Some Universal Characteristics of Intertidal Bacterial Diversity as Revealed by 16S rRNA Gene-Based PCR Clone Analysis

  • Shuang, J.L. (State Key Laboratory of Pharmaceutical Biotechnology, State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University) ;
  • Liu, C.H. (State Key Laboratory of Pharmaceutical Biotechnology, State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University) ;
  • An, S.Q. (State Key Laboratory of Pharmaceutical Biotechnology, State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University) ;
  • Xing, Y. (State Key Laboratory of Pharmaceutical Biotechnology, State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University) ;
  • Zheng, G.Q. (State Key Laboratory of Pharmaceutical Biotechnology, State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University) ;
  • Shen, Y.F. (State Key Laboratory of Pharmaceutical Biotechnology, State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University)
  • Published : 2006.12.30


A 16S rDNA clone library was generated to investigate the bacterial diversity in intertidal sediment from the coast of the Yellow Sea, P. R. China. A total of 102 clones were sequenced and grouped into 73 OTUs using a phylogenetic approach. The sequenced clones fell into 11 bacterial lineages: Proteobacteria, Bacteroidetes, Planctomycetes, Chloroflexi, Acidobacteria, Actinobacteria, Firmicutes, Spirochaetes, and candidate divisions of BRCl, OP3, and OP1l. Based on a phylogenetic analysis of these bacteria, together with the ten most closely related sequences deposited in the GenBank, it was concluded that intertidal bacteria are most likely derived from marine bacteria with a remarkable diversity, and some are particularly abundant in intertidal sediment.


