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Functional & Integrative Genomics

, Volume 18, Issue 5, pp 533–543 | Cite as

Genome annotation and comparative genomic analysis of Bacillus subtilis MJ01, a new bio-degradation strain isolated from oil-contaminated soil

  • Touraj Rahimi
  • Ali NiaziEmail author
  • Tahereh Deihimi
  • Seyed Mohsen Taghavi
  • Shahab Ayatollahi
  • Esmaeil EbrahimieEmail author
Original Article

Abstract

One of the main challenges in elimination of oil contamination from polluted environments is improvement of biodegradation by highly efficient microorganisms. Bacillus subtilis MJ01 has been evaluated as a new resource for producing biosurfactant compounds. This bacterium, which produces surfactin, is able to enhance bio-accessibility to oil hydrocarbons in contaminated soils. The genome of B. subtilis MJ01 was sequenced and assembled by PacBio RS sequencing technology. One big contig with a length of 4,108,293 bp without any gap was assembled. Genome annotation and prediction of gene showed that MJ01 genome is very similar to B. subtilis spizizenii TU-B-10 (95% similarity). The comparison and analysis of orthologous genes carried out between B. subtilis MJ01, reference strain B. subtilis subsp. subtilis str. 168, and close relative spizizenii TU-B-10 by microscope platform and various bioinformatics tools. More than 88% of 4269 predicted coding sequences in MJ01 had at least one similar sequence in genome of reference strain and spizizenii TU-B-10. Despite this high similarity, some differences were detected among encoding sequences of non-ribosome protein and bacteriocins in MJ01 and spizizenii TU-B-10. MJ01 has unique nucleotide sequences and a novel predicted lasso-peptide bacteriocin; it also has not any similar nucleotide sequence in non-redundant nucleotide data base.

Keywords

Bacillus subtilis Whole genome Biodegradation Genome interpretation Genomics comparison Biosurfactant Micro scope platform 

Notes

Acknowledgements

We thank to the LABGeM and the National Infrastructure « France Genomique », for their useful MicroScope platform tools and providing genome annotation and comparative analysis for MJ01 genome. We would also thanks to Mr. Moien Jahanbani Veshareh for providing MJ01 strain bacteria. This study was supported by Department of Biotechnology, Agriculture Faculty of Shiraz University.

Supplementary material

10142_2018_604_MOESM1_ESM.docx (102 kb)
ESM 1 (DOCX 101 kb)

