Degradation of Hydrocarbons and Lignin-like compounds by Alcaligenes sp. strain 3k isolated from Ilorin

Document Type : Original Research Paper


1 Department of Microbiology and Molecular Genetics Oklahoma State University, Stillwater, OK, USA Department of Microbiology, Faculty of Life Sciences, University of Ilorin, Ilorin, Nigeria

2 Department of Microbiology and Molecular Genetics Oklahoma State University, Stillwater, OK, USA

3 Department of Microbiology, Faculty of Life Sciences, University of Ilorin, Ilorin, Nigeria


The primary goal of this study was to isolate hydrocarbon-degrading organisms and assess their ability to bioremediate petroleum-contaminated soil and water. Nigeria is one of the major oil producing countries and petroleum contamination is widespread in agricultural soil. Alcaligenes sp. strain 3k was isolated from a kerosene-polluted soil in Ilorin, Nigeria. We also assessed its ability to degrade plant lignin, as lignin is a complex aromatic heteropolymer commonly found in soil and aquifer environment.  Strain 3k was originally grown on mineral salts medium with kerosene as a sole energy and carbon source. The capacity of the isolate to degrade both aromatic, aliphatic hydrocarbons and lignin-like compounds was tested. Among the tested compounds, the organism utilized kerosene, hexadecane, cyclohexane, phenol and benzoate as the sole sources of carbon. In addition, strain 3k also degraded various lignocellulose compounds as the sole source of carbon.  However, hexane, benzene, toluene, ethylbenzene and xylene were not metabolized. Our study demonstrates that soil organisms like Alcaligenes could play important role in the reclamation of petroleum-contaminated soil and water.  Utilization capacity of lignin as the sole carbon source suggest that these organisms can survive on plant detritus and also have the ability to degrade hydrocarbons upon accidental or deliberate contamination of agricultural soil and water.


