Adaptatie aan veranderende omgevingen in eukaryote en prokaryote modelorganismen

Microorganisms are often confronted with changes in their environment. Adapting to these changes in the environment is required to ensure their survival and reproductive success. Research done on the adaptation of microorganisms to environmental changes as well as the influence of the rate, frequency and predictability in which the environment changes, lead to an increased understanding of the evolution of adaptive strategies and some of the underlying mechanisms of these adaptive strategies to deal with environmental changes. However, these studies often investigated these adaptative strategies independently from one another or overlooked the implications of varying rates of adaptation within a species to the same environmental change. There is now the opportunity to investigate if the evolution of one adaptive strategy could facilitate the evolution of the other adaptive strategy and the investigation of benefits and trade-offs linked to slow and fast adaptation to environmental changes. In this project the adaptation of two model microorganisms, E. coli and S. cerevisiae, is studied in changing environments. For E. coli, it is well known that persistence and resistance are the two major adaptive strategies to survive and overcome antibiotic treatments. In this work, we investigated if and in which conditions one strategy could further facilitate the evolution of the other. In addition, how different nutrient and antibiotic concentrations can affect the evolution of persistence and resistance. By building a stochastic model to mimic the outcomes of experimental evolution in a range of different combinations of antibiotic a nutrient concentrations, we could determine the evolutionary paths taken to adapt to antibiotic treatments. These simulated paths show that persistence evolution precedes the evolution of resistance. These results suggest that at high antibiotic dosages, persistence evolution facilitates the evolution of resistance. The model further shows that the high and low nutrient concentrations select for resistance and persistence evolution respectively. This model has the potential, to aid in the evaluation of new antibiotic treatments. For S. cerevisiae, it is seen that when the environment changes in carbon source there is a period of reduced or no growth in which cells need to adapt to the new carbon source, called the lag phase. Which is a result of the time and energy it takes to adapt their metabolism. However, It has been shown that for the same change in carbon source, genetically different yeast strains show a large variation in the duration of their lag phase. This variation in adaption rate to a new nutrient raises the question of whether having a slow rate of adaptation has fitness benefits or if there are ecological niches that select for slow rates of adaptation. Previous research indicated that genetic variation in the gene YLR108C is at the basis of variation in the rate of adaption to a shift in carbon sources. This allows us to further investigate the trade-offs and fitness benefits linked to varying adaptation rates by carrying out experiments with strains only varying in the YLR108C allele. Competing these strains against each other in different environments, resulted in strains with a fast adaptation having the highest fitness in changing environments, while strains with a slow adaptation rate have the highest fitness in environments in which the population can grow to high densities. Furthermore, by analyzing genetic variation in YLR108C across 1,011 natural S. cerevisiae strains suggests a link between specific SNPs in YLR108C and the ecological niche of the strain. In which strains with a YLR108C allele associated with a slow adaptation rate are often isolated from niches with high concentrations of preferred carbon sources (e.g. glucose) and limited availability of oxygen. The niches of strains with a fast adaptation rate can contain a wide range of carbon sources from simple sugars to complex polysaccharides and these niches are often open-air fermentations. Taken together, these results suggest that the adaptation rate to changing carbon environments is evolutionarily tuned to specific ecological niches as well as a slow adaptation rate carrying fitness benefits.