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.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 Applications
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
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
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
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
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
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
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
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
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
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
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.
Author information
Authors and Affiliations
Corresponding authors
Electronic supplementary material
ESM 1
(DOCX 101 kb)
Rights and permissions
About this article
Cite this article
Rahimi, T., Niazi, A., Deihimi, T. et al. Genome annotation and comparative genomic analysis of Bacillus subtilis MJ01, a new bio-degradation strain isolated from oil-contaminated soil. Funct Integr Genomics 18, 533–543 (2018). https://doi.org/10.1007/s10142-018-0604-1
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10142-018-0604-1