Skip to main content
SpringerLink
Log in

Draft Genome Sequence of a Biosurfactant-Producing Bacillus subtilis UMX-103 Isolated from Hydrocarbon-Contaminated Soil in Terengganu, Malaysia

  • Published:
Current Microbiology Aims and scope Submit manuscript

Abstract

The draft genome here presents the sequence of Bacillus subtilis UMX-103. The bacterial strain was isolated from hydrocarbon-contaminated soil from Terengganu, Malaysia. The whole genome of the bacterium was sequenced using Illumina HiSeq 2000 sequencing platform. The genome was assembled using de novo approach. The genome size of UMX-103 is 4,234,627 bp with 4399 genes comprising 4301 protein-coding genes and 98 RNA genes. The analysis of assembled genes revealed the presence of 25 genes involved in biosurfactant production, where 14 of the genes are related to biosynthesis and 11 of the genes are in the regulation of biosurfactant productions. This draft genome will provide insights into the genetic bases of its biosurfactant-producing capabilities.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Banat IM, Franzetti A, Gandolfi I, Bestetti G, Martinotti MG, Fracchia L, Smyth TJ, Marchant R (2010) Microbial biosurfactants production, applications and future potential. Appl Microbiol Biotechnol 87(2):427–444

    Article  CAS  PubMed  Google Scholar 

  2. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W (2011) Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27(4):578–579

    Article  CAS  PubMed  Google Scholar 

  3. Boetzer M, Pirovano W (2012) Toward almost closed genomes with GapFiller. Genome Biol 13(6):R56

    Article  PubMed  PubMed Central  Google Scholar 

  4. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Cai Q, Zhang B, Chen B, Song X, Zhu Z, Cao T (2015) Screening of biosurfactant-producing bacteria from offshore oil and gas platforms in North Atlantic Canada. Environ Monit Assess 187(5):1–12

    Article  CAS  Google Scholar 

  6. Choudhary DK, Johri BN (2009) Interactions of Bacillus spp. and plants—with special reference to induced systemic resistance (ISR). Microbiol Res 164(5):493–513

    Article  CAS  PubMed  Google Scholar 

  7. Joshi SJ, Suthar H, Yadav AK, Hingurao K, Nerurkar A (2012) Occurrence of biosurfactant producing Bacillus spp. in diverse habitats. ISRN biotechnology 2013

  8. Kunst F, Ogasawara N, Moszer I, Albertini A, Alloni G, Azevedo V, Bertero M, Bessieres P, Bolotin A, Borchert S (1997) The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390(6657):249–256

    Article  CAS  PubMed  Google Scholar 

  9. Lagesen K, Hallin P, Rødland EA, Stærfeldt H-H, Rognes T, Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35(9):3100–3108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25(5):0955–0964

    Article  CAS  Google Scholar 

  11. Mulligan CN (2009) Recent advances in the environmental applications of biosurfactants. Curr Opin 14(5):372–378

    CAS  Google Scholar 

  12. Nakano MM, Corbell N, Besson J, Zuber P (1992) Isolation and characterization of sfp: a gene that functions in the production of the lipopeptide biosurfactant, surfactin, in Bacillus subtilis. Mol Gen Genet 232(2):313–321

    CAS  PubMed  Google Scholar 

  13. Pereira JF, Gudiña EJ, Costa R, Vitorino R, Teixeira JA, Coutinho JA, Rodrigues LR (2013) Optimization and characterization of biosurfactant production by Bacillus subtilis isolates towards microbial enhanced oil recovery applications. Fuel 111:259–268

    Article  CAS  Google Scholar 

  14. Płaza G, Chojniak J, Rudnicka K, Paraszkiewicz K, Bernat P (2015) Detection of biosurfactants in Bacillus species: genes and products identification. J Appl Microbiol 119(4):1023–1034

    Article  PubMed  Google Scholar 

  15. Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30(14):2068–2069

    Article  CAS  PubMed  Google Scholar 

  16. Vaz DA, Gudiña EJ, Alameda EJ, Teixeira JA, Rodrigues LR (2012) Performance of a biosurfactant produced by a Bacillus subtilis strain isolated from crude oil samples as compared to commercial chemical surfactants. Colloids Surf B 89:167–174

    Article  CAS  Google Scholar 

  17. Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18(5):821–829

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

This research was supported by the University of Malaya Research Grant (UMRG: RG353-15AFR) and Postgraduate Research Grant (PG195-2016A).

Author information

Authors and Affiliations

  1. Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia

    Yousri Abdelmutalab Abdelhafiz, Saharuddin BinMohamad & Amir Feisal Merican

  2. Centre of Research for Computational Sciences & Informatics for Biology, Bioindustry, Environment, Agriculture and Healthcare (CRYSTAL), University of Malaya, 50603, Kuala Lumpur, Malaysia

    Thamilvaani Manaharan, Saharuddin BinMohamad & Amir Feisal Merican

Authors
  1. Yousri Abdelmutalab Abdelhafiz
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Thamilvaani Manaharan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Saharuddin BinMohamad
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Amir Feisal Merican
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Amir Feisal Merican.

Ethics declarations

Conflict of interest

The authors have declared there was no conflict of interest.

Additional information

Nucleotide Sequence Accession Numbers

The complete genome sequences are deposited in DDBJ/EMBL/GenBank under the Accession No. BDCV01000000. The version described in this paper is the first version with Accession No. BDCV01000000.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Abdelhafiz, Y.A., Manaharan, T., BinMohamad, S. et al. Draft Genome Sequence of a Biosurfactant-Producing Bacillus subtilis UMX-103 Isolated from Hydrocarbon-Contaminated Soil in Terengganu, Malaysia. Curr Microbiol 74, 803–805 (2017). https://doi.org/10.1007/s00284-017-1249-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00284-017-1249-3

Keywords

Search

Navigation