Microbial Degradation of Petroleum Hydrocarbons

  • Ghada Abd-Elmonsef MahmoudEmail author
  • Magdy Mohmed Khalil Bagy


Nowadays, petroleum hydrocarbon pollutants keep on being a genuine natural worry because of the managed development of petroleum oil extraction, related generation which ends up noticeably with ecological issue. The expanding in industrial progression causes expanding in a petroleum-essential product consistently to cover the human needs. Continuous growing, development and improvement of industrial exercises over the whole world make petroleum-based products the most significant issue in this century. Oil spills frequently happen by mishaps amid pumping, transportation and refining. Nearness of these petrochemicals in the environment makes huge risks to human health for their lethal, mutagenic, cancer-causing impacts and their capacity of aggregation in food chain. Researchers keep searching for sustainable remediation techniques for polluted sites. As of now physical and chemical remediation advances are by all accounts facing a few issues like transferring pollutants from one phase to another and not having the ability for complete removal of contaminants which turn into another problem. Among the varieties of the remediation techniques, microbial utilization of microorganisms in biodegradation processes demonstrated the achievement in degrading xenobiotic compounds contrasted with physico-chemical strategies in terms of money-related costs, efficiency, energy efficiency, versatility and simplicity to apply and seems to be the environment sound solution. The key factor for successful bioremediation involves selecting appropriate microbes with high capability of pollutant degradation. Microorganisms like fungi, bacteria and yeast are considered as promising dynamic remarkable microbes involved in biodegradation of petroleum aliphatic and aromatic hydrocarbons.



Polycyclic aromatic hydrocarbons


Sulphur, nitrogen, oxygen


Total petroleum hydrocarbons


  1. Adebusoye SA, Ilori MO, Amund OO, Teniola OD, Olatope SO (2006) Microbial degradation of petroleum hydrocarbons in a polluted tropical stream. J Am Sci 2(3):48–57Google Scholar
  2. Adenipekun CO (2008) Bioremediation of engine-oil polluted soil by Pleurotus tuber-regium singer, a Nigerian white-rot fungus. Afr J Biotechnol 7:55–58Google Scholar
  3. Adenipekun CO, Isikhuemhen OS (2008) Bioremediation of engine oil polluted soil by the tropical white rot fungus, Lentinus squarrosulus Mont. (singer). Pak J Biol Sci 11:1637–1643CrossRefGoogle Scholar
  4. Adeniyi A, Afolabi J (2002) Determination of total petroleum hydrocarbons and heavy metals in soils within the vicinity of facilities handling refined petroleum products in Lagos metropolis. Environ Int 28:79–82CrossRefPubMedPubMedCentralGoogle Scholar
  5. Ahearn DG, Crow SA (1980) Yeasts from the North Sea and Amoco Cadiz oil. Bot Mar 23:125–127CrossRefGoogle Scholar
  6. Ahearn DG, Meyers SP (1972) The role of fungi in the decomposition of hydrocarbons in the marine environment. In: Walters AH, Hueck-van der Plas EH (eds) Biodeterioration of materials. Wiley, New York, pp 12–18Google Scholar
  7. Ahearn DG, Meyers SP, Standard PG (1971) The role of yeasts in the decomposition of oils in marine environments. Dev Ind Microbiol 12:126–134Google Scholar
  8. Al-Baldawi IA, Abdullah SRS, Suja F, Anuar N, Mushrifah I (2013) Effect of aeration on hydrocarbon phytoremediation capability in pilot sub-surface flow constructed wet land operation. Ecol Eng 61:496–500CrossRefGoogle Scholar
  9. Antizar-Ladislao B, Lopez-Real JM, Beck AJ (2004) Bioremediation of polycyclic aromatic hydrocarbon (PAH)-contaminated waste using composting approaches. Crit Rev Environ Sci Technol 34:249–289CrossRefGoogle Scholar
  10. Atlas RM (1981) Microbial degradation of petroleum hydrocarbons: an environmental perspective. Microbiol Rev 45(1):180–209PubMedPubMedCentralGoogle Scholar
  11. Atlas RM (1985) Effects of hydrocarbons on micro-organisms and biodegradation in Arctic ecosystems. In: Engelhardt FR (ed) Petroleum effects in the Arctic environment. Elsevier, London, pp 63–99Google Scholar
  12. Atlas RM (1988) Microbiology-fundamentals and applications, 2nd edn. Macmillan, New York, pp 352–353Google Scholar
  13. Atlas RM, Bartha R (1987) Microbial Ecology Fundamentals and applications, 2nd edn. Benjamin Cummings, Menlo ParkGoogle Scholar
  14. Atlas RM, Cerniglia CE (1995) Bioremediation of petroleum pollutants. Biosci 45:332–338CrossRefGoogle Scholar
  15. Atlas RM, Sexstone A, Gustin P, Miller O, Linkins P, Everett K (1980) Biodegradation of crude oil by tundra soil microorganisms. In: Oxley TA, Becker G, Allsop D (eds) Proceedings of the 4th international biodeterioration symposium. Pitman Publishing, London, pp 21–28Google Scholar
