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Microorganisms are among the most important organisms to the ecology of salt marsh estuaries; however, fundamental questions regarding their distribution, environmental controls, and interactions with phytoplankton remain unanswered. We used denaturing gradient gel electrophoresis (DGGE) of bacterial rRNA genes and high performance liquid chromatography (HPLC) of phytoplankton photopigments to characterize planktonic communities from the Ashepoo, Combahee, and Edisto (ACE) Basin and North Inlet (NI) estuaries on the South Carolina coast, USA. Multivariate comparisons of the planktonic community profiles revealed that the 2 estuaries supported distinct bacterial communities. Furthermore, bacterial communities in both systems were partitioned into separate particle-associated (PA) and free-living (FL) components. Differences in bacterial populations were also observed along the salinity gradient within each system. Comparisons of water physicochemistry with bacterial profiles indicated significant correlation of PA bacterial community structures with temperature, salinity, organic carbon, total phosphorus, and ammonium, whereas FL communities were affected by nitrate, ammonium, total phosphorus and orthophosphate. PA bacterioplankton community structures were also associated with diatoms, dinoflagellates, haptophytes and cryptophytes, while FL assemblages corresponded to prasinophytes, chlorophytes, and cyanobacteria. Comparisons between estuaries further demonstrated that ACE Basin communities were mostly associated with the same pigments as PA samples, and that NI assemblages correlated with FLassociated phytoplankton, suggesting different trophodynamics of particles in the 2 systems.

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