Robust detection of rare species using environmental DNA: the importance of primer specificity

Advances in environmental DNA monitoring: standardization, automation, and emerging technologies in aquatic ecosystems

Environmental DNA (eDNA) monitoring, a rapidly advancing technique for assessing biodiversity and ecosystem health, offers a noninvasive approach for detecting and quantifying species from various environmental samples. In this review, a comprehensive overview of current eDNA collection and detection technologies is provided, emphasizing the necessity for standardization and automation in aquatic ecological monitoring. Furthermore, the intricacies of water bodies, from streams to the deep sea, and the associated challenges they pose for eDNA capture and analysis are explored. The paper delineates three primary eDNA survey methods, namely, bringing back water, bringing back filters, and bringing back data, each with specific advantages and constraints in terms of labor, transport, and data acquisition. Additionally, innovations in eDNA sampling equipment, including autonomous drones, subsurface samplers, and in-situ filtration devices, and their applications in monitoring diverse taxa are discussed. Moreover, recent advancements in species-specific detection and eDNA metabarcoding are addressed, highlighting the integration of novel techniques such as CRISPR-Cas and nanopore sequencing that enable precise and rapid detection of biodiversity. The implications of environmental RNA and epigenetic modifications are considered for future applications in providing nuanced ecological data. Lastly, the review stresses the critical role of standardization and automation in enhancing data consistency and comparability for robust long-term biomonitoring. We propose that the amalgamation of these technologies represents a paradigm shift in ecological monitoring, aligning with the urgent call for biodiversity conservation and sustainable management of aquatic ecosystems.

Exploring uncharted territory: new frontiers in environmental DNA for tropical fisheries management

Tropical ecosystems host a significant share of global fish diversity contributing substantially to the global fisheries sector. Yet their sustainable management is challenging due to their complexity, diverse life history traits of tropical fishes, and varied fishing techniques involved. Traditional monitoring techniques are often costly, labour-intensive, and/or difficult to apply in inaccessible sites. These limitations call for the adoption of innovative, sensitive, and cost-effective monitoring solutions, especially in a scenario of climate change. Environmental DNA (eDNA) emerges as a potential game changer for biodiversity monitoring and conservation, especially in aquatic ecosystems. However, its utility in tropical settings remains underexplored, primarily due to a series of challenges, including the need for a comprehensive barcode reference library, an understanding of eDNA behaviour in tropical aquatic environments, standardized procedures, and supportive biomonitoring policies. Despite these challenges, the potential of eDNA for sensitive species detection across varied habitats is evident, and its global use is accelerating in biodiversity conservation efforts. This review takes an in-depth look at the current state and prospects of eDNA-based monitoring in tropical fisheries management research. Additionally, a SWOT analysis is used to underscore the opportunities and threats, with the aim of bridging the knowledge gaps and guiding the more extensive and effective use of eDNA-based monitoring in tropical fisheries management. Although the discussion applies worldwide, some specific experiences and insights from Indian tropical fisheries are shared to illustrate the practical application and challenges of employing eDNA in a tropical context.

Sources and Prevalence of Cyclospora cayetanensis in Southeastern U.S. Growing Environments

Recent cyclosporiasis outbreaks associated with fresh produce grown in the United States highlight the need to better understand Cyclospora cayetanensis prevalence in U.S. agricultural environments. In this study, C. cayetanensis occurrence was assessed in municipal wastewater sludge, on-farm portable toilets, irrigation pond water, and spent packing house dump tank water in a Southeastern Georgia growing region over two years. Detection of the C. cayetanensis 18S rRNA qPCR gene target in pond samples was 0%, 28%, and 42% (N = 217) depending on the detection definition used, and ≤1% in dump tank samples (N = 46). However, no qPCR detections were confirmed by sequencing, suggesting false detection occurred due to cross-reactions. C. cayetanensis qPCR detections were confirmed in 9% of wastewater sludge samples (N = 76). The human-specific fecal markers HF183 and crAssphage were detected in 33% and 6% of pond samples, respectively, and 4% and 0% of dump tank samples, respectively. Despite community Cyclospora shedding and evidence of human fecal contamination in irrigation water, there was no correlation between C. cayetanensis and HF183 qPCR detections, further supporting that 18S gene target qPCR amplifications were due to cross-reactions. When evaluating C. cayetanensis qPCR environmental detection data, the impact of assay specificity and detection criteria should be considered. Moreover, additional sequence-based testing may be needed to appropriately interpret Cyclospora qPCR environmental data.

The unknown unknown: A framework for assessing environmental DNA assay specificity against unsampled taxa

Taxon-specific quantitative PCR (qPCR) assays are commonly used for environmental DNA sampling-based inference of animal presence. These assays require thorough validation to ensure that amplification truly indicates detection of the target taxon, but a thorough validation is difficult when there are potentially many non-target taxa, some of which may have incomplete taxonomies. Here, we use a previously published, quantitative model of cross-amplification risk to describe a framework for assessing qPCR assay specificity when there is missing information and it is not possible to assess assay specificity for each individual non-target confamilial. In this framework, we predict assay specificity against unsampled taxa (non-target taxa without sequence data available) using the sequence information that is available for other confamilials. We demonstrate this framework using four case study assays for: (1) An endemic, freshwater arthropod (meltwater stonefly; Lednia tumana), (2) a globally distributed, marine ascidian (Didemnum perlucidum), (3) a continentally distributed freshwater crustacean (virile crayfish; Faxonius virilis, deanae and nais species complex) and (4) a globally distributed freshwater teleost (common carp; Cyprinus carpio and its close relative C. rubrofuscus). We tested the robustness of our approach to missing information by simulating application of our framework for all possible subsamples of 20-all non-target taxa. Our results suggest that the modelling framework results in estimates which are largely concordant with observed levels of cross-amplification risk using all available sequence data, even when there are high levels of data missingness. We explore potential limitations and extensions of this approach for assessing assay specificity and provide users with an R Markdown template for generating reproducible reports to support their own assay validation efforts.

In silico assessment of 18S rDNA metabarcoding markers for the characterization of nematode communities

Nematodes are keystone actors of soil, freshwater and marine ecosystems, but the complexity of morphological identification has limited broad-scale monitoring of nematode biodiversity. DNA metabarcoding is increasingly used to assess nematode diversity but requires universal primers with high taxonomic coverage and high taxonomic resolution. Several primers have been proposed for the metabarcoding of nematode diversity, many of which target the 18S rRNA gene. In silico analyses have a great potential to assess key parameters of primers, including taxonomic coverage, resolution and specificity. Based on a recently-available reference database, we tested in silico the performance of fourteen commonly used and one newly optimized primer for nematode metabarcoding. Most primers showed very good coverage, amplifying most of the sequences in the reference database, while four markers showed limited coverage. All primers showed good taxonomic resolution. Resolution was particularly good if the aim was the identification of higher-level taxa, such as genera or families. Overall, species-level resolution was higher for primers amplifying long fragments. None of the primers was highly specific for nematodes as, despite some variation, they all amplified a large number of other eukaryotes. Differences in performance across primers highlight the complexity of the choice of markers appropriate for the metabarcoding of nematodes, which depends on a trade-off between taxonomic resolution and the length of amplified fragments. Our in silico analyses provide new insights for the identification of the most appropriate primers, depending on the study goals and the origin of DNA samples. This represents an essential step to design and optimize metabarcoding studies assessing nematode diversity.

