Establishing Molecular Methods to Quantitatively Profile Stomach Diet Items of Fish—Application to the Invasive Blue Catfish (Ictalurus furcatus) Active
USGS scientists are collaborating with the Maryland Department of Natural Resources (MDDNR) to develop and evaluate a genetic assay for blue catfish fish diets that will allow us to design a cost-effective monitoring program for determining the diet of wild fish.
We will test the utility of this method and, once fully developed, these methods could be generally applied in many other piscivorous species of management importance across our Nation. Similar to previous USGS pioneering of environmental DNA detection methodologies in aquatic biotic surveys, our work will be at the forefront of this emerging field of molecular ecology.
Amplicon sequencing methods use a set of genetic barcodes to amplify all contributing components in a DNA sample at one time, and next generation sequencing platforms can analyze thousands to hundreds of thousands of individuals per run. These technologies allow detectability and quantification of diet components at levels not achieved with microscopy. While such sequencing techniques have been developed and successfully employed frequently with carnivores, herbivorous and piscivorous animals may present additional challenges due to chemical inhibitors present in plants, and fewer genetic barcoding resources for local plant communities. As a consequence, there are very few examples of piscivorous and herbivorous PCR-based diet studies currently found in the scientific literature.
Objectives:
We will test and apply amplicon sequencing assays for dietary analyses of blue catfish collected from the Mattawoman Creek and the Potomac River, MD.
- Overview
USGS scientists are collaborating with the Maryland Department of Natural Resources (MDDNR) to develop and evaluate a genetic assay for blue catfish fish diets that will allow us to design a cost-effective monitoring program for determining the diet of wild fish.
Sources/Usage: Public Domain. View Media DetailsBiologist Branson Williams netted this 40+ pound blue catfish during a electrofishing survey in Mattawoman Creek, a tributary to the Potomac River. We will test the utility of this method and, once fully developed, these methods could be generally applied in many other piscivorous species of management importance across our Nation. Similar to previous USGS pioneering of environmental DNA detection methodologies in aquatic biotic surveys, our work will be at the forefront of this emerging field of molecular ecology.
Amplicon sequencing methods use a set of genetic barcodes to amplify all contributing components in a DNA sample at one time, and next generation sequencing platforms can analyze thousands to hundreds of thousands of individuals per run. These technologies allow detectability and quantification of diet components at levels not achieved with microscopy. While such sequencing techniques have been developed and successfully employed frequently with carnivores, herbivorous and piscivorous animals may present additional challenges due to chemical inhibitors present in plants, and fewer genetic barcoding resources for local plant communities. As a consequence, there are very few examples of piscivorous and herbivorous PCR-based diet studies currently found in the scientific literature.
Objectives:
We will test and apply amplicon sequencing assays for dietary analyses of blue catfish collected from the Mattawoman Creek and the Potomac River, MD.
Sources/Usage: Public Domain. View Media DetailsThe search for blue catfish. Result of low-frequency electrofishing on the tidal Potomac River near Washington DC. This photograph was taken using a GoPro camera mounted on a 20 ft. staff. This configuration was used to acquire an accurate count of all blue catfish affected by the electric current before they recover from galvanotaxis. - Partners