Journal of Microbiology and Biotechnology

  • 제14권1호
  • /
  • Pages.205-211
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  • 2004
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  • 1017-7825(pISSN)
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  • 1738-8872(eISSN)
한국미생물·생명공학회 (The Korean Society for Microbiology and Biotechnology)
권호 표지

Remarkable Bacterial Diversity in the Tidal Flat Sediment as Revealed by 16S rDNA Analysis

  • Chun, Jong-Sik (School of Biological Sciences, Seoul National University) ;
  • Kim, Bong-Soo (School of Biological Sciences, Seoul National University) ;
  • Oh, Huyn-Myung (School of Biological Sciences, Seoul National University) ;
  • Kang, Ho-Jeong (Department of Environmental Science and Engineering, School of Engineering, Ewha Womans University) ;
  • Park, Seok-Soon (Department of Environmental Science and Engineering, School of Engineering, Ewha Womans University)
  • 발행 : 2004.02.01
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초록

A 16S rDNA clone library was generated to investigate the bacterial diversity in tidal flat sediment in Ganghwa Island, Republic of Korea. A total of 103 clones were sequenced and analyzed by comprehensive phylogenetic analyses. No clones were identical to any of known 16S rRNA sequences in public databases. Sequenced clones fell into thirteen lineages of the domain Bacteria: the alpha, beta, gamma, delta, and epsilon Proteobacteria, Actinobacteria, CFB group, Chloroflexi, Acidobacteria, Planctomycetes, Verrucomicrobia, and known uncultured candidate divisions (OP11, BRC1, KSB1, and WS1). Two clones were not associated with any known bacterial divisions. The majority of clones belonged to the gamma and delta Proteobacteria (46.7%). Clones of Actinobacteria were distantly related to known taxa. It is evident from 16S rDNA-based community analysis that the bacterial community in tidal flat sediment is remarkably diverse and unique among other marine environments examined so far.

