eDNA profile of fecal contaminated surface waters by mitochondrial 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 surface waters. PCR primers were designed to target the mitochondrial 16S ribosomal RNA genes of a broad range of terrestrial and aquatic animal species, with a particular attention to mammals and birds. These primers were used to amplify mitochondrial DNA (mtDNA) from environmental DNA extracted from surface waters, from which some were fecally contaminated, and from the inflow of wastewater treatment plant. The resulting PCR amplicons were composed of multiple sequences representing the local animal diversity at the time of the sampling. The amplicons were sequenced by the Illumina MiSeq PE-250 platform.