Skip to main content
SpringerLink
Log in

Characterization of benthic bacterial assemblages in a polluted stream using denaturing gradient gel electrophoresis

  • Published:
Hydrobiologia Aims and scope Submit manuscript

Abstract

To study differences in bacterial assemblages among sites with different environmental conditions, sediment samples were collected from three sites along a South Carolina (U.S.A.) coastalplain stream with varying levels of anthropogenic perturbation. The objective of this study was to compare the bacterial assemblages among these sites to detect possible impacts from the disturbance. To accomplish this comparison, DNA was extracted from the samples and subjected to the polymerase chain reaction using primers designed to amplify bacterial 16S rRNA genes. Relative measures of bacterial genetic diversity, assessed using denaturing gradient gel electrophoresis (DGGE), revealed greater numbers of unique sequences at the disturbed sites. The number of bands, which is analogous to species richness, did not vary predictably among sites. Similarity indices revealed a high level of similarity among replicate samples from each site and low similarity between samples from different sites. This study demonstrated that bacterial assemblages differed among sites and that the presence or absence of certain species, represented by unique DGGE bands, differed among sites; unique bands were most commonly encountered at the disturbed sites. Based on the evidence gathered, we conclude that benthic bacterial assemblages vary longitudinally and that anthropogenic disturbance may alter the bacterial component of streams.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Arnett, M. W. (ed.), (1994). Savannah River Site Environmental Data for 1994. Publication WSRC-95-077. USDOE Westinghouse Savannah River CO., Aiken, S.C.

    Google Scholar 

  • Brosius, J., T. J. Dull &; D. D. Sleeter, 1981. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J. Mol. Biol. 148: 107–127.

    Google Scholar 

  • Bull, A. T., M. Goodfellow &; J. H. Slater, 1992. Biodiversity as a source of innovation in biotechnology. Ann. Rev. Microbiol. 46: 219–252.

    Google Scholar 

  • Duineveld, B. M., A. S. Rosado, J. D. Van Elsas &; J. A. Van Veen, 1998. Analysis of the dynamics of bacterial communities in the rhizosphere of the chrysanthemum via denaturing gradient gel electrophoresis and substrate utilization patterns. Appl. envir. Microbiol. 64: 4950–4957.

    Google Scholar 

  • Ferris, M. J., G. Muyzer &; D. M. Ward, 1996. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl. envir. Microbiol. 62: 340–346.

    Google Scholar 

  • Ferris, M. J. &; D. M. Ward, 1997. Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis. Appl. envir. Microbiol. 63: 1375–1381.

    Google Scholar 

  • Gillan, D. C., A. G. C. L. Speksnijder, G. Zwart &; C. D. Ridder, 1998. Genetic diversity of the biofilm covering Montacuta ferruginosa (Mollusca, Bivalvia) as evaluated by denaturing gradient gel electrophoresis analysis and cloning of PCR-amplified gene fragments coding for 16S rRNA. Appl. envir. Microbiol. 64: 3464–3472.

    Google Scholar 

  • Heuer, H., M. Krsek, P. Baker, K. Smalla &; E. Wellington, 1997. Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation on denaturing gradients. Appl. envir. Microbiol. 63: 3233–3241.

    Google Scholar 

  • Kowalchuk, G. A., H. R. Stephen, W. De Boer, J. I. Prosser, T. M. Embley &; J. W. Woldendorp, 1997. Analysis of ammoniaoxidizing bacteria of the ß subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments Appl. envir. Microbiol. 63: 1489–1497.

    Google Scholar 

  • Krebs, C. J., 1978. Ecology: the Experimental Analysis of Distribution and Abundance, 2nd edn. Harper &; Row Publisher, New York N.Y.

    Google Scholar 

  • Leff, L., 1994. Stream bacterial ecology: A neglected field? Am. Soc. Microb. News. 60: 135–138.

    Google Scholar 

  • Leff, L. G. &; M. J. Lemke, 1998. Ecology of aquatic bacterial populations: lessons from applied microbiology. J. n. am. Benthol. Soc. 17: 261–271.

    Google Scholar 

  • Lemke, M. J., B. J. Brown &; L. G. Leff, 1997. The response of three bacterial populations to pollution in a stream. Microb. Ecol. 34: 224–231.

