The Service’s environmental DNA Processing Facility
Whitney Genetics Laboratory
BY EMY MONROE, WHITNEY GENETICS LAB
Credit: Becky Lasee, USFWS
As a result of Asian carps being identified as a serious threat to the ecological and economic water resources of the United States, the US Fish and Wildlife Service (Service), along with federal and state partners, is participating in a comprehensive plan to monitor and manage feral populations of Asian carps.
One of the newest tools in aquatic invasive species monitoring is the use of environmental DNA (eDNA) to survey for the presence or absence of target species. eDNA is shed by an organism into its environment, and using this DNA to detect rare fish is more efficient than traditional electroshocking or netting of fish. Developed at the University of Notre Dame, the eDNA method for Asian carps was first used for regular eDNA monitoring of the Chicago Area Waterway System (CAWS) and was carried out by the US Army Corps of Engineers (ACOE), the Service, and the State of Illinois from 2010-2012.
The Grand Opening of the Whitney Genetics Lab in April of 2013 marked the successful culmination of two years of planning, building, and staffing of the facility under the guidance of the Asian Carp Regional Coordinating Committee, the Service’s Midwest Region leadership and the La Crosse Fish Health Center’s Project Leader, Becky Lasee (recently retired). Funding for the lab was provided by the Great Lakes Restoration Initiative.
The 5300-square foot addition houses three multi-purpose labs, ten offices, and six state-of-the art DNA labs that create separate areas for each step in the DNA workflow to minimize contamination risk. Six new hires started during summer and fall of 2012 and the new building was occupied in November 2012. After a few weeks of moving in supplies, instruments, and equipment, the lab staff commenced training at the bench the first week of the New Year.
amplification plate, where a process, polymerase
chain reaction (PCR) makes hundreds of copies
of target DNA from the water samples.
Credit: Nick Grueneis, USFWS
In order to successfully assume responsibility for processing eDNA samples, the Service and the ACOE prepared a transition plan that would test and validate the new staff and facility. Transition was successfully completed in June, official monitoring samples were processed the first week of July, and results were posted for public consumption August 15, 2013.
Over the next few months, the lab will process samples from 25 different field sites, mostly from the Great Lakes or CAWS, but also from the Upper Mississippi and Ohio Rivers. These cases will consist of nearly 2800 samples, which translate into several thousand DNA extractions, tens of thousands of polymerase chain reactions, and hundreds of gels processed by electrophoresis in the lab.
The lab has also collaborated with biologists at the US Geological Survey (USGS) and the ACOE to validate new methods and markers to improve eDNA methods. These projects have resulted in updates to the Quality Assurance Project Plan (QAPP), the standard operating procedures for eDNA sample collection and processing the lab follows. Two major updates to the QAPP include the addition of centrifugation as an option for processing water samples which will save time for field crews and reduce the risk of cross-contamination in the field. Another major update is the switch to a different DNA extraction kit, which not only resulted in a 75% cost savings for the lab, but also reduced processing time.
Through collaborations with others within and outside of the Service, the staff of the WGL is excited to contribute to the successful implementation of the Asian carp monitoring and control plan. The lab would not have any samples to analyze without the cooperation with Service staff at the Fish and Wildlife Conservation Offices of the Midwest Region who collect and process water samples, and we also depend on the continued research of the ACOE and USGS to improve eDNA as a detection tool.
The Whitney Genetics Lab was named in memory of John M. Whitney, who served as a Fisheries Biologist at the La Crosse Fish Health Center for 21 years.