IMAGEN3D · The hidden majority: high-resolution imaging and genomics of the most ecologically important microbial eukaryotes in the ocean

How have eukaryotes evolved into the vast diversity we see nowadays? At present this simple question remains a mystery, mostly due to the vast uncharted microbial environmental diversity recurrently unveiled by molecular surveys. This gap in knowledge hinders a deep understanding of basic eukaryotic diversity, evolution and biology, and creates a biased perception towards well-characterized organisms of human interest. Yet, since the beginning of microbial research, from Leeuwenhoek and Haeckel, unicellular eukaryotes have been largely studied by optical methods, describing an extensive variety of shapes and morphologies. We therefore need new and different approaches to explore unknown eukaryote diversity.The goal of this project is to better understand early and enigmatic eukaryotic evolution by studying the morphology and genomes of the most informative undescribed eukaryotic lineages. Studies of novel eukaryotic diversity have historically relied on arbitrary factors regardless of their environmental abundance due to the lack of data. Yet, abundant groups are the most practical to explore. I will first identify the most environmentally abundant species that are distantly related to morphologically described groups. Next, I will develop a novel approach that allows the acquisition of 3D morphological data by imaging group-specific fluorescence in situ hybridization probes in combination with a set of fluorescent dyes labeling relevant subcellular features. Finally, I will sequence and assemble their genomes to better resolve the eukaryotic tree of life, by filling out poorly represented lineages that are distantly related to well-characterized species. This project will bring for the first time the link between already available environmental short sequences and their organismal morphology and genomic data.