Environmental DNA & Barcodes (DP IB Biology)

Environmental DNA & Barcodes

DNA barcodes

• A DNA barcode is a DNA sequence that can be used to quickly identify a species

  • DNA barcodes are short sequences, usually just a few hundred base pairs in length

  • The base sequences that are used for barcodes are often taken from mitochondrial DNA in eukaryotes, and ribosomal RNA in prokaryotes

Environmental DNA (eDNA)

• DNA barcodes can be used to determine which species are present in a particular habitat; this can be necessary for various reasons, e.g:

  • For researchers investigating the biodiversity of different habitats

  • Predicting the impact of development on an area of land

  • Assessing the impact of land use change

• Using eDNA to identify species can be much quicker than observing and manually identifying organisms

  • Plants can be difficult to identify if they are not in flower, or have no leaves

  • Some insect larvae may be very similar in appearance

  • It may not be possible to physically capture all of the species that are present

• The process of extracting DNA from a habitat is known as eDNA sampling

• eDNA sampling can be used to identify species present in a habitat as follows:

  1. Multiple eDNA samples are taken from the habitat of interest, e.g. water samples from a body of water, or soil samples from a terrestrial habitat

     • Traces left by the organisms will be present in the samples, e.g:

       • Cells that have brushed off an animal's skin

       • Fur or feathers lost by mammals or birds

       • Waste that has been released into the environment

       • Leaves that have fallen to the ground and partially broken down

  2. DNA in the samples is amplified using PCR

  3. The amplified DNA is sequenced to determine the order of bases present

  4. The specific sequence within the DNA that forms the barcode is compared to a database of known sequences

     • DNA sequencing technology means that the DNA sequences of many species are now known, and are stored in easily accessible databases

     • E.g. the Barcode of Life Data System (BOLD)

  5. A strong match with a known sequence means that researchers can confidently say that a species is present at a sample site

  6. A less-strong match may mean that further sampling is required

Environmental DNA sampling diagram

eDNA samples can be amplified and sequenced, and then compared to a database of known sequences to allow identification of unknown species present in an environment