New answers in optimizing techniques to capture and extract environmental DNA for detection and quantification of carp
Aquatic invasive species are already a vexing challenge: they’re new, they don’t have very many predators, and they often move freely and quickly among waters. Add to that the difficulty of determining whether a species is present in an area without being able to physically see it. That’s the challenge that MAISRC researchers who study eDNA are working to address.
Environmental DNA (eDNA) is a method used to measure the presence – and in some cases, the abundance – of invasive species by detecting fragments of DNA shed by the organism in water. It is likely much more sensitive than traditional AIS monitoring techniques – a primary reason why eDNA is currently used to monitor for Asian carp.
There are many methods in use today to capture (concentrate eDNA from water) and extract (purify the DNA in a water sample prior to analysis) eDNA, but few studies have sufficiently examined which techniques are optimal. Identification of optimal methods is extremely important for sensitive detection – use of sub-optimal methods could result in the failure to detect eDNA and the failure to recognize and take action in the early stages of AIS invasion.
In order to determine the optimal eDNA methodology, MAISRC researchers Jessica Eichmiller, Loren Miller, and Peter Sorensen studied several widely used eDNA capture methods as well as six commercially available DNA extraction kits. They were all evaluated for their ability to detect and quantify common carp mitochondrial DNA.
MAISRC researchers determined that optimal capture and extraction methods differed based on the goal– whether quantification or detection of the carp. While filtration capture performed better than precipitation and centrifugation for both detection and quantification, filter characteristics, such as pore size, affected the recovery of eDNA. In addition, researchers found tradeoffs among DNA extraction kits between the total DNA yield and the kit’s ability to remove inhibitors. When present, inhibitors – compounds that inhibit the enzymatic reactions that we use to measure the DNA in a sample – make it difficult to detect the DNA and can lead to inaccurate measurements.
MAISRC researchers are currently using the results of this study in a larger-scale field study aimed at improving the ability to measure quantities of common carp through their eDNA. Eventually, the researchers hope to use their findings on common carp to improve methods for detecting and quantifying Asian carp.
“Having more sensitive and reliable detection and quantification techniques, such as eDNA, will allow managers to make informed decisions about appropriate management actions for invasive species,” said Eichmiller. For detailed recommendations for eDNA capture and extraction methods, read the full paper, “Optimizing techniques to capture and extract environmental DNA for detection and quantification of fish,” online.