Complete Genome Sequence of a Moderately Thermophilic Facultative Chemolithoautotrophic Hydrogen-Oxidizing Bacterium, Hydrogenophilus thermoluteolus TH-1.

Hydrogenophilus spp., which are moderately thermophilic aerobic betaproteobacteria, are widely distributed in geothermal environments. They fix carbon dioxide via the Calvin-Benson-Bassham cycle and exhibit rapid autotrophic growth using hydrogen as an energy source. Here, we report the complete genome sequence of Hydrogenophilus thermoluteolus strain TH-1.

ANNOUNCEMENT

Hydrogenophilus thermoluteolus (formerly Pseudomonas hydrogenothermophila) strain TH-1 is a moderately thermophilic aerobic betaproteobacterium isolated from the soil around a hot spring in Izu Peninsula, Japan (1, 2). This facultative chemolithoautotroph can grow not only autotrophically on hydrogen or sulfur compounds as the electron donor and carbon dioxide as the carbon source but also heterotrophically in organic media (1, 3). It fixes carbon dioxide via the Calvin-Benson-Bassham (CBB) cycle (4). The optimal temperature for the growth of strain TH-1 is 52°C. The maximum specific growth rate under optimal autotrophic conditions was determined to be 0.68 h−1, which is the highest among autotrophs (1). Bacteria of the genus Hydrogenophilus have appeared in geothermal areas worldwide (5–7), and H. thermoluteolus DNA has also been identified in accretion ice in Antarctic subglacial Lake Vostok (8, 9).

The whole genome of strain TH-1, subcultured in our laboratory, was sequenced using a Roche 454 GS FLX Titanium genome sequencer and Illumina GAIIx genome analyzer. Total DNA was isolated from the cells cultivated autotrophically, with hydrogen as an energy source, according to the methods described previously (2). Library preparation, sequencing reactions, and runs were carried out according to the manufacturer’s instructions. The Roche sequencing yielded 96,761,814 bases from 304,337 single reads, with an average read length of 317.9 bp, and 300,670 of these reads were assembled into 43 contigs of >500 bp using Velvet version 1.2.08, with default settings (10). Genome coverage was 42-fold, and the average contig length and N50 size were 52,414 bp and 124,172 bp, respectively. Contig gaps were closed by sequencing DNA fragments amplified by PCR from genomic DNA with an ABI 3730xl DNA analyzer (Applied Biosystems, Foster City, CA). Error correction was performed by mapping the Illumina sequencing data (34,180,094 single reads of 38 bp) onto the assembled sequence using GENETYX, with default settings (Software Development Co., Tokyo, Japan). The genes were annotated using the DDBJ Microbial Genome Annotation Pipeline. Protein-coding sequences and rRNAs were confirmed based on comparison with the public databases. tRNAscan-SE (11) was used to identify tRNA genes.

The complete genome of H. thermoluteolus strain TH-1 comprises a circular chromosome of 2,223,143 bp, with 61.7% GC content, and a plasmid, designated pTH1, of 65,637 bp, with 58.3% GC content. The numbers of predicted protein-coding genes were 2,077 and 71 for the chromosome and plasmid, respectively. The genome contains three sets of the 16S-23S-5S rRNA genes and 49 tRNA genes. Genome analyses identified the genes for the enzymes involved in the CBB cycle, including the cbbLS genes encoding ribulose-1,5-bisphosphate carboxylase/oxygenase (4). The hoxFUYH genes encoding NAD+-reducing hydrogenase (12) were clustered with two other hydrogenase genes, hupABC and hupUV, and hydrogenase accessory genes. Strain TH-1 was found to have only the cbb3-type cytochrome c oxidase as the terminal oxidase for aerobic respiration. The plasmid pTH1 carries a gene cluster encoding urease and a urea transporter.

Data availability.

The complete genome sequence of H. thermoluteolus TH-1 has been deposited at DDBJ/ENA/GenBank under accession numbers AP018558 (chromosome) and AP018559 (plasmid).