Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes

Abstract

The deep ocean is the largest biome on Earth and faces increasing anthropogenic pressures from climate change and commercial fisheries. Our ability to sustainably manage this expansive habitat is impeded by our poor understanding of its inhabitants and by the difficulties in surveying and monitoring these areas. Environmental DNA (eDNA) metabarcoding has great potential to improve our understanding of this region and to facilitate monitoring across a broad range of taxa. Here, we evaluate two eDNA sampling protocols and seven primer sets for elucidating fish diversity from deep sea water samples. We found that deep sea water samples (> 1400 m depth) had significantly lower DNA concentrations than surface or mid-depth samples necessitating a refined protocol with a larger sampling volume. We recovered significantly more DNA in large volume water samples (1.5 L) filtered at sea compared to small volume samples (250 mL) held for lab filtration. Furthermore, the number of unique sequences (exact sequence variants; ESVs) recovered per sample was higher in large volume samples. Since the number of ESVs recovered from large volume samples was less variable and consistently high, we recommend the larger volumes when sampling water from the deep ocean. We also identified three primer sets which detected the most fish taxa but recommend using multiple markers due the variability in detection probabilities and taxonomic resolution among fishes for each primer set. Overall, fish diversity results obtained from metabarcoding were comparable to conventional survey methods. While eDNA sampling and processing need be optimized for this unique environment, the results of this study demonstrate that eDNA metabarcoding can facilitate biodiversity surveys in the deep ocean, require less dedicated survey effort per unit identification, and are capable of simultaneously providing valuable information on other taxonomic groups.

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

“…Fish eDNA stratification in the ocean responds to fish vertical distribution Despite the complexity of the vertical structuring of pelagic communities (Sutton 2013) and the call for studies focusing on the deep-sea ecosystem (Mengerink et al 2014;St. John et al 2016;Martin et al 2020), to date just a few studies have used eDNA sampling to explore the deep sea (Thomsen et al 2016;Easson et al 2020;Laroche et al 2020;McClenaghan et al 2020;Govindarajan et al 2021), and none has provided insights on the deep, vertical stratification of eDNA in the ocean. Here, we observed a consistent detection of DNA of the most abundant epipelagic fish species along the water column (e.g., European anchovy is detected down to > 1000 m depth), whereas detection of DNA from deep-sea fish was restricted to the upper depth at which they were assumed to occur and below.…”

“…This material can be analyzed through metabarcoding, which allows community characterization by simultaneously sequencing a short region of the genome of multiple species, which is then compared to a reference database (Hansen et al 2018). eDNA collected from water samples can provide biodiversity information of virtually any marine habitat (Thomsen et al 2012) including deep-sea environments (Thomsen et al 2016;Laroche et al 2020;McClenaghan et al 2020). However, inferring the macroorganisms present in marine ecosystems by analyzing their DNA released into the environment requires an understanding of how DNA traces behave in the water column, and many factors related to extra-organismal DNA production rate, degradation and transport have been reported to influence its detection and concentration in the ocean (Hansen et al 2018).…”

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

“…Despite the complexity of the vertical structuring of pelagic communities (Sutton 2013) and the call for studies focusing on the deep-sea ecosystem (Mengerink et al 2014;St. John et al 2016;Martin et al 2020), to date just a few studies have used eDNA sampling to explore the deep-sea (Thomsen et al 2016;Laroche et al 2020;McClenaghan et al 2020), and none has provided insights on the deep, vertical stratification of eDNA in the ocean. Here, we observed a consistent detection of DNA of the most abundant epipelagic fish species along the water column (e.g.,…”

“…This material can be analyzed through metabarcoding, which allows community characterization by simultaneously sequencing a short region of the genome of multiple species, which is then compared to a reference database. eDNA collected from water samples can provide biodiversity information of virtually any marine habitat (Thomsen et al 2012) including deep-sea environments (Thomsen et al 2016;Laroche et al 2020;McClenaghan et al 2020).…”

Airborne Environmental DNA Metabarcoding Detects More Diversity, More Efficiently, Than a Traditional Plant Community Survey

“…For example, in aquatic systems, Valentini et al (26) found that eDNA metabarcoding could more accurately detect both bony sh and amphibians compared to auditory, visual, and collection-based methods. Recently, McClenaghen et al (27) used eDNA metabarcoding to detect deep sea sh and found that the eDNA method gave similar results to conventional eld surveys while having a much lower sampling effort requirement. Additionally, eDNA metabarcoding has also been used for sediment analysis such as the study from Yoccoz et al (16) where after metabarcoding, terrestrial sediment samples were shown to correctly detect present species at the surface.…”