Bacterial and viral adaptation in ecologically complex systems

Abstract

If we want to understand microbial diversity and find new ways to control infectious disease, it is important that we consider the variety of ecological factors that microorganisms normally encounter and how this influences their evolution. Our understanding of interactions between abiotic (e.g. antibiotics) and biotic (e.g. parasites) conditions, and how they affect microbial adaptation remains limited. Specifically, the role of viruses that infect bacteria (phages) in the evolution of antibiotic resistance is an area of growing interest. Not only because viral parasites are important in bacterial ecology and evolution, but also because they have the potential to be used therapeutically. In this thesis I develop and test hypotheses relating to bacterial and viral adaptation in ecologically complex systems. In chapter 1 I give a general introduction to the thesis. In chapter 2, I investigated the role of antibiotic resistance alleles in bacterial responses to parasitic viruses (phages). I show that although some antibiotic resistance alleles can impede the evolution of resistance to phages via growth costs, the overall effect of resistance alleles is relatively weak, as compared to the strong effect of a mutator allele. In chapter 3 I investigated the counteracting effects of antibiotics on bacterial adaptation, specifically, the alteration of mutation supply rates via changes in bacterial population size or bacterial mutation rates. I present evidence that positive mutagenic effects are relatively weak, as compared to the strong negative effects of antibiotics in reducing population size. In chapter 4 I investigated phage host shifting across a range of different bacterial hosts. I used experimental evolution to evolve phage in the presence of novel bacterial host strains. I provide evidence that evolution can result in host shifts, but also in a variety of changes in virulence towards other hosts. In chapter 5 I outline some of the broad themes that emerge from these research projects and point out some of the potential areas for future work.