Biodegradation of crude oil by Halomonas elongata strain KWPA-12: a moderately halophilic strain detected in oil spills around Garo sulfidic springs, MIS Oilfield, Iran

Abstract

The oil spills in the vicinity of the Garo sulfidic springs in Golgir region, MIS oilfield, Iran, were investigated for halotolerant/halophilic microorganisms capable of crude oil biodegradation. Screenings resulted in an isolate capable of growth on crude oil of the local Asmari reservoir in media containing 30–100 g/L NaCl at 28 °C. The isolate, designed as KWPA-12, was an aerobic, motile, oxidase and catalase positive, Gram-negative rod. It was shown that strain KWPA-12 can utilize crude oil as the carbon and sulfur sources with a significant efficiency. The Asmari crude oil biodegradation in 90 g/L NaCl containing media was investigated by turbidity measurement, GC-FID and TPH analyses. The results showed that the aliphatic hydrocarbons including: small C11–C12 and long chains: C31–C33, are mostly favored by strain KWPA-12. Anthracene: a tri-ring and one of the most dominant poly-aromatic compounds of Asmari crude oil, was reduced down to about 1.1% of the starting moiety. Phylogenetic investigations performed on the partial 16S rRNA gene sequence indicated that the strain belongs to the genus Halomonas and it fell into the Halomonas elongata clade.

Keywords

Halomonas spp. / Degradation / Petroleum / Halophiles / PAHs / Saline

References

[1] Atlas RM. Microbial degradation of petroleum hydrocarbons: an environmental perspective. Microbiol Rev, 1981, 45: 180-209

[2] Atlas RM, Bartha R. Hydrocarbon biodegradation and oil spill bioremediation. Adv Microb Ecol, 1992, 12: 287-338

[3] Badamchi A, Papizadeh M. Comparative phylogeny of the genus Bordetella using sequence analysis of 16S rRNA and ompA genes. J Med Bacteriol, 2017, 6(1): 1-13

[4] Berendes F, Gottschalk G, Heine-Dobbernack E, Moore ERB, Tindall BJ. Halomonas desiderata sp. nov, a new alkaliphilic, halotolerant and denitrifying bacterium isolated from a municipal sewage work. Syst Appl Microbiol, 1996, 19: 158-167

[5] Bouchotroch S, Quesada E, Del Moral A, Liamas I, Béjar V. Halomonas maura sp. nov., a novel moderately halophilic, exopolysaccharide-producing bacterium. Int J Syst Evol Microbiol, 2001, 51: 1625-1632

[6] Brooijmans RJW, Pastink MIM, Siezen RJ. Hydrocarbon-degrading bacteria: the oilspill clean-up crew. J Microbial Biotech, 2009, 2(6): 587-594

[7] Bukin SV, Pavlova ON, Manakov AY, Kostyreva EA, Chernitsyna SM, Mamaeva EV, Pogodaeva TV, Zemskaya TI. The ability of microbial community of lake Baikal bottom sediments associated with gas discharge to carry out the transformation of organic matter under thermobaric conditions. Front Microbiol, 2016, 7: 690

[8] Chhatre SA, Purohit HJ, Shanker R, Chakrabarti T, Khanna P. Bacterial consortia for crude oil spill remediation. Wat Sci Tech, 1996, 34: 187-193

[9] Chitsazan M, Ghaderi G, Mirzaee Y, Papizadeh M. Oil field brine pollution and biological removal of arsenic from Garo springs (Masjed Soleiman, Khuzestan). Adv Appl Geol, 2012, 3(1): 83-93 (in Persian)

[10] Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras- Alfaro A, Kuske CR, Tiedje JM. Ribosomal database project: data and tools for high throughput rRNA analysis. Nucl Acids Res, 2013, 42: D633-D642

[11] Crous PW, Wingfield MJ, Schumacher RK, Summerell BA, Giraldo A, Gené J, Guarro J, Wanasinghe DN, Hyde KD, Camporesi E, Jones EBG, Thambugala KM, Malysheva EF, Malysheva VF, Acharya K, Álvarez J, Alvarado P, Assefa A, Barnes CW, Bartlett JS, Blanchette RA, Burgess TI, Carlavilla JR, Coetzee MPA, Damm U, Decock CA, den Breeÿen A, de Vries B, Dutta AK, Holdom DG, Rooney-Latham S, Manjón JL, Marincowitz S, Mirabolfathy M, Moreno G, Nakashima C, Papizadeh M, Shahzadeh Fazeli SA, Amoozegar MA, Romberg MK, Shivas RG, Stalpers JA, Stielow B, Stukely MJC, Swart WJ, Tan YP, van der Bank M, Wood AR, Zhang Y, Groenewald JZ. Fungal planet description sheets: 281–319. Persoonia, 2014, 33: 212-289

