Quantifying massively parallel microbial growth with spatially mediated interactions

Quantitative understanding of microbial growth is an essential prerequisite for successful control of pathogens as well as various biotechnology applications. Even though the growth of cell populations has been extensively studied, microbial growth remains poorly characterised at the spatial level. Indeed, even isogenic populations growing at different locations on solid growth medium typically show significant location-dependent variability in growth. Here we show that this variability can be attributed to the initial physiological states of the populations, the interplay between populations interacting with their local environment and the diffusion of nutrients and energy sources coupling the environments. We further show how the causes of this variability change throughout the growth of a population. We use a dual approach, first applying machine learning regression models to discover that location dominates growth variability at specific times, and, in parallel, developing explicit population growth models to describe this spatial effect. In particular, treating nutrient and energy source concentration as a latent variable allows us to develop a mechanistic resource consumer model that captures growth variability across the shared environment. As a consequence, we are able to determine intrinsic growth parameters for each local population, removing confounders common to location-dependent variability in growth. Importantly, our explicit low-parametric model for the environment paves the way for massively parallel experimentation with configurable spatial niches for testing specific eco-evolutionary hypotheses.Author summary: Image-based platforms allow obtaining population size estimates for massively parallel growth experiments on substrate plates at a relatively low cost. However, such population size data has been shown to display a high degree of spatial variability, which occurs even with isogenic populations. Here we first quantified the importance of spatial location on growth variation using a machine learning approach, and then developed spatially aware population growth models to explain the spatial structure of the growth data. Ultimately, we show that a spatial resource consumer model with local microhabitats connected via diffusion, and a parameter capturing the initial physiological state of a population, can fully explain the observed spatial variation in growth while allowing the inference of intrinsic growth parameters of specific populations. This result provides a method for systematic extraction of spatial growth models and paves the way for massively parallel eco-evolutionary experimentation.