Assessment of mixed human, livestock and wildlife sources of fecal contamination in surface waters by mitochondrial DNA metagenomics

Fecal contaminations of surface waters and groundwater can occur by more than one animal species in areas where urban and agricultural activities overlapped. We use mitochondrial metagenomics for source tracking fecal contamination in 86surface water samples. These PCR primers target the mitochondrial 16S ribosomal RNA genes from mammals, birds and fishes, and majority of amphibians or reptiles. These primers were used to amplify mitochondrial DNA (mtDNA) among eDNA in surface waters to identify homeotherms as a potential source of fecal pollution. The amplicons were sequenced by the Illumina MiSeq PE-250 platform.