Establishing Molecular Methods to Quantitatively Profile Stomach Diet Items of Fish—Application to the Invasive Blue Catfish (Ictalurus furcatus)
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.
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.