Eukaryotic and bacterial communities were characterized and quantified in microalgal photobioreactor cultures of freshwater Chlorella vulgar-is and marine Dunaliella tertiolecta. The microalgae exhibited good growth, whilst both cultures contained diverse bacterial communities. Both cultures included Proteobacteria and Bacteroidetes, while C. vulgar-is cultures also contained Actinobacteria. The bacterial genera present in the cultures were different due to different growth medium salinities and possibly different extracellular products. Bacterial community profiles were relatively stable in D. tertiolecta cultures but not in C. vulgar-is cultures likely due to presence of ciliates (Colpoda sp.) in the latter. The presence of ciliates did not, however, cause decrease in total number of C. vulgar-is or bacteria during 14 days of cultivation. Quantitative PCR (qPCR) reliably showed relative microalgal and bacterial cell numbers in the batch cultures with stable microbial communities, but was not effective when bacterial communities varied. Raw culture samples were successfully used as qPCR templates. (C) 2012 Elsevier Ltd. All rights reserved.