Catalyzed reporter deposition fluorescence in situ hybridization combined with microautoradiography (MICRO-CARD-FISH) is increasingly being used to obtain qualitative information on substrate uptake by individual members of specific prokaryotic communities. Here we evaluated the potential for using this approach quantitatively by relating the measured silver grain area around cells taking up 3 H-labeled leucine to bulk leucine uptake measurements. The increase in the silver grain area over time around leucineassimilating cells of coastal bacterial assemblages was linear during 4 to 6 h of incubation. By establishing standardized conditions for specific activity levels and concomitantly performing uptake measurements with the bulk community, MICRO-CARD-FISH can be used quantitatively to determine uptake rates on a single-cell level. Therefore, this approach allows comparisons of single-cell activities for bacterial communities obtained from different sites or growing under different ecological conditions.In situ hybridization with fluorescently labeled oligonucleotide probes (FISH) allows enumeration of specific prokaryotic groups or individual phylotypes with a microscope. Recently, this technique was modified to enhance the detection efficiency, and the new method was called catalyzed reporter deposition FISH (CARD-FISH) (25). CARD-FISH uses oligonucleotide probes labeled with horseradish peroxidase, which results in a sensitivity comparable to that obtained with FISH with polynucleotide probes (26). The CARD-FISH protocol includes a permeabilization step for bacterial cells using lysozyme (25) or for Archaea using proteinase K (28). This CARD-FISH protocol combined with microautoradiography (MICRO-CARD-FISH) was used to determine the number of bacterial and archaeal cells taking up the enantiomeric amino acid aspartic acid in waters of the North Atlantic down to a depth of 4,000 m (29).Microautoradiography combined with FISH is increasingly being used to obtain qualitative information on the substrate utilization by specific prokaryotic populations in complex natural communities (6, 24). Cottrell and Kirchman (6) demonstrated that the method commonly used to assess the prokaryotic activity of entire communities (leucine and thymidine incorporation) indeed covers the entire prokaryotic community. Using MICRO-FISH, it has been shown that some groups in a bacterial community are more active than expected based on their relative abundance (7,11,(17)(18)(19). Also, it has been shown that Cytophaga utilizes high-molecular-weight material more efficiently (7), while members of the SAR11 cluster and Roseobacter sp. apparently also efficiently utilize dimethylsulfoniopropionate (18,19).Generally, however, our knowledge about the phylogenetic composition of prokaryotic communities is increasing much faster than our understanding of the function of these phylotypes in their natural environments. Thus, methods that more closely link phylogenetic information with functional aspects are required, and one of these methods is...