Can environmental DNA (eDNA) be used for detection and monitoring of introduced crab species in the Baltic Sea?

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.

Development of a real-time PCR (qPCR) method for the identification of the invasive paddle crab Charybdis japonica (Crustacea, Portunidae)

Crabs can be transported beyond their native range via anthropogenic-mediated means such as aquarium trade, live seafood trade and shipping. Once introduced into new locations, they can establish persisting populations and become invasive, often leading to negative impacts on the recipient environment and native species. Molecular techniques are increasingly being used as complementary tools in biosecurity surveillance and monitoring plans for invasive species. Molecular tools can be particularly useful for early detection, rapid identification and discrimination of closely related species, including when diagnostic morphological characters are absent or challenging, such as early life stages, or when only part of the animal is available. In this study, we developed a species-specific qPCR assay, which targets the cytochrome c oxidase subunit 1 (CO1) region of the Asian paddle crab Charybdis japonica. In Australia, as well as many parts of the world, this species is considered invasive and routine biosecurity surveillance is conducted to reduce the risk of establishment. Through rigorous testing of tissue from target and non-target species we demonstrate that this assay is sensitive enough to detect as little as two copies per reaction and does not cross amplify with other closely related species. Field samples and environmental samples spiked with C. japonica DNA in high and low concentrations indicate that this assay is also a promising tool for detecting trace amounts of C. japonica eDNA in complex substrates, making it a useful complementary tool in marine biosecurity assessments.

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

Background

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

Methods

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

Results

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

Conclusion

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

Exploring the eDNA dynamics of the host-pathogen pair Pacifastacus leniusculus (Decapoda) and Aphanomyces astaci (Saprolegniales) under experimental conditions

The oomycete Aphanomyces astaci causes crayfish plague, a disease threatening native European crayfish. It is carried and transmitted by American crayfish species, which are the original hosts of A. astaci. In recent years, environmental DNA (eDNA) methods have been successfully implemented to monitor the spread of both A. astaci and its hosts. However, still little is known about how population density and other environmental factors influence the detectability of this host-pathogen complex. In a mesocosm experiment, we tested the influence of crayfish density, temperature and food availability on the detectability of eDNA for A. astaci and its host, signal crayfish Pacifastacus leniusculus. We also compared eDNA results with crayfish population density measured by catch per unit effort (CPUE) from two lakes with varying crayfish density and A. astaci prevalence. The mesocosm experiment revealed that a limited set of controlled factors can substantially change the detectable amount of eDNA, even though the physical presence of the target organisms remains the same. In cold, clear water, eDNA quantities of both targets increased far more than in a linear fashion with increased crayfish density. However, the presence of food decreased the detectability of crayfish eDNA, presumably through increased microbial-induced eDNA degradation. For A. astaci, where eDNA typically represents living spores, food did not affect the detectability. However, high water temperature strongly reduced it. The increased complexity and variability of factors influencing eDNA concentration under natural conditions, compared to a controlled experimental environment, suggests that establishing a reliable relationship between eDNA quantities and crayfish density is difficult to achieve. This was also supported by field data, where we found minimal correspondence between eDNA quantity and CPUE data. A comparison between quantitative real-time PCR (qPCR) analysis and droplet-digital PCR (ddPCR) analysis revealed higher detection success of the targets in field samples when using qPCR. Overall, our results support eDNA as an effective tool for presence-absence monitoring, but it seems less suited for biomass quantification and population density estimates. Detection of A. astaci and P. leniusculus is not influenced uniformly by respective environmental factors. Consequently, we recommend a strategy of monitoring both targets, where the detection of one may point towards the presence of the other.

