Using population dynamics to count bacteriophages and their lysogens

Abstract

Traditional assays for counting bacteriophages and their lysogens are labor-intensive and highly perturbative to the host cells. Here, we present a high-throughput infection method where all steps—cell growth, viral encounters, and post-infection recovery—take place in a microplate reader, and the growth dynamics of the infected culture are measured continuously using the optical density (OD). We find that the post-infection dynamics are reproducible and interpretable. In particular, the OD at which the culture lyses scales linearly with the logarithm of the initial phage concentration, providing a way of measuring phage numbers in unknown samples over nine decades and down to single-phage sensitivity. Interpreting the measured dynamics using a mathematical model for the coupled kinetics of phages and bacteria further allows us to infer the rates of viral encounters and cell lysis. Adding a single step of antibiotic selection provides the ability to measure the rate of host lysogenization. To demonstrate the application of our assay, we characterized the effect of bacterial growth rate on the propensity of lambda phage to lysogenizeE. coli. When infected by a single phage, the probability of lysogenization is found to decrease approximately exponentially with the host growth rate. In growing, but not in stationary, cells, the propensity to lysogenize increases ~50-fold when multiple phages co-infect the cell. These findings illuminate how host physiology feeds into the lysis/lysogeny decision circuit, and demonstrate the utility of high-throughput infection to interrogating phage-host interactions.