Scientists go fishing for fish DNA

It seems you can tell how many fish there are in the sea (or at least a part of it) from what they leave behind.

In a recent US study, scientists found that floating bits of DNA in small water samples revealed the relative biomass of fish roughly as well as a “gold standard” government trawl with nets – with each method yielding information the other missed.

While environmental DNA (eDNA) has shown itself to be a reliable way to determine the variety of fish in an area of water, this is the first study, the authors say, to show that it also can disclose the relative abundance of a species.

During four voyages by the New Jersey Ocean Trawl Survey in 2019, a team from Rockefeller University, Monmouth University and the New Jersey Bureau of Marine Fisheries, led by Rockefeller’s Mark Stoeckle, drew one-litre samples from various depths just before the trawler’s nets were lowered.

In a paper in the Journal of Marine Science, they report that they gained as much information from each sample as from a 66-million-litre trawl sweep.

Most species (70% to 87%) detected by trawl in a given month were also detected by eDNA, and vice versa, including nearly all (92% to 100%) abundant species. Conversely, most dropouts were relatively rare taxa. Trawl and eDNA peak seasonal abundance agreed for about 70% of species.

Fish shed DNA like dandruff, Stoeckle says, leaving an invisible trail wherever they swim. This eDNA can be skin cells, droppings, urine, eggs or other biological residues that last in the ocean for a few days.

The testing involves extracting and sequencing the DNA in a laboratory, then matching the results found in an online DNA reference library.

“The bioinformatic tools used by the team are the same ‘barcode’ analysis pipelines commonly used by microbiologists but were adapted for the study of marine vertebrates,” says Rockefeller’s Zachary Charlop-Powers, who led the software design.

He notes that the year of sampling and DNA extraction required an investment of just $12,000, exclusive of salaries.

Stoeckle says eDNA offers an inexpensive complement to nets, acoustics and other established ways to monitor the health of fish stocks and/or the shifting diversity, distribution and abundance of aquatic life.

“To put this in perspective,” he says, “if we thought of a trawl as a full medical CAT or MRI scan, then eDNA can be thought of as a pocket ultrasound. It can be carried and used anywhere in the hospital, without the time and expense of scheduling a full-scale exam.

“And eDNA surveys will become better and more informative every year as the technique improves and the DNA reference library grows.”

Among work still to be done, the researchers say, is better calibration of eDNA “reads” to fish body mass, and determining how to account for reads that may be the result of injury due to a predator attack.