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Environmental DNA

Environmental DNA (eDNA) is genetic material originating from organisms that is released into environmental samples such as water, soil, sediment, or air through processes like shedding of skin cells, excretion, or decomposition, allowing for the detection and monitoring of biodiversity without the need for direct capture or observation of the organisms themselves.^[1]^[2] This material persists in the environment for varying durations—up to several weeks in aquatic settings—depending on factors like temperature, pH, and UV exposure, enabling non-invasive sampling from diverse ecosystems.^[2] The concept of eDNA emerged in the early 2000s, building on advances in polymerase chain reaction (PCR) and high-throughput sequencing technologies that made it feasible to amplify and identify trace DNA from bulk environmental samples.^[1] Early applications focused on aquatic environments, with seminal studies demonstrating its use for detecting invasive species like Asian carp in the Great Lakes region of North America.^[2] By the 2010s, eDNA analysis expanded to terrestrial and aerial sampling, incorporating methods such as metabarcoding—which targets specific genetic markers like the cytochrome c oxidase I (COI) gene—to assess entire biological communities rather than single species.^[3] These techniques involve filtering environmental samples, extracting DNA, amplifying target regions via PCR, and sequencing to match against reference databases for taxonomic identification.^[1]^[2] eDNA has revolutionized biodiversity monitoring by offering a cost-effective, scalable alternative to traditional survey methods like netting, trapping, or visual counts, which can be labor-intensive and disruptive to sensitive habitats.^[3] It is particularly valuable for detecting rare, elusive, or endangered species—such as amphibians in Japanese wetlands or fish in remote ponds—providing higher sensitivity and earlier detection of presence or invasion risks.^[2] Applications extend to ecosystem health assessments, including pathogen surveillance (e.g., viruses and bacteria in rivers) and tracking responses to environmental changes like pollution or climate shifts, with thousands of peer-reviewed studies published since 2003 highlighting its efficacy across taxa from microbes to macro-organisms.^[3]^[4] As of 2025, eDNA is increasingly integrated into large-scale national surveys and fisheries stock assessments.^[5]^[6] Despite these advantages, eDNA methods face challenges, including potential false positives from contamination during sampling or lab processing, variability in DNA shedding rates among species, and degradation in harsh environmental conditions that can limit detection windows.^[1]^[2] It also cannot quantify population sizes or precise locations, necessitating integration with complementary approaches for comprehensive ecological insights.^[1] Ongoing research emphasizes standardization of protocols, expansion of genetic reference libraries, and addressing geographic biases—such as underrepresentation in low-income regions—to enhance reliability and global applicability.^[3] As sequencing costs continue to decline, eDNA holds promise for real-time monitoring and supporting conservation efforts amid accelerating biodiversity loss.^[2]

Fundamentals

Definition and Overview

Environmental DNA (eDNA) refers to genetic material released by organisms into their surrounding environment, including water, soil, air, sediments, or other media, through sources such as skin cells, feces, gametes, hair, or decomposition products. This DNA is isolated directly from environmental samples rather than from captured organisms, capturing traces from microbial, meiofaunal, and macrofaunal life forms. Unlike traditional biodiversity sampling methods, such as netting, trapping, or electrofishing, which involve direct capture and can be invasive and labor-intensive, eDNA analysis provides a non-invasive approach to indirectly detect species presence, relative abundance, and community diversity by examining these shed genetic traces. Key to eDNA's utility is its role as a proxy for organismal biomass and community structure, where DNA concentrations often correlate with species abundance, though modulated by factors like shedding rates and transport dynamics. eDNA persistence varies widely by environmental conditions—ranging from hours to days in dynamic aquatic systems due to degradation from UV light, temperature, and microbial activity, to months or years in stable sediments or soils where it binds to particles for protection. In metabarcoding applications, amplified eDNA sequences enable simultaneous identification of multiple taxa from a single sample, enhancing biodiversity assessments. eDNA exists in forms such as intracellular DNA within intact cells or extracellular DNA as free-floating fragments. The advantages of eDNA over conventional techniques include greater cost-effectiveness, with studies showing reduced expenses for equivalent or superior detection rates; improved sensitivity for rare or elusive species that are hard to observe directly; and scalability for broad-scale monitoring across ecosystems. The standard eDNA workflow begins with non-destructive environmental sampling, followed by DNA extraction, targeted amplification using polymerase chain reaction (PCR), high-throughput sequencing, and bioinformatics pipelines for taxonomic classification and analysis.

Historical Development

The concept of environmental DNA (eDNA) originated in microbial ecology during the 1980s, with pioneering work focusing on extracting and analyzing DNA directly from environmental samples to assess uncultured microbial communities. Norman Pace and colleagues advanced this approach by using ribosomal RNA gene sequences to characterize natural microbial populations in sediments and other matrices, enabling the first molecular surveys of microbial diversity without cultivation.^[7] This foundational technique, detailed in Pace's 1986 review, laid the groundwork for community DNA analysis by demonstrating the feasibility of amplifying and sequencing genetic material from complex environmental mixtures. By the 1990s, these methods expanded to broader sediment studies, such as Ogram et al.'s 1987 protocol for purifying microbial DNA from marine sediments, which established extraction standards still influential in eDNA workflows. A breakthrough in the 2000s extended eDNA applications to macroorganisms, beginning with sediment-based analyses. In 2003, Willerslev et al. analyzed Holocene and Pleistocene permafrost and lake sediments, detecting DNA from diverse plants, mammals, birds, and insects, thus bridging microbial to metazoan detection.^[8] This work demonstrated eDNA's potential for reconstructing ancient communities. Further extensions to aquatic environments followed, with targeted PCR assays for elusive species in water samples emerging in the late 2000s, such as Ficetola et al.'s 2008 detection of invasive bullfrog (Lithobates catesbeianus) DNA in ponds using mitochondrial markers, highlighting non-invasive monitoring without direct capture.^[9] The 2010s saw rapid expansion through metabarcoding advancements and practical applications, particularly for conservation and invasive species management. Thomsen et al.'s 2011 study was seminal, detecting diverse endangered freshwater taxa—including mammals like otters—in river water via eDNA, proving its efficacy for multi-species monitoring in lotic systems.^[10] For fish, Thomsen et al. (2012) introduced an optimized filtration protocol (often referred to as the FiLo method for filter-low volume sampling) that enhanced eDNA recovery from streams, enabling reliable metabarcoding of fish assemblages. Concurrently, eDNA proved valuable for invasive species, as shown in Dejean et al.'s 2012 work detecting American bullfrog (Lithobates catesbeianus) in ponds, where water samples amplified bullfrog DNA in 38 of 49 sites, outperforming traditional surveys for early invasion detection.^[11] These developments transitioned eDNA from targeted PCR to high-throughput next-generation sequencing (NGS), allowing simultaneous analysis of multiple taxa and addressing limitations in resolution and throughput. Recent developments up to 2025 have integrated eDNA with advanced NGS and expanded to novel matrices like air and ancient sediments. Airborne eDNA emerged in 2021 with Johnson et al.'s metabarcoding of air samples, detecting greater plant diversity—including pollen from both wind- and insect-pollinated species—than traditional surveys, with less sampling effort.^[12] For ancient eDNA, Froese et al. (2023) analyzed permafrost cores from Yukon, recovering DNA from Ice Age megafauna like mammoths and horses, alongside insects and pollen, to reconstruct mammoth steppe ecosystems and their collapse.^[13] This evolution from PCR-based detection to NGS-driven metabarcoding has transformed eDNA into a versatile tool for contemporary and paleoecological research, with ongoing refinements in sequencing depth and bioinformatics enhancing its scalability.

Types of eDNA

Intracellular eDNA

Intracellular eDNA refers to genetic material contained within the intact cells of living or recently viable organisms, such as bacteria, protists, fungi, or macroorganism cells including sperm, eggs, sloughed skin cells, or tissue fragments, which are released into the environment through processes like shedding, excretion, or natural sloughing.^[14] Unlike free-floating DNA, this form is protected by cellular membranes or walls, preserving its integrity until extraction procedures disrupt the cells.^[15] In environmental samples like water, soil, or sediment, intracellular eDNA originates from viable communities, providing insights into active populations rather than merely historical presence. A key aspect of intracellular eDNA is its representation of viable, intracellular DNA, which contrasts with degraded extracellular forms by indicating ongoing biological activity.^[14] This viable DNA enables assessment of active populations, such as bacterial communities in soil biofilms or metazoan gametes during reproduction, where it signals current ecological dynamics rather than relic signals.^[16] Common sources include feces, urine, mucus secretions, gametes, and intact microbial cells; for instance, in aquatic environments, fish sperm released during spawning serves as a prominent example, where nuclear DNA from these intact cells spikes in river water post-reproduction, allowing detection of breeding events.^[17] Similarly, in terrestrial settings, bacterial community DNA extracted from soil via metagenomic approaches captures intracellular material from viable microbes, revealing active soil microbiomes.^[18] Detecting intracellular eDNA presents specific challenges, as it necessitates cell lysis during DNA extraction to access the protected genetic material, often using mechanical or enzymatic methods in protocols like sequential filtration or centrifugation to separate it from extracellular fractions.^[14] Failure to distinguish it from extracellular DNA can lead to overestimation of viable organisms, as dormant or dead cells may still yield amplifiable DNA, potentially biasing interpretations of population activity.^[15] Techniques like propidium monoazide treatment can help target intact cells by inhibiting PCR amplification from compromised membranes, enhancing accuracy for viable assessments.^[19] Regarding persistence, intracellular eDNA generally exhibits shorter environmental half-life compared to extracellular forms once released, due to its initial cellular protection delaying degradation but rapid breakdown upon lysis via nucleases or environmental factors; however, while encased, it remains more stable, with studies showing less fragmentation in intact cells versus free DNA.^[15] This property underscores its utility for near-real-time monitoring of active biota, though accumulation of older intracellular material in sediments can complicate temporal inferences without size-based or viability assays.^[14]

