We study the interaction between Emiliania huxleyi, a bloom-forming alga, and its specific virus (EhV), an ecologically important host-virus model system in the ocean. Almost all of our current understanding of the molecular mechanisms that govern host-virus interactions in the ocean, is derived from experiments carried out at the population level, assuming synchrony and uniformity of the cell populations and neglecting any heterogeneity. We quantified host and virus gene expression on a single-cell resolution during the course of infection, using cutting edge technologies for single-cell transcriptomics that were applied, for the first time, to marine microbes. Simultaneous measurements of expression profiles of host and virus genes at a single-cell level allowed mapping of infected cells into newly defined infection states and detection of specific host responses in a subpopulation of infected cell. We showed that photosynthetically active cells chronically release viruses through non-lytic infection and that viral-induced cell lysis can occur without viral release, thus challenging major assumptions regarding the life cycle of giant viruses. A major achievement was the ability to apply these advanced methods to natural populations. We were able to quantify the fraction of cells that were actively infected, and demonstrated that only 25% of the population were infected by EhV, despite the synchronized demise of the entire population. Further, we developed innovative approaches to map the metabolic landscape that is generated during viral infection and revealed a systematic metabolic shift during infection towards lipids containing the odd-chain fatty acid pentadecanoic acid (C15:0). This shift might be part of the viral strategy to hijack host metabolism during infection. Next, we developed a platform that allows to analyze that metabolites profiles of environmental samples. We specifically aimed to uncover the bouquet of metabolites generated during viral infection of E. huxleyi in natural blooms. We discovered a set of chlorine-iodine–containing metabolites that were induced by viral infection and released during bloom demise. We proposed that these halometabolites are a distinct hallmark of the virus-induced exometabolome of E. huxleyi, providing insights into the metabolic consequences of the viral shunt.
Extracellular vesicles (EVs) have recently been discovered as a new mode of communication across in the marine environment. We found that EVs are highly produced during viral infection or when bystander cells are exposed to infochemicals derived from infected cells. These vesicles have a unique lipid composition and their cargo is composed of specific small RNAs that are predicted to target sphingolipid metabolism and cell-cycle pathways. We applied EVs to natural E. huxleyi populations and showed that they promote viral infection, leading to a faster infection dynamic and prolong EhV half-life in the marine environment. This novel mode of communication may influence the fate of the blooms and, consequently, the composition and flow of nutrients in marine microbial food webs.
