An Outlook for the Acquisition of Marine Sedimentary Ancient DNA (sedaDNA) From North Atlantic Ocean Archive Material

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.

From the Surface Ocean to the Seafloor: Linking Modern and Paleo‐Genetics at the Sabrina Coast, East Antarctica (IN2017_V01)

“…Basidiomycota and Ascomycota were detected, especially at KC06, and also occurred in the water column, suggesting they may survive in both environments. Careful interpretation is required, however, as especially fungi have been linked to contamination in sed aDNA from deep seafloor archive samples stored over many years prior to analyses (Selway et al., 2022), although our samples were freshly collected, thus the latter possibility seems unlikely.…”

A blueprint for integrating scientific approaches and international communities to assess basin-wide ocean ecosystem status

“…(5) Ancient environmental DNA (aDNA) uses eDNA methods and metabarcoding on sediment cores to reproduce temporal changes in pelagic plankton. Using cores from five sites in the North Atlantic, Selway et al 58 presented clear evidence of aDNA from the ubiquitous coccolithophore Emiliania huxleyi, demonstrating the potential of this technique but also highlighting the importance of minimising contamination during sample collection and storage.…”

Recovering short DNA fragments from minerals and marine sediments: A comparative study evaluating lysis and isolation approaches

“…To date, studies employing aeDNA as a climate and biodiversity proxy in sediments mostly focused on lacustrine deposits (Nguyen et al, 2023), with a marked increase in aeDNA research on marine deposits observed recently (e.g., De Schepper et al, 2019;Selway et al, 2022;Zimmermann et al, 2020Zimmermann et al, , 2021, including latest reports of 1-million years old diatom DNA isolated from a marine sediment core (Armbrecht et al, 2022) and record 2-million years old DNA from Kap København formation, which in part includes old marine sediments (Kjaer et al, 2022). Although fossilizing taxa (e.g., foraminifera, diatoms, and coccolithophores) offer a well-established proxy for marine paleoclimate reconstructions, aeDNA adds to a deeper understanding of past ecosystem structure, capturing diversity beyond the fossilized repository and often complementing it (Lejzerowicz et al, 2013;Parducci et al, 2019).…”