Using eDNA to survey amphibians: Methods, applications, and challenges

In recent years, environmental DNA (eDNA) has received attention from biologists due to its sensitivity, convenience, labor and material efficiency, and lack of damage to organisms. The extensive application of eDNA has opened avenues for the monitoring and biodiversity assessment of amphibians, which are frequently small and difficult to observe in the field, in areas such as biodiversity survey assessment and detection of specific, rare and threatened, or alien invasive species. However, the accuracy of eDNA can be influenced by factors such as ambient temperature, pH, and false positives or false negatives, which makes eDNA an adjunctive tool rather than a replacement for traditional surveys. This review provides a concise overview of the eDNA method and its workflow, summarizes the differences between applying eDNA for detecting amphibians and other organisms, reviews the research progress in eDNA technology for amphibian monitoring, identifies factors influencing detection efficiency, and discusses the challenges and prospects of eDNA. It aims to serve as a reference for future research on the application of eDNA in amphibian detection.

Use of passive sampling in environmental DNA metabarcoding technology: Monitoring of fish diversity in the Jiangmen coastal waters

Environmental DNA (eDNA) metabarcoding technology is proving to be the most up-to-date and promising method for monitoring marine fish diversity. Fish eDNA is usually collected on a filter membrane after the filtration of water. Not only does this require the use of specialized equipment, but the amount of filtered water needed is also difficult to meet. The recently proposed passive eDNA collection method can expand the sampling scale, providing new perspectives for monitoring marine biodiversity. The role of collection methods in eDNA surveys, however, remains unclear. In this study, a low-cost custom framework with two types of filter membrane materials was used to conduct passive submersion samplings at the north and south ends of Shangchuan Island, Jiangmen, China. After defined periods of submersion, the filter membranes were recovered and eDNA extracted. Metabarcoding techniques were applied to detect fish species information in the eDNA samples. A total of 106 marine fish species from 27 orders, 53 families, and 92 genera, including one cartilaginous fish, were identified in the samples. The majority of fish detected by active filtration were also found in the passively collected samples, within the same location. Both sampling methods, therefore, showed similar species richness. Passive sampling was effective in identifying fish species diversity and provided a higher spatial resolution owing to the sample replicates. Passive sampling was also more sensitive in detecting species that differ significantly in abundance (biomarkers) between different sampling depths. When active filtration is not possible, or when large-scale sampling is the purpose of the study, passive sampling methods certainly provide a promising alternative. The findings of our study provide guidance for fish surveys and continuous bio-stereoscopic monitoring in coastal waters.

eDNA-based detection reveals invasion risks of a biofouling bivalve in the world's largest water diversion project

Environmental DNA (eDNA) has increasingly been used to detect rare species (e.g., newly introduced nonindigenous species) in both terrestrial and aquatic ecosystems, often with distinct advantages over traditional methods. However, whether water eDNA signals can be used to inform invasion risks remains debatable owing to inherent uncertainties associated with the methods used and the varying conditions among study systems. Here, we sampled eDNA from canals of the central route of the South-to-North Water Diversion Project (hereafter SNWDP) in China to investigate eDNA distribution and efficacy to inform invasion risks in a unique lotic system. We first conducted a total of 16 monthly surveys in this system (two sites in the source reservoir and four sites in the main canal) to test if eDNA could be applied to detect an invasive, biofouling bivalve, the golden mussel Limnoperna fortunei. Second, we initiated a one-time survey in a sub-canal of the SNWDP using refined sampling (12 sites in ~22 km canal) and considered a few environmental predictors. We found that detection of target eDNA in the main canal was achieved up to 1100 km from the putative source population but was restricted to the warmer months (May-November). Detection probability exhibited a significant positive relationship with average daily minimum air temperature and with water temperature, consistent with the expected spawning season. eDNA concentration in the main canal generally fluctuated across months and sites and was generally higher in warmer months. Golden mussel eDNA concentration in the sub-canal decreased significantly with distance from the source and with increasing water temperature and became almost undetectable at ~22 km distance. Given the enormity of the SNWDP, golden mussels may eventually expand their distribution in the main canal, with established "bridgehead" populations facilitating further spread. Our findings suggest an elevated invasion risk of golden mussels in the SNWDP in warm months, highlighting the critical period for spread and, possibly, management.

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.

Environmental DNA unveiling the fish community structure and diversity features in the Yangtze River basin

Fish, as top predators in aquatic ecosystems, play an important role in maintaining the structure and functioning of these ecosystems, making their diversity a topic of great interest. This study focused on the Yangtze River Basin to investigate the fish community structure and diversity using environmental DNA (eDNA) technology. The results showed that a total of 71616 fish operational taxonomic units (OTUs) and 90 fish belonging to 23 families were detected, with the Cyprinidae family being the dominant group, followed by the Cobitidae, Amblycipitidae, etc. Compared to historical traditional morphological fish surveys, the quantity of fish detected using eDNA was relatively low, but the overall distribution pattern of fish communities was generally consistent. The highest fish Shannon-Wiener diversity index in the Yangtze River Basin sites reaches 2.60 with an average value of 1.25. The fish diversity index was higher in the downstream compared to the middle and upstream regions, and there were significant differences among different sampling sites. Significant environmental factors influencing α-diversity included chlorophyll-a, chemical oxygen demand, dissolved oxygen, total nitrogen, and elevation. Non-metric multidimensional scaling (NMDS) analysis revealed significant differences in fish community composition between the upstream and middle/lower reaches of the Yangtze River, while the composition of fish communities in the middle and lower reaches was more similar. Redundancy analysis (RDA) indicated that total organic carbon (TOC) was positively correlated with fish community distribution in the upstream, while water temperature and NO3-N were negatively correlated with fish distribution in the upstream. NH3-N and CODMn were negatively correlated with fish distribution in the middle and downstream regions, indicating a relatively severe water pollution in these areas. Additionally, fish communities in the Yangtze River displayed a typical distance decay pattern.

Using environmental DNA to better inform decision making around decommissioning alternatives for offshore oil and gas infrastructure

Artificial reefs are being utilised globally to aid in natural resource management, conservation, restoration or the creation of unique marine habitats. There is discussion around the optimal construction materials and designs for artificial reefs, the influences these have on biological communities, and the resulting ecological and social benefits. This discussion also includes the ecological value of repurposed marine infrastructure, such as decommissioned oil and gas platforms. Platforms often have an operational life spanning multiple decades, over which time they can develop extensive and unique community assemblages. The creation of artificial reefs by repurposing oil and gas platforms can have ecological, economic and sociological merit. However, with >12,000 platforms requiring decommissioning globally, there is the need for holistic assessment of biological communities associated with these platforms to inform the potential outcomes of different decommissioning options. We use environmental DNA metabarcoding (eDNA) of water, bio-foul and sediment samples to census broad eukaryotic diversity at eight platforms in the Gulf of Thailand (GoT) and five nearby soft sediment habitat locations. We sampled three target depths at sites (shallow, mid, deep) and detected 430 taxa at platforms, with higher diversity in shallow (near-surface) samples (313 taxa), compared to mid (30 m collection depth; 261 taxa) and deep (50 m; 273 taxa). Three percent of taxa were shared among all depths at platforms with distinct assembles at each depth. Introduced species are an ongoing risk for platforms, however the eDNA detected no known introduced species. While the eDNA data provide broad taxon coverage and significant assemblage patterns, ongoing sampling innovation, assay design and local reference material still require development to obtain the maximum benefit of the technique. This study highlights the versatility and scalability of eDNA metabarcoding to holistically census marine infrastructure and inform the management and potential conservation of extant communities.

