Skip to main content
SpringerLink
Log in

Biosurfactant-Producing Capability and Prediction of Functional Genes Potentially Beneficial to Microbial Enhanced Oil Recovery in Indigenous Bacterial Communities of an Onshore Oil Reservoir

  • Published:
Current Microbiology Aims and scope Submit manuscript

Abstract

Microbial enhanced oil recovery (MEOR) is a bio-based technology with economic and environmental benefits. The success of MEOR depends greatly on the types and characteristics of indigenous microbes. The aim of this study was to evaluate the feasibility of applying MEOR at Mae Soon Reservoir, an onshore oil reservoir experiencing a decline in its production rate. We investigated the capability of the reservoir’s bacteria to produce biosurfactants, and evaluated the potentials of uncultured indigenous bacteria to support MEOR by means of prediction of MEOR-related functional genes, based on a set of metagenomic 16s rRNA gene data. The biosurfactant-producing bacteria isolated from the oil-bearing sandstones from the reservoir belonged to one species: Bacillus licheniformis, with one having the ability to decrease surface tension from 72 to 32 mN/m. Gene sequences responsible for biosurfactant (licA3), lipase (lipP1) and catechol 2,3-dioxygenase (C23O) were detected in these isolates. The latter two, and other genes encoding MEOR-related functional proteins such as enoyl-CoA hydratase and alkane 1-monooxygenase, were predicted in the bacterial communities residing the reservoir’s sandstones. Exposure of these sandstones to nutrients, consisting of KNO3 and NaH2PO4, resulted in an increase in the proportions of some predicted functional genes. These results indicated the potentials of MEOR application at Mae Soon site. Using the approaches demonstrated in this study would also assist evaluation of the feasibility of applying MEOR in oil reservoirs, which may be enhanced by an appropriate nutrient treatment.

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

Similar content being viewed by others

References

  1. Afrapoli MS, Crescente C, Alipour S, Torsaeter O (2009) The effect of bacterial solution on the wettability index and residual oil saturation in sandstone. J Petrol Sci Eng 69:255–260. https://doi.org/10.1016/j.petrol.2009.09.002

    Article  CAS  Google Scholar 

  2. Agari Y, Kashihara A, Yokoyama S, Kuramitsu S, Shinkai A (2008) Global gene expression mediated by Thermus thermophilus SdrP, a CRP/FNR family transcriptional regulator. Mol Microbiol 70:60–75

    Article  CAS  PubMed  Google Scholar 

  3. Almeida P, Moreira R, Almeida R, Guimarães AK, Carvalho AS, Quintella C, Esperidiã CMC, Taft CA (2004) Selection and application of microorganisms to improve oil recovery. Eng Life Sci 4:319–325

    Article  CAS  Google Scholar 

  4. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Arai H, Kodama T, Igarashi Y (1997) Cascade regulation of the two CRP/FNR-related transcriptional regulators (ANR and DNR) and the denitrification enzymes in Pseudomonas aeruginosa. Mol Microbiol 25:1141–1148

    Article  CAS  PubMed  Google Scholar 

  6. Atlas RM (2005) Handbook of media for environmental microbiology. CRC Press, Boca Raton

    Book  Google Scholar 

  7. Auerbach G, Ostendorp R, Prade L, Korndörfer I, Dams T, Huber R, Jaenicke R (1998) Lactate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima: the crystal structure at 2.1 Å resolution reveals strategies for intrinsic protein stabilization. Structure 6:769–781

    Article  CAS  PubMed  Google Scholar 

  8. Aurepatipan N, Champreda V, Kanokratana P, Chitov T, Bovonsombut S (2018) Assessment of bacterial communities and activities of thermotolerant enzymes produced by bacteria indigenous to oil-bearing sandstone cores for potential application in Enhanced Oil Recovery. J Pet Sci Eng 163:295–302

    Article  CAS  Google Scholar 

  9. Azubuike CC, Chikere CB, Okpokwasil GC (2016) Bioremediation techniques—classification based on site of application: principles, advantages, limitations and prospects. World J Microbiol Biotechnol 32:180. https://doi.org/10.1007/s11274-016-2137-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Bahnson BJ, Anderson VE, Petsko GA (2002) Structural mechanism of enoyl-CoA hydratase: three atoms from a single water are added in either an E1cb stepwise or concerted fashion. Biochemetry 41:2621–2629

