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Archives of Virology

, Volume 162, Issue 6, pp 1671–1676 | Cite as

The “Giant Virus Finder” discovers an abundance of giant viruses in the Antarctic dry valleys

Original Article

Abstract

Mimivirus was identified in 2003 from a biofilm of an industrial water-cooling tower in England. Later, numerous new giant viruses were found in oceans and freshwater habitats, some of them having 2,500 genes. We have demonstrated their likely presence in four soil samples taken from the Kutch Desert (Gujarat, India). Here we describe a bioinformatics work-flow, called the “Giant Virus Finder” that is capable of discovering the likely presence of the genomes of giant viruses in metagenomic shotgun-sequenced datasets. The new workflow is applied to numerous hot and cold desert soil samples as well as some tundra- and forest soils. We show that most of these samples contain giant viruses, especially in the Antarctic dry valleys. The results imply that giant viruses could be frequent not only in aqueous habitats, but in a wide spectrum of soils on our planet.

Keywords

Mojave Desert Word Size Metagenomic Dataset Metagenomic Sample Giant Virus 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Compliance with ethical standards

Conflict of interest

C. Kerepesi and V. Grolmusz declare no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

705_2017_3286_MOESM1_ESM.docx (68 kb)
Supplementary material 1 (DOCX 68 kb)

References

  1. 1.
    Altschul SF, Wootton JC, Gertz EM, Agarwala R, Morgulis A, Schaffer AA, Yu Y-K (2005) Protein database searches using compositionally adjusted substitution matrices. FEBS J 272(20):5101–5109CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Boyer M, Yutin N, Pagnier I, Barrassi L, Fournous G, Espinosa L, Robert C, Azza S, Sun S, Rossmann MG, Suzan-Monti M, La Scola B, Koonin EV, Raoult D (2009) Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms. Proc Natl Acad Sci USA 106(51):21848–21853CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Claverie J-M, Ogata H, Audic S, Abergel C, Suhre K, Fournier P-E (2006) Mimivirus and the emerging concept of “giant” virus. Virus research 117(1):133–144CrossRefPubMedGoogle Scholar
  4. 4.
    Colson P, Gimenez G, Boyer M, Fournous G, Raoult D (2011) The giant cafeteria roenbergensis virus that infects a widespread marine phagocytic protist is a new member of the fourth domain of life. PLoS One 6(4):e18935CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Colson P, de Lamballerie X, Fournous G, Raoult D (2011) Reclassification of giant viruses composing a fourth domain of life in the new order megavirales. Intervirology 55(5):321–332CrossRefGoogle Scholar
  6. 6.
    Colson P, Yutin N, Shabalina SA, Robert C, Fournous G, Scola BL, Raoult D, Koonin EV (2011) Viruses with more than 1,000 genes: Mamavirus, a new Acanthamoeba polyphaga mimivirus strain, and reannotation of Mimivirus genes. Genome Biol Evol 3:737–742CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Desnues C, La Scola B, Yutin N, Fournous G, Robert C, Azza S, Jardot P, Monteil S, Campocasso A, Koonin EV et al (2012) Provirophages and transpovirons as the diverse mobilome of giant viruses. Proceed Nat Acad Sci 109(44):18078–18083CrossRefGoogle Scholar
  8. 8.
    Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, Lauber CL, Owens S, Gilbert JA, Wall DH, Caporaso JG (2012) Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci USA 109(52):21390–21395CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Fischer MG, Suttle CA (2011) A virophage at the origin of large DNA transposons. Science 332(6026):231–234CrossRefPubMedGoogle Scholar
  10. 10.
    Fischer MG, Allen MJ, Wilson WH, Suttle CA (2010) Giant virus with a remarkable complement of genes infects marine zooplankton. Proc Natl Acad Sci USA 107(45):19508–19513CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Garza DR, Suttle CA (1995) Large double-stranded DNA viruses which cause the lysis of a marine heterotrophic nanoflagellate (bodo sp.) occur in natural marine viral communities. Aquat Microb Ecol 9(3):203–210CrossRefGoogle Scholar
  12. 12.
    Huson DH, Mitra S, Ruscheweyh H-J, Weber N, Schuster SC (2011) Integrative analysis of environmental sequences using MEGAN4. Genome Res 21(9):1552–1560CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Jachiet P-A, Colson P, Lopez P, Bapteste E (2014) Extensive gene remodeling in the viral world: new evidence for nongradual evolution in the mobilome network. Genom Biol Evol 6(9):2195–2205CrossRefGoogle Scholar
  14. 14.
    Kerepesi C, Grolmusz V (2016) Giant viruses of the Kutch desert. Arch Virol 161(3):721–724CrossRefPubMedGoogle Scholar
  15. 15.
    Pandit AS, Joshi MN, Bhargava P, Ayachit GN, Shaikh IM, Saiyed ZM, Saxena AK, Bagatharia SB (2014) Metagenomes from the saline desert of Kutch. Genome Announc 2(3):e00439-14CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Philippe N, Legendre M, Doutre G, Couté Y, Poirot O, Lescot M, Arslan D, Seltzer V, Bertaux L, Bruley C, Garin J, Claverie J-M, Abergel C (2013) Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes. Science 341(6143):281–286CrossRefPubMedGoogle Scholar
  17. 17.
    Raoult D, Audic S, Robert C, Abergel C, Renesto P, Ogata H, Scola BL, Suzan M, Claverie J-M (2004) The 1.2-megabase genome sequence of Mimivirus. Science 306(5700):1344–1350CrossRefPubMedGoogle Scholar
  18. 18.
    Wilhelm SW, Coy SR, Gann ER, Moniruzzaman M, Stough JMA (2016) Standing on the shoulders of giant viruses: Five lessons learned about large viruses infecting small eukaryotes and the opportunities they create. PLoS Pathogens 12:e1005752CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Williams TA, Embley TM, Heinz E (2011) Informational gene phylogenies do not support a fourth domain of life for nucleocytoplasmic large DNA viruses. PLoS One 6(6):e21080CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Yau S, Lauro FM, DeMaere MZ, Brown MV, Thomas T, Raftery MJ, Andrews-Pfannkoch C, Lewis M, Hoffman JM, Gibson JA, Cavicchioli R (2011) Virophage control of antarctic algal host-virus dynamics. Proc Natl Acad Sci USA 108(15):6163–6168CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Yutin N, Wolf YI, Koonin EV (2014) Origin of giant viruses from smaller DNA viruses not from a fourth domain of cellular life. Virology 466–467:38–52CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Wien 2017

Authors and Affiliations

  1. 1.PIT Bioinformatics GroupEötvös UniversityBudapestHungary
  2. 2.Uratim Ltd.BudapestHungary
  3. 3.Institute for Computer Science and ControlHungarian Academy of SciencesBudapestHungary

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