AsianScientist (Could. 6, 2022) – One morning within the fall of 2016, conservation geneticist Professor Jonathan Fong picked his approach via the slopy and rocky nation parks on the outskirts of Hong Kong metropolis to achieve a river stream. He was on the lookout for the endangered big-headed turtle. However as a substitute of recognizing a turtle, Fong took out a sterilized tube from his bag, leaned over the stream, and stuffed the tube with river water. He then packed it up in an envelope and headed towards his lab at Lingnan College, the place he would study the water for the presence of the turtles’ eDNA.
All organisms shed their DNA of their pure surroundings in a number of kinds together with feces, mucus, gametes, pores and skin, or hair. Such DNA is named Environmental DNA or eDNA. Researchers like Fong amplify eDNA utilizing gene sequencing instruments to establish the species to which the DNA belongs.
Researchers in Western international locations began utilizing the expertise within the Nineteen Eighties to detect microbial biodiversity in marine sediments, however within the current years eDNA has been extensively used within the conservation of animals. As a substitute of spending hours on the lookout for a reside animal, it’s a lot simpler to gather their environmental samples, say researchers.
Analyzing eDNA is “like being a detective,” Fong instructed Asian Scientist Journal. “They’re imperfect items of proof but have an enormous potential.” However the rising use of the expertise can be revealing its drawbacks and potential misuse.
The potential
The traditional approach of doing a turtle discipline survey is tiresome. Researchers stroll a number of kilometers carrying traps. Then they set the traps at completely different areas and monitor them for days. Compared to that, eDNA expertise helps direct the place the researchers ought to focus their assets and power, says Fong.
Like Fong, researchers on the Wildlife Institute of India (WII) are additionally utilizing eDNA to observe river dolphins throughout the Ganges and Brahmaputra rivers, the place even hiring a ship for a day may value shut to twenty,000 Indian Rupees, or 360 SGD.
“Think about attempting to survey 3000 kilometers of the river,” stated Vishnupriya Kolipakam, conservation biologist at WII. Since final yr, Kolipakam and her group have been utilizing eDNA with higher ends in monitoring the dolphins than earlier.
The researchers are additionally utilizing the instrument to evaluate the inhabitants of many aquatic and terrestrial species. Conventional sampling strategies embrace researchers using fishing nets to seize fish at a number of websites. With eDNA, after the researchers have collected sufficient knowledge, they use their understanding of how typically a species sheds DNA and the way exterior elements might impression eDNA degradation, to calculate a tentative inhabitants.
“It’s only a matter of logical evaluation—placing knowledge in an equation and doing the mathematics,” Anish Kirtane, an Indian researcher at present pursuing a PhD in environmental methods science at ETH Zurich, instructed Asian Scientist Journal.
False positives
Environmental DNA expertise, nonetheless, shouldn’t be excellent but. The challenges embrace false optimistic outcomes and misinterpretations by the researchers. When researchers detect an animal’s DNA in an surroundings the place that animal shouldn’t be truly current, the outcomes are stated to be false optimistic.
Whereas monitoring the big-headed turtles, Fong collected water samples from 34 completely different streams in Hong Kong. Though his group confirmed the presence of latest turtle populations, additionally they had some false positives. “There have been few locations the place we discovered turtle DNA but once we went again and arrange traps for monitoring, we couldn’t discover any,” he stated.
“False positives may even flip pricey in eDNA research,” stated Ying Kin Ken So, a conservation biologist from the College of Hong Kong. “It is because many conservation administration choices are made based mostly on the interpretation of those outcomes.”
An inaccurate interpretation may even end in implementing measures to preserve a non-existent endangered species or to even take away non-existent invasive species.
Generally, even true outcomes may be misinterpreted as a consequence of quite a lot of causes. For instance, directional move of a river can direct eDNA to combination in sure areas, giving a false thought in regards to the abundance of a species.
The character and conduct of animals additionally issues. Fish which keep in water on a regular basis have a completely completely different DNA shedding charge than semi-aquatic creatures like frogs and turtles. Animals can shed extra DNA relying on climate, season, time of the day and their life stage. “So, researchers ought to have a agency understanding of ecology and conduct of the species earlier than decoding any outcomes from eDNA,” stated Kirtane.
Regardless of these challenges, eDNA research have been utilized in conservation administration and coverage making. In 2011, some researchers detected eDNA of an invasive Asian carp species in lake Michigan within the US. This led to a heated debate about whether or not the species had truly invaded the Nice Lakes.
Later, the conservationists proposed to separate the Nice Lakes and Mississippi river basin by closing the ship canal, regardless of oppositions of waterway operators and present customers of the canal. Now, the conservationists within the space routinely use eDNA expertise to observe the presence the Asian carp within the Nice Lakes.
Getting higher
Fairly like every other expertise, enhancing eDNA would require “extra testing and discovering developments or consistencies for reliability,” Fong stated. Extra and rigorous testing and evaluating knowledge over a number of seasons and amongst comparable animal teams will assist discover patterns and solidify knowledge interpretation.
Extra use may also convey down the price of the expertise and make it accessible to a wider set of researchers throughout Asia. At the moment, gene sequencing machines are costly and making a species-specific assay takes money and time.
“For us it took about 6 months to develop the reagents and will have value someplace between $5000-$10,000 only for the reagents,” Fong stated.
However the discipline is advancing quick and there are teams “engaged on making moveable PCR machines for onsite DNA detection, whereas others are engaged on simplification of DNA extraction processes,” stated Masayuki Ushio, microbial ecologist at Kyoto College in Japan.
Ushio believes that within the close to future, the approach “might even be utilized by widespread folks in detecting microbial pathogens in fisheries and agriculture lands.”
Regardless of the present challenges, most researchers consider that the approach is a brand new frontier of biodiversity evaluation. It’s exhausting to say how the expertise will evolve and will likely be used within the subsequent decade or so. For Kirtane “it’s tremendous thrilling to be in the midst of it and seeing issues change.”
———
Copyright: Asian Scientist Journal; Illustration: Shelly Liew/Asian Scientist Journal.
