Search USGS⌕ Search

SEARCH · Search USGS

Results for “Environmental DNA”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 55 records · Page 3Linked to original sources
USGS2022

Gaining decision-maker confidence through community consensus: Developing environmental DNA standards for data display on the USGS Nonindigenous Aquatic Species database

To advance national efforts for the detection and biosurveillance of aquatic invasive species (AIS), we employed a community consensus process to enable the incorporation of environmental DNA (eDNA) detection data into the U.S. Geological Survey’s (USGS) Nonindigenous Aquatic Species (NAS) database (https://nas.er.usgs.gov/eDNA/). Our goal was to identify minimum standards and best practices for the verification of eDNA data by working closely with AIS eDNA community practitioners and natural resource managers across government, private and academic sectors. To better inform management decisions, verified AIS eDNA data will be displayed on a separate mapping layer alongside visual sighting data with the inclusion of additional information on the eDNA methods employed to collect and produce the data. To allow for eDNA data display, we produced consensus derived online documents including a submission application and data submission template and are developing a guidance document for detailing the eDNA data submission process. We also developed a communication plan including a mechanism for reporting detections to appropriate managers for consideration prior to display. The products of these efforts are an application and data submission process that will be used in the new environmental DNA data layer on the Nonindigenous Aquatic Species (NAS) database. Herein, we detail how we engaged the eDNA community for consensus of our standards, share lessons learned from the process, and describe the benefits of such an approach at instilling confidence among the research and decision-maker community.

Management of Biological Invasions↗
USGS2022

Environmental DNA methods for ecological monitoring and biodiversity assessment in estuaries

Environmental DNA (eDNA) detection methods can complement traditional biomonitoring to yield new ecological insights in aquatic systems. However, the conceptual and methodological frameworks for aquatic eDNA detection and interpretation were developed primarily in freshwater environments and have not been well established for estuaries and marine environments that are by nature dynamic, turbid, and hydrologically complex. Environmental context and species life history are critical for successful application of eDNA methods, and the challenges associated with eDNA detection in estuaries were the subject of a symposium held at the University of California Davis on January 29, 2020 ( https://marinescience.ucdavis.edu/engagement/past-events/edna ). Here, we elaborate upon topics addressed in the symposium to evaluate eDNA methods in the context of monitoring and biodiversity studies in estuaries. We first provide a concise overview of eDNA science and methods, and then examine the San Francisco Estuary (SFE) as a case study to illustrate how eDNA detection can complement traditional monitoring programs and provide regional guidance on future potential eDNA applications. Additionally, we offer recommendations for enhancing communication between eDNA scientists and natural resource managers, which is essential for integrating eDNA methods into existing monitoring programs. Our intent is to create a resource that is accessible to those outside the field of eDNA, especially managers, without oversimplifying the challenges or advantages of these methods.

Estuaries and Coasts↗
USGS2025

Environmental DNA metabarcoding for monitoring fish biodiversity in remote lakes

Objective Environmental DNA (eDNA) metabarcoding provides an attractive option for monitoring biodiversity in remote freshwater ecosystems, where the deployment of conventional gears encounters major logistical constraints. We evaluated eDNA metabarcoding for monitoring fish communities and early detection of nonnative species in three remote lakes on Isle Royale, Michigan, USA. Methods At each of the three lakes, we collected surface, midwater, and lake bottom samples from 10 sites during spring and fall sampling events. We performed metabarcoding on all the water samples, targeting the 12S region of all fish species. Results Despite a relatively small sample size ( N = 60 samples per lake across two visits; 10 locations with three depths per location), we recovered 70% of all the species that were previously observed using conventional methods. We recovered several detections of putative Cisco Coregonus artedi , a vulnerable coldwater species, providing evidence that Cisco have persisted in these lakes. However, we found disentangling likely false positives from rare species challenging, which we overcame by employing multiple types of detection thresholds and a species-specific quantitative PCR assay. Conclusions Although we were able to successfully characterize the fish communities using eDNA metabarcoding, more attention needs to be given to the detection thresholds and communication protocols that provide guidance in interpretating new eDNA detections and using eDNA detections to inform management decisions. Although eDNA metabarcoding has limitations that should be accounted for at the outset of the project, the ease of sample collection makes eDNA metabarcoding an option for monitoring freshwater biodiversity in remote systems.

