New DNA tool 'changes everything in marine science'

Take a cup of water from any river, lake, or oceanside beach and environmental DNA fingerprinting can reveal which species of fish were recently swimming there. It used to take a lab a month or more to get those results, but now a new tool can identify a specific species in three days or less. That could be a gamechanger for science.

“If you took a water sample from New York Harbor on Tuesday morning, by the end of day Thursday you’ll know whether winter flounder are back,” said Jesse Ausubel, director of the Program for the Human Environment at Rockefeller University in New York City.

New York Harbor restricts dredging if winter flounder are present.

Not only is the “Go Fish eDNA” (environmental DNA) tool fast, it costs just $15 per sample for one species, and $8 for additional species. In a few years time an early morning water sample from a beach could tell lifeguards by midmorning if tiger or white sharks were around, Ausubel said. “It’d be a kind of DNA dipstick.”

Rockefeller University hosted the first National Conference on Marine Environmental DNA Nov. 29-30, in which scientists discussed how they are using and improving the technology.

"Over 1,000 miles from shore we were able in 48 hours to identify the presence of white sharks in the water column beneath the ship using nanopore eDNA sequencing at sea,” said Barbara Block, a marine scientist at Stanford University.

The Go Fish eDNA tool was developed by Mark Stoeckle, a senior research associate at Rockefeller University. He named it after the children's game Go Fish, in which one player asks another if they have a specific card in their hand, as in, “do you have any jacks?”

The ability to identify animals by their genetic trail without having to catch them is “a breakthrough with major environmental and economic implications,” said Stoeckle. (See how scientists are tracking animals on land with eDNA.)

Tracking a fish’s genetic trail

Humans lose between 30,000 and 40,000 skin cells every hour. The dust that collects on tables, shelves, and in corners of rooms in our homes is mostly dead human skin cells. Fish and other marine species also shed skin and other cells. These cells eventually sink or degrade, but research shows this genetic trail stays in the water column for 24 hours on average.

A water sample from a column of water goes through an extremely fine filter. DNA is extracted from the remaining "goo,“ explains Ausubel. DNA (Deoxyribonucleic acid) is found in every cell—from heart to skin, blood to bone—of every living organism. It contains genetic information that helps determine physical characteristics such as fins, fur, or skin.

The extracted DNA may amount to tens of millions of DNA fragments in a single sample. Fortunately, certain combinations of DNA called genetic markers are unique to each species. For example, a phone number with a 212 area code tells you the person lives in New York City. The DNA genetic markers are isolated and then matched against a DNA database that acts like a phone number directory to precisely identify the species found in the sample.

It’s a very reliable identification tool, and provides an index of the abundance of a particular species, says Ausubel. It is also revealing great levels of biodiversity in the oceans. Researchers using a traditional net seine to learn what lives in the oceans might catch 20 different species, while eDNA might find 100 species in the same waters, he said.

“If we had eDNA during the 11-year, $650 million Census of Marine Life project that ended in 2010 we could have done it better, for less money and much faster,” said Ausubel, one of the leaders of the Census.

“It changes everything in marine science. You just collect a few cups of water.”

So easy kids can do it

That’s just what New York high school students did on a weekly basis from the fishing pier at Coney Island during the spring and summer of 2017. They discovered 34 species of marine life had passed by, including sharks and rays.

Students from Boynton Middle School, in a collaboration with Cornell University, are taking water samples and using eDNA to find invasive fish species in their part of upstate New York.

In Wisconsin, researchers documented five invasive species of marine zooplankton in the ballast water of ships plying Lake Superior, including the eDNA of a bloody red shrimp originally from the Black Sea area.

"eDNA opens the door to cheap, frequent, widespread, potentially automated monitoring of the diversity, distribution, and abundance of aquatic life,” said Paul Gaffney, a retired Navy Vice-Admiral and former president and Urban Coast Institute Ocean Policy Fellow at Monmouth University.

“Government agencies need to take notice."