Theory and application of pulse amplitude modulated chlorophyll fluorometry in coral health assessment

Peter J. Ralph*, Ross Hill, Martina A. Doblin, Simon K. Davy

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

13 Citations (Scopus)


Scleractinian corals exist in symbiosis with dinoflagellate alga (genus Symbiodinium), which provides access to nutrients by the host but also makes it makes the holobiont vulnerable to photosynthetic stress, providing an opportunity for rapid health assessment using chlorophyll a (chl-a) fluorescence techniques. Common photosynthetic stressors of corals are high irradiance, ultraviolet light, temperature extremes, chemical pollution and low salinity, which are further compounded by other major anthropogenic pressures on coral reefs. Coral Symbiodinium cells contain chlorophyll (chl) a, c2 and a range of accessory pigments. The chl-a within the pigment complex absorbs light maximally in the blue (peak at 440 nm) and red (peak at 678 nm) regions of the spectrum and re-emits light energy in the form of fluorescence, maximally in the red bandwidth (630 to 770 m with a peak at 680 nm). In vivo chl-a has a variable fluorescence yield that is dependent upon the wavelength of excitation irradiance and varies over time as a result of the complex interaction of the photosynthetic pathways (Kautsky effect). When a chloroplast captures a photon of energy, the chl a molecule is excited from its ground state to an excited state. There are three competing and complementary energy dissipation processes for that excited molecule: (i) driving photosynthesis via the electron transport chain leading to carbon fixation, (ii) heat dissipation, or (iii) returning to the ground state and re-emitting some of the energy as fluorescence. This is why chl a fluorescence can be used as a proxy for photochemistry (and energy dissipation). During periods of high incident irradiance, if the amount of absorbed light exceeds the maximum rate of electron transport, then the excess energy must be dissipated, or photodamage can occur. Pulse-amplitude modulated (PAM) fluorometry provides a versatile technique for monitoring and assessing zooxanthellae health. It measures the photophysiological state of zooxanthellae noninvasively and often before more conspicuous indicators of deteriorating holobiont health are apparent. With multiple stressors, PAM fluorometry provides an integrated measure of coral condition, responding to the photosynthetic stress of algal symbionts. Because many types of fluorometers exist, it is imperative to be fully versed in their intended application and limitations before using one of these instruments. Four fundamental variables in PAM fluorescence data are Fo, Fm, Ft and Fm'; it is imperative that the entire system is set up correctly to ensure reliable measurements. Fo is dark-adapted and Ft is light-adapted minimum fluorescence. During a saturating flash of light, the fluorescence yield increases to a maximum called Fm, in the dark-adapted samples and Fm' in samples under ambient light, and the PSII reaction centers close. The difference between Fo and Fm is the variable fluorescence (Fv). The ratio of the variable fluorescence (Fv) to the maximum fluorescence (Fm) can be quantitatively related to the efficiency of photochemistry, also called maximum quantum yield of photosystem II (Fv/Fm). For coral disease states that directly or indirectly cause photosynthetic dysfunction, PAM fluorometry can be a valuable tool for monitoring the progression of coral disease in the field, and elucidating the impacts of microbial pathogens on the physiology of corals and their symbionts. Used in conjunction with other health assessment methods (e.g., cellular diagnostics, histology), PAM fluorometry can assist in elucidating the sequence of events and primary causes of symptoms observed in some diseases of corals.

Original languageEnglish
Title of host publicationDiseases of Coral
EditorsCheryl M. Woodley, Craig A. Downs, Andrew W. Bruckner, James W. Porter, Sylvia B. Galloway
Place of PublicationHoboken, New Jersey
PublisherJohn Wiley & Sons
Number of pages18
ISBN (Electronic)9781118828502
ISBN (Print)9780813824116
Publication statusPublished - 2016
Externally publishedYes


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