  16. Austin B, Calomiris JJ, Walker JD, Colwell RR (1977) Numerical taxonomy and ecology of petroleum degrading bacteria. Appl Environ Microbiol 34:60–68PubMedPubMedCentralGoogle Scholar
  17. Azadpour-Keeley A, Keeley JW, Russell HH, Sewell GW (2001) Monitored natural attenuation of contaminants in the subsurface: processes. Ground Water Monit Remediat 21:97–107CrossRefGoogle Scholar
  18. Baelum J, Borglin S, Chakraborty R, Fortney JL, Lamendella R, Mason OU, Auer M, Zemla M, Bill M, Conrad ME, Malfatti SA, Tringe SG, Holman HY, Hazen TC, Jansson JK (2012) Deep-sea bacteria enriched by oil and dispersant from the Deepwater horizon spill. Environ Microbiol 14:2405–2416CrossRefPubMedPubMedCentralGoogle Scholar
  19. Bagia A, Pampanin DM, Brakstad OG, Roald Kommedal R (2013) Estimation of hydrocarbon biodegradation rates in marine environments: a critical review of the Q10 approach. Mar Environ Res 89:83–90CrossRefGoogle Scholar
  20. Baheri H, Meysami P (2002) Feasibility of fungi bioaugmentation in composting a flare pit soil. J Hazard Mater 89:279–286CrossRefPubMedPubMedCentralGoogle Scholar
  21. Bailey NJL, Jobson AM, Rogers MA (1973) Bacterial degradation of crude oil: comparison of field and experimental data. Chem Geol 11:203–221CrossRefGoogle Scholar
  22. Bartha R, Atlas RM (1977) The microbiology of aquatic oil spills. Adv Appl Microbiol 22:225–266CrossRefPubMedPubMedCentralGoogle Scholar
  23. Bartha R, Bossert I (1984) The treatment and disposal of petroleum wastes. In: Atlas RM (ed) Petroleum microbiology. Macmillan, New York, pp 553–578Google Scholar
  24. Bhattacharya D, Sarma PM, Krishnan S, Mishra S, Lal B (2003) Evaluation of the genetic diversity among the strains of Pseudomonas citronellolis isolated from oily sludge contaminated sites. Appl Environ Microbiol 60:1435–1441CrossRefGoogle Scholar
  25. Boehm PD, Fiest DL(1980) Aspects of the transport of petroleum hydrocarbons to the offshore benthos during the IXTOC-I blowout in the Bay of Campeche, pp 207–236Google Scholar
  26. Bogusławska-Was E, Da Browski W (2001) The seasonal variability of yeasts and yeast-like organisms in water and bottom sediment of the Szczecin Lagoon. Int J Hyg Environ Health 203(5–6):451–458CrossRefPubMedPubMedCentralGoogle Scholar
  27. Bordoloi S, Basumatary B (2015) Phytoremediation of Hydrocarbon-contaminated soil using sedge species. In: Ansari A, Gill S, Gill R, Lanza G, Newman L (eds) Phytoremediation. Springer, ChamGoogle Scholar
  28. Bossert I, Bartha R (1984) The fate of petroleum in soil ecosystems. In: Atlas RM (ed) Petroleum microbiology. Macmillan, New York, pp 434–476Google Scholar
  29. Boyd SA, Shelton DR (1984) Anaerobic biodegradation of chlorophenols in fresh and acclimated sludge. Appl Environ Microbiol 47:272–277PubMedPubMedCentralGoogle Scholar
  30. Britton LN (1984) Microbial degradation of aliphatic hydrocarbons. In: Gibson DT (ed) Microbial degradation of organic compounds. Marcel Dekker, New York, pp 89–129Google Scholar
  31. Brooijmans RJW, Pastink MI, Siezen RJ (2009) Hydrocarbon-degrading bacteria: the oil-spill clean-up crew. Microb Biotechnol 2(6):587–594CrossRefPubMedPubMedCentralGoogle Scholar
  32. Brune KD, Bayer TS (2012) Engineering microbial consortia to enhance biomining and bioremediation. Front Microbiol 3:1–6CrossRefGoogle Scholar
  33. Burgin AJ, Hamilton SK (2007) Have we overemphasized the role of denitrification in aquatic ecosystems? A review of nitrate removal pathways. Front Ecol Environ 5:89–96CrossRefGoogle Scholar
  34. Callaghan AV, Morris BEL, Pereira IAC, McInerney MJ, Austin RN, Groves JT, Kukor JJ, Suflita JM, Young LY, Zylstra GJ, Wawrik B (2012) The genome sequence of Desulfatibacillumalkenivorans AK-01: a blueprint for anaerobic alkane oxidation. Environ Microbiol 14:101–113CrossRefPubMedPubMedCentralGoogle Scholar
  35. Cappello S, Denaro R, Genovese M, Giuliano L, Yakimov MM (2007) Predominant growth of Alcanivorax during the experiment on “oil spill bioremediation” in mesocosms. Microbiol Res 162:185–190CrossRefPubMedPubMedCentralGoogle Scholar
  36. Cappello S, Calogero R, Santisi S, Genovese M, Denaro R, Genovese L, Giuliano L, Mancini G, Yakimov MM (2015) Bioremediation of oil polluted marine sediments: a bio-engineering treatment. Int Microbiol 18:127–134PubMedPubMedCentralGoogle Scholar
  37. Cerniglia CE (1984) Microbial transformation of aromatic hydrocarbons. In: Atlas RM (ed) Petroleum microbiology. Macmillan, New York, pp 99–128Google Scholar
  38. Cerniglia CE, Perry JJ (1973) Crude oil degradation by microorganisms isolated from the marine environment. J Basic Microbiol 13:299–306Google Scholar
  39. Cerniglia C, Sutherland J (2010) Degradation of polycyclic aromatic hydrocarbons by fungi. In: McGenity TJ, van der Meer JR, de Lorenzo V (eds) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin/Heidelberg, pp 2079–2110CrossRefGoogle Scholar
  40. Cerniglia CE, Gibson DT, van Baalen C (1980) Oxidation of naphthalene by cyanobacteria and microalgae. J Gen Microbiol 116:495–500Google Scholar
