Fluorescence in situ hybridization (FISH) is currently a standard technique for detecting, identifying, and enumerating microorganisms. The method allows for visualization of cell morphology as well as in situ localization of microorganisms at single-cell resolution. Although FISH has been used for more than 20 years, many challenges remain with regard to improving the technique for understanding microbial ecology and physiology. This chapter describes the recent developments in this field, such as improved sensitivity by catalyzed reporter deposition (CARD)-FISH and in situ DNA-hybridization chain reaction (HCR). Highly sensitive methods for detecting mRNA and/or functional genes are also described. Moreover, methods combining isotope probing to reveal microbial metabolic activities are introduced.
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