Data from: New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems
Metabarcoding approaches use total and typically degraded DNA from environmental samples to analyse biotic assemblages and can potentially be carried out for any kinds of organisms in an ecosystem. These analyses rely on specific markers, here called metabarcodes, which should be optimized for taxon...
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Dryad
2020
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Online Access: | https://doi.org/10.5061/dryad.37s6bb42 |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::8fc1fa73aff38d1f35f697b1b78651bd 2023-05-15T15:16:02+02:00 Data from: New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems Epp, Laura S. Boessenkool, Sanne Bellemain, Eva P. Haile, James Esposito, Alfonso Riaz, Tiayyba Erséus, Christer Gusarov, Vladimir I. Edwards, Mary E. Johnsen, Arild Stenøien, Hans K. Hassel, Kristian Kauserud, Håvard Yoccoz, Nigel G. Bråthen, Kari Anne Willerslev, Eske Taberlet, Pierre Coissac, Eric Brochmann, Christian 2020-07-05 https://doi.org/10.5061/dryad.37s6bb42 en eng Dryad http://dx.doi.org/10.5061/dryad.37s6bb42 https://dx.doi.org/10.5061/dryad.37s6bb42 lic_creative-commons 10.5061/dryad.37s6bb42 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:81630 oai:easy.dans.knaw.nl:easy-dataset:81630 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 re3data_____::r3d100000044 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c Fungi Metabarcoding Environmental DNA Coleoptera Enchytraeidae Bryophyta ancient DNA Aves primers Holocene Pleistocene Life sciences medicine and health care Arctic envir geo Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2020 fttriple https://doi.org/10.5061/dryad.37s6bb42 2023-01-22T16:53:33Z Metabarcoding approaches use total and typically degraded DNA from environmental samples to analyse biotic assemblages and can potentially be carried out for any kinds of organisms in an ecosystem. These analyses rely on specific markers, here called metabarcodes, which should be optimized for taxonomic resolution, minimal bias in amplification of the target organism group and short sequence length. Using bioinformatic tools, we developed metabarcodes for several groups of organisms: fungi, bryophytes, enchytraeids, beetles and birds. The ability of these metabarcodes to amplify the target groups was systematically evaluated by (1) in silico PCRs using all standard sequences in the EMBL public database as templates, (2) in vitro PCRs of DNA extracts from surface soil samples from a site in Varanger, northern Norway, and (3) in vitro PCRs of DNA extracts from permanently frozen sediment samples of late-Pleistocene age (~ 16 000–50 000 yr BP) from two Siberian sites, Duvanny Yar and Main River. Comparison of the results from the in silico PCR with those obtained in vitro showed that the in silico approach offered a reliable estimate of the suitability of a marker. All target groups were detected in the environmental DNA, but we found large variation in the level of detection among the groups and between modern and ancient samples. Success rates for the Pleistocene samples were highest for fungal DNA, whereas bryophyte, beetle and bird sequences could also be retrieved, but to a much lesser degree. The metabarcoding approach has considerable potential for biodiversity screening of modern samples and also as a paleoecological tool. Epp_etal_metabarcodes_dryadThis file contains all consensus sequences retrieved from clones of environmental samples and referred to in Table S6 of the Supplementary material. Dataset Arctic Northern Norway Varanger Unknown Arctic Norway Yar ENVELOPE(151.300,151.300,70.917,70.917) |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
English |
topic |
Fungi Metabarcoding Environmental DNA Coleoptera Enchytraeidae Bryophyta ancient DNA Aves primers Holocene Pleistocene Life sciences medicine and health care Arctic envir geo |
spellingShingle |
Fungi Metabarcoding Environmental DNA Coleoptera Enchytraeidae Bryophyta ancient DNA Aves primers Holocene Pleistocene Life sciences medicine and health care Arctic envir geo Epp, Laura S. Boessenkool, Sanne Bellemain, Eva P. Haile, James Esposito, Alfonso Riaz, Tiayyba Erséus, Christer Gusarov, Vladimir I. Edwards, Mary E. Johnsen, Arild Stenøien, Hans K. Hassel, Kristian Kauserud, Håvard Yoccoz, Nigel G. Bråthen, Kari Anne Willerslev, Eske Taberlet, Pierre Coissac, Eric Brochmann, Christian Data from: New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems |
