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

Authors

  • LAURA S. EPP,

    1. National Centre for Biosystematics, Natural History Museum, University of Oslo, PO Box 1172, Blindern, NO-0318 Oslo, Norway
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    • Contributed equally.

  • SANNE BOESSENKOOL,

    1. National Centre for Biosystematics, Natural History Museum, University of Oslo, PO Box 1172, Blindern, NO-0318 Oslo, Norway
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    • Contributed equally.

  • EVA P. BELLEMAIN,

    1. National Centre for Biosystematics, Natural History Museum, University of Oslo, PO Box 1172, Blindern, NO-0318 Oslo, Norway
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  • JAMES HAILE,

    1. The Centre of Excellence for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
    2. Ancient DNA Research Laboratory, Murdoch University, South Street, Perth, WA 6150 Australia
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  • ALFONSO ESPOSITO,

    1. National Centre for Biosystematics, Natural History Museum, University of Oslo, PO Box 1172, Blindern, NO-0318 Oslo, Norway
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    • Present address: Faculty of Science and Technology, Free University of Bozen, Sernesistrasse, 1, I-39100 Bozen, Italy.

  • TIAYYBA RIAZ,

    1. Laboratoire d’Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
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  • CHRISTER ERSÉUS,

    1. Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30 Göteborg, Sweden
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  • VLADIMIR I. GUSAROV,

    1. National Centre for Biosystematics, Natural History Museum, University of Oslo, PO Box 1172, Blindern, NO-0318 Oslo, Norway
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  • MARY E. EDWARDS,

    1. Geography and Environment, University of Southampton, University Road, Southampton SO17 1BJ, UK
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  • ARILD JOHNSEN,

    1. National Centre for Biosystematics, Natural History Museum, University of Oslo, PO Box 1172, Blindern, NO-0318 Oslo, Norway
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  • HANS K. STENØIEN,

    1. Systematics and Evolution Group, Museum of Natural History and Archeology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
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  • KRISTIAN HASSEL,

    1. Systematics and Evolution Group, Museum of Natural History and Archeology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
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  • HÅVARD KAUSERUD,

    1. Microbial Evolution Research Group (MERG), Department of Biology, University of Oslo, PO Box 1066 Blindern, N-0316, Oslo, Norway
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  • NIGEL G. YOCCOZ,

    1. Department of Arctic and Marine Biology, University of Tromsø, NO-9037 Tromsø, Norway
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  • KARI ANNE BRÅTHEN,

    1. Department of Arctic and Marine Biology, University of Tromsø, NO-9037 Tromsø, Norway
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  • ESKE WILLERSLEV,

    1. The Centre of Excellence for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
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  • PIERRE TABERLET,

    1. Laboratoire d’Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
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  • ERIC COISSAC,

    1. Laboratoire d’Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
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    • Shared senior authorship.

  • CHRISTIAN BROCHMANN

    1. National Centre for Biosystematics, Natural History Museum, University of Oslo, PO Box 1172, Blindern, NO-0318 Oslo, Norway
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    • Shared senior authorship.


Laura Epp, Fax: +47 22851835; E-mail: laura.epp@nhm.uio.no

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.

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