The chapter discusses the fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes, and describes probe designing and testing. Fluorescence FISH with rRNA-targeted probes is a staining technique that allows phylogenetic identification of bacteria in mixed assemblages without prior cultivation by means of epifluorescence and confocal laser scanning microscopy, or by flow cytometry. FISH with oligonucleotide probes is for the purpose of bacterial identification that is to analyze bacterial community structure, and to follow the spatial and temporal dynamics of individual microbial populations in their habitat. Numerous aspects and applications of this method are discussed. FISH is successfully applied in freshwater, coastal, and offshore marine planktonic habitats, and in coastal sediments. It is shown that the fraction of bacteria detectable by FISH corresponds well with the abundance of active cells as determined by microautoradiography in coastal marine bacterioplankton.
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