The degradation of organic matter in the deep-sea is a critical microbial process that facilitates global carbon cycling and affects all organisms. Typically, deep-sea microbial communities experience very low organic carbon availability, however, at deep-sea whalefalls these bacteria are provided with organic carbon levels ~2000x greater than usual. This creates an ideal environment in which to examine the metabolism of marine microbes and to further understand carbon cycling on and within the deep-sea floor. Only a handful of papers have investigated marine sediments, thus, we first had to develop a method for measuring enzymatic activity. We focused on proteases, enzymes responsible for the breakdown of proteins, one of a number of organic carbon sources in the environment. Protease activity was measured in marine sediments associated with a whalefall at 1800 meters depth in Monterey Bay, collected at zero, three and ten meters distance. As expected, the highest protease activity was found directly under the whalefall and within the top 9cm of sediment. Protease activity was still elevated in samples collected at 17 months, yet almost negligible at 54 months, suggesting that enzymatic breakdown of proteins takes place within a few years of deposition on the sea floor. Molecular analysis of bacterial community composition within these sediments suggests a predominance of heterotrophic bacterial groups, likely responsible for the protease activity. This research allowed us to compare, both metabolically and phylogenetically, the effects of carbon load on deep-sea microbial communities, as well as factors that create and sustain these unique environments.