Genetic identification of hydrocarbons degrading bacteria isolated from oily sludge? and petroleum-contaminated soil in Basrah City, Iraq
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Abstract. Aboud EM, Burghal AA, Laftah AH. 2021. Genetic identification of hydrocarbons degrading bacteria isolated from oily sludge? and petroleum-contaminated soil in Basrah City, Iraq. Biodiversitas 22: 1934-1939. Petroleum is a major problem for environmental pollution due to the extensive use, which can reach all parts of the environment. Contaminated environments are required to identify bacterial diversity that has a remarkable ability to tolerate and biodegrade toxic compounds. The process of oil degradation by microorganisms in their natural environment is affected by certain chemical, physical and biological conditions. Bioremediation techniques are powerful for removing oil pollution, which reflects the ability of microorganisms to destroy organic pollutants. In the current study, six bacterial isolates (S1-S6) were isolated from oil-contaminated soils. mineral salt medium (MSM) was used to carry out biodegradation, crude oil degradation was an evaluation by the gravimetric method. After two weeks of incubation showed S5 isolate the greatest efficiency in oil degradation 53.6%, S1 and S6 also gave good capability degradation (47.31% and 44.9%) respectively, while isolates S2 and S3 gave the lowest percentage. All isolates were identified by 16S rDNA amplicons as Pseudomonas stutzeri, Psychrobacter faecalis, Pseudomonas songnenensis, Bacillus cereus, Psychrobacter quanticus strain E9R, and Psychrobacter quanticus strain EA422 according to molecular identification. The current study indicated that hydrocarbon-degrading bacteria specially Psychrobacter can be used to clean soil from crude oil and other industrial discharges.
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References
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Kumari N, Vashishtha A, Saini P, Menghani E. 2013. Isolation, identification and characterization of oil ?degrading ?bacteria isolated from the contaminated sites of Barmer, Rajasthan. Int J Biotechnol ?Bioeng Res 4 (5): 429-436.?
Lane D.J. 1991. 16S/23S rRNA sequencing in: Nucleic acid techniques in bacterial systematic. (eds). Stackebrandt E, ?Goodfellow M. John Wiley & Sons, Ltd. Chichester England.?
Li H, Wang X-L, Mu B-Z, et al. 2013. Molecular detection, quantification and distribution of alkane-?degrading bacteria in ?production water from low temperature oilfields. Int Biodeterior ?Biodegradation. 76: 49-57.? DOI: ??10.1016/j.ibiod.2012.06.007?
Litvinenko V. 2020. The role of hydrocarbons in the global energy agenda: The focus on liquefied natural gas. ?Resources ??9 (5): 59.? DOI: 10.3390/resources9050059?
Liu J, Xie X, Xiao S, Wang X, Zhao W, Tian Z. 2007. Isolation of Leptospirillum ferriphilum by single-layered ?solid ?medium. J Cent South Univ Technol 14 (4): 467-473.? DOI: 10.1007/s11771-007-0091-3?
Mansur AA, Taha M, Shahsavari E, Haleyur N, Adetutu EM, Ball AS. 2016. An effective soil slurry ?bioremediation ?protocol for the treatment of Libyan soil contaminated with crude oil tank bottom ?sludge. Int Biodeterior ?Biodegradation 115: 179-185.? DOI: 10.1016/j.ibiod.2016.08.015?
Margesin R, Schinner F. 2001. Biodegradation and bioremediation of hydrocarbons in extreme environments. ?Appl ?Microbiol Biotechnol 56 (5): 650-663.? DOI: 10.1007/s002530100701.?
Maruyama A, Honda D, Yamamoto H, Kitamura K, Higashihara T. 2000. Phylogenetic analysis of ?psychrophilic bacteria ?isolated from the Japan Trench, including a description of the deep-sea ?species Psychrobacter pacificensis sp. nov. Int ?J Syst Evol Microbiol 50 (2): 835-846.? DOI: 10.1099/00207713-50-2-835.?
