What is eDNA?
Biodiversity (biological diversity), a wide range of animals, plants, and microorganisms, is crucial for supporting life on Earth at different levels. The health of socio-ecological systems, and ecosystems as a whole, depends on this factor, for example, in ensuring food security, fighting diseases, supporting communities, cultural life, and the sustainability of wildlife itself.
Due to climate change and other human-induced threats, biodiversity is now endangered and in need of careful management and protection. However, today we have only a simple understanding of how ecosystems and biodiversity respond to different stressors and need to be studied more closely. For that, surveys are developed in different ecosystems, traditionally involving the physical observation (what the eye can see) of the species that are being looked for. But this methodology can have some limitations (microorganisms are not visible) and may have negative effects. But, there is an alternative to this: environmental DNA (eDNA).
When an organism, for example, an octopus, moves through the environment, it leaves behind some bits of itself, just as a fingerprint on the sand. The traces that an organism leaves can be dead skin cells, mucus, faeces, and hair, which all contain the DNA of the organism. This is what is called environmental DNA, or eDNA for short, and allows scientists to detect that these organisms were there.
Molecular methods refer to scientific techniques that involve the analysis and manipulation of molecules, particularly focusing on DNA. The DNA is read using DNA sequencing that “reads” the DNA code. DNA is unique to every organism out there and thus allows us to see the DNA fingerprint of all the organisms that passed through the water.
eDNA, like a silent detective, unveils a hidden world. It’s the key to discovering small invertebrates and microorganisms, often overlooked due to their size, but that play pivotal roles in their ecosystems, which is why the traditional methods, such as physical observation, might be limiting when studying biodiversity.
Why is eDNA important?
As mentioned before, monitoring biodiversity is important due to the effect it has on ecosystems. For example, if a species lacks or changes in a certain environment, it can affect the whole dynamics of an ecosystem.
eDNA can identify species that are not visible to the naked eye, but that can be crucial to an ecosystem, for example, algae or phytoplankton in aquatic environments; therefore, for small, rare, secretive, and other species that are difficult to detect, eDNA provides an attractive alternative. Therefore, applying eDNA methodologies is important for biodiversity surveying.
How is eDNA sampled?
Sampling environmental DNA (eDNA) is like taking a genetic snapshot of the environment. It all starts with the collection of a sample of the environment a scientist wants to study, for example, a lake. Once the scientist has the sample, it can be either analysed in place or back in the laboratory. The next step is the use of a filter to separate the genetic material (DNA) from the rest of what is in the sample. It’s like using a sieve to catch tiny pieces. After the DNA is preserved in a special container to keep it safe for analysis, and finally in the laboratory, the DNA is analysed to learn about the species present in the sampled environment. The result is like looking at a DNA puzzle to see which pieces (organisms) are there.
Different methodologies exist out there concerning the analysis of eDNA, notably in aquatic environments there even exists the possibility to do it without the filtering or to use innovative sampling tools such as the Metaprobe, a nimble, low-cost environmental DNA sampler for upscaling aquatic monitoring based on a hollow perforated spherical probe that when filled with rolls of gauze is used as a low-cost and low-effort eDNA sampler in aquatic environments.
What are DNA-based reference libraries/repositories?
Once the DNA puzzle is in the hands of the scientist is time to compare the available information about DNA, which means looking at a big book filled with genetic information to identify the species that are in the sample. This big book is called a reference library or reference repository, and there are different ones, usually dedicated to particular groups of species.
The reference library/repository is organized and made available to everyone, like a library anyone can visit. Scientists, researchers, and curious people can use it to identify and learn about different species. When scientists find unknown eDNA in a water sample, for example, they can look it up in this big book (library/repository) to figure out which species it belongs to. It’s like solving a mystery by checking the genetic code.
DNA-based libraries/repositories are the cornerstones since they are the key to knowing which species are present. Without them, scientists would not be able to identify which species are out there. Our ability to use DNA today is limited by how many known species we have in the reference libraries. If there is no reference, a sequence will be labelled as unknown. It is therefore crucial to have very complete and standardised references to ensure we can use DNA as an effective tool to study, understand, and preserve our natural environment.