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).

The removal of unwanted nutrients, such as carbon, nitrogen and phosphorus from wastewater, is crucial in maintaining our waterways and preventing eutrophication. The enhanced biological phosphorus removal (EBPR) process is a highly applied and globally important biological process for the removal of phosphorus and treatment of wastewater. FISH has been regularly used to assess the bacteria present in EBPR-activated sludge biomass, and to link EBPR process performance with resident microbial communities (Daims et al., 2006). This assessment has substantial implications for EBPR, specifically relating to the identification of two critical, relatively abundant and competing bacterial populations of ‘Candidatus Accumulibacter phosphatis’ (henceforth Accumulibacter) (Crocetti et al., 2000) and ‘Candidatus Competibacter phosphatis’ (henceforth Competibacter) (Crocetti et al., 2002), members of the Betaproteobacteria and Gammaproteobacteria, respectively. Accumulibacter is responsible for the majority of phosphorus removal in EBPR wastewater treatment processes, as Competibacter is detrimental for this vital nutrient removal process, through competition for carbon while not removing phosphorus.

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