SPECIES DETECTION: FISH
Jerde C. L., Mahon A. R., Chadderton W. L., Lodge D. M. (2011): “Sight‐unseen” detection of rare aquatic species using environmental DNA. Conservation Letters 4: 150-157.
FULL TEXT
Abstract
Effective management of rare species, including endangered native species and recently introduced nonindigenous species, requires the detection of populations at low density. For endangered species, detecting the localized distribution makes it possible to identify and protect critical habitat to enhance survival or reproductive success. Similarly, early detection of an incipient invasion by a harmful species increases the feasibility of rapid responses to eradicate the species or contain its spread. Here we demonstrate the efficacy of environmental DNA (eDNA) as a detection tool in freshwater environments. Specifically, we delimit the invasion fronts of two species of Asian carps in Chicago, Illinois, USA area canals and waterways. Quantitative comparisons with traditional fisheries surveillance tools illustrate the greater sensitivity of eDNA and reveal that the risk of invasion to the Laurentian Great Lakes is imminent.
Takahara T., Minamoto T., Doi H. (2013): Using environmental DNA to estimate the distribution of an invasive fish species in ponds. Plos One 8: e56584.
FULL TEXT
Abstract
Knowledge of the presence of an invasive species is critical to monitoring the sustainability of communities and ecosystems. Environmental DNA (eDNA), DNA fragments that are likely to be bound to organic matters in the water or in shed cells, has been used to monitor the presence of aquatic animals. Using an eDNA-based method, we estimated the presence of the invasive bluegill sunfish, Lepomis macrochirus, in 70 ponds located in seven locales on the Japanese mainland and on surrounding islands. We quantified the concentration of DNA copies in a 1 L water sample using quantitative real-time polymerase chain reaction (qPCR) with a primer/probe set. In addition, we visually observed the bluegill presence in the ponds from the shoreline. We detected bluegill eDNA in all the ponds where bluegills were observed visually and some where bluegills were not observed. Bluegills were also less prevalent on the islands than the mainland, likely owing to limited dispersal and introduction by humans. Our eDNA method simply and rapidly detects the presence of this invasive fish species with less disturbance to the environment during field surveys than traditional methods.
Hänfling B., Lawson Handley L., Read D. S., Hahn C., Li J., Nichols P., Blackman R. C., Oliver A., Winfield I. J. (2016): Environmental DNA metabarcoding of lake fish communities reflects long‐term data from established survey methods. Molecular Ecology 25: 3101-3119.
FULL TEXT
Abstract
Organisms continuously release DNA into their environments via shed cells, excreta, gametes and decaying material. Analysis of this ‘environmental DNA’ (eDNA) is revolutionizing biodiversity monitoring. eDNA outperforms many established survey methods for targeted detection of single species, but few studies have investigated how well eDNA reflects whole communities of organisms in natural environments. We investigated whether eDNA can recover accurate qualitative and quantitative information about fish communities in large lakes, by comparison to the most comprehensive long‐term gill‐net data set available in the UK. Seventy‐eight 2L water samples were collected along depth profile transects, gill‐net sites and from the shoreline in three large, deep lakes (Windermere, Bassenthwaite Lake and Derwent Water) in the English Lake District. Water samples were assayed by eDNA metabarcoding of the mitochondrial 12S and cytochrome b regions. Fourteen of the 16 species historically recorded in Windermere were detected using eDNA, compared to four species in the most recent gill‐net survey, demonstrating eDNA is extremely sensitive for detecting species. A key question for biodiversity monitoring is whether eDNA can accurately estimate abundance. To test this, we used the number of sequence reads per species and the proportion of sampling sites in which a species was detected with eDNA (i.e. site occupancy) as proxies for abundance. eDNA abundance data consistently correlated with rank abundance estimates from established surveys. These results demonstrate that eDNA metabarcoding can describe fish communities in large lakes, both qualitatively and quantitatively, and has great potential as a complementary tool to established monitoring methods.
Bakker J., Wangensteen O. S., Chapman D. D., Boussarie G., Buddo D., Guttridge T. L., Hertler H., Mouillot D., Vigliola L., Mariani S. (2017): Environmental DNA reveals tropical shark diversity in contrasting levels of anthropogenic impact. Scientific Reports 7: 16886.
FULL TEXT
Abstract
Sharks are charismatic predators that play a key role in most marine food webs. Their demonstrated vulnerability to exploitation has recently turned them into flagship species in ocean conservation. Yet, the assessment and monitoring of the distribution and abundance of such mobile species in marine environments remain challenging, often invasive and resource-intensive. Here we pilot a novel, rapid and non-invasive environmental DNA (eDNA) metabarcoding approach specifically targeted to infer shark presence, diversity and eDNA read abundance in tropical habitats. We identified at least 21 shark species, from both Caribbean and Pacific Coral Sea water samples, whose geographical patterns of diversity and read abundance coincide with geographical differences in levels of anthropogenic pressure and conservation effort. We demonstrate that eDNA metabarcoding can be effectively employed to study shark diversity. Further developments in this field have the potential to drastically enhance our ability to assess and monitor elusive oceanic predators, and lead to improved conservation strategies.
Klobucar S. L., Rodgers T. W., Budy P. (2017): At the forefront: evidence of the applicability of using environmental DNA to quantify the abundance of fish populations in natural lentic waters with additional sampling considerations. Canadian Journal of Fisheries and Aquatic Sciences 74: 2030-2034.
FULL TEXT
Abstract
Environmental DNA (eDNA) sampling has proven to be a valuable tool for detecting species in aquatic ecosystems. Within this rapidly evolving field, a promising application is the ability to obtain quantitative estimates of relative species abundance based on eDNA concentration rather than traditionally labor-intensive methods. We investigated the relationship between eDNA concentration and Arctic char (Salvelinus alpinus) abundance in five well-studied natural lakes; additionally, we examined the effects of different temporal (e.g., season) and spatial (e.g., depth) scales on eDNA concentration. Concentrations of eDNA were linearly correlated with char population estimates and exponentially correlated with char densities. Across lakes, eDNA concentrations were greater and more homogeneous in the water column during mixis; however, when stratified, eDNA concentrations were greater in the hypolimnion. Overall, our findings demonstrate that eDNA techniques can produce effective estimates of relative fish abundance in natural lakes. These findings can guide future studies to improve and expand eDNA methods while informing research and management using rapid and minimally invasive sampling.
