Two experiments were conducted to test whether viruses, small auto- and heterotrophic nanoflagellates were key factors regulating at relatively short-term (4 days) and nearby periods (April vs. May) the bacterial community in surface waters of Lake Geneva. 2.5 L containing polycarbonate bottles were incubated in situ with either <2 μm or <10μm filtered water with additions of either virus-free water or a viral concentrate. Abundances of viruses, prokaryotes and small autotrophs were obtained each day using flow cytometry, while bacterial richness was assessed using 16S rDNA PCR-DGGE and auto- and heterotrophic flagellates counted with epifluorescence microscopy at t0 and t96. Transmission electron microscopy was also used to assess virus-induced bacterial mortality at the start and the end of the experiments. Cloning-sequencing was applied on PCR products obtained after excision of selected DGGE bands to highlight more specifically the identity of bacteria of interest in the context of the experiment. The autotrophs and grazer presence and/or the virus enrichment resulted in different effects on the structure of the bacterial community and the impact was also different with the period. In May, bacterial structure changes seemed to be related to the impact or influence of the eukaryotes (including nanoflagellate grazers), while viruses might have a higher impact on the bacterial community structure the month before. This study provides new persuasive evidence that the presence of viruses and small eukaryotes are likely to drive bacterial community composition and shifts on the short-term in lacustrine ecosystems. More interestingly, such effects seem to be different between viruses and grazers, the ones sustaining, the others reducing bacterial community composition.
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