Extracellular eDNA

Extracellular eDNA consists of free, cell-free DNA fragments released into the environment from living or recently deceased organisms through processes such as cell lysis, apoptosis, active secretion, and extrusion via membrane vesicles in bacteria or mucus and sloughing in macroorganisms.^[20] In macroorganisms, sources include epithelial cells from skin, scales, gametes, feces, and urine, while in microorganisms, it often arises from autolysis or vesicular release.^[21] These naked DNA molecules exist independently of intact cells, distinguishing them from intracellular eDNA protected within viable or non-viable cells.^[14] Mechanisms of extracellular eDNA release are diverse and include predation leading to carcass decomposition, excretion through bodily wastes, and environmental stresses such as temperature fluctuations or predation pressure that induce cell lysis.^[22] For instance, macroorganisms like fish release eDNA via sloughed scales and mucus during normal activity, with release rates increasing with organism density and behavioral activity levels.^[23] Concentrations are thus influenced by local biomass and ecological dynamics, providing a proxy for recent organismal presence rather than long-term historical signals.^[24] This form of eDNA offers advantages for biodiversity detection, as its cell-free nature allows simpler extraction without the need to disrupt cell walls or membranes, reducing contamination risks during processing.^[25] It typically reflects contemporary ecological conditions, persisting for days to weeks in water columns before degradation, and longer—up to months—in sediments where it binds to particles.^[26] Examples include eDNA from fish scales and mucus detected in pond water, enabling species identification without direct capture, and from amphibian skin sloughing in streams, which signals breeding activity.^[23] A notable 2014 study demonstrated its utility by detecting invasive bighead and silver carp in river systems through water column sampling, confirming presence at low densities where traditional methods failed. To differentiate extracellular eDNA from intracellular forms, researchers employ viability dyes such as propidium monoazide (PMA), which penetrates compromised cells or binds free DNA to inhibit its amplification during downstream analyses like quantitative PCR (qPCR).^[19] This approach ensures that detected signals primarily represent released, extracellular material, minimizing overestimation from intact cells.^[27] Ecologically, extracellular eDNA serves as an indicator of biomass turnover, with shedding rates correlating to population sizes and health, and reveals trophic interactions through elevated levels following predation events that liberate prey DNA.^[22] Such patterns highlight dynamic processes like community structure and energy flow in ecosystems.^[28]

Ancient eDNA

Ancient environmental DNA (aeDNA) consists of highly fragmented, post-mortem genetic material from organisms that has persisted through degradation processes over timescales ranging from centuries to millennia, often preserved in stable environmental archives like permafrost, sediments, or cave deposits under low-oxygen, cold, and anoxic conditions.^[29] This form of environmental DNA arises from the remains of past biota, including intracellular and extracellular sources that have undergone extensive postmortem breakdown, distinguishing it from viable contemporary signals.^[29] Key preservation mechanisms include adsorption of DNA molecules to mineral surfaces, such as clay particles, which shields them from enzymatic degradation and physical damage, alongside low temperatures that inhibit hydrolysis and microbial activity.^[30] Anoxic environments further enhance longevity by limiting oxidative processes. Empirical models of DNA decay provide quantitative insights; for example, Allentoft et al. (2012) calculated a half-life of approximately 521 years for a 242 bp mammalian mitochondrial DNA fragment at 13.1°C, based on analysis of dated moa bones, offering a baseline for predicting relic eDNA survival in similar cold, mineral-rich settings. Extraction of ancient eDNA is complicated by its degradation into short fragments, typically 50-200 base pairs, which demands optimized lysis and isolation techniques to desorb DNA from minerals without further fragmentation.^[30] Contamination from modern sources poses a major risk due to the low endogenous DNA yields, necessitating cleanroom protocols, UV irradiation, and chemical treatments during processing. Authentication relies on cross-verification with multiple genetic markers, damage patterns like cytosine deamination, and independent replication to confirm ancient origin over contemporary artifacts.^[31] In contrast to modern eDNA, which captures current biodiversity dynamics, ancient eDNA emphasizes paleoecological reconstructions of extinct or shifted communities, supported by degradation models that estimate persistence and differentiate historical from recent inputs.^[29] A prominent application involves permafrost cores from northern Greenland, where ancient eDNA analysis revealed a lush Pliocene-Pleistocene ecosystem with mastodons, hares, and diverse vegetation, highlighting Arctic biodiversity changes over 2 million years.^[32] Similarly, sedimentary eDNA from European caves has uncovered Neanderthal-associated flora and fauna, such as woodland plants and herbivores, illustrating Ice Age environmental contexts around 40,000 years ago. These findings underscore ancient eDNA's role in tracing paleoecological responses to climatic shifts, with broader implications for modeling future ecosystem alterations.

Sampling Methods

Terrestrial Sampling

Terrestrial sampling for environmental DNA (eDNA) focuses on collecting material from soil, leaf litter, and surface matrices to detect biodiversity in land-based ecosystems, particularly for soil-dwelling microbes, invertebrates, and plants. Primary techniques include soil coring to depths of 0–20 cm, which captures vertical gradients in eDNA distribution, bulk collection of sediments or litter, and swab sampling from surfaces such as tree bark or foliage.^[33] Sample volumes typically range from 0.25–1 kg for field collection to address spatial heterogeneity, with smaller subsamples (0.25–2 g) processed for extraction to optimize DNA recovery.^[34] These methods target both intracellular eDNA from resident organisms and extracellular eDNA shed by transient species, enabling non-invasive surveys of cryptic terrestrial communities. Preservation immediately following collection is essential to mitigate nuclease degradation and microbial breakdown. Common approaches involve freezing samples at −20°C or storing them in 100% ethanol, which stabilizes DNA by halting enzymatic activity; for suspensions with particulates, filtration separates eDNA for targeted preservation.^[35] Drying is an alternative in remote settings but less effective for long-term integrity compared to cold storage. Sampling protocols must account for environmental matrices and variability, such as the rhizosphere for plant-microbe interactions, forest floors for fungal and detritivore assemblages, or agricultural soils to evaluate management effects on biodiversity.^[33] Seasonal fluctuations influence eDNA yield, with elevated detection during wetter periods due to heightened biological activity and reduced degradation, as observed in winter-to-summer shifts in soil mammal diversity.^[36] A key example is the application of soil eDNA metabarcoding to arthropod diversity in grassland and forest ecosystems, where a 2022 study across Amazonian sites detected 410 arthropod operational taxonomic units, highlighting community responses to soil physicochemical properties and advantages for monitoring elusive invertebrates.^[37] Such approaches excel in revealing multitrophic interactions in soils that traditional trapping overlooks. Contamination controls are critical, including the use of field blanks—such as processing empty tubes or distilled water alongside samples—and physical separation of field collection from laboratory PCR areas to prevent airborne or cross-sample transfer.^[35] eDNA yields vary by soil characteristics, with higher concentrations in organic-rich environments due to increased biomass and binding to humic substances that slow degradation, contrasted by lower yields in arid regions where desiccation accelerates DNA breakdown.^[34]

