The ecology and evolution of complex microbial communities

Microbial communities colonise virtually every habitable environment on earth. They live on us, inside us, and all around us, and are key components of the earth’s ecosystem. However, due to the complexity of microbial communities we still understand relatively little about the mechanisms that drive their ecology and evolution. The aim of this thesis is to develop novel experimental and mathematical approaches, in order to investigate complex microbial communities. Specifically, this thesis is split into two parts, focussing in turn on how environmental complexity, and interspecies interactions shape microbial ecology and evolution. In the first part I have studied microbial evolution in porous environments such as one might find in soil or aquifers. Here I have combined microfluidic experiments, mechanistic models, and game theory to study how hydrodynamics mediate competition between bacterial genotypes. With these I have demonstrated how even subtle environmental complexity can fundamentally affect microbial competition, enabling slow growing genotypes to outcompete their faster counterparts. In the second part of this thesis I have investigated how interspecies interactions influence the stability and initial assembly of microbial communities. Here I have developed new tools – from theoretical ecology – in order to study the microbial communities within the mammalian gastro-intestinal tract. With these I have demonstrated how strong, cooperative interactions between species can undermine both the stability, and the assembly of communities. Moreover, I have illustrated how these tools can be applied to real microbiome data, in order to better understand these important communities. In sum, this thesis explores two key drivers of microbial ecology and evolution, and presents a new set of tools for the future investigation of complex microbial communities.