Microbial Degradation of Recalcitrant PAHs-Microbial Diversity Involving Remediation Process

  • Shelly Sinha
  • Pritam Chattopadhyay
  • Sukanta K. Sen
Part of the Environmental Science and Engineering book series (ESE)


Domestic pollutants, largely due to population explosion and industrial inputs lead to the accumulation of various types of recalcitrant xenobiotic compounds (Hadibarata et al. 2009; Igwo-Ezikpe et al. 2010). As majority of them persist for longer period of time and are carcinogenic in nature, their disposal is a matter of global concern (Jain et al. 2005). Primarily, xenobiotic compounds are anonymous to living organisms and also have a tendency to get accumulated in the environment (Sinha et al. 2009). They encompass pesticides, fuels, solvents, alkanes, synthetic azo dyes, polyaromatic, nitroaromatic, chlorinated and polycyclic hydrocarbons. Amongst them, the presence of polycyclic aromatic hydrocarbons (PAHs) in the environment causes acute health hazard with their intrinsic chemical stability, high recalcitrance ability against different types of degradation and high toxicity to living organisms for their mutagenic or carcinogenic properties (Zhang et al. 2006). Apart from it, they are ubiquitous and prevail as persistent bioaccumulative toxins (PBT) (NiChadhain et al. 2006). For instance, phenanthrene, a lipophilic and relatively insoluble in water, is skin photosensitizer and mild allergenic to human (Hafez et al. 2008). It is also found as an inducer of the sister chromatid exchange process (Popp et al. 1997) and a potent inhibitor of gap-junction intercellular communications (Bláha et al. 2002).


Metagenomic Library Catabolic Gene Pyrene Degradation Phenanthrene Degradation Naphthalene Degradation 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



Authors are thankful to Department of Botany (DST-FIST and UGC-DRS sponsored), Visva-Bharati, for necessary support.


