Quantification of Environmental DNA (eDNA) Shedding and Decay Rates for Three Marine Fish

Spatio-temporal distribution of environmental DNA from amphibian and turtle species in a pond ecosystem

Environmental DNA (eDNA) analysis has emerged as a transformative tool for biodiversity monitoring and conservation. However, uncertainties in the ecological processes of eDNA in aquatic environments decrease the reliability of eDNA-based surveys. Understanding the distribution and persistence patterns of eDNA is essential to effectively correlate eDNA data with species occurrence across spatial and temporal scales. Here, we investigated the spatio-temporal distribution of eDNA from amphibian and turtle species in a pond ecosystem, by establishing controlled eDNA sources from American bullfrogs (Lithobates catesbeianus) and red-eared sliders (Trachemys scripta elegans), and quantifying eDNA concentrations from different water layers and sediment samples using droplet digital PCR. Our results showed that eDNA from both species was highly concentrated within 2-5 m of the biological sources, with dispersal distance independent of the duration of organism' presence in the pond and exhibiting a vertically increasing trend over time. eDNA concentration and persistence varied significantly depending on species and substrate type, with bullfrogs showing notably higher eDNA detectability. The average eDNA concentration in sediment was 1.4 × 104 times higher than in water, and eDNA persisted approximately one week longer. Our findings demonstrate that the strong aggregation patterns of eDNA can provide valuable insights into the spatial distribution of amphibians and turtles in pond systems. eDNA from surface water showed greater timeliness for biodiversity monitoring and aquatic invasive species management. The specificity of target taxa and the temporal complementarity of sedimentary eDNA should be carefully considered in future eDNA sampling designs.

The Long and the Short of It: Nanopore-Based eDNA Metabarcoding of Marine Vertebrates Works; Sensitivity and Species-Level Assignment Depend on Amplicon Lengths

To monitor the effect of nature restoration projects in North Sea ecosystems, accurate and intensive biodiversity assessments are vital. DNA-based techniques and especially environmental (e)DNA metabarcoding is becoming a powerful monitoring tool. However, current approaches rely on genetic target regions under 500 bp, offering limited taxonomic resolution. We developed a method for long-read eDNA metabarcoding, using Nanopore sequencing of a longer amplicon and present DECONA, a read processing pipeline to enable improved identification of marine vertebrate species. We designed a universal primer pair targeting a 2 kb region of fish mitochondrial DNA and compared it to the commonly used MiFish primer pair targeting a ~ 170 bp region. In silico testing showed that 2 kb fragments improved accurate identification of closely related species. Analysing eDNA from a North Sea aquarium showed that sequences from both primer pairs could be assigned to most species, and additional species level assignments could be made through the 2 kb primer pair. Interestingly, this difference was opposite in eDNA from the North Sea, where not the 2 kb but the MiFish primer pair detected more species. This study demonstrates the feasibility of using long-read metabarcoding for eDNA vertebrate biodiversity assessments. However, our findings suggests that longer fragments are less abundant in environmental settings, but not in aquarium settings, suggesting that longer fragments may provide a more recent snapshot of the community. Thus, long-read metabarcoding can expand the molecular toolbox for biodiversity assessments by improving species-level identification and may be especially useful when the temporal origin of the eDNA signal is better understood.

Integrating temperature-dependent production of environmental DNA into its relationship with organism abundance

Despite a consensus on the correlative relationship between environmental DNA (eDNA) concentration and organism abundance, precise and reliable abundance estimation using eDNA analysis is in its infancy. Previous studies suggested that water temperature could drive both eDNA degradation and production, but it remains unclarified how the eDNA-abundance relationship is influenced by water temperatures. To address the knowledge gap, numerical simulations considering temperature-dependent eDNA production and degradation were conducted by re-analyzing a previous dataset estimating fish eDNA production and decay rates at different water temperatures, followed by generating population-level eDNA concentrations depending on a given temperature, the number of individuals, and their mass distribution. Results showed that water temperatures had a positive, but relatively small, effect on the strength (R2 value) of the eDNA-abundance relationship, regardless of eDNA production scenarios. In contrast, the sensitivity (regression slope) of the relationship was enhanced by warmer temperatures when temperature-dependent eDNA production was considered, but it decreased unless it was considered. Although further efforts should be required to integrate organism physiology into eDNA production, the present study implied the importance of linking the production mechanism of eDNA particles to organism physiology, offering a groundwork for theorizing the eDNA-abundance relationship depending on environmental conditions, including temperatures, for making eDNA signals more quantitative and reliable.

Biodiversity monitoring in remote marine environments: Advancing environmental DNA/RNA sampling workflows

Understanding biodiversity is crucial for protecting unique environments, but acquiring this knowledge is challenging in isolated areas due to limited availability of easy-to-implement biomonitoring tools. To determine optimal sampling strategies in remote regions, environmental DNA and RNA (eDNA and eRNA) sampling workflows were evaluated at 12 sites in three fiords within Fiordland National Park, Aotearoa-New Zealand. For filtration comparison, a modified cruising speed net was used to concentrate eDNA/eRNA onto 20 μm nylon filters, while water from the net's cod-end was filtered through a 5 μm Smith-Root self-preserving filter using the eDNA Citizen Scientist Sampler. To compare preservation methods, Smith-Root filters were cut in half, with one half preserved in the self-preserving unit and the other in DNA/RNA Shield™ buffer. Biodiversity screening was performed by sequencing the 18S rRNA gene for eukaryotes and two mitochondrial 16S rRNA genes for fish and marine vertebrates. Comparable amplicon sequence variant (ASVs) richness was observed between methods, yet samples preserved with buffer showed higher richness of fish and marine vertebrate taxa and higher PCR amplification success. There was little variation in community composition, except for 16S rRNA targeting fish, where distinct patterns emerged based on preservation methods. Overall, sampling workflows showed similar community composition and alpha diversity across both nucleic acids. These results confirm that enhancing eDNA/eRNA yields for sparse taxa requires consideration of collection and preservation methods. However, abundant taxa biodiversity is captured consistently, allowing for adjustments without compromising robustness. These insights support streamlined eDNA/eRNA sampling, emphasizing adaptive strategies based on targeted taxa.

Investigating passive eDNA samplers and submergence times for marine surveillance

Passive environmental DNA (eDNA) samplers offer a cost-effective and scalable approach to marine biodiversity monitoring, potentially aiding detections of non-indigenous species. This study explored the efficiency of passive eDNA samplers to detect a variety of globally problematic marine invasive species in field conditions: Sabella spallanzanii, Styela clava, Bugula neritina and Undaria pinnatifida. Four passive sampler substrates, nylon filters, positively charged nylon discs, nylon mesh, and artificial sponges, were tested across six submergence times, ranging from 10 to 720 min, against standard filtration-based approaches. Our results demonstrated that passive samplers could achieve comparable or even higher eDNA yields than traditional active filtration methods, indicating their potential for biosecurity surveillance. Species-specific droplet-digital PCR (ddPCR) assays provided sensitive and quantifiable eDNA signals, though assay validation remains crucial to avoid false negatives. Significant variation in eDNA signal detection highlighted the importance of considering both material selection and submersion time, depending on the targeted organisms. Furthermore, 18S rRNA metabarcoding was undertaken to assess how the overall detected biodiversity might interfere with species-specific detections. Certain sessile organisms, such as ascidians and polychaetes, dominated early representation on the passive filters but did not interfere with species-specific detection. By optimizing material selection, submersion time, and assay validation, passive eDNA sampling can enhance the sensitivity and reliability of eDNA-based monitoring, contributing to improved marine biosecurity and conservation efforts.