Naik MG, Duraphe MD. 2012. Review paper on-Parameters affecting bioremediation. Int J life Sci pharma Res 2 (3): ?L77-L80.?
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 ?Biodegradation 63 (3): 273-279.? DOI: 10.1016/j.ibiod.2008.10.004.?
Perdigão R, Almeida CMR, Santos F, Carvalho MF, Mucha AP. 2021. Optimization of an Autochthonous ?Bacterial ?Consortium Obtained from Beach Sediments for Bioremediation of Petroleum ?Hydrocarbons. Water 13 (1): 66.? DOI: ??10.3390/w13010066.?
Romaniuk K, Ciok A, Decewicz P, et al. 2018. Insight into heavy metal resistome of soil psychrotolerant bacteria ??originating from King George Island (Antarctica). Polar Biol 41 (7): 1319-1333.? DOI: 10.1007/s00300-018-2287-4?
Sarshad D D, Shiraf N, Arjunan, S E. 2015. Isolation And Characterization Of Hydrocarbon Degrading ?Bacteria. Int J ?Pharm ?Bio Sci 6 (3): (B) 469-478.?
Truskewycz A, Gundry TD, Khudur LS, et al. 2019. Petroleum hydrocarbon contamination in terrestrial ?ecosystems-fate ?and microbial responses. Molecules 24 (18): 3400.? DOI: 10.3390/molecules24183400.?
Turner S, Pryer KM, Miao VPW, Palmer JD. 1999. Investigating deep phylogenetic relationships among ?cyanobacteria ?and plastids by small subunit rRNA sequence analysis 1. J Eukaryot Microbiol 46 (4): 327-338.? DOI: 10.1111/j.1550-??7408.1999.tb04612.x?
Wang W, Li Z, Zeng L, Dong C, Shao Z. 2020. The oxidation of hydrocarbons by diverse heterotrophic and ?mixotrophic ?bacteria that inhabit deep-sea hydrothermal ecosystems. ISME J 14 (8): 1994-??2006. DOI: 10.1038/s41396-020-0662-?y
Allamin IA, Halmi MIE, Yasid NA, Ahmad SA, Abdullah SRS, Shukor Y. 2020. Rhizodegradation of petroleum ?oily ?sludge-contaminated soil using Cajanus cajan increases the diversity of soil microbial ?community. Sci Rep 10 (1): 1-??11.? DOI: 10.1038/s41598-020-60668-1?
Anaukwu CG, Ezemba CC, Anakwenze VN, et al. 2016. Influence of anionic, cationic and non-ionic surfactants ?on ?growth of hydrocarbon utilizing bacteria. Am J Curr Microbiol 4 (1): 10-16.?
Ayala-del-Río HL, Chain PS, Grzymski JJ, et al. 2010. The genome sequence of Psychrobacter arcticus 273-4, a ??psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-?temperature growth. Appl ?Environ Microbiol 76 (7): 2304-2312.? DOI: 10.1128/AEM.02101-09?
Azevedo JSN, Correia A, Henriques I. 2013. Molecular analysis of the diversity of genus Psychrobacter present ?within a ?temperate estuary. FEMS Microbiol Ecol 84 (3): 451-460.? DOI: 10.1111/1574-6941.12075?
Baird RB. 2017. Standard Methods for the Examination of Water and Wastewater, 23rd. Water Environment Federation, ?American Public Health Association, American Water Works Association.??
Barathi S, Vasudevan N. 2001. Utilization of petroleum hydrocarbons by Pseudomonas fluorescens isolated ?from a ?petroleum-contaminated soil. Environ Int 26 (5-6): 413-416.? DOI: 10.1016/s0160-4120(01)00021-6.?
Boshui CB, Nan Z, Jiang W, Jiu W, Jianhua F. 2012. Biodegradation of petroleum hydrocarbon by Pseudomonas ??aeruginosa. China Petro Proc Petrochem Technol 14: 66-70.?
