Rock-Paper-Scissors: Competition and stability in engineered microbial communities

The diversity and impact of the human microbiome has catalyzed interest in how microbial communities can be engineered for applications ranging from human health, to bioproduction and bioremediation. An important aspect of such a forward engineering approach is a detailed understanding of how inter-species bacterial competition affects community com-position and stability. In order to study this, I design a three-strain bacterial community that exhibits “rock-paper-scissors” competition dynamics. Using these engineered bacterial strains, I explore genetic stability, evolution in bacterial competition, and ecological stability. In Chapter Two, I discuss the construction and characterization of these “rock-paper-scissors” genetic circuits. I characterize the dynamics of the competition among strain pairs in microfluidic devices. Next, I integrate the “rock-paper-scissors” bacterial strains with the synchronized lysis circuit. When combined, this circuit exhibits both community level “rock-paper-scissors” dynamics, as well as population level synchronized lysis. In Chapter Three, I demonstrate that cyclical population control can be engineered to stabilize the functionality of intracellular gene circuits. The “rock-paper-scissors dynamic demonstrates rapid cycling of strains in microfluidic devices and leads to an increase in the stability of gene circuit functionality in cell culture. In Chapter Four, I use the “rock-paper-scissors” bacteria strains in order to study competition and community stability. I demonstrate that intrinsic differences in three major mechanisms of bacterial warfare lead to an unbalanced community that is dominated by the weakest strain. The engineering of active warfare between microbial species establishes a framework for exploration of the underlying principles that drive com-plex ecological interactions. In Chapter Five, I investigate bacterial competition between a toxin producing and sensitive wild type E. coli strain in a hybrid growth model. I show that environmental perturbations such as stress or predation can drastically improve the fitness advantage that toxin producing strains have over their sensitive wild type counterparts