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

Citation

Armbrecht, L and Herrando-Perez, S and Eisenhofer, R and Hallegraeff, GM and Bolch, CJS and Cooper, A, An optimized method for the extraction of ancient eukaryote DNA from marine sediments, Molecular Ecology Resources, 20, (4) pp. 906-919. ISSN 1755-098X (2020) [Refereed Article]

Copyright Statement

Copyright 2020 John Wiley & Sons Ltd.

DOI: doi:10.1111/1755-0998.13162

Abstract

Marine 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.

Item Details

Item Type:Refereed Article
Keywords:molecular aDNA methods, ancient DNA, diatoms, dinoflagellates, haptophytes, Maria Island, metagenomics, plankton, seafloor, Tasmania
Research Division:Biological Sciences
Research Group:Ecology
Research Field:Palaeoecology
Objective Division:Environmental Management
Objective Group:Coastal and estuarine systems and management
Objective Field:Assessment and management of coastal and estuarine ecosystems
UTAS Author:Hallegraeff, GM (Professor Gustaaf Hallegraeff)
UTAS Author:Bolch, CJS (Associate Professor Christopher Bolch)
ID Code:138953
Year Published:2020
Funding Support:Australian Research Council (DP170102261)
Deposited By:Ecology and Biodiversity
Deposited On:2020-05-14
Last Modified:2020-12-08
Downloads:0

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