Pew Marine Fellow Harnesses Biomedical Science Techniques to Study Coral Reefs

Insights into coral genetics may support marine conservation efforts

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Pew Marine Fellow Harnesses Biomedical Science Techniques to Study Coral Reefs
In a white-walled lab with violet-hued lighting in the background, Phillip Cleves looks at several rows of clear tanks that are filled about halfway with water. Light blue translucmarineent hoses, each connected to a PVC pipe with a bright blue plastic valve, are inserted in a small hole in the lid on each of the tanks.
Phillip Cleves looks at his aquarium systems in the lab. Cleves is a principal investigator at the Carnegie Institution for Science and an adjunct professor at Johns Hopkins University.
Navid Marvi

When marine biologist Phillip Cleves, Ph.D., began studying coral genetics seven years ago, he had a limited window of just a few critical days each year to run experiments. Corals—living organisms that are essential to the health and sustainability of oceans—can be genetically modified only when they spawn, which typically occurs once a year, in the middle of the night, and after a full moon.

But as ocean temperatures rise because of climate change, coral reefs are at greater risk of dying, making Cleves’ research more urgent. So he and his team at the Carnegie Institution for Science in Baltimore looked for ways to study coral outside of this short spawning window. Today, employing gene-editing technology traditionally used in biomedical research, they’ve pioneered a way to grow and genetically modify corals in a lab setting at any time of the year, in hopes of better understanding how these organisms operate and survive.

Cleves is the inaugural recipient of the Pew Marine and Biomedical Science Fellowship—a new, crosscutting partnership between the Pew Fellows Program in Marine Conservation and the Pew Scholars Program in the Biomedical Sciences that supports the application of biomedical science to enhance marine conservation.

This interview has been edited for length and clarity.

What role do corals play in the ocean’s ecosystem?

Corals serve a similar purpose to trees in the forest. They are primary food producers, create a habitat for animals, and promote nutrient cycling. If it weren’t for corals and the algae growing inside them, there would be far less structure to tropical ecosystems. In fact, it’s thought that about 25% of all marine life is supported by coral reefs. They really are essential. And we know this because we are seeing the effects of corals dying due to climate change.

Your lab is studying the relationship between algae and coral. Why is this connection so important?

Microscopic algae live within the cells of coral tissue and play an important role in their survival. Because most corals occupy crystal clear, tropical waters where there aren’t a lot of nutrients, these algae produce food for coral through the process of photosynthesis.

A multicolored coral reef with variegated shapes appears in the foreground in clear blue waters.
A healthy coral reef gets its food—and color—from the microscopic algae that live inside its cells.
Courtesy of Phillip Cleves

You mentioned climate change. How is it threatening coral?

This symbiosis between the algae and corals breaks down during heat stress. When water temperatures get one or two degrees higher, algae are expelled from the coral cells. If the water temperatures stay high and the corals can’t repopulate their tissues with algae, they’ll starve to death and die. We call this coral bleaching.

Because of human activity and climate change, we are seeing more severe and frequent heat waves causing acute bleaching events. A particularly dramatic example hit the world’s reefs in 2016, when we lost approximately 30% of the Great Barrier Reef in about two weeks. Losing a third of that reef, and in such a short time span, is really a crisis given all the services these corals provide.

And this is where your lab’s work comes in?

Exactly. We really don’t know much about the genes and molecular pathways behind why some corals bleach and some don’t. These are the questions we focus on in my lab. Just like it’s important for us to understand the genes that cause human illness so that we can predict disease and inspire therapeutics, if we understand more basic mechanisms of coral biology and bleaching, we can both better predict what’s going to happen in the future and maybe even inspire conservation strategies.

What’s challenging about studying corals?

Scientists generally study organisms that reproduce well in the lab. Corals are not those animals. To genetically modify coral, we need coral eggs at the one-cell stage. Corals spawn only once a year, so you need to be at the right place at the right time to run these experiments.

When we started this work, this meant packing suitcases of lab equipment and flying to Australia, where we waited for the corals to spawn in November, over three nights, a few days after the full moon. Being able to do experiments once a year under those conditions is challenging, so we became interested in building a lab system that allows us to get better access to coral spawning and make more rapid progress.

A mass of gray, twig-like bleached coral lies on the ocean floor in murky blue water.
A bed of bleached coral sits on the bottom of the ocean. Bleaching occurs when water temperatures rise, causing corals to expel the algae that give them both their food and their color.
Courtesy of Phillip Cleves

Tell us about this lab system.

Through a collaboration with Jamie Craggs at the Horniman Museum, we’ve designed facilities at Carnegie that allow us to trick corals into thinking they are at different times of the year by manipulating temperature, light, and “moonlight” through blue LEDs. Now, instead of waiting for November by the full moon, we can reliably spawn corals many times throughout the year.

What biomedical science techniques are you applying to this work?

This work is a true intersection of biomedicine and conservation. The ability to manipulate gene function in model organisms has led to the discovery of nearly all the gene functions that we know in humans. Gene-editing technology has existed in medicine for some time and has recently expanded our ability to study diverse organisms, including corals. Using CRISPR-Cas9—a programmable RNA/protein complex used to alter an organism’s genome—we can precisely test the function of coral genes and explore our hypotheses for why bleaching happens.

What is the long-term goal of this research?

The goal posts keep moving. When we first started this work, I just wanted to see if we could inject corals with CRISPR-Cas9 and see mutations. Now that we can do that, I’m most excited about trying to understand what genes make corals bleach, why stress causes the breakdown of the relationship between the coral and algae, and why some corals bleach while others don’t. If we could use genetic information to predict whether coral will survive or die during the next bleaching event, we could use this knowledge for critical marine conservation.

Any final thoughts?

I believe that we are in a molecular biology renaissance. We can study any organism on the planet—from butterflies and squids to tropical fish and humans—and we can understand their genes and molecular pathways in a way that wasn’t possible before. But I also think that, as humans, we are in an existential crisis. We are seeing the impacts of human activity on biodiversity and ecosystems—and both the chronic and acute impacts of those changes on human health. So I’m excited that Pew gave me this opportunity to merge these two fields. This Pew Marine and Biomedical Science Fellowship is leading what I believe to be the path forward: approaching environmental health as human health.

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