| Summary: | Numerous microorganisms may be present in the water distribution system. This is associated with the imperfection of purification processes, or secondary water pollution. Not only it results in the deterioration of water quality parameters, but it also increases threat of epidemiological problems. The water that is biologically unstable creates ideal conditions for colonization of the microorganisms to the inner surface of pipelines which may form biofilm. The key issue, enabling prevention and control of the impact of the development of biofilms, is to assess the biodiversity of microbiocenosis. In order to obtain comprehensive characteristics of microorganisms communities on a particular substrate, it is necessary to combine several techniques. Further analysis using molecular biology methods are usually after traditional methods of assessing the microbiological quality of water. Standard methods do not reflect the actual species composition, because they are targeted at the bacteria that can be isolated and cultured in the laboratory. Conventional methods are capable of detecting less than 10% of the organisms in the sample. In order to study the biodiversity of organisms inhabiting a biofilm (apart from the conventional methods) analyses of the diversity of nucleic acids should be used. The first method could be the polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE). Another way may be fluorescence in situ hybridization, which allows to detect determined DNA sequence using specially labeled oligonucleotide probes. Visualization of the material is performed using a fluorescence microscope. The main purpose of this article is to present rapid and precise identification groups of microorganisms in their natural habitat in biofilm using fluorescent in situ hybridization method (FISH) . FISH method can be successfully used to visualize these microorganisms, which show difficulties in culturing, as well as to provide knowledge on the phylogenetic structure in different habitats. FISH technique allows the quantitative description of environmental samples.
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