  41. Chaillan F, Le Flèche A, Bury E, Phantavong YH, Grimont P, Saliot A, Oudot J (2004) Identification and biodegradation potential of tropical aerobic hydrocarbon degrading microorganisms. Res Microbiol 155:587–595CrossRefPubMedPubMedCentralGoogle Scholar
  42. Chaillan F, Chaîneau CH, Point V, Saliot A, Oudot J (2006) Factors inhibiting bioremediation of soil contaminated with weathered oils and drill cuttings. Environ Pollut 144(1):255–265CrossRefGoogle Scholar
  43. Chen M, Hong CS, Bush B, Rhee GY (1988) Anaerobic biodegradation of polychlorinated biphenyls by bacteria from Hudson River sediments. Ecotoxicol Environ Saf 16:95–105CrossRefPubMedPubMedCentralGoogle Scholar
  44. Chen M, Xua P, Zeng G, Yang C, Huang D, Zhang J (2015) Bioremediation of soils contaminated with polycyclic aromatic hydrocarbons, petroleum, pesticides, chlorophenols and heavy metals by composting: applications, microbes and future research needs. Biotechnol Adv 33:745–755CrossRefPubMedPubMedCentralGoogle Scholar
  45. Colwell RR, Walker JD (1977) Ecological aspects of microbial degradation of petroleum in the marine environment. Crit Rev Microbiol 5:423–445CrossRefGoogle Scholar
  46. Cook FD, Westlake DWS (1974) Microbiological degradation of northern crude oils. Environmental-social committee; northern pipelines, task force on northern oil development, report no. 74–1. Catalog no. R72–12774. Information Canada, OttawaGoogle Scholar
  47. Cook WL, Massey JK, Ahearn DJ (1973) The degradation of crude oil by yeasts and its effects on Lebistes reticulatus. In: Ahearn DG, Meyers SP (eds) The microbial degradation of oil pollutants. Publication no. LSU-SG-73-01. Center for Wetland Resources, Louisiana State University, Baton Rouge, pp 279–282Google Scholar
  48. Cooney JJ (1984) The fate of petroleum pollutants in fresh water ecosystems. In: Atlas RM (ed) Petroleum microbiology. Macmillan, New York, pp 399–434Google Scholar
  49. Cooney JJ, Edmonds P, Brenner QM (1968) Growth and survival of fuel isolates in hydrocarbon-fuel emulsions. Appl Microbiol 16:569–571PubMedPubMedCentralGoogle Scholar
  50. Cundell AM, Traxler RW (1974) Hydrocarbon degrading bacteria associated with Arctic oil seeps. Dev Ind Microbiol 15:250–255Google Scholar
  51. Daane LL, Harjono I, Barns SM, Launen LA, Palleroni NJ, Haggblom MM (2002) PAH-degradation by Paenibacillus spp. and description of Paenibacillus naphthalenovorans sp. nov., a naphthalene degrading bacterium from the rhizosphere of salt marsh plants. Int J Syst Evol Microbiol 52:131–139CrossRefPubMedPubMedCentralGoogle Scholar
  52. Daghio M, Tatangelo V, Franzetti A, Gandolfi I, Papacchini M, Careghini A, Sezenna E, Saponaro S, Bestetti G (2015) Hydrocarbon degrading microbial communities in bench scale aerobic biobarriers for gasoline contaminated groundwater treatment. Chemosphere 130:34–39CrossRefPubMedPubMedCentralGoogle Scholar
  53. Das N, Chandran P (2011) Microbial degradation of petroleum hydrocarbon contaminants: an overview. Biotechnol Res Int 2011:1–13Google Scholar
  54. Das K, Mukherjee AK (2007) Crude petroleum-oil biodegradation efficiency of Bacillus subtilis and Pseudomonas aeruginosa strains isolated from a petroleum-oil contaminated soil from north-East India. Bioresour Technol 98:1339–1345CrossRefPubMedPubMedCentralGoogle Scholar
  55. Das D, Baruah R, Roy AS, Singh AK, Boruah HPD, Kalita J, Bora TC (2015) Complete genome sequence analysis of Pseudomonas aeruginosa N002 reveals its genetic adaptation for crude oil degradation. Genomics 105:182–190CrossRefPubMedPubMedCentralGoogle Scholar
  56. Daugulis AJ, McCracken CM (2003) Microbial degradation of high and low molecular weight polyaromatic hydrocarbons in a two-phase partitioning bioreactor by two strains of Sphingomonas sp. Biotechnol Lett 25:1441–1444CrossRefPubMedPubMedCentralGoogle Scholar
  57. Davies JS, Westlake DWS (1979) Crude oil utilization by fungi. Can J Microbiol 25:146–156CrossRefPubMedPubMedCentralGoogle Scholar
  58. Dellagnezze BM, Sousa GV, Martins LL, Domingos DF, Limache EEG, Vasconcellos SP, Cruz GF, Oliveira VM (2014) Bioremediation potential of microorganisms derived from petroleum reservoirs. Mar Pollut Bull 89:191–200CrossRefPubMedPubMedCentralGoogle Scholar
  59. Deng MC, Li J, Liang FR, YiMS XXM, Yuan JP, Peng J, Wu CF, Wang JH (2014) Isolation and characterization of a novel hydrocarbon-degrading bacterium Achromobacter sp. HZ01 from the crude oil-contaminated seawater at the Daya Bay, southern China. Mar Pollut Bull 83:79–86CrossRefPubMedPubMedCentralGoogle Scholar
  60. Dibble JT, Bartha R (1979) Effect of environmental parameters on the biodegradation of oil sludge. Appl Environ Microbiol 37:729–739PubMedPubMedCentralGoogle Scholar
