Communication between microorganisms in the marine environment has immense ecological impact by mediating trophic-level interactions and thus determining community structure1. Extracellular vesicles (EVs) are produced by bacteria2,3, archaea4, protists5 and metazoans, and can mediate pathogenicity6 or act as vectors for intercellular communication. However, little is known about the involvement of EVs in microbial interactions in the marine environment7. Here we investigated the signalling role of EVs produced during interactions between the cosmopolitan alga Emiliania huxleyi and its specific virus (EhV, Phycodnaviridae)8, which leads to the demise of these large-scale oceanic blooms9,10. 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 that differs from that of viruses and their infected host cells, and their cargo is composed of specific small RNAs that are predicted to target sphingolipid metabolism and cell-cycle pathways. EVs can be internalized by E. huxleyi cells, which consequently leads to a faster viral infection dynamic. EVs can also prolong EhV half-life in the extracellular milieu. We propose that EVs are exploited by viruses to sustain efficient infectivity and propagation across E. huxleyi blooms. As these algal blooms have an immense impact on the cycling of carbon and other nutrients11,12, this mode of cell–cell communication may influence the fate of the blooms and, consequently, the composition and flow of nutrients in marine microbial food webs.
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Pohnert, G., Steinke, M. & Tollrian, R. Chemical cues, defence metabolites and the shaping of pelagic interspecific interactions. Trends Ecol. Evol. 22, 198–204 (2007).
Kulp, A. & Kuehn, M. J. Biological functions and biogenesis of secreted bacterial outer membrane vesicles. Annu. Rev. Microbiol. 64, 163–184 (2010).
Brown, L., Wolf, J. M., Prados-Rosales, R. & Casadevall, A. Through the wall: extracellular vesicles in Gram-positive bacteria, mycobacteria and fungi. Nat. Rev. Microbiol. 13, 620–630 (2015).
Soler, N., Marguet, E., Verbavatz, J. M. & Forterre, P. Virus-like vesicles and extracellular DNA produced by hyperthermophilic archaea of the order Thermococcales. Res. Microbiol. 159, 390–399 (2008).
Szempruch, A. J., Dennison, L., Kieft, R., Harrington, J. M. & Hajduk, S. L. Sending a message: extracellular vesicles of pathogenic protozoan parasites. Nat. Rev. Microbiol. 14, 669–675 (2016).
Yáñez-Mó, M. et al. Biological properties of extracellular vesicles and their physiological functions. J. Extracell. Ves. 4, 27066 (2015).
Biller, S. J. et al. Bacterial vesicles in marine ecosystems. Science 343, 183–186 (2014).
Wilson, W. H., Tarran, G. & Zubkov, M. V. Virus dynamics in a coccolithophore-dominated bloom in the North Sea. Deep Sea Res. II 49, 2951–2963 (2002).
Bratbak, G., Egge, J. & Heldal, M. Viral mortality of the marine alga Emiliania huxleyi (Haptophyceae) and the termination of the algal bloom. Mar. Ecol. Prog. Ser. 93, 39–48 (1993).
Lehahn, Y. et al. Decoupling physical from biological processes to assess the impact of viruses on a mesoscale algal bloom. Curr. Biol. 24, 2041–2046 (2014).
Rost, B. & Riebesell, U. in Coccolithophores: from Molecular Processes to Global Impact (eds Thierstein, H. R. & Young, J. R.) 99–125 (Springer-Verlag, Berlin, Heidelberg, 2004).
Collins, J. R. et al. The multiple fates of sinking particles in the North Atlantic Ocean. Global Biogeochem. Cycles 29, 1471–1494 (2015).
Malitsky, S. et al. Viral infection of the marine alga Emiliania huxleyi triggers lipidome remodeling and induces the production of highly saturated triacylglycerol. New Phytol. 210, 88–96 (2016).
Schatz, D. et al. Hijacking of an autophagy-like process is critical for the life cycle of a DNA virus infecting oceanic algal blooms. New Phytol. 204, 854–863 (2014).
Deatherage, B. L. & Cookson, B. T. Membrane vesicle release in bacteria, eukaryotes, and archaea: a conserved yet underappreciated aspect of microbial life. Infect. Immun. 80, 1948–1957 (2012).
Tkach, M. & Théry, C. Communication by extracellular vesicles: where we are and where we need to go. Cell 164, 1226–1232 (2016).
Zhang, X. et al. Characterization of the small RNA transcriptome of the marine coccolithophorid, Emiliania huxleyi. PLoS ONE 11, e0154279 (2016).
Spangenburg, E. E., Pratt, S. J. P., Wohlers, L. M. & Lovering, R. M. Use of BODIPY (493/503) to visualize intramuscular lipid droplets in skeletal muscle. J. Biomed. Biotechnol. 2011, 598358 (2011).
Daboussi, F. et al. Genome engineering empowers the diatom Phaeodactylum tricornutum for biotechnology. Nat. Commun. 5, 3831 (2014).
Frada, M. J. et al. Zooplankton may serve as transmission vectors for viruses infecting algal blooms in the ocean. Curr. Biol. 24, 2592–2597 (2014).
Manning, A. J. & Kuehn, M. J. Contribution of bacterial outer membrane vesicles to innate bacterial defense. BMC Microbiol. 11, 1–15 (2011).
Tzipilevich, E., Habusha, M. & Ben-Yehuda, S. Acquisition of phage sensitivity by bacteria through exchange of phage receptors. Cell 168, 186–199 (2017).
Ruiz, E., Oosterhof, M., Sandaa, R.-A., Larsen, A. & Pagarete, A. Emerging interaction patterns in the Emiliania huxleyi–EhV system. Viruses 9, 61 (2017).
