Bacteria-driven biotechnology is a powerful approach for engineering porous materials and processes across industries. This project focused on two key ideas: 1) precise control of the properties of porous systems can be obtained by exploiting bacteria and their remarkable capabilities; 2) porous media, with their high surface-to-volume ratios and complex structures, could be a major part of bacterial synthetic biology, serving as a scaffold enabling controlled, large-scale sessile microorganism cultivation.
The main scientific obstacle to precise control of such processes was the lack of understanding of complex biophysical mechanisms in complex porous structures, even in the case of single-strain biofilms. We hypothesized that deeper insight into the fundamentals of biofilm biomechanics and physical ecology in porous media would provide a novel theoretical basis for engineering and control.
Our first objective was to unravel the interactions between fluid flow, transport phenomena, and biofilms within connected multiscale heterogeneous structures. We developed novel microfluidic platforms integrated with online instrumentation, advanced imaging, and multi-scale modeling approaches, achieving accurate measurements in controlled conditions and detailed characterization of the spatio-temporal dynamics of biofilm development and bacterial ecology in porous media flows.
The second scientific objective was to create the primary building blocks toward a control theory of bacteria in porous media. Through a combination of experiments and mathematical modeling, we identified key variables governing biomass dynamics and global porous media properties. We also developed a novel porous micro-bioreactor technology that makes it possible to test new control strategies, e.g. bacterial predators or quorum-sensing inhibition, in a miniaturized system.
This work advances the field by developing microfluidic methods and multi-scale modeling approaches for studying biologically active porous media, while revealing fundamental new physics governing flow-biofilm interactions. These advances will enable applications in wastewater processing, soil bioremediation, and self-regulating construction materials, while providing a pathway from synthetic biology proof-of-concept to production.
