Scientists turn to eDNA to curtail the freshwater extinction crisis – Mongabay.com

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  • Freshwater ecosystems are understudied and underfunded, resulting in a lack of information on what species are at risk of extinction.
  • The eBioAtlas program, a partnership between the IUCN and NatureMetrics, uses environmental DNA gathered from freshwater samples to figure out what freshwater ecosystems to conserve and what species to prioritize.
  • So far, a pilot study in southeast Liberia has successfully picked up environmental DNA from nearly 170 species, including some that are critically endangered.
  • The new data will provide up-to-date information for the IUCN Red List of Threatened Species and empower local communities to maintain ownership of their land and water resources.

Drifting down the Dubo River through Sapo National Park in Liberia, Shadrach Kerwillain, a project manager for Fauna & Flora International (FFI), takes a sample of fresh river water. It’s hard to see what lies beneath the surface of the turbid, fast-moving river, but the importance of that water is clear.

Freshwater ecosystems supply drinking water, support inland fisheries, offer flood control and deliver nutrients to forests. Yet historically, they are understudied, underfunded and undervalued. Scientists rely on data gathered three to four decades ago while working in a race against time to figure out what freshwater ecosystems to conserve and what wildlife to prioritize.

An eDNA survey team traveling to a freshwater survey point along the Dubo River in Liberia. Image courtesy of Fauna & Flora International.

“If you don’t know where something is, it’s very hard to conserve it,” said Will Darwall, the head of freshwater biodiversity in the IUCN Global Species Program.

To curtail the extinction crisis and support conservation efforts, IUCN and NatureMetrics announced a new partnership: the eBioAtlas program. Program partners will look at environmental DNA, or eDNA — the traces of genetic material left in the water by animals — to get information on biodiversity fast, especially from places lacking data.

However, the eBioAtlas program is still in need of funding for the team to reach its goal of collecting 30,000 samples over the next three years. EBioAtlas partners are working to raise $15 million to reach their goal, Darwall said.

A Sapo National Park biologist filtering a water sample to collect genetic material along the Dubo River in Liberia. Image courtesy of Fauna & Flora International.

Out of sight, out of mind

Despite their importance, freshwater ecosystems are being lost three times more rapidly than tropical rainforests. Experts estimate that freshwater populations — mammals, birds, amphibians, reptiles and fishes — declined 84% since 1970, equating to about 4% each year.

There are about 26,000 freshwater species currently on the IUCN Red List of Threatened Species and about a quarter of those species are classified as data deficient, where there is not enough information to assess a species’ conservation status, Darwall said. One-third are threatened with extinction.

The lack of data is most likely attributed to the lack of funding. An analysis by the European Foundation Centre revealed that European foundations give only about 3% of environmental funding to freshwater ecosystems. North American foundations give around 8%, and the vast majority of that funding remains there.

For West African countries like Liberia, it’s not that there is a lack of support for freshwater conservation; rather there is a lack of awareness about the risks they face, Kerwillain said.

“Freshwater species are a good marker of how well an ecosystem is doing, especially during these times of changing climate,” he added.

A pygmy hippopotamus photo captured on a camera trap in the Wonegizi Proposed Protected Area. Nearby, Fauna & Flora International performed a pilot study for the eBioAtlas program where they collected freshwater along the Dubo and Dugbe rivers in southeast Liberia. They detected DNA from nearly 170 species, including the pygmy hippo. Image courtesy of Fauna & Flora International.

Microbes to megafauna

As part of a pilot study in 2020, the FFI team took water samples along the Dubo and Dugbe rivers, flowing through Sapo National Park and the Grand-Kru River Gee Proposed Protected Area in southeast Liberia. Before the expedition, the team learned from local communities that pygmy hippos (Choeropsis liberiensis) might be in the area.

The team took water samples from 20 sites and detected DNA from nearly 170 species, including the endangered pygmy hippo. They also picked up the first record of the endangered Tai toad (Sclerophrys taiensis) in Liberia and a critically endangered species of killifish (Scriptaphyosemion schmitti). They uncovered the presence of four other endangered species: the African gray parrot (Psittacus erithacus), the Diana monkey (Cercopithecus diana), the Western red colobus (Piliocolobus badius) and Jentink’s duiker (Cephalophus jentinki).

“One liter of river water can give you as much data on fish as 10 years of electrofishing effort,” said Kat Bruce, founder of NatureMetrics.

The eDNA approach gets data faster and cheaper than traditional methods, like camera traps, Darwell said. The technology is also novel because it picks up any genetic material in the water or catchment, from microbes to fish to elephants. Land animals can leave their genetic fingerprint when they walk through the water, or their DNA can be washed into the water when it rains.

Historically, one barrier in collecting data is getting specialist teams to the field. However, gathering freshwater samples for eDNA doesn’t require an expert. Schoolchildren, people in the tourism industry, or scientists already working in the field can easily participate.

To gather eDNA, the team collects freshwater at multiple spots using a large syringe, and then pushes the water through a filter that captures the DNA. NatureMetrics extracts the DNA and sequences it, obtaining a complex data set of both land and freshwater wildlife.

Still, there are drawbacks. With eDNA, experts can’t get precise counts or measure the abundance of particular fish or animals. Fish that live in water give off genetic material consistently, while mammals on land introduce DNA into the water sporadically. The technology is meant to add to the information that scientists gather from field observations.

A used filter containing eDNA, which is ready to be sent to the lab for analysis. Image courtesy of NatureMetrics.

“We’ve always been very clear about saying we’re not actually trying to replace traditional methods. There are always times when it’s better to go out there and actually observe the animals,” Bruce said.

To figure out what species DNA belongs to, NatureMetrics uses a reference database. But the reference databases are fairly incomplete because of the lack of information on freshwater ecosystems. Over time they will grow, adding more species when more information is captured.

A way forward

The vital part of the program is translating data to change on the ground. The new data, such as the presence of those endangered species, will provide up-to-date information for the IUCN Red List. NatureMetrics also plans to make the data freely available, especially to local stakeholders and policymakers.

Knowing where fish and animals are located could help direct conservation resources and create protected areas where they are needed.

For example, the information from this tool could be used to stop extractive industries, like mining. In some cases, mining companies will claim that an animal isn’t found in a desirable spot or that the area isn’t biodiverse. The in-depth coverage that eDNA delivers can empower local communities to fight back and tell companies they can’t move forward until they perform more targeted surveys.

While conversations on colonialism in field science emerge, programs like eBioAtlas can also help people rethink how science is done. International survey teams don’t always need to be flown in to gather data. Instead, it’s an opportunity to allow local communities to maintain ownership and stewardship of the environment, driving real change.

“It has a softer touch on communities compared to other surveying techniques,” Kerwillain said. “It puts the power of science in the hands of ordinary people.”

A laboratory technician processing eDNA samples in the lab to figure out what species can be detected through their DNA in the freshwater sample. Image courtesy of NatureMetrics.

Banner image of a FFI biodiversity officer filtering freshwater to collect eDNA along the Dubo River in Liberia, courtesy of Fauna & Flora International.

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