Developing an effective marine eDNA monitoring: eDNA detection at pre-outbreak densities of corallivorous seastar (Acanthaster cf. solaris)

Outbreaks of the corallivorous Crown-of-Thorns Seastar (CoTS) Acanthaster cf. solaris contribute significantly to coral reef loss. Control of outbreaks is hampered because standard monitoring techniques do not detect outbreaks at early (low density) stages, thus preventing early intervention. We previously demonstrated that eDNA monitoring can detect CoTS at intermediate densities. Here, we test whether detection probability can be improved by (i) targeted site selection or collection at specific times and (ii) moving from an average eDNA copy number approach (based on the limit of quantification) to a presence/absence approach (based on the limit of detection). Using a dataset collected over three years and multiple reef sites, we demonstrated that adding water residence age, sea surface level and temperature into generalized linear models explained low amounts of variance of eDNA copy numbers. Site specific CoTS density, by contrast, was a significant predictor for eDNA copy numbers. Bayesian multi-scale occupancy modelling of the presence/absence data demonstrated that the probability of sample capture (θ) on most reefs with intermediate or high CoTS densities was >0.8. Thus, confirming CoTS presence on these reefs would only require 2-3 samples. Sample capture decreased with decreasing CoTS density. Collecting ten filters was sufficient to reliably (based on the lower 95 % Credibility Interval) detect CoTS below nominal outbreak levels (3 Ind. ha^-1). Copy number-based estimates may be more relevant to quantify CoTS at higher densities. Although water residence age did contribute little to our models, sites with higher residence times may serve as sentinel sites accumulating eDNA. The approach based on presence or absence of eDNA facilitates eDNA monitoring to detect CoTS densities below outbreak thresholds and we continue to further develop this method for quantification.

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.

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

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

Fish Diversity Monitored by Environmental DNA in the Yangtze River Mainstream

Surveys and assessments based on environmental DNA are not only efficient and time-saving, but also cause less harm to monitoring targets. Environmental DNA has become a common tool for the assessment and monitoring of aquatic organisms. In this study, we investigated fish resources in the Yangtze River mainstream using environmental DNA, and the variations in fish during two seasons (spring and autumn) were compared. The results showed that 13 species were identified in spring, and nine species of fish were identified in autumn. The fish with higher eDNA detection were Sinibotia superciliaris, Tachysurus fulvidraco, Cyprinus carpio, Ctenopharyngodon Idella, Monopterus albus, Acanthogobius hasta, Saurogobio dabryi, Oncorhynchus mykiss, Mugil cephalus, Odontamblyopus rubicundus. Seasonal variation between spring and autumn was not significant, and the environmental factors had different effects on fish assemblages during the two seasons. Our study used the eDNA technique to monitor the composition of fish in the spring and autumn in the Yangtze River mainstream, providing a new technology for the long-term management and protection of fishery resources in the region. Of course, problems such as pollution and insufficient databases are the current shortcomings of environmental DNA, which will be the focus of our future research and study.

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.

Complex interactions between environmental DNA (eDNA) state and water chemistries on eDNA persistence suggested by meta-analyses

Understanding the processes of environmental DNA (eDNA) persistence and degradation is essential to determine the spatiotemporal scale of eDNA signals and accurately estimate species distribution. The effects of environmental factors on eDNA persistence have previously been examined; however, the influence of the physiochemical and molecular states of eDNA on its persistence is not completely understood. Here, we performed meta-analyses including 26 previously published papers on the estimation of first-order eDNA decay rate constants, and assessed the effects of filter pore size, DNA fragment size, target gene, and environmental conditions on eDNA decay rates. Almost all supported models included the interactions between the filter pore size and water temperature, between the target gene and water temperature, and between the target gene and water source, implying the influence of complex interactions between the eDNA state and environmental conditions on eDNA persistence. These findings were generally consistent with the results of a reanalysis of a previous tank experiment which measured the time-series changes in marine fish eDNA concentrations in multiple size fractions after fish removal. Our results suggest that the mechanism of eDNA persistence and degradation cannot be fully understood without knowing not only environmental factors but also cellular and molecular states of eDNA in water. Further verification of the relationship between eDNA state and persistence is required by obtaining more information on eDNA persistence in various experimental and environmental conditions, which will enhance our knowledge on eDNA persistence and support our findings.

