Increasing Efficiency and Throughput of eDNA

Science Center Objects

The results from this study will provide protocols for the collection, processing and analysis of environmental deoxyribonucleic acids (eDNA) samples for monitoring aquatic invasive species like Asian carp. These protocols have the potential to be used by fishery management agencies to monitor aquatic invasive species throughout the United States.

Environmental deoxyribonucleic acids (eDNA) has been used to monitor for the possible presence of Asian carp, bighead carp Hypophthalmichthys nobilis and silver carp H. molitrix, DNA throughout the Chicago Area Waterway System (CAWS), Des Plaines River, near shore waters of Lake Michigan and Upper Mississippi River. This technique is potentially useful for early detection and identification of distribution patterns of DNA in the waterway because it can presumably detect the presence of DNA in water when populations of targeted animals are at very low levels of abundance.  A positive eDNA sample indicates the presence of DNA and the possible presence of live organisms, allowing for resource managers to implement the appropriate management strategies. Unfortunately, eDNA cannot currently provide precise, real-time information on where the animals might be due to the requisite two-week sample processing time.  Additionally, this technology requires the collection on large amounts of water due to the low efficiency of the assay.  This study will help to improve the efficiency of this assay and increase the throughput to allow for more real-time results; thus, enabling resource managers to implement appropriate management actions in the most efficient manner.

The goal of this study is to develop a protocol that provides results in less time. Since the current eDNA protocol has several steps, improvements at each stage (collection, homogenization and extraction) will be explored.  

Objectives

Objective 1: Determine the most efficient method for collecting eDNA
Objective 2: Determine if bead-beater technologies can be used to improve the throughput of homogenizing eDNA samples
Objective 3: Identify the most efficient method for extracting DNA from environmental samples 

 

USGS Scientist Nate Jensen labeling eDNA samples taken from barge

(Public domain.)