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참고문헌

  1. Amann, R. I., W. Ludwig, and K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143- 169
  2. Carling, P. A. 1982. Temporal and spatial variation in intertidal sedimentation rates. Sedimentol. 29: 17-23 https://doi.org/10.1111/j.1365-3091.1982.tb01705.x
  3. Choi, H.-P., H.-J. Kang, H.-C. Seo, and H.-C. Sung. 2002. Isolation and identification of photosynthetic bacterium useful for waste water treatment. J. Microbiol. Biotechnol. 12: 643-648
  4. Chun, J. and M. Goodfellow. 1995. A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int. J. Syst. Bacteriol. 45: 240-245
  5. Chun, J., A. Huq, and R. R. Colwell. 1999. Analysis of 16S- 23S rRNA intergenic spacer regions of Vibrio cholerae and Vibrio mimicus. Appl. Environ. Microbiol. 65: 2202-2208
  6. Cifuentes, A., J. Anton, S. Benlloch, A. Donnelly, R. A. Herbert, and F. Rodriguez-Valera. 2000. Prokaryotic diversity in Zostera noltii-colonized marine sediments. Appl. Environ. Microbiol. 66: 1715-1719
  7. Crump, B. C., E. V. Armbrust, and J. A. Baross. 1999. Phylogenetic analysis of particle-attached and free-living bacterial communities in the columbia river, its estuary, and the adjacent coastal ocean. Appl. Environ. Microbiol. 65: 3192-3204
  8. Derakshani, M., T. Lukow, and W. Liesack. 2001. Novel bacterial lineages at the (sub)division level as detected by signature nucleotide-targeted recovery of 16S rRNA genes from bulk soil and rice roots of flooded rice microcosms. Appl. Environ. Microbiol. 67: 623-631
  9. Devereux, R., M. Delaney, F. Widdel, and D. A. Stahl. 1989. Natural relationships among sulfate-reducing eubacteria. J. Bacteriol. 171: 6689-6695
  10. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791
  11. Freitag, T. E. and J. I. Prosser. 2003. Community structure of ammonia-oxidizing bacteria within anoxic marine sediments. Appl. Environ. Microbiol. 69: 1359-1371
  12. Gray, J. P. and R. P. Herwig. 1996. Phylogenetic analysis of the bacterial communities in marine sediments. Appl. Environ. Microbiol. 62: 4049-4059
  13. Hedlund, B. P., A. D. Geiselbrecht, T. J. Bair, and J. T. Staley. 1999. Polycyclic aromatic hydrocarbon degradation by a new marine bacterium, Neptunomonas naphthovorans gen. nov., sp. nov. Appl. Environ. Microbiol. 65: 251-259
  14. Holben, W. E., J. K. Jansso, B. K. Chelm, and J. M. Tiedje. 1988. DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl. Environ. Microbiol. 54: 703-711
  15. Huber, J. A., D. A. Butterfield, and J. A. Baross. 2003. Bacterial diversity in a subseafloor habitat following a deepsea volcanic eruption. FEMS Microbiol. Ecol. 43: 393-409
  16. Hugenholtz, P., C. Pitulle, K. L. Hershberger, and N. R. Pace. 1998. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180: 366-376
  17. Hurst, C. J. 1997. Recovery of bacterial community DNA from soil, pp. 433-434. In Hurst, C. J., R. L. Crawford, G. R. Knudsen, M. J. McInerney and L. D. Stetzenbach (eds.), Manual of Environmental Microbiology, 2nd ed. ASM Press, Washington DC, U.S.A
  18. Jorgensen, B. B. 1982. Ecology of the bacteria of the sulphur cycle with special reference to anoxic-oxic interface environments. Philos. Trans. R Soc. Lond. B Biol. Sci. 298: 543-561 https://doi.org/10.1098/rstb.1982.0096
  19. Jukes, T. H. and C. R. Cantor. 1969. Evolution of protein molecules, pp. 21-132. In Munro, H. N. (ed.), Mammalian Protein Metabolism. Academic Press, New York, U.S.A
  20. LaPara, T. M., C. H. Nakatsu, L. Pantea, and J. E. Alleman. 2000. Phylogenetic analysis of bacterial communities in mesophilic and thermophilic bioreactors treating pharmaceutical wastewater. Appl. Environ. Microbiol. 66: 3951-3959
  21. Lee, W. J. and K. S. Bae. 2001. The phylogenetic relationship of several oscillatorian cyanobacteria, forming blooms at Daecheong reservoirs, based on partial 16S rRNA gene sequences. J. Microbiol. Biotechnol. 11: 504-507
  22. Li, L., C. Kato, and K. Horikoshi. 1999. Bacterial diversity in deep-sea sediments from different depths. Biodivers. Conserv. 8: 659-677
  23. Li, L., C. Kato, and K. Horikoshi. 1999. Microbial diversity in sediments collected from the deepest cold-seep area, the Japan Trench. Mar. Biotechnol. 1: 391-400 https://doi.org/10.1007/PL00011793
  24. 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
  25. Llobet-Brossa, E., R. Rossello-Mora, and R. Amann. 1998. Microbial community composition of Wadden Sea sediments as revealed by fluorescence in situ hybridization. Appl. Environ. Microbiol. 64: 2691-2696
  26. 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 oil spill. Appl. Environ. Microbiol. 65: 3566-3574
  27. Maidak, B. L., G. J. Olsen, N. Larsen, R. Overbeek, M. J. McCaughey, and C. R. Woese. 1997. The RDP (Ribosomal Database Project). Nucleic Acids Res. 25: 109-111
  28. Mullins, T. D., T. B. Britschgi, R. L. Krest, and S. J. Giovannoni. 1995. Genetic comparisons reveal the same unknown bacterial lineages in atlantic and pacific bacterioplankton communities. Limnol. Oceanogr. 40: 148-158 https://doi.org/10.4319/lo.1995.40.1.0148
  29. Page, A. L., R. H. Miller, and D. R. Keeney. 1982. Methods of Soil Analysis. Part 2: Chemical and Microbiological Properties, 2nd ed. American Society of Agronomy, Madison, WI, U.S.A
  30. Park, J., B., H. Lee, W., S.-Y. Lee, J. O. Lee, I. S. Bang, E. S. Choi, D. H. Park, and Y. K. Park. 2002. Microbial community analysis of 5-stage biological nutrient removal process with step feed system. J. Microbiol. Biotechnol. 12: 929-935
  31. Phelps, C. D., L. J. Kerkhof, and L. Y. Young. 1998. Molecular characterization of a sulfate-reducing consortium which mineralizes benzene. FEMS Microbiol. Ecol. 27: 269-279
  32. Ravenschlag, K., K. Sahm, C. Knoblauch, B. B. Jorgensen, and R. Amann. 2000. Community structure, cellular rRNA content, and activity of sulfate- reducing bacteria in marine arctic sediments. Appl. Environ. Microbiol. 66: 3592-3602
  33. Ravenschlag, K., K. Sahm, J. Pernthaler, and R. Amann. 1999. High bacterial diversity in permanently cold marine sediments. Appl. Environ. Microbiol. 65: 3982-3989
  34. Sahm, K., C. Knoblauch, and R. Amann. 1999. Phylogenetic affiliation and quantification of psychrophilic sulfatereducing isolates in marine arctic sediments. Appl. Environ. Microbiol. 65: 3976-3981
  35. Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425
  36. Smith, W. 1993. Ecological actions of sulfate-reducing bacteria, pp. 161-188. In Odom, J. M. and R. Singleton (eds.), The Sulfate-Reducing Bacteria: Contemporary Perspectives. Springer-Verlag, New York, U.S.A
  37. Tanner, M. A., C. L. Everett, W. J. Coleman, M. M. Yang, and D. C. Youvan. 2000. Complex microbial consortia inhabiting hydrogen sulfide-rich black mud from marine coastal environments. Biotechnol. et alia 8: 1-16
  38. Torsvik, V., J. Goksoyr, and F. L. Daae. 1990. High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56: 782- 787
  39. Urakawa, H., K. Kita-Tsukamoto, and K. Ohwada. 1999. Microbial diversity in marine sediments from Sagami Bay and Tokyo Bay, Japan, as determined by 16S rRNA gene analysis. Microbiology 145: 3305-3315
  40. Yanagibayashi, M., Y. Nogi, L. Li, and C. Kato. 1999. Changes in the microbial community in Japan Trench sediment from a depth of 6292 m during cultivation without decompression. FEMS Microbiol. Lett. 170: 271-279
  41. Yi, H. and J. Chun. 2002. Remarkable cultured bacterial biodiversity in getbol, the tidal flat of Korea. IUMS World Congress, Paris, France