Aquatic Sampling

Aquatic sampling for environmental DNA (eDNA) targets water bodies such as rivers, lakes, and oceans, where eDNA from aquatic macro-organisms is collected from the water column and sediments to assess biodiversity and species presence. Much of the eDNA in these environments is extracellular, originating from sloughed cells, feces, or gametes.^[38] Methods emphasize non-invasive collection to minimize disturbance while maximizing detection sensitivity for rare or elusive species. In the water column, filtration is the predominant technique, involving passage through membrane filters with pore sizes typically between 0.2 and 1.5 μm to retain eDNA fragments, though larger pores up to 10 μm may be used in less turbid waters to process higher volumes efficiently.^[38] Sample volumes range from 1 to 100 L, with smaller amounts (250–1,000 mL) common in high-concentration lentic systems and larger volumes requiring peristaltic pumps to handle flow without clogging; pre-filtration through coarser meshes addresses suspended particles in rivers or coastal areas. As an alternative for smaller volumes (<1 L), precipitation methods using ethanol with sodium acetate or commercial DNA-binding kits concentrate eDNA directly from unfiltered water, though these have declined in favor of filtration due to higher yields.^[38] Sediment sampling captures accumulated eDNA in benthic layers, particularly useful for detecting organisms in low-flow or profundal zones where DNA persists longer. Grab samplers, such as the Van Veen device, collect surface sediments (top 1–2 cm) from soft lake or river beds, while core samplers (4–13 cm diameter) enable vertical profiling up to 10 cm to target layered deposition in stratified waters.^[39] Subsamples are extracted with sterile tools to avoid cross-contamination, focusing on the oxic surface for recent eDNA signals. Preservation begins on-site to halt degradation: filters from water column sampling are folded and stored in ethanol or lysis buffers (e.g., Longmire's solution), while sediment cores are sectioned and flash-frozen at -80°C when possible.^[38] Humic acids and other inhibitors prevalent in organic-rich aquatic matrices are managed through immediate preservation and later use of kits like PowerSoil during processing, which bind and remove contaminants.^[38] Notable applications include riverine eDNA filtration in the Thames River, where 2018 sampling detected Atlantic salmon (Salmo salar) across approximately 346 km, revealing distributions undetectable by electrofishing.^[40] In lentic systems, pond water filtration has enabled amphibian monitoring, such as confirming California tiger salamander (Ambystoma californense) presence in wetlands via 1–2 L samples preserved in ethanol.^[41] Transport and storage protocols maintain sample integrity: filtered or precipitated materials are refrigerated at 4°C for up to 5 days or frozen at -20°C for longer durations, with sediment cores kept on ice during transit.^[38] In lotic environments, high flow rates dilute eDNA concentrations, reducing detectability downstream and requiring site-specific volume adjustments or multiple replicates to account for hydrological variability.

Aerial and Other Sampling

Aerial environmental DNA (eDNA) sampling involves the use of air pumps equipped with filters, typically 0.2 μm pore size, to capture airborne particles containing DNA fragments from organisms such as pollen, fungal spores, and arthropod fragments. These devices, often operating at high flow rates like thousands of liters per minute, are deployed in diverse settings including forests for fungal pathogen surveillance and urban areas for broader biodiversity assessment. For instance, in forest ecosystems, such sampling has detected a wider range of fungal taxa compared to soil methods, revealing stronger ecological signals in community composition. Similarly, arthropod eDNA has been identified through air filtration, enabling non-invasive monitoring of insect populations without direct capture. Snow and ice sampling for eDNA targets transient deposits, such as animal tracks or wind-transported material, by melting the sample and applying filtration to concentrate DNA. In Arctic regions, this approach has successfully extracted eDNA from polar bear snow tracks, yielding nuclear DNA in 87.5% of samples and enabling genotyping at multiple loci for individual identification. The method proved effective for other mammals like the Eurasian lynx, with 59.1% of wild tracks providing amplifiable eDNA, demonstrating its utility for non-invasive monitoring in remote, snowy environments. Preservation involves fixing samples in ethanol and storing at -20°C to mitigate degradation, though low yields (e.g., 0.02–7.06 ng/μL for polar bears) remain a hurdle. Other unconventional media for eDNA collection include dust accumulation and guano deposits, which capture settled airborne or excretory DNA for assessing indoor or localized biodiversity. Dust sampling, often via passive collectors or vacuum methods, has revealed vertebrate species presence in indoor settings, complementing active air filtration by detecting bioaerosols including pollen and microbial DNA. Guano from mammals like cattle contains substantial eDNA quantities (approximately 202.4 μg/g), allowing metabarcoding to profile associated microbial communities. Emerging vacuum sampling techniques further enable indoor biodiversity surveys, identifying terrestrial species in enclosed spaces with minimal disturbance. Challenges in aerial and other sampling stem from inherently low eDNA concentrations (e.g., as low as 0.87 copies/L in some airborne cases) and environmental factors like wind dispersion, which can dilute or alter sample composition. Wind effects particularly complicate detection in open areas, reducing reproducibility across sites. To optimize yields, collections are timed to coincide with peak organism activity, such as dawn for insects or midday for fungal spore release, enhancing detection rates in applications like vineyard insect monitoring. Preservation strategies, including dry filter storage or silica desiccation, are essential to maintain DNA integrity during transport and processing. Briefly, relic eDNA preserved in ice cores extends these methods to paleoenvironmental reconstructions of ancient Arctic biota.

Analytical Techniques

DNA Extraction and Preparation

The extraction and preparation of environmental DNA (eDNA) from environmental samples is a foundational laboratory process that isolates intact DNA molecules while minimizing degradation and removing matrix-specific contaminants such as humic acids, metals, and proteins. This step ensures sufficient yield and purity for subsequent analytical techniques, with protocols tailored to the sample matrix to optimize recovery from diverse sources like water, soil, or sediment.^[42] Extraction begins with cell lysis to release intracellular DNA from microbial, plant, or animal cells embedded in the sample. Mechanical methods, such as bead-beating with tungsten carbide or ceramic beads at frequencies around 25-30 Hz for 1-5 minutes, are widely used to disrupt robust cell walls, particularly in gram-positive bacteria and fungal spores common in terrestrial matrices.^[43] ^[44] Chemical lysis complements this through buffers containing detergents like cetyltrimethylammonium bromide (CTAB) at 2% concentration, sodium dodecyl sulfate (SDS) at 0.5-1%, or chaotropic salts such as guanidine thiocyanate, often combined with enzymes like Proteinase K for enzymatic digestion.^[42] ^[43] Commercial kits, such as the DNeasy PowerSoil Kit from Qiagen, integrate bead-beating with proprietary lysis buffers (e.g., C1 buffer with SDS) to handle inhibitor-rich soils, yielding up to 10-50 ng/μL DNA from 250 mg samples.^[44] ^[45] For sediments, CTAB-based protocols involve incubation at 42-65°C for 10-60 minutes with 2-mercaptoethanol to reduce polyphenolic interference, enhancing lysis efficiency in clay-heavy subsoils.^[43] Purification follows lysis to separate DNA from cellular debris and environmental inhibitors. Column-based methods, using silica membranes in kits like DNeasy PowerSoil or NucleoSpin Soil, bind DNA under high-salt conditions, followed by washes with ethanol or guanidine hydrochloride to remove humic substances and metals; elution typically occurs in 50-200 μL of low-salt buffer like TE or AE.^[42] ^[44] Magnetic bead purification, as in AMPure XP beads, provides scalable cleanup by selectively binding DNA in polyethylene glycol-sodium chloride solutions, allowing magnetic separation and removal of contaminants without centrifugation.^[42] In humic-rich sediments, additional steps like phenol-chloroform-isoamyl alcohol extraction (25:24:1 ratio) or CTAB-precipitation with 30% polyethylene glycol (PEG 6000) and 5 M NaCl precipitate DNA while excluding polysaccharides.^[43] These processes can achieve typical yields of 700 ng/g wet weight from marine sediments using optimized phosphate-CTAB buffers, though values vary from 0.3-200 μg/g total eDNA depending on soil type and depth.^[46] ^[47] Environmental inhibitors, prevalent in soils and turbid waters, can suppress enzymatic reactions; mitigation strategies include post-extraction dilution (1:10 to 1:100) to lower concentrations below inhibitory thresholds or application of dedicated removal kits like Zymo One-Step PCR Inhibitor Removal, which use proprietary resins to bind humics.^[42] Bovine serum albumin (BSA) addition during lysis or direct PCR enhancement further neutralizes residual tannins and phenolics without yield loss.^[45] Quality assessment verifies extract suitability. Fluorometric quantification with Qubit dsDNA assays provides precise measurement of double-stranded DNA yields, avoiding overestimation from single-stranded contaminants.^[42] Spectrophotometric analysis targets A260/A280 ratios of 1.8-2.0 for protein-free DNA and A260/A230 ratios above 2.0 to confirm low organic contaminant levels, with deviations indicating residual humics.^[42] ^[44] Agarose gel electrophoresis (0.8-1.5%) under UV light evaluates fragment integrity, revealing smears around 100-10,000 bp typical for eDNA, with smearing below 100 bp signaling degradation.^[43] Best practices emphasize contamination control and reproducibility. Extractions should occur in dedicated clean rooms with UV sterilization and separate workspaces for pre- and post-PCR handling; field and extraction blanks serve as negative controls to detect cross-contamination.^[42] Internal positive controls, such as spiked synthetic DNA, monitor lysis efficiency and inhibition throughout the workflow.^[45] Protocol variations accommodate matrix differences: aquatic samples from filtered water favor milder biochemical lysis with Proteinase K in kits like PowerWater to preserve fragile extracellular DNA, yielding 5,000-10,000 gene copies/2 μL from 15 mL volumes without harsh mechanical disruption.^[45] In contrast, terrestrial soils and sediments demand aggressive bead-beating and CTAB for penetration of organic aggregates, as gentler methods recover only 20-50% of bacterial diversity in humic clays.^[43] ^[44]

