A Blueprint for Genetically Engineering a Super Coral

Why some researchers are proposing a drastic measure to save a threatened ecosystem

In a healthy reef, coral symbionts make food for the coral animal. Juergen Freund / Alamy

A coral reef takes thousands of years to build, yet can vanish in an instant.

The culprit is usually coral bleaching, a disease exacerbated by warming waters that today threatens reefs around the globe. The worst recorded bleaching event struck the South Pacific between 2014 and 2016, when rising ocean temperatures followed by a sudden influx of warm El Niño waters traumatized the Great Barrier Reef. In just one season bleaching decimated nearly a quarter of the vast ecosystem, which once sprawled nearly 150,000 square miles through the Coral Sea. 

“As awful as it was, that bleaching event was a wake-up call,” says Rachel Levin, a molecular biologist who recently proposed a bold technique to save these key ecosystems. Her idea, published in the journal Frontiers in Microbiology, is simple: Rather than finding healthy symbionts to repopulate bleached coral in nature, engineer them in the lab instead. Given that this would require tampering with nature in a significant way, the proposal is likely to stir controversial waters.

But Levin argues that with time running out for reefs worldwide, the potential value could well be worth the risk. 

Levin studied cancer pharmacology as an undergraduate, but became fascinated by the threats facing aquatic life while dabbling in marine science courses. She was struck by the fact that, unlike in human disease research, there were far fewer researchers fighting to restore ocean health. After she graduated, she moved from California to Sydney, Australia to pursue a Ph.D. at the Center for Marine Bio-Innovation in the University of New South Wales, with the hope of applying her expertise in human disease research to corals. 

In medicine, it often takes the threat of a serious disease for researchers to try a new and controversial treatment (i.e. merging two womens’ healthy eggs with one man’s sperm to make a “three-parent baby”). The same holds in environmental scienceto an extent. “Like a terrible disease [in] humans, when people realize how dire the situation is becoming researchers start trying to propose much more,” Levin says. When it comes to saving the environment, however, there are fewer advocates willing to implement risky, groundbreaking techniques. 

When it comes to reefs—crucial marine regions that harbor an astonishing amount of diversity as well as protect land masses from storm surges, floods and erosion—that hesitation could be fatal. 

Coral bleaching is often presented as the death of coral, which is a little misleading. Actually, it’s the breakdown of the symbiotic union that enables a coral to thrive. The coral animal itself is like a building developer who constructs the scaffolding of a high rise apartment complex. The developer rents out each of the billions of rooms to single-celled, photosynthetic microbes called Symbiodinium.

But in this case, in exchange for a safe place to live, Symbiodinium makes food for the coral using photosynthesis. A bleached coral, by contrast, is like a deserted building. With no tenants to make their meals, the coral eventually dies.     

Though bleaching can be deadly, it’s actually a clever evolutionary strategy of the coral. The Symbiodinium are expected to uphold their end of the bargain. But when the water gets too warm, they stop photosynthesizing. When that food goes scarce, the coral sends an eviction notice. “It’s like having a bad tenant—you’re going to get rid of what you have and see if you can find better,” Levin says. 

But as the oceans continue to warm, it’s harder and harder to find good tenants. That means evictions can be risky. In a warming ocean, the coral animal might die before it can find any better renters—a scenario that has decimated reef ecosystems around the planet. 

Levin wanted to solve this problem, by creating a straightforward recipe for building a super-symbiont that could repopulate bleached corals and help them to persist through climate change—essentially, the perfect tenants. But she had to start small. At the time, “there were so many holes and gaps that prevented us from going forward,” she says. “All I wanted to do was show that we could genetically engineer [Symbiodinium].”

Even that would prove to be a tall order. The first challenge was that, despite being a single-celled organism, Symbiodinium has an unwieldy genome. Usually symbiotic organisms have streamlined genomes, since they rely on their hosts for most of their needs. Yet while other species have genomes of around 2 million base pairs, Symbiodinium’s genome is 3 orders of magnitude larger.

“They’re humongous,” Levin says. In fact, the entire human genome is only slightly less than 3 times as big as Symbiodinium’s. 

