Community metabolism plays a crucial role in the carbon dynamics of continental aquatic ecosystems. In the present work, two Mediterranean reservoirs (Southern Spain) with different trophic status were monitored during the stratified phase over two consecutive years (2009 and 2010) to evaluate community metabolic dynamics and potential controlling factors. Dark and light incubations were performed in order to estimate the daily rates of gross production (GP), community respiration (CR) and net community production (NCP). Temperature, irradiance, chlorophyll, phosphorus and carbon concentration were also measured at different depths within the mixed layer. On average, results showed heterotrophic behavior (GP < CR) in both reservoirs, which was particularly evident in the more eutrophic reservoir. Interannual climate variability was high due to the exceptionally rainy winter of 2010. This resulted in a significant decrease in the magnitude of the heterotrophic balance in both reservoirs. The change in NCP was especially evident in the most eutrophic reservoir where high water renewal rates lead to a lower CR. In general, NCP was found to be directly related to the ratio between the euphotic layer depth and the mixed layer depth, and inversely related to the particulate phosphorus concentration. Autotrophic behavior was only found in conditions of high irradiance (mixed layer shallower than euphotic layer), relatively low concentrations of dissolved organic carbon (<6 mg L−1) and particulate phosphorus (<10 μg L−1), and moderate chlorophyll concentration (2–9 μg L−1), albeit these conditions did not always lead to a net autotrophic balance.

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