Michigan↗
USGS2020

Capture of environmental DNA (eDNA) from water samples by flocculation

The analysis of environmental DNA (eDNA) has become a widely used approach to problem solving in species management. The detection of cryptic species including invasive and (or) species at risk is the goal, typically accomplished by testing water and sediment for the presence of characteristic DNA signatures. Reliable and efficient procedures for the capture of eDNA are required, especially those that can be performed easily in the field by personnel with limited training and citizen scientists. The capture of eDNA using membrane filtration is widely used currently. This approach has inherent issues that include the choice of filter material and porosity, filter fouling, and time required on site for the process to be performed. Flocculation offers an alternative that can be easily implemented and applied to sampling regimes that strive to cover broad territories in limited time.

JOVE Journal Of Visualized Experiments↗
USGS2026

Environmental DNA pilot monitoring program for invasive species and biodiversity assessments on Santa Cruz Island: Interim report, September 2025

The U.S. Geological Survey (USGS) and Southern California Coastal Water Research Project supported Channel Islands National Park, The Nature Conservancy’s (TNC) Santa Cruz Island Preserve, and University of California San Diego (UCSD) researchers in using environmental DNA sampling to monitor for invasive Argentine ant ( Linepithema humile ) and to describe spatial biodiversity patterns in a freshwater stream on Santa Cruz Island that is colloquially known as Cañada del Puerto Creek (hydrologic unit code 12 number 180600140201). An eDNA autosampler was deployed May 27–June 02, 2025, which filtered and preserved four 2-L water samples every 12 hours (n = 48 samples). These samples were extracted by USGS and shipped to UCSD for targeted eDNA analyses of Argentine ant. Environmental DNA sampling kits were used to filter and preserve water samples at four sites along the creek spanning ~ 5 km of stream distance. Six 1-L samples were collected at each site May 27–28 and samples were analyzed for eDNA metabarcoding using a comprehensive panel, which encompasses species across the tree of life. In these samples, eDNA from 2,134 unique taxa spanning 30 taxonomic groups (e.g., amoebas, insects, plants) were found. These sampling efforts demonstrated how eDNA autonomous and manual sampling approaches can be applied by National Park Service, TNC, and partners at scale to provide otherwise difficult and expensive to acquire information about biological threats and biodiversity.

California↗
USGS2019

Environmental DNA as a tool to help inform zebra mussel, Dreissena polymorpha, management in inland lakes

Zebra mussels ( Dreissena polymorpha ) are an aquatic invasive species that plague much of North America and are difficult to impossible to eradicate once they become established. Therefore, prevention and monitoring are key elements in the control of these organisms. Traditional microscopy is commonly used in monitoring but requires the presence of larval veligers. This limits the times when resource managers can monitor for the presence in northern lakes. A new monitoring tool, environmental DNA (eDNA), may allow for a more efficient and cost-effective monitoring program for zebra mussels. We developed and tested an environmental DNA assay in the fall and spring for zebra mussels in two Minnesota lakes, one heavily infested and another newly infested. We found that DNA copy numbers tended to be higher near the lake bottom and DNA was more concentrated in softer substrates. We also found that the amount of zebra mussel DNA sampling in winter resulted in similar results to when sampled in fall. This suggests that one could collect and analyze eDNA for zebra mussels during winter months to help inform future efforts in monitoring and control.

Minnesota↗
USGS2020

Use of environmental DNA to detect grass carp spawning events

The timing and location of spawning events are important data for managers seeking to control invasive grass carp populations. Ichthyoplankton tows for grass carp eggs and larvae can be used to detect spawning events; however, these samples can be highly debris-laden, and are expensive and laborious to process. An alternative method, environmental DNA (eDNA) technology, has proven effective in determining the presence of aquatic species. The objectives of this project were to assess the use of eDNA collections and quantitative eDNA analysis to assess the potential spawning of grass carp in five reservoir tributaries, and to compare those results to the more traditional method of ichthyoplankton tows. Grass carp eDNA was detected in 56% of sampling occasions and was detected in all five rivers. Concentrations of grass carp eDNA were orders of magnitude higher in June, corresponding to elevated discharge and egg presence. Grass carp environmental DNA flux (copies/h) was lower when no eggs were present and was higher when velocities and discharge increased and eggs were present. There was a positive relationship between grass carp eDNA flux and egg flux. Our results support the further development of eDNA analysis as a method to detect the spawning events of grass carp or other rheophilic spawners.