  61. Feng L, Wang W, Cheng J, Ren Y, Zhao G, Gao C, Tang Y, Liu X, Han W, Peng X, Liu R, Wang L (2007) Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir. Proc Natl Acad Sci USA 104:5602–5607CrossRefPubMedPubMedCentralGoogle Scholar
  62. Floodgate G (1984) The fate of petroleum in marine ecosystems. In: Atlas RM (ed) Petroleum microbiology. Macmillan, New York, pp 355–398Google Scholar
  63. Foght J (2008) Anaerobic biodegradation of aromatic hydrocarbons: pathways and prospects. J Mol Microbiol Biotechnol 15:93–120CrossRefPubMedPubMedCentralGoogle Scholar
  64. Foght JM, Westlake DWS, Johnson WM, Ridgway HF (1996) Environmental gasoline-utilizing isolates and clinical isolates of Pseudomonas aeruginosa are taxonomically indistinguishable by chemotaxonomic and molecular techniques. Microbiology 142(9):2333–2340CrossRefPubMedPubMedCentralGoogle Scholar
  65. Fusey P, Oudot J (1984) Relative influence of physical removal and biodegradation in the depuration of petroleum-contaminated seashore sediments. Mar Pollut Bull 15:136–141CrossRefGoogle Scholar
  66. Geetha SJ, Joshi SJ, Kathrotiya S (2013) Isolation and characterization of hydrocarbon degrading bacterial isolate from oil contaminated sites. APCBEE Procedia 5:237–241CrossRefGoogle Scholar
  67. Gesinde AF, Agbo EB, Agho MO, Dike EFC (2008) Bioremediation of some Nigerian and Arabian crude oils by fungal isolates. Int J Pure Appl Sci 2:37–44Google Scholar
  68. Ghazali FM, Abdul Rahman RNZ, Salleh AB, Basri M (2004) Biodegradation of hydrocarbons in soil by microbial consortium. Int Biodeterior Biodegrad 54:61–67CrossRefGoogle Scholar
  69. Guarino C, Spada V, Sciarrillo R (2017) Assessment of three approaches of bioremediation (natural attenuation, landfarming and bioagumentation – assistited landfarming) for a petroleum hydrocarbons contaminated soil. Chemosphere 170:10–16CrossRefPubMedPubMedCentralGoogle Scholar
  70. Habe H, Omori T (2003) Genetics of polycyclic aromatic hydrocarbon metabolism in diverse aerobic bacteria. Biosci Biotechnol Biochem 67:225–243CrossRefPubMedPubMedCentralGoogle Scholar
  71. Hambrick GA, DeLaune RD, Patrick WH (1980) Effect of estuarine sediment pH and oxidation-reduction potential on microbial hydrocarbon degradation. Appl Environ Microbiol 40:365–369PubMedPubMedCentralGoogle Scholar
  72. Hamdi H, Benzarti S, Manusadzianas L, Aoyama I, Jedidi N (2007) Solid-phase bioassays and soil microbial activities to evaluate PAH-spiked soil ecotoxicity after a long-term bioremediation process simulating landfarming. Chemosphere 70:135–143CrossRefPubMedPubMedCentralGoogle Scholar
  73. Hamzah A, Rabu A, Farzarul R, Yussoff NA (2010) Isolation and characterization of bacteria degrading Sumandak and south Angsi oils. Sains Malays 39(2):161–168Google Scholar
  74. Hamzah A, Phan CW, Abu Bakar NF, Wong KK (2013) Biodegradation of crude oil by constructed bacterial consortia and the constituent single bacteria isolated from Malaysia. Biorem J 17:1–10CrossRefGoogle Scholar
  75. Haritash AK, Kaushik CP (2009) Biodegradation aspects of polycyclic aromatic hydrocarbons (PAHs): a review. J Hazard Mater 169:1–15CrossRefGoogle Scholar
  76. Harms H, Schlosser D, Wick LY (2011) Untapped potential: exploiting fungi in bioremediation of hazardous chemicals. Nat Rev Microbiol 9:177–192CrossRefGoogle Scholar
  77. Hasinger M, Scherr KE, Lundaa T, Brauer L, Zach C, Loibner AP (2012) Changes in iso- and n-alkane distribution during biodegradation of crude oil under nitrate and sulphate reducing conditions. J Biotechnol 157:490–498CrossRefPubMedPubMedCentralGoogle Scholar
  78. Hidayat A, Tachibana S (2012) Biodegradation of aliphatic hydrocarbon in three types of crude oil by Fusarium sp. F092 under stress with artificial sea water. J Environ Sci Technol 5:64–73CrossRefGoogle Scholar
  79. Hill EC (1978) Biodegradation of hydrocarbon-based products in industrial use. In: Watkinson JR (ed) Developments in biodegradation of hydrocarbons-1. Applied Science Publishers, London, pp 201–226Google Scholar
  80. Hill EC, Thomas AR (1976) Microbiological aspects of supersonic aircraft fuel. In: Sharpley JM, Kaplan AM (eds) Proceedings of the third international biodegradation symposium. Applied Science Publishers, Ltd., London, pp 157–174Google Scholar
  81. Hollaway SL, Faw GM, Sizemore RK (1980) The bacterial community composition of an active oil field in the northwestern Gulf of Mexico. Mar Pollut Bull 11:153–156CrossRefGoogle Scholar
  82. Hong YH, Deng MC, Xua XM, Wu CF, Xiao X, Zhua Q, Sun XX, Zhou QZ, Peng J, Yuan JP, Wang JH (2016) Characterization of the transcriptomeof Achromobacter sp. HZ01with the outstanding hydrocarbon-degrading ability. Gene 584:185–194CrossRefPubMedPubMedCentralGoogle Scholar
  83. Horowitz A, Atlas RM (1980) Microbial seeding to enhance petroleum hydrocarbon biodegradation in aquatic Arctic ecosystems. In: Oxley TA, Becker G, Allsopp D (eds) Proceedings of the 4th international biodeterioration symposium. Pitman Publishing, London, pp 15–20Google Scholar
