Abstract
Microbes are distributed all over the world, in the air, under the ground, on and in other species, like plants, animals and human. They live in heterogeneous environments with complex interactions with both abiotic factors (e.g. temperature, water, and minerals) and biotic factors in many different ways (e.g. cooperation and competition). Significant effects of microbial interactions have been recognized in influencing both ecological and evolutionary dynamics of single species and communities. By using the model organism budding yeast, Saccharomyces cerevisiae, I studied microbes involved in relationships of cooperation, competition over ecological time scales, and interactions between spatially distributed metapopulations and environment after long term evolution.
The first chapter, entitled “Microbial expansion–collision dynamics promote cooperation and coexistence on surfaces”, proposed a novel mechanism for the maintenance of cooperation and co-existence (i.e., expansion-collision dynamics during microbial colonization of a surface). Expansion-collision dynamics is a common phenomenon of clonal microbial growth on a 2-dimensional surface, consisting of two regimes: expansion competition regime and boundary competition regime. During the expansion competition regime, individual founder cells divide clonally and expand to empty territory while boundary competition takes place at the genetically heterogeneous boundary where neighboring colonies have collided. We predict theoretically that expansion competition regime favors cooperators, while boundary competition regime favors defectors. We then tested our predictions empirically and verified experimental results computationally. We further showed that time-varying negative frequencydependence allows mutual invasion of types, promoting stable co-existence of microbes involved in a cooperative interaction.
The second chapter, entitled “Luxury uptake of synthesizable resources diminishes diversity and productivity in an experimental yeast microcosm”, described and investigated a new phenomenon, namely “luxury uptake of synthesizable resource (LUSR), that a cell uptakes a nutrient molecule from the environment while it can be synthesized intracellularly. Examples include simultaneous encoding of transporters and biosynthesis pathways for 20 necessary amino acids in Escherichia coli and S. cerevisiae. We studied the ecological consequences of LUSR in engineered yeast system with high throughput competition assays, uptake assays, theory and simulations, and found that LUSR diminishes both diversity and productivity, but is a competitive strategy and favored by natural selection in exploitative competitions.
The third chapter, entitled “Experimental evolution of antimicrobial resistance and pleiotropy in spatially distributed metapopulations with dispersal”, is a quantitative study of the evolution of antimicrobial resistance and pleiotropy when spatially distributed metapopulations interact with their environments. Specifically, we evolved spatially distributed metapopulations of barcoded yeast strains, each of which consists of 16 demes, in varying distributions of antifungal (fluconazole) in space with different dispersal patterns (local and global) and rates (low and high), for 960 generations. Then, we quantified the evolutionary consequences of dispersal pattern, dispersal rate, and environmental heterogeneity in the evolution of antimicrobial resistance and pleiotropy using high throughput competition assays. Our results indicate that clustered environmental heterogeneity impedes the evolution of antibiotic resistance and selects against positive environmental pleiotropy, while promotes local adaptation, in locally dispersing metapopulations.
My thesis identified and investigated two novel mechanisms that contribute to the ecological dynamics of cooperative and competitive communities, and advanced our knowledge of evolutionary dynamics of spatially distributed metapopulations influenced by environmental heterogeneity and dispersal.