Applied Biochemistry and Biotechnology

, Volume 187, Issue 2, pp 518–530 | Cite as

Genome Sequencing and Analysis of Strains Bacillus sp. AKBS9 and Acinetobacter sp. AKBS16 for Biosurfactant Production and Bioremediation

  • Niti B. Jadeja
  • Prachiti Moharir
  • Atya KapleyEmail author


Microbial genomics facilitates the analysis of microbial attributes, which can be applied in bioremediation of pollutants and oil recovery process. The biosurfactants derived from microbes can replace the chemical surfactants, which are ecologically detrimental. The aim of this work was to study the genetic organization responsible for biodegradation of aromatics and biosurfactant production in potential microbes isolated from polluted soil. Bacterial isolates were tested for biosurfactant production, wherein Bacillus sp. AKBS9 and Acinetobacter sp. AKBS16 exhibited highest biosurfactant production potential. Whole genome sequencing and annotations revealed the occurrence of sfp and NPRS gene in the Bacillibactin biosynthetic gene cluster in AKBS9 strain and emulsan biosynthetic gene cluster in AKBS16 strain for biosurfactant production. Various aromatic compound ring cleaving oxygenases scavenging organic molecules could be annotated for strain AKBS16 using RAST annotations.


Biosurfactant Surfactin PCR Microbial genomics 



The authors acknowledge the Council of Scientific and Industrial Research, India, CSIR-network project ESC-0108-MESER, for supporting this research. Niti B Jadeja (SRF) is grateful to the CSIR. We are also grateful to Director, CSIR-NEERI, Nagpur, for the support. The manuscript has been checked for plagiarism using iThenticate Software under assigned KRC No.: CSIR-NEERI/KRC/2018/JAN/DRC/1.

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Supplementary material

12010_2018_2828_MOESM1_ESM.docx (13 kb)
Supplementary Table 1 Results of confirmatory tests for Biosurfactant production in strains AKBS9 and AKBS16. (DOCX 12 kb)
12010_2018_2828_Fig4_ESM.png (172 kb)
Supplementary Figure 1

In-silico steps involved in the analysis of AKBS9 and AKBS16 draft genomes. (PNG 171 kb)

12010_2018_2828_MOESM2_ESM.tif (678 kb)
High Resolution (TIF 677 kb)
12010_2018_2828_Fig5_ESM.png (821 kb)
Supplementary Figure 2

Graphical representation of gene ontologies for draft genome assemblies a) AKBS9 and b) AKBS16. (PNG 820 kb)

12010_2018_2828_Fig6_ESM.png (1020 kb)
Supplementary Figure 2

Graphical representation of gene ontologies for draft genome assemblies a) AKBS9 and b) AKBS16. (PNG 820 kb)

12010_2018_2828_MOESM3_ESM.tif (2.9 mb)
High Resolution (TIF 3010 kb)
12010_2018_2828_MOESM4_ESM.tif (3.4 mb)
High Resolution (TIF 3457 kb)
12010_2018_2828_Fig7_ESM.png (4.3 mb)
Supplementary Figure 3

Circos plot of AKBS9 and closest reference match Bacillus cereusb) Circos plot of AKBS16 with closest reference match Acinetobacter pittii. (PNG 4396 kb)

12010_2018_2828_Fig8_ESM.png (4.7 mb)
Supplementary Figure 3

Circos plot of AKBS9 and closest reference match Bacillus cereusb) Circos plot of AKBS16 with closest reference match Acinetobacter pittii. (PNG 4396 kb)

12010_2018_2828_MOESM5_ESM.tif (6.1 mb)
High Resolution (TIF 6295 kb)
12010_2018_2828_MOESM6_ESM.tif (7.1 mb)
High Resolution (TIF 7273 kb)


