Replicate samples collected from the same location exhibited consistently similar DGGE profiles, demonstrating the degree of reproducibility of the results (Figure 1). DGGE banding patterns exhibited some similarities among sites, but the method was sensitive enough to detect some differences among sites. Analysis of the number of bands, the number of unique site-specific bands, and similarity in banding patterns provided a relatively complete representation of differences among sites.
In some cases, bands detected were less well defined than other bands and appeared fuzzy on the gel images and as broad peaks on the gel profile graphs. Selection of PCR primers that amplify a smaller DNA fragment and use of a GC clamp is recommended to correct this problem.
DGGE analysis of PCR products demonstrated that in many ways bacterial assemblages differed among sites. In general, more total and more unique bands were detected at the polluted sites. Other methods used to examine the bacterial assemblages at these same sites also revealed site-specific differences.5
Interpretation of DGGE results should be performed with the knowledge
that DGGE provides a relative measure of species diversity. As was the
case in this study, DGGE was intimately dependent on the efficiency of
the DNA extraction procedure and on an unbiased high fidelity PCR. To
more accurately understand the roles of bacterial populations to natural
environments, it is necessary to be able to measure the microbial community