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

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

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

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

Permalink

Publication Type:: Journal Article
Citation:: Earth-Science Reviews, 2019, 196
Issue Date:: 2019-09-01

Open Access

Copyright Clearance Process

Recently Added
In Progress
Open Access

This item is open access.

Adobe PDF

Download Accepted Manuscript VersionAdobe PDF (2.16 MB)

View on publisher's site

View statistics

Full metadata record

Field	Value	Language
dc.contributor.author	Armbrecht, LH	en_US
dc.contributor.author	Coolen, MJL	en_US
dc.contributor.author	Lejzerowicz, F	en_US
dc.contributor.author	George, SC	en_US
dc.contributor.author	Negandhi, K	en_US
dc.contributor.author	Suzuki, Y https://orcid.org/0000-0001-7872-9289	en_US
dc.contributor.author	Young, J	en_US
dc.contributor.author	Foster, NR	en_US
dc.contributor.author	Armand, LK	en_US
dc.contributor.author	Cooper, A	en_US
dc.contributor.author	Ostrowski, M https://orcid.org/0000-0002-4357-3023	en_US
dc.contributor.author	Focardi, A	en_US
dc.contributor.author	Stat, M	en_US
dc.contributor.author	Moreau, JW	en_US
dc.contributor.author	Weyrich, LS	en_US
dc.date.available	2021-08-12T19:01:10Z
dc.date.issued	2019-09-01	en_US
dc.identifier.citation	Earth-Science Reviews, 2019, 196	en_US
dc.identifier.issn	0012-8252	en_US
dc.identifier.uri	http://hdl.handle.net/10453/134221
dc.description.abstract	© 2019 Elsevier B.V. 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.	en_US
dc.relation.ispartof	Earth-Science Reviews	en_US
dc.relation.isbasedon	10.1016/j.earscirev.2019.102887	en_US
dc.rights	info:eu-repo/semantics/embargoedAccess
dc.subject.classification	Geology	en_US
dc.title	Ancient DNA from marine sediments: Precautions and considerations for seafloor coring, sample handling and data generation	en_US
dc.type	Journal Article
utslib.citation.volume	196	en_US
utslib.for	0603 Evolutionary Biology	en_US
utslib.for	0604 Genetics	en_US
utslib.for	0405 Oceanography	en_US
utslib.for	04 Earth Sciences	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
utslib.copyright.status	open_access	*
pubs.publication-status	Published	en_US
pubs.volume	196	en_US

Abstract:

© 2019 Elsevier B.V. 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.

Please use this identifier to cite or link to this item:

http://hdl.handle.net/10453/134221