Date of Completion


Embargo Period


Major Advisor

Biofilm, microfluidic device, antimicrobial susceptibility, soil water retention, biofilm respiratory

Co-Major Advisor

Leslie M. Shor

Associate Advisor

Jeffrey McCutcheon

Associate Advisor

Daniel Gage

Associate Advisor

Ranjan Srivastava

Associate Advisor

Yong Wang

Field of Study

Chemical Engineering


Doctor of Philosophy

Open Access

Open Access


Biofilms are aggregated bacteria embedded in extracellular polymeric substances (EPS). Biofilms are the dominant growth form of bacteria in most natural environments, and are also important in many industrial and in vivo settings. The function of a biofilm system is inherently different from the function of the same cells dispersed in liquid culture. Existing methods to study biofilm either do not maintain the essential biofilm architecture or do not capture the dynamic nature of their responses. This research describes the development of a set of biofilm microenvironment analysis systems that maintain the essential micro-scale structure of biofilms. These systems are relevant to both medical and environmental applications. Many critical enabling technologies were developed as part of this work, include contact printing for patterning arrays of identical bacterial biofilms; wide field and confocal microscopy and white light interferometry for characterization of biofilm geometry; development of a spatially continuous non-destructive optical oxygen sensor; soft lithography and photolithography to create synthetic biofilm microenvironments with controlled nonlinear gradients and realistic soil microstructures; optical analysis and high-throughput digital image processing methods; thermogravimetric analysis and dynamic vapor sorption to measure water retention in biofilms; and three-dimensional dynamic mass transport and reaction modeling to infer bulk oxygen respiration rates in

intact biofilms. In the medical context, this research offers practical methods for high-throughput screening of antimicrobials and antimicrobial dosing rates, and a tool for better understanding the relationships among antimicrobial concentration, antimicrobial flux, and exposure time in inhibiting bacterial biofilms, and thereby a strategy to minimize induced resistance. In the agricultural context, emulated soil micromodels were developed to directly observe the effects of biofilm EPS on pore-scale water retention. Experiments with a synthetic microenvironment confirmed that EPS and micromodel geometry act together to limit evaporation at pore throats. Conservation of the biofilm microenvironment enables emergent properties of the biofilm to be studied systematically in a laboratory setting. By conserving the complex and micro-structured features of the biofilm system, microbial systems engineering approaches offer new approaches to finding more effective treatments to disease, and for more sustainable and resilient food production.