Skip to main content

Protocols for the Isolation and Preliminary Characterization of Bacteria for Biodesulfurization and Biodenitrogenation of Petroleum-Derived Fuels

  • Protocol
  • First Online:
Hydrocarbon and Lipid Microbiology Protocols

Part of the book series: Springer Protocols Handbooks ((SPH))

Abstract

The use of microorganisms to improve fuel quality has been proposed, and in this chapter we describe basic experimental procedures for the isolation and characterization of bacteria for biodesulfurization and biodenitrogenation with dibenzothiophene and carbazole as model compounds for each application, respectively. The presented protocols should be considered as a starting point and adapted to other problematic compounds and conditions. Basic protocols for the evaluation of the treatment of real oil fractions are also presented.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    ASTM D4629-08 Standard test method for trace nitrogen in liquid petroleum hydrocarbons by syringe/inlet oxidative combustion and chemiluminescence detection

References

  1. Morales M, Ayala M, Vazquez-Duhalt R, Le Borgne S (2010) Application of microorganisms to the processing and upgrading of crude oil and fractions. In: Timmis KN, McGenity TJ, Meer JR, de Lorenzo V (eds) Consequences of microbial interactions with hydrocarbons, oils and lipids, vol 4, Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 2768–2785

    Google Scholar 

  2. Mohebali G, Ball AS (2008) Biocatalytic desulfurization (BDS) of petrodiesel fuels. Microbiology 154:2169–2183

    Article  CAS  PubMed  Google Scholar 

  3. Kabe T, Akamatsu K, Ishihara A, Otsuki S, Godo M, Zhang Q, Qian W (1997) Deep hydrodesulfurization of light gas oil. 1. Kinetics and mechanisms of dibenzothiophene hydrodesulfurization. Ind Eng Chem Res 36:5146–5152

    Article  CAS  Google Scholar 

  4. Monticello DJ, Finnerty WR (1985) Microbial desulfurization of fossil fuels. Annu Rev Microbiol 39:371–389

    Article  CAS  PubMed  Google Scholar 

  5. Le Borgne S, Ayala M (2010) Microorganisms utilizing sulfur-containing hydrocarbons. In: Timmis KN, McGenity TJ, Meer JR, de Lorenzo V (eds) Microbes and communities utilizing hydrocarbons, oils and lipids, vol 3, Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 2130–2141

    Google Scholar 

  6. Kilbane JJ (1992) Mutant microorganisms useful for cleavage of organic C-S bonds. US Patent No. 5,104,801

    Google Scholar 

  7. Denis-Larose C, Labbe D, Bergeron H, Jones AM, Creer CW, Al-Hawari J, Grossman MJ, Sankey BM, Lau PCK (1997) Conservation of plasmid-encoded dibenzothiophene desulfurization genes in several Rhodococci. Appl Environ Microbiol 63:2915–2919

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Izumi Y, Ohshiro T, Ogino H, Hine Y, Shimao M (1994) Selective desulphurization of dibenzothiophene by Rhodococcus erythropolis D-1. Appl Environ Microbiol 60:223–226

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Castorena G, Suárez C, Valdez I, Amador G, Fernández L, Le Borgne S (2002) Sulfur-selective desulfurization of dibenzothiophene and diesel oil by newly isolated Rhodococcus sp. strains. FEMS Microbiol Lett 215:157–161

    Article  CAS  PubMed  Google Scholar 

  10. Rhee SK, Chang JH, Chang YK, Chang HN (1998) Desulfurization of dibenzothiophene and diesel oils by a newly isolated Gordonia strain, CYKS1. Appl Environ Microbiol 64:2327–2331

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Chang JH, Rhee SK, Chang YK, Chang HN (1998) Desulfurization of diesel oils by a newly isolated dibenzothiophene-degrading Nocardia sp. strain CYKS2. Biotechnol Prog 14:851–855

    Article  CAS  PubMed  Google Scholar 

  12. Darzins A, Mrachko GT (2000) Sphingomonas biodesulfurization catalyst. US Patent No. 6,133,016

    Google Scholar 

  13. Bhatia S, Sharma DK (2010) Biodesulfurization of dibenzothiophene, its alkylated derivatives and crude oil by a newly isolated strain Pantoea agglomerans D23W3. Biochem Eng J 50:104–109

