Browse > Article

Analysis of Bacterial Diversity and Community Structure in Forest Soils Contaminated with Fuel Hydrocarbon  

Ahn Jae-Hyung (School of Agricultural Biotechnology, Seoul National University)
Kim Mi-Soon (School of Agricultural Biotechnology, Seoul National University)
Kim Min-Cheol (School of Agricultural Biotechnology, Seoul National University)
Lim Jong-Sung (National Instrumentation Center for Environmental Management, Seoul National University)
Lee Goon-Taek (National Instrumentation Center for Environmental Management, Seoul National University)
Yun Jun-Ki (Research Institute of Technology, Samsung Corporation)
Kim Tae-Sung (Ecosystem Disturbance Assessment Division, Nature and Ecology Research Department, National Institute of Environmental Research)
Kim Tae-San (Genetic Resources Division, National Institute of Agricultural Biotechnology, Rural Development Administration)
Ka Jong-Ok (School of Agricultural Biotechnology, Seoul National University)
Publication Information
Journal of Microbiology and Biotechnology / v.16, no.5, 2006 , pp. 704-715 More about this Journal
Abstract
Oil spill was found in 1999 from a diesel storage facility located near the top of Baekun Mountain in Uiwang City. Application of bioremediation techniques was very relevant in removing oil spills in this site, because the geological condition was not amenable for other onsite remediation techniques. For efficient bioremediation, bacterial communities of the contaminated site and the uncontaminated control site were compared using both molecular and cultivation techniques. Soil bacterial populations were observed to be stimulated to grow in the soils contaminated with diesel hydrocarbon, whereas fungal and actinomycetes populations were decreased by diesel contamination. Most of the dieseldegrading bacteria isolated from contaminated forest soils were strains of Pseudomonas, Ralstonia, and Rhodococcus species. Denaturing gradient gel electrophoresis (DGGE) analysis revealed that the profiles were different among the three contaminated sites, whereas those of the control sites were identical to each other. Analysis of 16S rDNA sequences of dominant isolates and clones showed that the bacterial community was less diverse in the oil-contaminated site than at the control site. Sequence analysis of the alkane hydroxylase genes cloned from soil microbial DNAs indicated that their diversity and distribution were different between the contaminated site and the control site. The results indicated that diesel contamination exerted a strong selection on the indigenous microbial community in the contaminated site, leading to predominance of well-adapted microorganisms in concurrence with decrease of microbial diversity.
Keywords
Bioremediation; fuel; 16S rRNA; soil DNA; DGGE; bacterial community;
Citations & Related Records
Times Cited By KSCI : 3  (Citation Analysis)
Times Cited By Web Of Science : 10  (Related Records In Web of Science)
연도 인용수 순위
1 Atlas, R. M., P. D. Boehm, and J. A. Calder. 1981. Chemical and biological weathering of oil from the Amoco Cadiz spillage, within the littoral zone. Estuar. Coast Shelf Sci. 12: 589-608   DOI
2 Buckley, D. H. and T. M. Schmidt. 2002. Exploring the biodiversity of soil - a microbial rain forest, p. 183-208. In J. T. Staley and A. L. Reysenbach (eds.), Biodiversity of Microbial Life. Wiley-Liss, New York, U.S.A.
3 Felsenstein, J. 2004. PHYLIP (Phylogenetic Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle
4 Kim, M. S., J. H. Ahn, M. K. Jung, J. H. Yu, D. H. Joo, M. C. Kim, H. C. Shin, T. S. Kim, T. H. Ryu, T. S. Kim, D. H. Kim, and J. O. Ka. 2005. Molecular- and cultivationbased characterization of bacterial community structure in rice field soil. J. Microbiol. Biotechnol. 15: 1087-1093   과학기술학회마을
5 Kim, T. S., M. S. Kim, M. K. Jung, J. H. Ahn, M. J. Joe, K. H. Oh, M. H. Lee, M. K. Kim, and J. O. Ka. 2005. Analysis of plasmid pJP4 horizontal transfer and its impact on bacterial community structure in natural soil. J. Microbiol. Biotechnol. 15: 376-383   과학기술학회마을
6 Ludwig, W., S. H. Bauer, I. Held, G. Kirchhof, R. Schulze, I. Huber, S. Spring, A. Hartmann, and K.-H. Schleifer. 1997. Detection and in situ identification of representatives of a widely distributed new bacterial phylum. FEMS Microbiol. Lett. 153: 181-190   DOI
