The aim of this study was to quantify different bacteria in drinking water production wells that supply the city of Mainz (capital of Rhineland-Palatinate, Germany). Knowledge of the counts of individual microorganisms is important for the appraisal of the hygienic and sensory quality of drinking water. Specific 16S rRNA probes were designed for 14 previously identified but non-cultured bacterial species (Ferribacterium limneticum, Hydrogenophaga sp., Methylotenera sp., Janthinobacterium sp., Pseudomonas sp., Rhizobium selenireducens, Rhodoferax sp., Nitrosomonadaceae bacterium, Thauera sp. and five strains which could not be identified to species level). With fluorescence in situ hybridization the titer of these species was determined. Total bacterial counts were 4.3 × 104 cells/mL (April) and 4.0 × 104cells/mL (December). The highest relative counts were observed for Methylotenera sp. (4.6–21.7%), F. limneticum (6.1–10.2%), Janthinobacterium sp. (6.1–7.1%), strain K-S10-Sep02 (5.8–5.9%) and Nitrosomonadaceae bacterium (4.8–5.9%). These organisms accounted for 50% (April) and 29% (December) of the total counts. Finally, single water production wells that supply drinking water were studied for the counts of Methylotenera sp., F. limneticum and Janthinobacterium sp. These counts differed between the wells and did not reflect counts in the drinking water treatment plant.

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