Environmental DNA metabarcoding: Current applications and future prospects for freshwater fish monitoring

Fish, as the top predators in freshwater, greatly contribute to maintain ecosystem stability. There has been a sharp decline in freshwater fish stocks due to multiple factors, both natural and anthropogenic. Effective and accurate monitoring of freshwater fish is necessary to inform on ecosystem health and guide environmental management practices. Traditional survey methods are gradually unable to meet the growing monitoring needs. Environmental DNA (eDNA) metabarcoding provides a high sensitivity, fast and affordable approach for surveying and monitoring of aquatic biology. However, due to the limitations of incomplete databases and non-standardized procedures, the use of eDNA techniques for monitoring freshwater fish remains less mature compared to traditional fish monitoring methods. To systematically review the current applications and future prospects of the eDNA metabarcoding for freshwater fish monitoring, this article: (i) summarizes relevant researches on freshwater fish monitoring using eDNA technology (e.g., methodologies, resource surveys, habitat assessments, etc.) over the past decade. (ii) outlines the methodology of eDNA metabarcoding in freshwater fish monitoring, proposes a standardized process for eDNA methods, and suggests ways to eliminate detection errors. (iii) analyzes the current challenges of the eDNA metabarcoding application in resource surveys and ecological quality assessments of freshwater fish. The eDNA technology can be used as a better alternative or supplement to traditional survey methods for monitoring the diversity, biomass, population distribution, and spawning behaviors of freshwater fish, in particular, it has a prominent advantage in monitoring endangered and rare fish species. (iv) investigates the application of eDNA technology in investigating the impact of human activities and invasive species on freshwater fish, and emphasizes the eDNA's potential in assessing the impacts of water projects (e.g., dam construction or removal, water diversion project) on fish habitats, and the effectiveness of fish passage and invasive fish control efforts. (v) discusses the future prospects of eDNA-based freshwater fish monitoring, both in terms of technology and application. This review provides a guidance for the future development and application of eDNA technology in freshwater fish monitoring and ecological quality assessments.

Revealing Elasmobranch Distributions in Turbid Coastal Waters: Insights From Environmental DNA and Particle Tracking

Many sharks, rays and skates are highly threatened and vulnerable to overexploitation, as such reliable monitoring of elasmobranchs is key to effective management and conservation. The mobile and elusive nature of these species makes monitoring challenging, particularly in temperate waters with low visibility. Environmental DNA (eDNA) methods present an opportunity to study these species in the absence of visual identification or invasive techniques. However, eDNA data alone can be difficult to interpret for species monitoring, particularly in a marine setting where its distribution can be influenced by water currents. In this study, we investigated the spatial and temporal distribution of elasmobranch species in two Special Areas for Conservation (SAC) off the coast of Wales. We took monthly eDNA samples for 1 year (starting September 2020 and March 2022 for the northern and southern SACs, respectively), and used metabarcoding to reveal the presence of elasmobranch species. We combined these data with hydrodynamic modelling and particle tracking methods to simulate the potential origins of the detected eDNA. We detected 11 elasmobranch species, including the critically endangered angelshark (Squatina squatina) and tope (Galeorhinus galeus). Most detections were in the spring and the fewest in the autumn. The particle tracking simulations predicted that eDNA was shed, on average, approximately 7 km and 15 km (in the northern and southern SACs, respectively) from the sampling stations at which it was detected. These results show that the two SACs represent important areas for elasmobranchs in the United Kingdom and demonstrate that eDNA methods combined with particle tracking simulations can represent a new frontier for monitoring marine species.

Experimental assessment of Acanthopagrus schlegelii biomass based on environmental DNA technology

The Environmental DNA (eDNA) technology has attracted significant attention due to its convenience and high sensitivity. However, the variations of eDNA across diverse environments and biological species remain complex. Therefore, a detailed exploration of the release patterns of eDNA for specific species under different environments is crucial for the scientific utilization of eDNA detection techniques. This study conducted an experiment involving the aquaculture of Acanthopagrus schlegelii to explore the release and degradation mechanisms of eDNA. It also analyzed the influence of salinity and biomass on the concentration of eDNA in water. Through model simulations, the variation patterns of A. schlegelii eDNA were revealed. The study achieved three key findings: (1) The research on the release and degradation mechanisms of A. schlegelii eDNA indicated that the Generalized Additive Model (GAM) effectively fits the variation patterns of eDNA concentration. The peak concentration of eDNA released by A. schlegelii was observed at 42 h, and the degradation process exhibited two stages: rapid and slow degradation, with a negative correlation between eDNA concentration and time. (2) By investigating the relationship between the concentration of A. schlegelii eDNA and biomass, it was demonstrated that Linear Models (LM) effectively captured this relationship, indicating a correlation between eDNA concentration and biomass. (3) The detection of A. schlegelii eDNA concentration under different salinity conditions revealed that the GAM model better reflected the relationship between eDNA and salinity, exhibiting a negative correlation. As salinity increased, the concentration of eDNA decreased. This study lays a foundation for future assessments of the A. schlegelii biomass in natural waters using eDNA quantitative detection techniques, and provides relevant references for quantitative eDNA detection techniques in other marine fish species.

Quantifying the Detection Sensitivity and Precision of qPCR and ddPCR Mechanisms for eDNA Samples

Environmental DNA (eDNA) detection employing quantitative PCR (qPCR) and droplet digital PCR (ddPCR) offers a non-invasive and efficient approach for monitoring aquatic organisms. Accurate and sensitive quantification of eDNA is crucial for tracking rare and invasive species and understanding the biodiversity abundance and distribution of aquatic organisms. This study compares the sensitivity and quantification precision of qPCR and ddPCR for eDNA surveys through Bayesian inference using latent parameters from both known concentration (standards) and environmental samples across three teleost fish species assays. The results show that ddPCR offers higher sensitivity and quantification precision, particularly at low DNA concentrations (< 1 copy/μL reaction), than qPCR. These findings highlight the superior performance of ddPCR for eDNA detection at low concentrations, guiding researchers towards more reliable methods for effective species monitoring. Additionally, this study indicates that a two-step (detection and concentration) model increased the precision of qPCR results, useful for enhancing the robustness of eDNA quantification. Furthermore, we investigated the lower limit of quantification for ddPCR, providing insights on how such limit can be extended, which could also be applied to qPCR.

Ecological forensic testing: Using multiple primers for eDNA detection of marine vertebrates in an estuarine lagoon subject to anthropogenic influences

Many critical aquatic habitats are in close proximity to human activity (i.e., adjacent to residences, docks, marinas, etc.), and it is vital to monitor biodiversity in these and similar areas that are subject to ongoing urbanization, pollution, and other environmental disruptions. Environmental DNA (eDNA) metabarcoding is an accessible, non-invasive genetic technique used to detect and monitor species diversity and is a particularly useful approach in areas where traditional biodiversity monitoring methods (e.g., visual surveys or video surveillance) are challenging to conduct. In this study, we implemented an eDNA approach that used a combination of three distinct PCR primer sets to detect marine vertebrates within a canal system of Biscayne Bay, Florida, an ecosystem representative of challenging sampling conditions and a myriad of impacts from urbanization. We detected fish species from aquarium, commercial, and recreational fisheries, as well as invasive, cryptobenthic, and endangered vertebrate species, including charismatic marine mammals such as the protected West Indian manatee, Trichechus manatus. Our results support the potential for eDNA analyses to supplement traditional biodiversity monitoring methods and ultimately serve as an important tool for ecosystem management. This approach minimizes stress or disturbance to organisms and removes the intrinsic risk and logical limitations of SCUBA diving, snorkeling, or deploying sensitive equipment in areas that are subject to high vessel traffic and/or low visibility. Overall, this work sets the framework to understand how biodiversity may change over different spatial and temporal scales in an aquatic ecosystem heavily influenced by urbanization and validates the use of eDNA as a complementary approach to traditional ecological monitoring methods.

