ABSTRACT
Marinobacter sp. strain ANT_B65 was isolated from sponge collected in King George Island, Antarctica. The draft genome of 4,173,840 bp encodes 3,743 protein-coding open reading frames. The genome will provide insights into the strain’s potential use in the production of natural products.
GENOME ANNOUNCEMENT
The genus Marinobacter comprises 41 species of Gram-negative bacteria isolated from marine and saline environments. Marinobacter species can survive in different conditions, such as oil-polluted saline soil (1) and hydrothermal sediment (2), and they can be psychrotolerant (3) or psychrophilic (4).
Marinobacter sp. strain ANT-B65 was isolated from sponge collected in Admiralty Bay, King George Island, Antarctica (62°05,130′S 58°23,356′W), during an expedition in the austral summer of 2010. Strain ANT_B65 was isolated using M1 medium (10 g · liter−1 soluble starch, 4 g · liter−1 yeast extract, 2 g · liter−1 peptone, and 15 g · liter−1 agar) prepared with artificial sea water (0.1 g · liter−1 KBr, 23.48 g · liter−1 NaCl, 10.61 g · liter−1 MgCl2-6H2O, 1.47 g · liter−1 CaCl2-2H2O, 0.66 g · liter−1 KCl, 0.04 g · liter−1 SrCl2-6H2O, 3.92 g · liter−1 Na2SO4, 0.19 g · liter−1 NaHCO3, and 0.03 g · liter−1 H3BO3) at the Multidisciplinary Center for Chemical, Biological and Agricultural Research, University of Campinas (Campinas, São Paulo, Brazil).
A paired-end library was sequenced using the HiSeq 2500 system and yielded 8,229,346 reads of 251 bp. The reads were assembled with SeqMan NGen version 14.0 software (DNASTAR, Inc., WI, USA), resulting in a total genome length of 4,173,840 bp in 8 contigs, with an N50 of 2,216,721 bp and a GC content of 53.7%.
The genome was annotated using Prokka (5), the NCBI Prokaryotic Genome Annotation Pipeline (PGAP), and the Rapid Annotations using Subsystems Technology (RAST) server version 4.0 (6, 7). Prokka identified 3,817 coding sequences (CDSs), 25 tRNAs, 5 rRNAs, and 25 miscellaneous RNAs. PGAP identified 3,743 protein-coding genes, 44 tRNAs, 12 rRNAs, and 580 pseudogenes. RAST identified 3,959 CDSs, 45 tRNAs, 12 rRNAs, and 443 subsystems and predicted that 3 proteins are phage components.
RAST and the Kyoto Encyclopedia of Genes and Genomes (KEGG) identified secondary metabolites related to an auxin biosystem. The antiSMASH v.4.0 (8) analysis revealed one known secondary metabolite cluster, an ectoine. This is a natural compound used by the microorganism to survive in osmotic stress and found mainly in halophilic bacteria (9, 10). The NaPDos (11) analysis revealed four gene clusters related to the ketosynthase domain, three gene clusters related to fatty acid synthesis, and one gene cluster related to a spinosad. This cluster was associated with a macrolide produced by Saccharopolyspora spinosa (12) and used in agriculture as a potent insecticide.
The genome of Marinobacter sp. ANT_B65 provides insights into its potential use in the production of natural products.
Accession number(s).
This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number NXGV00000000. The version described in this paper is the first version, NXGV01000000.
ACKNOWLEDGMENTS
This research was supported by the São Paulo Research Foundation (FAPESP), PROANTAR Program, and Coordination for the Improvement of Higher Education Personnel (CAPES).
Footnotes
Citation de França P, Camilo E, Fantinatti-Garboginni F. 2018. Draft genome sequence of Marinobacter sp. strain ANT_B65, isolated from Antarctic marine sponge. Genome Announc 6:e01404-17. https://doi.org/10.1128/genomeA.01404-17.
REFERENCES
- 1.Gu J, Cai H, Yu SL, Qu R, Yin B, Guo YF, Zhao JY, Wu XL. 2007. Marinobacter gudaonensis sp. nov., isolated from an oil-polluted saline soil in a Chinese oilfield. Int J Syst Evol Microbiol 57:250–254. doi: 10.1099/ijs.0.64522-0. [DOI] [PubMed] [Google Scholar]
- 2.Handley KM, Héry M, Lloyd JR. 2009. Marinobacter santoriniensis sp. nov., an arsenate-respiring and arsenite-oxidizing bacterium isolated from hydrothermal sediment. Int J Syst Evol Microbiol 59:886–892. doi: 10.1099/ijs.0.003145-0. [DOI] [PubMed] [Google Scholar]
- 3.Shivaji S, Gupta P, Chaturvedi P, Suresh K, Delille D. 2005. Marinobacter maritimus sp. nov., a psychrotolerant strain isolated from seawater off the subAntarctic Kerguelen Islands. Int J Syst Evol Microbiol 55:1453–1456. doi: 10.1099/ijs.0.63478-0. [DOI] [PubMed] [Google Scholar]
- 4.Zhang DC, Li HR, Xin YH, Chi ZM, Zhou PJ, Yu Y. 2008. Marinobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from the Arctic. Int J Syst Evol Microbiol 58:1463–1466. doi: 10.1099/ijs.0.65690-0. [DOI] [PubMed] [Google Scholar]
- 5.Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. doi: 10.1093/bioinformatics/btu153. [DOI] [PubMed] [Google Scholar]
- 6.Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. doi: 10.1186/1471-2164-9-75. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R. 2014. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 42:D206–D214. doi: 10.1093/nar/gkt1226. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ, Kautsar SA, Suarez Duran HG, de los Santos ELC, Kim HU, Nave M, Dickschat JS, Mitchell DA, Shelest E, Breitling R, Takano E, Lee SY, Weber T, Medema MH. 2017. antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res 45:W36–W41. doi: 10.1093/nar/gkx319. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Zaccai G, Bagyan I, Combet J, Cuello GJ, Demé B, Fichou Y, Gallat FX, Galvan Josa VM, von Gronau S, Haertlein M, Martel A, Moulin M, Neumann M, Weik M, Oesterhelt D. 2016. Neutrons describe ectoine effects on water H-bonding and hydration around a soluble protein and a cell membrane. Sci Rep 6:31434. doi: 10.1038/srep31434. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Bernard T, Jebbar M, Rassouli Y, Himdi-Kabbab S, Hamelin J, Blanco C. 1993. Ectoine accumulation and osmotic regulation in Brevibacterium linens. J Gen Microbiol 139:129–136. doi: 10.1099/00221287-139-1-129. [DOI] [Google Scholar]
- 11.Ziemert N, Podell S, Penn K, Badger JH, Allen E, Jensen PR. 2012. The natural product domain seeker NaPDoS: a phylogeny based bioinformatic tool to classify secondary metabolite gene diversity. PLoS One 7:e34064. doi: 10.1371/journal.pone.0034064. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Waldron C, Matsushima P, Rosteck PR Jr, Broughton MC, Turner J, Madduri K, Crawford KP, Merlo DJ, Baltz RH. 2001. Cloning and analysis of the Spinosad biosynthetic gene cluster of Saccharopolyspora spinosa. Chem Biol 8:487–499. doi: 10.1016/S1074-5521(01)00029-1. [DOI] [PubMed] [Google Scholar]