Ecological and Evolutionary Aspects of Microbial Population Growth in Confined Spaces

Spatial structure can play a pivotal role in defining an ecosystem's biodiversity, as well as its stability and adaptive capabilities. Emerging in the 1960s, a new theoretical framework was developed in the field of ecology aimed at describing island ecosystems (MacArthur & Wilson, 1967), which quickly gained popularity and was applied to a wide range of ecosystems and even influenced policy-making (Wu & Vankat, 1995). Despite its impact, it largely remained a theoretical framework and many of its claims or hypotheses remained unverified experimentally (Wu & Vankat, 1995; Levin, 1992). In fact, later work pointed to some of the gaps in island theory and stressed the need to couple ecological and evolutionary dynamics, as well as emphasizing the relevance of the correct choice of scale in describing ecosystems (Levin, 1992). More recently, studies have emerged in the field of microbial ecology and evolution with an explicit focus on the effects of spatial structure (Hallatschek & Nelson, 2008). Still, many open questions remain regarding eco-evolutionary dynamics in systems with a strong spatial dependence. In this work, we study a microbial ecosystem at the micro-scale consisting of an elongated cavity with one open and one closed end, whose tight spatial constraints confer it with very particular ecological properties. We generalize the study of Karita and coauthors (Karita et al., 2021) of these microbial communities by extending the study of a scale-dependent transition from a gaseous to a jammed state for the case of non-exponential microbial growth, in particular under the influence of resource depletion and an Allee-type cooperation. We also developed a novel, individual-based model based on the distinction between self-diffusion and collective diffusion. In particular, we use the model to study the stability of band-like structures and the takeover of cavities by strains with a high selective advantage, and we point to the presence of pinning impurities as band stabilizers in cavities, showing good agreement between the predictions of the simulations and experimental results. We also analyze Clone Size Distributions (CSD) in both jammed and gaseous cavities, uncovering fundamental differences in the dynamics leading up to them and showing how the jammed state of larger cavities leads to lower diversity than the gaseous state, in direct contrast with island theory. Lastly, we discuss a novel mechanism, Invader-Sustained Jamming (ISJ), by which an invading strain can stabilize the resident population of a cavity into a jammed state without itself being able to take over the system, even for large selection advantages. Our results support the view that the properties of ecosystems can be highly sensitive to scale or spatial structure, especially close to transitions like the one between gas and jamming. In particular, the transition to jamming points to a tradeoff between stability and adaptation, as it leads to stabler populations and increased levels of resistance against invasion at the expense of a lower speed of adaptation.