A preliminary study on detecting human DNA in aquatic environments: Potential of eDNA in forensics

Human environmental DNA (eDNA) application have not been fully applied or adequately considered in the fields of eDNA and forensics. Nonetheless, this technique holds great potential as a complementary tool for detecting human DNA in aquatic environments, particularly in cases involving crimes connect to such environments. However, the detectability or stability of eDNA can vary depending on several factors. Therefore, this preliminary study investigates the detection and degradation rates of human eDNA, as well as the recovery of nuclear short tandem repeat (STR) profiles and mitochondrial DNA (mtDNA) sequencing, using water samples from both saltwater and freshwater sources. To conduct the experiment, whole human blood was spiked into the water samples. Water samples were then filtered using a 5 µm pore size filter, and samples were collected at various time intervals up to 23 days. A human specific qPCR assay targeting HV1 region of human mtDNA was used to detect human eDNA. Results demonstrated that human eDNA remains detectable for up to 36 hours in freshwater samples and up 84 hours in saltwater samples. The limit of detection (LOD) of human eDNA, (205 copies/µl), was achieved after 60 hours in freshwater and 180 hours in saltwater samples. Partial STR profiles could be recovered up to 24 hours for freshwater and saltwater. Results from mtDNA sequencing indicate that full mtDNA profiles could be recovered from freshwater samples up to 48 hours and remained detectable up to 72 hours in saltwater. Overall, the findings of this study underscore the importance of considering and incorporating human eDNA analysis as a valuable tool in forensic practice. By harnessing the power of eDNA, law enforcement agencies can enhance their investigation capabilities, improve the accuracy of forensic reconstructions, and ultimately contribute to the resolution of cases involving aquatic environments. Further research and validation are needed to optimize and expand the utilization of eDNA techniques in forensic investigations.

Is it worthy to use environmental DNA instead of scientific trawling or video survey to monitor taxa in soft-bottom habitats?

Non-extractive techniques such as video analysis are increasingly used by scientists to study marine communities instead of extractive methods such as trawling. Currently, environmental DNA (eDNA) analysis is seen as a revolutionary tool to study taxonomic diversity. We aimed to determine which method is the most appropriate to describe fish and commercial invertebrate diversity comparing bottom trawl hauls, video transects and seawater eDNA. Our results reveal that video detected the lowest number of taxa and trawling the highest. eDNA analysis is powerful to describe marine bony fish communities, but some taxa of importance for the ecosystem such as elasmobranchs, crustaceans or molluscs are poorly detected. This may be due to several factors such as marker specificity, incomplete reference gene databases or low DNA release in the environment. For now, the various methods provide different information and none is exhaustive enough to be used alone for biodiversity characterisation.

Detection, movement and persistence of invertebrate eDNA in groundwater

Sampling groundwater biodiversity is difficult because of limited access and issues with species identification. Environmental DNA (eDNA) provides a viable alternative to traditional sampling approaches, however limited knowledge of the abundance and fate of DNA in groundwater hinders the interpretation of data from these environments. Groundwater environments are dark and have lower oxygen concentrations and microbial activity than surface waters. Consequently, assumptions about DNA fate in surface ecosystems may not apply to groundwaters. Here, we test the longevity and transport of eDNA in groundwater within a static microcosm and a flow-through mesocosm. A variety of invertebrates were placed within a mesocosm and microcosm to enable DNA shedding, and then removed. DNA persisted for up to 5 weeks after their removal in the static experiment and was detected between 9 and 33 days in the flow-through experiment. Sediments and water both proved important for eDNA detection. Crustacean DNA was detected sporadically and unpredictably, whereas non-crustacean DNA was detected more frequently despite their lower densities. We suggest that detecting crustaceans poses a challenge to utilising eDNA approaches for stygofauna monitoring. This is confounded by the scarcity of sequences for stygofauna in reference databases. Further research is needed before eDNA alone can be routinely employed for stygofauna detection.

Emerging use of air eDNA and its application to forensic investigations - A review

Biological material is routinely collected at crime scenes and from exhibits and is a key type of evidence during criminal investigations. Improvements in DNA technologies allow collection and profiling of trace samples, comprised of few cells, significantly expanding the types of exhibits targeted for DNA analysis to include touched surfaces. However, success rates from trace and touch DNA samples tend to be poorer compared to other biological materials such as blood. Simultaneously, there have been recent advances in the utility of environmental DNA collection (eDNA) in identification and tracking of different biological organisms and species from bacteria to naked mole rats in different environments, including, soil, ice, snow, air and aquatic. This paper examines the emerging methods and research into eDNA collection, with a special emphasis on the potential forensic applications of human DNA collection from air including challenges and further studies required to progress implementation.

Up in the air: Presence and collection of DNA from air and air conditioner units

Biological material is routinely collected at crime scenes and from exhibits and is a key type of evidence during criminal investigations. Touch or trace DNA samples from surfaces and objects deemed to have been contacted are frequently collected. However, a person of interest may not leave any traces on contacted surfaces, for example, if wearing gloves. A novel means of sampling human DNA from air offers additional avenues for DNA collection. In the present study, we report on the results of a pilot study into the prevalence and persistence of human DNA in the air. The first aspect of the pilot study investigates air conditioner units that circulate air around a room, by sampling units located in four offices and four houses at different time frames post-cleaning. The second aspect investigates the ability to collect human DNA from the air in rooms, with and without people, for different periods of time and with different types of collection filters. Results of this pilot study show that human DNA can be collected on air conditioner unit surfaces and from the air, with air samples representing the more recent occupation while air conditioner units showing historic use of the room.

Enhancing amphibian biomonitoring through eDNA metabarcoding

Surveying biodiversity has taken a quantum leap with environmental DNA (eDNA) metabarcoding, an immensely powerful approach lauded for its efficiency, sensitivity, and non-invasiveness. This approach emerges as a game-changer for the elusive realm of endangered and rare species-think nocturnal, environmentally elusive amphibians. Here, we have established a framework for constructing a reliable metabarcoding pipeline for amphibians, covering primer design, performance evaluation, laboratory validation, and field validation processes. The Am250 primer, located on the mitochondrial 16S gene, was optimal for the eDNA monitoring of amphibians, which demonstrated higher taxonomic resolution, smaller species amplification bias, and more extraordinary detection ability compared to the other primers tested. Am250 primer exhibit an 83.8% species amplification rate and 75.4% accurate species identification rate for Chinese amphibians in the in silico PCR and successfully amplified all tested species of the standard samples in the in vitro assay. Furthermore, the field-based mesocosm experiment showed that DNA can still be detected by metabarcoding even days to weeks after organisms have been removed from the mesocosm. Moreover, field mesocosm findings indicate that eDNA metabarcoding primers exhibit different read abundances, which can affect the relative biomass of species. Thus, appropriate primers should be screened and evaluated by three experimental approaches: in silico PCR simulation, target DNA amplification, and mesocosm eDNA validation. The selection of a single primer set or multiple primers' combination should be based on the monitoring groups to improve the species detection rate and the credibility of results.

A comparative study on eDNA-based detection of Siamese bat catfish (Oreoglanis siamensis) in wet and dry conditions

The use of environmental DNA (eDNA) analysis has demonstrated notable efficacy in detecting the existence of freshwater species, including those that are endangered or uncommon. This application holds significant potential for enhancing environmental monitoring and management efforts. However, the efficacy of eDNA-based detection relies on several factors. In this study, we assessed the impact of rainfall on the detection of eDNA for the Siamese bat catfish (Oreoglanis siamensis). Quantitative polymerase chain reaction (qPCR) analysis indicated that samples from days with average rainfall exceeding 35 mm (classified as heavy and very heavy rain) yielded negative results. While eDNA detection remains feasible on light or moderate rainy days, a noteworthy reduction in eDNA concentration and qPCR-positive likelihood was observed. Analysis across 12 sampling sites established a statistically significant negative relationship (p < 0.001) between eDNA detection and rainfall. Specifically, for each 1 mm increase in rainfall, there was an observed drop in eDNA concentration of 0.19 copies/mL (±0.14). The findings of this study provide definitive evidence that precipitation has a significant impact on the detection of eDNA in Siamese bat catfish. However, in the case of adverse weather conditions occurring on the day of sampling, our research indicates that it is acceptable to continue with the task, as long as the rainfall is not heavy or very heavy. To enhance the effectiveness of an eDNA survey, it is crucial to consider many factors related to climatic conditions. The aforementioned factor holds significant importance not only for the specific species under scrutiny but also for the broader dynamics of the climate.