    Article  CAS  Google Scholar 

  11. Banat IM, Franzetti A, Gandolfi I, Bestetti G, Martinotti MG, Fracchia L, Smyth TJ, Marchant R (2010) Microbial biosurfactants production, applications and future potential. Appl Microbiol Biotechnol 87:427–444

    Article  CAS  PubMed  Google Scholar 

  12. Barstow DA, Clarke AR, Chia WN, Wigley D, Sharman AF, Holbrook JJ, Atkinson T, Minton NP (1986) Cloning, expression and complete nucleotide sequence of the Bacillus stearothermophilusl-lactate dehydrogenase gene. Gene 46:47–55

    Article  CAS  PubMed  Google Scholar 

  13. Black PN, DiRusso CC (2003) Transmembrane movement of exogenous long-chain fatty acids: proteins, enzymes, and vectorial esterification. Microbiol Mol Biol Rev 67:454–472

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Bordoloi N, Konwar B (2008) Microbial surfactant-enhanced mineral oil recovery under laboratory conditions. Colloid Surf B 63:73–82

    Article  CAS  Google Scholar 

  15. Brown L, Vadie A (1998) The utilization of the microflora indigenous to and present in oil-bearing formations to selectively plug the more porous zones thereby increasing oil recovery during waterflooding. Department of Energy, Washington, DC. https://doi.org/10.2172/16011

    Book  Google Scholar 

  16. Brown L, Vadie A, Stephens J (2000) Slowing production decline and extending the economic life of an oil field: new MEOR technology. SPE J. https://doi.org/10.2523/59306-MS

    Article  Google Scholar 

  17. Brown L (2010) Microbial enhanced oil recovery (MEOR). Curr Opin Microbiol 13:316–320

    Article  CAS  PubMed  Google Scholar 

  18. Da Cunha CD, Rosado AS, Sebastián GV, Seldin L, von der Weid I (2006) Oil biodegradation by Bacillus strains isolated from the rock of an oil reservoir located in a deep-water production basin in Brazil. Appl Microbiol Biotechnol 73:949–959

    Article  CAS  PubMed  Google Scholar 

  19. Das P, Mukherjee S, Sen R (2008) Genetic regulations of the biosynthesis of microbial surfactants: an overview. Biotechnol Genet Eng Rev 25:165–186

    Article  CAS  PubMed  Google Scholar 

  20. De Clerck E, Gevers D, De Ridder K, De Vos P (2004) Screening of bacterial contamination during gelatine production by means of denaturing gradient gel electrophoresis, focussed on Bacillus and related endospore-forming genera. J Appl Microbiol 96:1333–1341

    Article  CAS  PubMed  Google Scholar 

  21. Donaldson EC, Chilingarian GV, Yen TF (1989) Microbial enhanced oil recovery. Elsevier Science, New York

    Google Scholar 

  22. Duhamel M, Wehr SD, Yu L, Rizvi H, Seepersad D, Dworatzek S, Cox EE, Edwards EA (2002) Comparison of anaerobic dechlorinating enrichment cultures maintained on tetrachloroethene, trichloroethene, cis-dichloroethene and vinyl chloride. Water Res 36:4193–4202

    Article  CAS  PubMed  Google Scholar 

  23. El-Sheshtawy HS, Aiad I, Osman ME, Abo-Elnasr AA, Kobisy AS (2016) Production of biosurfactant from Bacillus licheniformis for microbial enhanced oil recovery and inhibition the growth of sulfate reducing bacteria. Egypt J Pet 24:155–162. https://doi.org/10.1016/j.ejpe.2015.05.005

    Article  Google Scholar 

  24. Garvie EI (1980) Bacterial lactate dehydrogenases. Microbiol Rev 44:106

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Gudiña EJ, Pereira JF, Costa R, Coutinho JA, Teixeira JA, Rodrigues LR (2013) Biosurfactant-producing and oil-degrading Bacillus subtilis strains enhance oil recovery in laboratory sand-pack columns. J Hazard Mater 261:106–113

