Sulfate Reduction in Underground Horizons of a Flooded Coal Mine in Kuzbass

Panova, I. A.; Rusanov, Igor I; Kadnikov, Vitaly V.; Latygolets, E. A.; Avakyan, Marat R.; Иванов, М. В.; Zyusman, V. C.; Kovaleva, A. A.; Ravin, Nikolai V.; Пименов, Н. В.; Карначук, О. В.

doi:10.1134/s0026261720050185

Cited by 5 publications

(2 citation statements)

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“…Previously, we analyzed the microbial community of a bacterial mat from a hydrogen sulfide drainage well of the flooded Severnaya mine in Kemerovo, Russia, by subjecting the 16S rRNA gene fragments to high-throughput sequencing [30]. However, all obtained sequences belonging to Thiothrix had more than 97% similarity with several previously described species, which did not allow us to assess the species diversity of Thiothrix.…”

Section: Application Of the Tils Gene To Analyze The Diversity Of Bac...mentioning

confidence: 99%

tilS and rpoB: New Molecular Markers for Phylogenetic and Biodiversity Studies of the Genus Thiothrix

Ravin,

Smolyakov,

Markov

et al. 2023

Microorganisms

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Currently, the phylogeny of the genus Thiothrix is based on comparative whole genome analysis because of the high homology of the 16S ribosomal RNA gene sequences within the genus. We analyzed the possibility of using various conservative genes as phylogenetic markers for the genus Thiothrix. We found that the levels of similarity of the nucleotide sequences of the tRNA(Ile)-lysidine synthase (tilS) and the β subunit of RNA polymerase (rpoB) genes are in good agreement with the average nucleotide identity (ANI) values between the genomes of various representatives of the genus Thiothrix. The genomes of Thiothrix strains MK1, WS, DNT52, DNT53, and H33 were sequenced. Taxonomic analysis using both whole genomes and the tilS gene consistently showed that MK1 and WS belong to Thiothrix lacustris, while DNT52, DNT53, and H33 belong to Thiothrix subterranea. The tilS gene fragments were subjected to high-throughput sequencing to profile the Thiothrix mat of a sulfidic spring, which revealed the presence of known species of Thiothrix and new species-level phylotypes. Thus, the use of tilS and rpoB as phylogenetic markers will allow for rapid analyses of pure cultures and natural communities for the purpose of phylogenetic identification of representatives of the genus Thiothrix.

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Section: Application Of the Tils Gene To Analyze The Diversity Of Bac...mentioning

confidence: 99%

tilS and rpoB: New Molecular Markers for Phylogenetic and Biodiversity Studies of the Genus Thiothrix

Ravin,

Smolyakov,

Markov

et al. 2023

Microorganisms

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“…The known range of habitats of the genus Thiothrix is now actively expanding. Metagenomic analysis of groundwater and cave lakes has shown the presence of representatives of the genus Thiothrix (Macalady et al, 2008;Rossmassler et al, 2016;Panova et al, 2020). Also members of this genus were found in hydrothermal marine ecosystems, wastewater treatment bioreactors (Mardanov et al, 2020), and as ectosymbionts of invertebrates (Konkol et al, 2010;Bauermeister et al, 2012;Li et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Comparative Genome Analysis of the Genus Thiothrix Involving Three Novel Species, Thiothrix subterranea sp. nov. Ku-5, Thiothrix litoralis sp. nov. AS and “Candidatus Thiothrix anitrata” sp. nov. A52, Revealed the Conservation of the Pathways of Dissimilatory Sulfur Metabolism and Variations in the Genetic Inventory for Nitrogen Metabolism and Autotrophic Carbon Fixation

