Brook trout are commonly used as an indicator species because they are very sensitive to environmental changes.
COURTESY: R.J. BURNSIDE & ASSOCIATES
Environmental DNA or eDNA biomonitoring is a breakthrough technology that has begun to revolutionize how industry can reduce monitoring cost and efforts, evaluate risk, and meet or exceed environmental regulations and permit requirements. Access to eDNA technology had been previously restricted to research institutions and affiliated corporations; this is no longer the case. After over a decade of research and development, eDNA biomonitoring is now at the point of commercialization. Mining and industry now have access to a new tool that can cut the cost of environmental assessments and monitoring from 25% to 68% and offers more reliable results.
What is eDNA?
As animals interact with their environment, they leave behind a trail of genetic material that lasts for days to a few weeks. This genetic material that is left in the water, soil, or even guano (bat feces), is called environmental DNA (eDNA).
It contains a code that is specific to that species, thus it can be distinguished from other species’ DNA by using specialized genetic tests. By sampling the environment and not the species itself, eDNA can determine if the species is or was present very recently. Testing is done using molecular biology tools developed for medical diagnostics, and that have now been adapted for fieldwork in rugged environments.
While the technology is sophisticated, the concept is simple; with millions of cells shed from a single organism, it is far more probable to find DNA than it is to find the organism that left it there.
It requires a fraction of the time taken by conventional methods to determine the presence or absence of a particular species, and the amount of time spent in the field can be cut significantly. In the case of rare, cryptic, or endangered species, confirming that the species is present or absent using conventional methods can be very difficult. Furthermore, the risk of a false negative, that is, concluding that a species is absent when it is in fact present, is considerable with conventional methods. False negatives can translate to unforeseen financial commitments associated with site remediation, in addition to project delays and negative publicity.
And, eDNA can be used to detect both aquatic and terrestrial species, including: fish, amphibians, turtles, bats, birds, salamanders, mussels and benthic invertebrates.
Suppose that a protected species of frog is believed to occupy a proposed development site for mining activity. The conventional approach would be to conduct acoustic surveys at specific times of year, over several months listening for the frog’s nightly call. This method is not only inefficient and expensive, but it is open to tremendous misidentification error by the observer, which could result in the wrong outcomes, and wrong management decision downstream. Environmental DNA methods, however, could confirm the presence or absence of the frog with confidence, in just a matter of days.
“Used correctly, eDNA has the potential to revolutionize how we conduct environmental assessments,” says Jay Cashubec, an aquatic ecologist with AECOM. “It has proven more accurate, costs less, and can be done in a fraction of the time of a regular survey, allowing us to accomplish more with less.”
Environmental DNA biomonitoring represents the pinnacle of environmental responsibility. With properly designed tests and sound surveying approaches, much higher confidence in the accuracy of results can be obtained. Achieving this level of accuracy requires rigorously validated tests, or “assays,” which are designed to detect the target species, and only that species. Species-specific DNA assays can now be designed with such precision that even a single strand of DNA in a test sample can be detected.
With extremely sensitive DNA detection tests, it becomes a question of collecting enough water samples from the right locations to confirm that a species is using a given environment. Determining these locations will soon be automated thanks to the development of an eDNA design software program which use advanced statistical models and machine learning to help guide eDNA survey designs.
Some key attributes to eDNA biomonitoring are reduced monitoring effort and cost; work outside regulatory timing windows; there is no species capture and handling, which reduces the risk to disrupting the habitat or harming the animal, this is especially valuable with rare and cryptic species detection, which is facilitated considering eDNA allows for early detection of life-stages, and increases the window of probability for confirming presence. Envioronmental DNA has significantly faster sample turnaround times; and allows for a high degree of efficacy. In addition, it allows for early detection of invasive species.
Environmental DNA can help to evaluate the risk of proposed developments and expansions without exhaustive conventional methods of assessment. Sample turn-around times can be within hours, not days nor weeks; and eDNA can also help anticipate compensation costs by identifying sensitive areas (i.e. Lake Trout spawning shoals, Salmon nursery habitat, turtle wintering ponds, etc.) that may be impacted by development. Costs and effort for ecological monitoring as required by environmental permits can also be significantly reduced through use of eDNA biomonitoring.
