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Microbes are increasingly considered in trophic ecology among aquatic ecosystems due to their high productivity possibly leading to significant implications in both consumer dynamics and carbon recycling. These organisms can hence represent an overlooked resource for a large array of species that should be accounted for when addressing species trophic relationships through network perspectives. Understanding the networks of interactions that are at work within lake ecosystems is a very promising research front, yet little explored, despite the potential for knowledge and applications that results from it. There is a whole procession of microorganisms living closely with each other and responding dynamically to environmental biotic and abiotic disturbances. These responses correspond to and/or result in a change in the composition of microorganisms and their interactions (competition, commensalism, amensalism and mutualism) constituting a network whose modulations can impact the functioning and health of ecosystems. Identifying and characterizing these networks of microbial interactions thus provides a better understanding of the complex underlying mechanisms that influence them and impact the functioning of lakes. Diverse analytical tools are mobilized to highlight the microbial implication in the trophic functioning of lakes (e.g. stable isotopes, fatty acid and molecular analyses).