A Reef Under Pressure

Last year, an unprecedented marine heat wave swept across Western Australia, pushing ocean temperatures at the World Heritage-listed Nyinggulu (Ningaloo) Reef as much as 4 degrees Celsius above normal.

As a result, vast stretches of coral along the 300-kilometer reef turned a ghostly white in one of the worst bleaching events ever recorded there. The vibrant coral ecosystems that support thousands of marine species faded into dull, skeletal landscapes, a distress signal from one of the planet’s most extraordinary marine environments.

Yet scientists say the reef is not beyond saving.

Kate Quigley is a principal scientist at the Minderoo Foundation. She has poured her working life into coral research. 

“As climate change impact accelerates, conservation genetics will have an increasingly important role in helping to support critical ecosystems, like coral reefs, to recover,” Quigley said. 

This year, Quigley invited TACC’s Kelsey Beavers to collaborate in Exmouth, a remote coastal town where the outback meets the Indian Ocean. Beavers is a computational biologist specializing in genomics and transcriptomics, using high performance computing to analyze how corals respond to environmental stress.

For Quigley and Beavers, this was an opportunity to do important genetic work with the corals at the Minderoo Exmouth Research Lab (MERL), which plays a critical role in safeguarding local ocean ecosystems in Ningaloo Reef and adjacent Exmouth Gulf regions. 

For just a few nights each year, corals reproduce in a synchronized spawning event triggered by lunar cycles, water temperature, and light. The scientists were there to capture this extraordinary and specific moment. 

“This was a special opportunity to safeguard genetic material from corals living in one of the world’s most iconic reef ecosystems,” Beavers said.

They do this through cryopreservation, which has recently become one of the most important tools in coral conservation — many coral species are declining faster than they can adapt to warming oceans. By freezing their reproductive cells, scientists are creating a living archive of their genetic material. That archive buys important time — time for scientists to figure out how to protect these species, and time for the world to get emissions and ocean warming under control. 

“For me personally,” Beavers said, “it can be emotionally challenging to work with endangered species at a time when the future is so uncertain, so knowing that we were able to preserve those cells for generations to come filled the whole team with a huge sense of relief and hope. Some of us even shed a few tears of joy watching the samples go into the liquid nitrogen.”  

Holding Their Breath For The Reef To Respond 

To prepare for this moment, research teams collected small samples of healthy coral from the seabed. Carefully, these were brought to water tanks at the MERL, where the conditions of Ningaloo Reef were meticulously re-created. The water temperature, currents, and even the moonlight were adjusted to closely match conditions  at sea. Scientists worked under red light to prevent any disruption to the coral's natural behavior.

And then they waited.

Beavers arrived in Exmouth four days before the corals started spawning, but the rest of the team had been watching and waiting for two weeks.

“Every night when we headed to the lab around 6 p.m., we would say, ‘Tonight’s the night!’ but after two weeks of waiting, I could tell the team was starting to get a little nervous that the corals would not cooperate,” Beavers said. “When things finally did start happening, there was an overwhelming wave of excitement, and it was all hands on deck.” 

“When spawning is about to start, you can see egg bundles start to form on the surface of the coral. When we see that, we carefully move the corals into buckets, wait for them to spawn, and then sit hunched over on the ground collecting those bundles into test tubes.” 

The team of scientists then went to work separating the eggs from the sperm, isolating enough sperm to cryopreserve, and then performing genetic crosses (fertilizing eggs from one coral with sperm from another).

During the next few days, they monitored the fertilized eggs under microscopes, watching them develop until they reached the larval stage. Coral larvae are small, free-swimming “baby" corals — this is the life stage where they would naturally be carried by ocean currents until they find a place to settle and grow into an adult coral. It is also a vulnerable stage in their life cycle, which makes it a critical window for studying heat tolerance. If larvae cannot survive in warmer waters, they will never make it to adulthood, and the reef cannot replenish itself. 

Once they had larvae, Beavers explained, the team started the heat stress experiment.

For each genetic cross, they pipetted exactly 20 larvae into six small floating chambers — called “wells” or “boats” — that sit on the surface of a larger tank. Three of those boats went into a tank kept at a normal ocean temperature at 27.1 degrees Celsius, and the other three went into a tank headed to 35.5 C to simulate a marine heatwave. Because they had larvae from 34 genetic crosses, that added up to 204 of these wells in total.

At the heart of the research are pressing questions: Can scientists breed corals that survive a warming ocean, and which pairings yield the strongest next generation? 

“Some genetic crosses showed remarkable heat tolerance during the experiment, which was very exciting for us,” Beavers said.

The spawning had never been guaranteed, but in the end, it gave them something unprecedented: the first coral samples ever cryopreserved from Ningaloo Reef. Those samples will now take their place in the Taronga CryoDiversity Bank, the world’s largest wildlife cryopreservation facility, alongside genetic material preserved from species across the entire animal kingdom. 

Using HPC To Turn Genetic Data Into Answers About Coral Survival 

As part of the experiment, Beavers collected larval samples for DNA and RNA sequencing. DNA reveals each coral’s genome, the genetic blueprint inherited from its parents, while RNA provides a snapshot of which genes were actively switched on during heat stress. Together, these two layers of data allow us to answer a critical question: What enables some coral larvae to survive heat stress while others do not? 

By comparing survivors with nonsurvivors, the scientists can pinpoint genetic variants linked to heat tolerance and identify the genes activated to cope with stress. This shows not just which corals are more resilient, but why, and that insight can guide efforts to protect, selectively breed, and restore reefs in a warming ocean. 

“This is where my work at TACC comes in,” Beavers concluded. “Sequencing these samples generates an enormous volume of data, and TACC’s supercomputers make it possible to process it at scale. The next phase is turning that raw data into biological insight, using high performance computing to uncover the genetic patterns that could help safeguard coral reefs.”