In vitro degradation of polycyclic aromatic hydrocarbons by Sphingobium xenophagum, Bacillus pumilus and Pseudomonas plecoglossicida

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Research Paper 01/04/2015
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In vitro degradation of polycyclic aromatic hydrocarbons by Sphingobium xenophagum, Bacillus pumilus and Pseudomonas plecoglossicida

Imaneh Amini, Arezoo Tahmourespour, Atousa Abdollahi, Mansour Bayat
J. Bio. Env. Sci.6( 4), 246-259, April 2015.
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Polycyclic aromatic hydrocarbons are a class of organic compounds with carcinogenic and genotoxic properties. Biodegradation of such pollutants using microorganisms, especially bacteria, would be a cheap and environmentally safe clean up method. In the present study, a total of 30 anthracene, phenanthrene and pyrene degrading bacteria were isolated from two petroleum contaminated soils in Isfahan-Iran using enrichment technique. Three isolates, showing the highest growth and the lowest pH in their media, were considered as the best hydrocarbon degraders. These isolates were identified to be Sphingobium xenophagum ATAI16, Bacillus pumilus ATAI17 and Pseudomonas plecoglossicida ATAI18 using 16S rDNA gene sequences analyses, and were submitted to GenBank under accession number of KF040087, KF040088 and KF113842, respectively. They were able to degrade 43.31% of phenanthrene, 56.94% of anthracene and 45.32% of pyrene after 9 days, respectively. Strain ATAI18 produced dioxygenase enzyme as an important metabolite for hydrocarbon degradation. The production of biosurfactant was reported positive for both strains of ATAI17 and ATAI18. It was concluded that these three new strains could be used to improve the bioremediation process in a polluted area.


Arulazhagan P, Vasudevan N, Yeom IT. 2010. Biodegradation of polycyclic aromatic hydrocarbon by a halotolerant bacterial consortium isolated from marine environment. International Journal of Environmental Science & Technology 7, 639-652.

Bahrami AR, Mohammad Fam I, Donaldson J. 2004. Development of a thermal desorption method for the analysis of particle associated polycyclic aromatic hydrocarbons in ambient air. International Journal of Environmental Science & Technology 1, 165-169.

Balogun SA, Fagade OE. 2008. Screening for surface-active agent producing bacteria from diesel oil polluted tropical soil. World Applied Science Journal 3, 930-933.

Bennett RM, Dagamac NHA, Fernandez EVM, Uba MO, Ching MW. 2012. In vitro degradation of anthracene by Mycobacterium sp. GIPAH-01 isolated from Guimaras island, Philippines. Asian journal of experimental biological sciences 3, 682-687.

Bin M, Huai HC, Yan H, Jian MX. 2010. Isolations and consortia of PAH-degrading bacteria from the rhizosphere of four crops in PAH-contaminated field. Paper presented in 19th World Congress of Soil Science, Soil Solutions for a Changing World, Australia: Brisbane, August 63-66.

Bin TY, Xu Y, Yan CF, ling JR, gang WX. 2011. Screening, identification and degrading gene assignment of a chrysene-degrading strain. African Journal of Biotechnology 10, 6549-6557.

Chadhain SMN, Norman RS, Pesce KV, Kukor JJ, Zylstra GJ. 2006. Microbial dioxygenase gene population shifts during polycyclic aromatic hydrocarbon biodegradation. Applied and Environmental Microbiology 72, 4078-4087.

Coral G, Karagoz S. 2005. Isolation and characterization of phenanthrene degrading bacteria from a petroleum refinery soil. Annals of Microbiology 55, 255-259.

Cui CZ, Zeng C, Wan X, Chen D, Zhang JY, Shen P. 2008. Effect of rhamnolipids on degradation of anthracene by two newly isolated strains, Sphingomonassp. 12A and Pseudomonas sp. 12B. Journal of Microbiology and Biotechnology 18, 63-66.

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. Bioresource Technology 98, 1339–1345.

Das N, Chandran P. 2011. Microbial degradation of petroleum hydrocarbon contaminants: an overview. Biotechnology Research International 2011, 1-13.

De Salle R, Giribet G, Wheeler W. 2002. Techniques in Molecular Systematics and Evolution.Birkhäuser. Basel: springer.

Fritsche W, Hofrichter M. 2008. Aerobic Degradation by Microorganisms. In: Rehm HJ, Reed G (ed) Biotechnology, 2nd edn., Weinheim, Germany: Wiley-VCH Verlag GmbH, 145-155.

