The Department of Defense (DoD) has responsibility for numerous facilities in tropical and subtropical environments that are adjacent to coral reefs. Coral reefs are susceptible to anthropogenic insult and are rapidly degrading worldwide. Documenting the physiological state of reef communities is critical for developing remediation strategies that can both reduce anthropogenic impact and distinguish between natural stress and anthropogenic factors potentially related to military activity. The ability to characterize, assess, and monitor underwater benthic communities associated with DoD sites or activities is required in order to document compliance with promulgated national policy and to ensure that DoD operations do not lead to natural resource degradation, particularly with respect to coral reefs.

The objectives of this project were to (1) develop advanced techniques for non-destructive assessment of the viability and health of coral reef communities with the capabilities of identification and quantification of natural and anthropogenic stresses; (2) design “bench scale” prototypes of Fluorescence Induction and Relaxation (FIRe) fluorosensors for permanent underwater monitoring stations and remotely operated vehicles (ROVs); and (3) collect baseline data on physiological, biophysical, biooptical, and genetic diversity of coral reef communities in the Caribbean and the Indo-Pacific regions.

Technical Approach

The novel FIRe technique and instrumentation were developed for measuring photosynthetic characteristics and assessing the physiological status of coral and other benthic organisms. This advanced technique relies on the established relationship between fluorescence emission and the efficiency of photosynthetic processes and provides a comprehensive suite of fluorescent and photosynthetic parameters of the target. The measured parameters reflect the physiological status of various components of the photosynthetic machinery, including the primary photochemical reaction in Photosystem II reaction centers and the electron transport within and down to Photosystem II (i.e., secondary photosynthetic reactions). These photosynthetic processes and related fluorescent parameters are particularly sensitive to environmental stresses, such as nutrient availability, irradiance, temperature, and anthropogenic insults, thus providing a biophysical background for non-invasive fluorescence monitoring of the organisms.


A bench-top version of the FIRe system was developed, constructed, and employed in the laboratory and field research. On the second stage of the instrument development, an underwater multi-receiver FIRe system for long-term underwater monitoring stations was designed and tested. This system permits simultaneous monitoring in situ of multiple targets, a crucial factor in sampling diverse coral reef communities. Finally, a bench-scale prototype of the laser-based FIRe sensor was designed for autonomously operated vehicles (AOVs). Based on the experiments in coral tanks, the specifications for a future operational ROV/AOV FIRe sensor have been defined.

Coral Cultivation Facilities were built at Rutgers University to conduct controlled manipulation experiments on live coral in the laboratory. The biophysical and biochemical parts of the project were completed both in the laboratory and in the field with the aim to elucidate the impact of common natural stresses (such as elevated temperature and excess light) and selected anthropogenic stresses (such as heavy metal contamination) on coral. The cellular and molecular mechanisms, together with the optical signatures of the stresses, had previously been established. On this background, bio-optical algorithms for detection and assessment of the stresses were developed and evaluated. During the field studies in the Caribbean and Indo-Pacific regions, baseline information on the variability in fluorescent and photosynthetic properties of corals was collected.

The molecular biology and genetic part of the project included identification, isolation, as well as spectroscopic, genetic, and biochemical characterization of major color determinants in corals, as well as sequencing, cloning, and characterization of 30 new fluorescent proteins from corals. Empirical correlation between individual allelomorphs and the photosynthetic and physiological variability retrieved using the FIRe variable fluorescence techniques were further examined. Although further research is needed to understand the physiological function and variability of expression of fluorescent proteins in coral, this part of the project provides scientific background for understanding the optical diversity of coral reef ecosystems and interpreting the results of optical monitoring of benthic communities using spectral fluorescence and reflectance measurements.


The FIRe system can be used to assess the physiological status of benthic organisms, including coral. Together with spectral fluorescence and novel molecular biology techniques, it provides a comprehensive and detailed assessment of DoD coral reef ecosystems. The research revealed that the method is very sensitive to changes in the coral physiology and records detrimental changes at early stages of the stress development—before any visible changes in coral coloration appear. Because the technique records an extensive suite of physiological parameters, there is also a possibility to diagnose what kind of stress is involved. For instance, the developed protocols were successfully employed to distinguish between common natural stresses and selected anthropogenic stresses such as metal toxicities.

The best strategy for operational use of this technology would be production and installation of underwater systems for permanent underwater stations at several locations with continuous recording and analysis. Such measurements are conducted in a fully automatic mode and would alert marine biologists and environmental policy makers as to potential detrimental changes in the coral. The technology transfer of the bench-top version of the FIRe system to a small high-tech company, Satlantic Inc., has been completed (www.satlantic.com/fire).