Application of Microorganisms to the Processing and Upgrading of Crude Oil and Fractions

  • M. Morales
  • M. Ayala
  • R. Vazquez-Duhalt
  • S. Le Borgne

Abstract:

The first review describing microorganisms capable of degrading hydrocarbons appeared on 1946 by ZoBell (Bacteriol Rev 10:1–49, 1946). Since then, the amount and depth of the information on the metabolic pathways responsible for the degradation or mineralization of hydrocarbons have greatly increased. Bacterial and enzyme degradation of alkanes, aromatics, heterocyles, and even asphaltenes, the most recalcitrant molecules in crude oil, has been studied at the molecular level. The ability to transfer an entire pathway in stable vehicles such as plasmids has contributed to spreading the hydrocarbon-degrading phenotype to different genera, colonizing different environments. The opportunity and relevance of applying such microorganisms to the oil industry are discussed in this chapter, specifically regarding the processing and upgrading of problematic fractions. Both advantages and limitations of these biotechnologies are presented.

Keywords

Surfactant Ozone Hydrocarbon Immobilization Magnetite 

References

  1. Arensdorf JJ, Loomis AK, DiGrazia PM, Monticello DJ, Pienkos PT (2002) Chemostat approach for the directed evolution of biodesulfurization gain-of-function mutants. Appl Environ Microbiol 68: 691–698.PubMedCrossRefGoogle Scholar
  2. Atlas RM, Aislabie J (1992) Process for biotechnological upgrading of shale oil. US Patent No. 5,143,827.Google Scholar
  3. Ayala M, Le Borgne S (2009) Microorganisms utilizing sulfur-containing hydrocarbons. In Handbook of Hydrocarbon and Lipid Microbiology. Timmis, Kenneth N (ed.). Springer.Google Scholar
  4. Ayala M, Robledo NR, Lopez-Munguia A, Vazquez-Duhalt R (2000) Substrate specificity and ionization potential in chloroperoxidase-catalyzed oxidation of diesel fuel. Environ Sci Technol 34: 2804–2809.CrossRefGoogle Scholar
  5. Ayala M, Tinoco R, Hernandez V, Bremauntz P, Vazquez-Duhalt R (1998) Biocatalytic oxidation of fuel as an alternative to biodesulfurization. Fuel Process Technol 57: 101–111.CrossRefGoogle Scholar
  6. Ayala M, Verdin J, Vazquez-Duhalt R (2007) The prospects for peroxidase-based biorefining of petroleum fuels. Biocatal Biotrans 25: 114–129.CrossRefGoogle Scholar
  7. Bej SK, Dalai AK, Adjaye J (2001) Comparison of hydrogenation of basic and nonbasic nitrogen compounds present in oil sands derived heavy gas oil. Energy Fuel 15: 377–383.CrossRefGoogle Scholar
  8. Bertrand JC, Rambeloarisoa E, Rontani JF, Giusti G, Mattei G (1983) Microbial degradation of crude oil in sea water in continuous culture. Biotechnol Lett 5: 567–572.CrossRefGoogle Scholar
  9. Bonde SE, Nunn D (2003a) Technical Progress Report for The Biocatalytic Desulfurization Project. DOE Award Number: DE-FC26-02NT15340 Report Start Date: 9/19/2002 – Report End Date: 12/19/2002.Google Scholar
  10. Bonde SE, Nunn D (2003b) Technical Progress Report for The Biocatalytic Desulfurization Project. DOE Award Number: DE-FC26-02NT15340. Report Start Date: 03/20/2003 – Report End Date: 06/19/2003.Google Scholar
