Skip to main content
SpringerLink
Log in

Phylogenomic characterization and pangenomic insights into the surfactin-producing bacteria Bacillus subtilis strain RI4914

  • Environmental Microbiology - Research Paper
  • Published:
Brazilian Journal of Microbiology Aims and scope Submit manuscript

Abstract

Bacillus subtilis is a versatile bacterial species able to produce surfactin, a lipopeptide biosurfactant. We carried out the phylogenomic characterization and pangenomic analyses using available B. subtilis complete genomes. Also, we report the whole genome of the biosurfactant-producing B. subtilis strain RI4914 that was isolated from effluent water from an oil exploration field. We applied a hybrid sequencing approach using both long- and short-read sequencing technologies to generate a highly accurate, single-chromosome genome. The pangenomics analysis of 153 complete genomes classified as B. subtilis retrieved from the NCBI shows an open pangenome composed of 28,511 accessory genes, which agrees with the high genetic plasticity of the species. Also, this analysis suggests that surfactin production is a common trait shared by members of this species since the srfA operon is highly conserved among the B. subtilis strains found in most of the assemblies available. Finally, increased surfactin production corroborates the higher srfAA gene expression in B. subtilis strain RI4914.

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

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  1. Van Hamme JD, Singh A, Ward OP (2006) Physiological aspects. Biotechnol Adv 24:604–620. https://doi.org/10.1016/j.biotechadv.2006.08.001

  2. Abbasi H, Hamedi MM, Lotfabad TB, Zahiri HS, Sharafi H, Masoomi F et al (2012) Biosurfactant-producing bacterium, Pseudomonas aeruginosa MA01 isolated from spoiled apples: physicochemical and structural characteristics of isolated biosurfactant. J Biosci Bioeng 113:211–219

    Article  PubMed  CAS  Google Scholar 

  3. Desai JD, Banat IM (1997) Microbial production of surfactants and their commercial potential. Microbiol Mol Biol Rev 61:47–64

    PubMed  PubMed Central  CAS  Google Scholar 

  4. Lima TMS, Procópio LC, Brandão FD, Leão BA, Tótola MR, Borges AC (2011) Evaluation of bacterial surfactant toxicity towards petroleum degrading microorganisms. Bioresour Technol 102:2957–2964

    Article  PubMed  CAS  Google Scholar 

  5. Lima TMS, Procópio LC, Brandão FD, Carvalho AMX, Tótola MR, Borges AC (2011) Biodegradability of bacterial surfactants. Biodegradation 22:585–592. https://doi.org/10.1007/s10532-010-9431-3

  6. Maia M, Capão A, Procópio L (2019) Biosurfactant produced by oil-degradingPseudomonas putidaAM-b1 strain with potential for microbial enhanced oil recovery. Bioremediat J 23:302–310

    Article  CAS  Google Scholar 

  7. Harwood CR, Mouillon J-M, Pohl S, Arnau J (2018) Secondary metabolite production and the safety of industrially important members of the Bacillus subtilis group. FEMS Microbiol Rev 42:721–738

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  8. Fernandes PL, Rodrigues EM, Paiva FR, Ayupe BAL, McInerney MJ, Tótola MR. (2016) Biosurfactant, solvents and polymer production by Bacillus subtilis RI4914 and their application for enhanced oil recovery. Fuel 180:551–557. https://doi.org/10.1016/j.fuel.2016.04.080

  9. Willenbacher J, Yeremchuk W, Mohr T, Syldatk C, Hausmann R (2015) Enhancement of Surfactin yield by improving the medium composition and fermentation process. AMB Express 5:145

    Article  PubMed  Google Scholar 

  10. Zhi Y, Wu Q, Xu Y (2017) Genome and transcriptome analysis of surfactin biosynthesis in Bacillus amyloliquefaciens MT45. Sci Rep 7:40976

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  11. Wu B, Xiu J, Yu L, Huang L, Yi L, Ma Y (2022) Biosurfactant production by Bacillus subtilis SL and its potential for enhanced oil recovery in low permeability reservoirs. Sci Rep 12:7785

