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
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 sul...
Published in: | Frontiers in Microbiology |
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Language: | English |
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2021
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Online Access: | https://doi.org/10.3389/fmicb.2021.760289 https://doaj.org/article/8e003ad6659247a7b320ddb4becf7d6e |
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ftdoajarticles:oai:doaj.org/article:8e003ad6659247a7b320ddb4becf7d6e 2023-05-15T18:43:55+02:00 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 Nikolai V. Ravin Tatyana S. Rudenko Dmitry D. Smolyakov Alexey V. Beletsky Andrey L. Rakitin Nikita D. Markov Alexey Fomenkov Luo Sun Richard J. Roberts Andrey A. Novikov Olga V. Karnachuk Margarita Y. Grabovich 2021-10-01T00:00:00Z https://doi.org/10.3389/fmicb.2021.760289 https://doaj.org/article/8e003ad6659247a7b320ddb4becf7d6e EN eng Frontiers Media S.A. https://www.frontiersin.org/articles/10.3389/fmicb.2021.760289/full https://doaj.org/toc/1664-302X 1664-302X doi:10.3389/fmicb.2021.760289 https://doaj.org/article/8e003ad6659247a7b320ddb4becf7d6e Frontiers in Microbiology, Vol 12 (2021) Thiothrix genome phylogeny comparative genomics metagenome-assembled genome Microbiology QR1-502 article 2021 ftdoajarticles https://doi.org/10.3389/fmicb.2021.760289 2022-12-31T09:14:43Z 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. Article in Journal/Newspaper White Sea Directory of Open Access Journals: DOAJ Articles White Sea Calvin ENVELOPE(165.100,165.100,-71.283,-71.283) Frontiers in Microbiology 12 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Thiothrix genome phylogeny comparative genomics metagenome-assembled genome Microbiology QR1-502 |
spellingShingle |
Thiothrix genome phylogeny comparative genomics metagenome-assembled genome Microbiology QR1-502 Nikolai V. Ravin Tatyana S. Rudenko Dmitry D. Smolyakov Alexey V. Beletsky Andrey L. Rakitin Nikita D. Markov Alexey Fomenkov Luo Sun Richard J. Roberts Andrey A. Novikov Olga V. Karnachuk Margarita Y. Grabovich 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 |
topic_facet |
Thiothrix genome phylogeny comparative genomics metagenome-assembled genome Microbiology QR1-502 |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Nikolai V. Ravin Tatyana S. Rudenko Dmitry D. Smolyakov Alexey V. Beletsky Andrey L. Rakitin Nikita D. Markov Alexey Fomenkov Luo Sun Richard J. Roberts Andrey A. Novikov Olga V. Karnachuk Margarita Y. Grabovich |
author_facet |
Nikolai V. Ravin Tatyana S. Rudenko Dmitry D. Smolyakov Alexey V. Beletsky Andrey L. Rakitin Nikita D. Markov Alexey Fomenkov Luo Sun Richard J. Roberts Andrey A. Novikov Olga V. Karnachuk Margarita Y. Grabovich |
author_sort |
Nikolai V. Ravin |
title |
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 |
title_short |
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 |
title_full |
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 |
title_fullStr |
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 |
title_full_unstemmed |
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 |
title_sort |
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 |
publisher |
Frontiers Media S.A. |
publishDate |
2021 |
url |
https://doi.org/10.3389/fmicb.2021.760289 https://doaj.org/article/8e003ad6659247a7b320ddb4becf7d6e |
long_lat |
ENVELOPE(165.100,165.100,-71.283,-71.283) |
geographic |
White Sea Calvin |
geographic_facet |
White Sea Calvin |
genre |
White Sea |
genre_facet |
White Sea |
op_source |
Frontiers in Microbiology, Vol 12 (2021) |
op_relation |
https://www.frontiersin.org/articles/10.3389/fmicb.2021.760289/full https://doaj.org/toc/1664-302X 1664-302X doi:10.3389/fmicb.2021.760289 https://doaj.org/article/8e003ad6659247a7b320ddb4becf7d6e |
op_doi |
https://doi.org/10.3389/fmicb.2021.760289 |
container_title |
Frontiers in Microbiology |
container_volume |
12 |
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1766234446914125824 |