  11. Bublitz F, Guenther T, Fritsche W (1994) Screening of fungi for the biological modification of hard coal and coal derivatives. Fuel Proc Technol 40: 347–354.CrossRefGoogle Scholar
  12. Castorena G, Mugica 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.PubMedCrossRefGoogle Scholar
  13. 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.PubMedCrossRefGoogle Scholar
  14. Chen H, Zhang WJ, Chen JM, Cai YB, Li W (2008) Desulfurization of various organic sulfur compounds and the mixture of DBT+4,6-DMDBT by Mycobacterium sp. ZD-19. Bioresour Technol 99: 3630–3634.PubMedCrossRefGoogle Scholar
  15. Choi KH, Korai Y, Mochida I, Ryub JW, Min W (2004). Impact of removal extent of nitrogen species in gas oil on its HDS performance: an efficient approach to its ultra deep desulfurization. Appl Catal B-Environ 50: 9–16.CrossRefGoogle Scholar
  16. Choudhary TV, Parrott S, Johnson B (2008) Unraveling heavy oil desulfurization chemistry: targeting clean fuels. Environ Sci Technol 42: 1944–1947.PubMedCrossRefGoogle Scholar
  17. Coco WM, Levinson WE, Crist MJ, Hektor HJ, Darzins A, Pienkos PK, Squires CH, Monticello DJ (2001) DNA shuffling method for generating highly recombined genes and evolved enzymes. Nat Biotechnol 19: 354–359.PubMedCrossRefGoogle Scholar
  18. Conesa A, Punt PJ, van den Hondel CAMJJ (2002) Fungal peroxidases: molecular aspects and applications. J Biotechnol 93: 143–158.PubMedCrossRefGoogle Scholar
  19. Davies JJ, Evans WC (1964) Oxidative metabolism of naphthalene by soil pseudomonads. The ring-fission mechanism. Biochem J 9: 251–261.Google Scholar
  20. Ellis LBM, Roe D, Wackett LP (2006) The University of Minnesota Biocatalysis Biodegradation Database: The First Decade. Nucl Acids Res 34: D517–D521.PubMedCrossRefGoogle Scholar
  21. Fedorak PM, Semple KM, Vazquez-Duhalt R, Westlake DWS (1993) Chloroperoxidase mediated modifications of petroporphyrins and asphaltenes. Enzyme Microb Technol 15: 429–437.CrossRefGoogle Scholar
  22. Foght JM (2004) Whole-cell bioprocessing of aromatic compounds in crude oil and fuels. In Studies in Surface Science and Catalysis: Petroleum Biotechnology: Developments and Perspectives, vol. 151. R Vazquez-Duhalt and R Quintero-Ramirez (eds.). Amsterdam: Elsevier, pp. 145–175.CrossRefGoogle Scholar
  23. Folsom BR, Schieche DR, DiGrazia PM, Werner J, Palmer S (1999) Microbial desulfurization of alkylated dibenzothiophenes from a hydrodesulfurized middle distillate by Rhodococcus erythropolis I-19. Appl Environ Microbiol 65: 4967–4972.PubMedGoogle Scholar
  24. Gai Z, Yu B, Li L, Wang Y, Ma C, Feng J, Deng Z, Xu P (2007) Cometabolic degradation of dibenzofuran and dibenzothiophene by a newly isolated carbazole-degrading Sphingomonas sp. strain. Appl Environ Microbiol 73: 2832–2838.PubMedCrossRefGoogle Scholar
  25. Garcia-Arellano H, Buenrostro-Gonzalez E, Vazquez-Duhalt R (2004) Biocatalytic transformation of petroporphyrins by chemical modified cytochrome c. Biotechnol Bioeng 85: 790–798.PubMedCrossRefGoogle Scholar
  26. Groenzin H, Mullins OC (2000) Molecular size and structures of asphaltenes from various sources. Energy Fuels 14: 677–684.CrossRefGoogle Scholar
