Journal of Applied & Environmental Microbiology
ISSN (Print): 2373-6747 ISSN (Online): 2373-6712 Website: http://www.sciepub.com/journal/jaem Editor-in-chief: Sankar Narayan Sinha
Open Access
Journal Browser
Go
Journal of Applied & Environmental Microbiology. 2016, 4(1), 1-20
DOI: 10.12691/jaem-4-1-1
Open AccessArticle

Microbial Community Profiling of Active Oleophilic Bacteria involved in Bioreactor-based Crude-oil Polluted Sediment Treatment

Chioma Blaise Chikere1, , Amara Ukamaka Okoye1 and Gideon Chijioke Okpokwasili1

1Department of Microbiology, Faculty of Biological science, College of Natural and Applied Sciences, University of Port Harcourt, Rivers State, Nigeria, P.M.B. 5323, East-West Road, Choba, Port Harcourt, Rivers State, Nigeria

Pub. Date: January 30, 2016

Cite this paper:
Chioma Blaise Chikere, Amara Ukamaka Okoye and Gideon Chijioke Okpokwasili. Microbial Community Profiling of Active Oleophilic Bacteria involved in Bioreactor-based Crude-oil Polluted Sediment Treatment. Journal of Applied & Environmental Microbiology. 2016; 4(1):1-20. doi: 10.12691/jaem-4-1-1

Abstract

Petroleum hydrocarbon pollution has been a major environmental challenge in the coastal areas, Niger-Delta, Nigeria. In this study, culture dependent and molecular techniques were used to monitor bioremediation over a-64 day period in seven microcosms setup in 2.5 L stirred tank bioreactors with each tank containing either Poultry droppings (BPOUT), NPK fertilizer (BNPK), Cow dung (BCD) or Urea fertilizer (BUREA). One bioreactor (BAUG) was bioaugmented while two others served as unamended (BUNa) and heat-killed (BHKD) controls. A decrease in petroleum hydrocarbon concentration and a concomitant increase in biomass was observed in all treatments at varying levels. BNPK (97.2%; 97.1%) showed highest reduction percentage while BHKD (82.34%, 81.3%) was the least for total petroleum hydrocarbon and polycyclic aromatic hydrocarbon amongst all treatment. Screening of isolates for aromatic hydrocarbon ring cleavage functional gene (catechol 2,3-dioxygenase) revealed that catechol 2,3-dioxygenase (C23D0) gene was detected in the following genera: Pseudomonas spp. (3), Rhodococcus sp. (2), Bacillus spp.(2)., Achromobacter sp., Serratia sp., Aeromonas sp., Micrococcus sp. and Acinetobacter sp. Sequences obtained from amplification of 16S rRNA gene gave a total number of 24 hydrocarbon utilizing bacterial species which showed 96-100% similarity with those deposited in GenBank and are identified as Brevundimonas naejangsanensis, Pseudomonas pseudoalcaligenes, Pseudomonas spp. (6), Aquitalea magnusonii, Achromobacter sp., Halomonas lutea, Pseudomonas aeruginosa (8), Shewanella sp, Achromobacter sp., Gordonia sp., Sphingobacterium sp. and Bacillus sp. Our result revealed that these extant indigenous bacterial population in the crude oil-polluted sediment habour the relevant aromatic hydrocarbon ring cleavage genes (catechol 2,3-dioxygenase) and may have a key role in bioremediation of crude oil-polluted sediment.

Keywords:
bioreactor-based hydrocarbon microbial community oleophilic bacteria sediment

Creative CommonsThis work is licensed under a Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

References:

[1]  United Nation Environmental Programme (UNEP0 (2011). Environmental setting in Ogonilannd and Niger Delta. Environmental Assessment of Ogoniland. UNEP, Nairobi, Kenya.
 
[2]  Environmental Guidelines and Standards for Petroleum Industries in Nigeria (EGASPIN) (1992). Issued by the Department of Petroleum Resources, Nigeria. (Revised edition, 2002).
 