    Article  CAS  Google Scholar 

  14. Papizadeh M, Ardakani MR, Motamedi H, Rasouli I, Zarei M (2011) C-S targeted biodegradation of dibenzothiophene by Stenotrophomonas sp. NISOC-04. Appl Biochem Biotechnol 165:938–948

    Article  CAS  PubMed  Google Scholar 

  15. Gunam IB, Yamamura K, Sujaya IN, Antara NS, Aryanta WR, Tanaka M, Tomita F, Sone T, Asano K (2013) Biodesulfurization of dibenzothiophene and its derivatives using resting and immobilized cells of Sphingomonas subarctica T7b. J Microbiol Biotechnol 23:473–482

    Article  CAS  PubMed  Google Scholar 

  16. Nassar HN, El-Gendy NS, Abo-State MA, Mostafa YM, Mahdy HM, El- Temtamy SA (2013) Desulfurization of dibenzothiophene by a novel strain Brevibacillus invocatus C19 isolated from Egyptian coke. Biosci Biotechnol Res Asia 10:29–46

    Article  CAS  Google Scholar 

  17. Konishi J, Ishii Y, Onaka T, Okumura K, Suzuki M (1997) Thermophilic carbon-sulfur-bond-targeted biodesulfurization. Appl Environ Microbiol 63:3164–3169

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Kirimura K, Furuya T, Nishii Y, Ishii Y, Kino K, Usami S (2001) Biodesulfurization of dibenzothiophene and its derivatives through the selective cleavage of carbon-sulfur bonds by a moderately thermophilic bacterium Bacillus subtilis WU-S2B. J Biosci Bioeng 91:262–266

    Article  CAS  PubMed  Google Scholar 

  19. Furuya T, Kirimura K, Kino K, Usami S (2001) Thermophilic biodesulfurization of dibenzothiophene and its derivatives by Mycobacterium phlei WU-F1. FEMS Microbiol Lett 204:129–133

    Article  CAS  PubMed  Google Scholar 

  20. Bhatia S, Sharma DK (2012) Thermophilic desulfurization of dibenzothiophene and different petroleum oils by Klebsiella sp. 13T. Environ Sci Pollut Res Int 19:3491–3497

    Article  CAS  PubMed  Google Scholar 

  21. Bhatia S, Sharma DK (2010) Mining of genomic databases to identify novel biodesulfurizing microorganisms. J Ind Microbiol Biotechnol 37:425–429

    Article  CAS  PubMed  Google Scholar 

  22. Éigenson AS, Ivchenko EG (1977) Distribution of sulfur and nitrogen in fractions from crude oil and residues. Chem Technol Fuels Oils 13:542–544

    Article  Google Scholar 

  23. Laredo GC, Leyva S, Alvarez R, Mares MT, Castillo JJ, Cano JL (2002) Nitrogen compounds characterization in atmospheric gas oil and light cycle oil from a blend of Mexican crudes. Fuel 81:1341–1350

    Article  CAS  Google Scholar 

  24. Morales M, Le Borgne S (2010) Microorganisms utilizing nitrogen-containing hydrocarbons. In: Timmis KN, McGenity TJ, Meer JR, de Lorenzo V (eds) Microbes and communities utilizing hydrocarbons, oils and lipids, vol 3, Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 4554–4562

    Google Scholar 

  25. Yu B, Xu P, Zhu S, Cai X, Wang Y, Li L, Li F, Liu X, Ma C (2006) Selective biodegradation of S and N heterocycles by a recombinant Rhodococcus erythropolis strain containing carbazole dioxygenase. Appl Environ Microbiol 72:2235–2238

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Ouchiyama N, Zhang Y, Omori T, Kodama T (1993) Biodegradation of carbazole by Pseudomonas spp. CA06 and CA10. Biosci Biotechnol Biochem 57:455–460

    Article  CAS  Google Scholar 

  27. Hisatsuka K, Sato M (1994) Microbial transformation of carbazole to anthranilic acid by Pseudomonas stutzeri. Biosci Biotechnol Biochem 58:213–214

    Article  CAS  PubMed  Google Scholar 

  28. Li L, Li Q, Li F, Shi Q, Yu B, Liu F, Xu P (2006) Degradation of carbazole and its derivatives by a Pseudomonas sp. Appl Microbiol Biotechnol 73:941–948

    Article  CAS  PubMed  Google Scholar 

  29. Larentis AL, Sampaio HCC, Carneiro CC, Martins OB, Alves TLM (2011) Evaluation of growth, carbazole biodegradation and anthranilic acid production by Pseudomonas stutzeri. Braz J Chem Eng 28(01):37–44

