Further limitations of phylogenetic group-specific probes used for detection of bacteria in environmental samples

Fluorescence in situ hybridization (FISH) with fluorochrome-labelled oligonucleotides targeting rRNA is a powerful tool for the identification and quantification of micro-organisms that are important in environmental and industrial processes (Amann,1995). Phylogenetic group-specific (PGS) oligonucleotide probes, targeting rRNA of many different taxa, are commonly used to screen environmental samples. The use of broad-spectrum PGS FISH probes is quite limited because they might detect micro-organisms outside the PGS group containing the target sequence (false positives), and they frequently miss micro-organisms within the group lacking the target sequence (false negatives)(Loy et al., 2007; Amann and Fuchs, 2008).