Highfield, A., Evans, C., Walne, A., Miller, P. I. & Schroeder, D. C. How many Coccolithovirus genotypes does it take to terminate an Emiliania huxleyi bloom? Virology 466–467, 138–145 (2014).
Ziv, C. et al. Viral serine palmitoyltransferase induces metabolic switch in sphingolipid biosynthesis and is required for infection of a marine alga. Proc. Natl Acad. Sci. USA 113, E1907–E1916 (2016).
Rosenwasser, S. et al. Rewiring host lipid metabolism by large viruses determines the fate of Emiliania huxleyi, a bloom-forming alga in the ocean. Plant Cell 26, 2689–2707 (2014).
Weitz, J. S. et al. A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes. ISME J. 9, 1352–1364 (2015).
Jover, L. F., Effler, T. C., Buchan, A., Wilhelm, S. W. & Weitz, J. S. The elemental composition of virus particles: implications for marine biogeochemical cycles. Nat. Rev. Micro. 12, 519–528 (2014).
Keller, M. D., Selvin, R. C., Claus, W. & Guillard, R. R. L. Media for the culture of oceanic ultraphytoplankton. J. Phycol. 23, 633–638 (1987).
Schroeder, D. C., Oke, J., Malin, G. & Wilson, W. H. Coccolithovirus (Phycodnaviridae): characterisation of a new large dsDNA algal virus that infects Emiliania huxleyi. Arch. Virol. 147, 1685–1698 (2002).
Pagarete, A., Allen, M. J., Wilson, W. H., Kimmance, S. A. & de Vargas, C. Host–virus shift of the sphingolipid pathway along an Emiliania huxleyi bloom: survival of the fattest. Environ. Microbiol. 11, 2840–2848 (2009).
Bligh, E. G. & Dyer, W. J. A rapid method of total lipid extraction and purification. Can. J. Biochem. Physiol. 37, 911–917 (1959).
Hummel, J. et al. Ultra performance liquid chromatography and high resolution mass spectrometry for the analysis of plant lipids. Front. Plant Sci. 2, 54 (2011).
Degenkolbe, T. et al. Differential remodeling of the lipidome during cold acclimation in natural accessions of Arabidopsis thaliana. Plant J. 72, 972–982 (2012).
Giavalisco, P. et al. Elemental formula annotation of polar and lipophilic metabolites using 13C, 15N and 34S isotope labelling, in combination with high-resolution mass spectrometry. Plant J. 68, 364–376 (2011).
Samarakoon, T. et al. in High-Throughput Phenotyping in Plants: Methods and Protocols (ed. Normanly, J.) 179–268 (Humana, New York, 2012).
Gasulla, F. et al. The role of lipid metabolism in the acquisition of desiccation tolerance in Craterostigma plantagineum: a comparative approach. Plant J. 75, 726–741 (2013).
Fulton, J. M. et al. Novel molecular determinants of viral susceptibility and resistance in the lipidome of Emiliania huxleyi. Environ. Microbiol. 16, 1137–1149 (2014).
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10–12 (2011).
Feldmesser, E., Rosenwasser, S., Vardi, A. & Ben-Dor, S. Improving transcriptome construction in non-model organisms: integrating manual and automated gene definition in Emiliania huxleyi. BMC Genomics 15, 1–16 (2014).
Alcolombri, U. et al. Identification of the algal dimethyl sulfide–releasing enzyme: a missing link in the marine sulfur cycle. Science 348, 1466–1469 (2015).
Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).
Gene Ontology Consortium. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 38, D331–335 (2010).
Conesa, A. et al. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21, 3674–3676 (2005).
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
Bauer, S., Grossmann, S., Vingron, M. & Robinson, P. N. Ontologizer 2.0—a multifunctional tool for GO term enrichment analysis and data exploration. Bioinformatics 24, 1650–1651 (2008).
Taylor, J. The estimation of numbers of bacteria by tenfold dilution series. J. Appl. Bacteriol. 25, 54–61 (1962).
George, T. C. et al. Quantitative measurement of nuclear translocation events using similarity analysis of multispectral cellular images obtained in flow. J. Immunol. Methods 311, 117–129 (2006).
Spitzer, M., Wildenhain, J., Rappsilber, J. & Tyers, M. BoxPlotR: a web tool for generation of box plots. Nat. Meth. 11, 121–122 (2014).
Wilson, W. H. et al. Isolation of viruses responsible for the demise of an Emiliania huxleyi bloom in the English Channel. J. Mar. Biol. Assoc. UK 82, 369–377 (2002).
We thank Z. Porat from the Life Sciences Core Facilities, the Weizmann Institute of Science for assistance with ImageStream analysis, C. Bessudo from the Department of Plant and Environmental Sciences at the Weizmann Institute of Science for support with confocal microscopy and O. Yaron, currently at Bar Ilan University, for constructing the small RNA libraries. We also thank S. Graf van Creveld from the Vardi lab for the initial design of the model, I. Sher from the Design, Photography and Printing Branch at the Weizmann Institute of Science for assistance in designing the graphs for this manuscript and J. Weitz from the Georgia Institute of Technology for fruitful discussion. This research was supported by the European Research Council StG (INFOTROPHIC grant no. 280991) and CoG (VIROCELLSPHERE grant no. 681715) and by generous support from the Edith and Nathan Goldenberg Career Development Chair to A.V. The EM studies were supported in part by the Irving and Cherna Moskowitz Center for Nano and Bio-Nano Imaging at the Weizmann Institute of Science.