In Situ Analysis of Structure and Activity of the Nitrifying Community in Biofilms, Aggregates, and Sediments

This review summarizes the state of microscale in situ analyses of nitrification. Microsensors and fluorescence in situ hybridization (FISH) have both become important methods for microbial ecology. In combination, they have offered a variety of exciting insights into structure and activity of microbial communities, including nitrifying biofilms, aggregates, and sediments. Several levels of information can be obtained: (a) identification of microenvironments or environmental conditions (such as concentrations of oxygen, ammonium, nitrite) favored by particular microorganisms; (b) qualitative evidence of certain metabolic activities of particular microorganisms, e.g., nitrite oxidation by Nitrospira sp.; and (c) quantification of cell-specific reaction rates and estimation of the in situ kinetics of uncultivated microorganisms. Potential, limitations, and future perspectives of such combined microsensor/FISH approaches for the study of nitrification are discussed.