Article

Fungal Diversity

, Volume 49, Issue 1, pp 113-123

First online:

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

  • Guillaume LentenduAffiliated withLaboratoire d’Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, Grenoble 1Department Soil Ecology, UFZ—Helmholtz Centre for Environmental Research
  • , Lucie ZingerAffiliated withLaboratoire d’Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, Grenoble 1Max Plank Institute for Marine Microbiology
  • , Stéphanie ManelAffiliated withLaboratoire d’Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, Grenoble 1Laboratoire Population Environnement Développement, UMR 151 UP/IRD, Université de ProvenceLaboratoire d’Ecologie Alpine, CNRS UMR 5553, Université de Grenoble
  • , Eric CoissacAffiliated withLaboratoire d’Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, Grenoble 1
  • , Philippe CholerAffiliated withLaboratoire d’Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, Grenoble 1Station Alpine J. Fourier, Grenoble Univ, CNRS UMS 2925
  • , Roberto A. GeremiaAffiliated withLaboratoire d’Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, Grenoble 1 Email author 
  • , Christelle MelodelimaAffiliated withLaboratoire d’Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, Grenoble 1

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Abstract

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.

Keywords

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