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  12. Madsen JK, Pihl R, Møller AH, Madsen AT, Otzen DE and Andersen KK (2015) The anionic biosurfactant rhamnolipid does not denature industrial enzymes. Front Microbiol 6:292. https://doi.org/10.3389/fmicb.2015.00292

  13. Kim Y, Koh I, Young Lim M, Chung W-H, Rho M (2017) Pan-genome analysis of Bacillus for microbiome profiling. Sci Rep 7:10984

    Article  PubMed  PubMed Central  Google Scholar 

  14. Brito PH, Chevreux B, Serra CR, Schyns G, Henriques AO, Pereira-Leal JB (2018) Genetic competence drives genome diversity in Bacillus subtilis. Genome Biol Evol 10:108–124

    Article  PubMed  CAS  Google Scholar 

  15. Borriss R, Danchin A, Harwood CR, Médigue C, Rocha EPC, Sekowska A, et al. (2018) Bacillus subtilis,the model Gram-positive bacterium: 20 years of annotation refinement. Microb Biotechnol 11:3–17. https://doi.org/10.1111/1751-7915.13043

  16. Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V et al (1997) The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390:249–256

    Article  PubMed  CAS  Google Scholar 

  17. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948. https://doi.org/10.1093/bioinformatics/btm404

  18. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29:e45

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  19. Steibel JP, Poletto R, Coussens PM, Rosa GJM (2009) A powerful and flexible linear mixed model framework for the analysis of relative quantification RT-PCR data. Genomics 94:146–152

    Article  PubMed  CAS  Google Scholar 

  20. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM (2017) Canu: scalable and accurate long-read assembly via adaptive -mer weighting and repeat separation. Genome Res 27:722–736

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  21. Vaser R, Sović I, Nagarajan N, Šikić M (2017) Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res 27:737–746

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  22. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  23. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  24. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M (2021) TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res. https://doi.org/10.1093/nar/gkab902

    Article  PubMed Central  Google Scholar 

  25. 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 32:929–931

    Article  PubMed  CAS  Google Scholar 

  26. Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL et al (2014) PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res 42:D581–D591

    Article  PubMed  CAS  Google Scholar 

  27. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L et al (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  28. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  29. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755

    Article  PubMed  CAS  Google Scholar 

  30. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MTG et al (2015) Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31:3691–3693

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  31. Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. https://doi.org/10.1093/bioinformatics/btu153

  32. Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  33. Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  34. Sohail R, Jamil N. (2019) Isolation of biosurfactant producing bacteria from Potwar oil fields: effect of non-fossil fuel based carbon sources. Green Process Synth 9:77–86. https://doi.org/10.1515/gps-2020-0009

  35. Alvarez VM, Jurelevicius D, Marques JM, de Souza PM, de Araújo LV, Barros TG et al (2015) Bacillus amyloliquefaciens TSBSO 3.8, a biosurfactant-producing strain with biotechnological potential for microbial enhanced oil recovery. Colloids Surf B Biointerfaces 136:14–21

    Article  PubMed  CAS  Google Scholar 

  36. Wu H, Wang D, Gao F (2021) Toward a high-quality pan-genome landscape of Bacillus subtilis by removal of confounding strains. Brief Bioinform 22:1951–1971. https://doi.org/10.1093/bib/bbaa013

  37. Rasmussen S, Nielsen HB, Jarmer H (2009) The transcriptionally active regions in the genome of Bacillus subtilis. Mol Microbiol 73:1043–1057

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  38. Adékambi T, Drancourt M, Raoult D (2009) The rpoB gene as a tool for clinical microbiologists. Trends Microbiol 17:37–45

    Article  PubMed  Google Scholar 

  39. Ki J-S, Zhang W, Qian P-Y (2009) Discovery of marine Bacillus species by 16S rRNA and rpoB comparisons and their usefulness for species identification. J Microbiol Methods 77:48–57