  1. 1.
    Deleu, M., & Paquot, M. (2004). From renewable vegetables resources to microorganisms: New trends in surfactants. Comptes Rendus Chimie, 7(6-7), 641–646.CrossRefGoogle Scholar
  2. 2.
    Owsianiak, M., Chrzanowski, Ł., Szulc, A., Staniewski, J., Olszanowski, A., Olejnik-Schmidt, A. K., & Heipieper, H. J. (2009). Biodegradation of diesel/biodiesel blends by a consortium of hydrocarbon degraders: Effect of the type of blend and the addition of biosurfactants. Bioresource Technology, 100(3), 1497–1500.CrossRefGoogle Scholar
  3. 3.
    Bezza, F. A., & Chirwa, E. M. N. (2016). Biosurfactant-enhanced bioremediation of aged polycyclic aromatic hydrocarbons (PAHs) in creosote contaminated soil. Chemosphere, 144, 635–644.CrossRefGoogle Scholar
  4. 4.
    Perez-Ameneiro, M., Vecino, X., Cruz, J. M., & Moldes, A. B. (2015). Wastewater treatment enhancement by applying a lipopeptide biosurfactant to a lignocellulosic biocomposite. Carbohydrate Polymers, 131, 186–196.CrossRefGoogle Scholar
  5. 5.
    Desai, J. D., & Banat, I. M. (1997). Microbial production of surfactants and their commercial potential. Microbiology and Molecular Biology Reviews, 61(1), 47–64.Google Scholar
  6. 6.
    Kapley, A., De Baere, T., & Purohit, H. J. (2007). Eubacterial diversity of activated biomass from a common effluent treatment plant. Research in Microbiology, 158(6), 494–500.CrossRefGoogle Scholar
  7. 7.
    Kapley, A., Prasad, S., & Purohit, H. J. (2007). Changes in microbial diversity in fed-batch reactor operation with wastewater containing nitroaromatic residues. Bioresource Technology, 98(13), 2479–2484.CrossRefGoogle Scholar
  8. 8.
    Kapley, A., & Purohit, H. J. (2009). Diagnosis of treatment efficiency in industrial wastewater treatment plants: A case study at a refinery ETP. Environmental Science & Technology, 43(10), 3789–3795.CrossRefGoogle Scholar
  9. 9.
    Thangaraj, K., Kapley, A., & Purohit, H. J. (2008). Characterization of diverse Acinetobacter isolates for utilization of multiple aromatic compounds. Bioresource Technology, 99(7), 2488–2494.CrossRefGoogle Scholar
  10. 10.
    Kapley, A., Liu, R., Jadeja, N. B., Zhang, Y., Yang, M., & Purohit, H. J. (2015). Shifts in microbial community and its correlation with degradative efficiency in a wastewater treatment plant. Applied Biochemistry and Biotechnology, 176(8), 2131–2143.CrossRefGoogle Scholar
  11. 11.
    Nwaguma, I. V., Chikere, C. B., & Okpokwasili, G. C. (2016). Isolation, characterization, and application of biosurfactant by Klebsiella pneumoniae strain IVN51 isolated from hydrocarbon-polluted soil in Ogoniland, Nigeria. Bioresources and Bioprocessing, 3(1), 40.CrossRefGoogle Scholar
  12. 12.
    Shoeb, E., Ahmed, N., Akhter, J., Badar, U., Siddiqui, K., Ansari, F., Waqar, M., Imtiaz, S., Akhtar, N., Shaikh, Q. U. A., & BAIG, R. (2015). Screening and characterization of biosurfactant-producing bacteria isolated from the Arabian Sea coast of Karachi. Turkish Journal of Biology, 39, 210–216.CrossRefGoogle Scholar
  13. 13.
    Morikawa, M., Daido, H., Takao, T., Murata, S., Shimonishi, Y., & Imanaka, T. (1993). A new lipopeptide biosurfactant produced by Arthrobacter sp. strain MIS38. Journal of Bacteriology, 175(20), 6459–6466.CrossRefGoogle Scholar
  14. 14.
    Overbeek, R., Olson, R., Pusch, G. D., Olsen, G. J., Davis, J. J., Disz, T., Edwards, R. A., Gerdes, S., Parrello, B., Shukla, M., & Vonstein, V. (2013). The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Research, 42, 206–214.CrossRefGoogle Scholar
  15. 15.
    Darzentas, N. (2010). Circoletto: Visualizing sequence similarity with Circos. Bioinformatics, 26(20), 26202621.CrossRefGoogle Scholar
