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Microbial Degradation of Petroleum Hydrocarbons: An Overview

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Abstract

Petroleum hydrocarbon contamination is severe in both terrestrial and aquatic environments. Hydrocarbon contamination affects both vertebrates and invertebrates in the environment under threat by oil spills. Several microbes participate in the decomposition of petroleum hydrocarbons (PH) under natural conditions. Microbes’ ability to remove PH has been studied extensively and exploited in the restoration of various spots affected by liquid hydrocarbon spills. Microbes involved in the decomposition of petroleum products consist of several bacteria and fungi. Almost 175 genera of bacteria, haloarchaeal bacteria, and eukarya are capable of degrading hydrocarbons into carbon dioxide and water. A consortium of microbes, rather than single species, is involved in degrading petroleum products as hydrocarbonoclastic microbes rarely function alone. Microbes isolated from terrestrial and marine environments contaminated with PH have proven to be excellent biodegraders of PH. Some of the Gram-negative hydrocarbonoclastic bacteria are Pseudomonas aeruginosa, P. fluorescens, Vibrio, Haemophilus spp., Marinobacter, Cycloclasticus, Pseudoalteromonas, Marinomonas, and Halomonas, whereas Mycobacterium spp., Rhodococcus spp., Paenibacillus spp., and Bacillus subtilis are some of the Gram-positive hydrocarbonoclastic bacteria. Hydrocarbonoclastic fungi include Phanerochaete chrysosporium, Bjerkandera adusta, Penicillium sp., Aspergillus sp., and Pleurotus ostreatus. It has been observed that bacteria, fungi, and microalgae are in close association while degrading PH, and it has been observed that the close association of bacteria and microalgae improves the degradation of PH. Enzymes produced by microbes which decompose PH comprise bacterial oxygenases and fungal exoenzymes such as lignin-modifying peroxidases like lignin peroxidases (LiPs), manganese peroxidases (MPs), and monocopper oxidases like laccases and epoxide hydrolases. Biodegradation of PH depends on various abiotic factors such as pH, temperature, oxygen, salinity, pressure, nutrients such as nitrogen and phosphorous, and their physical state. This review focuses on the microbes capable of degrading PH, the microbial processes involved in the degradation of PH, factors affecting the bioremediation, case studies involving bioremediation, and the recent strategies employed in in situ removal of PH.

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References

  • Adebusoye SA, Ilori MO, Amund OO, Teniola OD, Olatope SO (2007) Microbial degradation of petroleum hydrocarbons in a polluted tropical stream. World J Microbiol Biotechnol 23:1149–1159

    Article  CAS  Google Scholar 

  • Adoki A, Orugbani T (2007) Removal of crude petroleum hydrocarbons by heterotrophic bacteria in soils amended with nitrogenous fertilizer plant effluents. Afr J Biotechnol 6(13)

    Google Scholar 

  • Andersson BE, Lundstedt S, Tornberg K, Schnurer Y, Oberg LG, Mattiasson B (2003) Incomplete degradation of polycyclic aromatic hydrocarbons in soil inoculated with wood-rotting fungi and their effect on the indigenous soil bacteria. Environ Toxicol Chem 22:1238–1243

    Article  CAS  PubMed  Google Scholar 

  • April TM, Foght JM, Currah RS (1999) Hydrocarbon-degrading filamentous fungi isolated from flare pit soils in northern and western Canada. Can J Microbiol 46:38–49

    Article  Google Scholar 

  • Atlas RM (1981) Microbial degradation of petroleum hydrocarbons: an environmental perspective. Microbiol Rev 45:180–209

    CAS  PubMed  PubMed Central  Google Scholar 

  • Atlas RM (1995) Petroleum biodegradation and oil spill bioremediation. Mar Pollut Bull 31:178–182

    Article  CAS  Google Scholar 

  • Baik MH, Newcomb M, Friesner RA, Lippard SJ (2003) Mechanistic studies on the hydroxylation of methane by methane monooxygenase. Chem Rev 103:2385–2419

    Article  CAS  PubMed  Google Scholar 

  • Bartha R, Atlas RM (1977) The microbiology of aquatic oil spills. Adv Appl Microbiol 22:225–266

    Article  CAS  PubMed  Google Scholar 

  • Bezalel L, Hadar Y, Cerniglia CE (1997) Enzymatic mechanisms involved in phenanthrene degradation by the white rot fungus Pleurotus ostreatus. Appl Environ Microbiol 63:2495–2501

