Isolation and characterization of a bacterium affiliated with the hitherto uncultured candidate phylum WOR-3 from a deep-sea hydrothermal fluid.

A pure cultured representative, designated strain sy37, in the candidate WOR-3 lineage was obtained from a deep-sea hydrothermal fluid. This lineage was named as the candidate phylum, "Candidatus Caldipriscota," "Candidatus Hydrothermota," or "Candidatus Stahliibacteriota," based on metagenome-assembled genomes of samples from various environments. The isolated strain was a thermophilic, microaerophilic, and chemoheterotrophic rod and obtained energy through aerobic/anaerobic respiration using oxygen and elemental sulfur. The strain could not use thiosulfate, sulfate, sulfite, fumarate, nitrate, nitrite, selenate, selenite, arsenate, ferric citrate, or ferrihydrite as an electron acceptor. Genomic annotation suggested that strain sy37 possesses a novel sulfur reduction mechanism. Among members of the WOR-3 lineage, only the group containing strain sy37 possessed the oxidative phosphorylation pathway with V-type ATPase and cytochrome c oxidase and may be capable of evolving to adapt to modern oxidative environments.

Importance: Genome analysis from various environments has revealed the overall diversity of microorganisms. However, there are many lineages for which culture representatives do not yet exist, and the characteristics and ecological significance of many of these microorganisms remain unclear: the WOR-3 lineage is one of these and has been found in various environments through the 16S rRNA gene analysis. In recent years, the metagenome-assembled genomes have been determined from the environments. In this study, we report on the successful isolation of a thermophilic microaerobic chemoorganoheterotroph, strain sy37, which is phylogenetically belonging to the WOR-3 lineage, from a deep-sea hydrothermal environment for the first time.