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...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | English |
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ELSEVIER
2019
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| Online Access: | http://purl.org/au-research/grants/arc/LP160100839 http://hdl.handle.net/20.500.11937/90975 |
| _version_ | 1848765476758355968 |
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| author | Armbrecht, L.H. Coolen, Marco Lejzerowicz, F. George, S.C. Negandhi, K. Suzuki, Y. Young, J. Foster, N.R. Armand, L.K. Cooper, A. Ostrowski, M. Focardi, A. Stat, Michael Moreau, J.W. Weyrich, L.S. |
| author_facet | Armbrecht, L.H. Coolen, Marco Lejzerowicz, F. George, S.C. Negandhi, K. Suzuki, Y. Young, J. Foster, N.R. Armand, L.K. Cooper, A. Ostrowski, M. Focardi, A. Stat, Michael Moreau, J.W. Weyrich, L.S. |
| author_sort | Armbrecht, L.H. |
| building | Curtin Institutional Repository |
| collection | Online Access |
| 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. |
| first_indexed | 2025-11-14T11:35:52Z |
| format | Journal Article |
| id | curtin-20.500.11937-90975 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-14T11:35:52Z |
| publishDate | 2019 |
| publisher | ELSEVIER |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-909752023-06-13T09:16:21Z Ancient DNA from marine sediments: Precautions and considerations for seafloor coring, sample handling and data generation Armbrecht, L.H. Coolen, Marco Lejzerowicz, F. George, S.C. Negandhi, K. Suzuki, Y. Young, J. Foster, N.R. Armand, L.K. Cooper, A. Ostrowski, M. Focardi, A. Stat, Michael Moreau, J.W. Weyrich, L.S. Science & Technology Physical Sciences Geosciences, Multidisciplinary Geology Ancient DNA Marine sediments Deep biosphere Phytoplankton Contamination Seafloor IODP Biomarkers Mars GREEN SULFUR BACTERIA EXTRACELLULAR DNA BLACK-SEA ENVIRONMENTAL DNA GENOME SEQUENCE NUCLEIC-ACIDS PLANT DNA SOIL CONTAMINATION PRESERVATION 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. 2019 Journal Article http://hdl.handle.net/20.500.11937/90975 10.1016/j.earscirev.2019.102887 English http://purl.org/au-research/grants/arc/LP160100839 ELSEVIER restricted |
| spellingShingle | Science & Technology Physical Sciences Geosciences, Multidisciplinary Geology Ancient DNA Marine sediments Deep biosphere Phytoplankton Contamination Seafloor IODP Biomarkers Mars GREEN SULFUR BACTERIA EXTRACELLULAR DNA BLACK-SEA ENVIRONMENTAL DNA GENOME SEQUENCE NUCLEIC-ACIDS PLANT DNA SOIL CONTAMINATION PRESERVATION Armbrecht, L.H. Coolen, Marco Lejzerowicz, F. George, S.C. Negandhi, K. Suzuki, Y. Young, J. Foster, N.R. Armand, L.K. Cooper, A. Ostrowski, M. Focardi, A. Stat, Michael Moreau, J.W. Weyrich, L.S. Ancient DNA from marine sediments: Precautions and considerations for seafloor coring, sample handling and data generation |
| title | 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_short | 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 |
| topic | Science & Technology Physical Sciences Geosciences, Multidisciplinary Geology Ancient DNA Marine sediments Deep biosphere Phytoplankton Contamination Seafloor IODP Biomarkers Mars GREEN SULFUR BACTERIA EXTRACELLULAR DNA BLACK-SEA ENVIRONMENTAL DNA GENOME SEQUENCE NUCLEIC-ACIDS PLANT DNA SOIL CONTAMINATION PRESERVATION |
| url | http://purl.org/au-research/grants/arc/LP160100839 http://hdl.handle.net/20.500.11937/90975 |