Time to speed up coral evolution?

The Australian Institute of Marine Science is a glorious place. From sultry Townsville in far north Queensland, it’s a lush 50 km drive east through sugar cane and mango plantations, across an estuary and through scrub till finally you crest a hill and are hit by the blue expanse of the Pacific Ocean.

A primeval atmosphere reigns at Cape Ferguson. Signs on the dock warn of crocodiles, sharks and snakes. Everything is protected and thrillingly feral.

Something quite wild is happening inside the buildings too. Here, marine biologist Madeleine van Oppen and colleagues are pursuing a bold, and controversial, goal – to speed up the evolution of corals to ensure the survival of the world’s reefs, particularly the one on the institute’s doorstep, the 2,300 km-long Great Barrier Reef.

Their research, once considered fringe, has gone mainstream. In January the Australian government committed $6 million to a study on the feasibility of helping the reef adapt to climate change. AIMS and CSIRO, the national science agency, are leading this study, which brings together leading reef conservation and research bodies: the Great Barrier Reef Marine Park Authority (GBRMPA), which manages the reef; the Great Barrier Reef Foundation, which raises funds for scientific research; the University of Queensland; the Queensland University of Technology; and James Cook University.

Assisting the evolution of coral is a radical departure from the historically conservative agenda of the reef’s custodians. Mostly the efforts have been to combat local threats, like agricultural runoff and predatory starfish. But the back-to-back bleaching events of 2016 and 2017 rammed home the greater existential threat from global warming. “The narrative that it will be our kids who have to deal with climate change is obsolete,” says Paul Hardisty, the head of AIMS. “We’re out of time; action has to happen now.”

The funding is just one-tenth of a $60 million reef protection package announced by the federal government, with the bulk dedicated to reducing industry impacts on water quality and managing starfish. But the results of the feasibility study may open the funding flood gates.

How much is it worth spending to save the reef? Its ecological value is immeasurable, but its economic value can be calculated. According to an analysis by Deloitte Access Economics, reef tourism contributes more than $6 billion a year to the Australian economy. Add in the services to fisheries and coastal protection, and it is an asset valued at $56 billion. Surely, worth a sizeable chunk of research dollars to save it.

Marine scientists, however, are hardly comrades in arms on the merits of accelerated evolution.

While some feel compelled to try and preserve a ‘functional’ reef, others think the ambition is flawed and futile. They say the scale of the reef is too vast for science to slow its decline, and any success may well defeat the purpose. Rather than preserving the diversity of its 400-plus hard coral species, it might produce a reef dominated by a few coral ‘superweeds’.

“One of my main objections is it’s more likely to do more harm than good,” says Andrew Baird, an ecologist at James Cook University.

Yet others point to the dazzling march of technology and say we must at least explore outlandish possibilities. The advent of CRISPR gene editing is an oft-cited example. Six years ago no one would have predicted there would be a cheap, precise, universally deployable tool for rewriting the code of genes, or that ‘gene drives’ would be capable of rapidly altering the genetic makeup of entire populations.

Maybe within the next few decades, the argument goes, science will deliver the tools to drive evolution just where we want it to go.

Of course nothing will save coral if greenhouse gas emissions don’t cease. Coral is the canary in the coalmine. It is exquisitely sensitive to increases in water temperature – just a degree above the normal maximum for several weeks is enough to cause bleaching and death.

If the Paris climate accord holds and emissions cease by 2050, the hope is assisted evolution will buy time for corals to adapt to 1-2 degrees of warming.

The scientists contemplating such possibilities say it is not just up to them to decide; they are looking to the public for permission. “We try to engage the public at forums and talk openly to the media. It’s about being transparent,” says van Oppen.

So sooner or later, we’re all going to have to ask this question: How far should we go to try to save our reefs?

Assist the evolution of coral? It’s a simple enough proposition. We know the Great Barrier Reef is a resilient ecosystem. Around 100,000 years ago, there was no Great Barrier Reef. Vast ice sheets had locked up the planet’s water and left an ancient earlier reef high and dry. As the ice sheets thawed and sea levels rose, the reef slowly returned over the last 8,000 to 9,000 years with species adapted to the new conditions. No doubt the reef will ultimately evolve new species and recover this time too, but we don’t want to wait 9,000 years.