Boussarie G., Bakker J., Wangensteen O. S., Mariani S., Bonnin L., Juhel J. B., Kiszka J. J., Kulbicki M., Manel S., Robbins W. D., Vigliola L. (2018): Environmental DNA illuminates the dark diversity of sharks. Science Advances 4: eaap9661.
FULL TEXT
Abstract
In the era of “Anthropocene defaunation,” large species are often no longer detected in habitats where they formerly occurred. However, it is unclear whether this apparent missing, or “dark,” diversity of megafauna results from local species extirpations or from failure to detect elusive remaining individuals. We find that despite two orders of magnitude less sampling effort, environmental DNA (eDNA) detects 44% more shark species than traditional underwater visual censuses and baited videos across the New Caledonian archipelago (south-western Pacific). Furthermore, eDNA analysis reveals the presence of previously unobserved shark species in human-impacted areas. Overall, our results highlight a greater prevalence of sharks than described by traditional survey methods in both impacted and wilderness areas. This indicates an urgent need for large-scale eDNA assessments to improve monitoring of threatened and elusive megafauna. Finally, our findings emphasize the need for conservation efforts specifically geared toward the protection of elusive, residual populations.
Li Y., Evans N. T., Renshaw M. A., Jerde C. L., Olds B. P., Shogren A. J., Deiner K., Lodge D. M., Lamberti G. A., Pfrender M. E. (2018): Estimating fish alpha-and beta-diversity along a small stream with environmental DNA metabarcoding. Metabarcoding and Metagenomics 2: 24262.
FULL TEXT
Abstract
Environmental DNA (eDNA) metabarcoding has been increasingly applied to biodiversity surveys in stream ecosystems. In stream networks, the accuracy of eDNA-based biodiversity assessment depends on whether the upstream eDNA influx affects downstream detection. Biodiversity assessment in low-discharge streams should be less influenced by eDNA transport than in high-discharge streams. We estimated α- and β-diversity of the fish community from eDNA samples collected in a small Michigan (USA) stream from its headwaters to its confluence with a larger river. We found that α-diversity increased from upstream to downstream and, as predicted, we found a significant positive correlation between β-diversity and physical distance (stream length) between locations indicating species turnover along the longitudinal stream gradient. Sample replicates and different genetic markers showed similar species composition, supporting the consistency of the eDNA metabarcoding approach to estimate α- and β-diversity of fishes in low-discharge streams.
Parrondo M., Clusa L., Mauvisseau Q., Borrell Y. J. (2018): Citizen warnings and post checkout molecular confirmations using eDNA as a combined strategy for updating invasive species distributions. Journal for Nature Conservation 43: 95-103.
FULL TEXT
Abstract
Citizen warnings alerting about the presence of invasive species has been claimed as fundamental in the strategies addressed to manage aquatic invasions. A great volume of online information coming from fishermen and ordinary citizens, about detection of new species in their communities is currently available. Unfortunately, it is not always implemented as a useful tool by agencies, and within stakeholders protocols, to prevent and manage biological invasions. In this work, we have used as a case study the wels catfish Silurus glanis Linnaeus, 1758. Online blogs, webpages, videos, magazines, and newspapers, were searched for news about the presence and spread of S. glanis in the Iberian Peninsula until June 2016. This information was compiled with official reports (scientific papers and regional and national governmental reports) to create a map showing the putative current pattern of S. glanis invasion through Iberian freshwater ecosystems. The current situation pointed to Silurus’s presence in six of the seven main river basins of the Iberian territory. Since non-official reports need post-alerts confirmations, we have also set up a molecular pilot study designing genus specific primers to detect this species in environmental DNA (eDNA) from the reported locations. In the pilot study, primers were tested on eDNA samples extracted from experimental aquariums and on real environmental samples taken from different basins in Spain (Ebro, Douro and Tagus). In all these basins S. glanis was detected. Official Silurus reports were confirmed with two molecular markers in five out of the six cases (83%) assayed in this work, and in two out of three non-official reports (66%) coming from fishermen websites and newspaper reports. The proposed combined strategy (citizen alerts and the eDNA detection method) can be a helpful tool in early detection of invasive species allowing fast and effective management actions by stakeholders.
Ostberg C. O., Chase D. M., Hoy M. S., Duda J. J., Hayes M. C., Jolley J. C., Silver G. S., Cook‐Tabor C. (2019): Evaluation of environmental DNA surveys for identifying occupancy and spatial distribution of Pacific Lamprey (Entosphenus tridentatus) and Lampetra spp. in a Washington coast watershed. Environmental DNA 1: 131-143.
FULL TEXT
Abstract
Surveys of environmental DNA (eDNA) have become an important and multifaceted tool for monitoring and identifying distributions and occupancy of aquatic species. This tool is attractive because it is powerful, easy to apply, and provides an alternative to traditional field survey methods. However, validating eDNA survey methods against traditional field survey methods is warranted prior to their application. We used eDNA and electrofishing to survey 10 sites in 3 tributaries of the Chehalis River, Washington, to infer distribution and occupancy of Entosphenus tridentatus and Lampetra spp. Both methods produced similar detection rates for E. tridentatus, and Lampetra spp. were detected at slightly greater frequency with eDNA in the Black River and Skookumchuck River. Within each of the three tributaries, eDNA concentration was negatively related to sample distance from the Chehalis River mainstem for E. tridentatus but not for Lampetra spp., which indicates E. tridentatus and Lampetra spp. may be distributed differently within tributaries. Application of lamprey eDNA data to a multiscale occupancy model indicated high probability of detecting eDNA in water samples and quantitative PCR (qPCR) assays. Broad distribution and high detection of E. tridentatus and Lampetra spp. suggest robust populations inhabit the Chehalis River basin. Our findings suggest eDNA surveys may be comparable to electrofishing for informing lamprey occupancy and distributions. Such sampling is efficient and cost-effective and we anticipate that eDNA surveys will become a valuable tool in addressing key research and monitoring needs for conservation and restoration of lampreys in general.
