Environmental DNA (eDNA) barcoding identifies species by collecting DNA that organisms leave in an environment, sequencing selected DNA regions and comparing those sequences with a reference database. This is Additional Higher Level (AHL) content in A3.1 Diversity of organisms.
Organisms release DNA into water, soil or air through skin cells, mucus, faeces, gametes, hair and decomposing tissue. A sample can therefore provide evidence that a species is present without the organism being captured or directly observed.
| Stage | What happens |
|---|---|
| Environmental sampling | Water, soil or another environmental material is collected. Multiple samples improve reliability because eDNA may be unevenly distributed. |
| DNA extraction | DNA fragments are separated from the environmental sample. Strict contamination controls are required because very small amounts of foreign DNA can produce false results. |
| Amplification | Polymerase chain reaction (PCR) uses primers to amplify a selected barcode region. For a mixed sample, primers may amplify DNA from many species. |
| Sequencing | The base sequences of the amplified DNA fragments are determined. |
| Database comparison | Sequences are compared with reference barcodes from identified organisms. A close match provides evidence for the species or taxonomic group present. |
A DNA barcode is a relatively short, standardized DNA sequence that varies sufficiently between species to support identification but is similar within members of the same species. When many barcode sequences from a mixed environmental sample are analysed together, the process is often called eDNA metabarcoding.
A common misconception is that eDNA barcoding counts organisms directly. It usually provides evidence of presence, not an exact population size: DNA may persist after an organism leaves or dies, and the amount released differs among species and environmental conditions. Identification also depends on the completeness and accuracy of the reference database.
Exam technique: For an “outline” question, give the sequence sample → extract DNA → PCR → sequence → compare with a database → identify species. For “evaluate,” add benefits such as rapid, non-invasive biodiversity surveys and limitations such as contamination, DNA degradation and incomplete reference databases.