Researchers Analyzing eDNA In Water Samples Brought Back From Papahānaumokuākea

Aug 21, 2019

Scientists are using an established DNA technique to discover just what lives in the deep coral reefs of the Northwestern Hawaiian Islands. Think of it as a CSI for marine ecosystems.

Researchers with the National Oceanic and Atmospheric Administration returned to Oahu last week after a three-week expedition to the Papahānaumokuākea Marine National Monument. It was there they found invasive algae outbreaks in the shallow reefs of the Pearl and Hermes Atoll, and a reef destroyed by Hurricane Walaka, a Category 3 storm.

But there was also good news.

Researchers found a new form of coral reef habitat at a depth of 300 feet off the Pearl and Hermes Atoll. That's where they found lush beds of the Sargassum algae, which is typically found in tidepools and very shallow reef habitats off the main Hawaiian islands. It was the first time the algae was found at such depths as a habitat-forming species.

But to better understand what lives in the deep waters, the expedition team brought back samples to conduct an intriguing test.

"We collected water samples for eDNA analysis," said Richard Pyle of the Bishop Museum. EDNA refers to environmental DNA.

"EDNA samples all the free DNA floating out in an environment. In our case that environment was the deep coral reefs," Pyle said. "And what it will tell you is not just what single species has what DNA, but the whole suite of organisms that live on a reef. They're shedding slime and scales, and all kinds of their DNA is just permeating the water."

EDNA is not a new concept. Pyle says it has been used for years on shallow coral reefs and on land, but it's only recently that researchers began turning to it for deep reef environments. According to Pyle, the recent expedition was the first extensive eDNA sample collection for the Northwest Hawaiian Islands.

To obtain the samples, researchers collect the water in a clean, sterilized tube. Scientists then use a vacuum pump to suck the water sample through a tiny filter to capture DNA molecules.

"So we take that little piece of paper, that filter, stick in a vial of preservative, and analyze it," said Pyle.

New DNA sequencing technology allows scientists to not only target a specific organism, but analyze all the DNA collected in the sample. Pyle says this speeds up the process of learning what organisms live below the surface.

"Historically, the way we find out what species live on a reef is we go dive on them, we look at them, and we write [the organism] down or we take pictures. That's the conspicuous stuff that you can see," said Pyle. "What you can't see is all the little things hiding in the holes. But all of those things, their DNA gets in the water, just like the conspicuous things does.

"So this technique seems very promising for figuring out who else is on the reef, besides what we saw there."

Scientists are in the process of analyzing the water samples from deep and shallow coral reefs taken during the expedition. The results will help researchers better understand reef ecosystems of the Northwestern Hawaiian Islands, and beyond.