A recent evolution in the direct amplification and analysis of ribosomal RNA genes is the use of specific primers, which allows to amplify and analyse the 16S rRNA genes of defined groups within a complex microbial community. The analysis of these group-specific PCR fragments on a DGGE gel provides a valuable tool for monitoring the structure and dynamics of microbial populations over time or under the influence of environmental changes. This approach has already been used in a few studies, which investigated specific microbial groups such as methanotrophic members of the alpha- and gamma-Proteobacteria [11], actinomycetes [10], alpha- and beta -Proteobacteria [12], ammonia-oxidising bacteria [13], Archaea [14] and fungi