How eDNA can support regulatory and policy decisions

Dr. Mehrdad Hajibabaei, PhD
Founder and Chief Scientific Officer, eDNAtec

Dr. Mehrdad Hajibabaei

Within the DNA – or genome – of organisms there are gene sequences that are unique to each species.

These are known as barcode regions and can serve as reliable identifiers for entire species.All organisms shed some of their DNA in their environment. We call this environmental DNA (eDNA). Using advanced sequencing technologies and computer programs we can sequence and identify any species from environmental samples such as water, soil or even air. We can draw a clear picture of what organisms populate an ecosystem – from the smallest microbe to the largest whale – by collecting and analyzing water samples. 

In this interview, Dr. Hajibabaei highlights why eDNA technology is of particular interest to government regulators and policy makers, who seek quick and reliable ways to assess biodiversity and the overall health of ecosystems.

Can you help us understand how eDNA has important implications for regulators and policy makers?

Absolutely. Genomics technologies have revolutionized biological sciences. For example, identification and surveillance of disease-causing viruses and bacteria relies heavily on molecular diagnostic tools. Without genomics we would not be able to track various strains of coronavirus during the pandemic. In the environmental sector, eDNA can provide biodiversity data for environmental assessment (EA) and regulatory regimes. As compared to traditional approaches, eDNA analysis provides faster turn-around and is far more cost-effective than traditional techniques. Additionally, we can deploy eDNA at much larger scales because the workflow relies on automation and computational analysis. While eDNA has significant advantages for regulatory use, eDNA can also provide new insights for understanding environmental change. These can shape new policies and regulatory frameworks as we mobilize resources to mitigate the effects of climate change, for example.

Can you elaborate on how eDNA can help us understand environmental change?

Let’s focus on biodiversity loss, which traditionally has been very difficult to measure. Conventional approaches have included the collection of physical, chemical, biological and geological data to extrapolate what is happening in an ecosystem. However, with potentially thousands of species in an ecosystem, it is virtually impossible to precisely understand changes in the environment using those techniques. Some biodiversity analysis has been done on key species, but in order to really understand what’s going on with biodiversity loss you need to directly measure species – from bacteria to mammals – and this is where eDNA can play a key role. Combined in a hybrid way with algorithms and machine learning tools, we can basically use eDNA to quickly and accurately measure the entire biodiversity of an ecosystem.

With regard to climate change, obviously we want to know how that is affecting an ecosystem. Whether in marine or freshwater environments, what we need is a good measure of diversity and its dynamics, especially with local systems that might be under various types of stressors. For example, we also need to take into account potential human utilization of resources and any other sources of impact beyond climate change. So fundamentally, we need the most accurate measure of biodiversity that we can get. Operationally, using conventional techniques, this would be very difficult but with eDNA we can get very close to that. We can understand locally what is happening in an environment where we have all sorts of potential stressors happening, on top of climate change. Using eDNA, we can generate biological data that can be useful in understanding how climate change is influencing ecosystems, on both a local and global scale.

So, you would use eDNA to establish benchmarks and then monitor any changes that may take place going forward?

Correct. In an ideal scenario you would be starting in a pristine environment where there have been no environmental impacts, but of course that is very rare. What we would identify is more of a functional baseline; you analyze the first sample collection and repeat the measurement across time, then use statistical analysis and modelling to understand the trajectory of change.  These findings would be used to  maintain sustainable use of that ecosystem over time. Canada is working to preserve 25 percent of its coastal territories as marine protected areas by 2025, and 30 percent by 2030. What will we do to measure and confirm that we really are protecting these areas? Certainly, eDNA and meta barcoding can play a key role in enabling us to understand this question. As well, indigenous communities and not-for-profit organizations who are involved in Environmental Assessments are all converging on the benefits of eDNA approaches for these kinds of quick and reliable measurements.

A typical EA, such as for an offshore exploration project, can take many months. How much more quickly can eDNA approaches complete the same parcel of work?

That’s a critical point. In the case of eDNA, we only need a small amount of water. We don’t need to access the organisms, catch the fish or harvest large quantities of sediments and look through the microscope. Once the water samples have been collected we can generate the data in a matter of days, depending on where the samples are collected. When it gets to the lab we can process hundreds of samples in the span of a week. We will produce charts, tables of what we found in the environment, along with names of any species that we have in the reference library. Some might not have names but we can at least associate them to general groups of organisms. Generally speaking, we can supply data for hundreds of sites in about a week. And this can be accelerated by adding more lab staff and equipment. In our own facility we are constantly improving methods and finding easier and faster ways to provide data. This is backed by the whole genomics enterprise which is working on similar problems and establishing platforms. We have built the eDNA genomics approaches on top of what has been established for medical diagnostics and infectious diseases. In other words, this is not an artisanal, small-scale operation – it is backed by larger-scale investments and world-class companies.

Can eDNA approaches be used in the Arctic to assess the environment?

Absolutely. This question has been put to us by various levels of government and other stakeholders, and the answer is always ‘yes, 100 percent.’ We have had projects in the past in the Arctic and this is one of the key regions on Earth where eDNA is highly effective whereas some other tools may have serious limitations. Scientists haven’t had a chance to do as many traditional surveys in the Arctic as we would want, due to the extreme physical challenges. With eDNA we only need to acquire some water samples and ice cores. Again, when you are trying to assess the impact of rapid climate change in the Arctic, this is the kind of tool that can deliver the data to understand how melting of the ice or any changes in the environment might impact the ecosystems there. So the Arctic is a key area where deploying an eDNA solution would make a huge difference.

If you were at a conference and met an influential political leader in the elevator, what message would you want to leave with them?

I would say that the current data collection tools that we have are fantastic but simply not enough and eDNA can be added to the toolbox to bring important characteristics which will allow us to rapidly and precisely measure the biological layers of any ecosystem. And that is key to understanding the impacts of climate change, for example. Climate change is urgent and we need rapid action. Without understanding the problem we can’t enforce mitigation or strategies to deal with it. I think eDNA can do that for us. But it is crucial that we involve clients as partners in our projects. I participated recently in a workshop with representatives from the federal fisheries department, and a key point came out in a very crisp way during a panel discussion in which I participated. When advancing technologies for regulatory applications, someone suggested that we do more than present research findings to policy makers or managers. Rather, this person suggested a co-development model, where we actually work very closely with regulators and their policy people to advance these tools from the design phase all the way to delivering results and implementation. This idea was echoed and supported by one of the policy leads in DFO. We have been very successful in spearheading this approach. We believe it is the way of the future for eDNAtec.

Dr. Hajibabaei is an internationally recognized leader in molecular biodiversity and genomics technologies with over 150 peer-reviewed publications. He is an Associate Professor at the Centre for Biodiversity Genomics and Department of Integrative Biology of the University of Guelph, specializing in the development and application of cutting-edge technologies for rapid and accurate analysis of biological diversity from genes to ecosystems. Dr. Hajibabaei has served on advisory and review panels for various international organizations and funding agencies and has collaborated with regulatory agencies, NGOs and industry.

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