  27. Grossman MJ, Lee MK, Prince RC, Garrett KK, George GN, Pickering IJ (1999) Microbial desulfurization of a crude oil middle-distillate fraction: analysis of the extent of sulfur removal and the effect of removal on remaining sulfur. Appl Environ Microbiol 65: 181–188.PubMedGoogle Scholar
  28. Grossman MJ, Lee MK, Prince RC, Minak-Bernero V, George GN, Pickering IJ (2001) Deep desulfurization of extensively hydrodesulfurized middle distillate oil by Rhodococcus sp. strain ECRD-1. Appl Environ Microbiol 67: 1949–1952.PubMedCrossRefGoogle Scholar
  29. Guobin S, Huaiying Z, Weiquan C, Jianmin X, Huizhou L (2005) Improvement of biodesulfurization rate by assembling nanosorbents on the surfaces of microbial cells. Biophys J 89: L58–L60.PubMedCrossRefGoogle Scholar
  30. Hirasawa K, Ishii Y, Kobayashi M, Koizumi K, Maruhashi K (2001) Improvement of desulfurization activity in Rhodococcus erythropolis KA2-5-1 by genetic engineering. Biosci Biotechnol Biochem 65: 239–246.PubMedCrossRefGoogle Scholar
  31. Hofrichter M, Bublitz F, Fritsche W (1997) Fungal attack on coal: I. Modification of hard coal by fungi. Fuel Proc Technol 52: 43–53.CrossRefGoogle Scholar
  32. 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.CrossRefGoogle Scholar
  33. Kayser KJ, Kilbane JJ II (2004) Method for metabolizing carbazole in petroleum US Patent No. 6,943,006.Google Scholar
  34. Kilbane JJ (1992) Mutant microorganisms useful for cleavage of organic C-S bonds. US Patent No. 5,104,801.Google Scholar
  35. Kilbane JJ (2006) Microbial biocatalyst developments to upgrade fossil fuels. Curr Opin Biotech 17: 305–314.PubMedCrossRefGoogle Scholar
  36. Kilbane JJ II, Ranganathan R, Cleveland L (2000) Selective removal of nitrogen from quinoline and petroleum by Pseudomonas ayucida IGTN9M. Appl Environ Microbiol 66: 688–693.PubMedCrossRefGoogle Scholar
  37. Kilbane JJ II, Ribeiro, CMS, Linhares MONM (2001) Pseudomonas ayucida useful for cleavage of organic C-N bonds. US Patent No. 6,221,651.Google Scholar
  38. Kilbane JJ II, Ribeiro, CMS, Linhares MONM (2003) Bacterial cleavage of only organic C-N bonds of carbonaceous materials to reduce nitrogen content. US Patent No. 6,541,240.Google Scholar
  39. Kim JS, Crowley DE (2007) Microbial diversity in natural asphalts of the Rancho La Brea tar pits. Appl Environ Microbiol 73: 4579–4591.PubMedCrossRefGoogle Scholar
  40. Konishi J, Ishii Y, Onaka T, Okumura K, Suzuki M (1997) Thermophilic carbon-sulfur-bond-targeted biodesulfurization. Appl Environ Microbiol 63: 3164–3169.PubMedGoogle Scholar
  41. Kotlar HK, Brakstad OG, Markussen S, Winnberg A (2004) Use of petroleum biotechnology throughout the value chain of an oil company: an integrated approach. In Studies in Surface Science and Catalysis: Petroleum Biotechnology: Developments and Perspectives, vol. 151. R Vazquez-Duhalt and R Quintero-Ramirez (eds.). Amsterdam: Elsevier, pp. 1–27.CrossRefGoogle Scholar
  42. Lacotte DJ, Mille G, Acquaviva M, Bertrand JC (1996) Arabian light 150 asphaltene biotransformation with n-alkanes as co-substrate. Chemosphere 32: 1755–1761.CrossRefGoogle Scholar
  43. Laredo G, Montesinos A, De los Reyes JA (2004) Inhibition effects observed between dibenzothiophene and carbazole during the hydrotreating process. Appl Catal A-Gen 265: 171–183.CrossRefGoogle Scholar
