Environmental DNA (eDNA)
- NOTOC**
Environmental DNA (eDNA)
Environmental DNA, commonly called eDNA, is genetic material collected directly from environmental samples rather than from organisms that have been captured or physically observed. Organisms continually release DNA through skin cells, mucus, scales, feces, urine, reproductive material, tissues, pollen, spores, and other biological material. Scientists can recover these genetic traces from water, sediment, soil, air, vegetation, biofilms, and many other substrates.
Environmental DNA has developed from an experimental technique for detecting individual species into a broad system for monitoring biodiversity. It can reveal organisms that are rare, elusive, endangered, invasive, difficult to capture, or present only temporarily. High-throughput sequencing and metabarcoding have expanded eDNA analysis beyond individual species, allowing researchers to identify many organisms from a single environmental sample.
The rapid development of eDNA has important implications for conservation biology, ecological research, fisheries management, invasive-species surveillance, protected-area monitoring, ecosystem-health assessment, and large-scale biodiversity observation.
What Environmental DNA Is
Environmental DNA occurs in many forms. It may consist of free DNA fragments in water or soil, intact cells, tissues, microorganisms, pollen, fecal material, or fragments attached to sediments and other environmental particles.
Different sampling methods can therefore capture different portions of the environmental DNA present at a location. Water filtration may emphasize recently transported biological material, while sediments can accumulate DNA over longer periods. Soil, bark, leaves, flowers, spider webs, air filters, animal drinking sites, and even owl pellets have all been investigated as potential sources of environmental DNA.
Because environmental DNA can persist after an organism has moved away, an eDNA detection does not always indicate that the organism was physically present at the exact sampling point at the moment the sample was collected. Understanding the origin, transport, persistence, degradation, and physical state of eDNA is therefore essential when interpreting results.
From Species Detection to Biodiversity Monitoring
Early eDNA studies demonstrated that small water samples could detect fish, amphibians, mammals, crustaceans, and other aquatic organisms without physically capturing them. These successes established eDNA as a potentially powerful method for finding rare or difficult-to-observe species.
The field subsequently expanded through DNA metabarcoding. Instead of searching for one species with a species-specific genetic assay, metabarcoding uses broadly targeted genetic primers and high-throughput sequencing to identify many species simultaneously.
This has allowed environmental DNA surveys to reconstruct entire biological communities, including fish, amphibians, mammals, plants, insects, plankton, mollusks, microorganisms, and other organisms.
Large-scale eDNA monitoring can now reveal patterns of biodiversity across rivers, lakes, coastlines, wetlands, forests, protected areas, and other ecosystems.
Sampling and Laboratory Methods
Reliable eDNA monitoring depends heavily on how samples are collected, preserved, filtered, extracted, amplified, sequenced, and analyzed.
Water is one of the most widely used environmental substrates. Researchers commonly collect water and pass it through filters that retain biological material. DNA is then extracted from the filter and analyzed using techniques such as quantitative PCR, digital PCR, metabarcoding, or increasingly portable molecular detection systems.
Studies have demonstrated that filter material, pore size, sample volume, preservation method, storage conditions, DNA extraction procedures, and laboratory protocols can substantially alter which organisms are detected.
Environmental conditions can also influence DNA survival. Temperature, ultraviolet radiation, acidity, microbial activity, water movement, and other factors affect how quickly DNA degrades.
Sediments often contain higher concentrations of DNA than surface water and may preserve genetic signals for longer periods. This can be useful for reconstructing ecological conditions but may also make it more difficult to determine exactly when an organism was present.
Quality Control and Standardization
Contamination is one of the most important challenges in environmental DNA research. Tiny amounts of DNA transferred between samples, equipment, laboratories, or researchers can create misleading detections.
For this reason, rigorous negative controls, laboratory separation, equipment cleaning, replication, assay validation, and transparent reporting are essential components of eDNA studies.
Researchers have also emphasized the importance of clearly defining analytical limits of detection and quantification. A molecular assay may detect extremely small amounts of DNA, but deciding whether that signal represents meaningful evidence of species presence requires careful statistical and ecological interpretation.
Standardized procedures are increasingly important as eDNA moves from research laboratories into government monitoring and management programs.
Freshwater Ecosystems
Freshwater environments have been among the most important testing grounds for environmental DNA.
Rivers, streams, lakes, wetlands, reservoirs, and estuaries contain DNA from fish, amphibians, mussels, crayfish, aquatic insects, microorganisms, and other organisms. Water sampling can often detect species that conventional electrofishing, netting, trapping, or visual surveys fail to observe.
River systems present both opportunities and challenges. Flowing water can transport DNA downstream, meaning a sample may contain genetic information from organisms located some distance upstream.
This characteristic has led researchers to describe rivers as conveyors of biodiversity information. By sampling river networks strategically, scientists may be able to infer biological diversity across large watersheds.
Lake studies have demonstrated that eDNA can reveal spatial and seasonal changes in biological communities. Repeated sampling can document changes associated with spawning, migration, precipitation, temperature, and seasonal ecological cycles.
Fish Monitoring and Fisheries
Fish are among the most intensively studied organisms in environmental DNA research.
eDNA has been used to detect endangered salmon, trout, sturgeon, eels, tropical fishes, invasive carp, and numerous other species. Metabarcoding studies frequently detect more fish species than individual conventional survey methods.
Researchers are also investigating whether eDNA concentration can provide information about abundance or biomass. Controlled experiments and field studies have sometimes found relationships between DNA concentration and fish abundance, although environmental conditions, DNA production, transport, and degradation complicate quantitative interpretation.
Environmental DNA may eventually complement fisheries surveys, stock assessments, catch monitoring, bycatch detection, and ecosystem-based fisheries management.
Amphibians, Reptiles, Mussels, and Other Difficult-to-Detect Species
Environmental DNA is particularly useful for organisms that are cryptic, rare, endangered, nocturnal, subterranean, or otherwise difficult to observe.
Amphibian studies have demonstrated successful detection of salamanders, frogs, and other species from water and terrestrial samples. Species-specific assays can identify populations that might be missed by seasonal calling surveys or visual searches.
Freshwater mussels are another major application. Many mussel species are threatened or endangered and can be difficult to locate using conventional surveys. eDNA offers a non-destructive method for locating populations and potentially monitoring changes in their distribution.
Reptiles, including turtles, snakes, crocodilians, and lizards, have also been studied using environmental DNA.
Invasive Species Detection
Early detection is crucial for managing invasive species because eradication becomes increasingly difficult once populations become widespread.
Environmental DNA can detect species when population densities are extremely low, making it especially attractive for invasive-species surveillance.
Examples include invasive fish, zebra mussels, signal crayfish, Burmese pythons, agricultural pests, and other organisms.
Sensitive eDNA assays may identify an invasion front before conventional surveys detect the organism. Portable technologies may eventually allow managers to test environmental samples directly in the field and respond more rapidly to emerging invasions.
At the same time, managers must distinguish between true populations and DNA transported from another source. A positive eDNA detection does not automatically prove that a reproducing population exists at the sampling location.
Marine and Coastal Biodiversity
Environmental DNA has rapidly expanded into marine science.
Seawater can contain genetic material from fish, sharks, rays, whales, plankton, corals, mollusks, microorganisms, and many other marine organisms. Metabarcoding allows broad biological communities to be assessed from relatively small volumes of seawater.
Applications include coral reefs, estuaries, seagrass beds, mangroves, kelp forests, marine protected areas, coastal fisheries, deep-sea environments, and open-ocean ecosystems.
Marine eDNA surveys have documented geographic differences in biodiversity and temporal changes associated with seasons, environmental gradients, habitat structure, marine heatwaves, and human disturbance.
Coral Reefs, Mangroves, Seagrasses, and Kelp Forests
Complex coastal habitats can be difficult and expensive to survey comprehensively using traditional methods.
Coral-reef eDNA surveys can detect fish and small cryptic organisms that may escape visual surveys. Studies also suggest that reef structure and habitat complexity influence the biological communities detected through environmental DNA.
Mangrove and seagrass research demonstrates that eDNA can distinguish fish assemblages among neighboring habitats and support restoration and conservation planning.
Kelp-forest research similarly shows that sampling location, depth, timing, biological replication, and water movement influence which species are detected.
These studies reinforce the need for carefully designed sampling strategies when using environmental DNA for ecosystem comparisons.
The Deep Ocean
The deep ocean remains one of Earth's least thoroughly surveyed environments.
Environmental DNA may provide a comparatively efficient method for investigating biodiversity at depths where conventional sampling requires expensive vessels, submersibles, remotely operated vehicles, or specialized trawling equipment.
Researchers have recovered eDNA from deep-sea water, sediments, submarine canyons, seamounts, and mesopelagic environments.
Studies suggest that DNA communities can vary substantially with depth, indicating that careful vertical sampling is needed to characterize deep-ocean biodiversity.
Pumped deep-sea water and automated sampling infrastructure may eventually support repeated long-term monitoring of deep marine ecosystems.
Terrestrial Environmental DNA
Environmental DNA research was initially dominated by aquatic ecosystems, but terrestrial methods are developing rapidly.
Soil contains DNA from plants, animals, fungi, microorganisms, and other organisms. Soil metabarcoding can reveal broad patterns in plant communities and terrestrial biodiversity.
DNA can also be recovered from tree bark, leaves, forest surfaces, sediments, animal waterholes, and other terrestrial substrates.
Studies comparing terrestrial eDNA with camera traps and traditional wildlife surveys suggest that molecular methods can provide valuable complementary information, particularly for elusive mammals and small organisms.
Airborne Environmental DNA
One of the most rapidly developing areas of environmental DNA research is airborne eDNA.
Animals, plants, fungi, and microorganisms continuously release biological particles into the atmosphere. Air filtration and passive dust collectors can capture some of this material.
Early experiments demonstrated that airborne DNA could detect vertebrates in zoological parks. Subsequent studies showed that the approach also works in natural forests, grasslands, and other environments.
Airborne eDNA has detected mammals, birds, amphibians, reptiles, insects, and other organisms.
Environmental conditions such as wind, rainfall, humidity, and animal activity can affect airborne DNA concentration and transport, making sampling design important.
Plants, Pollinators, and Arthropods
Environmental DNA also creates new opportunities for monitoring plants and insects.
Soil DNA can reproduce broad patterns of plant diversity, while DNA collected from surfaces can help identify terrestrial arthropods.
