A drop in the ocean: Monitoring fish communities in spawning areas using environmental DNA

Abstract

Early life stages of aquatic organisms are particularly vulnerable to climatic stressors; however, they are difficult to monitor due to challenges in sampling and morphological identification. Environmental DNA (eDNA) from water samples represents an opportunity for rapid, nondestructive monitoring of aquatic community composition as well as single species monitoring. eDNA can also detect spawning events, although has not been yet tested in offshore spawning grounds. Here, we used metabarcoding of water samples to detect the presence of key fish taxa in spawning areas that are difficult to monitor using traditional means. We analyzed DNA from water samples and fish larvae samples at 14 offshore sites, using 12S mitochondrial metabarcoding and compared taxa detections, diversity, and community structure estimated by both sample types. Species richness and diversity did not differ between water and larvae samples. Both sample types detected a core of 12 taxa across the survey, with an average agreement in detections of 75% at sampling site level. Water samples detected two of the three most abundant taxa, the sandeel, Ammodytes marinus, and clupeids, Clupea harengus/Sprattus sprattus, at 31% and 38% more sites than larvae samples respectively, while Callionymus sp. was more prevalent in larvae samples. Mackerel (Scomber scombrus) and blue whiting (Micromestius poutassou) were only detected in water samples despite sampling taking place at peak spawning times for these species. Our results demonstrate that eDNA metabarcoding provides a rapid and feasible monitoring method for the management of key taxa, such as sandeel, that cannot be easily monitored using traditional capture surveys.

Biodiversity assessment across a dynamic riverine system: A comparison of eDNA metabarcoding versus traditional fish surveying methods

“…Mock communities constructed using pooled genomic DNA, which are then PCR amplified, represent a much more informative analog to biases which may occur in eDNA samples during the amplification process. Studies which have used this approach reiterate that relative abundances estimated from metabarcoding reads should be interpreted with caution (Lamb et al, 2019; Leray & Knowlton, 2017; Ratcliffe et al, 2021).…”

The future of biodiversity monitoring and conservation utilizing environmental DNA

“…For example, Ratcliffe et al. (2021) used eDNA metabarcoding in fish spawning areas in the Irish and Celtic seas. Concurrent larval fish sampling by netting produced equivalent estimates of species richness and diversity with eDNA metabarcoding with 75% agreement.…”

Multiparametric monitoring of fish activity rhythms in an Atlantic coastal cabled observatory

“…Like any other approach, there are a number of limitations that still affect eDNA's full potential and these can be overcome by further refining the method itself (Zaiko et al, 2018) but also by corroborating it with other types of data (e.g. Ratcliffe et al, 2020). Thus, cabled observatories such as SmartBay offer a unique opportunity to conduct multi-disciplinary studies combining video, oceanographic, physical (audio-visual) approaches for cross validation with eDNA, hence obtaining an augmented status of such sites, leading to a result that is greater than the sum of parts.…”