Fishes↗
USGS2017

Experimental observations on the decay of environmental DNA from bighead and silver carps

Interest in the field of environmental DNA (eDNA) is growing rapidly and eDNA surveys are becoming an important consideration for aquatic resource managers dealing with invasive species. However, in order for eDNA monitoring to mature as a research and management tool, there are several critical knowledge gaps that must be filled. One such gap is the fate of eDNA materials in the aquatic environment. Understanding the environmental factors that influence the decay of eDNA and how these factors impact detection probabilities over time and space could have significant implications for eDNA survey design and data interpretation. Here we experimentally explore decay of eDNA associated with bighead carp ( Hypophthalmichthys nobilis ) biological waste collected from an aquaculture filtration system and with sperm collected from captive silver carp ( H. molitrix ), and how decay may be influenced by differing levels of water turbulence, temperature, microbial load, and pH. We found that the decay patterns of eDNA associated with both H. nobilis biological waste and H. molitrix milt significantly fit monophasic exponential decay curves. Secondly, we observed that the highest temperature we tested resulted in a decay half-life as much as 5.5× more rapid than the lowest temperature we tested. When we suppressed microbial loads in eDNA samples, we observed that overall losses of eDNA were reduced by about 2.5×. When we amended eDNA samples with pond water the half-life of eDNA was reduced by about 2.25×, despite relatively little apparent increase in the overall microbial load. This pattern indicated that species constituency of the microbial community, in addition to microbial load, might play a critical role in eDNA degradation. A shift in pH from 6.5 to 8.0 in the samples resulted in a 1.6× reduction in eDNA halflife. Water turbulence in our study had no apparent effect on eDNA decay. When we combined different temperature, pH, and microbial load treatments to create a rapid decay condition and a slow decay condition, and tracked eDNA decay over 91 days, we observed a 5.0× greater loss of eDNA by Day 5 under rapid decay conditions than under slow decay conditions. At the end of the trials, the differences in eDNA loss between the rapid decay and baseline and slow decay conditions were 0.1× and 3.3×, respectively. Our results strongly demonstrate the potential for environmental factors to influence eDNA fate and, thus, the interpretation of eDNA survey results.

Management of Biological Invasions↗
USGS2022

Environmental DNA metabarcoding read numbers and their variability predict species abundance, but weakly in non-dominant species

Metabarcoding of environmental DNA (eDNA) provides more comprehensive, efficient, and non-invasive sampling of biological communities than conventional methods. However, limitations of metabarcoding include taxon-specific biases in amplification and sequencing that distort assessments of community composition. Further, hyper-abundant species may disproportionately affect community composition assessments and impair the detection of rare species (i.e., “species masking”). In this study, we examine methodological approaches to improve eDNA metabarcoding assessments of community structure using fish community diversity in a pond in south Florida using MiFish primers modified to improve cichlid detection. Mitochondrial 12S eDNA amplicon sequencing via Illumina NovaSeq was analyzed using the DADA2 model-based exact sequence inference. The fish species and abundances in the system were recorded during piscicide treatment and subsequent native species restocking. Our results demonstrate that (1) ultra-high-throughput sequencing on the newer NovaSeq patterned flow cell provided reliable detection of very rare taxa—with detections of a single individual. (2) Read numbers were significantly correlated to the total surface area of the fish population, and numerical abundance to a lesser degree; however, dominant taxa largely drove those correlations, and simulations showed that biases in the most abundant taxa will have disproportionate effects on the strength of the correlation. (3) The read number coefficient of variation for each species across spatially separated replicate samples may provide less biased abundance estimates compared with estimates based on average read counts. Finally, (4) exact sequence inference detected multiple haplotypes and population genetic diversity within a species. Our results demonstrate the real-world metabarcoding capacity to reveal community structure and reliably detect rare species and unique haplotypes and shows that read numbers can, to a limited degree, be used to infer the size of fish populations. Careful examination of detection biases among dominant taxa and spatial variation among samples are required for rigorous eDNA-based estimates of community structure. Our results demonstrate the capacity of NovaSeq metabarcoding to reveal freshwater fish community structure and reliably detect rare species and unique haplotypes. Metabarcoding read numbers were significantly correlated to the total surface area of the fish species' populations, allowing for conditional inferences of population sizes. However, dominant taxa largely drove those correlations, and simulations indicated that biases toward the most abundant taxa will have disproportionate effects on the strength of the correlation.