    Google Scholar 

  • Lemke, M. J. &; L. G. Leff, 1999. Bacterial populatiosn in an anthropogenically disturbed stream: Comparison of different seasons. Microb. Ecol. 38: 234–243.

    Google Scholar 

  • McArthur, J. V. &; R. Tuckfield, 1997. Information length: spatial and temporal parameters among stream bacterial assemblages. J. n. am. Benthol. Soc. 16: 347–357.

    Google Scholar 

  • Miller, K. M., T. J. Ming, A. D. Schultz &; R. E. Withler, 1999. Denaturing gradient gel electrophoresis (DGGE): A rapid and sensitive technique to screen nucleotide sequence variation in populations. BioTechniques 27: 1016–1030.

    Google Scholar 

  • Murray, A. E., C. M. Preston, R. Massana, L. T. Taylor, A. Blakis, K. Wu &; E. F. DeLong. 1998. Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica. Appl. envir. Microbiol. 64: 2585–3595.

    Google Scholar 

  • Muyzer, G., E. C. De Waal &; A. G. Uitterlinden, 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. envir. Microbiol. 59: 695–700.

    Google Scholar 

  • Muyzer, G. &; K. Smalla, 1998. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Anton. Leeuw. Int. J. Gen Mol. Microbiol. 73: 127–141.

    Google Scholar 

  • Olsen, G. J., D. J. Lane, S. J. Giovannoni, N. R. Pace &; D. A. Stahl, 1986. Microbial Ecology and evolution: a ribosomal RNA approach. Ann. Rev. Microbiol. 40: 337–65.

    Google Scholar 

  • Ovreas, L., L. Forney, L. F. Daae &; V. Torsvik, 1997. Distribution of bacterioplankton in meromictic Lake Saelinvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S-rRNA. Appl. envir. Microbiol. 63: 3367–3373.

    Google Scholar 

  • Porter, K. &; Y. Feig, 1980, The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanogr. 25: 943–948.

    Google Scholar 

  • Rolleke, S., G. Muyzer, C. Wawer, G. Wanner &; W. Lubitz, 1996. Identification of bacteria in a biodegraded wall painting by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl. envir. Microbiol. 62: 2059–2065.

    Google Scholar 

  • Sambrook, J., E. F. Fritsch &; T. Maniatis, 1989. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory.

  • Santegoeds, C. M., S. C. Nold &; D. M. Ward, 1996. Denaturing gradient gel electrophoresis used to monitor the enrichment culture of aerobic chemoorganotrophic bacteria from a hot spring cyanobacterial mat. Appl. envir. Microbiol. 62: 3922–3928.

    Google Scholar 

  • Sayler, G. L. &; A. L. Layton, 1990. Environmental application of nucleic acid hybridization. Ann. Rev. Microbiol. 44: 625–648.

    Google Scholar 

  • Teske, A., C. Wawer, G. Muyzer &; N. B. Ramsing, 1996. Distribution of sulfate-reducing bacteria in a stratified fjord (Mariager Fjord, Denmark) as evaluated by most-probable-number counts and denaturing gradient gel electrophoresis of PCR-amplified ribosomal DNA fragments. Appl. envir. Microbiol. 62: 1405–1415.

    Google Scholar 

  • Tsai, Y. &; B. H. Olson, 1991. Rapid method for direct extraction of DNA from soil and sediments. Appl. envir. Microbiol. 57: 1070–1074.

    Google Scholar 

  • Tsai, Y. &; B. H. Olson, 1992. Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction. Appl. envir. Microbiol. 58: 2292–2295.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biological Sciences, Kent State University, Kent, OH, 44242, U.S.A.

    Derek G. Cody & Robert T. Heath

  2. Department of Biological Sciences, Kent State University, Kent, OH, 44242, U.S.A.

    Laura G. Leff

Authors
  1. Derek G. Cody
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Robert T. Heath
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Laura G. Leff
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Laura G. Leff.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Cody, D.G., Heath, R.T. & Leff, L.G. Characterization of benthic bacterial assemblages in a polluted stream using denaturing gradient gel electrophoresis. Hydrobiologia 432, 207–215 (2000). https://doi.org/10.1023/A:1004075120018

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1004075120018

Search

Navigation