Abstracts Earth and Environmental Sciences

Understanding how gas-producing biosensors can be used in living soils to study biological processes in situ

by Emily M. Fulk

Soil microbes regulate critical Earth system processes, including mediating the transformation of biogeochemical cycle intermediates, regulating the production and consumption of greenhouse gases, and forming essential plant symbioses. However, little is known about how macroscale conditions, including soil properties like or- ganic matter content or climactic properties like hydration, influence the microscale environment and microbial behavior in soils. Engineered microbes that function as biosensors present an opportunity to understand how microbial consortia members re- spond to dynamic conditions within a spatially and temporally heterogeneous matrix environment. In this thesis, I review opportunities to engineer microbial biosensors that can sense the microscale environment and produce a detectable signal to report on their experiences. Then, I describe my work to enable ultrasensitive detection of a volatile gas signal produced by biosensing cells, enabling non-invasive monitoring of microbial behavior within a living soil. I show that these tools enable non-destructive detection of a sugar in bulk soil at biosensor cell titers that are orders of magnitude below the abundance of native microbial consortia in soils. I also describe my efforts to expand the use of gas-producing enzymes to report on post-translational protein interactions, and show my progress towards developing a nitrate biosensor for in situ applications in soil. Finally, I discuss opportunities to further advance applications of synthetic biology to address Earth and environmental science questions.