Improving the efficiency of adaptive management methods in multiple fishways using environmental DNA

Dams and weirs impede the continuity of rivers and transit of migratory fish. To overcome this obstacle, fishways are installed worldwide; however, management after installation is important. The Miyanaka Intake Dam has three fish ladders with different flow velocities and discharges and has been under adaptive management since 2012. Fish catch surveys, conducted as an adaptive management strategy, place a heavy burden on fish. Furthermore, a large number of investigators must be mobilized during the 30-day investigation period. Thus, a monitoring method using environmental DNA that exerts no burden on fish and requires only a few surveyors (to obtain water samples) and an in-house analyst was devised; however, its implementation in a fishway away from the point of analysis and with limited flow space and its effective water sampling frequency have not been reported. Therefore, in 2019, we started a trial aiming to evaluate the methods and application conditions of environmental DNA surveys for the continuous and long-term monitoring of various fish fauna upstream and downstream of the Miyanaka Intake Dam. To evaluate the fish fauna, the results of an environmental DNA survey (metabarcoding method) for 2019 to 2022 were compared to those of a catch survey in the fishway from 2012 to 2022. The results confirmed the use of environmental DNA surveys in evaluating the contribution of fishways to biodiversity under certain conditions and introduced a novel method for sample collection.

Changes in the level of biofilm development significantly affect the persistence of environmental DNA in flowing water

As one of the powerful tools of species biomonitoring, the utilization of environmental DNA (eDNA) technology is progressively expanding in both scope and frequency within the field of ecology. Nonetheless, the growing dissemination of this technology has brought to light a multitude of intricate issues. The complex effects of environmental factors on the persistence of eDNA in water have brought many challenges to the interpretation of eDNA information. In this study, the primary objective was to examine how variations in the presence and development of biofilms impact the persistence of grass carp eDNA under different sediment types and flow conditions. This investigation encompassed the processes of eDNA removal and resuspension in water, shedding light on the complex interactions involved. The findings reveal that with an elevated biofilm development level, the total removal rate of eDNA gradually rose, resulting in a corresponding decrease in its residence time within the mesocosms. The influence of biofilms on the persistence of grass carp eDNA is more pronounced under flowing water conditions. However, changes in bottom sediment types did not significantly interact with biofilms. Lastly, in treatments involving alternating flow conditions between flowing and still water, significant resuspension of grass carp eDNA was not observed due to interference from multiple factors, including the effect of biofilms. Our study offers preliminary insights into the biofilm-mediated mechanisms of aquatic eDNA removal, emphasizing the need for careful consideration of environmental factors in the practical application of eDNA technology for biomonitoring in natural aquatic environments.

eDNA based bycatch assessment in pelagic fish catches

Pelagic fish like herring, sardines, and mackerel constitute an essential and nutritious human food source globally. Their sustainable harvest is promoted by the application of precise, accurate, and cost-effective methods for estimating bycatch. Here, we experimentally test the new concept of using eDNA for quantitative bycatch assessment on the illustrative example of the Baltic Sea sprat fisheries with herring bycatch. We investigate the full pipeline from sampling of production water on vessels and in processing factories to the estimation of species weight fractions. Using a series of controlled mixture experiments, we demonstrate that the eDNA signal from production water shows a strong, seasonally consistent linear relationship with herring weight fractions, however, the relationship is influenced by the molecular method used (qPCR or metabarcoding). In four large sprat landings analyzed, despite examples of remarkable consistency between eDNA and visual reporting, estimates of herring bycatch biomass varied between the methods applied, with the eDNA-based estimates having the highest precision for all landings analyzed. The eDNA-based bycatch assessment method has the potential to improve the quality and cost effectiveness of bycatch assessment in large pelagic fisheries catches and in the long run lead to more sustainable management of pelagic fish as a precious marine resource.

Evaluating environmental DNA detection of a rare fish in turbid water using field and experimental approaches

Detection sensitivity of aquatic species using environmental DNA (eDNA) generally decreases in turbid water but is poorly characterized. In this study, eDNA detection targeted delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish associated with turbid water. eDNA sampling in the field was first paired with a trawl survey. Species-specific detection using a Taqman qPCR assay showed concordance between the methods, but a weak eDNA signal. Informed by the results of field sampling, an experiment was designed to assess how turbidity and filtration methods influence detection of a rare target. Water from non-turbid (5 NTU) and turbid (50 NTU) estuarine sites was spiked with small volumes (0.5 and 1 mL) of water from a delta smelt tank to generate low eDNA concentrations. Samples were filtered using four filter types: cartridge filters (pore size 0.45 μm) and 47 mm filters (glass fiber, pore size 1.6 μm and polycarbonate, pore sizes 5 and 10 μm). Prefiltration was also tested as an addition to the filtration protocol for turbid water samples. eDNA copy numbers were analyzed using a censored data method for qPCR data. The assay limits and lack of PCR inhibition indicated an optimized assay. Glass fiber filters yielded the highest detection rates and eDNA copies in non-turbid and turbid water. Prefiltration improved detection in turbid water only when used with cartridge and polycarbonate filters. Statistical analysis identified turbidity as a significant effect on detection probability and eDNA copies detected; filter type and an interaction between filter type and prefilter were significant effects on eDNA copies detected, suggesting that particulate-filter interactions can affect detection sensitivity. Pilot experiments and transparent criteria for positive detection could improve eDNA surveys of rare species in turbid environments.

Non-invasive real-time genomic monitoring of the critically endangered kākāpō

We used non-invasive real-time genomic approaches to monitor one of the last surviving populations of the critically endangered kākāpō (Strigops habroptilus). We first established an environmental DNA metabarcoding protocol to identify the distribution of kākāpō and other vertebrate species in a highly localized manner using soil samples. Harnessing real-time nanopore sequencing and the high-quality kākāpō reference genome, we then extracted species-specific DNA from soil. We combined long read-based haplotype phasing with known individual genomic variation in the kākāpō population to identify the presence of individuals, and confirmed these genomically informed predictions through detailed metadata on kākāpō distributions. This study shows that individual identification is feasible through nanopore sequencing of environmental DNA, with important implications for future efforts in the application of genomics to the conservation of rare species, potentially expanding the application of real-time environmental DNA research from monitoring species distribution to inferring fitness parameters such as genomic diversity and inbreeding.

Current status and topical issues on the use of eDNA-based targeted detection of rare animal species

Animal detection through DNA present in environmental samples (eDNA) is a valuable tool for detecting rare species, that are difficult to observe and monitor. eDNA-based tools are underpinned by molecular evolutionary principles, key to devising tools to efficiently single out a targeted species from an environmental sample. Here, we present a comprehensive review of the use of eDNA-based methods for the detection of targeted animal species, such as rare, endangered, or invasive species, through the analysis of 549 publications (2008-2022). Aquatic ecosystems have been the most surveyed, in particular, freshwaters (74 %), and to a less extent marine (14 %) and terrestrial systems (10 %). Vertebrates, in particular, fish (38 %), and endangered species, have been the focus of most of these studies, and Cytb and COI are the most employed markers. Among invertebrates, assays have been mainly designed for Mollusca and Crustacea species (21 %), in particular, to target invasive species, and COI the most employed marker. Targeted molecular approaches, in particular qPCR, have been the most adopted (75 %), while eDNA metabarcoding has been rarely used to target single or few species (approx. 6 %). However, less attention has been given in these studies to the effects of environmental factors on the amount of shed DNA, the differential amount of shed DNA among species, or the sensitivity of the markers developed, which may impact the design of the assays, particularly to warrant the required detection level and avoid false negatives and positives. The accuracy of the assays will also depend on the availability of genetic data and vouchered tissue or DNA samples from closely related species to assess both marker and primers' specificity. In addition, eDNA-based assays developed for a particular species may have to be refined for use in a new geographic area taking into account site-specific populations, as well as any intraspecific variation.

