Estimating fish abundance and biomass from eDNA concentrations: variability among capture methods and environmental conditions

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.

Human activities strengthen the influence of deterministic processes in the mechanisms of fish community assembly in tropical rivers of Yunnan, China

Human-induced global alterations have worsened the severe decrease in fish biodiversity in rivers. To successfully reduce the pace of reduction in fish diversity, it is crucial to prioritize the understanding of how human activities impact the processes that shape and maintain fish diversity. Traditional fish survey methods are based on catch collection and morphological identification, which is often time-consuming and ineffective. Hence, these methods are inadequate for conducting thorough and detailed large-scale surveys of fish ecology. The rapid progress in molecular biology techniques has transformed environmental DNA (eDNA) technique into a highly promising method for studying fish ecology. In this work, we conducted the first systematic study of fish diversity and its formation and maintenance mechanism in the Xishuangbanna section of the Lancang River using eDNA metabarcoding. The eDNA metabarcoding detected a total of 159 species of freshwater fishes spanning 13 orders, 34 families, and 99 genera. The fishes in the order cypriniformes were shown to be overwhelmingly dominant. At different intensities of anthropogenic activity, we found differences in fish community composition and assembly. The analysis of the Sloan's neutral community model fitting revealed that stochastic processes were the dominant factor in the shaping of fish communities in the Xishuangbanna section of the Lancang River. We have further confirmed this result by using the phylogenetic normalized stochasticity ratio. Furthermore, our findings indicate that as human activities get more intense, the influence of stochastic processes on the shaping of fish communities decreases, while the influence of deterministic processes eventually becomes more prominent. Finally, we discovered that salinity positively correlated with fish community changes in the high-intensity anthropogenic sample sites, but all environmental factors had little effect on fish community changes in the low-intensity and moderate-intensity anthropogenic sample sites. Our study not only validated the potential application of eDNA metabarcoding for monitoring fish diversity in tropical rivers, but also revealed how fish communities respond to human activities. This knowledge will serve as a solid foundation for the protection of fish resources in tropical rivers.

Environmental DNA concentrations vary greatly across productive and degradative conditions, with implications for the precision of population estimates

Population size is an important metric to inform the conservation and management of species. For aquatic species, environmental DNA (eDNA) concentration has been suggested for non-invasively estimating population size. However, many biotic and abiotic factors simultaneously influence the production and degradation of eDNA which can alter the relationship between population size and eDNA concentration. We investigated the influence of temperature, salinity, and ranavirus infection on eDNA concentrations using tadpole mesocosms. Using linear regression models, we tested the influence of each experimental treatment on eDNA concentrations at three time points before and during epidemics. Prior to infection, elevated temperatures lowered eDNA concentrations, indicating that degradation was the driving force influencing eDNA concentrations. During early epidemics, no treatments strongly influenced eDNA concentrations and in late epidemics, productive forces dominated as ranavirus intensity and dead organisms increased eDNA concentrations. Finally, population size was only an important predictor of eDNA concentration in late epidemics and we observed high levels of variation between samples of replicate mesocosms. We demonstrate the complexities of several interacting factors influencing productive and degradative forces, variation in influences on eDNA concentration over short time spans, and examine the limitations of estimating population sizes from eDNA with precision in semi-natural conditions.

The forensic potential of environmental DNA (eDNA) in freshwater wildlife crime investigations: From research to application

Environmental DNA (eDNA) is widely used in biodiversity, conservation, and ecological studies but despite its successes, similar approaches have not yet been regularly applied to assist in wildlife crime investigations. The purpose of this paper is to review current eDNA methods and assess their potential forensic application in freshwater environments considering collection, transport and persistence, analysis, and interpretation, while identifying additional research required to present eDNA evidence in court. An extensive review of the literature suggests that commonly used collection methods can be easily adapted for forensic frameworks providing they address the appropriate investigative questions and take into consideration the uniqueness of the target species, its habitat, and the requirements of the end user. The use of eDNA methods to inform conservationists, monitor biodiversity and impacts of climate change, and detect invasive species and pathogens shows confidence within the scientific community, making the acceptance of these methods by the criminal justice system highly possible. To contextualise the potential application of eDNA on forensic investigations, two test cases are explored involving i) species detection and ii) species localisation. Recommendations for future work within the forensic eDNA discipline include development of suitable standardised collection methods, considered collection strategies, forensically validated assays and publication of procedures and empirical research studies to support implementation within the legal system.

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.

Harnessing eDNA metabarcoding to investigate fish community composition and its seasonal changes in the Oslo fjord

In the face of global ecosystem changes driven by anthropogenic activities, effective biomonitoring strategies are crucial for mitigating impacts on vulnerable aquatic habitats. Time series analysis underscores a great significance in understanding the dynamic nature of marine ecosystems, especially amidst climate change disrupting established seasonal patterns. Focusing on Norway's Oslo fjord, our research utilises eDNA-based monitoring for temporal analysis of aquatic biodiversity during a one year period, with bi-monthly sampling along a transect. To increase the robustness of the study, a taxonomic assignment comparing BLAST+ and SINTAX approaches was done. Utilising MiFish and Elas02 primer sets, our study detected 63 unique fish species, including several commercially important species. Our findings reveal a substantial increase in read abundance during specific migratory cycles, highlighting the efficacy of eDNA metabarcoding for fish composition characterization. Seasonal dynamics for certain species exhibit clear patterns, emphasising the method's utility in unravelling ecological complexities. eDNA metabarcoding emerges as a cost-effective tool with considerable potential for fish community monitoring for conservation purposes in dynamic marine environments like the Oslo fjord, contributing valuable insights for informed management strategies.

