A 20 d seawater mesocosm experiment was conducted to study microbial loop and carbon cycling dynamics in 3 experimental systems of different trophic status. Two mesocosms were supplemented with phytoplankton (Phaeocystis in one mesocosm and diatoms in another). This report details the variations in bacterial community composition and in carbon utilization potential investigated via assays measuring the hydrolysis of complex polysaccharides and a simple peptide compound. The first half of the study period was dominated by bacterial growth and large shifts in community composition coinciding with utilization of the organic carbon present at the beginning of the experiment, as shown by hydrolysis of specific polysaccharides and drawdown of labile dissolved organic carbon. During the second half of the experiment, bacterioplankton abundance, composition, and enzymatic activities changed in response to the experimental treatments. Multiple correlation analyses implicated co-variation between rRNA gene DGGE phylotypes (e.g. Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes) and specific combinations of environmental parameters and carbon resources, indicating phylotypic specialization to the experimental mesocosm conditions. Similarly, hydrolysis of 3 polysaccharides (xylan, chondroitin, and Isochrysis extract) correlated significantly with particular phylotypes, providing evidence of species-specific influences on carbon utilization that varied temporally over the experiment period. Aminopeptidase activity mirrored biomass accumulation, as indicated by positive correlations (>0.80) with most biomass indicators determined. These results illustrate that combined molecular and biochemical analysis of active microbial communities can illuminate linkages between specific organisms and important ecosystem processes such as carbon utilization. Additionally, our findings show that trophic status was reflected in community composition and carbon utilization activities.