[12] Dando PR, O’Hara SCM, Schuster U, Taylor LJ, Clayton CJ, Baylis S, Laier T. Gas seepage from a carbonate-cemented sandstone reef on the Kattegat coast of Denmark. Mar Pet Geol, 1994, 11: 182-189

[13] Das N, Chandran P. Microbial degradation of petroleum hydrocarbon contaminants: an overview. Biotechnol Res Int, 2011, 2011: 1-13

[14] Díaz MP, Boyd KG, Grigson SJW, Burgess JG. Biodegradation of crude oil across a wide range of salinities by an extremely halotolerant bacterial consortium MPD-M, immobilized onto polypropylene fibers. Biotechnol Bioeng, 2002, 79(2): 145-153

[15] Doboş L, Carmen P. The effect of bioremediation on the microbial consortia of oil polluted soil. ProEnvironment, 2011, 4: 264-267

[16] Dott W, Feidieker D, Kämpfer P, Schleibinger H, Strechel S. Comparison of autochtonous bacteria and commercially available cultures with respect to their effectiveness in fuel oil degradation. J Ind Microbiol, 1989, 4: 365-374

[17] Englert CJ, Kenzie EJ, Dragun J. Calabrese EJ, Kostecki PT. Bioremediation of petroleum products in soil. Principles and practices for petroleum contaminated soils, 1993 Chelsea Lewis Publishers 111-130

[18] García MT, Mellado E, Ostos JC, Ventosa A. Halomonas organivorans sp. nov., a moderate halophile able to degrade aromatic compounds. Int J Syst Evol Microbiol, 2004, 54: 1723-1728

[19] Guo T, Wang HC, Xue WQ, Zhao J, Yang ZL. Phylogenetic analyses of Armillaria reveal at least 15 phylogenetic lineages in China, seven of which are associated with cultivated Gastrodia elata. PLoSOne, 2016, 11(5): e0154794

[20] Hao RX, Lu AH. Biodegradation of heavy oils by halophilic bacterium. Prog Nat Sci Mater Int, 2009, 19: 997-1001

[21] Hassanshahian M, Emtiazi G, Cappello S. Isolation and characterization of crude -oil -degrading bacteria from the Persian Gulf and the Caspian Sea. Mar Poll Bull, 2012, 64: 7-12

[22] Hawle-Ambrosch E, Riepe W, Dornmayr-Pfaffenhuemer M, Radax C, Holzinger A, Stan-Lotter H. Biodegradation of fuel oil hydrocarbons by a mixed bacterial consortium in sandy and loamy soils. Biotechnol J, 2007, 2(12): 1564-1568

[23] Huelsenbeck JP, Ronqvist F. MrBayes: bayesian inference of phylogeny. Bioinformatics, 2001, 17: 754-755

[24] Hyde KD, Hongsanan S, Jeewon R, Bhat DJ, McKenzie EHC, Jones EBG, Phookamsak R, Ariyawansa HA, Boonmee S, Zhao Q, Abdel-Aziz FA, Abdel-Wahab MA, Banmai S, Chomnunti P, Cui BK, Daranagama DA, Das K, Dayarathne MC, de Silva NL, Dissanayake AJ, Doilom M, Ekanayaka AH, Gibertoni TB, Góes-Neto A, Huang SK, Jayasiri SC, Jayawardena RS, Konta S, Lee HB, Lim WJ, Lin CG, Liu JK, Lu YZ, Luo ZL, Manawasinghe IS, Manimohan P, Mapook A, Niskanen T, Norphanphoun C, Papizadeh M, Perera RH, Phukhamsakda C, Richter C, de Santiago ALCMA, Drechsler-Santos ER, Senanayake IC, Tanaka K, Tennakoon TMDS, Thambugala KM, Tian Q, Tibpromma S, Thongbai B, Vizzini A, Wanasinghe DN, Wijayawardene NN, Wu H, Yang J, Zeng XY, Zhang H, Zhang JF, Bulgakov TS, Camporesi E, Bahkali AH, Amoozegar AM, AraujoNeta LS, Ammirati JF, Baghela A, Bhatt RP, Bojantchev S, Buyck B, da Silva GA, de Lima CLF, de Oliveira RJV, de Souza CAF, Dai YC, Dima B, Duong TT, Ercole E, Mafalda-Freire F, Ghosh A, Hashimoto A, Kamolhan S, Kang JC, Karunarathna SC, Kirk PM, Kytövuori I, Lantieri A, Liimatainen K, Liu ZY, Liu XZ, Lücking R, Medardi G, Mortimer PE, Nguyen TTT, Promputtha I, Raj KNA, Reck MA, Lumyong S, Shahzadeh Fazeli SA, Stadler M, Soudi MR, Su HY, Takahashi T, Tangthirasunun N, Uniyal P, Wang Y, Wen TC, Xu JC, Zhang ZK, Zhao YC, Zhou JZ, Zhu L. Fungal diversity notes 367–490: taxonomic and phylogenetic contributions to fungal taxa. Fungal Divers, 2016, 80: 1-270

