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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Data Archiving and Networked Services (DANS)
2012
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Online Access: | https://doi.org/10.5061/dryad.m346b576 |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::58cd44deacc2ae17398b800b88eb1215 2023-05-15T17:43:35+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 2012-01-01 https://doi.org/10.5061/dryad.m346b576 undefined unknown Data Archiving and Networked Services (DANS) http://dx.doi.org/10.5061/dryad.m346b576 https://dx.doi.org/10.5061/dryad.m346b576 lic_creative-commons oai:easy.dans.knaw.nl:easy-dataset:81511 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:81511 10.5061/dryad.m346b576 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 re3data_____::r3d100000044 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c Life sciences medicine and health care plant diversity functional diversity biodiversity assessment Environmental sequencing DNA metabarcoding Angiosperms Northern Norway French Alps French Guiana envir geo Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2012 fttriple https://doi.org/10.5061/dryad.m346b576 2023-01-22T16:52:41Z 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. Yoccoz_et_al_Table_S1Supplementary Table with description of the results obtained for the Boreal site.Yoccoz_et_al_Table_S2Supplementary Table showing the results obtained for the Tropical site.Boreal_sequence_datafasta file.Tropical_sequence_dataFasta file.Temperate_sequence_dataFasta ... Dataset Northern Norway Unknown Norway |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
Life sciences medicine and health care plant diversity functional diversity biodiversity assessment Environmental sequencing DNA metabarcoding Angiosperms Northern Norway French Alps French Guiana envir geo |
spellingShingle |
Life sciences medicine and health care plant diversity functional diversity biodiversity assessment Environmental sequencing DNA metabarcoding Angiosperms Northern Norway French Alps French Guiana envir geo 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 |
Life sciences medicine and health care plant diversity functional diversity biodiversity assessment Environmental sequencing DNA metabarcoding Angiosperms Northern Norway French Alps French Guiana envir geo |
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. Yoccoz_et_al_Table_S1Supplementary Table with description of the results obtained for the Boreal site.Yoccoz_et_al_Table_S2Supplementary Table showing the results obtained for the Tropical site.Boreal_sequence_datafasta file.Tropical_sequence_dataFasta file.Temperate_sequence_dataFasta ... |
format |
Dataset |
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 |
publisher |
Data Archiving and Networked Services (DANS) |
publishDate |
2012 |
url |
https://doi.org/10.5061/dryad.m346b576 |
geographic |
Norway |
geographic_facet |
Norway |
genre |
Northern Norway |
genre_facet |
Northern Norway |
op_source |
oai:easy.dans.knaw.nl:easy-dataset:81511 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:81511 10.5061/dryad.m346b576 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 re3data_____::r3d100000044 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c |
op_relation |
http://dx.doi.org/10.5061/dryad.m346b576 https://dx.doi.org/10.5061/dryad.m346b576 |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.m346b576 |
_version_ |
1766145701948948480 |