  1. Adriaens P, Vogel TM (1995) Biological treatment of chlorinated organics. In: Young LY, Cerniglia CE (eds) Microbial transformation and degradation of toxic organic chemicals. Wiley-Liss, New York, pp 435–486Google Scholar
  2. Basta T, Buerger S, Stolz A (2005) Structural and replicative diversity of large plasmids from sphingomonads that degrade polycyclic aromatic compounds and xenobiotics. Microbiology 151:2025–2037CrossRefGoogle Scholar
  3. Bedessem ME, Swoboda-Colberg NG, Colberg PJS (1997) Naphthalene mineralization coupled to sulfate reduction in aquifer-derived enrichments. FEMS Microbiol Lett 152:213–218CrossRefGoogle Scholar
  4. Bláha L, Kapplová P, Vondrá?ek J, Upham B, Machala M (2002) Inhibition of gap-junctional intercellular communication by environmentally occurring polycyclic aromatic hydrocarbons. Toxicol Sci 65:43–51CrossRefGoogle Scholar
  5. Bosch R, García-Valdés E, Moore ERB (1999) Genetic characterization and evolutionary implications of a chromosomally encoded naphthalene-degradation upper pathway from Pseudomonas stutzeri AN10. Gene 236:149–157CrossRefGoogle Scholar
  6. Bosch R, García-Valdés E, Moore ERB (2000) Complete nucleotide sequence and evolutionary significance of a chromosomally encoded naphthalene-degradation lower pathway from Pseudomonas stutzeri AN10. Gene 245:65–74CrossRefGoogle Scholar
  7. Boyd DR, Sharma ND, Hempenstal F, Kennedy MA, Malone JF, Allen CCR, Rensnick SM, Gibson DT (1999) Bis-cis-dihydrodiols: a new class of metabolites from biphenyl dioxygenase-catalyzed sequential asymmetric cis-dihydroxylation of polycyclic arenas and heteroarenes. J Org Chem 64:4005–4011CrossRefGoogle Scholar
  8. Caldini G, Cenci G, Manenti R, Morozzi G (1995) The ability of an environmental isolate of Pseudomonas fluorescens to utilize chrysene and other four-ring polynuclear aromatic hydrocarbons. J Appl Microbiol Biotechnol 44:225–229CrossRefGoogle Scholar
  9. Cerniglia CE (1984) Microbial metabolism of polycyclic aromatic hydrocarbons. Adv Appl Microbiol 30:31–71CrossRefGoogle Scholar
  10. Cerniglia CE (1992) Biodegradation of polycyclic aromatic hydrocarbons. Biodegradation 3:351–368CrossRefGoogle Scholar
  11. Chang W, Um Y, Hoffman B, Holoman TCR (2005) Molecular characterization of polycyclic aromatic hydrocarbon (PAH) degrading methanogenic communities. Biotechnol Prog 21:682–688CrossRefGoogle Scholar
  12. Chauhan A, Faziur R, Oakeshott JG, Jain RK (2008) Bacterial metabolism of polycyclic aromatic hydrocarbons: strategies for bioremediation. J Ind Microbiol 48:95–113CrossRefGoogle Scholar
  13. Chen SH, Aitken MD (1999) Salicylate stimulates the degradation of high molecular weight polycyclic aromatic hydrocarbons by Pseudomonas saccharophila P15. Environ Sci Technol 33:435–439CrossRefGoogle Scholar
  14. Cho JC, Kim SJ (2001) Detection of mega plasmid from polycyclic aromatic hydrocarbon-degrading Sphingomonas sp. strain KS14. J Mol Microbiol Biotechnol 3:503–506Google Scholar
  15. Chowdhury A, Pradhan S, Saha M, Sanyal N (2008) Impact of pesticides on soil microbiological parameters and possible bioremediation strategies. J Ind Microbiol 48:114–127CrossRefGoogle Scholar
  16. Dennis JJ, Zylstra GJ (2004) Complete sequence and genetic organization of pDTG1, the 83 kilobase naphthalene degradation plasmid from Pseudomonas putida strain NCIB 9816-4. J Mol Biol 341:753–768CrossRefGoogle Scholar
  17. Dhote M, Juwarkar A, Kumar A, Kanade GS, Chakrabarti T (2010) Biodegradation of chrysene by the bacterial strains isolated from oily sludge. World J Microbiol Biotechnol 26:329–335CrossRefGoogle Scholar
  18. Diaz E (2004) Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility. Ind Microbiol 7:173–180Google Scholar
  19. Dunn NW, Gunsalus IC (1973) Transmissible plasmid coding early enzymes of naphthalene oxidation in Pseudomonas putida. J Bacteriol 114:974–979Google Scholar
  20. Evans WC, Fernley HN, Griffiths E (1965) Oxidative metabolism of phenanthrene and anthracene by soil pseudonads. Biochem J 95:819–831Google Scholar
  21. Fetzer JC (2000) The chemistry and analysis of the large polycyclic aromatic hydrocarbons. In: Fetzer JC (ed) Polycyclic aromatic compounds. Wiley, New York, pp 27–143Google Scholar
  22. Gibson J, Harwood CS (2002) Metabolic diversity in aromatic compound utilization by anaerobic microbes. Ann Rev Microbiol 56:345–369CrossRefGoogle Scholar
  23. Hadibarata T, Tachibana S, Itoh K (2009) Biodegradation of chrysene, an aromatic hydrocarbon by Polyporus sp. S133 in liquid medium. J Hazard Mater 164:911–917CrossRefGoogle Scholar
