Functional inferences of environmental coccolithovirus biodiversity

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.

This is a preview of subscription content, access via your institution.

References

  1. Abrescia N G, Bamford D H, Grimes J M, and Stuart D I. 2012. Structure unifies the viral universe. Annu Rev Biochem, 81: 795–822.

    PubMed  Article  CAS  Google Scholar 

  2. Allen M J, Schroeder D C, Holden M T, and Wilson W H. 2006. Evolutionary History of the Coccolithoviridae. Mol Biol Evol, 23: 86–92.

    PubMed  Article  CAS  Google Scholar 

  3. Allen M J, Schroeder D C, Donkin A, Crawfurd K J, and Wilson W H. 2006. Genome comparison of two Coccolithoviruses. Virol J, 3: 15.

    PubMed  Article  Google Scholar 

  4. Allen M J, Martinez-Martinez J, Schroeder D C, Somerfield P J, and Wilson W H. 2007. Use of microarrays to assess viral diversity: from genotype to phenotype. Environ Microbiol, 9: 971–982.

    PubMed  Article  CAS  Google Scholar 

  5. Allen M J, Forster T, Schroeder D C, Hall M, Roy D, Ghazal P, and Wilson W H. 2006. Locus-specific gene expression pattern suggests a unique propagation strategy for a giant algal virus. J Virol, 80: 7699–7705.

    PubMed  Article  CAS  Google Scholar 

  6. Bamford D H, Grimes J M, and Stuart D I. 2005. What does structure tell us about virus evolution?. Curr Opin Struct Biol, 15: 655–663.

    PubMed  Article  CAS  Google Scholar 

  7. Bidle K D, and Vardi A. 2011. A chemical arms race at sea mediates algal host-virus interactions. Curr Opin Microbiol, 14: 449–457.

    PubMed  Article  Google Scholar 

  8. Bidle K D, Haramaty L, Barcelos E R J, and Falkowski P. 2007. Viral activation and recruitment of metacaspases in the unicellular coccolithophore, Emiliania huxleyi. Proc Natl Acad Sci U S A, 104: 6049–6054.

    PubMed  Article  CAS  Google Scholar 

  9. Brussaard C P, Marie D, and Bratbak G. 2000. Flow cytometric detection of viruses. J Virol Methods, 85: 175–182.

    PubMed  Article  CAS  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, and Wommack K E. 2008. Global-scale processes with a nanoscale drive: the role of marine viruses. ISME J, 2: 575–578.

    PubMed  Article  CAS  Google Scholar 

  11. Chen F, Suttle C A, and Short S M. 1996. Genetic diversity in marine algal virus communities as revealed by sequence analysis of DNA polymerase genes. Appl Environ Microbiol, 62: 2869–2874.

    PubMed  CAS  Google Scholar 

  12. Coolen M J. 2011. 7000 years of Emiliania huxleyi viruses in the Black Sea. Science, 333: 451–452.

    PubMed  Article  CAS  Google Scholar 

  13. de Wit R, and Bouvier T. 2006. ‘Everything is everywhere, but, the environment selects’; what did Baas Becking and Beijerinck really say?. Environ Microbiol, 8: 755–758.

    PubMed  Article  Google Scholar 

  14. Falkowski P G, Fenchel T, and Delong E F. 2008. The microbial engines that drive Earth’s biogeochemical cycles. Science, 320: 1034–1039.

    PubMed  Article  CAS  Google Scholar 

  15. Guex N, and Peitsch M C. 1997. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis, 18: 2714–2723.

    PubMed  Article  CAS  Google Scholar 

  16. Han G, Gable K, Yan L, Allen M J, Wilson W H, Moitra P, Harmon J M, and Dunn T M. 2006. Expression of a novel marine viral single-chain serine palmitoyltransferase and construction of yeast and mammalian single-chain chimera. J Biol Chem, 281: 39935–39942.

    PubMed  Article  CAS  Google Scholar 

  17. Hanson R. 2010. Jmol — a paradigm shift in crystallographic visualization. Journal of Applied Crystallography, 43: 1250–1260.