Metabarcoding and Sequencing

Metabarcoding of environmental DNA (eDNA) involves high-throughput sequencing to identify multiple taxa simultaneously by targeting conserved genetic marker genes within environmental samples. Following DNA extraction and preparation, the process typically begins with polymerase chain reaction (PCR) amplification using universal primers designed for specific markers, such as the cytochrome c oxidase subunit I (COI) gene for metazoans or the 16S ribosomal RNA (16S rRNA) gene for bacteria.^[48]^[49] These primers flank variable regions that provide taxonomic resolution, allowing amplification of short DNA fragments suitable for degraded eDNA. Amplified products undergo library preparation, including adapter ligation and indexing for multiplexing, before sequencing on next-generation sequencing (NGS) platforms like the Illumina MiSeq, which generates millions of short reads (typically 200-500 base pairs) per sample.^[48]^[50] The bioinformatics pipeline processes raw sequencing data to generate reliable taxonomic profiles. Initial steps include demultiplexing reads based on unique index sequences and quality filtering to remove low-quality or short reads. Chimera detection and removal, often using tools like USEARCH, eliminate artifactual sequences formed during PCR. Reads are then clustered into operational taxonomic units (OTUs) or amplicon sequence variants (ASVs) at 97-99% similarity thresholds, followed by taxonomic assignment against reference databases such as BOLD for COI-based metazoan identification or SILVA for 16S-based microbial classification.^[51]^[52] This pipeline enables the reconstruction of community composition from complex mixtures, though incomplete reference databases can limit resolution for understudied taxa.^[53] Primer design is critical to minimize biases in metabarcoding, with universal primers enabling broad amplification but often favoring dominant taxa due to mismatches in annealing efficiency. To address host or dominant species bias, blocking oligonucleotides can be incorporated to suppress unwanted amplification, such as vertebrate-specific blockers in aquatic samples dominated by fish DNA.^[54] These strategies improve detection of rare or target taxa without exhaustive custom primer development. A key advantage of metabarcoding is its capacity for simultaneous detection of hundreds of species from a single sample, far surpassing traditional surveys, while sequencing read depth allows semi-quantitative estimates of relative abundance based on read counts proportional to biomass or occurrence.^[35]^[55] For instance, in a 2018 study across 39 sites in French Guiana's species-rich freshwater systems, eDNA metabarcoding identified 132 fish species, demonstrating its utility in high-diversity environments.^[56] Despite these strengths, challenges include error sources like index switching during Illumina sequencing, which can introduce false positives by misassigning reads across samples at rates of 0.1-2%, necessitating unique dual indices and negative controls for validation.^[57]^[58] Quantitative analysis of diversity often employs rarefaction curves, which standardize sequencing effort by subsampling reads to compare species richness across samples, revealing whether sufficient depth was achieved to capture community structure without overestimation.^[59] This approach prioritizes conceptual insights into biodiversity patterns over absolute counts, supporting applications in ecosystem monitoring.

Targeted Detection Methods

Targeted detection methods in environmental DNA (eDNA) analysis focus on assays designed to identify and quantify specific organisms or genetic markers, offering high sensitivity for rare or low-abundance targets. These approaches typically employ polymerase chain reaction (PCR)-based techniques, such as quantitative PCR (qPCR) and droplet digital PCR (ddPCR), which use species-specific primers and probes to amplify and detect target DNA sequences from environmental samples. For instance, TaqMan probes in qPCR enable real-time fluorescence monitoring during amplification, allowing for the determination of cycle threshold (Ct) values that indicate the initial quantity of target DNA. Assay design emphasizes selecting loci with high sensitivity, often from mitochondrial DNA (mtDNA) due to its abundance and maternal inheritance, which enhances detection probability in eDNA samples. Primers are tailored to unique genetic regions, such as the cytochrome b gene for fish species, to minimize cross-amplification with non-target taxa. Limits of detection (LOD) for these assays typically range from 1 to 10 target DNA copies per reaction, enabling reliable identification even at trace concentrations. ddPCR further improves precision by partitioning samples into thousands of droplets for absolute quantification without standard curves, outperforming qPCR in low-DNA scenarios like pond water eDNA for bluegill sunfish.^[60] These methods have been pivotal in applications for early invasive species detection, such as the 2013 qPCR surveillance for Asian carp in the Great Lakes basin, where eDNA signals confirmed presence in the Chicago Area Waterway System and western Lake Erie, guiding barrier reinforcements. Compared to metabarcoding, targeted assays provide superior sensitivity for low-abundance invaders, reducing false negatives in sparse populations. Validation involves rigorous in vitro and in situ testing: specificity is assessed by screening against related taxa to ensure no cross-reactivity, while sensitivity is quantified via serial dilutions to establish LOD and limits of quantification (LOQ). Environmental validation often incorporates occupancy models, which account for imperfect detection by estimating site occupancy probability (ψ) and detection probability (p) from replicate samples, as demonstrated in stream surveys for amphibians.^[61]^[62]^[63] Emerging techniques like loop-mediated isothermal amplification (LAMP) offer field-deployable alternatives, amplifying DNA at a constant temperature (around 65°C) without thermocyclers, suitable for on-site eDNA testing. LAMP assays for aquatic invasive species, such as round goby, achieve detection limits comparable to qPCR while enabling rapid, visual readout via colorimetric or turbidity changes. Data from targeted methods should be interpreted cautiously: a positive detection indicates occupancy probability rather than absolute population density, as eDNA persistence varies with environmental factors like temperature and flow.^[64]^[65]

Applications in Biodiversity Monitoring

Terrestrial Species Monitoring

Environmental DNA (eDNA) has become a vital tool for monitoring terrestrial species, particularly in assessing declines in arthropod populations and detecting elusive mammals. By analyzing genetic material from soil, air, feces, and snow, eDNA enables non-invasive detection of biodiversity changes across land ecosystems, providing baselines for conservation efforts amid ongoing global insect losses.^[28] In arthropod decline monitoring, eDNA from soil and archived leaves has revealed significant temporal shifts in insect diversity, offering insights into the arthropod crisis. A 2022 study using eDNA metabarcoding on archived leaf samples from German forests demonstrated temporal turnover and biotic homogenization in arthropod communities over approximately 30 years, with relative read abundance declining for about 7% of taxa and increasing for 10%.^[66] Similarly, a 2025 analysis of archived leaf samples showed arthropod diversity decline in South Korean forests but stability in German ones, underscoring regional variations in insect loss and the value of eDNA for comparative monitoring.^[67] Airborne eDNA sampling has complemented these efforts; for instance, a 2025 national survey in Japan detected over 1,000 arthropod taxa via air filters, correlating with traditional trap data to track flying insect communities and support biomass decline assessments, such as those linked to a reported 75% reduction in German flying insect biomass since 1989.^[5]^[68] Recent 2024-2025 studies indicate global insect abundance losses of up to 72% in even protected, untouched ecosystems over two decades; eDNA research provides baselines to quantify such regional declines and the ongoing crisis.^[67]^[69] For mammal detection, eDNA from fecal and soil samples excels in identifying elusive species without disturbance. In Scandinavia, DNA analysis of wolverine (Gulo gulo) scats collected in 2016-2017 confirmed population distribution and genetic diversity across Norway and Sweden, enabling non-invasive tracking of this low-density carnivore in remote habitats. Soil eDNA has similarly aided in detecting soil-associated mammals, providing community-level insights into terrestrial biodiversity. Snow track eDNA analysis further enhances winter surveys; a 2019 study in Japan successfully identified mammalian species like sika deer from melted snow prints using universal primers and metabarcoding, achieving species-level resolution in multiple samples.^[70] In North American contexts, such as Yellowstone, eDNA from wolf snow tracks has been tested for species and sex identification, supporting monitoring of packs and individuals like wolves and pumas during seasonal surveys.^[71] Key advantages of eDNA in terrestrial monitoring include its non-invasive nature, ideal for protected areas where traditional trapping could harm sensitive species, and its support for temporal replication through repeated sampling to track population trends.^[72] Metrics like species richness—often higher in eDNA surveys than traditional methods—and community turnover rates from multi-year sampling provide quantitative context for decline assessments, with eDNA detecting up to 30% more taxa in repeated terrestrial plots.^[73]^[74] These approaches have established eDNA as a cornerstone for addressing the arthropod crisis and mammal conservation, with case studies demonstrating its role in baseline creation and trend analysis.^[67]

