Shaping Function Through Space: The Role of Spatial Organization in Microbial Communities

Abstract

Spatial organization plays a critical role in microbial community function, influencing how cells exchange metabolites, coordinate behavior, and compete for resources. This thesis investigates the consequences of spatial structure in natural microbial systems and introduces a novel method to engineer these systems with high precision and scalability. First, we examine the colonization of chitin particles by marine bacteria, a model for particulate organic matter degradation. Using high-throughput phenotyping of natural isolates, we show that vitamin cross-feeding is essential for successful colonization of chitin-particles by many auxotrophic strains. We then model two distinct vitamin cross-feeding mechanisms: lysis and secretion. Using a resource-explicit modeling approach, we leverage metabolic-flux and physiological measurements to predict the colonization success of auxotrophic cross-feeders in this spatially structured environment. Second, we introduce a new chemical method for engineering microbial cell surfaces that enables covalent attachment of molecules such as enzymes and DNA strands to the cell surface. We show that this surface functionalization procedure leads to the acquisition of new phenotypes like antibiotic resistance and programmable adhesion. Altogether, this work reinforces the importance of spatial organization for microbial community function and introduces a new technique to harness this community feature and turn it into a design principle for synthetic microbial systems.