Using Experimental Evolution to Evaluate Environmental Effects on Microbial Mutation and Adaptation

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PROJECT SUMMARY In nature and human microbiomes, microbes regularly face challenges due to fluctuations in the availability of resources and nutrients - a lifestyle termed feast/famine. Previous studies investigating microbial adaptation to feast/famine have focused on the specific adaptations that allow microbes to survive extreme starvation, often overlooking how the eventual replenishment of resources affects evolution. However, due to evolutionary tradeoffs between growth and survival, the molecular, cellular, and behavioral phenotypes that evolve in response to feast/famine may vary based on the duration and severity of starvation. Common adaptations to resource limitation include expanding metabolic capability through nutritional competence and increasing efficiency by diversification into cross-feeding ecotypes. As microbial metabolism can be constrained by many biologically relevant factors, including the presence of oxygen, this can complicate evolution and limit potential adaptive trajectories. Research in my lab focuses on how microbes adapt and diversify in novel complex environments by applying multi-omic, systems microbiology approaches to experimental evolution. We plan to investigate how oxygen availability shapes microbial evolution to feast/famine by conducting an adaptive laboratory evolution experiment with two bacterial species, the facultative anaerobe Escherichia coli, and the fastidious aerotolerant anaerobe Lactobacillus crispatus. We will characterize populations for fitness outcomes, common adaptive mutations, and patterns of diversification to determine how oxygen influences adaptation to feast/famine conditions. We will follow up by characterizing the effects of common adaptive mutations on microbial physiology using transcriptomics and high-throughput phenotyping. Further, as oxygen can shift the topography of the adaptive landscape by affecting the rate and spectra of mutations, we will also perform mutation accumulation experiments on facultatively anaerobic, aerotolerant anaerobic, and obligately anaerobic bacterial species in the presence and absence of oxygen. Studies of microbial evolution have historically neglected fastidious microorganisms and anaerobic environments due to the challenges associated with their culture. Our research will provide fundamental knowledge about evolutionary processes in a neglected fraction of the microbial tree of life that accounts for a significant proportion of the human microbiome.