Environmental DNA (eDNA)
Applications, Workflow and the Role of NGS
Key Takeaways
Summary
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Every organism leaves a genetic fingerprint in its environment. Environmental DNA (eDNA) is transforming how we monitor biodiversity, detect invasive species, and protect ecosystems at planetary scale. Combined with the speed and scale of modern next-generation sequencing (NGS), it is one of the most significant methodological advances in ecology and conservation science of the past two decades.
What Is Environmental DNA?
Every living organism continuously sheds genetic material into its surroundings. Fish release DNA through mucus and scales into the water column; soil invertebrates leave traces through faeces and decomposing tissue; plants disperse pollen carrying their full genomic signature. This shed material — collected from the environment rather than from the organism itself — is what scientists call environmental DNA, or eDNA.
The concept is not new. Microbial ecologists have been extracting and analysing DNA from soil and water for decades. What has changed is the resolution and scale at which we can work. The dramatic fall in sequencing costs since the early 2010s means a single water sample can now be screened against databases of millions of reference sequences, identifying not just one target species but entire biological communities simultaneously.
eDNA degrades over time under the influence of UV radiation, temperature, microbial activity, and pH. In most freshwater systems, detectable eDNA persists for between 24 hours and a few weeks — meaning a positive detection reflects genuinely recent biological presence. eDNA can be collected from:
Aquatic environments
Rivers, lakes, estuaries, and marine systems, where DNA is shed continuously via mucus, faeces, urine, gametes, and cells
Soil and sediment
Rich in microbial and fungal eDNA; also used for terrestrial vertebrate detection and agricultural pathogen surveillance
Air
Pollen, fungal spores, and fine aerosols carry eDNA detectable via filtration; an emerging frontier for allergen monitoring and biosecurity
Ice and permafrost
Ancient eDNA preserved in ice cores can reconstruct past ecosystems, offering a palaeogenomic archive through time
The eDNA Workflow: From Field to Result
An eDNA study involves five conceptually distinct phases, each with its own quality controls. The sequencing platform selected in phase four directly determines the throughput, cost, and taxonomic resolution of the final data.
- ✓ Step 1 — Sample Collection: Water samples (typically 1–5 litres) collected using sterile containers or peristaltic pumps. Strict contamination protocols are essential: field blanks, gloves, and equipment decontamination between sites. Soil cores, air filters, or sediment grabs are used for terrestrial applications.
- ✓ Step 2 — Filtration and DNA Extraction: Water is filtered through membranes to capture cells and DNA. Filters are preserved in lysis buffer or liquid nitrogen. DNA is extracted using commercial kits optimised for environmental samples, eluted in low-EDTA TE buffer to preserve integrity.
- ✓ Step 3 — Library Preparation: Target gene amplicons are amplified by PCR with dual-indexed, barcoded primers. MGI's MGIEasy Universal DNA Library Prep Set and MGIEasy Fast FS Library Prep Set V2.0 are validated for low-input environmental DNA.
- ✓ Step 4 — NGS Sequencing: Pooled libraries are sequenced on an NGS platform, generating tens to hundreds of millions of reads per run — enabling large sample cohorts at a cost per read orders of magnitude lower than first-generation Sanger sequencing.
- ✓ Step 5 — Bioinformatics and Reporting: Raw reads are quality-filtered, primers trimmed, and assembled. Taxonomy is assigned against curated reference databases. Results feed into biodiversity indices, species occurrence matrices, or statutory regulatory reports.
Technologies for eDNA Analysis
The choice of analytical method depends on the biological question, required resolution, and budget. Four major approaches are in active use.
| Approach | Best For |
|---|---|
| NGS — High Throughput | Large sample cohorts at low cost per read; backbone of metabarcoding and metagenomics workflows. |
| Metabarcoding | Community-level surveys recovering hundreds of taxa simultaneously from a single environmental sample. |
| Shotgun Metagenomics | Full taxonomic, functional, and phylogenetic resolution including unculturable microbes and rare species missed by amplicon approaches. |
| qPCR / ddPCR | Single-species detection with high sensitivity — invasive species surveillance, pathogen monitoring, and critically endangered species presence/absence confirmation. |
Key Applications and Impact Areas
Biodiversity monitoring and assessment
Traditional biosurveys — electrofishing, kick-sampling, transect counts — are labour-intensive, seasonal, and observer-dependent. eDNA metabarcoding can survey entire aquatic communities from a morning’s sampling effort, with data reproducible across laboratories and comparable across years. For national park agencies, water utilities, and conservation organisations managing hundreds of sites, this scalability is transformative.
Invasive species early detection
eDNA can detect invasive species from environmental samples weeks before visual sighting becomes possible, when population densities are still low enough for management intervention to be effective. The US Geological Survey has deployed eDNA surveillance across the Great Lakes basin for Asian carp since 2009; European programmes are applying the same principle to signal crayfish, quagga mussel, and topmouth gudgeon.
Endangered and protected species monitoring
For species where disturbance itself is a conservation risk — cryptic amphibians, nocturnal mammals, deep-sea fish — eDNA allows presence/absence confirmation without trapping, handling, or habitat disruption. This is particularly valuable in legally protected areas where survey licences are difficult to obtain, or in habitats that are physically inaccessible.
Regulatory and statutory bioassessment
Regulatory adoption is accelerating. eDNA-based assessment of fish communities is now accepted under several national implementations of the EU Water Framework Directive. Environmental consultancies routinely include eDNA surveys in Environmental Impact Assessments for infrastructure, dredging, and development projects. Standardisation bodies including CEN and ISO are actively developing formal eDNA protocols.
Wastewater and pathogen surveillance
The COVID-19 pandemic demonstrated that wastewater eDNA surveillance can provide population-level epidemiological signals days before clinical case reporting — a capability now being extended to influenza, antimicrobial resistance genes, and enteric pathogens. The same analytical infrastructure used for biodiversity surveys can be repurposed for public health monitoring.
Published 1 June 2026
References
- Bohmann et al. (2014). Environmental DNA for wildlife biology and biodiversity monitoring. Trends in Ecology & Evolution, 29(6), 358–367.
- Callahan et al. (2016). DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods, 13(7), 581–583.
- Deiner et al. (2017). Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Molecular Ecology, 26(21), 5872–5895.
- Ficetola et al. (2008). Species detection using environmental DNA from water samples. Biology Letters, 4(4), 423–425.
- Medema et al. (2020). Presence of SARS-CoV-2 RNA in sewage and correlation with reported COVID-19 prevalence. Environmental Science & Technology Letters, 7(7), 511–516.
- Metzker, M. L. (2010). Sequencing technologies — The next generation. Nature Reviews Genetics, 11(1), 31–46.
- Taberlet et al. (2012). Environmental DNA. Molecular Ecology, 21(8), 1789–1793.
- Thomsen & Willerslev (2015). Environmental DNA — An emerging tool in conservation for monitoring past and present biodiversity. Biological Conservation, 183, 4–18.
- U.S. Geological Survey. Environmental DNA (eDNA) surveillance for Asian carp.
- European Commission. Water Framework Directive (WFD).
- World Health Organization (2022). Environmental surveillance for SARS-CoV-2 to complement public health surveillance.