Multifunctional polydopamine - Zn2+-curcumin coated additively manufactured ceramic bone grafts with enhanced biological properties

The lack of site-specific chemotherapeutic agents after osteosarcoma surgeries often induces severe side effects. We propose the utilization of curcumin as an alternative natural chemo-preventive drug for tumor-specific delivery systems with 3D printed tricalcium phosphate (TCP) based artificial bone grafts. The poor bioavailability and hydrophobic nature of curcumin restrict its clinical use. We have used polydopamine (PDA) coating with Zn2+ functionalization to enhance the curcumin release in the biological medium. The obtained PDA-Zn2+ complex is characterized by X-ray photoelectron spectroscopy (XPS). The presence of PDA-Zn2+ coating leads to ~2 times enhancement in curcumin release. We have computationally predicted and validated the optimized surface composition by a novel multi-objective optimization method. The experimental validation of the predicted compositions indicates that the PDA-Zn2+ coated curcumin immobilized delivery system leads to a ~12 folds decrease in osteosarcoma viability on day 11 as compared to only TCP. The osteoblast viability shows ~1.4 folds enhancement. The designed surface shows the highest ~90 % antibacterial efficacy against gram-positive and gram-negative bacteria. This unique strategy of curcumin delivery with PDA-Zn2+ coating is expected to find application in low-load bearing critical-sized tumor-resection sites.

Freshwater connectivity transforms spatially integrated signals of biodiversity

Aquatic ecosystems offer a continuum of water flow from headwater streams to inland lakes and coastal marine systems. This spatial connectivity influences the structure, function and dynamics of aquatic communities, which are among the most threatened and degraded on the Earth. Here, we determine the spatial resolution of environmental DNA (eDNA) in dendritic freshwater networks, which we use as a model for connected metacommunities. Our intensive sampling campaign comprised over 420 eDNA samples across 21 connected lakes, allowing us to analyse detections at a variety of scales, from different habitats within a lake to entire lake networks. We found strong signals of within-lake variation in eDNA distribution reflective of typical habitat use by both fish and zooplankton. Most importantly, we also found that connecting channels between lakes resulted in an accumulation of downstream eDNA detections in lakes with a higher number of inflows, and as networks increased in length. Environmental DNA achieves biodiversity surveys in these habitats in a high-throughput, spatially integrated way. These findings have profound implications for the interpretation of eDNA detections in aquatic ecosystems in global-scale biodiversity monitoring observations.

Heterogeneity of Fish Taxonomic and Functional Diversity Evaluated by eDNA and Gillnet along a Mangrove-Seagrass-Coral Reef Continuum

The effective and reliable monitoring of fish communities is important for the management and protection of marine ecosystems. Environmental DNA (eDNA) metabarcoding is a relatively new method that has been widely used in recent years, while traditional sampling via fish catching (i.e., gillnets) is one of the most common and reliable fish monitoring methods used to date. We compared the taxonomic and functional diversity of fish detected within a mangrove-seagrass-coral reef continuum using both survey methods. One liter seawater and gillnet samples were collected in August 2021 from mangrove forests, seagrass meadows and coral reef habitats (n = 3 each) in Hainan, China. Surveys using eDNA and gillnets identified 139 genera belonging to 66 families and 58 genera belonging to 42 families, respectively. Regardless of the survey method, fish detected in mangrove, seagrass and coral reef habitats were heterogeneous in their communities; however, the shared species between habitats suggest some degree of connectivity. There were no significant differences between habitats in terms of taxonomic and functional diversity, but a higher taxonomic diversity was detected using eDNA. Both methods were able to distinguish fish assemblages between different habitats; however, gillnet surveys performed better than eDNA surveys for distinguishing mangrove from seagrass assemblages. Therefore, the concurrent use of eDNA and gillnet survey methods provides a more comprehensive approach to understanding the heterogeneity of fish taxonomic and functional diversity along mangrove-seagrass-coral reef continuums.

Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution

Environmental DNA (eDNA) is the fastest growing biomonitoring tool fuelled by two key features: time efficiency and sensitivity. Technological advancements allow rapid biodiversity detection at both species and community levels with increasing accuracy. Concurrently, there has been a global demand to standardise eDNA methods, but this is only possible with an in-depth overview of the technological advancements and a discussion of the pros and cons of available methods. We therefore conducted a systematic literature review of 407 peer-reviewed papers on aquatic eDNA published between 2012 and 2021. We observed a gradual increase in the annual number of publications from four (2012) to 28 (2018), followed by a rapid growth to 124 publications in 2021. This was mirrored by a tremendous diversification of methods in all aspects of the eDNA workflow. For example, in 2012 only freezing was applied to preserve filter samples, whereas we recorded 12 different preservation methods in the 2021 literature. Despite an ongoing standardisation debate in the eDNA community, the field is seemingly moving fast in the opposite direction and we discuss the reasons and implications. Moreover, by compiling the largest PCR-primer database to date, we provide information on 522 and 141 published species-specific and metabarcoding primers targeting a wide range of aquatic organisms. This works as a user-friendly 'distillation' of primer information that was hitherto scattered across hundreds of papers, but the list also reflects which taxa are commonly studied with eDNA technology in aquatic environments such as fish and amphibians, and reveals that groups such as corals, plankton and algae are under-studied. Efforts to improve sampling and extraction methods, primer specificity and reference databases are crucial to capture these ecologically important taxa in future eDNA biomonitoring surveys. In a rapidly diversifying field, this review synthetises aquatic eDNA procedures and can guide eDNA users towards best practice.

Using eDNA sampling for species-specific fish detection in tropical oceanic samples: limitations and recommendations for future use

Background

Over the past decade, environmental DNA (eDNA) has become a resourceful tool in conservation and biomonitoring. Environmental DNA has been applied in a variety of environments, but the application to studies of marine fish, particularly at tropical latitudes, are limited. Since many commercially important Caribbean fishes are overexploited, these species are optimal candidates to explore the use of this method as a biomonitoring tool. Specifically, for many of these species, the formation of fish spawning aggregations (FSAs) marks a critical life history event where fishes will gather in large numbers for reproduction. These FSAs are ephemeral in nature, lasting only a few days, but are predictable in time and space which makes them susceptible to overfishing.

Methods

In this study, we test the feasibility of using an eDNA sampling approach (water and sediment collection) to detect the presence of known FSAs off the west coast of Puerto Rico, with cytochrome c oxidase subunit 1 (CO1) and 12S rRNA (12S) primers designed to target specific species. A total of 290 eDNA samples were collected and, of those, 206 eDNA samples were processed. All eDNA samples varied in DNA concentration, both between replicates and collection methods. A total of 12 primer sets were developed and tested using traditional PCR and qPCR.

Results

Despite validation of primer accuracy and sample collection during known peak spawning times, the use of traditional PCR and qPCR with both molecular markers failed to produce species-specific amplification. Thus, a trial test was conducted using the CO1 primers in which target fish DNA was 'spiked' at various concentrations into the respective eDNA samples to determine the target species DNA concentration limit of detection. Upon successful amplification of the trial, results indicated that eDNA samples were below the detection threshold of our methods, suggesting that the number of fish present at the spawning aggregations was inadequate for single-species detection methods. In addition, elements such as the unavoidable presence of non-target DNA, oceanic environmental conditions, shedding rates of target fish, among other biotic and abiotic factors could have affected DNA persistence and degradation rates at the sites.

Conclusion

We provide recommendations for species-specific fish detection in lower latitudes, and suggestions for studies aiming to monitor or detect fish spawning aggregations using eDNA sampling.

Optimal sample type and number vary in small shallow lakes when targeting non-native fish environmental DNA

Non-native fish have been shown to have deleterious impacts on freshwater ecosystems in New Zealand. Early detection is critical for their effective management. Traditional capture-based techniques may not detect newly introduced fish, especially if they are present in low abundance. Molecular techniques that target environmental DNA (eDNA) have been shown, in many instances, to be more sensitive, cost-effective and require lower sampling effort. However, appropriate sampling strategies are needed to ensure robust and interpretable data are obtained. In this study we used droplet digital PCR assays to investigate the presence of two non-native fish in New Zealand, the European perch (Perca fluviatilis) and rudd (Scardinius erythrophthalmus) in three small lakes. Samples were collected from water and surface sediment at near-shore and mid-lake sites. Probabilistic modelling was used to assess the occupancy of fish eDNA and develop guidance on sampling strategies. Based on the detection probability measures from the present study, at least six sites and five replicates per site are needed to reliably detect fish eDNA in sediment samples, and twelve sites with eight replicates per site for water samples. The results highlight the potential of developing monitoring and surveillance programs adapted to lakes, that include the use of assays targeting eDNA. This study focused on small shallow lakes, and it is likely that these recommendations may vary in larger, deeper, and more geomorphologically complex lakes, and this requires further research.

