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High Level of Bacterial Diversity and Novel Taxa in Continental Shelf Sediment

  • Hong, Jin-Kyung (Institute of Environmental Sciences and Department of Environmental Sciences, Hankuk University of Foreign Studies) ;
  • Cho, Jae-Chang (Institute of Environmental Sciences and Department of Environmental Sciences, Hankuk University of Foreign Studies)
  • 투고 : 2011.12.02
  • 심사 : 2012.01.27
  • 발행 : 2012.06.28

초록

The bacterial diversity of the continental shelf sediment in the Yellow Sea was investigated by the cloning and sequencing of PCR-amplified 16S rRNA genes. The majority of the cloned sequences were distinct phylotypes that were novel at the species level. The richness estimator indicated that the sediment sample might harbor up to 32 phylum-level taxa. A large number of low-abundance, phylum-level taxa accounted for most of the observed phylogenetic diversity at our study site, suggesting that these low-abundance taxa might play crucial roles in the shelf sediment ecosystem.

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참고문헌

  1. Arrigo, K. R. 2005. Marine microorganisms and global nutrient cycles. Nature 437: 349-355. https://doi.org/10.1038/nature04159
  2. Ashelford, K. E., N. A. Chuzhanova, J. C. Fry, A. J. Jones, and A. J. Weightman. 2005. At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl. Environ. Microbiol. 71: 7724-7736. https://doi.org/10.1128/AEM.71.12.7724-7736.2005
  3. Bowman, J. P., S. A. McCammon, J. A. Gibson, L. Robertson, and P. D. Nichols. 2003. Prokaryotic metabolic activity and community structure in Antarctic continental shelf sediments. Appl. Environ. Microbiol. 69: 2448-2462. https://doi.org/10.1128/AEM.69.5.2448-2462.2003
  4. Bowman, J. P. and R. D. McCuaig. 2003. Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic continental shelf sediment. Appl. Environ. Microbiol. 69: 2463-2483. https://doi.org/10.1128/AEM.69.5.2463-2483.2003
  5. Chao, A. 1984. Non-parametric estimation of the number of classes in a population. Scand. J. Stat. 11: 265-270.
  6. Cho, J. C. and J. M. Tiedje. 2000. Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil. Appl. Environ. Microbiol. 66: 5448-5456. https://doi.org/10.1128/AEM.66.12.5448-5456.2000
  7. Colwell, R. K. and J. A. Coddington. 1994. Estimating terrestrial biodiversity through extrapolation. Philos. Trans. R. Soc. Lond. B Biol. Sci. 345: 101-118. https://doi.org/10.1098/rstb.1994.0091
  8. Dhillon, A., A. Teske, J. Dillon, D. A. Stahl, and M. L. Sogin. 2003. Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin. Appl. Environ. Microbiol. 69: 2765-2772. https://doi.org/10.1128/AEM.69.5.2765-2772.2003
  9. Elshahed, M. S., N. H. Youssef, A. M. Spain, C. Sheik, F. Z. Najar, L. O. Sukharnikov, et al. 2008. Novelty and uniqueness patterns of rare members of the soil biosphere. Appl. Environ. Microbiol. 74: 5422-5428. https://doi.org/10.1128/AEM.00410-08
  10. Fry, J. C., R. J. Parkes, B. A. Cragg, A. J. Weightman, and G. Webster. 2008. Prokaryotic biodiversity and activity in the deep subseafloor biosphere. FEMS Microbiol. Ecol. 66: 181-196. https://doi.org/10.1111/j.1574-6941.2008.00566.x
  11. Gray, J. P. and R. P. Herwig. 1996. Phylogenetic analysis of the bacterial communities in marine sediments. Appl. Environ. Microbiol. 62: 4049-4059.
  12. Heijs, S. K., R. R. Haese, P. W. van der Wielen, L. J. Forney, and J. D. van Elsas. 2007. Use of 16S rRNA gene based clone libraries to assess microbial communities potentially involved in anaerobic methane oxidation in a Mediterranean cold seep. Microb. Ecol. 53: 384-398. https://doi.org/10.1007/s00248-006-9172-3
  13. Hugenholtz, P., B. M. Goebel, and N. R. Pace. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180: 4765-4774.
  14. 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.
  15. Hunter, E. M., H. J. Mills, and J. E. Kostka. 2006. Microbial community diversity associated with carbon and nitrogen cycling in permeable shelf sediments. Appl. Environ. Microbiol. 72: 5689-5701. https://doi.org/10.1128/AEM.03007-05
  16. Jin, J. H. and S. K. Chough. 1998. Partitioning of transgressive deposites in the southeastern Yellow Sea: A sequence stratigraphic interpretation. Mar. Geol. 149: 79-92. https://doi.org/10.1016/S0025-3227(98)00023-1
