Estuaries draining densely populated watersheds experience significant anthropogenic pressure and sustain large autotrophic and heterotrophic production owing to an increased input of nutrients and organic matter. Polluted estuaries are often net heterotrophic systems. Our objective was to study the relative contributionof autotrophic and heterotrophic food webs in sustaining the high productivity of pelagic estuarine ecosystems along the estuarine gradient of the Scheldt estuary. We concentrated on the nature of the primary food sources of calanoid and cyclopoid copepods and on the organic substrates supporting heterotrophic production. An extensive study of the monthly variation of delta15N and delta 13C of suspended matter and copepods over a period of two year showed that variations in the relative contribution and isotopic signature of phytoplankton were probably the main factors controlling the seasonal and spatial variation in the delta15N and delta13C signature of suspended organic matter. Comparisons between the seasonal delta 15N and delta13C patterns of suspended matter and copepods showed that the nature of the primary food sources differed between calanoid and cyclopoid copepods and between freshwater and oligohaline-mesohaline reaches. In the oligohaline and mesohaline reaches, calanoid and cyclopoid copepods were mainly supported by autotrophic and heterotrophic biomass, respectively, whereby the latter probably thrived on dissolved organic matter derived from local phytoplankton. In the freshwater section, cyclopoid copepods dominated the copepod community. The important discrepancy between delta15N of cyclopoid copepods and the mode led delta15N of phytoplankton in the freshwater reaches eliminated local phytoplankton or heterotrophs thriving on dissolved organic matter derived from local phytoplankton as a possible food source. This situation was explained via a scenario where bacteria thriving on phytoplankton detritus imported from the tributaries formed the main food source of local cyclopoid copepods. Our observations highlighted a very different ecosystem functioning for the freshwater part compared to the oligo- and mesohaline waters of the estuary proper. In this work, we constructed an isotopic baseline for future studies on the diet and trophic level of planktivorous fish by calculating the annual mean delta15N and delta13C of copepods. However, the highly variable nature of the annual mean delta15N hampers the use of stable N isotopes as a tool to study fish migration between freshwater and marine reaches. Nevertheless, mesohaline stations showed sufficiently distinct delta15N signatures to allow tracing of migration between this habitat and the freshwater reaches.
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