Insights in Pharmaceutical Pollution: The Prospective Role of eDNA Metabarcoding

Environmental pollution is a growing threat to natural ecosystems and one of the world's most pressing concerns. The increasing worldwide use of pharmaceuticals has elevated their status as significant emerging contaminants. Pharmaceuticals enter aquatic environments through multiple pathways related to anthropogenic activity. Their high consumption, insufficient waste treatment, and the incapacity of organisms to completely metabolize them contribute to their accumulation in aquatic environments, posing a threat to all life forms. Various analytical methods have been used to quantify pharmaceuticals. Biotechnology advancements based on next-generation sequencing (NGS) techniques, like eDNA metabarcoding, have enabled the development of new methods for assessing and monitoring the ecotoxicological effects of pharmaceuticals. eDNA metabarcoding is a valuable biomonitoring tool for pharmaceutical pollution because it (a) provides an efficient method to assess and predict pollution status, (b) identifies pollution sources, (c) tracks changes in pharmaceutical pollution levels over time, (d) assesses the ecological impact of pharmaceutical pollution, (e) helps prioritize cleanup and mitigation efforts, and (f) offers insights into the diversity and composition of microbial and other bioindicator communities. This review highlights the issue of aquatic pharmaceutical pollution while emphasizing the importance of using modern NGS-based biomonitoring actions to assess its environmental effects more consistently and effectively.

Exploring the relationship between environmental DNA concentration and biomass in Asian giant softshell turtle (Pelochelys cantorii)

In recent years, environmental DNA (eDNA) technology has become an accepted approach for investigating rare and endangered species because of its economic efficiency, high sensitivity, and non-invasiveness. The Asian giant softshell turtle (Pelochelys cantorii) is a first-class protected aquatic animal in China, and traditional resource survey methods have not identified its natural populations for many years. In this study, primers and a TaqMan probe targeting ND5 were designed, reaction conditions were optimized, a standard curve was constructed using synthetic DNA, and an eDNA quantitative PCR (qPCR) detection method was established. The eDNA detection technology for P. cantorii revealed that the number of species in the experimental pools showed a significant linear relationship with the eDNA concentration (p < 0.05). The eDNA concentration was negatively correlated with the length of time after the removal of P. cantorii and retention in the water body for 9 days. The qPCR detection method for P. cantorii eDNA established in this study can be applied to the qualitative detection of P. cantorii in water bodies, as well as to preliminary evaluation of its relative biomass. This can serve as a baseline for the investigation of natural P. cantorii population and the evaluation of its wild release effects.

A species-specific digital PCR assay for the endangered blue racer (Coluber constrictor foxii) in Canada

The only population of the endangered blue racer (Coluber constrictor foxii) in Canada occurs on Pelee Island, Ontario. The species is threatened by multiple factors, including habitat degradation and loss, road mortality, persecution, and potentially predation. We designed and evaluated the performance of an environmental DNA droplet digital PCR assay that can be used for multiple facets of conservation of this species. We tested the assay in silico and in vitro using DNA of blue racers and co-occurring snake species and estimated the LOD and LOQ using synthetic DNA. As wild turkey predation has been suggested to negatively affect racers, we tested the assay on eight wild turkey faecal samples. Our assay is specific, can detect the target species at very low levels of concentration (0.002 copies/µL), and can accurately quantify copy numbers ≥ 0.26 copies/µL. We detected no racer DNA in any wild turkey faecal sample. More faecal samples collected at strategic locations during snake peak activity on Pelee Island would enable a more thorough assessment of the possibility of turkey predation. Our assay should be effective for other environmental samples and can be used for investigating other factors negatively affecting blue racers, for example, helping to quantify blue racer habitat suitability and site occupancy.

Catchment-based sampling of river eDNA integrates terrestrial and aquatic biodiversity of alpine landscapes

Monitoring of terrestrial and aquatic species assemblages at large spatial scales based on environmental DNA (eDNA) has the potential to enable evidence-based environmental policymaking. The spatial coverage of eDNA-based studies varies substantially, and the ability of eDNA metabarcoding to capture regional biodiversity remains to be assessed; thus, questions about best practices in the sampling design of entire landscapes remain open. We tested the extent to which eDNA sampling can capture the diversity of a region with highly heterogeneous habitat patches across a wide elevation gradient for five days through multiple hydrological catchments of the Swiss Alps. Using peristaltic pumps, we filtered 60 L of water at five sites per catchment for a total volume of 1800 L. Using an eDNA metabarcoding approach focusing on vertebrates and plants, we detected 86 vertebrate taxa spanning 41 families and 263 plant taxa spanning 79 families across ten catchments. For mammals, fishes, amphibians and plants, the detected taxa covered some of the most common species in the region according to long-term records while including a few more rare taxa. We found marked turnover among samples from distinct elevational classes indicating that the biological signal in alpine rivers remains relatively localised and is not aggregated downstream. Accordingly, species compositions differed between catchments and correlated with catchment-level forest and grassland cover. Biomonitoring schemes based on capturing eDNA across rivers within biologically integrated catchments may pave the way toward a spatially comprehensive estimation of biodiversity.

Development and validation of an environmental DNA assay to detect federally threatened groundwater salamanders in central Texas

The molecular detection of DNA fragments that are shed into the environment (eDNA) has become an increasingly applied tool used to inventory biological communities and to perform targeted species surveys. This method is particularly useful in habitats where it is difficult or not practical to visually detect or trap the target organisms. Central Texas Eurycea salamanders inhabit both surface and subterranean aquatic environments. Subterranean surveys are challenging or infeasible, and the detection of salamander eDNA in water samples is an appealing survey technique for these situations. Here, we develop and validate an eDNA assay using quantitative PCR for E. chisholmensis, E. naufragia, and E. tonkawae. These three species are federally threatened and constitute the Septentriomolge clade that occurs in the northern segment of the Edwards Aquifer. First, we validated the specificity of the assay in silico and with DNA extracted from tissue samples of both target Septentriomolge and non-target amphibians that overlap in distribution. Then, we evaluated the sensitivity of the assay in two controls, one with salamander-positive water and one at field sites known to be occupied by Septentriomolge. For the salamander-positive control, the estimated probability of eDNA occurrence (ψ) was 0.981 (SE = 0.019), and the estimated probability of detecting eDNA in a qPCR replicate (p) was 0.981 (SE = 0.011). For the field control, the estimated probability of eDNA occurring at a site (ψ) was 0.938 (95% CRI: 0.714-0.998). The estimated probability of collecting eDNA in a water sample (θ) was positively correlated with salamander relative density and ranged from 0.371 (95% CRI: 0.201-0.561) to 0.999 (95% CRI: 0.850- > 0.999) among sampled sites. Therefore, sites with low salamander density require more water samples for eDNA evaluation, and we determined that our site with the lowest estimated θ would require seven water samples for the cumulative collection probability to exceed 0.95. The estimated probability of detecting eDNA in a qPCR replicate (p) was 0.882 (95% CRI: 0.807-0.936), and our assay required two qPCR replicates for the cumulative detection probability to exceed 0.95. In complementary visual encounter surveys, the estimated probability of salamanders occurring at a known-occupied site was 0.905 (SE = 0.096), and the estimated probability of detecting salamanders in a visual encounter survey was 0.925 (SE = 0.052). We additionally discuss future research needed to refine this method and understand its limitations before practical application and incorporation into formal survey protocols for these taxa.

