Although the method is not new, it is only in recent years that it has started to become established. The first attempts to identify bacteria on the basis of DNA traces in water and soil samples date back to the late 1980s. But it wasn’t until 2008 that European researchers first demonstrated the presence of frog DNA in a sample of water. Since then, this method has taken off.
At the same time, the emergence of new techniques for rapid and comprehensive DNA sequencing has provided a further boost for scientists working on environmental DNA. These include Kristy Deiner, Professor of Environmental DNA at ETH Zurich. She heads up the group that includes Anish Kirtane, Cátia Pereira and Zora Doppmann.
As of 2015, high-throughput sequencers have been routinely used for environmental DNA analysis. These devices can rapidly decode unsorted mixtures containing millions of different DNA molecules in just one run. “We used to have to separate each strand of DNA from the others and purify it before we could analyse its sequence,” Deiner explains. “This is the technical revolution that really set the ball rolling.”
Cheap and fast
In the meantime, the three researchers have delivered their samples to the lab. Pereira and Doppmann are in the clean room. Dressed in white protective suits, they look like astronauts. Through a pane of glass, Kirtane watches his colleagues process the filter pad and treat it with solutions to wash out material containing DNA. They then purify and prepare the samples so that the solution contains only DNA.
“It’s vital to prevent any contamination,” Doppmann explains. Even a minuscule trace of DNA, either from themselves or from outside, could render the samples useless. Before entering the clean room, the researchers must therefore pass through an airlock and put on protective suits, all of which takes time. Furthermore, all the air pumped into the clean room is first filtered. At night, UV lamps are turned on to break down any DNA molecules that might have been accidentally introduced. After each test, all the surfaces must be cleaned with bleach.