Environmental DNA methylation of Lymnaea stagnalis varies with age and is hypermethylated compared to tissue DNA

Environmental DNA (eDNA) approaches contributing to species identifications are quickly becoming the new norm in biomonitoring and ecosystem assessments. Yet, information such as age and health state of the population, which is vital to species biomonitoring, has not been accessible from eDNA. DNA methylation has the potential to provide such information on the state of a population. Here, we measured the methylation of eDNA along with tissue DNA (tDNA) of Lymnaea stagnalis at four life stages. We demonstrate that eDNA methylation varies with age and allows distinguishing among age classes. Moreover, eDNA was globally hypermethylated in comparison to tDNA. This difference was age-specific and connected to a limited number of eDNA sites. This differential methylation pattern suggests that eDNA release with age is partially regulated through DNA methylation. Our findings help to understand mechanisms involved in eDNA release and shows the potential of eDNA methylation analysis to assess age classes. Such age class assessments will encourage future eDNA studies to assess fundamental processes of population dynamics and functioning in ecology, biodiversity conservation and impact assessments.

Out of thin air: surveying tropical bat roosts through air sampling of eDNA

Understanding roosting behaviour is essential to bat conservation and biomonitoring, often providing the most accurate methods of assessing bat population size and health. However, roosts can be challenging to survey, e.g., physically impossible to access or presenting risks for researchers. Disturbance during monitoring can also disrupt natural bat behaviour and present material risks to the population such as disrupting hibernation cycles. One solution to this is the use of non-invasive monitoring approaches. Environmental (e)DNA has proven especially effective at detecting rare and elusive species particularly in hard-to-reach locations. It has recently been demonstrated that eDNA from vertebrates is carried in air. When collected in semi-confined spaces, this airborne eDNA can provide remarkably accurate profiles of biodiversity, even in complex tropical communities. In this study, we deploy novel airborne eDNA collection for the first time in a natural setting and use this approach to survey difficult to access potential roosts in the neotropics. Using airborne eDNA, we confirmed the presence of bats in nine out of 12 roosts. The identified species matched previous records of roost use obtained from photographic and live capture methods, thus demonstrating the utility of this approach. We also detected the presence of the white-winged vampire bat (Diaemus youngi) which had never been confirmed in the area but was long suspected based on range maps. In addition to the bats, we detected several non-bat vertebrates, including the big-eared climbing rat (Ototylomys phyllotis), which has previously been observed in and around bat roosts in our study area. We also detected eDNA from other local species known to be in the vicinity. Using airborne eDNA to detect new roosts and monitor known populations, particularly when species turnover is rapid, could maximize efficiency for surveyors while minimizing disturbance to the animals. This study presents the first applied use of airborne eDNA collection for ecological analysis moving beyond proof of concept to demonstrate a clear utility for this technology in the wild.

Genetic Detection and a Method to Study the Ecology of Deadly Cubozoan Jellyfish

Cubozoan jellyfish pose a risk of envenomation to humans and a threat to many businesses, yet crucial gaps exist in determining threats to stakeholders and understanding their ecology. Environmental DNA (eDNA) provides a cost-effective method for detection that is less labour intensive and provides a higher probability of detection. The objective of this study was to develop, optimise and trial the use of eDNA to detect the Australian box jellyfish, Chironex fleckeri. This species was the focus of this study as it is known to have the strongest venom of any cubozoan; it is responsible for more than 200 recorded deaths in the Indo-Pacific region. Further, its ecology is poorly known. Herein, a specific and sensitive probe-based assay, multiplexed with an endogenous control assay, was developed, and successfully utilised to detect the deadly jellyfish species and differentiate them from closely related taxa. A rapid eDNA decay rate of greater than 99% within 27 h was found with no detectable influence from temperature. The robustness of the technique indicates that it will be of high utility for detection and to address knowledge gaps in the ecology of C. fleckeri; further, it has broad applicability to other types of zooplankton.

Environmental DNA study on aquatic ecosystem monitoring and management: Recent advances and prospects

Environmental DNA (eDNA) is organismal DNA that can be detected in the environment and is derived from cellular material of organisms shed into aquatic or terrestrial environments. It can be sampled and monitored using molecular methods, which is important for the early detection of invasive and native species as well as the discovery of rare and cryptic species. While few reviews have summarized the latest findings on eDNA for most aquatic animal categories in the aquatic ecosystem, especially for aquatic eDNA processing and application. In the present review, we first performed a bibliometric network analysis of eDNA studies on aquatic animals. Subsequently, we summarized the abiotic and biotic factors affecting aquatic eDNA occurrence. We also systematically discussed the relevant experiments and analyses of aquatic eDNA from various aquatic organisms, including fish, molluscans, crustaceans, amphibians, and reptiles. Subsequently, we discussed the major achievements of eDNA application in studies on the aquatic ecosystem and environment. The application of eDNA will provide an entirely new paradigm for biodiversity conservation, environment monitoring, and aquatic species management at a global scale.

Assessing the use of environmental DNA (eDNA) as a tool in the detection of human DNA in water

Environmental DNA (eDNA) is a highly sensitive and cost-effective tool that is increasingly being applied to studies of biodiversity and species detection. This non-invasive method relies on the collection of environmental samples that contain genetic material being shed into surrounding environment by the target organism/s. While forensic science has a long history of using molecular tools for collecting DNA from the environment, the detection of human DNA from environmental water samples has been limited. This study investigated the detection and degradation rates of human eDNA in water samples under controlled laboratory conditions. Using a human-specific qPCR assay targeting the ND1 region of human mitochondrial DNA, eDNA degradation over time in water spiked with human blood was assessed. Recovery of nuclear DNA was investigated by determining if routine DNA short tandem repeat (STR) profiles of the blood source could be generated. Results demonstrated that human eDNA remains detectable for up to 11 days under laboratory conditions in environmental water and up to 35 days in distilled water. Partial STR profiles could be recovered from environmental water only up to 24 h, while, in distilled water, partial profiles continued to be recovered up to 840 h. These findings demonstrate that sampling human eDNA from aquatic samples can provide reliable human DNA detection within relatively short time windows, assisting law enforcement agencies by providing information about the potential time an individual may have been present in an area or assisting in the detection and location of a body or remains in aquatic environments.

Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods. Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and cost-effective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.

Detection and persistence of environmental DNA (eDNA) of the different developmental stages of a vector mosquito, Culex pipiens pallens

Preventing mosquito-borne infectious diseases requires that vector mosquitoes are monitored and controlled. Targeting immature mosquitoes (eggs, larvae, and pupae), which have less mobility than adults, is an effective management approach. However, conducting these surveys is often difficult due to the limitations of morphological classification and survey costs. The application of environmental DNA (eDNA) analysis can solve these issues because it allows easy estimation of species distribution and morphology-independent species identification. Although a few previous studies have reported mosquito eDNA detection, there is a gap in knowledge regarding the dynamics related to the persistence of immature mosquito eDNA. We used Culex pipiens pallens, a vector of West Nile fever, as a model species. First, we developed a species-specific detection assay and confirmed its specificity using in silico and in vitro tests. Next, we conducted laboratory experiments using breeding tanks. Water samples were collected at each developmental stage. In addition, water samples were collected daily until the seventh day after emergence from the pupae. We quantified eDNA using real-time PCR with the developed assay to investigate the dynamics of mosquito eDNA. The specificity of the developed assay was confirmed by in silico and in vitro tests. Mosquito eDNA was detected at all developmental stages and detected up to seven days after emergence of pupae. In particular, high concentrations of eDNA were detected immediately after hatching from eggs and after emergence from pupae. Highly frequent positive eDNA signals were continuously detected between egg hatching and pupa hatching. Mosquito eDNA was detected immediately after the eggs were introduced, and eDNA-positive detections continued until pupae emergence, suggesting that eDNA analysis is useful for monitoring mosquito larvae. In the future, monitoring immature mosquitoes using eDNA analysis will contribute to prevent mosquito-borne infectious diseases.

