Polyunsaturated aldehydes (PUAs), produced as secondary metabolites by diatoms, have been shown to induce toxic effects on a variety of organisms, including copepods and phyto- and bacterioplankton. However, the nature of and the players in this interaction remain poorly under- stood. We tested the effect of 3 PUAs commonly produced by marine diatoms—2E,4E/Z-heptadienal (HEPTA), 2E,4E/Z-octadienal (OCTA), 2E,4E/Z-decadienal (DECA) and a mix of HEPTA and OCTA (MIX)—on a natural bacterial community from a coastal area of the NW Mediterranean Sea (Blanes Bay, Spain). Little effect on total or relative cell abundance or bulk bacterial production was observed after 6 or 24 h exposure to 7.5 nM of the 3 different PUAs for the different bacterial phylogenetic groups (Gammaproteobacteria, Bacteroidetes, Rhodobacteraceae and SAR11), assessed by catalysed reporter deposition (CARD)-fluorescence in situ hybridisation (FISH). Metabolic activity, i.e. single- cell activity as determined by microautoradiography combined with CARD-FISH (MAR-CARD- FISH), was least affected by the addition of single PUAs in Gammaproteobacteria, markedly in Bac- teroidetes and most markedly in Rhodobacteraceae, leading to a decrease in Rhodobacteraceae abundance by 21% (by 38% of the active cells assessed by leucine uptake) compared to the control. Bacteroidetes, although markedly affected in single-cell activity, were the most abundant group (54% of total cell counts). The addition of a mixture of OCTA and HEPTA produced a more pro- nounced decrease in the metabolic activity of all groups than the incubation with the single PUAs, suggesting a synergistic effect. Our results demonstrate that PUAs have a differential effect on the single-cell activity of distinct bacterial groups in natural communities. PUAs may therefore play an important role in shaping bacterial community composition by conferring a competitive advantage to PUA-resistant groups, allowing them to preferentially use the organic matter released by diatoms.