Draft genome sequence of Vitellibacter aquimaris D-24T isolated from seawater

Suganthi Thevarajoo Chitra Selvaratnam Kok-Gan Chan Kian Mau Goh Chun Shiong Chong About the authors

ABSTRACT

Vitellibacter aquimaris D-24T (=KCTC 42708T = DSM 101732T), a halophilic marine bacterium, was isolated from seawater collected from Desaru beach, Malaysia. Here, we present the draft genome sequence of D-24T with a genome size of approximately 3.1 Mbp and G + C content of 39.93%. The genome of D-24T contains genes involved in reducing a potent greenhouse gas (N2O) in the environment and the degradation of proteinaceous compounds. Genome availability will provide insights into potential biotechnological and environmental applications of this bacterium.

Keywords:
Vitellibacter aquimaris; Genome sequence; Denitrification; Proteases

Over the last few decades, marine microorganisms have received considerable attention for their applications in biotechnology. Prime focus has been given on identification of halophilic enzymes with potential applications.11 Dalmaso GZL, Ferreira D, Vermelho AB. Marine extremophiles: a source of hydrolases for biotechnological applications. Mar Drugs. 2015;13(4):1925-1965.,22 Gomes J, Steiner W. The biocatalytic potential of extremophiles and extremozymes. Food Technol Biotechnol. 2004;42(4):223-235. Halophilic enzymes boast unique properties such as the sustainability at extreme ranges of salt concentration, temperature, pH, and organic solvents.33 Kumar S, Karan R, Kapoor S, Singh S, Khare S. Screening and isolation of halophilic bacteria producing industrially important enzymes. Braz J Microbiol. 2012;43(4):1595-1603.,44 Moreno M, Pérez D, García MT, Mellado E. Halophilic bacteria as a source of novel hydrolytic enzymes. Life. 2013;3(1):38-51. Characterization of marine bacteria through their genome sequence has provided great opportunities for mining and identifying of enzymes with biotechnological importance.

Vitellibacter aquimaris D-24T, previously isolated from seawater, was confirmed as a new species in genus Vitellibacter.55 Thevarajoo S, Selvaratnam C, Goh KM, et al. Vitellibacter aquimaris sp. nov., a marine bacterium isolated from sea water. Int J Syst Evol Microbiol. 2016;66(9):3662-3668. This bacterium is a Gram negative, rod-shape and yellow-orange pigmented bacterium. In this study, we report the draft genome of V. aquimaris D-24T.

V. aquimaris D-24T was grown in Marine Broth 2216 (BD Difco) and the genomic DNA was extracted using the DNeasy Blood and Tissue kit (Qiagen, Hilden, Germany) per manufacturer instructions. The genome of the V. aquimaris D-24T sequence was generated using pair-end sequencing in an Illumina MiSeq sequencing platform (Illumina, California, USA). De novo assembly was performed using IDBA-UD version 1.0.9,66 Peng Y, Leung HC, Yiu S-M, Chin FY. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 2012;28:1420-1428. obtaining 66 contigs with a N50 contig length of 439,587. Genome annotations were carried out using NCBI Prokaryotic Genome Annotation Pipeline 2.877 Angiuoli SV, Gussman A, Klimke W, et al. Toward an online repository of standard operating procedures (SOPs) for (meta)genomic annotation. OMICS. 2008;12:137-141. and Integrated Microbial Genomes Expert Review (IMG-ER).88 Markowitz VM, Mavromatis K, Ivanova NN, Chen I-MA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics. 2009;25(17):2271-2278. Protein coding sequences were predicted by using GeneMarkS+ version 2.8 with the best-placed reference protein method99 Besemer J, Borodovsky M. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res. 2005;33:W451-W454. and Prodigal,1010 Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinf. 2010;11:119. respectively.

The draft genome of V. aquimaris D-24T is comprised of 3,147,268 nucleotides with a mean G + C content of 39.93%. A total of 2967 genes were predicted, of which 2790 (94.03%) protein-coding genes were assigned with putative function or hypothetical proteins. The genome consists of three 5S rRNA, one 16S rRNA, one 23 rRNA, and 35 tRNA genes (Table 1). The genome V. aquimaris D-24T contains genes encoded for nitrite reductase (nirK) (WP_045079976.1), nitric oxide reductase subunit B (norB) (WP_062619270.1), nitric oxide reductase subunit C (norC) (WP_062619272.1), and nitrous oxide reductase (nosZ) (WP_062619280.1), all of which are involved in the denitrification pathway (NO2- to N2). Nitrous oxide (N2O) is a potent greenhouse gas which also damages the Earth's ozone layer. Due to intensive agricultural and industrial practices, the release of this gas into the atmosphere has greatly increased.1111 Zumft WG, Kroneck PM. Respiratory transformation of nitrous oxide (N2O) to dinitrogen by Bacteria and Archaea. Adv Microb Physiol. 2006;52:107-227.,1212 Jones CM, Graf DR, Bru D, Philippot L, Hallin S. The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink. ISME J. 2013;7:417-426. Nitrous-oxide reductase plays an important role in catalyzing the reduction of nitrous oxide to nitrogen (N2).1313 Pauleta SR, Dell'Acqua S, Moura I. Nitrous oxide reductase. Coord Chem Rev. 2013;257:332-349. The nitrous oxide reductase (nosZ) from V. aquimaris D-24T is a promising candidate for removing nitrous oxide, a potent greenhouse gas, from the environment.

