Genetic markers derived from Bacteroidales spp. have been proposed as promising indicators for fecal contamination in the water environment. However, little is known about the persistency of Bacteroidales spp. 16S rRNA genetic markers in the natural environment, which hampers the precise identification of fecal contamination sources. In this study, the persistency of human-specific Bacteroidales spp. genetic markers in river water was investigated during a 3-week agitation. The copy number of Bacteroidales spp. genetic marker was decreased with agitation time, and was very sensitive to water temperature. After the 3-week agitation, three clones of 18S rRNA gene related to Glaucoma scintillans, Spumella-like flagellate, and Colpidium campylum were acquired. The presence of predators that can prey on target bacteria could also be a critical factor affecting the quantified value of genetic markers. It is very important to take these factors, water temperature and the presence of predator, into account for predicting the fate of genetic markers to accurately identify fecal pollution sources.

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