eDNA Sampling For Species Identification: 7 Examples

Environmental DNA (eDNA) sampling for species identification has revolutionized biodiversity monitoring by enabling highly accurate, cost-effective, non-invasive detection of organisms across aquatic, terrestrial, and atmospheric environments.

As biodiversity monitoring continues to evolve, eDNA sampling for species identification provides a transformative tool for researchers, conservationists, and environmental managers. By extracting genetic material from environmental samples such as water, soil, and air, eDNA metabarcoding and qPCR analysis can rapidly detect target species, assess community composition, and inform conservation interventions without direct organism handling.

At Cmbio, we support this evolving field through cutting-edge eDNA Metabarcoding Research and analysis.

This blog examines multiple applications, data points, and integration strategies across environments, answering the key questions: how do eDNA methods work, and how do they compare to traditional approaches in detection rates, accuracy, cost and time.

Aquatic eDNA Applications: Water Sample Species Detection

Water-based eDNA approaches rely on filtration of 1-2 liters using 0.7 μm glass fiber filters, capturing molecular traces from fish, invertebrates, and other aquatic taxa for qPCR and metabarcoding analysis targeting COI and 18S markers.

• Long Island Sound Case Study: In a benchmark comparison, 42 fish species were identified using eDNA sampling, far exceeding the counts from traditional trawl nets, which detected only 33 species. Sensitivity rates approached 82% for eDNA, confirming superior performance in complex estuarine ecologies.
• Spanish Rivers Comparative Survey: Across major Iberian river systems, eDNA sampling identified 22 species versus 19 by electrofishing, confirming a 77% higher sensitivity. Furthermore, 27.95% of total freshwater fish species were detected exclusively by eDNA analyses, completely missed in standard regulatory field efforts.
• Protocol Optimization: Standard sample volumes range from 1–2 L, enabling high-throughput detection while controlling for contamination. The use of targeted primers enhances detection of both dominant and rare fish, maximizing accuracy across different aquatic systems.
• Cost and Timeline Comparison: On average, eDNA studies report 33.4% lower project costs (when compared to electrofishing or net surveys) and can deliver survey results in as little as 2–4 weeks, supporting rapid management response.
• False Negatives: Built-in negative controls reduce risk of false positives, and advanced reference database assignment has further reduced false negatives compared to organismal surveys.

Marine Environment Fish Community Assessment

• Comprehensive Marine Surveys: Marine eDNA metabarcoding identifies 16 out of 17 species detected by trawl sampling, plus 55 additional native fish unique to the genetic protocol. Sediment eDNA assays reveal markedly different marine assemblages compared to water column samples, offering multidomain community detection in a single analysis round.
• Detection Sensitivity: Marine studies in coral and kelp ecosystems report eDNA sensitivity rates up to 94.1%, detecting rare sharks, rays, and cryptic reef fish not captured in conventional netting or visual dives.
• Processing Advantages: Marine eDNA protocols allow for longitudinal monitoring, uncovering both seasonal migratory patterns and stable resident populations, supporting long-term population management and conservation compliance.

Freshwater River and Lake Monitoring

• Multi-Seasonal Monitoring: In European river networks, 83.33% of monitored sites demonstrated significantly higher freshwater fish detection rates by eDNA compared to traditional electrofishing which is crucial for endangered, migratory, or nocturnal species. eDNA sampling for species identification avoids seasonal gaps and improves regulatory species lists.
• Data Integration: Advanced eDNA methods are used across lakes, reservoirs, and riverine catchments to quantify population abundance, migration cycles, and site-specific occupancy. Quantitative PCR results correlate with observed biomass for key indicator species, improving the reliability of ecological forecasting.
• Exclusive Species Detection: 27.95% of species were found solely by eDNA, outpacing conventional surveys, a priority for restoration or compliance programs.

Terrestrial eDNA Applications: Soil and Surface Sampling

• Wildlife Detection: Soil sampling protocols (bulk extraction, surface swabbing) have documented detection of 16 mammalian species across 94 independent UK survey sites, outperforming camera trap records, especially for small, elusive, or burrow-dwelling animals. 
• Species Richness: 60%+ of expected community diversity can be reliably identified in surface or subsurface soil analyses. Read depth for arboreal vs. non-arboreal mammals averaged 2466 vs. 289, underlining taxon-specific sensitivity.