Sepulveda A. J., Schabacker J., Smith S., Al‐Chokhachy R., Luikart G., Amish S. J. (2019): Improved detection of rare, endangered and invasive trout in using a new large‐volume sampling method for eDNA capture. Environmental DNA 1: 227-237.
FULL TEXT
Abstract
Environmental DNA (eDNA) detection probability increases with volume of water sampled. Common approaches for collecting eDNA samples often require many samples since these approaches usually use fine filters, which restrict the volume of water that can be sampled. An alternative to collecting many, small volume water samples using fine filters may be to collect fewer, large volume water samples using coarse filters that do not clog as rapidly. We used mesocosm experiments and field evaluations to compare coarse filter-large water volume samples (hereafter large volume filter samples) versus fine filter-small water volume samples (hereafter small volume filter samples) for detection and quantification of rainbow trout (Oncorhynchus mykiss) and bull trout (Salvelinus confluentus) DNA. We found that large volume filter sampling can be an effective approach for detecting DNA of low-density target taxa. In mesocosm experiments, large-volume and small-volume water samples detected similar quantities of rainbow trout DNA. In the field, large volume samples more frequently detected bull trout DNA, had higher bull trout DNA copy number, and higher total DNA concentrations than small volume samples. However, sampling higher water volumes increased the potential for PCR inhibition so the DNA workflow had to be altered for large volume samples. Combining larger water volume samples with other strategies, like increasing PCR sensitivity and the number of PCR replicates, will improve detection of rare species, which is crucial for advancing conservation and ecological understanding.
Thalinger B., Wolf E., Traugott M., Wanzenböck J. (2019): Monitoring spawning migrations of potamodromous fish species via eDNA. Scientific Reports 9: 15388.
FULL TEXT
Abstract
Potamodromous fish are considered important indicators of habitat connectivity in freshwater ecosystems, but they are globally threatened by anthropogenic impacts. Hence, non-invasive techniques are necessary for monitoring during spawning migrations. The use of environmental DNA (eDNA) potentially facilitates these efforts, albeit quantitative examinations of spawning migrations remain so far mostly uncharted. Here, we investigated spawning migrations of Danube bleak, Alburnus mento, and Vimba bream, Vimba vimba, and found a strong correlation between daily visual fish counts and downstream eDNA signals obtained from filtered water samples analysed with digital PCR and end-point PCR coupled with capillary electrophoresis. By accounting for daily discharge fluctuations, it was possible to predict eDNA signal strength from the number of migrating fish: first, the whole spawning reach was taken into account. Second, the model was validated using eDNA signals and fish counts obtained from the upper half of the examined river stretch. Consequently, fish counts and their day-to-day changes could be described via an eDNA-based time series model for the whole migration period. Our findings highlight the capability of eDNA beyond delivering simple presence/absence data towards efficient and informative monitoring of highly dynamic aquatic processes such as spawning migrations of potamodromous fish species.
Truelove N. K., Andruszkiewicz E. A., Block B. A. (2019): A rapid environmental DNA method for detecting white sharks in the open ocean. Methods in Ecology and Evolution 10: 1128-1135.
FULL TEXT
Abstract
Environmental DNA (eDNA) research often requires returning to the laboratory for processing, which can delay species identification by weeks–months. Using a portable Oxford Nanopore MinIon sequencer, eDNA from white shark (Carcharodon carcharias) was rapidly identified from seawater samples collected in the high seas where they have historically been identified with biologging datasets. A total of 10 sequencing runs were performed on the MinIon onboard an oceanographic vessel with a turnaround time from water collection to sequence results and annotation of ~48 hr. Identifying vertebrates by amplifying eDNA from seawater provides a novel approach for sampling and detecting the presence of elusive species of conservation importance in remote locations.
Adams K. R., Gibbs L., Knott N. A., Broad A., Hing M., Taylor M. D., Davis A. R. (2020): Coexisting with sharks: a novel, socially acceptable and non-lethal shark mitigation approach. Scientific Reports 10: 17497.
FULL TEXT
Abstract
Conflict between humans and large predators is a longstanding challenge that can present negative consequences for humans and wildlife. Sharks have a global distribution and are considered to pose a potential threat to humans; concurrently many shark species are themselves threatened. Developing strategies for coexistence between humans and this keystone group is imperative. We assess blimp surveillance as a technique to simply and effectively reduce shark encounters at ocean beaches and determine the social acceptance of this technique as compared to an established mitigation strategy—shark meshing. We demonstrate the suitability of blimps for risk mitigation, with detection probabilities of shark analogues by professional lifeguards of 0.93 in ideal swimming conditions. Social surveys indicate strong social acceptance of blimps and preference for non-lethal shark mitigation. We show that continuous aerial surveillance can provide a measurable reduction in risk from sharks, improving beach safety and facilitating coexistence between people and wildlife.
Cardás J. B., Deconinck D., Márquez I., Torre P. P., Garcia-Vazquez E., Machado-Schiaffino G. (2020): New eDNA based tool applied to the specific detection and monitoring of the endangered European eel. Biological Conservation 250: 108750.
