A groundbreaking advancement in marine biology and underwater imaging has emerged from researchers at UC San Diego’s Scripps Institution of Oceanography: a revolutionary underwater microscope called the Benthic Underwater Microscope Imaging PAM, or BUMP. This innovative technology transcends previous limitations by allowing scientists to peer directly into the microcosm of coral reefs and observe critical photosynthetic processes in situ, without disturbing these delicate ecosystems. The development of BUMP opens unprecedented possibilities to understand coral health at the microscopic level, marking a significant leap forward in the fight to protect and preserve the world’s rapidly declining coral reefs.
Traditional methods for studying coral bleaching and photosynthesis have largely relied on destructive sampling or low-resolution techniques that fail to capture the fine-scale physiological dynamics of coral-algal symbiosis. However, BUMP employs pulse amplitude modulated (PAM) light measurement techniques integrated within a diver-operable microscope system. This approach enables researchers to quantify photosynthetic efficiency and visualize fluorescence emitted by individual symbiotic microalgae residing within coral tissues, all while maintaining the structural and functional integrity of the living reefs. This is especially crucial, considering that coral bleaching—a stress response characterized by loss of symbiotic algae—remains a poorly understood phenomenon due to the challenges in accessing and monitoring processes at the micro-scale in situ.
BUMP’s design represents an engineering masterpiece. Developed by the Jaffe Lab for Underwater Imaging at Scripps Oceanography, the microscope is both compact and user-friendly, incorporating a high-magnification lens array paired with focused LED excitation sources and sensitive fluorescence detectors. The entire system is controlled via a waterproof touchscreen interface and powered by an onboard battery pack, enabling divers to transport and deploy the device at the seafloor without relying on heavy, ship-based instrumentation. This portability empowers marine scientists to conduct non-invasive, real-time assessments of coral health across diverse reef ecosystems globally.
The microscope detects and maps the red fluorescence originating from chlorophyll within the photosynthetic microalgae, which serve as symbionts and vital energy sources for corals. By measuring the intensity of this fluorescence through PAM techniques, BUMP provides a quantitative index of photosynthetic efficiency at micron-scale resolution—an ability never before achieved in natural underwater environments. Additionally, the system captures cyan and green fluorescence emitted by specialized proteins produced by the corals themselves, shedding light on their physiological state and potential adaptive responses to environmental stressors.
Testing of this device spanned multiple iconic reef locations, including Hawaii, the Red Sea, and Palmyra Atoll. In partnership with the Smith Lab, the researchers calibrated and validated BUMP’s sensitivity and accuracy, ensuring that measurements are robust and representative of natural conditions. Lead author Or Ben-Zvi, a marine biologist, reported surprising observations during in-field deployments, such as dynamic changes in coral polyp volume and complex behaviors reminiscent of “kissing” or “fighting” between adjacent polyps. These behavioral insights, combined with photosynthetic data, provide new dimensions in understanding coral ecology and response mechanisms.
BUMP not only reveals the microstructure of coral tissue but also permits the non-invasive tracking of photosynthetic performance in real time. This is particularly critical given the accelerating frequency and severity of marine heatwaves, which trigger coral bleaching and widespread reef degradation. Through early detection of subtle declines in algal photosynthetic function, the microscope offers a potential warning system that could inform timely conservation interventions before irreversible damage occurs. This capability aligns closely with ecological management goals amid the climate crisis.
Beyond coral research, BUMP holds tremendous promise for investigating other photosynthetic marine organisms at micro-scales. For instance, researchers are already leveraging this technology to study the initial life stages of giant kelp, a keystone species along the California coast. Understanding photosynthetic efficiency and growth dynamics in these species under changing ocean conditions will provide broader insights into marine ecosystem health and productivity.
The development of BUMP underscores the vital role of federal funding and scientific innovation in addressing pressing environmental challenges. Instrumentation such as this not only enhances our fundamental knowledge of marine biology but also equips the scientific community with tools essential for developing informed strategies to protect vulnerable habitats. Researchers emphasize that continued investment in technology is indispensable for unraveling complex physiological mysteries—such as why corals bleach—and for crafting responsive mitigation efforts.
Scripps Oceanography’s interdisciplinary collaboration between engineers, marine biologists, and oceanographers that culminated in BUMP illustrates the power of converging expertise to confront multifaceted scientific problems. By merging cutting-edge microscopy, optical physics, and ecological fieldwork, this project sets a new standard for in situ marine imaging. The capacity to visualize interactions between coral hosts and their algal symbionts at unprecedented spatial and temporal resolution fundamentally transforms our approach to marine conservation science.
As coral reef ecosystems globally face existential threats from warming oceans, acidification, and human disturbance, innovative tools like BUMP provide a beacon of hope. The knowledge it generates will help shape effective policies and restoration practices by illuminating the mechanisms underlying coral health and resilience. Its ability to non-invasively monitor the delicate balance of coral-algal relationships promises advances in how researchers and conservationists assess and respond to environmental stressors on reef systems worldwide.
In summary, the Benthic Underwater Microscope Imaging PAM (BUMP) emerges as a transformative technology in marine science, enabling direct, real-time visualization and quantification of photosynthetic processes deep within live coral tissues. It represents a monumental technological breakthrough, fostering new understanding of coral physiology at microscopic scales and offering a vital tool to help protect these keystone ecosystems amid mounting global change pressures. The research published by UC San Diego scientists ushers in a new era for oceanographic imaging and coral reef conservation.
Subject of Research: Animals
Article Title: The Benthic Underwater Microscope Imaging PAM (BUMP): A Non-invasive Tool for In Situ Assessment of Microstructure and Photosynthetic Efficiency
News Publication Date: 3-Jul-2025
Web References:
https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.70078
https://jaffeweb.ucsd.edu/
https://seaweedecologylab.ucsd.edu/
References:
Ben-Zvi, O., Jaffe, J., Roberts, P., Deheyn, D., Lertvilai, P., Ratelle, D., Smith, J., Snyder, J., & Wangpraseurt, D. (2025). The Benthic Underwater Microscope Imaging PAM (BUMP): A Non-invasive Tool for In Situ Assessment of Microstructure and Photosynthetic Efficiency. Methods in Ecology and Evolution. DOI: 10.1111/2041-210x.70078
Image Credits: Or Ben-Zvi
Keywords: Reef building corals; Coral bleaching; Coral reefs; Marine photosynthesis; Microbiology; Microalgae; Fluorescence microscopy; Research methods; Observational studies; Imaging