Development and Testing of Species-Specific Primers for Detecting the Presence of the Northern Pacific Sea Star (Asterias amurensis) from Environmental DNA

The starfish Asterias amurensis, a well-known predator of molluscan species in intertidal ecosystems, has caused substantial ecological and economic losses in North China such as offshore Qingdao. Effective monitoring and prevention measures are urged to minimize its negative impacts. Compared with traditional biomonitoring methods, environmental DNA technology has emerged as a powerful and cost-efficient tool for inferring species' presence and abundance. In this study, we developed a pair of species-specific primers (i.e., Ast-F and Ast-R) for the A. amurensis mitochondrial COI gene and tested its utility in amplifying and quantifying the DNA fragments from environmental samples under both laboratory and field conditions. The results of controlled water tank experiments demonstrated that the amount of eDNA released by A. amurensis was positively related to its biomass; after the removal of the starfish, the eDNA degraded significantly in 24 h and remained detectable for 8 days. The number of eDNA copies enriched tended to increase with smaller pore size of filter membrane and larger volume of filtered water. For field tests, we confirmed the validation of our approach in six locations in Qingdao by filtering 1000 ml water per sample with a 0.45-µm pore size filtration. All the amplification products generated a single and bright band via gel electrophoresis, and the quantitative PCR results unveiled significant differences in eDNA copies. This study provided an eDNA-based approach for investigating the distribution and biomass of A. amurensis, which may help to formulate early warning and management strategies in coastal Qingdao and other regions.

Genomics for monitoring and understanding species responses to global climate change

All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These environmental changes are happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish a species' potential to adapt to future environments. Understanding and monitoring how organisms respond to human-driven climate change is therefore a major priority for the conservation of biodiversity in a rapidly changing environment. Recent developments in genomic, transcriptomic and epigenomic technologies are enabling unprecedented insights into the evolutionary processes and molecular bases of adaptation. This Review summarizes methods that apply and integrate omics tools to experimentally investigate, monitor and predict how species and communities in the wild cope with global climate change, which is by genetically adapting to new environmental conditions, through range shifts or through phenotypic plasticity. We identify advantages and limitations of each method and discuss future research avenues that would improve our understanding of species' evolutionary responses to global climate change, highlighting the need for holistic, multi-omics approaches to ecosystem monitoring during global climate change.

Vertical eDNA distribution of cold-water fishes in response to environmental variables in stratified lake

In summer, the survival zones of cold-water species are predicted to narrow by both increasing water temperatures from the surface and by expanding hypoxic zones from the lake bottom. To examine how the abundance of cold-water fishes changes along environmental gradients, we assessed the vertical environmental DNA (eDNA) distributions of three salmonid species which may have different water temperature tolerances during both stratification and turnover periods using quantitative PCR (qPCR). In addition, we examined on the vertical distribution of diverse fish fauna using an eDNA metabarcoding assay. The results suggested that the kokanee salmon (Oncorhynchus nerka) eDNA were abundant in deep, cold waters. On the other hand, rainbow trout (O. mykiss) eDNA were distributed uniformly throughout the water column, suggesting that they may have high water-temperature tolerance compared with kokanee salmon. The eDNA concentrations of masu salmon (O. masou) were below the detection limit (i.e., <10 copies μL-1) at all stations and depths and hence could not be quantified during stratification. Together with the finding that the eDNA distributions of other prey fish species were also constrained vertically in species-specific ways, our results suggest that climate change will result in substantial changes in the vertical distributions of lake fish species and thus affect their populations and interactions.

Monitoring of multiple fish species by quantitative environmental DNA metabarcoding surveys over two summer seasons

Periodic monitoring can provide important information for the protection of endangered fish, sustainable use of fishery resources and management of alien species. Previous studies have attempted to monitor fish using non-invasive environmental DNA (eDNA) technology, generally employing quantitative PCR to quantify the eDNA concentration. However, the throughput was limited. High-throughput metabarcoding technology can detect the DNA of multiple species simultaneously in a single experiment but does not provide sufficient quantification. In this study, we applied a quantitative metabarcoding approach to simultaneously quantify the eDNA concentration of an entire fish assemblage in a small reservoir over two summer seasons. Traditional surveys were also conducted to investigate the individuals of fish. The eDNA concentrations were quantified using quantitative metabarcoding, and the fish species detected using this approach were highly consistent with the results of traditional fish monitoring. A significant positive relationship was observed between the eDNA concentration and fish species abundance. Seasonal changes in fish community structure were estimated using eDNA concentrations, which may reveal the activity seasons of different fish. The eDNA concentrations of different fish species peaked at different water temperatures, reflecting the differential responses of fish species to this environmental factor. Finally, by detecting outlier eDNA concentrations, the spawning activities of 13 fish species were estimated, 12 of which were roughly consistent with the current knowledge of fish spawning periods. These results indicate that quantitative eDNA metabarcoding with dozens of sampling times is useful for the simultaneous ecological monitoring of multiple fish species.

Correlation between the Density of Acipenser sinensis and Its Environmental DNA

Since the construction of the Gezhouba Dam, Chinese sturgeon (Acipenser sinensis) numbers have gradually declined, rendering this species critically endangered according to the International Union for the Conservation of Nature. Environmental DNA (eDNA) technology plays an important role in monitoring the abundance of aquatic organisms. Species density and biomass have been proven to be estimable by researchers, but the level of accuracy depends on the specific species and ecosystem. In this study, juvenile A. sinensis, an endangered fish, were selected as the research target. Under controlled laboratory conditions in an aquarium, one, two, four, six, and eight juvenile A. sinensis were cultured in five fish tanks, respectively. Water samples were filtered at eight different time points for eDNA content analysis. Additionally, eDNA yield was tested at six different time points after a 0.114 ind./L density of A. sinensis was removed, and the employed degradation model was screened using the Akaike information criterion (AIC) and the Bayesian information criterion (BIC). The results showed that eDNA content remained stable after 3 days and exhibited a significant positive linear correlation with the density of A. sinensis (R2 = 0.768~0.986). Furthermore, eDNA content was negatively correlated with the 3-day period after the removal of A. sinensis. The power function had the smallest AIC and BIC values, indicating better fitting performance. This study lays a momentous foundation for the application of eDNA for monitoring juvenile A. sinensis in the Yangtze Estuary and reveals the applicability of eDNA as a useful tool for assessing fish density/biomass in natural environments.