Seasonal Variation and Assessment of Fish Resources in the Yangtze Estuary Based on Environmental DNA

In the past few years, environmental DNA (eDNA) techniques have been used to monitor marine communities. Research indicates that eDNA is an effective tool for monitoring fishery resources. This study analyzed the seasonal variations in fish resources in the Yangtze Estuary, China, using eDNA. A total of 103 water samples were collected from the Yangtze Estuary across the four seasons in 2019—20 samples in February, 28 in May, 28 in August and 27 in November. Our research successfully detected the fishery resources of the Yangtze Estuary. We found significant differences according to the season. The results showed that 59 species were identified in 2019 (20 in February, 16 in May, 5 in August and 45 in November) and fish species varied widely over the four seasons. Furthermore, our samples revealed significant differences in annual fish stocks in the Yangtze Estuary, compared with eDNA data from 2018 and with traditional surveys from past years. Overall, eDNA is a useful emerging tool to assist with monitoring and protecting fish resources for the Yangtze Estuary.

Simultaneous detection of native and invasive crayfish and Aphanomyces astaci from environmental DNA samples in a wide range of habitats in Central Europe

Crayfish of North American origin are amongst the most prominent high-impact invasive invertebrates in European freshwaters. They contribute to the decline of European native crayfish species by spreading the pathogen causing crayfish plague, the oomyceteAphanomyces astaci. In this study we validated the specificity of four quantitative PCR (qPCR) assays, either published or newly developed, usable for environmental DNA (eDNA) screening for widely distributed native and non-native crayfish present in Central Europe:Astacus astacus,Pacifastacus leniusculus,Faxonius limosusandProcambarus virginalis. We then conducted an eDNA monitoring survey of these crayfish as well as the crayfish plague pathogen in a wide variety of habitat types representative for Central and Western Europe. The specificity of qPCR assays was validated against an extensive collection of crayfish DNA isolates, containing most crayfish species documented from European waters. The three assays developed in this study were sufficiently species-specific, but the published assay forF. limosusdisplayed a weak cross-reaction with multiple other crayfish species of the family Cambaridae. In the field study, we infrequently detected eDNA ofA. astacitogether with the three non-native crayfish species under examination. We never detected eDNA fromA. astacitogether with native crayfish, but in a few locations eDNA from both native and non-native crayfish was captured, due either to passive transport of eDNA from upstream populations or co-existence in the absence of infected crayfish carriers ofA. astaci. In the study, we evaluated a robust, easy-to-use and low-cost version of the eDNA sampling equipment, based mostly on items readily available in garden stores and hobby markets, for filtering relatively large (~5 l) water samples. It performed just as well as the far more expensive equipment industrially designed for eDNA water sampling, thus opening the possibility of collecting suitable eDNA samples to a wide range of stakeholders. Overall, our study confirms that eDNA-based screening for crayfish and their associated pathogen is a feasible alternative to traditional monitoring.

eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystem

Environmental DNA (eDNA) metabarcoding, a technique for retrieving multispecies DNA from environmental samples, can detect a diverse array of marine species from filtered seawater samples. There is a growing potential to integrate eDNA alongside existing monitoring methods in order to establish or improve the assessment of species diversity. Remote island reefs are increasingly vulnerable to climate-related threats and as such there is a pressing need for cost-effective whole-ecosystem surveying to baseline biodiversity, study assemblage changes and ultimately develop sustainable management plans. We investigated the utility of eDNA metabarcoding as a high-resolution, multitrophic biomonitoring tool at the Cocos (Keeling) Islands, Australia (CKI)-a remote tropical coral reef atoll situated within the eastern Indian Ocean. Metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes, as well as the 18S rRNA nuclear gene, were applied to 252 surface seawater samples collected from 42 sites within a 140 km² area. Our assays successfully detected a wide range of bony fish and elasmobranchs (244 taxa), crustaceans (88), molluscs (37) and echinoderms (7). Assemblage composition varied significantly between sites, reflecting habitat partitioning across the island ecosystem and demonstrating the localisation of eDNA signals, despite extensive tidal and oceanic movements. In addition, we document putative new occurrence records for 46 taxa and compare the efficiency of our eDNA approach to visual survey techniques at CKI. Our study demonstrates the utility of a multimarker metabarcoding approach in capturing multitrophic biodiversity across an entire coral reef atoll and sets an important baseline for ongoing monitoring and management.

