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. 2024 Feb 5;14(1):2976.
doi: 10.1038/s41598-024-52543-0.

eDNA based bycatch assessment in pelagic fish catches

Paulina Urban  1 , Magnus Wulff Jacobsen  2 , Dorte Bekkevold  2 , Anders Nielsen  3 , Marie Storr-Paulsen  4 , Reindert Nijland  5 , Einar Eg Nielsen  6
Affiliations

eDNA based bycatch assessment in pelagic fish catches

Paulina Urban et al. Sci Rep. .

Abstract

Pelagic fish like herring, sardines, and mackerel constitute an essential and nutritious human food source globally. Their sustainable harvest is promoted by the application of precise, accurate, and cost-effective methods for estimating bycatch. Here, we experimentally test the new concept of using eDNA for quantitative bycatch assessment on the illustrative example of the Baltic Sea sprat fisheries with herring bycatch. We investigate the full pipeline from sampling of production water on vessels and in processing factories to the estimation of species weight fractions. Using a series of controlled mixture experiments, we demonstrate that the eDNA signal from production water shows a strong, seasonally consistent linear relationship with herring weight fractions, however, the relationship is influenced by the molecular method used (qPCR or metabarcoding). In four large sprat landings analyzed, despite examples of remarkable consistency between eDNA and visual reporting, estimates of herring bycatch biomass varied between the methods applied, with the eDNA-based estimates having the highest precision for all landings analyzed. The eDNA-based bycatch assessment method has the potential to improve the quality and cost effectiveness of bycatch assessment in large pelagic fisheries catches and in the long run lead to more sustainable management of pelagic fish as a precious marine resource.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Outline of the study consisting of experimental eDNA to weight assessment, molecular method selection, and ground truth assessment through comparison to other bycatch assessment methods.
Figure 2
Figure 2
Comparison of the repeated experiments used to determine the eDNA-to-biomass relationship for ship production water (a) and factory production water (b). The solid line represents the model prediction and dotted lines the 95% confidence interval. Both experiments were prepared for fishing seasons relevant to the Baltic Sea sprat fisheries (March and November). In both water types, estimated herring DNA fraction was underrepresented in the November, compared to the March experiment.
Figure 3
Figure 3
Comparison of the three molecular methods applied to the experimental samples (ship production water (a,b); factory production water (c,d)) for March (a,c) and November (b,d) experiment. Both qPCR based methods (singleplex, black dots, and multiplex, grey triangles) could be used interchangeably to derive accurate estimates of DNA fractions. The solid line represents the model prediction and dotted lines the 95% confidence interval. The DNA-metabarcoding approach, grey squares, showed differences in performance between the two water types analyzed. It appears that reliable DNA fractions can be estimated from “eDNA at factory” samples only.
Figure 4
Figure 4
Shows the fit of each model March (pink) and November (green), to on-site test samples collected at each landing, and compares the predicted weight fraction to the true herring fraction found in the total on-site test sample (black). Each on-site test represented three replicates (each between 2–4 kg of the catch), that were first rinsed with freshwater and then sampled after 10 min, 2 h and 4 h. Each point in the graph represents the mean fraction for each time per landing and 95% confidence intervals across the three replicates. The weight numbers on top show the total amount of catch used for the on-site test sample.
Figure 5
Figure 5
Overview of the herring bycatch estimated for each landing assessed using different methods. Estimates for landing 1 covered both eDNA based estimates; two different logbook estimates, the 3rd party assessment and additional estimated performed by the fisheries control agency that inspected the catch. For landing 2 no ship production water samples could be obtained, hence only factory production water. Error bars represent the standard error of the estimated bycatch rates per method.
Figure 6
Figure 6
Detailed overview of the herring fractions estimated for each tank holding fish in landing 4. The eDNA estimates (orange) from ship production water are compared to additional fisher’s estimates (yellow). For all tanks, the estimates show substantial similarity.
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