Magnetic resonance insights into engineered biofilm-inspired systems

Abstract

This dissertation explores how nuclear magnetic resonance (NMR) techniques can be applied to study engineered biofilm-inspired systems in environmental and geologic settings. Two systems were investigated: (1) aerobic granular sludge (AGS), biofilm aggregates used in wastewater treatment, and (2) microbially-induced calcium carbonate precipitation (MICP), a biofilm-based sealing strategy applied to seal fractures in subsurface shale rock formations. In the first system, magnetic resonance imaging (MRI) was used to characterize the relaxation-weighted contrast of model biofilms (or "phantoms") constructed to mimic the extracellular polymeric substances (EPS) found in AGS. Key biofilm components were studied for their contributions to T1 and T2 contrast, including gel-forming polysaccharides, extracellular proteins, and bacterial cells. Results revealed that biopolymer structure and composition can play a major role in MRI contrast, demonstrating the potential of relaxation-weighted MRI to study biofilm heterogeneity without invasive labeling or sectioning. In the second system, NMR relaxometry and magnetic resonance velocimetry (MRV) was used to monitor MICP-treatment in shale fractures at elevated temperatures (60 °C). T2 relaxation profiles tracked porosity changes during biomineralization and 3D velocity mapping provided insight into the evolution of flow channeling and tortuosity as sealing progressed. NMR findings were also complemented by X-ray microtomography (micro-CT) imaging analysis and 2D local cubic law (LCL) flow simulations. Overall, effective permeability reductions were observed, though polymer additives and surfactants were explored to make MICP-treatment more efficient. Together, these studies highlight the versatility of NMR in assessing both biological structure and reactive transport processes in opaque systems. Future work should build on these methods by incorporating additional imaging contrast mechanisms (for example, CEST and CHESS) and exploring dynamic in situ measurements.