Deep‐sea sponge derived environmental DNA analysis reveals demersal fish biodiversity of a remote Arctic ecosystem

Abstract

The deep‐sea is vast, remote, and largely underexplored. However, methodological advances in environmental DNA (eDNA) surveys could aid in the exploration efforts, such as using sponges as natural eDNA filters for studying fish biodiversity. In this study, we analyzed the eDNA from 116 sponge tissue samples and compared these to 18 water eDNA samples and visual surveys obtained on an Arctic seamount. Across survey methods, we revealed approximately 30% of the species presumed to inhabit this area and 11 fish species were detected via sponge derived eDNA alone. These included commercially important fish such as the Greenland halibut and Atlantic mackerel. Fish eDNA detection was highly variable across sponge samples. Highest detection rates were found in sponges with low microbial activity such as those from the class Hexactinellida. The different survey methods also detected alternate fish communities, highlighted by only one species overlap between the visual surveys and the sponge eDNA samples. Therefore, we conclude that sponge eDNA can be a useful tool for surveying deep‐sea demersal fish communities and it synergises with visual surveys improving overall biodiversity assessments. Datasets such as this can form comprehensive baselines on fish biodiversity across seamounts, which in turn can inform marine management and conservation practices in the regions where such surveys are undertaken.

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

“…Additionally, no significant differences in vertebrate eDNA signals were reported between marine sponges and water eDNA when collected from the same location simultaneously (Jeunen, Cane, et al, 2023). Finally, variability in the efficiency of eDNA accumulation between different marine sponge species has been observed (Cai et al, 2022;Turon et al, 2020) and potentially linked to filtration rates and microbial activity (Brodnicke et al, 2023).…”

“…Since the use of optimized protocols is linked to increased DNA concentration, diversity detection consistency, and probability of rare taxa (Spens et al, 2016), additional research into protocol optimization for sponge eDNA surveys is required. Furthermore, differences in eDNA accumulation efficiency have been observed for various sponge species (Cai et al, 2022;Turon et al, 2020) and linked to filtration rates and microbial activity (Brodnicke et al, 2023). While our survey targeted a sponge species with a form suited for obtaining tissue biopsies using an ROV with minimal disturbance, to limit negative impacts on the benthic community, increasing our knowledge on which species are most suitable for eDNA monitoring would enhance species detection through sponge eDNA metabarcoding surveys.…”

“…Further exacerbating the time commitment for water filtration is the increased water volume required to be processed in marine eDNA studies compared to freshwater ecosystems (Bowers et al, 2021). To circumvent the need for water filtration, multiple alternative methods have been successfully trialed, including passive filtration (Bessey et al, 2021;Kirtane et al, 2020;Verdier et al, 2021), autonomous sampling (Hansen et al, 2020;Yamahara et al, 2019), and direct sampling of filter-feeding organisms such as marine sponges (Brodnicke et al, 2023;Cai et al, 2022;Harper et al, 2023;Jeunen, Cane, et al, 2023;Mariani et al, 2019;Neave et al, 2023;Turon et al, 2020).…”

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

“…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(Jeunen et al , 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). The observed variability in the efficiency of capturing and retaining eDNA signals across species within the phylum Porifera (Cai et al 2022;Brodnicke et al 2023) has been linked to microbial activity (Brodnicke et al 2023).…”

“…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). The observed variability in the efficiency of capturing and retaining eDNA signals across species within the phylum Porifera (Cai et al 2022;Brodnicke et al 2023) has been linked to microbial activity (Brodnicke et al 2023).…”