Adetitun, D.O., Akinmayowa, O.V., Atolani, O. and Olayemi, A.B. (2018): Biodegradation of jet
fuel by three Gram negative bacilli isolated from kerosene contaminated soil. Pollution, 4(2), 291-303.
Agarry, S. E., Durojaiye, A. O., Yusuf, R. O. and Aremu, M. O. (2008). Biodegradation
of phenol in refinery wastewater by pure cultures of Pseudomonas aeruginosa NCIB 950 and Pseudomonas fluorescence NCIB 3756. International Journal of Environment and Pollution, 32(1), 3-11.
Ampe, F., Uribelarrea, J., Aragao, G. M. F. and Lindley, N. D. (1997). Benzoate Degradation via
the ortho Pathway in Alcaligenes eutrophus is perturbed by Succinate. Applied and Environmental Microbiology, 63(7), 2765–2770.
Annachatre, A.P., Gheewala, S.H. (1996) Biodegradation of chlorinated phenolic compounds.
Biotechnology Advances, 14, 35–56.
Bai, J., Wen, J., Li, H. and Jiang, Y. (2007). Kinetic modeling of growth and biodegradation of
Phenol and m-cresol using Alcaligenes faecalis. Process Biochemistry, 42, 510-517.
Brown, M. E. and Chang, M. C. (2014). Exploring Bacterial Lignin Degradation. Current Opinion in Chemical Biology, 19, 1–7.
Bugg, T. D. and Rahmanpour, R. (2015). Enzymatic Conversion of Lignin into Renewable
Chemicals. Current Opinion in Chemical Biology, 29, 10–17.
Bugg, T.D., Ahmad, M., Hardiman, E.M. and Rahmanpour, R. (2011)a. Pathways for
degradation of lignin in bacteria and fungi. Natural Product Reports, 28, 883-1896.
Bugg, T. D., Ahmad, M., Hardiman, E. M. and Singh, R. (2011)b. The Emerging Role for
Bacteria in Lignin Degradation and Bio-product Formation. Current Opinion in Biotechnology, 22, 394–400.
Caldwell, M. E. and Suflita, J. M. (2000). Detection of Phenol and Benzoate as Intermediates of
Anaerobic Benzene Biodegradation under Different Terminal Electron-Accepting Conditions. Environmental Science and Technology, 34, 1216–1220.
Chakraborty, S., Bhattacharya, T., Patel, T. N. and Tiwari, K. K. (2010). Biodegradation of
Phenol by Native Microorganisms Isolated from Coke Processing Wastewater. Journal of Environmental Biology, 31(3), 293-6.
Chénier, M, R., Beaumier, D., Roy, R., Driscoll, B.T., Lawrence, J.R., Greer, C.W. (2003).
Impact of seasonal variations and nutrient inputs on nitrogen cycling and degradation of hexadecane by replicated river biofilms. Applied Environmental Microbiology, 69, 5170–       5177.
Cao, B., Nagarajan, K. and Loh, K.C. (2009). Biodegradation of aromatic compounds: current status and opportunities for biomolecular approaches. Applied Microbiology and Biotechnology, 85, 207-228.
Carmona, M., Zamarro, M. T., Blázquez, B., Durante-Rodríguez, G., Juárez, J. F., Valderrama, J.
A., Barragán, M. J., García, J. L. and Díaz, E. (2009). Anaerobic Catabolism of Aromatic Compounds. A Genetic and Genomic View. Microbiology and Molecular Biology Reviews, 73, 71–133.
Chilcott, R. P. (2006). Compendium of Chemical Hazards: Kerosene (Fuel Oil). Health
Protection Agency. Didcot, Oxfordshire, OX11 0RQ, United Kingdom. 36P.
Dalvi, S., Youssef, N. H. and Fathepure, B. Z. (2016). Microbial Community Structure Analysis
of a Benzoate‑Degrading Halophilic Archaeal Enrichment. Extremophiles, 20, 311–321.
Dean, B. J. (1985). Recent Findings on the Genetic Toxicology of Benzene, Toluene, Xylenes
and Phenols. Mutation Research, 145, 153–181.
Datta, R., Kelkar, A., Baraniya, D., Molaei, A., Moulick, A., Meena, R.S. and Formanek,             P.
(2017). Enzymatic degradation of lignin in soil: a review. Sustainability, 9, 1163.
Falade, A.O., Nwodo, U.U., Iweriebor, B.C., Green, E., Mabinya, L.V. and Okoh, A.I., (2017). Lignin peroxidase functionalities and prospective applications. Microbiology Open, 6(1); p.e00394.
Feist, C. F. and Hegeman, G. D. (1969). Phenol and Benzoate Metabolism by Pseudomonas
putida: Regulation of Tangential Pathways. Journal of Bacteriology, 100, 869– 877.
Gibson, J. and Harwood, C. S. (2002). Metabolic Diversity in Aromatic Compound
Utilization by Anaerobic Microbes. Annual Review of Microbiology, 56, 345–369.
Gleixner, G.; Czimczik, C.J.; Kramer, C.; Lühker, B.; Schmidt, M.W.I. (2001). Plant compounds
and their turnover and stabilization as soil organic matter. Global Biogeochemical Cycles in the Climate System, 201–215.
Gouda, M. K, Omar, S. H, Nour-Eldin, H. M. and Chekroud, Z. A. (2008). Bioremediation of
Kerosene II: A Case Study in Contaminated Clay (Laboratory and Field: Scale Microcosms). World Journal of Microbiology and Biotechnology, 24, 1451-1460.
Harayama, S., Kasai, Y. and Hara, A. (2004). Microbial Communities in Oil-Contaminated
Seawater. Current Opinion in Biotechnology, 15, 205–214.
Harwood, C. S. and Parales, R. E. (1996). The β-ketoadipate Pathway and the Biology of
Self-Identity. Annual Review of Microbiology, 50, 553–590.
Head, I. M., Jones, D. M. and Roling, W. F. (2006). Marine Microorganisms make a Meal of Oil.
Nature Reviews Microbiology, 4, 173–182.
Igwo-Ezikpe, M. N., Gbenle, O. G., Ilori, M. O., Okpuzor, J and Osuntoki, A. A. (2009).
Evaluation of Alcaligenes faecalis Degradation of Chrysene and Diesel Oil with Concomitant Production of Biosurfactant. Research Journal of Environmental Toxicology, 3, 159-169.
