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Over the last few decades, molecular methods have vastly improved our ability to study the diversity of microbial communities. In molecular diversity surveys, the function of protists is often inferred from phylogeny. Yet these surveys are unable to distinguish between different trophic modes among closely related taxa. Here we present results from a culture-independent study linking bacterivory to the diversity of pelagic protists from 3 depths of a stratified mesotrophic lake. Bacteria were labeled with bromodeoxyuridine (BrdU) and added to lakewater samples; after incubation, total DNA was extracted from filtered samples. Part of the DNA extract was subjected to immunoprecipitation with anti-BrdU antibodies, and then both whole DNA and BrdU-labeled sam- ples were analyzed using 454-pyrosequencing of the v9 region of 18S small subunit rRNA gene am- plicons. The results show that a different community of protists exists at each depth, with limited overlap of taxonomic composition between depths. The community of BrdU-labeled protists, deemed putative bacterivores, is largely a subset of the community found in the whole DNA sam- ples. Many of these BrdU-labeled taxa are poorly represented in GenBank and thus are probably rarely isolated and/or uncultured species. Several of the taxa identified as bacterivores are also phototrophs, highlighting the important role of mixotrophy among eukaryotic microbes. Definitive identity of functional traits among taxa requires careful experimentation, yet this method allows a first-pass assay of the trophic role of microbial eukaryotes from environmental samples.

Linking bacterivory and phyletic diversity of protists with a marker gene survey and experimental feeding with BrdU-labeled bacteria