Even after advances in DNA sequencing made deciphering these genomes possible, scientists still had no idea what 80 percent of the genes were for. “We needed to backtrack and piece together which gene was doing what in this organism,” Levin says. A member of a group of phytoplankton called dinoflagellates, Symbiodinium are incredibly diverse. Levin turned her attention to two key Symbiodinium strains she could grow in her lab. 

The first strain, like most Symbiodinium, was vulnerable to the high temperatures that cause coral bleaching. Turn up the heat dial a few notches, and this critter was toast. But the other strain, which had been isolated from the rare corals that live in the warmest environments, seemed to be impervious to heat. If she could figure out how these two strains wielded their genes during bleaching conditions, then she might find the genetic keys to engineering a new super-strain. 

When Levin turned up the heat, she saw that the hardy Symbiodinium escalated its production of antioxidants and heat shock proteins, which help repair cellular damage caused by heat. Unsurprisingly, the normal Symbiodinium didn’t. Levin then turned her attention to figuring out a way to insert more copies of these crucial heat tolerating genes into the weaker Symbiodinium, thereby creating a strain adapted to live with corals from temperate regions—but with the tools to survive warming oceans. 

Getting new DNA into a dinoflagellate cell is no easy task. While tiny, these cells are protected by armored plates, two cell membranes, and a cell wall. “You can get through if you push hard enough,” Levin says. But then again, you might end up killing the cells. So Levin solicited help from an unlikely collaborator: a virus. After all, viruses “have evolved to be able to put their genes into their host’s genome—that’s how they survive and reproduce,” she says. 

Levin isolated a virus that infected Symbiodinium, and molecularly altered it it so that it no longer killed the cells. Instead, she engineered it to be a benign delivery system for those heat tolerating genes. In her paper, Levin argues that the virus’s payload could use CRISPR, the breakthrough gene editing technique that relies on a natural process used by bacteria, to cut and paste those extra genes into a region of the Symbiodinium’s genome where they would be highly expressed. 

It sounds straightforward enough. But messing with a living ecosystem is never simple, says says Dustin Kemp, professor of biology at the University of Alabama at Birmingham who studies the ecological impacts of climate change on coral reefs. “I’m very much in favor of these solutions to conserve and genetically help,” says Kemp. But “rebuilding reefs that have taken thousands of years to form is going to be a very daunting task.”

Considering the staggering diversity of the Symbiodinium strains that live within just one coral species, even if there was a robust system for genetic modification, Kemp wonders if it would ever be possible to engineer enough different super-Symbiodinium to restore that diversity. “If you clear cut an old growth forest and then go out and plant a few pine trees, is that really saving or rebuilding the forest?” asks Kemp, who was not involved with the study. 

But Kemp agrees that reefs are dying at an alarming rate, too fast for the natural evolution of Symbiodinium to keep up. “If corals were rapidly evolving to handle [warming waters], you’d think we would have seen it by now,” he says. 

Thomas Mock, a marine microbiologist at the University of East Anglia in the UK and a pioneer in genetically modifying phytoplankton, also points out that dinoflagellate biology is still largely enshrouded in mystery. “To me this is messing around,” he says. “But this is how it starts usually. Provocative argument is always good—it’s very very challenging, but let’s get started somewhere and see what we can achieve.” Recently, CSIRO, the Australian government’s science division, has announced that it will fund laboratories to continue researching genetic modifications in coral symbionts.

When it comes to human health—for instance, protecting humans from devastating diseases like malaria or Zika—scientists have been willing to try more drastic techniques, such as releasing mosquitoes genetically programmed to pass on lethal genes. The genetic modifications needed to save corals, Levin argues, would not be nearly as extreme. She adds that much more controlled lab testing is required before genetically modified Symbiodinium could be released into the environment to repopulate dying corals reefs. 

“When we’re talking ‘genetically engineered,’ we’re not significantly altering these species,” she says. “We’re not making hugely mutant things. All we’re trying to do is give them an extra copy of a gene they already have to help them out ... we’re not trying to be crazy scientists.”

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