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bogan BW, Lamar RT, Hammel KE (1996) Fluorene oxidation in vivo by phanerochaetechrysosporium and in vitro during manganese peroxidase-dependent lipid peroxidation. Appl Environ Microbiol 62:1788–1792

    CAS  PubMed  PubMed Central  Google Scholar 

  • Boguslawska-Ws E, Dbrowski 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 203:451–458

    Article  Google Scholar 

  • Boopathy R, Shields S, Nunna S (2012) Biodegradation of crude oil from the BP oil spill in the marsh sediments of southeast Louisiana, USA. Appl Biochem Biotechnol 67:1560–1568

    Article  CAS  Google Scholar 

  • Cerniglia CE, Sutherland JB (2010) Degradation of polycyclic aromatic hydrocarbons by fungi. In: Timmis KN, TJ MG, van der Meer JR, de Lorenzo V (eds) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 2080–2110

    Google Scholar 

  • Chikere CB, Okpokwasili GC, Chikere BO (2011) Monitoring of microbial hydrocarbon remediation in the soil. 3 Biotech 1:117–138

    Article  PubMed  PubMed Central  Google Scholar 

  • Chouychai W, Lee H (2012) Phytotoxicity assay of crop plants to lindane and alpha-endosulfan contaminants in alkaline Thai soil. Int J Agric Biol 14(5):734–738

    CAS  Google Scholar 

  • Chouychai W, Thongkukiatkul A, Upatham S, Lee H, Pokethitiyook P, Kruatrachue M (2009) Plant-enhanced phenanthrene and pyrene biodegradation in acidic soil. J Environ Biol 30:139–144

    CAS  PubMed  Google Scholar 

  • Darsa KV, Thatheyus AJ (2014) Biodegradation of petroleum compound using Pseudomonas aeruginosa. OALibJ 1(5):1–9. https://doi.org/10.4236/oalib.1100735

  • Darsa KV, Thatheyus AJ, Ramya D (2014) Biodegradation of petroleum compound using the bacterium Bacillus subtilis. Sci Int 2(1):20–25

    Google Scholar 

  • Fathepure BZ. (2014) Recent studies in microbial degradation of petroleum hydrocarbons in hypersaline environments. Front Microbiol 5:173

    Google Scholar 

  • Gallego S, Vila J, Tauler M, Nieto JM, Breugelmans P, Springael D, Grifoll M (2014) Community structure and PAH ring-hydroxylating dioxygenase genes of a marine pyrene-degrading microbial consortium. Biodegradation 25:543–556

    Article  CAS  PubMed  Google Scholar 

  • Ghosal D, Ghosh S, Dutta TK, Ahn Y (2016) Current state of knowledge in microbial degradation of polycyclic aromatic hydrocarbons (PAHs): a review. Front Microbiol 7:1369

    PubMed  PubMed Central  Google Scholar 

  • Giebel HA, Kalhoefer D, Lemke A et al (2011) Distribution of Roseobacter RCA and SAR11 lineages in the North Sea and characteristics of an abundant RCA isolate. ISME J 5:8–19

    Article  PubMed  Google Scholar 

  • Gkorezis P, Daghio M, Franzetti A, Van Hamme JD, Sillen W, Vangronsveld J (2016) The interaction between plants and bacteria in the remediation of petroleum hydrocarbons: an environmental perspective. Front Microbiol 7:1836

    Article  PubMed  PubMed Central  Google Scholar 

  • Hammel KE (1995) Organopollutant degradation by ligninolytic fungi. In: Young LY, Cerniglia KE (eds) Microbial transformation and degradation of toxic organic chemicals. Wiley-Liss Inc, New York, pp 331–346

    Google Scholar 

  • Harayama S, Kasai Y, Hara A (2004) Microbial communities in oil contaminated seawater. Curr Opin Biotechnol 15:205–214

    Article  CAS  PubMed  Google Scholar 

  • Hoffman DJ, Rattner BA, Burton GA Jr, Cairns J Jr (eds) (2002) Handbook of ecotoxicology. CRC press, Hoboken

    Google Scholar 

  • Hong SH, Ryu H, Kim J, Cho KS (2011) Rhizoremediation of diesel-contaminated soil using the plant growth-promoting rhizobacterium Gordonia sp. S2RP-17. Biodegradation 22(3):593–601

