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Data from: New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems

Data from: New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems
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 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.,
DRYAD
Epp, Laura S.
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Boessenkool, Sanne
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Bellemain, Eva P.
d62cd2b8-01fd-403e-9d06-0c621854ad09
Haile, James
831f077c-daae-4aa1-b4b7-c4c76a2f6c00
Esposito, Alfonso
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Riaz, Tiayyba
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Erséus, Christer
367907f1-96aa-4bff-9b3f-188fab72f110
Gusarov, Vladimir I.
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Edwards, Mary E.
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Johnsen, Arild
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Stenøien, Hans K.
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Hassel, Kristian
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Kauserud, Håvard
7fa12650-214e-4c2b-9118-337e521f4517
Yoccoz, Nigel G.
77470e98-046b-4edc-9ca9-d41428b02126
Bråthen, Kari Anne
35789f60-9819-45ee-a4fe-ff4a9f2108a5
Willerslev, Eske
3815b419-7ba2-4827-a7a7-e97dd7118ee6
Taberlet, Pierre
f5769360-3873-49b1-b4ce-56e14b1d3aa0
Coissac, Eric
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Brochmann, Christian
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Epp, Laura S.
d7c2dd0c-c6be-4dfa-a1a8-3f76187fcc6c
Boessenkool, Sanne
6a24c3b2-94e2-4722-bd5a-33041ce5e6c9
Bellemain, Eva P.
d62cd2b8-01fd-403e-9d06-0c621854ad09
Haile, James
831f077c-daae-4aa1-b4b7-c4c76a2f6c00
Esposito, Alfonso
0149748d-9b55-4c9c-b9e7-11384c67fc10
Riaz, Tiayyba
b05c1a5c-5a98-4cfb-99b7-1280051481cc
Erséus, Christer
367907f1-96aa-4bff-9b3f-188fab72f110
Gusarov, Vladimir I.
99720fab-58bd-4364-a061-ffdc4c0af74c
Edwards, Mary E.
4b6a3389-f3a4-4933-b8fd-acdfef72200e
Johnsen, Arild
d5e74f06-e873-4b91-91bb-44cb3d4e5ac7
Stenøien, Hans K.
9c8030b2-abed-468b-bd14-0615f69fd7f6
Hassel, Kristian
2951dc6d-56d0-42b3-ae2b-fa8ab4342427
Kauserud, Håvard
7fa12650-214e-4c2b-9118-337e521f4517
Yoccoz, Nigel G.
77470e98-046b-4edc-9ca9-d41428b02126
Bråthen, Kari Anne
35789f60-9819-45ee-a4fe-ff4a9f2108a5
Willerslev, Eske
3815b419-7ba2-4827-a7a7-e97dd7118ee6
Taberlet, Pierre
f5769360-3873-49b1-b4ce-56e14b1d3aa0
Coissac, Eric
66ae82c0-bd94-4446-8d1b-af0d15732d0b
Brochmann, Christian
82cfe10a-4506-4340-a219-8ee809f52d5e

Epp, Laura S., Boessenkool, Sanne, Haile, James, Erséus, Christer, Stenøien, Hans K., Yoccoz, Nigel G., Bråthen, Kari Anne, Willerslev, Eske, Taberlet, Pierre, Coissac, Eric and Brochmann, Christian (2012) Data from: New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems. DRYAD doi:10.5061/dryad.37s6bb42 [Dataset]

Record type: Dataset

Abstract

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.,

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More information

Published date: 1 January 2012

Identifiers

Local EPrints ID: 449258
URI: http://eprints.soton.ac.uk/id/eprint/449258
PURE UUID: e3f0ddd7-9663-4f24-aca4-ce2f9a718ba3
ORCID for Mary E. Edwards: ORCID iD orcid.org/0000-0002-3490-6682

Catalogue record

Date deposited: 20 May 2021 16:33
Last modified: 21 May 2021 01:38

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Contributors

Creator: Laura S. Epp
Creator: Sanne Boessenkool
Contributor: Eva P. Bellemain
Creator: James Haile
Contributor: Alfonso Esposito
Contributor: Tiayyba Riaz
Creator: Christer Erséus
Contributor: Vladimir I. Gusarov
Contributor: Mary E. Edwards ORCID iD
Contributor: Arild Johnsen
Creator: Hans K. Stenøien
Contributor: Kristian Hassel
Contributor: Håvard Kauserud
Creator: Nigel G. Yoccoz
Creator: Kari Anne Bråthen
Creator: Eske Willerslev
Creator: Pierre Taberlet
Creator: Eric Coissac
Creator: Christian Brochmann

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