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. 2013 Aug 28;28(5):291–302. doi: 10.1007/s12250-013-3362-1

Functional inferences of environmental coccolithovirus biodiversity

Jozef I Nissimov 1,2, Mark Jones 1, Johnathan A Napier 3, Colin B Munn 4, Susan A Kimmance 1, Michael J Allen 1,✉
PMCID: PMC8208406  PMID: 24006045

Abstract

The cosmopolitan calcifying alga Emiliania huxleyi is one of the most abundant bloom forming coccolithophore species in the oceans and plays an important role in global biogeochemical cycling. Coccolithoviruses are a major cause of coccolithophore bloom termination and have been studied in laboratory, mesocosm and open ocean studies. However, little is known about the dynamic interactions between the host and its viruses, and less is known about the natural diversity and role of functionally important genes within natural coccolithovirus communities. Here, we investigate the temporal and spatial distribution of coccolithoviruses by the use of molecular fingerprinting techniques PCR, DGGE and genomic sequencing. The natural biodiversity of the virus genes encoding the major capsid protein (MCP) and serine palmitoyltransferase (SPT) were analysed in samples obtained from the Atlantic Meridional Transect (AMT), the North Sea and the L4 site in the Western Channel Observatory. We discovered nine new coccolithovirus genotypes across the AMT and L4 site, with the majority of MCP sequences observed at the deep chlorophyll maximum layer of the sampled sites on the transect. We also found four new SPT gene variations in the North Sea and at L4. Their translated fragments and the full protein sequence of SPT from laboratory strains EhV-86 and EhV-99B1 were modelled and revealed that the theoretical fold differs among strains. Variation identified in the structural distance between the two domains of the SPT protein may have an impact on the catalytic capabilities of its active site. In summary, the combined use of ‘standard’ markers (i.e. MCP), in combination with metabolically relevant markers (i.e. SPT) are useful in the study of the phylogeny and functional biodiversity of coccolithoviruses, and can provide an interesting intracellular insight into the evolution of these viruses and their ability to infect and replicate within their algal hosts.

Keywords: Coccolithovirus, Major capsid protein, Serine palmitoyltransferase, Functional biodiversity