The challenge of implementing environmental DNA metabarcoding to detect elasmobranchs in a resource-limited marine protected area

Elasmobranchs are threatened and eDNA metabarcoding is a powerful tool that can help efforts to better understand and conserve them. Nevertheless, the inter-calibration between optimal methodological practices and its implementation in resource-limited situations is still an issue. Based on promising results from recent studies, the authors applied a cost-effective protocol with parameters that could be easily replicated by any conservationist. Nonetheless, the results with fewer elasmobranchs detected than expected reveal that endorsed primers and sampling strategies still require further optimization, especially for applications in resource-limited conservation programmes.

Decoding dissolved information: environmental DNA sequencing at global scale to monitor a changing ocean

The use of environmental DNA (eDNA) technology for environmental monitoring is rapidly expanding, with applications for fisheries, coral reefs, harmful algal blooms, invasive and endangered species, and biodiversity monitoring. By enabling detection of species over space and time, eDNA fulfills a fundamental need of environmental surveys. Traditional surveys are expensive, require significant capital expenditure, and can be destructive; eDNA offers promise for cheaper, less invasive, and higher-resolution (i.e. genetic) assessments of environments and stocks. However, challenges in quantification, detection limits, biobanking capacity, reference databases, and data management and integration remain significant hurdles to efficient eDNA monitoring at global and decadal scale. Here, we consider the current state of eDNA technology and its suitability for the problems for which it is being used. We explore the current best practices, the logistical and social challenges that prevent eDNA from widespread adoption and benefit, and the emerging technologies that may address those challenges.

Comparative analysis of fish environmental DNA reveals higher sensitivity achieved through targeted sequence-based metabarcoding

Environmental DNA (eDNA)-based methods of species detection are enabling various applications in ecology and conservation including large-scale biomonitoring efforts. qPCR is widely used as the standard approach for species-specific detection, often targeting a fish species of interest from aquatic eDNA. However, DNA metabarcoding has the potential to displace qPCR in certain eDNA applications. In this study, we compare the sensitivity of the latest Illumina NovaSeq 6000 NGS platform to qPCR TaqMan assays by measuring limits of detection and by analysing eDNA from water samples collected from Churchill River and Lake Melville, NL, Canada. Species-specific, targeted next generation sequencing (NGS) assays had significantly higher sensitivity than qPCR, with limits of detection 14- to 29-fold lower. For example, when analysing eDNA, qPCR detected Gadus ogac (Greenland cod) in 21% of samples, but targeted NGS detected this species in 29% of samples. General NGS assays were as sensitive as qPCR, while simultaneously detecting 15 fish species from eDNA samples. With over 34,000 fish species on the planet, parallel and sensitive methods such as NGS will be required to support effective biomonitoring at both regional and global scales.

Environmental DNA Assay for the Detection of the American Bullfrog (Lithobates catesbeianus) in the Early Stages of the Invasion in the Ebre Delta

The American bullfrog (Lithobates catesbeianus) is considered to be one of the most harmful invasive species. In the Iberian Peninsula, this species had been cited occasionally until the year 2018, when L. catesbeianus appeared in the Ebre Delta, and, for the first time, it started breeding in a territory of the Peninsula. Using environmental DNA (eDNA) analysis and visual surveys, the American bullfrog invasion in the Ebre Delta was monitored across two consecutive years (2019-2020). No specimens were observed in 2019, and results for the eDNA survey also failed to detect this species in the Delta. In 2020, two individuals were captured and, under the most conservative criteria to constrain the number of positive detections, eDNA analyses detected the presence of the American bullfrog in at least five locations. Performing an eDNA assay yielded a higher sensitivity with a lower sampling effort than traditional methods. Although the American bullfrog does not appear to still be well-established in the Ebre Delta, only a few bullfrog individuals could be enough for their establishment in suitable habitats. In this context, eDNA assays are essential tools to facilitate the detection, control, and eradication of this species in the first stage of the invasion process.

Assessing the breeding phenology of a threatened frog species using eDNA and automatic acoustic monitoring

Background

Climate change has driven shifts in breeding phenology of many amphibians, causing phenological mismatches (e.g., predator-prey interactions), and potentially population declines. Collecting data with high spatiotemporal sensitivity on hibernation emergence and breeding times can inform conservation best practices. However, monitoring the phenology of amphibians can be challenging because of their cryptic nature over much of their life cycle. Moreover, most salamanders and caecilians do not produce conspicuous breeding calls like frogs and toads do, presenting additional monitoring challenges.

Methods

In this study, we designed and evaluated the performance of an environmental DNA (eDNA) droplet digital PCR (ddPCR) assay as a non-invasive tool to assess the breeding phenology of a Western Chorus Frog population (Pseudacris maculata mitotype) in Eastern Ontario and compared eDNA detection patterns to hourly automatic acoustic monitoring. For two eDNA samples with strong PCR inhibition, we tested three methods to diminish the effect of inhibitors: diluting eDNA samples, adding bovine serum albumin to PCR reactions, and purifying eDNA using a commercial clean-up kit.

Results

We recorded the first male calling when the focal marsh was still largely frozen. Chorus frog eDNA was detected on April 6^th, 6 days after acoustic monitoring revealed this first calling male, but only 2 days after males attained higher chorus activity. eDNA signals were detected at more sampling locales within the marsh and eDNA concentrations increased as more males participated in the chorus, suggesting that eDNA may be a reasonable proxy for calling assemblage size. Internal positive control revealed strong inhibition in some samples, limiting detection probability and quantification accuracy in ddPCR. We found diluting samples was the most effective in reducing inhibition and improving eDNA quantification.

Conclusions

Altogether, our results showed that eDNA ddPCR signals lagged behind male chorusing by a few days; thus, acoustic monitoring is preferable if the desire is to document the onset of male chorusing. However, eDNA may be an effective, non-invasive monitoring tool for amphibians that do not call and may provide a useful complement to automated acoustic recording. We found inhibition patterns were heterogeneous across time and space and we demonstrate that an internal positive control should always be included to assess inhibition for eDNA ddPCR signal interpretations.

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.