Florida↗
USGS2018

Tradeoffs of a portable, field-based environmental DNA platform for detecting invasive northern pike (Esox lucius) in Alaska

Environmental DNA (eDNA) has improved detection probabilities of aquatic invasive species but lab-based analytical platforms for eDNA analyses slow opportunities for rapid response. Effective approaches that address this analytical bottleneck and improve capacity for rapid response are urgently needed. We tested the sensitivity of a portable, field-based eDNA platform relative to widely used lab-based eDNA approaches for detecting invasive northern pike (Esox lucius) in eight lakes on Alaska’s Kenai Peninsula. The portable, field-based platform takes ~ 1 hr from sample collection to final results and uses a field-based DNA extraction kit, a shelf-stable assay, and a portable real-time PCR thermocycler. Lab-based approaches take days to weeks to months for final results and use lab-based DNA extraction kits, lab-bound assays, and benchtop real-time thermocyclers. We found that the portable, field-based approach was less sensitive than lab-based approaches and was more prone to inhibition, thus increasing potential for false-negatives. Until sensitivity and inhibition issues can be resolved, this portable, field-based approach is best viewed as a complement to rather than a replacement of standard eDNA lab-based approaches.

Alaska↗
USGS2023

Dead-end hollow fiber ultrafiltration capture of environmental DNA for freshwater mussel (Unionidae) species detection with metabarcoding

Insufficient water sample volumes can be a limiting factor for detecting species with environmental DNA (eDNA) from aquatic habitats. We compared detections of freshwater mussel (Unionidae) communities using large water sample volumes and dead-end hollow fiber ultrafiltration (D-HFUF or DEUF) with traditional eDNA filtration methods that use relatively small water sample volumes. Unionid species were detected in approximately 50-L D-HFUF eDNA samples with two mitochondrial DNA metabarcoding markers (COI and ND1) and compared to species detection results from eDNA captured from commonly used 1-L samples filtered with polyethersulfone (PES) filters at three lotic sites in Georgia and Missouri. Of the 431,560 COI and 1,035,472 ND1 reads from all environmental samples of both filter types that passed quality control, 95% (410,755 reads) of COI reads and 85% (883,472 reads) of ND1 reads were assigned to a unionid species. Nineteen different freshwater mussel species were detected across all D-HFUF samples, and 11 species were detected across all PES samples. Reads assigned to the genus Elliptio could not be resolved beyond the genus level with either marker. From D-HFUF samples, 15 and 16 mussel species were detected with the COI and ND1 markers, respectively. From PES samples, nine and seven species were detected with the COI and ND1 markers, respectively. More mussel species were detected at each site in D-HFUF samples than in PES samples regardless of whether results from both markers were combined or evaluated separately. Our results demonstrate the merit of further exploration and optimization of D-HFUF for capturing eDNA from high-volume water samples to facilitate detection of unionids and likely other aquatic organisms.

Environmental DNA↗
USGS2024

Environmental DNA reveals invasion of Puerto Rican waterways by non-native Clarias catfish

The Sharptooth walking catfish ( Clarias gariepinus ) is native to parts of the Middle East, Asia, and Africa but is one of the world's most invasive freshwater fish species. The species’ ability to invade is partly due to its ability to breathe atmospheric oxygen, thereby avoiding hypoxia or poor water quality in receiving waterbodies; further, it can crawl over moist land to disperse to new systems. In 2018, two individuals purported to be Sharptooth walking catfish were collected and identified within the Canal de Patillas, a canal in the Guayama municipality in southeastern Puerto Rico. Several other specimens were also collected the following year. Given that this invasion was in its infancy, environmental DNA (eDNA) surveillance was employed as a rapid and efficient surveillance tool to help delineate the extent of this invasion. Water samples were collected and analyzed for Clarias eDNA from 66 sites encompassing a wide range of habitats in canals, lakes, and a river surrounding the area where they were first reported. Using eDNA-metabarcoding, we detected Clarias eDNA at 40 of the 63 sites throughout the sampled waterbodies. Furthermore, our molecular analysis indicated that the Whitespotted Clarias ( C. fuscus ) is the likely invader, and the original specimens, classified as C. gariepinus , were misidentified based on the use of morphological rather than genetic features for species classification. Environmental DNA surveillance indicated that the distribution of Clarias catfish in this system is substantially more extensive than previously documented. These findings suggest that additional survey efforts could help determine the invasion's full spatial extent and leading edge to inform the scope and scale of any potential management responses.

