Details on oligonucleotide probes are available at probe-
Base (Loy et al., 2007). All the probes were synthesized with 50-
FITC and -Cy3 labels and purchased from MWG AG Biotech
(Germany). Slides were examined under an epifluorescence
microscope (Olympus BX51).
All microscopic analyses of SBBGR samples were performed
on crushed biomass (biofilm and granules). The ratio
of bacteria (EUB338mix) over the total number of cells (DAPI
stained cells) was considered as a gross parameter to assess
the overall physiological state of bacterial communities and
define biomass activity (De Sanctis et al., 2010). In fact, DAPI
staining detects all the cells containing DNA (active, not active
or even dead). Differently, cell detection by FISH requires that
the cell contains at least 103 copies of 16S rRNA (ribosomal
RNA) and the presence of several ribosomes approximately
indicates that cells are metabolically active.