Pigment Dynamics In a Coastal Bottom Boundary Layer and Its Relation to the Physical Regime: Measurements Using an In Situ Fiber-Optic Fluorometer

Date of Award


Degree Type


Degree Name

Doctor of Philosophy (PhD)


Marine Science

First Advisor

Steven E. Lohrenz

Advisor Department

Marine Science


An understanding of the processes which control the near-bottom distribution and transport of particulate organic matter produced by phytoplankton is essential in determining its fate and the linkages of carbon budgets between the various shelf regions. A variety of evidence suggests such linkages may be important in the Cape Hatteras shelf and slope regions. Time series observations of chlorophyll fluorescence in the bottom boundary layer are examined in relation to physical processes over the inner continental shelf at a 20 m site near Cape Hatteras, North Carolina for a 29 d period from 24 July to 22 August 1994. An autonomous multisensor in situ fiber-optic fluorometer was developed and deployed in the bottom boundary layer in conjunction with a BASS (benthic acoustic stress sensor) tripod for estimating the vertical photosynthetic pigment structure on sampling scales that were directly compatible with physical observations. Performance evaluation of the instrument showed stable operation during long-term field operations. Simulation analysis of particle size and a theoretical model of the phytoplankton package effect on fluorescence measurements by the dual fiber-optic sensor of the fluorometer indicated variability of fluorescence yield which were minimized by multiple sampling. Time series estimates of near-bottom pigment concentrations near Cape Hatteras were variable with high maxima (exceeding 100 mg m$\sp{-3}$). Periods of increased sediment suspensions and transient episodes of high pigment concentrations during the first half of the deployment period were associated with increased wind and wave activity in the region. High pigment concentration in surficial sediments were measured at deployment time and may have been available for resuspension during this period. A storm front on 7 August 1994, subsequent stratification and occurrence of low salinity events at the experiment site determined the pigment field in the near bottom waters for the remainder of the deployment period. Pigment fluxes were dominated by episodic transport events and relatively high magnitudes of net carbon transport onshore (3.9 g chl m$\sp{-2}$ day$\sp{-1}$) and to the south (4.5 g chl m$\sp{-2}$ day$\sp{-1}$). Fluorescence measurements with the multisensor fiber-optic fluorometer provided small-scale descriptions of the pigment field in relation to the physical processes and an accurate assessment of near-bottom pigment transport.