, 2003). Sulphate-reducing bacteria are a large group belonging find protocol to Deltaproteobacteria and known to be widely distributed in oxygen-depleted aquatic environments (Madigan et al., 2003). In our study, we found sulphate-reducing bacteria in two benthic samples, TPDEEP_215m and LL12_81m, but not in LL7_101m. This is in accordance with anoxia and the occurrence of H2S being very infrequent in the central Gulf of Finland compared with the two more westerly locations. In TPDEEP, Desulfobacterium, a strict anaerobe, as well as Desulfobacula and Desulfobacter were present, all belonging to the Order Desulfobacterales. In LL12_81m, sulphate-reducing bacteria were found belonging to three orders: Desulfobacterales, Desulfuromonales, and Desulfovibrionales, of which the Desulfobacterales was the most common. The latter order was comprised of genera, including Desulfobacterium, Desulfobacula, Desulfobacter, Desulfocella, and Desulfonema, which are indigenous to anoxic marine and freshwater habitats. However, sulphate-reducing bacteria did not dominate, consisting of only around 2?C4% of all sequences in both samples, depending on the method used to characterize the genera (Classifier/blastn) (Zhang et al., 2000; Wang et al., 2007). The sulphate-oxidizing Sulfurimonas (Inagaki et al., 2003) was present in deep water in TPDEEP and LL12 and was the eighth most abundant genus in the entire Alectinib mw dataset. Additionally, Sulfurovum and Sulfurospirillum were detected in TPDEEP_215m. Sulfurimonas is Gemcitabine an aerobic and mesophilic genus (Inagaki et al., 2003), but our data suggest there are species of this genus capable of growing in anoxic and cold environments as well. Our findings correspond to previous studies in stratified water columns, where microbial communities have been found to differ between oxygen-rich surface water and oxygen-depleted deeper layers (DeLong et al., 2006; Zaikova et al., 2010). Although Beggiatoa alba is known to be common in the Baltic Sea at the hypoxic sediment?Cwater interface (Mu?mann et al., 2007), it was not detected in the benthic communities studied here. Because cyanobacterial blooms have been considered a serious problem in the Baltic Sea region (Forsberg, 1991), we were interested in their occurrence also outside of the main blooming season of toxic cyanobacteria. In our dataset, cyanobacteria were present in all samples, but they constituted only a minority (<2%) of all the sequence reads. They were more common in pelagic surface waters than in estuarine (station KV) and benthic communities. The genus Nodularia, known to produce mass occurrences and occasional toxic blooms in the Baltic Sea (Sivonen et al., 1989a), was not detected. However, Anabaena and Aphanizomenon were detected at sites LL7 (1 and 30?m) and TPDEEP (30?m) even if the total number of sequence reads assigned to these groups was marginal.