The next step in the molecular characterization
of microbial communities is the extraction of nucleic
acids from bacterial cells present in the samples;
also this step is not free from biases. Problems are
encountered with the reliable and reproducible lysis of
all bacterial cells as well as with the extraction of intact
nucleic acid, and the removal of substances, such as
humic acids and bacterial exopolysaccharides, which
may inhibit DNA digestion with restriction enzymes
and PCR amplification (e.g.,Wheeler & Stahl, 1996).