    Article  CAS  PubMed  Google Scholar 

  26. Hall C, Tharakan P, Hallock J, Cleveland C, Jefferson M (2003) Hydrocarbons and the evolution of human culture. Nature 426:318–322

    Article  CAS  PubMed  Google Scholar 

  27. Hao R, Lu A, Wang G (2004) Crude-oil-degrading thermophilic bacterium isolated from an oil field. Can J Microbiol 50:175–182

    Article  CAS  PubMed  Google Scholar 

  28. Head IM, Jones DM, Larter SR (2003) Biological activity in the deep subsurface and the origin of heavy oil. Nature 426:344

    Article  CAS  PubMed  Google Scholar 

  29. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32:277–280

    Article  CAS  Google Scholar 

  30. Kanwar L, Gogoi BK, Goswami P (2002) Production of a Pseudomonas lipase in n-alkane substrate and its isolation using an improved ammonium sulfate precipitation technique. Bioresour Technol 84:207–211

    Article  CAS  PubMed  Google Scholar 

  31. Kato T, Haruki M, Imanaka T, Morikawa M, Kanaya S (2001) Isolation and characterization of long-chain-alkane degrading Bacillus thermoleovorans from deep subterranean petroleum reservoirs. J Biosci Bioeng 91:64–70

    Article  CAS  PubMed  Google Scholar 

  32. Kaur G, Singh A, Sharma R, Sharma V, Verma S, Sharma PK (2016) Cloning, expression, purification and characterization of lipase from Bacillus licheniformis, isolated from hot spring of Himachal Pradesh, India. 3 Biotech 6:49. https://doi.org/10.1007/s13205-016-0369-y

    Article  PubMed  PubMed Central  Google Scholar 

  33. Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Thurber RLV, Knight R, Beiko RG, Huttenhower C (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31:814–821

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Lin SC, Lin KG, Lo CC, Lin YM (1998) Enhanced biosurfactant production by a Bacillus licheniformis mutant. Enzym Microb Technol 23:267–273

    Article  CAS  Google Scholar 

  35. Lin SC, Minton MA, Sharma MM, Georgiou G (1994) Structural and immunological characterization of a biosurfactant produced by Bacillus licheniformis JF-2. Appl Environ Microbiol 60:31–38

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Maier R, Soberon-Chavez G (2000) Pseudomonas aeruginosa rhamnolipids: biosynthesis and potential applications. Appl Microbiol Biotechnol 54:625–633

    Article  CAS  PubMed  Google Scholar 

  37. Meyer M, Stenzel U, Hofreiter M (2008) Parallel tagged sequencing on the 454 platform. Nat Protoc 3:267–278. https://doi.org/10.1038/nprot.2007.520

    Article  CAS  PubMed  Google Scholar 

  38. Miller CE, Williams PH, Ketley JM (2009) Pumping iron: mechanisms for iron uptake by Campylobacter. Microbiol 155:3157–3165

    Article  CAS  Google Scholar 

  39. Mishra S, Singh S (2012) Microbial degradation of n-hexadecane in mineral salt medium as mediated by degradative enzymes. Bioresour Technol 111:148–154

    Article  CAS  PubMed  Google Scholar 

  40. Nasiri H (2011) Enzymes for enhanced oil recovery (EOR). Dissertation, Technical University of Denmark

  41. Pallant J (2013) SPSS survival manual. McGraw-Hill Education, London

    Google Scholar 

  42. Pereira JF, Gudiña EJ, Costa R, Vitorino R, Teixeira JA, Coutinho JAP, Rodrigues LR (2013) Optimization and characterization of biosurfactant production by Bacillus subtilis isolates towards microbial enhanced oil recovery applications. Fuel 111:259–268

    Article  CAS  Google Scholar 

  43. Petersen H, Nytoft H, Ratanasthien B, Foopatthanakamol A (2007) Oils from cenozoic rift-basins in central and northern Thailand: source and thermal maturity. J Pet Geol 30:59–78

    Article  CAS  Google Scholar 

  44. Phetcharat T, Dawkrajai P, Chitov T, Wongpornchai P, Saenton S, Mhuantong W, Kanokratana P, Champreda V, Bovonsombut S (2018) Effect of inorganic nutrients on bacterial community composition in oil-bearing sandstones from the subsurface strata of an onshore oil reservoir and its potential use in Microbial Enhanced Oil Recovery. PLoS ONE 13:e0198050. https://doi.org/10.1371/journal.pone.0198050