We have been assisting the evolution of species ever since we began domesticating crops and animals some 10,000 years ago. Today’s wheat varieties, for example, bear little resemblance to their weedy ancestors. Coral, however, is not wheat. It is the keystone species of a wild ecosystem, and the ethos for conserving wilderness – forests, savannahs, seagrass meadows or reefs – has always been to preserve, not change.

Historically the custodians of the Great Barrier Reef have adhered to this ethos. They cordoned off areas, stopped overfishing, regulated tourism, tried to keep waters clean and battled outbreaks of the Crown of Thorns starfish. The strategy seemed to be working.

In 2010, for example, global bleaching events triggered by warm oceans hammered reefs across the Pacific, the Indian Ocean, the Caribbean and the Arabian Gulf.  But the Great Barrier Reef was largely spared. Some thought the reef was too big to fail.

Not so. The back-to-back bleaching events of 2016 and 2017 delivered the global coral apocalypse to Australian shores. The 2016 event, like previous mass bleachings, was linked to the warming of Pacific waters produced by an El Nino weather pattern. The second was not. It took everyone by surprise.

Adding up the damage from the onslaught, GBRMPA estimates about half the reef has died.

“The scale at which these impacts are operating is like nothing we’ve ever seen before,” says David Wachenfeld, GBRMPA’s director of reef recovery. For Wachenfeld, business as usual is no longer an option. “It’s a moment in history where [when it comes] to the protection of reef systems, even one as big and robust as the Great Barrier Reef, we have to rethink how we’re doing this.”

When it comes to assisting the evolution of coral, van Oppen, an athletic and affable woman in her early 50s, has been ahead of the curve. “I felt it was just a matter of time,” she says.

Originally from the Netherlands, one of her first projects led her to East Africa’s Lake Malawi to plumb the mystery of how its 700 species of cichlid fish had evolved so rapidly. She never dreamed that 20 years on, she would use her knowledge to speed up the evolution of the corals of Australia’s Great Barrier Reef.

In 2008, based at AIMS, she began trying to interbreed the more heat-resistant Acropora millepora corals of Orpheus Island with their southerly relatives in the Keppel islands. With the first attempt, floodwaters washed away the experimental hybrids, and yet again the following year. It was hard to find the funding to repeat the experiment – the key focus at the time was managing the clear and present dangers of the Crown of Thorns invasion and the run-off  from rivers that clouded and contaminated the waters of the in-shore reefs. Corals, especially juveniles, need clear, clean water to thrive and repair the incessant damage wrought by starfish and cyclones.

Van Oppen found a like mind in coral researcher Ruth Gates at the University of Hawaii. Hawaiian reefs, though never as biodiverse as the Great Barrier Reef, had been decimated by bleaching events and sewage run-off.

In 2013 the collaborators attracted the attention of Microsoft co-founder Paul Allen’s philanthropic foundation, winning a small $10,000 exploratory grant. Two years later in 2015, after a 2014 bleaching event had hammered corals in Kane’ohe Bay, the foundation kicked the research into high gear with a $4 million, five-year grant to “develop a biological toolbox for creating a stockpile of corals with improved environmental stress resilience, which can then be used to stabilise and restore reefs”.

When the first bleaching event hit Australia in 2016, van Oppen found herself in the right place at the right time. As the global media reported apocalyptic scenes of mass bleaching, tepid waters thick with the ooze of dying corals, weeping scientists and widespread reef grief, van Oppen’s once obscure research was showcased by the BBC’s David Attenborough and the Australian ABC’s Catalyst program.

But it wasn’t just the media that began taking serious interest in her work. As the reef’s custodian, GBRMPA wrestled with how to manage the national treasure in the face of a coral apocalypse and began to take note of van Oppen’s work, helping to recast it from fringe to trailblazing.

The current 18-month feasibility study is a hard-headed assessment of the tools available to help the reefscape adapt, how it could be done at scale, and at what cost. Besides larval seeding, underwater fans and shade cloth, these tools also include the biological toolbox developed by van Oppen.

So what exactly does the coral biological toolbox contain? Lots. It involves tweaking the genes of coral, as well as the community of organisms that resides within it. The problem is that no one has ever tried to tweak these genes before. “We have to be careful not to overpromise,” says van Oppen.

