Severely increasing anthropic pressure on natural water bodies sets a societal context where it is urgent to better understand the role of microbial biodiversity in aquatic ecosystem dynamics and resilience to perturbations. Micro-organisms regulate the chemical composition of the biosphere, influence climates, recycle nutrients, and decompose pollutants. The diversity of microbial communities and their ecological and metabolic functions are being explored in a variety of natural ecosystems, including extreme environments. Because of technical constraints, microbiologists have focused their efforts mainly on prokaryotes. In the environment, and particularly in aquatic ecosystems, the diversity and dynamics of microbial eukaryotes are still poorly understood. Among the new paradigms and challenges constantly emerging in aquatic sciences, probing the unexplored reservoir of novel ‘species’, genes, and metabolic pathways from microbial eukaryotes offers, perhaps, the most exciting research opportunity for the future. These were discussed during the topical session # 11 of the ASLO 2009 aquatic sciences meeting held at Nice, France, through a combination of invited and selected talks and posters. This book brings together part of these talks and presents contributions on ‘disregarded’ microbial eukaryote diversity and its ecological potential in aquatic ecosystems. We hope that this collection of papers will greatly expand our knowledge of the roles of eukaryotic microbes in aquatic ecosystems and will serve as a basis for significant research in the future. We believe that the decade to come promises exciting ecology on the interactions between microbial diversity, hidden genes and functions, and food web dynamics in aquatic systems.

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