Genetic sampling finds 'species richness' hiding in coastal eelgrass beds

Environmental DNA sampling (eDNA) in Pacific and Atlantic coastal waters has revealed an unseen "species richness" — detecting twice as many fish species as a traditional net survey, according to a new Canadian study.

Scientists behind the research say the findings point to eDNA as a cheaper, easier and less intrusive way to measure biodiversity and monitor the northward movement of fish caused by climate change.

Nineteen eelgrass beds — 10 in Nova Scotia and nine on southern Vancouver Island — were sampled in 2019.

A lengthy beach seine net was used to capture fish. At the same time and place, seawater samples were collected to test for trace amounts of genetic material shed by passing fish.

The goal was to compare the sampling methods to measure biodiversity.

"We actually captured more diversity, almost twice as much. So for every seine, if we were to capture 10 species, we would sequence on average 20 species out of the DNA," said Ryan Stanley, a Fisheries and Oceans Canada biologist at the Bedford Institute of Oceanography in Nova Scotia.

Stanley is co-author of a paper which published the findings in the Canadian Journal of Fisheries and Aquatic Sciences.

Scientists used a process known as eDNA metabarcoding.

This system converts a genetic sequence into a barcode that can identify a species for comparison in a genetic reference database, the same way a Universal Product Code (UPC) is used by a supermarket scanner to identify products.

Unlike the UPC code at the store, not every species has an exact barcode match in the genetic reference.

Of the 129 fish types detected by eDNA, there were only four not associated with the record in their respective region.

One was a giant wrymouth, an elongated eel-like fish with a broad head, detected in Nova Scotia by eDNA even though it is a Pacific species.

It may have been another species of wrymouth known in the Atlantic, but not in their reference database.

Fisheries and Oceans Canada geneticist Cathryn Abbott, at the Pacific Biological Station in Nanaimo, B.C., says researchers were careful to test their findings but found few gaps where a detected DNA did not match the local reference.

"We found it to be really effective," said Abbott.

"This was our first shot at this method, in this context. And eDNA performed incredibly well in my mind. I was amazed that we detected twice as many species, but immediately they all made ecological sense and were plausible."

In Nova Scotia, eelgrass beds were sampled from Taylor Head on the eastern shore to McNabs Island in the mouth of Halifax Harbour to Rosebay on the south shore.

"We got a few species we weren't expecting," Stanley said in an interview at Taylor Head.

There, the 25-metre beach seine net captured a tiny northern pufferfish and a slightly larger northern barracuda — both of which are semi-tropical.

The eDNA did not detect the puffer fish, but did pick up the barracuda, several types of jack and a spotfin butterfly fish not captured in the seine.

"These species have been observed along the coast sometimes, particularly more in the southern part of the province by recreational divers. But they're exceedingly rare," said Stanley.

"The eDNA did a very good job, particularly at Taylor Head here, identifying diversity that we didn't otherwise catch directly in the net."

In British Columbia, researchers detected five species of Pacific salmon that were not captured in the beach seines. Chinook salmon were detected at eight of nine sites, but not captured in seines at any site.

As an example of efficiency, scientists said eDNA barcoding at the nine sites detected 84 per cent of species captured by a previous beach seine survey that involved 89 locations over a much larger area.

In Canada, with the world's longest coastline — 240,000 kilometres — that has advantages.

"It's a perfect way to go out into an environment and have a quick look at what might be there or what isn't there. And when I say, quick, look, it's because we're going out with a bottle to capture a litre of water, which is a lot easier than a big vessel obviously, that needs to go with a big net and a bunch of crew," said Abbott.

eDNA has its limitations. It does not count fish, cannot detect age, sex or size, but it is a way to screen for the presence or absence of a species.

Abbott said this can help monitor changes in the ecosystem, like climate change.

"We are expecting more northward expansion of fish as waters warm and more northern ranges become tolerant to what is more tropical and subtropical species. We do expect eDNA would be a good tool to detect those range expansions early, potentially earlier than we might happen to catch them in a net."