    Article  PubMed  CAS  Google Scholar 

  40. Zhang S-J, Du X-P, Zhu J-M, Meng C-X, Zhou J, Zuo P (2020) The complete genome sequence of the algicidal bacterium Bacillus subtilis strain JA and the use of quorum sensing to evaluate its antialgal ability. Biotechnol Rep 25:e00421. https://doi.org/10.1016/j.btre.2020.e00421

  41. Stice SP, Stumpf SD, Gitaitis RD, Kvitko BH, Dutta B (2018) Genetic diversity analysis reveals limited genomic diversity as well as accessory genes correlated with onion pathogenicity. Front Microbiol 9:184

    Article  PubMed  PubMed Central  Google Scholar 

  42. Snipen L, Almøy T, Ussery DW (2009) Microbial comparative pan-genomics using binomial mixture models. BMC Genomics 10:385

    Article  PubMed  PubMed Central  Google Scholar 

  43. Rouli L, Merhej V, Fournier P-E, Raoult D (2015) The bacterial pangenome as a new tool for analysing pathogenic bacteria. New Microbes New Infect 7:72–85

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  44. Coleman JJ, Rounsley SD, Rodriguez-Carres M, Kuo A, Wasmann CC, Grimwood J et al (2009) The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genet 5:e1000618

    Article  PubMed  PubMed Central  Google Scholar 

  45. Choi HJ, Shin D, Shin M, Yun B, Kang M, Yang H-J et al (2020) Comparative genomic and functional evaluations of Bacillus subtilis newly isolated from Korean traditional fermented foods. Foods 9:1805. https://doi.org/10.3390/foods9121805

    Article  PubMed Central  CAS  Google Scholar 

Download references

Funding

This work was supported by the National Council for Scientific and Technological Development (Conselho Nacional de Desenvolvimento Científico e Tecnológico/CNPq—project grant number 404651/2018–6). AMV received a research fellowship from the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) (#303061/2019–7). JKLF also received a research fellowship from the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) (#133550/2019–2). This research was supported by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior — Brasil (CAPES) — Finance Code 001. This work was also supported by the Brazilian Microbiome Project (http://www.brmicrobiome.org).

Author information

Authors and Affiliations

  1. Department of Biology, Federal University of Lavras - UFLA, Lavras, Minas Gerais, Brazil

    Julie Kennya de Lima Ferreira, Dirceu de Sousa Melo, Cristina Ferreira Silva e Batista, Antonio Chalfun-Junior, Kellen Kauanne Pimenta de Oliveira & Victor Satler Pylro

  2. Departamento de Tecnologia, Faculdade de Ciências Agrárias E Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, Sao Paulo, Brazil

    Alessandro de Mello Varani

  3. Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Minas Gerais, Viçosa, Brazil

    Marcos Rogério Tótola & Michelle Fernandes Almeida

  4. Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA

    Luiz Fernando Wurdig Roesch

Authors
  1. Julie Kennya de Lima Ferreira
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Alessandro de Mello Varani
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Marcos Rogério Tótola
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Michelle Fernandes Almeida
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Dirceu de Sousa Melo
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Cristina Ferreira Silva e Batista
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Antonio Chalfun-Junior
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Kellen Kauanne Pimenta de Oliveira
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Luiz Fernando Wurdig Roesch
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Victor Satler Pylro
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Victor Satler Pylro.

Ethics declarations

Conflict of interest

The authors declare no competing interests.

Additional information

Publisher's note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Responsible Editor: Luiz Henrique Rosa

Supplementary Information

Rights and permissions

Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

de Lima Ferreira, J.K., de Mello Varani, A., Tótola, M.R. et al. Phylogenomic characterization and pangenomic insights into the surfactin-producing bacteria Bacillus subtilis strain RI4914. Braz J Microbiol 53, 2051–2063 (2022). https://doi.org/10.1007/s42770-022-00815-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s42770-022-00815-0

Keywords

Search

Navigation