Spatially differing bacterial communities in water columns of the northern Baltic Sea

The Baltic Sea is a large, shallow and strongly stratified brackish water basin. It suffers from eutrophication, toxic cyanobacterial blooms and oxygen depletion, all of which pose a threat to local marine microbial communities. In this study, the diversity and community structure of the northern Baltic Sea bacterial communities in the water column were − for the first time − thoroughly studied by 454-sequencing. The spring and autumn bacterial communities were one order of magnitude less diverse than those in recently studied oceanic habitats. Patchiness and strong stratification were clearly detectable, since only less than 1% of OTUs were shared among eleven samples. The community composition was more uniform horizontally (at a fixed depth) at different sites than vertically within one sampling site. Taxonomic affiliations revealed a total of 23 bacterial classes and 169 genera, and five percent of the sequences were assigned unclassified. The cyanobacteria constituted less than two percent of the sequences and potentially toxic cyanobacterial genera were practically absent during the sampling seasons.