Genome Sequence of Kosmotoga olearia Strain TBF 19.5.1, a Thermophilic Bacterium with a Wide Growth Temperature Range, Isolated from the Troll B Oil Platform in the North Sea

Abstract

Kosmotoga olearia strain TBF 19.5.1 is a member of the Thermotogales that grows best at 65°C and very well even at 37°C. Information about this organism is important for understanding the evolution of mesophiles from thermophiles. Its genome sequence reveals extensive gene gains and a large content of mobile genetic elements. It also contains putative hydrogenase genes that have no homologs in the other member of the Thermotogales.

GENOME ANNOUNCEMENT

Kosmotoga olearia strain TBF 19.5.1 is a thermophilic anaerobic bacterium belonging to the order Thermotogales and was isolated from oil production fluid collected at the Troll B oil platform in the North Sea. It grows at temperatures from 20 to 80°C with a doubling time of 103 ± 8 min at its optimum growth temperature of 65°C on its preferred carbon source, pyruvate (2). It shows an unusual ability to grow well at suboptimal temperatures, with a doubling time on pyruvate of 175 ± 59 min at 37°C (2). Phylogenetic analyses place it as a close relative to the apparently mesophilic Thermotogales, known as the mesotogas (11). Given this phylogenetic position and its ability to grow well over such a range of temperatures, it represents an interesting opportunity to examine the evolutionary transition from a thermophilic to a mesophilic lifestyle.

The genome of K. olearia was sequenced using a combination of Sanger (8-kbp and 40-kbp fosmids) and 454 sequencing. All general aspects of library construction and sequencing can be found at the Joint Genome Institute website (www.jgi.doe.gov). Reads from all libraries were assembled using the Phred/Phrap/Consed assembler (3–5). Possible misassemblies were corrected and gaps between contigs were closed by editing in Consed or by custom primer walks from subclones or PCR products.

Genes were identified using Prodigal (7) as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline (12). In order to determine a product description for each of the predicted coding sequences, they were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database and the UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Noncoding genes and miscellaneous features were predicted using tRNAscan-SE (10), RNAMMer (9), Rfam (6), TMHMM (8), and signalP (1).

The complete K. olearia genome consists of 2,302,126 bp in a single circular chromosome, making it one of the largest sequenced Thermotogales genomes. The genome has an average G+C content of 41.5%, and there are a total of 2,118 predicted protein-coding genes, two ribosomal operons, 46 tRNAs, and 51 pseudogenes.

Compared to the other sequenced genomes in this order, the K. olearia genome has many unique mobile genetic elements, including transposons and group II introns. The large number of mobile genetic elements suggests that this genome undergoes frequent recombination, rearrangement, and gene gain/loss events. This apparent genome instability associated with mobile genetic elements may have allowed K. olearia to acquire genes that allow it to grow at a wide range of temperatures and may also have contributed to its relatively large genome size.

The K. olearia genome contains 21 open reading frames transcribed in the same direction (Kole_0555 to Kole_575), comprising a region unique among the Thermotogales. Encoded in this region are a putative Ni-Fe hydrogenase, NADH:quinone reductase complex, and cation antiporter. These annotations raise the possibility of an uncharacterized phenotype for this organism and perhaps an energy conservation mechanism novel among the Thermotogales.

Nucleotide sequence accession number.

The complete genome sequence of Kosmotoga olearia strain TBF 19.5.1 is available in GenBank under accession number CP001634.