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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.


Maximum-likelyhood phylogenetic tree based on CLUSTALW alignment of 16S rRNA gene sequences of the Acidithiobacillia. Type strains of each species of Acidithiobacillus are used, along with that of Thermithiobacillus (emboldened). Thermithiobacillus sp. NCIMB 8349 (the only other Thermithiobacillus sp. in culture) is given for the sake of completeness. Sequences pertaining to organisms for which a publically available genome sequence exists are underlined. Accession numbers for the GenBank database are in parentheses. Alignment and tree were constructed in MEGA 6 [30] using 1,509 positions and pairwise deletion. Tree was drawn using the Tamura-Nei model for maximum-likelyhood trees [31]. Values at nodes are based on 5,000 bootstrap replicates. Scale-bar indicates 2 substitutions per 100. Thiobacillus thioparus DSM 505T is used as the outgroup
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Fig1: Maximum-likelyhood phylogenetic tree based on CLUSTALW alignment of 16S rRNA gene sequences of the Acidithiobacillia. Type strains of each species of Acidithiobacillus are used, along with that of Thermithiobacillus (emboldened). Thermithiobacillus sp. NCIMB 8349 (the only other Thermithiobacillus sp. in culture) is given for the sake of completeness. Sequences pertaining to organisms for which a publically available genome sequence exists are underlined. Accession numbers for the GenBank database are in parentheses. Alignment and tree were constructed in MEGA 6 [30] using 1,509 positions and pairwise deletion. Tree was drawn using the Tamura-Nei model for maximum-likelyhood trees [31]. Values at nodes are based on 5,000 bootstrap replicates. Scale-bar indicates 2 substitutions per 100. Thiobacillus thioparus DSM 505T is used as the outgroup

Mentions: This strain was isolated from sulfidic groundwater flowing into a Roman bathhouse (Temple of Sulis-Minerva, now The Roman Baths, Bath, UK) – the only other strain of this genus held in a culture collection (Thermithiobacillus sp. NCIMB 8349) came from decomposing concrete in the Melbourne sewers in the 1940s [5]. The authors have detected at least 6 OTUs representing probably other Thermithiobacillus spp. in 16S rRNA gene libraries from the Roman Baths and have isolated a number of strains to date, indicating that Thermithiobacillus spp. are no more difficult to isolate than other sulfur-oxidising autotrophs and may thus simply be rare or confined to rare ecosystems. It forms white colonies of 2–5 mm diameter in 48 h that smell faintly of elementary sulfur if grown on thiosulfate-containing basal salts agar. In batch cultures, thiosulfate is oxidized stoichiometrically to tetrathionate early in the exponential phase, resulting in an increase in culture pH from pH 6.8 to pH 7.5–8.0 – a hallmark of the genus – before being fully oxidized to sulfate, with concomitant fall in culture pH, usually ending at pH 5.2. In continuous cultures, no intermediates accumulate in the medium. In the authors’ hands, trithionate has also been observed very early in the growth phase in batch culture, prior to tetrathionate production. Substrate-level phosphorylation appears not to participate in the energy conservation of this strain and all ATP is thus formed through oxidative phosphorylation [2]. The type – and only – strain was isolated from an enrichment culture comprising water obtained from the inflow of the Great Bath (Roman Baths, Bath, UK) in 1983 (Ann P. Wood, personal communication) added to a basal salts medium supplemented with thiosulfate and monomethylamine hydrochloride, before plating onto basalt salts agar containing 5 mM thiosulfate as sole energy source and incubated under air enriched with 5 % (v/v) carbon dioxide as sole carbon source. Key features of this organism are summarized in Table 1. A phylogenetic tree based on the 16S rRNA gene sequence, showing the position of the organism with regard to the Acidithiobacillia, rooted with Thiobacillus thioparus, is given in Fig. 1.Table 1


Permanent draft genome of Thermithiobaclillus tepidarius DSM 3134 T , a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia
Maximum-likelyhood phylogenetic tree based on CLUSTALW alignment of 16S rRNA gene sequences of the Acidithiobacillia. Type strains of each species of Acidithiobacillus are used, along with that of Thermithiobacillus (emboldened). Thermithiobacillus sp. NCIMB 8349 (the only other Thermithiobacillus sp. in culture) is given for the sake of completeness. Sequences pertaining to organisms for which a publically available genome sequence exists are underlined. Accession numbers for the GenBank database are in parentheses. Alignment and tree were constructed in MEGA 6 [30] using 1,509 positions and pairwise deletion. Tree was drawn using the Tamura-Nei model for maximum-likelyhood trees [31]. Values at nodes are based on 5,000 bootstrap replicates. Scale-bar indicates 2 substitutions per 100. Thiobacillus thioparus DSM 505T is used as the outgroup
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig1: Maximum-likelyhood phylogenetic tree based on CLUSTALW alignment of 16S rRNA gene sequences of the Acidithiobacillia. Type strains of each species of Acidithiobacillus are used, along with that of Thermithiobacillus (emboldened). Thermithiobacillus sp. NCIMB 8349 (the only other Thermithiobacillus sp. in culture) is given for the sake of completeness. Sequences pertaining to organisms for which a publically available genome sequence exists are underlined. Accession numbers for the GenBank database are in parentheses. Alignment and tree were constructed in MEGA 6 [30] using 1,509 positions and pairwise deletion. Tree was drawn using the Tamura-Nei model for maximum-likelyhood trees [31]. Values at nodes are based on 5,000 bootstrap replicates. Scale-bar indicates 2 substitutions per 100. Thiobacillus thioparus DSM 505T is used as the outgroup
Mentions: This strain was isolated from sulfidic groundwater flowing into a Roman bathhouse (Temple of Sulis-Minerva, now The Roman Baths, Bath, UK) – the only other strain of this genus held in a culture collection (Thermithiobacillus sp. NCIMB 8349) came from decomposing concrete in the Melbourne sewers in the 1940s [5]. The authors have detected at least 6 OTUs representing probably other Thermithiobacillus spp. in 16S rRNA gene libraries from the Roman Baths and have isolated a number of strains to date, indicating that Thermithiobacillus spp. are no more difficult to isolate than other sulfur-oxidising autotrophs and may thus simply be rare or confined to rare ecosystems. It forms white colonies of 2–5 mm diameter in 48 h that smell faintly of elementary sulfur if grown on thiosulfate-containing basal salts agar. In batch cultures, thiosulfate is oxidized stoichiometrically to tetrathionate early in the exponential phase, resulting in an increase in culture pH from pH 6.8 to pH 7.5–8.0 – a hallmark of the genus – before being fully oxidized to sulfate, with concomitant fall in culture pH, usually ending at pH 5.2. In continuous cultures, no intermediates accumulate in the medium. In the authors’ hands, trithionate has also been observed very early in the growth phase in batch culture, prior to tetrathionate production. Substrate-level phosphorylation appears not to participate in the energy conservation of this strain and all ATP is thus formed through oxidative phosphorylation [2]. The type – and only – strain was isolated from an enrichment culture comprising water obtained from the inflow of the Great Bath (Roman Baths, Bath, UK) in 1983 (Ann P. Wood, personal communication) added to a basal salts medium supplemented with thiosulfate and monomethylamine hydrochloride, before plating onto basalt salts agar containing 5 mM thiosulfate as sole energy source and incubated under air enriched with 5 % (v/v) carbon dioxide as sole carbon source. Key features of this organism are summarized in Table 1. A phylogenetic tree based on the 16S rRNA gene sequence, showing the position of the organism with regard to the Acidithiobacillia, rooted with Thiobacillus thioparus, is given in Fig. 1.Table 1

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.