Unveiling the hidden diversity of marine eukaryotes in the Ross Sea: A comparative analysis of seawater and sponge eDNA surveys

Abstract

The Ross Sea, Antarctica, while largely pristine, is experiencing increased anthropogenic pressures, necessitating enhanced biomonitoring efforts for conservation purposes. Environmental DNA (eDNA) extracted from marine sponges provides a promising approach for biodiversity monitoring in remote areas by circumventing the need for time‐consuming water filtration. Investigations into the efficacy of eDNA signal detection across the tree of life from marine sponges have yet to be fully explored. Here, we conducted a seawater and sponge eDNA metabarcoding survey at seven coastal locations in the Ross Sea to assess spatial eukaryote biodiversity patterns and investigate eDNA signal differences between both substrates. In total, we detected 1450 operational taxonomic units (OTUs) across 30 phyla. Significant differences in water and sponge eDNA signal richness and composition were observed, with a partial overlap in OTU detection between both substrates and, thereby, underscoring the crucial role of substrate selection in eDNA metabarcoding surveys. Furthermore, alpha and beta diversity analyses revealed distinct eDNA signals among sampling locations, which were corroborated by known species distributions. However, only 135 OTUs (9%) could be successfully assigned to species level, and 574 OTUs (40%) were unable to be taxonomically classified, due to limitations in the reference database. Our results provide evidence for the potential of eDNA monitoring in remote areas, demonstrate the need to consider more sophisticated sampling strategies whereby multiple eDNA substrates are incorporated, and highlight the importance of complete reference databases for robust taxonomy assignment of eDNA signals.

Unlocking Antarctic molecular time-capsules – recovering historical environmental DNA from museum-preserved sponges

“…Obtaining quantitative spatial and temporal information on Antarctic species is more than ever critical, with the region forecast to see major physical and biological changes in response to climate change and anthropogenic pressures (Chown and Brooks 2019;Convey and Peck 2019). While eDNA has been successfully implemented to monitor contemporary biodiversity patterns of the Antarctic marine biome (Cowart et al 2018;Clarke et al 2021;Jeunen et al 2023b;Liao et al 2023;Suter et al 2023), a lack of long-term, quantitative observations limits our understanding of the natural variability in Antarctic ecosystems and complicates future policy making (Howell et al 2021;Suter et al 2023). Hence, investigating historical and ancient DNA has the potential to provide the missing information for successful conservation efforts in Antarctica.…”

“…Additionally, multiple mismatches at the 3’ end of the forward PCR primer-binding region (S8 FIG) could have significantly reduced the amplification efficiency for this taxonomic group, resulting in false-negative detections (Stadhouders et al 2010). While universal metabarcoding approaches have been reported to be an inefficient solution due to the co-amplification of sponge host DNA (Jeunen et al 2023b), a multi-marker targeted metabarcoding approach has previously been proposed for aquatic eDNA research to increase species detection accuracy and reduce the impact of amplification bias (McElroy et al 2020).…”

“…In particular, marine sponges have been shown to naturally accumulate environmental DNA by continuously filtering large volumes of water to capture particulate matter as a food source (Godefroy et al 2019). Compared to aquatic eDNA, marine sponges have been observed to hold near-identical vertebrate and eukaryotic diversity patterns within small spatial scales (Jeunen et al 2023a, 2023b), as well as mirroring temporal resolutions in a controlled mesocosm experiment (Cai et al 2022). Similarly to comparisons between aquatic eDNA and traditional survey approaches, a partial overlap between sponge eDNA and visual surveys has been observed, with sponge eDNA recovering a larger fraction of the fish community in deep-sea and polar regions (Brodnicke et al 2023; Jeunen et al 2024).…”