Benthic invertebrates in Svalbard fjords-when metabarcoding does not outperform traditional biodiversity assessment

To protect and restore ecosystems and biodiversity is one of the 10 challenges identified by the United Nations's Decade of the Ocean Science. In this study we used eDNA from sediments collected in two fjords of the Svalbard archipelago and compared the taxonomic composition with traditional methods through metabarcoding, targeting mitochondrial CO1, to survey benthos. Clustering of 21.6 mill sequence reads with a d value of 13 in swarm, returned about 25 K OTU reads. An identification search with the BOLD database returned 12,000 taxonomy annotated sequences spanning a similarity range of 50% to 100%. Using an acceptance filter of minimum 90% similarity to the CO1 reference sequence, we found that 74% of the ca 100 taxon identified sequence reads were Polychaeta and 22% Nematoda. Relatively few other benthic invertebrate species were detected. Many of the identified sequence reads were extra-organismal DNA from terrestrial, planktonic, and photic zone sources. For the species rich Polychaeta, we found that, on average, only 20.6% of the species identified from morphology were also detected with DNA. This discrepancy was not due to missing reference sequences in the search database, because 90-100% (mean 96.7%) of the visually identified species at each station were represented with barcodes in Boldsystems. The volume of DNA samples is small compared with the volume searched in visual sorting, and the replicate DNA-samples in sum covered only about 2% of the surface area of a grab. This may considerably reduce the detection rate of species that are not uniformly distributed in the sediments. Along with PCR amplification bias and primer mismatch, this may be an important reason for the limited congruence of species identified with the two approaches. However, metabarcoding also identified 69 additional species that are usually overlooked in visual sample sorting, demonstrating how metabarcoding can complement traditional methodology by detecting additional, less conspicuous groups of organisms.

A manager's guide to using eDNA metabarcoding in marine ecosystems

Environmental DNA (eDNA) metabarcoding is a powerful tool that can enhance marine ecosystem/biodiversity monitoring programs. Here we outline five important steps managers and researchers should consider when developing eDNA monitoring program: (1) select genes and primers to target taxa; (2) assemble or develop comprehensive barcode reference databases; (3) apply rigorous site occupancy based decontamination pipelines; (4) conduct pilot studies to define spatial and temporal variance of eDNA; and (5) archive samples, extracts, and raw sequence data. We demonstrate the importance of each of these considerations using a case study of eDNA metabarcoding in the Ports of Los Angeles and Long Beach. eDNA metabarcoding approaches detected 94.1% (16/17) of species observed in paired trawl surveys while identifying an additional 55 native fishes, providing more comprehensive biodiversity inventories. Rigorous benchmarking of eDNA metabarcoding results improved ecological interpretation and confidence in species detections while providing archived genetic resources for future analyses. Well designed and validated eDNA metabarcoding approaches are ideally suited for biomonitoring applications that rely on the detection of species, including mapping invasive species fronts and endangered species habitats as well as tracking range shifts in response to climate change. Incorporating these considerations will enhance the utility and efficacy of eDNA metabarcoding for routine biomonitoring applications.

Environmental DNA detects Spawning Habitat of an ephemeral migrant fish (Anadromous Rainbow Smelt: Osmerus mordax)

BACKGROUND

Anadromous rainbow smelt (Osmerus mordax) have experienced a large range reduction in recent decades and the status of remnant spawning populations is poorly known in Maine, where these fish have significant ecological, cultural, and commercial relevance. Defining the remnant range of anadromous smelt is more difficult than for many declining fish species because adults are only ephemerally present while spawning in small coastal streams at night during spring runoff periods when traditional assessments can be unreliable or even hazardous. We hypothesized that eDNA might facilitate improved survey efforts to define smelt spawning habitat, but that detection could also face challenges from adult eDNA quickly flushing out of these small stream systems. We combined daytime eDNA sampling with nighttime fyke netting to ascertain a potential window of eDNA detection before conducting eDNA surveys in four streams of varying abundance. Hierarchical occupancy modeling was in turn employed to estimate eDNA encounter probabilities relative to numbers of sampling events (date), samples within events, and qPCR replicates within samples.

RESULTS

Results from the combined eDNA and fyke net study indicated eDNA was detectable over an extended period, culminating approximately 8-13 days following peak spawning, suggesting developing smelt larvae might be the primary source of eDNA. Subsequently, smelt eDNA was readily detected in eDNA surveys of four streams, particularly following remediation of PCR inhibitors. Hierarchical occupancy modeling confirmed our surveys had high empirical detection for most sites, and that future surveys employing at least three sampling events, three samples per event, and six qPCR replicates can afford greater than 90% combined detection capability in low abundance systems.

CONCLUSIONS

These results demonstrate that relatively modest eDNA sampling effort has high capacity to detect this ephemerally present species of concern at low to moderate abundances. As such, smelt eDNA detection could improve range mapping by providing longer survey windows, safer sampling conditions, and lower field effort in low density systems, than afforded by existing visual and netting approaches.

National eDNA-based monitoring of Batrachochytrium dendrobatidis and amphibian species in Norway

Freshwaters represent the most threatened environments with regard to biodiversity loss and, therefore, there is a need for national monitoring programs to effectively document species distribution and evaluate potential risks for vulnerable species. The monitoring of species for effective management practices is, however, challenged by insufficient data acquisition when using traditional methods. Here we present the application of environmental DNA (eDNA) metabarcoding of amphibians in combination with quantitative PCR (qPCR) assays for an invasive pathogenic chytrid species (Batrachochytrium dendrobatidis -Bd), a potential threat to endemic and endangered amphibian species. Statistical comparison of amphibian species detection using either traditional or eDNA-based approaches showed weak correspondence. By tracking the distribution of Bd over three years, we concluded that the risk for amphibian extinction is low since Bd was only detected at five sites where multiple amphibians were present over the sampled years. Our results show that eDNA-based detection can be used for simultaneous monitoring of amphibian diversity and the presence of amphibian pathogens at the national level in order to assess potential species extinction risks and establish effective management practices. As such our study represents suggestions for a national monitoring program based on eDNA.

Saint Peter and Saint Paul Archipelago barcoded: Fish diversity in the remoteness and DNA barcodes reference library for metabarcoding monitoring

In order to monitor the effects of anthropogenic pressures in ecosystems, molecular techniques can be used to characterize species composition. Among molecular markers capable of identifying species, the cytochrome c oxidase I (COI) is the most used. However, new possibilities of biodiversity profiling have become possible, in which molecular fragments of medium and short-length can now be analyzed in metabarcoding studies. Here, a survey of fishes from the Saint Peter and Saint Paul Archipelago was barcoded using the COI marker, which allowed the identification of 21 species. This paved the way to further investigate the fish biodiversity of the archipelago, transitioning from barcoding to metabarcoding analysis. As preparatory steps for future metabarcoding studies, the first extensive COI library of fishes listed for these islands was constructed and includes new data generated in this survey as well as previously available data, resulting in a final database with 9,183 sequences from 169 species and 63 families of fish. A new primer specifically designed for those fishes was tested in silico to amplify a region of 262 bp. The new approach should guarantee a reliable surveillance of the archipelago and can be used to generate policies that will enhance the archipelago’s protection.

