Monitoring of Microorganisms Added into Oil-Contaminated Microenvironments by Terminal-Restriction Fragment Length Polymorphism Analysis |
JUNG SEONG-YOUNG
(Microbiology Laboratory, Korea Ocean Research & Development Institute, Department of Biochemistry, Hanyang University)
LEE JUNG-HYUN (Microbiology Laboratory, Korea Ocean Research & Development Institute) CHAI YOUNG-GYU (Department of Biochemistry, Hanyang University) KIM SANG-JIN (Microbiology Laboratory, Korea Ocean Research & Development Institute) |
1 | Avaniss-Aghajani, E., K. Jones, D. Chapman, and C. Brunk. 1994. A molecular technique for identification of bacteria using small subunit ribosomal RNA sequences. BioTechniques 17: 144-149 |
2 | Bertani, G. 1951. Studies of lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J. Bacteriol. 62: 293-300 |
3 | Chin, K.-J., T. Lukow, and R. Conrad. 1999. Effect of temperature on structure and function of the methanogenic archaeal community in an anoxic rice field soil. Appl. Environ. Microbiol. 65: 2341-2349 |
4 | Choi, S.-C., K. K. Kwon, J. H. Sohn, and S.-J. Kim. 2002. Evaluation of fertilizer additions to stimulate oil biodegradation in sand seashore mesocosms. J. Microbiol. Biotechnol. 12: 431-436 |
5 | Jackman, S. C., H. Lee, and J. T. Trevors. 1992. Survival, detection and containment of bacteria. Microbial Releases 1: 125-154 |
6 | Kim, T.-H., J.-H. Lee, Y.-S. Oh, K.-S. Bae, and S.-J. Kim. 1999. Identification and characterization of an oil-degrading yeast, Yarrowia lipolytica 180. J. Microbiol. 37: 128-135 |
7 | Ludemann, H., I. Arth, and W. Liesack. 2000. Spatial changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores. Appl. Environ. Microbiol. 66: 754-762 DOI ScienceOn |
8 | Maidak, B. L., J. R. Cole, C. T. Parker, Jr. G. M. Garrity, N. Larsen, B. Le, T. G. Lilburn, M. J. McCaughey, G. J. Olsen, R. Overbeek, S. Pramanik, T. M. Schmidt, J. M. Tiedje, and C. R. Woese. 1999. A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res. 27: 171-173 DOI ScienceOn |
9 | Moeseneder, M. M., J. M. Arrieta, G. Muyzer, C. Winter, and G. J. Herndl. 1999. Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 65: 3518-3525 |
10 | Marsh, T. L. 1999. Terminal restriction fragment length polymorphism (T-RFLP): An emerging method for characterizing diversity among homologous populations of amplification products. Curr. Opin. Microbiol. 2: 323-327 DOI PUBMED ScienceOn |
11 | Osborn, A. M., E. R. B. Moore, and K. N. Timmis. 2000. An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ. Microbiol. 2: 39-50 DOI ScienceOn |
12 | Oh, Y.-S., D.-S. Sim, and S.-J. Kim. 2003. Effectiveness of bioremediation on oil-contaminated sand in intertidal zone. J. Microbiol. Biotechnol. 13: 437-443 |
13 | Marsh, T. L., W.-T. Liu, L. J. Forney, and H. Cheng. 1998. Beginning a molecular analysis of the eukaryal community in activated sludge. Wat. Sci. Tech. 37: 455-460 DOI ScienceOn |
14 | Bartha, R. and D. Pramer. 1965. Features of a flask and method for measuring the persistence and biological effects of pesticides in soil. Soil Sci. 100: 68-70 DOI |
15 | Dunbar, J., L. O. Ticknor, and C. R. Kuske. 2000. Assessment of microbial diversity in four southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis. Appl. Environ. Microbiol. 66: 2943-2950 DOI ScienceOn |
16 | Lee, J.-H., S.-Y. Jung, and S.-J. Kim. 2001. Specific detection of an oil-degrading bacterium, Corynebacterium sp. IC10, in sand microcosms by PCR using species-specific primers based on 16S rRNA gene sequences. Biotechnol. Lett. 23: 1741-1748 DOI ScienceOn |
17 | Nam, K., H. S. Moon, J. Y. Kim, and J. J. Kukor. 2002. Linkage between biodegradation of polycyclic aromatic hydrocarbons and phospholipid profiles in soil isolates. J. Microbiol. Biotechnol. 12: 77-83 |
18 | Farrelly, V., F. A. Rainey, and E. Stackebrandt. 1995. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl. Environ. Microbiol. 61: 2798-2801 |
19 | Clement, B. G., L. E. Kehl, K. L. Debord, and C. L. Kitts. 1998. Terminal restriction fragment patterns (TRFPs), a rapid, PCR-based method for the comparison of complex bacterial communities. J. Microbiol. Meth. 31: 135-142 DOI ScienceOn |
20 | Kim, T.-H., Y.-S. Oh, and S.-J. Kim. 2000. The possible involvement of the cell surface in aliphatic hydrocarbon utilization by an oil-degrading yeast, Yarrowia lipolytica 180. J. Microbiol. Biotechnol. 10: 333-337 |
21 | Dunbar, J., L. O. Ticknor, and C. R. Kuske. 2001. Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities. Appl. Environ. Microbiol. 67: 190-197 DOI ScienceOn |
22 | Lee, J.-H., H.-H. Shin, H.-K. Lee, K.-K. Kwon, and S.-J. Kim. 1998. Efficient removal of humic substances in preparing DNA extract from marine sediments. Kor. J. Microbiol. 34: 132-136 |
