Fluorescence in situ hybridization for the detection of prokaryotes

Determining the structure and dynamics of microbial communities is a core component of microbial ecology. Traditionally, microbiologists used timeconsuming cultivation-based methods to detect prokaryotes in the environment and to estimate their abundance. However, today it is common knowledge that the vast majority of prokaryotes cannot be cultured in the laboratory by applying standard methods (1). Furthermore, cultivation approaches underestimate the actual environmental abundance even of culturable bacteria since efficient dispersal of biofilms is not always possible and many bacteria that are in principle culturable can occur in a so-called Viable but not culturable’ state (2). Therefore, for most ecosystems the majority of numerically and functionally important microbial community members are not available as pure cultures. This situation might improve with the more widespread implementation of innovative cultivation techniques (3-7) but detailed censuses of complex microbial communities require a fundamentally different approach.