References

  1. Abrescia N G, Bamford D H, Grimes J M, Stuart D I. Structure unifies the viral universe. Annu Rev Biochem. 2012;81:795–822. doi: 10.1146/annurev-biochem-060910-095130. [DOI] [PubMed] [Google Scholar]
  2. Allen M J, Schroeder D C, Holden M T, Wilson W H. Evolutionary History of the Coccolithoviridae. Mol Biol Evol. 2006;23:86–92. doi: 10.1093/molbev/msj010. [DOI] [PubMed] [Google Scholar]
  3. Allen M J, Schroeder D C, Donkin A, Crawfurd K J, Wilson W H. Genome comparison of two Coccolithoviruses. Virol J. 2006;3:15. doi: 10.1186/1743-422X-3-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Allen M J, Martinez-Martinez J, Schroeder D C, Somerfield P J, Wilson W H. Use of microarrays to assess viral diversity: from genotype to phenotype. Environ Microbiol. 2007;9:971–982. doi: 10.1111/j.1462-2920.2006.01219.x. [DOI] [PubMed] [Google Scholar]
  5. Allen M J, Forster T, Schroeder D C, Hall M, Roy D, Ghazal P, Wilson W H. Locus-specific gene expression pattern suggests a unique propagation strategy for a giant algal virus. J Virol. 2006;80:7699–7705. doi: 10.1128/JVI.00491-06. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bamford D H, Grimes J M, Stuart D I. What does structure tell us about virus evolution? Curr Opin Struct Biol. 2005;15:655–663. doi: 10.1016/j.sbi.2005.10.012. [DOI] [PubMed] [Google Scholar]
  7. Bidle K D, Vardi A. A chemical arms race at sea mediates algal host-virus interactions. Curr Opin Microbiol. 2011;14:449–457. doi: 10.1016/j.mib.2011.07.013. [DOI] [PubMed] [Google Scholar]
  8. Bidle K D, Haramaty L, Barcelos E R J, Falkowski P. Viral activation and recruitment of metacaspases in the unicellular coccolithophore, Emiliania huxleyi. Proc Natl Acad Sci U S A. 2007;104:6049–6054. doi: 10.1073/pnas.0701240104. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Brussaard C P, Marie D, Bratbak G. Flow cytometric detection of viruses. J Virol Methods. 2000;85:175–182. doi: 10.1016/S0166-0934(99)00167-6. [DOI] [PubMed] [Google Scholar]
  10. Brussaard C P, Wilhelm S W, Thingstad F, Weinbauer M G, Bratbak G, Heldal M, Kimmance S A, Middelboe M, Nagasaki K, Paul J H, Schroeder D C, Suttle C A, Vaque D, Wommack K E. Global-scale processes with a nanoscale drive: the role of marine viruses. ISME J. 2008;2:575–578. doi: 10.1038/ismej.2008.31. [DOI] [PubMed] [Google Scholar]
  11. Chen F, Suttle C A, Short S M. Genetic diversity in marine algal virus communities as revealed by sequence analysis of DNA polymerase genes. Appl Environ Microbiol. 1996;62:2869–2874. doi: 10.1128/aem.62.8.2869-2874.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Coolen M J. 7000 years of Emiliania huxleyi viruses in the Black Sea. Science. 2011;333:451–452. doi: 10.1126/science.1200072. [DOI] [PubMed] [Google Scholar]
  13. de Wit R, Bouvier T. ‘Everything is everywhere, but, the environment selects’; what did Baas Becking and Beijerinck really say? Environ Microbiol. 2006;8:755–758. doi: 10.1111/j.1462-2920.2006.01017.x. [DOI] [PubMed] [Google Scholar]
  14. Falkowski P G, Fenchel T, Delong E F. The microbial engines that drive Earth’s biogeochemical cycles. Science. 2008;320:1034–1039. doi: 10.1126/science.1153213. [DOI] [PubMed] [Google Scholar]
  15. Guex N, Peitsch M C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis. 1997;18:2714–2723. doi: 10.1002/elps.1150181505. [DOI] [PubMed] [Google Scholar]
  16. Han G, Gable K, Yan L, Allen M J, Wilson W H, Moitra P, Harmon J M, Dunn T M. Expression of a novel marine viral single-chain serine palmitoyltransferase and construction of yeast and mammalian single-chain chimera. J Biol Chem. 2006;281:39935–39942. doi: 10.1074/jbc.M609365200. [DOI] [PubMed] [Google Scholar]
  17. Hanson R. Jmol — a paradigm shift in crystallographic visualization. Journal of Applied Crystallography. 2010;43:1250–1260. doi: 10.1107/S0021889810030256. [DOI] [Google Scholar]
  18. Hartshorn M J. AstexViewer: a visualisation aid for structure-based drug design. J Comput Aided Mol Des. 2002;16:871–881. doi: 10.1023/A:1023813504011. [DOI] [PubMed] [Google Scholar]
  19. Kelley L A, Sternberg M J. Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc. 2009;4:363–371. doi: 10.1038/nprot.2009.2. [DOI] [PubMed] [Google Scholar]
  20. Krupovic M, Bamford D H. Virus evolution: how far does the double beta-barrel viral lineage extend? Nat Rev Microbiol. 2008;6:941–948. doi: 10.1038/nrmicro2033. [DOI] [PubMed] [Google Scholar]
  21. Krupovic M, Bamford D H. Double-stranded DNA viruses: 20 families and only five different architectural principles for virion assembly. Curr Opin Virol. 2011;1:118–124. doi: 10.1016/j.coviro.2011.06.001. [DOI] [PubMed] [Google Scholar]
  22. Larsen J B, Larsen A, Bratbak G, Sandaa R A. Phylogenetic analysis of members of the Phycodnaviridae virus family, using amplified fragments of the major capsid protein gene. Appl Environ Microbiol. 2008;74:3048–3057. doi: 10.1128/AEM.02548-07. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Martinez J M, Schroeder D C, Wilson W H. Dynamics and genotypic composition of Emiliania huxleyi and their co-occurring viruses during a coccolithophore bloom in the North Sea. FEMS Microbiol Ecol. 2012;81:315–323. doi: 10.1111/j.1574-6941.2012.01349.x. [DOI] [PubMed] [Google Scholar]