Development of a ddPCR assay for the detection of the Smoky Madtom (Noturus baileyi) from eDNA in stream water samples

The Smoky Madtom Noturus baileyi is a federally endangered species, whose native distribution includes lower Abrams Creek in Great Smoky Mountains National Park (GRSM) and Citico Creek in nearby Cherokee National Forest. Due to challenges for bio-monitoring posed by its nocturnality and cryptic life history, an environmental DNA (eDNA)-based approach for detection would be useful to complement existing electrofishing and seining efforts to better understand the distribution of this species. We developed a probe-based droplet digital PCR (ddPCR) assay to detect Smoky Madtoms from non-invasively collected water samples. The assay was specific to N. baileyi and did not amplify concentrated genomic DNA of 16 co-occurring or regional fish species, including the yellowfin madtom N. flavipinnis and stonecat N. flavus. The assay limit of detection (LOD) was determined to be 4.18 copies (95% CI: 3.95, 4.41). Several 2 L water samples collected from throughout various streams in GRSM in 2016 and 2017 were tested for the presence of N. baileyi using the ddPCR assay. N. baileyi was detected at two different sites in 2016 and 2017 within Abrams Creek previously known to contain N. baileyi, but no novel detections in other sampled streams were observed. This assay should prove useful for continued surveys of N. baileyi in GRSM.

Can nuclear aquatic environmental DNA be a genetic marker for the accurate estimation of species abundance?

Environmental DNA (eDNA) analysis is a promising tool for the sensitive and effective monitoring of species distribution and abundance. Traditional eDNA analysis has targeted mitochondrial DNA (mtDNA) fragments due to their abundance in cells; however, the quantification may vary depending on cell type and physiology. Conversely, some recent eDNA studies have targeted multi-copy nuclear DNA (nuDNA) fragments, such as ribosomal RNA genes, in water, and reported a higher detectability and more rapid degradation than mitochondrial eDNA (mt-eDNA). These properties suggest that nuclear eDNA (nu-eDNA) may be useful for the accurate estimation of species abundance relative to mt-eDNA, but which remains unclear. In this study, we compiled previous studies and re-analyzed the relationships between mt- and nu-eDNA concentration and species abundance by comparing the R² values of the linear regression. We then performed an aquarium experiment using zebrafish (Danio rerio) to compare the relationships across genetic regions, including single-copy nuDNA. We found more accurate relationships between multi-copy nu-eDNA and species abundance than mt-eDNA in these datasets, although the difference was not significant upon weighted-averaging the R² values. Moreover, we compared the decay rate constants of zebrafish eDNA across genetic regions and found that multi-copy nu-eDNA degraded faster than mt-eDNA under pH 7, implying a quick turnover of multi-copy nu-eDNA in the field. Although further empirical studies of nu-eDNA applications are necessary to support our findings, this study provides the groundwork for improving the estimation accuracy of species abundance via eDNA analysis.

eDNAssay: a machine learning tool that accurately predicts qPCR cross-amplification

Environmental DNA (eDNA) sampling is a highly sensitive and cost-effective technique for wildlife monitoring, notably through the use of qPCR assays. However, it can be difficult to ensure assay specificity when many closely related species cooccur. In theory, specificity may be assessed in silico by determining whether assay oligonucleotides have enough base-pair mismatches with nontarget sequences to preclude amplification. However, the mismatch qualities required are poorly understood, making in silico assessments difficult and often necessitating extensive in vitro testing-typically the greatest bottleneck in assay development. Increasing the accuracy of in silico assessments would therefore streamline the assay development process. In this study, we paired 10 qPCR assays with 82 synthetic gene fragments for 530 specificity tests using SYBR Green intercalating dye (n = 262) and TaqMan hydrolysis probes (n = 268). Test results were used to train random forest classifiers to predict amplification. The primer-only model (SYBR Green-based) and full-assay model (TaqMan probe-based) were 99.6% and 100% accurate, respectively, in cross-validation. We further assessed model performance using six independent assays not used in model training. In these tests the primer-only model was 92.4% accurate (n = 119) and the full-assay model was 96.5% accurate (n = 144). The high performance achieved by these models makes it possible for eDNA practitioners to more quickly and confidently develop assays specific to the intended target. Practitioners can access the full-assay model via eDNAssay (https://NationalGenomicsCenter.shinyapps.io/eDNAssay), a user-friendly online tool for predicting qPCR cross-amplification.

A review of applications of environmental DNA for reptile conservation and management

Reptile populations are in decline globally, with total reptile abundance halving in the past half century, and approximately a fifth of species currently threatened with extinction. Research on reptile distributions, population trends, and trophic interactions can greatly improve the accuracy of conservation listings and planning for species recovery, but data deficiency is an impediment for many species. Environmental DNA (eDNA) can detect species and measure community diversity at diverse spatio‐temporal scales, and is especially useful for detection of elusive, cryptic, or rare species, making it potentially very valuable in herpetology. We aim to summarize the utility of eDNA as a tool for informing reptile conservation and management and discuss the benefits and limitations of this approach. A literature review was conducted to collect all studies that used eDNA and focus on reptile ecology, conservation, or management. Results of the literature search are summarized into key discussion points, and the review also draws on eDNA studies from other taxa to highlight methodological challenges and to identify future research directions. eDNA has had limited application to reptiles, relative to other vertebrate groups, and little use in regions with high species richness. eDNA techniques have been more successfully applied to aquatic reptiles than to terrestrial reptiles, and most (64%) of studies focused on aquatic habitats. Two of the four reptilian orders dominate the existing eDNA studies (56% Testudines, 49% Squamata, 5% Crocodilia, 0% Rhynchocephalia). Our review provides direction for the application of eDNA as an emerging tool in reptile ecology and conservation, especially when it can be paired with traditional monitoring approaches. Technologies associated with eDNA are rapidly advancing, and as techniques become more sensitive and accessible, we expect eDNA will be increasingly valuable for addressing key knowledge gaps for reptiles.

Effects of forest cover on richness of threatened fish species in Japan

Estuaries--one of the most vulnerable ecosystems globally--face anthropogenic threats, including biodiversity loss and the collapse of sustainable fisheries. Determining the factors contributing to the maintenance of estuarine biodiversity, especially that of fish, is vital for promoting estuarine conservation and sustainability. We used environmental DNA metabarcoding analysis to determine fish species composition in 22 estuaries around Japan and measured watershed-scale land-use factors (e.g., population size, urban area percentage, and forest area percentage). We sought to test the hypothesis that the richness of the most vulnerable estuarine fish species (i.e., registered by the Japanese Ministry of the Environment in the national species red-list) is determined by watershed-scale land-use factors. The richness of such species was greater, where forest cover was highest; thus, forest cover contributes to their conservation. The proportion of agriculture cover was associated with low species richness of red-listed fishes (redundancy analysis, adjusted R² = 43.9% of total variance, df = 5, F = 5.3843, p = 0.0001). The number of red-listed species increased from 3 to 11 along a watershed land-use gradient ranging from a high proportion of agriculture cover to a large proportion of forest cover. Furthermore, the results showed that throughout Japan all the examined watersheds that were covered by >74.8% forest had more than the average (6.7 species per site) richness of red-listed fish species. This result can be attributed to the already high average forest cover in Japan of 67.2%. Our results demonstrate how the land use of watersheds can affect the coastal sea environment and its biodiversity and suggest that proper forest management in conjunction with land-use management may be of prime importance for threatened fish species and coastal ecosystems in general.

