The traditional model of marine pelagic food webs based on phytoplankton, zooplankton and predatory fish, is changing fast from being a three-step food chain, to becoming a complex and dynamic network of species interactions. Microorganisms play a vital part in the cycling of energy and nutrients in the oceans, and are consequently drivers of several global biogeochemical processes. The lack of mechanistic understanding of the microbial communities has been identified as one of the major knowledge gaps for predicting both vulnerability of local marine ecosystems as well as global climatic feedback alterations. Using Next Generation Sequencing (NGS) metabarcoading and metagenomics, we are developing a method for studying marine food web interactions among the microbial community and upper trophic levels. Our aim is to increase the mechanistic understanding of trophic feeding-, parasitic- and symbiotic interactions and to identify what species are the key players in the transport of organic compounds to the upper food web. We use simple laboratory feeding interactions to enhance the quantitative properties of the NGS methods and for validating NGS analysis of field samples under different environmental conditions. The methods used in this study are expected to shred new light on the complexity and dynamics of the plankton food webs and facilitate the study of the key players. These insights are prerequisite for further investigation of the mechanistic impacts of warming, ocean acidification and other anthropogenic factors on the marine microbial community.