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Lysed cell material of Synechococcus (open ocean strain WH7803) was prepared using French press (Glenn Mills, Clifton, NJ, USA), filtered through a glass fiber filter (GF/F Whatman), and then added to 20 L of Gulf Stream surface water. Triplicate samples and controls were incubated at room temperature and in the dark for over 500 days. Optical properties were determined at specific time intervals throughout the experiment and revealed fluorescent dissolved organic matter (FDOM) similar to deep ocean FDOM, confirming results from an earlier shorter incubation experiment. New insights in the behavior of statistically-derived Parallel Factor Analysis (PARAFAC)components revealed processing of the initially produced fluorophores and the accumulation of a molecularly modified degradation product that maintained the core fluorescence, with slight spectral shifts indicated by a change from one PARAFAC components to another over time. Microbially transformed FDOM derived from of <em>Synechococcus</em> can therefore accumulate in the dark ocean over long-time periods and hence is confirmed to be a viable source of marine FDOM. Ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry supports the notion that the core fluorescence could be derived from pyrrole substructures.