Doctoral Dissertations

Date of Award


Degree Type


Degree Name

Doctor of Philosophy


Energy Science and Engineering

Major Professor

Scott R. Retterer

Committee Members

Jennifer L. Morrell-Flavey, Steven M. Abel, Jaan Mannik


Studies that estimate more than 90% of bacteria subsist in a biofilm state to survive environmental stressors. These biofilms persist on man-made and natural surfaces, and examples of the rich biofilm diversity extends from the roots of bioenergy crops to electroactive biofilms in bioelectrochemical reactors. Efforts to optimize microbial systems in the bioeconomy will benefit from an improved fundamental understanding of bacterial biofilms. An understanding of these microbial systems shows promise to increase crop yields with precision agriculture (e.g. biosynthetic fertilizer, microbial pesticides, and soil remediation) and increase commodity production yields in bioreactors. Yet conventional laboratory methods investigate these micron-scale biofilms with macro-scale vessels and are limited in experimental throughput. This dissertation leverages nanofabrication techniques to engineer novel platforms for the study of bacterial biofilms from the bioeconomy. Nanofabrication can create micron-scale environments for bacterial biofilm studies and gain measurements inaccessible to conventional laboratory methods. Nanofabrication techniques can control physical and chemical influences (e.g. fluid flow, topography, confinement, surface roughness, chemistry, etc.) to mimic features of the natural environment. Platform design can also be aligned with microscopy and custom image processing algorithms to amass large datasets. Silane functionalization, together with image processing, investigated Pantoea YR343 biofilm propagation and enumerated the honeycomb biofilm morphology.

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