Genetic Barcoding of Gut Contents: From Partially-Digested Tissue to Species Identity

Genetic barcoding has the potential to substantially reduce the proportion of unidentified, partially-digested tissue in gut content analyses and improve information on trophic interactions. The focus of our study is to understand the trophic impacts of non-native Blue Catfish (Ictalurus furcatus) in upper Chesapeake Bay (CB). The Blue Catfish is a large, long-lived, moderately salt-tolerant top predator that often feeds extensively on important fishery and prey resources. To investigate trophic dynamics of Blue Catfish in upper CB, tidal fresh areas within the Nanticoke River, Patuxent River, Sassafras River and Susquehanna Flats were sampled during summer/fall 2013 and 2014 using boat electrofishing. Gut contents were initially identified using standard morphological methods. Unidentified vertebrate tissue was subsequently analyzed using genetic barcoding (sequencing of the cytochrome c oxidase 1 gene) and compared against a DNA barcode library of Chesapeake Bay fishes to determine species identity. To date, genetic barcoding has provided identifications for 21 fish species including several species of management concern (Striped Bass, American Eel, River Herring, Menhaden) and one bird. Genetic barcoding is a powerful tool for species-level identification of partially-digested gut contents that can improve the quality of data underpinning food web models and management decisions.