Abstract
Here, we report the draft 2,261,881-bp genome sequence of Caloranaerobacter sp. TR13, isolated from a deep-sea hydrothermal vent on the East Pacific Rise. The sequence will be helpful for understanding the genetic and metabolic features, as well as potential biotechnological application in the genus Caloranaerobacter.
GENOME ANNOUNCEMENT
Thermophilic anaerobic microorganisms can thrive at temperatures over 50°C and do not require the use of O2 as a terminal electron acceptor for growth (1, 2). A growing number of anaerobic thermophilic bacteria have been isolated and studied from the deep-sea for their physiological properties and potential applications (3, 4). The anaerobic thermophilic bacterial genus Caloranaerobacter was first described by Wery et al. (5). It contains two type species: Caloranaerobacter azorensis MV1087 and Caloranaerobacter ferrireducens DY22619 (6). Recently, Caloranaerobacter spp. are reported to play an important role in biological hydrogen generation (7). Caloranaerobacter sp. TR13 (=MCCC 1A00790), an anaerobic, thermophilic, chemo-organotrophic bacterium, was isolated from a deep-sea hydrothermal vent sediment sample collected on the East Pacific Rise. It can grow at temperatures ranging from 37 to 75°C (optimum, 60°C), and at salinities of 0.5 to 7.0% (wt/vol) NaCl (optimum, 3.0% NaCl). Strain TR13 showed highest 16S rDNA sequence similarity with C. ferrireducens DY22619 (99.5%). To date, there is no reference C. ferrireducens genome sequence available publicly. Here, we report the draft genome sequence of strain TR13, the first released C. ferrireducens genome sequence. The sequence will be helpful for understanding the genetic and metabolic features, as well as potential biotechnological application in the genus Caloranaerobacter.
The genomic DNA of Caloranaerobacter sp. TR13 was extracted using a bacterial DNA kit (Omega) according to the manufacturer’s instructions. TR13 genome was sequenced by whole-genome shotgun sequencing using the Illumina MiSeq system at Shanghai Majorbio Bio-pharm Technology Co., Ltd. (Shanghai, China). A total of 346,433,714 reads were generated, representing approximately 153-fold coverage of the genome. These reads were assembled using SOAPdenovo v2.0 (8) and resulted in 52 contigs with an N50 of 259,980 bp. The longest contig size was 644,929 bp. The draft genome of strain TR13 was analyzed and annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/).
The draft genome sequence of Caloranaerobacter sp. TR13 was 2,261,881 bp in total length, with a G+C content of 29.5%. The genome contains 2,170 predicted open reading frames (ORFs) and 2,126 predicted protein-coding sequences (CDSs). There were 21 tRNA genes, 3 rRNA genes (5S, 16S, and 23S), and 1 noncoding RNA (ncRNA) gene predicted from this assembly.
Strain TR13 could utilize yeast extract, tryptone, and peptone for its growth. Sequence analysis revealed that the TR13 genome encodes forty peptidases and twenty-six proteases including two subtilisin-like serine proteases. TR13 genome also encodes different types of amylases for polysaccharide hydrolysis. Compared to C. azorensis H53214 and C. ferrireducens DY22619, TR13 possesses more [FeFe] hydrogenase genes (seventeen) involved in biological hydrogen production (7). TR13 contains one superoxide reductase Sor, one rubredoxin, two rubrerythrin, two NADH oxidases, three disulfide oxidoreductases, and one thioredoxin reductase against oxygen stress (9). A heat shock protein GrpE and two chaperone DnaJ proteins in response to hyperosmotic and high temperature were also found in TR13 genome.
Nucleotide sequence accession numbers.
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number JXLL00000000. The version described in this paper is version JXLL01000000.
ACKNOWLEDGMENTS
This work was supported by grants from the National Basic Research Program of China (973 Program 2012CB722209) and the Fundamental Research Funds of the Third Institute of Oceanography, State Oceanic Administration of China (2011001).
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Footnotes
Citation Zhou M, Xie Y, Dong B, Liu Q, Chen X. 2015. Draft genome sequence of Caloranaerobacter sp. TR13, an anaerobic thermophilic bacterium isolated from a deep-sea hydrothermal vent. Genome Announc 3(6):e01491-15. doi:10.1128/genomeA.01491-15.
REFERENCES
- 1.Canganella F, Wiegel J. 2014. Anaerobic thermophiles. Life 4:77–104. doi: 10.3390/life4010077. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Wagner ID, Wiegel J. 2008. Diversity of thermophilic anaerobes. Ann N Y Acad Sci 1125:1–43. doi: 10.1196/annals.1419.029. [DOI] [PubMed] [Google Scholar]
- 3.Lin L, Xu J. 2013. Dissecting and engineering metabolic and regulatory networks of thermophilic bacteria for biofuel production. Biotechnol Adv 31:827–837. doi: 10.1016/j.biotechadv.2013.03.003. [DOI] [PubMed] [Google Scholar]
- 4.Frock AD, Kelly RM. 2012. Extreme thermophiles: moving beyond single-enzyme biocatalysis. Curr Opin Chem Eng 1:363–372. doi: 10.1016/j.coche.2012.07.003. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Wery N, Moricet JM, Cueff V, Jean J, Pignet P, Lesongeur F, Cambon-Bonavita MA, Barbier G. 2001. Caloranaerobacter azorensis gen. nov., sp. nov., an anaerobic thermophilic bacterium isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 51:1789–1796. doi: 10.1099/00207713-51-5-1789. [DOI] [PubMed] [Google Scholar]
- 6.Zeng X, Zhang Z, Li X, Jebbar M, Alain K, Shao Z. 2015. Caloranaerobacter ferrireducens sp. nov., an anaerobic, thermophilic, iron (III)-reducing bacterium isolated from deep-sea hydrothermal sulfide deposits. Int J Syst Evol Microbiol 65:1714–1718. doi: 10.1099/ijs.0.000165. [DOI] [PubMed] [Google Scholar]
- 7.Jiang L, Xu H, Zeng X, Wu X, Long M, Shao Z. 2015. Thermophilic hydrogen-producing bacteria inhabiting deep-sea hydrothermal environments represented by Caloranaerobacter. Res Microbiol 166:677–687. doi: 10.1016/j.resmic.2015.05.002. [DOI] [PubMed] [Google Scholar]
- 8.Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW. 2012. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1:18. doi: 10.1186/2047-217X-1-18. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Jenney FE Jr, Verhagen MF, Cui X, Adams MW. 1999. Anaerobic microbes: oxygen detoxification without superoxide dismutase. Science 286:306–309. doi: 10.1126/science.286.5438.306. [DOI] [PubMed] [Google Scholar]