Ancient DNA from marine sediments: precautions and considerations for seafloor coring, sample handling and data generation
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...
Published in: | Earth-Science Reviews |
---|---|
Main Authors: | , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Elsevier
2019
|
Subjects: | |
Online Access: | http://hdl.handle.net/2440/126125 https://doi.org/10.1016/j.earscirev.2019.102887 |
id |
ftunivadelaidedl:oai:digital.library.adelaide.edu.au:2440/126125 |
---|---|
record_format |
openpolar |
spelling |
ftunivadelaidedl:oai:digital.library.adelaide.edu.au:2440/126125 2023-12-17T10:48:39+01:00 Ancient DNA from marine sediments: precautions and considerations for seafloor coring, sample handling and data generation Armbrecht, L. Coolen, M. Lejzerowicz, F. George, S. Negandhi, K. Suzuki, Y. Young, J. Foster, N. Armand, L. Cooper, A. Ostrowski, M. Focardi, A. Stat, M. Moreau, J. Weyrich, L. 2019 http://hdl.handle.net/2440/126125 https://doi.org/10.1016/j.earscirev.2019.102887 en eng Elsevier http://purl.org/au-research/grants/arc/DP160102587 http://purl.org/au-research/grants/arc/DP18100982 http://purl.org/au-research/grants/arc/LE160100067 http://purl.org/au-research/grants/arc/DP15012326 http://purl.org/au-research/grants/arc/FL14010021 http://purl.org/au-research/grants/arc/LP160100839 http://purl.org/au-research/grants/arc/DP110103668 http://purl.org/au-research/grants/arc/FL140100260 http://purl.org/au-research/grants/arc/FT180100407 http://purl.org/au-research/grants/arc/CE170100015 Earth-Science Reviews, 2019; 196:102887-1-102887-13 1872-6828 http://hdl.handle.net/2440/126125 doi:10.1016/j.earscirev.2019.102887 Armbrecht, L. [0000-0002-1213-1257] Foster, N. [0000-0001-7159-7391] Cooper, A. [0000-0002-7738-7851] © 2019 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.earscirev.2019.102887 Ancient DNA marine sediments deep biosphere phytoplankton contamination seafloor IODP biomarkers Mars Journal article 2019 ftunivadelaidedl https://doi.org/10.1016/j.earscirev.2019.102887 2023-11-20T23:21:57Z 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. Linda H. Armbrecht, Marco J.L. Coolen, Franck Lejzerowicz, Simon C. George, Karita Negandhi, Yohey Suzuki, Jennifer Young, Nicole R. Foster, Leanne K. Armand, Alan Coopera, Martin Ostrowski, Amaranta ... Article in Journal/Newspaper permafrost The University of Adelaide: Digital Library Earth-Science Reviews 196 102887 |
institution |
Open Polar |
collection |
The University of Adelaide: Digital Library |
op_collection_id |
ftunivadelaidedl |
language |
English |
topic |
Ancient DNA marine sediments deep biosphere phytoplankton contamination seafloor IODP biomarkers Mars |
spellingShingle |
Ancient DNA marine sediments deep biosphere phytoplankton contamination seafloor IODP biomarkers Mars Armbrecht, L. Coolen, M. Lejzerowicz, F. George, S. Negandhi, K. Suzuki, Y. Young, J. Foster, N. Armand, L. Cooper, A. Ostrowski, M. Focardi, A. Stat, M. Moreau, J. Weyrich, L. Ancient DNA from marine sediments: precautions and considerations for seafloor coring, sample handling and data generation |
topic_facet |
Ancient DNA marine sediments deep biosphere phytoplankton contamination seafloor IODP biomarkers Mars |
description |
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. Linda H. Armbrecht, Marco J.L. Coolen, Franck Lejzerowicz, Simon C. George, Karita Negandhi, Yohey Suzuki, Jennifer Young, Nicole R. Foster, Leanne K. Armand, Alan Coopera, Martin Ostrowski, Amaranta ... |
format |
Article in Journal/Newspaper |
author |
Armbrecht, L. Coolen, M. Lejzerowicz, F. George, S. Negandhi, K. Suzuki, Y. Young, J. Foster, N. Armand, L. Cooper, A. Ostrowski, M. Focardi, A. Stat, M. Moreau, J. Weyrich, L. |
author_facet |
Armbrecht, L. Coolen, M. Lejzerowicz, F. George, S. Negandhi, K. Suzuki, Y. Young, J. Foster, N. Armand, L. Cooper, A. Ostrowski, M. Focardi, A. Stat, M. Moreau, J. Weyrich, L. |
author_sort |
Armbrecht, L. |
title |
Ancient DNA from marine sediments: precautions and considerations for seafloor coring, sample handling and data generation |
title_short |
Ancient DNA from marine sediments: precautions and considerations for seafloor coring, sample handling and data generation |
title_full |
Ancient DNA from marine sediments: precautions and considerations for seafloor coring, sample handling and data generation |
title_fullStr |
Ancient DNA from marine sediments: precautions and considerations for seafloor coring, sample handling and data generation |
title_full_unstemmed |
Ancient DNA from marine sediments: precautions and considerations for seafloor coring, sample handling and data generation |
title_sort |
ancient dna from marine sediments: precautions and considerations for seafloor coring, sample handling and data generation |
publisher |
Elsevier |
publishDate |
2019 |
url |
http://hdl.handle.net/2440/126125 https://doi.org/10.1016/j.earscirev.2019.102887 |
genre |
permafrost |
genre_facet |
permafrost |
op_source |
http://dx.doi.org/10.1016/j.earscirev.2019.102887 |
op_relation |
http://purl.org/au-research/grants/arc/DP160102587 http://purl.org/au-research/grants/arc/DP18100982 http://purl.org/au-research/grants/arc/LE160100067 http://purl.org/au-research/grants/arc/DP15012326 http://purl.org/au-research/grants/arc/FL14010021 http://purl.org/au-research/grants/arc/LP160100839 http://purl.org/au-research/grants/arc/DP110103668 http://purl.org/au-research/grants/arc/FL140100260 http://purl.org/au-research/grants/arc/FT180100407 http://purl.org/au-research/grants/arc/CE170100015 Earth-Science Reviews, 2019; 196:102887-1-102887-13 1872-6828 http://hdl.handle.net/2440/126125 doi:10.1016/j.earscirev.2019.102887 Armbrecht, L. [0000-0002-1213-1257] Foster, N. [0000-0001-7159-7391] Cooper, A. [0000-0002-7738-7851] |
op_rights |
© 2019 Elsevier B.V. All rights reserved. |
op_doi |
https://doi.org/10.1016/j.earscirev.2019.102887 |
container_title |
Earth-Science Reviews |
container_volume |
196 |
container_start_page |
102887 |
_version_ |
1785572878920450048 |