Bacterial Evolution under 3D physical confinement

Abstract

Microorganisms inhabit diverse ecosystems and exhibit remarkable adaptability to extreme environmental conditions, largely due to their rapid generation times and substantial population sizes. To understand how microorganisms adapt over time, examining the mechanisms behind these adaptations is essential. Traditionally, these mechanisms are studied using homogeneous shaken liquid cultures or 2D agar pads, which, while suitable for investigating biochemical signalling, do not consider the complexities that arise due to the mechanical landscape of the microbiome. In environments like gut mucus and soil, microbes are suspended in a three-dimensional space and must navigate narrow crevices to access nutrients and oxygen. Previous studies investigated the short-term effects of altering the degree of physical confinement on bacterial growth, which reported that an increase in confinement hinders growth. In this study, we expand on these works by exploring the long-term effects of confinement and how bacteria can adapt and evolve when subjected to physical confinement. We subjected MG1655 E. coli to experimental evolution under physical confinement by serially passaging them in 3D gel matrices of different degrees of confinement. Our observations indicate that when compared to unconfined conditions, mutation accumulation is low under physical confinement. We speculate this could be due to the reduction in population dispersal and constraints on colony size imposed by confinement itself, posing implications for the rate of adaptation in three-dimensional microbiomes found in nature.