Environmental DNA and its Bioinformatics Component

By: Anurag Jakkula


When organisms move through their habitats, vital and powerful information is left behind. This information can tell us the organism’s past, present, and future. This highly valuable data comes in the form of environmental DNA or eDNA. Environmental DNA has a bright, influential future in the fields of environmental science, paleontology, agriculture, public health, and ecology.


Environmental DNA’s scope has been proven several times with huge breakthroughs in science and conservation. First off, environmental DNA allows humans to study animal species in the least invasive way possible. In a particular study, 93 days of electrofishing effort was put into finding a single specimen of a rare species of fish. However, it only took 4 hours to detect a specimen with the help of eDNA. Recently, the Wildlife Conservation Society used eDNA to discover the fourth known living Rafetus Swinhoei. The Rafetus Swinhoei is the world’s rarest turtle.


Environmental DNA is also a huge component of environmental conservation. Conservationists don’t need to disturb nature in order to help it anymore. Using eDNA, conservationists can determine the growth and decline in animal populations without having to trap and tag animals. This can be done by measuring the quantity of DNA, relative to the organism’s rate of DNA shedding and environment. Furthermore, the abundance of invasive species can be measured in the same way.


Environmental DNA is also used to protect human health. The U.S. Department of the Interior uses eDNA to monitor indicators of contamination, such as Coliforms, escherichia coli, and enterococci in water. Environmental DNA samples from water systems have allowed for the more fine detection of the pathogen, legionella. legionella causes severe illness in the elderly. Various organizations in Michigan use eDNA testing to detect schistosomes in the state’s lakes. Schistosomes burrow into the skin to cause swimmer’s itch.


There is no question about eDNA playing a vital role in many novel efforts. However, advanced bioinformatics algorithms are necessary to sequence and evaluate eDNA. For instance, organisms shed DNA at varying rates, which affects relative abundance. Also, environmental DNA is prone to degradation from temperature and other factors. Bioinformatics, being a field with wide application, plays a role of importance in the field of environmental science. Here at the Helyx Initiative, the motto is “Bioinformatics education for all.” A spot-on motto indeed!


Citations:

https://www.nature.com/articles/s42003-019-0330-9

https://biomeme.com/environmental-dna/

https://www.illumina.com/techniques/sequencing/dna-sequencing/targeted-resequencing/environmental-dna.html


Images:

https://pixabay.com/images/id-3325080/

https://pixabay.com/images/id-67659/

https://pixabay.com/images/id-5921814/



What did you learn?

1. How is eDNA used to non-invasively calculate the abundance of organisms?

The abundance of the organism’s eDNA is measured. Then, this calculation is measured up against the organism’s rate of DNA shedding environmental factors. From this, the number of a certain species in an area can be determined.


2. What role does bioinformatics play in environmental DNA?

To put it simply, bioinformatics turns eDNA into useful, valuable data. First, bioinformatics is necessary to sequence eDNA. Bioinformatics algorithms are also necessary to calculate relativity, with regards to environmental factors, species type, and geography.


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