When phytoplankton are bathed in the natural radiance field of
the ocean, some of the chlorophyll molecules emit red light in a
phenomenon known as sun-induced chlorophyll fluorescence
(SICF). In this thesis, I approach the study of SICF from several
perspectives. For field studies deploying floating
spectroradiometers, an inversion model of reflectance in the
fluorescence band is developed and applied. The model is used
in two optical regimes: in coastal waters of Nova Scotia, where
chromophoric dissolved organic matter absorption was
sufficiently high to prevent the retrieval of phytoplankton
biomass using standard ocean color algorithms; and in the
Bering Sea, where phytoplankton biomass dominated the optical
signal. In the first example, the retrieval of phytoplankton
biomass was possible using the fluorescence signal corrected for
changes in the quantum yield of fluorescence with irradiance. In
the second application, the accurate retrieval of phytoplankton
absorption from ocean color allowed the quantum yield of
fluorescence to be estimated. For global observations of
fluorescence from space (i.e., provided by the MODIS
spectroradiometer on the Aqua and Terra satellites), I created
and applied two algorithms for retrieving the quantum yield of
fluorescence or phytoplankton biomass. A comparison with the
MODIS chlorophyll data product showed that 86% of the
retrievals using the new fluorescence algorithm were within a
factor of two of the standard ocean color algorithm. The new
algorithm for the quantum yield will be an improvement in
regions where the 412 nm band is poorly retrieved, but will
perform similarly to the previous algorithm in other regions.
Lastly, in a theoretical study I developed a mechanistic model of
phytoplankton fluorescence at the level of the chloroplast. This
approach reconciles fluorescence emission with photosynthesis
and heat dissipation in phytoplankton on timescales varying
from seconds to days. The model includes photochemical and
non-photochemical quenching, damage and repair of
photosystem II (PSII), acclimation of the antenna size of PSII, the
ratio of photoprotective to photosynthetic pigments, and
nutrient limitation. The results of this thesis should allow better
retrieval and interpretation of the physiological and taxonomic
information contained in sun-induced fluorescence.