Microbial Evolution on a Virtual Grain of Sand

The microbial world is astonishingly diverse. Even a single soil particle, that has to be sampled with the tip of a needle, contains up to hundreds of different strains or species. Where does all this diversity come from, and how is it maintained on an area smaller than a grain of sand? In my thesis, I describe our work on the ecology and evolution of micro-organisms. Instead of going into the laboratory, however, we study these systems by designing "virtual laboratories", in which we implement the most important aspects of what microbes must do to survive and reproduce. By studying these models, we investigate microbial community formation, the impact of horizontal gene transfer (HGT), and the predictability of evolution, and many other intriguing details of the microbial world. Briefly, we find that even small microbial populations can harbour a lot of diversity and that certain patterns repeatedly emerge when we "replay the tape". These patterns include the evolution of anticipation in a serial transfer protocol, the emergence of metabolic cross-feeding, how microbes may benefit from differentially mobilising slightly beneficial genes, and the evolution of small and large genomes when microbes evolve with and without HGT. All in all, our work provides testable hypotheses and search images for experimental biologists in real laboratories, but also leave plenty of room for future experimentation in virtual laboratories.