Sampling and modelling rare species: Conceptual guidelines for the neglected majority

Biodiversity conservation faces a methodological conundrum: Biodiversity measurement often relies on species, most of which are rare at various scales, especially prone to extinction under global change, but also the most challenging to sample and model. Predicting the distribution change of rare species using conventional species distribution models is challenging because rare species are hardly captured by most survey systems. When enough data are available, predictions are usually spatially biased towards locations where the species is most likely to occur, violating the assumptions of many modelling frameworks. Workflows to predict and eventually map rare species distributions imply important trade-offs between data quantity, quality, representativeness and model complexity that need to be considered prior to survey and analysis. Our opinion is that study designs need to carefully integrate the different steps, from species sampling to modelling, in accordance with the different types of rarity and available data in order to improve our capacity for sound assessment and prediction of rare species distribution. In this article, we summarize and comment on how different categories of species rarity lead to different types of occurrence and distribution data depending on choices made during the survey process, namely the spatial distribution of samples (where to sample) and the sampling protocol in each selected location (how to sample). We then clarify which species distribution models are suitable depending on the different types of distribution data (how to model). Among others, for most rarity forms, we highlight the insights from systematic species-targeted sampling coupled with hierarchical models that allow correcting for overdispersion and spatial and sampling sources of bias. Our article provides scientists and practitioners with a much-needed guide through the ever-increasing diversity of methodological developments to improve the prediction of rare species distribution depending on rarity type and available data.

Advances in multiplex molecular detection technologies for harmful algae

As the eutrophication of natural water bodies becomes more and more serious, the frequency of outbreaks of harmful algal blooms (HABs) mainly formed by harmful algae also increases. HABs have become a global ecological problem that poses a serious threat to human health and food safety. Therefore, it is extremely important to establish methods that can rapidly detect harmful algal species for early warning of HABs. The traditional morphology-based identification method is inefficient and inaccurate. In recent years, the rapid development of molecular biology techniques has provided new ideas for the detection of harmful algae and has become a research hotspot. The current molecular detection methods for harmful algal species mainly include fluorescence in situ hybridization, sandwich hybridization, and quantitative PCR (qPCR), but all of these methods can only detect single harmful algal species at a time. The establishment of methods for the simultaneous detection of multiple harmful algal species has become a new trend in the development of molecular detection technology because various harmful algal species may coexist in the natural water environment. The established molecular techniques for multiple detections of harmful algae mainly include gene chip, multiplex PCR, multiplex qPCR, massively parallel sequencing, antibody chip, and multiple isothermal amplification. This review mainly focuses on the principles, advantages and disadvantages, application progress, and application prospects of these multiple detection technologies, aiming at providing effective references not only for the fisheries but also for economic activities, environment, and human health.

Environmental DNA analysis for macro-organisms: species distribution and more

In an era of severe biodiversity loss, biological monitoring is becoming increasingly essential. The analysis of environmental DNA (eDNA) has emerged as a new approach that could revolutionize the biological monitoring of aquatic ecosystems. Over the past decade, macro-organismal eDNA analysis has undergone significant developments and is rapidly becoming established as the golden standard for non-destructive and non-invasive biological monitoring. In this review, I summarize the development of macro-organismal eDNA analysis to date and the techniques used in this field. I also discuss the future perspective of these analytical methods in combination with sophisticated analytical techniques for DNA research developed in the fields of molecular biology and molecular genetics, including genomics, epigenomics, and single-cell technologies. eDNA analysis, which to date has been used primarily for determining the distribution of organisms, is expected to develop into a tool for elucidating the physiological state and behaviour of organisms. The fusion of microbiology and macrobiology through an amalgamation of these technologies is anticipated to lead to the future development of an integrated biology.

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.

Monitoring of environmental DNA from nonindigenous species of algae, dinoflagellates and animals in the North East Atlantic

Monitoring the distribution of marine nonindigenous species is a challenging task. To support this monitoring, we developed and validated the specificity of 12 primer-probe assays for detection of environmental DNA (eDNA) from marine species, all nonindigenous to Europe. The species include sturgeons, a Pacific red algae, oyster thief, a freshwater hydroid from the Black Sea, Chinese mitten crab, Pacific oyster, warty comb jelly, sand gaper, round goby, pink salmon, rainbow trout and North American mud crab. We tested all assays in the laboratory, on DNA extracted from both the target and non-target species to ensure that they only amplified DNA from the intended species. Subsequently, all assays were used to analyse water samples collected at 16 different harbours across two different seasons during 2017. We also included six previously published assays targeting eDNA from goldfish, European carp, two species of dinoflagellates of the genera Karenia and Prorocentrum, two species of the heterokont flagellate genus Pseudochattonella. Conventional monitoring was carried out alongside eDNA sampling but with only one sampling event over the one year. Because eDNA was relatively fast and easy to collect compared to conventional sampling, we sampled eDNA twice during 2017, which showed seasonal changes in the distribution of nonindigenous species. Comparing eDNA levels with salinity gradients did not show any correlation. A significant correlation was observed between number of species detected with conventional monitoring methods and number of species found using eDNA at each location. This supports the use of eDNA for surveillance of the distribution of marine nonindigenous species, where the speed and relative easy sampling in the field combined with fast molecular analysis may provide advantages compared to conventional monitoring methods. Prior validation of assays increases taxonomic precision, and laboratorial setup facilitates analysis of multiple samples simultaneously. The specific eDNA assays presented here can be implemented directly in monitoring programmes across Europe and potentially worldwide to infer a more precise picture of the dynamics in the distribution of marine nonindigenous species.

Honey Environmental DNA Can Be Used to Detect and Monitor Honey Bee Pests: Development of Methods Useful to Identify Aethina tumida and Galleria mellonella Infestations

Environmental DNA (eDNA) contained in honey derives from the organisms that directly and indirectly have been involved in the production process of this matrix and that have played a role in the hive ecosystems where the honey has been produced. In this study we set up PCR-based assays to detect the presence of DNA traces left in the honey by two damaging honey bee pests: the small hive beetle (Aethina tumida) and the greater wax moth (Galleria mellonella). DNA was extracted from 82 honey samples produced in Italy and amplified using two specific primer pairs that target the mitochondrial gene cytochrome oxidase I (COI) of A. tumida and two specific primer pairs that target the same gene in G. mellonella. The limit of detection was tested using sequential dilutions of the pest DNA. Only one honey sample produced in Calabria was positive for A. tumida whereas about 66% of all samples were positively amplified for G. mellonella. The use of honey eDNA could be important to establish early and effective measures to contain at the local (e.g., apiary) or regional scales these two damaging pests and, particularly for the small hive beetle, to prevent its widespread diffusion.