Comparative Evaluation of Common Materials as Passive Samplers of Environmental DNA

Environmental DNA (eDNA) technology has revolutionized biomonitoring in recent years; however, eDNA collection from aquatic environments generally relies on the time-consuming and equipment-dependent process of water filtration. Passive eDNA sampling deploys sorbent materials to capture eDNA from water, circumventing many problems associated with active filtration; yet, very few candidate materials have been systematically evaluated for this purpose. Here, we evaluated the ability of 12 different types of common loose sorbents and filter membranes to capture eDNA in laboratory and field experiments compared with conventional water filtration. Glass fiber filters (GF) outperformed all other materials in laboratory experiments with respect to their quantitative capacity to recover amphibian eDNA, with the eDNA yield increasing linearly with submersion time up to 72 h. Furthermore, GF rapidly (within 0.5 h) captured the eDNA of up to 71% of the total fish species in a lake, in addition to detecting the entire fish community by 8 h, as assessed by metabarcoding analysis. Our results demonstrate that GF could passively capture aqueous eDNA with a similar or greater efficiency than conventional methods, thus paving the way for convenient, effective, and eco-friendly eDNA sampling in aquatic environments.

Experimental study on the response relationship between environmental DNA concentration and biomass of Schizothorax prenanti in still water

The superiority of the environmental DNA (eDNA) method for estimating the biomass of aquatic species has been demonstrated. However, the relationship between eDNA concentration and biomass is difficult to clarify under the influence of complex water flow and habitat conditions. It seriously restricts the popularization and application of the eDNA method in estimating aquatic biomass. In this paper, a typical fish species of rivers in southwest China, Schizothorax prenanti, was selected as the target species. Under standardized laboratory hydrostatic conditions, two environmental factors, water pH and water temperature were firstly determined through pre-experiments. Then we investigated the correlation between eDNA concentration and biomass under different body sizes and different body size compositions. The experimental results showed that water pH and the water temperature had a great influence on eDNA concentration. Therefore, the effects of these environmental factors need to be considered simultaneously when using eDNA concentration to estimate biomass. Under the premise of consistent environmental conditions, the biomass of Schizothorax prenanti was positively correlated with the eDNA concentration when the individual body size was the same. For each 1% increase in biomass of the fish, the eDNA concentration of adult (larger size) fish increased by 0.98%, while the eDNA concentration of juvenile (smaller size) fish increased by 1.38%. The smaller the size of individual fish, the greater the increase of eDNA concentration with biomass, and the increase of juvenile fish was about 1.4 times that the adult fish. When the biomass was the same but the body size composition was different, the higher the proportion of small body size individuals in the population, the higher the eDNA concentration. Special attention needs to be paid to the body size composition of the population to avoid the biomass estimation being lower than the actual value when the smaller size fish are dominant. The experimental results provide a strong basis for a more accurate estimation of aquatic biomass in reservoirs, lakes, and other still water areas by using the eDNA method.

Temperature Controls eDNA Persistence across Physicochemical Conditions in Seawater

Environmental DNA (eDNA) quantification and sequencing are emerging techniques for assessing biodiversity in marine ecosystems. Environmental DNA can be transported by ocean currents and may remain at detectable concentrations far from its source depending on how long it persist. Thus, predicting the persistence time of eDNA is crucial to defining the spatial context of the information derived from it. To investigate the physicochemical controls of eDNA persistence, we performed degradation experiments at temperature, pH, and oxygen conditions relevant to the open ocean and the deep sea. The eDNA degradation process was best explained by a model with two phases with different decay rate constants. During the initial phase, eDNA degraded rapidly, and the rate was independent of physicochemical factors. During the second phase, eDNA degraded slowly, and the rate was strongly controlled by temperature, weakly controlled by pH, and not controlled by dissolved oxygen concentration. 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. The relationship between temperature and eDNA persistence is independent of the source species. We propose a general temperature-dependent model to predict the maximum persistence time of eDNA detectable through single-species eDNA quantification methods.

Filtration extraction method using microfluidic channel for measuring environmental DNA

The environmental DNA (eDNA) method, which is widely applied in biomonitoring, is limited to laboratory analysis and processing. In this study, we developed a filtration/extraction component using a microfluidic channel, the Biryu-Chip (BC), and a filtration/extraction method, the BC method, to minimize the volume of the sample necessary for DNA extraction and subsequent PCR amplification. We tested the performance of the BC method and compared it with that of the Sterivex filtration/extraction method using aquarium and river water samples. We observed that using the BC method, the same concentration of extracted DNA was obtained with 1/20-1/40 of the filtration volume of the Sterivex method, suggesting that the BC method can be widely used for eDNA measurement. In addition, we performed on-site measurements of eDNA within 30 min using a mobile PCR device, demonstrating that filtration and extraction can be performed easily and quickly using the BC method. The PCR results obtained using the BC method were similar to those obtained using the Sterivex method. The BC method requires fewer steps; therefore, the risk of DNA contamination can be reduced. When combined with mobile PCR, the BC method can be applied to easily detect eDNA within 30 min from the collection of water sample, even on-site.

Environmental DNA as a tool for biodiversity monitoring in aquatic ecosystems – a review

The monitoring of changes in aquatic ecosystems due to anthropogenic activities is of utmost importance to ensure the health of aquatic biodiversity. Eutrophication in water bodies due to anthropogenic disturbances serves as one of the major sources of nutrient efflux and consequently changes the biological productivity and community structure of these ecosystems. Habitat destruction and overexploitation of natural resources are other sources that impact the equilibrium of aquatic systems. Environmental DNA (eDNA) is a tool that can help to assess and monitor aquatic biodiversity. There has been a considerable outpour of research in this area in the recent past, particularly concerning conservation and biodiversity management. This review focuses on the application of eDNA for the detection and relative quantification of threatened, endangered, invasive and elusive species. We give a special emphasis on how this technique developed in the past few years to become a tool for understanding the impact of spatial-temporal changes on ecosystems. Incorporating eDNA based biomonitoring with advances in sequencing technologies and computational abilities had an immense role in the development of different avenues of application of this tool.

Holistic Impact Evaluation of Human Activities on the Coastal Fish Biodiversity in the Chinese Coastal Environment

Ecological qualities and resources in coasts are threatened by various human activities, such as pollution and fishery. Impact evaluation of environmental stressors over a wide coastal stretch has been limited due to lack of efficient and standardizable biodiversity monitoring and assessment tools. Integrating environmental DNA (eDNA) and ecological traits, a holistic approach was developed to assess the impact of pollution and aquaculture on fish biodiversity in Chinese coastal areas. Taking the Yalujiang Estuary (YLJK) from the Yellow Sea and the Nan'ao Island Area (NAO) from the South China Sea as cases, the performance of the eDNA biomonitoring workflow was validated. First, the eDNA results of 22 sampling sites reached more than 85% of the asymptotes of species or ASVs in each area. A total of 115 fish species in both areas were detected and NAO was 1.8 times richer than YLJK using eDNA and the fish eDNA composition was consistent with the historical data. eDNA recovered distinct variations of fish sequence, taxonomic and functional diversity, and the corresponding trends following the offshore distance between the two areas. Fish sequence diversity was decreased primarily by estuarine pollution factors (chemical oxygen demand and zinc) in the YLJK. Compared with no breeding areas, lower fish sequence diversity was in breeding areas in the NAO. By integrating ecological traits, the eDNA approach offers promising opportunities for future fish biodiversity monitoring and assessment in national and global coastal environments.