Demonstration of the Use of Environmental DNA for the Non-Invasive Genotyping of a Bivalve Mollusk, the European Flat Oyster (Ostrea edulis)

Accurate SNP (single nucleotide polymorphism) genotype information is critical for a wide range of selective breeding applications in aquaculture, including parentage assignment, marker-assisted, and genomic selection. However, the sampling of tissue for genetic analysis can be invasive for juvenile animals or taxa where sampling tissue is difficult or may cause mortality (e.g. bivalve mollusks). Here, we demonstrate a novel, non-invasive technique for sampling DNA based on the collection of environmental DNA using European Flat Oysters (Ostrea edulis) as an example. The live animals are placed in individual containers until sufficient genetic material is released into the seawater which is then recovered by filtration. We compared the results of tissue and eDNA derived SNP genotype calls using a PCR based genotyping platform. We found that 100% accurate genotype calls from eDNA are possible, but depend on appropriate filtration and the dilution of the sample throughout the workflow. We also developed an additional low-cost DNA extraction technique which provided >99% correct SNP genotype calls in comparison to tissue. It was concluded that eDNA sampling can be used in hatchery and selective breeding programs applicable to any aquatic organism for which direct tissue sampling may result in animal welfare concerns or mortality.

Combining ddPCR and environmental DNA to improve detection capabilities of a critically endangered freshwater invertebrate

Isogenus nubecula is a critically endangered Plecoptera species. Considered extinct in the UK, I. nubecula was recently rediscovered (in one location of the River Dee, Wales), after 22 years of absence. In a similar way to many other species of Perlodidae, I. nubecula could be utilised as a bio-indicator, for assessing water quality and health status of a given freshwater system. However, conventional monitoring of invertebrates via kick-sampling, is invasive and expensive (time consuming). Further, such methods require a high level of taxonomic expertise. Here, we compared the traditional kick-sampling method with the use of eDNA detection using qPCR and ddPCR-analyses. In spring 2018, we sampled eDNA from twelve locations on the River Dee. I. nubecula was detected using kick-sampling in five of these locations, three locations using both eDNA detection and kick-sampling and one location using eDNA detection alone – resulting in a total of six known and distinct populations of this critically endangered species. Interestingly, despite the eDNA assay being validated in vitro and in silico, and results indicating high sensitivity, qPCR analysis of the eDNA samples proved to be ineffective. In contrast, ddPCR analyses resulted in a clear detection of I. nubecula at four locations suggesting that inhibition most likely explains the large discrepancy between the obtained qPCR and ddPCR results. It is therefore important to explore inhibition effects on any new eDNA assay. We also highlight that ddPCR may well be the best option for the detection of aquatic organisms which are either rare or likely to shed low levels of eDNA into their environment.

A Brief Review of Non-Avian Reptile Environmental DNA (eDNA), with a Case Study of Painted Turtle (Chrysemys picta) eDNA Under Field Conditions

Environmental DNA (eDNA) is an increasingly used non-invasive molecular tool for detecting species presence and monitoring populations. In this article, we review the current state of non-avian reptile eDNA work in aquatic systems, and present a field experiment on detecting the presence of painted turtle (Chrysemys picta) eDNA. Thus far, turtle and snake eDNA studies have shown mixed results in detecting the presence of these animals under field conditions. However, some instances of low detection rates and non-detection occur for these non-avian reptiles, especially for squamates. We explored non-avian reptile eDNA quantification by sampling four lentic ponds with different densities (0 kg/ha, 6 kg/ha, 9 kg/ha, and 13 kg/ha) of painted turtles over three months to detect differences in eDNA using a qPCR assay amplifying the COI gene of the mtDNA genome. Only one sample of the highest-density pond amplified eDNA for a positive detection. Yet, estimates of eDNA concentration from pond eDNA were rank-order correlated with turtle density. We present the “shedding hypothesis”—the possibility that animals with hard, keratinized integument do not shed as much DNA as mucus-covered organisms—as a potential challenge for eDNA studies. Despite challenges with eDNA inhibition and availability in water samples, we remain hopeful that eDNA can be used to detect freshwater turtles in the field. We provide key recommendations for biologists wishing to use eDNA methods for detecting non-avian reptiles.