[3]  Youssef, M., El-Taweel G. E., A. Y. Naggar, S. E. El-Hawary, El- Meleigy, M. A. and Ahmed, S. A. (2010). Hydrocarbon Degrading Bacteria as Indicator of Petroleum Pollution in Ismailia Canal, Egypt. World Applied Sciences Journal 8 (10): 1226-1233.
 
[4]  Varjani S. J;. Rana Dolly P.; Bateja, S. and Upasani, V. N. (2013). Isolation and Screening for Hydrocarbon Utilizing Bacteria (HUB) from Petroleum Samples. Internal Journal of Current Microbiology and Applied Science 2(4): 48-60.
 
[5]  Das, N. and Chandran, P. (2011) Microbial degradation of petroleum hydrocarbon contaminants – an overview. Biotechnology Research International (11):1-13.
 
[6]  Paniagua-Michel, J. and Rosales, A. (2015) Marine Bioremediation - A Sustainable Biotechnology of Petroleum Hydrocarbons Biodegradation in Coastal and Marine Environments. Journal Bioremediation and Biodegradation 6:273.
 
[7]  Godleads, O. A.; Prekeyi T. F.; Samson E. O. and Igelenyah E. (2015). Bioremediation, Biostimulation and Bioaugmention: A Review International Journal of Environmental Bioremediation & Biodegradation 3 (1): 28-39.
 
[8]  Moscoso, F.; Teijiz, I.; Deive F. J. and Sanromán, M. A. (2012). Efficient PAHs biodegradation by a bacterial consortium at flask and bioreactor scale. Bioresource Technology, Elsavier 119: 270-276.
 
[9]  Sebiomo, A.; Bankole, S. A. and Awosanya, A. O. (2010). Determination of the ability of microorganisms isolated from mechanic soil to utilise lubricating oil as carbon source. African journal of microbiology research 4(21): 2257-2264.
 
[10]  Chikere, C. B.; Okpokwasili, G. C. and Ichiakor, O. (2009) Characterization of hydrocarbon utilizing bacteria in tropical marine sediments. African Journal of Biotechnology 8: 2541-2544.
 
[11]  Rojo, F. (2009). Degradation of alkanes by bacteria. Environ Microbiol 11:2477-2490.
 
[12]  Yakimov, M. M.; Timmis, K. N. and Golyshin, P. N. (2007) Obligate oil degrading marine bacteria. Current Opinion on Biotechnology. 18:257-268.
 
[13]  Gertler, C; Gerdts G; Timmis, K. N. and Golyshin, P. N. (2009). Microbial consortia in mesocosm bioremediation trial using oil sorbents, slow release fertilizer and bioaugmentation. FEMS Microbiology Ecology. 69:288-300.
 
[14]  Atlas, R. M. and Hazen, T.C. (2011).Oil biodegradation and bioremediation: A tale of the two worst spills in U.S. history. Environmental Science Technology,45:6709-6715.
 
[15]  Krishna, K..K.; Keryn, L.S.; Pawel, P.S.; Robert, B.M. and Andrew, S.B. (2012). A complementary approach to identifying and asssessing the remediation potential of hydrocarbonoclastic bacteria. Journal of Microbiological Methods 88:348-355.
 
[16]  Chikere, C.B. and C. C. Azubuike (2013). Catechol 2,3-dioxygenase screening in putative hydrocarbon utilizing bacteria. International Research Journal of Microbiology 4 (1): 1-6.
 
[17]  Guo-Chun, D.; Holger, H.; Sebastian, Z., Michael, S.; Geertje Johanna, P.; Katja Ko¨gel-Knabner, H. I. and Smalla, K. (2010). Soil Type-Dependent Responses to Phenanthrene as Revealed by Determining the Diversity and Abundance of Polycyclic Aromatic Hydrocarbon Ring-Hydroxylating Dioxygenase Genes by Using a Novel PCR Detection System. Polish Journal of Environmental Studies. 12 (1) :15-25.
 
