Development and validation of a microbial source tracking marker for the detection of fecal pollution by muskrats

Surface waters in mixed-activity watersheds can be compromised by fecal pollution from livestock production, sewage outflows or leaking septic systems, or avian or mammalian wildlife. While undertaking water quality research in Eastern Ontario Canada, we observed an abundance of muskrats (Ondatra zibethicus) in some waterways, and sought to determine their significance with respect to fecal pollution loads. To that end, we developed and validated here a sensitive and specific marker, designated MuBa01, based on the 16S rRNA gene that distinguishes muskrat feces from human, livestock, or other wildlife sources. DNA from waterways inhabited by muskrats carried the marker. The widely used pig-specific marker Pig-2-Bac yielded a product with some muskrat feces, suggesting that it lacks specificity required to establish the significance of swine production in areas inhabited by muskrats. Overall, the MuBa01 marker will be useful for distinguishing the significance of this wide-ranging semi-aquatic mammal in the context of other fecal pollution sources.

► Muskrat feces can contain human pathogens.
► We have designed primers and probe to detect this pollution by qPCR.
► The system shows a good sensitivity and a good specificity.
► Fecal pollution in environmental water has been successfully detected by our system
► This tool will be of broad interest to the community interested in water quality management.