et al. 2021

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Two strains of filamentous, colorless sulfur bacteria were isolated from bacterial fouling in the outflow of hydrogen sulfide-containing waters from a coal mine (Thiothrix sp. Ku-5) and on the seashore of the White Sea (Thiothrix sp. AS). Metagenome-assembled genome (MAG) A52 was obtained from a sulfidic spring in the Volgograd region, Russia. Phylogenetic analysis based on the 16S rRNA gene sequences showed that all genomes represented the genus Thiothrix. Based on their average nucleotide identity and digital DNA-DNA hybridization data these new isolates and the MAG represent three species within the genus Thiothrix with the proposed names Thiothrix subterranea sp. nov. Ku-5T, Thiothrix litoralis sp. nov. AST, and “Candidatus Thiothrix anitrata” sp. nov. A52. The complete genome sequences of Thiothrix fructosivorans QT and Thiothrix unzii A1T were determined. Complete genomes of seven Thiothrix isolates, as well as two MAGs, were used for pangenome analysis. The Thiothrix core genome consisted of 1,355 genes, including ones for the glycolysis, the tricarboxylic acid cycle, the aerobic respiratory chain, and the Calvin cycle of carbon fixation. Genes for dissimilatory oxidation of reduced sulfur compounds, namely the branched SOX system (SoxAXBYZ), direct (soeABC) and indirect (aprAB, sat) pathways of sulfite oxidation, sulfur oxidation complex Dsr (dsrABEFHCEMKLJONR), sulfide oxidation systems SQR (sqrA, sqrF), and FCSD (fccAB) were found in the core genome. Genomes differ in the set of genes for dissimilatory reduction of nitrogen compounds, nitrogen fixation, and the presence of various types of RuBisCO.

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Thiothrix

Grabovich

Ravin

Boden

2023

Bergey's Manual of Systematics of Archaea and Bacteria

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Thi'o.thrix. Gr. neut. n. theîon , brimstone, sulfur (Latin transliteration thium ); Gr. fem. n. thrix , hair; N.L. fem. n. Thiothrix , sulfur hair. Proteobacteria / Gammaproteobacteria / Thiotrichales / Thiotrichaceae / Thiothrix Gram‐stain‐negative, aerobic, and facultative anaerobic filamentous bacteria that can attach to surfaces. Distribution occurs with the help of gonidia. All species are capable of forming rosettes. Elemental sulfur is stored intracellularly. Nonmotile. Capable of chemolithoautotrophic and heterotrophic growth. Mixed metabolic modes are also observed, but it is not entirely clear if this is chemolithoheterotrophy or mixotrophy. Obligately respiratory metabolism. Molecular oxygen, nitrate, and thiosulfate can be used as terminal electron acceptors. CO 2 is fixed through the Calvin–Benson–Bassham cycle. Genomes encode all enzymes of the Krebs cycle, except for the canonical malate dehydrogenase (NAD + , mdh , EC 1.1.1.37) which is replaced by malate dehydrogenase (quinone, mqo , EC 1.1.5.4), which donates electrons to the quinone pool. Reduced sulfur compounds are oxidized to sulfate. Hydrogen sulfide is oxidized to elemental sulfur by bacterial sulfide:quinone reductase (Sqr, EC 1.8.5.4) and sulfide‐cytochrome c reductase (flavocytochrome c, FccAB, EC 1.8.2.3) enzymes; sulfur then oxidized to (bi)sulfite by dissimilatory sulfite reductase (DsrAB, EC 1.8.99.5), and then to sulfate via the direct route by sulfite dehydrogenase (quinone, SoeABC, EC 1.8.5.6) and the indirect one via sulfate adenylyltransferase (Sat, EC 2.7.7.4) and adenylyl‐sulfate reductase (AprAB, EC 1.8.99.2). Thiosulfate is oxidized through a branched version of the Lu‐Kelly cycle (SoxABXYZ). Mesophilic. Dominant fatty acids are C 16:1 ω7, C 16:0 , and C 18:1 ω7. Known habitats are sulfidic springs and lakes, coastal seawater, sulfidic groundwaters, deep‐sea hydrothermal vents, activated sludge, sewage, and exoskeletons of some Crustacea . DNA G + C content (mol%) : 49.3–54.9 (genome sequence). Type species : Thiothrix nivea Winogradsky 1888 AL ( Beggiatoa nivea Rabenhorst 1865).

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Sulfate Reduction in Underground Horizons of a Flooded Coal Mine in Kuzbass

Cited by 5 publications

References 24 publications

tilS and rpoB: New Molecular Markers for Phylogenetic and Biodiversity Studies of the Genus Thiothrix

tilS and rpoB: New Molecular Markers for Phylogenetic and Biodiversity Studies of the Genus Thiothrix

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