A Microcosm Study of Surface Sediment Environmental DNA: Decay Observation, Abundance Estimation, and Fragment Length Comparison

Interpretation of environmental DNA (eDNA) is a major problem hindering the application of this emerging technology for environmental monitoring. The decay characteristics and bioabundance estimation of different DNA fragment lengths are largely unknown, especially for eDNA captured from surface sediments. An estuarine amphipod, Grandidierella japonica, was used as the target species in this study. We conducted a lab-scale experiment using DNA extraction to clarify the effect of bacteria on eDNA decay. We also conducted a microcosm experiment using amphipods to clarify interpretations of information regarding eDNA decay and bioabundance estimation by using two fragments with different lengths (126 and 358 bp). It was found that the bacteria concentration accelerated eDNA decay, and long fragments were more susceptible to bacteria, thus decaying faster, than short fragments in the exponential decay period. The fresh eDNA (collected within 24 h of removing the amphipods) was more indicative of bioabundance than old eDNA (collected 240-480 h after removing amphipods), and short fragments better reflected bioabundance than long fragments. Finally, we compared the half-life of eDNA in surface sediment with that in a water sample and found that the temporal scales of surface sediment and water are similar (days to weeks). Our results suggest that surface sediment also has the potential to monitor the environment at a temporal scale similar to water.

Considerations for incorporating real-time PCR assays into routine marine biosecurity surveillance programmes: a case study targeting the Mediterranean fanworm (Sabella spallanzanii) and club tunicate (Styela clava) 1

Molecular techniques may provide effective tools to enhance marine biosecurity surveillance. Prior to routine implementation, evidence-based consideration of their benefits and limitations is needed. In this study, we assessed the efficiency and practicality of visual diver surveys and real-time PCR assays (targeting DNA and RNA) for detecting two marine invasive species whose infestation levels varied between species and location: Sabella spallanzanii and Styela clava. Filtered water samples (n = 171) were collected in parallel with dive surveys at two locations as part of the New Zealand Marine High Risk Site Surveillance programme: Nelson Harbour (27 sites) and Waitemata Harbour (30 sites). Diver surveys resulted in a greater number of detections compared to real-time PCR: S. clava - 21 versus 5 sites in Nelson, 6 versus 1 in Auckland; S. spallanzanii - 18 versus 10 in Auckland, no detections in Nelson. Occupancy modelling derived detection probabilities for the real-time PCR for S. clava were low (14%), compared to S. spallanzanii (66%). This could be related to abundances, or species-specific differences in DNA shedding. Only one RNA sample was positive, suggesting that most detections were from extracellular DNA or non-viable fragments. While molecular methods cannot yet replace visual observations, this study shows they provide useful complementary information.

Behavior and season affect crayfish detection and density inference using environmental DNA

Although the presence/absence of aquatic invertebrates using environmental DNA (eDNA) has been established for several species, inferring population densities has remained problematic. The invasive American signal crayfish, Pacifastacus leniusculus (Dana), is the leading cause of decline in the UK's only native crayfish species, Austropotamobius pallipes (Lereboullet). Methods to detect species at low abundances offer the opportunity for the early detection, and potential eradication, of P. leniusculus before population densities reach threatening levels in areas occupied by A. pallipes. Using a factorial experimental design with aquaria, we investigated the impacts of biomass, sex ratio, and fighting behavior on the amount of eDNA released by P. leniusculus, with the aim to infer density per aquarium depending on treatments. The amount of target eDNA in water samples from each aquarium was measured using the quantitative Polymerase Chain Reaction. We show that the presence of eggs significantly increases the concentration of crayfish eDNA per unit of mass, and that there is a significant relationship between eDNA concentration and biomass when females are egg-bearing. However, the relationship between crayfish biomass and eDNA concentration is lost in aquaria without ovigerous females. Female-specific tanks had significantly higher eDNA concentrations than male-specific tanks, and the prevention of fighting did not impact the amount of eDNA in the water. These results indicate that detection and estimate of crayfish abundance using eDNA may be more effective while females are ovigerous. This information should guide further research for an accurate estimation of crayfish biomass in the field depending on the season. Our results indicate that detection and quantification of egg-laying aquatic invertebrate species using eDNA could be most successful during periods when eggs are developing in the water. We recommend that practitioners consider the reproductive cycle of target species when attempting to study or detect aquatic species using eDNA in the field.

