Environmental DNA (eDNA) from a Consultant's Perspective
By: Jared Hobbs, M.Sc., R.P.Bio.,
Senior Technical Expert / Biologist
Outline
1) Challenges and opportunities in Environmental Assessment Processes
2) The Importance of Rigour and Standards
3) Implementationa) Responsible Adoption
b) Proof of Concept
4) Looking Ahead
Challenges and Opportunities in Environmental assessment Processes
Conventional methods
• Environmental resource management requires accurate ecological information regarding the health of a given ecosystem and the distributions of the species that occupy it.
• Conventional survey techniques used to collect and analyze a species’ distribution are characterized as: labour intensive,
require skilled experts to design and lead the program,
susceptible to observer bias,
offer relatively limited capabilities to confirm species’ distributions
invasive to target taxa and / or destructive to their sensitive habitats
PRAGMATIC ADVANTAGES OF eDNA
More accurate / sensitive and less subjective to bias Synchronous study of multiple species with less
restrictive timing windows Retro-active addition of focal taxa Less invasive to species and ecosystems, no risk of
pathogen transfer. Also safer for field staff. No permitting requirements
When to use eDNA?
Cost / Benefit Analysis (CBA)
• Cost Benefit Analysis (CBA): a systematic evaluation to comparatively asses the strengths and weaknesses associated with the application of eDNA vs. conventional methods.
Cost / Benefit Analysis (CBA)
Vs.
The Importance of Rigour and Standards
Developing Lab Standards / Publishing Results• In collaboration with the University of
Victoria (Helbing Lab) we developed provincial standards for eDNA that set requirements for qPCR sample testing and assay development.
• Our methods were published in PLOS One.
UVic / Maxxam Lab Standards for qPCR Analysis – A more rigorous approach
3 Runs
Most labs conduct 3 runs on each sample for the target taxa.
e”Target”
We also use plate controls: 2 pos/1 neg
8 technical replicates/sample
eTarget
Increased confidence in results (90-
100%)
4 technical replicates/sample
ePlant
Poor quality samplePerform inhibitor cleanup
&Retest with ePlant
UVic conduct 16 runs on each sample to control for false negatives
Standardized Approach: MOE Standards
• We authored provincial MOE RISC standards that detail procedures for sample collection, filtration and preservation.
• We provide(d) internal training, through courses and collaborative project implementation, to facilitate consistency and rigour during application.
TRC Review Panel Feedback regarding the protocol? a. It seems to be thorough, and gives lots of
information in regards to what affects detection rates and common sources of contamination.
b. My overall impression is that it is a solid protocol that has had input from two strong labs (the Goldberg and Helbing labs) that are leading the way (with Hemmera) in eDNA research on the west coast.
2. Are the protocols technically sound? a. Yes, they are good. 3. Is the protocol easy to follow? a. Yes
Implementation: Responsible Adoption
We recognized the need to engage regulatory agencies first – if they didn’t adopt this method we couldn’t apply it to meet our clients needs.
We also needed to provide guidance to our staff to ensure rigour in our application: we developed an internal SOP; this later became a provincial standard.
2014 (8 projects)GMT eDNA Assessment 2014
SFPR eDNA Assessment 2014
Spadefoot and Tiger Salamander
Rocky Mountain Tailed Frog-Flathead 2014
Pacific Water Shrew eDNA
Giant Salamander Sunshine Coast PWS and ASTR eDNA
Woodfibre LNG
eDNA in BC: Year One - 2014
eDNA in BC: Year Two - 2015
We expanded our application to Yukon, engaged more deeply with more academic labs (Yukon College, Helbing Lab-UVic and Montana).
We also expanded focus to additional target taxa and environments.
2015 (8 projects)GMT eDNA Assessment 2015SFPR eDNA Assessment 2015
Port Metro Vancouver S@Risk InventoryColony Farms eDNA Assessment
Rocky Mountain Tailed Frog-wigwam
CDC Yukon eDNA for Western Toad and Columbia Spotted Frog
CDC Yukon Pathogen assessment
eDNA Standards DevelopmentYukon SIF (salmon project with Yukon college)
eDNA in BC: Year Three - 2016
We continued to expand focus on new species, in new geographies, for new clients and with new partnerships.
2016 (8 projects)Arctic Greyling
MLNG eDNA (amphib's at risk)
SFPR/GMT eDNA Assessment 2016
FWCP coastal tailed frog - Lillooet
Rocky Mountain Tailed Frog-Yahk
CDC Pathogens/Training
Creston Bullfrog
HCTF Red-legged frog
In 2016, we also began to develop fish primers!
eDNA in BC: Year Four - 2017
2017 (21 projects)Yukon Grayling and Chinook (3 collections in 2017)
Stave eDNA
Carmanah / Walbran lentic eDNA
CRD Bullfrog Assessment
HCTF Oregon spotted frog/Cascades frog (year 2)
Yukon Env. Western Toad (Watson Lake)
Atlin Western Toad
Okanagan Invasive Species-Sampling
PMV Sp@Risk
SRWS Chinook Barrier Assessment
Bayonne Creek Mine SAR assessment
Stulkawhits coastal tailed frog assessment
Fraser Leachate Lagoons eDNA assessment
Dollarton Pacific water shrew/coastal tailed frog eDNA
Prince Rupert Port Authority South Kaien Island
Rocky Mountain Tailed Frog-Yahk
Kitimat coastal tailed frog and efish
Rivers Inlet Salmon and coastal tailed frog
BCIC Ignite provides funding to Hemmera/Uvic to accelerate commercialization of new technologies and innovations in the natural resources and applied sciences in British Columbia. Awarded $188K of funding to support development and research of eDNA.
