Dokument

Summary:
Bacteria commonly live in communities, embedded in a self-produced matrix, termed as biofilms. Bacterial biofilms are involved in many processes in natural, clinical and industrial settings. They, for example, influence environmental biochemical cycles, increase the persistence and resistance to antibiotics in the context of infection, and are commonly associated with the damage of food and pipelines in industry. The study of biofilms, particularly the process of formation, cellular metabolism of biofilm-dwelling bacteria, and their collective stress response, is instrumental for the development of new methods to combat biofilms, as well as for understanding bacterial physiology in natural environments. This dissertation addresses and contributes to answering some of the open questions in the field of biofilm research: how are biofilms formed and what determines their architecture? How do biofilm heterogeneity and biofilm metabolism interplay? How do different microbial subpopulations interact within a single-species biofilm? How do biofilms respond to stress at the single-cell and multicellular levels, and what are the consequences of such responses? In chapter 2, we showed that mechanical cell-cell interactions determine biofilm architecture in surface-attached Vibrio cholerae biofilms. Using single-cell segmentation of microscopy images and in silico simulations we defined an interaction potential that predicts the overall biofilm architecture. To study biofilm heterogeneity and metabolic interactions between subpopulations within bacterial biofilms, we searched for novel metabolic amino acid cross-feeding in isogenic Escherichia coli biofilm colonies. In chapter 3, using metabolomics, global and spatial transcriptomics, and confocal fluorescence imaging, we found new evidence suggesting alanine cross-feeding between different regions of the biofilm. This cross-feeding interaction had important consequences for colony growth and morphology, and for bacterial survival within the biofilm. Biofilms are hypothesized to have an enrichment of slow-growing cells caused by environmental heterogeneity. Due to a lack of techniques for monitoring spatial metabolism this idea has however not been validated in vivo. We developed a new method to study slow-growing cells. In chapter 4, as a proof of concept, slow growing cells were enriched from a CRISPRi library by sorting them according to a fluorescent growth rate reporter. This technique could be applied to study slow growing cells within bacterial biofilms. In chapter 5, we focused on how biofilms respond to antibiotic stress. Using V. cholerae biofilms, we found that bacteria respond at the single-cell level and at the multicellular level when exposed to translational inhibitors. Specifically, the cell volume and cell-cell spacing increased upon protein synthesis inhibition. These architectural changes had important consequences for the ecology of biofilms, in particular antibiotic-treated biofilms were prone to invasion by other bacterial cells and bacteriophages. In conclusion, this dissertation contributes to answer important questions in the field of biofilm research. It improves our understanding of bacterial biofilms, and could facilitate the development of new strategies to combat biofilms in clinical and industrial settings. Furthermore, this work highlights the importance of applying techniques with single-cell resolutions to study biofilms.

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