  44. Laredo GC, Altamirano E, De los Reyes JA (2003) Inhibitions effects of nitrogen compounds on the hydrodesulfurization of dibenzothiophene: Part 2. Appl Catal A-Gen 243: 207–214.CrossRefGoogle Scholar
  45. Laredo GC, Leyva S, Alvarez R, Mares MT, Castillo JJ, Cano JL (2002) Nitrogen compounds characterization in atmospheric gasoil and light cycle oil from a blend of Mexican crudes. Fuel 81: 1341–1350.CrossRefGoogle Scholar
  46. Larkin MJ, Kulakov LA, Allen CC (2005) Biodegradation and Rhodococcus--masters of catabolic versatility. Curr Opin Biotechnol 16: 282–290.PubMedCrossRefGoogle Scholar
  47. Le Borgne S, Quintero R (2003) Biotechnological processes for the refining of petroleum. Fuel Process Technol 81: 155–169.CrossRefGoogle Scholar
  48. Leliveld RG, Eijsbouts SE (2008) How a 70-year-old catalytic refinery process is still ever dependent on innovation. Catal Today 130: 183–190.CrossRefGoogle Scholar
  49. Li GQ, Li SS, Zhang ML, Wang J, Zhu L, Liang FL, Liu RL, Ma T (2008a) Genetic rearrangement strategy for optimizing the dibenzothiophene biodesulfurization pathway in Rhodococcus erythropolis. Appl Environ Microbiol 74: 971–976.PubMedGoogle Scholar
  50. Li GQ, Ma T, Li SS, Li H, Liang FL, Liu RL (2007) Improvement of dibenzothiophene desulfurization activity by removing the gene overlap in the dsz operon. Biosci Biotechnol Biochem 71: 849–854.PubMedCrossRefGoogle Scholar
  51. Li L, Xu P, Blankerspoor HD (2004) Degradation of carbazole in the presence of non-aqueous phase liquids by Pseudomonas sp. Biotechnol Lett 26: 581–584.PubMedCrossRefGoogle Scholar
  52. Li YG, Xing JM, Xiong XC, Li WL, Gao HS, Liu HZ (2008b) Improvement of biodesulfurization activity of alginate immobilized cells in biphasic systems. J Ind Microbiol Biotechnol 35: 145–150.PubMedCrossRefGoogle Scholar
  53. Matsubara T, Ohshiro T, Nishina Y, Izumi Y (2001) Purification, characterization, and overexpression of flavin reductase involved in dibenzothiophene desulfurization by Rhodococcus erythropolis D-1. Appl Environ Microbiol 67: 1179–1184.PubMedCrossRefGoogle Scholar
  54. Mogollon L, Rodriguez R, Larrota W, Ortiz C, Torres R (1998) Biocatalytic removal of nickel and vanadium from petroporphyrins and asphaltenes. Appl Biochem Biotechnol 70–72: 765–777.PubMedCrossRefGoogle Scholar
  55. Monot F, Abbad-Andaloussi S, Warzywoda M (2002) Biological culture containing Rhodococcus erythropolis and/or Rhodococcus rhodnii and process for desulfurization of petroleum fraction, U.S. Patent No. 6,337,204.Google Scholar
  56. Monticello DJ (2000) Biodesulfurization and the upgrading of petroleum distillates. Curr Opin Biotechnol 11: 540–546.PubMedCrossRefGoogle Scholar
  57. Monticello DJ, Finnerty WR (1985) Microbial desulfurization of fossil fuels. Annu Rev Microbiol 39: 371–389.PubMedCrossRefGoogle Scholar
  58. Morales M, Le Borgne S (2009) Microorganisms utilizing nitrogen-containing hydrocarbons. In Handbook of Hydrocarbon and Lipid Microbiology. Timmis, Kenneth N. (ed.). Springer.Google Scholar