References

  1. Ali A, Soares SC, Barbosa E, Santos AR, Barh D, Bakhtiar SM et al (2013) Microbial comparative genomics: an overview of tools and insights into the genus Corynebacterium. J Bacteriol Parasitol 4(2):1–16.  https://doi.org/10.4172/2155-9597.1000167 CrossRefGoogle Scholar
  2. Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, Wishart DS (2016) PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 1–6.  https://doi.org/10.1093/nar/gkw387
  3. Auch AF, von Jan M, Klenk H-P, Göker M (2010) Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2(1):117–134.  https://doi.org/10.4056/sigs.531120 CrossRefPubMedPubMedCentralGoogle Scholar
  4. Ben Ayed H, Hmidet N, Béchet M, Chollet M, Chataigné G, Leclère V, Jacques P, Nasri M (2014) Identification and biochemical characteristics of lipopeptides from Bacillus mojavensis A21. Process Biochem 49(10):1699–1707.  https://doi.org/10.1016/j.procbio.2014.07.001 CrossRefGoogle Scholar
  5. Bezza FA, Chirwa EMN (2015) Production and applications of lipopeptide biosurfactant for bioremediation and oil recovery by Bacillus subtilis CN2. Biochem Eng J 101:168–178.  https://doi.org/10.1016/j.bej.2015.05.007 CrossRefGoogle Scholar
  6. de Silva R, CFS, Almeida DG, Rufino RD, Luna JM, Santos VA, Sarubbo LA (2014) Applications of biosurfactants in the petroleum industry and the remediation of oil spills. Int J Mol Sci Multidiscip Digit Publ Inst (MDPI) 15:12523–12542.  https://doi.org/10.3390/ijms150712523
  7. Dhillon BK, Laird MR, Shay JA, Winsor GL, Lo R, Nizam F, Pereira SK, Waglechner N, McArthur AG, Langille MGI, Brinkman FSL (2015) IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis. Nucleic Acids Res 43(W1):W104–W108.  https://doi.org/10.1093/nar/gkv401 CrossRefPubMedPubMedCentralGoogle Scholar
  8. Harvey AL, Edrada-Ebel R, Quinn RJ (2015) The re-emergence of natural products for drug discovery in the genomics era. Nat Rev Drug Discov 14(2):111–129.  https://doi.org/10.1038/nrd4510 CrossRefPubMedGoogle Scholar
  9. Hutchison CA, Chuang R-YR-Y, Noskov VN, Assad-Garcia N, Deerinck TJ, Ellisman MH et al (2016) Design and synthesis of a minimal bacterial genome. Science 351(6280):aad6253–aad6253.  https://doi.org/10.1126/science.aad6253 CrossRefPubMedGoogle Scholar
  10. Jha SS, Joshi SJ, Geetha SJ (2016) Lipopeptide production by Bacillus subtilis R1 and its possible applications. Braz J Microbiol 47(4):955–964.  https://doi.org/10.1016/j.bjm.2016.07.006 CrossRefPubMedPubMedCentralGoogle Scholar
  11. Jolley KA, Maiden MCJ (2010) BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11(1):595.  https://doi.org/10.1186/1471-2105-11-595 CrossRefPubMedPubMedCentralGoogle Scholar
  12. Kamada M, Hase S, Sato K, Toyoda A, Fujiyama A, Sakakibara Y (2014) Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads. PLoS One 9(10):e109999.  https://doi.org/10.1371/journal.pone.0109999 CrossRefPubMedPubMedCentralGoogle Scholar
  13. Kamada M, Hase S, Fujii K, Miyake M, Sato K, Kimura K, Sakakibara Y (2015) Whole-genome sequencing and comparative genome analysis of bacillus subtilis strains isolated from non-salted fermented soybean foods. PLoS One 10(10):e0141369.  https://doi.org/10.1371/journal.pone.0141369 CrossRefPubMedPubMedCentralGoogle Scholar
  14. Koren S, Harhay GP, Smith TP, Bono JL, Harhay DM, Mcvey SD, Radune D, Bergman NH, Phillippy AM (2013) Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biol 14(9):R101.  https://doi.org/10.1186/gb-2013-14-9-r101 CrossRefPubMedPubMedCentralGoogle Scholar
  15. Land M, Hauser L, Jun S-R, Nookaew I, Leuze MR, Ahn T-H, Karpinets T, Lund O, Kora G, Wassenaar T, Poudel S, Ussery DW (2015) Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics 15(2):141–161.  https://doi.org/10.1007/s10142-015-0433-4 CrossRefPubMedPubMedCentralGoogle Scholar
  16. Liang Y, Zhao H, Deng Y, Zhou J, Li G, Sun B (2016) Long-term oil contamination alters the molecular ecological networks of soil microbial functional genes. Front Microbiol 7:60.  https://doi.org/10.3389/fmicb.2016.00060 PubMedPubMedCentralCrossRefGoogle Scholar
