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Data from: DNA from soil mirrors plant taxonomic and growth form diversity

Data from: DNA from soil mirrors plant taxonomic and growth form diversity
Data from: DNA from soil mirrors plant taxonomic and growth form diversity
Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call metabarcoding: high-throughput and simultaneous taxa identification based on a very short (usually less than 100 base pairs) but informative DNA fragment. Short DNA fragments allow the use of degraded DNA from environmental samples. All analyses included amplification using plant-specific versatile primers, sequencing and estimation of taxonomic diversity. We tested in three steps whether degraded DNA from dead material in soil has the potential of efficiently assessing biodiversity in different biomes. First, soil DNA from eight boreal plant communities located in two different vegetation types (meadow and heath) was amplified. Plant diversity detected from boreal soil was highly consistent with plant functional and structural diversity estimated from conventional above-ground surveys. Second, we assessed DNA persistence using samples from formerly cultivated soils in temperate environments. We found that number of crop DNA sequences retrieved strongly varied with years since last cultivation, and crop sequences were absent from nearby, uncultivated plots. Third, we assessed the universal applicability of DNA metabarcoding using soil samples from tropical environments: a large proportion of species and families from the study site was efficiently recovered. The results open unprecedented opportunities for large-scale DNA-based biodiversity studies across a range of taxonomic groups using standardized metabarcoding approaches.
Zenodo
Brysting, Anne K.
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Cruaud, Corinne
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Thuiller, Wilfried
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Haile, James
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Taberlet, Pierre
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Wincker, Patrick
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von Stedingk, H.
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Coissac, Eric
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Goslar, Tomasz
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Orlando, Ludovic
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Brathen, Kari-Anne
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Miquel, Christian
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Chave, Jérôme
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Gavory, Frederick
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Valentini, Alice
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Yoccoz, Nigel G.
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Edwards, Mary E.
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Sønstebø, J. H.
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De Bello, Francesco
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Willerslev, Eske
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Brochmann, Christian
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Gilbert, M. Thomas P.
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Pompanon, Francois
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Gielly, Ludovic
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Rasmussen, Morten
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Brysting, Anne K.
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Cruaud, Corinne
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Thuiller, Wilfried
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Haile, James
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Taberlet, Pierre
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Wincker, Patrick
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von Stedingk, H.
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Coissac, Eric
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Goslar, Tomasz
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Orlando, Ludovic
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Brathen, Kari-Anne
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Miquel, Christian
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Chave, Jérôme
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Gavory, Frederick
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Valentini, Alice
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Yoccoz, Nigel G.
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Edwards, Mary E.
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Sønstebø, J. H.
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De Bello, Francesco
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Willerslev, Eske
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Brochmann, Christian
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Gilbert, M. Thomas P.
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Pompanon, Francois
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Gielly, Ludovic
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Rasmussen, Morten
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(2012) Data from: DNA from soil mirrors plant taxonomic and growth form diversity. Zenodo doi:10.5061/dryad.m346b576 [Dataset]

Record type: Dataset

Abstract

Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call metabarcoding: high-throughput and simultaneous taxa identification based on a very short (usually less than 100 base pairs) but informative DNA fragment. Short DNA fragments allow the use of degraded DNA from environmental samples. All analyses included amplification using plant-specific versatile primers, sequencing and estimation of taxonomic diversity. We tested in three steps whether degraded DNA from dead material in soil has the potential of efficiently assessing biodiversity in different biomes. First, soil DNA from eight boreal plant communities located in two different vegetation types (meadow and heath) was amplified. Plant diversity detected from boreal soil was highly consistent with plant functional and structural diversity estimated from conventional above-ground surveys. Second, we assessed DNA persistence using samples from formerly cultivated soils in temperate environments. We found that number of crop DNA sequences retrieved strongly varied with years since last cultivation, and crop sequences were absent from nearby, uncultivated plots. Third, we assessed the universal applicability of DNA metabarcoding using soil samples from tropical environments: a large proportion of species and families from the study site was efficiently recovered. The results open unprecedented opportunities for large-scale DNA-based biodiversity studies across a range of taxonomic groups using standardized metabarcoding approaches.

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More information

Published date: 10 February 2012

Identifiers

Local EPrints ID: 449323
URI: http://eprints.soton.ac.uk/id/eprint/449323
PURE UUID: 6d9d5c0d-214c-4f48-bb3a-59819bfbe13e
ORCID for Mary E. Edwards: ORCID iD orcid.org/0000-0002-3490-6682

Catalogue record

Date deposited: 24 May 2021 16:32
Last modified: 18 May 2023 01:36

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Contributors

Contributor: Anne K. Brysting
Contributor: Corinne Cruaud
Contributor: Wilfried Thuiller
Contributor: James Haile
Contributor: Pierre Taberlet
Contributor: Patrick Wincker
Contributor: H. von Stedingk
Contributor: Eric Coissac
Contributor: Tomasz Goslar
Contributor: Ludovic Orlando
Contributor: Kari-Anne Brathen
Contributor: Christian Miquel
Contributor: Jérôme Chave
Contributor: Frederick Gavory
Contributor: Alice Valentini
Contributor: Nigel G. Yoccoz
Contributor: Mary E. Edwards ORCID iD
Contributor: J. H. Sønstebø
Contributor: Francesco De Bello
Contributor: Eske Willerslev
Contributor: Christian Brochmann
Contributor: M. Thomas P. Gilbert
Contributor: Francois Pompanon
Contributor: Ludovic Gielly
Contributor: Morten Rasmussen

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