    Article  CAS  PubMed  Google Scholar 

  • Hua SF, Song YY, Xia CG, Li SB (2011) Sequencing analysis of 16S rDNA and soluble methane monooxygenase genes from a methanotroph Methylosinus trichosporium IMV 3011. Ann Microbiol 61:391–396

    Article  CAS  Google Scholar 

  • Jenkins ME, Adams MA (2011) Respiratory quotients and Q10 of soil respiration in sub-alpine Australia reflect influences of vegetation types. Soil Biol Biochem 43:1266–1274

    Article  CAS  Google Scholar 

  • Jerina DM (1983) Metabolism of aromatic hydrocarbons by the cytochrome P450 system and epoxide hydrolase. Drug Metab Dispos 11:1–4

    CAS  PubMed  Google Scholar 

  • Jiang H, Chen Y, Murrell JC, Jiang P, Zhang C, Xing XH et al (2011) Methanotrophs: multifunctional bacteria with promising applications in environmental bioengineering. In: Comprehensive biotechnology: environmental biotechnology and safety, vol 6, 2nd edn. Elsevier, Amsterdam, pp 249–262

    Chapter  Google Scholar 

  • Kniemeyer O, Fischer T, Wilkes H, Glockner FO, Widdel F (2003) Anaerobic degradation of ethylbenzene by a new type of marine sulfate reducing bacterium. Appl Environ Microbiol 69:760–768

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kotani T, Yamamoto T, Yurimoto H, Sakai Y, Kato N (2003) Propane monooxygenase and NAD (+)-dependent secondary alcohol dehydrogenase in propane metabolism by Gordonia sp. strain TY-5. J Bacteriol 185:7120–7128

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • LabbĂ© D, Margesin R, Schinner F, Whyte LG, Greer CW (2007) Comparative phylogenetic analysis of microbial communities in pristine and hydrocarbon-contaminated Alpine soils. FEMS Microbiol Ecol 59(2):466–475

    Article  CAS  PubMed  Google Scholar 

  • Launen L, Pinto L, Wiebe C, Kiehlmann E, Moore M (1995) The oxidation of pyrene and benzo [a] pyrene by non-basidiomycete soil fungi. Can J Microbiol 41(6):477–488

    Article  CAS  PubMed  Google Scholar 

  • Leahy JG, Colwell RR (1990) Microbial degradation of hydrocarbons in the environment. Microbiol Rev 54(3):305–315

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lieberman RL, Shrestha DB, Doan PE, Hoffman BM, Stemmler TL, Rosenzweig AC (2003) Purified particulate methane monooxygenase from Methylococcus capsulatus (Bath) is a dimer with both mononuclear copper and a copper-containing cluster. Proc Natl Acad Sci U S A 100:3820–3825s

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lo Piccolo L, De Pasquale C, Fodale R, Puglia AM, Quatrini P (2011) Involvement of an alkane hydroxylase system of Gordoniasp strain SoCg in degradation of Solid n-Alkanes. Appl Environ Microbiol 77:1204–1213

    Article  CAS  PubMed  Google Scholar 

  • Margesin R, Schinner F (2001) Biodegradation and bioremediation of hydrocarbons in extreme environments. Appl Microbiol Biotechnol 56:650–663

    Article  CAS  PubMed  Google Scholar 

  • Margesin R, Labbe D, Schinner F, Greer CW, Whyte LG (2003) Characterization of hydrocarbon-degrading microbial populations in contaminated and pristine alpine soils. Appl Environ Microbiol 69:3085–3092

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Marin MM, Yuste L, Rojo F (2003) Differential expression of the components of the two alkane hydroxylases from Pseudomonas aeruginosa. J Bacteriol 185:3232–3237

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • May R, Schroder P, Sandermann HJ (1997) Ex-situ process for treating PAH contaminated soil with Phanerochaete chrysosporium. Environ Sci Technol 31:2626–2633

    Article  CAS  Google Scholar 

  • Medina-Bellver JI, MarĂ­n P, Delgado A, RodrĂ­guez-Sánchez A, Reyes E, Ramos JL, Marques S (2005) Evidence for in situ crude oil biodegradation after the Prestige oil spill. Environ Microbiol 7(6):773–779

