Today DGGE/TGGE is a well-established molecular tool
in environmental microbiology that allows the study of
complcxity and behavior of microbial communities. The
technique is reliable, reproducible, rapid and inexpensive.
DGGE/TGGE allows the simultaneous analysis of multi-
ple samples making it possible to follow community
changes over time. An additional strong feature of these
techniques is the possibility of identifying community
members by sequencing of excised bands or by hybridiza-
tion analysis with specific probes, which is not possible
with other fingerprinting techniques, such as terminal
restriction fragment length polymorphism n'-RFLP) [43"].
Moreover, probes can be designed after sequencing of
excised DGGE/TGGE bands and used in hybridization
analysis [44] (see also Figure 1), or even be generated with-
out prior sequence knowledge by 'nested' amplification of
excised bands [11]. DGGE and TGGE, however, also have
their limitations. Apart from the general potential biases,
which most of the molecular techniques in microbial ecol-
ogy face (e.g. those produced by sample handling, uneven
cell lysis or peR [Zl··]), DGGE/TGGE also have some
specific limitations [6··]; for instance, the detection of het-
eroduplex molecules [Z.1] and molecules produced by