title: 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity.
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.
authors.affiliation: INRA, UMR 1136 INRA/Nancy Université Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France.
authors.forename: M
authors.initials: M
authors.lastname: Buée
authors.affiliation: INRA, UMR 1136 INRA/Nancy Université Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France.
authors.forename: M
authors.initials: M
authors.lastname: Reich
authors.affiliation: INRA, UMR 1136 INRA/Nancy Université Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France.
authors.forename: C
authors.initials: C
authors.lastname: Murat
authors.affiliation: INRA, UMR 1136 INRA/Nancy Université Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France.
authors.forename: E
authors.initials: E
authors.lastname: Morin
authors.affiliation: Department of Plant and Environmental Sciences, University of Gothenborg, Box 461, 405 30 Gothenborg, Sweden.
authors.forename: R H
authors.initials: RH
authors.lastname: Nilsson
authors.affiliation: INRA, UMR 1136 INRA/Nancy Université Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France.
authors.forename: S
authors.initials: S
authors.lastname: Uroz
authors.affiliation: INRA, UMR 1136 INRA/Nancy Université Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France.
authors.forename: F
authors.initials: F
authors.lastname: Martin
mesh_terms: D001483:Base Sequence; D044822:Biodiversity; D004271:DNA, Fungal; D021903:DNA, Ribosomal Spacer; D017753:Ecosystem; D005658:Fungi / Q000145:classification* / Q000235:genetics; D005800:Genes, Fungal; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods; D012987:Soil; D012988:Soil Microbiology; D013045:Species Specificity; D014197:Trees
chemical_list: D004271:DNA, Fungal; D021903:DNA, Ribosomal Spacer; D012987:Soil
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