Ikpeme, E. M., Nfongeh, J. F. and Etim, L. (2007). Comparative Bioremediation Enhancement
Procedures on Kerosene Polluted ultisol from Niger Delta Region, Southern Nigeria. Research Journal of Microbiology, 2 (11), 856-860.
Jiang, Y., Wen, J., Bai, J., Jia, X. and Hu, Z. (2007). Biodegradation of phenol at high initial concentration by Alcaligenes faecalis. Journal of Hazardous Materials, 147, 672-        676.
Ji, Y., Mao, G., Wang, Y. and Bartlam, M. (2013). Structural Insights into Diversity and
n-alkane Biodegradation Mechanisms of Alkane Hydroxylases. Frontiers in Microbiology, 4, 1–13.
Jyothi, K., Babu, S. K., Nancy Clara, K. and Kashyap, A. (2012). Identification and Isolation of
Hydrocarbon Degrading Bacteria by Molecular Characterization. Helix, 2, 105-111.
Kubicek, C.P. The Plant Biomass (2012). In Fungi and Lignocellulosic Biomass; Kubicek, C.P., Ed.; Wiley-Blackwell: Oxford, UK, 2012; pp. 1–28
Marco-Urrea, E. and Reddy, C. A. (2012). Degradation of chloro-organic pollutant by white-rotfungi. In S. N. Singh (Ed.), Microbial degradation of xenobiotics (pp. 31–66).        Berlin: Springer.
Marques-Rocha, F. J., Hernandez-Rodrigues, V. and Lamela, M. A. T. (2000). Biodegradation of
Diesel Oil by Microbial Consortium. Water, Soil and Air Pollution, 128, 313-20.
Martinez, A.T., Ruiz-Duenas, F.J., Martínez, M.J., del Rio, J.C. and Gutierrez, A. (2009). Enzymatic delignification of plant cell wall: from nature to mill. Current Opinion in Biotechnology, 20, 348-357.
Mosier, N., Wyman, C., Dale, B., Elander, R., Lee, Y.Y., Holtzapple, M. and Ladisch, M. (2005). Features of promising technologies for pretreatment of lignocellulosic biomass. Bioresource technology, 96, 673-686.
Nakazawa, T. and Yokota, T. (1973). Benzoate Metabolism in Pseudomonas putida (arvilla) mt-
2, Demonstration of Two Benzoate Pathways. Journal of Microbiology, 115; 262–267.
Nicholson, C. A. and Fathepure, B. Z. (2004). Biodegradation of benzene by halophilic and halotolerant bacteria under aerobic conditions. Applied Environmental Microbiology, 70, 1222- 1225.
Okoro, C. C. and Amund, O. O. (2010). Biodegradation of Produce Water Hydrocarbons by Pure
Cultures of Alcaligenes sp. Journal of American Science, 6, 107-112
Pepi, M., Minacci, A., Cello, F. D., Baldi, F. and Fani, R. (2003). Long Term Analysis of
Diesel Fuel Consumption in a Co-Culture of Acinetobacter venetianus, Pseudomonas putida and Alcaligenes faecalis. Antonie van Leeuwenhoek, 89, 3-9.
Phelps, C. D. and Young, L. Y. (1999). Anaerobic Biodegradation of BTEX and Gasoline
in Various Aquatic Sediments. Biodegradation, 10, 15–25.
Płaza, G.A., Wypych, J., Berry, C. and Brigmon, R.L. (2007). Utilization of monocyclic aromatic hydrocarbons individually and in mixture by bacteria isolated from petroleum-contaminated soil. World Journal of Microbiology and Biotechnology, 23, 533-542
Puentes-Téllez, P.E and Salles, J.F. (2018). Construction of effective minimal active microbial
consortia for lignocellulose degradation. Microbial Ecology, 76, 419–429.
Ralph, J., Lundquist, K., Brunow, G., Lu, F., Kim, H., Schatz, P.F., Marita, J.M., Hatfield, R.D., Ralph, S.A., Christensen, J.H. and Boerjan, W. (2004). Lignins: natural polymers from oxidative coupling of 4-hydroxyphenyl-propanoids. Phytochemistry Reviews, 3, 29-60.
Rojo, F. (2009). Degradation of Alkanes by Bacteria. Environmental Microbiology, 11, 2477–
Santhini, K., Myla, J., Sajani, S. and Usharani, G. (2009). Screening of Micrococcus sp from Oil
Contaminated Soil with Reference to Bioremediation. Botany Research International, 2(4), 248-252.
Saratale, G. D., Bhosale, S. K., Kalme, S. D. and Govindwar, S. P. (2007). Biodegradation of
Kerosene in Aspergillus ochraceus (NCIM-1146). Journal of Basic Microbiology, 47, 400-405.
Schnitzer, M. and Monreal, C.M. (2011). Quo vadis soil organic matter research? A biological link to the chemistry of humification. In Advances in agronomy, 113, 143-217.
So, C. M. and Young, L. Y. (1999). Isolation and Characterization of a Sulfate-Reducing
Bacterium that Anaerobically Degrades Alkanes. Applied Environmental Microbiology, 65, 2969–2976.
van Beilen, J. B., Li, Z., Duetz, W. A., Smits, T. H. M. and Witholt, B. (2003). Diversity
of Alkane Hydroxylase System in the Environment.Oil and Gas Science and Technology, 58(4), 427-440.
Yeom, S.H. and Yoo, Y.J. (2002). Analysis of microbial adaptation at enzyme level for enhancing biodegradation rate of BTX. Korean Journal of Chemical Engineering, 19, 780-782.
Zampolli, J., Collina, E., Lasagni, M. and Di Gennaro, P. (2014). Biodegradation of Variable-Chain-Length n-Alkanes in Rhodococcus opacus R7 and the Involvement of an Alkane Hydroxylase System in the Metabolism.AMB Express, 4(73), 1-9.
Zhenghui, L., Wenyu, X., Dehao, L., Yang, P., Zesheng, L. and Shusi, L. (2016). Biodegradation of Phenol by Bacteria Strain Acinetobacter calcoaceticus PA Isolated from Phenolic Wastewater. International Journal of Environmental Research and Public Health,13(300), 1-8.