Using free-living protozoan biodiversity to resolve deep eukaryote evolution

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Eukaryotes are the lifeforms with complex cells. The most familiar eukaryotes are animals, fungi and land plants. Yet these represent only a small fraction of the `kingdoms' of eukaryotes - there are dozens of groups of algae, parasites and free-living protozoa that are equivalently distinct parts of Earth's biodiversity. In fact, free-living protozoa represent most of the diversity of eukaryote groups alive today, and have the most ancient roots: they gave rise to all the other eukaryotic lifeforms. They are also tremendously important parts of the ecosystem, as major predators of other microbes. Nonetheless, we know far less about free-living protozoa than other eukaryotes. The proposed research program consists of 3 projects that resolve fundamental questions about the biodiversity and evolution of free-living protozoa: Project 1: We will isolate protozoa that potentially represent `new kingdoms', using cell-culturing as well as methods to obtain large amounts of genetic data from cells that cannot be cultivated. We will then infer evolutionary trees from large databases of genetic information to place these new groups on the evolutionary tree of life. Project 2: We aim to resolve a profound mystery in the deep-level evolution of eukaryotes. We will examine the internal architecture (cytoskeleton) of cells from certain groups that are thought to be distantly related, yet seem to share a particular set of structures related to the feeding system. We will also compare the genomes of species with and without these structures to identify novel proteins that they might be made from. We aim to understand whether all living eukaryotes descended from an ancient ancestor with these same structures. Project 3: We will assess the biodiversity of free-living protozoa in water and sediments of a large hypersaline (i.e. briny) lake, using genetic sequences collected directly from the environment, as well from observed and/or cultivated cells. We will test whether we find new groups that are specialist predators of other complex cells (due to the limited diversity of animals in these systems), and whether we can infer their prey from patterns in the genetic data. We will also test whether oxygen-poor sediment levels have similar species to those found previously in oxygen-free brine pools on the sea floor. These projects together will literally `redraw the evolutionary tree' of complex-celled life, as it appears in all biology textbooks for example, and greatly improve our knowledge of how complex lifeforms diversified on Earth. Many other researchers will use our findings in future studies aimed at understanding how the myriad different parts of complex cells arose and changed over time. Some are likely to use some of our new cultures for various cell experiments. Our results will also be used by microbial ecologists worldwide to allow them to correctly identify species in their own genetic datasets.