Some mines across Canada have already begun to use eDNA in their annual biomonitoring initiatives. Much of the eDNA work done on mine sites to date has focused on various species of trout, such as the Brook trout. Brook trout are commonly used as indicator species because they are very sensitive to environmental changes. Thus, monitoring populations of Brook trout can reveal important information about the health of entire ecosystems, and the effect that mining activity may have on these systems.
Recently, eDNA biomonitoring was incorporated alongside conventional electrofishing techniques at a mine site in northern Ontario. The objective was to conduct population assessments to determine the viability of a Brook trout spawning habitat restoration project.
Environmental DNA has consistently yielded better detection results than electrofishing, with only a fraction of the time commitment, and no physical impact on the aquatic system.
Two genetic approaches are being used in the eDNA game. The first approach is a targeted approach, known as quantitative polymerase chain reaction (qPCR).
This is the gold-standard DNA diagnostic method used in medicine for over 25 years. The qPCR technique is an extremely accurate technique to detect between one and three target species at a time. These target species are usually selected based on their ecological significance, but practically any organism can be detected based on the question being asked. The qPCR technique can be used to detect endangered species, a variety of indicator species, and invasive species, and is proven for its sensitivity, accuracy, and low cost.
The other approach in eDNA biomonitoring is known as metabarcoding.
This technique is often used in broadscale biomonitoring to characterize entire ecosystems and bacterial communities.
Meta-barcoding can be used to simultaneously monitor most animal species in an aquatic system; and, in addition to changes in microbial activity as a result of chemical or effluent spills.
While both techniques have complementary benefits, what is most important is that they are used correctly. Like most emerging technologies, eDNA biomonitoring encompasses sophisticated processes, from designing robust surveys and accurate tests, to extracting the DNA from samples onsite. The methods used to carry out these important steps are crucial for the successful integration of eDNA technologies into routine biomonitoring.
Surveys should always be customized to the project and the species of interest; and sample timing and locations must reflect the biology and the ecology of the species of interest. Likewise, species-specific DNA tests need to be designed using specimens obtained from the geographic region of interest, and should always go through a series of rigorous validation steps to ensure confidence in results. Best practice is to conduct surveys using third party verified assays, robust survey designs, and sampling processes to reduce DNA degradation and contamination. With field-ready eDNA tools now available, water filtration, DNA extraction, and sample analyses can be done on site, which significantly reduce concerns around DNA degradation, and sources of contamination. DNA degradation in the samples is a common concern in eDNA biomonitoring if the samples are shipped to a central lab. The trace amounts of DNA in a water sample can degrade rapidly after collection if not extracted onsite in a thermostable buffer.
This degradation can be the result of high temperature, microbial activity, and UV light exposure. Fortunately, new DNA extraction protocols have enabled on-site extraction and stabilization of DNA, opening the door for eDNA surveys to be conducted in even the most remote locations, without the need to ship samples to a lab. This brings the eDNA lab to the field.
Environmental DNA biomonitoring answers the questions:
- What species are present on site?
- Are endangered species present?
- What specific areas do they inhabit?
- Have species migration patterns changed?
- Are invasive species present?
All of these factors require careful consideration and can benefit from use of eDNA biomonitoring. As the global demand for resources rise, so too does the need for technological innovation that accommodates more accurate and efficient environmental measures, and offset costs. Environmental DNA biomonitoring offers these benefits, with significant cost savings of up to 68% compared to conventional methods, and with reliable and accurate results.
In addition, new applications for eDNA continue to be discovered, and eDNA has yet to see its full suite of applications and potential.
Kevin Romanick is the head of field operations at Precision Biomonitoring Inc. (PBI). He is a biotechnology in ecology expert a graduate of the master of biotechnology program at the university of Guelph. At PBI, Kevin leads eDNA surveys for several industrial applications, including compliance surveys for mining operations.