Not all those who evolve are adapted: The ecology and evolution of microbial interactions within synthetic communities and phage therapy

Abstract

Evolutionary ecology defines mechanisms shaping adaptations across all orders of life. Much of this research area has used microbes as model systems for testing hypotheses, owing to their ability to rapidly evolve in vitro. However, the relevance of this work in broader ecology, both in microbes and multicellular organisms, is questionable as many evolution experiments are conducted with single or pairs of species. In reality, species exist in complex communities with interactions from competition and trophic networks. In this thesis, I conduct a series of experimental works and critically review on a series of knowledge gaps related to this shortcoming. Within two chapters, I examine how competition affects adaptation of a focal species and multiple coexisting species. Building on this work, I introduce trophic interactions. In a critical review, I evaluate the relative importance of bacteriophages (“phages”; bacteria killing viruses) in shaping microbial communities. In two further chapters I examine how phages interact with plasmids (a second antagonist) to shape community composition and how bacteria adapt to phages under multispecies competitive interactions. Finally, we focus on the applied aspects of these knowledge gaps with the uses of phages to treat bacterial infections. We first examine how starting genetic diversity of phage populations affect bacterial adaptation to phage. Then, we compare bacteria and phage (co)evolution in vivo and in vitro using samples from a phage prophylaxis patient. To conclude, we examine how macrophages influence bacteria-phage (co)evolution in vitro. These results highlight that even small increases in community complexity can change evolutionary outcomes. Community context is therefore of vital importance when predicting evolution from in vitro experiments in theoretical and applied contexts.