Vertical stratification of environmental DNA in the open ocean captures ecological patterns and behavior of deep‐sea fishes

Abstract

The deep sea provides global vital functions such as sequestration of carbon from the atmosphere. The increased anthropogenic pressures and interest in expanding deep-sea fisheries make this pristine ecosystem particularly vulnerable, whose conservation largely depends on rapid knowledge acquisition. In view of the limitations of traditional methods to explore the biodiversity of this vast ecosystem, the analysis of traces of macroorganismal DNA released into the water column arises as a cost-effective, noninvasive alternative. Yet, the success of this approach requires understanding of the stratification of DNA traces in the ocean. This study provides evidence that fish DNA traces can be used to establish depth-specific fish diversity and abundance throughout the water column, opening a promising avenue for gathering knowledge about the deep-sea ecosystem.Establishing the foundations for a sustainable use of deep-sea resources relies on increasing knowledge on this inaccessible ecosystem, which is challenging with traditional methods. The analysis of environmental DNA (eDNA) emerges as an alternative, but it has been scarcely applied to deep-sea fish. Here, we have analyzed the fish eDNA contained in oceanic vertical profile samples (up to 2000 m depth) collected throughout the continental slope of the Bay of Biscay. We detected 52 different fish species, of which 25 were classified as deep-sea fish. We found an increase of deep-sea fish richness and abundance with depth, and that eDNA reflects daynight community patterns and species-specific vertical distributions that are consistent with the known diel migratory behavior of many mesopelagic fishes. These findings highlight the potential of eDNA to improve knowledge on the fish species inhabiting the dark ocean before this still pristine ecosystem is further exploited.

Environmental DNA persistence and fish detection in captive sponges

“…As for the resident species, sponge nsDNA may pro- When there is no bar at the corresponding time point, it represents that no fish species were detected. Colour codes refer to the experimental fish species for each tank (three species for each tank, two of which ubiquitous) detection (Allan et al, 2021;Canals et al, 2021). Thus, the sessile nature of sponges could more exhaustively track the diel fluctuations and other behaviours of fishes.…”

Environmental DNA persistence and fish detection in captive sponges

“…Our evidence further demonstrates how certain sponges could help monitor these more elusive species (preserving eDNA for longer), which may be missed by other monitoring methods. As for the resident species, sponge nsDNA may provide insightful fish detection compared to aquatic eDNA because spatial and temporal variability of aquatic eDNA may affect species detection (Allan et al, 2021; Canals et al, 2021). Thus, the sessile nature of sponges could more exhaustively track fish’s diel fluctuations and other behaviours.…”

Framing Cutting-Edge Integrative Deep-Sea Biodiversity Monitoring via Environmental DNA and Optoacoustic Augmented Infrastructures

“…eDNA metabarcoding approaches are revolutionizing marine biodiversity assessment and monitoring because they can be used to simultaneously determine entire species communities, even when the exact composition of these assemblages is unknown (e.g., Deiner et al, 2017;Djurhuus et al, 2017;Stefanni et al, 2018;Eble et al, 2020;Kolda et al, 2020;McClenaghan et al, 2020;Seymour et al, 2020;Kawato et al, 2021). eDNA metabarcoding is becoming a particularly valuable tool for deep-sea biodiversity research and monitoring given high species diversity, low animal numbers, difficulties in taxonomic identification due to limited taxonomic expertise, large and remote location, and associated logistical constraints for sample/specimen acquisition (Thomsen et al, 2016;Kersten et al, 2019;Atienza et al, 2020;Canals et al, 2021;Kawato et al, 2021;Merten et al, 2021).…”

“…Recent eDNA advancements allow us to study a wide range of taxa (including vertebrates) that are otherwise inaccessible by direct capture or optoacoustic technologies (e.g., Lacoursière-Roussel et al, 2018;Cowart et al, 2020;Laroche et al, 2020b;Canals et al, 2021). Though still limited to the near surface waters, the combined use of video-monitoring and eDNA metabarcoding has also been successfully applied using Baited Remote Underwater Video Systems (BRUVs) to monitor Marine Protected Areas (MPAs) (Stat et al, 2019) or integrated in cabled observatories (Mirimin et al, 2021).…”