Death And Chemotaxis: Dynamics of Phage-Bacteria Interactions in Crowded Environments

Bacteriophages (“phages”) are viruses that infect and kill bacteria; thus, phage-bacteria interactions shape microbiomes, with critical implications for agriculture, food, and medicine. However, laboratory studies typically use “well-mixed” cultures in test tubes or Petri dishes, which do not mimic nature’s complexities. In nature, bacteria and phages exist in crowded 3D environments, like soil and biological tissue, that impact behaviors. Furthermore, phage-bacteria interactions are typically studied at limited timepoints due to the experimental challenges of real-time analysis, further limiting understanding of how they influence microbiomes in practice.

Here, we address this gap in knowledge using direct visualization of phage-bacteria interactions in transparent crowded matrices composed of packed hydrogel microparticles. We use confocal microscopy to visualize the real-time dynamics of motile E. coli populations encountering lytic T4 phages as a function of the initial spatial distributions and concentrations. Additionally, we develop a theoretical framework that can predict our experimental observations, thereby helping to reveal the profound impact phages have on bacterial population dynamics.