Environmental DNA (eDNA) removal rates in streams differ by particle size under varying substrate and light conditions

The use of environmental DNA (eDNA) as a sampling tool offers insights into the detection of invasive and/or rare aquatic species and enables biodiversity assessment without traditional sampling approaches, which are often labor-intensive. However, our understanding of the environmental factors that impact eDNA removal (i.e., how rapidly eDNA is removed from the water column by the combination of decay and physical removal) in flowing waters is limited. This limitation constrains predictions about the location and density of target organisms after positive detection. To address this question, we spiked Common Carp (Cyprinus carpio) eDNA into recirculating mesocosms (n = 24) under varying light (shaded versus open) and benthic substrate conditions (no substrate, bare substrate, and biofilm-colonized substrate). We then collected water samples from each mesocosm at four time points (40 min, 6 h, 18 h, and 48 h), and sequentially filtered the samples through 10, 1.0, and 0.2 μm filters to quantify removal rates for different eDNA particle sizes under varying light and substrate conditions. Combining all size classes, total eDNA removal rates were higher for mesocosms with biofilm-colonized substrate compared to those with no substrate or bare (i.e., no biofilm) substrate, which is consistent with previous findings linking biofilm colonization with increased eDNA removal and degradation. Additionally, when biofilm was present, light availability increased eDNA removal; eDNA levels fell below detection after 6-18 h for open mesocosms versus 18-48 h for shaded mesocosms. Among size classes, larger particles (>10 μm) were removed faster than small particles (1.0-0.2 μm). These results suggest that changes in the distribution of eDNA size classes over time (e.g., with downstream transport) and with differing environmental conditions could be used to predict the location of target organisms in flowing waters, which will advance the use of eDNA as a tool for species monitoring and management.

Environmental DNA metabarcoding serves as a promising method for aquatic species monitoring and management: A review focused on its workflow, applications, challenges and prospects

Marine and freshwater biodiversity is under threat from both natural and manmade causes. Biological monitoring is currently a top priority for biodiversity protection. Given present limitations, traditional biological monitoring methods may not achieve the proposed monitoring aims. Environmental DNA metabarcoding technology reflects species information by capturing and extracting DNA from environmental samples, using molecular biology techniques to sequence and analyze the DNA, and comparing the obtained information with existing reference libraries to obtain species identification. However, its practical application has highlighted several limitations. This paper summarizes the main steps in the environmental application of eDNA metabarcoding technology in aquatic ecosystems, including the discovery of unknown species, the detection of invasive species, and evaluations of biodiversity. At present, with the rapid development of big data and artificial intelligence, certain advanced technologies and devices can be combined with environmental DNA metabarcoding technology to promote further development of aquatic species monitoring and management.

Using environmental DNA metabarcoding to monitor fish communities in small rivers and large brooks: Insights on the spatial scale of information

Monitoring fish communities is central to the evaluation of ecological health of rivers. Both presence/absence of fish species and their relative quantity in local fish assemblages are crucial parameters to measure. Fish communities in lotic systems are traditionally monitored via electrofishing, characterized by a known limited efficiency and high survey costs. Analysis of environmental DNA could serve as a non-destructive alternative for detection and quantification of lotic fish communities, but this approach still requires further insights in practical sampling schemes incorporating transport and dilution of the eDNA particles; optimization of predictive power and quality assurance of the molecular detection method. Via a controlled cage experiment, we aim to extend the knowledge on streamreach of eDNA in small rivers and large brooks, as laid out in the European Water Framework Directive's water typology. Using a high and low source biomass in two river transects of a species-poor river characterized by contrasting river discharge rates, we found strong and significant correlations between the eDNA relative species abundances and the relative biomass per species in the cage community. Despite a decreasing correlation over distance, the underlying community composition remained stable from 25 to 300 m, or up to 1 km downstream of the eDNA source, depending on the river discharge rate. Such decrease in similarity between relative source biomass and the corresponding eDNA-based community profile with increasing distance downstream from the source, might be attributed to variation in species-specific eDNA persistence. Our findings offer crucial insights on eDNA behaviour and characterization of riverine fish communities. We conclude that water sampled from a relatively small river offers an adequate eDNA snapshot of the total fish community in the 300-1000 m upstream transect. The potential application for other river systems is further discussed.

eDNA testing reveals surprising findings on fish population dynamics in Thailand

COVID-19, a global health concern, has an effect on all aspects of the economy. The aquaculture and fishing industries were severely harmed as a result of the closures in multiple nations. Regular systems for inventory monitoring, production, and supply were disrupted. Cancellation of programmes for research, fieldwork, sampling, and tagging influences management-required data. For effective species management, fish dispersion assessments are indispensable. However, due to the difficulty of accessing sampling sites and the associated costs, there is frequently a lack of comprehensive information regarding the distribution and abundance of organisms. The COVID-19 prohibition made fish monitoring more problematic. Due to constant pressure, populations of the stone lapping minnow (Garra cambodgiensis), one of Thailand's overfished fish, are rapidly declining. Therefore, eDNA-based monitoring was devised and implemented to reveal the likely dispersal of the species in Thailand prior to and following the lockdown. At 28 locations within the Chao Phraya River Basin, water samples were collected. qPCR was used to determine the presence or absence of G. cambodgiensis in water samples. In 78 of 252 water samples, a wide range of computed copy numbers for G. cambodgiensis eDNA was observed. It was discovered that samples collected in 2021 (after the lockdown) contain a higher concentration of G. cambodgiensis eDNA than samples collected in 2018 or 2019 (prior to the lockdown). The closure appears to be a boon and may result in a substantial restocking of the fish we have studied. Overall, eDNA-based analysis is an extremely promising new survey instrument.

Wildlife Population Assessment: Changing Priorities Driven by Technological Advances

Advances in technology are having a large effect on the priorities for innovation in statistical ecology. Collaborations between statisticians and ecologists have always been important in driving methodological development, but increasingly, expertise from computer scientists and engineers is also needed. We discuss changes that are occurring and that may occur in the future in surveys for estimating animal abundance. As technology advances, we expect classical distance sampling and capture-recapture to decrease in importance, as camera (still and video) survey, acoustic survey, spatial capture-recapture and genetic methods continue to develop and find new applications. We explore how these changes are impacting the work of the statistical ecologist.

