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Genomic and functional features of the biosurfactant producing Bacillus sp. AM13

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An Erratum to this article was published on 25 November 2016

Abstract

Genomic studies provide deeper insights into secondary metabolites produced by diverse bacterial communities, residing in various environmental niches. This study aims to understand the potential of a biosurfactant producing Bacillus sp. AM13, isolated from soil. An integrated approach of genomic and chemical analysis was employed to characterize the antibacterial lipopeptide produced by the strain AM13. Genome analysis revealed that strain AM13 harbors a nonribosomal peptide synthetase (NRPS) cluster; highly similar with known biosynthetic gene clusters from surfactin family: lichenysin (85 %) and surfactin (78 %). These findings were substantiated with supplementary experiments of oil displacement assay and surface tension measurements, confirming the biosurfactant production. Further investigation using LCMS approach exhibited similarity of the biomolecule with biosurfactants of the surfactin family. Our consolidated effort of functional genomics provided chemical as well as genetic leads for understanding the biochemical characteristics of the bioactive compound.

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References

  • Al-Bahry SN, Al-Wahaibi YM, Elshafie AE, Al-Bemani AS, Joshi SJ, Al-Makhmari HS, Al-Sulaimani HS (2013) Biosurfactant production by Bacillus subtilis B20 using date molasses and its possible application in enhanced oil recovery. Int Biodeterior Biodegrad 81:141–146. doi:10.1016/j.ibiod.2012.01.006

    Article  CAS  Google Scholar 

  • Aleti G, Sessitsch A, Brader G (2015) Genome mining: prediction of lipopeptides and polyketides from bacillus and related firmicutes. Comput Struct Biotechnol J 13:192–203. doi:10.1016/j.csbj.2015.03.003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity G, Kodira CD, Kyrpides N, Madupu R, Markowitz V, Tatusova T, Thomson N, White O (2008) Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. Omi A J Integr Biol 12:137–141. doi:10.1089/omi.2008.0017

    Article  CAS  Google Scholar 

  • Ansari MZ, Yadav G, Gokhale RS, Mohanty D (2004) NRPS-PKS: a knowledge-based resource for analysis of NRPS-PKS megasynthases. Nucleic Acids Res 32:405–413. doi:10.1093/nar/gkh359

    Article  Google Scholar 

  • Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F et al (2008) The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. doi:10.1186/1471-2164-9-75

    Article  PubMed  PubMed Central  Google Scholar 

  • Ben Ayed H, Jridi M, Maalej H, Nasri M, Hmidet N (2014) Characterization and stability of biosurfactant produced by bacillus mojavensis A21 and its application in enhancing solubility of hydrocarbon. J Chem Technol Biotechnol 89:1007–1014. doi:10.1002/jctb.4192

    Article  CAS  Google Scholar 

  • Bergmann S, Schümann J, Scherlach K, Lange C, Brakhage AA, Hertweck C (2007) Genomics-driven discovery of PKS-NRPS hybrid metabolites from Aspergillus nidulans. Nat Chem Biol 3:213–217. doi:10.1038/nchembio869

    Article  CAS  PubMed  Google Scholar 

  • Branquinho R, Sousa C, Lopes J, Pintado ME, Peixe LV, Osorio (2014) Differentiation of Bacillus pumilus and Bacillus safensis using MALDI-TOF-MS. PLoS One 9:e116426. doi:10.1371/journal.pone.0110127

    Article  Google Scholar 

  • Carrillo PG, Mardaraz C, Pitta-Alvarez SI, Giulietti AM (1996) Isolation and selection of biosurfactant-producing bacteria. World J Microbiol Biotechnol 12:82–4. doi:10.1007/BF00327807

    Article  CAS  PubMed  Google Scholar 

  • Chevreux B, Wetter T, Suhai S (1999) Genome sequence assembly using trace signals and additional sequence information. Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99:45–56

    Google Scholar 

  • Chun J, Lee JH, Jung Y, Kim M, Kim S, Kim BK, Lim YW (2007) EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57:2259–2261. doi:10.1099/ijs.0.64915-0

    Article  CAS  PubMed  Google Scholar 

  • Dhillon BK, Laird MR, Shay JA, Winsor GL, Lo R, Nizam F, Pereira SK, Waglechner N, McArthur AG, Langille MG, Brinkman FS (2015) IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis. Nucleic Acids Res 43:W104–8. doi:10.1093/nar/gkv401