  17. McArthur AG, Wright GD (2015, October) Bioinformatics of antimicrobial resistance in the age of molecular epidemiology. Curr Opin Microbiol 27:45–50.  https://doi.org/10.1016/j.mib.2015.07.004 CrossRefPubMedGoogle Scholar
  18. Rhoads, A., & Au, K. F. (2015). PacBio sequencing and its applications. Genomics, Proteomics and Bioinformatics, pp. 278–289. 10.1016/j.gpb.2015.08.002, PacBio Sequencing and Its ApplicationsGoogle Scholar
  19. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J (2016) JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32(6):929–931.  https://doi.org/10.1093/bioinformatics/btv681 CrossRefPubMedGoogle Scholar
  20. Shaligram S, Kumbhare SV, Dhotre DP, Muddeshwar MG, Kapley A, Joseph N, Purohit HP, Shouche YS, Pawar SP (2016) Genomic and functional features of the biosurfactant producing Bacillus sp. AM13. Functional and Integrative Genomics 1–10.  https://doi.org/10.1007/s10142-016-0506-z
  21. Sharma A, Satyanarayana T (2013) Comparative genomics of Bacillus species and its relevance in industrial microbiology. Genomics Insights Libertas Academica 6:GEI.S12732.  https://doi.org/10.4137/GEI.S12732 CrossRefGoogle Scholar
  22. Shibulal B, Al-Bahry SN, Al-Wahaibi YM, Elshafie AE, Al-Bemani AS, Joshi SJ (2014) Microbial enhanced heavy oil recovery by the aid of inhabitant spore-forming Bacteria: an insight review. Sci World J 2014:1–12.  https://doi.org/10.1155/2014/309159 CrossRefGoogle Scholar
  23. Vallenet D, Engelen S, Mornico D, Cruveiller S, Fleury L, Lajus A et al (2009) MicroScope: a platform for microbial genome annotation and comparative genomics. Database 2009:bap021.  https://doi.org/10.1093/database/bap021 CrossRefPubMedPubMedCentralGoogle Scholar
  24. van Heel AJ, de Jong A, Montalbán-López M, Kok J, Kuipers OP (2013) BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides. Nucleic Acids Res 41(Web Server issue):W448–W453.  https://doi.org/10.1093/nar/gkt391
  25. Vallenet D, Belda E, Calteau A, Cruveiller S, Engelen S, Lajus A, le Fèvre F, Longin C, Mornico D, Roche D, Rouy Z, Salvignol G, Scarpelli C, Thil Smith AA, Weiman M, Médigue C (2013) MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. Nucleic Acids Res 41(Database issue):D636–D647.  https://doi.org/10.1093/nar/gks1194 CrossRefPubMedGoogle Scholar
  26. Wang Y, Coleman-Derr D, Chen G, Gu YQ (2015) OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res 43(W1):W78–W84.  https://doi.org/10.1093/nar/gkv487 CrossRefPubMedPubMedCentralGoogle Scholar
  27. Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Müller R, Wohlleben W, Breitling R, Takano E, Medema MH (2015) antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 43(W1):W237–W243.  https://doi.org/10.1093/nar/gkv437 CrossRefPubMedPubMedCentralGoogle Scholar
  28. Yu G, Wang XC, Tian WH, Shi JC, Wang B, Ye Q, Dong SG, Zeng M, Wang JZ (2015) Genomic diversity and evolution of Bacillus subtilis. Biomed Environ Sci : BES 28(8):620–625.  https://doi.org/10.3967/bes2015.087 PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Touraj Rahimi
    • 1
  • Ali Niazi
    • 1
    Email author
  • Tahereh Deihimi
    • 1
  • Seyed Mohsen Taghavi
    • 2
  • Shahab Ayatollahi
    • 3
  • Esmaeil Ebrahimie
    • 1
    • 4
    • 5
    • 6
    Email author
  1. 1.Institute of BiotechnologyShiraz UniversityShirazIran
  2. 2.Department of Crop ProtectionShiraz UniversityShirazIran
  3. 3.School of Chemical and Petroleum EngineeringSharif University of TechnologyTehranIran
  4. 4.School of Information Technology and Mathematical Sciences, Division of Information Technology, Engineering and the EnvironmentThe University of South AustraliaAdelaideAustralia
  5. 5.Adelaide Medicine SchoolThe University of AdelaideAdelaideAustralia
  6. 6.School of Biological Sciences, Faculty of Science and EngineeringFlinders UniversityAdelaideAustralia

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