Abstract
This chapter discusses two techniques of analyzing microbial community structure in tropical and temperate river waters: fluorescent vital staining and fluorescent in situ hybridization (FISH), and denaturing gradient gel electrophoresis (DGGE). Microbes process and degrade various compounds in the environment, i.e., they directly purify the polluted environments. 6-carboxyfluorescein diacetate (6CFDA) staining for the enumeration of esterase-active bacterial cells and 2-hydroxy-3-naphthoic acid-2'-phenylanilide phosphate (HNPP) and Fast Red TR in situ hybridization (HNPP-FISH) techniques are used for the analysis of bacterial community structure in natural rivers. Certain fluorescent dyes are available for the detection of physiologically active bacterial cells by epifluorescence microscopy and flow cytometry. 5-cyano-2,3-ditolyl tetrazolium chloride (CTC), a tetrazolium salt is used as an indicator of bacterial respiratory function. DGGE analyzes the bacterial community structure of river water samples. DGGE can separate DNA fragments whose length are the same but sequences are different. The number of bands observed in DGGE profiles provides an estimate of species' richness.
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