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New discoveries about the unexpected lifestyles of aquatic microbial eukaryotes (protists) are advancing rapidly through the targeted exploration of cultured isolates and whole communities using molecular sequencing and imaging techniques in concert with evolutionary theory and geochemical analysis. Three major contributions to microeukaryote biology, ecology, and evolution that are catapulting the field forward are the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP), the Tara Oceans Expeditions, and the Malaspina Expedition. Although these three efforts focused on marine organisms, they have provided an unprecedented wealth of new data to the broader protist ecology, evolution, biogeochemistry, and model system research communities. Moreover, these efforts are enabling development of new concepts about the interactions of protists with viruses, bacteria, and archaea.