Guy Schleyer

Virophages are small double-stranded DNA viruses that co-infect eukaryotic cells along with giant viruses. They are widespread in aquatic ecosystems and can influence microbial population dynamics by acting as an adaptive antiviral defense system, limiting production of giant virus progeny. Giant viruses extensively reprogram host metabolism to support their replication, yet little is known about how this process is altered by virophages. Characterizing these alterations may reveal the metabolic mechanisms underlying virophage-mediated changes in infection outcomes. Here, we used one of the few established host–giant virus–virophage experimental systems, consisting of the marine heterotrophic flagellate Cafeteria burkhardae , its giant virus CroV, and the virophage mavirus, to investigate lipid remodeling during viral infection and virophage co-infection. We found that infection by the giant virus strongly induced triacylglycerols containing furan fatty acids (FuFAs), a class of potent antioxidants that may protect infected cells and newly formed virions from oxidative damage. These lipids were also detected in purified giant virus particles, linking their accumulation to virus production. Co-infection with the virophage reduced the FuFA response and was instead characterized by pronounced accumulation of the betaine lipid diacylglyceryltrimethylhomoserine (DGTS). Most of the induced DGTS species were also present in the giant virus particles, suggesting that their accumulation during co-infection may be associated with altered giant virus production and lipid utilization. Together, these findings show that virophage co-infection reshapes giant virus-induced remodeling of the host lipidome, revealing a potential metabolic basis for their effects on virus production and infection outcomes.

Background: Lipidomics and its branch epilipidomics are rapidly advancing fields that explore the roles of native and modified lipids (e.g., oxidized, nitrated and halogenated lipid species), respectively, in biological systems. Dysregulation of lipid metabolism and signaling contributes to numerous diseases, including cardiovascular, metabolic, neurodegenerative, and inflammatory conditions. However, multiple challenges, including lack of standardization, limited data integration, and poor clinical translation, hinder progress. To address these, the COST Action EpiLipidNET (CA19105) established a pan-European network fostering collaboration across disciplines to accelerate lipid science and its application to health and disease. Aim of review: This review outlines the achievements of EpiLipidNET over its four-year duration, highlights key scientific contributions across five thematic working groups, and presents the future direction of its ongoing activities. The aim is to demonstrate how a collaborative, interdisciplinary framework can catalyze innovation in lipidomics and epilipidomics, enhance methodological harmonization, support early-career researchers, and bridge the gap between basic science, clinical translation, industry, stakeholders, and public engagement. Key scientific concepts of review: EpiLipidNET structured its networking activities around (i) harmonization of analytical workflows, (ii) development of epilipidomics tools and data integration strategies, (iii) translational studies for clinical lipid biomarkers, (iv) investigation of lipid signaling mechanisms, and (v) dissemination and outreach. The network supported over 460 members globally, launched multiple training schools and scientific missions, produced 110+ publications, and fostered new initiatives in endothelial membrane lipidomics, food lipidomics, plant and algae lipids, and redox lipid biology. Its integrative approach sets a foundation for continued progress toward precision medicine and sustainable health interventions through lipid science.

The viral shunt is a fundamental ecosystem process which diverts the flux of organic carbon fixed through photosynthesis during algal bloom events from heterotrophic grazers to bacteria. Through the extracellular release of metabolites, lytic viral infections supply 2 to 10% of photosynthetically fixed carbon in the ocean for bacterial respiration. Despite its significance for the carbon cycle, we lack tools to detect the viral shunt in the natural environment and assess its ecological impact. Here, we investigated the use of exometabolites as biomarkers for the viral shunt by applying molecular, metabolomics, and oceanographic tools to study bloom dynamics of the cosmopolitan microalga Gephyrocapsa huxleyi (formerly Emiliania huxleyi ) across the Atlantic Ocean, spanning four biogeochemical provinces between Iceland and Patagonia. We mapped the distinct metabolic footprint of its viral infections using exo- and endometabolomics and detected nineteen organohalogen metabolites across the blooms, showing their global distribution. A time-resolved comparison of particulate and dissolved metabolite pools during an induced mesocosm bloom revealed that virocells—actively infected host cells—were the source of the halogenated metabolites. Three trichloro-iodo metabolites were present during the demise of all virus-infected oceanic blooms, highlighting them as suitable metabolic biomarkers for the viral shunt. The environmental stability of these halometabolites in the dissolved organic matter pool over a few days can recapitulate viral infections at earlier stages of phytoplankton bloom succession. The chloro-iodo metabolites thereby expand the existing repertoire of metabolic biomarkers for viral infections at sea and may advance efforts to trace the biogeochemical impact of alga–virus interactions in the ocean.

