carbon coated copper grid before washing with further saline and staining in 50 mM uranyl acetate for 5 mins and washing again. Stained grids were visualized in a JEOL JEM-1400Plus transmission electron microscope, operating at 120 kV
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5037610&req=5

Fig2: Transmission electron micrograph of T. tepidarius from a thiosulfate-limited chemostat (20 mM, 0.15 h-1). Cells were obtained from a chemostat-culture at steady-state by centrifugation and were washed and suspended in sterile 150 mM sodium chloride solution and applied to Formvar® and carbon coated copper grid before washing with further saline and staining in 50 mM uranyl acetate for 5 mins and washing again. Stained grids were visualized in a JEOL JEM-1400Plus transmission electron microscope, operating at 120 kV
Mentions: Cells are 0.6 – 1.0 by 0.2 to 0.4 μm and stain Gram negative. They are rapidly motile by means of a single polar flagellum up to 4 μm in length, as shown in Fig. 2. Ubiquinone-8 is the dominant respiratory quinone and cells fix carbon dioxide via the Calvin-Benson-Bassham cycle at the expense of inorganic sulfur oxidation. Cells accumulate polyphosphate (‘volutin’) granules when grown in batch culture but are typically free from storage granules when grown in energy-source-limited chemostats. Anaerobic growth is not observed with tetrathionate as the electron donor and nitrate, nitrite, nitrous oxide, elementary sulfur, sulfate, tetrathionate or pyruvate as terminal electron acceptors, but cultures can reduce nitrate to nitrite. Experimental estimations of G + C content of genomic DNA are 66.6 ± 0.5 mol% by buoyant density [1] or 65.9 ± 0.8 mol% by acid denaturation [9] in our hands. Dry biomass is 47 % (w/w) C regardless of the energy source used. T. tepidariusDSM 3134T does not grow on any organic carbon compound tested, including sugars (glucose, ribose, fructose, sucrose), intermediates of Krebs cycle (citrate, succinate, fumarate, malate, oxaloacetate), carboxylates (glycolate, formate, acetate, propionate, pyruvate), C1 compounds (monomethylamine, dimethylamine, trimethylamine, methanol, methane), structural amino acids (all 20), substituted thiophenes (thiophene-2-carboxylate, thiophene-3-carboxylate) or complex media (yeast extract, nutrient broth, brain-heart infusion, Columbia sheep blood agar, chocolate agar). Energy sources that support autotrophic growth are elementary sulfur, sulfide, trithionate, tetrathionate, hexathionate, heptathionate and thiosulfate. Fe(II), Mn(II), Cu(I), U(IV), pentathionate, dithionate, thiocyanate, sulfite, carbon disulfide, carbonyl sulfide, dimethylsulfide, dimethylsulfoxide, dimethylsulfone and formate do not support autotrophic growth as energy sources. The high growth yields and tetrathionate-accumulation in the early phases of growth make this strain a very interesting model organism for elucidation of sulfur oxidation pathways and their evolution.Fig. 2

View Article: PubMed Central - PubMed

ABSTRACT

Thermithiobacillus tepidarius DSM 3134T was originally isolated (1983) from the waters of a sulfidic spring entering the Roman Baths (Temple of Sulis-Minerva) at Bath, United Kingdom and is an obligate chemolithoautotroph growing at the expense of reduced sulfur species. This strain has a genome size of 2,958,498 bp. Here we report the genome sequence, annotation and characteristics. The genome comprises 2,902 protein coding and 66 RNA coding genes. Genes responsible for the transaldolase variant of the Calvin-Benson-Bassham cycle were identified along with a biosynthetic horseshoe in lieu of Krebs’ cycle sensu stricto. Terminal oxidases were identified, viz. cytochrome c oxidase (cbb3, EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). Metalloresistance genes involved in pathways of arsenic and cadmium resistance were found. Evidence of horizontal gene transfer accounting for 5.9 % of the protein-coding genes was found, including transfer from Thiobacillus spp. and Methylococcus capsulatus Bath, isolated from the same spring. A sox gene cluster was found, similar in structure to those from other Acidithiobacillia – by comparison with Thiobacillus thioparus and Paracoccus denitrificans, an additional gene between soxA and soxB was found, annotated as a DUF302-family protein of unknown function. As the Kelly-Friedrich pathway of thiosulfate oxidation (encoded by sox) is not used in Thermithiobacillus spp., the role of the operon (if any) in this species remains unknown. We speculate that DUF302 and sox genes may have a role in periplasmic trithionate oxidation.

No MeSH data available.


Related in: MedlinePlus