A Walk through eDNA Research from the Conservation Genetics and Wildlife Forensics Lab

All organisms, from bacteria to humans, leave a genetic fingerprint in their environment, and recent advances in environmental DNA (eDNA) analysis are allowing scientists to detect these signals in samples of air, water, and soil. One type of eDNA analysis, metabarcoding, allows for the detection of species using a single primer set that can target entire taxonomic groups. Over the past year, we have developed a 16S rRNA metabarcoding protocol that can detect vertebrate species eDNA from water samples and have piloted this technique in three aquatic systems in Central Arizona: Upper Verde River, Fossil Creek native fish restoration, and the Willow Lake Important Bird Area. Water samples taken from these systems were vacuum filtered, the eDNA was extracted, and primers were used to amplify the 16S rRNA mitochondrial gene. Amplified DNA was prepared for sequencing on an Illumina MiSeq FGx Forensic Genomics Systems. The resulting paired-end sequence reads were merged, quality filtered, and assigned to OTUs at 97% sequence identity using USEARCH. OTUs were then identified to the species-level using the NCBI BLAST tool. Thus far, we have detected 93 vertebrate species, including members from all groups: fish, amphibians, reptiles, birds, and mammals. Based on these results, we believe that eDNA metabarcoding is a valuable tool with applications for monitoring vertebrate communities in a diversity of aquatic ecosystems. This talk will serve as an introduction to on-going eDNA metabarcoding projects in the Conservation Genetics and Wildlife Forensics Lab