Florida Bay is a shallow, lagoonal estuary located at the southern tip of Florida. An inverse analysis approach was used to examine carbon flows and trophic interactions in the planktonic system of two contrasting regions of Florida Bay, the eastern and north- central regions. The eastern region has relatively low phytoplankton concentrations, while the north-central region exhibits sporadic blooms of the picoplanktonic cyanobacterium Synechococcus. The overall goal of the study was to obtain a biologically realistic plank- tonic food web for Florida Bay that can be coupled to results of seagrass modeling and studies of inter-basin exchange. Estimated rates of carbon flow through the planktonic food webs differed greatly between regions, but not between seasons. Assumptions about the food preferences of the microzooplankton resulted in different paths of carbon through the food web, but had relatively little effect on total export from the planktonic system. The microbial loop played an important role in carbon cycling through the food webs of both the eastern and north-central regions. Despite active recycling, calculated carbon export rates were high from the north-central region (82–128 mg C m-3 d-1 ); export from the eastern region was lower by a factor of 12–14. Production by small (< 5 mm) phy- toplankton accounted for the majority of carbon exported from the north-central region. The contribution of the picoplankton to export from this region contrasts with their more conventional role in recycling of organic matter within the water column. The inverse models helped identify gaps in knowledge of the Florida Bay planktonic ecosystem, and pointed to areas for future research including the characterization of protozoan bacterivory and the extent of microzooplankton grazing on picoplanktonic cyanobacteria versus het- erotrophic bacteria.
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