Fluorescence in reef corals

Abstract

Fluorescence can be a powerful tool for probing biological systems. Prior measurements from Caribbean corals identified five fluorescing pigments in reef corals. In this thesis I study coral fluorescence spectra. I wanted to learn if fluorescence could be useful for large scale mapping and monitoring of the reef as a part of an effort to stop the recently reported global decline in coral reefs condition. 3D excitation I emission spectra, average wavelength locations and shape variability studies of each of the pigments is presented. I also present an in situ corrununity study of the species Montastraea cavernosa and investigate the variability of fluorescence emission among colonies of one species at one location. Coral's fluorescence emission spectrum can result from the excitation of one or more fluorescing pigments. A mathematical algorithm was developed to separate coral fluorescence spectra into individual components. The un-mixing algorithm was combined with a prediction model whose purpose was to predict the response that will be produced by any excitation light source given knowledge of the response produced by a different light source. Energy coupling between two of the pigments was discovered. An empirical coupling efficiency factor was defined and calculated to account for this energy transfer. The energy coupling between these pigments may have important consequences in future investigation of coral's evolution. A new experimental method to separate the reflectance and fluorescence spectral components of fluorescing corals was developed for in vivo and in situ data. Two experimental methods are proposed to measure and calculate a newly defined quantity, "practical fluorescence efficiency". This efficiency factor is essential for correct prediction of coral spectra under different illumination conditions. This part of my work will benefit optical models that calculate light interaction with the bottom of the ocean in shallow waters. Lastly I present a prototype Fluorescence Imaging Laser Line Scanner system and discuss its potential use as a remote sensing system for reef mapping and monitoring. Recommendations are made to better tune the system to the fluorescence characteristics of reef corals.