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.

Investigating the Potential Utility of Environmental DNA to Provide a Relative Abundance Index for the Depleted Teleost, Mulloway, Argyrosomus japonicus

Non-invasive, low-cost methods for censusing depleted fish populations are being prioritised among many jurisdictions worldwide. Collecting environmental DNA (eDNA) could offer one such option for augmenting fish population assessments. However, candidate species need to be carefully selected because species-specific DNA shedding and decay rates are affected by many biotic and abiotic factors that may influence relative abundance estimates. In this study, we sought to ascertain if the eDNA of a depleted Australian teleost, mulloway, Argyrosomus japonicus, reflects its weight under controlled aquaria conditions. With four experiments, we investigated the relationships between mulloway eDNA concentrations and their weight tank−1 as a function of: (1) time post-tank establishment; (2) water temperatures (within the species’ tolerance range); (3) stocking densities; and (4) among individual, similar-sized fish. The concentrations of eDNA in tanks stabilised after six days, and a positive relationship was found between fish weight and eDNA concentration, despite some variability in shedding rates by similar-sized fish. There was also a positive effect of water temperature on eDNA concentrations, which reinforces the need to control for such abiotic factors. We conclude that there is strong utility in applying eDNA concentrations as an index of relative abundance for mulloway under controlled conditions, which justifies future field-based investigations.

Signal and noise in metabarcoding data

Metabarcoding is a powerful molecular tool for simultaneously surveying hundreds to thousands of species from a single sample, underpinning microbiome and environmental DNA (eDNA) methods. Deriving quantitative estimates of underlying biological communities from metabarcoding is critical for enhancing the utility of such approaches for health and conservation. Recent work has demonstrated that correcting for amplification biases in genetic metabarcoding data can yield quantitative estimates of template DNA concentrations. However, a major source of uncertainty in metabarcoding data stems from non-detections across technical PCR replicates where one replicate fails to detect a species observed in other replicates. Such non-detections are a special case of variability among technical replicates in metabarcoding data. While many sampling and amplification processes underlie observed variation in metabarcoding data, understanding the causes of non-detections is an important step in distinguishing signal from noise in metabarcoding studies. Here, we use both simulated and empirical data to 1) suggest how non-detections may arise in metabarcoding data, 2) outline steps to recognize uninformative data in practice, and 3) identify the conditions under which amplicon sequence data can reliably detect underlying biological signals. We show with both simulations and empirical data that, for a given species, the rate of non-detections among technical replicates is a function of both the template DNA concentration and species-specific amplification efficiency. Consequently, we conclude metabarcoding datasets are strongly affected by (1) deterministic amplification biases during PCR and (2) stochastic sampling of amplicons during sequencing-both of which we can model-but also by (3) stochastic sampling of rare molecules prior to PCR, which remains a frontier for quantitative metabarcoding. Our results highlight the importance of estimating species-specific amplification efficiencies and critically evaluating patterns of non-detection in metabarcoding datasets to better distinguish environmental signal from the noise inherent in molecular detections of rare targets.

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.

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.

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.

Similarities and Differences in Fish Community Composition Accessed by Electrofishing, Gill Netting, Seining, Trawling, and Water eDNA Metabarcoding in Temperate Reservoirs

It is difficult to understand the composition and diversity of biological communities in complex and heterogeneous environments using traditional sampling methods. Recently, developments in environmental DNA metabarcoding have emerged as a powerful, non-invasive method for comprehensive community characterization and biodiversity monitoring in different types of aquatic ecosystems. In this study, water eDNA targeting fish (wf-eDNA) and four traditional fish sampling methods (electrofishing, gill netting, seining, trawling) were compared to evaluate the reliability and efficiency of wf-eDNA (vertebrate mitochondrial 12S ribosomal RNA (rRNA) as an alternative approach to assess the diversity and composition of freshwater fish communities. The results of wf-eDNA showed a consistency between the traditional sampling methods regarding species detection. However, some fish species detected using wf-eDNA assay were not detected using traditional sampling methods and vice versa. Comparison of wf-eDNA and traditional sampling methods revealed spatial homogeneity in fish community composition in all reservoirs. Ordination analysis showed that the wf-eDNA approach covers all traditional sampling methods and occupies an intermediate position. In addition, based on the Shannon diversity index, we found that in one reservoir the wf-eDNA method yielded similar fish community diversity to traditional sampling methods. However, in other reservoirs, the calculated Shannon diversity index of the wf-eDNA method was significantly higher than traditional sampling methods. In general, significant positive correlations were found between the wf-eDNA method and almost all traditional sampling methods. We conclude that wf-eDNA seems to be a reliable and complementary approach for biomonitoring and ecosystem management of freshwater ichthyofauna.

Complementary molecular and visual sampling of fish on oil and gas platforms provides superior biodiversity characterisation

Offshore oil and gas platforms have the potential to provide complex refugia for fish and benthic colonisers. We compare two methods of biodiversity assessment for fish and elasmobranchs at seven decommissioned oil and gas platforms as well as five sediment sites, located 5 km from platforms, in the Gulf of Thailand. Using surveys from stereo-video ROV transects, and data from Environmental DNA (eDNA) water-column samples, we detected fish and elasmobranch taxa from 39 families and 66 genera across both platform and sediment sites with eDNA, compared with 18 families and 29 genera by stereo-ROV with platforms yielding significantly greater species richness. This study demonstrates that the combination of stereo-video ROV and eDNA provide effective, non-extractive and complementary methods to enhance data capture. This approach sets new benchmarks for evaluating fish assemblages surrounding platforms and will enhance measurements of biota to inform decisions on the fate of oil/gas infrastructure.

