Structure, function and dynamics of microbial communities: The molecular biological approach

Molecular biological methods, such as PCR, fluorescent in situ hybridizatio n and DNA sequencing, are nowadays routinely used to detect and identify mi croorganisms in their natural environment and to explore microbial diversit y. The use of these methods has become necessary, because it is now recogni zed that cultivation-based methods do not retrieve the enormous microbial d iversity existing in nature. Although successful the molecular methods are not free from limitations and biases. This paper describes the potentials a nd problems of molecular methods, and gives examples of their application t o study the structure, function, and dynamics of microbial communities. Reg arding the limitations of both the microbiological as well as the molecular approach, I would argue for an integrated approach combining both approach es with a detailed investigation of environmental parameters, to fully unde rstand the role of microbes in ecosystem functioning.