Flowers represent a particularly interesting environmental DNA substrate. Bees and other pollinators leave traces of DNA when they visit flowers. Researchers can collect this DNA without capturing the pollinators themselves.
Flower-derived eDNA may therefore provide information about pollinator diversity, species abundance, and plant-pollinator interactions.
Environmental DNA has also been recovered from pan-trap water, leaf surfaces, forest vegetation, and agricultural plants to detect insects and other arthropods.
Natural Passive Samplers
Researchers increasingly recognize that biological and physical structures can act as natural environmental DNA collectors.
Spider webs can capture airborne biological particles and DNA from nearby vertebrates.
Marine sponges continuously filter seawater and may accumulate DNA from surrounding organisms.
Biofilms can trap DNA over time and provide information about aquatic communities.
Flowers collect DNA from visiting insects, while owl pellets contain genetic material from prey species.
These approaches could reduce the need for active sampling and expand environmental DNA monitoring into habitats where conventional collection is difficult.
Conservation Biology
Environmental DNA has important potential for conservation because many threatened species are difficult to monitor using conventional methods.
Non-invasive sampling can reduce disturbance to endangered populations while increasing the geographic scale of monitoring.
Applications include locating rare populations, identifying biodiversity hotspots, assessing protected areas, monitoring restoration, documenting species rediscoveries, tracking migration, and measuring ecological responses to environmental change.
Environmental DNA can also complement traditional ecological knowledge, field surveys, camera trapping, acoustic monitoring, and direct species observation.
Most researchers therefore view eDNA as a powerful addition to conventional biodiversity monitoring rather than a universal replacement for traditional ecological methods.
Protected Areas and Citizen Science
The scalability of environmental DNA makes it attractive for monitoring large protected areas.
Marine protected areas, World Heritage sites, freshwater reserves, and terrestrial conservation landscapes can potentially be sampled repeatedly using standardized protocols.
Citizen-science programs provide another opportunity. Volunteers can collect environmental samples following standardized procedures, while specialized laboratories conduct the genetic analysis.
Programs involving whale-watching vessels and UNESCO marine World Heritage sites demonstrate how researchers, conservation organizations, and members of the public may participate in large-scale eDNA biodiversity monitoring.
Detecting Ecological Change
Environmental DNA is increasingly used not merely to compile species lists but to measure ecological change.
Repeated sampling can reveal seasonal shifts, species migrations, changes in community composition, and biological responses to disturbances.
Researchers have used archived environmental samples to reconstruct changes associated with marine heatwaves.
Other studies have examined biodiversity responses to bottom trawling, marine litter, urbanization, water chemistry, habitat differences, temperature, hydrology, and other environmental factors.
Long-term eDNA monitoring could therefore become an important component of ecological early-warning systems.
Food Webs and Ecosystem Health
Because metabarcoding can simultaneously detect large numbers of organisms, researchers are beginning to reconstruct ecological networks from environmental DNA.
Community data can potentially be combined with food-web and network analysis to examine relationships among predators, prey, competitors, parasites, and other organisms.
Environmental DNA is also being investigated as an indicator of ecological health.
Instead of relying on a small number of indicator species, future monitoring programs may use broad molecular profiles of entire biological communities to assess ecosystem condition.
Wildlife Disease and Pathogens
Environmental DNA and environmental RNA can detect pathogens as well as free-living organisms.
Water samples can be screened for multiple disease-causing organisms without repeatedly capturing wildlife.
Large-scale pathogen surveillance may therefore allow researchers to create disease-risk maps and detect emerging outbreaks.
Aquaculture systems are another promising application because circulating water can be sampled repeatedly to detect pathogens affecting fish populations.
Environmental RNA may be particularly useful because RNA generally degrades more rapidly than DNA and may sometimes provide information about more recent biological activity.
Emerging Molecular Technologies
Technological advances are making environmental DNA analysis faster and more portable.
Traditional eDNA workflows often require samples to be transported to centralized laboratories. New field systems combine filtration, DNA extraction, amplification, and detection in portable equipment.
CRISPR-based assays have been developed for rapid detection of organisms including salmon and jellyfish.
Automated environmental sample processors can collect, analyze, and transmit results from remote marine environments.
Future systems may permit increasingly continuous or near-real-time biodiversity monitoring.
Bioinformatics and Reference Databases
Collecting environmental DNA is only the first step. Genetic sequences must be compared with reference databases to determine which organisms produced them.
Incomplete or inaccurate reference databases remain a major limitation.
Some organisms have extensive barcode records, while others are poorly represented. A DNA sequence may therefore be recovered successfully but remain impossible to identify precisely.
Primer choice also affects the organisms detected. A primer that performs well for one group may fail to amplify another.
New primer-development tools, multiplexed assays, improved reference databases, and visualization methods are being developed to improve taxonomic coverage and reliability.
Quantifying Species Abundance
One of the major goals of environmental DNA research is moving from simple detection toward estimating abundance.
The basic idea is that more organisms may release more DNA into their environment.
In practice, the relationship is complicated. Organisms differ in how much DNA they shed, while temperature, sunlight, microbial activity, currents, sedimentation, and other processes affect how quickly DNA is transported or destroyed.
Consequently, a high DNA concentration does not always correspond directly to a large population.
Despite these limitations, several fish studies have found meaningful relationships between eDNA concentration, abundance, and biomass. Quantitative applications are likely to remain an important area of research.
False Positives, False Negatives, and Interpretation
Environmental DNA is highly sensitive, which is both an advantage and a challenge.
A false positive occurs when DNA is detected even though the organism of interest is not actually present in the population being studied. Contamination, transported DNA, laboratory errors, or misidentification can contribute to false positives.
A false negative occurs when an organism is present but its DNA is not detected. Low population density, insufficient sample volume, poor primer performance, DNA degradation, PCR inhibition, or inadequate sampling can all contribute.
Replication and appropriate controls are therefore essential.
Environmental DNA results must be interpreted within ecological context rather than treated as unquestionable evidence of species presence or absence.
eDNA Transport and Persistence
DNA does not remain stationary after being released.
In rivers, genetic material can move downstream. In oceans, currents can transport DNA vertically and horizontally. Wind may move airborne DNA across terrestrial landscapes.
DNA can also bind to sediments and mineral particles, altering its persistence and transport.
Environmental DNA therefore represents a combination of biological and physical processes.
Understanding those processes is necessary before researchers can reliably translate genetic detections into precise information about organism location, abundance, or timing.
Environmental DNA and Ancient Ecosystems
Environmental DNA is not limited to monitoring living organisms.
DNA preserved in lake sediments, marine sediments, soils, ice, and other environments can remain detectable for long periods.
Sedimentary ancient DNA can provide information about past biological communities and ecological change.
Researchers can use these records to reconstruct vegetation, animal communities, ecosystem functions, and environmental responses over historical or prehistoric timescales.
Statistical methods including occupancy models, clustering, ordination, and other analytical techniques help extract ecological information from ancient environmental DNA datasets.
Human DNA and Privacy
An unexpected ethical issue has emerged from highly sensitive environmental DNA sequencing.
Samples collected for biodiversity research can contain human DNA. Deep sequencing may sometimes recover substantial amounts of human genomic information even when researchers were not attempting to collect it.
This phenomenon has been described as human genomic bycatch.
Potential applications include forensic investigation, public-health research, and biosecurity monitoring, but the same capabilities raise serious concerns about privacy, consent, surveillance, genetic discrimination, data ownership, and the collection of genetic information from people who never agreed to participate in a study.
Environmental DNA research may therefore require ethical safeguards that historically were not considered necessary for ecological sampling.
Policy and Regulation
As environmental DNA moves into government and conservation decision-making, questions are emerging about how molecular evidence should be used.
A positive eDNA detection could potentially influence invasive-species management, endangered-species protection, development decisions, fisheries regulation, or habitat management.
However, regulators must determine how much evidence is necessary before taking action.
Standardized sampling procedures, validated assays, quality-control requirements, transparent reporting, and clear decision frameworks will be important if eDNA evidence is used routinely in environmental regulation.
Advantages of Environmental DNA
Environmental DNA offers several major advantages over conventional biological surveys.
It can be:
- Non-invasive.
- Sensitive to rare organisms.
- Effective for cryptic or elusive species.
- Useful across large geographic areas.
- Capable of detecting many species simultaneously.
- Less dependent on physically capturing organisms.
- Applicable in inaccessible habitats.
- Compatible with repeated long-term monitoring.
- Potentially less expensive for large biodiversity surveys.
- Capable of preserving samples that can later be reanalyzed as genetic technology improves.
These characteristics make eDNA especially attractive in biodiversity-rich or difficult-to-survey ecosystems.
Limitations of Environmental DNA
Environmental DNA also has important limitations.
Detection depends on sampling design, sample volume, DNA shedding, environmental conditions, transport, degradation, laboratory procedures, primer choice, sequencing technology, and reference databases.
A DNA detection does not necessarily reveal:
- The exact location of the organism.
- Whether the organism is alive.
- How many individuals are present.
- Whether a population is reproducing.
- How recently the organism occupied the area.
- Whether transported DNA originated somewhere else.
Traditional ecological expertise therefore remains essential for interpreting environmental DNA results.
Combining eDNA with Conventional Surveys
Many studies comparing environmental DNA with traditional ecological surveys find that the methods detect overlapping but not identical communities.
eDNA may identify species missed by nets, electrofishing, camera traps, visual surveys, microscopy, or other techniques.
Traditional surveys may also detect organisms that eDNA fails to identify.
Rather than viewing the approaches as competitors, many researchers emphasize their complementary value.
Combining environmental DNA with camera traps, acoustic monitoring, microscopy, netting, visual surveys, remote underwater video, and conventional taxonomy can provide a more complete understanding of biodiversity than any single method.
The Future of Biodiversity Monitoring
Environmental DNA is moving toward increasingly large-scale and automated biodiversity observation.
Future monitoring networks may combine field sensors, automated water samplers, portable molecular laboratories, DNA sequencing, artificial intelligence, remote sensing, ecological models, and centralized biodiversity databases.
Repeated sampling could create molecular time series showing how biological communities change from days to decades.
Environmental DNA may also become increasingly important for evaluating climate change, habitat restoration, protected areas, invasive species, fisheries, pollution, urban development, agricultural systems, and ecosystem resilience.
