Non-Native Fish Detection in the Central Arizona Project Canal Using eDNA Metabarcoding

Authors: Yale Passamaneck, William Stewart, Kent Mosher

Year: 2021

Abstract

The Central Arizona Project (CAP) is a 336-mile-long aqueduct that extends though Arizona, delivering water to municipal, tribal, agricultural, and industrial customers. After the completion of the CAP in 1993, the U.S. Fish and Wildlife Service determined that the transportation and delivery of CAP water had the potential to introduce and spread non-native aquatic species into the Gila River basin. Under this 1994 Biological Opinion and two later revisions, the U.S. Bureau of Reclamation was required to develop and implement a long-term monitoring program to examine the presence and distribution of non-native fish in the CAP and its primary connected waters. Over the years, sampling in the CAP using traditional methods (boat electrofishing, trammel nets, minnow traps, etc.) has proven to be resource intensive and logistically challenging. Environmental DNA (eDNA) metabarcoding provides the potential to identify the presence of non-native fish in a cost-effective manner with reduced field sampling effort. To evaluate the information available from eDNA metabarcoding, sampling was conducted at approximately 5-mile intervals along the canal, including at pumping plant forebays, in conjunction with traditional sampling methods. DNA barcode fragments were amplified using universal primers and subjected to high-throughput DNA sequencing. Resultant data were compared to a reference database of fish DNA sequences to identify source taxa. Results of eDNA metabarcoding were compared to data from traditional sampling efforts to evaluate the comparative benefits and costs of the two approaches.