The intricate, hidden processes that sustain coral life are being revealed through a new microscope developed by scientists at UC San Diego’s Scripps Institution of Oceanography.
The diver-operated microscope — called the Benthic Underwater Microscope imaging PAM, or BUMP — incorporates pulse amplitude modulated (PAM) light techniques to offer an unprecedented look at coral photosynthesis on micro-scales.
In a new study, researchers describe how the BUMP imaging system makes it possible to study the health and physiology of coral reefs in their natural habitat, advancing longstanding efforts to uncover precisely why corals bleach.
Engineers and marine researchers in the Jaffe Lab for Underwater Imaging at Scripps Oceanography designed and built the cutting-edge microscope with funding from the U.S. National Science Foundation. The microscope is already yielding new insights into the relationship between corals and the symbiotic microalgae that support their health, revealing for the first time how well individual algae photosynthesize within coral tissue.
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Their findings were published July 3 in the journal Methods in Ecology and Evolution.
“This microscope is a huge technological leap in the field of coral health assessment,” said Or Ben-Zvi, a postdoctoral researcher at Scripps Oceanography and lead author of the study. “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, non-invasively and in their natural environment.”
Corals are reef-building animals that can’t photosynthesize on their own. Instead, they rely on microalgae living inside their tissues to do it for them. These symbiotic algae use sunlight, carbon dioxide and water to produce oxygen and energy-rich sugars that support coral growth and reef formation.
At just 10 micrometers across, or about one-tenth the width of a human hair, these algae are far too small to be seen with the naked eye. When corals are stressed by warming waters or poor environmental conditions, they lose these microalgae, leading to a pale appearance (“coral bleaching”) and eventual starvation of the coral. Although this process is known, scientists don’t fully understand why, and it hasn’t been possible to study at appropriate scales in the field — until now.
“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 jeopardized. In this case, NSF funding allowed us to fabricate a device so we can solve the physiological mystery of why corals bleach, and ultimately, use these insights to inform remediation efforts.”
The new imaging system builds upon previous technology developed by the Jaffe Lab, notably the Benthic Underwater Microscope, or BUM, from 2016. The main component of the BUMP is a microscope unit that is controlled via a touch screen and powered by a battery pack. Through an array of high-magnification lenses and focused LED lights, the microscope captures vivid color and fluorescence images and videos, and it now has the ability to measure photosynthesis and map it in higher resolution via focal scans.
With this tool, scientists are literally shining a light on biological processes underwater, using PAM light measurement techniques to visualize fluorescence and measure photosynthesis, and using imaging to create high-resolution 3D scans of corals.
When viewing the corals under the microscope, the red fluorescence of corals is attributed to the presence of chlorophyll, a photosynthetic pigment in the microalgae. With the PAM technique, the red fluorescence is measured, providing an index of how efficiently the microalgae are using light to produce sugars. The cyan/green fluorescence, concentrated around specific areas such as the mouth and tentacles of the coral, is attributed to special fluorescent proteins produced by the corals themselves and play multiple roles in the coral’s life functions.
The tool is small enough to fit in a carry-on suitcase and light enough for a diver to transport to the seafloor without requiring ship-based assistance. In collaboration with the Smith Lab at Scripps Oceanography, Ben-Zvi, a marine biologist, tested and calibrated the instrument at several coral reef hot spots around the globe: Hawaii, the Red Sea and Palmyra Atoll.
Peering through the microscope, she was surprised by how active the corals were, noting that they changed their volume and shape constantly. Coral behavior that looks like kissing or fighting has been previously documented by the Jaffe Lab, and Ben-Zvi was able to add some new observations to the mix, such as seeing a coral polyp seemingly trying to capture or remove a particle that was passing by, by rapidly contracting its tentacles.
“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,” said Ben-Zvi. “We are visualizing photosynthesis, something that was previously unseen at the scales we are examining, and that feels like magic.”
Because scientists can bring the instrument directly into underwater study sites, their work is non-invasive — they don’t need to collect samples or even touch the corals.
“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.”
The researchers said that data collected with the new microscope can reveal early warning signs that appear before corals experience irreversible damage from global climate change events, such as marine heat waves. These insights could help guide mitigation strategies to better protect corals.
Beyond corals, the tool has widespread potential for studying other small-scale marine organisms that photosynthesize, such as baby kelp. Several researchers at Scripps Oceanography are already using the BUMP imaging system to study the early life stages of the elusive giant kelp off 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 addition to Ben-Zvi and Jaffe, this study was co-authored by Paul Roberts — formerly with Scripps Oceanography and now at the Monterey Bay Aquarium Research Institute — along with Dimitri Deheyn, Pichaya Lertvilai, Devin Ratelle, Jennifer Smith, Joseph Snyder and Daniel Wangpraseurt of Scripps Oceanography.
Source: University of California, San Diego
Published on July 3, 2025