    Article  CAS  PubMed  Google Scholar 

  • Mishra S, Jyot J, Kuhad RC, Lal B (2001) Evaluation of inoculum addition to stimulate in situ bioremediation of oily-sludge-contaminated soil. Appl Environ Microbiol 67:1675–1681

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 56:197–205

    Article  CAS  Google Scholar 

  • Pizarro-TobĂ­as P, Niqui JL, Roca A, Solano J, Fernández M, Bastida F, GarcĂ­a C, Ramos JL (2015) Field trial on removal of petroleum-hydrocarbon pollutants using a microbial consortium for bioremediation and rhizoremediation. Environ Microbiol Rep 7(1):85–94

    Article  CAS  PubMed  Google Scholar 

  • Rabus R, Kube M, Beck A, Widdel F, Reinhardt R (2002) Genes involved in the anaerobic degradation of ethylbenzene in a denitrifying bacterium, strain EbN1. Arch Microbiol 178:506–516

    Article  CAS  PubMed  Google Scholar 

  • Rahman KSM, Thahira-Rahman J, Lakshmanaperumalsamy P, Banat IM (2002) Towards efficient crude oil degradation by a mixed bacterial consortium. Bioresour Technol 85:257–261

    Article  CAS  PubMed  Google Scholar 

  • Rajasekar A, Anandkumar B, Maruthamuthu S, Ting YP, Rahman PKSM (2010) Characterization of corrosive bacterial consortia isolated from petroleum product transporting pipelines. Appl Microbiol Biotechnol 85:1175–1188

    Article  CAS  PubMed  Google Scholar 

  • Sarma PM, Bhattacharya D, Krishnan S, Lal B (2004) Degradation of polycyclic aromatic hydrocarbons by a newly discovered enteric bacterium, Leclercia adecarboxylata. Appl Environ Microbiol 70:3163–3166

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schneiker S, dos Santos VA, Bartels D, Bekel T, Brecht M, Buhrmester J, Chernikova TN, Denaro R, Ferrer M, Gertler C, Goesmann A (2006) Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat Biotechnol 24(8):997–1004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sierra-Garcia IN, de Oliveira VM (2013) Microbial hydrocarbon degradation: efforts to understand biodegradation in petroleum reservoirs. In: Biodegradation-engineering and technology. pp 47–72

    Google Scholar 

  • Silva IS, Grossman M, Durrant LR (2009) Degradation of polycyclic aromatic hydrocarbons (2–7 rings) under microaerobic and very-low-oxygen conditions by soil fungi. Int Biodeterior Biodegrad (2):224–229

    Google Scholar 

  • Singh H (2006) Mycoremediation: fungal bioremediation. Wiley, Hoboken

    Book  Google Scholar 

  • Singh SN (ed) (2012) Microbial degradation of xenobiotics, environmental science and engineering. Springer, Berlin/Heidelberg

    Google Scholar 

  • So CM, Phelps CD, Young LY (2003) Anaerobic transformation of alkanes to fatty acids by a sulfate-reducing bacterium, strain Hxd3. Appl Environ Microbiol 69:3892–3900

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sood N, Patle S, Lal B (2010) Bioremediation of acidic oily sludge-contaminated soil by the novel yeast strain Candida digboiensis TERI ASN6. Environ Sci Pollut Res 17:603–610

    Article  CAS  Google Scholar 

  • Steliga T, Jakubowicz P, Kapusta P (2012) Changes in toxicity during in situ bioremediation of weathered drill wastes contaminated with petroleum hydrocarbons. Bioresour Technol 125:1–10

    Article  CAS  PubMed  Google Scholar 

  • Sutherland JB, Rafii F, Khan AA, Cerniglia CE (1995) Mechanisms of polycyclic aromatic hydrocarbon degradation. In: Young LY, Cerniglia KE (eds) Microbial transformation and degradation of toxic organic chemicals. Wiley-Liss, New York, pp 269–306

    Google Scholar 

  • Swannell RPJ, Mitchell D, Lethbridge G, Jones D, Heath D, Hagley M, Jones M, Petch S, Milne R, Croxford R, Lee K (1999) A field demonstration of the efficacy of bioremediation to treat oiled shorelines following the Sea Empress incident. Environ Technol 20:863–873

    Article  CAS  Google Scholar 

  • Tortella GR, Diez MC, Duran N (2005) Fungal diversity and use in decomposition of environmental pollutants. Crit Rev Microbiol 31:197–212

