AUTHOR=Ravin Nikolai V. , Rudenko Tatyana S. , Smolyakov Dmitry D. , Beletsky Alexey V. , Rakitin Andrey L. , Markov Nikita D. , Fomenkov Alexey , Sun Luo , Roberts Richard J. , Novikov Andrey A. , Karnachuk Olga V. , Grabovich Margarita Y. 

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

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.760289

DOI=10.3389/fmicb.2021.760289

ISSN=1664-302X

ABSTRACT=<p>Two strains of filamentous, colorless sulfur bacteria were isolated from bacterial fouling in the outflow of hydrogen sulfide-containing waters from a coal mine (<italic>Thiothrix</italic> sp. Ku-5) and on the seashore of the White Sea (<italic>Thiothrix</italic> 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 <italic>Thiothrix</italic>. Based on their average nucleotide identity and digital DNA-DNA hybridization data these new isolates and the MAG represent three species within the genus <italic>Thiothrix</italic> with the proposed names <italic>Thiothrix subterranea</italic> sp. nov. Ku-5<sup>T</sup>, <italic>Thiothrix litoralis</italic> sp. nov. AS<sup>T</sup>, and “<italic>Candidatus</italic> Thiothrix anitrata” sp. nov. A52. The complete genome sequences of <italic>Thiothrix fructosivorans</italic> Q<sup>T</sup> and <italic>Thiothrix unzii</italic> A1<sup>T</sup> were determined. Complete genomes of seven <italic>Thiothrix</italic> isolates, as well as two MAGs, were used for pangenome analysis. The <italic>Thiothrix</italic> 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 (<italic>SoxAXBYZ</italic>), direct (<italic>soeABC</italic>) and indirect (<italic>aprAB</italic>, <italic>sat</italic>) pathways of sulfite oxidation, sulfur oxidation complex Dsr (<italic>dsrABEFHCEMKLJONR</italic>), sulfide oxidation systems SQR (<italic>sqrA</italic>, <italic>sqrF</italic>), and FCSD (<italic>fccAB</italic>) 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.</p>