Characterizing Antarctic fish assemblages using eDNA obtained from marine sponge bycatch specimens

Abstract

International conservation goals have been set to mitigate Southern Ocean ecosystem deterioration, with multiple monitoring programs evaluating progress towards those goals. The scale of continuous monitoring through visual observations, however, is challenged by the remoteness of the area and logistical constraints. Given the ecological and economic importance of the Southern Ocean, it is imperative that additional biological monitoring approaches are explored. Recently, marine sponges, which are frequently caught and discarded in Southern Ocean fisheries, have been shown to naturally accumulate environmental DNA (eDNA). Here, we compare fish eDNA signals from marine sponge bycatch specimens to fish catch records for nine locations on the continental shelf (523.5–709 m) and 17 from the continental slope (887.5–1611.5 m) within the Ross Sea, Antarctica. We recorded a total of 20 fishes, with 12 fishes reported as catch, 18 observed by eDNA, and ten detected by both methods. While sampling location was the largest contributor to the variation observed in the dataset, eDNA obtained significantly higher species richness and displayed a significantly different species composition compared to fish catch records. Overall, eDNA read count correlated more strongly with fish abundance over biomass. Species composition correlated on a regional scale between methods, however eDNA signal strength was a low predictor of catch numbers at the species level. Our results highlight the potential of sponge eDNA monitoring in the Southern Ocean by detecting a larger fraction of the fish community compared to catch recordings, thereby increasing our knowledge of this understudied ecosystem and, ultimately, aiding conservation efforts.

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

“…We were able to identify a diverse profile of Actinopterygii and Chondrichthyes from Antarctic sponge specimens, irrespective of the preservation method used. The Antarctic fish community constituted 64 taxa ranging from Nototheniidae (cod icefishes) and Channichthyidae (icefishes), to Bathydraconidae (Antarctic dragonfishes), all of which are known to occur in the Ross Sea according to Antarctic toothfish bycatch records (Pinkerton and Bradford-Grieve 2014;Jeunen et al 2024).…”

“…We were able to identify a diverse profile of Actinopterygii and Chondrichthyes from Antarctic sponge specimens, irrespective of the preservation method used. The Antarctic fish community constituted 64 taxa ranging from Nototheniidae (cod icefishes) and Channichthyidae (icefishes), to Bathydraconidae (Antarctic dragonfishes), all of which are known to occur in the Ross Sea according to Antarctic toothfish bycatch records (Pinkerton and Bradford-Grieve 2014; Jeunen et al 2024). Interestingly, one notably absent taxonomic group, besides two signals of Gymnoscopelus sp., from sponge specimens collected in deeper waters are the myctophids, the most diverse and abundant group of mesopelagic fishes globally, including in the Southern Ocean (Duhamel et al 2014; Woods et al 2023; Vasiliadis et al 2024).…”

“…A custom-curated reference database was generated using CRABS v 0.1.5 (Jeunen et al 2022). The custom curated reference database consisted of sequences downloaded from multiple online repositories using the ‘ db_download ’ function and in-house generated barcodes of Southern Ocean fish species (Jeunen et al 2024) using the ‘ db_import ’ function. Amplicon regions were extracted from sequences through in silico PCR analysis (‘ insilico_pcr ’ function) and pairwise global alignments (‘ pga ’ function).…”

“…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).…”