FULL TEXT
Abstract
European eel (Anguilla anguilla) populations have declined drastically over the last decades and it has been included in the IUCN red list of endangered species as critically endangered since 2007. Thus, continuous population monitoring is crucial in order to warrant the conservation of this emblematic species. Environmental DNA (eDNA) has been recently implemented as a powerful method for the detection and monitoring of freshwater species, particularly for endangered species, where eDNA methods have shown to be less invasive than other methods (e.g. electrofishing). In this study, we developed and validated, under controlled conditions, a new species-specific tool for detecting A. anguilla from water samples by means of eDNA. Furthermore, we applied a semi-quantitative approach for monitoring of glass eel at different depths (surface and bottom) during different seasons in two rivers of northern Spain (Nalón and Sella rivers). We detected a significantly higher proportion of positive DNA amplifications in bottom than surface samples. Moreover, the proportion of replicas with positive amplification varied along the estuaries sections examined, and especially in the different sampling months. The temporal detection trends found in this study were compatible with the known upstream migration pattern of this species. Altogether, this study contributes to the establishment of a simple, easy and cheap system based on eDNA, that could be routinely applied in conservation research and management programs to monitoring wild populations of endangered species.
Miya M., Gotoh R. O., Sado T. (2020): MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples. Fisheries Science 86: 939-970.
FULL TEXT
Abstract
We reviewed the current methodology and practices of the DNA metabarcoding approach using a universal PCR primer pair MiFish, which co-amplifies a short fragment of fish DNA (approx. 170 bp from the mitochondrial 12S rRNA gene) across a wide variety of taxa. This method has mostly been applied to biodiversity monitoring using environmental DNA (eDNA) shed from fish and, coupled with next-generation sequencing technologies, has enabled massively parallel sequencing of several hundred eDNA samples simultaneously. Since the publication of its technical outline in 2015, this method has been widely used in various aquatic environments in and around the six continents, and MiFish primers have demonstrably outperformed other competing primers. Here, we outline the technical progress in this method over the last 5 years and highlight some case studies on marine, freshwater, and estuarine fish communities. Additionally, we discuss various applications of MiFish metabarcoding to non-fish organisms, single-species detection systems, quantitative biodiversity monitoring, and bulk DNA samples other than eDNA. By recognizing the MiFish eDNA metabarcoding strengths and limitations, we argue that this method is useful for ecosystem conservation strategies and the sustainable use of fishery resources in “ecosystem-based fishery management” through continuous biodiversity monitoring at multiple sites.
Nester G. M., De Brauwer M., Koziol A., West K. M., DiBattista J. D., White N. E., Power M., Heydenrych M. J., Harvey E., Bunce M. (2020): Development and evaluation of fish eDNA metabarcoding assays facilitate the detection of cryptic seahorse taxa (family: Syngnathidae). Environmental DNA 2: 614-626.
FULL TEXT
Abstract
Environmental DNA (eDNA) metabarcoding methods have demonstrated their potential as noninvasive techniques for the monitoring and conservation of marine fishes, including rare and endangered taxa. However, the majority of these investigations have focused on large‐bodied taxa such as sharks and sturgeons. In contrast, eDNA studies on small‐bodied cryptic taxa are much less common. As a case in point, seahorses (members of the Syngnathidae family) have never been detected by eDNA, despite the fact that globally there are 14 species classified as “Threatened” by the IUCN. Here, we critically evaluate the ability of two existing broad‐spectrum fish metabarcoding assays (MiFish and 16S Fish) and explore the efficacy of two newly designed fish metabarcoding assays (16S_FishSyn_Short and 16S_FishSyn_Long) to detect Syngnathidae amidst a wide spectrum of fish species. Furthermore, a custom Western Australian 16S rRNA fish database was created to increase the likelihood of correct taxonomic assignments. With the newly designed assays, we detected four Syngnathidae species in a targeted eDNA survey of the Perth metropolitan area (Western Australia). These detections include the seahorse species Hippocampus subelongatus and Hippocampus breviceps, which represents the first time seahorse species have been detected using eDNA. The existing MiFish and 16S Fish assays did not detect any Syngnathidae. This evaluation of all four fish metabarcoding assays reinforces the view that every PCR assay has “blind spots”. In the context of complex environmental samples, no assay is universal and false negatives will occur due to a combination of PCR efficacy, primer binding, assay sensitivity, degeneracies in the primers, template competition, and amplicon length. Taken together, these data indicate that eDNA methodologies, with ongoing optimizations, will become an integral part of monitoring small‐bodied cryptic taxa such as seahorses, gobies, and blennies and can assist in mapping species’ distributions and prioritizing conservation areas.
Schweiss K. E., Lehman R. N., Drymon J. M., Phillips N. M. (2020): Development of highly sensitive environmental DNA methods for the detection of Bull Sharks, Carcharhinus leucas (Müller and Henle, 1839), using Droplet Digital™ PCR. Environmental DNA 2: 3-12.
FULL TEXT
Abstract
As apex and mesopredators, elasmobranchs play a crucial role in maintaining ecosystem function and balance in marine systems. Elasmobranch populations worldwide are in decline as a result of exploitation via direct and indirect fisheries mortalities and habitat degradation; however, a lack of information on distribution, abundance, and population biology for most species hinders their effective management. Environmental DNA analysis has emerged as a cost-effective and non-invasive technique to fill some of these data gaps, but often requires the development of species-specific methodologies. Here, we established eDNA methodology appropriate for targeted species detections of Bull Sharks, Carcharhinus leucas, in estuarine waters in the northern Gulf of Mexico. We compared different QIAGEN®DNeasy® extraction kit protocols and developed a species-specific Droplet Digital™ PCR (ddPCR) assay by designing primers and an internal probe to amplify a 237 base pair portion of the ND2 gene in the mitochondrial genome of C. leucas. To validate the developed methods, water samples were collected from known C. leucas habitat and from an ex situ closed environment containing a single C. leucas individual. The effectiveness of the assay in an open environment was then assessed by placing one C. leucas into a flow-through mesocosm system and water samples were collected every 30 min for 3 hr. The developed C. leucas -specific assay has the ability to detect target DNA concentrations in a reaction as low as 0.6 copies/μl. DdPCR reactions performed on water samples from known habitat and 30 min after a shark was added to the closed environment contained 1.62 copies/μl and 166.6 copies/μl of target C. leucas eDNA, respectively. Carcharhinus leucas eDNA was detected in the flow-through system within 30 min, but concentrations remained low and variable throughout the duration of the experiment.