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Pornsunthorntawee O, Arttaweeporn N, Paisanjit S, Somboonthanate P, Abe M, Rujiravanit R, Chavadej S (2008) Isolation and comparison of biosurfactants produced by Bacillus subtilis PT2 and Pseudomonas aeruginosa SP4 for microbial surfactant-enhanced oil recovery. Biochem Eng J 42:172–179

    Article  CAS  Google Scholar 

  46. Prabhu Y, Phale P (2003) Biodegradation of phenanthrene by Pseudomonas sp. strain PP2: novel metabolic pathway, role of biosurfactant and cell surface hydrophobicity in hydrocarbon assimilation. Appl Microbiol Biotechnol 61:342–351

    Article  CAS  PubMed  Google Scholar 

  47. Racey A (2011) Chap. 13 petroleum geology. In: Ridd MF, Barber AJ, Crow MJ (eds) The geology of Thailand. Geological Society of London, London

    Google Scholar 

  48. Rojo F (2009) Degradation of alkanes by bacteria. Environ Microbiol 11:2477–2490

    Article  CAS  PubMed  Google Scholar 

  49. Ron EZ, Rosenberg E (2001) Natural roles of biosurfactants. Environ microbiol 3:229–236

    Article  CAS  PubMed  Google Scholar 

  50. Sait M, Hugenholtz P, Janssen PH (2002) Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ Microbiol 4:654–666

    Article  CAS  PubMed  Google Scholar 

  51. Sakai Y, Maeng JH, Tani Y, Kato N (1994) Use of long-chain n-alkanes (C13–C44) by an isolate, Acinetobacter sp. M-1. Biosci Biotechnol Biochem 58:2128–2130

    Article  CAS  Google Scholar 

  52. Sen R (2008) Biotechnology in petroleum recovery: The microbial EOR. Progr Energy Combust Sci 34:714–724. https://doi.org/10.1016/j.pecs.2008.05.001

    Article  CAS  Google Scholar 

  53. Sepahy AA, Assadi MM, Saggadian V, Noohi A (2005) Production of biosurfactant from Iranian oil fields by isolated Bacilli. Int J Environ Sci Technol 1:287–293

    Article  CAS  Google Scholar 

  54. Simou OM, Pantazaki AA (2014) Evidence for lytic transglycosylase and β-N-acetylglucosaminidase activities located at the polyhydroxyalkanoates (PHAs) granules of Thermus thermophilus HB8. Appl Microbiol Biotechnol 98:1205–1221

    Article  CAS  PubMed  Google Scholar 

  55. Simpson DR, Natraj NR, McInerney MJ, Duncan KE (2011) Biosurfactant-producing Bacillus are present in produced brines from Oklahoma oil reservoirs with a wide range of salinities. Appl Microbiol Biotechnol 91:1083–1093

    Article  CAS  PubMed  Google Scholar 

  56. Swaathy S, Kavitha V, Pravin AS, Mandal AB, Gnanamani A (2014) Microbial surfactant mediated degradation of anthracene in aqueous phase by marine Bacillus licheniformis MTCC 5514. Biotechnol Rep 4:162–170

    Google Scholar 

  57. Thaniyavarn J, Roongsawang N, Kameyama T, Haruki M, Imanaka T, Morikawa M, Kanaya S (2003) Production and characterization of biosurfactants from Bacillus licheniformis F2. 2. Biosci Biotechnol Biochem 67:1239–1244

    Article  CAS  PubMed  Google Scholar 

  58. Thomas S (2008) Enhanced oil recovery—an overview. Oil Gas Sci Technol Rev IFP 63:9–19. https://doi.org/10.2516/ogst:2007060

    Article  CAS  Google Scholar 

  59. Tomita T, Kuzuyama T, Nishiyama M (2006) Alteration of coenzyme specificity of lactate dehydrogenase from Thermus thermophilus by introducing the loop region of NADP(H)-dependent malate dehydrogenase. Biosci Biotechnol Biochem 70:2230–2235

