Hawaii scientists develop technique using DNA to study coral reefs

With coral reefs coming under increasing threat from climate change, University of Hawaii at Manoa scientists have developed a technique that could help the biologists working to save them.

The technique, described in a paper published in Environmental DNA journal, allows for a quick and inexpensive assessment of the condition of coral reefs through an analysis of DNA taken from small samples of water.

The new research comes from Patrick Nichols, a UH graduate student in the marine biology graduate program, and Peter Marko, an associate professor in the university’s Department of Biology.

Visual surveys are the current standard for measuring the health of underwater ecosystems and have been growing in importance as coral decline under increasing acidification and warmer water temperatures linked to climate change, as well as from local pressures.

But traditional surveys, which measure the living coral on a reef, generally rely on time-consuming, logistically challenging and relatively expensive estimates by teams of scuba divers or by using drone technology.

Environmental DNA — commonly known as eDNA — is already an established conservation tool that takes advantage of the fact that all organisms shed DNA into their environment. The technique detects this genetic residue and analyzes it for identification.

But until now the tool had yet to be tested for measuring living coral organisms, according to the paper.

In an interview, Nichols said the project used “metabarcoding,” a technique in which all of the DNA in a water sample is analyzed in one step with DNA sequencing.

Coral DNA sequences are identified and counted to find out how many different types of coral are at each reef. Degraded reefs have very little coral eDNA while healthy reefs exhibit a much stronger coral eDNA signature.

In their paper, the authors said the new technique can track changes in coral reef health and composition over time, as well as detect species that can be missed by traditional surveys.

“If you (had) asked me 10 years ago if this was possible, I would have said, ‘No way,’” Marko said in a UH news release. “But advances in technology and falling costs of highly sensitive DNA sequencing methods have opened the door to all kinds of important ecological questions.”

Nichols, a UH marine biology graduate assistant, said the new technique has been proven effective on coral in Hawaiian waters and will need further testing for accuracy elsewhere.

Used as a complement to traditional monitoring methods, he said, the technique will allow biologists to conduct more surveys and open new frontiers — such as the health and composition of deep-water reefs.

“We know very little about the deeper depths,” Nichols said.

According to the International Union for Conservation of Nature, coral reefs are among the most threatened ecosystems on Earth, largely due to climate change in combination with local pressures.