Plant Species Identification Through Root Systems

• Year-Round Botanical Surveys: Plant-root eDNA sampling delivers full community surveys outside narrow flowering windows. Endangered taxa such as Sapria himalayana, often missed in seasonal visual surveys, were reliably detected in root and bulk soil DNA enabling managers to overcome limitations of traditional botanic methodology.
• Population Monitoring: Surface eDNA assays yield rapid detection of dozens to hundreds of plant taxa from small soil volumes, enabling effective restoration and compliance monitoring for land managers.

Airborne eDNA Applications: Atmospheric Species Sampling

• Airborne Species Capture: Passive and active air filtration (dust traps, cyclone filtration, Big Spring dust traps) have been shown to detect wind-pollinated and non-wind-pollinated plant taxa, including Bouteloua and Prosopis glandulosa, at distances up to several kilometers. DNA from terrestrial vertebrates and fungi is also captured, often with seasonal and geographic specificity.

Conservation and Management Applications

• Early Invasive Species Detection: Marinas, rivers, and estuaries have implemented early detection eDNA programs to identify non-indigenous and previously unrecorded species, improving rapid response and successful management outcomes by >40% over direct capture surveys.
• Threatened Populations: Amazon River basin eDNA monitoring has yielded detection of 675 vertebrates (including 155 mammals, 375 fish), enabling large-scale, non-invasive census for endangered megafauna.

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Future Developments and Integration Strategies

• Multi-Environment Integrations: UNESCO’s marine mapping program detected 4,500 species, with studies identifying 100+ per 1.5L sample. Cross-environment eDNA sampling delivers higher detection rates and supports comprehensive ecosystem connectivity analysis, aligning with the latest international standardization efforts.
• Methodological Advances: Integration of aquatic, soil, and airborne sampling methods results in more complete biodiversity assessments, driving future research and regulatory practice.

Unlock eDNA Analysis with Cmbio

Cmbio’s suite of eDNA, genomics, and bioinformatics services prepare policy-makers, regulators, and conservationists for rapid, scalable, and evidence-led biodiversity monitoring.

Explore our full eDNA Metabarcoding Research services or contact us to discuss your project needs.

FAQs

How does eDNA detection increase sensitivity and accuracy in field sampling compared to traditional methods?

eDNA detection utilizes molecular techniques to survey organisms by collecting genetic traces from water, soil, or air, often detecting target species at much lower population densities than conventional field sampling. When using eDNA, research routinely demonstrates higher sensitivity: more than 94% detection rates and reduced false negatives in aquatic environments, especially for cryptic or low-abundance organisms. The process is non-invasive and quick, enabling sampling in areas where visual or capture methods are impractical, and standardized protocols (gloves, field blanks, new tubes per site, interval sampling for large areas) greatly minimize contamination risks.

Can eDNA collection reliably detect rare species in environmental samples? What factors influence this potential?

Yes, using eDNA enables reliable detection of rare species through targeted qPCR and metabarcoding, supporting biodiversity assessments, conservation monitoring, and ecological research. eDNA collection protocols (such as filtering water or sampling soil from suitable habitats) have consistently revealed species that remain undetected in standard surveys, including critically endangered fish and elusive amphibians. The potential for detection depends on sampling design (e.g., site selection, frequency, primer specificity) and ecological factors like species secretion rates, water flow, and DNA degradation, all of which affect eDNA concentration and detection reliability.

How can eDNA field sampling methods support multi-species monitoring in a single survey event?

eDNA field sampling supports multi-species identification in a single collection by employing broad-range or multiple primer sets to amplify genetic material from various taxa (fish, plants, invertebrates, and even microbes) in the same sample. A single eDNA collection (such as a filtered water or bulk soil sample) can be split for several analyses, delivering full community profiles and enhanced biodiversity monitoring potential. Stored extracts allow for additional species targeting long after initial collection, making eDNA strategies highly scalable for environmental surveys, restoration projects, and compliance reporting. Field protocols recommend interval sampling, repetition, and careful documentation to maximize accuracy and compare results across locations.