Sedimentary ancient DNA to unlock Arctic marine biodiversity during the Holocene Thermal Maximum

Greenland’s west coast is highly vulnerable to the impacts of climate change, with profound implications for marine ecosystems and their services. Projections suggest significant restructuring of Arctic marine ecosystems due to ongoing sea ice decline, yet uncertainties remain regarding the biosphere-specific responses of these ecosystems. The Arctic cryosphere has undergone significant changes throughout the Holocene, with the Holocene Thermal Maximum (HTM) representing a key period of reduced sea ice and warmer conditions. These past environmental shifts provide a valuable analogue for understanding the ongoing impacts of climate warming on Arctic marine ecosystems. Understanding past climate impacts on marine species is essential for predicting future changes and informing policy decisions.

While traditional microfossil records have advanced our knowledge of past ecosystems, they are biased toward species with hard body parts and are insufficiently covered in time and space. To address these limitations, we use sedimentary ancient DNA (sedaDNA) to track HTM marine biodiversity dynamics. This method allows for the detection of a broad range of organisms, including soft-bodied species such as ciliates and jellyfish, which are not preserved in the fossil record. To enhance the taxonomic resolution of marine eukaryotes across all trophic levels, from primary producers to marine mammals, we developed custom hybridization capture probes targeting barcoding regions. This approach enables the retrieval of short DNA fragments and the assessment of postmortem damage to validate the sedaDNA signal. We employed a two-step methodology: (1) compiling databases such as GBIF and WoRMS to identify knowledge gaps in Arctic marine biodiversity, and (2) evaluating various barcoding genes (e.g., 18S, rbcL, ITS2, COI) for taxonomic resolution and reference availability. Using the SILVA-NR99 database, we focused on the V7 region of the small subunit ribosomal RNA gene as a universal marker, while applying alternative markers for groups lacking sufficient resolution. We generated 46,804 80bp-long probes targeting 11,389 species, which we tested both in silico and on marine surface sediment samples collected from 25 sites around Greenland before their application to Holocene sediment cores from western Greenland.

This approach holds great potential for identifying key marine Arctic species across trophic levels and optimizing their taxonomic resolution during the HTM, revealing ecosystem responses to warming. By providing new insights into Arctic marine ecosystem dynamics and their long-term responses to climate change, we aim to offer valuable information for developing adaptive management strategies aimed at ensuring the ecological sustainability of the region.