Abstract Marine algae contribute about half of the global biological carbon fixation, and thereby provide the basis of the marine food web of micro-, meio- and macrofauna from protists to fishes, as well as the heterotrophic bacterioplankton. We studied the response of the bacterioplankton to spring phytoplankton blooms in the German Bight and observed swift responses of Flavobacteria and Gammaproteobacteria with different niche specializations in macromolecule degradation, in particular carbohydrates. Initially, we used a combination of biodiversity assessments, metagenomics, metaproteomics, and environmental parameter measurements for our studies. Lately we complemented this repertoire by targeted cultivation efforts in conjunction with draft genome sequencing and proteomics, as well as environmental carbohydrate-detection. In the near future we also plan to add enzyme functional and structural analyses. Initial results demonstrate that this combined data integration approach bears the potential to uncover the niches of environmentally relevant carbohydrate-degrading bacteria in an as yet unseen level of detail, and thus to substantially deepen our understanding of an as yet under-researched aspect of the global carbon cycle.