    Article  CAS  Google Scholar 

  18. Hartshorn M J. 2002. AstexViewer: a visualisation aid for structure-based drug design. J Comput Aided Mol Des, 16: 871–881.

    PubMed  Article  CAS  Google Scholar 

  19. Kelley L A, and Sternberg M J. 2009. Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc, 4: 363–371.

    PubMed  Article  CAS  Google Scholar 

  20. Krupovic M, and Bamford D H. 2008. Virus evolution: how far does the double beta-barrel viral lineage extend? Nat Rev Microbiol, 6: 941–948.

    PubMed  Article  CAS  Google Scholar 

  21. Krupovic M, and Bamford D H. 2011. Double-stranded DNA viruses: 20 families and only five different architectural principles for virion assembly. Curr Opin Virol, 1: 118–124.

    PubMed  Article  CAS  Google Scholar 

  22. Larsen J B, Larsen A, Bratbak G, and Sandaa R A. 2008. Phylogenetic analysis of members of the Phycodnaviridae virus family, using amplified fragments of the major capsid protein gene. Appl Environ Microbiol, 74: 3048–3057.

    PubMed  Article  CAS  Google Scholar 

  23. Martinez J M, Schroeder D C, and Wilson W H. 2012. Dynamics and genotypic composition of Emiliania huxleyi and their co-occurring viruses during a coccolithophore bloom in the North Sea. FEMS Microbiol Ecol, 81: 315–323.

    PubMed  Article  CAS  Google Scholar 

  24. Martinez J M, Schroeder D C, Larsen A, Bratbak G, and Wilson W H. 2007. Molecular dynamics of Emiliania huxleyi and cooccurring viruses during two separate mesocosm studies. Appl Environ Microbiol, 73: 554–562.

    PubMed  Article  CAS  Google Scholar 

  25. Michaelson L V, Dunn T M, and Napier J A. 2010. Viral trans-dominant manipulation of algal sphingolipids. Trends Plant Sci, 15: 651–655.

    PubMed  Article  CAS  Google Scholar 

  26. Monier A, Pagarete A, de Vargas C, Allen M J, Read B, Claverie J M, and Ogata H. 2009. Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus. Genome Res, 19: 1441–1449.

    PubMed  Article  CAS  Google Scholar 

  27. Nissimov J I, Worthy C A, Rooks P, Napier J A, Kimmance S A, Henn M R, Ogata H, and Allen M J. 2011. Draft genome sequence of the coccolithovirus EhV-84. Stand Genomic Sci, 5: 1–11.

    PubMed  Article  CAS  Google Scholar 

  28. Nissimov J I, Worthy C A, Rooks P, Napier J A, Kimmance S A, Henn M R, Ogata H, and Allen M J. 2011. Draft genome sequence of the Coccolithovirus Emiliania huxleyi virus 203. J Virol, 85: 13468–13469.

    PubMed  Article  CAS  Google Scholar 

  29. Nissimov J I, Worthy C A, Rooks P, Napier J A, Kimmance S A, Henn M R, Ogata H, and Allen M J. 2012. Draft genome sequence of the coccolithovirus Emiliania huxleyi virus 202. J Virol, 86: 2380–2381.

    PubMed  Article  CAS  Google Scholar 

  30. Nissimov J I, Worthy C A, Rooks P, Napier J A, Kimmance S A, Henn M R, Ogata H, and Allen M J. 2012. Draft genome sequence of four coccolithoviruses: Emiliania huxleyi virus EhV-88, EhV-201, EhV-207, and EhV-208. J Virol, 86: 2896–2897.

    PubMed  Article  CAS  Google Scholar 

  31. Pagarete A, Allen M J, Wilson W H, Kimmance S A, and de Vargas C. 2009. Host-virus shift of the sphingolipid pathway along an Emiliania huxleyi bloom: survival of the fattest. Environ Microbiol, 11: 2840–2848.