Brinkrolf K, Brune I, Tauch A. 2006. Transcriptional regulation of catabolic pathways for aromatic compounds ?in ?Corynebacterium glutamicum. Genet Mol Res 5 (4): 773-789.?
Chaillan F, Le Flèche A, Bury E, et al. 2004. Identification and biodegradation potential of tropical aerobic ?hydrocarbon-?degrading microorganisms. Res Microbiol 155 (7): 587-595.? DOI: 10.1016/j.resmic.2004.04.006.?
Chandra S, Sharma R, Singh K, Sharma A. 2013. Application of bioremediation technology in the environment ??contaminated with petroleum hydrocarbon. Ann Microbiol 63 (2): 417-431.? DOI: 10.1007/s13213-012-0543-3?
Das N, Chandran P. 2011. Microbial degradation of petroleum hydrocarbon contaminants: an overview. ?Biotechnol Res ?Int ? 2011: 941810. DOI: 10.4061/2011/941810.?
Deng Z, Jiang Y, Chen K, Gao F, Liu X. ??2020. Petroleum depletion property and microbial community shift after ??bioremediation using Bacillus halotolerans T-04 and Bacillus cereus 1-1. Front Microbiol 11: 353.? DOI: ??10.3389/fmicb.2020.00353?
Devatha CP, Vishal AV, Rao JPC. 2019. Investigation of physical and chemical characteristics on soil due to ?crude oil ?contamination and its remediation. Appl Water Sci 9: 89. DOI: 10.1007/s13201-019-0970-4?
Eaton AD, Clesceri LS, Rice EW, Greenberg AE, Franson MAH. 2005. Standard methods for the examination of ?water ?and wastewater: centennial edition, 21st edn Washington. DC: American Public Health Association. ?
Ehis-Eriakha CB, Chikere CB, Akaranta O. 2020. Functional Gene Diversity of Selected Indigenous ?Hydrocarbon-?Degrading Bacteria in Aged Crude Oil. Int J Microbiol 2020.? DOI: 10.1155/2020/2141209?
Ezeonu CS, Tagbo R, Anike EN, Oje OA, Onwurah INE. 2012. Biotechnological tools for environmental ?sustainability: ?prospects and challenges for environments in Nigeria—a standard review. ?Biotechnol Res Int 2012.? DOI: ??10.1155/2012/450802?
Federation WE, Association APH. 2005. Standard methods for the examination of water and wastewater. Am ?Public Heal ?Assoc Washington, DC, USA.?
Folk RL. 1974. Petrologie of sedimentary rocks. Texas, USA Hemphill’s, Austin Folk, R. L: 128-182.?
Kashi FJ, Owlia P, Amoozegar MA, Yakhchali B, Kazemi B. 2020. Diversity of cultivable microorganisms in the ?eastern ?part of Urmia salt lake, Iran. J Microbiol Biotechnol Food Sci 9 (4): 36-43.? DOI:10.15414/jmbfs.2014.4.1.36-43?
Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: a novel method for rapid multiple sequence alignment ?based on ?fast Fourier transform. Nucleic Acids Res 30 (14): 3059-3066.? DOI: 10.1093/nar/gkf436?
Koshlaf E, Ball AS. 2017. Soil bioremediation approaches for petroleum hydrocarbon polluted environments. ?AIMS ?Microbiol 3 (1): 25-49.? DOI: 10.3934/microbiol.2017.1.25?
Kumari N, Vashishtha A, Saini P, Menghani E. 2013. Isolation, identification and characterization of oil ?degrading ?bacteria isolated from the contaminated sites of Barmer, Rajasthan. Int J Biotechnol ?Bioeng Res 4 (5): 429-436.?
Lane D.J. 1991. 16S/23S rRNA sequencing in: Nucleic acid techniques in bacterial systematic. (eds). Stackebrandt E, ?Goodfellow M. John Wiley & Sons, Ltd. Chichester England.?