  24. Martinez J M, Schroeder D C, Larsen A, Bratbak G, Wilson W H. Molecular dynamics of Emiliania huxleyi and cooccurring viruses during two separate mesocosm studies. Appl Environ Microbiol. 2007;73:554–562. doi: 10.1128/AEM.00864-06. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Michaelson L V, Dunn T M, Napier J A. Viral trans-dominant manipulation of algal sphingolipids. Trends Plant Sci. 2010;15:651–655. doi: 10.1016/j.tplants.2010.09.004. [DOI] [PubMed] [Google Scholar]
  26. Monier A, Pagarete A, de Vargas C, Allen M J, Read B, Claverie J M, Ogata H. Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus. Genome Res. 2009;19:1441–1449. doi: 10.1101/gr.091686.109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Nissimov J I, Worthy C A, Rooks P, Napier J A, Kimmance S A, Henn M R, Ogata H, Allen M J. Draft genome sequence of the coccolithovirus EhV-84. Stand Genomic Sci. 2011;5:1–11. doi: 10.4056/sigs.1884581. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Nissimov J I, Worthy C A, Rooks P, Napier J A, Kimmance S A, Henn M R, Ogata H, Allen M J. Draft genome sequence of the Coccolithovirus Emiliania huxleyi virus 203. J Virol. 2011;85:13468–13469. doi: 10.1128/JVI.06440-11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Nissimov J I, Worthy C A, Rooks P, Napier J A, Kimmance S A, Henn M R, Ogata H, Allen M J. Draft genome sequence of the coccolithovirus Emiliania huxleyi virus 202. J Virol. 2012;86:2380–2381. doi: 10.1128/JVI.06863-11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Nissimov J I, Worthy C A, Rooks P, Napier J A, Kimmance S A, Henn M R, Ogata H, Allen M J. Draft genome sequence of four coccolithoviruses: Emiliania huxleyi virus EhV-88, EhV-201, EhV-207, and EhV-208. J Virol. 2012;86:2896–2897. doi: 10.1128/JVI.07046-11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. 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. 2009;11:2840–2848. doi: 10.1111/j.1462-2920.2009.02006.x. [DOI] [PubMed] [Google Scholar]
  32. Pagarete A, Le Corguille G, Tiwari B, Ogata H, de Vargas C, Wilson W H, Allen M J. Unveiling the transcriptional features associated with coccolithovirus infection of natural Emiliania huxleyi blooms. FEMS Microbiol Ecol. 2011;78:555–564. doi: 10.1111/j.1574-6941.2011.01191.x. [DOI] [PubMed] [Google Scholar]
  33. Pagarete A, Lanzen A, Puntervoll P, Sandaa R A, Larsen A, Larsen J B, Allen M J, Bratbak G. Genomic Sequence and Analysis of EhV-99B1, a New Coccolithovirus from the Norwegian Fjords. 2012. [DOI] [PubMed] [Google Scholar]
  34. Rowe J M, Fabre M F, Gobena D, Wilson W H, Wilhelm S W. Application of the major capsid protein as a marker of the phylogenetic diversity of Emiliania huxleyi viruses. FEMS Microbiol Ecol. 2011;76:373–380. doi: 10.1111/j.1574-6941.2011.01055.x. [DOI] [PubMed] [Google Scholar]
  35. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406–425. doi: 10.1093/oxfordjournals.molbev.a040454. [DOI] [PubMed] [Google Scholar]
  36. Schroeder D C, Oke J, Hall M, Malin G, Wilson W H. Virus succession observed during an Emiliania huxleyi bloom. Appl Environ Microbiol. 2003;69:2484–2490. doi: 10.1128/AEM.69.5.2484-2490.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Schroeder D C, Biggi G F, Hall M, Davy J, Martínez J M, Richardson A J, Malin G, Wilson W H. A GENETIC MARKER TO SEPARATE EMILIANIA HUXLEYI (PRYMNESIOPHYCEAE) MORPHOTYPES1. Journal of Phycology. 2005;41:874–879. doi: 10.1111/j.1529-8817.2005.04188.x. [DOI] [Google Scholar]
  38. Suttle C A. Viruses in the sea. Nature. 2005;437:356–361. doi: 10.1038/nature04160. [DOI] [PubMed] [Google Scholar]
  39. Suttle C A. Marine viruses—major players in the global ecosystem. Nat Rev Microbiol. 2007;5:801–812. doi: 10.1038/nrmicro1750. [DOI] [PubMed] [Google Scholar]
  40. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 2007;24:1596–1599. doi: 10.1093/molbev/msm092. [DOI] [PubMed] [Google Scholar]
  41. van Rijssel M, Gieskes W W C. Temperature, light, and the dimethylsulfoniopropionate (DMSP) content of Emiliania huxleyi (Prymnesiophyceae) Journal of Sea Research. 2002;48:17–27. doi: 10.1016/S1385-1101(02)00134-X. [DOI] [Google Scholar]
  42. Vardi A, Van Mooy B A, Fredricks H F, Popendorf K J, Ossolinski J E, Haramaty L, Bidle K D. Viral glycosphingolipids induce lytic infection and cell death in marine phytoplankton. Science. 2009;326:861–865. doi: 10.1126/science.1177322. [DOI] [PubMed] [Google Scholar]
  43. Vardi A, Haramaty L, Van Mooy B A, Fredricks H F, Kimmance S A, Larsen A, Bidle K D. Proc Natl Acad Sci U S A. 2012. Host-virus dynamics and subcellular controls of cell fate in a natural coccolithophore population. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Wilson W H, Tarran G, Zubkov M V. Virus dynamics in a coccolithophore-dominated bloom in the North Sea. Deep Sea Research Part II: Topical Studies in Oceanography. 2002;49:2951–2963. doi: 10.1016/S0967-0645(02)00065-6. [DOI] [Google Scholar]
  45. Wilson W H, Schroeder D C, Allen M J, Holden M T, Parkhill J, Barrell B G, Churcher C, Hamlin N, Mungall K, Norbertczak H, Quail M A, Price C, Rabbinowitsch E, Walker D, Craigon M, Roy D, Ghazal P. Complete genome sequence and lytic phase transcription profile of a Coccolithovirus. Science. 2005;309:1090–1092. doi: 10.1126/science.1113109. [DOI] [PubMed] [Google Scholar]

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