  24. Hafez EE, Rashad M, Abd-Elsalam HE, Hanafy AA (2008) The polyaromatic hydrocarbons as a serious environmental pollutants and the role of bioremediation to overcome this problem. In: Basu SK, Datta BS (eds) Environment, health and nutrition—global issues. APH Publishing Corporation, New DelhiGoogle Scholar
  25. Heitkamp MA, Cerniglia CE (1988) Mineralization of polycyclic aromatic hydrocarbons by a bacterium isolated from sediment below an oil field. Appl Environ Microbiol 54:1612–1614Google Scholar
  26. Hilyard EJ, Jones-Meehan JM, Spargo BJ, Hill RT (2008) Enrichment, isolation, and phylogenetic identification of polycyclic aromatic hydrocarbon-degrading bacteria from Elizabeth river sediments. Appl Environ Microbiol 74:1176–1182CrossRefGoogle Scholar
  27. Hinchee RE, Leeson A, Ong SK, Semprini L (1994) Bioremediation of chlorinated and polycyclic aromatic hydrocarbon compounds. Lewis Publishers, LondonGoogle Scholar
  28. Igwo-Ezikpe MN, Gbenle OG, Ilori MO (2006) Growth study on chrysene degraders isolated from polycyclic aromatic hydrocarbon polluted soils in Nigeria. Afr J Biotechnol 5:823–828Google Scholar
  29. Igwo-Ezikpe MN, Gbenle OG, Ilori MO, Okpuzor J, Osuntoki AA (2010) High molecular weight polycyclic aromatic hydrocarbons biodegradation by bacteria isolated from contaminated soils in Nigeria. Res J Environ Sci 4:127–137CrossRefGoogle Scholar
  30. Jain RK, Kapur M, Labana S, Lal B, Sarma PM, Bhattacharya D, Thakur IS (2005) Microbial diversity: application of micro-organisms for the biodegradation of xenobiotics. Curr Sci 89:101–112Google Scholar
  31. Johnsen AR, Wickb JY, Harms H (2005) Principles of microbial PAH-degradation in soil. Environ Pollut 133:71–84CrossRefGoogle Scholar
  32. Juhasz AL, Naidu R (2000) Bioremediation of high molecular weight polycyclic aromatic hydrocarbons: a review of the microbial degradation of benzo[?]pyrene. Int Biodeterior Biodegrad 45:57–88CrossRefGoogle Scholar
  33. Kanaly RA, Bartha R, Watanabe K, Harayama S (2000a) Rapid mineralization of benzo[?]pyrene by a microbial consortium growing on diesel fuel. Appl Environ Microbiol 66:4205–4211CrossRefGoogle Scholar
  34. Kanaly RA, Harayama S, Watanabe K (2000b) Biodegradation of high molecular-weight polycyclic aromatic hydrocarbons by bacteria. J Bacteriol 182:2059–2067CrossRefGoogle Scholar
  35. Karthikeyan R, Bhandari A (2001) Anaerobic biotransformation of aromatic and polycyclic aromatic hydrocarbons in soil microcosms: a review. J Hazard Subst Res 3:1–19Google Scholar
  36. Khan AA, Wang RF, Cao WW, Doerge DR, Wennerstrom D, Cerniglia CE (2001) Molecular cloning, nucleotide sequence and expression of genes encoding a polycyclic ring dioxygenase from Mycobacterium sp. strain PYR-1. Appl Environ Microbiol 67:3577–3585CrossRefGoogle Scholar
  37. Kim JD, Shim SH, Lee CG (2005a) Degradation of phenanthrene by bacterial strains isolated from soil in oil refinery fields in Korea. J Microbiol Biotechnol 15:337–345Google Scholar
  38. Kim YH, Freeman JP, Moody JD, Engesser KH, Cerniglia CE (2005b) Effects of pH on the degradation of phenanthrene and pyrene by Mycobacterium vanbaalenii PYR-1. Appl Microbiol Biotechnol 67:275–285CrossRefGoogle Scholar
  39. Kim SJ, Kweon O, Jones RC, Edmondson RD, Cerniglia CE (2007) Complete and integrated pyrene degradation pathway in Mycobacterium vanbaalenii PYR-1 based on system biology. J Bacteriol 189:464–472CrossRefGoogle Scholar
  40. Kim SJ, Kweon O, Jones RC, Edmondson RD, Cerniglia CE (2008) Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1. Biodegradation 19:259–881CrossRefGoogle Scholar
  41. Kumar G, Singla R, Kumar R (2010) Plasmid associated anthracene degradation by Pseudomonas sp isolated from filling station site. Nat Sci 8:89–94Google Scholar
  42. Liang Y, Gardener D, Miller CD, Chen D, Anderson AJ, Weimer BC, Sims RC (2006) Study of biochemical pathways and enzymes involved in pyrene degradation by Mycobacterium sp. strain KMS. Appl Environ Microbiol 72:7821–7828CrossRefGoogle Scholar
  43. Liu SL, Luo YM, Cao ZH, Wu LH, Ding KQ, Christie P (2004) Degradation of benzo[?]pyrene in soil with arbuscular mycorrhizal alfalfa. Environ Geochem Health 26:285–293CrossRefGoogle Scholar
  44. Lloyd-Jones G, Laurie AD, Hunter DWF, Fraser R (1999) Analysis of catabolic genes for naphthalene and phenanthrene degradation in contaminated New Zealand soils. FEMS Microbiol Ecol 29:69–79CrossRefGoogle Scholar
  45. Luch A (2005) The carcinogenic effects of polycyclic aromatic hydrocarbons. Imperial College Press, LondonCrossRefGoogle Scholar
  46. Ma Y, Wang L, Shao Z (2006) Pseudomonas, the dominant polycyclic aromatic hydrocarbon-degrading bacteria isolated from Antarctic soils and the role of large plasmids in horizontal gene transfer. Environ Microbiol 8:455–465CrossRefGoogle Scholar
