Community ecology of phages on a clonal bacterial host

Abstract Bacteriophages are the most abundant and diverse biological entities on Earth, yet the ecological mechanisms that sustain this extraordinary diversity remain unclear. Here, we have discovered a general mechanism that allows phage diversity to outstrip the diversity of their bacterial hosts. We assembled and passaged dozens of diverse phage communities on a single, non-coevolving strain of Escherichia coli until the phage communities reached equilibrium. In all cases, we found multiple phage species coexisted stably, despite competition for a single, clonal host population. Coexistence within these communities was supported through host phenotypic heterogeneity, whereby phages specialized on cells adopting different growth phenotypes. Our experiments reveal a rich community ecology of bacteriophages where multiple phage species coexist and interact at the scale of a single bacterial host. One-Sentence Summary Diverse communities of phages emerge stably and consistently on a clonal bacterial host, enabled by phenotypic heterogeneity.