Persistence of marine fish environmental DNA and the influence of sunlight

Harnessing information encoded in environmental DNA (eDNA) in marine waters has the potential to revolutionize marine biomonitoring. Whether using organism-specific quantitative PCR assays or metabarcoding in conjunction with amplicon sequencing, scientists have illustrated that realistic organism censuses can be inferred from eDNA. The next step is establishing ways to link information obtained from eDNA analyses to actual organism abundance. This is only possible by understanding the processes that control eDNA concentrations. The present study uses mesocosm experiments to study the persistence of eDNA in marine waters and explore the role of sunlight in modulating eDNA persistence. We seeded solute-permeable dialysis bags with water containing indigenous eDNA and suspended them in a large tank containing seawater. Bags were subjected to two treatments: half the bags were suspended near the water surface where they received high doses of sunlight, and half at depth where they received lower doses of sunlight. Bags were destructively sampled over the course of 87 hours. eDNA was extracted from water samples and used as template for a Scomber japonicus qPCR assay and a marine fish-specific 12S rRNA PCR assay. The latter was subsequently sequenced using a metabarcoding approach. S. japonicus eDNA, as measured by qPCR, exhibited first order decay with a rate constant ~0.01 hr ^-1 with no difference in decay rate constants between the two experimental treatments. eDNA metabarcoding identified 190 organizational taxonomic units (OTUs) assigned to varying taxonomic ranks. There was no difference in marine fish communities as measured by eDNA metabarcoding between the two experimental treatments, but there was an effect of time. Given the differences in UVA and UVB fluence received by the two experimental treatments, we conclude that sunlight is not the main driver of fish eDNA decay in the experiments. However, there are clearly temporal effects that need to be considered when interpreting information obtained using eDNA approaches.

Monitoring of noble, signal and narrow-clawed crayfish using environmental DNA from freshwater samples

For several hundred years freshwater crayfish (Crustacea-Decapoda-Astacidea) have played an important ecological, cultural and culinary role in Scandinavia. However, many native populations of noble crayfish Astacus astacus have faced major declines during the last century, largely resulting from human assisted expansion of non-indigenous signal crayfish Pacifastacus leniusculus that carry and transmit the crayfish plague pathogen. In Denmark, also the non-indigenous narrow-clawed crayfish Astacus leptodactylus has expanded due to anthropogenic activities. Knowledge about crayfish distribution and early detection of non-indigenous and invasive species are crucial elements in successful conservation of indigenous crayfish. The use of environmental DNA (eDNA) extracted from water samples is a promising new tool for early and non-invasive detection of species in aquatic environments. In the present study, we have developed and tested quantitative PCR (qPCR) assays for species-specific detection and quantification of the three above mentioned crayfish species on the basis of mitochondrial cytochrome oxidase 1 (mtDNA-CO1), including separate assays for two clades of A. leptodactylus. The limit of detection (LOD) was experimentally established as 5 copies/PCR with two different approaches, and the limit of quantification (LOQ) were determined to 5 and 10 copies/PCR, respectively, depending on chosen approach. The assays detected crayfish in natural freshwater ecosystems with known populations of all three species, and show promising potentials for future monitoring of A. astacus, P. leniusculus and A. leptodactylus. However, the assays need further validation with data 1) comparing traditional and eDNA based estimates of abundance, and 2) representing a broader geographical range for the involved crayfish species.