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

The New phytologist, 2009-10, Vol.184 (2), p.449-456 [Peer Reviewed Journal]

Copyright 2009 New Phytologist ;The Authors (2009). Journal compilation © New Phytologist (2009) ;Distributed under a Creative Commons Attribution 4.0 International License ;ISSN: 0028-646X ;EISSN: 1469-8137 ;DOI: 10.1111/j.1469-8137.2009.03003.x ;PMID: 19703112

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Title:
454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity
Author: Buée, M. ; Reich, M. ; Murat, C. ; Morin, E. ; Nilsson, R. H. ; Uroz, S. ; Martin, F.
Subjects: 454 pyrosequencing ; Annan industriell bioteknik ; Ascomycota ; Base Sequence ; Biochemistry and Molecular Biology ; Biodiversity ; Bioinformatics and Systems Biology ; Bioinformatik och systembiologi ; Biokemi och molekylärbiologi ; Biological Sciences ; Biological Systematics ; Biological taxonomies ; Biologisk systematik ; Biologiska vetenskaper ; community structure ; Cryptococcus ; DNA, Fungal ; DNA, Ribosomal Spacer ; Ecology ; Ecosystem ; ectomycorrhizal fungi ; Ekologi ; environmental samples ; Forest soils ; fungal diversity ; Fungi ; Fungi - classification ; Fungi - genetics ; Genes, Fungal ; Internal transcribed spacers ; Lactarius ; Life Sciences ; Mycology ; nuclear ribosomal internal transcribed spacers ; Other Industrial Biotechnology ; Phytopathology and phytopharmacy ; Plantations ; Polymerase Chain Reaction ; Sequence Analysis, DNA - methods ; Sequencing ; Soil ; Soil fungi ; Soil Microbiology ; Soil samples ; Species Specificity ; Trees ; Vegetal Biology
Is Part Of: The New phytologist, 2009-10, Vol.184 (2), p.449-456
Description: 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.
Publisher: Oxford, UK: Oxford, UK : Blackwell Publishing Ltd
Language: English
Identifier: ISSN: 0028-646X
EISSN: 1469-8137
DOI: 10.1111/j.1469-8137.2009.03003.x
PMID: 19703112
Source: IngentaConnect Free/Open Access Journals
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454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity

Copyright 2009 New Phytologist ;The Authors (2009). Journal compilation © New Phytologist (2009) ;Distributed under a Creative Commons Attribution 4.0 International License ;ISSN: 0028-646X ;EISSN: 1469-8137 ;DOI: 10.1111/j.1469-8137.2009.03003.x ;PMID: 19703112

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