Hunting hidden salamanders with eDNA | Science News for Students

Hunting hidden salamanders with eDNA

Three teens use genetic techniques to pinpoint a new population of these very rare animals
May 31, 2018 — 5:33 pm EST
Yuka Tsuzuku (left), Kota Tsuchida (middle), and Yusuke Sakai (right)

From left: Yuka Tsuzuku,Yusuke Sakai, and Kota Tsuchida pose at Intel ISEF with model salamanders and model salamander eggs.

C. AYERS PHOTOGRAPHY/SOCIETY FOR SCIENCE & THE PUBLIC

PITTSBURGH, Pa. — Salamanders are small, often camouflaged amphibians. How do you find them hiding in their environment? Three teens used a combination of geographic sleuthing, bits of shed DNA and their own eyeballs. And their approach paid off. They found a new population of an especially rare species of these animals.

As their name suggests, Japanese clouded salamanders are native to Japan. But they are not commonly found throughout the country. Indeed, notes Yuka Tsuzuku, 17, in her prefecture of Gifu, “There were only three [known] habitats in 2016.” Like Yosuke Sakai, 17, and Kota Tsuchida, 18, she was worried about these animals.

All three teens are seniors at Gifu Senior High School in Gifu City, Japan. And they knew why the species had been struggling. These salamanders need wet conditions — like the rice paddies found around Gifu Prefecture — to breed. However, Yuka notes, “Paved roads prevent the adult salamander from going to their spawning grounds.” The students noticed new apartment complexes and roads were replacing wet rice paddies with dry asphalt. This made it hard for the salamanders to reach their habitat.

(Story continues below image)

This is a Japanese clouded salamander.
This is a Japanese clouded salamander. 
I, Kempei/Wikimedia Commons (CC-BY-SA-3.0)

“Gifu is the northern edge of the salamander’s habitat,” Yuka explains. If the animals couldn’t survive in this province, the teens worried that their region of Japan could soon become salamander-free.

Their high school’s biology club has dedicated itself to saving the local clouded salamanders. To do their part, these three students decided to scout for unknown populations of the animals in Gifu. But hunting salamanders is a tough task. “Manual field surveys, such as going to the mountains, [are] very hard,” Kota notes. It takes a very long time, he says. Indeed, Gifu Prefecture is so large, he observes, that such a field survey “might take 30 years.”

Kota, Yusuke and Yuka did not have 30 years. They needed something faster. They started with a geographic information system, or GIS. This is a computer program that can store a mountain of data about some region’s geography. Without the computer, so much data would have been hard to sort quickly. But with it, the teens now could narrow down their search by focusing on sites with environmental features that the salamanders needed.

They started their search with 6,000 potential sites. The teens then narrowed these down to just five sites with prime salamander habitat.

The teens then headed out to each one. At each site they collected samples of water and soil. They shared these with Minamoto Toshifumi.

Toshihumi is an environmental scientist at Kobe University, several hours away. He graduated from the teens' high school. But more importantly, he studies genetic material known as environmental DNA, or eDNA. DNA contains the instructions for living things. It’s normally found inside cells. But organisms shed some cells — and their DNA — all the time. Some of that eDNA will end up littering any environment in which an organism had lived. So a savvy scientist (or three) can take a sample from the environment, and hunt through the many types of eDNA in it, searching for genetic evidence of a target species. 

Toshihumi helped Yuka, Yusuke and Kota extract DNA from the water and soil. The teens were in luck. Two of their samples had clouded salamander eDNA. That means one or more of these amphibians might be nearby. The teens headed back to the site and began searching. Soon, they found a few clear, slimy, transparent packets.

Jackpot!  These were clouded salamander eggs — and proof that animals were living nearby.

Thrilled, Yusuke notes that “we found a new population of clouded salamander in a year.” They handed off the eggs to a local zookeeper. “The young salamander is very sensitive,” Yusuke says. The zookeeper raised the hatchlings and released the animals back into the wild once they became adults.

The three teens described their newly discovered salamander population here, earlier this month, at the Intel International Science and Engineering Fair (ISEF). This year, the fair brought together nearly 1,800 students from 81 countries to share their science fair projects. The competition was created and is run by Society for Science & the Public. The fair is sponsored by Intel this year. (The Society also publishes Science News for Students and this blog.) For their salamander project, the trio took home a second place award of $1,500 in the Animal Sciences category.

Yusuke, Yuka and Kota still have two other promising sites in which to hunt for salamanders. In the meantime, they have contacted their local government, asking them to preserve the newly discovered salamander habitat.