    Article  PubMed  PubMed Central  Google Scholar 

  • Domingos DF, de Faria AF, de Souza GR, Eberlin MN, Greenfield P, Zucchi TD, Melo IS, Tran-Dinh N, Midgley D, de Oliveira VM (2015) Genomic and chemical insights into biosurfactant production by the mangrove-derived strain Bacillus safensis CCMA-560. Appl Microbiol Biotechnol 99:3155–3167. doi:10.1007/s00253-015-6377-8

    Article  CAS  PubMed  Google Scholar 

  • Donio MBS, Ronica FA, Viji VT, Velmurugan S, Jenifer JS, Michaelbabu M, Dhar P, Citarasu T (2013) Halomonas sp. BS4, a biosurfactant producing halophilic bacterium isolated from solar salt works in India and their biomedical importance. Springerplus 2:149. doi:10.1186/2193-1801-2-149

    Article  PubMed  PubMed Central  Google Scholar 

  • Doroghazi JR, Albright JC, Goering AW, Ju KS, Hainess RR, Tchalukov KA, Labeda DP, Kelleher NL, Metcalf WW (2014) A roadmap for natural product discovery based on large-scale genomics and metabolomics. Nat Chem Biol 10:963–8. doi:10.1038/nchembio.1659

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grant JR, Stothard P (2008) The CGView server: a comparative genomics tool for circular genomes. Nucleic Acids Res 36:181–184. doi:10.1093/nar/gkn179

    Article  Google Scholar 

  • 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 14:111–129. doi:10.1038/nrd4510

    Article  CAS  PubMed  Google Scholar 

  • Heerklotz H, Seelig J (2007) Leakage and lysis of lipid membranes induced by the lipopeptide surfactin. Eur Biophys J 36:305–314. doi:10.1007/s00249-006-0091-5

    Article  CAS  PubMed  Google Scholar 

  • Kapley A, Tanksale H, Sagarkar S, Prasad AR, Kumar RA, Sharma N, Qureshi A, Purohit HJ (2016) Antimicrobial activity of Alcaligenes sp. HPC 1271 against multidrug resistant bacteria. Funct Integr Genomics 16:57–65. doi:10.1007/s10142-015-0466-8

    Article  CAS  PubMed  Google Scholar 

  • Konz D, Doekel S, Marahiel M a (1999) Molecular and biochemical characterization of the protein template controlling biosynthesis of the lipopeptide lichenysin molecular and biochemical characterization of the protein template controlling biosynthesis of the lipopeptide lichenysin. J Bacteriol 181:133–140, doi: 0021-9193/99/$04.0010

    CAS  PubMed  PubMed Central  Google Scholar 

  • Koumoutsi A, Chen X, Henne A, Lieseqang H, Hitzeroth G, Franke P, Vater J, Borriss R (2004) Structural and functional characterization of gene clusters directing nonribosomal synthesis of bioactive cyclic lipopeptides in Bacillus amyloliquefaciens strain FZB42. J Bacteriol 186:1084–1096. doi:10.1128/JB.186.4.1084

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108. doi:10.1093/nar/gkm160

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lam KS (2007) New aspects of natural products in drug discovery. Trends Microbiol 15:279–289. doi:10.1016/j.tim.2007.04.001

    Article  CAS  PubMed  Google Scholar 

  • Land M, Hauser L, Jun SR, Nookaew I, Leuze MR, Ahn TH, Karpinets T, Lund O, Kora G, Wassenaar T, Poudel S, Ussery DW (2015) Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics 15:141–61. doi:10.1007/s10142-015-0433-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lavermicocca P, Valerio F, Evidente A, Lazzaroni S, Corsetti A, Gobbetti M (2000) Purification and characterization of novel antifungal compounds from the sourdough lactobacillus plantarum strain 21B. Appl Environ Microbiol 66:4084–4090. doi:10.1128/AEM.66.9.4084-4090.2000

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu Y, Lai Q, Dong C, Sun F, Wang L, Li G, Shao Z (2013) Phylogenetic diversity of the Bacillus pumilus group and the marine ecotype revealed by multilocus sequence analysis. PLoS One 8:1–11. doi:10.1371/journal.pone.0080097

