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The Evidence of Things Not Seen: eDNA and Fisheries Stocks

Knudsen, S. W., Ebert, R. B., Hesselsøe, M., Kuntke, F., Hassingboe, J., Mortensen, P. B., … Møller, P. R. (2019). Species-specific detection and quantification of environmental DNA from marine fishes in the Baltic Sea. Journal of Experimental Marine Biology and Ecology, 510 (October 2018), 31–45. doi:10.1016/j.jembe.2018.09.004

Trawler Hauling Nets. NOAA, 1968. https://commons.wikimedia.org/

Say you walked to the ocean and filled a jar with ocean water. From that sample, could you confidently say there are no fish in the ocean? No, you couldn’t. Logic says your sampling method is flawed, or you were unlucky and grabbed a sample without a fish in it. However, just because there’s no fish in your jar doesn’t mean microscopic evidence isn’t there—enter the world of environmental DNA, or eDNA (fragments of DNA left behind in the environment by an organism), and see how this new technology could help in scientific assessments throughout the ocean.

Traditionally, estimating fish populations requires trawling through large swaths of ocean. Not only can trawling be harmful to the local environment (e.g. bottom trawling where heavy nets disturb the sea floor), but it is also very expensive. Given the size of the ocean, a catch is not always guaranteed. Different species can escape nets more easily, or show up disproportionally between trawl surveys, while other species look nearly identical and can be misidentified.

Steen Knudsen and a team of scientists decided to develop and test a method to better detect eDNA to find a more efficient approach to estimate fish stocks. The team paired both trawl surveys and eDNA sampling to figure out if eDNA was capable of revealing the presence of six commercial species in the Eastern North Atlantic. Specifically, the species they were looking for were Atlantic cod, mackerel, and herring, as well as European eel, flounder, and plaice. While trawl surveys were going on, the team collected water samples at the same depths where nets were collecting live samples. Afterwards, species collected in the trawl survey were separately counted, while the water samples underwent filtration to allow DNA extraction.

Fig. 1: Basics of PCR, showing double-stranded DNA being broken apart and reforming (through heating and cooling of the solution). Primers and other nucleotides fill the gaps of the single strands, forming new double strands. (Enzoklop, 2014. https://commons.wikimedia.org/)

The amount of DNA left behind in the environment by marine creatures varies depending on the number of organisms sloughing it off in a given area. The “loose” eDNA degrades within days or weeks based on light, temperature, and enzymes in the water. To account for tiny amounts of DNA, samples were amplified using qPCR, a type of polymerase chain reaction. PCR is a way of creating copies of DNA by repeatedly breaking the double strands apart in a solution of nucleotides and known genome sequences (primers and probes). These nucleotides attach to the newly broken single strands, forming new double-stranded DNA. The cycle of breaking and reforming these strands continues until millions of copies are made.

Of the six species the team was looking for, four were present in the trawl surveys conducted, while the remaining two (Atlantic mackerel and European eel) only appeared in the eDNA analysis. Mackerel are fast fish, often swimming large distances, so their physical absence and eDNA presence was not surprising—they left a DNA trail in the sampled water. The low amounts of eel eDNA were also not surprising given the species can easily slip through the trawl net sizes used, and because the species is found in greater numbers in shallower waters that were not trawled in the current study.

Fig. 2: Fig. 3, Knudsen et al., (2018). Locations of 17 trawl and eDNA sampling sites; circles represent catch per unit effort (CPUE) while yellow-red coloration indicates the amount of eDNA snippets found in water samples taken at mid-water and bottom depths. Species guide: A. Atlantic herring; B. Atlantic cod; C. European flounder; D. European plaice.

The team noted a correlation between the catch per unit effort (CPUE) and eDNA from Atlantic cod, mackerel, and European plaice. The correlation between Atlantic cod catch and eDNA was stronger than that of the mackerel, which was unexpected, but the scientists suggested the mackerel’s weaker catch:eDNA relationship could have been due to the mackerel’s preference for swimming in the water column, away from the bottom. Knudsen went on to discuss that there are many factors that complicate how eDNA results are interpreted, from how finicky primers can be during the PCR process, to shifts in fish behavior with age that result in migration to a different environment.

Just because the eDNA and trawl count comparisons did not always match, doesn’t mean eDNA is a flawed method for assessing fisheries stocks. Knudsen’s team emphasized that the specificity of the DNA makes species identification easier, even if it’s not great for approximating fish counts. Confident identification of species found in an area can be tough, especially if an expert isn’t on board examining the trawl samples. The eDNA also bodes well for detecting species that cannot be caught in a particular trawl, or for those that live in environments where trawling is impossible—like marine protected areas.

In addition, the team suggested eDNA quantification should focus on variations of one target species between samples, instead of looking at different target species in one sample. Overall, the team concluded that many more trawls and accompanying eDNA sampling would have to occur to hone the methodology, but they are hopeful that this route could lead to a change in how we estimate local populations of many species that are hard to access. It really does make you rethink all the information contained in one jar of water, doesn’t it?



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