Ecological investigations of diatom viruses: bridging environmental and laboratory studies

Viruses are generally more abundant than their cellular counterparts and represent the largest reservoir of genetic diversity within the marine environment. It has been estimated that each day 10²⁸ viral infections occur in the world’s oceans releasing upwards of 10⁹ tons of carbon from cellular organisms. Importantly, during infection they are a major force in driving changes in host physiology and evolution that ultimately leads to genetic diversity within populations. To investigate the cellular mechanisms of infection, combined approaches of environmental and laboratory studies were used focusing on pennate diatom populations. Diatoms represent a broad group of phytoplankton that account for between 35-75% of marine primary production and have unique viruses that infect them, those with ssDNA and +ssRNA genomes. Evidence from environmental assays suggests episodic upwelling leads to coastal diatom blooms correlated with significant estimates of virus-induced lysis, including sequence data confirming host/virus systems. Multiple methods for single cell RNA sequencing of diatom cells were developed and used on recently isolated laboratory strains, including techniques to target those actively growing and infected. These data provide empirical evidence, with temporal resolution, that only a portion of cells within a population are infected and there is significant differences of transcriptional activity among subpopulations in time. Moreover, data from these studies provide robust measurements of RNA virus physiology and impacts on their host transcriptional activity that are being incorporated into genome-scale models to elucidate responsive genetic markers during viral infection. These cellular and population-level changes move up the ecological ladder to community shifts in diversity and availability of resources, thereby altering microbial food webs with the ability to change the functional capacity and ecological niche for phytoplankton communities.