[18]  Anthony, D. K.; YinWei, .; Ryan, J.; Newton, I.; van Nostrand, J. D. and Jizhong Zhou, Sandra.L. McLellan and Krassimira. R..H.(2014). The polycyclic aromatic hydrocarbon degradation potential of Gulf of Mexico native coastal microbial communities after the Deep water Horizon oil spill. Frontiers in Microbiology. 5 (205):1-12.
 
[19]  Ma, Y.; Wang, L. and 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. National Center for Biotechnology Information, 8 (3):455-65.
 
[20]  Tullio, B.; Sara ,B.; Fabrizio, F.; Claudia, S.; Cesare, C. and Daniele, D. (2001) Aromatic hydrocarbon degradation patterns and catechol 2,3-dioxygenase genes in microbial cultures from deep anoxic hypersaline lakes in the eastern Mediterranean sea Microbiology Research. 156, 49-57.
 
[21]  Van Elsa, J. D.; Jansson, J. K. and Trevors, J. K. (2007) Modern Soil Microbiology. 2nd ed. New York: CRC Press,. p. 387-429.
 
[22]  Chikere, C. B., Chikere , B. O and Okpokwasili, G. C.(2012). Bioreactor-based bioremediation of hydrocarbon-polluted Niger Delta marine sediment, Nigeria 3 Biotechecnology 2:53-66.
 
[23]  Bergey. D. H. and Holt, J. G. (1994). Bergey's Manual of Determinative Bacteriology. 9th edition. Williams and Wacket, Baltimore, Washington DC.
 
[24]  Luis, M.; Maria, T. P.; Janet, S.; Grace, T. and Eilana (2013). Colour Atlas of Medical Bacteriology. ASM Press, Washigton DC.
 
[25]  Jyothi k., Surendra B., Nancy CK., Anita k.(2012) Identification and Isolation of Hydrocarbon Degrading Bacteria by Molecular Characterization. Helix. 2: 105-111.
 
[26]  Mnif, S.; Chamkha, M. and Sayadi, S. (2009). Isolation and characterization of Halomonas sp. Strain C2SS100, a hydrocarbon degrading bacterium under hypersaline conditions. Journal of Applied Microbiology. 107:785-794.
 
[27]  Mesarch, B. M.; Nakatsu, C. H. and Niles, L.(2000): Development of catechol 2,3-dioxygenase-specific primers for monitoring bioremediation by competitive quantitative PCR. Applied Environmental Microbiology. 66: 678-683.
 
[28]  Aparna, A.; Srinikethan, G. and Smitha, H. (2012). Production and characterization of biosurfactant produced by a novel Pseudomonas sp. 2B. Colloids Surf B. Journal of Environmental Science and Pollution Research. 95: 23-29.
 
[29]  Quatrini, P.; Scaglione, G.; De Pasquale, C.; Reila, S. and Puglia, A.M. (2008) Isolation of Gram-positive n-alkane degraders from a hydrocarbon contaminated Mediterranean shoreline. Journal of Applied Microbiology 104:251-259.
 
[30]  Atlas, R.M. and Philip. J.(2005). Bioremediation: Applied Solution for Real-World Environmental Clean-up. American Society for Microbiology (ASM). 75-105.
 
[31]  Collina. E., G.; Bestetti, P.; Gennaro, D.; Franzetti, A.; Gugliersi, F.; Lasagni, M. and Pitea. D. (2005) Naphthalene biodegradation kinetics in an aerobic slurry-phase bioreactor, Environmental international 31:167-171.
 
[32]  van Hamme J. D.; Singh, A. and Ward, O. P. (2003) Recent advances in petroleum microbiology. Microbiology Molecular Biology Review 67:503-549.
 
[33]  Singh, A. K; Sherry, A.; Gray, N. D.; Jones, D. M.; Bowler, B. F. J. and Head, I. M. (2014). Kinetic parameters for nutrient enhanced crude oil biodegradation in intertidal marine sediments. Frontier in Microbiology. 5:160.
 