If the Paris climate accord holds and emissions cease by 2050, the hope is that assisted evolution will buy time for corals to adapt to 1–2 degrees of further warming.

Let’s be clear. Coral is not a wheat plant. We’ve had thousands of years’ experience tweaking the genes of wheat. We can make cross-breeds at will, map out desired traits in the DNA and usher them into new varieties. Breeding has produced fantastic successes. Modern wheats have more than doubled their yield since the 1950s, and every few years breeders bring out new varieties better adapted to the latest strain of fungus or better able to tolerate drought or salt.

Nothing like this is possible with any coral species – let alone the hundreds of Great Barrier Reef species one would want to assist. Van Oppen and colleagues are hoping to contract thousands of years of wheat-tweaking experience into a decade.

Their source of optimism lies in the fact that coral naturally has some tricks up its sleeve. On any bleached reef, some corals will survive. The question is why.

It all comes down to ecosystems. A mature coral head is a colony of millions of genetically identical polyps – tiny, delicate, anemone-like organisms that build limestone ‘houses’ around themselves, which form the structure of coral reefs. Every tiny pinprick in the limestone is a place a living polyp calls home.

Each polyp houses an invisible community of diverse microbes within its body tissues. “Life did not take over the world by combat but by networking,” wrote evolutionary biologist Lynn Margulis. Corals take networking to a whole new level.

What that means is that researchers have to consider more than just the coral’s genes if they want to speed up their evolution.

For starters, there are the genes of their most famous cohabitants – various types of single-celled algae, collectively known as zooxanthellae or the Symbiodinium. Juvenile polyps swallow these algae but instead of digesting them, they usher them into purpose-built compartments within the outer cells of the polyp. Like all plants, algae make sugar from sunlight via a set of chemical reactions called photosynthesis and they provide their coral host with 90% of its calorie requirements. That powers the corals’ monumental limestone-building project in waters that are otherwise low in nutrients. The need for sunlight is why corals are so vulnerable to poor water quality. Sediments can smother the coral and block the sun.

Heat is the worst stress of all. When temperatures stay high for more than a week or two, the vital coral-algae partnership starts to break down. The heat plays havoc with the algae’s photosynthetic reactions, causing them to release increased amounts of damaging chemicals called oxidants. In the face of this toxic assault, the polyps begin evicting the resident Symbiodinium. Some corals fluoresce a dazzling shade of electric blue in the process, perhaps an attempt to soak up the excessive energy of the oxidants. But the show is short-lived. Once the algae are evicted, the tan brown colour of healthy coral bleaches to white. It is possible for the polyps to be recolonised; if they are not, the coral starves to death over a few weeks.

But eviction is not always the outcome, and there’s evidence to suggest that the genes of the algae play a role in determining how well the partnership survives. For instance, back in 2006, van Oppen and colleague Ray Berkelmans transplanted temperature-sensitive corals from the Keppel islands to the warmer waters of Magnetic Island, 600 km further north. The corals that survived had traded their old algal partners, Clade C, for the more heat-tolerant Clade D types.

The Symbiodinium partnership is crucial to the coral polyp but it is not the only one. Turns out, microbes play an important role in polyp health, much like they do in human health. Once considered invaders, the microbial community that inhabits our body’s orifices – the microbiome – is now linked to an ever-growing list of vital functions including taming our immune system and contributing to the health of the gut, liver and even the brain. The latest thinking is that the coral polyp, sitting right at the base of the evolutionary tree next to sponges, also relies on its microbiome for its health and immunity.

The coral microbiome resides in the coral’s mucus coating, gut and skeleton. It is effectively a chemical factory that produces a diverse range of products, including nitrogen and sulfur-containing compounds. Van Oppen suspects the repertoire extends to anti-oxidants – chemicals that could neutralise the oxidants produced during coral bleaching. If that’s the case, it might just be the genes of the coral microbiome that help it survive heat stress.

The latest thinking is that the coral polyp, sitting right at the base of the evolutionary tree next to sponges, also relies on its microbiome for its health and immunity.

