Figure 4 - available via license: Creative Commons Attribution 4.0 International
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Digital unique expression. Proportional Venn diagram of the genes expressed in each of the strains in exponential growth, and their overlaps. The diagram was drawn using BioVenn (https:// www. biove nn. nl/ index. php).
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Emiliania huxleyi is a cosmopolitan coccolithophore widespread in temperate oceans. This unicellular photoautotroph forms massive recurring blooms that play an important role in large biogeochemical cycles of carbon and sulfur, which play a role in climate change. The mechanism of bloom formation and demise, controlled by giant viruses that routine...
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... and CCMP379 each have one additional unique heterozygous SNP (position 520 G/A and position 889 C/T respectively). We compared all of the Emiliania huxleyi 18S sequences from different strains that we could identify in GenBank to our starting sequence, a total of 30 sequences ( Supplementary Fig. S4). There are only two positions in the entire alignment where there are SNPs that occur in more than one strain. ...
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... during exponential growth, we wanted to compare the three strains CCMP373, CCMP374 and CCMP2090. Since the CCMP2090 experiment was performed using a different version of the sequencing instrument and had strong batch effects when compared to the second experiment, we looked at genes that were expressed uniquely in each one of the three strains (Fig. 4) in each experiment separately. Genes that had at least 7 normalized reads in two replicates from day 2 for strains CCMP373 and CCMP374 or in the non-infected CCMP2090 sample from day 1, were considered expressed in exponential ...
Citations
... For the host, an integrated transcriptome reference of E. huxleyi was used as a ref. 65. Viral transcripts in the database were identified using a homology search against a customized protein database as described above. ...
Giant viruses (phylum Nucleocytoviricota) are globally distributed in aquatic ecosystems. They play fundamental roles as evolutionary drivers of eukaryotic plankton and regulators of global biogeochemical cycles. However, we lack knowledge about their native hosts, hindering our understanding of their life cycle and ecological importance. In the present study, we applied a single-cell RNA sequencing (scRNA-seq) approach to samples collected during an induced algal bloom, which enabled pairing active giant viruses with their native protist hosts. We detected hundreds of single cells from multiple host lineages infected by diverse giant viruses. These host cells included members of the algal groups Chrysophycae and Prymnesiophycae, as well as heterotrophic flagellates in the class Katablepharidaceae. Katablepharids were infected with a rare Imitervirales-07 giant virus lineage expressing a large repertoire of cell-fate regulation genes. Analysis of the temporal dynamics of these host–virus interactions revealed an important role for the Imitervirales-07 in controlling the population size of the host Katablepharid population. Our results demonstrate that scRNA-seq can be used to identify previously undescribed host–virus interactions and study their ecological importance and impact.
... Indeed, there was a decrease in genes involved in photosynthesis at 6, 12 and 24 HPI, although some cells seemed to be intact and photosynthesizing 148 . Enriched functions associated with E. huxleyi responding to viral infection included modified amino acid, lipid binding, porin activity, calcium channel activity, pore complex, cell outer membrane, bacterial-type flagellum functions, among others 154 . High expression of glycolysis and nucleotides biosynthesis related genes were reported when studying single protist cells from a coccolithophore bloom 151 . ...
... Apart from inducing the expression of viral genes, viruses can elevate the expression of host genes associated with processes such as DNA synthesis, energy generation, and the modification of lipid, protein, and nucleic acid biosynthesis pathways. These alterations collectively contribute to the complex interplay between viruses and host cells during infection 62,117,[135][136][137][138]140,144,153,154,167 . Still, deeper exploration of virus-host dynamics is much needed, and can help elucidate host factors influencing susceptibility, pathogenicity, resistance, and protists basic cytology. ...
Protists encompass a vast widely distributed group of organisms, surpassing the diversity observed in metazoans. Their diverse ecological niches and life forms are intriguing characteristics that render them valuable subjects for in-depth cell biology studies. Throughout history, viruses have played a pivotal role in elucidating complex cellular processes, particularly in the context of cellular responses to viral infections. In this comprehensive review, we provide an overview of the cellular alterations that are triggered in specific hosts following different viral infections and explore intricate biological interactions observed in experimental conditions using different host-pathogen groups.
... For the virus, the predicted CDSs in the EhV201, EhV163, EhVice, and EhVM1 genome sequence (58) were used as reference. For the host, an integrated transcriptome reference of E. huxleyi (59). In addition to the nuclear sequences, the transcriptome reference contains chloroplast and mitochondrial transcripts, which were identified by the basic local alignment search tool (BLAST) (60) searches against the respective organellar genome sequences (61). ...
Giant viruses infect many unicellular eukaryotes, including algae that form massive oceanic blooms. Despite the major impact of viruses on the marine ecosystem, the ability to quantify and assess active viral infection in nature remains a major challenge. We applied single-cell RNA sequencing, to profile virus and host transcriptomes of 12,000 single algal cells from a coccolithophore bloom. Viral infection was detected already at early exponential bloom phase, negatively correlating with the bloom intensity. A consistent percent of infected coccolithophores displayed the early phase of viral replication for several consecutive days, indicating a daily turnover and continuous virocell-associated metabolite production, potentially affecting the surrounding microbiome. Linking single-cell infection state to host physiology revealed that infected cells remained calcified even in the late infection stage. These findings stress the importance of studying host-virus dynamics in natural populations, at single-cell resolution, to better understand virus life cycle and its impact on microbial food webs.
