Journal
FRONTIERS IN MICROBIOLOGY
Volume 12, Issue -, Pages -Publisher
FRONTIERS MEDIA SA
DOI: 10.3389/fmicb.2021.760289
Keywords
Thiothrix; genome; phylogeny; comparative genomics; metagenome-assembled genome
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Funding
- Russian Science Foundation [20-14-00137]
- Ministry of Education and Science of the Russian Federation
- Gubkin Russian State University of Oil and Gas [0768-2020-0007]
- Russian Science Foundation [20-14-00137] Funding Source: Russian Science Foundation
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Two strains of filamentous, colorless sulfur bacteria were isolated from a coal mine and the White Sea, while a metagenome-assembled genome was obtained from a sulfidic spring in Russia. Phylogenetic analysis showed that all genomes belonged to the genus Thiothrix, with three proposed new species identified. The core genome of Thiothrix includes genes for metabolism, respiration, and sulfur oxidation pathways.
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-5(T), Thiothrix litoralis sp. nov. AS(T), and Candidatus Thiothrix anitrata sp. nov. A52. The complete genome sequences of Thiothrix fructosivorans Q(T) and Thiothrix unzii A1(T) 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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