  84. Hou J, Liu W, Wanga B, Wang Q, Luo Y, Franks AE (2015) PGPR enhanced phytoremediation of petroleum contaminated soil and rhizosphere microbial community response. Chemosphere 138:592–598CrossRefPubMedPubMedCentralGoogle Scholar
  85. Hutchins SR (1991) Biodegradation of monoaromatic hydrocarbons by aquifer microorganisms using oxygen, nitrate, or nitrous oxide as the terminal electron acceptor. Appl Environ Microbiol 57:2403–2407PubMedPubMedCentralGoogle Scholar
  86. Huu NB, Denner EBM, Ha DTC, Wanner G, Stan-Lotter H (1999) Marinobacter aquaeolei sp. nov., a halophilic bacterium isolated from a Vietnamese oil producing well. Int J Syst Bacteriol 49:367–375CrossRefPubMedGoogle Scholar
  87. Jain PK, Gupta VK, Pathak H, Lowry M, Jaroli DP (2010) Characterization of 2T engine oil degrading indigenous bacteria, collected from high altitude Mussoorie region of India. World J Microbiol Biotechnol 26:1419–1426CrossRefGoogle Scholar
  88. Jamison VM, Raymond RL, Hudson JO (1975) Biodegradation of high-octane gasoline in groundwater. Dev Ind Microbiol 16:305–312Google Scholar
  89. Jesubunmi CO (2014) Isolation of oil – degrading microorganisms in spent engine oil – contaminated soil. J Biol Agric Healthc 4:191–195Google Scholar
  90. Jobson A, Cook FD, Westlake DWS (1972) Microbial utilization of oil. Appl Microbiol 23:1082–1089PubMedPubMedCentralGoogle Scholar
  91. Johnsen AR, Wick LY, Harms H (2005) Principles of microbial PAH degradation in soil. Environ Pollut 133:71–84CrossRefPubMedPubMedCentralGoogle Scholar
  92. Jones JG, Eddington MA (1968) An ecological survey of hydrocarbon-oxidizing microorganisms. J Gen Microbiol 52:381–390CrossRefGoogle Scholar
  93. Joo HS, Ndegwa PM, Shoda M, Phae CG (2008) Bioremediation of oil-contaminated soil using Candida catenulata and food waste. Environ Pollut 156:891–896CrossRefPubMedPubMedCentralGoogle Scholar
  94. Kadali KK, Simons KL, Skuza PP, Moore RB, Ball AS (2012) A complementary approach to identifying and assessing the remediation potential of hydrocarbonoclastic bacteria. J Microbiol Methods 88:348–355CrossRefPubMedPubMedCentralGoogle Scholar
  95. Kauppi S, Sinkkonen A, Romantschuk M (2011) Enhancing bioremediation of diesel-fuel-contaminated soil in a boreal climate: comparison of biostimulation and bioaugmentation. Int Biodeter Biodegr 65:359–368CrossRefGoogle Scholar
  96. Khan AHA, Tanveer S, Anees M, Muhammad YS, Iqbal M, Yousaf S (2016) Role of nutrients and illuminance in predicting the fate of fungal mediated petroleum hydrocarbon degradation and biomass production. J Environ Manag 176:54–60CrossRefGoogle Scholar
  97. Kharusi SA, Abed RMM, Dobretsov S (2016) EDTA addition enhances bacterial respiration activities and hydrocarbon degradation in bioaugmented and nonbioaugmented oil-contaminated desert soils. Chemosphere 147:279–286CrossRefPubMedPubMedCentralGoogle Scholar
  98. Khashayar T, Mahsa T (2010) Biodegradation potential of petroleum hydrocarbons by bacterial diversity in soil. World Appl Sci J 8(6):750–755Google Scholar
  99. Komagata K, Nakase T, Katsuya N (1964) Aimilation of hydrocarbons by yeasts. I. Preliminary screening. J Gen Appl Microbiol 10:313–321CrossRefGoogle Scholar
  100. Kriipsalu M, Marques M, Nammaria DR, Hogland W (2007) Bio-treatment of oily sludge: the contribution of amendment material to the content of target contaminants, and the biodegradation dynamics. J Hazard Mater 148:616–622CrossRefPubMedPubMedCentralGoogle Scholar
  101. Krutz LJ, Beyrouty CA, Gentry TJ, Wolf DC, Reynolds CM (2005) Selective enrichment of a pyrene degrader population and enhanced pyrene degradation in Bermuda grass rhizosphere. Biol Fertil Soils 41:359–364CrossRefGoogle Scholar
  102. Kuznetsov VD, Zaitseva TA, Vakulenko LV, Filippova SN (1992) Streptomyces albiaxialis sp. nov.: a new petroleum hydrocarbon-degrading species of thermo- and halotolerant Streptomyces. Microbiology 61:62–67Google Scholar
  103. Leahy JG, Colwell RR (1990) Microbial degradation of hydrocarbons in the environment. Microbiol Rev 54(3):305–315PubMedPubMedCentralGoogle Scholar
  104. Liu B, Jua M, Liu J, Wua W, Li X (2016) Isolation, identification, and crude oil degradation characteristics of a high-temperature, hydrocarbon-degrading strain. Mar Pollut Bull 106:301–307CrossRefPubMedPubMedCentralGoogle Scholar
  105. Llanos C, Kioller A (1976) Changes in the flora of soil fungi following oil waste application. Oikos 27:337–382CrossRefGoogle Scholar
  106. Ma J, Yang Y, Dai X, Chen Y, Deng H, Zhou H, Guo S, Yan G (2016) Effects of adding bulking agent, inorganic nutrient and microbial inocula on biopile treatment for oil-field drilling waste. Chemosphere 150:17–23CrossRefPubMedPubMedCentralGoogle Scholar
  107. Mahmoud GA, Koutb MMM, Morsy FM, Bagy MMK (2015a) Mycoflora isolated from Mazot and solar polluted soils in upper Egypt. Egypt J Soil Sci 55(1):15–30CrossRefGoogle Scholar
