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(212) Assessing microbial diversity using denaturing gradient gel electrophoresis (DGGE) in ecotoxicology - problems and solutions. Dahllöf, Ingela1, 1 ABSTRACT- Change in community structure is a useful tool when assessing effects of pollutants in the environment, or in experiments with high community complexity. For larger flora and fauna the method is straightforward, identifying and counting. For smaller organisms like bacteria the determination of community structure in a large amount of sample has been made possible with the advent of molecular techniques. The most common approach is through DNA extraction, PCR of a fragment from 16S ribosomal DNA, and subsequent separation of fragments on DGGE that gives a picture of the community composition. These pictures of banding patterns can be used as indirect measures of community diversity and thereby also for assessing change. However, there are several considerations that have to be made before these techniques can work as standard tools with good statistical backing. There are problems with heterogeneity of genes, quantitative DNA extraction and PCR, as well as selectivity in the whole process. Examples from DGGE-analysis of the bacterial community from mesocosm experiments involving the anti-fouling Sea-nine, as well as from the bacterial community from experiments with marine sediment samples, will be presented where attempts to solve these problems have been made. Key words: microbial community diversity, DGGE, 16S, rpoB |