7 Maidak, B. L., J. R. Cole, T. G. Lilburn, C. T. Parker Jr, P. R. Saxman, J. M. Stredwick, G. M. Garrity, B. Li, G. J. Olsen, S. Pramanik, T. M. Schmidt, and J. M. Tiedje. 2000. The RDP (Ribosomal Database Project) continues. Nucleic Acids Res. 28: 173-174   DOI
8 Norris, T. B., J. M. Wraith, R. W. Castenholz, and T. R. McDermott. 2002. Soil microbial community structure across a thermal gradient following a geothermal heating event. Appl. Environ. Microbiol. 68: 6300-6309   DOI
9 Pinholt, Y. S., S. Struwe, and A. Kjoller. 1979. Microbial changes during oil decomposition in soil. Holarct. Ecol. 2: 195-200
10 Rojo, F. 2005. Specificity at the end of the tunnel: Understanding substrate length discrimination by the alkB alkane hydroxylase. J. Bacteriol. 187: 19-22   DOI   ScienceOn
11 Roling, W. F. M., M. G. Milner, D. M. Jones, K. Lee, F. Daniel, R. J. P. Swannell, and I. M. Head. 2002. Robust hydrocarbon degradation and dynamics of bacterial communities during nutrient-enhanced oil spill bioremediation. Appl. Environ. Microbiol. 68: 5537-5548   DOI
12 Saul, D.J., J. M. Aislabie, C. E. Brown, L. Harris, and J. M. Foght. 2005. Hydrocarbon contamination changes the bacterial diversity of soil from around Scott Base, Antarctica. FEMS Microbiol. Ecol. 53: 141-155   DOI   ScienceOn
13 Lane, D. J. 1991. 16S/23S rRNA sequencing, pp. 115-148. In E. Stackebrandt and M. Goodfellow (eds.), Nucleic Acid Techniques in Bacterial Systematics. John Wiley and Sons, Chichester, England
14 Swannell, R. P. J., D. Mitchell, G. Lethbridge, D. Jones, D. Heath, M. Hagley, M. Jones, S. Petch, R. Croxford, and K. Lee. 1999. A field demonstration of the efficacy of bioremediation to treat oiled shorelines following the Sea Empress incident. Environ. Technol. 20: 863-873   DOI   ScienceOn
15 van Beilen, J. B., F. Mourlane, M. A. Seeger, J. Kovac, Z. Li, T. H. Smits, U. Fritsche, and B. Witholt. 2003. Cloning of Baeyer-Villiger monooxygenases from Commamonas, Xanthobacter and Rhodococcus using polymerase chain reaction with highly degenerate primers. Environ. Microbiol. 5: 174-182   DOI   ScienceOn
16 Xiang, S., T. Yao, L. An, B. Xu, and J. Wang. 2005. 16S rRNA sequences and differences in bacteria isolated from the Muztag Ata glacier at increasing depths. Appl. Environ. Microbiol. 71: 4619-4627   DOI   ScienceOn
17 Venkatrswaran, K., S. Kanai, H. Tanaka, and S. Miyachi. 1993. Vertical distribution and biodegradation activity of oil degrading bacteria in the Pacific Ocean. J. Marine Biotechnol. 1: 33-39
18 Chaineau, C. H., J. Morel, J. Dupont, E. Bury, and J. Oudot. 1999. Comparison of the fuel oil biodegradation potential of hydrocarbon-assimilating microorganisms isolated from a temperate agricultural soil. Sci. Total Environ. 227: 237-247   DOI   ScienceOn
19 Powell, S. M., J. P. Bowman, I. Snape, and J. S. Stark. 2003. Microbial community variation in pristine and polluted nearshore Antarctic sediments. FEMS Microbiol. Ecol. 45: 135-145   DOI   ScienceOn
20 Kasai, Y., H. Kishira, K. Syutsubo, and S. Harayama. 2001. Molecular detection of marine bacterial populations on beaches contaminated by the Nakhodka tanker oil-spill accident. Environ. Microbiol. 3: 246-255   DOI
21 Sei, K., Y. Sugimoto, K. Mori, H. Maki, and T. Kohno. 2003. Monitoring of alkane-degrading bacteria in a sea-water microcosm during oil degradation by polymerase chain reaction based on alkane-catabolic genes. Environ. Microbiol. 5: 517-522   DOI   ScienceOn
22 Atlas, R. M. and C. E. Cerniglia. 1995. Bioremediation of petroleum pollutants: Diversity and environmental aspects of hydrocarbon biodegradation. BioScience 45: 332-338   DOI   ScienceOn
23 van Beilen, J. B., S. Panke, S. Lucchini, A. G. Franchini, M. Rothlisberger, and B. Witholt. 2001. Analysis of Pseudomonas putida alkane degradation gene clusters and flanking insertion sequences: Evolution and regulation of the alk-genes. Microbiology 147: 1621-1630   DOI
24 Alexander, M. 1982. Most probable number methods for microbial populations, pp. 815-820. In A. L. Page (ed.), Method of Soil Analysis, Part 2: Chemical and Microbiological Properties. Soil Science Society of America, Wisconsin, U.S.A
25 Fujii, T., T. Narikawa, K. Takeda, and J. Kato. 2004. Biotransformation of various alkanes using Escherichia coli expressing an alkane hydroxylase system from Gordonia sp. TF6. Biosci. Biotechnol. Biochem. 68: 2171-2177   DOI   ScienceOn
26 Van Hamme, J. D., A. Singh, and O. P. Ward. 2003. Recent advances in petroleum microbiology. Microbiol. Mol. Biol. Rev. 67: 503-549   DOI