  16. 16.
    Tatusova, T., DiCuccio, M., Badretdin, A., Chetvernin, V., Nawrocki, E. P., Zaslavsky, L., Lomsadze, A., Pruitt, K. D., Borodovsky, M., & Ostell, J. (2016). NCBI prokaryotic genome annotation pipeline. Nucleic Acids Research, 44(14), 6614–6624.CrossRefGoogle Scholar
  17. 17.
    Weber, T., Blin, K., Duddela, S., Krug, D., Kim, H. U., Bruccoleri, R., Lee, S. Y., Fischbach, M. A., Müller, R., Wohlleben, W., & Breitling, R. (2015). antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Research, 43, 237–243.CrossRefGoogle Scholar
  18. 18.
    Santos, D. K. F., Rufino, R. D., Luna, J. M., Santos, V. A., & Sarubbo, L. A. (2016). Biosurfactants: Multifunctional biomolecules of the 21st century. International Journal of Molecular Sciences, 17(3), 401.CrossRefGoogle Scholar
  19. 19.
    Shaligram, S., Kumbhare, S. V., Dhotre, D. P., Muddeshwar, M. G., Kapley, A., Joseph, N., Purohit, H. P., Shouche, Y. S., & Pawar, S. P. (2016). Genomic and functional features of the biosurfactant producing Bacillus sp. AM13. Functional & Integrative Genomics, 16(5), 557–566.CrossRefGoogle Scholar
  20. 20.
    Koumoutsi, A., Chen, X. H., Henne, A., Liesegang, 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. Journal of Bacteriology, 186(4), 1084–1096.CrossRefGoogle Scholar
  21. 21.
    Bach, H., Berdichevsky, Y., & Gutnick, D. (2003). An exocellular protein from the oil-degrading microbe Acinetobacter venetianus RAG-1 enhances the emulsifying activity of the polymeric bioemulsifier emulsan. Applied and Environmental Microbiology, 69(5), 2608–2615.CrossRefGoogle Scholar
  22. 22.
    Nakar, D., & Gutnick, D. L. (2001). Analysis of the wee gene cluster responsible for the biosynthesis of the polymeric bioemulsifier from the oil-degrading strain Acinetobacter lwoffii RAG-1. Microbiology, 147(7), 1937–1946.CrossRefGoogle Scholar
  23. 23.
    Bhardwaj, P., Sharma, A., Sagarkar, S., & Kapley, A. (2015). Mapping atrazine and phenol degradation genes in Pseudomonas sp. EGD-AKN5. Biochemical Engineering Journal, 102, 125–134.CrossRefGoogle Scholar
  24. 24.
    Fondi, M., Maida, I., Perrin, E., Orlandini, V., La Torre, L., Bosi, E., Negroni, A., Zanaroli, G., Fava, F., Decorosi, F., & Giovannetti, L. (2016). Genomic and phenotypic characterization of the species Acinetobacter venetianus. Scientific Reports, 6(1), 21985.Google Scholar
  25. 25.
    Gu, Q., Wu, Q., Zhang, J., Guo, W., Wu, H., & Sun, M. (2017). Acinetobacter sp. DW-1 immobilized on polyhedron hollow polypropylene balls and analysis of transcriptome and proteome of the bacterium during phenol biodegradation process. Scientific Reports, 7, 4863.CrossRefGoogle Scholar
  26. 26.
    Rudrashetti, A. P., Jadeja, N. B., Gandhi, D., Juwarkar, A. A., Sharma, A., Kapley, A., & Pandey, R. A. (2017). Microbial population shift caused by sulfamethoxazole in engineered-Soil Aquifer Treatment (e-SAT) system. World Journal of Microbiology and Biotechnology, 33(6), 121.CrossRefGoogle Scholar
  27. 27.
    Mukherjee, A., Chettri, B., Langpoklakpam, J. S., Basak, P., Prasad, A., Mukherjee, A. K., Bhattacharyya, M., Singh, A. K., & Chattopadhyay, D. (2017). Bio informatic approaches including predictive metagenomic profiling reveal characteristics of bacterial response to petroleum hydrocarbon contamination in diverse environments. Scientific Reports, 7(1), 1108.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Niti B. Jadeja
    • 1
  • Prachiti Moharir
    • 1
  • Atya Kapley
    • 1
    Email author
  1. 1.Director Research CellNational Environmental Engineering Research Institute CSIRNagpurIndia

Personalised recommendations