The greatest transformation may be a shift from occasional surveys of selected organisms toward more continuous observation of entire ecological communities.
Conclusion
Environmental DNA has changed how scientists can observe life in the environment. Genetic traces collected from water, sediment, soil, air, plants, and other environmental materials can reveal organisms that might otherwise remain undetected.
The technique has progressed from detecting individual aquatic species to monitoring complex freshwater, marine, terrestrial, and airborne communities. It is increasingly being applied to endangered species, invasive organisms, fisheries, protected areas, pollinators, wildlife disease, ecological restoration, and ecosystem-health assessment.
At the same time, environmental DNA is not a simple substitute for conventional biological surveys. DNA transport, degradation, contamination, imperfect reference databases, methodological differences, and uncertainty about abundance and location require careful interpretation.
Standardization, improved reference libraries, stronger statistical methods, portable molecular technologies, and better integration with conventional ecological knowledge will determine how widely eDNA can be incorporated into routine environmental management.
The field also demonstrates that technological advances can create unexpected social questions. The ability to recover incidental human genetic information from ordinary environmental samples introduces important issues involving privacy, consent, data ownership, and surveillance.
Environmental DNA is therefore more than a new biodiversity survey technique. It is emerging as a broad environmental-observation technology capable of changing how ecosystems are measured, monitored, understood, and managed.
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Environmental DNA (eDNA): Foundations and Major Reviews
1. Environmental DNA as a Tool for Ecosystem Monitoring and Conservation Biology
| Basanta Kumar Das, Biswajit Mandal, Vikash Kumar | Frontiers in Marine Science | 2026-07
Environmental DNA offers a non-invasive and increasingly cost-effective way to detect organisms and assess biodiversity, with applications ranging from individual threatened species to entire ecological communities.
2. Environmental DNA (eDNA) Technology in Biodiversity and Ecosystem Health Research: Advances and Prospects
| Authors et al. | Ecology and Evolution | 2026
This broad review examines aquatic, terrestrial, soil, and airborne eDNA methods while addressing sampling, extraction, bioinformatics, standardization, and reference-database limitations.
3. Passive Environmental DNA Sampling: A Review of Current Practices, Limitations and Future Directions for Biodiversity Monitoring
| Fidji Sandré, Marie-Pier Brochu, Valérie S. Langlois | Methods in Ecology and Evolution | 2026
Passive samplers such as membranes, sponges, activated carbon, and dust-collecting materials may simplify eDNA collection and allow biodiversity monitoring in locations where conventional filtration is difficult.
4. A Systematic Review Evaluating the Performance of eDNA Methods Relative to Conventional Methods for Biodiversity Monitoring
| Nicholas J. Iacaruso et al. | Ecography | 2026
A systematic comparison finds that eDNA often improves species detection and reduces sampling effort, although its communities do not always perfectly match those recorded using conventional surveys.
5. Environmental DNA: The Next Chapter
| Rosetta Blackman et al. | Molecular Ecology | 2024-06
This perspective reviews the expansion of eDNA from experimental species detection toward large-scale ecological monitoring and increasingly sophisticated analyses of biodiversity.
6. What Is Environmental DNA?
| Haylea Power et al. | Environmental DNA | 2023-12-02
The study emphasizes that eDNA exists in many physical forms, including extracellular fragments, cells, tissues, biofilms, and organisms, and that sampling methods can preferentially collect different fractions.
7. Environmental DNA Surveys of African Biodiversity: State of Knowledge, Challenges, and Opportunities
| Sophie von der Heyden | Environmental DNA | 2023
This review examines the potential for eDNA to address major biodiversity-monitoring gaps across Africa while discussing infrastructure, reference databases, training, and research capacity.
8. Environmental DNA Metabarcoding: Transforming How We Survey Animal and Plant Communities
| Kristy Deiner et al. | Molecular Ecology | 2017-11
This influential review explains how high-throughput sequencing and metabarcoding can reconstruct multi-species communities from environmental samples.
9. The Ecology of Environmental DNA and Implications for Conservation Genetics
| Matthew A. Barnes, Cameron R. Turner | Conservation Genetics | 2016
The authors develop a framework for understanding eDNA origin, state, transport, persistence, and degradation, all of which influence how detections should be interpreted.
10. Environmental DNA – An Emerging Tool in Conservation for Monitoring Past and Present Biodiversity
| Philip Francis Thomsen, Eske Willerslev | Biological Conservation | 2015-03
A foundational review describes how environmental samples can reveal both contemporary and ancient biodiversity and discusses eDNA's conservation potential and limitations.
11. Environmental DNA for Wildlife Biology and Biodiversity Monitoring
| Kristine Bohmann et al. | Trends in Ecology & Evolution | 2014-06
The authors review emerging applications of environmental DNA for detecting common, endangered, invasive, elusive, and otherwise difficult-to-survey organisms.
12. Ancient and Modern Environmental DNA
| Eske Willerslev et al. | Philosophical Transactions of the Royal Society B | 2014
Environmental DNA from sediments, ice, soil, and water provides information on both modern biodiversity and ecological communities extending thousands of years into the past.
13. The Detection of Aquatic Animal Species Using Environmental DNA – A Review of eDNA as a Survey Tool in Ecology
| Helen C. Rees et al. | Journal of Applied Ecology | 2014
This early review evaluates the rapidly expanding use of aquatic eDNA and identifies methodological and interpretive challenges that must be addressed for routine ecological monitoring.
14. Monitoring Endangered Freshwater Biodiversity Using Environmental DNA
| Philip Francis Thomsen et al. | Molecular Ecology | 2012-06
A landmark experiment showed that DNA collected from small water samples could detect threatened amphibians, fish, mammals, insects, and crustaceans.
15. The Future of Environmental DNA in Ecology
| Nigel G. Yoccoz | Molecular Ecology | 2012
This early perspective recognized environmental DNA as a potentially transformative approach for documenting ecological communities and biodiversity.
Sampling, Laboratory Methods, Quantification, Bioinformatics, Quality Control, and Standards
16. Using Gap Visualization to Navigate Multivariate Metabarcode Data, Select Primer Pairs, and Enhance Reference Data Quality
| Xin-Yi Chua et al. | Environmental DNA | 2024-12-10
Visualization of DNA barcode gaps can help researchers compare metabarcoding primers, identify taxonomic ambiguity, and detect errors or deficiencies in reference databases.
17. Preservation of Aquatic Environmental DNA Using Cationic Detergents
| Viresh Thamke et al. | Environmental DNA | 2024-11-23
Experiments show that particular cationic surfactants can significantly prolong DNA persistence in collected water, potentially reducing the need for immediate field filtration.
18. V9 Hypervariable Region Metabarcoding Primers for Euglenozoa and Metamonada
| Jiří Novák et al. | Environmental DNA | 2024-10-12
Newly designed primers improve metabarcoding coverage of microbial eukaryotic groups that may be poorly amplified by commonly used universal primers.
19. Environmental DNA Concentrations Vary Greatly Across Productive and Degradative Conditions, with Implications for the Precision of Population Estimates
| Meghan B. Parsley et al. | Scientific Reports | 2024-07-29
Experimental results demonstrate how both DNA shedding and environmental degradation can substantially influence measured concentrations independently of organism abundance.
20. Rapid, Contamination-Less, and Efficient Environmental DNA Filtration System
| Authors et al. | MethodsX | 2024-06
A large-volume filtration system processes numerous water replicates simultaneously while reducing handling, filtration time, and contamination risk in low-eDNA environments such as the deep ocean.
21. Development of Environmental DNA Metabarcoding Primers for Marine Mollusks and Comparison with Published Primers
| Xiaojing Shi et al. | BMC Ecology and Evolution | 2024-05-31
Newly developed metabarcoding primers improve molecular surveys of highly diverse marine mollusk communities.
22. Streamside Detection of Chinook Salmon Environmental DNA with CRISPR Technology
| Blasko et al. | Environmental DNA | 2024-04-15
CRISPR-Cas12a technology enables rapid field detection of Chinook salmon DNA and could reduce dependence on centralized laboratory testing.
23. Single Metabarcoding Multiplex Captures Community-Level Freshwater Biodiversity and Beyond
| Nicholas Eastwood et al. | Environmental DNA | 2024-02-15
Multiplexed primers offer a way to survey multiple taxonomic groups simultaneously rather than conducting separate assays for each component of freshwater biodiversity.
24. Environmental DNA Storage and Extraction Method Affects Detectability for Multiple Aquatic Invasive Species
| García et al. | Environmental DNA | 2024
Comparisons of storage buffers and extraction protocols demonstrate that laboratory workflow decisions can materially affect invasive-species detection rates.
25. Enhancing Metabarcoding of Freshwater Biotic Communities: A New Online Tool for Primer Selection and Exploring Data from 14 Primer Pairs
| Tournayre et al. | Environmental DNA | 2024
The SNIPe tool helps researchers compare metabarcoding primers and identify efficient combinations capable of detecting broad portions of freshwater biodiversity.
26. Quantitative Environmental DNA Metabarcoding Shows High Potential as a Novel Approach to Quantitatively Assess Fish Community
| Satsuki Tsuji et al. | Scientific Reports | 2022-12-13
Quantitative metabarcoding produced eDNA estimates that correlated positively with fish abundance and biomass measured using conventional field surveys.
27. Relationships Between the eDNA Concentration Obtained from Metabarcoding and Stream Fish Abundance Estimated by the Removal Method Under Field Conditions
| Hikaru Nakagawa et al. | Environmental DNA | 2022-08-08
Quantitative metabarcoding using internal standards is tested against conventional abundance estimates for several fish species living in flowing streams.
28. Environmental DNA Metabarcoding for Benthic Monitoring: A Review of Sediment Sampling and DNA Extraction Methods
| Authors et al. | Science of the Total Environment | 2022-04-20
This review evaluates sediment collection, preservation, extraction, DNA persistence, and other methodological issues important for standardized benthic eDNA monitoring.
29. Time to Get Real with qPCR Controls: The Frequency of Sample Contamination and the Informative Power of Negative Controls in Environmental DNA Studies
| Patrick R. Hutchins, Leah N. Simantel, Adam J. Sepulveda | Molecular Ecology Resources | 2022
The study quantifies contamination risks across an eDNA workflow and examines how effectively negative controls reveal sporadic and systemic contamination.