27 Kohno, T., Y. Sugimoto, K. Sei, and K. Mori. 2002. Design of PCR primers and gene probes for general detection of alkane-degrading bacteria. Microb. Environ. 17: 114-121   DOI   ScienceOn
28 Margesin, R. and F. Shinner. 1999. Biological decontamination of oil spills in cold environments. J. Chem. Technol. Biotechnol. 74: 381-389   DOI   ScienceOn
29 Venosa, A. D., M. T. Suidan, B. A. Wrenn, K. L. Strohmeier, J. R. Haines, B. L. Eberhart, D. King, and E. Holder. 1996. Bioremediation of an experimental oil spill on the shoreline of Delaware Bay. Environ. Sci. Technol. 30: 1764-1775   DOI   ScienceOn
30 Gelsomino, A., A. C. Keijzer-Wolters, G. Cacco, and J. D. van Elsas. 1999. Assessment of bacterial community structure in soil by polymerase chain reaction and denaturing gradient gel electrophoresis. J. Microbiol. Methods 38: 1-15   DOI   ScienceOn
31 Johnson, D. B., S. Rolfe, K. B. Hallberg, and E. Iversen. 2001. Isolation and phylogenetic characterization of acidophilic microorganisms indigenous to acidic drainage waters at an abandoned Norwegian copper mine. Environ. Microbiol. 3: 630-637   DOI   ScienceOn
32 Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25: 4876-4882   DOI
33 MacNaughton, S. J., J. R. Stephen, A. D. Venosa, G. A. Davis, Y.-J. Chang, and D. C. White. 1999. Microbial population changes during bioremediation of an experimental dil spill. Appl. Environ. Microbiol. 65: 3566-3574
34 Suzuki, M., T. Hayakawa, J. P. Shaw, M. Rekik, and S. Harayama. 1991. Primary structure of xylene monooxygenase: Similarities to and differences from the alkane hydroxylation system. J. Bacteriol. 173: 1690-1695   DOI
35 Weaver, R. W., J. S. Angle, and P. S. Bottomley. 1994. Methods of Soil Analysis: Part 2-Microbiological and Biochemical Properties. Soil Science Society of America, Madison, U.S.A
36 Bossert, I. and R. Bartha. 1984. The fate of petroleum in soil ecosystems, pp. 434-476. In R. M. Atlas (ed.), Petroleum Microbiology. Macmillan Publishing Co., New York, U.S.A
37 Cho, M. J., Y. K. Kim, and J. O. Ka. 2004. Molecular differentiation of Bacillus spp. antagonistic against phytopathogenic fungi causing damping-off disease. J. Microbiol. Biotechnol. 14: 599-606
38 Floodgate, G. 1984. The fate of petroleum in marine ecosystems, pp. 355-398. In R. M. Atlas (ed.), Petroleum Microbiology. Macmillan Publishing Co., New York, U.S.A
39 Ferris, M. J., G. Muyzer, and D. M. Ward. 1996. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl. Environ. Microbiol. 62: 340-346
40 Smit, E., P. Leefang, S. Gommans, and J. Van Den Broek. 2001. Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl. Environ. Microbiol. 67: 2284-2291   DOI   ScienceOn
41 Whyte, L. G., C. W. Greer, and W. E. Innis. 1995. Assessment of the biodegradation potential of psychrotrophic microorganisms. Can. J. Microbiol. 42: 99-106
42 Bakken, L. R. and R. A. Olsen. 1987. The relationship between cell size and viability of soil bacteria. Microb. Ecol. 13: 103-114   DOI   ScienceOn
43 Smits, T. H. M., M. Rothlisberger, B. Witholt, and J. B. van Beilen. 1999. Molecular screening for alkane hydroxylase genes in gram-negative and gram-positive strains. Environ. Microbiol. 1: 307-317   DOI   ScienceOn
44 Balkwill, D. L. 1990. Deep-aquifer microorganisms, pp. 183-211. In D. P. Labeda (ed.), Isolation of Biotechnological Organisms from Nature. McGraw-Hill Publ. Co., New York, U.S.A
45 Leahy, J. G. and R. R. Colwell. 1990. Microbial degradation of hydrocarbons in the environment. Microbiol. Rev. 54: 305-315
46 Sotsky, J. B., C. W. Greer, and R. M. Atlas. 1994. Frequency of genes in aromatic and aliphatic hydrocarbon biodegradation pathways within bacterial populations from Alaskan sediments. Can. J. Microbiol. 40: 981-985   DOI   ScienceOn
47 Hattori, T., H. Mitsui, H. Haga, N. Wakao, S. Shikano, K. Gorlach, Y. Kasahara, A. El-Beltagy, and R. Hattori. 1997. Advances in soil microbial ecology and the biodiversity. Antonie van Leeuwenhoek 72: 21-28   DOI   ScienceOn
48 Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipmann. 1990. Basic local alignment tool. J. Mol. Biol. 215: 403-410   DOI
49 de Bruijn, F. J. 1992. Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria. Appl. Environ. Microbiol. 58: 2180-2187
50 Felske, A., A. Wolterink, R. V. Lis, and A. D. L. Akkermans. 1998. Phylogeny of the main bacterial 16S rRNA sequences in Drentse A grassland soils (The Netherlands). Appl. Environ. Microbiol. 64: 871-879