Detection of Invasive Mussel Environmental DNA (eDNA) by Polymerase Chain Reaction (PCR)

Project ID: 8912
Principal Investigator: Denise Hosler
Research Topic: Invasive Species
Priority Area Assignments: 2014 (Zebra and Quagga Mussels)
Funded Fiscal Years: 2014
Keywords: quagga mussel, zebra mussel, invasive mussel, edna, pcr

Research Question

Reclamation has analyzed over 11,000 samples and utilizes both microscopy and polymerase chain reaction (PCR) to detect and identify invasive mussel larvae (veligers) in water samples. Occasionally, a water sample may yield a positive DNA result without visual identification of a veliger body by microscopy; this has only occurred in samples where a veliger body was discovered previously. These results have led to confusion among water managers, since PCR can only give presence/absence data, and cannot quantify the number of organisms in a sample. Indication of DNA does not mean a full-scale infestation will occur, but it does mean that quagga or zebra mussel DNA was present in the system.

One possible explanation for veliger DNA in a sample with no veliger bodies could be the presence of environmental DNA (eDNA) in the sample; eDNA is the genetic material that sheds off of an organism, in the feces, mucus or dead cells. Veliger bodies can be degraded or destroyed by field and laboratory techniques, or improper preservation methods at sample collection. This study will determine the effectiveness of PCR at detecting degraded and destroyed veligers that are not detectable by cross-polarized microscopy. This data will determine what amount of eDNA is needed to achieve a positive PCR result.

Need and Benefit

Environmental DNA (eDNA) is the genetic material that sheds off every organism, through the organism's feces, mucus, urine and tissue. In samples where an organisms body is not found it may be possible to achieve a positive PCR result if eDNA is present. In the case of early detection samples for invasive mussels, it is possible that a damaged and undetectable veliger is the eDNA that may lead to a positive PCR result. A positive PCR result with no veliger body found in the water sample may be an indication that veligers are in the area, or were in the area recently, or that a smoldering adult population is thriving undetected in the water body.

To test for eDNA we propose degrading the veliger body beyond the point of detection for microscopy and also destroying the veliger body and testing the sample for the presence/absence of mussel tissue. If degraded and/or destroyed veligers yield positive PCR results this study may indicate that PCR is a more sensitive test than microscopy for early detection, when veligers have been damaged or have lost their bifringence. A sample that is positive by PCR with no veliger body can only indicate presence of mussel tissue; it does not quantify the number of organisms present in the sample. All Reclamation regions will benefit from this research as it will help to clarify what a positive PCR result means to water managers.

Contributing Partners

Contact the Principal Investigator for information about partners.

Research Products

Bureau of Reclamation Review

The following documents were reviewed by experts in fields relating to this project's study and findings. The results were determined to be achieved using valid means.

PCR Detection of Quagga Mussel Intracellular (final, PDF, 917KB)
By Ms. Jamie Carmon, Sherri Pucherelli and Dr. Jacque Keele
Report completed on November 03, 2014

The Reclamation Detection Laboratory for Exotic Species (RDLES) utilizes both microscopy and
PCR to detect presence of dreissenid mussels in western water bodies. PCR results are variable and there are times
where it is possible to get a negative result by microscopy and a positive by PCR on the same sample. The goal of
this study was to demonstrate how multiple factors (extraction kit type, amount of DNA in the sample, days to
analysis, and the presence or absence inhibitors) impact the suc

Detecting Free-Floating Quagga Mussel DNA (final, PDF, 1.0MB)
By Jamie Carmon
Publication completed on September 30, 2015

This bulletin summarizes the research results and potential application to Reclamation's mission.

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Last Updated: 6/22/20