Marine eukaryote sedaDNA extractions

The aim of this study was to optimize sedaDNA extraction protocols to maximize the yield of small DNA fragments typical of ancient DNA (aDNA) over a broad diversity of marine eukaryotes. We compared seven combinations of sedaDNA extraction treatments and sequencing library preparations using a set of three sediment samples collected in a 104 m deep water column 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 liquid silica, diluted versus undiluted DNA in shotgun library preparations, and the advantage of using size-selection versus no size-selection of low molecular weight (LMW) DNA in these libraries. We present an optimized extraction protocol integrating these steps in the associated publication. 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.