Table 1
Genome features of Vitellibacter aquimaris D-24T.

Genome analysis also revealed a total of twelve genes encoded for proteases, including two metalloproteases (KXO00999.1; KXN98592.1); two serine proteases (KXO01375.1; KXN97930.1); five proteases (KXO00989.1; KXO00819.1; KXN99950.1; KXN99951.1; KXO00100.1); two zinc metalloproteases (KXO00568.1; KXN98177.1); and an acid protease (KXO00796.1). Genes encoding proteases were also present in the genome of another species of Vitellibacter.1414 Thevarajoo S, Selvaratnam C, Chan K-G, Goh KM, Chong CS. Draft genome sequence of Vitellibacter vladivostokensis KMM 3516T: a protease-producing bacterium. Mar Gen. 2015;23:49-50. The draft genome sequence of V. aquimaris D-24T will facilitate understanding and development of potential applications of Vitellibacter species.

The Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number JRWG00000000. The first version (accession number JRWG01000000) is described in this paper.

Acknowledgments

This work was financially supported by Ministry of Education Malaysia (grant number: 4F265) and Universiti Teknologi Malaysia RU grants (grant number: 07H43 and 14H67). Suganthi Thevarajoo and Chitra Selvaratnam acknowledge the PhD Zamalah scholarship from Universiti Teknologi Malaysia. Kok-Gan Chan acknowledges the University of Malaya High Impact Research Grants (UM.C/625/1/HIR/MOHE/CHAN/01, Grant No. A-000001-50001 and UM-MOHE HIR Grant UM.C/625/1/HIR/MOHE/CHAN/14/1, no. H-50001-A000027).

References

  • 1
    Dalmaso GZL, Ferreira D, Vermelho AB. Marine extremophiles: a source of hydrolases for biotechnological applications. Mar Drugs 2015;13(4):1925-1965.
  • 2
    Gomes J, Steiner W. The biocatalytic potential of extremophiles and extremozymes. Food Technol Biotechnol 2004;42(4):223-235.
  • 3
    Kumar S, Karan R, Kapoor S, Singh S, Khare S. Screening and isolation of halophilic bacteria producing industrially important enzymes. Braz J Microbiol 2012;43(4):1595-1603.
  • 4
    Moreno M, Pérez D, García MT, Mellado E. Halophilic bacteria as a source of novel hydrolytic enzymes. Life 2013;3(1):38-51.
  • 5
    Thevarajoo S, Selvaratnam C, Goh KM, et al. Vitellibacter aquimaris sp. nov., a marine bacterium isolated from sea water. Int J Syst Evol Microbiol 2016;66(9):3662-3668.
  • 6
    Peng Y, Leung HC, Yiu S-M, Chin FY. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 2012;28:1420-1428.
  • 7
    Angiuoli SV, Gussman A, Klimke W, et al. Toward an online repository of standard operating procedures (SOPs) for (meta)genomic annotation. OMICS 2008;12:137-141.
  • 8
    Markowitz VM, Mavromatis K, Ivanova NN, Chen I-MA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009;25(17):2271-2278.
  • 9
    Besemer J, Borodovsky M. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res 2005;33:W451-W454.
  • 10
    Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinf 2010;11:119.
  • 11
    Zumft WG, Kroneck PM. Respiratory transformation of nitrous oxide (N2O) to dinitrogen by Bacteria and Archaea. Adv Microb Physiol 2006;52:107-227.
  • 12
    Jones CM, Graf DR, Bru D, Philippot L, Hallin S. The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink. ISME J 2013;7:417-426.
  • 13
    Pauleta SR, Dell'Acqua S, Moura I. Nitrous oxide reductase. Coord Chem Rev 2013;257:332-349.
  • 14
    Thevarajoo S, Selvaratnam C, Chan K-G, Goh KM, Chong CS. Draft genome sequence of Vitellibacter vladivostokensis KMM 3516T: a protease-producing bacterium. Mar Gen 2015;23:49-50.

Publication Dates

  • Publication in this collection
    Jan-Mar 2018

History

  • Received
    26 Oct 2016
  • Accepted
    28 Mar 2017
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