Project: Collaborative Research: Drivers and effects of latent phage activation in marine SAR11

NSF Award Abstract:

Viruses are the most abundant biological entities in the ocean. When they infect plankton, they can alter food webs, induce shifts in nutrient cycles, and enhance genetic exchange. However, the mechanisms that control these important processes are largely unknown, which has limited our ability to predict infection outcomes in nature. The primary goal of this study is to identify key chemical, physical, and biological factors that influence host-virus interactions in cultured bacterioplankton and to use this information to build mathematical models that predict infection dynamics in diverse marine ecosystems. Most of the marine viruses available for detailed study kill bacteria following infection. This novel study focuses on SAR11, the most abundant marine bacteria, which harbor dormant viruses called prophages, to determine what causes prophage activation and host death. Specifically, the research team uses field surveys and laboratory experiments with SAR11-prophage pairs to generate data and mathematical models to predict the outcomes of viral infections in SAR11 and other marine microbes.

The conditions that trigger prophage activation and their corresponding contributions to ecosystem processes are largely hypothetical, due primarily to difficulties identifying and culturing host cells with prophages. It is becoming increasingly clear that the impact and importance of these infections are under-characterized and under-estimated. The proposed research revises estimates of prophage activation in globally-important SAR11 by quantifying infection occurrence, identifying prophage activation inducers, and testing the effects of maintaining virus DNA in the host genomes. The frequency of prophage infections is determined by analyzing bacterial metagenomes generated with long-read sequencing technology. Controlled growth experiments under a range of conditions that cause stress (physical, chemical, and biological) and evaluation of shifts in gene expression are employed to identify drivers of prophage activation. The outcomes of prophage infections in culture serve to parameterize key interactions in numerical models that can then predict outcomes in nature. This study fills critical gaps in knowledge about the mechanisms that maintain the large and genetically diverse populations of bacteria and viruses in the ocean and has the potential to change our understanding and capacity to predict host-virus interactions under changing environmental conditions.