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Despite their relative low volume on a global scale, lakes represent a valuable reserve of accessible freshwaters. Any increase in our understanding of their functioning is a step towards their better exploitation and preservation. Microorganisms drive the metabolic processes that regulate the biogeochemical cycles in lakes; here, I will focus on Archaea and Cyanobacteria as micro-players playing macro-roles in lake ecosystems. In particular, I will present two examples to demonstrate the importance of prokaryotes in lakes: picocyanobacteria and mesophilic archaea. The role of prokaryotes in lakes will be discussed in relation to their taxonomy, dynamics and ecology using these two examples. The challenge, now, is to better understand the relationship between the diversity and the physiology of various ecotypes, how these interact with each other and with environmental factors allowing the proliferation of the most competitive genotypes.
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