30. Environmental DNA for Biomonitoring
| Jan Pawlowski et al. | Molecular Ecology | 2021-06-27
This article reviews the growing transition of environmental DNA from experimental ecology into practical biological monitoring programs.
31. An Illustrated Manual for Environmental DNA Research: Water Sampling Guidelines and Experimental Protocols
| Toshifumi Minamoto et al. | Environmental DNA / eDNA Society | 2021
This standardized manual provides practical procedures for field sampling, filtration, contamination prevention, laboratory analysis, and environmental DNA research.
32. Application of eDNA as a Tool for Assessing Fish Population Abundance
| Michael J. Spear et al. | Environmental DNA | 2020-06-07
This study investigates the conditions under which eDNA concentration can move beyond simple species detection and provide useful information about fish abundance.
33. A System for Rapid eDNA Detection of Aquatic Invasive Species
| Andrew C. Thomas et al. | Environmental DNA | 2020
Portable filtration, DNA extraction, and qPCR equipment were combined into a field system capable of rapidly detecting invasive New Zealand mudsnails.
34. Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies
| Ryan P. Kelly, Andrew Olaf Shelton, Ramón Gallego | Scientific Reports | 2019-08-20
PCR amplification can distort relationships between DNA concentrations and ecological abundance, making careful interpretation essential when using metabarcoding data.
35. Reporting the Limits of Detection and Quantification for Environmental DNA Assays
| Katy E. Klymus et al. | Environmental DNA | 2019
The authors propose standardized procedures for determining and reporting limits of detection and quantification in quantitative-PCR eDNA studies.
36. Environmental DNA Filtration Techniques Affect Recovered Biodiversity
| Markus Majaneva et al. | Scientific Reports | 2018-03-16
Different filter materials and filtration strategies can significantly alter the diversity recovered from the same environmental water samples.
37. Methods to Maximise Recovery of Environmental DNA from Water Samples
| Aryo Hinlo et al. | PLOS ONE | 2017-06-12
Experiments compare water collection, preservation, filtration, extraction, and amplification approaches to determine which combinations maximize recovery of low-concentration eDNA.
38. Detection Limits of Quantitative and Digital PCR Assays and Their Influence in Presence–Absence Surveys of Environmental DNA
| Margaret E. Hunter et al. | Molecular Ecology Resources | 2017
The research demonstrates why clearly defined analytical detection thresholds are essential when using eDNA to infer species presence or absence.
39. Critical Considerations for the Application of Environmental DNA Methods to Detect Aquatic Species
| Caren S. Goldberg et al. | Methods in Ecology and Evolution | 2016
The authors provide practical recommendations covering study design, controls, contamination avoidance, assay validation, replication, and interpretation.
40. Choice of Capture and Extraction Methods Affect Detection of Freshwater Biodiversity from Environmental DNA
| Kristy Deiner et al. | Biological Conservation | 2015-03
Comparisons of capture and DNA-extraction protocols demonstrate that methodological choices can substantially alter which organisms are detected.
41. Quantifying Effects of UV-B, Temperature, and pH on eDNA Degradation in Aquatic Microcosms
Controlled experiments show that temperature, ultraviolet radiation, and pH influence how quickly environmental DNA disappears from aquatic environments.
42. Fish Environmental DNA Is More Concentrated in Aquatic Sediments Than Surface Water
| Cameron R. Turner, Karen Uy Le, Robert C. Everhart | Biological Conservation | 2015-03
Fish DNA can persist at much higher concentrations and for longer periods in sediment than in overlying water, creating different temporal signals of species presence.
43. Effects of Sample Processing on the Detection Rate of Environmental DNA from the Common Carp
| Authors et al. | Biological Conservation | 2015-03
Sample freezing, DNA volume, and other processing decisions can influence whether low-concentration fish eDNA is successfully detected.
44. Moving Environmental DNA Methods from Concept to Practice for Monitoring Aquatic Macroorganisms
| Caren S. Goldberg, Katherine M. Strickler, David S. Pilliod | Biological Conservation | 2015-03
This introduction to a major eDNA special issue outlines the methodological advances needed to transform eDNA into a routine biodiversity-monitoring tool.
45. The Effect of Dilution and Post-Extraction Purification on Environmental DNA Samples
| Anna M. McKee, Stephen F. Spear, Todd W. Pierson | Biological Conservation | 2015
This study evaluates practical approaches for reducing PCR inhibition while preserving enough DNA for reliable ecological detection.
Freshwater Fish, Rivers, Lakes, Wetlands, and Aquatic Biodiversity
46. Optimization of Environmental DNA-Based Methods: A Case Study for Detecting Brook Trout
| Erika Myler et al. | PeerJ | 2026-02-11
The study systematically optimizes sampling and molecular procedures for detecting low concentrations of brook trout DNA.
47. Comparing Sediment and Water eDNA Metabarcoding for Monitoring Aquatic Biodiversity in a Plateau Lake
| Xiu Feng et al. | Environmental DNA | 2026-01-27
Comparing water and sediments across multiple taxonomic groups shows that the two substrates capture different components of lake biodiversity.
48. Environmental DNA Metabarcoding: Current Applications and Future Prospects for Freshwater Fish Monitoring
| Authors et al. | Journal of Environmental Management | 2025-03
This review evaluates freshwater fish applications, methodological workflows, habitat assessment, ecological monitoring, and remaining challenges in standardization and reference databases.
49. Environmental DNA Barcoding Reveals General Biodiversity Patterns in the Large Tropical Rift Lake Albert
| Miklós Bálint et al. | Science of the Total Environment | 2024-11-13
eDNA metabarcoding provides a broad biodiversity baseline for Lake Albert, an African ecosystem where comprehensive conventional biological surveys are difficult.
50. Development of eDNA Protocols for Detection of Endangered White Sturgeon in the Wild
| James A. Crossman et al. | Environmental DNA | 2024-09-10
Laboratory and field validation establishes sensitive protocols for detecting endangered white sturgeon across habitats where population abundance varies substantially.
51. Effectiveness of eDNA for Monitoring Riverine Macroinvertebrates
| Authors et al. | Science of the Total Environment | 2024-09-01
A review finds substantial promise but concludes that current eDNA methods may miss important invertebrate groups and should not yet fully replace conventional monitoring.
52. eDNA Is a Useful Environmental Monitoring Tool for Assessing Stream Ecological Health
| Alastair M. Suren et al. | Environmental DNA | 2024-08-28
Community-level eDNA data can complement established indicators when evaluating biological condition and ecological health in stream networks.
53. Developing an eDNA Approach for Wetland Biomonitoring: Insights on Technical and Conventional Approaches
| Starsha Bird et al. | Environmental DNA | 2024-06-17
Research in a New Zealand wetland examines filter size, DNA transport, temporal variation, and how molecular monitoring complements conventional surveys.
54. An Integrated Spatio-Temporal View of Riverine Biodiversity Using Environmental DNA Metabarcoding
| William Bernard Perry et al. | Nature Communications | 2024-05-23
Intensive sampling across several rivers shows that eDNA can detect meaningful biodiversity turnover through both space and time.
55. A Comparative Study on eDNA-Based Detection of Siamese Bat Catfish in Wet and Dry Conditions
| Maslin Osathanunkul and Chatmongkon Suwannapoom | Scientific Reports | 2024-04-17
Detection of a rare freshwater catfish varies with seasonal conditions, demonstrating that survey timing can strongly affect eDNA monitoring performance.
56. Environmental DNA as a Tool for Better Understanding the Distribution, Abundance, and Health of Atlantic and Pacific Salmon
| Ora L. Russ, J. Andrés López et al. | Fisheries | 2024
A review of dozens of studies considers how eDNA can contribute not only to salmon detection but also to abundance estimates, disease monitoring, and fisheries management.
57. Environmental DNA Dynamics of Three Species of Unionid Freshwater Mussels
| Ruiz-Ramos et al. | Environmental DNA | 2024
Experiments measure DNA shedding and degradation in three mussel species, including the federally endangered spectaclecase, to improve interpretation of field detections.
58. Enumeration Potential of Environmental DNA for Pacific Salmon Stock Assessments
| Geoffrey Y. Su et al. | Environmental DNA | 2023-12-29
Daily eDNA measurements closely tracked large spawning runs of pink salmon, indicating possible future applications in salmon enumeration and stock assessment.
59. Conservation Assessment Based on Large-Scale Monitoring of eDNA: Application to Freshwater Mussels
| Authors et al. | Biological Conservation | 2023-07
Standardized metabarcoding across 260 sites produced distribution and detection information useful for reassessing the conservation status of freshwater mussel species.
60. eDNA Metabarcoding from Aquatic Biofilms Allows Studying Spatial and Temporal Fluctuations of Fish Communities from Lake Geneva
| Sinziana F. Rivera et al. | Environmental DNA | 2023-04-03
Biofilms function as passive DNA collectors and reveal seasonal and spatial changes in lake fish communities, including signals associated with spawning periods.
61. River Benthic Macroinvertebrates and Environmental DNA Metabarcoding: A Scoping Review
| Aristeidis Parmakelis et al. | Biodiversity and Conservation | 2023
A review of dozens of studies documents considerable methodological variation in eDNA sampling, extraction, amplification, and sequencing of river macroinvertebrates.
62. Development and Validation of Two Environmental DNA Assays for American Eel
| Gregory R. Moyer et al. | Environmental DNA | 2022-10-26
Two species-specific qPCR markers were developed and tested to improve monitoring of the widely distributed but increasingly conservation-sensitive American Eel.
63. Comparison of Fish Communities Using Environmental DNA Metabarcoding and Capture Methods in a Freshwater Lake
| Authors et al. | Fisheries Research | 2022-09
Newly developed 16S primers and conventional capture surveys detected overlapping but distinct portions of the fish community in China's Lake Gehu.
64. Using eDNA to Assess the Fish Diversity and Spatial Characteristics in the Changjiang River-Shijiu Lake Connected System
| Authors et al. | Ecological Indicators | 2022
Environmental DNA detected dozens of fish taxa and helped characterize biodiversity across interconnected river, channel, and lake habitats.
65. Biodiversity Assessment Across a Dynamic Riverine System: A Comparison of eDNA Metabarcoding Versus Traditional Fish Surveying Methods
| Jane Hallam et al. | Environmental DNA | 2021-07-21
Across the Thames River system, eDNA metabarcoding detected more freshwater fish species than traditional sampling despite extensive conventional survey effort.
