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Most of the groundwaters used for drinking water production in northern Germany belong to reduced water types and part of them contain methane. If methane is not sufficiently removed in the course of drinking water treatment, methane oxidizing bacteria (methanotrophs) grow and inhibit drinking water treatment processes, resulting in inferior quality of final treated water. Methanotrophs were detected by fluorescence in situ hybridization (FISH) with 16S rRNA targeted group- and genus-specific oligonucleotide probes at different sampling sites in waterworks treating raw water with methane concentrations between 0.14 and 70 mg/L. In investigations of 7 treatment plants, primarily type I methanotrophs of the family Methylococcaceae were detected. With individual probes, up to 46.5% of total bacteria were found to be type I methanotrophs. The presence of methanotrophs in the waterworks samples was confirmed by enrichment cultures grown under methane atmosphere, isolation of methanotrophic bacteria and identification of representative isolates as Methylomonas methanica. Furthermore, methane degradation rates of original samples from waterworks showed high methane degradation activities in batch culture experiments. Thus, in situ probing of methanotrophs with fluorescent oligonucleotide probes seems to be a promising tool for detection and quantification of methanotrophs in waterworks and for relation of problems in drinking water treatment to the occurrence of methane in groundwater. Includes 23 references, tables, figures.