Phage evolution and ecology

Abstract

Bacteriophages (phages) are the viruses of bacteria and the study of phage biology can be differentiated, roughly, into molecular, environmental, evolutionary, ecological, and applied aspects. While for much of the past fifty-plus years molecular and then applied aspects have dominated the field, more recently environmental concerns, especially the phage impact on biogeochemical cycles, have driven an increase in the appreciation of phage ecology. Over approximately the same time frame, decreasing sequencing costs have combined with phage molecular characterization to give rise to an inescapable consideration of phage comparative genomics. That, along with environmental metagenomics, has stimulated, especially among molecular biologists, a more general interest in phage evolutionary biology. However, while reviews of phage ecology have become exceedingly common, overviews of phage evolutionary biology are comparatively rare, and broad considerations of phage evolutionary biology drawn from an ecological perspective rarer still. In this chapter I jump into this latter void, providing an overview of phage evolutionary biology as viewed from the perspective of phage-environment interactions, that is, from the perspective of phage ecology. This I do over five sections constituting (1) an introduction to phages and how, phenotypically, they can be differentiated into three basics types that correlate, more or less, with genomic size, that is, tailed (generally larger genomes), lipid-containing (medium-sized genomes), and single-stranded (small genomes); (2) a brief introduction to phage ecology as considered particularly from a classical ecological perspective; (3) an extended introduction to evolutionary biology as viewed from a phage and phage-ecological standpoint; (4) phage evolutionary ecology, that is, consideration of phage adaptations from the vantage of why, in terms of phage fitness, those adaptations may have evolved; and (5) phage evolutionary biology, including evolutionary ecology, as viewed from the perspective of phage genomics.