66. Environmental DNA Metabarcoding Uncovers Environmental Correlates of Fish Communities in Spatially Heterogeneous Freshwater Habitats
| Authors et al. | Ecological Indicators | 2021-07
Fish distributions inferred from eDNA were associated with environmental conditions including temperature, trophic status, and water age.
67. Mapping Biodiversity Hotspots of Fish Communities in Subtropical Streams Through Environmental DNA
| Rosetta C. Blackman et al. | Scientific Reports | 2021-05-14
A basin-wide eDNA survey across Thailand's Chao Phraya system detected more than one hundred fish taxa and identified important biodiversity patterns.
68. Space-Time Dynamics in Monitoring Neotropical Fish Communities Using eDNA Metabarcoding
| Authors et al. | Science of the Total Environment | 2021-02-01
River eDNA from Brazil shows that precipitation, season, hydrology, and sampling location can substantially alter apparent fish-community composition.
69. eDNA Metabarcoding Outperforms Traditional Fisheries Sampling and Reveals Fine-Scale Heterogeneity in a Temperate Freshwater Lake
| Gehri et al. | Environmental DNA | 2021
Intensive water sampling detected every fish species captured by conventional nets plus numerous additional taxa and revealed spatial community differences missed by traditional gear.
70. Environmental DNA Allows Upscaling Spatial Patterns of Biodiversity in Freshwater Ecosystems
| Luca Carraro et al. | Nature Communications | 2020-07-17
Modeling and field data demonstrate how river eDNA can be used to reconstruct biodiversity patterns across large freshwater networks.
71. Evaluation of Fish Biodiversity in Estuaries Using Environmental DNA Metabarcoding
| Authors et al. | PLOS ONE | 2020
Water samples from five Japanese estuaries revealed extensive fish diversity and demonstrated the usefulness of metabarcoding for estuarine monitoring.
72. Testing the Performance of Environmental DNA Metabarcoding for Surveying Highly Diverse Tropical Fish Communities: A Case Study from Lake Tanganyika
| Christopher J. Doble et al. | Environmental DNA | 2020
This study evaluates whether metabarcoding can effectively survey the exceptionally species-rich fish communities of an African Great Lake.
73. Usefulness and Limitations of Sample Pooling for Environmental DNA Metabarcoding of Freshwater Fish Communities
| Hirotoshi Sato, Yuki Sogo, Hideyuki Doi, Hiroki Yamanaka | Scientific Reports | 2017-11-01
The study evaluates whether pooling water samples can lower large-scale survey costs without sacrificing too much information about freshwater fish communities.
74. Annual Time-Series Analysis of Aqueous eDNA Reveals Ecologically Relevant Dynamics of Lake Ecosystem Biodiversity
| Iliana Bista et al. | Nature Communications | 2017-01-18
Repeated eDNA sampling throughout a year captured seasonal changes in lake biodiversity and demonstrated the value of molecular monitoring through time.
75. Environmental DNA Reveals That Rivers Are Conveyer Belts of Biodiversity Information
| Kristy Deiner et al. | Nature Communications | 2016-08-30
River water contains DNA originating from both aquatic and terrestrial organisms, allowing streams to integrate biodiversity information across entire landscapes.
76. Efficacy of Environmental DNA to Detect and Quantify Brook Trout Populations in Headwater Streams
| Barry P. Baldigo et al. | Transactions of the American Fisheries Society / USGS | 2016
Brook trout eDNA detections are compared with electrofishing surveys to determine how accurately molecular sampling estimates fish occurrence and abundance.
77. Characterizing the Distribution of an Endangered Salmonid Using Environmental DNA Analysis
| Matthew B. Laramie, David S. Pilliod, Caren S. Goldberg | Biological Conservation | 2015
Landscape-scale water sampling successfully detects Chinook salmon and illustrates the potential of eDNA for mapping migratory fish across large river systems.
78. Estimation of Fish Biomass Using Environmental DNA
| Teruhiko Takahara et al. | PLOS ONE | 2012
Controlled experiments demonstrated a relationship between common carp abundance and DNA concentration in water, opening the possibility of estimating biomass from eDNA.
79. Sight-Unseen Detection of Rare Aquatic Species Using Environmental DNA
| Christopher L. Jerde et al. | Conservation Letters | 2011
One of the early invasive-fish applications showed that environmental DNA could detect rare aquatic organisms even when conventional surveys failed to observe them.
Amphibians, Reptiles, Mussels, and Invasive Species
80. Environmental DNA for Endangered Freshwater Mussel Monitoring: A Review on Global Synthesis of eDNA Methods, Challenges, and Innovative Strategies
A systematic review evaluates the rapidly expanding use of eDNA for detecting endangered freshwater mussels and considers its readiness for conservation and regulatory monitoring.
81. Environmental DNA Metabarcoding Facilitates Integrative Conservation Assessments and Species Rediscoveries in Tropical Biodiversity Hotspots
| Amadeus Plewnia et al. | Scientific Reports | 2026-03-03
Amphibian eDNA surveys in the Tropical Andes detect elusive and threatened species and help identify populations that had escaped conventional biodiversity surveys.
82. Burmese Python Environmental DNA Surveys in Southern Florida
| U.S. Geological Survey | USGS | 2024-11-29
USGS researchers use waterborne DNA to help determine the distribution and possible expansion routes of cryptic invasive Burmese pythons in southern Florida.
83. Development and Optimization of a Novel Environmental DNA-Based Method for Moor Frog Monitoring
| Suvi Olli et al. | Environmental DNA | 2024-02-06
A species-specific eDNA assay offers an alternative to short seasonal calling surveys for detecting protected moor frogs.
84. Development and Validation of an Environmental DNA Assay to Detect Federally Threatened Groundwater Salamanders in Central Texas
| Michelle E. Adcock et al. | PLOS ONE | 2023
eDNA provides a non-invasive method for detecting rare groundwater salamanders in habitats where direct observation and trapping are exceptionally difficult.
85. Using eDNA to Survey Amphibians: Methods, Applications, and Challenges
| Authors et al. | Biotechnology and Bioengineering | 2023
This review summarizes amphibian eDNA survey methods, conservation applications, environmental influences on detection, and risks of false positives and negatives.
86. Environmental DNA-Based Methods Detect the Invasion Front of an Advancing Signal Crayfish Population
| Jack A. Greenhalgh et al. | Environmental DNA | 2022-01-05
Sensitive eDNA methods reveal the leading edge of an invasive signal crayfish population where conventional detection can be especially difficult.
87. A Review of Applications of Environmental DNA for Reptile Conservation and Management
| Authors et al. | Ecology and Evolution | 2022
The review evaluates eDNA research involving turtles, snakes, crocodilians, and lizards and identifies major opportunities for monitoring cryptic reptile populations.
88. Strategic Considerations for Invasive Species Managers in the Utilization of Environmental DNA
| Authors et al. | Management of Biological Invasions | 2022
This practitioner-oriented article explains how managers can decide when eDNA is appropriate for invasive-species surveillance and how detections should be interpreted.
89. Environmental DNA as a Tool to Help Inform Zebra Mussel Management in Inland Lakes
| Jon Amberg et al. | Management of Biological Invasions | 2019-03-22
Zebra mussel eDNA can extend monitoring beyond periods when larval veligers are easily detected and may improve early-warning programs.
90. Environmental DNA Improves Eastern Hellbender Detection over Conventional Sampling Methods
| Sean M. Wineland et al. | Environmental DNA | 2019
Water sampling detects Eastern Hellbenders at sites where traditional searches may miss these large but cryptic aquatic salamanders.
91. Environmental DNA Applications for the Conservation of Imperiled Crayfish
| Authors et al. | Journal of Crustacean Biology | 2018-03-10
eDNA is used to monitor endangered Shasta crayfish, invasive signal crayfish, and management interventions intended to separate the two species.
92. Searching for a Signal: Environmental DNA for the Detection of Invasive Signal Crayfish
| Kirsten J. Harper et al. | Management of Biological Invasions | 2018
Researchers test eDNA as a rapid and non-invasive method for detecting invasive signal crayfish in Scottish freshwater systems.
93. Environmental DNA Sampling Improves Occurrence and Detection Estimates of Invasive Burmese Pythons
| Margaret E. Hunter et al. | PLOS ONE | 2015-04-15
Combining eDNA with occupancy modeling increases the ability to estimate Burmese python occurrence despite the exceptionally low detectability of these invasive snakes.
94. Molecular Detection of Vertebrates in Stream Water: A Demonstration Using Rocky Mountain Tailed Frogs and Idaho Giant Salamanders
| Caren S. Goldberg et al. | PLOS ONE | 2011
Stream-water DNA successfully detects cryptic amphibians and demonstrates that eDNA can function in flowing-water environments as well as ponds and lakes.
Marine, Coastal, Estuarine, Fisheries, Coral Reefs, and Deep-Sea eDNA
95. Application of Environmental DNA Technology in Monitoring Species Diversity at Multiple Biological Groups in Marine Protected Area
| Yukun Zhang et al. | Marine Environmental Research | 2026-08
Multi-marker eDNA sampling in a marine protected area simultaneously detects fish, phytoplankton, and invertebrates and provides a broad conservation baseline.
96. Environmental DNA Sampling from Whale-Watching Vessels for Cetacean Monitoring
| Belén G. Ovide et al. | Journal of Visualized Experiments | 2026-04-10
The protocol shows how researchers and trained citizen scientists aboard whale-watching vessels can systematically collect seawater for cetacean eDNA monitoring.
97. Environmental DNA as a Tool for the Assessment of Coral Composition in the Chagos Archipelago
| Boxian Wen et al. | Environmental DNA | 2026-02-05
Coral-focused metabarcoding evaluates whether seawater DNA can complement diver-based reef monitoring in the remote Chagos Archipelago.
98. Environmental DNA from Pumped Deep-Sea Water Enables Monitoring of Deep-Sea Fish Diversity
| Authors et al. | Scientific Reports | 2026
Water pumped from deep ocean intakes retains sufficient eDNA to characterize deep-sea fish assemblages, potentially enabling long-term monitoring from shore-based infrastructure.
99. Environmental DNA Reveals Diverse and Depth-Stratified Biodiversity in East Indian Ocean Submarine Canyons
| Georgia M. Nester et al. | Environmental DNA | 2026
Deep-water eDNA sampling reveals substantial biodiversity differences among ocean depths and illustrates its value for poorly explored submarine ecosystems.