Li H, Wang X-L, Mu B-Z, et al. 2013. Molecular detection, quantification and distribution of alkane-?degrading bacteria in ?production water from low temperature oilfields. Int Biodeterior ?Biodegradation. 76: 49-57.? DOI: ??10.1016/j.ibiod.2012.06.007?
Litvinenko V. 2020. The role of hydrocarbons in the global energy agenda: The focus on liquefied natural gas. ?Resources ??9 (5): 59.? DOI: 10.3390/resources9050059?
Liu J, Xie X, Xiao S, Wang X, Zhao W, Tian Z. 2007. Isolation of Leptospirillum ferriphilum by single-layered ?solid ?medium. J Cent South Univ Technol 14 (4): 467-473.? DOI: 10.1007/s11771-007-0091-3?
Mansur AA, Taha M, Shahsavari E, Haleyur N, Adetutu EM, Ball AS. 2016. An effective soil slurry ?bioremediation ?protocol for the treatment of Libyan soil contaminated with crude oil tank bottom ?sludge. Int Biodeterior ?Biodegradation 115: 179-185.? DOI: 10.1016/j.ibiod.2016.08.015?
Margesin R, Schinner F. 2001. Biodegradation and bioremediation of hydrocarbons in extreme environments. ?Appl ?Microbiol Biotechnol 56 (5): 650-663.? DOI: 10.1007/s002530100701.?
Maruyama A, Honda D, Yamamoto H, Kitamura K, Higashihara T. 2000. Phylogenetic analysis of ?psychrophilic bacteria ?isolated from the Japan Trench, including a description of the deep-sea ?species Psychrobacter pacificensis sp. nov. Int ?J Syst Evol Microbiol 50 (2): 835-846.? DOI: 10.1099/00207713-50-2-835.?
Naik MG, Duraphe MD. 2012. Review paper on-Parameters affecting bioremediation. Int J life Sci pharma Res 2 (3): ?L77-L80.?
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 ?Biodegradation 63 (3): 273-279.? DOI: 10.1016/j.ibiod.2008.10.004.?
Perdigão R, Almeida CMR, Santos F, Carvalho MF, Mucha AP. 2021. Optimization of an Autochthonous ?Bacterial ?Consortium Obtained from Beach Sediments for Bioremediation of Petroleum ?Hydrocarbons. Water 13 (1): 66.? DOI: ??10.3390/w13010066.?
Romaniuk K, Ciok A, Decewicz P, et al. 2018. Insight into heavy metal resistome of soil psychrotolerant bacteria ??originating from King George Island (Antarctica). Polar Biol 41 (7): 1319-1333.? DOI: 10.1007/s00300-018-2287-4?
Sarshad D D, Shiraf N, Arjunan, S E. 2015. Isolation And Characterization Of Hydrocarbon Degrading ?Bacteria. Int J ?Pharm ?Bio Sci 6 (3): (B) 469-478.?
Truskewycz A, Gundry TD, Khudur LS, et al. 2019. Petroleum hydrocarbon contamination in terrestrial ?ecosystems-fate ?and microbial responses. Molecules 24 (18): 3400.? DOI: 10.3390/molecules24183400.?
Turner S, Pryer KM, Miao VPW, Palmer JD. 1999. Investigating deep phylogenetic relationships among ?cyanobacteria ?and plastids by small subunit rRNA sequence analysis 1. J Eukaryot Microbiol 46 (4): 327-338.? DOI: 10.1111/j.1550-??7408.1999.tb04612.x?
Wang W, Li Z, Zeng L, Dong C, Shao Z. 2020. The oxidation of hydrocarbons by diverse heterotrophic and ?mixotrophic ?bacteria that inhabit deep-sea hydrothermal ecosystems. ISME J 14 (8): 1994-??2006. DOI: 10.1038/s41396-020-0662-?y