PhD Defense by Mireia Cordero

Title: How bacteria conquer, compete, and cooperate
Subtitle: A study on spatial dynamics and self-organisation of Escherichia coli communities

Abstract: This thesis explores the emergence of spatial self-organisation within bacterial communities and its impact on their spreading dynamics. By combining novel experimental setups with stochastic numerical simulations, I quantify the influence of specific bacterial interactions and environmental conditions on their community formation. I do so by studying three distinct experimental systems of Escherichia coli with increasing complexity between interactions of their constituents.

The first study examines the three-dimensional organisation of isogenic colonies within semi-solid media. In this setting, environmental factors are the main driver of self-organisation. This study reveals the formation of satellite colonies due to flagellar motility, an enhancing mechanism for bacterial invasion that allows cells to conquer new territories while maintaining the protection benefits of the main colony.

The second study addresses the effect of cell morphology on spreading competition, revealing a competitive advantage of slender cells in two-dimensional settings. Those cells align due to mechanical interactions, which promote their takeover of the colony edge. Likewise, this thesis proves that cell morphology is a key factor in the efficiency of processes that require cell-to-cell contact within subpopulations of cells.

The third study investigates the origin of indirect antibiotic resistance as a consequence of the spatial arrangement of cells. When the detoxification of the environment occurs locally, cells require close contact to gain protection against the antibiotic. Here, three-dimensional configurations are shown to increase the tolerance of the sensitive cells to an antibiotic compared to their two-dimensional counterparts. The significance of cell contacts is further highlighted as the environment shifts from promoting competition at low antibiotic levels to enhancing cooperation via indirect resistance at high ones. This transition leads to the rearrangement of subpopulations in space, resulting in increased cell interactions.

Overall, this thesis emphasises the importance of spatial factors in studies of bacterial communities and reveals how physical interactions and environmental conditions shape their behaviour. The results presented aim to offer new insights into bacterial self-organisation and resistance mechanisms that may have been previously overlooked.