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PMID: 19703112 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity.

The New phytologist ·Vol. 184 ·No. 2 ·2009-10-00 ·Pages 449-456

Buée M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S, Martin F

Abstract

* Soil fungi play a major role in ecological and biogeochemical processes in forests. Little is known, however, about the structure and richness of different fungal communities and the distribution of functional ecological groups (pathogens, saprobes and symbionts). * Here, we assessed the fungal diversity in six different forest soils using tag-encoded 454 pyrosequencing of the nuclear ribosomal internal transcribed spacer-1 (ITS-1). No less than 166 350 ITS reads were obtained from all samples. In each forest soil sample (4 g), approximately 30 000 reads were recovered, corresponding to around 1000 molecular operational taxonomic units. * Most operational taxonomic units (81%) belonged to the Dikarya subkingdom (Ascomycota and Basidiomycota). Richness, abundance and taxonomic analyses identified the Agaricomycetes as the dominant fungal class. The ITS-1 sequences (73%) analysed corresponded to only 26 taxa. The most abundant operational taxonomic units showed the highest sequence similarity to Ceratobasidium sp., Cryptococcus podzolicus, Lactarius sp. and Scleroderma sp. * This study validates the effectiveness of high-throughput 454 sequencing technology for the survey of soil fungal diversity. The large proportion of unidentified sequences, however, calls for curated sequence databases. The use of pyrosequencing on soil samples will accelerate the study of the spatiotemporal dynamics of fungal communities in forest ecosystems.

MeSH Terms
Base Sequence Biodiversity DNA, Fungal DNA, Ribosomal Spacer Ecosystem Fungi/classification,genetics Genes, Fungal Polymerase Chain Reaction Sequence Analysis, DNA/methods Soil Soil Microbiology Species Specificity Trees
Chemicals
DNA, Fungal DNA, Ribosomal Spacer Soil
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Buée M
INRA, UMR 1136 INRA/Nancy Université Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France.
Reich M
INRA, UMR 1136 INRA/Nancy Université Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France.
Murat C
INRA, UMR 1136 INRA/Nancy Université Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France.
Morin E
INRA, UMR 1136 INRA/Nancy Université Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France.
Nilsson R H
Department of Plant and Environmental Sciences, University of Gothenborg, Box 461, 405 30 Gothenborg, Sweden.
Uroz S
INRA, UMR 1136 INRA/Nancy Université Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France.
Martin F
INRA, UMR 1136 INRA/Nancy Université Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France.
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Article Info
Journal
The New phytologist
Abbr.
New Phytol
ISSN
1469-8137
DOI
10.1111/j.1469-8137.2009.03003.x
Published
2009-10-00
Epub
2009-00-22
Pages
449-456
Language
English
Region
England
NLM ID
9882884
Subset
IM
Corrections
CommentIn
PMID: 19796334
External Links
PubMed source DOI: 10.1111/j.1469-8137.2009.03003.x View journal details
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