UC San Diego

The power of a single engineered organism is limited by its capacity for genetic modification. In order to circumvent the constraints of any singular microbe, a new frontier in synthetic biology is emerging: synthetic ecology, or the engineering of microbial consortia. In this thesis, we focus on engineering tools to facilitate communication and coexistence of microbial species in a synthetic ecosystem. Engineered microbial consortia are already being used to solve problems of waste recycling (Fulget et al., 1999), industrial fermentation (Chen, 2011; Patle and Lal, 2007), bioremediation (Dejonghe et al., 2003), and human health (Petrof et al., 2013; Khoruts et al., 2010; Shahinas et al., 2012), and we believe our tools will continue to further these advances. In Chapter One, I introduce the history and importance of synthetic biology and how engineering microbial ecosystems became the "second wave" of synthetic biology. In Chapter Two, I discuss the quorum sensing communication systems I developed in an effort to allow for complex social behavior across different members of a community. In Chapter Three, I discuss several applications utilizing the myriad of described quorum sensing systems. In Chapter Four, I discuss a method to stably co-culture two metabolically competitive species using a recently developed population control circuit (Din et al., 2016) in conjunction with my novel quorum sensing systems. We posit that such engineered microbial communities will outpace monocultures in their ability to perform complicated tasks, and these chapters combine to enumerate the tools we’ve created to accelerate this emerging effort.