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Ancient DNA pp 31-44 | Cite as

Sampling and Extraction of Ancient DNA from Sediments

  • Laura S. Epp
  • Heike H. Zimmermann
  • Kathleen R. Stoof-Leichsenring
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1963)

Abstract

Environmental DNA preserved in sediments is rapidly gaining importance as a tool in paleoecology. Sampling procedures for sedimentary ancient DNA (sedaDNA) have to be well planned to ensure clean subsampling of the inside of sediment cores and avoid introducing contamination. Additionally, ancient DNA extraction protocols may need to be optimized for the recovery of DNA from sediments, which may contain inhibitors. Here we describe procedures for subsampling both nonfrozen and frozen sediment cores, and we describe an efficient method for ancient DNA extraction from such samples.

Key words

Sedimentary ancient DNA (sedaDNA) Environmental DNA (eDNA) Sediment cores Permafrost Metagenomics Metabarcoding 

Notes

Acknowledgments

This work was supported by the DFG grant EP98/2-1 to LSE. We thank Inger G. Alsos for exchange of experiences concerning the DNA extraction protocols.

References

  1. 1.
    Willerslev E, Hansen AJ, Binladen J, Brand TB, Gilbert MTP, Shapiro B, Bunce M, Wiuf C, Gilichinsky DA, Cooper A (2003) Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science 300(5620):791–795.  https://doi.org/10.1126/Science.1084114CrossRefPubMedGoogle Scholar
  2. 2.
    Coolen MJL, Muyzer G, Rijpstra WIC, Schouten S, Volkman JK, Damste JSS (2004) Combined DNA and lipid analyses of sediments reveal changes in Holocene haptophyte and diatom populations in an Antarctic lake. Earth Planet Sci Lett 223(1–2):225–239.  https://doi.org/10.1016/j.epsl.2004.04.014CrossRefGoogle Scholar
  3. 3.
    Haile J, Froese DG, MacPhee RDE, Roberts RG, Arnold LJ, Reyes AV, Rasmussen M, Nielsen R, Brook BW, Robinson S, Demuro M, Gilbert MTP, Munch K, Austin JJ, Cooper A, Barnes I, Moller P, Willerslev E (2009) Ancient DNA reveals late survival of mammoth and horse in interior Alaska. Proc Natl Acad Sci U S A 106(52):22352–22357.  https://doi.org/10.1073/Pnas.0912510106CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Willerslev E, Davison J, Moora M, Zobel M, Coissac E, Edwards ME, Lorenzen ED, Vestergard M, Gussarova G, Haile J, Craine J, Gielly L, Boessenkool S, Epp LS, Pearman PB, Cheddadi R, Murray D, Brathen KA, Yoccoz N, Binney H, Cruaud C, Wincker P, Goslar T, Alsos IG, Bellemain E, Brysting AK, Elven R, Sonstebo JH, Murton J, Sher A, Rasmussen M, Ronn R, Mourier T, Cooper A, Austin J, Moller P, Froese D, Zazula G, Pompanon F, Rioux D, Niderkorn V, Tikhonov A, Savvinov G, Roberts RG, MacPhee RDE, Gilbert MTP, Kjaer KH, Orlando L, Brochmann C, Taberlet P (2014) Fifty thousand years of Arctic vegetation and megafaunal diet. Nature 506(7486):47–51.  https://doi.org/10.1038/nature12921CrossRefPubMedGoogle Scholar
  5. 5.
    Epp LS, Gussarova G, Boessenkool S, Olsen J, Haile J, Schröder-Nielsen A, Ludikova A, Hassel K, Stenoien HK, Funder S, Willerslev E, Kjaer K, Brochmann C (2015) Lake sediment multi-taxon DNA from North Greenland records early post-glacial appearance of vascular plants and accurately tracks environmental changes. Quat Sci Rev 117:152–163.  https://doi.org/10.1016/j.quascirev.2015.03.027CrossRefGoogle Scholar
  6. 6.
    Alsos IG, Sjogren P, Edwards ME, Landvik JY, Gielly L, Forwick M, Coissac E, Brown AG, Jakobsen LV, Foreid MK, Pedersen MW (2016) Sedimentary ancient DNA from Lake Skartjorna, Svalbard: assessing the resilience of arctic flora to Holocene climate change. The Holocene 26(4):627–642.  https://doi.org/10.1177/0959683615612563CrossRefGoogle Scholar
  7. 7.
    Pedersen MW, Ruter A, Schweger C, Friebe H, Staff RA, Kjeldsen KK, Mendoza MLZ, Beaudoin AB, Zutter C, Larsen NK, Potter BA, Nielsenlo R, Rainville RA, Orlando L, Meltzer DJ, Kjaer KH, Willerslev E (2016) Postglacial viability and colonization in North America’s ice-free corridor. Nature 537(7618):45–49.  https://doi.org/10.1038/nature19085CrossRefPubMedGoogle Scholar
  8. 8.