[25] Ijah UJJ. Studies on relative capabilities of bacterial and yeast isolates from tropical soil in degrading crude oil. Waste Manag, 1998, 18: 293-299

[26] Katoh K, Asimenos G, Toh H. Posada D. Bioinformatics for DNA sequence analysis. Methods in molecular biology, 2009 Totowa Humana Press, Springer

[27] Kimes NE, Callaghan AV, Suflita JM, Morris PJ. Microbial transformation of the Deepwater Horizon oil spill—past, present, and future perspectives. Front Microbiol, 2014, 5: 603

[28] Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol, 2016, 33(7): 1870-1874

[29] Lal B, Khanna S. Degradation of crude oil by Acinetobacter calcoaceticus and Alcaligenes odorans. J Appl Bacteriol, 1996, 81(4): 355-362

[30] Malik ZA, Ahmed S. Degradation of petroleum hydrocarbons by oil field isolated bacterial consortium. Afr J Biotechnol, 2012, 11: 650-658

[31] Martínez-Cánovas MJ, Quesada E, Llamas I, Béjar V. Halomonas ventosae sp. nov., a moderately halophilic, denitrifying, exopolysaccharide-producing bacterium. Int J Syst Evol Microbiol, 2004, 54: 733-737

[32] McGenity TJ, Folwell BD, McKew BA, Sanni GO. Marine crude-oil: a central role for interspecies interactions. Aquat Biosyst, 2012, 8: 10

[33] McWilliam H, Li W, Uludag M, Squizzato S, Park YM, Buso N, Cowley AP, Lopez R. Analysis tool web services from the EMBL-EBI. Nucleic Acids Res, 2013, 41: 597-600

[34] Mellado E, Moore ERB, Nieto JJ, Ventosa A. Phylogenetic inferences and taxonomic consequences of 16S ribosomal DNA sequence comparison of Chromohalobacter marismortui, Volcaniella eurihalina, and Deleya salina and reclassification of V. eurihalina as Halomonas eurihalina comb. nov. Int J Syst Bacteriol, 1995, 45: 712-716

[35] Miller MA, Pfeiffer W, Schwartz T (2010) Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In Proceedings of the gateway computing environments workshop (GCE), 14 Nov 2010, New Orleans, LA, pp 1–8

[36] Mnif S, Chamkha M, Sayadi S. Isolation and characterization of a Halomonas sp. strain C2SS100 a hydrocarbon degrading bacterium under hypersaline condition. J Appl Microbiol, 2009, 107: 785-794

[37] Mormile MR, Romine MF, Garcia MT, Ventosa A, Bailey TJ, Peyton BM. Halomonas campisalis sp. nov., a denitrifying, moderately haloalkaliphilic bacterium. Syst Appl Microbiol, 1999, 22: 551-558

[38] Nylander JAA. MrModeltest 2. Program distributed by the author, 2004 Uppsala Evolutionary Biology Centre, Uppsala University

[39] Ollivier B, Magot M. Petroleum microbiology, 2005 USA Blackwell

[40] Papizadeh M (2012) Geomicrobiological aspects of Gachsaran formation affected the hydrochemistry of Garo springs and Tembi River. National ground water association (NGWA), stream-aquifer interactions session, USA

