Microscope reveals coral health in unprecedented detail

Coral reefs are in trouble. As oceans warm and environments shift, the vibrant ecosystems built by corals are turning pale and dying off.

While scientists have known for years that coral bleaching is linked to the loss of symbiotic algae, they’ve never been able to watch the process unfold at the cellular level in realtime – until now.

Underwater microscope for studying coral

Researchers at the Scripps Institution of Oceanography at UC San Diego have created a handheld underwater microscope. The device makes it possible to study coral photosynthesis right where it happens – in the ocean, inside living coral tissue – without causing any damage.

The team named the device the Benthic Underwater Microscope imaging PAM – BUMP, for short.

The Jaffe Lab for Underwater Imaging at Scripps Oceanography built the microscope with support from the U.S. National Science Foundation.

The tool combines imaging with a light-based technique known as pulse amplitude modulated (PAM) fluorometry to measure how efficiently tiny algae inside corals are photosynthesizing.

Coral depends on glowing algae

The algae, called symbionts, are essential for coral survival. They live within coral tissue and convert sunlight, water, and carbon dioxide into sugars and oxygen.

The coral, in turn, uses that energy to grow and build reefs. But when stressed by warming seas or pollution, corals eject these algae. Without them, corals appear white and slowly starve – known as the bleaching effect.

The BUMP microscope makes it possible to monitor this relationship in real-time and in natural environments – something that couldn’t be done before.

A huge technological leap

“This microscope is a huge technological leap in the field of coral health assessment,” said study lead author Or Ben-Zvi, a postdoctoral researcher at Scripps Oceanography.

“Coral reefs are rapidly declining, losing their photosynthetic symbiotic algae in the process known as coral bleaching.”

“We now have a tool that allows us to examine these microalgae within the coral tissue, noninvasively and in their natural environment.”

The microscope is small enough to fit in a carry-on suitcase. It’s light enough for a diver to bring to the seafloor without a ship’s help.

Controlled with a touchscreen and powered by a battery pack, the microscope uses focused LED lights and high-magnification lenses to capture vivid images and videos. It also creates detailed 3D scans and maps photosynthesis in high resolution.

Microscope reveals corals’ inner glow

At just 10 micrometers wide – one-tenth the width of a human hair – coral symbionts are invisible to the naked eye. But when corals are viewed under the microscope, the algae glow red due to chlorophyll, the pigment that powers photosynthesis.

PAM technology measures this glow to calculate how efficiently the algae are converting light into energy. Other glowing areas, like cyan and green patches, come from fluorescent proteins that the coral produces, often around its mouth and tentacles.

The images help researchers “see” coral health without touching or harming them. “We get a lot of information about their health without the need to interrupt nature,” said Ben-Zvi.

“It’s similar to a nurse who takes your pulse and tells you how well you’re doing. We’re checking the coral’s pulse without giving them a shot or doing an intrusive procedure on them.”

Observing corals at unseen scales

Ben-Zvi and her colleagues tested the microscope at coral hotspots around the world – including Hawaii, the Red Sea, and Palmyra Atoll – in collaboration with the Smith Lab at Scripps Oceanography.

What they saw surprised them. Corals weren’t passive. They moved constantly, changing shape, reacting to particles, and even behaving in ways that looked like fighting or kissing.

Ben-Zvi observed coral polyps contracting their tentacles, possibly trying to remove or capture something floating by.

“The more time we spend with this microscope, the more we hope to learn about corals and why they do what they do under certain conditions,” she said.

“We are visualizing photosynthesis, something that was previously unseen at the scales we are examining, and that feels like magic.”

Early detection of coral stress

Corals face serious threats from climate change, and once bleaching begins, it can be hard to stop. But this microscope might help researchers catch problems earlier.

“The microscope facilitates previously unavailable, underwater observations of coral health, a breakthrough made possible thanks to the National Science Foundation and its critical investment in technology development,” said Jules Jaffe, a research oceanographer at Scripps and co-author of the study.

Without continued federal funding, scientific research is at risk. In this case, however, support from NSF enabled the team to build a device that helps solve the physiological mystery of coral bleaching and, ultimately, inform efforts to reverse it.

By detecting signs of stress before the coral reaches the tipping point, the researchers hope to create better strategies for protecting reefs from events like marine heatwaves.

Studying kelp and ocean algae

The potential doesn’t stop with corals. Scientists at Scripps Oceanography are already using the BUMP microscope to study other tiny marine life that rely on photosynthesis, including baby kelp off the coast of California.

“Since photosynthesis in the ocean is important for life on earth, a host of other applications are imaginable with this tool, including right here off the coast of San Diego,” said Jaffe.

In short, the BUMP microscope gives scientists something they’ve never had before: a new way to look at life underwater – close up, in motion, and alive. And with this new perspective, scientists are hoping to find better ways to protect some of the most fragile ecosystems on the planet.

The full study was published in the journal Methods in Ecology and Evolution.

About the image: The photo features the coral Stylophora pistillata taken with the new micrsope, BUMP. Each polyp has a mouth and a set of tentacles, and the red dots are individual microalgae residing inside the coral tissue. Credit: Or Ben-Zvi

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