Physiological and Genomic Characterization of a Novel Obligately Chemolithoautotrophic, Sulfur-Oxidizing Bacterium of Genus Thiomicrorhabdus Isolated from a Coastal Sediment

Thiomicrorhabdus species, belonging to the family Piscirickettsiaceae in the phylum Pseudomonadotav are usually detected in various sulfur-rich marine environments. However, only a few bacteria of Thiomicrorhabdus have been isolated, and their ecological roles and environmental adaptations still require further understanding. Here, we report a novel strain, XGS-01T, isolated from a coastal sediment, which belongs to genus Thiomicrorhabdus and is most closely related to Thiomicrorhabdus hydrogeniphila MAS2T, with a sequence similarity of 97.8%. Phenotypic characterization showed that XGS-01T is a mesophilic, sulfur-oxidizing, obligate chemolithoautotrophy, with carbon dioxide as its sole carbon source and oxygen as its sole electron acceptor. During thiosulfate oxidation, strain XGS-01T can produce extracellular sulfur of elemental α-S8, as confirmed via scanning electron microscopy and Raman spectromicroscopy. Polyphasic taxonomy results indicate that strain XGS-01T represents a novel species of the genus Thiomicrorhabdus, named Thiomicrorhabdus lithotrophica sp. nov. Genomic analysis confirmed that XGS-01T performed thiosulfate oxidation through a sox multienzyme complex, and harbored fcc and sqr genes for sulfide oxidation. Comparative genomics analysis among five available genomes from Thiomicrorhabdus species revealed that carbon fixation via the oxidation of reduced-sulfur compounds coupled with oxygen reduction is conserved metabolic pathways among members of genus Thiomicrorhabdus.

nov., a mesophilic sulfur-oxidizing bacterium isolated from sediment of a brackish lake in northern Japan

A novel sulfur-oxidizing bacterium, strain Am19^T, was isolated from sediment of a brackish lake. Strain Am19^T grew chemolithoautotrophically on inorganic sulfur compounds, and heterotrophic growth was not observed. Cells were rod-shaped with length of 1.1-3.0 μm and diameter of 0.5-0.8 μm. Growth was observed at 5-37 °C with an optimum growth temperature of 30 °C. The pH range for growth was 5.6-8.5 with an optimum pH of 6.6-7.0. Major fatty acids were summed feature 3 (C_{16: 1}ω7c and/or C_{16: 1}ω6c), summed feature 8 (C_{18: 1}ω7c and/or C_{18: 1}ω6c) and C_{16: 0}. The sole respiratory quinone was ubiquinone-8. The complete genome of strain Am19^T is composed of a circular chromosome with length of 2.5 Mbp and G + C content of 42.7 mol%. Phylogenetic analysis based on genomic data indicated that strain Am19^T belongs to the genus Thiomicrorhabdus but is distinct from any existing species. Analysis of the 16S rRNA gene supported creation of a new species to accommodate strain Am19^T. On the basis of genomic and phenotypic characteristics, strain Am19^T (= NBRC 114602 ^T = BCRC 81336 ^T) is proposed as the type strain of a new species, with name of Thiomicrorhabdus immobilis sp. nov.

nov.: novel sulphur-oxidizing chemolithoautotrophs isolated from the chemocline of Hospital Hole, an anchialine sinkhole in Spring Hill, Florida, USA

Two sulphur-oxidizing, chemolithoautotrophic aerobes were isolated from the chemocline of an anchialine sinkhole located within the Weeki Wachee River of Florida. Gram-stain-negative cells of both strains were motile, chemotactic rods. Phylogenetic analysis of the 16S rRNA gene and predicted amino acid sequences of ribosomal proteins, average nucleotide identities, and alignment fractions suggest the strains HH1^T and HH3^T represent novel species belonging to the genus Thiomicrorhabdus. The genome G+C fraction of HH1^T is 47.8 mol% with a genome length of 2.61 Mb, whereas HH3^T has a G+C fraction of 52.4 mol% and 2.49 Mb genome length. Major fatty acids of the two strains included C_16 : 1, C_18 : 1 and C_16 : 0, with the addition of C_10:0 3-OH in HH1^T and C_12 : 0 in HH3^T. Chemolithoautotrophic growth of both strains was supported by elemental sulphur, sulphide, tetrathionate, and thiosulphate, and HH1^T was also able to use molecular hydrogen. Neither strain was capable of heterotrophic growth or use of nitrate as a terminal electron acceptor. Strain HH1^T grew from pH 6.5 to 8.5, with an optimum of pH 7.4, whereas strain HH3^T grew from pH 6 to 8 with an optimum of pH 7.5. Growth was observed between 15-35 °C with optima of 32.8 °C for HH1^T and 32 °C for HH3^T. HH1^T grew in media with [NaCl] 80-689 mM, with an optimum of 400 mM, while HH3^T grew at 80-517 mM, with an optimum of 80 mM. The name Thiomicrorhabdus heinhorstiae sp. nov. is proposed, and the type strain is HH1^T (=DSM 111584^T=ATCC TSD-240^T). The name Thiomicrorhabdus cannonii sp. nov is proposed, and the type strain is HH3^T (=DSM 111593^T=ATCC TSD-241^T).

Thiosulfativibrio zosterae gen. nov., sp. nov., and Thiosulfatimonas sediminis gen. nov., sp. nov

Aerobic, Gram-stain-negative, obligately chemolithoautotrophic thiosulfate-oxidizing bacteria, strains AkT22^T and aks77^T were isolated from a brackish lake in Japan. Strains AkT22^T and aks77^T were isolated from samples of eelgrass and sediment, respectively. Growth on sulfide, tetrathionate, elemental sulfur, and organic substrates was not observed for both strains. Growth of the strains was observed at 5 °C or higher temperature, with optimum growth at 22 °C. Strain AkT22^T grew at a pH range of 5.8-8.0, with optimum growth at pH 6.7-7.8. Strain aks77^T grew at a pH range of 5.8-8.5, with optimum growth at pH 7.0-7.9. Major cellular fatty acids (> 10% of total) of strain AkT22^T were C_16:1, C_18:1, and C_16:0. The sole respiratory quinone was ubiquinone-8 in both strains. The genome of strain AkT22^T consisted of a circular chromosome, with size of approximately 2.6 Mbp and G + C content of 43.2%. Those values of the genome of strain aks77^T were ca. 2.7 Mbp and 45.5%, respectively. Among cultured bacteria, Thiomicrorhabdus aquaedulcis HaS4^T showed the highest sequence identities of the 16S rRNA gene, to strains AkT22^T (94%) and aks77^T (95%). On the basis of these results, Thiosulfativibrio zosterae gen. nov., sp. nov. and Thiosulfatimonas sediminis gen. nov., sp. nov. are proposed, with type strains of AkT22^T (= BCRC 81184^T = NBRC 114012^T = DSM 109948^T) and aks77^T (= BCRC 81183^T = NBRC 114013^T), respectively.