Environmental DNA detection of aquatic invasive plants in lab mesocosm and natural field conditions
Aquatic invasive plant species cause negative impacts to economies and ecosystems worldwide. Traditional survey methods, while necessary, often do not result in timely detections of aquatic invaders, which can be cryptic, difficult to identify, and exhibit very rapid growth and reproduction rates. Environmental DNA (eDNA) is a relatively new method that has been used to detect multiple types of animals in freshwater and marine ecosystems through tissues naturally shed from the organism into the water column or sediment. While eDNA detection has proven highly effective in the detection of aquatic animals, we know less about the efficacy of eDNA as an effective surveillance tool for aquatic plants. To address this disparity, we designed mesocosm experiments with Elodea species to determine the ability to detect accumulation and degradation of the DNA signal for aquatic plants, followed by field surveillance of the highly invasive Hydrilla verticillata in freshwaters across several U.S. geographic regions. In both lab and field experiments, we designed a high sensitivity quantitative PCR assay to detect the aquatic plant species. In both experiments, plant eDNA detection was successful; we saw accumulation of DNA when plants were introduced to tanks and a decrease in DNA over time after plants were removed. We detected eDNA in the field in areas of known Hydrilla distribution. Employing eDNA detection for aquatic plants will strengthen efforts for early detection and rapid response of invaders in global freshwater ecosystems.
KeywordseDNA Aquatic plants Hydrilla Elodea Herbivory Nuclear DNA Chloroplast DNA qPCR
We would like to thank Haley Erickson and Eric Larson for field assistance and Lizz Radican and Bill Wang for laboratory assistance with this project. Kelley Morris, Cullen Ondracek, Mark Webb from Texas Parks and Wildlife helped with Hydrilla field sites in Texas. Kristen Heyer and Bill Hamilton of the Maryland DNR provided the boat and sampling assistance at Mattawoman Creek. Joseph Love, Bruce Michael, and John Mullican of the Maryland DNR provided sampling coordinates and advice for sampling. Ryan Argo, Ohio River Valley Water Sanitation Commission (ORSANCO), provided location coordinates for sampling in the Ohio River. Eric Fischer, Indiana Department of Natural Resources, assisted with collection permits and information about Lake Manitou. Sudeep Chandra provided information about Clear Lake in California. John Madsen (USDA) provided Hydrilla tissue for the assay. Linyi Zhang created the map figures. Partial support was provided to CAG by the Strecker Lab at Portland State University. This research was supported by US Environmental Protection Agency Grant EPA-R5-GL2012-1 to SPE and DML and Biotechnology Risk Assessment Grant Program Competitive Grant Nos. 2013-33522-21007 and 2016-33522-25629 to SPE from the USDA National Institute of Food and Agriculture and the Agricultural Research Service. Angela Strecker, Meredith Holgerson, and Ariana Chiapella provided helpful comments on earlier drafts of the manuscript. We would especially like to thank the associate editor and two anonymous reviewers for their thoughtful attention to this manuscript.
- Fisher E (2015) GLP update: Indiana Hydrilla eradication & Starry stonewort battle. Update to the Great Lakes Panel. http://glc.org/files/projects/ais/GLPMeeting-April2015-Fisher-SSW.pdf. Accessed 19 July 2016
- Global Invasive Species Database (2016) Species profile: Hydrilla verticillata. http://www.iucngisd.org/gisd/species.php?sc=272. Accessed 21 July 2016
- Jacono CC, Richerson MM, Morgan VH, Pfingsten IA (2015) Hydrilla verticillata. USGS Nonindigenous Aquatic Species Database, Gainesville, FL. http://nas.er.usgs.gov/queries/FactSheet.aspx?SpeciesID=6. Accessed 21 July 2016
- Kratville D (2013) The California Department of Food and Agriculture Hydrilla eradication program annual progress report 2013. California Department of Food and Agriculture, Sacramento, CA. https://www.cdfa.ca.gov/plant/ipc/hydrilla/pdfs/2013HydrillaAnnualReport.pdf. Accessed 15 September 2015
- Lake County Department of Public Works, Water Resources Division (2004) Clear lake integrated aquatic plant management plan. http://www.co.lake.ca.us/Assets/WaterResources/Aquatic+Plant+Management+Areas/Aquatic+Plant+Management+Plan.pdf. Accessed 15 Sept 2015
- Langeland KA (1996) Hydrilla verticillata (LF) Royle (Hydrocharitaceae), “The Perfect Aquatic Weed”. Castanea 61(3):293–304Google Scholar
- Lodge DM, Simonin PW, Burgiel SW, Keller RP, Bossenbroek JM, Jerde CL, Kramer AM, Rutherford ES, Barnes MA, Wittmann ME, Chadderton WL, Apriesnig JL, Beletsky D, Cooke R, Drake JM, Egan SP, Finnoff DC, Gantz CA, Grey EK, Hoff MH, Howeth JG, Jensen RA, Larson ER, Mandrak NE, Mason DM, Martinez FA, Newcomb TJ, Rothlisberger JD, Tucker AJ, Warziniack TW, Zhang H (2016) Risk analysis and bioeconomics of invasive species to inform policy and management. Annu Rev Environ Resour 41:453–488CrossRefGoogle Scholar
- Longmire JL, Maltbie M, Baker RJ (1997) Use of “lysis buffer” in DNA isolation and its implication for museum collections. Mus Tex Tech Univ 163:1–3Google Scholar
- Office of Technology Assessment (OTA) (1993) Harmful non-indigenous species in the United States. Publication No. OTA-F-565, OTA, U.S. Congress, Washington, DCGoogle Scholar
- SAS Institute Inc (2013) Using JMP 11. SAS Institute Inc, CaryGoogle Scholar
- Trebitz A, Hoffman J, Darling J, Pilgrim E, Kelly J, Schardt J, Brown E, Chadderton L, Egan SP, Grey E, Hashsham S, Klymus K, Mahon A, Ram J, Schultz M, Stepien C (2017) Science status and needs for implementing early detection monitoring of aquatic non-indigenous species. J Environ Manag 202:299–310CrossRefGoogle Scholar
- UNEP (2006) Africa Environment Outlook 2. Division of Early Warning and Assessment, United Nations Environment Programme, NairobiGoogle Scholar