Bacteriophage genomes rapidly evolve via mutation and horizontal gene transfer to counter evolving bacterial host defenses; such arms race dynamics should lead to divergence between phages from similar, geographically isolated ecosystems. However, near-identical phage genomes can reoccur over large geographical distances and several years apart, conversely suggesting many are stably maintained. Here, we show that phages with near-identical core genomes in distant, discrete aquatic ecosystems maintain diversity by possession of numerous flexible gene modules, where homologous genes present in the pan-genome interchange to create new phage variants. By repeatedly reconstructing the core and flexible regions of phage genomes from different metagenomes, we show a pool of homologous gene variants co-exist for each module in each location, however, the dominant variant shuffles independently in each module. These results suggest that in a natural community, recombination is the largest contributor to phage diversity, allowing a variety of host recognition receptors and genes to counter bacterial defenses to co-exist for each phage.
Bibliographical noteFunding Information:
This work was supported by the Leverhulme Trust (RPG-2012-624) to A.M.A. and C.M.B. C.M.B. was also supported by the Austrian Science Fund (FWF, M 2299-B32). A.M.A. was also supported by NE/J02399X/1 and Aarhus University Research Funding (AuFF). A.E. was supported by NE/S001034/1.
© 2020, The Author(s).