Optimized analysis of variable chlorophyll fluorescence in algal physiology under stress conditions : measuring nothing with confidence

Nicole Bobco, California State University, Monterey Bay

Thesis (M.A.) Teacher Education Department


The detection and determination of viable phytoplankton are fundamental assays in oceanographic and limnological fields. Assessing phytoplankton physiology allows for insight into how cells might respond to different environmental or physical stressors, making it an important subject for ecological research and applied sciences, where the physiological status of photautotrophs must be known. In particular, maritime operations have been identified as major vectors in the spread of aquatic invasive species through ballast water transport. To mitigate this environmental hazard, shipborne systems are required to effectively sterilize ballast water to comply with emerging regulations regarding the transport of ballast water. Common oceanographic tools must now be reassessed for their capacity to quantify the treatment based reduction in viable biomass for organisms, like phytoplankton, to determine efficacy and compliance of treatment systems with ballast water regulations. Pulse Amplitude Modulated (PAM) fluorometry offers one method to assess the phytoplankton component of ballast water. This technology measures chlorophyll fluorescence to provide various indices (e.g. Fv/Fm) of photosystem activity, a proxy of cell viability or phytoplankton health. This thesis describes the development and testing of a series of custom algorithms developed in MATLAB to enable robust assessment of PAM rapid light curves trends in order to quantify the absence of biological activity in treated ballast water samples. The series of algorithms provide a simple user interface and has practical applications in a wide range of academic as well as regulatory applications.