Aquatic and Marine Species Monitoring

Environmental DNA (eDNA) has revolutionized monitoring of aquatic and marine species by enabling non-invasive detection of organisms through water samples, offering higher sensitivity than traditional methods for elusive or low-density populations. In freshwater and marine environments, eDNA facilitates early identification of species presence, supporting conservation efforts and ecosystem management without disturbing habitats. This approach is particularly valuable for tracking dynamic aquatic communities where physical capture is challenging due to water currents, depth, or species behavior.^[75] For invasive species detection, eDNA provides early alerts by identifying low-abundance individuals before population explosions occur. A seminal application involved quantitative PCR (qPCR) assays for detecting Asian carp (Hypophthalmichthys spp.) in the Great Lakes region, where eDNA signals allowed surveillance of upstream migration barriers as early as 2014, outperforming traditional netting in sensitivity and cost-efficiency. Such targeted eDNA methods have since been adapted for other invasives like the killer shrimp (Dikerogammarus villosus) in European rivers, enabling rapid response to prevent establishment.^[76]^[77] Monitoring endangered aquatic species benefits from eDNA's ability to survey large river and lake networks efficiently. In the United States, eDNA sampling revealed the presence of the critically endangered hellbender salamander (Cryptobranchus alleganiensis) in Missouri rivers, detecting it at sites where visual surveys failed due to the species' cryptic habits and habitat preferences under rocks. This method increased detection probability by over 300% compared to manual searches, informing targeted habitat restoration. Similar successes have been reported for amphibians like the northern leopard frog (Lithobates pipiens) in prairie pothole wetlands, where eDNA confirmed occupancy in fragmented landscapes.^[78]^[79] In marine environments, eDNA captured via ocean drifters and filters has illuminated planktonic and megafaunal distributions. The Tara Oceans expedition, culminating in analyses around 2020, used eDNA metabarcoding on global seawater samples to detect megafauna like whales and sharks alongside plankton, revealing co-occurrence patterns across ocean basins that traditional sighting surveys miss. Recent advances, such as the 2025 eDNA Expeditions Phase II led by UNESCO, integrate citizen science with autonomous drifters to map marine biodiversity hotspots in real-time, enhancing global ocean health assessments.^[80]^[81] Biodiversity assessments in complex habitats like coral reefs and estuaries rely on eDNA metabarcoding to delineate community structures. In the Indo-Pacific, seawater eDNA from coral reefs identified over 200 fish species per site, capturing depth gradients and habitat-specific assemblages that visual censuses underestimate by 40-50%. Estuarine studies in Japan using similar techniques quantified fish diversity across salinity gradients, detecting rare migrants and revealing seasonal shifts in community composition. These approaches provide baseline data for tracking reef degradation or estuarine health amid climate pressures.^[82]^[83] Temporal dynamics of eDNA signals inform species persistence and local extinctions in aquatic systems. For fish, eDNA typically degrades within 1-4 weeks post-individual removal, influenced by temperature and flow; in temperate rivers, signals from common carp (Cyprinus carpio) persisted up to 21 days, allowing estimates of recent occupancy. This decay rate contrasts with longer persistence in stagnant lakes (up to months), aiding in distinguishing active populations from historical remnants.^[84]^[85] Integration of eDNA data with occupancy models enhances distribution mapping by accounting for imperfect detection. Hierarchical models, first applied to aquatic eDNA in 2013 for stream amphibians, estimate true species occupancy while incorporating environmental covariates like flow rate, improving accuracy for rare fish distributions in rivers by 20-30%. In marine contexts, multi-scale occupancy frameworks applied to 2020s coastal eDNA surveys map cetacean ranges, predicting habitat suitability amid ocean warming.^[86]^[87]

Fisheries and Resource Management

Environmental DNA (eDNA) has emerged as a valuable tool in fisheries and resource management by enabling non-invasive assessments of fish stocks, which supports sustainable harvesting practices and compliance with regulations. In stock biomass estimation, eDNA concentrations have shown strong correlations with actual fish abundance and catch data, allowing for more accurate predictions of population dynamics. For instance, a 2018 study on Pacific salmon demonstrated a quantitative relationship between eDNA levels in streams and the number of spawning sockeye salmon, with eDNA signals reflecting fine-scale spatial and temporal variations in abundance that aligned with observed escapement counts.^[88] This approach has been applied to forecast salmon runs, integrating eDNA data with hydrological models to estimate upstream biomass distribution and inform harvest quotas.^[89] In addressing bycatch and illegal trade, eDNA sampling from port waters and vessel holds provides forensic evidence of traded species, helping to detect undeclared catches and enforce international agreements. A 2021 pilot study used eDNA metabarcoding on meltwater from industrial and artisanal fishing vessels to profile catch compositions, identifying tuna species such as yellowfin and bigeye alongside bycatch, which revealed discrepancies with reported landings indicative of potential illegal activities.^[90] Similarly, water sampling in fish markets has uncovered mislabeling and illegal sourcing, with eDNA detecting traces of protected or overexploited species in seafood products, thereby aiding traceability and reducing incentives for illicit trade.^[91] For aquaculture monitoring, eDNA facilitates the early detection of pathogens and escapees in pond systems, minimizing disease outbreaks and ecological risks from non-native introductions. Studies have successfully used eDNA to identify fish pathogens like viral hemorrhagic septicemia virus in freshwater ponds, with detection sensitivities surpassing traditional culturing methods and enabling rapid response to infections.^[92] In escapee detection, eDNA metabarcoding of pond effluents has traced non-indigenous species releases, supporting containment protocols and biosecurity in intensive farming operations.^[93] The economic impacts of eDNA in fisheries are significant, as it reduces survey costs compared to conventional methods like trawling by requiring only water filtration and lab analysis. Research indicates eDNA surveys can be up to twice as cost-efficient for biodiversity and abundance assessments in marine environments, with lower operational expenses for fieldwork and equipment.^[94] A case study from 2023 in the North Atlantic illustrated this in cod management, where eDNA-based assessments complemented trawl surveys to map Gadus morhua distributions, leading to refined quota settings and estimated savings of 40-60% in monitoring budgets through targeted sampling.^[95]^[96] Regulatory adoption of eDNA is advancing, with integration into guidelines from bodies like the FAO and regional fisheries management organizations to enhance stock assessments and sustainability. The FAO has incorporated eDNA protocols into recommendations for monitoring illegal, unreported, and unregulated fishing, emphasizing its role in verifying compliance with catch limits.^[97] By 2025, updated sustainability metrics from NOAA's eDNA roadmap highlight a 30% improvement in stock assessment accuracy for overfished species, driven by standardized eDNA workflows that align with IUCN Red List criteria for threat evaluations.^[6] Despite these benefits, challenges in calibrating eDNA for precise abundance estimates persist, particularly in dynamic aquatic environments where dilution affects signal strength. Flow-adjusted models have been developed to correct for hydrological variations, as shown in Pacific salmon studies where eDNA concentrations were normalized against discharge rates to improve correlations with biomass by up to 50%.^[98] These models incorporate allometric scaling of eDNA shedding rates across species, enabling more reliable quantitative inferences for management decisions.^[99]

Advanced and Specialized Applications

Deep-Sea and Sedimentary Analysis

Environmental DNA (eDNA) analysis has revolutionized the study of deep-sea ecosystems by enabling the detection of microbial and metazoan communities in extreme environments where traditional sampling is challenging. In deep-sea habitats, samples are often collected using remotely operated vehicles (ROVs) to gather sediments or water from depths exceeding 4,000 meters, allowing for non-invasive assessment of biodiversity in hydrothermal vent communities. For instance, a 2019 study utilizing eDNA metabarcoding on hard substrates from deep-sea vents, including those in the Mid-Atlantic Ridge, identified diverse assemblages of bacteria, archaea, and eukaryotes, highlighting the role of chemosynthetic processes in supporting unique microbial and faunal diversity.^[100] Sedimentary profiling employs vertical coring techniques to extract layered sediment cores, which preserve temporal sequences of eDNA deposition and facilitate the reconstruction of benthic community dynamics over time. These cores, often obtained via ROVs or submersibles, reveal shifts in invertebrate assemblages, such as polychaetes and crustaceans, by targeting eDNA from successive stratigraphic layers that reflect environmental changes or faunal migrations. A 2022 investigation in the Mediterranean demonstrated how sediment core eDNA metabarcoding uncovered temporal patterns in metazoan diversity, including benthic invertebrates, providing insights into community stability without disturbing the habitat.^[101] Despite these advances, deep-sea eDNA applications face significant challenges, including the extreme high pressure that complicates sample collection and preservation, as well as the inherently low biomass in abyssal zones, which results in dilute eDNA signals requiring high-sensitivity amplification methods. For example, a 2022 optimization study of pumped seawater eDNA from deep-sea sites emphasized the need for larger sample volumes to overcome low eDNA concentrations in oligotrophic waters, where biomass can be orders of magnitude lower than in surface layers. In the Atlantic abyssal plains, a 2025 eDNA survey of equatorial sediments unveiled unprecedented eukaryotic diversity, including potential new species of protists and invertebrates previously undetected by visual methods, underscoring the technique's value despite these hurdles.^[102]^[103] Integrating eDNA data with oceanographic models enhances understanding of how physical processes influence deep-sea biodiversity distribution. By correlating eDNA profiles with current patterns and upwelling events, researchers can trace larval dispersal and nutrient-driven community assembly in abyssal regions; a 2023 mesocosm study in an eastern boundary upwelling system used multi-marker eDNA to link eukaryotic community divergence to hydrodynamic variability. A 2025 data release from the California Current Large Marine Ecosystem described eDNA metabarcoding assessments of deep-sea habitats (~800-3,200 m) using samples collected via Niskin bottles on ROVs or CTD rosettes during West Coast research cruises, addressing gaps in biodiversity surveys of seafloor communities.^[104]^[105] Biodiversity hotspots like hydrothermal vents and cold seeps are particularly amenable to eDNA characterization through 16S rRNA for prokaryotes and 18S rRNA for eukaryotes, capturing the chemosynthesis-based food webs that sustain endemic species. A 2023 eDNA metabarcoding effort at the Formosa Ridge cold seep employed 18S rRNA (V4, V9 regions) and 12S rRNA markers to document multi-trophic diversity, including invertebrates, demonstrating higher resolution than morphological surveys alone. Similarly, applications at hydrothermal vents have identified novel microbial consortia and associated metazoans, emphasizing eDNA's role in mapping these isolated, high-biomass oases amid vast low-productivity expanses.^[106]