Hemmera was awarded recognition, at RemTech 2017, for leadership in “innovation” for our work with eDNA development.
Implementation: Proof of Concept
eDNA Projects: BC and Beyond
Tailed Frog: Two examples
• Occur in cool, permanent well oxygenated mountain streams with a step-pool morphology
• Prefer cobble substrate with lots of interstitial spaces; low tolerance for sedimentation.
• Adults use riparian habitats for terrestrial foraging.
• Eggs laid under large rocks in the thalwag.
Coastal Tailed Frog: Distribution
Coastal Tailed Frog: 2016 eDNA Project
• In 2016 we used eDNA to survey suitable habitats in the Cascades, along the eastern limit of the species’ range in British Columbia.
List Status
BC CDC Blue listed
COSEWIC Threatened
SARA Endangered S.1
2016 FWCP Project location
Coastal Tailed Frog
Coastal Tailed Frog
Rocky Mountain Tailed Frog: Distribution
• Global distribution from BC, Montana, Idaho, Washington and Oregon
• Two geographically disparate populations in BC; Yahk & Flathead Rivers; in 39 stream reaches.
List Status
BC CDC Red listed
COSEWIC Endangered
SARA Endangered S.1
Previous Inventory Results
Study YearTotal TCS
SitesPositive
Detections
1996-1998 239 19
2001 220 79
2003 204 63
2004 50 0
Total 713 161
(Previous) Canadian Distribution
Yahk Flathead
eDNA Results
Yahk
Flathead
Current Canadian Distribution
YahkFlathead
Tiger Salamander - Okanagan
• Extralimital site at Ritchie Lake tested positive in 2014 however eDNA was new, so there was some skepticism and reticence to trust the result.
• Three years later a govt biologist found, photographed and reported a tiger salamander at Ritchie Lake!
• Objective: to assess presence of tiger salamander in the Okanagan Valley, BC.
• 2014: 35 sites sampled, 11 positive
• 2017: 19 sites sampled, 10 positive
Email from Bryn White (BC MOE)April 16, 2018“Hi Jared - look at this fat little beauty I found at Ritchie Lake in Garnet Valley north of Summerland (we fenced it) -that was the one that you tested with E DNA and came up positive for SPIN and AMTI. “
Tiger Salamander -Okanagan
Invasive Species Applications: American Bullfrog
• Objective: to assess presence of American bullfrog in the Okanagan Valley, BC.
• 2017: 10 sites sampled, 1 positive & 1 suspected
• This result was after an intensive multi-year eradication program that was purported to have eliminated American bullfrog from the Okanagan
Looking Forward: The Path Ahead
Application Opportunities
UVic and Hemmera have made important technical advancements to mitigate type one and type two errors?With our advancements in application of this method eDNA now provides a potentially powerful solution to more confidently inform many of the challenges faced by environmental professionals:
Better inform operational designs
Create efficiencies in compliance monitoring to assess effectiveness of mitigation activities
Identify appropriate compensatory habitat
Efficiently inform effectiveness assessment of site reclamation and functional restoration efforts
Facilitate broad scale inventory to better understand species distribution, and inform risk assessment to wildlife at a population level, or landscape scale
How can eDNA be applied to realize efficiencies in new geographies? Can we help proponents
understand the advantages conferred by eDNA ?
Can we help proponents, and their QEPs, identify opportunities for more efficient and cost effective solutions?
Collaborative Engagement
Sharing our Advances: Training
Training is provided, through NRTG , to Environmental practitioners, regulatory agencies and clients to ensure rigorous, accurate and cost-effective application of eDNA methods.
Recognizing Opportunities to Support
Who’s interested in eDNA?
Really? Who’s not???
• Regulators (gain improved understanding, using potentially the most cost-effective, non-detrimental methods available)
• Resource managers who want to ensure rigor in baseline studies and are looking for cost-effective methods.
• Practitioners with interests in applied conservation and research
• Academic institutions
eDNA Methods in BC: A Summary
• Environmental DNA (eDNA) is a proven powerful and efficient method for conducting aquatic survey for species of management concern (e.g. species at risk, introduced species, wildlife pathogens).
• Hemmera (working with C. Helbing and C. Goldberg) was the first to apply eDNA in a commercial (non-academic) setting in western Canada. We’re excited by its potential to:
greatly enhance knowledge to conserve (aquatic) species at risk
assess restoration program effectiveness
support environmental assessment processes
assess invasive species control programs
support development of monitoring programs for management purposes
Available eDNA PrimersSpecies Common Name
Anaxyrus (Bufo) boreas Western toad
Ascaphus montanus Rocky mountain tailed frog
Ascaphus truei Pacific (Coastal) tailed frog
Lithobates (Rana) catesbeiana North American bullfrog
Lithobates (Rana) pipiens Northern leopard frog
Oncorhynchus kisutch Coho salmon
Oncorhynchus tschawytscha Chinook salmonRana aurora Northern red-legged frog
Rana cascadae Cascades frog
Rana luteiventris Columbia spotted frog
Rana pretiosa Oregon spotted frog
Sorex bendirii Pacific water shrew
Thymallus arcticus Arctic Grayling
eFish FisheFrog Frog
eMammal Mammal
ePlant Plant
Spea intermontana Great Basin spadefoot
Ambystoma mavortium Tiger Salamander
Oncorhynchus clarkii Cutthroat trout
Oncorhynchus mykiss Rainbow trout
Oncorhynchus nerka Sockeye Salmon
Contact Us
Jared Hobbs
Hemmera Envirochem Inc.18th Floor, 4730 Kingsway Burnaby, BCT: [email protected]
Thank you