Ocean acidification resulting from the uptake of anthropogenic carbon dioxide (CO2) by the ocean is considered a major threat to marine ecosystems. Here we examined the effects of ocean acidification on microbial community dynamics in the eastern Baltic Sea during the summer of 2012 when inorganic nitrogen and phosphorus were strongly depleted. Large-volume in situ mesocosms were employed to mimic present, future and far future CO2 scenarios. All six groups of phytoplankton enumerated by flow cytometry (<20 µm cell diameter) showed distinct trends in net growth and abundance with CO2 enrichment. The picoeukaryotic phytoplankton groups Pico-I and Pico-II displayed enhanced abundances, whilst Pico-III, Synechococcus and the nanoeukaryotic phytoplankton groups were negatively affected by elevated fugacity of CO2 (fCO2). Specifically, the numerically dominant eukaryote, Pico-I, demonstrated increases in gross growth rate with increasing fCO2 sufficient to double its abundance. The dynamics of the prokaryote ... : Supplement to: Crawfurd, Katharine J; Alvarez-Fernandez, Santiago; Mojica, Kristina D A; Riebesell, Ulf; Brussaard, Corina P D (2017): Alterations in microbial community composition with increasing fCO2: a mesocosm study in the eastern Baltic Sea. Biogeosciences, 14(16), 3831-3849 ...