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.

eDNA in subterranean ecosystems: Applications, technical aspects, and future prospects

Monitoring of biota is pivotal for the assessment and conservation of ecosystems. Environments worldwide are being continuously and increasingly exposed to multiple adverse impacts, and the accuracy and reliability of the biomonitoring tools that can be employed shape not only the present, but more importantly, the future of entire habitats. The analysis of environmental DNA (eDNA) metabarcoding data provides a quick, affordable, and reliable molecular approach for biodiversity assessments. However, while extensively employed in aquatic and terrestrial surface environments, eDNA-based studies targeting subterranean ecosystems are still uncommon due to the lack of accessibility and the cryptic nature of these environments and their species. Recent advances in genetic and genomic analyses have established a promising framework for shedding new light on subterranean biodiversity and ecology. To address current knowledge and the future use of eDNA methods in groundwaters and caves, this review explores conceptual and technical aspects of the application and its potential in subterranean systems. We briefly introduce subterranean biota and describe the most used traditional sampling techniques. Next, eDNA characteristics, application, and limitations in the subsurface environment are outlined. Last, we provide suggestions on how to overcome caveats and delineate some of the research avenues that will likely shape this field in the near future. We advocate that eDNA analyses, when carefully conducted and ideally combined with conventional sampling techniques, will substantially increase understanding and enable crucial expansion of subterranean community characterisation. Given the importance of groundwater and cave ecosystems for nature and humans, eDNA can bring to the surface essential insights, such as study of ecosystem assemblages and rare species detection, which are critical for the preservation of life below, as well as above, the ground.

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.

From Cave Dragons to Genomics: Advancements in the Study of Subterranean Tetrapods

Throughout most of the kingdom Animalia, evolutionary transitions from surface life to a life permanently bound to caves and other subterranean habitats have occurred innumerous times. Not so in tetrapods, where a mere 14 cave-obligate species-all plethodontid and proteid salamanders-are known. We discuss why cave tetrapods are so exceptional and why only salamanders have made the transition. Their evolution follows predictable and convergent, albeit independent pathways. Among the many known changes associated with transitions to subterranean life, eye degeneration, starvation resistance, and longevity are especially relevant to human biomedical research. Recently, sequences of salamander genomes have become available opening up genomic research for cave tetrapods. We discuss new genomic methods that can spur our understanding of the evolutionary mechanisms behind convergent phenotypic change, the relative roles of selective and neutral evolution, cryptic species diversity, and data relevant for conservation such as effective population size and demography.

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.

Using eDNA techniques to find the endangered big-headed turtle (Platysternon megacephalum)

We evaluate the efficacy of environmental DNA (eDNA) techniques to locate wild populations and estimate the population size of the endangered big-headed turtle (Platysternon megacephalum) in Hong Kong. The results from this study are important for identifying priority sites for protection and further research. Additionally, we assess the impact of two environmental variables (temperature and pH) on eDNA quantity. We surveyed 34 streams for three years, sampling four times each year. Four new populations were first identified with eDNA analysis, and then verified by field surveys. Our multi-year survey highlights that eDNA detection can be inconsistent over time, even in streams with known populations. There was no significant relationship between eDNA quantity and the environmental variables tested. Lastly, our results suggest that eDNA methods remain promising to estimate population size, since number of positive detections were positively correlated with population size in streams with known populations. We conclude that eDNA methods are powerful, but care must be taken when interpreting field results as they are affected by species ecology and environmental conditions.

Monitoring newt communities in urban area using eDNA metabarcoding

Newts are amphibians commonly present in small ponds or garden pools in urban areas. They are protected in many countries and their presence is monitored through visual observation and/or trapping. However, newts are not easy to spot as they are small, elusive and often hidden at the bottom of water bodies. In recent years, environmental DNA (eDNA) has become a popular tool for detecting newts, with a focus on individual species using qPCR assays. Here, we assess the effectiveness of eDNA metabarcoding compared to conventional visual surveys of newt diversity in 45 ponds within urban areas of Geneva canton, Switzerland. We designed newt-specific mitochondrial 16S rRNA primers, which assign the majority of amplicons to newts, and were able to detect four species known to be present in the region, including the invasive subspecies Lissotriton vulgaris meridionalis, native to the Italian peninsula, that has been introduced in the Geneva area recently. The obtained eDNA results were congruent overall with conventional surveys, confirming the morphological observations in the majority of cases (67%). In 25% of cases, a species was only detected genetically, while in 8% of cases, the observations were not supported by eDNA metabarcoding. Our study confirms the usefulness of eDNA metabarcoding as a tool for the effective and non-invasive monitoring of newt community and suggests its broader use for the survey of newt diversity in urban area at larger scales.

A New Approach to Evaluate and Reduce Uncertainty of Model-Based Biodiversity Projections for Conservation Policy Formulation

Biodiversity projections with uncertainty estimates under different climate, land-use, and policy scenarios are essential to setting and achieving international targets to mitigate biodiversity loss. Evaluating and improving biodiversity predictions to better inform policy decisions remains a central conservation goal and challenge. A comprehensive strategy to evaluate and reduce uncertainty of model outputs against observed measurements and multiple models would help to produce more robust biodiversity predictions. We propose an approach that integrates biodiversity models and emerging remote sensing and in-situ data streams to evaluate and reduce uncertainty with the goal of improving policy-relevant biodiversity predictions. In this article, we describe a multivariate approach to directly and indirectly evaluate and constrain model uncertainty, demonstrate a proof of concept of this approach, embed the concept within the broader context of model evaluation and scenario analysis for conservation policy, and highlight lessons from other modeling communities.