While these teens think the salamanders are cute, Yuka says they have another reason to protect these tiny amphibians. “Our ancestors lived in harmony with nature,” she says. “The Japanese clouded salamander lives in that habitat and conserving the salamander will conserve the traditional habitat.”

Editor’s Note: This article was updated at 10:15AM on 6/4/18 to correct the order in which the names of the teens appear in the top photograph, to clarify the source of the quote in paragraph two and to correct the spelling of Toshifumi’s name.

Power Words

(for more about Power Words, click here)

amphibians     A group of animals that includes frogs, salamanders and caecilians. Amphibians have backbones and can breathe through their skin. Unlike reptiles, birds and mammals, unborn or unhatched amphibians do not develop in a special protective sac called an amniotic sac.

biology     The study of living things. The scientists who study them are known as biologists.

breed     (noun) Animals within the same species that are so genetically similar that they produce reliable and characteristic traits. German shepherds and dachshunds, for instance, are examples of dog breeds. (verb) To produce offspring through reproduction.

cell     The smallest structural and functional unit of an organism. Typically too small to see with the unaided eye, it consists of a watery fluid surrounded by a membrane or wall. Depending on their size, animals are made of anywhere from thousands to trillions of cells. Most organisms, such as yeasts, molds, bacteria and some algae, are composed of only one cell.

criteria     (sing. criterion) The standards, rules, traits or other things used to make a judgment or determination about something.

DNA     (short for deoxyribonucleic acid) A long, double-stranded and spiral-shaped molecule inside most living cells that carries genetic instructions. It is built on a backbone of phosphorus, oxygen, and carbon atoms. In all living things, from plants and animals to microbes, these instructions tell cells which molecules to make.

engineering     The field of research that uses math and science to solve practical problems.

environment     The sum of all of the things that exist around some organism or the process and the condition those things create. Environment may refer to the weather and ecosystem in which some animal lives, or, perhaps, the temperature and humidity (or even the placement of components in some electronics system or product).

environmental DNA (eDNA )     Genetic material (DNA) retrieved from the environment. Its presence serves as evidence that a living species left it behind — even if there is no other physical sighting of that species.

field     An area of study, as in: Her field of research was biology. Also a term to describe a real-world environment in which some research is conducted, such as at sea, in a forest, on a mountaintop or on a city street. It is the opposite of an artificial setting, such as a research laboratory.

geographic information system      A system used to capture, hold, and manipulate information about a particular spatial (geographical) area.

geography     The study of Earth’s features and how the living and nonliving parts of the planet affect one another.

habitat     The area or natural environment in which an animal or plant normally lives, such as a desert, coral reef or freshwater lake. A habitat can be home to thousands of different species.

Intel International Science and Engineering Fair (Intel ISEF)     Initially launched in 1950, this competition is one of three created (and still run) by the Society for Science & the Public. Each year now, approximately 1,800 high school students from more than 80 countries, regions, and territories are awarded the opportunity to showcase their independent research at Intel ISEF and compete for an average of almost $5 million in prizes. 

molecule     An electrically neutral group of atoms that represents the smallest possible amount of a chemical compound. Molecules can be made of single types of atoms or of different types. For example, the oxygen in the air is made of two oxygen atoms (O2), but water is made of two hydrogen atoms and one oxygen atom (H2O).

native     Associated with a particular location; native plants and animals have been found in a particular location since recorded history began. These species also tend to have developed within a region, occurring there naturally (not because they were planted or moved there by people). Most are particularly well adapted to their environment.

organism     Any living thing, from elephants and plants to bacteria and other types of single-celled life.

population     (in biology) A group of individuals from the same species that lives in the same area.

savvy     The quality of possessing useful and clever knowledge.

Society for Science and the Public     A nonprofit organization created in 1921 and based in Washington, D.C. Since its founding, the Society has been promoting not only public engagement in scientific research but also the public understanding of science. It created and continues to run three renowned science competitions: the Regeneron Science Talent Search (begun in 1942), the Intel International Science and Engineering Fair (initially launched in 1950) and Broadcom MASTERS (created in 2010). The Society also publishes award-winning journalism: in Science News (launched in 1922) and Science News for Students (created in 2003). Those magazines also host a series of blogs (including Eureka! Lab).

species     A group of similar organisms capable of producing offspring that can survive and reproduce.

survey     (v.) To ask questions that glean data on the opinions, practices (such as dining or sleeping habits), knowledge or skills of a broad range of people. Researchers select the number and types of people questioned in hopes that the answers these individuals give will be representative of others who are their age, belong to the same ethnic group or live in the same region. (n.) The list of questions that will be offered to glean those data.