Re-evaluation of the EUK516 probe for the domain eukarya results in a suitable probe for the detection of kinetoplastids, an important group of parasitic and free-living flagellates.

Two frequently used universal eukaryote probes, EUK1209 and EUK516, are not consistent with one branch of the eukaryotic phylogenetic tree, the Kinetoplastida, which has undergone rapid evolution of their small subunit rRNA gene. Kinetoplastids include medically important parasitic organisms (e.g. Trypanosoma, Leishmania) and free-living flagellates that occur in all aquatic environments and in soils (e.g. Bodo, Neobodo, Rhynchomonas). A modified probe presented here as KIN516, now based on the kinetoplastid sequence, provides a strong signal with Neobodo designis, Leishmania donovani, and Trypanosoma cruzi using the catalyzed reporter deposition protocol. EUK516 and KIN516 function as competitor probes, thereby greatly increasing discriminatory power when used in combination. The probe pair was tested in field samples collected in a freshwater pond in Norfolk, the mesohaline Elizabeth River, Norfolk, Virginia, and a tropical lagoon in Belize. The combined probes bound to 58-84% of organisms identified as eukaryotic based on having large DAPI-stained nuclei. The contribution of kinetoplastids to total eukaryotes (positive signal of EUK516+KIN516) was much higher in marine samples (ca. 17%) than in either the freshwater or brackish water sites (<0.2%).