ROME is a basic research project that will focus on Rare and Overlooked Microbial Eukaryotes, an unexplored reservoir of novel 'species', genes, and metabolic pathways. We will focus on the ecological functions and roles of “rare” (i.e., below 0.01 to 1% of the total number of pyrosequence reads) and “neglected abundant” (primarily zoosporic organisms) species in two contrasting, well-circumscribed and well-studied systems, Lake Pavin and the Eastern English Channel. Deep environmental sequencing, coupled with experimental manipulations and microscopic observations, will unveil the ecological potentials of rare and neglected “ microbial eukaryotes in aquatic ecosystems. Our central hypothesis is that abrupt environmental changes result in novel communities. Among the neglected abundant eukaryotes, zoosporic chytrid pathogens of phytoplankton likely play a key and hitherto unrecognised role in food web dynamics. To explore this possibility, the genomes of one host-pathogen system will be sequenced, annotated and used as a reference to explore gene function in the environment. This information will be combined with functional ecological measurements performed on field communities and mesocosm experiments, in order to model fluxes in the ecosystems under study. We will combine analytical, biochemical, microbiological, and molecular biological techniques in an integrative study of organisms with neglected ecological functions. ROME is a unique collaboration between researchers with complementary expertise in microbial food web interactions and trophic relations, purification/culture and microscope identification of protists and zoosporic organisms, molecular ecology, functional genomics, analysis of community structure, and food web modelling.