    Google Scholar 

  • Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964. doi:10.1093/nar/25.5.955

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lu L, Wang J, Xu Y, Wang K, Hu Y, Tian R, Yang B, Lai Q, Li Y, Zhang W, Shao Z, Lam H, Qian PY (2014) A high-resolution LC-MS-based secondary metabolite fingerprint database of marine bacteria. Sci Rep 4:6537. doi:10.1038/srep06537

    Article  CAS  PubMed  Google Scholar 

  • Morikawa M, Hirata Y (2000) A study on the structure-function relationship of lipopeptide biosurfactants. 1488:211–218. doi:10.1016/S1388-1981(00)00124-4

  • Mukherjee S, Das P, Sivapathasekaran C, Sen R (2009) Antimicrobial biosurfactants from marine bacillus circulans: extracellular synthesis and purification. Lett Appl Microbiol 48:281–288. doi:10.1111/j.1472-765X.2008.02485.x

    Article  CAS  PubMed  Google Scholar 

  • Naruse N, Tenmyo O, Kobaru S, Kamei H, Miyaki T, Konishi M, Oki T (1990) Pumilacidin, a complex of new antiviral antibiotics. Production, isolation, chemical properties, structure and biological activity. J Antibiot (Tokyo) 43:267–280. doi:10.7164/antibiotics.43.267

    Article  CAS  Google Scholar 

  • Nerurkar AS (2010) Structural and Molecular Characteristics of Lichenysin and Its Relationship with Surface Activity. In: Sen R (ed) Biosurfactants, vol 672. New York, Springer, pp 304–315. doi:10.1007/978-1-4419-5979-9_23

    Chapter  Google Scholar 

  • Ongena M, Jacques P (2008) Bacillus lipopeptides: versatile weapons for plant disease biocontrol. Trends Microbiol 16:115–125. doi:10.1016/j.tim.2007.12.009

    Article  CAS  PubMed  Google Scholar 

  • Pal RR, Khardenavis AA, Purohit HJ (2015) Identification and monitoring of nitrification and denitrification genes in Klebsiella pneumoniae EGD-HP19-C for its ability to perform heterotrophic nitrification and aerobic denitrification. Funct Integr Genomics 15:63–76. doi:10.1007/s10142-014-0406-z

    Article  CAS  PubMed  Google Scholar 

  • Payne DJ, Gwynn MN, Holmes DJ, Pompliano DL (2007) Drugs for bad bugs: confronting the challenges of antibacterial discovery. Nat Rev Drug Discov 6:29–40. doi:10.1038/nrd2201

    Article  CAS  PubMed  Google Scholar 

  • Prakash O, Green SJ, Jasrotia P, Ovreholt WA, Canion A, Watson DB, Brooks SC, Kostka JE (2012) Rhodanobacter denitrificans sp. nov., isolated from nitrate-rich zones of a contaminated aquifer. Int J Syst Evol Microbiol 62:2457–2462. doi:10.1099/ijs.0.035840-0

    Article  CAS  PubMed  Google Scholar 

  • Raaijmakers JM, de Bruijn I, Nybroe O, Ongena M (2010) Natural functions of lipopeptides from bacillus and pseudomonas: More than surfactants and antibiotics. FEMS Microbiol Rev 34:1037–1062. doi:10.1111/j.1574-6976.2010.00221.x

    Article  CAS  PubMed  Google Scholar 

  • Rey MW, Ramaiya P, Nelson BA, Brody-Karpin SD, Zaretsky EJ, Tang M, Lopez de Leon A, Xiang H, Gusti V, Clausen IG et al (2004) Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species. Genome Biol 5:R77. doi:10.1186/gb-2004-5-10-r77

    Article  PubMed  PubMed Central  Google Scholar 

  • Richter M, Rosselló-Móra R, Glöckner FO, Peplies J (2015) JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32:929–31. doi:10.1093/bioinformatics/btv681

    Article  PubMed  Google Scholar 

  • Rodrigues L, Banat IM, Teixeira J, Oliveira R (2006) Biosurfactants: potential applications in medicine. J Antimicrob Chemother 57:609–618. doi:10.1093/jac/dkl024