... Resistance to viral infection has been described in several E. huxleyi strains and was previously attributed to ploidy level, genome and transcriptome variations between the strains (13,33), to expression and activity of specific enzymes, such as DMSP-lyase, and to metacaspase expression (34,35). Resistant cells were also identified in low numbers (<1%) in infected E. huxleyi cultures (36), revealing that resistance can also be triggered by viral infection. ...
... E. huxleyi Strains. To identify lipids that are characteristic of resistant strains, we compared the lipidome of four E. huxleyi strains that differ in their susceptibility to viral infection by EhV201: the resistant E. huxleyi strains CCMP373 and CCMP379 and the susceptible E. huxleyi strains CCMP2090 and CCMP374 (hereinafter, E. huxleyi strains 373, 379, 2090, and 374, respectively) (31,33,34). Previous studies reported that following infection of E. huxleyi cultures by EhV, a small proportion of the population (< 1%) survives and acquires resistance to the virus (13,36). ...
... Phylogenetic analysis of the conserved domain of the SLD proteins revealed three distinct clades (I-III, SI Appendix, Fig. S20A and Table S5), each consisting of diverse taxonomic groups. We further examined the expression of these genes using previous transcriptomics experiments with E. huxleyi strains 373, 379, 2090, and 374 (33,42). Out of the five putative E. huxleyi sld genes, sld1 and sld4 were expressed in the resistant E. huxleyi strains 373 and 379 and not in the susceptible strains (SI Appendix, Figs. ...
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 alga Emiliania huxleyi to its specific virus, E. huxleyi virus (EhV). By applying an untargeted lipidomics approach, we identified a group of glycosphingolipid (GSL) biomarkers that characterize resistant E. huxleyi strains and were thus termed resistance-specific GSLs (resGSLs). Further, we detected these lipid biomarkers in E. huxleyi isolates collected from induced E. huxleyi blooms and in samples collected during an open-ocean E. huxleyi bloom, indicating that resistant cells predominantly occur during the demise phase of the bloom. Last, we show that the GSL composition of E. huxleyi cultures 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.
Since the discovery of the first “giant virus,” particular attention has been paid toward isolating and culturing these large DNA viruses through Acanthamoeba spp. bait systems. While this method has allowed for the discovery of plenty novel viruses in the Nucleocytoviricota , environmental -omics-based analyses have shown that there is a wealth of diversity among this phylum, particularly in marine datasets. The prevalence of these viruses in metatranscriptomes points toward their ecological importance in nutrient turnover in our oceans and as such, in depth study into non-amoebal Nucleocytoviricota should be considered a focal point in viral ecology. In this review, we report on Kratosvirus quantuckense (née Aureococcus anophagefferens Virus), an algae-infecting virus of the Imitervirales . Current systems for study in the Nucleocytoviricota differ significantly from this virus and its relatives, and a litany of trade-offs within physiology, coding potential, and ecology compared to these other viruses reveal the importance of K. quantuckense . Herein, we review the research that has been performed on this virus as well as its potential as a model system for algal-virus interactions.
Giant viruses (phylum Nucleocytoviricota) are globally distributed in aquatic ecosystems 1,2 . They play major roles as evolutionary drivers of eukaryotic plankton ³ and regulators of global biogeochemical cycles ⁴ . Recent metagenomic studies have significantly expanded the known diversity of marine giant viruses 1,5–7 , but we still lack fundamental knowledge about their native hosts, thereby hindering our understanding of their lifecycle and ecological importance. Here, we aim to discover the native hosts of giant viruses using a novel, sensitive single-cell metatranscriptomic approach. By applying this approach to natural plankton communities, we unraveled an active viral infection of several giant viruses, from multiple lineages, and identified their native hosts. We identify a rare lineage of giant virus (Imitervirales-07) infecting a minute population of protists (class Katablepharidaceae) and revealed the prevalence of highly expressed viral-encoded cell-fate regulation genes in infected cells. Further examination of this host-virus dynamics in a temporal resolution suggested this giant virus controls its host population demise. Our results demonstrate how single-cell metatranscriptomics is a sensitive approach for pairing viruses with their authentic hosts and studying their ecological significance in a culture-independent manner in the marine environment.
Viruses are the most abundant biological entity in the ocean and play a significant role in shaping the marine ecosystem. The past two decades have revealed an outstanding diversity of giant viruses infecting protists across the tree of life and, in particular, algae that form massive blooms in the ocean. Virus-induced bloom demise significantly impacts marine ecology and biogeochemistry, as well as the associated microbial community. Nevertheless, little is known about the infection dynamics of these giant viruses in the natural environment and their role in regulating algal blooms. Here, we provide evidence for a daily life cycle of giant viral infection in algal blooms by processing the transcriptome of over 12,000 single algal cells during different phases of interaction with their giant viruses. We revealed that viral infection occurs already at the exponential phase of the bloom and that the timing of infection can determine the magnitude of the bloom but not the fraction of infected cells. We further revealed that the same proportion of infected cells are in the early phase of the viral replication program (13.5%) throughout several consecutive days of the bloom, suggesting that a daily turnover of infection is at play during the bloom and demise phases of the algal population. This may imply that a continuous source of virocell-associated metabolites diffuses throughout the bloom succession and could fuel the microbial food webs. Finally, we link single cell infection state to host physiology and show that infected cells remained calcified even in the late stage of infection, contradicting common observation of bulk population in which viral infection is directly linked with decalcification. Together, these results highlight the importance of studying host-virus dynamics in natural populations at a single-cell resolution, which can provide a fresh view of the dynamics and propagation of viral infection. This approach will enable quantification of the impact of marine viruses on microbial food webs.