Oka S. I., Doi H., Miyamoto K., Hanahara N., Sado T., Miya M. (2021): Environmental DNA metabarcoding for biodiversity monitoring of a highly diverse tropical fish community in a coral reef lagoon: Estimation of species richness and detection of habitat segregation. Environmental DNA 3: 55-69.
FULL TEXT
Abstract
An environmental DNA (eDNA) metabarcoding approach has been widely used for biodiversity monitoring of fishes, although it has rarely been applied to tropical and subtropical aquatic ecosystems, where species diversity is remarkably high. This study examined the extent to which species richness can be estimated in a small coral reef lagoon (1,500 × 900 m) near Okinawa Island, southern Japan, where the surrounding waters are likely to harbor more than 1,500 species of fish. During 2015–2017, a total of 16 capture-based surveys were conducted to create a faunal list of fish species, followed by eDNA metabarcoding based on seawater samples taken from 11 sites in the lagoon on a day in May 2019. We also tested whether eDNA metabarcoding could detect differences between adjacent fish communities inhabiting the offshore reef edge and shore-side seagrass beds within the lagoon. A total of 217 fish species were confirmed by the capture-based samplings, while 291 fish species were detected by eDNA metabarcoding, identifying a total of 410 species distributed across 119 families and 193 genera. Of these 410 species, only 96 (24% of the total) were commonly identified by both methods, indicating that capture-based surveys failed to collect a number of species detected by eDNA metabarcoding. Interestingly, two different approaches to estimate species richness based on eDNA data yielded values close to the 410 species, including one that suggested an additional three or more eDNA surveys from 11 sites (36 samples) would detect 90% of the 410 species. In addition, nonmetric multidimensional scaling for fish assemblages clearly distinguished between the fish communities of the offshore reef edge and those of the shore-side seagrass beds. This study demonstrates that an eDNA metabarcoding approach is useful for estimating species richness and detection of habitat segregation even in ecosystems with remarkably high species diversity.
Ratcliffe F. C., Uren Webster T. M., Garcia de Leaniz C., Consuegra S. (2021): A drop in the ocean: Monitoring fish communities in spawning areas using environmental DNA. Environmental DNA 3: 43-54.
FULL TEXT
Abstract
Early life stages of aquatic organisms are particularly vulnerable to climatic stressors; however, they are difficult to monitor due to challenges in sampling and morphological identification. Environmental DNA (eDNA) from water samples represents an opportunity for rapid, nondestructive monitoring of aquatic community composition as well as single species monitoring. eDNA can also detect spawning events, although has not been yet tested in offshore spawning grounds. Here, we used metabarcoding of water samples to detect the presence of key fish taxa in spawning areas that are difficult to monitor using traditional means. We analyzed DNA from water samples and fish larvae samples at 14 offshore sites, using 12S mitochondrial metabarcoding and compared taxa detections, diversity, and community structure estimated by both sample types. Species richness and diversity did not differ between water and larvae samples. Both sample types detected a core of 12 taxa across the survey, with an average agreement in detections of 75% at sampling site level. Water samples detected two of the three most abundant taxa, the sandeel, Ammodytes marinus, and clupeids, Clupea harengus/Sprattus sprattus, at 31% and 38% more sites than larvae samples respectively, while Callionymus sp. was more prevalent in larvae samples. Mackerel (Scomber scombrus) and blue whiting (Micromestius poutassou) were only detected in water samples despite sampling taking place at peak spawning times for these species. Our results demonstrate that eDNA metabarcoding provides a rapid and feasible monitoring method for the management of key taxa, such as sandeel, that cannot be easily monitored using traditional capture surveys.
van Rooyen A., Miller A. D., Clark Z., Sherman C. D., Butcher P. A., Rizzari J. R., Weeks A. R. (2021): Development of an environmental DNA assay for detecting multiple shark species involved in human–shark conflicts in Australia. Environmental DNA 3: 940-949.
FULL TEXT
Abstract
The number of human–shark interactions has increased worldwide during the past decade resulting in injuries and fatalities. In Australia, the white shark (Carcharodon carcharias), tiger shark (Galeocerdo cuvier), and bull shark (Carcharhinus leucas) are responsible for the majority of fatal incidents. On the southeast coast of Australia, monitoring programs currently rely on SMART (Shark-Management-Alert-in-Real-Time) drumlines and mesh nets to catch, tag, and monitor shark movement. However, these methods are laborious, costly, and involve the capture of only a fraction of the total shark population. Here, we develop a multiplex environmental DNA assay capable of detecting all three shark species simultaneously from water samples by targeting conserved but specific mitochondrial sequences that are characteristic of each species. The specificity of the assay was validated by testing for cross-amplification across a range of non-target but co-occurring shark species from eastern Australia. We test the sensitivity of the assay on water samples collected from shark capture events and sites where these shark species are known to frequent, and undertake DNA sequencing on positive samples to confirm species haplotype authenticity. Samples collected from one of these sites also demonstrate that eDNA detections are dependent on shark activity in the area. This assay will allow for rapid detection of DNA from each shark species in water samples, providing a cost-effective alternative for monitoring sharks along the east coast of Australia and potentially elsewhere.
Cole V. J., Harasti D., Lines R., Stat M. (2022): Estuarine fishes associated with intertidal oyster reefs characterized using environmental DNA and baited remote underwater video. Environmental DNA 4: 50-62.
