The impact of ecological complexity on bacterial evolution

Bacteria successfully colonize almost any environment on our planet like the oceans, soils or the guts of animals. Their success is in part due to their ability to adapt to a vast range of environmental conditions and has resulted in a stunning bacterial diversity found in virtually every ecosystem on earth. Indeed, laboratory experiments have shown just how rapidly bacteria can evolve to cope with conditions under which they could previously not grow, such as the presence of harmful chemicals or antibiotics, high temperature or novel food sources. Yet such laboratory evolution experiments typically involve only single species of bacteria that are studied in isolation. In reality, however, bacteria grow as part of dense communities made up of many different species. Within these diverse communities microorganisms compete for nutrients and space but are sometimes also found to work together, for instance to break down hard- to digest food sources. This is especially true for the human gut, which harbours trillions of bacterial cells belonging to hundreds of different species. Understanding how evolution proceeds in the bacterial community of our guts is directly relevant to human health: It is in this complex community that bacteria will evolve new capabilities to any challenges they may face, for instance a course of antibiotics they are exposed to. My project goal is therefore to systematically tackle a major unanswered question in microbiology and evolution: how does living in a complex community made up of many species affect bacterial adaptation? To close this gap, I will assemble a range of simple to more complex bacterial communities in the laboratory. I will study how changing the complexity of a bacterial community impacts the evolution of a focal bacterium, namely Escherichia coli. E.coli is normally a harmless natural resident of the human gut but also holds the potential to cause disease. Incidentally, its resistance to treatment by antibiotics is on the rise worldwide. Therefore, in my project I will elucidate the impacts of community species diversity on the evolutionary dynamics of E. coli 1) in response to other members of the gut community and 2) in the presence of an additional selection pressure in the form of an antibiotic. To study its evolution, I will grow the different bacterial communities in continuous-flow culture models, a laboratory system that allows to mimic important aspects of the human gut, such as the absence of oxygen, a slow but steady growth and a controlled pH. The use of a precisely controllable experimental system will allow me to establish causal relations and build up complexity systematically to study its effects. With this project I aim to shed light onto a question, which is considered one of the major open challenges for 21st century biology, namely how evolution proceeds in complex ecosystems.