  1. Acinas, S. G., V. Klepac-Ceraj, D. E. Hunt, C. Pharino, I. Ceraj, D. L. Distel, and M. F. Polz. 2004. Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430: 551-554
  2. Alain, K., M. Zbinden, N. Le Bris, F. Lesongeur, J. Querellou, F. Gaill, and M. A. Cambon-Bonavita. 2004. Early steps in microbial colonization processes at deep-sea hydrothermal vents. Environ. Microbiol. 6: 227-241
  3. Bahr, M., B. C. Crump, V. Klepac-Ceraj, A. Teske, M. L. Sogin, and J. E. Hobbie. 2005. Molecular characterization of sulfate-reducing bacteria in a New England salt marsh. Environ. Microbiol. 7: 1175-1185
  4. Buchan, A., S. Y. Newell, M. Butler, E. J. Biers, J. T. Hollibaugh, and M. A. Moran. 2003. Dynamics of bacterial and fungal communities on decaying salt marsh grass. Appl. Environ. Microbiol. 69: 6676-6687
  5. Felsenstein, J. 1988. Phylogenies from molecular sequences: Inference and reliability. Annu. Rev. Genet. 22: 521-565
  6. Hines, M. E., R. S. Evans, B. R. S. Genthner, S. G. Willis, S. Friedman, J. N. Rooney-Varga, and R. Devereux. 1999. Molecular phylogenetic and biogeochemical studies of sulfate-reducing bacteria in the rhizosphere of Spartina alterniflora. Appl. Environ. Microbiol. 65: 2209-2216
  7. Hold, G. L., E. A. Smith, M. S. Rappe, E. W. Maas, E. R. B. Moore, C. Stroempl, J. R. Stephen, J. I. Prosser, T. H. Birkbeck, and S. Gallacher. 2001. Characterization of bacterial communities associated with toxic and non-toxic dinoflagellates: Alexandrium spp. and Scrippsiella trochoidea. FEMS Microbiol. Ecol. 37: 161-173
  8. 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
  9. Hurt, R. A., X. Qiu, L. Wu, Y. Roh, A. V. Palumbo, J. M. Tiedje, and J. Zhou. 2001. Simultaneous recovery of RNA and DNA from soils and sediments. Appl. Environ. Microbiol. 67: 4495-4503
  10. Juretschko, S., A. Loy, A. Lehner, and M. Wagner. 2002. The microbial community composition of a nitrifyingdenitrifying activated sludge from an industrial sewage treatment plant analyzed by the full-cycle rRNA approach. Syst. Appl. Microbiol. 25: 84-99
  11. Kim, B. S., H. M. Oh, H. Kang, S. S. Park, and J. Chun. 2004. Remarkable bacterial diversity in the tidal sediment as revealed by 16S rDNA analysis. J. Microbiol. Biotechnol. 14: 205-211
  12. Klepac-Ceraj, V., M. Bahr, B. C. Crump, A. P. Teske, J. E. Hobbie, and M. F. Polz. 2004. High overall diversity and dominance of microdiverse relationships in salt marsh sulphate-reducing bacteria. Environ. Microbiol. 6: 686-698
  13. 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
  14. Lowe, M., E. L. Madsen, K. Schindler, C. Smith, S. Emrich, F. Robb, and R. U. Halden. 2002. Geochemistry and microbial diversity of a trichloroethene-contaminated Superfund site undergoing intrinsic in situ reductive dechlorination. FEMS Microbiol. Ecol. 40: 123-134
  15. Lueders, T., B. Pommerenke, and M. W. Friedrich. 2004. Stable-isotope probing of microorganisms thriving at thermodynamic limits: Syntrophic propionate oxidation in flooded soil. Appl. Environ. Microbiol. 70: 5778-5786
  16. Lydell, C., L. Dowell, M. Sikaroodi, P. Gillevet, and D. Emerson. 2004. A population survey of members of the phylum Bacteroidetes isolated from salt marsh sediments along the east coast of the United States. Microb. Ecol. 48: 263-273
  17. Macbeth, T. W., D. E. Cummings, S. Spring, L. M. Petzke, and K. S. Sorenson Jr. 2004. Molecular characterization of a dechlorinating community resulting from in situ biostimulation in a trichloroethene-contaminated deep, fractured basalt aquifer and comparison to a derivative laboratory culture. Appl. Environ. Microbiol. 70: 7329- 7341
  18. Mussmann, M., K. Ishii, R. Rabus, and R. Amann. 2005. Diversity and vertical distribution of cultured and uncultured Deltaproteobacteria in an intertidal mud flat of the Wadden Sea. Environ. Microbiol. 7: 405-418
  19. Nakagawa, S., K. Takai, F. Inagaki, H. Chiba, J. Ishibashi, S. Kataoka, H. Hirayama, T. Nunoura, K. Horikoshi, and Y. Sako. 2005. Variability in microbial community and venting chemistry in a sediment-hosted backarc hydrothermal system: Impacts of subseafloor phase-separation. FEMS Microbiol. Ecol. 54: 141-155
  20. Nercessian, O., Y. Fouquet, C. Pierre, D. Prieur, and C. Jeanthon. 2005. Diversity of bacteria and Archaea associated with a carbonate-rich metalliferous sediment sample from the Rainbow vent field on the Mid-Atlantic Ridge. Environ. Microbiol. 7: 698-714
  21. Nesbo, C. L., Y. Boucher, M. Dlutek, and F. W. Doolittle. 2005. Lateral gene transfer and phylogenetic assignment of environmental fosmid clones. Environ. Microbiol. 7: 2011- 2026
  22. Okabe, S., T. Ito, K. Sugita, and H. Satoh. 2005. Succession of internal sulfur cycles and sulfur-oxidizing bacterial communities in microaerophilic wastewater biofilms. Appl. Environ. Microbiol. 71: 2520-2529
  23. Purdy, K. J., D. B. Nedwell, and T. M. Embley. 2003. Analysis of the sulfate-reducing bacterial and methanogenic Archaeal populations in contrasting Antarctic sediments. Appl. Environ. Microbiol. 69: 3181-3191
  24. Ravenschlag, K., K. Sahm, J. Pernthaler, and R. Amann. 1999. High bacterial diversity in permanently cold marine sediments. Appl. Environ. Microbiol. 65: 3982-3989
  25. Saiki, R. K., D. H. Gelfand, S. Stoffel, S. J. Scharf, R. Higuchi, G. T. Horn, K. B. Mullis, and H. A. Erlich. 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239: 487-491
  26. Saitou, N. and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425
  27. Schloetelburg, C., C. von Wintzingerode, R. Hauck, F. von Wintzingerode, W. Hegemann, and U. B. Goebel. 2002. Microbial structure of an anaerobic bioreactor population that continuously dechlorinates 1,2-dichloropropane. FEMS Microbiol. Ecol. 39: 229-237
  28. Selenska-Pobell, S., G. Kampf, K. Hemming, G. Radeva, and G. Satchanska. 2001. Bacterial diversity in soil samples from two uranium waste piles as determined by rep-APD, RISA and 16S rDNA retrieval. Antonie Van Leeuwenhoek 79: 149-161
  29. Singleton, D. R., M. A. Furlong, S. L. Rathbun, and W. W. B. 2001. Quantitative comparisons of 16S rDNA sequence libraries from environmental samples. Appl. Environ. Microbiol. 67: 4373-4376
  30. Stubner, S., T. Wind, and R. Conrad. 1998. Sulfur oxidation in rice field soil: Activity, enumeration, isolation and characterization of thiosulfate-oxidizing bacteria. Syst. Appl. Microbiol. 21: 569-578
  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
  32. Volossiouk, T., E. J. Robb, and R. N. Nazar. 1995. Direct DNA extraction for PCR-mediated assays of soil organisms. Appl. Environ. Microbiol. 61: 3972-3976
  33. Watanabe, K., Y. Kodama, K. Syutsubo, and S. Harayama. 2000. Molecular characterization of bacterial populations in petroleum-contaminated groundwater discharged from underground crude oil storage cavities. Appl. Environ. Microbiol. 66: 4803-4809
  34. 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
  35. Zhou, J., M. A. Bruns, and J. M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62: 316-322