The Impact of Endosymbiosis on Genome Structure and Content

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Endosymbiosis is the process where a host cell takes up and retains another cell, resulting in a long-term intracellular association. Endosymbiosis is widely accepted to have impacted evolution and cell function significantly, but we have a surprisingly superficial understanding of how the process actually works, or the ultimate fate of most endosymbionts. We study the gain or loss of endosymbionts and how partners integrate, to better explain the process and its impact on the partners.      Sub-cellular organelles (mitochondria and plastids) are are the best-studied endosymbionts, but are also limited as mechanistic models by their extreme age and integration. Indeed, work on more recent insect-bacterial endosymbioses has challenged many longstanding assumptions about the process, including its mutualistic nature. Insects, however, represent a narrow spectrum of endosymbiotic diversity: protist-bacterial endosymbioses are much more diverse, but for most we have few functional or genomic insights. Using single-cell genomics to study even uncultivated microbial endosymbioses, we can develop a broader understanding of how this process unfolds, using two lines of research to balance depth and breadth: 1. Endosymbiont replacement in Euplotes. The ciliate Euplotes harbours an essential endosymbiont, Polynucleobacter, which we have shown is constantly degraded and re-established from free-living strains. But some Euplotes lack Polynucleobacter, and possess different endosymbionts, while others still have extra "accessory" endosymbionts. We will test if the dominant process of repeated replacement extends to these endosymbionts, and whether accessory endosymbionts increase functional complexity of the system.  2. Diverse systems to study protist-bacterial endosymbiosis. To examine a wide breadth of endosymbiotic contexts, we will also explore endosymbiotic integration in diverse protist hosts. One classic system is cellulose-digesting protists in termite hindguts. We will characterize bacterial endosymbionts from several recently-diverged hosts to determine how common are gains, losses, and replacements, and whether they persist through host speciation. Another system is anaerobic ciliates with hydrogen-producing relict mitochondria, "hydrogenosomes". These can associate with methanogenic archaeal endosymbionts for hydrogen-exchange, and we find genomic reduction of hydrogenosomes may be accelerated by the presence of endosymbionts. We will test this by examining a wide range of ciliate hosts, with and without endosymbionts. Lastly, we will carry out pilot studies on under-explored systems to identify candidates for further development: free-living diplonemids with nucleus- and mitochondrion-associated endosymbionts, and a classic lab-timescale system in Amoeba.        These studies will collectively provided significant insights into what are general principles in diverse stages and contexts of an important evolutionary process.