Abstract
Marinomonas sp. strain D104 was isolated from a polycyclic aromatic hydrocarbon-degrading consortium enriched from deep-sea sediment from the Arctic Ocean. The draft genome sequence of D104 (approximately 3.83 Mbp) contains 62 contigs and 3,576 protein-encoding genes, with a G+C content of 44.8%.
GENOME ANNOUNCEMENT
Marinomonas spp. are marine bacteria of wide distribution. Up to now, 22 type strains from different species have been identified in this genus (http://www.bacterio.net/marinomonas.html). According to the NCBI genome and assembly databases, only four genome sequences of Marinomonas have been reported, those of two type strains, Marinomonas mediterranea MMB-1T and Marinomonas posidonica IVIA-Po-181T (1, 2), as well as two nontype strains, Marinomonas sp. strain MED121 and Marinomonas sp. strain MWYL1. Here, we report the genome sequence of another Marinomonas strain, designated Marinomonas sp. D104. This strain was isolated from a polycyclic aromatic hydrocarbon (PAH)-degrading consortium, which was enriched from the deep-sea subsurface sediment of the Makarov Basin (170°29′W, 87°04′N, water depth of 4,000 m) in the Arctic Ocean. Although only one primary study indicated that Marinomonas can mineralize PAHs (3), our previous studies showed that strain D104 can degrade a wide variety of PAHs, such as naphthalene, fluorene, phenanthrene, anthracene, and pyrene at 25°C (unpublished data). In addition, strain D104 shows the highest sequence similarity, 97.72%, to Marinomonas ushuaiensis DSM 15871T (4), followed by another 21 type species of the genus Marinomonas (94.51 to 96.94% similarity). These results indicate that strain D104 is a potential new species within the genus Marinomonas.
Genomic DNA was purified from strain D104 with an AxyPrep bacterial genomic DNA miniprep kit (Axygen) according to the manual instructions. The genome was sequenced using the Genome Analyzer IIx system at Shanghai Majorbio Bio-pharm Technology Co., Ltd. (Shanghai, China), which produced 1,471 Mbp paired-end reads of 80 bp with an insert size of 300 bp. Approximately 1,356-Mbp high-quality reads were assembled with SOAPdenovo version 1.05 (5). The final genome assembly has 353-fold coverage and contains 62 scaffolds composed of 49 contigs (>1,000 bp), with a total size of 3,833,369 bp, an N50 contig length of 207,434 bp, and a mean G+C content of 44.8%.
Gene prediction and annotation of the draft genome were carried out using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html) (6). The draft genome is composed of 3,576 putative protein-encoding genes (2,822 with annotated functions) and contains 4 rRNA genes, 5 small noncoding RNA genes, and a total of 63 tRNA genes for all 20 amino acids. Furthermore, 27 pseudogenes were also identified in the draft genome.
According to the annotation results, many genes possibly involved in the degradation of aromatic compounds were found in the genome of Marinomonas sp. D104, including one aromatic ring-cleaving dioxygenase and five naphthalene 1,2-dioxygenase genes (7, 8). Moreover, three genes encoding protocatechuate 3,4-dioxygenase and five genes encoding protocatechuate 4,5-dioxygenase were also found. They carry out the oxidative cleavage of protocatechuate, which is an important intermediate metabolite during the degradation of aromatic compounds (9). In addition, one cytochrome P450 gene was present in the genome. A previous study demonstrated that cytochrome P450 is also involved in the degradation of PAHs (10). The genome sequence of Marinomonas sp. D104 helps to improve understanding of the PAH-degrading mechanism of Marinomonas spp.
Nucleotide sequence accession number.
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. AYOZ00000000. The version described in this paper is the first version.
ACKNOWLEDGMENTS
This work was financially supported by the Young Marine Science Foundation of SOA (no. 2012142), the High-Tech Research and Development Program of China (no. 2012AA092102), the National Natural Science Foundation of China (no. 41206158, 41076105), the Public Welfare Project of SOA (no. 201005032), the Scientific Research Foundation of the Third Institute of Oceanography, SOA (2011), and the China Polar Environment Investigation and Estimate Project (2012–2015).
