Biofysische modellen voor de eco-evolutionaire dynamiek van microbiële collectieven

The majority of microbes inhabit multicellular communities rather than existing as unicellular organisms. These microbial collectives are ubiquitous on Earth and profoundly impact virtually all ecosystems, including human society. While the regulatory and biochemical aspects of microbial community formation have been extensively studied, it remains unclear how the structure and functions of these communities emerge from the microscopic properties of individual microorganisms. This dissertation examines the structural dynamics of microbial community formation by developing computational models based on empirically quantified mechanical properties of microorganisms at the single-cell level. These models are further extended to explore how microbial structural organization influences the evolution of these collectives. This work focuses on two microbes: Saccharomyces cerevisiae, commonly known as baker's yeast, and Salmonella enterica Typhimurium , a common gastroenteric pathogen. In S. cerevisiae, the FLO1 gene encodes cell wall proteins that enable cells to adhere to neighboring cells, initiating the formation of multicellular groups, known as flocs, which can protect the constituent cells. FLO1 also functions as a 'green beard' gene, facilitating both cooperation, through the formation of protective groups, and kin recognition by selectively binding other FLO1 -expressing cells. Here, single-cell adhesion measurements reveal that Flo1p preferentially binds to fellow FLO1-expressing cells (cooperators) over defectors lacking FLO1 expression. In an individual cell-based simulation of cluster formation in shear flow, a trade-off emerges in the "green beard" mechanism, where reduced bond stability enhances kin recognition but diminishes group size. Additionally, the fitness of FLO1 cooperators decreases as their frequency in the population rises, due to the permissive character (F+– = 0.5 F++) of the Flo1p bond. Given the costs associated with FLO1 expression, this asymmetric selection often leads to a stable coexistence between cooperators and defectors. Salmonella forms multicellular communities, or biofilms, which are encased in a self-produced matrix of extracellular polymeric substances (EPS). These biofilms are notorious for complicating treatment and disinfection in both the medical sector and the feed/food industry. Although the intricate three-dimensional structure is a hallmark of biofilm formation, it is unclear how this structure emerges from the properties of single bacteria and how it provides protection against external stresses, such as antimicrobial treatment. This study quantifies the thickness and density of EPS surrounding individual bacteria using confocal microscopy on a set of strains with increasing expression of csgD, the master regulator of biofilm formation. Increased EPS production results in a thicker layer of EPS surrounding bacteria, and individual-cell based modeling shows that this increase in thickness leads to sparser, yet more nematically aligned, biofilms. Contrary to current paradigms, increasing EPS production results in biofilms with lower tolerance to antimicrobial treatment. Additionally, this dissertation evaluates the effect of biofilm architecture on the penetration of functionalized nanoparticles, which is proposed as a novel antimicrobial delivery strategy. Combining single-particle tracking with Brownian dynamics modeling, where the EPS surrounding individual bacteria acts as a local viscous sink, our results indicate that both biofilm architecture and EPS production influence nanoparticle drug delivery, with low EPS levels potentially aiding delivery by immobilizing nanoparticles closer to bacteria, while higher levels hinder delivery due to shielding effects. Finally, the selective pressure of antimicrobial treatment on mixed biofilms of resistant and susceptible cells is investigated, specifically focusing on the effects of biofilm architecture and treatment conditions. In the case of extended-spectrum ß-lactamases (ESBLs), resistant cells can protect close by susceptible cells during antimicrobial treatment by locally detoxifying the environment. Using in vitro experiments and in silico models, the protection conferred by ESBL production is found to be weak and act on relatively long spatial scales. Although selection against resistance via ESBLs is possible, this only occurs when the resistant cells protect the entire microbial community.