FULL TEXT
Abstract
It has been widely shown that oyster reefs enhance local biodiversity and fisheries production. To determine the importance of intertidal remnant estuarine oyster reefs compared to unstructured sandy habitats over small spatial scales (<1 km) to fishes, assemblages were sampled with two nondestructive methods: baited underwater remote videos (BRUVs) and environmental DNA (eDNA) metabarcoding. Fish diversity from eDNA was characterized using three metabarcoding assays, and the assemblages differed with each, as well as to that detected by BRUVs. Overall, 112 fish genera were identified, with 78 more genera detected using eDNA metabarcoding than those observed with BRUVs. Both eDNA and BRUVs resolved a higher number of fish genera associated with oyster reefs than with sand sites, and a different fish composition between habitats was also resolved using each method. Furthermore, eDNA was shown to be useful toward characterizing the gamma diversity of the estuary, due to the intertidal nature and hydrodynamics of the system, as well as the alpha diversity associated with oyster reefs and sand sites. This study reinforces the importance of using multiple metabarcoding assays along-side BRUVs for sampling assemblages of fishes and demonstrates the utility of using both methods in studies of biodiversity and future management of intertidal estuarine systems.
Czachur M. V., Seymour M., Creer S., von der Heyden S. (2022): Novel insights into marine fish biodiversity across a pronounced environmental gradient using replicated environmental DNA analyses. Environmental DNA 4: 181-190.
FULL TEXT
Abstract
Safeguarding marine ecosystems is essential for maintaining ecosystem function and biodiversity, but effective monitoring of marine habitats can be logistically challenging, costly, and difficult to regularly implement. Environmental DNA-based biomonitoring is a rapidly growing tool that is non-destructive, cost-effective, and reliable. However, discrepancies in eDNA sampling protocols and methodology persist, which can greatly impact the interpretations of biomonitoring results, particularly across highly diverse ecosystems with historically elevated biodiversity. The South African coastal system is a unique and highly diverse ecoregion consisting of two ocean boundary currents creating one of the most diverse biological regions on the planet. Here, we present the first eDNA-based metabarcoding assessment of South African coastal fishes while also providing key management insights into study and sample design. We observed strong ecological associations with fish species richness across the extent of the South African coast, along with weaker associations with seasonality. We detected 466 operational taxonomic units across 112 of the 270 families described previously from the region, with greater species richness on the eastern subtropical coast compared to the western coast, which follows expected species richness patterns. Additionally, we provide evidence that biological replication is necessary to detect intra-site fish diversity and that three biological replicates are sufficient for capturing species diversity dynamics. Our work highlights the value of eDNA biomonitoring across space and time enabling biodiversity characterizations for the management of a gradient of coastal marine environments.
de Bruyn M., Barbato M., Broadhurst M. K. (2022): Metabarcoding gillnets to assess unaccounted catch depredation or escape. Environmental DNA 4: 157-166.
FULL TEXT
Abstract
Gillnets are the world’s most common net-based fishing gear, comprising walls of light mesh designed to entangle fish. Gillnets are often retrieved with holes in the netting, which means some animals escape or are depredated unseen, but with some mortality. To effectively manage fisheries around the world, information is required on not only the harvested and discarded mortalities, but also problematic interactions and mortalities caused by the fishing gear and especially those involving protected species. This study sought to assess a novel method for determining such interactions by sampling five adjacent pieces of netting around each of ten holes in two bather-protection polyethylene gillnets for environmental DNA or “eDNA”. Here we show that eDNA correctly identified all previously entangled-and-landed species. Also, eDNA from three uncaptured taxa were recorded: bull shark, Carcharhinus leucas, white shark, Carcharodon carcharias and dolphins (Delphindae), illustrating the potential to reveal previously cryptic gillnet interactions. We propose that as scientific methods evolve and autonomous real-time DNA surveillance becomes routine, eDNA testing of fishing gears and vessels could provide a novel, complementary fishery-monitoring tool.
Desgarnier L., Mouillot D., Vigliola L., Chaumont M., Mannocci L. (2022): Putting eagle rays on the map by coupling aerial video-surveys and deep learning. Biological Conservation 267: 109494.
FULL TEXT
Abstract
Reliable and efficient techniques are urgently needed to monitor elasmobranch populations that face increasing threats worldwide. Aerial video-surveys provide precise and verifiable observations for the rapid assessment of species distribution and abundance in coral reefs, but the manual processing of videos is a major bottleneck for timely conservation applications. In this study, we applied deep learning for the automated detection and mapping of vulnerable eagle rays from aerial videos. A light aircraft dedicated to touristic flights allowed us to collect 42 h of aerial video footage over a shallow coral lagoon in New Caledonia (Southwest Pacific). We extracted the videos at a rate of one image per second before annotating them, yielding 314 images with eagle rays. We then trained a convolutional neural network with 80% of the eagle ray images and evaluated its accuracy on the remaining 20% (independent data sets). Our deep learning model detected 92% of the annotated eagle rays in a diversity of habitats and acquisition conditions across the studied coral lagoon. Our study offers a potential breakthrough for the monitoring of ray populations in coral reef ecosystems by providing a fast and accurate alternative to the manual processing of aerial videos. Our deep learning approach can be extended to the detection of other elasmobranchs and applied to systematic aerial surveys to not only detect individuals but also estimate species density in coral reef habitats.
Dubreuil T., Baudry T., Mauvisseau Q., Arqué A., Courty C., Delaunay C., Sweet M., Grandjean F. (2022): The development of early monitoring tools to detect aquatic invasive species: eDNA assay development and the case of the armored catfish Hypostomus robinii. Environmental DNA 4: 349-362.
FULL TEXT
Abstract
Introductions of invasive non-native species (and their subsequent impacts) are recognized as a major threat to native flora and fauna. This is especially true in island ecosystems such as the tropical island of Martinique. In 2018, one such aquatic invasive species, the suckermouth catfish Hypostomus robinii (Loricariidae), was reported for the first time in two of the islands rivers. H. robinii is a popular freshwater aquarium fish and native to tropical and sub-tropical South America. Since its initial discovery, a growing number of populations have been found, suggesting a larger distribution of this species through Martinique’s hydrographic network. Here, we developed a novel survey technique (utilizing environmental DNA) and conducted a widespread survey across the island to assess the distribution of this invasive species. We were able to detect H. robinii in 22% of sites surveyed (18 out of 83) via our eDNA-based assay. The presence of these fish was confirmed using traditional trapping at 14 of these sites. Additionally, we used occupancy modeling to investigate the impact of different environmental covariates on the detection efficiency of the novel assay and the potential impacts of false positives and negatives. We highlight a decrease in the detection probability when water volume filtered increases. That said, the eDNA-based method proves a useful tool for the detection of this invasive fish species and monitoring its spread for management purposes.
