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An outlook for the acquisition of marine sedimentary ancient DNA (sedaDNA) from North Atlantic Ocean archive material

Citation

Selway, CA and Armbrecht, L and Thornalley, D, An outlook for the acquisition of marine sedimentary ancient DNA (sedaDNA) from North Atlantic Ocean archive material, Paleoceanography and Paleoclimatology, 37, (5) Article e2021PA004372. ISSN 2572-4517 (2022) [Refereed Article]


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DOI: doi:10.1029/2021PA004372

Abstract

Studies incorporating sedimentary ancient DNA (sedaDNA) analyses to investigate paleo-environments have increased considerably over the last few years, and the possibility of utilizing archived sediment cores from previous field campaigns could unlock an immense resource of sampling material for such paleo-investigations. However, sedaDNA research is at a high risk of contamination by modern environmental DNA, as sub-optimal sediment storage conditions may allow for contaminants (e.g., fungi) to grow and become dominant over preserved sedaDNA in the sample. Here, we test the feasibility of sedaDNA analysis applied to archive sediment material from five sites in the North Atlantic, collected between 1994 and 2013. We analyzed two samples (one younger and one older) per site using a metagenomic shotgun approach and were able to recover eukaryotic sedaDNA from all samples. We characterized the authenticity of each sample through sedaDNA fragment size and damage analyses, which allowed us to disentangle sedaDNA and contaminant DNA. Although we determined that contaminant sequences originated mainly from Ascomycota (fungi), most samples were dominated by Emiliania huxleyi, a haptophyte species that commonly blooms in the study region. We attribute the presence of contaminants to non-ideal sampling and sample storage conditions of the investigated samples. Therefore, while we demonstrate that sedaDNA analysis of archival North Atlantic seafloor sediment samples are generally achievable, we stress the importance of best-practice ship-board sampling techniques and storage conditions to minimize contamination. We highly recommend the application of robust bioinformatic tools that help distinguish ancient genetic signals from modern contaminants, especially when working with archive material.

Item Details

Item Type:Refereed Article
Keywords:sedimentary ancient DNA, North Atlantic, phytoplankton, metagenomics, fungi, contamination, DNA damage
Research Division:Biological Sciences
Research Group:Ecology
Research Field:Palaeoecology
Objective Division:Environmental Management
Objective Group:Marine systems and management
Objective Field:Marine biodiversity
UTAS Author:Armbrecht, L (Dr Linda Armbrecht)
ID Code:150408
Year Published:2022
Deposited By:Ecology and Biodiversity
Deposited On:2022-06-13
Last Modified:2022-06-15
Downloads:0

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