Finally, corals seem to have one more trick up their sleeve. Some colonies appear to adjust to heat stress in the same way that tomato plants do: they gradually get used to it. Gardeners harden tomato seedlings by gradually exposing them to warmer and warmer temperatures. The mechanism, dubbed epigenetics, does not alter the DNA code but reprograms it (by attaching chemicals such as methyl groups). There are glimmers of hope that corals can acclimatise to gradual change based on what happened to the reefs exposed to the devastating Indian Ocean mass bleaching event that occurred in 1998. When the 2010 bleaching event arrived 12 years later, those corals that had survived the earlier event appeared to be more resistant.

However, the bleaching events of 2016 and 2017 dashed any such hope for the Great Barrier Reef; whatever hardening took place, it was not enough to protect the reef.

Van Oppen and her colleagues are now tinkering with these four components of the coral genetic toolbox – coral genes, algal genes, microbial genes and epigenetic hardening. Most of the tinkering is taking place at AIMS in the wilds of Cape Ferguson.

Away from the crocodiles, sharks and snakes, scientists can safely carry out their experiments in what may be the world’s most sophisticated simulation of the sea – the $40 million SeaSim aquarium, which has a state-of-the-art control room with the same design specs as those in a nuclear reactor. Scientists can observe remarkable things by  programming the slow-ramping rhythms of the sea, the waxing and waning of daylight and temperature, and the CO₂ levels that climb gradually at night as plants cease photosynthesis and their consumption of the gas. The computers can also precisely simulate the deposition of fine sediments, a feat that revealed for the first time how corals shed their mucus coating like a glove to rid their surface of sediment. Before scientists unleash any evolutionarily fast-tracked coral on the reef, its impact will be simulated at SeaSim first.

SeaSim may be safer than the waters of Cape Ferguson, but things get pretty feral here at spawning season. Once a year, generally on a November night after the full moon, corals spawn. On the reef it happens en masse, the waters turning cloudy with trillions of eggs and sperm. Before November, scientists from around the world pluck corals from the reef and bring them into SeaSim. But not every coral species joins in on cue; they may be out of sync by hours or weeks. So breeders will stay up all night watching and waiting for the first signs that the coral are about to eject their tiny bundles of sperm and eggs. They collect the bundles, strain the sperm from the eggs and wait for the next species to spawn. It’s a harrowing wait: they have only a couple of hours before their captured sperm and eggs die.

AIMS researcher Lesa Peplow shows me a tank bearing the results of cross-breeding experiments with four species of Acropora: tenuis, loripes, sarmentosa and florida. She, van Oppen and PhD student Wing Chan have tested juvenile corals under the conditions of today and those predicted for the middle of the century (+1 degree and 685 ppm CO₂). Encouragingly, some of the hybrid crosses showed greater survival than their parents under both conditions.

In another corner of SeaSim, I am guided by Line Bay, a Dane who visited the Great Barrier Reef on a snorkelling holiday in 1994 and never left. Bay, together with Kate Quigley, is testing the genes of corals that survived the February 2016 mass bleaching of the northern reefs. They took cuttings of Acropora survivors and brought them into SeaSim. When they spawned, they were crossed with Acropora from a more southerly locale. The offspring are being tested to see if they have inherited the heat-resistance genes.

Bay also takes me into an external area of SeaSim, where the tanks are covered by shade cloth. Here hardening experiments are under way in an experiment dubbed Evolution 21. A mix of reef species will be followed under different climatic conditions, for five years. Bay has a long-standing interest in “how corals tune to their local environment”. She points out that coral larvae the size of rice grains can last for up to 100 days in the ocean and are attracted to the smell of coral. They may reach another reef with conditions quite different to those of the parents. Perhaps, like tomato seedlings, corals rely on hardening for local tuning? And could such tuning be inherited? The Spiny Damselfish, for instance, appears to pass on its heat-acclimatisation to its offspring.

“What we’re facing now is the terrible realisation that, by not doing anything, we’re risking the reef as much as if we intervene.”

To test coral hardening and inheritance, Bay is studying the coral species Acropora loripes and Platygyra daedalea, reared under extreme climatic regimes. If she can establish heat-hardening of the larvae, it could have an impact. More than 90% of larvae die in their first nine months, so seeding reefs with heat-hardened larvae could boost populations.

