Fluorescently-labeled oligonucleotide probes can be used to identify protistan food vacuole contents.

In situ hybridization using fluorescent oligonucleotide probes complementary to unique regions of 16S rRNA molecules provides a way of identifying the food vacuole contents of bactivorous protists. Laboratory experiments with Tetrahymena showed rRNAs in food vacuoles are degraded slowly enough to permit their use as hybridization targets for such probes. A probe specific for a hypervariable region of the small subunit rRNA of an unnamed proteobacterium abundant in a local lake was then synthesized. It was used to probe the food vacuoles of the ciliates present in fixed water samples collected from the same lake. The vacuoles of several filter-feeding ciliates bound the probe, indicating that such probes can be used to identify the food vacuole contents of ciliates collected from natural samples.