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 metabarcod...
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ftdryad:oai:v1.datadryad.org:10255/dryad.37742 2023-05-15T17:43:33+02:00 Data from: DNA from soil mirrors plant taxonomic and growth form diversity Yoccoz, Nigel G. Brathen, Kari-Anne Gielly, Ludovic Haile, James Edwards, Mary E. Goslar, Tomasz von Stedingk, H. Brysting, Anne K. Coissac, Eric Pompanon, Francois Sønstebø, J. H. Miquel, Christian Valentini, Alice De Bello, Francesco Chave, Jérôme Thuiller, Wilfried Wincker, Patrick Cruaud, Corinne Gavory, Frederick Rasmussen, Morten Gilbert, M. Thomas P. Orlando, Ludovic Brochmann, Christian Willerslev, Eske Taberlet, Pierre Northern Norway French Alps French Guiana 2012-02-10T16:48:57Z http://hdl.handle.net/10255/dryad.37742 https://doi.org/10.5061/dryad.m346b576 unknown doi:10.5061/dryad.m346b576/1 doi:10.5061/dryad.m346b576/2 doi:10.5061/dryad.m346b576/3 doi:10.5061/dryad.m346b576/4 doi:10.5061/dryad.m346b576/5 doi:10.5061/dryad.m346b576/6 doi:10.1111/j.1365-294X.2012.05545.x PMID:22507540 doi:10.5061/dryad.m346b576 Yoccoz NG, Brathen K, Gielly L, Haile J, Edwards ME, Goslar T, von Stedingk H, Brysting AK, Coissac E, Pompanon F, Sønstebø JH, Miquel C, Valentini A, De Bello F, Chave J, Thuiller W, Wincker P, Cruaud C, Gavory F, Rasmussen M, Gilbert MTP, Orlando L, Brochmann C, Willerslev E, Taberlet P (2012) DNA from soil mirrors plant taxonomic and growth form diversity. Molecular Ecology 21(15): 3647-3655. http://hdl.handle.net/10255/dryad.37742 environmental sequencing DNA metabarcoding plant diversity functional diversity biodiversity assessment Article 2012 ftdryad https://doi.org/10.5061/dryad.m346b576 https://doi.org/10.5061/dryad.m346b576/1 https://doi.org/10.5061/dryad.m346b576/2 https://doi.org/10.5061/dryad.m346b576/3 https://doi.org/10.5061/dryad.m346b576/4 https://doi.org/10.5061/dryad.m346b576/5 ; 2020-01-01T14:55:37Z 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. Article in Journal/Newspaper Northern Norway Dryad Digital Repository (Duke University) Norway |
institution |
Open Polar |
collection |
Dryad Digital Repository (Duke University) |
op_collection_id |
ftdryad |
language |
unknown |
topic |
environmental sequencing DNA metabarcoding plant diversity functional diversity biodiversity assessment |
spellingShingle |
environmental sequencing DNA metabarcoding plant diversity functional diversity biodiversity assessment Yoccoz, Nigel G. Brathen, Kari-Anne Gielly, Ludovic Haile, James Edwards, Mary E. Goslar, Tomasz von Stedingk, H. Brysting, Anne K. Coissac, Eric Pompanon, Francois Sønstebø, J. H. Miquel, Christian Valentini, Alice De Bello, Francesco Chave, Jérôme Thuiller, Wilfried Wincker, Patrick Cruaud, Corinne Gavory, Frederick Rasmussen, Morten Gilbert, M. Thomas P. Orlando, Ludovic Brochmann, Christian Willerslev, Eske Taberlet, Pierre Data from: DNA from soil mirrors plant taxonomic and growth form diversity |
topic_facet |
environmental sequencing DNA metabarcoding plant diversity functional diversity biodiversity assessment |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Yoccoz, Nigel G. Brathen, Kari-Anne Gielly, Ludovic Haile, James Edwards, Mary E. Goslar, Tomasz von Stedingk, H. Brysting, Anne K. Coissac, Eric Pompanon, Francois Sønstebø, J. H. Miquel, Christian Valentini, Alice De Bello, Francesco Chave, Jérôme Thuiller, Wilfried Wincker, Patrick Cruaud, Corinne Gavory, Frederick Rasmussen, Morten Gilbert, M. Thomas P. Orlando, Ludovic Brochmann, Christian Willerslev, Eske Taberlet, Pierre |
author_facet |
Yoccoz, Nigel G. Brathen, Kari-Anne Gielly, Ludovic Haile, James Edwards, Mary E. Goslar, Tomasz von Stedingk, H. Brysting, Anne K. Coissac, Eric Pompanon, Francois Sønstebø, J. H. Miquel, Christian Valentini, Alice De Bello, Francesco Chave, Jérôme Thuiller, Wilfried Wincker, Patrick Cruaud, Corinne Gavory, Frederick Rasmussen, Morten Gilbert, M. Thomas P. Orlando, Ludovic Brochmann, Christian Willerslev, Eske Taberlet, Pierre |
author_sort |
Yoccoz, Nigel G. |
title |
Data from: DNA from soil mirrors plant taxonomic and growth form diversity |
title_short |
Data from: DNA from soil mirrors plant taxonomic and growth form diversity |
title_full |
Data from: DNA from soil mirrors plant taxonomic and growth form diversity |
title_fullStr |
Data from: DNA from soil mirrors plant taxonomic and growth form diversity |
title_full_unstemmed |
Data from: DNA from soil mirrors plant taxonomic and growth form diversity |
title_sort |
data from: dna from soil mirrors plant taxonomic and growth form diversity |
publishDate |
2012 |
url |
http://hdl.handle.net/10255/dryad.37742 https://doi.org/10.5061/dryad.m346b576 |
op_coverage |
Northern Norway French Alps French Guiana |
geographic |
Norway |
geographic_facet |
Norway |
genre |
Northern Norway |
genre_facet |
Northern Norway |
op_relation |
doi:10.5061/dryad.m346b576/1 doi:10.5061/dryad.m346b576/2 doi:10.5061/dryad.m346b576/3 doi:10.5061/dryad.m346b576/4 doi:10.5061/dryad.m346b576/5 doi:10.5061/dryad.m346b576/6 doi:10.1111/j.1365-294X.2012.05545.x PMID:22507540 doi:10.5061/dryad.m346b576 Yoccoz NG, Brathen K, Gielly L, Haile J, Edwards ME, Goslar T, von Stedingk H, Brysting AK, Coissac E, Pompanon F, Sønstebø JH, Miquel C, Valentini A, De Bello F, Chave J, Thuiller W, Wincker P, Cruaud C, Gavory F, Rasmussen M, Gilbert MTP, Orlando L, Brochmann C, Willerslev E, Taberlet P (2012) DNA from soil mirrors plant taxonomic and growth form diversity. Molecular Ecology 21(15): 3647-3655. http://hdl.handle.net/10255/dryad.37742 |
op_doi |
https://doi.org/10.5061/dryad.m346b576 https://doi.org/10.5061/dryad.m346b576/1 https://doi.org/10.5061/dryad.m346b576/2 https://doi.org/10.5061/dryad.m346b576/3 https://doi.org/10.5061/dryad.m346b576/4 https://doi.org/10.5061/dryad.m346b576/5 ; |
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