Beyond the futuristic contours of the SeaSim facility lie some more ordinary looking buildings. One houses a lab where van Oppen and her colleagues are trying to breed algae that hang in there with their coral partner when the heat is on. They extracted algae from corals and then grew them for 80 generations at temperatures of 31 degrees – conditions that should select for heat-tolerant individuals. These survivors were inoculated into coral larvae, then the partners tested for their heat tolerance. So far only a small benefit has been seen. The next step will be to accelerate the mutation rate of the algae using mutagenic chemicals.

For the final tool in the kit, I visit van Oppen at the University of Melbourne lab that she runs jointly with microbiologist Linda Blackall. It is nestled away in what used to be the botany building – an ivy-covered, redbrick pile with cross-hatched white window panes and gothic oversized wooden doors set into a stone archway with the year 1929 carved above. It is a quaint setting for some decidedly avant garde experiments.

You’ve heard of probiotics for human health – concoctions of healthy bacteria to be taken as yoghurt, pills or even faecal transplants to treat conditions like inflammatory bowel disease? Here the goal is to develop a probiotic for coral.

The model animal upon which these probiotics will be tested is the starburst-like pale anemone Exaiptaisia pallida, best known as an aquarium pest. Like its coral polyp cousins, it relies on symbiosis with algae, and bleaches when temperatures rise too high. In its mucus, tissue and stomach, it also houses a community of bacteria. PhD student Leon Hartman has been learning how to grow these pretty creatures for the past two years. It’s a major job: filtering Melbourne’s water, adding sea salt and hatching brine shrimp to feed them – they prefer their food live. He is growing the anemones under elevated temperatures to see what sort of bacteria associate with the survivors.

Ashley Dungan, another PhD student, takes Hartman’s carefully tended anemones and mercilessly squashes them – pretty easy given their skin is only four cell layers thick. Dungan streaks out the anemone soup onto agar-coated petri dishes, spreading it so thinly that single bacteria will grow into round pink-brown colonies. Did any of these bacteria help their anemone host resist bleaching? Dungan is testing each bacterial clone for its ability to neutralise oxidants. The hope is to find a soothing concoction that can make coral less prone to boot out hot and bothered algae.

Van Oppen and her colleagues are testing all four coral tools to see if they can tighten the nuts and bolts of the multi-component coral organism to create individuals that can withstand conditions predicted for the rest of the century. How many fast-tracked coral species would be needed to maintain a functional reef? Van Oppen guesses several dozen, spanning the range of morphologies – branched, massive and encrusting.

Seeding strategies, like one now being tested on a degraded patch of reef at Heron Island, would be scaled up to deliver the genetically, epigenetically or microbially hardened new recruits. To disperse them across the vast distances, a strategic set of reefs would be targeted – those known to be part of an ocean highway whose currents connect key reefs within the 3000-strong chain.

Though it is very early days, many researchers hope science can deliver a solution that buys coral time. AIMS’ Paul Hardisty says simply: “I’m an optimist.”

Other researchers are not. At AIMS’s closest neighbour, the ARC Centre of Excellence for Coral Reef Studies at James Cook University, it’s not hard to find researchers deeply sceptical of assisted evolution.

The director, Terry Hughes, has expressed concerns that any idea of an engineered solution for threatened reefs distracts from the main game, which is reducing carbon dioxide emissions.

But the key scientific riposte is that assisted evolution represents a futile ambition. JCU ecologist Baird offers a reality check. “Think of how much time and money it took for Monsanto just to engineer a soybean, probably more effort than has gone into ecology in the history of the universe.” He concludes, “I honestly believe the time, energy and intellect required is well and truly beyond anything the reef community can muster.”

Ove Hoegh-Guldberg, a bleaching expert and now Director of the Global Change Institute at the University of Queensland, sees the merit of both positions. While he likens the assisted evolution project to “gardening on the scale of Italy”, he’s not willing to turn his back on anything. “All options are on the table and we’ll put a ruler over them.”

Emma Johnston, a marine ecologist at the University of NSW, has felt the weight of divided views more than most. As a GBRMPA board member, she had to decide whether to back the option of assisted evolution. She chose to support it. “What we’re facing now is the terrible realisation that, by not doing anything, we’re risking the reef as much as if we intervene,” she says.

But that decision wasn’t easy. “I’ve had to struggle,” she says. “I think all these people are right.”