Despite the intensive development of microbial ecology methods in the last decades and the recognition of the importance of the linkage between viral and prokaryotic community dynamics, the two groups are rarely studied together. The present project aims to increase our understanding of the linkage between viral and prokaryotic communities in aquatic environments and initiate a framework were the two are studied together in a multidisciplinary way with special focus on the factors determining the nature and strength of the connections between them and their ecosystem function modifying capacities. To achieve this goal a multidisciplinary microbial ecologist will be trained and the following 3 major research objectives will be addressed:1: analysis of the global distribution of marine ssDNA phages and its correlation to the biogeography of prokaryotes coupled with the identification of the possible hosts of these phages by comparing their distribution with the distribution of other planktonic organisms. The goal will be achieved by analyzing the diversity of hundreds of samples from a global oceanic survey through a set of state-of-the-art molecular techniques and statistical tools.2: assessment of the role of viral communities in determining the establishment success of dispersed bacterial communities. The goal will be achieved by performing several virus-free and virus-containing microcosm experiments on a diverse set of aquatic samples and comparing bacterial community composition and function in the light of viral abundance and diversity.3: joint investigation of viral and prokaryotic diversity and biogeography of freshwaters, and assessment of the effect of the viral shunt on boreal lakes’ carbon flux. The goal will be achieved by analyzing the viral and prokaryotic diversity of subtropical and boreal lakes; measuring the viral shunt’s effect by chemostat experiments; and evaluating it in light of the viral and prokaryotic diversity and distribution results.