  59. Mushrush GW, Beal EJ, Hardy DR, Hughes JM (1999) Nitrogen compound distribution in middle distillate fuels derived from petroleum, oil shale, and tar sand sources Fuel Process Technol 61: 197–210.CrossRefGoogle Scholar
  60. Ohshiro T, Ohkita R, Takikawa T, Manabe M, Lee WC, Tanokura M, Izumi Y (2007) Improvement of 2’-hydroxybiphenyl-2-sulfinate desulfinase, an enzyme involved in the dibenzothiophene desulfurization pathway, from Rhodococcus erythropolis KA2-5-1 by site-directed mutagenesis. Biosci Biotechnol Biochem 71: 2815–2821.PubMedCrossRefGoogle Scholar
  61. ORNL (2000) An emissions mission: solving the sulfur problem. Oak Ridge Natl Lab Rev 33: 6–8.Google Scholar
  62. Phale PS, Basu A, Majhi PD, Deversyshetty J, Vamsee-Krishna C, Shrivastava R (2007) Metabolic diversity in bacterial degradation of aromatic compounds. OMICS 11: 252–279.PubMedCrossRefGoogle Scholar
  63. Reichmuth DS, Blanch HW, Keasling JD (2004) Dibenzothiophene biodesulfurization pathway improvement using diagnostic GFP fusions. Biotechnol Bioeng 88: 94–99.PubMedCrossRefGoogle Scholar
  64. Reichmuth DS, Hittle JL, Blanch HW, Keasling JD (2000) Biodesulfurization of dibenzothiophene in Escherichia coli is enhanced by expression of a Vibrio harveyi oxidoreductase gene. Biotechnol Bioeng 67: 72–79.PubMedCrossRefGoogle Scholar
  65. Rhee SK, Chang JH, Chang YK, Chang HN (1998) Desulfurization of dibenzothiophene and diesel oils by a newly isolated Gordona strain, CYKS1. Appl Environ Microbiol 64: 2327–2331.PubMedGoogle Scholar
  66. Rontani JF, Bosser-Joulak F, Rambeloarisoa E, Bertrand JC, Giusti G, Faure R (1985) Analytical study of Asyhart crude oil biodegradation. Chemosphere 14: 1413–1422.CrossRefGoogle Scholar
  67. Rossini S (2003) The impact of catalytic materials on fuel reformulation. Catal Today 77: 467–484.CrossRefGoogle Scholar
  68. Santos SCC, Alviano DS, Alviano CS, Pádula M, Leitao AC, Martins OB, Ribeiro CMS, Sassaki MYM, Matta CPS, 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.PubMedCrossRefGoogle Scholar
  69. Shan G, Xing J, Zhang H, Liu H (2005) Biodesulfurization of dibenzothiophene by microbial cells coated with magnetite nanoparticles. Appl Environ Microbiol 71: 4497–4502.PubMedCrossRefGoogle Scholar
  70. Shin S, Sakanishi K, Mochida I. (2000) Identification and reactivity of nitrogen molecular species in gas oils. Energy Fuels 14: 539–544.CrossRefGoogle Scholar
  71. Soleimani M, Bassi A, Margaritis A (2007) Biodesulfurization of refractory organic sulfur compounds in fossil fuels. Biotechnol Adv 25: 570–596.PubMedCrossRefGoogle Scholar
  72. Song C (2003) An overview of new approaches to deep desulfurization for ultra-clean gasoline, diesel fuel and jet fuel. Catal Today 86: 211–263.CrossRefGoogle Scholar
  73. Sood N, Lal B (2008) Isolation and characterization of a potential paraffin-wax degrading thermophilic bacterial strain Geobacillus kaustophilus TERI NSM for application in oil wells with paraffin deposition problems. Chemosphere 70: 1445–1451.PubMedCrossRefGoogle Scholar
  74. Sugaya K, Nakayama O, Hinata N, Kamekura K, Ito A, Yamagiwa K, Ohkawa A (2001) Biodegradation of quinoline in crude oil. J Chem Technol Biotechnol 76: 603–611.CrossRefGoogle Scholar