Garrity GM, Brenner DJ, Krieg NR, Staley JT. 2005.  Bergey’s  Manual  of  Systematic  Bacteriology. New York: Springer.

Guo C, Dang Z, Wong Y, Tam NF. 2010. Biodegradation ability and dioxgenase genes of PAH-degrading Sphingomonas and Mycobacterium strains isolated from mangrove sediments. International Biodeterioration & Biodegradation 64, 419-426.

Hertel RF, Rosner G, Kielhorn J, Menichini E, Grover PL, Blok J. 1998. Selected non-heterocyclic polycyclic aromatic hydrocarbon. World Health Organization, Geneva, Environmental Health Criteria

Jain PK, Bajpai V. 2012. Biotechnology of bioremediation- a review. International Journal of Environmental Sciences 3, 535-549.

John RC, Essien JP, Akpan SB, Okpokwasili GC. 2012. Polycyclic Aromatic Hydrocarbon-degrading Bacteria from Aviation Fuel Spill Site at Ibeno, Nigeria. Bulletin of Environmental Contamination and Toxicology 88, 1014–1019.

Kertesz MA, Kawasaki A. 2010.  Hydrocarbon-Degrading Sphingomonads: Sphingomonas, Sphingobium, Novosphingobium, and Sphingopyxis. In: Timmis KN (ed) Handbook of Hydrocarbon and Lipid Microbiology. Berlin: Springer-Verlag, 1693-1705.

Khanna P, Goyal D, Khanna S. 2012. Characterization of pyrene utilizing Bacillus spp. from crude oil contaminated soil. Brazilian Journal of Microbiology 43, 606-617.

Kumar A, Munjal A, Sawhney R. 2011. Crude oil constitution, degradation pathway and associated bioremediation microflora: an overview. International Journal of Environmental Sciences 1, 1420-1439.

Kumar M, Leona V, Materano AS, Ilzinsa O, Castro IG, Fuenmayor SL. 2006. Polycyclic aromatic hydrocarbon degradation by biosurfactant-producing Pseudomonas sp. IR1. Z. Naturforsch 61, 203-212.

Lily MK, Bahuguna A, Dangwal K, Garg V. 2009. Degradation of benzo[a]pyrene by a novel strain Bacillus subtilis BMT4i (MTCC 9447). Brazilian Journal of Microbiology 40, 884-892.

Madueno L, Coppotelli BM, Alvarez HM, Morelli IS. 2011. Isolation and characterization of indigenous soil bacteria for bioaugmentation of PAH contaminated soil of semiarid Patagonia, Argentina. International Biodeterioration & Biodegradation 65, 345-351.

Naama JH, Khalil N, Fattal AH. 2010. Study of Degrading Some Petroleum Cuts by Bacteria. Journal of Chemical and Pharmaceutical Research 2, 772-784.

Nie M, Yin X, Ren C, Wang Y, Xu F, Shen Q. 2010. Novel rhamnolipidbiosurfactants produced by a polycyclic aromatic hydrocarbon-degrading bacterium Pseudomonas aeruginosa strain NY3. Biotechnology advances 28, 635-43.

Nishimori E, Kita-Tsukamoto K, Wakabayashi H. 2000. Pseudomonas plecoglossicidasp. nov., the causative agent of bacterial haemorrhagic ascites of ayu, Plecoglossusaltivelis. International Journal of Systematic and Evolutionary Microbiology 50, 83– 89.

Nnamchi CI, Obeta JAN, Ezeogu LI. 2006. Isolation and characterization of some polycyclic aromatic hydrocarbon degrading bacteria from Nsukka soils in Nigeria. International Journal of Environmental Science & Technology 3, 181-190.

Nwinyi OC. 2012. Molecular and physiological studies on bacterial degradation of polynuclear aromatic hydrocarbons. Ph.D thesis, University of Ota, Nigeria.

Obayori OS, Ilori MO, Adebusoye SA, Oyetibo GO, Amund OO. 2008. Pyrene-degradation potentials of Pseudomonas species isolated from polluted tropical soils. World Journal of Microbiology and Biotechnology 24, 2639-2646.

Ping L, Zhang C, Zhu Y, Wu M, Hu X, Li Z, Zhao H. 2011. Biodegrading of pyrene by a newly isolated Pseudomonas putidaPL2. Biotechnology and Bioprocess Engineering 16, 1000-1008.

