Fungal Diversity

, Volume 49, Issue 1, pp 113–123 | Cite as

Assessment of soil fungal diversity in different alpine tundra habitats by means of pyrosequencing

  • Guillaume Lentendu
  • Lucie Zinger
  • Stéphanie Manel
  • Eric Coissac
  • Philippe Choler
  • Roberto A. Geremia
  • Christelle Melodelima


Studying fungal diversity is vital if we want to shed light on terrestrial ecosystem functioning. However, there is still poor understanding of fungal diversity and variation given that Fungi are highly diversified and that most of fungal species remain uncultured. In this study we explored diversity with 454 FLX sequencing technology by using the Internal Transcribed Spacer 1 (ITS1) as the fungal barcode marker in order to evaluate the effect of 11 environmental conditions on alpine soil fungal diversity, as well as the consistency of those results by taking into account rare or unidentified Molecular Operational Taxonomic Units (MOTUs). In total we obtained 205131 ITS1 reads corresponding to an estimated fungal gamma diversity of between 5100 and 12 000 MOTUs at a 98% similarity threshold when considering respectively only identified fungal and all MOTUs. Fungal beta-diversity patterns were significantly explained by the environmental conditions, and were very consistent for abundant/rare and fungal/unidentified MOTUs confirming the ecological significance of rare/unidentified MOTUs, and therefore the existence of a fungal rare biosphere. This study shows that a beta-diversity estimation based on pyrosequencing is robust enough to support ecological studies. Additionally, our results suggest that rare MOTUs harbour ecological information. Thus the fungal rare biosphere may be important for ecosystem dynamics and resilience.


Multiple-tag parallel pyrosequencing Fungal communities MOTUs Rare biosphere Alpine tundra Landscape 



This research was conducted on the long-term research site Zone Atelier Alpes, a member of the ILTER-Europe network. We thank David Lejon for his help in the lab work, Armelle Monier for technical assistance, Serge Aubert and the staff of Station Alpine J. Fourier for providing logistics facilities during the field-work and two anonymous reviewers for comments on earlier version of the manuscript. This work was funded by the ANR-06-BLAN-0301 “Microalpes” and the “CNRS Programme Ingénierie Ecologique” funded in 2008.

Supplementary material

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Copyright information

© Kevin D. Hyde 2011

Authors and Affiliations

  • Guillaume Lentendu
    • 1
    • 4
  • Lucie Zinger
    • 1
    • 5
  • Stéphanie Manel
    • 1
    • 2
    • 6
  • Eric Coissac
    • 1
  • Philippe Choler
    • 1
    • 3
  • Roberto A. Geremia
    • 1
  • Christelle Melodelima
    • 1
  1. 1.Laboratoire d’Ecologie Alpine, CNRS UMR 5553Université Joseph Fourier, Grenoble 1Grenoble Cedex 09France
  2. 2.Laboratoire Population Environnement Développement, UMR 151 UP/IRDUniversité de ProvenceMarseille Cedex 03France
  3. 3.Station Alpine J. FourierGrenoble Univ, CNRS UMS 2925Grenoble Cedex 9France
  4. 4.Department Soil EcologyUFZ—Helmholtz Centre for Environmental ResearchHalle/SaaleGermany
  5. 5.Max Plank Institute for Marine MicrobiologyBremenGermany
  6. 6.Laboratoire d’Ecologie Alpine, CNRS UMR 5553Université de GrenobleGrenoble Cedex 09France

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