Integrating physiology and environmental dynamics to operationalize environmental DNA (eDNA) as a means to monitor freshwater macro-organism abundance

Research has demonstrated consistent positive correlations between organism abundance and absolute environmental DNA (eDNA) concentrations. Robust correlations in laboratory experiments indicate strong functional links, suggesting the potential for eDNA to monitor organism abundance in nature. However, correlations between absolute eDNA concentrations and organism abundance in nature tend to be weaker because myriad biotic and abiotic factors influence steady-state eDNA concentrations, decoupling its direct functional link with abundance. Additional technical challenges can also weaken correlations between relative organism abundance and relative eDNA data derived from metabarcoding. Future research must account for these factors to improve the inference of organism abundance from eDNA, including integrating the effects of organism physiology on eDNA production, eDNA dynamics in lentic/lotic systems, and key environmental parameters that impact estimated steady-state concentrations. Additionally, it is critical to manage expectations surrounding the accuracy and precision that eDNA can provide - eDNA, for example, cannot provide abundance estimates comparable to intensively managed freshwater fisheries that enumerate every individual fish. Recent developments, however, are encouraging. Current methods could provide meaningful information regarding qualitative conservation thresholds and emergent research has demonstrated that eDNA concentrations in natural ecosystems can provide rough quantitative estimates of abundance, particularly when models integrate physiology and/or eDNA dynamics. Operationalizing eDNA to infer abundance will probably require more than simple correlations with organism biomass/density. Nevertheless, the future is promising - models that integrate eDNA dynamics in nature could represent an effective means to infer abundance, particularly when traditional methods are considered too "costly" or difficult to obtain.

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.

A workflow for the relative quantification of multiple fish species from oceanic water samples using environmental DNA (eDNA) to support large-scale fishery surveys

While the number of published marine studies using environmental DNA (eDNA) has increased substantially in recent years, marine fish surveys are still scarce. To examine the potential for eDNA to support marine fisheries monitoring surveys, we optimized an eDNA isolation method, developed a multispecies assay and tested it on eDNA samples collected along the Pacific coast of the United States. Four commercial DNA extraction kits that exploit the capability of the nucleic acids binding a solid phase (two using a silica matrix and two magnetic beads) as well an organic separation method were tested. A species-specific multiplex qPCR assay was developed and tested to simultaneously target Pacific hake (Merluccius productus), Pacific lamprey (Entosphenus tridentatus) and eulachon (Thaleichthys pacificus). The specificity of the assay was tested in silico, in vitro and in natura. Environmental DNA isolation using phenol:chloroform:isoamyl purification with a phase lock was optimized and yielded the highest amount of total and target DNA and was used to extract 46 marine water samples for the detection of the three species of interest. The multiplex qPCR assay used in the quantification process was also optimized to provide convenience and accuracy. Pacific hake was present in 44% of the eDNA samples while the other two species were absent. Here, we present a complete workflow for the simultaneous detection and quantification of multiple marine fish species using eDNA. This workflow supports large-scale at-sea sampling efforts with preservation at ambient temperatures and has demonstrated DNA extraction efficiency and reliability. The multiplex qPCR assay is shown to be sensitive and specific for the purposes of simultaneously monitoring the relative abundance of multiple targeted fish species.

Persistence and accumulation of environmental DNA from an endangered dragonfly

Detection of environmental DNA (eDNA) has become a commonly used surveillance method for threatened or invasive vertebrates in both aquatic and terrestrial environments. However, most studies in this field favor vertebrate target species. Environmental DNA protocols can be especially useful for endangered invertebrates such as the Hine’s emerald dragonfly (Somatochlora hineana) where conservation efforts have been greatly hindered by training, time, overall costs, and environmental impacts associated with conducting surveys in the calcareous fens occupied by this species. An essential step in developing such a protocol is to evaluate the dynamics of eDNA concentration under controlled conditions. We used the quantitative polymerase chain reaction (qPCR) to examine seasonal shifts in the persistence and net-accumulation of eDNA from captive S. hineana larvae in experimental mesocosms at temperatures corresponding with their overwintering (5.0 °C) and active (16.0 °C) seasons. Environmental DNA persisted longer at 5.0 °C but accumulated more readily at 16.0 °C. Differences in the accumulation and persistence of eDNA reflect differences in the longevity of eDNA at different temperatures and seasonal differences in larval S. hineana behavior. This study highlights the importance of considering how seasonal changes in temperature influence not only the speed of eDNA degradation but also the target species’ eDNA shedding rates.

Development of a Quantitative PCR Assay for Four Salmon Species Inhabiting the Yangyangnamdae River Using Environmental DNA

Simple Summary

Regular surveys provide essential information to establish strategies for the effective conservation of salmon resources. As an alternative to conventional fish surveys, which are costly and laborious, quantitative PCR (qPCR) assays were established for the analysis of four salmon species inhabiting the Korean Peninsula. We designed four species-specific primer sets that showed high specificity and sensitivity in both tissue and environmental DNA (eDNA) samples collected from the Yangyangnamdae River. After normalization for PCR inhibition in each sample, the established qPCR assays produced standardized and realistic eDNA profiles for the four salmon species, suggesting that the newly developed qPCR assays are a useful tool for the management of Oncorhynchus resources in Korean waters.

Abstract

A species-specific quantitative PCR (qPCR) assay using environmental DNA (eDNA) is a promising tool for both qualitative and quantitative analyses of target species directly from water samples. Despite its reliability, an eDNA-based qPCR assay pipeline has not yet developed to monitor salmon species inhabiting Korean waters, which have been rapidly decreasing. We designed species-specific primers for four Oncorhynchus species inhabiting the eastern coastal waters along the Korean Peninsula. These include primers for two native species (Oncorhynchus keta and O. masou) and two that were introduced (O. mykiss and O. kisutch). The limit of detection and limit of quantification for the four qPCR assays ranged from 4.11 to 10.38 copies and from 30 to 81 copies, respectively, indicating a high sensitivity and specificity across all four species. Following optimization, the qPCR assays were used for the quantitative analyses of the four Oncorhynchus species in the Yangyangnamdae River during the spawning and non-spawning seasons in the year 2019–2020, one of the main rivers where salmon migrate during the spawning season in Korea. The raw copy numbers in all of the examined samples were normalized by PCR inhibition rates to standardize and compare with other studies. Among the four Oncorhynchus species examined, the eDNA concentration of O. keta increased significantly (63.60-fold, p < 0.0001) during the spawning season (November) compared with that in the non-spawning season (March), suggesting that O. keta is the main salmon species migrating through the Yangyangnamdae River. In contrast, we did not detect any differences in eDNA concentration for the other three Oncorhynchus species between the spawning and non-spawning seasons, indicating that their presence does not alter during the year. Their eDNA concentration is also relatively low compared to O. keta, which suggests that small numbers of these three species are present in the river. Overall, these newly developed qPCR assays represent useful monitoring tools for the management of four salmon species in Korean waters.

