To characterize the long-chain cyclic alkane ( c -alkane) degradation of bacteria in Rhodococcus , we analyzed the relationship between the alkane hydroxylase gene ( alkB ) and long-chain c-alkane degradation in 19 species. Eleven strains which were isolated from nature using long-chain c-alkane as a substrate were identified as R. erythropolisc , and all were shown to carry the alkB [ alkB R2 type]. This gene type was also carried by two other species, R. rhodochrous and R. baikonurensis . In total, 17 species of the genus Rhodococcus carried alkB , but the gene types differed from each other. The two species R. rhodnii and R. coprophilus did not carry alkB , and their long-chain c -alkane degradation levels were low.
Usman, M., Faure, P., Hanna, K., Abdelmoula, M. and Ruby, C. (2012) Application of Magnetite Catalyzed Chemical Oxidation (Fenton-Like and Persulfate) for the Remediation of Oil Hydrocarbon Contamination. Fuel, 96, 270-276. https://doi.org/10.1016/j.fuel.2012.01.017
Hatayama, K., Sakihama, Y., Matsumiya, Y. and Kubo, M. (2008) Construction of an Efficient Bioremediation System for Petroleum Hydrocarbon-Contaminated Soils Using Specific Hydrocarbon-Degrading Bacteria and Bacterial Biomass Monitoring. In: Domínguez, J.B., Ed., Soil Contamination Research Trends, Nova Science Publishers, NY, 143-160.
Dua, M., Johri, A.K., Singh, A. and Sethunathan, N. (2002) Biotechnology and Bioremediation: Successes and Limitations. Applied Microbiology and Biotechnology, 59, 143-152. https://doi.org/10.1007/s00253-002-1024-6
Vidali, M. (2001) Bioremediation. An Overview. Pure and Applied Chemistry, 73, 1163-1172. https://doi.org/10.1351/pac200173071163
Stroud, J.L., Paton, G.I. and Semple, K.T. (2007) Microbe-Aliphatic Hydrocarbon Interactions in Soil: Implications for Biodegradation and Bioremediation. Journal of Applied Microbiology, 102, 1239-1253. https://doi.org/10.1111/j.1365-2672.2007.03401.x
Kissin, Y.V. (1990) Catagenesis of Light Cycloalkanes in Petroleum. Organic Geochemistry, 15, 575-594. https://doi.org/10.1016/0146-6380(90)90103-7
Korda, A., Santas, P., Tenente, A. and Santas, R. (1997) Petroleum Hydrocarbon Bioremediation: Sampling Analytical Techniques, in Situ Treatment and Commercial Microorganisms Currently Used. Applied Microbiology and Biotechnology, 48, 677-686. https://doi.org/10.1007/s002530051115
Pritchard, P.H., Mueller, J.G., Rogers, J.C., Kremer, F.V. and Glaser, J.A. (1992) Oil Spill Bioremediation: Experiences, Lessons and Results from the Exxon Valdez Oil Spill in Alaska. Biodegradation, 3, 315-335. https://doi.org/10.1007/BF00129091
Adhikari, D., Perwira, I.Y., Araki, K.S. and Kubo, M. (2016) Sitimulation of Soil Microorganisms in Pesticide-Contaminated Soil Using Organic Materials. AIMS Bioengineering, 3, 379-388. https://doi.org/10.3934/bioeng.2016.3.379
Blakley, E.R. (1978) The Microbial Degradation of Cyclohexanecarboxylic Acid by a β-Oxidation Pathway with Simultaneous Induction to the Utilization of Benzoate. Canadian Journal of Microbiology, 24, 847-855. https://doi.org/10.1139/m78-141
Blakley, E.R. and Papish, B. (1982) The Metabolism of Cyclohexanecarboxylic Acid and 3-Cyclohexenecarboxylic Acid by Pseudomonas putida. Canadian Journal of Microbiology, 28, 1324-1329. https://doi.org/10.1139/m82-198
Komukai-Nakamura, S., Sugiura, K., Yamauchi-Inomata, Y., Toki, H., Venkateswaran, K., Yamamoto, S., Tanaka, H. and Harayama, S. (1996) Construction of Bacterial Consortia That Degrade Arabian Light Crude Oil. Journal of Fermentation and Bioengineering, 82, 570-574. https://doi.org/10.1016/S0922-338X(97)81254-8
Aislabie, J., Saul, D.J. and Foght, J.M. (2006) Bioremediation of Hydrocarbon-Contaminated Polar Soils. Extremophiles, 10, 171-179. https://doi.org/10.1007/s00792-005-0498-4