    Article  CAS  PubMed  Google Scholar 

  60. Tugrul T, Cansunar E (2005) Detecting surfactant-producing microorganisms by the drop-collapse test. World J Microbiol Biotechnol 21:851–853

    Article  CAS  Google Scholar 

  61. Ueki A, Ueki K, Oguma A, Ohtsuki C (1989) Partition of electrons between methanogenesis and sulfate reduction in the anaerobic digestion of animal waste. J Gen Appl Microbiol 35:151–162

    Article  CAS  Google Scholar 

  62. Van Hamme JD, Singh A, Ward OP (2003) Recent advances in petroleum microbiology. Microbiol Mol Biol Rev 67:503–549

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman W (2011) Bergey’s manual of systematic bacteriology. Vol 3: The Firmicutes. Springer, New York

    Google Scholar 

  64. Wang J, Ma T, Zhao L, Lv J, Li G, Zhang H, Zhao B, Liang F, Liu R (2008) Monitoring exogenous and indigenous bacteria by PCR-DGGE technology during the process of microbial enhanced oil recovery. J Ind Microbiol Biotechnol 35:619–628

    Article  CAS  PubMed  Google Scholar 

  65. Wang LY, Ke WJ, Sun XB, Liu JF, Gu JD, Mu BZ (2014) Comparison of bacterial community in aqueous and oil phases of water-flooded petroleum reservoirs using pyrosequencing and clone library approaches. Appl Microbiol Biotechnol 98:4209–4221. https://doi.org/10.1007/s00253-013-5472-y

    Article  CAS  PubMed  Google Scholar 

  66. Youssef N, Elshahed MS, McInerney MJ (2009) Microbial processes in oil fields: culprits, problems, and opportunities. In: Laskin AI, Sariaslani S, Gadd GM (eds) Advances in applied microbiology. Academic Press, Burlington, pp 141–251

    Google Scholar 

  67. Youssef N, Simpson DR, Duncan KE, McInerney MJ, Folmsbee M, Fincher T, Knapp RM (2007) In situ biosurfactant production by Bacillus strains injected into a limestone petroleum reservoir. Appl Environ microbiol 73:1239–1247

    Article  CAS  PubMed  Google Scholar 

  68. Zhou J, Bruns MA, Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62:316–322

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This research work was facilitated and partially supported by Chiang Mai University (CMU), Northern Petroleum Development Center (NPDC), The National Center for Genetic Engineering and Biotechnology (BIOTEC), and was financially funded by the National Research Council of Thailand, NPDC, and CMU Graduate School. The authors would like to thank the staff members of the NPDC, Chiang Mai, Thailand, for their assistance in the field sampling and Dr. Denis Sweatman (CMU) for his kind assistance in proofreading the manuscript.

Author information

Authors and Affiliations

  1. Interdisciplinary Program in Biotechnology, Graduate School, Chiang Mai University, Chiang Mai, 50200, Thailand

    Thanachai Phetcharat

  2. Defence Energy Department, Northern Petroleum Development Center, Fang, Chiang Mai, 50110, Thailand

    Pinan Dawkrajai

  3. Division of Microbiology, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand

    Thararat Chitov & Sakunnee Bovonsombut

  4. Enzyme Technology Laboratory, The National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, 12120, Thailand

    Wuttichai Mhuantong & Verawat Champreda

  5. Environmental Science Research Center (ESRC), Chiang Mai University, Chiang Mai, 50200, Thailand

    Thararat Chitov & Sakunnee Bovonsombut

  6. Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand

    Sakunnee Bovonsombut

Authors
  1. Thanachai Phetcharat
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Pinan Dawkrajai
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Thararat Chitov
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Wuttichai Mhuantong
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Verawat Champreda
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Sakunnee Bovonsombut
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Sakunnee Bovonsombut.

Additional information

Publisher’s Note

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

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (XLSX 25 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Phetcharat, T., Dawkrajai, P., Chitov, T. et al. Biosurfactant-Producing Capability and Prediction of Functional Genes Potentially Beneficial to Microbial Enhanced Oil Recovery in Indigenous Bacterial Communities of an Onshore Oil Reservoir. Curr Microbiol 76, 382–391 (2019). https://doi.org/10.1007/s00284-019-01641-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00284-019-01641-8

Search

Navigation