    PubMed  Article  CAS  Google Scholar 

  32. Pagarete A, Le Corguille G, Tiwari B, Ogata H, de Vargas C, Wilson W H, and Allen M J. 2011. Unveiling the transcriptional features associated with coccolithovirus infection of natural Emiliania huxleyi blooms. FEMS Microbiol Ecol, 78: 555–564.

    PubMed  Article  CAS  Google Scholar 

  33. Pagarete A, Lanzen A, Puntervoll P, Sandaa R A, Larsen A, Larsen J B, Allen M J, and Bratbak G. 2012. Genomic Sequence and Analysis of EhV-99B1, a New Coccolithovirus from the Norwegian Fjords. Intervirology.

    Google Scholar 

  34. Rowe J M, Fabre M F, Gobena D, Wilson W H, and Wilhelm S W. 2011. Application of the major capsid protein as a marker of the phylogenetic diversity of Emiliania huxleyi viruses. FEMS Microbiol Ecol, 76: 373–380.

    PubMed  Article  CAS  Google Scholar 

  35. Saitou N, and Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol, 4: 406–425.

    PubMed  CAS  Google Scholar 

  36. Schroeder D C, Oke J, Hall M, Malin G, and Wilson W H. 2003. Virus succession observed during an Emiliania huxleyi bloom. Appl Environ Microbiol, 69: 2484–2490.

    PubMed  Article  CAS  Google Scholar 

  37. Schroeder D C, Biggi G F, Hall M, Davy J, Martínez J M, Richardson A J, Malin G, and Wilson W H. 2005. A GENETIC MARKER TO SEPARATE EMILIANIA HUXLEYI (PRYMNESIOPHYCEAE) MORPHOTYPES1. Journal of Phycology, 41: 874–879.

    Article  CAS  Google Scholar 

  38. Suttle C A. 2005. Viruses in the sea. Nature, 437: 356–361.

    PubMed  Article  CAS  Google Scholar 

  39. Suttle C A. 2007. Marine viruses—major players in the global ecosystem. Nat Rev Microbiol, 5: 801–812.

    PubMed  Article  CAS  Google Scholar 

  40. Tamura K, Dudley J, Nei M, and Kumar S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol, 24: 1596–1599.

    PubMed  Article  CAS  Google Scholar 

  41. van Rijssel M, and Gieskes W W C. 2002. Temperature, light, and the dimethylsulfoniopropionate (DMSP) content of Emiliania huxleyi (Prymnesiophyceae). Journal of Sea Research, 48: 17–27.

    Article  Google Scholar 

  42. Vardi A, Van Mooy B A, Fredricks H F, Popendorf K J, Ossolinski J E, Haramaty L, and Bidle K D. 2009. Viral glycosphingolipids induce lytic infection and cell death in marine phytoplankton. Science, 326: 861–865.

    PubMed  Article  CAS  Google Scholar 

  43. Vardi A, Haramaty L, Van Mooy B A, Fredricks H F, Kimmance S A, Larsen A, and Bidle K D. 2012. Host-virus dynamics and subcellular controls of cell fate in a natural coccolithophore population. Proc Natl Acad Sci U S A.

    Google Scholar 

  44. Wilson W H, Tarran G, and Zubkov M V. 2002. Virus dynamics in a coccolithophore-dominated bloom in the North Sea. Deep Sea Research Part II: Topical Studies in Oceanography, 49: 2951–2963.

    Article  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, and Ghazal P. 2005. Complete genome sequence and lytic phase transcription profile of a Coccolithovirus. Science, 309: 1090–1092.

    PubMed  Article  CAS  Google Scholar 

Download references

Author information

Affiliations

Authors

Corresponding author

Correspondence to Michael J. Allen.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Nissimov, J.I., Jones, M., Napier, J.A. et al. Functional inferences of environmental coccolithovirus biodiversity. Virol. Sin. 28, 291–302 (2013). https://doi.org/10.1007/s12250-013-3362-1

Download citation

Keywords

  • Coccolithovirus
  • Major capsid protein
  • Serine palmitoyltransferase
  • Functional biodiversity