Zampolli, J., Collina, E., Lasagni, M. and Gennaro1, P.G. (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. https://doi.org/10.1186/s13568-014-0073-4
Throne-Holst, M., Wentzel, A., Ellingsen, T.E., Kotlar, H.K. and Zotchev, S.B. (2007) Identification of Novel Genes Involved in Long-Chain n-Alkane Degradation by Acinetobacter sp. Strain DSM 17874. Applied and Environmental Microbiology, 73, 3327-3332. https://doi.org/10.1128/AEM.00064-07
Lal, B. and Khanna, S. (1996) Degradation of Crude Oil by Acinetobacter calcoaceticus and Alcaligenes odorans. Journal of Applied Microbiology, 81, 355-362. https://doi.org/10.1111/j.1365-2672.1996.tb01926.x
Sakai, Y., Maeng, J.H., Tani, Y. and Kato, N. (1994) Use of Long-Chain n-alkanes (C13-C44) by an Isolate, Acinetobacter sp. M-1. Bioscience, Biotechnology and Biochemistry, 58, 2128-2130. https://doi.org/10.1271/bbb.58.2128
Táncsics, A., Benedek, T., Szoboszlay, S., Veres, P.G., Farkas, M., Máthé, I., Márialigeti, K., Kukolya, J., Lányi, S. and Kriszt, B. (2015) The Detection and Phylogenetic Analysis of the Alkane 1-Monooxygenase Gene of Members of the Genus Rhodococcus. Systematic and Applied Microbiology, 38, 1-7. https://doi.org/10.1016/j.syapm.2014.10.010
Kubota, K., Koma, D., Matsumiya, Y., Chung, S.Y. and Kubo, M. (2008) Phylogenetic Analysis of Long-Chain Hydrocarbon-Degrading Bacteria and Evaluation of Their Hydrocarbon-Degradation by the 2,6-DCPIP Assay. Biodegradation, 19, 749-757. https://doi.org/10.1007/s10532-008-9179-1
Koma, D., Sakashita, Y., Kubota, K., Fujii, Y., Hasumi, F., Chung, S.Y. and Kubo, M. (2004) Degradation Pathways of Cyclic Alkanes in Rhodococcus sp. NDKK48. Applied Microbiology and Biotechnology, 66, 92-99. https://doi.org/10.1007/s00253-004-1623-5
Kostichka, K., Thomas, S.M., Gibson, K.J., Nagarajan, V. and Cheng, Q. (2001) Cloning and Characterization of a Gene Cluster for Cyclododecanone Oxidation in Rhodococcus ruber SC1. Journal of Bacteriology, 183, 6478-6486. https://doi.org/10.1128/JB.183.21.6478-6486.2001
van Hamme, J.D., Odumeru, J.A. and Ward, O.P. (2000) Community Dynamics of a Mixed-Bacterial Culture Growing on Petroleum Hydrocarbons in Batch Culture. Canadian Journal of Microbiology, 46, 441-450. https://doi.org/10.1139/w00-013
van Beilen, J.B., Smits, T.H.M., Roos, F.F., Brunner, T., Balada, S.B., Rothlisberger, M. and Witholt, B. (2005) Identification of an Aminno Acid Position That Determines the Substrate Range of Integral Membrane Alkane Hydroxylases. Journal of Bacteriology, 187, 85-91. https://doi.org/10.1128/JB.187.1.85-91.2005
van Beilen, J.B. and Funhoff, E.G. (2007) Alkane Hydroxylases Involved in Microbial Alkane Degradation. Applied Microbiology and Biotechnology, 74, 13-21. https://doi.org/10.1007/s00253-006-0748-0
Whyte, L.G., Smits, T.H.M., Labbé, D., Witholt, B., Greer, C.W. and van Beilen, J.B. (2002) Gene Cloning and Characterization of Multiple Alkane Hydroxylase Systems in Rhodococcus Strains Q15 and NRRL B-16531. Applied and Environmental Microbiology, 68, 5933-5942. https://doi.org/10.1128/AEM.68.12.5933-5942.2002
Fujii, T., Narikawa, T., Takeda, K. and Kato, J. (2004) Biotransformation of Various Alkanes Using the Escherichia coli Expressing an Alkane Hydroxylase System from Gordonia sp. TF6. Bioscience, Biotechnology and Biochemistry, 68, 2171-2177. https://doi.org/10.1271/bbb.68.2171
Vomberg, A. and Klinner, U. (2000) Distribution of alkB Genes within n-Alkane-Degrading Bacteria. Journal of Applied Microbiology, 89, 339-348. https://doi.org/10.1046/j.1365-2672.2000.01121.x
Whyte, L.G., Hawari, J., Zhou, E., Bourbonniére, L., Inniss, W. and Greer, C.W. (1998) Biodegradation of Variable-Chain-Length Alkanes at Low Temperatures by a Psychrotrophic Rhodococcus sp. Applied and Environmental Microbiology, 64, 2578-2584.
