AsianScientist (May. 6, 2022) – One morning in the fall of 2016, conservation geneticist Professor Jonathan Fong picked his way through the slopy and rocky country parks on the outskirts of Hong Kong city to reach a river stream. He was looking for the endangered big-headed turtle. But instead of spotting a turtle, Fong took out a sterilized tube from his bag, leaned over the stream, and filled the tube with river water. He then packed it up in an envelope and headed toward his lab at Lingnan University, where he would examine the water for the presence of the turtles’ eDNA.
All organisms shed their DNA in their natural environment in several forms including feces, mucus, gametes, skin, or hair. Such DNA is called Environmental DNA or eDNA. Researchers like Fong amplify eDNA using gene sequencing tools to identify the species to which the DNA belongs.
Researchers in Western countries started using the technology in the 1980s to detect microbial biodiversity in marine sediments, but in the recent years eDNA has been extensively used in the conservation of animals. Instead of spending hours looking for a live animal, it’s much easier to collect their environmental samples, say researchers.
Analyzing eDNA is “like being a detective,” Fong told Asian Scientist Magazine. “They are imperfect pieces of evidence yet have a huge potential.” But the increasing use of the technology is also revealing its drawbacks and potential misuse.
The potential
The conventional way of doing a turtle field survey is tiresome. Researchers walk several kilometers carrying traps. Then they set the traps at different locations and monitor them for days. In comparison to that, eDNA technology helps direct where the researchers should focus their resources and energy, says Fong.
Like Fong, researchers at the Wildlife Institute of India (WII) are also using eDNA to monitor river dolphins across the Ganges and Brahmaputra rivers, where even hiring a boat for a day could cost close to 20,000 Indian Rupees, or 360 SGD.
“Imagine trying to survey 3000 kilometers of the river,” said Vishnupriya Kolipakam, conservation biologist at WII. Since last year, Kolipakam and her team have been using eDNA with better results in tracking the dolphins than earlier.
The researchers are also using the tool to assess the population of many aquatic and terrestrial species. Traditional sampling methods include researchers employing fishing nets to capture fish at multiple sites. With eDNA, after the researchers have collected enough data, they use their understanding of how often a species sheds DNA and how external factors may impact eDNA degradation, to calculate a tentative population.
“It is just a matter of logical analysis—putting data in an equation and doing the math,” Anish Kirtane, an Indian researcher currently pursuing a PhD in environmental systems science at ETH Zurich, told Asian Scientist Magazine.
False positives
Environmental DNA technology, however, is not perfect yet. The challenges include false positive results and misinterpretations by the researchers. When researchers detect an animal’s DNA in an environment where that animal is not actually present, the results are said to be false positive.
While tracking the big-headed turtles, Fong collected water samples from 34 different streams in Hong Kong. Although his team confirmed the presence of new turtle populations, they also had some false positives. “There were few places where we found turtle DNA yet when we went back and set up traps for monitoring, we couldn’t find any,” he said.
“False positives can even turn costly in eDNA studies,” said Ying Kin Ken So, a conservation biologist from the University of Hong Kong. “This is because many conservation management decisions are made based on the interpretation of these results.”
An inaccurate interpretation could even result in implementing measures to conserve a non-existent endangered species or to even remove non-existent invasive species.
Sometimes, even true results can be misinterpreted due to a variety of reasons. For example, directional flow of a river can direct eDNA to aggregate in certain locations, giving a false idea about the abundance of a species.
The nature and behavior of animals also matters. Fish which stay in water all the time have an entirely different DNA shedding rate than semi-aquatic creatures like frogs and turtles. Animals can shed more DNA depending on weather, season, time of the day and their life stage. “So, researchers should have a firm understanding of ecology and behavior of the species before interpreting any results from eDNA,” said Kirtane.
Despite these challenges, eDNA studies have been used in conservation management and policy making. In 2011, some researchers detected eDNA of an invasive Asian carp species in lake Michigan in the US. This led to a heated debate about whether the species had actually invaded the Great Lakes.
Later, the conservationists proposed to separate the Great Lakes and Mississippi river basin by closing the ship canal, despite oppositions of waterway operators and current users of the canal. Now, the conservationists in the area routinely use eDNA technology to monitor the presence the Asian carp in the Great Lakes.
Getting better
Quite like any other technology, improving eDNA will require “more testing and finding trends or consistencies for reliability,” Fong said. More and rigorous testing and comparing data over multiple seasons and among similar animal groups will help find patterns and solidify data interpretation.
More use will also bring down the cost of the technology and make it accessible to a wider set of researchers across Asia. Currently, gene sequencing machines are expensive and making a species-specific assay takes time and money.
“For us it took about 6 months to develop the reagents and may have cost somewhere between $5000-$10,000 just for the reagents,” Fong said.
But the field is advancing fast and there are groups “working on making portable PCR machines for onsite DNA detection, while others are working on simplification of DNA extraction processes,” said Masayuki Ushio, microbial ecologist at Kyoto University in Japan.
Ushio believes that in the near future, the technique “may even be used by common people in detecting microbial pathogens in fisheries and agriculture lands.”
Despite the current challenges, most researchers believe that the technique is a new frontier of biodiversity assessment. It is hard to say how the technology will evolve and will be used in the next decade or so. For Kirtane “it is super exciting to be in the middle of it and seeing things change.”
———
Copyright: Asian Scientist Magazine; Illustration: Shelly Liew/Asian Scientist Magazine.
