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

Abstract

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.

Two New Species of Filamentous Sulfur Bacteria of the Genus Thiothrix, Thiothrix winogradskyi sp. nov. and ‘Candidatus Thiothrix sulfatifontis’ sp. nov.

“…The data of physiological characteristics presented in this study were obtained by us earlier [ 26 , 27 ]. Data for Thiothrix sp.…”

“…Thiothrix sulfatifontis’ KT and T. winogradskyi CT3 T , along with the previously described species, was also analyzed by constructing a phylogenetic tree based on concatenated sequences of 120 conserved marker genes ( Figure 3 ). New genomes appeared to form distinct species-level lineages within the genus Thiothrix , and were most closely related to T. subterranea Ku-5 T , isolated from the outflow of sulfidic water from a drained well from the closed and flooded coal mine in Siberia [ 26 ]. These three species, along with T. litoralis AS T , T. lacustris BL T , T. fructosivorans Q T , and T. caldifontis G1 T form a distinct Clade 1.…”

“…Genome sequences for T. nivea JP2 T (GCF_000260135.1), T. lacustris BL T (GCF_000621325.1), and T. caldifontis G1 T (GCF_900107695.1) were obtained in 2012, 2014, and 2016. Later, in 2020–2021, whole genome sequences of type strains were obtained for T. unzii A1 T (ATCC 49747 T ) and T. fructosivorans Q T (ATCC 49748 T ), as well as for new isolates and MAG’s [ 24 , 25 , 26 ]. Thus, over the last few years, the genus Thiothrix has expanded to 10 species.…”

“…It was shown for many isolates from the genus Thiothrix , that the standard phylogenetic marker, the 16S rRNA gene, is not informative due to very high sequence identity [ 23 , 26 , 27 ]. The 16S rRNA gene sequence identity between Thiothrix sp.…”

“…However, the phylogenetic analysis based on a whole genome sequence showed that this strain represents a distinct species, T. litoralis sp. nov. [ 26 ]. Due to the current lack of reliable phylogenetic markers only the analysis of the whole genome sequences can clarify the phylogenetic status of representatives of the genus Thiothrix .…”