topic_facet |
Fungi Metabarcoding Environmental DNA Coleoptera Enchytraeidae Bryophyta ancient DNA Aves primers Holocene Pleistocene Life sciences medicine and health care Arctic envir geo |
description |
Metabarcoding approaches use total and typically degraded DNA from environmental samples to analyse biotic assemblages and can potentially be carried out for any kinds of organisms in an ecosystem. These analyses rely on specific markers, here called metabarcodes, which should be optimized for taxonomic resolution, minimal bias in amplification of the target organism group and short sequence length. Using bioinformatic tools, we developed metabarcodes for several groups of organisms: fungi, bryophytes, enchytraeids, beetles and birds. The ability of these metabarcodes to amplify the target groups was systematically evaluated by (1) in silico PCRs using all standard sequences in the EMBL public database as templates, (2) in vitro PCRs of DNA extracts from surface soil samples from a site in Varanger, northern Norway, and (3) in vitro PCRs of DNA extracts from permanently frozen sediment samples of late-Pleistocene age (~ 16 000–50 000 yr BP) from two Siberian sites, Duvanny Yar and Main River. Comparison of the results from the in silico PCR with those obtained in vitro showed that the in silico approach offered a reliable estimate of the suitability of a marker. All target groups were detected in the environmental DNA, but we found large variation in the level of detection among the groups and between modern and ancient samples. Success rates for the Pleistocene samples were highest for fungal DNA, whereas bryophyte, beetle and bird sequences could also be retrieved, but to a much lesser degree. The metabarcoding approach has considerable potential for biodiversity screening of modern samples and also as a paleoecological tool. Epp_etal_metabarcodes_dryadThis file contains all consensus sequences retrieved from clones of environmental samples and referred to in Table S6 of the Supplementary material. |
format |
Dataset |
author |
Epp, Laura S. Boessenkool, Sanne Bellemain, Eva P. Haile, James Esposito, Alfonso Riaz, Tiayyba Erséus, Christer Gusarov, Vladimir I. Edwards, Mary E. Johnsen, Arild Stenøien, Hans K. Hassel, Kristian Kauserud, Håvard Yoccoz, Nigel G. Bråthen, Kari Anne Willerslev, Eske Taberlet, Pierre Coissac, Eric Brochmann, Christian |
author_facet |
Epp, Laura S. Boessenkool, Sanne Bellemain, Eva P. Haile, James Esposito, Alfonso Riaz, Tiayyba Erséus, Christer Gusarov, Vladimir I. Edwards, Mary E. Johnsen, Arild Stenøien, Hans K. Hassel, Kristian Kauserud, Håvard Yoccoz, Nigel G. Bråthen, Kari Anne Willerslev, Eske Taberlet, Pierre Coissac, Eric Brochmann, Christian |
author_sort |
Epp, Laura S. |
title |
Data from: New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems |
title_short |
Data from: New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems |
title_full |
Data from: New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems |
title_fullStr |
Data from: New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems |
title_full_unstemmed |
Data from: New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems |
title_sort |
data from: new environmental metabarcodes for analysing soil dna: potential for studying past and present ecosystems |
publisher |
Dryad |
publishDate |
2020 |
url |
https://doi.org/10.5061/dryad.37s6bb42 |
long_lat |
ENVELOPE(151.300,151.300,70.917,70.917) |
geographic |
Arctic Norway Yar |
geographic_facet |
Arctic Norway Yar |
genre |
Arctic Northern Norway Varanger |
genre_facet |
Arctic Northern Norway Varanger |
op_source |
10.5061/dryad.37s6bb42 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:81630 oai:easy.dans.knaw.nl:easy-dataset:81630 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 re3data_____::r3d100000044 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c |
op_relation |
http://dx.doi.org/10.5061/dryad.37s6bb42 https://dx.doi.org/10.5061/dryad.37s6bb42 |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.37s6bb42 |
_version_ |
1766346356463501312 |