An optimized method for the extraction of ancient eukaryote DNA from marine sediments

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dc.contributor.authorArmbrecht, L.
dc.contributor.authorHerrando-Pérez, S.
dc.contributor.authorEisenhofer, R.
dc.contributor.authorHallegraeff, G.M.
dc.contributor.authorBolch, C.J.S.
dc.contributor.authorCooper, A.
dc.date.issued2020
dc.description.abstractMarine sedimentary ancient DNA (sedaDNA) provides a powerful means to reconstruct marine palaeo-communities across the food web. However, currently there are few optimized sedaDNA extraction protocols available to maximize the yield of small DNA fragments typical of ancient DNA (aDNA) across a broad diversity of eukaryotes. We compared seven combinations of sedaDNA extraction treatments and sequencing library preparations using marine sediments collected at a water depth of 104 m off Maria Island, Tasmania, in 2018. These seven methods contrasted frozen versus refrigerated sediment, bead-beating induced cell lysis versus ethylenediaminetetraacetic acid (EDTA) incubation, DNA binding in silica spin columns versus in silica-solution, diluted versus undiluted DNA in shotgun library preparations to test potential inhibition issues during amplification steps, and size-selection of low molecular-weight (LMW) DNA to increase the extraction efficiency of sedaDNA. Maximum efficiency was obtained from frozen sediments subjected to a combination of EDTA incubation and bead-beating, DNA binding in silica-solution, and undiluted DNA in shotgun libraries, across 45 marine eukaryotic taxa. We present an optimized extraction protocol integrating these steps, with an optional post-library LMW size-selection step to retain DNA fragments of ≤500 base pairs. We also describe a stringent bioinformatic filtering approach for metagenomic data and provide a comprehensive list of contaminants as a reference for future sedaDNA studies. The new extraction and data-processing protocol should improve quantitative paleo-monitoring of eukaryotes from marine sediments, as well as other studies relying on the detection of highly fragmented and degraded eukaryote DNA in sediments.
dc.description.statementofresponsibilityLinda Armbrecht, Salvador Herrando-Pérez, Raphael Eisenhofer, Gustaaf M. Hallegraeff, Christopher J. S. Bolch, Alan Cooper
dc.identifier.citationMolecular Ecology Resources, 2020; 20(4):906-919
dc.identifier.doi10.1111/1755-0998.13162
dc.identifier.issn1755-098X
dc.identifier.issn1755-0998
dc.identifier.orcidArmbrecht, L. [0000-0002-1213-1257]
dc.identifier.orcidHerrando-Pérez, S. [0000-0001-6052-6854]
dc.identifier.orcidCooper, A. [0000-0002-7738-7851]
dc.identifier.urihttp://hdl.handle.net/2440/126163
dc.language.isoen
dc.publisherWiley
dc.relation.granthttp://purl.org/au-research/grants/arc/CE170100015
dc.relation.granthttp://purl.org/au-research/grants/arc/DP170102261
dc.relation.granthttp://purl.org/au-research/grants/arc/FL140100260
dc.rights© 2020 John Wiley & Sons Ltd
dc.source.urihttps://doi.org/10.1111/1755-0998.13162
dc.subjectancient DNA
dc.subjectdiatoms
dc.subjectdinoflagellates
dc.subjecthaptophytes
dc.subjectMaria Island
dc.subjectmetagenomics
dc.subjectplankton
dc.subjectseafloor
dc.subjectTasmania
dc.titleAn optimized method for the extraction of ancient eukaryote DNA from marine sediments
dc.typeJournal article
pubs.publication-statusPublished

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