Research on bacteria in their biofilm form is limited by the ability to artificially culture bacterial biofilms in a system that permits the visualization of individual cells. The experiments comprising this thesis research are on-going investigations of bacterial culture systems engineered to provide an environment that mimics biofilms while enabling real-time microscopy. Specifically, the microfluidic systems developed and assessed as part of this thesis permit the visualization of individual bacteria cells within consortia growing within a narrow space provided by a microfluidic device. This research demonstrates the versatility of these microfluidic systems across potentially high-throughput microbiological experiments utilizing genetically engineered Escherichia coli. Before demonstrating the efficacy of these systems, the development of the field of synthetic biology over the past half century is reviewed, focusing on synthetic genetic circuits and their applications (Chapter 2). The first and main microfluidic device explored in this research was developed to mimic the nutrient-deficient conditions within biofilms by forcing media to enter the culture area through a narrow, torturous channel. The microfluidic channel was thin enough (0.97 μm) to prevent the motility of 1-μm-wide E. coli cells, enabling visualization of individual cells. The bacteria cultured in the device contained either a simple Plux-driven quorum sensing receiver (Chapters 3 and 5) or a LacI- and TetR-driven genetic toggle switch (Chapter 4). Under the culture conditions, the quorum sensing reporter signal was detected even without addition of the signaling molecule (Chapter 3). The genetic toggle switch was stable when the system began in the high-LacI expression state, but after 5 days of culture, >5% of high-TetR expression cells began to consistently express the high-LacI state (Chapter 4). This system was also employed to track lineages of cells using real-time microscopy, which successfully characterized the inheritance of aberrant, enlarged cell phenotypes under stress (Chapter 5). Another microfluidic device, a droplet bioreactor, was also developed to culture small numbers of cells in an aqueous bubble suspended in oil (Chapter 6). Quorum sensing receiver cellswere cultured in this device, demonstrating that it is well suited for testing the effects of compounds on biofilms within water-in-oil droplets. / Ph. D. / Bacteria are the most abundant organisms globally, yet relatively little is understood about the basic biology of biofilms, one of the most common natural states of bacteria. Biofilms are ubiquitous consortia of individual microbial cells that send and received chemical signals from one another to carry out group behaviors such as quorum sensing. The impacts of biofilms range from the contamination of food processing equipment to antibiotic resistant bacterial infections. The vast majority of microbiological research has been conducted on bacteria in their planktonic state as individual cells cultured in a liquid medium. This form of culture does not permit the types of research that can help address the impacts of biofilms on human health and economic activities, never mind examine the biological mechanism of random gene and morphological expression within bacterial biofilm. This thesis presents research utilizing two microfluidic devices that will enable further large-scale studies to unravel the mechanisms that create biofilms as well as permit high-throughput testing of chemical compounds to control the growth and development of biofilms. Moreover, these devices permit the use of real-time microscopy to track cells and their growth over time. The first microfluidic device utilized in this research mimics the nutrient-limiting conditions of biofilms. This biofilm-mimicking device was used to culture a common research bacteria, Escherichia coli, with one of two engineered genetic circuits (reviewed in Chapter 2): a quorum sensing receiver (Chapters 3 and 5) or genetic toggle switch (Chapter 4). Both of these genetic circuits demonstrated stochasticity in their gene expression states under the culture conditions in the biofilm-mimicking device. The second microfluidic device successfully permitted the culture of small numbers of isolated cells within a small bubble of bacterial media suspended in oil (Chapter 6). Additionally, this device enabled the addition of chemical compounds to influence the growth and metabolism of the trapped cells. Collectively, these microfluidic devices provide the ability to effectively study both the mechanisms underlying random gene expression within biofilms as well as explore the chemical factors that can be used to control and mitigate biofilm formation and growth.