23 | Rainey, F. A., N. Ward, L. I. Sly, and E. Stackebrandt. 1994. Dependence of the taxon composition of clone libraries for PCR amplified, naturally occurring 16S rDNA, on the primer pair and the cloning system used. Experientia 50: 796-797 |
24 | Amann, R. I., W. Ludwig, and K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 9: 143-169 |
25 | Kim, J.-S., S.-W. Kwon, F. Jordan, and J.-C. Ryu. 2003. Analysis of bacterial community structure in bulk soil, rhizosphere soil, and root samples of hot pepper plants using FAME and 16S rDNA clone libraries. J. Microbiol. Biotechnol. 13: 236-242 |
26 | Liu, W.-T., T. L. Marsh, H. Cheng, and L. J. Forney. 1997. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl. Environ. Microbiol. 63: 4516-4522 |
27 | Matsuki, T., K. Watanabe, R. Tanaka, M. Fukuda, and H. Oyaizu. 1999. Distribution of bifidobacterial species in human intestinal microflora examined with 16S rRNA-genetargeted species-specific primers. Appl. Environ. Microbiol. 65: 4506-4512 |
28 | Suzuki, M. T. and S. J. Giovannoni. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62: 625-630 |
29 | Liu, W.-T., T. L. Marsh, and L. J. Forney. 1998. Determination of the microbial diversity of anaerobic-aerobic activated sludge by a novel molecular biological technique. Wat. Sci. Tech. 37: 417-422 DOI ScienceOn |
30 | Zhou, J., A. V. Palumbo, and J. M. Tiedje. 1997. Sensitive detection of a novel class of toluene degrading denitrifiers, Azoarcus tolulyticus, with small-subunit rRNA primers and probes. Appl. Environ. Microbiol. 63: 2384-2390 |
31 | Leser, T. D., M. Boye, and N. B. Hendriksen. 1995. Survival and activity of Pseudomonas sp. strain B13 (FR1) in a marine microcosm determined by quantitative PCR and an rRNA-targeting probe and its effect on the indigenous bacterioplankton. Appl. Environ. Microbiol. 61: 1201-1207 |
32 | Reysenbach, A.-L., L. J. Giver, G. S. Wickham, and N. R. Pace. 1992. Differential amplification of rRNA genes by polymerase chain reaction. Appl. Environ. Microbiol. 58: 3417-3418 |
33 | Bruce, K. D. 1997. Analysis of mer gene subclasses within bacterial communities in soils and sediments resolved by fluorescent-PCR-restriction fragment length polymorphism profiling. Appl. Environ. Microbiol. 63: 4914-4919 |
34 | Tsai, Y.-L. and B. H. Olson. 1992. Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Appl. Environ. Microbiol. 58: 754-757 |
35 | Vionis, A. P., E. A. Katsifas, and A. D. Karagouni. 1998. Survival, metabolic activity and conjugative interactions of indigenous and introduced streptomycete strains in soil microcosm. Antonie Van Leeuwenhoek 73: 103-115 DOI ScienceOn |
36 | van der Maarel, M. J. E. C., R. R. E. Artz, R. Haanstra, and L. J. Forney. 1998. Association of marine archaea with the digestive tracts of two marine fish species. Appl. Environ. Microbiol. 64: 2894-2898 |
37 | Marsh, T. L., P. Saxman, J. Cole, and J. Tiedje. 2000. Terminal restriction fragment length polymorphism analysis program, a Web-based research tool for microbial community analysis. Appl. Environ. Microbiol. 66: 3616-3620 DOI ScienceOn |
38 | Moeseneder, M. M., C. Winter, J. M. Arrieta, and G. J. Herndl. 2001. Terminal-restriction fragment length polymorphism (T-RFLP) screening of a marine archaeal clone library to determine the different phylotypes. J. Microbiol. Meth. 44: 159-172 DOI ScienceOn |
39 | Wagner, M., R. Amann, H. Lemme, and K. Schleife. 1993. Probing activated sludge with oligonucleotides specific for proteobacteria: Inadequacy of culture-dependent methods for describing microbial community structure. Appl. Environ. Microbiol. 59: 1520-1525 |
40 | Fogel, G. B., C. R. Collins, J. Li, and C. F. Brunk. 1999. Prokaryotic genome size and SSU rDNA copy number: Estimation of microbial relative abundance from a mixed population. Microbiol. Ecol. 38: 93-113 DOI ScienceOn |
41 | Meckenstock, R., P. Steinle, J. R. Van de Meer, and M. Snozzi. 1998. Quantification of bacterial mRNA involved in degradation of 1,2,4-trichlorobenzene by Pseudomonas sp. strain P51 from liquid culture and from river sediment by reverse transcriptase PCR (RT/PCR). FEMS Microbiol. Lett. 167: 123-129 DOI ScienceOn |
42 | Kuske, C. R., K. L. Banton, D. L. Adorada, P. C. Stark, K. K. Hill, and P. J. Jackson. 1998. Small-scale DNA sample preparation method for field PCR detection of microbial cells and spores in soil. Appl. Environ. Microbiol. 64: 2463- 2472 |
43 | Shin, S. K., Y.-S. Oh, and S.-J. Kim. 1999. Biodegradation of phenanthrene by Sphingomonas sp. strain KH3-2. J. Microbiol. 37: 185-192 |