    Article  CAS  PubMed  Google Scholar 

  • Satpute SK, Banpurkar AG, Dhakephalkar PK, Banat IM, Chopade BA (2010) Methods for investigating biosurfactants and bioemulsifiers: a review. Crit Rev Biotechnol 30:127–144. doi:10.3109/07388550903427280

    Article  CAS  PubMed  Google Scholar 

  • Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M (2006) ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 34:D32–6. doi:10.1093/nar/gkj014

    Article  CAS  PubMed  Google Scholar 

  • Van Lanen SG, Shen B (2006) Microbial genomics for the improvement of natural product discovery. Curr Opin Microbiol 9:252–260. doi:10.1016/j.mib.2006.04.002

    Article  PubMed  Google Scholar 

  • Villanueva J, Switala J, Ivancich A, Loewen PC (2014) Genome sequence of Bacillus pumilus MTCC B6033. Genome Announc 2:e00327–14. doi:10.1128/genomeA.00327-14

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang H, Fewer DP, Holm L, Rouhiainen L, Sivonen K (2014) Atlas of nonribosomal peptide and polyketide biosynthetic pathways reveals common occurrence of nonmodular enzymes. Proc Natl Acad Sci U S A 111:9259–9264. doi:10.1073/pnas.1401734111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Weber T, Blin K, Duddela S, Krug D, Hu K, Bruccoleri R, Lee SY, Fischback MA, Muller 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 43:1–7. doi:10.1093/nar/gkv437

    Article  Google Scholar 

  • Yakimov MM, Timmis KN, Wray V, Fredrickson HL (1995) Characterization of a new lipopeptide surfactant produced by thermotolerant and halotolerant subsurface Bacillus licheniformis BAS50. Appl Environ Microbiol 61:1706–1713, doi: 0099-2240/95/$04.0010

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zerikly M, Challis GL (2009) Strategies for the discovery of new natural products by genome mining. ChemBioChem 10:625–633. doi:10.1002/cbic.200800389

    Article  CAS  PubMed  Google Scholar 

  • Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS (2011) PHAST: a fast phage search tool. Nucleic Acids Res 39:1–6. doi:10.1093/nar/gkr485

    Article  Google Scholar 

  • 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 7:1–9. doi:10.1371/journal.pone.0034064

    Article  Google Scholar 

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Acknowledgments

Authors are thankful to Dr. Kiran Mahale (National Centre for Cell Science, Pune) and Dr. Sneha Sagarkar (Department of Biotechnology, Savitribai Phule University of Pune) for their valuable technical inputs. Authors are grateful to Mrs. Ashwini Rane (Department of Microbiology, Savitribai Phule University of Pune) for her assistance in conducting biosurfactant assay, and Datar Genetics Limited, Nashik, India for their support in Genome sequencing. We would also like to thank Dr. Ranadhir Chakraborty (North Bengal University) for providing the MDR isolates used in the study. This study was funded by Department of Biotechnology, Government of India, under the project of Microbial Culture Collection (Grant number: BT/PR10054/NDB/52/94/2007).

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The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Department of Biochemistry, Government Medical College, Nagpur, 440009, Maharashtra, India

    Shraddha Shaligram & Manohar G. Muddeshwar

  2. Microbial Culture Collection, National Centre for Cell Science, Pune, 411007, Maharashtra, India

    Shraddha Shaligram, Shreyas V. Kumbhare, Dhiraj P. Dhotre, Neetha Joseph, Yogesh S. Shouche & Shrikant P. Pawar

  3. Environmental Genomics Division, National Environmental Engineering Research Institute, CSIR Nehru Marg, Nagpur, 440020, India

    Atya Kapley & Hemant P. Purohit

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  1. Shraddha Shaligram
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  2. Shreyas V. Kumbhare
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  4. Manohar G. Muddeshwar
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Correspondence to Manohar G. Muddeshwar or Shrikant P. Pawar.

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An erratum to this article is available at http://dx.doi.org/10.1007/s10142-016-0528-6.

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Shaligram, S., Kumbhare, S.V., Dhotre, D.P. et al. Genomic and functional features of the biosurfactant producing Bacillus sp. AM13. Funct Integr Genomics 16, 557–566 (2016). https://doi.org/10.1007/s10142-016-0506-z

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