We thank the whole team of the fourth Arctic Research Expedition of the “Xuelong” icebreaker.
Footnotes
Citation Dong C, Bai X, Lai Q, Xie Y, Chen X, Shao Z. 2014. Draft genome sequence of Marinomonas sp. strain D104, a polycyclic aromatic hydrocarbon-degrading bacterium from the deep-sea sediment of the Arctic Ocean. Genome Announc. 2(1):e1211-13. doi:10.1128/genomeA.01211-13.
REFERENCES
- 1. Lucas-Elio P, Goodwin L, Woyke T, Pitluck S, Nolan M, Kyrpides NC, Detter JC, Copeland A, Lu M, Bruce D, Detter C, Tapia R, Han S, Land ML, Ivanova N, Mikhailova N, Johnston AW, Sanchez-Amat A. 2012. Complete genome sequence of Marinomonas posidonica type strain (IVIA-Po-181T). Stand. Genomic Sci. 7:31–43. 10.4056/sigs.2976373 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2. Lucas-Elio P, Goodwin L, Woyke T, Pitluck S, Nolan M, Kyrpides NC, Detter JC, Copeland A, Teshima H, Bruce D, Detter C, Tapia R, Han S, Land ML, Ivanova N, Mikhailova N, Johnston AW, Sanchez-Amat A. 2012. Complete genome sequence of the melanogenic marine bacterium Marinomonas mediterranea type strain (MMB-1T). Stand. Genomic Sci. 6:63–73. 10.4056/sigs.2545743 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Melcher RJ, Apitz SE, Hemmingsen BB. 2002. Impact of irradiation and polycyclic aromatic hydrocarbon spiking on microbial populations in marine sediment for future aging and biodegradability studies. Appl. Environ. Microbiol. 68:2858–2868. 10.1128/AEM.68.6.2858-2868.2002 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4. Prabagaran SR, Suresh K, Manorama R, Delille D, Shivaji S. 2005. Marinomonas ushuaiensis sp. nov., isolated from coastal sea water in Ushuaia, Argentina, sub-Antarctica. Int. J. Syst. Evol. Microbiol. 55:309–313. 10.1099/ijs.0.63363-0 [DOI] [PubMed] [Google Scholar]
- 5. 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, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J. 2012. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1:18. 10.1186/2047-217X-1-18 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity G, Kodira CD, Kyrpides N, Madupu R, Markowitz V, Tatusova T, Thomson N, White O. 2008. Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. OMICS 12:137–141. 10.1089/omi.2008.0017 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Kauppi B, Lee K, Carredano E, Parales RE, Gibson DT, Eklund H, Ramaswamy S. 1998. Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase. Structure 6:571–586. 10.1016/S0969-2126(98)00059-8 [DOI] [PubMed] [Google Scholar]
- 8. Barriault D, Sylvestre M. 1999. Catalytic activity of Pseudomonas putida strain G7 naphthalene 1,2-dioxygenase on biphenyl. Int. Biodeterior. Biodegrad. 44:33–37. 10.1016/S0964-8305(99)00049-9 [DOI] [Google Scholar]
- 9. Fuchs G, Boll M, Heider J. 2011. Microbial degradation of aromatic compounds—from one strategy to four. Nat. Rev. Microbiol. 9:803–816. 10.1038/nrmicro2652 [DOI] [PubMed] [Google Scholar]
- 10. Brezna B, Kweon O, Stingley RL, Freeman JP, Khan AA, Polek B, Jones RC, Cerniglia CE. 2006. Molecular characterization of cytochrome P450 genes in the polycyclic aromatic hydrocarbon degrading Mycobacterium vanbaalenii PYR-1. Appl. Microbiol. Biotechnol. 71:522–532. 10.1007/s00253-005-0190-8 [DOI] [PubMed] [Google Scholar]