100. Depth-Driven Biodiversity Patterns and Community Structure in the Beipo Seamount Revealed by Environmental DNA
| Authors et al. | Ecological Indicators | 2026
Multi-depth sampling demonstrates that eDNA can identify strong vertical patterns in seamount biodiversity that would be expensive to document using conventional deep-sea surveys.
101. Environmental DNA Reveals Coastal Fish Biodiversity Response Across the Atlantic-Indian Ocean Environmental Transition Gradient
| Authors et al. | Ecological Indicators | 2025-10
A roughly 2,800-kilometer survey of South Africa's coast uses eDNA to identify large-scale changes in fish-community structure across environmental regions.
102. Spatiotemporal eDNA Monitoring of Marine Biodiversity in a Hyperurbanised Coastal Environment
| Zhi Ting Yip et al. | Environmental DNA | 2025-08-14
Repeated sampling around heavily urbanized Singapore demonstrates how eDNA can track biodiversity patterns despite intense coastal development.
103. How Fragmented Is eDNA? A Case Study on Shark DNA in Tropical Reef Seawater
| Katrina M. West, Bruce Deagle et al. | Environmental DNA | 2025-08-02
Tiger shark DNA recovered from seawater shows that some eDNA fragments are substantially longer than commonly assumed, potentially enabling finer genetic analyses.
104. Environmental DNA Analysis at Multiple Taxonomic Levels Highlights Geographic Variation in Subtropical Coastal Marine Communities
| Kodai Gibu et al. | Scientific Reports | 2025-07-01
Multi-marker eDNA surveys reveal geographic differences in coastal communities across several taxonomic levels and illustrate the value of broad ecosystem-scale sampling.
105. Fish Diversity Assessment and Semi-Quantitative Biomass Estimation Through Metabarcoding of Environmental DNA
| Authors et al. | Ecological Indicators | 2025-04
Comparisons with bottom trawls indicate that eDNA metabarcoding may provide useful information about both marine fish diversity and relative biomass.
106. Application of eDNA Metabarcoding in the Assessment of Fish Biodiversity in Philippine Mangroves
| Camila Frances P. Naputo et al. | Regional Studies in Marine Science | 2024-12-10
This study evaluates the advantages and practical difficulties of applying eDNA to biodiversity monitoring and restoration planning in Philippine mangrove ecosystems.
107. Detection of the Jellyfish Chrysaora pacifica by RPA-CRISPR-Cas12a Environmental DNA Assay
| Authors et al. | Science of the Total Environment | 2024-12-10
A portable CRISPR-based assay provides highly sensitive detection of jellyfish DNA and could improve early warning of problematic blooms.
108. Environmental DNA Metabarcoding Reveals the Influence of Environmental Heterogeneity on Microeukaryotic Plankton in the Offshore Waters of East China Sea
| Authors et al. | Environmental Research | 2024-12-01
eDNA shows how nutrient conditions and other environmental gradients influence plankton diversity, community assembly, and ecological stability.
109. Complementary Roles of eDNA Metabarcoding and Microscopy in Plankton Monitoring Across Seven Habitats
| Xingyu Chen et al. | Journal of Plankton Research | 2024-10-02
Molecular and microscope-based surveys detect overlapping but different elements of plankton biodiversity, supporting their complementary use.
110. Environmental DNA Reveals the Impact of Submarine Groundwater Discharge on the Spatial Variability of Coastal Fish Diversity
| Authors et al. | Biology | 2024-08-11
Coastal eDNA surveys show that freshwater and nutrient inputs from submarine groundwater discharge can structure nearby fish communities.
111. Environmental DNA Reveals Fine-Scale Spatial and Temporal Variation of Marine Mammals and Their Prey Species in a Scottish Marine Protected Area
| Elizabeth Boyse et al. | Environmental DNA | 2024-07-22
Repeated seawater sampling reveals changes in marine mammal detections and prey communities across space and time within a protected area.
112. Vertical and Horizontal Environmental DNA Patterns of Fish in a Shallow and Well-Mixed North Sea Area
| Nergiz Dukan et al. | Scientific Reports | 2024-07-20
Even in shallow, mixed coastal waters, sampling position and depth can affect fish eDNA patterns and therefore influence monitoring design.
113. Applying Environmental DNA Approaches to Inform Marine Biodiversity Conservation: The Ocean Twilight Zone
| Authors et al. | Marine Policy | 2024-07
The article considers how scalable eDNA monitoring could fill biodiversity-data gaps in the mesopelagic ocean and support high-seas conservation policy.
114. Exploring Microbiome and Plankton Responses and Interactions in the Mangrove Ecosystem Through eDNA and Network Analysis
| Authors et al. | Science of the Total Environment | 2024-06-20
Multi-marker sequencing simultaneously characterizes microbes, plankton, and fish and reveals biological interaction networks within mangrove systems.
115. Field Collections and Environmental DNA Surveys Reveal Topographic Complexity of Coral Reefs as a Predictor of Cryptobenthic Biodiversity
| O. B. Brodnicke et al. | Environmental DNA | 2024-05-17
Combining physical collections and eDNA demonstrates that structurally complex coral reefs support distinctive communities of small and often overlooked organisms.
116. Environmental DNA as a Tool to Reconstruct Catch Composition for Longline Fisheries Vessels
| M. E. Green et al. | Scientific Reports | 2024-05-03
DNA collected from vessel brine tanks successfully reconstructed target and bycatch species, offering another tool for fisheries monitoring and compliance.
117. Environmental DNA Metabarcoding Reveals the Effects of Seafloor Litter and Trawling on Marine Biodiversity
| Alice Sbrana et al. | Marine Environmental Research | 2024-04
Metabarcoding reveals shifts in seafloor biological communities associated with bottom trawling and marine litter.
118. DNA from Dives: Species Detection of Humpback Whales from Flukeprint eDNA
| C. V. Robinson et al. | Environmental DNA | 2024-03-12
Water collected from the turbulent footprint left after a whale dives can contain enough DNA for reliable humpback-whale detection.
119. Detecting Kelp-Forest Associated Metazoan Biodiversity with eDNA Metabarcoding
| Emma I. Rossouw et al. | npj Biodiversity | 2024-02-21
South African kelp-forest sampling demonstrates that eDNA can inventory diverse marine organisms in a region where the technique has historically been underused.
120. Environmental DNA Captures Diurnal Fluctuations of Surface Eukaryotes on a Tropical Coral Reef
| Rosalie Dowell et al. | Environmental DNA | 2024-02-18
Repeated reef-water sampling shows that detectable eDNA communities can change over the course of a single day, making sampling time an important survey consideration.
121. eDNA Based Bycatch Assessment in Pelagic Fish Catches
| Paulina Urban et al. | Scientific Reports | 2024-02-05
Molecular analysis of commercial catches provides an alternative method for identifying otherwise difficult-to-document bycatch in pelagic fisheries.
122. Conventional Net Tow Versus Environmental DNA for Metabarcoding-Based Analysis of Plankton-Environment Interactions
| Authors et al. | Ecological Indicators | 2024-01
eDNA recovered broad plankton diversity efficiently and identified many of the same environmental drivers detected through conventional net sampling.
123. The Effect of Spatio-Temporal Sampling and Biological Replication on the Detection of Kelp Forest Fish Communities Using eDNA Metabarcoding
| Courtaillac et al. | Environmental DNA | 2024
South African field experiments show how sampling location, depth, time, replication, and pooling affect fish-community detection in kelp forests.
124. Environmental DNA Metabarcoding for Fish Diversity Assessment in a Macrotidal Estuary
| Authors et al. | Estuarine, Coastal and Shelf Science | 2023-11-05
eDNA identifies more estuarine fish species than individual conventional netting techniques and captures ecological changes associated with season and salinity.
125. Integration of Environmental DNA Metabarcoding Technique to Reinforce Fish Biodiversity Assessments in Seagrass Ecosystems: Gazi Bay
| Samuel Mwakisha Mwamburi et al. | Environmental DNA | 2023-10-17
eDNA surveys of Kenyan seagrass, mangrove-seagrass, and coral-seagrass habitats complement conventional observations and document substantial differences in fish diversity.
126. Addressing Data-Deficiency of Threatened Sharks and Rays in a Highly Dynamic Coastal Ecosystem Using Environmental DNA
| Authors et al. | Ecological Indicators | 2023-10
eDNA surveys of Guinea-Bissau's Bijagós Archipelago documented numerous threatened sharks and rays in a turbid and logistically difficult coastal ecosystem.
127. Extending Deep-Sea Benthic Biodiversity Inventories with Environmental DNA Metabarcoding
| Authors et al. | Marine Biology | 2023-04-13
Sedimentary eDNA expands biodiversity inventories in deep-sea habitats that are difficult and expensive to study using conventional sampling.
128. Archived DNA Reveals Marine Heatwave-Associated Shifts in Fish Assemblages
| Zachary Gold et al. | Environmental DNA | 2023-03-28
Archived environmental samples allow researchers to reconstruct fish-community changes associated with major marine heatwaves.
129. Optimized DNA Isolation from Marine Sponges for Natural Sampler DNA Metabarcoding
| Lynsey R. Harper et al. | Environmental DNA | 2023-01-20
Because sponges continuously filter seawater, DNA accumulated in their tissues can provide a natural passive record of surrounding marine biodiversity.
130. Seas the DNA? Limited Detection of Cetaceans by Low-Volume Environmental DNA Transect Surveys
| C. V. Robinson et al. | Environmental DNA | 2023
Low-volume sampling successfully detected several cetaceans but also demonstrated that inadequate water volume can substantially reduce detection probability.
131. Elasmobranch Diversity Across a Remote Coral Reef Atoll Revealed Through Environmental DNA Metabarcoding
| Authors et al. | Zoological Journal of the Linnean Society | 2022-04-14
Seawater metabarcoding around the Chagos Archipelago identifies numerous sharks and rays and reveals differences among habitats and sampling depths.
132. Environmental DNA Metabarcoding: A Novel Method for Biodiversity Monitoring of Marine Fish Communities
| Masaki Miya | Annual Review of Marine Science | 2022
This major review examines the development of fish-focused metabarcoding, including the widely used MiFish primers and applications to marine biodiversity monitoring.