Algal blooms are hotspots for diverse microbial interactions affecting bloom dynamics. Viral infections often regulate the demise of these blooms, recycling >25% of oceanic fixed carbon. Although these blooms collapse synchronously, only 10-30% of algal cells show active viral infection, suggesting additional mortality agents. Using microbial communities from natural coccolithophore blooms, we discovered that bacteria significantly enhanced virus-mediated algal mortality. We quantified this interaction using two novel metrics: the Synergy Index (SI) measuring viral-bacterial interaction strength, and the Benefit Index (BI) assessing changes in bacterial fitness. We identified Alteromonas bacteria as drivers of viral-bacterial coinfection, with consistently high SI and BI. In natural communities, Alteromonas exhibited chemoattraction towards infected algal cells, leading to their enrichment in bloom demise particles. This viral-bacterial synergy represents a previously unrecognized mortality agent controlling bloom termination, modulating the balance between the carbon-recycling viral shunt and the carbon-exporting viral shuttle pathways, likely influencing global carbon cycling.

The viral shunt is a fundamental ecosystem process which diverts the flux of organic carbon from grazers to heterotrophic microorganisms. Through the extracellular release of metabolites, lytic viral infections supply 2-10% of photosynthetically fixed carbon in the ocean for bacterial respiration. Despite its significance for the carbon cycle, we lack tools to detect the viral shunt in the natural environment and assess its ecological impact. Here, we study the use of exometabolites as biomarkers for the viral shunt by applying molecular, metabolomics, and oceanographic tools in blooms of the cosmopolitan microalga Gephyrocapsa huxleyi across the Atlantic Ocean, spanning four biogeochemical provinces between Iceland and Patagonia. We mapped the distinct metabolic footprint of its viral infections using exo- and endometabolomics approaches and detected nineteen organohalogen metabolites across the blooms, showing their global formation. Time-resolved comparison of particulate and dissolved metabolite pools during an induced mesocosm bloom indicated virocells – actively infected host cells – as the source of the halogenated metabolites. Three trichloro-iodo metabolites were present during demise of all virus-infected blooms, highlighting them as suitable metabolic biomarkers. The environmental stability of these halometabolites in the DOM pool over a few days can recapitulate viral infections at earlier stages of phytoplankton bloom succession.

Summary: In the marine environment, seaweeds (i.e. marine macroalgae) provide a wide range of ecological services and economic benefits. Like land plants, seaweeds do not provide these services in isolation, rather they rely on their associated microbial communities, which together with the host form the seaweed holobiont. However, there is a poor understanding of the mechanisms shaping these complex seaweed–microbe interactions, and of the evolutionary processes underlying these interactions. Here, we identify the current research challenges and opportunities in the field of seaweed holobiont biology. We argue that identifying the key microbial partners, knowing how they are recruited, and understanding their specific function and their relevance across all seaweed life history stages are among the knowledge gaps that are particularly important to address, especially in the context of the environmental challenges threatening seaweeds. We further discuss future approaches to study seaweed holobionts, and how we can apply the holobiont concept to natural or engineered seaweed ecosystems.

