Flexible genes establish widespread bacteriophage pan-genomes in cryoconite hole ecosystems

Christopher M. Bellas (), Declan C. Schroeder, Arwyn Edwards, Gary Barker and Alexandre M. Anesio
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Christopher M. Bellas: University of Innsbruck
Declan C. Schroeder: University of Minnesota
Arwyn Edwards: Aberystwyth University
Gary Barker: University of Bristol
Alexandre M. Anesio: Aarhus University

Nature Communications, 2020, vol. 11, issue 1, 1-10

Abstract: Abstract 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.

Date: 2020
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DOI: 10.1038/s41467-020-18236-8

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