  108. Mahmoud GA, Koutb MMM, Morsy FM, Bagy MMK (2015b) Characterization of lipase enzyme produced by hydrocarbons utilizing fungus Aspergillus terreus. Euro J Biol Res 5(3):70–77Google Scholar
  109. Malik ZA, Ahmed S (2012) Degradation of petroleum hydrocarbons by oil field isolated bacterial consortium. Afr J Biotechnol 11:650–658Google Scholar
  110. Mancera-Lopez ME, Esparza-Garcia F, Chavez-Gomez B, Rodriguez-Vazquez R, Saucedo-Castaneda G, Barrera-Cortes J (2008) Bioremediation of an aged hydrocarbon-contaminated soil by a combined system of biostimulation-bioaugmentation with filamentous fungi. Int Biodeterior Biodegrad 61:151–160CrossRefGoogle Scholar
  111. Masood N, Zakaria MP, Ali MM, Magam SM, Alkhadher S, Keshavarzifard M, Vaezzadeh V, Hussein MA (2014) Distribution of petroleum hydrocarbons in surface sediments from selected locations in Kuala Selangor River, Malaysia. From sources to solution. SpringerGoogle Scholar
  112. Mittal A, Singh P (2009) Isolation of hydrocarbon degrading bacteria from soils contaminated with crude oil spills. Indian J Exp Biol 47:760–765PubMedPubMedCentralGoogle Scholar
  113. Mnif S, Chamkha M, Sayadi S (2009) Isolation and characterization of Halomonas sp. strain C2SS100, a hydrocarbon-degrading bacterium under hypersaline conditions. J Appl Microbiol 107:785–794CrossRefPubMedGoogle Scholar
  114. Namkoong W, Hwang EY, Park JS, Choi JY (2002) Bioremediation of diesel-contaminated soil with composting. Environ Pollut 119:23–31CrossRefPubMedPubMedCentralGoogle Scholar
  115. Narro ML, Cerniglia CE, Baalen CV, Gibson DT (1992a) Evidence of NIH shift in naphthalene oxidation by the marine cyanobacterium, Oscillatoria species strain JCM. Appl Environ Microbiol 58:1360–1363PubMedPubMedCentralGoogle Scholar
  116. Narro ML, Cerniglia CE, Baalen CV, Gibson DT (1992b) Metabolism of phenanthrene by the marine cyanobacterium Agmenellum quadruplicatum strain PR-6. Appl Environ Microbiol 58:1351–1359PubMedPubMedCentralGoogle Scholar
  117. Nie Y, Chi CQ, Fang H, Liang JL, Lu SL, Lai GL, Tang YQ, Wu XL (2014) Diverse alkane hydroxylase genes in microorganisms and environments. Sci Rep 4:49–68Google Scholar
  118. O’Brien PY, Dixon PS (1976) The effects of oil and oil components on algae; a review. Br Phycol J 11:115–142CrossRefGoogle Scholar
  119. Obuekwe CO, Badrudeen AM, Al-Saleh E, Mulder JL (2005) Growth and hydrocarbon degradation by three desert fungi under conditions of simultaneous temperature and salt stress. Int Biodeterior Biodegrad 56:197–205CrossRefGoogle Scholar
  120. Obuekwe CO, Al-Jadi ZK, Al-Saleh ES (2009) Hydrocarbon degradation in relation to cell-surface hydrophobicity among bacterial hydrocarbon degraders from petroleum-contaminated Kuwait desert environment. Int Biodeterior Biodegrad 63:273–279CrossRefGoogle Scholar
  121. Okolo JC, Amadi EN, Odu CTI (2005) Effects of soil treatments containing poultry manure on crude oil degradation in a sandy loam soil. Appl Ecol Env Res 3(1):47–53CrossRefGoogle Scholar
  122. Olivieri R, Bacchin P, Robertiello A, Oddo N, Degen L, Tonolo A (1976) Microbial degradation of oil spills enhanced by a slow-release fertilizer. Appl Environ Microbiol 31:629–634PubMedPubMedCentralGoogle Scholar
  123. Perry JJ (1984) Microbial metabolism of cyclic alkanes. In: Atlas RM (ed) Petroleum microbiology. Macmillan, New York, pp 61–98Google Scholar
  124. Pinedo-Rivilla C, Aleu J, Collado I (2009) Pollutants biodegradation by fungi. Curr Org Chem 13:1194–1214CrossRefGoogle Scholar
  125. Priya A, Mandal AK, Ball AS, Manefield M, Lal B, Sarma PM (2015) Mass culture strategy for bacterial yeast co-culture for degradation of petroleum hydrocarbons in marine environment. Mar Pollut Bull 100:191–199CrossRefPubMedPubMedCentralGoogle Scholar
  126. Raza C, Billal A, Jahan N (2010) Evaluation of biodegradation potential of bacteria in crude oil contaminated soil. Biologia (Pakistan) 5(1&2):77–85Google Scholar
  127. Riis V, Kleinsteuber S, Babel W (2003) Influence of high salinities on the degradation of diesel fuel by bacteria consortia. Can J Microbiol 49:713–721CrossRefPubMedPubMedCentralGoogle Scholar
  128. Romero MC, Urrutia MI, Reinoso HE, Kiernan MM (2010) Benzo[a]pyrene degradation by soil filamentous fungi. J Yeast Fungal Res 1:25–29Google Scholar
  129. Ron EZ, Rosenberg E (2014) Enhanced bioremediation of oil spills in the sea. Curr Opin Biotechnol 27:191–194CrossRefPubMedPubMedCentralGoogle Scholar
  130. Ruberto L, Vazquez SC, MacCormack WP (2003) Effectiveness of the natural bacterial flora, biostimulation and bioaugmentation on the bioremediation of a hydrocarbon contaminated Antarctic soil. Int Biodeterior Biodegrad 52:115–125CrossRefGoogle Scholar
