Periodic Reporting for period 4 - Virocellsphere (Host-virus chemical arms race during algal bloom in the ocean at a single cell resolution)
Periodo di rendicontazione: 2021-05-01 al 2021-10-31
Phytoplankton are unicellular alga that form massive oceanic blooms covering thousands of square kilometers. Half of the photosynthetic activity on Earth is performed in the ocean by these microscopic organisms, and their influence on global cycles of carbon, nitrogen and sulfur is immense. The short life span of these organisms makes them a sensitive proxy for evaluating the impact of climate change on marine ecosystems. Microbial interactions that regulate the fate of algal blooms play a profound role in determining carbon and nutrient cycling in the ocean and feedback to the atmosphere. Some of the key mortality agents of algal cells are marine viruses, bacteria and grazers. Viral infection that leads to demise of a bloom will have a unique footprint on the environment and is predicted to influence the carbon export to the deep ocean, recycling of nutrients available to the rest of the marine organisms, biodiversity and even influence the atmosphere above the dying bloom. The latter occurs when dying algal cells produce volatile chemicals that are emitted to the atmosphere as aerosols and can modulate cloud formation.
Viruses are the most abundant biological entities in the marine environment and are hypothesized to be major ecological, evolutionary and biogeochemical engines. Algae-infecting viruses were estimated to turn-over more than a quarter of the total photosynthetically fixed carbon, thereby fueling microbial food webs, short-circuiting carbon transfer to higher trophic levels and promoting export to the deep sea. As major evolutionary drivers, marine viruses enhance the diversity of microbial life, affect species composition, and are responsible for widespread lateral gene transfer with their hosts. Despite the huge ecological importance of host-virus interactions, the ability to assess their ecological impact is limited to current approaches, which focus mainly on quantification of viral abundance and diversity. A major challenge in our current understanding of host-virus interactions in the marine environment is to decode the wealth of genomic and metagenomics data and translate it into cellular mechanisms that mediate host susceptibility and resistance to viral infection.
Extensive work conducted in our lab in the past few years focused on the molecular mechanisms underlying the interaction between the alga Emiliania huxleyi and its specific giant virus. By combining advanced cell biology, genome-enabled technologies and analytical chemistry approaches, we were able to identify several fundamental metabolic pathways that mediate these host-virus interactions.
The overarching objectives of our proposal are:
1. To characterize distinct cell-states within a population of infected host cells that respond differentially to viral infection.
2. To reveal the composition of the information-conveying chemicals, generated by virus-infected cells and their role in determining cell fate and susceptibility to infection.
3. Comprehensive characterization of phenotypic heterogeneity during host-virus interactions and its ecological significance during natural E. huxleyi blooms.
Viruses are the most abundant biological entities in the marine environment and are hypothesized to be major ecological, evolutionary and biogeochemical engines. Algae-infecting viruses were estimated to turn-over more than a quarter of the total photosynthetically fixed carbon, thereby fueling microbial food webs, short-circuiting carbon transfer to higher trophic levels and promoting export to the deep sea. As major evolutionary drivers, marine viruses enhance the diversity of microbial life, affect species composition, and are responsible for widespread lateral gene transfer with their hosts. Despite the huge ecological importance of host-virus interactions, the ability to assess their ecological impact is limited to current approaches, which focus mainly on quantification of viral abundance and diversity. A major challenge in our current understanding of host-virus interactions in the marine environment is to decode the wealth of genomic and metagenomics data and translate it into cellular mechanisms that mediate host susceptibility and resistance to viral infection.
Extensive work conducted in our lab in the past few years focused on the molecular mechanisms underlying the interaction between the alga Emiliania huxleyi and its specific giant virus. By combining advanced cell biology, genome-enabled technologies and analytical chemistry approaches, we were able to identify several fundamental metabolic pathways that mediate these host-virus interactions.
The overarching objectives of our proposal are:
1. To characterize distinct cell-states within a population of infected host cells that respond differentially to viral infection.
2. To reveal the composition of the information-conveying chemicals, generated by virus-infected cells and their role in determining cell fate and susceptibility to infection.
3. Comprehensive characterization of phenotypic heterogeneity during host-virus interactions and its ecological significance during natural E. huxleyi blooms.
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.
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.
A major achievement of the Virocellsphere project was the development single-cell whole transcriptome analyses of infected cells. This novel approach enabled the discovery of the different phases of viral infection and genes associated with host response to the infection. We shed light on the resistance mechanisms of the minority of host cells and gained insights into the cellular programs that lead to the death of infected cells and, consequently, the demise of algal blooms. We were able to probe for expression of specific E. huxleyi and EhV genes within cells collected from natural populations, thus enabling specific detection of the level of infection within the E.huxleyi sub-population of phytoplankton. Using a metabolomics approach we were able to detect small molecules that are produced specifically during infection. Additionally, we developed novel lipid-based biomarkers to detect virus-sensitive and resistant subpopulations in the environment. We have recently characterized extracellular vesicles produced by E. huxleyi during viral infection and used as a communication signal to modify the dynamic of infection in culture and natural assemblages.