Uncovering Bacterial Metabolites Involved in Eukaryotic Development

Abstract

Microorganisms are ubiquitous. They crowd the soils, the oceans, even deserts and glaciers, and they make up the microbiota that live in and on the bodies of animals. Crammed into their environment with many other competing species of microorganism, they form alliances and disputes, often mediated by secreted molecules. For evolutionary biologists, such interactions can reveal how organisms compete for resources, how finely tuned association may aid their fitness in diverse environments, and whether such interactions are conserved in other organisms. Chemists have traditionally focused on the mediation of such symbioses via the production of, or response to, secondary metabolites. Such studies further our understanding of the natural world and may also reveal novel biologically active molecules that can be used to treat human disease.

The focus of this thesis is the relationship between bacteria and eukaryotic organisms. While traditionally bacteria were associated with pathogenesis, they are increasingly viewed as essential contributors to eukaryotic health. Chapter 1 discusses a handful of symbiotic relationships that have provided chemical ecologists with opportunities to discover new chemistry and increase their understanding of the impact of microorganisms on eukaryotes. In Chapters 2 and 3 both chemical and evolutionary questions are addressed through the study of chemical communication between bacteria and the choanoflagellate, Salpingoeca rosetta. Choanoflagellates are aquatic eukaryotes and are the closest living relatives of animals. This unique phylogenetic positioning and their ability to switch between a unicellular state and multicellular “rosettes” make choanoflagellates an ideal model organism for studying the emergence of multicellularity in animals. We found that the co-isolated bacteria, Algoriphagus machipongonensis, produces lipids that affect multicellular development in choanoflagellates through a complex set of synergistic and inhibitory activities.

Finally, Chapter 4 focuses on a symbiotic relationship between a social amoeba, Dictyostelium discoideum, and co-isolated bacteria. Certain D. discoideum isolates have been shown to engage in “primitive farming,” in which D. discoideum engulf bacteria, which are subsequently released upon spore dispersal. While some of the farmed bacteria are a food source for the amoeba, the rest do not serve a readily apparent function in the symbiosis. Additionally, not all of the D. discoideum isolates are capable of farming. We examine how small molecules isolated from the farmed bacteria affect D. discoideum “fitness” and we also develop a screen for bacterial genes that have toxic effects on D. discoideum.

The overarching theme of the research presented herein is that relationships are complicated. Of the two major symbiotic systems explored, we have found that bacterial-eukaryotic interactions cannot be defined as obviously negative or positive; usually they are both. While developing model systems for studying symbiosis often requires simplicity, the underlying intricacies should not be ignored, as these are what often provide the clearest insight into the nature of the relationship.