Ancient DNA from marine sediments: precautions and considerations for seafloor coring, sample handling and data generation

• Published in: Earth-Science Reviews
• Main Authors: Armbrecht, LH, Coolen, MJL, Lejzerowicz, F, George, SC, Negandhi, K, Suzuki, Y, Young, J, Foster, NR, Armand, LK, Cooper, A, Ostrowski, M, Focardi, A, Stat, M, Moreau, JW, Weyrich, LS
• Format: Article in Journal/Newspaper
• Language: English
• Published: Elsevier Science Bv 2019
• Subjects: Biological Sciences; Genetics; Genomics; permafrost
• Online Access: https://doi.org/10.1016/j.earscirev.2019.102887; http://ecite.utas.edu.au/146469

The study of ancient DNA (aDNA) from sediments ( sed aDNA) offers great potential for paleoclimate interpretation, and has recently been applied as a tool to characterise past marine life and environments from deep ocean sediments over geological timescales. Using sed aDNA, palaeo-communities have been detected, including prokaryotes and eukaryotes that do not fossilise, thereby revolutionising the scope of marine micropalaeontological research. However, many studies to date have not reported on the measures taken to prove the authenticity of sed aDNA-derived data from which conclusions are drawn. aDNA is highly fragmented and degraded and extremely sensitive to contamination by non-target environmental DNA. Contamination risks are particularly high on research vessels, drilling ships and platforms, where logistics and facilities do not yet allow for sterile sediment coring, and due consideration needs to be given to sample processing and analysis following aDNA guidelines. This review clarifies the use of aDNA terminology, discusses common pitfalls and highlights the urgency behind adopting new standards for marine sed aDNA research, with a focus on sampling optimisation to facilitate the incorporation of routine sed aDNA research into International Ocean Discovery Program (IODP) operations. Currently available installations aboard drilling ships and platforms are reviewed, improvements suggested, analytical approaches detailed, and the controls and documentation necessary to support the authenticity of aDNA retrieved from deep-sea sediment cores is outlined. Beyond practical considerations, concepts relevant to the study of past marine biodiversity based on sed aDNA, and the applicability of the new guidelines to the study of other contamination-susceptible environments (permafrost and outer space) are discussed.