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The Suisun Bay Phenomenon


Active Fluorescence

Photosynthetic yield is measured in an effort to estimate the photosynthetic efficiency of primary producers, more specifically the organism’s  ability to use light for photosynthetic processes.  When phytoplankton are nutrient or light limited, stressed or exposed to biotoxins, their photosynthetic yield decreases indicating a blocking or degradation of the photosynthetic pathway resulting in a diminished ability to produce sugars or compounds necessary for  growth.  Typical yield values, calculated as the ratio of variable fluorescence to maximum fluorescence, range from 0.00 to 0.65.  Yields closer to 0.65 indicate healthy algal populations (i.e. not limited from growth; photosynthetic pathways open).

Turner Designs' PhytoFlash is an active fluorometer used to estimate photosynthetic yield.  It can be used in either stand alone mode or integrated into CTDs, dataloggers, or third party instruments.  Low power consumption, robust design, and relatively fast sampling rates make it ideal for rapidly assessing photosynthetic efficiency of phytoplankton in almost any aquatic habitat.     

Recently, data collected from Suisun Bay using a PhytoFlash exhibit suppressed yields within the Bay, increasing as you travel towards the Delta or San Pablo Bay.  The following data sets were collected by Raphael Kudela from UC Santa Cruz on May and July of 2012 and April 2013, respectively:


Suppressed yields in Suisin Bay were observed in all three profiles.   Is there some component to Suisun Bay waters that affects the efficiency of the phytoplankton community or are there interferences that affect the fluorescence detected by the phytoflash, resulting in lower yield estimates?  

We know with blue fluorimetry that Dissolved Organic Matter (DOM) is a primary interference factor.  Turner Designs offers a red excitation PhytoFlash which can be used for estimating eukaryotic activity in DOM-rich systems, eliminating interference from DOM.  Data collected below using both blue and red PhytoFlash instruments show no qualitative or statistic difference in blank corrected yield estimates.    


DOM interference can be corrected simply by subtracting the background fluorescence signal from the raw fluorescence signal, greatly increasing accuracy in estimates.  Because DOM isn't a factor once a proper blank is subtracted, even if Suisun Bay was a DOM-rich environment, it wouldn't account for the low yields observed.  

Suspended solids may interfere with the fluorescence signal detected by either blocking or scattering light.  Over multiple cruises, no correlations were found between yield and sediment load.  This is primarily due to the way yield is calculated.  Even if there was a drop in the fluorescence signal detected due to increased suspended sediments, the decrease in fluorescence would equivalently affect both parameters measured: Fo (background fluorescence) and Fm (maximum fluorescence).  Because PhytoFlash uses the difference between Fm and Fo to estimate yield, the unit is relatively insensitive to high sediment loads or turbidity, with no effect on yield estimates.  

The PhytoFlash was used to collect yield data across Suisun Bay during multiple cruises.  All sampling events recorded a drop in yield within Suisun, with increasing yields as you exit towards San Pablo Bay or the Delta.  Because PhytoFlash provides accurate yield estimates even when interferences such as dissolved organics and suspended sediments are present, there must be other factors contributing to the suppressed yields observed in Suisun Bay.  Exactly what those other factors are that cause the “Bad Suisun” phenomenon is the focus of several research groups.  The PhytoFlash provides the ability to easily monitor the extent and location of this lower yield, narrowing the search for the factor(s) that are ultimately responsible.



Suisun Bay, CA USA
UC Santa Cruz