A large fraction of the organic matter fixed in the oceans is transformed and remineralised by marine heterotrophic microorganisms. They, therefore, play a critical role in the marine carbon cycle. In this study, we set out to identify the roles played by individual heterotrophic bacteria in the degradation of high molecular weight polysaccharides. At five sites in the Atlantic Ocean, we investigated the processing of organic matter in microbial communities by tracking the changes in community composition (fluorescence in situ hybridisation (FISH), 16S rRNA tag sequencing) in substrate incubation using a defined concentration of a known fluorescently labelled polysaccharide (FLA-laminarin, FLA-xylan, and FLA-chondroitin sulfate). Additionally, we tracked the dynamics of substrate processing (selfish uptake and extracellular hydrolysis) within the microbial communities between sites. We found that the same substrate was processed in different ways by different members of a pelagic microbial community which points to significant follow-on effects for carbon cycling.