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Environmental DNA (eDNA) is DNA that is collected from an environmental sample, rather than an individual organism. Animals leave traces of their DNA in the environment through their feces, urine, skin or hair cells lost. This DNA can be collected in environmental samples (soil, seawater, sediment etc.) to get information on what species are recently present in the area. The analysis of collected eDNA is called Metagenomics. Scientists are able to analyze the DNA present by high-throughput DNA sequencing. The entire eDNA sample is usually sequenced by Shotgun sequencing or PCR directed sequencing. Information from the DNA sequences is then used to conduct a large scale, biodiversity survey on all of the animals that have been in the area without having to directly interact with the actual organisms. Collecting eDNA is a replacement to other surveying methods such as trapping and visual wildlife surveys.

Pros of Collecting eDNA

Some of the pros of collecting eDNA as a surveying method include;

• High Species Detection Rate - Species that are elusive or live in a low density, can be detected by eDNA analysis of areas they have recently been. Collecting eDNA can detect animals in an area that other surveying methods could not catch or observe. This is because the animal does not need to be present in order to detect it's presence in the ecosystem. If the animal has left behind a DNA sample, then it will be detected after DNA sequencing. eDNA analysis can also detect smaller organisms such as microbes, that are too small to detect visually.
• Accurate - Many species have different taxonomic groups that can be hard to differentiate between through only visual observation. eDNA collection provides the DNA of the organisms in the area, which is analyzed with species specific primers to determine individual species identification.
• Very Low Disturbance - No organisms need to be trapped or directly interfered with in order for their DNA to be collected. As a result someone could gather DNA samples of various species without any disturbance to the organisms. This helps protect the health of the organism and the ecosystem as a whole.

eDNA Collection Techniques

Although environmental DNA can be obtained from many different types of samples, using water samples is the most common and effective. Water samples can be analyzed to detect a specific species or to create a list of all species present.

Collecting water samples is the most common way to gather eDNA.

Specific Species Detection

For detection of a single species, first a water sample of the body of water in question is required. Usually there will be a very small amount of eDNA present so PCR amplification is done to create more copies of the DNA. Then primers that specifically anneal to the DNA sequence of the targeted species are used. A positive binding would create a separate bar in a gel once the results are viewed.

Multi-Species Detection

Analysis of eDNA in a water sample can determine all species that have recently been in the area. A universal primer is used in PCR amplification to increase the copies of DNA. Then Next-generation sequencing is conducted, and the sequences are checked with a reference database to establish a list of every species present.