A polyphasic approach to study ecophysiology of complex multispecies nitrifying biofilms

This chapter aims to highlight the great potential of the combined use of microautoradiography (MAR) combined with fluorescent in situ hybridization (FISH) and microsensor technology in studies of complex multispecies nitrifying biofilms. The combination of FISH and microsensor technology is a powerful and reliable tool to link the spatial organization of microbial communities and their in situ function at community levels. MAR-FISH can be used to simultaneously examine the 16S rRNA-based phylogenetic identity and specific metabolic activity of cultivable or uncultivable microorganisms within complex microbial communities at a single-cell level. Information obtained at both resolution levels must be combined to draw a clear picture of a complex multispecies biofilm ecosystem. In addition, ecophysiological interactions among community members in complex multispecies biofilms can be investigated by tracing the fate of radiolabeled [(14)C] atom incorporated in nitrifying bacteria with MAR-FISH. The structure, function, and ecophysiological interactions among community members in complex multispecies nitrifying biofilms will be illustrated as an example of the combined use of MAR-FISH and microsensor technology.