  131. Salminen JM, Hanninen PJ, Leveinen J, Lintinen PTJ, Jorgensen KS (2006) Occurrence and rates of terminal electron-accepting processes and recharge processes in petroleum hydrocarbon-contaminated subsurface. J Environ Qual 35:2273–2282CrossRefPubMedPubMedCentralGoogle Scholar
  132. Saraswathy A, Hallberg R (2002) Degradation of pyrene by indigenous fungi from a former gasworks site. FEMS Microbiol Lett 210:227–232CrossRefPubMedPubMedCentralGoogle Scholar
  133. Sarma PM, Bhattacharya D, Krishnan S, Banwari L (2004) Degradation of polycyclic aromatic hydrocarbons by a newly discovered enteric bacterium, Leclercia adecarboxylata. Appl Environ Microbiol 70(5):3163–3166CrossRefPubMedPubMedCentralGoogle Scholar
  134. Sathishkumar M, Binupriya AR, Balk S, Yun S (2008) Biodegradation of crude oil by individual bacterial strains and a mixed bacterial consortium isolated from hydrocarbon contaminated areas. Clean 36(1):92–96Google Scholar
  135. Sayler GS, Hooper SW, Layton AC, Henry King GM (1990) Catabolic plasmids of environmental and ecological significance. Microbiol Ecol 19:1–20CrossRefGoogle Scholar
  136. Schneiker S, dos Santos VAPM, Bartels D, Bekel T, Brecht M, Buhrmester J, Chernikova TN, Denaro R, Ferrer M, Gertler C, Goesmann A, Golyshina OV, Kaminski F, Khachane AN, Lang S, Linke B, McHardy AC, Meyer F, Nechitaylo T, Puehler A, Regenhardt D, Rupp O, Sabirova JS, Selbitschka W, Yakimov MM, Timmis KN, Vorhoelter FJ, Weidner S, Kaiser O, Golyshin PN (2006) Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat Biotechnol 24:997–1004CrossRefPubMedPubMedCentralGoogle Scholar
  137. Sepahi AA, Golpasha DI, Emami M, Nakhoda MA (2008) Isolation and characterization of crude oil degrading Bacillus spp. Iran J Environ Health Sci Eng 5(3):149–154Google Scholar
  138. Sheppard PJ, Simons KL, Adetutu EM, Kadali KK, Juhasz AL, Manefield M, Sarma PM, Lal B, Ball AS (2014) The application of carrier-based bioremediation strategy for marine oil spills. Mar Pollut Bull 84(1–2):339–346CrossRefPubMedPubMedCentralGoogle Scholar
  139. Sierra J, Renault P (1995) Oxygen consumption by soil microorganisms as affected by oxygen and carbon dioxide levels. Appl Soil Ecol 2:175–184CrossRefGoogle Scholar
  140. Sihag S, Pathak H, Jaroli DP (2014) Factors affecting the rate of biodegradation of polyaromatic hydrocarbons. Int J Pure Appl Biosci 2:185–202Google Scholar
  141. Singer ME, Finnerty WR (1984) Microbial metabolism of straight-chain and branched alkanes. In: Atlas RM (ed) Petroleum microbiology. Macmillan, New York, pp 1–60Google Scholar
  142. Singh H (2006) Mycoremediation: fungal bioremediation. Wiley- Interscience, New YorkCrossRefGoogle Scholar
  143. So CM, Youngm LY (2001) Anaerobic biodegradation of alkanes by enriched consortia under four different reducing conditions. Environ Toxicol Chem 20:473–478CrossRefPubMedPubMedCentralGoogle Scholar
  144. Steliga T, Jakubowicz P, Kapusta P (2012) Changes in toxicity during in situ bioremediation of weathered drill wastes contaminated with petroleum hydrocarbons. Bioresour Technol 125:1–10CrossRefPubMedPubMedCentralGoogle Scholar
  145. Sunita VJ, Dolly PR, Bateja S, Vivek UN (2013) Isolation and screening for hydrocarbon utilizing bacteria (HUB) from petroleum samples. Int J Curr Microbiol Appl Sci 2(4):48–60Google Scholar
  146. Taccari M, Milanovic V, Comitini F, Casucci C, Ciani M (2012) Effects of biostimulation and bioaugmentation on diesel removal and bacterial community. Int Biodeterior Biodegrad 66:39–46CrossRefGoogle Scholar
  147. Tang WW, Zeng GM, Gong JL, Liang J, Xu P, Zhang C, Gong JL, Liang J, Xu P, Zhang C, Huang BB (2014) Impact of humic/fulvic acid on the removal of heavy metals from aqueous solutions using nanomaterials: a review. Sci Total Environ 468:1014–1027CrossRefPubMedPubMedCentralGoogle Scholar
  148. Tejada M, Gonzalez JL, Hernandez MT, Garcia C (2008) Application of different organic amendments in a gasoline contaminated soil: effect on soil microbial properties. Bioresour Technol 99:2872–2880CrossRefPubMedPubMedCentralGoogle Scholar
  149. Thenmozhi R, Nagasathya A, Thajuddin N (2011) Studies on biodegradation of used engine oil by consortium cultures. Adv Environ Biol 5(6):1051–1057Google Scholar
  150. Throne-Holst M, Wentzel A, Ellingsen TE, Kotlar H-K, Zotchev SB (2007) Identification of novel genes involved in long-chain n-alkane degradation by Acinetobacter sp. strain DSM 17874. Appl Environ Microbiol 73:3327–3332CrossRefPubMedPubMedCentralGoogle Scholar
  151. Torlapati J, Boufadel MC (2014) Evaluation of the biodegradation of Alaska north slope oil in microcosms using the biodegradation model. BIOB Front Microbiol 5:1–15Google Scholar
  152. Trejo-Hernandez MR, Ortiz A, Okoh AI, Morales D, Quintero R (2007) Biodegradation of heavy crude oil Maya using spent compost and sugar cane bagasse wastes. Chemosphere 68:848–855CrossRefPubMedPubMedCentralGoogle Scholar
  153. Tyagi M, Fonseca MMR, de Carvalho CCCR (2010) Bioaugmentation and biostimulation strategies to improve the effectiveness of bioremediation processes. Biodegradation 22(2):231–241CrossRefPubMedPubMedCentralGoogle Scholar
