A diver‑operated microscope is giving scientists an unprecedented window into the hidden life of coral reefs, revealing how individual symbiotic algae within coral tissues harness sunlight to fuel their hosts. Developed at UC San Diego’s Scripps Institution of Oceanography, the Benthic Underwater Microscope imaging PAM (BUMP) uses pulse amplitude modulated light to map photosynthetic efficiency at nearly one‑micron resolution—small enough to visualize single microalgal cells embedded in living coral, all without collecting a single sample.
Traditionally, coral health assessments have relied on bulk fluorescence measurements or lab‑based imaging, limiting insights into micro‑scale variability. By combining high‑magnification optics, focused LED illumination, and real‑time fluorescence imaging in a single, waterproof unit, the BUMP can be carried by a scuba diver straight to the reef. Once submerged, it captures vivid color and chlorophyll‑a fluorescence images, then computes the minimal and maximal fluorescence of Photosystem II to generate pixel‑by‑pixel maps of Fv/Fm, a key proxy for photosynthetic efficiency.
“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,” says Or Ben‑Zvi, lead author and postdoctoral researcher at Scripps Oceanography.
In laboratory trials, the team validated the BUMP against a commercial Mini‑Imaging PAM, finding similar average Fv/Fm values but with the BUMP unveiling fine‑scale spatial differences within individual coral polyps. In field tests across Hawaii, the Red Sea, and Palmyra Atoll, the BUMP revealed how photosynthetic efficiency varies across different coral morphologies and microhabitats—data that were previously impossible to collect in situ.
“This microscope is a huge technological leap in the field of coral health assessment,” says Jules Jaffe, research oceanographer and co‑author.
Beyond mapping photosynthesis, the BUMP’s high‑resolution images capture coral behavior—such as polyps contracting or responding to particles—and the distribution of fluorescent proteins around mouths and tentacles, offering clues to coral stress responses. Its portability and non‑invasive design mean researchers can repeatedly monitor the same colony over time, spotting early warning signs of bleaching before visible damage occurs.
By peering into the microscopic engines that power coral reefs, the BUMP lays the groundwork for targeted conservation strategies, from identifying resilient coral strains to testing interventions that bolster symbiont performance. As ocean warming and pollution continue to threaten reefs worldwide, this new “underwater microscope” could be the magnifying glass scientists need to safeguard these vital ecosystems for generations to come.
The study has been published in the journal Methods in Ecology and Evolution.