    Article  CAS  Google Scholar 

  30. Singh GB, Srivastava A, Saigal A, Aggarwal S, Bisht S, Gupta S, Srivastava S, Gupta N (2011) Biodegradation of carbazole and dibenzothiophene by bacteria isolated from petroleum-contaminated sites. Biorem J 15(4):189–195

    Article  CAS  Google Scholar 

  31. Zhao C, Zhang Y, Li X, Wen D, Tang X (2011) Biodegradation of carbazole by the seven Pseudomonas sp. strains and their denitrification potential. J Haz Mat 190:253–259

    Article  CAS  Google Scholar 

  32. Nojiri H (2012) Structural and molecular genetic analyses of bacterial carbazole degradation system. Biosci Biotechnol Bochem 76:1–18

    Article  CAS  Google Scholar 

  33. Singh GB, Gupta S, Gupta N (2013) Carbazole degradation and biosurfactant production by newly isolated Pseudomonas sp. strain GBS.5. Int Biodeterior Biodegradation 84:35–43

    Article  CAS  Google Scholar 

  34. Schneider J, Grosser RJ, Jayasimhulu K, Xue W, Kinkle B, Warshawsky D (2000) Biodegradation of carbazole by Ralstonia sp. RJGII.123 isolated from hydrocarbon contaminated soil. Can J Microbiol 46:269–277

    Article  CAS  PubMed  Google Scholar 

  35. Li YW, Li WL, Huang JX, Xiong XCH, Gao HSH, Xing JM, Liu HZ (2008) Biodegradation of carbazole in oil/water biphasic system by a newly isolated bacterium Klebsiella sp. LSSE-H2. Biochem Eng J 41:166–170

    Article  CAS  Google Scholar 

  36. Fuse H, Takimura O, Murakami K, Inoue H, Yamaoka Y (2003) Degradation of chlorinated biphenyl, dibenzofuran, and dibenzo-p-dioxin by marine bacteria that degrade biphenyl, carbazole, or dibenzofuran. Biosci Biotechnol Biochem 67:1121–1125

    Article  CAS  PubMed  Google Scholar 

  37. Yamazoe A, Yagi O, Oyaizu H (2004) Biotransformation of fluorene, diphenyl ether, dibenzo-p-dioxin and carbazole by Janibacter sp. Biotechnol Lett 26:479–486

    Article  CAS  PubMed  Google Scholar 

  38. Singh GB, Gupta S, Srivastava S, Gupta N (2011) Biodegradation of carbazole by newly isolated Acinetobacter spp. Bull Environ Contam Toxicol 87:522–526

    Article  CAS  PubMed  Google Scholar 

  39. Inoue K, Habe H, Yamane H, Omori T, Nojiri H (2005) Diversity of carbazole-degrading bacteria having the car gene cluster: isolation of a novel gram-positive carbazole-degrading bacterium. FEMS Microbiol Lett 245:145–153

    Article  CAS  PubMed  Google Scholar 

  40. Castorena G, Múgica V, Le Borgne S, Acuña ME, Bustos- Jaimes I, Aburto J (2006) Carbazole biodegradation in gas oil/water biphasic media by a new isolated bacterium Burkholderia sp. strain IMP5GC. J Appl Microbiol 100:739–745

    Article  CAS  PubMed  Google Scholar 

  41. Castorena G, Acuña MA, Aburto J, Bustos-Jaimes I (2008) Semi-continuous biodegradation of carbazole in fuels by biofilm-immobilised cells of Burkholderia sp. strain IMP5GC. Process Biochem 43:1318–1321

    Article  CAS  Google Scholar 

  42. Habe H, Ashikawa Y, Saiki Y, Yoshida T, Nojiri H, Omori T (2002) Sphingomonas sp. strain KA1, carrying a carbazole dioxygenase gene homologue, degrades chlorinated dibenzo-p-dioxins in soil. FEMS Microbiol Lett 211:43–49

    Article  CAS  PubMed  Google Scholar 

  43. Kilbane JJ II, Daram A, Abbasian J, Kayser KJ (2002) Isolation and characterization of Sphingomonas sp. GTIN11 capable of carbazole metabolism in petroleum. Biochem Biophys Res Commun 297:242–248