Pinyakong O, Habe H, Supaka N, Pinpanichkarn P, Juntongjin K, Yoshida T, Furihata K, Nojiri H, Yamane H, Omori T. 2000. Identification of novel metabolites in the degradation of phenanthrene by Sphingomonas sp. strain P2. FEMS Microbiology Letters 191, 115-121.

Płociniczak MP, Płaza GA, Seget ZP, Cameotra SS. 2011. Environmental applications of biosurfactants: recent advances. International Journal of Molecular Sciences 12, 633-654.

Rasdy NFA, Sanagi MM, Ibrahim WAW, Abu Naim A. 2008. Determination of polycyclic aromatic hydrocarbons in palm oil mill effluent by soxhlet extraction and gas chromatography-flame ionization detection. The Malaysian Journal of Analytical Sciences 12, 16-21.

Richards LA. 1954. Diagnosis and improvement of saline and alkali soils. United States, Washington: USDA Agricultural Handbook.

Roy M, Khara P, Basu S, Dutta TK. 2013. Catabolic Versatility of Sphingobium sp. Strain PNB Capable of Degrading Structurally Diverse Aromatic Compounds. Bioremediation & Biodegradation 4, 1-6.

Safahiyeh AR, Mojoodi F, Zolgharnein H. 2011. Evaluation and Comparison of the Ability of Indigenous Pseudomonas Bacteria from Musa creek to remove poly Aromatic Compounds. Journal of Environmental Studies 37, 149-158.

Schuler L, Jouanneau Y, Chadhain SMN, Meyer C, Pouli M, Zylstra GJ, Hols P Agathos SN. 2009. Characterization of a ring- hydroxylatingdioxygenase from phenanthrene-degrading Sphingomonas sp. strain LH128 able to oxidize benz[a]anthracene. Applied Microbiology and Biotechnology 83, 465–475.

Seo JS, Keum YS, Li QX. 2009. Bacterial Degradation of Aromatic Compounds. International Journal of Environmental Research and Public Health 6, 278- 309.

Shokrollahzadeh S, Golmohammad F, Shokouhi H. 2012. Study of Sphingopyxisisolates in degradation of polycyclic aromatic hydrocarbons. Chemical Engineering Transactions 27, 55-60.

Stolz A, Maag CS, Denner EBM, Busse HJ, Egli T, Kampfer P. 2000. Description of Sphingomonasxenophagasp. nov.for strains BN6T and N,N which degrade xenobiotic aromatic compounds. International Journal of Systematic and Evolutionary Microbiology 50, 35–41.

Satomi  M,  La  Duc  MT,  Venkateswaran  K. 2006. Bacillus safensis sp. nov., isolated from spacecraft and assembly-facility surfaces. International Journal of Systematic and Evolutionary Microbiology 56, 1735–1740.

Story SP, Parker SH, Hayasaka SS, Riley MB, Kline EL. 2001. Convergent and divergent points in catabolic pathways involved in utilization of fluoranthene, naphthalene, anthracene, and phenanthrene by Sphingomonaspaucimobilisvar. EPA505. Journal of Industrial Microbiology and Biotechnology 26, 369-82.

Tao XQ, Lu GN, Dang Z, Yang C, Yi XY. 2007. A phenanthrene-degrading strain Sphingomonas sp. GY2B isolated from contaminated soils. Process Biochemistry 42, 401–408.

Toledo FL, Calvo C, Rodelas B, Gonzales-Lopez J. 2006. Selection and Identification of Bacteria Isolated from Waste Crude oil with Polycyclic Aromatic Hydrocarbons Removal Capacity. Systematic and Applied Microbiology 29, 244-252.

Tulevaa B, Christova N, Jordanov B, Damyanova BN, Petrov P. 2005. Naphthalene Degradation and Biosurfactant Activity by Bacillus cereus 28BN. Z Naturforsch 60, 577-582.

Vos  PD,  Garrity  GM,  Jones  D,  Krieg  NR, Ludwig W, Rainey FA, Schleifer KH. Whitman WB. 2009. Bergey’s  Manual of  Systematic Bacteriology. New York: Springer.

Ward  OP.  2010.  Microbial  biosurfactants  and biodegradation. Advances in Experimental Medicine and Biology 672, 65-74.

Wick AF, Haus NW, Sukkariyah BF, Haering KC, Daniel WL. 2011. Remediation of PAH- contaminated soils and sediments: A literature review. CSES Department, Internal Research Document.

Winter JP, Behan-Pelletier VM. 2007. Microarthropods. In: Gregorich EG, Carter MR (ed) Soil Sampling and Methods of Analysis. USA: CRC Press Taylor & Francis.