Bacteria and their viruses phages are abundant across diverse ecosystems and their interactions influence global biogeochemical cycles and incidence of disease. Problematically, both classical and metagenomic methods insufficiently assess the host specificity of phages and phage—host infection dynamics in nature.
Here we review emerging methods to study phage—host interaction and infection dynamics with a focus on those that offer resolution at the single-cell level. All three methods enable study of phage infection of uncultured bacteria from environmental samples, while the latter also discriminates between phage—host interaction outcomes e.
Together these techniques enable quantitative, spatiotemporal studies of phage—bacteria interactions from environmental samples of any ecosystem, which will help elucidate and predict the ecological and evolutionary impacts of specific phage—host pairings in nature. Phages and their bacterial hosts are abundant across diverse ecosystems wherever investigated, including fresh water Hennes and Simon, , sea water Bergh, ; Fuhrman, ; Wommack and Colwell, , sediment Danovaro et al.
Phages influence global biogeochemical cycling by manipulating host populations through mortality, horizontal gene transfer, and viral metabolic reprogramming. First, phage-induced lysis of microbial cells releases organic matter and contributes to carbon, nitrogen, and phosphorus cycling Shelford et al. Second, virus-mediated horizontal gene transfer can have major implications on host evolutionary trajectories. In the oceans, cyanobacterial viruses cyanophages have captured core photosystem genes that alter the evolutionary trajectory of these globally distributed photosystems Lindell et al.
In medicine, prophage-encoded virulence factors routinely transform hosts into pathogens e. Despite the apparent importance of virus—host interaction outcomes to ecosystem function, our knowledge has been largely bottlenecked by cultivation and technical limitations.
