Discovering Biodiversity Without Disturbance

Environmental DNA, or eDNA, is the genetic material that organisms release into the environment. Environmental DNA is collected from various environmental samples such as soil, water, snow or even air, rather than taken directly from an individual organism.

In short, eDNA is an accurate, sensitive and non-invasive biodiversity data collection method used to identify what types of organisms are or have recently been present in selected ecosystem samples, as well as to monitor and assess invasive species that may be altering or affecting natural ecosystems.

As technology advances, the applications of environmental DNA in the study and protection of nature are also evolving. It is now possible to obtain even three times as many species as would be detected with traditional methods.

Nerd fact: eDNA is a method that has even been used to confirm or demystify peculiar cases, such as the mysterious and legendary Loch Ness Monster, whose analysis of more than 250 water samples from around, in the center and in the depths of the loch, showed that it was not a “monster” but a considerable number of eels.

Our Data team conducted a pilot test of eDNA samples from Parque Oncol, located in Valdivia, Chile, together with the team of Ecogen, a startup that develops technology-based research using environmental DNA to generate monitoring and evaluation plans of natural resources, in order to understand, preserve and restore a part of Chile’s biodiversity.

Here’s what we’ve found.

How do you get eDNA?

Easy pie. The sample is extracted with a syringe that subtracts information from the water or soil. Then the DNA is subtracted and “washed” with isopropanol and ethanol so that it becomes visible.

Briefly, these steps are followed:

• Environmental sample collector
• DNA extraction
• DNA amplification using universal partitioners and gene library generation
• Massive high-throughput sequencing
• Bioinformatics analysis
• Species listing and obtaining amplification sequence variants
• Ecological Analysis

Environmental DNA has the potential to open up exciting and creative ways to learn about and help protect the wildlife around us. Here we tell you more about the pilot test we conducted at Parque Oncol and what we discovered in the samples.

Parque Oncol: Why is it important to have information about its biodiversity?

Parque Oncol is a protected wilderness area of 754 hectares located 28 km from Valdivia, Chile, and is an ancient area of high biological value due to its function as an interglacial climatic refuge -since it did not freeze, some of the species that remained here populated the rest of the territory-. This was our site of choice for our pilot test for 3 main reasons:

3 reasons why we took eDNA samples at Parque Oncol

• Oncol is part of the Valdivian Rainforest. A unique, one-of-its-kind ecosystem. It’s an evergreen and mixed rainforest, somehow similar to a tropical forest, but located in a temperate region.
• Oncol is home to 3 different types of forests: 1) Tepu or Tepual forest 2) Tepa-Tineo-Mañío Forest. 3) Renovales de Canelo (young forest)
• In Oncol there are more than 28 species of ferns, 9 species of amphibians and a diversity of birds, such as the Rayadito, Picaflor, Carpintero Grande, among many others. It is also the habitat of endemic mammals such as the recently discovered opossum, the puma, the pudú and the fox.

With regard to climate change and possible biological invasions, having a good baseline makes it possible to monitor what is happening in the park and to understand what elements are pressuring the ecosystem, in order to take action through public and private policies according to the results obtained. Thanks to that we can understand, protect, and even restore native biodiversity in the area.

Lemu & Ecogen: eDNA results in Parque Oncol

Through an exploratory analysis of remote environments within the park, close to camera traps for more representativeness, 0.25 mg of the selected samples were studied, being also the first time we tested this method in a conservation area.

The results indicated the presence of 732 species, including fungi, invertebrates, amphibians, fish, birds, and mammals: 727 native species and 5 introduced species, (Fish: Oncorhynchus mykiss (Rainbow trout), Salmon trutta (Trout), Cyprinus carpio (Common carp). Mammals Bos taurus (Cow), Ovis aries (Sheep), Sus scrofa (Pig) and Rattus norvegicus (Norway rat).

The overall species distribution was as follows:

• 597 fungal species: The most prominent were ascomycota, basidiobolomycota, basidiomycota, chytridiomycota and mortierellomycota.
• 105 invertebrate species: The most prominent were Annelida, Arthropoda, Tardigrada, and Nematoda.
• 11 species of amphibians: Among them were Alsodes gargola, Eupsophus emiliopugini and batrachyla leptopus.
• 8 species of fish: Among them were Salmo trutta, brachygalaxias bullocki and oncorhynchus mykiss.
• 4 species of birds: Among them were Thraupidae and Passeriformes.
• 7 species of mammals: Among them were Pudu puda, Leopardus guigna and Bos taurus.

The groups with the highest diversity were fungi in soil samples, while amphibians were found in water samples.

As for amphibians, 4 species that had never been recorded before in Parque Oncol were found: 2 of them qualify as wide distribution, which means that their habitat extends over a wider territory than previously stipulated.

The genetic results of the amphibians are still preliminary and must continue to be analyzed, since the taxonomic definition of the genus Alsodes (to which 3 of the 4 species found belong) is complex. Nevertheless, these are some data worth highlighting:

• Alsodes gargola, is a species described for Argentina mainly, but in 2012 they determined that 2 specimens collected near Futaleufú corresponded to A.garlola, so this record may be among the first for the species in Chile.
• Alsodes tumultosus (La Parva spiny-breasted toad), known only from its type locality, La Parva. Our analysis represents an enormous extent of its distribution.
• Alsodes verrucosus (Warty spiny-breasted toad). The only records in Chile correspond to the Type that Philippi in 1902, in the province of Cautín, and later in Wellington Island (in 1988) a specimen that is lost. The species is described for Argentina.
• Eupsophus emiliopugini (*Green-eyed leaf-frog). Its distribution extends from Puyehue in the province of Osorno, to the province of Aysén. Therefore, this record would be an extension of its distribution to the north.

The results show that the park offers a rich reservoir of diversity in fungi, invertebrates and amphibians, fish, birds and mammals. These results are striking and call for more intensive field surveys both for genetic sampling and for finding live specimens.

Despite the good news regarding native species, we had the unfortunate surprise of having found many invasive fish species. It is not only worrying because they have been introduced by humans, but also because of their adaptability and high efficiency as predators, which is killing the smaller native species.

Likewise, the presence of amphibians — whose distribution had not been contemplated in that area, surprises us and urges us to continue investigating the habitat and the relationship of these species with their environment.

Conclusions

Thanks to eDNA we can go deeper into the ecosystems and continue exploring biodiversity in order to understand and preserve it.

Undoubtedly, what the human eye perceives falls short of what the DNA sampling is able to capture, which is s pleasant surprise.

EDNA is a non-invasive method that allows us to better understand our ecosystems and even discover relationships between the environment and species, which are always changing and constantly evolving. Given its importance in conservation and environmental restoration, we will continue to invest time and resources and will give more advances of the next eDNA tests.

Let’s not waste nature’s unique potential. Let’s take care of it as the treasure it is.

If you want to know more details about our eDNA sampling pilot, feel free to send an email to hello@le.mu and we will be glad to answer your questions.