Hashemzadeh Segherloo I., Tabatabaei S. N., Abdolahi‐Mousavi E., Hernandez C., Normandeau E., Laporte M., Boyle B., Amiri M., GhaedRahmati N., Hallerman E., Bernatchez L. (2022): eDNA metabarcoding as a means to assess distribution of subterranean fish communities: Iranian blind cave fishes as a case study. Environmental DNA 4: 402-416.
FULL TEXT
Abstract
One of the most important steps in conservation of the subterranean life forms is to decipher their distribution and ecology, which is challenging using traditional approaches. Development of an environmental DNA (eDNA) assay provides an efficient means for discovering and monitoring subterranean life forms. In this study, the distribution of three Iranian blind cave fish species (blind Iran cave barb Garra typhlops, blind Lorestan cave barb Garra lorestanensis, and blind cave loach Eidinemacheilus smithi) was assessed using 12S rRNA eDNA metabarcoding performed using MiFish-U PCR primers and preliminary species distribution modeling (SDM) using bioclimatic data. The majority of sampling localities with positive detection of cave barb eDNA fall within suitable habitats in the Zagros Mountains of Iran. Our results revealed that Lorestan and Iran cave barbs have differential distribution patterns, with some extent of habitat overlap in the vicinity of the originally discovered cave barb locality. According to the observed distribution patterns, the blind Lorestan cave barb and cave loach are mostly distributed in habitats close to the Sezar River (Dez River drainage, Iran), and the blind Iran cave barb is distributed towards the west and probably in a few springs in the Karkheh River drainage. Our data support the previously proposed distribution pattern for the cave barbs, in which the species show partial niche separation and reproductive isolation, with the Lorestan cave barb being a water flow-dependent species and the Iran cave barb being a generalist species preferring variable flow rates. We showed eDNA metabarcoding to be a useful approach for ecological surveys of subterranean fish biodiversity with implications for conservation.
Liu Z., Collins R. A., Baillie C., Rainbird S., Brittain R., Griffiths A. M., Sims D. W., Mariani S., Genner M. J. (2022): Environmental DNA captures elasmobranch diversity in a temperate marine ecosystem. Environmental DNA 4: 1024-1038.
FULL TEXT
Abstract
Many sharks, skates, and rays (elasmobranchs) are highly threatened by the activities of commercial fisheries, and a clear understanding of their distributions, diversity, and abundance can guide protective measures. However, surveying and monitoring elasmobranch species can be highly invasive or resource-intensive, and utilization of non-invasive environmental DNA-based methods may overcome these problems. Here, we studied spatial and seasonal variation in the elasmobranch community of the Western English Channel using environmental DNA (eDNA) collected from surface and bottom waters periodically over an annual cycle (2017–2018). In total we recovered 13 elasmobranch species within eDNA samples, and the number of transformed eDNA reads was positively associated with species (hourly) catch data resolved from 105-year time series trawl data (1914–2018). These results demonstrate the ability of eDNA to detect and semi-quantitatively reflect the prevalence of historically dominant and rare elasmobranch species in this region. Notably, eDNA recorded a greater number of species per sampling event than a conventional trawl survey in the same area over the same sampling years (2017–2018). Several threatened species were recovered within the eDNA, including undulate ray, porbeagle shark, and thresher shark. Using eDNA, we found differences in elasmobranch communities among sampling stations and between seasons, but not between sampling depths. Collectively, our results suggest that non-invasive eDNA-based methods can be used to study the spatial and seasonal changes in the diversity and abundance of whole elasmobranch communities within temperate shelf habitats. Given the threatened status of many elasmobranchs in human-impacted marine environments, eDNA analysis is poised to provide key information on their diversity and distributions to inform conservation-focused monitoring and management.
Marwayana O. N., Gold Z., Meyer C. P., Barber P. H. (2022): Environmental DNA in a global biodiversity hotspot: Lessons from coral reef fish diversity across the Indonesian archipelago. Environmental DNA 4: 222-238.
FULL TEXT
Abstract
Indonesia is the heart of the Coral Triangle, the world’s most diverse marine ecosystem. Preserving the biological and economic value of this marine biodiversity requires efficient and economical ecosystem monitoring, yet our understanding of marine biodiversity in this region remains limited. This study uses environmental DNA (eDNA) to survey fish communities across a well-documented biodiversity gradient in Indonesia. A total of 6,608,693 sequence reads of MiFish 12S rRNA from 39 sites spanning seven regions of Indonesia revealed 1099 fish amplified sequence variants (ASVs), 80.4% of which could be identified to species. Regional fish diversity broadly conformed to expectations, with the highest fish biodiversity in Raja Ampat and lowest in Western Indonesia. Similarly, zeta diversity analysis showed greater community turnover in higher diversity reefs of Eastern Indonesia and greater community similarity in low diversity regions of Western Indonesia. However, despite a twofold difference in fish diversity between Eastern and Western Indonesia, mean ASVs recovered per 1-L seawater was relatively similar across all regions. Moreover, although ASV recovery from individual seawater samples saturated, ASV recovery did not saturate at the site or region level, indicating that sampling/sequencing efforts employed in lower diversity ecosystems are insufficient for biodiversity hotspots like the Coral Triangle. Despite these limitations, eDNA substantially increased (36.3%–84.1%; mean 57.1%) the number of fish species recorded during intensive visual surveys, adding pelagic (tuna, jacks, scads, mackerels), nocturnal (soldierfish, lanternfish), and crevice-dwelling species (eels, blennies, gobies) that are difficult to document in visual surveys. Results demonstrate the added value of eDNA in biodiversity hotspots like the Coral Triangle and highlight the need for research to understand how best to sample eDNA in high diversity regions to deliver on the promise of eDNA as a tool to monitor marine biodiversity effectively and efficiently.