Ancient DNA Reconstruction

Sedimentary ancient DNA (sedaDNA) enables the reconstruction of past ecosystems by analyzing DNA preserved in sediment layers, offering insights into environmental changes over millennia that complement traditional paleoecological proxies like pollen and macrofossils. Unlike modern environmental DNA, which captures contemporary biodiversity on short timescales, sedaDNA targets degraded genetic material from deceased organisms, facilitating the study of evolutionary histories, species migrations, and extinction events in contexts where fossils are scarce. This approach has revolutionized paleoecology by providing species-level resolution for vegetation dynamics, faunal assemblages, and human impacts on landscapes.^[107] Key methods for sedaDNA analysis account for the fragmented and chemically altered nature of ancient DNA, typically recovering short fragments under 100 base pairs. Targeted capture techniques, such as hybridization with bait probes specific to taxonomic groups (e.g., plants or mammals), enrich libraries for relevant sequences while minimizing off-target modern contaminants. Authentication relies on characteristic damage patterns, including cytosine-to-thymine (C-to-T) deamination at fragment ends, which increases with age and confirms endogenous ancient origin; these are quantified using tools like mapDamage to filter post-mortem modifications. Silica-based extraction protocols optimized for low-input samples further enhance recovery from mineral-bound sediments. In paleoecological applications, sedaDNA has revealed long-term vegetation shifts, such as continuous increases in terrestrial plant richness across northern Fennoscandia during the Holocene, driven by warming and nutrient availability, spanning over 11,000 years from lake sediments.^[107] For megafauna extinctions, sedaDNA from Alaskan sediments demonstrated woolly mammoth persistence until approximately 5,700 years ago in Beringia, challenging timelines of regional extirpation and highlighting isolated refugia amid post-glacial habitat loss.^[108] These findings underscore sedaDNA's role in tracing biodiversity responses to climatic transitions. Links to past climate variability are evident in sedaDNA records showing Holocene warming's effects on tundra biomes, with expansions of shrub and forb communities in the High Arctic replacing open steppe-tundra assemblages as temperatures rose by over 5°C from the late glacial period. In New Zealand, pollen records from lake cores document abrupt ecosystem shifts following Māori arrival around 700 years ago, including declines in native forest taxa and increases in disturbance indicators like bracken fern, reflecting deforestation and agricultural expansion. Recent 2025 studies from Laptev Sea permafrost deposits integrate sedaDNA with radiocarbon dating to assess thaw-induced paleoecological changes, revealing shifts in microbial and floral communities tied to deglacial warming.^[109] SedaDNA's temporal resolution operates on millennial scales, capturing cumulative signals from sediment accumulation rates of centimeters per century, in contrast to modern eDNA's ability to resolve seasonal or annual fluctuations in living communities. Relic eDNA preservation in permafrost or anoxic lake beds extends records to hundreds of thousands of years, though degradation limits resolution beyond this.

Societal and Emerging Aspects

Citizen Science Initiatives

Citizen science initiatives in environmental DNA (eDNA) research have democratized biodiversity monitoring by engaging volunteers in sample collection and data contribution, significantly expanding the scale and reach of eDNA studies beyond professional efforts.^[110] These programs leverage public participation to gather eDNA from diverse environments, fostering greater awareness of biodiversity loss while generating valuable datasets for conservation.^[111] By simplifying complex sampling protocols, such initiatives enable non-experts to contribute to scientific discovery, often through partnerships with research institutions and platforms like iNaturalist.^[112] Prominent programs include UNESCO's eDNA Expeditions, a global citizen science effort launched to assess marine biodiversity and climate impacts, where volunteers collect water samples using provided kits during expeditions and everyday activities.^[113] In 2024, the LeDNA project mobilized citizen scientists to sample environmental DNA from over 800 lakes worldwide in a single day, revealing undetected species and highlighting the method's scalability for freshwater ecosystems.^[114] Similarly, iNaturalist has integrated eDNA results into its platform through projects like the ProBleu Bulgaria BioBlitz, where participants combine traditional observations with eDNA sampling to monitor coastal wetlands, uploading data directly to shared databases for analysis.^[112] NatureMetrics supports public involvement via simplified eDNA kits distributed through partnerships, such as with travel companies for on-site sampling during citizen science trips, exemplified by their role in UK pond surveys in 2022 that detected conservation-priority mammals across multiple sites.^[115]^[116] Protocols for these initiatives emphasize user-friendly tools, such as portable filtration kits that allow volunteers to collect water or soil samples without specialized equipment, followed by mailing to labs for sequencing.^[117] Participants typically follow step-by-step guides for sterile sampling to avoid contamination, with apps or online portals facilitating data upload to centralized repositories like GBIF or project-specific databases, ensuring traceability and integration with broader eDNA networks.^[118] For amphibian-focused efforts, such as those targeting great crested newts in UK ponds, volunteers use bottle-based water collection at pond edges, which has been validated for detecting elusive species across citizen networks.^[119] These initiatives have markedly increased geographic coverage, with the 2024 LeDNA lake sampling providing eDNA data from remote and underrepresented regions, contributing to global assessments of amphibian and fish diversity.^[120] Educational outcomes are profound, as participants gain insights into biodiversity threats, with programs like eDNA Expeditions Phase II in 2025 extending to low-resource areas through community-led training in regions like the Global South, promoting equitable participation and local conservation action.^[81] Hybrid approaches, such as combining eDNA with trail camera data in mammal monitoring projects, further enhance detection rates; for instance, studies integrating camera trap images with soil eDNA have identified more species than either method alone, boosting public engagement in terrestrial surveys.^[121] Quality control is maintained through online training modules that teach proper sampling techniques and contamination prevention, with many programs supported by scientific advisory boards to ensure accuracy.^[113] Equity in participation is addressed by designing inclusive protocols, such as multilingual resources and subsidies for kits in underserved communities, as seen in ongoing expansions of eDNA networks in low-resource settings.^[117] These measures not only uphold data reliability but also build diverse contributor bases, amplifying the societal impact of eDNA citizen science.^[117]

Challenges and Future Directions

One major limitation in eDNA research is the rapid degradation of DNA in environmental samples, which can occur at rates influenced by factors such as temperature, UV exposure, and microbial activity, often leading to detection windows of days to weeks in aquatic systems.^[84] This degradation contributes to false negatives, particularly for species with low shedding rates or those present in low densities, as fragmented DNA may fail to amplify during PCR.^[122] Additionally, transport biases in eDNA distribution—driven by water currents, wind, or sedimentation—complicate spatial interpretations of species presence, requiring models to account for these dynamics.^[123] Quantification remains challenging, as eDNA concentrations do not directly correlate with biomass or abundance due to variable shedding and persistence rates, necessitating species-specific calibrations for reliable estimates.^[124]^[125] Contamination risks during sampling, extraction, and amplification pose significant hurdles, potentially introducing false positives that undermine result reliability.^[126] To address this, efforts toward standardization have intensified, with protocols like the 2023 NIWA guidelines for lotic systems providing national frameworks for consistent sampling and processing in freshwater environments.^[127] Similarly, the U.S. National Aquatic Environmental DNA Strategy (2024) outlines recommendations for interoperable methods and data sharing to enhance comparability across aquatic eDNA studies.^[128] The MIEM guidelines further promote minimum reporting standards for metabarcoding workflows, aiding reproducibility.^[129] Ethical concerns in eDNA applications include privacy risks for detected species, as identifying locations of endangered populations could facilitate poaching or habitat disruption if data are not securely managed.^[130] Over-reliance on eDNA technology in conservation may also marginalize traditional monitoring methods and local knowledge, potentially leading to incomplete assessments if not integrated thoughtfully.^[131] Looking ahead, portable nanopore sequencing technologies, such as Oxford Nanopore devices, enable real-time field analysis of eDNA, reducing turnaround times and logistical barriers in remote areas, as demonstrated in 2025 studies on vertebrate biodiversity.^[132] AI-driven bioinformatics pipelines are emerging to automate sequence processing and taxonomic assignment, improving accuracy and scalability for large datasets.^[133] Integration with remote sensing, including 2025 drone-based eDNA sampling for insect diversity on vegetation, promises hybrid approaches for broader spatial coverage.^[134] Research gaps persist in developing long-term eDNA databases, such as the NAMERS repository, which aim to standardize reference sequences for global metabarcoding but require expanded coverage for underrepresented taxa.^[135] Modeling eDNA dynamics under climate change—factoring in altered degradation and transport—remains underexplored, limiting predictive applications.^[4] Post-2023 advances in portable sequencers have accelerated field-deployable workflows, yet validation across ecosystems is needed.^[136] Policy recommendations advocate incorporating eDNA into international frameworks, such as updates to the Convention on Biological Diversity's Kunming-Montreal Global Biodiversity Framework, to support monitoring targets for genetic diversity and invasive species management.^[137] This includes standardized data protocols to ensure eDNA contributes verifiably to national biodiversity strategies.^[138]