Evaluating eDNA for Use within Marine Environmental Impact Assessments

In this review, the use of environmental DNA (eDNA) within Environmental Impact Assessment (EIA) is evaluated. EIA documents provide information required by regulators to evaluate the potential impact of a development project. Currently eDNA is being incorporated into biodiversity assessments as a complementary method for detecting rare, endangered or invasive species. However, questions have been raised regarding the maturity of the field and the suitability of eDNA information as evidence for EIA. Several key issues are identified for eDNA information within a generic EIA framework for marine environments. First, it is challenging to define the sampling unit and optimal sampling strategy for eDNA with respect to the project area and potential impact receptor. Second, eDNA assay validation protocols are preliminary at this time. Third, there are statistical issues around the probability of obtaining both false positives (identification of taxa that are not present) and false negatives (non-detection of taxa that are present) in results. At a minimum, an EIA must quantify the uncertainty in presence/absence estimates by combining series of Bernoulli trials with ad hoc occupancy models. Finally, the fate and transport of DNA fragments is largely unknown in environmental systems. Shedding dynamics, biogeochemical and physical processes that influence DNA fragments must be better understood to be able to link an eDNA signal with the receptor’s state. The biggest challenge is that eDNA is a proxy for the receptor and not a direct measure of presence. Nonetheless, as more actors enter the field, technological solutions are likely to emerge for these issues. Environmental DNA already shows great promise for baseline descriptions of the presence of species surrounding a project and can aid in the identification of potential receptors for EIA monitoring using other methods.

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.

Using environmental DNA methods to improve detectability in an endangered sturgeon (Acipenser sinensis) monitoring program

Background

To determine the presence and abundance of an aquatic species in large waterbodies, especially when populations are at low densities, is highly challenging for conservation biologists. Environmental DNA (eDNA) has the potential to offer a noninvasive and cost-effective method to complement traditional population monitoring, however, eDNA has not been extensively applied to study large migratory species. Chinese sturgeon (Acipenser sinensis), is the largest anadromous migratory fish in the Yangtze River, China, and in recent years its population has dramatically declined and spawning has failed, bringing this species to the brink of extinction. In this study, we aim to test the detectability of eDNA methods to determine the presence and relative abundance of reproductive stock of the species and whether eDNA can be used as a tool to reflect behavioral patterns. Chinese sturgeon eDNA was collected from four sites along the spawning ground across an eight month period, to investigate the temporal and spatial distribution using droplet digital PCR (ddPCR).

Results

We designed a pair of specific primers for Chinese sturgeon and demonstrated the high sensitivity of ddPCR to detect and quantify the Chinese sturgeon eDNA concentration with the limit of detection 0.17 copies/μl, with Chinese sturgeon eDNA been intermittently detected at all sampling sites. There was a consistent temporal pattern among four of the sampling sites that could reflect the movement characteristics of the Chinese sturgeon in the spawning ground, but without a spatial pattern. The eDNA concentration declined by approximately 2–3 × between December 2018 and December 2019.

Conclusions

The results prove the efficacy of eDNA for monitoring reproductive stock of the Chinese sturgeon and the e decreased eDNA concentration reflect that Chinese sturgeon may survive with an extremely small number of reproductive stock in the Yangtze River. Accordingly, we suggest future conservation measures should focus on both habitat restoration and matured fish restocking to ensure successful spawning. Overall, this study provides encouraging support for the application of eDNA methods to monitor endangered aquatic species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01948-w.

Reinforcement of Environmental DNA Based Methods (Sensu Stricto) in Biodiversity Monitoring and Conservation: A Review

Simple Summary

Worldwide biodiversity loss points to a necessity of upgrading to a fast and effective monitoring method that can provide quick conservation action. Newly developed environmental DNA (eDNA) based method found to be more cost-effective, non-invasive, quick, and accurate than traditional monitoring (spot identification, camera trapping). Although the eDNA based methods are proliferating rapidly, as a newly developed branch, it needs more standardization and practitioner adaptation. The present study aims to evaluate the eDNA based methods, and their potential achievements in biodiversity monitoring, and conservation for quick practitioners’ adaption. The investigation shows that the eDNA technique is applicable largely in (i) early detection of invasive species, (ii) species detection for conservation, (iii) community-level biodiversity monitoring, (iv) ecosystem health monitoring, (v) study on trophic interactions, etc. Thus, the eDNA technique shows a great promise with its high accuracy and authenticity, and will be applicable alone or alongside other methods in the near future.

Abstract

Recently developed non-invasive environmental DNA-based (eDNA) techniques have enlightened modern conservation biology, propelling the monitoring/management of natural populations to a more effective and efficient approach, compared to traditional surveys. However, due to rapid-expansion of eDNA, confusion in terminology and collection/analytical pipelines can potentially jeopardize research progression, methodological standardization, and practitioner adoption in several ways. Present investigation reflects the developmental progress of eDNA (sensu stricto) including highlighting the successful case studies in conservation management. The eDNA technique is successfully relevant in several areas of conservation research (invasive/conserve species detection) with a high accuracy and authentication, which gradually upgrading modern conservation approaches. The eDNA technique related bioinformatics (e.g., taxon-specific-primers MiFish, MiBird, etc.), sample-dependent methodology, and advancement of sequencing technology (e.g., oxford-nanopore-sequencing) are helping in research progress. The investigation shows that the eDNA technique is applicable largely in (i) early detection of invasive species, (ii) species detection for conservation, (iii) community level biodiversity monitoring, (iv) ecosystem health monitoring, (v) study on trophic interactions, etc. Thus, the eDNA technique with a high accuracy and authentication can be applicable alone or coupled with traditional surveys in conservation biology. However, a comprehensive eDNA-based monitoring program (ecosystem modeling and function) is essential on a global scale for future management decisions.

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.

Development of droplet digital Polymerase Chain Reaction assays for the detection of long-finned (Anguilla dieffenbachii) and short-finned (Anguilla australis) eels in environmental samples

Freshwater eels are ecologically, and culturally important worldwide. The New Zealand long-finned eel (Anguilla dieffenbachii) and short-finned eel (Anguilla australis) are apex predators, playing an important role in ecosystem functioning of rivers and lakes. Recently, there has been a national decline in their populations due to habitat destruction and commercial harvest. The emergence of targeted environmental DNA detection methodologies provides an opportunity to enhance information about their past and present distributions. In this study we successfully developed species-specific droplet digital Polymerase Chain Reaction (ddPCR) assays to detect A. dieffenbachii and A. australis DNA in water and sediment samples. Assays utilized primers and probes designed for regions of the mitochondrial cytochrome b and 16S ribosomal RNA genes in A. dieffenbachii and A. australis, respectively. River water samples (n = 27) were analyzed using metabarcoding of fish taxa and were compared with the ddPCR assays. The presence of A. dieffenbachii and A. australis DNA was detected in a greater number of water samples using ddPCR in comparison to metabarcoding. There was a strong and positive correlation between gene copies (ddPCR analyses) and relative eel sequence reads (metabarcoding analyses) when compared to eel biomass. These ddPCR assays provide a new method for assessing spatial distributions of A. dieffenbachii and A. australis in a range of environments and sample types.