Puerto Rico↗
USGS2015

Environmental DNA (eDNA) sampling improves occurrence and detection estimates of invasive Burmese pythons

Environmental DNA (eDNA) methods are used to detect DNA that is shed into the aquatic environment by cryptic or low density species. Applied in eDNA studies, occupancy models can be used to estimate occurrence and detection probabilities and thereby account for imperfect detection. However, occupancy terminology has been applied inconsistently in eDNA studies, and many have calculated occurrence probabilities while not considering the effects of imperfect detection. Low detection of invasive giant constrictors using visual surveys and traps has hampered the estimation of occupancy and detection estimates needed for population management in southern Florida, USA. Giant constrictor snakes pose a threat to native species and the ecological restoration of the Florida Everglades. To assist with detection, we developed species-specific eDNA assays using quantitative PCR (qPCR) for the Burmese python ( Python molurus bivittatus ), Northern African python ( P . sebae ), boa constrictor ( Boa constrictor ), and the green ( Eunectes murinus ) and yellow anaconda ( E . notaeus ). Burmese pythons, Northern African pythons, and boa constrictors are established and reproducing, while the green and yellow anaconda have the potential to become established. We validated the python and boa constrictor assays using laboratory trials and tested all species in 21 field locations distributed in eight southern Florida regions. Burmese python eDNA was detected in 37 of 63 field sampling events; however, the other species were not detected. Although eDNA was heterogeneously distributed in the environment, occupancy models were able to provide the first estimates of detection probabilities, which were greater than 91%. Burmese python eDNA was detected along the leading northern edge of the known population boundary. The development of informative detection tools and eDNA occupancy models can improve conservation efforts in southern Florida and support more extensive studies of invasive constrictors. Generic sampling design and terminology are proposed to standardize and clarify interpretations of eDNA-based occupancy models.

Florida↗
USGS2019

Evaluation of environmental DNA surveys for identifying occupancy and spatial distribution of Pacific Lamprey (Entosphenus tridentatus) and Lampetra spp. in a Washington coast watershed

Surveys of environmental DNA (eDNA) have become an important and multifaceted tool for monitoring and identifying distributions and occupancy of aquatic species. This tool is attractive because it is powerful, easy to apply, and provides an alternative to traditional field survey methods. However, validating eDNA survey methods against traditional field survey methods is warranted prior to their application. We used eDNA and electrofishing to survey 10 sites in 3 tributaries of the Chehalis River, Washington, to infer distribution and occupancy of Entosphenus tridentatus and Lampetra spp. Both methods produced similar detection rates for E . tridentatus , and Lampetra spp. were detected at slightly greater frequency with eDNA in the Black River and Skookumchuck River. Within each of the three tributaries, eDNA concentration was negatively related to sample distance from the Chehalis River mainstem for E . tridentatus but not for Lampetra spp., which indicates E . tridentatus and Lampetra spp. may be distributed differently within tributaries. Application of lamprey eDNA data to a multiscale occupancy model indicated high probability of detecting eDNA in water samples and quantitative PCR (qPCR) assays. Broad distribution and high detection of E. tridentatus and Lampetra spp. suggest robust populations inhabit the Chehalis River basin. Our findings suggest eDNA surveys may be comparable to electrofishing for informing lamprey occupancy and distributions. Such sampling is efficient and cost‐effective and we anticipate that eDNA surveys will become a valuable tool in addressing key research and monitoring needs for conservation and restoration of lampreys in general.