    Taberlet P, Coissac E, Pompanon F, Brochmann C, Willerslev E (2012) Towards next-generation biodiversity assessment using DNA metabarcoding. Mol Ecol 21(8):2045–2050.  https://doi.org/10.1111/j.1365-294X.2012.05470.xCrossRefPubMedGoogle Scholar
  9. 9.
    Sjögren P, Edwards ME, Gielly L, Langdon CT, Croudace IW, Merkel MKF, Fonville T, Alsos IG (2016) Lake sedimentary DNA accurately records 20th century introductions of exotic conifers in Scotland. New Phytol.  https://doi.org/10.1111/nph.14199
  10. 10.
    Jørgensen T, Haile J, Moller P, Andreev A, Boessenkool S, Rasmussen M, Kienast F, Coissac E, Taberlet P, Brochmann C, Bigelow NH, Andersen K, Orlando L, Gilbert MTP, Willerslev E (2012) A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability. Mol Ecol 21(8):1989–2003.  https://doi.org/10.1111/j.1365-294X.2011.05287.xCrossRefPubMedGoogle Scholar
  11. 11.
    Willerslev E, Cappellini E, Boomsma W, Nielsen R, Hebsgaard MB, Brand TB, Hofreiter M, Bunce M, Poinar HN, Dahl-Jensen D, Johnsen S, Steffensen JP, Bennike O, Schwenninger JL, Nathan R, Armitage S, de Hoog CJ, Alfimov V, Christl M, Beer J, Muscheler R, Barker J, Sharp M, Penkman KEH, Haile J, Taberlet P, Gilbert MTP, Casoli A, Campani E, Collins MJ (2007) Ancient biomolecules from deep ice cores reveal a forested Southern Greenland. Science 317(5834):111–114.  https://doi.org/10.1126/Science.1141758CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Giguet-Covex C, Pansu J, Arnaud F, Rey PJ, Griggo C, Gielly L, Domaizon I, Coissac E, David F, Choler P, Poulenard J, Taberlet P (2014) Long livestock farming history and human landscape shaping revealed by lake sediment DNA. Nat Commun 5:3211.  https://doi.org/10.1038/Ncomms4211CrossRefPubMedGoogle Scholar
  13. 13.
    Pansu J, Giguet-Covex C, Ficetola GF, Gielly L, Boyer F, Zinger L, Arnaud F, Poulenard J, Taberlet P, Choler P (2015) Reconstructing long-term human impacts on plant communities: an ecological approach based on lake sediment DNA. Mol Ecol 24(7):1485–1498.  https://doi.org/10.1111/mec.13136CrossRefPubMedGoogle Scholar
  14. 14.
    Boessenkool S, McGlynn G, Epp LS, Taylor D, Pimentel M, Gizaw A, Nemomissa A, Brochmann C, Popp M (2014) Use of ancient sedimentary DNA from a biodiversity hotspot in the humid tropics as a novel conservation tool. Conserv Biol 28(2):446–455CrossRefGoogle Scholar
  15. 15.
    Stoof-Leichsenring KR, Epp LS, Trauth MH, Tiedemann R (2012) Hidden diversity in diatoms of Kenyan Lake Naivasha: a genetic approach detects temporal variation. Mol Ecol 21(8):1918–1930.  https://doi.org/10.1111/j.1365-294X.2011.05412.xCrossRefPubMedGoogle Scholar
  16. 16.
    Haile J (2012) Ancient DNA extraction from soils and sediments. In: Shapiro B, Hofreiter M (eds) Ancient DNA: methods and protocols. Springer Science+Business Media, New York, pp 57–64.  https://doi.org/10.1007/978-1-61779-516-9CrossRefGoogle Scholar
  17. 17.
    Taberlet P, Prud’homme SM, Campione E, Roy J, Miquel C, Shehzad W, Gielly L, Rioux D, Choler P, Clement JC, Melodelima C, Pompanon F, Coissac E (2012) Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies. Mol Ecol 21(8):1816–1820.  https://doi.org/10.1111/j.1365-294X.2011.05317.xCrossRefPubMedGoogle Scholar
  18. 18.
    Paus A, Boessenkool S, Brochmann C, Epp LS, Fabel D, Haflidason H, Linge H (2015) Lake Store Finnsjøen—a key for understanding Late-Glacial/early Holocene vegetation and ice sheet dynamics in the central Scandes mountains. Quat Sci Rev 121:36–51CrossRefGoogle Scholar
  19. 19.
    Bálint M, Márton O, Schatz M, Düring RA, Grossart HP (2018) Proper experimental design requires randomization/balancing of molecular ecology experiments, Ecology and Evolution. 8:1786–1793. DOI: 10.1002/ece3.3687Google Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Laura S. Epp
    • 1
    • 2
  • Heike H. Zimmermann
    • 1
  • Kathleen R. Stoof-Leichsenring
    • 1
  1. 1.Alfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchPolar Terrestrial Environmental SystemsPotsdamGermany
  2. 2.Department of BiologyUniversity of KonstanzKonstanzGermany

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