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

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

doi:10.1111/j.1365-294X.2012.05537.x

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

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

143 Citations (Scopus)

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 (i) in silico PCRs using all standard sequences in the EMBL public database as templates, (ii) in vitro PCRs of DNA extracts from surface soil samples from a site in Varanger, northern Norway and (iii) in vitro PCRs of DNA extracts from permanently frozen sediment samples of late-Pleistocene age (∼16 000-50 000 years 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 palaeoecological tool.

Original language	English
Journal	Molecular Ecology
Volume	21
Issue number	8
Pages (from-to)	1821-1833
Number of pages	13
ISSN	0962-1083
DOIs	https://doi.org/10.1111/j.1365-294X.2012.05537.x
Publication status	Published - Apr 2012

Access to Document

10.1111/j.1365-294X.2012.05537.x

Cite this

Epp, L. S., Boessenkool, S., Bellemain, E. P., Haile, J. S., Esposito, A., Riaz, T., Erséus, C., Gusarov, V. I., Edwards, M. E., Johnsen, A., Stenøien, H. K., Hassel, K., Kauserud, H., Yoccoz, N. G., Bråthen, K. A., Willerslev, E., Taberlet, P., Coissac, E., & Brochmann, C. (2012). New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems. Molecular Ecology, 21(8), 1821-1833. https://doi.org/10.1111/j.1365-294X.2012.05537.x

Epp, LS, Boessenkool, S, Bellemain, EP, Haile, JS, Esposito, A, Riaz, T, Erséus, C, Gusarov, VI, Edwards, ME, Johnsen, A, Stenøien, HK, Hassel, K, Kauserud, H, Yoccoz, NG, Bråthen, KA, Willerslev, E, Taberlet, P, Coissac, E & Brochmann, C 2012, 'New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems', Molecular Ecology, vol. 21, no. 8, pp. 1821-1833. https://doi.org/10.1111/j.1365-294X.2012.05537.x

@article{83f2dd0e1bb543babc3660abeefd4e2e,

title = "New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems",

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 (i) in silico PCRs using all standard sequences in the EMBL public database as templates, (ii) in vitro PCRs of DNA extracts from surface soil samples from a site in Varanger, northern Norway and (iii) in vitro PCRs of DNA extracts from permanently frozen sediment samples of late-Pleistocene age (∼16 000-50 000 years 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 palaeoecological tool.",

author = "Epp, {Laura S.} and Sanne Boessenkool and Bellemain, {Eva P.} and Haile, {James Seymour} and Alfonso Esposito and Tiayyba Riaz and Christer Ers{\'e}us and Gusarov, {Vladimir I.} and Edwards, {Mary E.} and Arild Johnsen and Sten{\o}ien, {Hans K.} and Kristian Hassel and H{\aa}vard Kauserud and Yoccoz, {Nigel G.} and Br{\aa}then, {Kari Anne} and Eske Willerslev and Pierre Taberlet and Eric Coissac and Christian Brochmann",

note = "Special issue: environmental DNA",

year = "2012",

month = apr,

doi = "10.1111/j.1365-294X.2012.05537.x",

language = "English",

volume = "21",

pages = "1821--1833",

journal = "Molecular Ecology",

issn = "0962-1083",

publisher = "Wiley-Blackwell",

number = "8",

}

TY - JOUR

T1 - New environmental metabarcodes for analysing soil DNA

T2 - potential for studying past and present ecosystems

AU - Epp, Laura S.

AU - Boessenkool, Sanne

AU - Bellemain, Eva P.

AU - Haile, James Seymour

AU - Esposito, Alfonso

AU - Riaz, Tiayyba

AU - Erséus, Christer

AU - Gusarov, Vladimir I.

AU - Edwards, Mary E.

AU - Johnsen, Arild

AU - Stenøien, Hans K.

AU - Hassel, Kristian

AU - Kauserud, Håvard

AU - Yoccoz, Nigel G.

AU - Bråthen, Kari Anne

AU - Willerslev, Eske

AU - Taberlet, Pierre

AU - Coissac, Eric

AU - Brochmann, Christian

N1 - Special issue: environmental DNA

PY - 2012/4

Y1 - 2012/4

N2 - 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 (i) in silico PCRs using all standard sequences in the EMBL public database as templates, (ii) in vitro PCRs of DNA extracts from surface soil samples from a site in Varanger, northern Norway and (iii) in vitro PCRs of DNA extracts from permanently frozen sediment samples of late-Pleistocene age (∼16 000-50 000 years 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 palaeoecological tool.

AB - 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 (i) in silico PCRs using all standard sequences in the EMBL public database as templates, (ii) in vitro PCRs of DNA extracts from surface soil samples from a site in Varanger, northern Norway and (iii) in vitro PCRs of DNA extracts from permanently frozen sediment samples of late-Pleistocene age (∼16 000-50 000 years 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 palaeoecological tool.

U2 - 10.1111/j.1365-294X.2012.05537.x

DO - 10.1111/j.1365-294X.2012.05537.x

M3 - Journal article

C2 - 22486821

SN - 0962-1083

VL - 21

SP - 1821

EP - 1833

JO - Molecular Ecology

JF - Molecular Ecology

IS - 8

ER -

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

Abstract

Access to Document

Fingerprint

Cite this