  17. Johnson, J. E. and R. T. Hill. 2003. Sediment microbes of deepsea bioherms on the northwest shelf of Australia. Microb. Ecol. 46: 55-61. https://doi.org/10.1007/s00248-002-2031-y
  18. Jorgensen, B. B. 1983. Processes at the sediment-water interface, pp. 477-515. In B. Bolin, and R. B. Cook (eds.). The Major Biogeochemical Cycles and Their Interactions. John Wiley, Chichester.
  19. Karl, D. M. 2007. Microbial oceanography: Paradigms, processes and promise. Nat. Rev. Microbiol. 5: 759-769. https://doi.org/10.1038/nrmicro1749
  20. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111-120. https://doi.org/10.1007/BF01731581
  21. Kumar, S., K. Tamura, and M. Nei. 2004. MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5: 150-163. https://doi.org/10.1093/bib/5.2.150
  22. Lanoil, B. D., R. Sassen, M. T. La Duc, S. T. Sweet, and K. H. Nealson. 2001. Bacteria and Archaea physically associated with Gulf of Mexico gas hydrates. Appl. Environ. Microbiol. 67: 5143-5153. https://doi.org/10.1128/AEM.67.11.5143-5153.2001
  23. Massol-Deya, A. A., D. A. Odelson, R. F. Hickey, and J. M. Tiedje. 1995. Bacterial community fingerprinting of amplified 16S and 16S-23S ribosomal RNA gene sequences and restriction endonuclease analysis (ARDRA), pp. 1-8. Kluwer Academic Publisher, Dordrecht, The Netherlands.
  24. Rappe, M. S. and S. J. Giovannoni. 2003. The uncultured microbial majority. Annu. Rev. Microbiol. 57: 369-394. https://doi.org/10.1146/annurev.micro.57.030502.090759
  25. Ravenschlag, K., K. Sahm, J. Pernthaler, and R. Amann. 1999. High bacterial diversity in permanently cold marine sediments. Appl. Environ. Microbiol. 65: 3982-3989.
  26. Reed, D. W., Y. Fujita, M. E. Delwiche, D. B. Blackwelder, P. P. Sheridan, T. Uchida, and F. S. Colwell. 2002. Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. Appl. Environ. Microbiol. 68: 3759-3770. https://doi.org/10.1128/AEM.68.8.3759-3770.2002
  27. Scala, D. J. and L. J. Kerkhof. 2000. Horizontal heterogeneity of denitrifying bacterial communities in marine sediments by terminal restriction fragment length polymorphism analysis. Appl. Environ. Microbiol. 66: 1980-1986. https://doi.org/10.1128/AEM.66.5.1980-1986.2000
  28. Sogin, M. L., H. G. Morrison, J. A. Huber, D. Mark Welch, S. M. Huse, P. R. Neal, et al. 2006. Microbial diversity in the deep sea and the underexplored "rare biosphere." Proc. Natl. Acad. Sci. USA 103: 12115-12120. https://doi.org/10.1073/pnas.0605127103
  29. Stach, J. E., L. A. Maldonado, D. G. Masson, A. C. Ward, M. Goodfellow, and A. T. Bull. 2003. Statistical approaches for estimating actinobacterial diversity in marine sediments. Appl. Environ. Microbiol. 69: 6189-6200. https://doi.org/10.1128/AEM.69.10.6189-6200.2003
  30. Teske, A., K. U. Hinrichs, V. Edgcomb, A. de Vera Gomez, D. Kysela, S. P. Sylva, et al. 2002. Microbial diversity of hydrothermal sediments in the Guaymas Basin: Evidence for anaerobic methanotrophic communities. Appl. Environ. Microbiol. 68: 1994-2007. https://doi.org/10.1128/AEM.68.4.1994-2007.2002
  31. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680. https://doi.org/10.1093/nar/22.22.4673
  32. Torsvik, V., L. Ovreas, and T. F. Thingstad. 2002. Prokaryotic diversity - magnitude, dynamics, and controlling factors. Science 296: 1064-1066. https://doi.org/10.1126/science.1071698
  33. Vandamme, P., B. Pot, M. Gillis, P. de Vos, K. Kersters, and J. Swings. 1996. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev. 60: 407-438.
  34. Wang, Q., G. M. Garrity, J. M. Tiedje, and J. R. Cole. 2007. Nave Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73: 5261-5267. https://doi.org/10.1128/AEM.00062-07
  35. Webster, G., R. J. Parkes, J. C. Fry, and A. J. Weightman. 2004. Widespread occurrence of a novel division of bacteria identified by 16S rRNA gene sequences originally found in deep marine sediments. Appl. Environ. Microbiol. 70: 5708-5713. https://doi.org/10.1128/AEM.70.9.5708-5713.2004

피인용 문헌

  1. Novel PCR Primers for the Archaeal Phylum Thaumarchaeota Designed Based on the Comparative Analysis of 16S rRNA Gene Sequences vol.9, pp.5, 2012, https://doi.org/10.1371/journal.pone.0096197
  2. Bacterial community characterization and biogeochemistry of sediments from a tropical upwelling system (Cabo Frio, Southeastern Brazil) vol.130, pp.None, 2012, https://doi.org/10.1016/j.csr.2016.10.001