We can now collect environmental DNA — the genetic material contained in a sample of water, say, or soil or sediment
Imagine you are standing on the seashore. A fish jumps, then disappears. What kind of fish was it? If you know your marine life, you might guess it was some kind of mullet.
But how can we know for sure what kinds of fish live in the oceans and rivers around us? Answering this question requires considerable time and effort — you have to dive into the water and observe — or break out a fishing rod, net and other tackle, then see what you can catch.
Or at least you used to. Today, we have a new technique. We have new vocabulary, too. I’m going to teach you some. When we talk about ecosystems and the benefits they bestow upon us — like honey bees pollinating crops — we put these discussions under the “ecosystem services” header.
And we are talking more about ecosystem services these days, mostly because we are coming to understand them much better than we used to.
We have a new tool.
We can now collect environmental DNA — the genetic material contained in a sample of water, say, or soil or sediment. We all leave samples of our DNA behind as we go through our day, though us Homo sapiens might be the only species in the animal kingdom that flushes it away.
Other animals leave their DNA right out in the open where we can collect it (lucky us).
Once we collect it, however, we still need some kind of gauge to tell us stuff like what kind of fish that was which just jumped in front of us. The tool that allows us to do this and much more is called metabarcoding. It’s a really fast way to assess all the biodiversity that is in our ecosystem.
So, congratulations, you’ve already learned a new acronym, eDNA.
DNA, or deoxyribonucleic acid, remember, is the genetic material that nearly all living organisms pass from parent to child. Your junior high school biology teacher may have told you to think of it is “the blueprint of life.”
We have long been able to analyze microbes and other organisms so small they cannot be seen with the naked eye. We do this by extracting DNA directly from environmental media.
You’ve probably never thought of air, land and water as “environmental media” before, but since we’re reading it for signs of biodiversity, that is exactly what it is.
This media also contain eDNA that can be seen with the naked eye. Remember that mullet?
A few years ago, nobody had yet had the eureka moment of realizing all that eDNA was being published in all of our environmental media every day.
That would come when Dr. Toshifumi Minamoto of Kobe University, who was studying carp pathogens, placed carp in a tank and began conducting experiments. He noticed that DNA besides the pathogenic microbes proliferated. When he tried to determine where this DNA was coming from, he discovered the carp were, um, well, urinating.
There were myriad DNA floating in the water, and in attempting to determine the source of all this surprising DNA, Minamoto had his eureka moment: Ecosystems themselves can tell us exactly what lives in them. In 2012, he published a paper.
Initially, nobody thought ecosystems could be read like books and magazines. Large numbers of people, myself included, were skeptical of Minamoto’s research results.
Though skeptical, I found the concept of fish eDNA intriguing and thus set out to develop analysis technology. I would conduct my initial experiments in an aquarium. In these large tanks, the species of fish are predetermined, so if I could somehow work backward from their eDNA and my results matched the aquarium’s population, it might be possible to apply whatever technology I could come up with to a body of water in the natural environment.
I immediately proceeded to the Okinawa Churaumi Aquarium, famous for its three enormous whale sharks. I scooped out some water and forced it through a fine filter — each hole had a diameter of 1 micron or less — that allowed me to capture the eDNA. I then proceeded with ho-hum everyday molecular biological experiments.
However, with that approach the concentration of fish DNA was too small, so analysis was impossible. Moreover, eDNA deteriorates in water (four types of material known as “bases” are linked by the millions in chains, but these break apart). Accordingly, the target of analysis is nothing more than short DNA fragments.
What I succeeded in developing is a tool called a primer. I named it MiFish. Using this tool, short DNA fragments can be selectively amplified and — voila! — identify fish species. MiFish can amplify DNA from any of the more than 33,000 species of fish said to exist, and thus enable analysis in any body of water in the world.
By adding base sequences, called adapters, to both ends of the DNA fragments that were amplified, analysis becomes possible with the latest next-generation sequencers. When I promptly analyzed the eDNA obtained from the water of the Okinawa Churaumi Aquarium tanks using a next-generation sequencer, it became clear that I could detect at least 90% of the more than 250 species of fish living in the four tanks.
The technology has since been made increasingly easy to use. Only half a year after my paper was published, in July 2015, a private company began contracting analysis work. The private company sent in water samples. They were tested, and the species of fish that are living in that body of water were determined.
We have used the technology to create a complete picture of the species of fish living in Kyoto’s Maizuru Bay and the rivers surrounding Lake Biwa, northeast of Kyoto. In addition, we have learned that it is possible to use water sampled from depths of 600 meters to monitor deep-sea fish. Moreover, not only can we learn what species of fish are present, we also have the feeling that it could be possible to monitor their numbers and biomass.
At present, I am working with Satoko Seino, an associate professor at Kyushu University, on tests to use eDNA to learn how many fish are visiting seaweed beds offshore from Tsushima, Nagasaki Prefecture. As these waters warm, they seem to be attracting more fish, which feed on the seaweed farmers are hoping to harvest.
This technology is becoming simpler and more automated and could mature into something able to monitor changes in fish populations. By monitoring trends in fish populations over time and compiling the data, the day will likely come when near-future forecasts can be made, just like weather forecasts. Perhaps we’ll look at our fisheries app to check “tomorrow’s mackerel forecast” or the “weekly tuna forecast.”
If monitoring of ecosystems and aquatic resources becomes possible, it could be a means for us homo sapiens to utilize nature’s gifts to the fullest.
In other words, we might soon be able to put the unilateral exploitation of nature on the brink of extinction.
Masaki Miya is a senior research scientist at the Natural History Museum and Institute, in Chiba, Japan.