  75. Swaty TE (2005) Global refining industry trends: the present and future. Hydrocarbon Process 84: 35–46.Google Scholar
  76. Szymanska A, Lewandowski M, Sayag C, Djéga-Mariadassou G (2003) Kinetic study of the hydrodenitrogenation of carbazole over bulk molybdenum carbide. J Catal 218: 24–31.CrossRefGoogle Scholar
  77. Tanaka Y, Yoshikawa O, Maruhashi K, Kurane R (2002) The cbs mutant strain of Rhodococcus erythropolis KA2-5-1 expresses high levels of Dsz enzymes in the presence of sulfate. Arch Microbiol 178: 351–357.PubMedCrossRefGoogle Scholar
  78. Tao F, Yu B, Xu P, Ma CQ (2006) Biodesulfurization in biphasic systems containing organic solvents. Appl Environ Microbiol 72: 4604–4609.PubMedCrossRefGoogle Scholar
  79. Thouand G, Bauda P, Oudot J, Kirsh G, Sutton C, Vidalie JF (1999) Laboratory evaluation of crude oil biodegradation with commercial or natural microbial inocula. Can J Microbiol 45: 106–115.PubMedCrossRefGoogle Scholar
  80. US Department of Transportation, Federal Highway Administration (2009) Web site: http://www.fhwa.dot.gov/environment/freightaq/appendixa.htm
  81. Wammer KH, Peters CA (2005) Polycyclic aromatic hydrocarbon biodegradation rates: a structure-based study. Environ Sci Technol 39: 2571–2578.PubMedCrossRefGoogle Scholar
  82. Wammer KH, Peters CA (2006) A molecular modeling analysis of polyaromatic hydrocarbon biodegradation by naphthalene dioxygenase. Environ Toxicol Chem 25: 912–920.PubMedCrossRefGoogle Scholar
  83. Wyndham RC, Costerton JW (1981) In vitro microbial degradation of bituminous hydrocarbons and in situ colonization of bitumen surfaces within the Athabasca oil sands deposit. Appl Environ Microbiol 41: 791–800.PubMedGoogle Scholar
  84. Xiong X, Xing J, Li X, Bai X, Li W, Li Y, Liu H (2007) Enhancement of biodesulfurization in two-liquid systems by heterogeneous expression of Vitreoscilla hemoglobin. Appl Environ Microbiol 73: 2394–2397.PubMedCrossRefGoogle Scholar
  85. Yu B, Ma C, Zhou W, Zhu S, Wang Y, Qu J, Li F, Xu P (2006a) Simultaneous biodetoxification of S, N, and O pollutants by engineering of a carbazole-degrading gene cassette in a recombinant biocatalyst. Appl Environ Microbiol 72: 7373–7376.PubMedCrossRefGoogle Scholar
  86. Yu B, Xu P, Shi Q, Ma C (2006b) Deep desulfurization of diesel oil and crude oils by a newly isolated Rhodococcus erythropolis strain. Appl Environ Microbiol 72: 54–58.PubMedCrossRefGoogle Scholar
  87. Yu L, Meyer T, Folsom B (1998) Oil/water/biocatalyst three-phase separation process. US Patent No. 5,772,901.Google Scholar
  88. Zeuthen P, Knudsen KG, Whitehurst DD (2001) Organic nitrogen compounds in gasoil blends, their hydrotreated products and the importance to hydrotreatment. Catal Today 65: 307–314.CrossRefGoogle Scholar
  89. ZoBell CE (1946) Action of microorganisms on hydrocarbons. Bacteriol Rev 10: 1–49.Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • M. Morales
    • 1
  • M. Ayala
    • 2
  • R. Vazquez-Duhalt
    • 2
  • S. Le Borgne
    • 1
  1. 1.Department of Process and TechnologyUAM-CuajimalpaMexico CityMexico
  2. 2.Department of Cellular Engineering and BiocatalysisInstituto de BiotecnologiaUNAMMexico

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