The distribution of phytoplankton in the Baltic Sea assessed by a prokaryotic 16S rRNA gene primer system

Due to the evolutionary relationship between cyanobacteria and chloroplasts of all oxygenic eukaryotic photoautotrophs, both can be amplified by prokaryotic 16S rRNA gene primers. In marine water samples, chloroplast sequences often make up as much as 50% of a 16S rRNA gene library, yet because of the comparatively low phylogenetic resolution within limited chloroplast databases, they are usually removed from further analyses. However, chloroplast 16S rRNA gene databases are constantly improving and our aim was to test if the combined 16S rRNA gene sequences of phototrophic prokaryotes and eukaryotes generated by a prokaryotic primer set could be used to characterize their distribution. Using the phytoREF database, in situ 16S rRNA gene distribution characterization was performed for samples throughout the Baltic Sea (cells >0.2 μm) and compared to microscopic (cells >20 μm) as well as flow-cytometric (cells <7 μm) data. Generally, microscopic and molecular methods revealed similar distribution patterns of diatoms, chlorophytes and filamentous cyanobacteria. Although not directly comparable, flow cytometry delivered semi-quantitative patterns, on a very broad classification level, to the molecular approach. In conclusion, the combination of molecular and non-molecular analyses provided an improved overview of the phototrophic community, demonstrating its usefulness as a tool in monitoring strategies.