eDNA and metabarcoding—the future of effectively and rapidly surveying biodiversity

Traditionally, if we want to determine the presence of a species—say, an endangered species of fish or amphibian in a sensitive area—we must document that it’s there, which is typically done by capture. Not so with eDNA. Rather than having to sample the species, we sample the environment where that species lives, such as a pond or a lake, or where they may roost, like a cave, or the soils in a burrow where they might be denning. We sample that environment for DNA that has been shed, such as skin or fecal matter, and analyze the DNA to see which species was present. This avoids harm to organisms and can vastly improve our ability to detect what is at the location.

Metabarcoding moves beyond a targeted approach for single species and allows us to determine a full suite of species present—and well beyond what we can do using conventional tools.

Benefits of metabarcoding

Metabarcoding is a great way to explore the environment—and it’s very useful for rapid surveys of communities to learn what might be present. Instead of having to conduct three or four types of surveys to collect a wide variety of critters, with maybe three or four biology specialists, an eDNA survey can be conducted by a small team guided by a plan developed by specialists.

The eDNA team will sample the environment and the DNA will be analyzed to determine which species are there. Analysis is conducted by a specialized laboratory—and the turn-around time can be rapid. Since you don’t have to disturb the animals, this process is safer for them and involves fewer field staff, which is better for health and safety and reduces field costs.

Look back in time

Okay, so you can’t use metabarcoding to time travel. But the DNA you extract from a sample gives you a unique ability to look back a year or two later at the same sample to ask more questions.

How? We typically don’t use up all the DNA when we run an analysis, so we archive the remainder. DNA can be preserved for a long period of time. Say we collect samples at the baseline stage before a project is constructed, we can archive the DNA from those samples and then analyze them again in the future if new questions arise about what was present at the baseline stage. That’s time travel.

For example—consider a pipeline project. You’ve collected samples in a watercourse where the pipeline might cross, and you have analyzed the eDNA to learn about the fish communities at these locations to help you plan your project. Let’s say a year from now, when the pipeline is in place, a question comes up about amphibians. You can query the archived samples to see what amphibians were present before the pipeline was constructed.

Down to Earth

An important reminder: we’re sampling the environment, so we must design our sampling program well to be confident that we will detect what is truly present. As powerful as this science is, it’s not a Star Trek Tricorder—it won’t give you an absolute answer. We need to put on our ecologist hats to sample the environment at the right time and place to have the best chance of detecting the species we’re looking for to see if it is present.

And we must have a qualified laboratory on board to analyze the samples. In other words, we need to do our homework so that we can get a reliable answer to the questions being asked. This is important for all biological surveys and equally important for surveys that use DNA-based approaches like metabarcoding to assess biodiversity.

Biodiversity

Metabarcoding gives us a much broader picture of biodiversity than we’ve ever had before.

You may remember that old children’s song that goes something like this: “The green grass grows all around … and a hole in the grass, a tree in the hole, a limb on the tree, a nest on the limb, an egg in the nest, a bird in that egg, a feather on that bird, a bug on that feather, a germ on that bug …” and so on. You get the idea.

That song describes big to small in that ecosystem. Likewise, metabarcoding analysis can give us a much broader picture of biodiversity than any other tool. It will reveal much more about the organisms that are present than we can see with the naked eye and conventional tools. As a result, we get much more information to allow us to assess ecosystem health and to make responsible decisions about how to protect the environment.

Time is of the essence

Metabarcoding is a powerful tool. It can give us access to so much information—and we’re only just beginning to learn how to use it to its full potential. The data collected are rich and valuable. Looking to the future, what questions can we answer using eDNA sampling and metabarcoding analysis?

Time is of the essence. In this time of climate urgency and habitat loss, we need new ideas on how to effectively and rapidly survey biodiversity. DNA-based approaches, such as metabarcoding, will take us there.