Spatial microbial models

Keynote talks, Wednesday 10th July:

Uwe Täuber – Stochastic Population Dynamics of Competing Species in Driven and/or Spatially Inhomogeneous Systems (09:00-10:00)

Agent-based Monte Carlo simulations of simple lattice models constitute a versatile tool to investigate stochastic population dynamics subject to time- and/or space-dependent rate parameters. I will address two topics: (1) To represent seasonal oscillations in resource availability, we implement a periodically varying carrying capacity in a two-dimensional Lotka-Volterra predator-prey model. We find that two-species coexistence is enhanced through this periodic drive. The fast- and slow switching regimes can be described through different effective static environments. Yet we observe intriguing resonant features when the external switching rate matches the internal population oscillation frequency, inducing persistent spatial correlations. (2) Stochastic population dynamics in finite systems often ultimately terminates in an absorbing state. However, in sufficiently large spatially extended models, the time to reach species fixation or extinction becomes exceedingly long, effectively permitting coexistence. Yet tuning certain control parameters, e.g., increasing the predation rate in predator-prey systems or enhancing asymmetries in cyclic dominance models, may render coexistence states in finite systems highly vulnerable against stochastic fluctuations. Intriguingly, though, they can be efficiently stabilized through continuous influx from the system’s boundaries, which is generated via diffusive coupling of the vulnerable region to an adjacent stable patch. I will discuss (semi-)quantitative criteria that delineate the conditions for this remarkable boundary flow stabilization of finite-size absorbing-state instabilities in stochastic population dynamics with either cyclic or hierarchical competition.

Wolfram Möbius – Geometry as a predictor for evolutionary dynamics of populations undergoing range expansions in fragmented environments (11:45-12:45)

Evolution of microbial populations expanding into fragmented environments is a complex process shaped by the interplay of local population dynamics, mutation, migration, and environmental heterogeneity. Understanding the effects of environmental structure is challenging not least due to the vast number of different environments a population may encounter.
In a series of projects, we followed a bottom-up approach to uncover the consequences of environmental heterogeneity on neutral evolution as well as the dynamics of mutation and selection in the presence of unfavourable patches. Guided by simulations, we developed coarsened models which are closely associated with geometrical arguments. These highlight general principles and allow one to predict the dynamics in complex environments from the dynamics around individual heterogeneities. In addition to the theoretical work, we present experiments and experimental approaches that highlight the effects of environmental structure on microbial ecology and evolution.

Bartek Waclaw – The physics of growth and evolution in microbial biofilms (14:30-15:30)

Microbes in biofilms interact with each other and the environment in many ways, including mechanical repulsion, adhesion, and friction. In the last 10 years, these physics-like interactions have been shown to be as important for biofilm growth and evolution as biochemical interactions. In this talk, I will discuss mechanistic spatial models and experiments aimed at explaining how physical interactions affect population dynamics of genetic variants in the biofilm. I will also show how the physics of a growing biofilm can be used against it to reduce the chance that an undesired variant, e.g., an antibiotic-resistant mutant, spreads in the biofilm.

Contributed talks, Wednesday 10th July:

Rosalind Allen – Effect of spatial partitioning of a microbial population on collective antibiotic resistance (10:00-10:25)

János Juhász – Agent-based modelling of multi-strain yeast colony development in inhomogeneous environmental conditions (10:25-10:50)

Matthew Asker – Spatial Structure and Environmental Dynamics in Microbial Populations (10:50-11:15)

Bowen Li – NUFEB 2.0 – A massively parallel simulator for individual-based modelling of microbial communities (12:45-13:10)

Niklas Moser – A general likelihood-based method for the inferential analysis of agent-space reactant-catalyst-product models (15:30-15:55)