Biotechnology Letters

, Volume 22, Issue 5, pp 399–405 | Cite as

Digitization of DGGE (denaturing gradient gel electrophoresis) profile and cluster analysis of microbial communities

  • Tong Zhang
  • Herbert H.P. Fang

Abstract

Denaturing gradient gel electrophoresis (DGGE) of 16S rDNA profiles were objectively digitized using an image analyzer; the individual microbial species in a community can thus be precisely quantified. The similarity between various microbial communities was compared to the digitized DGGE profiles using the cluster analyses technique. The microbial community in a biofilm was considerably different from that in suspended sludge obtained from the same system.

biofilm cluster analysis DGGE microbial community 

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References

  1. Acinas SG, Anton J, Rodriguez VF (1999) Diversity of free-living and attached bacteria in offshore western Mediterranean waters as depicted by analysis of genes encoding 16S rRNA. Appl. Environ. Microbiol. 65: 514-522.Google Scholar
  2. Amann RI (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143-169.Google Scholar
  3. Costerson JW, Cheng KJ, Geesey GG, Ladd TJ, Nickel JC, Dasgupta M, Marrie T (1987) Bacterial biofilms in nature and disease. Ann. Rev. Microbiol. 41, 435-464.Google Scholar
  4. Curtis TP, Caine NG (1998) The comparison of the diversity of activated sludge plants. Wat. Sci. Tech. 37: 71-78.Google Scholar
  5. Devereux R, Hines ME, Stahl DA (1996) S cycling: characterization of natural communities of sulfate reducing bacteria by 16S rRNA sequence comparisons. Microbiol. Ecol. 32: 283-292.Google Scholar
  6. Fantroussi SEL, Verschuere L, Verstraete W, Top EM (1999) Effect of phenylurea herbicides on soil microbial communities estimated by analysis of 16S rRNA gene fingerprints and community-level physiological profiles. Appl. Environ. Microbiol. 65: 982-988.Google Scholar
  7. Ferris MJ, Muyzer G, Ward DM (1996) Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl. Environ. Microbiol. 62: 340-346.Google Scholar
  8. Fournier D, Lemieux R, Couiland D (1998) Genetic evidence for the diversified bacteria populations in wastewater sludge during biological leaching of metals. Biotechnol. Lett. 20: 27-31.Google Scholar
  9. Lee DH, Zo YG, Kim SJ (1996) Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-singlestranded-conformation polymorphism. Appl. Environ. Microbiol. 62: 3113-3120.Google Scholar
  10. Muyzer G (1998) Structure, function and dynamics of microbial community: the molecular biological approach. In: Carvalho GR (ed.), Advanced Molecular Ecology. New York: IOS Press, pp. 157-184.Google Scholar
  11. Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial population by DGGE analysis of polymerase chain reaction amplified genes encoding for 16S rRNA. Appl. Environ. Microbiol. 62: 2676-2680.Google Scholar
  12. Muyzer G, Teske A, Wirsen CO, Jannasch HW(1995) Phylogenetic relationship of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch. Microbiol. 164: 165-172.Google Scholar
  13. Myers RM, Fischer SG, Lerman LS, Maniatis T (1985) Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by the denaturing gradient gel electrophoresis. Nucl. Acid Res. 13: 3131-3145.Google Scholar
  14. Okabe S, Satoh H, Wantanabe Y (1999) In situ analysis of nitrifying biofilms as determined by the in situ hybridisation and the use of microeletrodes. Appl. Environ. Microbiol. 65: 3182-3191.Google Scholar
  15. Ovreas L, Forney L, Daae FL, Torsvik V (1997) Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl. Environ. Microbiol. 63: 3367-3373.Google Scholar
  16. Raskin, L, Amann RI, Poulsen LK, Rittmann BE, Stahl DA (1995) Use of ribosomal RNA-based molecular probes for characterisation of complex microbial communities in anaerobic biofilms. Wat. Sci. Technol. 31: 261-272.Google Scholar
  17. Riesner D, Steger G, Zimmat R, Owens RA, Wagenhofer M, Hillen W, Vollbach S, Henco K (1989). Temperature-gradient gel electrophoresis of nucleic acids: analysis of conformational transitions, sequence variations, and protein-nucleic acid interactions. Electrophoresis 10: 377-389.Google Scholar
  18. Rolleke S, Muyzer G. (1996) Identification of bacteria in biodegraded wall painting by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl. Environ. Microbiol. 62: 2059-2065.Google Scholar
  19. Santegoeds CM, Ferdelman TG, Muyzer G, de Beer D (1998a) Structural and functional dynamics of sulfate-reducing populations in bacterial biofilms. Appl. Environ. Microbiol. 64: 3731-3739.Google Scholar
  20. Sekiguchi Y, Kamagata Y, Syutsubo K, Ohashi A, Harada H, Nakamura K (1998) Phylogenetic diversity of mesophilic and thermophilic granular sludge determined by 16S rRNA gene analysis. Microbiology 144: 2655-2665.Google Scholar
  21. Stahl DA, Flesher B, Mansfield HR, Montgomery L (1988) Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl. Environ. Microbiol. 54: 1079-1084.Google Scholar
  22. Vallaeys T, Topp E, Muyzer G (1997) Evaluation of DGGE in the detection of 16S rDNA sequence variation in rhizobia and methanotrophs. FEMS Microbiol. Ecol. 61: 1444-1450.Google Scholar

Copyright information

© Kluwer Academic Publishers 2000

Authors and Affiliations

  • Tong Zhang
    • 1
  • Herbert H.P. Fang
    • 1
  1. 1.Centre for Environmental Engineering Research, Department of Civil EngineeringThe University of Hong KongHong Kong SAR, China

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