Microbial organisms (pro- and eukaryotes) play an essential role in freshwater and marine (but also terrestrial) ecosystems worldwide. They drive biogeochemical cycles, fuel food webs and sequester carbon. However, the abiotic, biotic and stochastic forces that regulate the assembly of their communities, their functioning in ecosystems, and the way they adapt to changing environments (including climate), remain little understood. During the past decades, aquatic microbial research has undergone a sea change thanks to the integration of molecular tools (omics approaches). In my research, I apply a wide range of microscopic, physiological and molecular tools to better understand diversity and occurrence patterns in microbes (mainly microalgae) and how they function in ecosystems and adapt to changing environments, with emphasis on interactions with other microbial organisms, and this in a wide range of aquatic environments, from Arctic fjords to the North Sea and Schelde estuary.