e-dna is short for environmental DNA, and as the name already indicates, e-dna is genetic material of organisms found in the environment. Multiple applications of eDNA are of increasing importance, especially in the field of ecology. E-dna is used to monitor species in a habitat of interest. To explain what e-dna is, an aquatic environment is taken as an example. Organisms living in it, like this fish, constantly lose genetic material, which is found in excrements or shed skin cells, and those contain DNA. This form of DNA from organisms found in the environment is referred to as e-dna. But what is eDNA used for? To determine which species are living in an environment like the sea, one would have to either catch those individuals to identify and count them, or one would have to identify them with other monitoring systems. Especially in a complex ecosystem such as the ocean, fishing can be considered invasive and laborious, and video surveillance systems may be extremely expensive. Besides those more classical monitoring methods, eDNA provides an additional layer of information.

some advantages since e-dna is present in the environment for about two weeks. It is possible to detect rare species, which might not have been caught in nets or fishing boats. How can such information be gained from eDNA? In the first step, the water sample is collected. From this sample, the DNA is extracted. The water sample contains eDNA from different organisms. However, at this moment, the species of origin of those DNA fragments are not known. In case one wants to determine the species composition in an environment, the next step usually involves metabarcoding. For simplicity, this example does not show the entire genome but a short sequence. A specific genetic marker needs to be amplified from the extracted DNA using PCR. To make sure that all animals can later be detected, the eDNA of all animals has to be amplified. A critical step is to select universal primers that bind to all animal DNA. Target genes for the primer design have to be highly conserved. A sequence with an extremely high degree of similarity among different species is often found in mitochondrial genes. Those primers bind

to the same sequence of animal edna. The primers have additional overhangs, which are used for the library preparation and the sequencing step later. But the details about this will not be covered in this video. Check out the indicated video here for more information about that. In brief, DNA fragments of various organisms are amplified in high quantity. And after millions of amplicons have been generated with PCR, those reads can be sequenced with an Illumina instrument at ease. After some data processing, including different bioinformatics steps such as the removal of primers and unwanted reads, the species can be classified using a database with reference sequences. At this step, it is very important to have a reference database of good quality. That is, it contains sequences from a large spectrum of animals. Those genome databases help to distinguish which species are present in the environment from which the eDNA was collected from. In those conserved gene regions, only single nucleotides may differ between the species. And each are like a fingerprint that allows species identification. Even though eDNA is a great tool for

ecologists. There are, of course, limitations. One is that the primers used to amplify eDNA material need to be universal and bind to DNA from all target animals, but they need to be specific enough to exclude animals from outside the target group. If for one organism the primer binding sequence is different, the primer may not bind anymore, and the DNA of the respective species will not be amplified. This species will not be detected in the study, even if the organism was present in the environment. Further, it is hard to draw conclusions about the abundance or biomass of animals. Much eDNA from one species could indicate that this species is abundant, but it could also have various other explanations. One might be that a dead individual of a rare species may release elevated levels of eDNA. Quantification of eDNA data is still questionable at this moment, also especially for rare or even undiscovered species. Another limitation is that the databases do not have good reference sequences of those species. Species identification might also be difficult if the target sequence of one

species is so conserved that it is identical to that of another. In this case, two species cannot be distinguished. If you could take something home today and know what edna is, please like this video. Also, feel free to subscribe to this channel and check out this video here. Thanks for watching.

Biomonitoring using eDNA (environmental DNA)

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Biomonitoring using eDNA (environmental DNA)

Biomonitoring using eDNA (environmental DNA)

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