Abstract
Viruses are the most abundant biological entities in the sea. Infecting marine organisms from oxygen-producing phytoplankton to whales, viruses regulate the populations of many marine organisms and play important roles in global biogeochemical fluxes. Thanks to the recent improvement of sequencing technology, billions of bases of sequences from marine microbial communities are being determined by different groups of researchers.
Those environmental sequence data, or “metagenomes,” now provide unprecedented opportunities to reconstruct and characterize the composition and the dynamics of mostly unculturable microorganisms in different habitats.
We recently developed a new computational method called phylogenetic mapping to obtain a comprehensive picture of the distributions of microorganisms contained in environmental samples. We used our method to investigate the distributions of large DNA viruses represented in the Sorcerer II Global Ocean Sampling Expedition microbial metagenomic data set. Using DNA polymerase genes as a taxonomic marker, we identified 811 homologous sequences of likely viral origins. Most of these sequences corresponded to phages, being consistent with the large number of phage-like particles in marine environments. Interestingly, the second largest viral group corresponded to the one containing mimivirus, the largest known virus (with 1.2 Mb-genome), which infects amoeba. Albeit only recently discovered, giant viruses of the mimivirus family appear to constitute a diverse, quantitatively important, and geographically ubiquitous component of the population of large eukaryotic DNA viruses in the sea. We also identified several DNA polymerase homologs closely related to African swine fever virus, a large virus pathogenic to domestic animals and until now limited to terrestrial animal hosts.
Finally, our approach allowed the identification of a new combination of genes in viral-like sequences. In conclusion, high throughput metagenomics is becoming a technique of choice to follow the changes of marine microbial environments induced by climatic changes and/or human activities.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Abergel C, Rudinger-Thirion J, Giege R, Claverie JM (2007) Virus-encoded aminoacyl-tRNA synthetases: structural and functional characterization of mimivirus TyrRS and MetRS. J Virol 81:12406–12417
Claverie JM (2006) Viruses take center stage in cellular evolution. Genome Biol 7:110
Claverie JM, Ogata H, Audic S, Abergel C, Suhre K, Fournier PE (2006) Mimivirus and the emerging concept of “giant” virus. Virus Res 117:133–144
Edwards RA, Rohwer F (2005) Viral metagenomics. Nat Rev Microbiol 3:504–510
Ghedin E, Claverie JM (2005) Mimivirus relatives in the Sargasso sea. Virol J 2:62
La Scola B, Audic S, Robert C, Jungang L, de Lamballerie X, Drancourt M, Birtles R, Claverie JM, Raoult D (2003) A giant virus in amoebae. Science 299:2033
La Scola B, Desnues C, Pagnier I, Robert C, Barrassi L, Fournous G, Merchat M, Suzan-Monti M, Forterre P, Koonin E, Raoult D (2008) The virophage as a unique parasite of the giant mimivirus. Nature 455:100–104
Monier A, Claverie JM, Ogata H (2008a) Taxonomic distribution of large DNA viruses in the sea. Genome Biol 9:R106
Monier A, Larsen JB, Sandaa RA, Bratbak G, Claverie JM, Ogata H (2008b) Marine mimivirus relatives are probably large algal viruses. Virol J 5:12
Ogata H, Claverie JM (2007) Unique genes in giant viruses: regular substitution pattern and anomalously short size. Genome Res 17:1353–1361
Ogata H, Claverie JM (2008) Microbiology. How to infect a Mimivirus. Science 321:1305–1306
Patel A, Noble RT, Steele JA, Schwalbach MS, Hewson I, Fuhrman JA (2007) Virus and prokaryote enumeration from planktonic aquatic environments by epifluorescence microscopy with SYBR Green I. Nat Protoc 2:269–276
Raoult D, Audic S, Robert C, Abergel C, Renesto P, Ogata H, La Scola B, Suzan M, Claverie JM (2004) The 1.2-megabase genome sequence of Mimivirus. Science 306:1344–1350
Renesto P, Abergel C, Decloquement P, Moinier D, Azza S, Ogata H, Fourquet P, Gorvel JP, Claverie JM (2006) Mimivirus giant particles incorporate a large fraction of anonymous and unique gene products. J Virol 80:11678–11685
Rohwer F (2003) Global phage diversity. Cell 113:141
Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcon LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, Platt T, Bermingham E, Gallardo V, Tamayo-Castillo G, Ferrari MR, Strausberg RL, Nealson K, Friedman R, Frazier M, Venter JC (2007) The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 5:e77
Suttle CA (2005) Viruses in the sea. Nature 437:356–361
Suzan-Monti M, La Scola B, Barrassi L, Espinosa L, Raoult D (2007) Ultrastructural characterization of the giant volcano-like virus factory of Acanthamoeba polyphaga Mimivirus. PLoS ONE 2:e328
Zauberman N, Mutsafi Y, Halevy DB, Shimoni E, Klein E, Xiao C, Sun S, Minsky A (2008) Distinct DNA exit and packaging portals in the virus Acanthamoeba polyphaga mimivirus. PLoS Biol 6:e114
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer Science+Business Media B.V.
About this paper
Cite this paper
Ogata, H., Monier, A., Claverie, JM. (2010). Distribution of Giant Viruses in Marine Environments. In: Ceccaldi, HJ., Dekeyser, I., Girault, M., Stora, G. (eds) Global Change: Mankind-Marine Environment Interactions. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-8630-3_28
Download citation
DOI: https://doi.org/10.1007/978-90-481-8630-3_28
Published:
Publisher Name: Springer, Dordrecht
Print ISBN: 978-90-481-8629-7
Online ISBN: 978-90-481-8630-3
eBook Packages: Earth and Environmental ScienceEarth and Environmental Science (R0)