In order to understand the function of the different microorganisms in activated sludge, it is important to know their identity, diversity and activity. In this paper we describe how microautoradiography (MAR) and fluorescent in situ hybridization (FISH) can be used to characterize and enumerate functionally important groups of microorganisms in activated sludge. The principles for the methods, some important methodological aspects and limitations of the procedures and some important results are discussed. Special focus is on the examination of the in situ physiology of certain filamentous microorganisms and a discussion about the use of such information in mathematical models of the activated sludge processes.

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