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Detection of Asian carp DNA as part of a Great Lakes basin-wide ...
Samples collected in the Chicago Area Waterway System and in the western basin of Lake Erie indicate the presence of Asian carp DNA in the Great Lakes.
[58]
A validation scale to determine the readiness of environmental DNA ...
Mar 16, 2021 · Generally, “targeted” eDNA assays must be specific to the species of interest and possess high sensitivity to allow detection at low densities, ...
[59]
Isothermal amplification of environmental DNA (eDNA) for direct ...
Loop-mediated isothermal amplification (LAMP) of aquatic invasive species environmental DNA (AIS eDNA) was used for rapid, sensitive, and specific detection ...
[60]
Development and validation of an eDNA protocol for monitoring ...
Apr 4, 2022 · Occupancy modeling is a powerful tool to estimate detection and site occupancy probabilities despite imperfect detection. It is challenging to ...
[61]
Environmental DNA from archived leaves reveals widespread ... - eLife
Nov 10, 2022 · This landmark study reveals novel temporal arthropod biodiversity insights that can be leveraged from environmental DNA traces.
[62]
eDNA metabarcoding of archived leaf samples reveals arthropod ...
Jul 4, 2025 · Hence, eDNA from leaf samples of both ESBs provides a unique opportunity to explore long-term forest arthropod diversity trends across ecosystem ...
[63]
First national survey of terrestrial biodiversity using airborne eDNA
Jun 2, 2025 · Sample collection Airborne eDNA was collected between September 2021 and October 2022 using 15 Digitel DPA-14 ambient air samplers on the UK ...
[64]
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0186462
[65]
(PDF) Environmental DNA Collected from Snow Tracks is Useful for ...
Aug 6, 2025 · Using Sanger sequencing, eDNA on snow tracks was recovered at the species level except for M. melampus using universal primers, while eDNA of M.
[66]
Testing environmental DNA from wolf snow tracks for species, sex ...
If individual wolves could be identified and sexed by the eDNA in their snow tracks, researchers should be able to determine population and family or group ...Missing: Yellowstone 2022 puma
[67]
Applications of environmental DNA (eDNA) to detect subterranean ...
eDNA-based biodiversity surveys have shown greater detection sensitivity, lower taxonomic selectivity, and superior cost-efficiency and these advantages make ...
[68]
A systematic review evaluating the performance of eDNA methods ...
Jun 19, 2025 · We found that eDNA is more likely to provide increased estimates of sensitivity metrics (i.e. species richness and detection probability) and ...
[69]
Environmental DNA provides higher resolution assessment of ... - NIH
May 3, 2021 · We found that eDNA provided greater resolution in assessing biodiversity dynamics in time and space, compared to traditional sampling.Missing: repeated | Show results with:repeated
[70]
The detection of aquatic animal species using environmental DNA ...
Jun 20, 2014 · We review recently published studies that use eDNA to monitor aquatic populations, discuss the methodologies used and the application of ...
[71]
Quantifying Environmental DNA Signals for Aquatic Invasive ...
In this study we present a comparison of three eDNA surveillance platforms: traditional polymerase chain reaction (PCR), quantitative PCR (qPCR) ...Missing: early | Show results with:early
[72]
[PDF] Using eDNA to detect freshwater invasive non-native species under ...
Feb 19, 2024 · These results demonstrate the potential for using eDNA as a detection method for killer shrimp and signal crayfish but also highlights that ...<|control11|><|separator|>
[73]
Using environmental DNA methods to improve detectability in a ...
We tested for presence of Hellbenders by extracting environmental DNA (eDNA). We investigated whether amount of eDNA was related to abundance or season.
[74]
https://pmc.ncbi.nlm.nih.gov/articles/PMC8093236/
[75]
Assessing patterns of metazoans in the global ocean using ...
Aug 14, 2024 · We used existing datasets from two global expeditions, Tara Oceans and Malaspina, that circumnavigated the oceans and sampled down to 4000 m to ...Missing: megafauna 2020
[76]
eDNA Expeditions Phase II Sets Sail at UNOC3: Citizen Scientists ...
Jun 13, 2025 · eDNA Expeditions Phase II, a global campaign using environmental DNA (eDNA) to observe and monitor marine species around the world.Missing: aquatic | Show results with:aquatic
[77]
Cross-ocean patterns and processes in fish biodiversity on coral ...
Apr 20, 2022 · We use environmental DNA metabarcoding to reconstruct well-known patterns of fish biodiversity on coral reefs and uncover hidden patterns.
[78]
Evaluation of fish biodiversity in estuaries using environmental DNA ...
Oct 6, 2020 · Here, we used environmental DNA (eDNA) metabarcoding to investigate fish biodiversity in five different estuaries in Japan.
[79]
Persistence of environmental DNA in marine systems - Nature
Nov 5, 2018 · We found that eDNA also degraded around 1.1 times faster in winter than in summer, although this difference was not statistically significant.
[80]
Temperature Controls eDNA Persistence across Physicochemical ...
Jun 3, 2022 · We demonstrate that marine eDNA can persist at quantifiable concentrations for over 2 weeks at low temperatures (≤10 °C) but for a week or less at ≥20 °C.
[81]
Site occupancy models in the analysis of environmental DNA ...
Mar 28, 2013 · The use of environmental DNA (eDNA) to detect species in aquatic environments such as ponds and streams is a powerful new technique with ...Summary · Introduction · Materials and Methods · DiscussionMissing: mapping | Show results with:mapping
[82]
A case study using coastal marine eDNA | PLOS One
Mar 19, 2020 · We developed a multi-scale, multi-species occupancy model for the analysis of community biodiversity data resulting from eDNA metabarcoding.Missing: specificity | Show results with:specificity
[83]
Concentrations of environmental DNA (eDNA) reflect spawning ...
Feb 8, 2018 · Here, we report a strong quantitative relationship between eDNA concentration and the abundance of spawning sockeye salmon in a small stream in ...Missing: forecasting | Show results with:forecasting
[84]
[PDF] Concentrations of environmental DNA (eDNA) reflect spawning ...
A particular challenge for predicting Pacific Salmon abundance is likely to be the differential contribution of eDNA from live and dead fish, which is ...
[85]
Characterizing Industrial and Artisanal Fishing Vessel Catch ... - NIH
We pilot an approach that uses forensic environmental DNA (eDNA) metabarcoding to profile fish species composition from the meltwater in fish holds.
[86]
Environmental DNA as a tool to reconstruct catch composition for ...
May 3, 2024 · The application of MM across fisheries is broad and includes detecting illegal trade of species in fish markets, food products ...
[87]
Detection of Fish Pathogens in Freshwater Aquaculture Using eDNA ...
eDNA and eRNA methods are being extensively used in aquaculture and fisheries settings to understand the presence of different fish species and pathogens in ...Missing: escapee | Show results with:escapee
[88]
Environmental DNA: A New Low-Cost Monitoring Tool for ... - Frontiers
The data we present suggest that eDNA metabarcoding of the 18S SSU rDNA v9 region can sensitively and specifically identify multiple aquaculture pathogens from ...Missing: escapee | Show results with:escapee<|separator|>
[89]
[PDF] Cost Efficiency of Environmental DNA as Compared to Conventional ...
As eDNA becomes more prevalent in detecting and monitoring aquatic biodiversity, it has been considered an effective, noninvasive, and cost-efficient ...
[90]
Atlantic cod (Gadus morhua) assessment approaches in ... - Frontiers
Mar 23, 2023 · The goal of this study was to comparatively analyze a newly developed, more sensitive real-time PCR based eDNA approach with bottom trawl fisheries catches.
[91]
Environmental DNA complements scientific trawling in surveys of ...
Sep 21, 2023 · In this study, we compared the results of eDNA metabarcoding and scientific bottom trawling for marine fish biodiversity monitoring in the Bay ...
[92]
Appraising deep-sea fish stocks when data are scarce
Jul 25, 2025 · Agreement signed with ICES to advance biological data collection and assessment methods for deep-sea fisheries in international waters.
[93]
A Roadmap for Using eDNA in Stock Assessments - NOAA Fisheries
Jul 9, 2025 · Environmental DNA (eDNA) is a valuable tool that can enhance fish stock assessments by providing a non-invasive, cost-effective, and scalable ...
[94]
[PDF] Environmental DNA for the enumeration and management of Pacific ...
Finally, noise in enumeration with eDNA can be caused by a lack of primer specificity. 398. Our assays are much more sensitive to sockeye and coho salmon DNA ...Missing: forecasting | Show results with:forecasting
[95]
Relationships between the eDNA concentration obtained from ...
Aug 8, 2022 · This study successfully determined the relationships between eDNA concentration and fish abundance using the allometric scaling model under ...2.2 Fish Sampling · 2.3 Edna Sampling · 3 Results