  154. US Environmental Protection Agency (1986) Test method for evaluating solid waste, SW-846, 3rd ed., 1A. U.S. EPA, Washington, DCGoogle Scholar
  155. van Beilen JB, Funhoff EG (2007) Alkane hydroxylases involved in microbial alkane degradation. Appl Microbiol Biotechnol 74:13–21CrossRefPubMedPubMedCentralGoogle Scholar
  156. van Beilen JB, Funhoff EG, van Loon A, Just A, Kaysser L, Bouza M, Holtackers R, Röthlisberger M, Li Z, Witholt B (2006) Cytochrome P450 alkane hydroxylases of the CYP153 family are common in alkane-degrading eubacteria lacking integral membrane alkane hydroxylases. Appl Environ Microbiol 72:59–65CrossRefPubMedPubMedCentralGoogle Scholar
  157. Venosa AD, Zhu X (2003) Biodegradation of crude oil contaminating marine shorelines and freshwater wetlands. Spill Sci Technol Bull 8(2):163–178CrossRefGoogle Scholar
  158. Verstraete W, Vanloocke R, DeBorger R, Verlinde A (1976) Modelling of the breakdown and the mobilization of hydrocarbons in unsaturated soil layers. In: Sharpley JM, Kaplan AM (eds) Proceedings of the 3rd international biodegradation symposium. Applied Science Publishers, London, pp 99–112Google Scholar
  159. von Wedel RJ, Mosquera JF, Goldsmith CD, Hater GR, Wong A, Fox TA, Hunt WT, Paules MS, Quiros JM, Wiegand JW (1988) Bacterial biodegradation of petroleum hydrocarbons in groundwater: in situ augmented bioreclamation with enrichment isolates in California. Water Sci Technol 20:501–503CrossRefGoogle Scholar
  160. Walker JD, Austin HF, Colwell RR (1975a) Utilization of mixed hydrocarbon substrate by petroleum-degrading microorganisms. J Gen Appl Microbiol 21:27–39CrossRefGoogle Scholar
  161. Walker JD, Colwell RR, Vaituzis Z, Meyer SA (1975b) Petroleum-degrading achlorophyllous alga Prototheca zopfii. Nature (London) 254:423–424CrossRefGoogle Scholar
  162. Walker JD, Colwell RR, Petrakis L (1976) Biodegradation of petroleum by Chesapeake Bay sediment bacteria. Can J Microbiol 22:423–428CrossRefPubMedPubMedCentralGoogle Scholar
  163. Wang YN, Cai H, Chi CQ, Lu AH, Lin XG, Jian ZF, Xl W (2007) Halomonas shengliensis sp. nov., a moderately halophilic, denitrifying, crude-oil-utilizing bacterium. Int J Syst Evol Microbiol 57:1222–1226CrossRefPubMedPubMedCentralGoogle Scholar
  164. Whang LM, Liu PWG, Ma CC, Cheng SS (2008) Application of biosurfactants, rhamnolipid, and surfactin, for enhanced biodegradation of diesel-contaminated water and soil. J Hazard Mater 151:155–163CrossRefPubMedPubMedCentralGoogle Scholar
  165. Whyte LG, Bourbonnie’re L, Greer CW (1997) Biodegradation of petroleum hydrocarbons by Psychrotrophic Pseudomonas strains possessing both alkane (alk) and naphthalene (nah) catabolic pathways. Appl Environ Microbiol 63:3719–3723PubMedPubMedCentralGoogle Scholar
  166. Wu M, Chen L, Tian Y, Ding Y, Dick WA (2013) Degradation of polycyclic aromatic hydrocarbons by microbial consortia enriched from three soils using two different culture media. Environ Pollut 178:152–158CrossRefPubMedGoogle Scholar
  167. Wu M, Dick WA, Li W, Wang X, Yang Q, Wang T, Xu L, Zhang M, Chen L (2016) Bioaugmentation and biostimulation of hydrocarbon degradation and the microbial community in a petroleum-contaminated soil. Int Biodeterior Biodegrad 107:158–164CrossRefGoogle Scholar
  168. Wu M, Li W, Dick WA, Ye X, Chen K, Kost D, Chen L (2017) Bioremediation of hydrocarbon degradation in a petroleum-contaminated soil and microbial population and activity determination. Chemosphere 169:124–130CrossRefPubMedPubMedCentralGoogle Scholar
  169. Wuerdemann H, Wittmaier M, Rinkel U, Hanert HH (1994) A simple method for determining deficiency of oxygen during soil remediation. In: Hinchee RE, Alleman BC, Hoeppel RE, Miller RN (eds) Hydrocarbon bioremediation. CRC Press, Boca Raton, FL, pp 454–485Google Scholar
  170. Yakimov MM, Timmis KN, Golyshin PN (2007) Obligate oil-degrading marine bacteria. Curr Opin Biotechnol 18:257–266CrossRefPubMedGoogle Scholar
  171. Yeung CW, van Stempvoort DR, Spoelstra J, Bickerton G, Voralek J, Greer CW (2013) Bacterial community evidence for anaerobic degradation of petroleum hydrocarbons in cold climate groundwater. Cold Reg Sci Technol 86:55–68CrossRefGoogle Scholar
  172. Zhou E, Crawford RL (1995) Effects of oxygen, nitrogen, and temperature on gasoline biodegradation in soil. Biodgradation 6:127–140CrossRefGoogle Scholar
  173. Zvyagintseva IS, Poglasova MN, Gotoeva MT, Belyaev SS (2001) Effect of the medium salinity on oil degradation by Nocardioform bacteria. Microbiology 70:652–656CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  • Ghada Abd-Elmonsef Mahmoud
    • 1
    Email author
  • Magdy Mohmed Khalil Bagy
    • 1
  1. 1.Botany and Microbiology Department, Faculty of ScienceAssiut UniversityAssiutEgypt

Personalised recommendations