133. Estuarine Fishes Associated with Intertidal Oyster Reefs Characterized Using Environmental DNA and Baited Remote Underwater Video
| Victoria J. Cole et al. | Environmental DNA | 2022
Combining eDNA with underwater video provides complementary information about fish assemblages associated with oyster reefs and nearby unvegetated habitats.
134. Modeling Characterization of the Vertical and Temporal Variability of Environmental DNA in the Mesopelagic Ocean
| Elizabeth Andruszkiewicz Allan et al. | Scientific Reports | 2021-10-28
Oceanographic modeling illustrates how biological processes, currents, depth, and time influence eDNA distributions in the difficult-to-monitor mesopelagic ocean.
135. Remote, Autonomous Real-Time Monitoring of Environmental DNA from Commercial Fish
| Brian K. Hansen et al. | Scientific Reports | 2020-08-06
An Environmental Sample Processor automatically collects, extracts, analyzes, and reports fish eDNA, demonstrating the possibility of near-real-time ocean monitoring.
136. Environmental DNA Survey Captures Patterns of Fish and Invertebrate Diversity Across a Tropical Seascape
| Bryan N. Nguyen et al. | Scientific Reports | 2020-04-21
Broad COI metabarcoding detected thousands of animal taxa and distinguished biological communities across neighboring Caribbean marine habitats.
137. Validating Environmental DNA Metabarcoding for Marine Fishes in Diverse Ecosystems Using a Public Aquarium
| Kevin C. Morey et al. | Environmental DNA | 2020-03-04
Aquarium systems containing known fish communities provide a controlled way to test metabarcoding accuracy before applying methods to highly diverse marine environments.
138. Environmental DNA Reveals Seasonal Shifts and Potential Interactions in a Marine Community
| Anni Djurhuus et al. | Nature Communications | 2020-01-14
Repeated seawater sampling detects seasonal marine-community turnover and illustrates how eDNA time series can reveal ecological dynamics.
139. Marine Water Environmental DNA Metabarcoding Provides a Comprehensive Fish Diversity Assessment and Reveals Spatial Patterns in a Large Oceanic Area
| Fraija-Fernández et al. | Ecology and Evolution | 2020
Large-area seawater sampling demonstrates the potential of eDNA to characterize marine fish diversity without the selectivity and physical disturbance of trawling.
140. Detection of Introduced and Resident Marine Species Using Environmental DNA Metabarcoding of Sediment and Water
| Luke E. Holman et al. | Scientific Reports | 2019-08-09
Comparing water and sediment samples demonstrates the usefulness of eDNA for detecting both native marine organisms and potentially invasive species.
141. Detection of a Diverse Marine Fish Fauna Using Environmental DNA from Seawater Samples
| Philip Francis Thomsen et al. | PLOS ONE | 2012-08-29
Although marine-focused, this landmark fish study helped establish metabarcoding as a practical method for detecting diverse vertebrate communities from water.
Terrestrial, Soil, Airborne, Plants, Mammals, Arthropods, and Pollinator eDNA
142. Soil eDNA Biomonitoring: Assessing Efficacy for Detecting Terrestrial Vertebrate and Plant Biodiversity
| Authors et al. | Environmental Science & Technology | 2026-07-07
Soil eDNA detects terrestrial vertebrates at levels comparable to camera trapping while recovering particularly rich plant biodiversity information.
143. Non-Destructive Environmental DNA Extracted from Owl Pellet Contents: A Valuable Tool for Monitoring Mammalian Species Richness
| Authors et al. | PLOS ONE | 2026
DNA extracted without destroying owl pellets provides information about mammalian prey communities and offers an additional terrestrial biodiversity-monitoring substrate.
144. Flower-Derived Environmental DNA Reveals Community Diversity, Species Abundances and Ecological Interactions in Bee Pollinators
| Arndt Schmidt et al. | Environmental DNA | 2025-08-18
DNA deposited on flowers by visiting insects can reveal bee communities and plant-pollinator interactions without needing to capture the pollinators themselves.
145. Environmental DNA as a Tool for Soil Health Monitoring and Unveiling New Ecological Frontiers
| Authors et al. | Ecological Indicators | 2025-05
This review considers soil eDNA applications in biodiversity conservation, sustainable agriculture, ecosystem-health assessment, climate studies, and landscape monitoring.
146. Using Flower eDNA Metabarcoding to Identify the Effects of Forest Structure and Microclimate on Flower-Visiting Arthropods
| Díaz-Calafat et al. | Environmental DNA | 2025
DNA left behind on flowers reveals highly localized arthropod communities and provides a way to investigate how forest structure and microclimate affect flower visitors.
147. Complementary Role of Environmental DNA for Line-Transect Bird Surveys: A Field Test in a Japanese Rice Landscape
| Authors et al. | Ecological Indicators | 2024-09
Paddy-water eDNA detected aquatic birds missed by visual surveys, while conventional transects remained superior for most terrestrial bird species.
148. Environmental DNA Metabarcoding of Pan Trap Water to Monitor Arthropod-Plant Interactions
| Joshua H. Kestel et al. | Environmental DNA | 2024-03-12
Water remaining inside insect pan traps contains useful environmental DNA that can supplement information obtained from the insects physically collected in the traps.
149. Spider Webs Capture Environmental DNA from Terrestrial Vertebrates
| Authors et al. | iScience | 2024
Spider webs act as passive collectors of vertebrate DNA and may provide an inexpensive new way to survey terrestrial animals.
150. Airborne Environmental DNA Captures Terrestrial Vertebrate Diversity in Nature
| Christina Lynggaard et al. | Molecular Ecology Resources | 2024
Forest air samples in Denmark detected dozens of wild vertebrate taxa, showing that airborne eDNA works outside controlled zoo environments.
151. Using Environmental DNA to Detect and Identify Sweetpotato Whitefly and Twospotted Spider Mite in Greenhouse-Grown Tomato Plants
| Lee-Rodriguez et al. | Environmental DNA | 2024
DNA washed from leaf surfaces enables sensitive detection of two economically significant agricultural pests without requiring visual identification.
152. Prospects of Pollinator Community Surveillance Using Terrestrial Environmental DNA Metagenetics
| Grace Avalos et al. | Environmental DNA | 2023-12-21
Flower and pollen eDNA detect bee taxa and demonstrate opportunities and remaining limitations for scaling molecular pollinator monitoring.
153. Using Surface Environmental DNA to Assess Arthropod Biodiversity within a Forested Ecosystem
| Michael C. Allen et al. | Environmental DNA | 2023-11-06
DNA collected from foliage and tree bark reveals hundreds of arthropod taxa and demonstrates a non-destructive approach to forest invertebrate inventories.
154. Monitoring Terrestrial Wildlife by Combining Hybridization Capture and Metabarcoding Data from Waterhole Environmental DNA
| Authors et al. | Biological Conservation | 2023-08
Combining metabarcoding with targeted hybridization capture increases the amount of genetic information recovered from wildlife DNA deposited at waterholes.
155. Answers Blowing in the Wind: Detection of Birds, Mammals, and Amphibians with Airborne Environmental DNA in a Natural Environment over a Yearlong Survey
| Mark D. Johnson et al. | Environmental DNA | 2023-01-20
Passive dust collectors deployed on a prairie throughout a year detected numerous vertebrates and showed that rainfall, wind, and animal activity influence airborne DNA signals.
156. Airborne eDNA Documents a Diverse and Ecologically Complex Tropical Bat and Other Mammal Community
| Garrett et al. | Environmental DNA | 2023-01-11
Air sampling successfully characterized a highly diverse tropical bat assemblage and demonstrates potential for monitoring dense or inaccessible roosting communities.
157. Sampling Environmental DNA from Trees and Soil to Detect Cryptic Arboreal Mammals
| Michael C. Allen et al. | Scientific Reports | 2023-01-05
Tree-bark and soil samples detect numerous mammal species, demonstrating that terrestrial eDNA surveys do not need to rely solely on nearby bodies of water.
158. Using eDNA for Mammal Inventories Still Needs Naturalist Expertise: A Meta-Analysis
| Authors et al. | Ecology and Evolution | 2023
A meta-analysis shows substantial promise for mammalian eDNA but concludes that traditional ecological knowledge and survey expertise remain important.
159. BeeDNA: Microfluidic Environmental DNA Metabarcoding as a Tool for Connecting Plant and Pollinator Communities
| Lynsey R. Harper et al. | Environmental DNA | 2022-10-19
DNA deposited by insects on flowers can identify pollinator visitors, while microfluidic metabarcoding allows multiple genetic markers to be processed simultaneously.
160. Environmental DNA as a Management Tool for Tracking Artificial Waterhole Use in Savanna Ecosystems
| Authors et al. | Biological Conservation | 2022-10
eDNA from artificial waterholes in South Africa's Kruger National Park is compared with camera traps to evaluate how reliably water samples record visiting mammals.
161. Accumulation and Diversity of Airborne, Eukaryotic Environmental DNA
| Martin Johannesen Klepke et al. | Environmental DNA | 2022-07-18
Air samples contain detectable DNA from numerous eukaryotic organisms, including vertebrates and insects, supporting the development of airborne biodiversity monitoring.
162. Metabarcoding of Soil Environmental DNA Replicates Plant Community Variation but Not Specificity
| Christopher James Barnes et al. | Environmental DNA | 2022-02-22
Soil metabarcoding reproduces broad variation among plant communities but also illustrates the difficulty of translating soil DNA directly into precise local vegetation inventories.
163. Airborne Environmental DNA for Terrestrial Vertebrate Community Monitoring
| Christina Lynggaard et al. | Current Biology | 2022-02-07
Air filtration around Copenhagen Zoo detected dozens of mammals, birds, fish, amphibians, and reptiles, establishing airborne DNA as a promising vertebrate-monitoring substrate.
164. Measuring Biodiversity from DNA in the Air
| Elizabeth L. Clare et al. | Current Biology | 2022-02-07
Airborne DNA recovered from a zoological park detected mammals and birds and demonstrated that vertebrate eDNA can disperse hundreds of meters from its source.
165. Environmental DNA Metabarcoding: A Novel Contrivance for Documenting Terrestrial Biodiversity
| Authors et al. | Plants | 2022
This review examines how soil, water, surfaces, and other terrestrial substrates can be exploited for DNA-based surveys of land-based biodiversity.