van Beilen, J.B., Smits, T.H.M., Whyte, L.G., Schorcht, S., Röthlisberger, M., Plaggemeier, T., Engesser, H. and Witholt, B. (2002) Alkane Hydroxylase Homologues in Gram-Positive Strains. Environmental Microbiology, 4, 676-682. https://doi.org/10.1046/j.1462-2920.2002.00355.x
Hara, A., Baik, S.H., Syutsubo, K., Misawa, N., Smits, T.H.M., van Beilen, J.B. and Harayama, S. (2004) Cloning and Functional Analysis of alkB Genes in Alcanivorax borkumensis SK2. Environmental Microbiology, 6, 191-197. https://doi.org/10.1046/j.1462-2920.2003.00550.x
Rehm, H.J. and Reiff, I. (1981) Mechanisms and Occurrence of Microbial Oxidation of Long-Chain Alkanes. In: Fiechter, A., Ed., Reactors and Reactions, Vol. 19: Advances in Biochemical Engineering, Springer, Berlin, 175-215. https://doi.org/10.1007/3-540-10464-X_18
Fukuhara, Y., Horii, S., Matsuno, T., Matsumiya, Y., Mukai, M. and Kubo, M. (2013) Distribution of Hydrocarbon-Degrading Bacteria in the Soil Environment and Their Contribution to Bioremediation. Applied Biochemistry and Biotechnology, 170, 329-339. https://doi.org/10.1007/s12010-013-0170-x
Koma, D., Sakashita, Y., Kubota, K., Fujii, Y., Hasumi, F., Chung, S.Y. and Kubo, M. (2003) Degradation of Car Engine Base Oil by Rhodococcus sp. NDKK48 and Gordonia sp. NDKY76A. Bioscience, Biotechnology and Biochemistry, 67, 1590-1593. https://doi.org/10.1271/bbb.67.1590
Koma, D., Hasumi, F., Yamamoto, E., Ohta, T., Chung, S.Y. and Kubo, M. (2001) Biodegradation of Long-Chain n-Paraffins from Waste Oil of Car Engine by Acinetobacter sp. Journal of Bioscience and Bioengineering, 91, 94-96. https://doi.org/10.1016/S1389-1723(01)80120-1
Koma, D., Hasumi, F., Chung, S.Y. and Kubo, M. (2003) Biodegradation of n-Alkylcyclohexanes by Co-Oxidation via Multiple Pathways in Acinetobacter sp. ODDK71. Journal of Bioscience and Bioengineering, 95, 641-644. https://doi.org/10.1016/S1389-1723(03)80178-0
Iwamoto, T. and Nasu, M. (2001) Current Bioremediation Practice and Perspective. Journal of Bioscience and Bioengineering, 92, 1-8. https://doi.org/10.1016/S1389-1723(01)80190-0
Sanpa, S., Sumiyoshi, S., Kujira, T., Matsumiya, Y. and Kubo, M. (2006) Isolation and Characterization of a Bluegill Degrading Microorganism, and Analysis of the Root Hair-Promoting Effect of the Degraded Products. Bioscience, Biotechnology and Biochemistry, 70, 340-347. https://doi.org/10.1271/bbb.70.340
van Beilen, J.B., Li, Z., Duetz, W.A. and Witholt, B. (2003) Diversity of Alkane Hydroxylase Systems in the Environment. Oil Gas Science and Technology, 58, 427-440. https://doi.org/10.2516/ogst:2003026
van Beilen, J.B., Funhoff, E.G., van Loon, A., Just, A., Kaysser, L., Bouza, M., Holtackers, R., Röthlisberger, M., Li, Z. and Witholt, B. (2006) Cytochrome P450 Alkane Hydroxylases of the CYP153 Family Are Common in Alkane-Degrading Eubacteria Lacking Integral Membrane Alkane Hydroxylases. Applied and Environmental Microbiology, 72, 59-65.
https://doi.org/10.1128/AEM.72.1.59-65.2006
Nie, Y., Chi, C.Q., Fang, H., Liang, J.L., Lu, S.L., Lai, G.L., Tang, Y.Q. and Wu, X.L. (2014) Diverse Alkane Hydroxylase Genes in Microorganisms and Environments. Scientific Reports, 4, Article No. 4968. https://doi.org/10.1038/srep04968