Date Thesis Awarded


Access Type

Honors Thesis -- Access Restricted On-Campus Only

Degree Name

Bachelors of Science (BS)




Margaret Saha

Committee Members

Greg Conradi Smith

Mark Forsyth

Dana Willner


Synthetic Biology has shown potential to address soil degradation and climate change through the design of microbes that can, for example, degrade pollutants, sequester greenhouse gasses, and increase crop yields. For Synthetic Biology to be a realistic solution, bioengineered bacteria must be able to survive, spread, and express genes of interest in soil environments. However, major gaps in knowledge exist about how inoculated bacteria behave in the soil.

This project takes three foundational steps toward fieldable soil synthetic biology. First, a soil microcosm experiment was conducted with engineered Mycobacterium smegmatis over 49 days, the first of its kind to incorporate bacteriophage, have a spatial component, and compare population dynamics across bacterial engineering methods as well as soil sterility. This experiment demonstrated the ability of bacteria, regardless of engineering type and soil sterility, to persist in soil. It also revealed statistically significant differences in bacteria and phage population dynamics over time across bacterial engineering types and soil sterility. Second, a Polycyclic Aromatic Hydrocarbon (PAH) pollutant degradation circuit was designed and constructed, and then integrated into M. smegmatis’s genome. And, third, an RNA extraction protocol was optimized for the simultaneous extraction of RNA from culture and from soil, which will enable RNA sequencing experiments comparing gene expression between these two environments.

Available for download on Monday, May 08, 2034

On-Campus Access Only