Advertisement

Ancient DNA pp 57-63 | Cite as

Ancient DNA Extraction from Soils and Sediments

  • James HaileEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 840)

Abstract

DNA contained in soils and sediments can provide novel insights into past environments and ecosystems. In this chapter, I describe an efficient and effective technique to extract total DNA from sediments in a manner that minimizes the coextraction of PCR-inhibitory compounds. I describe two different approaches: one that is suitable for large (up to 10 g wet weight) amounts of substrate, and a second that is more appropriate for small (up to 0.5 g) amounts of substrate. Finally, I discuss some of the obstacles that may be encountered in the process of extracting DNA from soils and sediments and suggest approaches to circumvent some common problems.

Key words

sediment soils ancient DNA metagenomics environmental sampling sedaDNA 

Notes

Acknowledgment

This work was supported by Murdoch University, Perth, Australia.

References

  1. 1.
    Haile J, MacPhee R, Roberts R, Arnold L, Brook B, Nielsen R, Gilbert M, Brock F, Munch K, Chivas A, Tikhonov A, Willerslev E (2009) Ancient DNA reveals late survival of mammoth and horse in interior Alaska. Proc Natl Acad Sci U S A 106:22363–22368CrossRefGoogle Scholar
  2. 2.
    Haile J, Larson G, Owens K, Dobney K, Shapiro B (2010) Ancient DNA typing of archaeological pig remains corroborates historical records. J Archaeol Sci 37:174–177CrossRefGoogle Scholar
  3. 3.
    Haile J, Holdaway R, Oliver K, Bunce M, Gilbert MTP, Nielsen R, Munch K, Ho S, Shapiro B, Willerslev E (2007) Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor? Mol Biol Evol 24:982–989PubMedCrossRefGoogle Scholar
  4. 4.
    Willerslev E, Hansen A, Binladen J, Brand T, Gilbert M, Shapiro B, Bunce M, Wiuf C, Gilichinsky D, Cooper A (2003) Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science 300:791–795PubMedCrossRefGoogle Scholar
  5. 5.
    Lydolph M, Jacobsen J, Arctander P, Gilbert M, Gilichinsky D, Hansen A, Willerslev E, Lange L (2005) Beringian paleoecology inferred from permafrost-preserved fungal DNA. Appl Environ Microbiol 71:1012–1017PubMedCrossRefGoogle Scholar
  6. 6.
    Crecchio C, Stotzky G (1998) Binding of DNA on humic acids: effect on transformation of Bacillus subtilis and resistance to DNase. Soil Biol Biochem 30:1061–1067CrossRefGoogle Scholar
  7. 7.
    Khanna M, Stotzky G (1992) Transformation of Bacillus subtilis by DNA bound on montmorillonite and effect of DNase on the transforming ability of bound DNA. Appl Environ Microbiol 58:1930–1939PubMedGoogle Scholar
  8. 8.
    Gilbert MTP, Bandelt HJ, Hofreiter M, Barnes I (2005) Assessing ancient DNA studies. Trends Ecol Evol 20:541–544PubMedCrossRefGoogle Scholar
  9. 9.
    Bulat S, Lubeck M, Alekhina I, Jensen F, Knudsen I, Lubeck P (2000) Identification of a universally primed-PCR-derived sequence-characterized amplified region marker for an antagonistic strain of Clonostachys rosea and development of a strain-specific PCR detection assay. Appl Environ Microbiol 66:4758–4763PubMedCrossRefGoogle Scholar
  10. 10.
    Voet D, Voet J (1995) Biochemistry. Wiley, New YorkGoogle Scholar
  11. 11.
    Vasan S, Zhang X, Zhang XN, Kapurniotu A, Bernhagen J, Teichberg S, Basgen J, Wagle D, Shih D, Terlecky I, Bucala R, Cerami A, Egan J, Ulrich P (1996) An agent cleaving glucose-derived protein crosslinks in vitro and in vivo. Nature 382:275–278PubMedCrossRefGoogle Scholar
  12. 12.
    Poinar HN, Hofreiter M, Spaulding WG, Martin PS, Stankiewicz BA, Bland H, Evershed RP, Possnert G, Paabo S (1998) Molecular coproscopy: dung and diet of the extinct ground sloth Nothrotheriops shastensis. Science 281:402–406PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Ancient DNA Laboratory, School of Biological Sciences and BiotechnologyMurdoch UniversityPerthAustralia

Personalised recommendations