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

• Published in: Frontiers in microbiology Vol. 12; p. 760289
• Main Authors: 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.
• Format: Journal Article
• Language: English
• Published: Frontiers Media S.A 22-10-2021
• Subjects: comparative genomics; genome; metagenome-assembled genome; Microbiology; phylogeny; Thiothrix
• ISSN: 1664-302X; 1664-302X
• DOI: 10.3389/fmicb.2021.760289

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.