Washington↗
USGS2024

A guide to environmental DNA extractions for non-molecular trained biologists, ecologists, and conservation scientists

Ecologists, biologists, and conservation scientists are increasingly interested in the use of environmental DNA (eDNA) data for research and potentially decision-making. While commercial DNA extraction kits are typically user-friendly and accessible, they may fail to deliver the desired results with inherently complex eDNA samples, necessitating protocol optimization or educated selection of alternative approaches. To this end, knowledge of the basic steps and principles of DNA extractions is essential, but traditional education tracks in ecology, conservation, and environmental management typically do not include in-depth training in molecular methods. The primary objective of this paper is to enable scientists with an ecological background and limited molecular training to understand the four key steps of eDNA isolations, and to use this expertise to their advantage. We describe the purpose of commonly used reagents and chemicals, point out alternatives for each key step, explain the impact of certain choices regarding isolation approaches on DNA integrity and purity, and highlight the possibility of a tailor-made “mix and match” approach. We anticipate that this paper will enable field ecologists to develop a deeper understanding of the mechanisms and chemistry underlying eDNA extractions, thus allowing them to make informed decisions regarding the best eDNA extraction method for their research goals. Our intention is not to provide comprehensive, step-by-step protocols, but to offer guiding principles while highlighting alternative solutions. Finally, we hope that this paper will act as a useful resource to support knowledge transfer and teaching.

Environmental DNA↗
USGS2020

The elephant in the lab (and field): Contamination in aquatic environmental DNA studies

The rapid evolution of environmental (e)DNA methods has resulted in knowledge gaps in smaller, yet critical details like proper use of negative controls to detect contamination. Detecting contamination is vital for confident use of eDNA results in decision-making. We conducted two literature reviews to summarize (a) the types of quality assurance measures taken to detect contamination of eDNA samples from aquatic environments, (b) the occurrence, frequency and attribution (i.e., putative sources) of unexpected amplification in these quality assurance samples, and (c) how results were interpreted when contamination occurred. In the first literature review, we reviewed 156 papers and found that 91% of targeted and 73% of metabarcoding eDNA studies reported inclusion of negative controls within their workflows. However, a large percentage of targeted (49%) and metabarcoding (80%) studies only reported negative controls for laboratory procedures, so results were potentially blind to field contamination. Many of the 156 studies did not provide critical methodological information and amplification results of negative controls. In our second literature review, we reviewed 695 papers and found that 30 targeted and 32 metabarcoding eDNA studies reported amplification of negative controls. This amplification occurred at similar proportions for field and lab workflow steps in targeted and metabarcoding studies. These studies most frequently used amplified negative controls to delimit a detection threshold above which is considered significant or provided rationale for why the unexpected amplifications did not affect results. In summary, we found that there has been minimal convergence over time on negative control implementation, methods, and interpretation, which suggests that increased rigor in these smaller, yet critical details remains an outstanding need. We conclude our review by highlighting several studies that have developed especially effective quality assurance, control and mitigation methods.

Frontiers in Ecology and Evolution↗
USGS2020

At Palmyra Atoll, the fish‐community environmental DNA signal changes across habitats but not with tides

At Palmyra Atoll, the environmental DNA (eDNA) signal on tidal sand flats was associated with fish biomass density and captured 98%–100% of the expected species diversity there. Although eDNA spilled over across habitats, species associated with reef habitat contributed more eDNA to reef sites than to sand‐flat sites, and species associated with sand‐flat habitat contributed more eDNA to sand‐flat sites than to reef sites. Tides did not disrupt the sand‐flat habitat signal. At least 25 samples give a coverage >97.5% at this diverse, tropical, marine system.

Journal of Fish Biology↗
USGS2025

O Romeo! Environmental DNA could prevent a tragedy for the elusive Chucky Madtom (Noturus crypticus)

Using environmental DNA (eDNA) surveillance methods, we report the first evidence of the persistence of the Chucky Madtom ( Noturus crypticus ) in Little Chucky Creek, Tennessee, which has been absent from conventional surveys since 2004, and in Dunn Creek, Tennessee, where it was last collected in 1940. This highlights the utility of eDNA for detecting cryptic, rare fish species that may persist at extremely low population densities when conventional surveys fail, as well as its effectiveness as a contemporary tool to guide targeted conventional sampling efforts; however, it is not intended to replace the ‘in hand’ detection of the species.

Tennessee↗