Quantitifaction and Modeling of Biofilm Development through Interferometry
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Bravo, Pablo
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Abstract
Biofilms are ubiquitous in nature and have significant impacts on ecosystems, human health, and various industries. However, their complex three-dimensional structure and heterogeneous composition pose challenges for accurate measurements and modeling. Using white light interferometry, we measure the heights and topographies of microbial colonies with nanometer precision from inoculation to their final equilibrium height, producing a detailed empirical characterization of the biofilm-air interface. We characterized that their vertical growth dynamics are defined by two regimes: exponentially early on until a given thickness, and then growth decreases linearly until it stops. We propose that this behavior is a direct consequence of nutrient gradients, given the geometric configuration of the colony. This leads to the formation of a finite-size growth layer. This model captures the vertical growth dynamics from short to long time scales (10 min to 14 d) of diverse microorganisms, including bacteria and fungi. After an initial period of increasing roughness, colony topographies freeze, even as the biofilm continues to grow. The observation of this freezing phenomenon across diverse bacterial species suggests that it arises due to a universal feature of biofilm development. We show that the amount cells are displaced by the emergence of a single new cell decays exponentially with distance; once biofilms grow tall enough, reproduction no longer affects topography. Finally, we corroborate this model by establishing a correlation between the freezing of the biofilm-air interface with their growth dynamics, highlighting the coupling between mechanical interactions and the developmental process. We also provide biophysical models for more complex three-dimensional scenarios. By incorporating horizontal expansion into the vertical growth model, we reproduce spherical cap geometry and constant contact angle at the biofilm edge. Diffusion-limited models are developed to investigate the role of nutrient gradients in the evolution of multicellularity and the effects of oxygen-binding proteins on the growth of yeast clusters.
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2024-05-23
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Dissertation