[34]  Li, D.; Midgley, D.J.; Ross, J. P.; Oytam, Y.; Abell, G. C. and Volk, H..(2012). Microbial biodiversity in a Malaysian oil field and a systematic comparison with oil reservoirs worldwide. Arch.Microbiol. 194:513-523.
 
[35]  Zhang, F.; She, Y. H.; Chai, L. J.; Banat, I. M.; Zhang, X. T. and Shu ,F.C.,(2012). Microbial diversity in long-term water-flooded oil reservoirs with different in situ temperatures in China. Sci.Rep. 2:760.
 
[36]  Berdugo-Clavijo, C. and Lisa, M.G. (2014) Conversion of crude oil to methane by a microbial consortium enriched from oil reservoir production water .Petroleum Microbiology Research Group,Department of Biological Sciences, 10: 3389-3342.
 
[37]  Rajendhran, J. and Gunasekaran, P. (2011). Microbial phylogeny and diversity: Small subunit ribosomal RNA sequence analysis and beyond. ScienceDirect Microbiological Research 166: 99-110.
 
[38]  Magali, S. M.; Mariana, L.; Walter, D.J.; Marzio, D.I. and Hebe, M. (2012). Abundance, Dynamic and Biographic Distribution of seven polycyclic Aromatic Hydrocarbon Dioxygenase Gene variant in coastal sediment of Patagonia. Applied and Environmental Microbiology 78(5): 1589-2514.
 
[39]  Garcia, M. T.; Ventosa, A. and Mellado, E. (2005) Catabolic versatility of aromatic compound-degrading halophilic bacteria. FEMS Microbiol. Ecol. 54, 97-109.
 
[40]  Agrawal, N. and Shahi, K. S. (2015). Review Article: An Environmental Cleanup Strategy Microbial Transformation of Xenobiotic Compounds. Int. Journ. Curr. Microbiol. App. Sci. 4(4):429-461.
 
[41]  Garcia-Sierra, I. N.; Correa, A., J.; Pantaroto de Vasconcellos, S.; Pereira de Souza, A.; dos Santos Neto , E.V. and Anete Pereira de Souza. (2014). New Hydrocarbon Degradation Pathways in the Microbial Metagenome from Brazilian Petroleum Reservoirs. PLoS ONE 9 (2): 1371-1382.
 
[42]  Kostka, J. E.; Prakash, O.; Overholt, W.A.; Green, S. J.; Freyer, G. and Canion, A. (2011). Hydrocarbon-degrading bacteria and the bacterial community response in Gulf of Mexico beach sands impacted by the Deepwater Horizon oil spill. Applied and Environmental Microbiology. 77:7962-7974.
 
[43]  Niepceron, M.; Martin-Laurent, F.; Crampon, M,; Portet-Koltalo, F, Akpa-Vinceslas, M.; Legras M.; Bru, D.; Bureau, F. and Bodilis, J. (2013). GammaProteobacteria as a potential bioindicator of a multiple contamination by polycyclic aromatic hydrocarbons (PAHs) in agricultural soils. Environmental Pollution. Elsevier. 180. 199-205.
 
[44]  Gallego, J. L. R..; Garcia-Martinez, M. J.; Llamas, J. F.; Belloch, C.; Pelaez, A.I. and Sanchez, J. (2007). Biodegradation of oil tank bottom sludge using microbial consortia. Biodegradation. 18 (3) : 269-281.
 
[45]  Surekha, K. S.; Arun, G. K.; Prashant, K. P.; Ibrahim, M. B .and Balu, A. C. (2010). Methods for investigating biosurfactants and bioemulsifiers: a review. Critical Reviews in Biotechnology. 30 (2): 127-144.
 
[46]  Chaillan. F.; Le Flèche, A.; Bury, E.; Phantavong, Y. H.; Grimont, P.; Saliot A, and Oudot, J. (2004). “Identification and biodegradation potential of tropical aerobic hydrocarbon-degrading microorganisms,” Research in Microbiology, 155 (7):587-595.