    Article  CAS  PubMed  Google Scholar 

  44. Shepherd JM, Lloyd-Jones G (1998) Novel carbazole degradation genes of Sphingomonas CB3: sequence analysis, transcription, and molecular ecology. Biochem Biophys Res Commun 247:129–135

    Article  CAS  PubMed  Google Scholar 

  45. Santos SC, Alviano DS, Alviano CS, Padula M, Leitao AC, Martins OB, Ribeiro CM, Sassaki MY, Matta CP, Bevilaqua J, Sebastian GV, Seldin L (2006) Characterization of Gordonia sp. strain F.5.25.8 capable of dibenzothiophene desulfurization and carbazole utilization. Appl Microbiol Biotechnol 71:355–362

    Article  CAS  PubMed  Google Scholar 

  46. Singh GB, Srivastava S, Gupta S, Gupta N (2011) Evaluation of carbazole degradation by Enterobacter sp. isolated from hydrocarbon contaminated soil. Recent Res Sci Technol 3:44–48

    CAS  Google Scholar 

  47. Pasternak G, Kolwzan B (2013) Surface tension and toxicity changes during biodegradation of carbazole by newly isolated methylotrophic strain Methylobacterium sp. GPE1. Int Biodeterior Biodegradation 84:143–149

    Article  CAS  Google Scholar 

  48. Szymanska A, Lewandowski M, Sayag C, Djega- Mariadassou G (2003) Kinetic study of the hydrodenitrogenation of carbazole over bulk molybdenum carbide. J Catal 218:24–31

    Article  CAS  Google Scholar 

  49. Bressler DC, Fedorak PM (2000) Bacterial metabolism of fluorene, dibenzofuran, dibenzothiophene, and carbazole. Can J Microbiol 46:397–409

    Article  CAS  PubMed  Google Scholar 

  50. Oldfield C (1998) Microorganisms which can desulphurise benzothiophenes. Patent WO/1998/004678

    Google Scholar 

  51. Li FL, Xu P, Ma CQ, Luo LL, Wang XS (2003) Deep desulfurization of hydrodesulfurization treated diesel oil by a facultative Thermophilic bacterium Mycobacterium sp. X7B. FEMS Microbiol Lett 223:301–307

    Article  CAS  PubMed  Google Scholar 

  52. Johnson JL (1994) Similarity analysis of rRNAs. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular microbiology. ASM Press, Washington, pp 683–700

    Google Scholar 

  53. Baker GC, Smith JJ, Cowan DA (2003) Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 55:541–555

    Article  CAS  PubMed  Google Scholar 

  54. Kayser KJ, Bielaga-Jones BA, Jackowski K, Odusan O, Kilbane JJ (1993) Utilization of organosulfur compounds by axenic and mixed cultures of Rhodococcus rhodochrous IGTS8. J Gen Microbiol 139:3123–3129

    Article  CAS  Google Scholar 

  55. Kirimura K, Nakagawa H, Tsuji K, Matsuda K, Kurane R, Usami S (1999) Selective and continuous degradation of carbazole contained in petroleum oil by resting cells of Sphingomonas sp. CDH-7. Biosci Biotechnol Biochem 63:1563–1568

    Article  CAS  PubMed  Google Scholar 

  56. Gieg L, Otter A, Fedorak P (1996) Carbazole degradation by Pseudomonas sp. LD2: metabolic characteristics and the identification of some metabolites. Environ Sci Technol 30:575–585

    Article  CAS  Google Scholar 

  57. Van Hamme JD, Fedorak PM, Foght JM, Gray MR, Dettman HD (2004) Use of a novel fluorinated organosulfur compound to isolate bacteria capable of carbon-sulfur bond cleavage. Appl Environ Microbiol 70:1487–1493

    Article  PubMed  PubMed Central  Google Scholar 

  58. Ovreas SL, Forney L, Daae FL, Torsvik V (1997) Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol 63:3367–3373

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Sylvie Le Borgne .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer-Verlag Berlin Heidelberg

About this protocol

Cite this protocol

Morales, M., Le Borgne, S. (2014). Protocols for the Isolation and Preliminary Characterization of Bacteria for Biodesulfurization and Biodenitrogenation of Petroleum-Derived Fuels. In: McGenity, T., Timmis, K., Nogales, B. (eds) Hydrocarbon and Lipid Microbiology Protocols. Springer Protocols Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/8623_2014_41

Download citation

  • DOI: https://doi.org/10.1007/8623_2014_41

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-53113-6

  • Online ISBN: 978-3-662-53115-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics