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The Río de la Plata is the world’s largest estuary, draining the second largest basin of South America. In spite of its key significance at the local and global scale, this is the first attempt made so far to characterize the bacterial diversity of this system. We employed a suite of molecular methods to analyze the bacterial diversity at different phylogenetic levels, both in terms of richness and evenness, and we related these findings to physicochemical parameters. A clear environmental gradient was observed with 3 distinctive zones (riverine, frontal, and marine). In turn, the bacterial communities appeared highly diverse and strongly structured by the environment. A high number (324) of different operational taxonomic units (OTUs) were identified by automated ribosomal intergenic spacer analysis (ARISA). The ARISA results suggested that the composition of bacterioplankton communities was strongly related to physicochemical water characteristics, and that the bacterioplankton had little overlap with the bacterial assemblage of the sediments. Catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) indicated that Betaproteobacteria and Actinobacteria were more abundant in the riverine zone, whereas Gammaproteobacteria and Planctomycetes preferred the marine waters. The relative abundance of Bacteroidetes peaked in the frontal zone, and Alphaproteobacteria were numerically dominant throughout the estuary. The analysis of about 300 almost full-length 16S rRNA gene sequences pointed to the existence of ubiquitous phylotypes, but also suggested habitat preferences among certain groups. This first look into the bacterial community of the Río de la Plata demonstrated marked diversity patterns, providing further insights into the ecology of globally distributed groups of aquatic bacteria

Multilevel analysis of the bacterial diversity along the environmental gradient Río de la Plata–South Atlantic Ocean