    Article  CAS  PubMed  Google Scholar 

  • Uhlik O, Wald J, Strejcek M, Musilova L, Ridl J, Hroudova M, Vlcek C, Cardenas E, Mackova M, Macek T (2012) Identification of bacteria utilizing biphenyl, benzoate, and naphthalene in long-term contaminated soil. PloS One 7(7):e40653

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • van Beilen JB, Marin MM, Smits THM, Rothlisberger M, Franchini AG, Witholt B, Rojo F (2004) Characterization of two alkane hydroxylase genes from the marine hydrocarbonoclastic bacterium Alcanivorax borkumensis. Environ Microbiol 6:264–273

    Article  CAS  PubMed  Google Scholar 

  • 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 

  • Vanishree M, Thatheyus AJ, Ramya D (2014a) Biodegradation of petrol using Aspergillus sp. Ann Res Rev Biol 4(6):914

    Article  Google Scholar 

  • Vanishree M, Thatheyus AJ, Ramya D (2014b) Biodegradation of petrol using fungus Penicillium sp. Forensic Sci Int 2(1):26–31

    Google Scholar 

  • Vila J, MarĂ­a Nieto J, Mertens J, Springael D, Grifoll M (2010) Microbial community structure of a heavy fuel oil-degrading marine consortium: linking microbial dynamics with polycyclic aromatic hydrocarbon utilization. FEMS Microbiol Ecol 73:349–362

    CAS  PubMed  Google Scholar 

  • Wang W, Shao Z (2012) Genes involved in alkane degradation in the Alcanivorax hongdengensis strain A-11-3. Appl Microbiol Biotechnol 94:437–448

    Article  CAS  PubMed  Google Scholar 

  • Widdel F, Rabus R (2001) Anaerobic biodegradation of saturated and aromatic hydrocarbons. Curr Opin Biotechnol 12(3):259–276

    Article  CAS  PubMed  Google Scholar 

  • Wilkes H, Rabus R, Fischer T, Armstroff A, Behrends A, Widdel F (2002) Anaerobic degradation of n-hexane in a denitrifying bacterium: further degradation of the initial intermediate (1-methylpentyl)succinate via C-skeleton rearrangement. Arch Microbiol 177:235–243

    Article  CAS  PubMed  Google Scholar 

  • Yakimov MM, Timmis KN, Golyshin PN (2007) Obligate oil-degrading marine bacteria. Curr Opin Biotechnol 18(3):257–266

    Article  CAS  PubMed  Google Scholar 

  • Yousaf V, Andria T, Reichenauer G, Smalla K, Sessitsch A (2010) Phylogenetic and functional diversity of alkane degrading bacteria associated with Italian ryegrass (Lolium multiflorum) and birds foot trefoil (Lotus corniculatus) in a petroleum oil contaminated environment. J Hazard Mater 184:523–532

    Article  CAS  PubMed  Google Scholar 

  • Yu XZ, Wu SC, Wu FY, Wong MH (2011) Enhanced dissipation of PAHs from soil using mycorrhizal ryegrass and PAH-degrading bacteria. J Hazard Mater 186(2):1206–1217

    Article  CAS  PubMed  Google Scholar 

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Acknowledgment

The authors would like to acknowledge the authorities of The American College, Madurai, Tamil Nadu, India, for their encouragement.

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Authors and Affiliations

  1. Department of Immunology and Microbiology, The American College, Madurai, India

    A. Deborah Gnana Selvam

  2. PG & Research Department of Zoology, The American College, Madurai, Tamil Nadu, India

    A. Joseph Thatheyus

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  1. A. Deborah Gnana Selvam
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Editors and Affiliations

  1. Himalayan School of Biosciences, Swami Rama Himalayan University, Dehradun, Uttarakhand, India

    Vivek Kumar

  2. Centre for Life Sciences, Central University of Jharkhand, Ranchi, Jharkhand, India

    Manoj Kumar

  3. Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh, India

    Ram Prasad

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Deborah Gnana Selvam, A., Thatheyus, A.J. (2018). Microbial Degradation of Petroleum Hydrocarbons: An Overview. In: Kumar, V., Kumar, M., Prasad, R. (eds) Microbial Action on Hydrocarbons. Springer, Singapore. https://doi.org/10.1007/978-981-13-1840-5_19

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