166. Environmental DNA Analysis as an Emerging Non-Destructive Method for Plant Biodiversity Monitoring
| Authors et al. | Botanical Review / Plant-focused review | 2022
The review finds considerable potential for using eDNA to detect rare, endangered, invasive, and otherwise difficult-to-monitor plant species.
167. eDNA Metabarcoding of Log Hollow Sediments and Soils Highlights the Importance of Substrate Type, Frequency of Sampling and Animal Size
| Ryan et al. | Environmental DNA | 2022
Sediment accumulating inside fallen tree hollows retains vertebrate DNA and can reveal animals that visited the location weeks or even months before sampling.
168. Terrestrial eDNA Survey Outperforms Conventional Approach for Detecting an Invasive Pest Insect Within an Agricultural Ecosystem
| Michael C. Allen et al. | Environmental DNA | 2021-08-02
DNA collected from environmental surfaces improves detection of an invasive agricultural insect compared with conventional visual surveillance.
169. The State, Transport, and Fate of Aboveground Terrestrial Arthropod eDNA
| Rafael E. Valentin et al. | Environmental DNA | 2021-07-09
Experiments investigate how sunlight, rainfall, DNA state, and filter pore size influence arthropod DNA deposited on vegetation.
170. Environmental DNA Metabarcoding as a Useful Tool for Evaluating Terrestrial Mammal Diversity in Tropical Forests
| José Luis Mena et al. | Ecological Applications | 2021-03-29
Molecular monitoring is compared with trapping, mist-netting, and camera surveys for documenting mammals in highly diverse Amazonian forests.
171. Detection of Endangered Aquatic Plants in Rapid Streams Using Environmental DNA
| Authors et al. | Frontiers in Ecology and Evolution | 2021-01-28
Species-specific eDNA provides a non-destructive method for locating endangered aquatic plants in fast-flowing streams where conventional botanical surveys may be difficult.
172. eDNAir: Proof of Concept That Animal DNA Can Be Collected from Air Sampling
| Elizabeth L. Clare et al. | PeerJ | 2021
Air sampling successfully captures mammal DNA and establishes proof of concept for monitoring terrestrial vertebrates without directly observing them.
173. eDNA Sampled from Stream Networks Correlates with Camera Trap Detection Rates of Terrestrial Mammals
| Authors et al. | Scientific Reports | 2021
Stream-water metabarcoding detected more mammal taxa than a dense camera-trap network in the same landscape and did so at substantially lower sampling cost.
174. Power and Limitations of Environmental DNA Metabarcoding for Surveying Leaf Litter Eukaryotic Communities
| Carla Martins Lopes et al. | Environmental DNA | 2020-10-06
Leaf litter contains DNA from exceptionally diverse terrestrial communities, but incomplete reference databases and differences in DNA recovery complicate precise species inventories.
175. Environmental DNA Metabarcoding of Pond Water as a Tool to Survey Conservation and Management Priority Mammals
| Authors et al. | Biological Conservation | 2019-10
Mammalian DNA deposited in ponds can reveal both semi-aquatic and terrestrial species, providing a relatively simple way to monitor difficult-to-detect mammals.
176. Methodological Considerations for Detection of Terrestrial Small-Body Salamander eDNA
| Authors et al. | Wildlife Society Bulletin / Conservation research | 2017
Experiments with soil, skin swabs, fecal material, and salamander DNA demonstrate both the promise and difficulty of recovering eDNA in terrestrial habitats.
177. DNA from Soil Mirrors Plant Taxonomic and Growth Form Diversity
| Nigel G. Yoccoz et al. | Molecular Ecology | 2012
Soil DNA profiles broadly reflect surrounding plant diversity and provided an early demonstration that terrestrial environmental samples could reconstruct vegetation communities.
Conservation, Management, Policy, Ethics, and Emerging Applications
178. Environmental DNA/RNA for Non-Invasive Early Detection and Monitoring of Pathogen Dynamics in Atlantic Salmon Recirculating Aquaculture Systems
| Dhiraj Krishna et al. | Aquaculture | 2026-01-01
Waterborne DNA and RNA detected several important salmon pathogens and demonstrated the possibility of continuous, non-lethal disease surveillance in aquaculture systems.
179. Environmental DNA as a Method to Reconstruct Food Webs and Assess Ecosystem Health
| Authors et al. | Ecological Indicators | 2025-04
Researchers combine eDNA-derived community information with ecological network analysis to reconstruct food webs and develop potential indicators of ecosystem condition.
180. DNA Fragments in Air, Soil and Water Could Be Used in the Investigation of Crime and Warn of Biosecurity Threats
| The Royal Society | The Royal Society | 2025-03-10
A Royal Society policy briefing explores environmental monitoring, agriculture, biosecurity, forensic uses, data infrastructure, privacy concerns, and the growing problem of unintended human DNA collection.
181. Environmental DNA
This overview emphasizes standardized data practices, quality assurance, improved reference libraries, and transparent interpretation as eDNA becomes increasingly integrated into conservation and wildlife management.
182. Environmental DNA Methods for Biosecurity and Invasion Biology in Terrestrial Ecosystems: Progress, Pitfalls, and Prospects
| Authors et al. | Science of the Total Environment | 2024-05-20
The review examines how terrestrial eDNA can support biosecurity from the initial detection of newly arriving invasive species through surveillance and confirmation of eradication.
183. Importance of eDNA Taphonomy and Sediment Provenance for Robust Ecological Inference
| K. K. Sand et al. | Environmental DNA | 2024-03-11
DNA interactions with minerals and sediments influence preservation, transport, and recovery, meaning sediment geochemistry must be considered when reconstructing ecological communities from eDNA.
184. Environmental DNA Expeditions in UNESCO World Heritage Marine Sites
UNESCO's international citizen-science program uses standardized seawater eDNA sampling across marine World Heritage sites to document biodiversity and investigate climate-related changes.
185. Deep Sequencing of Extracellular eDNA Enables Total Biodiversity Assessment of Ecosystems
| Authors et al. | Ecological Indicators | 2023-12
A PCR-free extracellular-DNA approach recovered organisms across broad sections of the tree of life from India's Chilika Lagoon and captured large-scale biodiversity changes.
186. Environmental DNA and RNA in Aquatic Community Ecology: Toward Methodological Standardization
| Ingrid V. Bunholi et al. | Environmental DNA | 2023-09-28
The authors examine the increasingly complementary use of environmental DNA and environmental RNA and call for standardized collection and analytical protocols.
187. Ethical Considerations for Human Sequences in Environmental DNA
| Hideyuki Doi and Ryan P. Kelly | Nature Ecology & Evolution | 2023-07-06
The authors argue that researchers must establish ethical safeguards as biodiversity surveys increasingly generate incidental human genetic information.
188. Applications of Environmental DNA to Detect Subterranean and Aquatic Invasive Species
| Authors et al. | Environmental Advances | 2023-07
This critical review examines eDNA metabarcoding for invasive species surveillance while emphasizing contamination, DNA transport, incomplete reference libraries, and interpretation challenges.
189. Inadvertent Human Genomic Bycatch and Intentional Capture Raise Beneficial Applications and Ethical Concerns with Environmental DNA
| Liam Whitmore et al. | Nature Ecology & Evolution | 2023-05-15
Deep sequencing of environmental samples can inadvertently recover surprisingly detailed human genomic information, creating significant questions about privacy, consent, surveillance, and data ownership.
190. The Ethics of Human Sequences in Environmental Samples
| Natalie Ram | Nature Ecology & Evolution | 2023-05-15
This commentary examines the legal and ethical implications of recovering human genetic material during environmental sampling.
191. Large-Scale eDNA Monitoring of Multiple Aquatic Pathogens as a Tool to Provide Risk Maps for Wildlife Diseases
| Natalie Sieber et al. | Environmental DNA | 2023-05-11
Simultaneously screening environmental samples for multiple pathogens can produce landscape-scale disease-risk maps without repeatedly capturing and examining wildlife.
192. eDNA in Subterranean Ecosystems: Applications, Technical Aspects, and Future Prospects
| Authors et al. | Science of the Total Environment | 2022
Environmental DNA could greatly expand knowledge of groundwater and cave biodiversity, where conventional sampling is particularly difficult and many organisms remain poorly documented.
193. Environmental DNA as a Tool for Invasive Species Detection and Management
| Sarah Burgiel and Carol Stepien | National Invasive Species Council / NOAA Repository | 2022
This management-oriented report examines how eDNA can strengthen surveillance, early detection, monitoring, and decision-making for invasive species.
194. Reinforcement of Environmental DNA Based Methods in Biodiversity Monitoring and Conservation
| Authors et al. | Biology | 2021
The review summarizes applications to invasive-species detection, endangered-species surveys, community monitoring, ecosystem health, and ecological interactions.
195. The Future of Biodiversity Monitoring and Conservation Utilizing Environmental DNA
| Kristy Deiner | Environmental DNA | 2020-12-21
This perspective describes how eDNA is progressing from species detection toward abundance estimates, population genetics, ecosystem monitoring, and conservation decision-making.
196. Numerical Methods for Sedimentary-Ancient-DNA-Based Study on Past Biodiversity and Ecosystem Functioning
| Wentao Chen and Gentile Francesco Ficetola | Environmental DNA | 2020-03-09
Statistical approaches including occupancy models, abundance estimation, clustering, ordination, and causal analysis can extract considerably more ecological information from sedimentary ancient DNA records.
197. Are Environmental DNA Methods Ready for Aquatic Invasive Species Management?
The authors argue that validated eDNA methods are sufficiently mature for management but that clearer decision frameworks are needed for translating detections into management actions.
198. Past, Present, and Future Perspectives of Environmental DNA Metabarcoding
| Authors et al. | Global Ecology and Conservation | 2019
A systematic review traces the rapid expansion of metabarcoding across aquatic and terrestrial ecosystems and discusses methodological trends and future applications.
199. Species-Level Biodiversity Assessment Using Marine Environmental DNA Metabarcoding Requires Protocol Optimization and Standardization
| Authors et al. | Ecology and Evolution | 2019
Marine experiments show that differences in filtration, DNA extraction, primers, and laboratory procedures can substantially influence species-level biodiversity results.
200. Uses and Misuses of Environmental DNA in Biodiversity Science and Conservation
| David L. Jerde et al. | Annual Review of Ecology, Evolution, and Systematics | 2018-11-02
This critical review emphasizes that eDNA is powerful but warns against overinterpreting detections without understanding DNA transport, persistence, contamination, and false-positive risks.
