Environmental DNA monitoring for detecting aquatic invasive species in Ontario

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1 Environmental DNA monitoring for detecting aquatic invasive species in Ontario Chris Wilson 1, Kristyne Wozney 1, Jenn Bronnenhuber 1, Caleigh Smith 1, and Chris Kyle 2 1 Aquatic Research and Development Section, OMNR 2 Biology Department, Trent University

2 Parallel issues in management of invasive and endangered species hard to find who s where? how many? habitat: range, occupancy, seasonal use critical habitat (SAR) entry points and invasion / expansion routes (AIS) evaluation of management efforts

3 Environmental DNA (edna) cells / DNA shed from living or dead organisms into surrounding environment molecular smoke alarm doesn t say what the source was living / dead; body parts; fluids, cells, free molecules, etc. doesn t tell re: age, sex, size, reproductive status, population info positive detection = DNA from the species was present at that location when the sample was collected barcoding gene

4 Barcode of Life (Guelph) BOL database (BOLD; Ratnasingham and Hebert 2007) < reference CO-I mtdna sequences + taxonomic samples for all Canadian freshwater fishes (Hubert et al. 2008) starting point for edna detection

5 OMNR Codrington research facility: methods testing multiple species; known biomass edna parameters for testing: species specificity spatial sensitivity quantitative sensitivity temporal sensitivity

6 Multiple sampling locations upstream (water supply) 50m downstream (outflow) 0.5, 1, 2, 5, and 10 km downstream Flow

7 Validation of species- and location-sensitivity 2km 1km 500m Codrington inflow outflow 500m 1km 2km

8 n=1 Quantitative sensitivity (density effects) n=2 n=4 n=8 n=16 species detection at all densities detection strength increased with population density L Tank density H

9 Emerging threats: aquatic invasive species Asian carp (4 species) edna detection of bighead + silver carp Chicago Shipping Canal Lake Erie ( ) grass carp in inland Michigan lakes; snakehead expansion in New England states multiple invertebrate invasives

10 edna surveillance for Asian Carp in Lake Erie: rapid response to prevent establishment August 2011 samples July 2012 samples MNR sampling (Sept-Nov 2012) (photo courtesy of MN DNR)

11 Quantitative PCR = faster + more sensitive More sensitive than standard PCR fewer processing steps quantitative detection able to define sensitivity, power of detection negative controls 1,

12 Lake Erie Asian Carp 2013 Sampling Plan St. Clair River, Lake St. Clair, Detroit River, and Lake Erie Western Basin will be sampled for Bighead and Silver Carp in summer Potential spawning rivers (Thames and Sydenham) will be sampled for Bighead and Silver Carp in spring Coastal wetlands will be sampled for Grass Carp in summer

13 Plant Invaders: Water Soldier (Stratiotes aloides) available in pond supply stores Trent River = only known wild infestation buoyant in summer; otherwise submerged both vegetative and sexual reproduction collaborative eradication effort underway edna markers developed to map distribution, support eradication efforts

14 Other Invaders: the next wave? water soldier grass carp black carp round goby tubenose goby northern snakehead rudd Hemimysis Bythotrephes Cercopagis (plus >50 other candidates: NOAA GLANSIS watchlist)

15 Community edna: species roll call not specific to a particular species (non-targeted detection) determine what species are present in edna samples; potential detection of new invasive or endangered species testing using DNA from 23 fish + mussel species determine the sensitivity and potential applications

16 Funding: COA, OMNR, DFO (indirect for AIS) Acknowledgements Support: OMNR Lake Erie Mgmt Unit, Biodiversity Section, Trent Univ (NRDPFC) People: lab members Andy Mahon, Chris Jerde Beth Wright

17 Contamination Concerns and Precautions potential contamination ( false positive results) field sampling gear thorough cleaning (bleach) of all field gear sample from low density areas first water filtration DNA extraction PCR setup dedicated work areas for water filtration disposable filters; clean all filtration equipment dedicated extraction work area and tools; wipe down with bleach before and after dedicated PCR work area and tools; use filter pipette tips

18 Contamination Concerns and Precautions potential contamination ( false positive results) field sampling gear thorough cleaning (bleach) of all field gear sample from low density areas first water filtration DNA extraction PCR setup dedicated work areas for water filtration disposable filters; clean all filtration equipment dedicated extraction work area and tools; wipe down with bleach before and after dedicated PCR work area and tools; use filter pipette tips

19 Spotted Gar (THR; COSEWIC 2005) Lk Erie (Pt Pelee, Rondeau, Long Pt) Lk Ontario (Bay of Quinte, East Lake, Hamilton Harbour) habitat protection needs assess habitat occupancy

20 Identifying seasonal habitat use of endangered species (spotted gar)

21 Moving Forward / Taking it Further continue to refine methods: quantitative ( real-time ) vs. regular PCR detection single species vs. community detection simplify methods for collecting + extracting DNA options for improving: cost throughput turnaround time

22 Prospects and Potential sensitive, rapid assessment tool for species detection (SAR/AIS) augment and focus field sampling efforts non-invasive sampling no negative impacts on SAR (handling, disturbance, mortality) improve distribution / occurrence data identify critical habitat map invasion / expansion routes inform management responses habitat regulations (SAR) restoration efforts (SAR) eradication/control programs (AIS)

23 Because we don't think about future generations, they will never forget us. -Henrik Tikkanen