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

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.