[41] Papizadeh M, Roayaei Ardakani M. Bio filtration of volatile sulphurous hydrocarbon -polluted air by hydrocarbon degrading Pseudomonas NISOC-11. J Biotechnol, 2010, 150: 209-210

[42] Papizadeh M, Roayaei Ardakani M, Ebrahimipour G, Motamedi H. Utilization of dibenzothiophene as sulfur source by Microbacterium sp. NISOC-06. World J Microbiol Biotechnol, 2010, 26: 1195-1200

[43] Papizadeh M, Roayaei Ardakani M, Motamedi H, Rasouli I, Zarei M. C-S targeted biodegradation of dibenzothiophene by Stenotrophomonas sp. NISOC-04. Biotechnol Appl Biochem, 2011, 165: 938-948

[44] Papizadeh M, Fakour H, Roayaei Ardakani M (2012) Unusual geohydrochemical properties of Golgir sulfur springs resulted in microbioecological deviation in Tembi River. Handbook of The First National congress of Biological and Genetic Resource, Tehran, Iran

[45] Papizadeh M, Roayaei Ardakani M, Fakour H (2013) Microbioecology of water and sediments of saline and sulfur springs associated with Tembi River. KWPA. 89-01-02-019

[46] Papizadeh M, Roayaei Ardakani M, Fakour H, Ghaderi G, Firouzei Y. Microbio-ecology and hydro-geochemistry of saline sulfur springs of Ghale-madreseh, Khuzestan, Iran. Pollution, 2017, 3(4): 623-637

[47] Papizadeh M, Roayaei Ardakani M, Motamedi H. Growth-phase dependent biodesulfurization of dibenzothiophene by Enterobacter sp. strain NISOC-03. Pollution, 2017, 3(1): 101-111

[48] Papizadeh M, Soudi MR, Amini L, Wijayawardene NN, Hyde KD. Pyrenochaetopsis tabarestanensis (Cucurbitariaceae, Pleosporales), a new species isolated from rice farms in north Iran. Phytotaxa, 2017, 291(1): 15-28

[49] Peng M, Zi X, Wang Q. Bacterial community diversity of oil-contaminated soils assessed by high throughput sequencing of 16S rRNA genes. Int. J. Environ. Res. Publ. Health, 2015, 12: 12002-12015

[50] Qin X, Tang J, Li D, Zhang Q. Effect of salinity on the bioremediation of petroleum hydrocarbons in a saline? Alkaline soil. Lett Appl Microbiol, 2012, 55: 210-217

[51] Rambaut A (2008) FigTree v1.1.1: Tree figure drawing tool. http://tree.bio.ed.ac.uk/software/figtree/. Accessed 20 June 2008

[52] Rambaut A, Drummond AJ (2016) Tracer v1.6: MCMC trace analyses tool. University of Edinburgh. http://beast.bio.ed.ac.uk/programs. Accessed 17 March 2016

[53] Saba F, Papizadeh M, Khansha J, Sedghi M, Rasooli M, Amoozegar MA, Soudi MR, Shahzadeh Fazeli SA. A safe, rapid, and reproducible genomic DNA extraction protocol for sequence-based identification of archaea, bacteria, cyanobacteria, diatoms, fungi, and green algae. J Med Bacteriol, 2016, 5(3, 4): 22-28

[54] Sousa JAB, Sorokin DY, Bijmans MFM, Plugge CM, Stams AJM. Ecology and application of haloalkaliphilic anaerobic microbial communities. Appl Microbiol Biotechnol, 2015, 99(22): 9331-9336

[55] Sugiura K, Ishihara M, Shimauchi T, Harayama S. Physicochemical properties and biodegradability of crude oil. Environ Sci Technol, 1997, 31: 45-51

[56] Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maxi-mum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol, 2011, 28: 2731-2739

[57] Wang YN, Cai H, Chi CQ, Lu AH, Lin XG, Jiang ZF, Wu XL. Halomonas shengliensis sp. nov., a moderately halophilic, denitrifying, crude-oil -utilizing bacterium. Int J Syst Evol Microbiol, 2007, 57: 1222-1226

[58] Yakubu M, Bello YM. Biodegradation of Lagoma crude oil using pig dung. Afr J Biotechnol, 2007, 6: 2821-2825

[59] Yang YY, Zhao Q, Cui YH, Wang Y, Xie S, Liu Y. Spatio-temporal variation of sediment methanotrophic microorganisms in a large eutrophic lake. Microb Ecol, 2015, 71: 9-17