  47. Mallick S, Chatterjee S, Dutta TK (2007) A novel degradation pathway in the assimilation of phenanthrene by Staphylococcus sp. strain PN/Y via meta-cleavage of 2-hydroxy-1-naphthoic acid: formation of trans-2,3-dioxo-5-(2?-hydroxyphenyl)-pent-4-enoic acid. Microbiology 153:2104–2115CrossRefGoogle Scholar
  48. Meckenstock RU, Annweiler E, Michaelis W, Richnow HH, Schink B (2000) Anaerobic naphthalene degradation by a sulfate reducing enrichment culture. Appl Environ Microbiol 66:2743–2747CrossRefGoogle Scholar
  49. Mishra V, Lal R, Srinivasan C (2001) Enzymes and operons mediating xenobiotic degradation in bacteria. Crit Rev Microbiol 27:133–166CrossRefGoogle Scholar
  50. Mrojik A, Piotrowska-Seget Z, Labuzek S (2003) Bacterial degradation and bioremediation of polycyclic aromatic hydrocarbons. Pol J Environ Stud 12:15–25Google Scholar
  51. NiChadhain SM, Norman RS, Pesce KV, Kukor JJ, Zylstra GJ (2006) Microbial dioxygenase gene population shifts during polycyclic aromatic hydrocarbon biodegradation. Appl Environ Microbiol 72:4078–4087CrossRefGoogle Scholar
  52. Peng RH, Xiong AS, Xue Y, Fu XY, Gao F, Zhao W, Tian YS, Yao QH (2008) Microbial biodegradation of polyaromatic hydrocarbons. FEMS Microbiol Rev 32:927–955CrossRefGoogle Scholar
  53. Pfeifer A, Mark G, Leung S, Dougherty M, Spillare E, Kasid U (1998) Effects of c-raf-1 and c-myc expression on radiation response in an in vitro model of human small-cell-lung carcinoma. Biochem Biophys Res Commun 252:481–486CrossRefGoogle Scholar
  54. Phale PS, Basu A, Majhi PD, Deveryshetty J, Vamsee-Krishna C, Shrivastava R (2007) Metabolic diversity in bacterial degradation of aromatic compounds OMICS. J Integr Biol 11:252–279Google Scholar
  55. Popp W, Vahrenholz C, Schell C, Grimmer G, Dettbarn G, Kraus R, Brauksiepe A, Schmeling B, Gutzeit T, Von-Bülow T, Norpoth K (1997) DNA single strand breakage, DNA adducts, and sister chromatid exchange in lymphocytes and phenanthrene and pyrene metabolites in urine of coke oven workers. Occup Environ Med 54:176–183CrossRefGoogle Scholar
  56. Sarma PM, Duraja P, Deshpande S, Lal B (2010) Degradation of pyrene by an enteric bacterium, Leclercia adecarboxylata PS4040. Biodegradation 21:59–69CrossRefGoogle Scholar
  57. Schloss PD, Handelsman J (2003) Biotechnological prospects from metagenomics. Curr Opin Microbiol 14:303–310Google Scholar
  58. Schneegurt-Mark A, Kulpa-Charler FJR (1998) The application of molecular techniques in environmental biotechnology for monitoring microbial systems. Biotechnol Appl Biochem 27:73–79CrossRefGoogle Scholar
  59. Sheng XF, He LY, Zhou L, Shen YY (2009) Characterization of Microbacterium sp. F10a and its role in polycyclic aromatic hydrocarbon removal in low-temperature soil. Can J Microbiol 55:529–535CrossRefGoogle Scholar
  60. Singh DK (2008) Biodegradation and bioremediation of pesticide in soil: concept, method and recent developments. Ind J Microbiol 48:35–40CrossRefGoogle Scholar
  61. Sinha S, Chattopadhyay P, Pan I, Chatterjee S, Chanda P, Bandyopadhyay D, Das K, Sen SK (2009) Microbial transformation of xenobiotics for environmental bioremediation. Afr J Biotechnol 8:6016–6027Google Scholar
  62. Smith JR, Nakles DV, Sherman DF, Neuhauser EF, Loehr RC (1989) Environmental fate mechanisms influencing biological degradation of coal-tar derived poly-nuclear-aromatic-hydrocarbons in soil system. In: Proceeding of 3rd international conference on new frontiers for hazardous waste management, US Environmental Protection Agency, Washington DC, pp 397–405Google Scholar
  63. Taranenko NI, Hurt R, Zhou J, Isola NR, Huang H, Lee SH, Chen CH (2002) Laser desorption mass spectrometry for microbial DNA analysis. J Microbiol Method 48:101–106CrossRefGoogle Scholar
  64. Walter U, Beyer M, Klein J, Rehm HJ (1991) Degradation of pyrene by Rhodococcus sp. UW1. Appl Microbiol Biotechnol 34:671–676CrossRefGoogle Scholar
  65. Xue W, Warshawsky D (2005) Metabolic activation of polycyclic and heterocyclic aromatic hydrocarbons and DNA damage: a review. Toxicol Appl Pharm 206:73–93CrossRefGoogle Scholar
  66. Zhang XX, Cheng SP, Zhu CJ, Sun SL (2006) Microbial PAH-degradation in soil: degradation pathways and contributing factors. Pedosphere 16:555–565CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg  2012

Authors and Affiliations

  • Shelly Sinha
    • 1
  • Pritam Chattopadhyay
    • 2
  • Sukanta K. Sen
    • 3
  1. 1.Rabindra MahavidyalayaChampadangaHooghlyIndia
  2. 2.Plant Biotechnology Laboratory, Department of BotanyVisva-BharatiSantiniketanIndia
  3. 3.Microbiology Division, Department of BotanyVisva-BharatiSantiniketanIndia

Personalised recommendations