eDNA Metabarcoding
Also known as: eDNA, metabarcoding, DNA metabarcoding, genetic monitoring
Environmental DNA (eDNA) metabarcoding detects and identifies species present in environmental samples (water, soil, air) by sequencing short DNA fragments released by organisms. Developed by Taberlet and colleagues (2012), this approach has revolutionized biodiversity monitoring: species can be surveyed without capture, observation, or complex sampling designs. Metabarcoding sequences millions of DNA fragments, identifies reads taxonomically, and assigns them to species. The method is non-invasive, rapid, and cost-effective, enabling large-scale biodiversity surveys and early detection of cryptic or rare species.
Key highlights
- Non-invasive and non-lethal: no capture or killing of organisms required
- Detects rare, cryptic, or early-life-stage organisms: any species that sheds DNA in the sample
- Rapid and cost-effective compared to traditional surveys, enabling large-scale sampling
- Unbiased in principle: detection does not depend on observer or sampling technique skill
- Can quantify relative abundance (if standardized carefully) or presence-absence
Intuition
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How it works
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When to use it
Use eDNA metabarcoding for non-invasive biodiversity surveys, early detection of invasive or rare species, assessment of community change, or monitoring of microhabitats. Ideal for cryptic, small, or aquatic species difficult to survey directly. Requires well-curated reference sequences for accurate taxonomic assignment.
Strengths & limitations
- Non-invasive and non-lethal: no capture or killing of organisms required
- Detects rare, cryptic, or early-life-stage organisms: any species that sheds DNA in the sample
- Rapid and cost-effective compared to traditional surveys, enabling large-scale sampling
- Unbiased in principle: detection does not depend on observer or sampling technique skill
- Can quantify relative abundance (if standardized carefully) or presence-absence
- Taxonomic accuracy depends on reference database quality; unsequenced species cannot be identified
- Does not provide spatial or behavioral information; eDNA does not reveal where organisms are or what they are doing
- Environmental DNA degrades rapidly; detection time window is limited (days to weeks for most organisms)
- Cannot distinguish live from dead organisms or viable from non-viable propagules; nucleic acids persist after death
- Quantification is difficult and relative (reads) rather than absolute (individuals or biomass)
Common pitfalls
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Applications
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Frequently asked
How long does eDNA persist in the environment?
This depends on environmental conditions. In water, eDNA typically persists for days to weeks; temperature, pH, UV exposure, and microbial degradation accelerate decay. In soil or sediment, eDNA persists longer (months to years). Document environmental conditions and validate persistence times for your study system using degradation experiments.
Can I use eDNA to estimate population abundance?
Not directly. eDNA read abundance is biased by many factors (PCR efficiency, primer binding, copy number, degradation, contamination). Relative abundance (comparing read proportions) is possible with careful standardization. For absolute abundance, combine eDNA with capture-mark-recapture or other density estimation methods.
What is the difference between OTU and ASV?
OTUs (operational taxonomic units) cluster reads at fixed similarity threshold (97%), which obscures sequence differences. ASVs (amplicon sequence variants) are exact sequence variants, each differing by one nucleotide. ASVs provide better resolution but assume errors have been corrected. Modern practice favors ASVs, but both are used depending on question and data quality.
Sources
- 1.Taberlet, P., Coissac, E., Hajibabaei, M., & Rieseberg, L. H. (2012). Environmental DNA. Molecular Ecology, 21(8), 1789-1793.
- 2.Deakin, G., Pettitt-Wade, H., & Waldick, R. C. (2016). Environmental DNA metabarcoding: A review of the application to fish biodiversity assessment in temperate freshwaters. Environmental DNA, 1(1), 4-14.
- 3.Ficetola, G. F., Miaud, C., Pompanon, F., & Taberlet, P. (2008). Species detection using environmental DNA from water samples. Biology Letters, 4(4), 423-425.
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Cite this page
ScholarGate. (2026, June 3). eDNA Metabarcoding. ScholarGate. https://scholargate.app/ecology/edna-metabarcoding