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

Linda H. Armbrecht, Marco J.L. Coolen, Franck Lejzerowicz, Simon C. George, Karita Negandhi, Y. Suzuki, Jennifer Young, Nicole R. Foster, Leanne K. Armand, Alan Cooper, Martin Ostrowski, Amaranta Focardi, Michael Stat, John W. Moreau, Laura S. Weyrich

Research output: Contribution to journalReview article

Abstract

The study of ancient DNA (aDNA) from sediments (sedaDNA) 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 sedaDNA, 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 sedaDNA-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 sedaDNA research, with a focus on sampling optimisation to facilitate the incorporation of routine sedaDNA 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 sedaDNA, and the applicability of the new guidelines to the study of other contamination-susceptible environments (permafrost and outer space) are discussed.

Original languageEnglish (US)
Article number102887
JournalEarth-Science Reviews
Volume196
DOIs
StatePublished - Sep 2019

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marine sediment
seafloor
DNA
sediment
research vessel
deep-sea sediment
prokaryote
ocean
eukaryote
terminology
paleoclimate
permafrost
sediment core
logistics
drilling
biodiversity
timescale
sampling
contamination
ship

All Science Journal Classification (ASJC) codes

  • Earth and Planetary Sciences(all)

Cite this

Armbrecht, Linda H. ; Coolen, Marco J.L. ; Lejzerowicz, Franck ; George, Simon C. ; Negandhi, Karita ; Suzuki, Y. ; Young, Jennifer ; Foster, Nicole R. ; Armand, Leanne K. ; Cooper, Alan ; Ostrowski, Martin ; Focardi, Amaranta ; Stat, Michael ; Moreau, John W. ; Weyrich, Laura S. / Ancient DNA from marine sediments : Precautions and considerations for seafloor coring, sample handling and data generation. In: Earth-Science Reviews. 2019 ; Vol. 196.
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abstract = "The study of ancient DNA (aDNA) from sediments (sedaDNA) 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 sedaDNA, 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 sedaDNA-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 sedaDNA research, with a focus on sampling optimisation to facilitate the incorporation of routine sedaDNA 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 sedaDNA, and the applicability of the new guidelines to the study of other contamination-susceptible environments (permafrost and outer space) are discussed.",
author = "Armbrecht, {Linda H.} and Coolen, {Marco J.L.} and Franck Lejzerowicz and George, {Simon C.} and Karita Negandhi and Y. Suzuki and Jennifer Young and Foster, {Nicole R.} and Armand, {Leanne K.} and Alan Cooper and Martin Ostrowski and Amaranta Focardi and Michael Stat and Moreau, {John W.} and Weyrich, {Laura S.}",
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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 2019, 'Ancient DNA from marine sediments: Precautions and considerations for seafloor coring, sample handling and data generation', Earth-Science Reviews, vol. 196, 102887. https://doi.org/10.1016/j.earscirev.2019.102887

Ancient DNA from marine sediments : Precautions and considerations for seafloor coring, sample handling and data generation. / Armbrecht, Linda H.; Coolen, Marco J.L.; Lejzerowicz, Franck; George, Simon C.; Negandhi, Karita; Suzuki, Y.; Young, Jennifer; Foster, Nicole R.; Armand, Leanne K.; Cooper, Alan; Ostrowski, Martin; Focardi, Amaranta; Stat, Michael; Moreau, John W.; Weyrich, Laura S.

In: Earth-Science Reviews, Vol. 196, 102887, 09.2019.

Research output: Contribution to journalReview article

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T1 - Ancient DNA from marine sediments

T2 - Precautions and considerations for seafloor coring, sample handling and data generation

AU - Armbrecht, Linda H.

AU - Coolen, Marco J.L.

AU - Lejzerowicz, Franck

AU - George, Simon C.

AU - Negandhi, Karita

AU - Suzuki, Y.

AU - Young, Jennifer

AU - Foster, Nicole R.

AU - Armand, Leanne K.

AU - Cooper, Alan

AU - Ostrowski, Martin

AU - Focardi, Amaranta

AU - Stat, Michael

AU - Moreau, John W.

AU - Weyrich, Laura S.

PY - 2019/9

Y1 - 2019/9

N2 - The study of ancient DNA (aDNA) from sediments (sedaDNA) 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 sedaDNA, 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 sedaDNA-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 sedaDNA research, with a focus on sampling optimisation to facilitate the incorporation of routine sedaDNA 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 sedaDNA, and the applicability of the new guidelines to the study of other contamination-susceptible environments (permafrost and outer space) are discussed.

AB - The study of ancient DNA (aDNA) from sediments (sedaDNA) 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 sedaDNA, 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 sedaDNA-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 sedaDNA research, with a focus on sampling optimisation to facilitate the incorporation of routine sedaDNA 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 sedaDNA, and the applicability of the new guidelines to the study of other contamination-susceptible environments (permafrost and outer space) are discussed.

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