Algal blooms drive global biogeochemical cycles of key nutrients in the oceans and serve as hotspots for biological interactions. The massive spring blooms of the cosmopolitan coccolithophore Emiliania huxleyi (E. huxleyi) are often infected by the lytic Emiliania huxleyi specific virus (EhV) which is a major mortality agent triggering bloom demise. Nonetheless, the multi-annual “boom and bust” pattern of E. huxleyi suggests that mechanisms of coexistence are essential for these host-virus dynamics. To investigate host-virus coexistence, we developed a new model system from an E. huxleyi culture which recovered from viral infection. The recovered population coexists with the virus, as host cells continue to grow in parallel to viral production. By applying a single-molecule fluorescence in situ hybridization (smFISH) approach to quantify the fraction of infected cells and assessing infection-specific lipid biomarkers, we identified a small subpopulation (5-7% of cells) that was infected and produced new virions, whereas the majority of the host population could resist infection. To further assess population heterogeneity, we generated monoclonal strain collections using single-cell sorting and subsequently phenotyped their susceptibility to EhV infection. This unraveled a substantial cell-to-cell heterogeneity across a continuum of susceptibility to resistance, suggesting that infection outcomes may vary depending on the individual cell. These results add a new dimension to our understanding of the complexity of host-virus interactions that are commonly assessed in bulk and described by binary definitions of resistance or susceptibility. We propose that phenotypic heterogeneity drives E. huxleyi -EhV coexistence and may potentially provide the coexisting strain an ecological advantage by killing competing susceptible strains.

Marine viruses play a key role in regulating phytoplankton populations, greatly affecting the biogeochemical cycling of major nutrients in the ocean. Resistance to viral infection has been reported for various phytoplankton species under laboratory conditions. Nevertheless, the occurrence of resistant cells in natural populations is underexplored due to the lack of sensitive tools to detect these rare phenotypes. Consequently, our current understanding of the ecological importance of resistance and its underlying mechanisms is limited. Here, we sought to identify lipid biomarkers for the resistance of the bloom-forming algaEmiliania huxleyito its specific virus,E. huxleyivirus (EhV). By applying an untargeted lipidomics approach, we identified a group of glycosphingolipid (GSL) biomarkers that characterize resistantE. huxleyistrains and were thus termed resistance-specific GSLs (resGSLs). Further, we detected these lipid biomarkers inE. huxleyiisolates collected from inducedE. huxleyiblooms and in samples collected during an open-oceanE. huxleyibloom, indicating that resistant cells predominantly occur during the demise phase of the bloom. Last, we show that the GSL composition ofE. huxleyicultures that recover following infection and gain resistance to the virus resembles that of resistant strains. These findings highlight the metabolic plasticity and coevolution of the GSL biosynthetic pathway and underscore its central part in this host–virus arms race.

Algal blooms are hotspots of marine primary production and play central roles in microbial ecology and global elemental cycling. Upon demise of the bloom, organic carbon is partly respired and partly transferred to either higher trophic levels, bacterial biomass production or sinking. Viral infection can lead to bloom termination, but its impact on the fate of carbon remains largely unquantified. Here, we characterize the interplay between viral infection and the composition of a bloom-associated microbiome and consequently the evolving biogeochemical landscape, by conducting a large-scale mesocosm experiment where we monitor seven induced coccolithophore blooms. The blooms show different degrees of viral infection and reveal that only high levels of viral infection are followed by significant shifts in the composition of free-living bacterial and eukaryotic assemblages. Intriguingly, upon viral infection the biomass of eukaryotic heterotrophs (thraustochytrids) rivals that of bacteria as potential recyclers of organic matter. By combining modeling and quantification of active viral infection at a single-cell resolution, we estimate that viral infection causes a 2–4 fold increase in per-cell rates of extracellular carbon release in the form of acidic polysaccharides and particulate inorganic carbon, two major contributors to carbon sinking into the deep ocean. These results reveal the impact of viral infection on the fate of carbon through microbial recyclers of organic matter in large-scale coccolithophore blooms.