How we can detect pretty much anything - Hélène Morlon and Anna Papadopoulou

For years, scientists have been staking out this remote forest in Montana for an animal that’s notoriously tricky to find. Camera traps haven’t offered definitive evidence, and even experts can't identify its tracks with certainty. But within the past decades, researchers have developed methods that can detect even the most elusive species. And so, in 2018, these scientists took a sample from some conspicuous snow tracks. Lab tests showed conclusive results: the Canada lynx was indeed present in the area.

Without seeing the cat, scientists had proof it was there because of environmental DNA or eDNA. Using a technique called DNA metabarcoding, researchers can take a sample from the environment and learn which organisms are in it or have recently passed through it. The world is covered in DNA. It’s all around us— on the ground, at the bottom of the ocean, and up in the clouds. Multicellular organisms are constantly shedding cells.

But until recently, eDNA wasn’t very useful to us. Traditional scientific techniques couldn’t parse environmental samples containing mixed genetic material from multiple species. But DNA metabarcoding can. DNA begins to degrade once it’s exposed to the environment. In the ocean, for example, it may only persist for a few days. So in many contexts, eDNA is useful for telling us about the recent past.

The process of DNA metabarcoding starts with an environmental sample like a core of soil, a vial of water, some feces, an insect trap, or even the blood from leeches’ stomachs. Researchers then sift out everything aside from DNA by blending the sample up and using enzymes that break down cellular proteins and release DNA, which they purify. The result is a “soup” of all the DNA in the sample. Scientists then apply the polymerase chain reaction or PCR, which uses artificial DNA strands called universal primers.

These primers bind to DNA sequences that are similar across species, then amplify genetic barcodes that are species-specific. High-throughput sequencing then reads millions of these DNA fragments, simultaneously. And finally, researchers compare them to reference databases and identify how many and which species are present— or if they’ve found entirely new ones. This method has led to the discovery of tens of thousands of species over the past decade.

While metabarcoding can detect elusive animals like the Canada lynx, it can also help scientists identify invasive species. In Yosemite, researchers used eDNA to track and remove invasive bullfrogs. Once no trace of these amphibians remained, they reintroduced a threatened native species, California red-legged frogs, which had disappeared from the area some 50 years prior.

Likewise, DNA metabarcoding can be used to monitor biodiversity. For example, using traditional approaches, categorizing all of the insects in a hectare of rainforest can take decades. But DNA from insect traps could yield these results in just a few months. One study compared insects from adjacent forest and plantation sites within China’s Yunnan province. It quickly found that not only were plantations less diverse, but deforestation affected insect groups unequally. Grasshoppers thrived in cleared areas while specialist forest beetles declined.

Using eDNA, scientists are able to investigate complex ecosystem interactions. Tracking thousands of insects as they visit flowers is impossible. Instead, researchers can study the DNA left on flowers and insects to map pollination networks. Before these techniques were available, we didn’t really know how much pollination was happening at night because we couldn’t observe it. Now scientists understand that moths are important nocturnal pollinators.

eDNA can even tell stories of long extinct species. Cold, dry, and low oxygen conditions are perfect for preserving genetic material. By digging deep into the Arctic permafrost, researchers found 50,000 year old DNA, which they matched to the nutrient-rich plants found in the stomachs of woolly mammoths. With eDNA, they also found that less nutritious grasses colonized the Arctic steppe during the last ice age, potentially contributing to the mammoth decline.

As we face another period of climate change— this time due to human activities— understanding our planet’s rapidly shifting biodiversity will be crucial to protecting it. Fortunately, eDNA and metabarcoding give us the tools to document rapid change in real time.