Advanced molecular-based surveillance of quagga and zebra mussels: A review of environmental DNA/RNA (eDNA/eRNA) studies and considerations for future directions

Sensitive methods, capable of rapidly and accurately detecting aquatic invasive species, are in demand. Molecular-based approaches, such as environmental DNA (eDNA) surveys, satisfy these requirements and have grown in popularity. As such, eDNA surveys could aid the effort to combat the colonisation and spread of two notoriously invasive freshwater mussel species, the quagga mussel (Dreissena rostriformis bugensis) and zebra mussel (D. polymorpha), through improved surveillance ability. Here, we provide a review of dreissenid eDNA literature (both grey and published), summarising efforts involved in the development of various assays for use in multiple different technologies (e.g. quantitative PCR, high-throughput sequencing and loop-mediated isothermal amplification) and sampling scenarios. We discuss important discoveries made along the way, including novel revelations involving environmental RNA (eRNA), as well as the advantages and limitations of available methods and instrumentation. In closing, we highlight critical remaining gaps, where further investigation could lead to advancements in dreissenid monitoring capacity.

Monthly eDNA Monitoring of an Invasive Bryozoan, Bugulina californica, in Seawater Using Species-Specific Markers

Simple Summary

Bugulina californica, marine invasive bryozoan, is hard to monitor the biomass and presence because of their habitat in underwater. Additionally, they have life stage difficult to find such as larva, and we need an effective survey method to detect whole life stages for monitoring early invasion stage. Therefore, we tried to applied environmental DNA to monitor the monthly changes of B. californica in harbors of Korea. We collect seawater environmental samples and developed a molecular target species detection method to detect B. californica DNA of monthly changes. We analyzed the environmental samples using our molecular markers and calculated the DNA copies. We determined method of environmental DNA assay as effectiveness survey technique for marine invasive species which has a non-visual life stage and spatial changes of whole biomass.

Abstract

Environmental DNA (eDNA) method used by many ecologists as effective investigation tool can detect endangered species, rare species, and invasive species. In case of invasive species, eDNA method help to monitor the target species when the species was hard to detect through the traditional survey such as the early stage of invasion, low abundance, and larva or juvenile stage. The bryozoan, Bugulina californica, was known as a marine fouling invasive species in Korea since its first reported in 1978. This species expanded nationwide, and damages to ascidian aquaculture through attached on the ship hulls and artificial facilities. To monitor the distribution and biomass of invasive bryozoan, B. californica, the qPCR analysis of environmental DNA was performed on seawater samples from 12 harbors. In this study, we designed species-specific markers which can calculate the detected DNA copies of B. californica, and the presence and monitoring of this species can be more accurately estimated by environmental DNA analysis than by traditional survey, in which it is difficult to identify the species. Real-time PCR analysis using environmental DNA is an effective monitoring method that can determine both the distribution and the monthly change in biomass of B. californica in Korea.

Environmental DNA metabarcoding primers for freshwater fish detection and quantification: In silico and in tanks

Environmental DNA (eDNA) techniques refer to utilizing the organisms' DNA extracted from environment samples to genetically identify target species without capturing actual organisms. eDNA metabarcoding via high-throughput sequencing can simultaneously detect multiple fish species from a single water sample, which is a powerful tool for the qualitative detection and quantitative estimates of multiple fish species. However, sequence counts obtained from eDNA metabarcoding may be influenced by many factors, of which primer bias is one of the foremost causes of methodological error. The performance of 18 primer pairs for COI, cytb, 12S rRNA, and 16S rRNA mitochondrial genes, which are all frequently used in fish eDNA metabarcoding, were evaluated in the current study. The ribosomal gene markers performed better than the protein-coding gene markers during in silico screening, resulting in higher taxonomic coverage and appropriate barcode lengths. Four primer pairs-AcMDB07, MiFish-U, Ve16S1, and Ve16S3-designed for various regions of the 12S and 16S rRNA genes were screened for tank metabarcoding in a case study targeting six freshwater fish species. The four primer pairs were able to accurately detect all six species in different tanks, while only MiFish-U, Ve16S1, and Ve16S3 revealed a significant positive relationship between species biomass and read count for the pooled tank data. The positive relationship could not be found in all species within the tanks. Additionally, primer efficiency differed depending on the species while primer preferential species varied in different fish assemblages. This case study supports the potential for eDNA metabarcoding to assess species diversity in natural ecosystems and provides an alternative strategy to evaluate the performance of candidate primers before application of eDNA metabarcoding in natural ecosystems.

Two hundred years of zooplankton vertical migration research

Vertical migration is a geographically and taxonomically widespread behaviour among zooplankton that spans across diel and seasonal timescales. The shorter-term diel vertical migration (DVM) has a periodicity of up to 1 day and was first described by the French naturalist Georges Cuvier in 1817. In 1888, the German marine biologist Carl Chun described the longer-term seasonal vertical migration (SVM), which has a periodicity of ca. 1 year. The proximate control and adaptive significance of DVM have been extensively studied and are well understood. DVM is generally a behaviour controlled by ambient irradiance, which allows herbivorous zooplankton to feed in food-rich shallower waters during the night when light-dependent (visual) predation risk is minimal and take refuge in deeper, darker waters during daytime. However, DVMs of herbivorous zooplankton are followed by their predators, producing complex predator-prey patterns that may be traced across multiple trophic levels. In contrast to DVM, SVM research is relatively young and its causes and consequences are less well understood. During periods of seasonal environmental deterioration, SVM allows zooplankton to evacuate shallower waters seasonally and take refuge in deeper waters often in a state of dormancy. Both DVM and SVM play a significant role in the vertical transport of organic carbon to deeper waters (biological carbon sequestration), and hence in the buffering of global climate change. Although many animal migrations are expected to change under future climate scenarios, little is known about the potential implications of global climate change on zooplankton vertical migrations and its impact on the biological carbon sequestration process. Further, the combined influence of DVM and SVM in determining zooplankton fitness and maintenance of their horizontal (geographic) distributions is not well understood. The contrasting spatial (deep versus shallow) and temporal (diel versus seasonal) scales over which these two migrations occur lead to challenges in studying them at higher spatial, temporal and biological resolution and coverage. Extending the largely population-based vertical migration knowledge base to individual-based studies will be an important way forward. While tracking individual zooplankton in their natural habitats remains a major challenge, conducting trophic-scale, high-resolution, year-round studies that utilise emerging field sampling and observation techniques, molecular genetic tools and computational hardware and software will be the best solution to improve our understanding of zooplankton vertical migrations.

