As the atmospheric CO2 concentration rises, more CO2 will dissolve in the oceans, leading to a reduction in pH. The consequences for marine organisms and especially heterotrophic bacteria remain under debate, and almost nothing is known concerning marine fungi. Both microbial groups are important players in organic matter decomposition and nutrient cycling, and their pH tolerance is known to be broad in relation to the predicted acidification range. At the community level however, even slight changes in pH may favour distinct groups, leading to compositional or even functional shifts. Effects of ocean acidification on microbial communities have mainly been studied in systems that reflect the natural situation but are biologically highly complex, namely the microbial community of corals or large-scale mesocosms. In coral microbial communities, shifts towards bacteria associated with stressed or diseased coral hosts together with a higher abundance of fungi were reported. Mesocosm studies in contrast did not reveal consistent effects on bacterial community composition, while fungi, to our knowledge, have not been considered so far. In these studies, indirect effects mediated through complex food webs or the host organism's physiology come into play, so that pH effects may be masked. Thus to reduce complexity and to look only at the direct pH effects on microbial communities, we conducted small-scale laboratory acidification experiments with the natural microbial community from Helgoland Roads (North Sea). For investigations of the bacterial community, three dilution approaches were used to select for different bacterial groups and seasonal variability was accounted for by repeating the experiment four times (spring, summer, autumn, winter). In a second experiment in spring, we investigated direct pH effects on fungal communities including yeasts. The pH levels used were in situ seawater pH, pH 7.82 and pH 7.67, representing the present-day situation and acidification at a pCO2 of 700 or 1000 ppm projected for the North Sea for the year 2100. For both bacteria and fungi, we studied alpha- and beta-diversity by automated ribosomal intergenic spacer analysis (ARISA). Based on ARISA results, selected bacterial community samples were further characterized by 16S amplicon pyrosequencing to identify the affected bacterial populations. Bacterial abundances were analyzed by flow cytometry and fungal abundances by colony forming unit counts. Marine yeasts isolated in the fungal experiment were screened by ARISA, protein spectra were compared among isolates by Matrix-assisted laser desorption/ionization-time-of-flight MS (MALDI-TOF MS) and representative isolates were selected for large-subunit rDNA D1/D2 domain sequence analysis. Bacterial communities were strongly influenced by season and dilution, demonstrating that diverse communities had been generated. Furthermore, significant influences of pH were found in two of the three dilution approaches for all seasons, mostly already at pH 7.82. The same pH influence was found for fungal communities. Additionally, fungal colony forming units were significantly higher for low pH treatments, while total bacterial abundances were not influenced by pH. Sequencing results are currently analyzed. Our findings suggest that already relatively small changes in pH affect microbial populations and may lead to higher abundances of marine fungi.