Engineered Biofilms for Environmental Applications

Abstract

As anthropogenic waste continues to pollute the environment with toxic metals, radionuclides and organic compounds, there is a need for new strategies of waste containment and waste management that are cost-effective and sustainable. This thesis explores the engineering of biofilms—populations of microorganisms in an extracellular matrix—as novel biotechnological tools for the removal of pollutants and the recovery of valuable resources from waste streams, using E. coli biofilms as a model system to highlight design principles. The guiding hypothesis is that we can program materials and living systems to be targeted biosorbents by genetic modification of both the cellular and the extracellular components of biofilms. We first demonstrate the environmentally-triggered production of a mercury biosorbent in E. coli using a synthetic gene circuit that couples mercury sensing to the production of curli fibers—extracellular protein amyloids that have a natural affinity for mercury. The circuit is sensitive to mercury in the presence of other metals, and tunes curli production according to environmental mercury concentrations. This response persists over multiple cell generations. The work suggests that biofilms could potentially operate as autonomous sensor-actuator systems for in situ bioremediation. We then describe the development of filters based on curli fibers that have been genetically programmed to display customizable tags. The filters were successfully applied towards the selective recovery of rare earth metals from complex metal mixtures. This work paves the way for designing extracellular amyloids in a range of biofilms for rapid, scalable and selective resource recovery from anthropogenic waste. Taken together, the results presented in this thesis show how a confluence of synthetic biology and materials science can potentially transform biofilms into specialized biosorbents for environmental applications.