New eDNA pilot study in Bhutan revolutionizes biodiversity assessment tools

A tiger walks in a forest

Deep in the heart of one of the world’s most biodiverse countries, a small group of scientists huddle together on the bank of the Mangde Chhu River in Bhutan.

Overshadowed by the majesty of the Himalayan mountains glimmering before them, the scientists appeared unassuming: small and insignificant compared to the pale and looming snow-covered peaks. They crouched intently over a thin, clear tube inserted into the stream—delicately, gingerly—as if trying to extract some secret of the mountains from its flowing waters.

And in fact, they were doing just that.

What is eDNA? 

Environmental DNA, or eDNA for short, provides scientists with the unique opportunity to assess biodiversity in isolated and remote regions in a noninvasive, holistic manner. The method involves extracting environmental samples like soil, water, air or snow to discover the presence of species in an area.

Bhutan is renowned for its rich biodiversity and commitment to protecting it. In fact, conservation is woven into the country’s national identity: his Majesty the Fourth King, Jigme Singye Wangchuck, designated environmental conservation as a pillar of his philosophy of “Gross National Happiness”.

Recently, the country collaborated with WWF, ETH-Zurich, and Spygen to pioneer a revolutionary pilot study on the effectiveness of eDNA sampling in assessing biodiversity. As such, Bhutan is poised to become a global leader in using eDNA technology for conservation purposes.

Collecting the secrets of the river

The study was conducted on a particular stretch of the Mangde Chhu river in Bhutan’s Royal Manas Park, chosen due to its high biodiversity and preexisting databases of the area’s species. The researchers acquired a total of 42 eDNA samples from 14 locations: six on the main Mangde Chhu channel and eight in surrounding tributaries.

With these water samples, the scientists hoped to shed light on Bhutan’s cryptic fauna, including some mammals, reptiles, fishes, and amphibians around the sample sites.

Given the novelty of this methodology, the researchers had a lot of groundwork to cover.

Determining taxonomic diversity

First, the team determined which animals were present and to what extent they could be taxonomically classified by comparing the DNA strands extracted from the samples to ones in an existing reference database. To do so, they sequenced the collected DNA and, from their results, determined to what taxonomic level the sequence could be assigned (be it species, genus, or higher). From this analysis, the scientists were able to identify 325 unique taxa: 131 mammals, 119 birds, 52 fish, 20 amphibians, and 3 reptiles.

Fish, frogs, and snow leopards: Species detection with eDNA

Second, the researchers sought to find out if eDNA extraction could reliably illuminate specific species of interest. To do so, they analyzed the differences in species recovered from different water sample types.

From this analysis, the scientists determined that samples from running water---such as rivers and tributaries---yielded four times more species than those from stagnant water---such as ponds---suggesting that sampling running water is more efficient.

Despite challenges presented by an incomplete reference database, the scientists successfully identified a total of 134 species: 16 fishes (26% of species known in the study area), 7 amphibians (35%), 51 birds (7%), and 60 mammals (39%). Of these 134 species, 33 of them are on the IUCN Red List.

So what?: Unlocking potential uses for eDNA

The success of the team’s study offers a host of new conservation opportunities for Bhutan. While some challenges remain in eDNA studies, they can be resolved with targeted research around eDNA such as beefing up reference databases. The cost effectiveness, noninvasive nature, and ability of eDNA sampling to detect elusive and rare species positions it as a prime tool for conservation researchers.

Complementary methods: eDNA and camera traps for biodiversity monitoring

Lastly, to understand how eDNA could complement traditional survey methods, scientists compared species detected via eDNA analysis to those captured by camera traps to assess how eDNA methods could complement current survey techniques. Their comparison focused on land mammals, including carnivores, ungulates, and smaller mammals like rodents and bats.

Results showed a positive correlation between eDNA sample reads and camera trap detections, particularly strong for ungulates. Both methods detected similar species, though each had its strengths and limitations: eDNA sampling identified some species missed by cameras, notably the Indian hog deer (Axis porcinus), while cameras captured some species not detected by eDNA. Encouragingly, eDNA analysis revealed the presence of seven carnivore species, including the Asian black bear (Ursus thibetanus), leopard cat (Prionailurus bengalensis), and tiger (Panthera tigris).

These findings suggest that eDNA and camera traps can complement each other, providing a more comprehensive picture of an area's biodiversity. This complementary approach is particularly valuable for monitoring elusive species like tigers.

Bhutan currently conducts tiger population surveys every four to five years using camera traps. However, this method can be expensive and may not provide a complete picture of the ecosystem’s richness. Integrating eDNA sampling with camera trapping offers a unique opportunity to enhance tiger monitoring efforts.

eDNA sampling presents several advantages for tiger monitoring:

  1. Cost-effectiveness: eDNA can detect a wide range of species more economically than camera trapping, allowing for broader coverage in Bhutan's vast landscapes.
  2. Preliminary distribution mapping: eDNA data can help create initial species distribution maps, including for elusive tigers, guiding the optimal placement of camera traps.
  3. Increased survey frequency: The cost efficiency of eDNA could enable annual surveys, providing more regular data on tiger range expansion or contraction.
  4. Comprehensive ecosystem assessment: Unlike camera traps, eDNA can identify a diverse array of organisms, including fish, amphibians, birds, invertebrates, plants, fungi, and bacteria, offering insights into the overall health of tiger habitats.
  5. Environmental change monitoring: Regular eDNA surveys can help track the impacts of habitat destruction and climate change on tiger landscapes.

By combining eDNA sampling with strategic camera trap placement, Bhutan can develop a more robust and efficient tiger monitoring program. This integrated approach not only enhances our understanding of tiger populations but also provides valuable data on the complex ecosystems that support these magnificent predators.

Bhutan’s biodiversity: The potential to perform a national survey

Perhaps the most exciting potential use of eDNA sampling is for a national survey of Bhutan’s biodiversity. Assessing all of Bhutan’s wildlife from every ecosystem—be it forest, freshwater, alpine, or even subterranean—is an essential step in planning effective conservation strategies. This type of survey would reveal the country’s biodiversity hotspots, areas where biodiversity is extremely concentrated and therefore protection is essential. These surveys could also measure the effects of changes on ecosystems from challenges like climate change, invasive species, or land use.

What’s next?: Study takeaways

All things considered, the study was a huge success. The researchers proved eDNA can produce reliable, quick, cost-efficient, and noninvasive biodiversity inventories. And in doing so, they completed Bhutan’s first and most comprehensive biodiversity inventory in record time.

And so, they had it: the secrets of the Himalayas. Slowly, they unraveled themselves, extracted from the river waters that carry the microscopic sluff from snow leopards, tigers, and musk deer; the degraded DNA of red pandas, white-bellied herons, and golden mahseer; the tiny, precious fragments that reveal the colorful world of biodiversity in Bhutan.

Now, the real work begins.