Amazonian mammal monitoring using aquatic environmental DNA

Environmental DNA (eDNA) metabarcoding has emerged as one of the most efficient methods to assess aquatic species presence. While the method can in theory be used to investigate nonaquatic fauna, its development for inventorying semi-aquatic and terrestrial fauna is still at an early stage. Here we investigated the potential of aquatic eDNA metabarcoding for inventorying mammals in Neotropical environments, be they aquatic, semi-aquatic or terrestrial. We collected aquatic eDNA in 96 sites distributed along three Guianese watersheds and compared our inventories to expected species distributions and field observations derived from line transects located throughout French Guiana. Species occurrences and emblematic mammalian fauna richness patterns were consistent with the expected distribution of fauna and our results revealed that aquatic eDNA metabarcoding brings additional data to line transect samples for diurnal nonaquatic (terrestrial and arboreal) species. Aquatic eDNA also provided data on species not detectable in line transect surveys such as semi-aquatic, aquatic and nocturnal terrestrial and arboreal species. Although the application of eDNA to inventory mammals still needs some developments to optimize sampling efficiency, it can now be used as a complement to traditional surveys.

Estimation of tuna population by the improved analytical pipeline of unique molecular identifier-assisted HaCeD-Seq (haplotype count from eDNA)

Many studies have investigated the ability to identify species from environmental DNA (eDNA). However, even when individual species are identified, the accurate estimation of their abundances by traditional eDNA analyses has been still difficult. We previously developed a novel analytical method called HaCeD-Seq (Haplotype Count from eDNA), which focuses on the mitochondrial D-loop sequence. The D-loop is a rapidly evolving sequence and has been used to estimate the abundance of eel species in breeding water. In the current study, we have further improved this method by applying unique molecular identifier (UMI) tags, which eliminate the PCR and sequencing errors and extend the detection range by an order of magnitude. Based on this improved HaCeD-Seq pipeline, we computed the abundance of Pacific bluefin tuna (Thunnus orientalis) in aquarium tanks at the Tokyo Sea Life Park (Kasai, Tokyo, Japan). This tuna species is commercially important but is at high risk of resource depletion. With the developed UMI tag method, 90 out of 96 haplotypes (94%) were successfully detected from Pacific bluefin tuna eDNA. By contrast, only 29 out of 96 haplotypes (30%) were detected when UMI tags were not used. Our findings indicate the potential for conducting non-invasive fish stock surveys by sampling eDNA.

Spatial Heterogeneity of eDNA Transport Improves Stream Assessment of Threatened Salmon Presence, Abundance, and Location

The integration of environmental DNA (eDNA) within management strategies for lotic organisms requires translating eDNA detection and quantification data into inferences of the locations and abundances of target species. Understanding how eDNA is distributed in space and time within the complex environments of rivers and streams is a major factor in achieving this translation. Here we study bidimensional eDNA signals in streams to predict the position and abundance of Atlantic salmon (Salmo salar) juveniles. We use data from sentinel cages with a range of abundances (3–63 juveniles) that were deployed in three coastal streams in New Brunswick, Canada. We evaluate the spatial patterns of eDNA dispersal and determine the effect of discharge on the dilution rate of eDNA. Our results show that eDNA exhibits predictable plume dynamics downstream from sources, with eDNA being initially concentrated and transported in the midstream, but eventually accumulating in stream margins with time and distance. From these findings we developed a fish detection and distribution prediction model based on the eDNA ratio in midstream versus bankside sites for a variety of fish distribution scenarios. Finally, we advise that sampling midstream at every 400 m is sufficient to detect a single fish at low velocity, but sampling efforts need to be increased at higher water velocity (every 100 m in the systems surveyed in this study). Studying salmon eDNA spatio-temporal patterns in lotic environments is essential to developing strong quantitative population assessment models that successfully leverage eDNA as a tool to protect salmon populations.

Exploring the Use of Environmental DNA (eDNA) to Detect Animal Taxa in the Mesopelagic Zone

Animal biodiversity in the ocean’s vast mesopelagic zone is relatively poorly studied due to technological and logistical challenges. Environmental DNA (eDNA) analyses show great promise for efficiently characterizing biodiversity and could provide new insight into the presence of mesopelagic species, including those that are missed by traditional net sampling. Here, we explore the utility of eDNA for identifying animal taxa. We describe the results from an August 2018 cruise in Slope Water off the northeast United States. Samples for eDNA analysis were collected using Niskin bottles during five CTD casts. Sampling depths along each cast were selected based on the presence of biomass as indicated by the shipboard Simrad EK60 echosounder. Metabarcoding of the 18S V9 gene region was used to assess taxonomic diversity. eDNA metabarcoding results were compared with those from net-collected (MOCNESS) plankton samples. We found that the MOCNESS sampling recovered more animal taxa, but the number of taxa detected per liter of water sampled was significantly higher in the eDNA samples. eDNA was especially useful for detecting delicate gelatinous animals which are undersampled by nets. We also detected eDNA changes in community composition with depth, but not with sample collection time (day vs. night). We provide recommendations for applying eDNA-based methods in the mesopelagic including the need for studies enabling interpretation of eDNA signals and improvement of barcode reference databases.