Divergence in bacterial ecology is reflected by difference in population genetic structure, phage-predator load and host range

Phages depend on their bacterial host to replicate, but how habitat, density and diversity of the host population drive phage ecology is not well understood. Here, we addressed this question by comparing two populations of marine bacteria and their phages collected during a time series sampling in an oyster farm. Vibrio crassostreae reproduces more specifically in oysters. This population is genetically structured into clades of near clonal strains favoring infection by closely related phages and leading to a modular structure of the phage-bacterial infection network. Vibrio chagasii, on the other hand, blooms in the water column from where it can colonize oysters via filter-feeding. We found higher phage predation pressure on V. chagasii that did not result from a broader host range of the phages but rather from a greater burst size generating more infectious particles in the environment. We showed that contrasting patterns of genetic diversity for host and phage lead to different infection network architectures. We also provided evidence that a bloom of phages generates epigenetic and genetic variability that can be selected to counteract host defense systems.