[96]
Exploring Environmental DNA (eDNA) to Assess Biodiversity of Hard ...
In this study, we explored the environmental DNA (eDNA) approach as a tool (1) to assess biodiversity of benthic communities associated with deep-sea hard ...
[97]
eDNA Reveals the Associated Metazoan Diversity of Mediterranean ...
The combination of eDNA and sediment cores allowed us to reconstruct temporal patterns of metazoan community diversity and provides a novel approach to ...2.2. Edna Analysis... · 3. Results · 4. DiscussionsMissing: coring | Show results with:coring
[98]
Optimization of environmental DNA analysis using pumped deep ...
Jan 16, 2023 · However, it is estimated that in the deep sea, where biomass is low, the amount of eDNA sources is lower than in coastal and surface seawater ( ...
[99]
Abyssal DNA: Eukaryotic Diversity in Atlantic Equatorial Deep-Sea ...
Here, we documented eukaryotic diversity as indicated by the sequence assignment of eDNA in abyssal Atlantic Ocean sediment sampled between the Brazilian ...
[100]
Ecological divergence of a mesocosm in an eastern boundary ... - BG
Apr 5, 2023 · Ecological divergence of a mesocosm in an eastern boundary upwelling system assessed with multi-marker environmental DNA metabarcoding.
[101]
Environmental DNA detections from deep seafloor habitats in the ...
Environmental DNA detections from deep seafloor habitats in the California Current Large Marine Ecosystem. February 14, 2025. View Data Release.
[102]
Biodiversity exploration of Formosa Ridge cold seep in the South ...
In the present study, we identified multi-trophic biodiversity using eDNA metabarcoding combined with multiple ribosomal RNA gene (rDNA) markers.
[103]
A National Scale “BioBlitz” Using Citizen Science and eDNA ...
Mar 27, 2022 · In an unprecedented study, we combined citizen science with eDNA metabarcoding to map coastal fish biodiversity at a national scale.
[104]
Citizen Scientists' Motivation to Participate in Environmental DNA ...
Citizen scientists carrying out the environmental DNA (eDNA) sampling. (a) Collecting eDNA water samples from the rivers' edge with a water bottle and (b) using ...
[105]
ProBleu Bulgaria - Coastal wetlands unveiled - iNaturalist
Welcome to the "Coastal wetlands unveiled: Empowering biodiversity monitoring through eDNA, ecoacoustics, and citizen science" Biobliz!
[106]
Environmental DNA Expeditions in UNESCO World Heritage Marine ...
UNESCO's Environmental DNA (eDNA) Expeditions is a global citizen science initiative aimed at advancing knowledge of marine biodiversity and the impacts of ...
[107]
Citizen Scientists Will Capture DNA From 800 Lakes In One Day
Apr 19, 2024 · The project aims to find species that have gone unnoticed by sampling the waters of hundreds of lakes worldwide for environmental DNA.
[108]
[PDF] BFER Citizen Science: Testing the WatereDNA Results 2022
eDNA surveys allow a wider range of freshwater habitats to be sampled across an entire catchment or landscape, from ponds and ditches, to rivers and lakes.
[109]
Citizen Science Departures - Exodus Travels
Using NatureMetrics' innovative eDNA sample-taking technique, we can find out the species present in different ecosystems, as well as their distributions across ...
[110]
Co‐design of a citizen science study: Unlocking the potential of ...
Sep 27, 2023 · Citizen science projects using eDNA analysis should develop user-friendly materials and instructions, recognising that citizen scientists may ...INTRODUCTION · CITIZEN SCIENTIST... · DISCUSSION · RECOMMENDATIONS
[111]
Exploring the potential of extreme citizen science with Danish high ...
Mar 4, 2024 · In this paper we will showcase the development of an existing citizen science project with focus on eDNA monitoring towards a more comprehensive ...Introduction · Method · Results · Discussion
[112]
Comparison of Two Citizen Scientist Methods for Collecting Pond ...
Aug 21, 2018 · We targeted the Great Crested Newt, a semi-aquatic amphibian that has been widely used as a study species within eDNA research and citizen ...Introduction · Field Samples · Discussion<|control11|><|separator|>
[113]
Why citizen scientists are gathering DNA from hundreds of lakes
Feb 21, 2024 · In a first-of-its-kind project, researchers are tapping into the power of citizen science to collect DNA samples from hundreds of lakes worldwide.Missing: projects | Show results with:projects
[114]
Trail cameras detect species better than soil eDNA
Dec 12, 2024 · The study reveals that trail cameras detected more species than soil eDNA analysis, but the latter still boosted the overall number of detections.Missing: hybrid citizen
[115]
The Role of Community Science in DNA‐Based Biodiversity ... - NIH
eDNA studies in the Global South are currently limited, with community scientists mostly contributing occurrence records, while researchers perform eDNA ...<|control11|><|separator|>
[116]
[PDF] Understanding and mitigating errors and biases in metabarcoding
In metabarcoding, the number of false positives arising from contamination can be reduced by only accepting species that are detected in multiple technical ...Missing: switching | Show results with:switching
[117]
Opportunities and inherent limits of using environmental DNA for ...
Aug 9, 2023 · Some of these limitations might be overcome with the development of new technologies or models that account for the specificities of eDNA.
[118]
Scaling from eDNA to biomass: controlling allometric relationships ...
Mar 14, 2023 · Here, primary research focus has been to estimate fish abundance or biomass in the wild from species-specific DNA copy numbers in environmental ...
[119]
A general framework to unify the estimation of numerical abundance ...
Dec 9, 2022 · Collectively, we show that quantitative eDNA data is unlikely to correspond exactly to either N or biomass, but can be 'corrected' to reflect ...
[120]
Application of Environmental DNA in Aquatic Ecosystem Monitoring
Environmental DNA (eDNA) technology is a method for identifying specific biological species by monitoring the presence of DNA fragments in the environment.
[121]
[PDF] eDNA Guidelines and field protocols for lotic systems - NIWA
Fish are suitable for detection using eDNA because they shed substantial amounts of DNA into the water, their genomic data are well represented bioinformatics ...
[122]
[PDF] Toward a national eDNA strategy for the United States
Apr 26, 2023 · follow standardization guidelines and produce freely accessible protocols. Specific activities might include (1) integrating eDNA monitoring ...
[123]
The MIEM guidelines: Minimum information for reporting of ...
Dec 30, 2024 · A working group of scientists have collaborated to produce a set of minimum reporting guidelines for the constituent steps of metabarcoding workflows.Missing: ENCODE | Show results with:ENCODE<|separator|>
[124]
Unveiling the Invisible: The Revolutionary World of eDNA
May 13, 2024 · Privacy concerns emerge when considering the potential for eDNA to inadvertently reveal information about protected or endangered species to ...
[125]
Prospects and challenges of environmental DNA (eDNA ... - Frontiers
Feb 26, 2023 · In this mini-review, we synthesize the viability, potentials, challenges and future prospects of applying eDNA metabarcoding approaches in ...
[126]
Evaluation of nanopore sequencing for increasing accessibility of ...
In summary, we show that nanopore sequencing technology can be used to reliably carry out eDNA-based biodiversity monitoring in remote locations, including in ...
[127]
Integrating AI, GIS, and eDNA for Real-Time and Biodiversity-Driven ...
This review proposes an integrated framework combining artificial intelligence (AI), geographic information systems (GISs), and environmental DNA (eDNA)3. Research Methodology · 4. Research Findings And... · 5. Discussion
[128]
Robot‐Aided Measurement of Insect Diversity on Vegetation Using ...
May 7, 2025 · We investigated a non‐invasive approach of combining the use of drones and environmental DNA (eDNA) to monitor insect biodiversity on vegetation.
[129]
NAMERS: a purpose-built reference DNA sequence database to ...
Nov 19, 2024 · Applied eDNA metabarcoding is increasingly being considered as a tool to inform management decisions, regulations, or policy development.
[130]
A systematic review on environmental DNA (eDNA) Science: An eco ...
eDNA represents all DNA present in the environment derived from biological tissue fragments and excrement. •. eDNA metabarcoding characterizes the DNA of ...
[131]
Shotgun sequencing of airborne eDNA achieves rapid ... - Nature
Jun 3, 2025 · Here we report the rapid application of shotgun long-read environmental DNA (eDNA) analysis for non-invasive biodiversity, genetic diversity and pathogen ...
[132]
From environmental DNA into actionable biodiversity data: Towards ...
Sep 23, 2025 · The review highlights eDNA's role in regional and global monitoring networks, its ability to protect sensitive data through intentional system ...
[133]
A vision for global eDNA-based monitoring in a changing world
Aug 22, 2024 · Here, we envision a global eDNA biomonitoring scheme, which could potentially revolutionize the understanding and conservation of life on Earth.