Systematic review and meta-analysis: water type and temperature affect environmental DNA decay

Environmental DNA (eDNA) has been used in a variety of ecological studies and management applications. The rate at which eDNA decays has been widely studied but at present it is difficult to disentangle study‐specific effects from factors that universally affect eDNA degradation. To address this, a systematic review and meta‐analysis was conducted on aquatic eDNA studies. Analysis revealed eDNA decayed faster at higher temperatures and in marine environments (as opposed to freshwater). DNA type (mitochondrial or nuclear) and fragment length did not affect eDNA decay rate, although a preference for <200 bp sequences in the available literature means this relationship was not assessed with longer sequences (e.g. >800 bp). At present, factors such as ultraviolet light, pH, and microbial load lacked sufficient studies to feature in the meta‐analysis. Moving forward, we advocate researching these factors to further refine our understanding of eDNA decay in aquatic environments.

Limitations of eDNA analysis for Carcinus maenas abundance estimations

Background

Environmental DNA (eDNA) is an effective tool for the detection and monitoring of presence or absence of rare and invasive species. These techniques have been extended to quantify biomass in vertebrates, particularly in fish species. However, the efficacy of eDNA techniques to quantify biomass in invertebrate species has rarely been examined. This study tested whether eDNA could be used to determine the biomass of the world-wide invasive green crab, Carcinus maenas. In a controlled laboratory study, the relationship between biomass and C. maenas eDNA concentration was examined in the context of different biotic (activity) and abiotic (temperature) parameters.

Results

When incubating different numbers of crabs in sterile saltwater for up to 7 days, a relationship between eDNA concentration and biomass was observed at temperatures of 6.7 ℃ and 18.7 ℃, but not at 12.8 ℃. Additionally, motor activity, aggression level, time of sampling, and features of organismal decay had significant impact on the concentration of C. maenas eDNA collected.

Conclusions

We show that eDNA concentration did not correlate with biomass, and that biomass, temperature, organismal characteristics, and potentially many more parameters affect shedding and degradation rates for eDNA in this species, thus, impacting the recoverable eDNA concentration. Therefore, eDNA techniques are not likely to provide a reliable signal of biomass in the invasive invertebrate species C. maenas.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-01969-z.

Environmental DNA from Marine Waters and Substrates: Protocols for Sampling and eDNA Extraction

Environmental DNA (eDNA) analysis has emerged in recent years as a powerful tool for the detection, monitoring, and characterization of aquatic metazoan communities, including vulnerable species. The rapid rate of adopting the eDNA approach across diverse habitats and taxonomic groups attests to its value for a wide array of investigative goals, from understanding natural or changing biodiversity to informing on conservation efforts at local and global scales. Regardless of research objectives, eDNA workflows commonly include the following essential steps: environmental sample acquisition, processing and preservation of samples, and eDNA extraction, followed by eDNA sequencing library preparation, high-capacity sequencing and sequence data analysis, or other methods of genetic detection. In this chapter, we supply instructional details for the early steps in the workflow to facilitate researchers considering adopting eDNA analysis to address questions in marine environments. Specifically, we detail sampling, preservation, extraction, and quantification protocols for eDNA originating from marine water, shallow substrates, and deeper sediments. eDNA is prone to degradation and loss, and to contamination through improper handling; these factors crucially influence the outcome and validity of an eDNA study. Thus, we also provide guidance on avoiding these pitfalls. Following extraction, purified eDNA is often sequenced on massively parallel sequencing platforms for comprehensive faunal diversity assessment using a metabarcoding or metagenomic approach, or for the detection and quantification of specific taxa by qPCR methods. These components of the workflow are project-specific and thus not included in this chapter. Instead, we briefly touch on the preparation of eDNA libraries and discuss comparisons between sequencing approaches to aid considerations in project design.

The particle size distribution of environmental DNA varies with species and degradation

Environmental DNA (eDNA) analysis is frequently used as a non-invasive method to investigate species and biodiversity in ecosystems. However, such eDNA may represent both organisms currently present as well as species that released their DNA some point in the past, thereby representing a mix of current and historic biodiversity. This may lead to a false-positive detection of organisms' presence. As the eDNA particle size distribution (PSD) changes along with the decay process, it may facilitate solving the above problem. Here, we set up tank experiments with snails, zebrafish and daphnids, respectively, to monitor the change in eDNA PSD and eDNA degradation through time after removing organisms. We found that zebrafish eDNA decays more slowly for larger particle sizes. Across all species tested, the percentage of large size ranges tended to increase over time while the smaller sizes showed relatively fast decay rates. As a result, PSD changed consistently with eDNA decay, although initial PSD varied between species. In combination, we propose that eDNA PSD can be used to assess the current prevalence of organisms at an eDNA sampling location while avoiding false-positives on the presence of species. Our findings expand the applicability of eDNA for monitoring target species in freshwater ecosystems.

Pathogens and disease vectors/hosts monitoring in aquatic environments: Potential of using eDNA/eRNA based approach

Infectious diseases are spreading in to previously unreported geographical regions, and are reappeared in regions 75 or 100 years after their last reported case, as a result of environmental changes caused by anthropogenic activities. A pathogen, vector/host monitoring methodology is therefore indispensable in identifying potential transmission sites, providing early warnings and evaluating the human health risks of these infectious diseases in a given area. Recently, environmental DNA (eDNA) and environmental RNA approach (eRNA) have become widespread in monitoring organisms in the environment due to advantages like lower cost, time, and labour requirements. However, eDNA/eRNA based monitoring of pathogens and vectors/hosts using aquatic samples is limited to very few studies. In this review, we summarized the currently available eDNA/eRNA based human and non-human pathogens and vectors/hosts detection studies in aquatic samples. Species-specific shedding, transport, and decay of eDNA/eRNA in aquatic environments which is essential in estimating the abundance of pathogen, vectors/host in focus is also summarized. We also suggest the usage of eDNA/eRNA approach in urban aquatic samples like runoff in identifying the disease vectors/hosts inhabiting in locations which are not accessible easily.

Development of an eDNA metabarcoding tool for surveying the world’s largest amphibian

Due to the overexploitation of farming, as well as habitat destruction, the wild population of Chinese giant salamander (CGS) Andrias davidianus, a species with seven genetically distinct lineages, has decreased by over 80% in the past 70 years. Traditional survey methods have proven to be unsuitable for finding this rare and elusive species. We evaluated the efficacy of environmental DNA (eDNA) sampling to detect CGS indirectly from its aquatic environment. We developed several species-specific primer sets; validated their specificity and sensitivity; and assessed their utility in silico, in the laboratory, and at two field sites harboring released farm-bred CGS. We detected the presence of CGS DNA by using polymerase chain reaction and Sanger sequencing. We also sequenced an amplicon mixture of seven haplotype-represented samples using high-throughput sequencing. Our eDNA methods could detect the presence of CGS at moderate densities reported across its range, proving them as a cost-effective way to establish broad-scale patterns of occupancy for CGS. In addition, our primers enabled the detection of mitochondrial lineage mixture or introduced individuals from geographically isolated populations of CGS.

eDNA captures depth partitioning in a kelp forest ecosystem

Environmental DNA (eDNA) metabarcoding is an increasingly important tool for surveying biodiversity in marine ecosystems. However, the scale of temporal and spatial variability in eDNA signatures, and how this variation may impact eDNA-based marine biodiversity assessments, remains uncertain. To address this question, we systematically examined variation in vertebrate eDNA signatures across depth (0 m to 10 m) and horizontal space (nearshore kelp forest and surf zone) over three successive days in Southern California. Across a broad range of teleost fish and elasmobranchs, results showed significant variation in species richness and community assemblages between surface and depth, reflecting microhabitat depth preferences of common Southern California nearshore rocky reef taxa. Community assemblages between nearshore and surf zone sampling stations at the same depth also differed significantly, consistent with known habitat preferences. Additionally, assemblages also varied across three sampling days, but 69% of habitat preferences remained consistent. Results highlight the sensitivity of eDNA in capturing fine-scale vertical, horizontal, and temporal variation in marine vertebrate communities, demonstrating the ability of eDNA to capture a highly localized snapshot of marine biodiversity in dynamic coastal environments.