Osathanunkul M., Madesis P. (2022): Environmental DNA detection of giant snakehead in Thailand’s major rivers for wild stock assessment. Plos One 17: e0267667.
FULL TEXT
Abstract
Capture-based aquaculture is now gaining much attention in Southeast Asia. This system was used to produce several fish species with social and economic implications, including the giant snakehead (Channa micropeltes). As wild harvesting of organisms for seed stock is one of main practices in capture-based aquaculture, abundance and distribution of the wild stock are essential for both environmental impact evaluation and stock management. Mark and recapture, visual observation and physical capture of target species are costly, ineffective, and labour intensive for fish surveys in several cases. Detection of target organisms using eDNA (environmental DNA) could be a good alternative as it has proved to be a non-invasive, rapid, and sensitive method for aquatic species monitoring and surveying. Here, we developed a TaqMan assay that targets the 16S region of giant snakehead DNA to amplify eDNA captured in water samples. 300 µl of water samples were collected from 15 sites located in the Chao Phraya River Basin (Ping, Wang, Yom, Nan, and Chao Phraya River) and filtered with 0.7 µm glass fibre membrane filter. Giant snakehead eDNA was detected in most tributaries (60%) with concentrations ranging from 74.0 copies/ml in Wang River sites to 7.4 copies/ml in Nan River sites. As intensification of capture-based aquaculture could lead to depleting of wild fish stocks, urgent management is needed. However, the existing conventional approaches for assessment of fish overexploitation, survey and monitoring have several limitations.
Searcy R. T., Boehm A. B., Weinstock C., Preston C. M., Jensen S., Roman B., Birch J. M., Scholin C. A., Van Houtan K. S., Kiernan J. D., Yamahara K. M. (2022): High‐frequency and long‐term observations of eDNA from imperiled salmonids in a coastal stream: Temporal dynamics, relationships with environmental factors, and comparisons with conventional observations. Environmental DNA 4: 776-789.
FULL TEXT
Abstract
A greater understanding of eDNA behavior in the environment is needed before it can be employed for ecosystem monitoring applications. The objectives of this study were to use autonomous sampling to conduct long-term, high-frequency monitoring of the eDNA of native salmonid species in a Californian coastal stream, describe temporal variation of eDNA on multiple scales and identify environmental factors that drive this variation, and evaluate the ability of the eDNA datasets to detect rare species and represent organismal abundance. Using high-throughput autonomous environmental sample processors (ESPs) and qPCR, we enumerated eDNA concentrations from 674 water samples collected at subdaily intervals over 360 days at a single site. We detected eDNA from two imperiled salmonids (coho salmon Oncorhynchus kisutch and steelhead/rainbow trout O. mykiss) in most samples; O. kisutch eDNA was generally in lower concentration and more variable than O. mykiss eDNA. High-frequency (i.e., subdaily and daily) variability in salmonid eDNA concentrations showed occasional patchiness (i.e., large differences between consecutive samples), while seasonal differences were observed consistent with the ecology of the species at this site. Salmonid eDNA concentrations were significantly associated with creek discharge, photoperiod, and whether the creek mouth was open or closed by a seasonal sandbar. The release of hatchery-origin O. kisutch parr into the stream was associated with a significant increase in eDNA concentration for the remainder of the study. We compared eDNA signals with fish abundance data collected from traps located at the site. Fish were detected more often by eDNA than from trapping. Significant positive associations between fish abundance and eDNA concentrations were observed for O. mykiss; however, no such associations were observed for O. kisutch. This study adds to our knowledge on the occurrence and behavior of fish eDNA in lotic systems and informs future biomonitoring efforts using automated sampling technology.
Wilms T. J., Jacobsen M. W., Hansen B. K., Baktoft H., Bollhorn J., Scharff‐Olsen C. H., Bertelsen J. L., García E. G. A., Støttrup J. G., Nielsen E. E., Svendsen J. C. (2022): Environmental DNA reveals fine‐scale habitat associations for sedentary and resident marine species across a coastal mosaic of soft‐and hard‐bottom habitats. Environmental DNA 4: 954-971.
FULL TEXT
Abstract
Accurate knowledge on spatiotemporal distributions of marine species and their association with surrounding habitats is crucial to inform adaptive management actions responding to coastal degradation across the globe. Here, we investigate the potential use of environmental DNA (eDNA) to detect species–habitat associations in a patchy coastal area of the Baltic Sea. We directly compare species-specific qPCR analysis of eDNA with baited remote underwater video systems (BRUVS), two non-invasive methods widely used to monitor marine habitats. Four focal species (cod Gadus morhua, flounder Platichthys flesus, plaice Pleuronectes platessa, and goldsinny wrasse Ctenolabrus rupestris) were selected based on contrasting habitat associations (reef- vs. sand-associated species), as well as differential levels of mobility and residency, to investigate whether these factors affected the detection of species–habitat associations from eDNA. To this end, a species-specific qPCR assay for goldsinny wrasse is developed and made available herein. In addition, potential correlations between eDNA signals and abundance counts (MaxN) from videos were assessed. Results from Bayesian multilevel models revealed strong evidence for a sand association for sedentary flounder (98% posterior probability) and a reef association for highly resident wrasse (99% posterior probability) using eDNA, in agreement with BRUVS. However, contrary to BRUVS, eDNA sampling did not detect habitat associations for cod or plaice. We found a positive correlation between eDNA detection and MaxN for wrasse (posterior probability 95%), but not for the remaining species and explanatory power of all relationships was generally limited. Our results indicate that eDNA sampling can detect species–habitat associations on a fine spatial scale, yet this ability likely depends on the mobility and residency of the target organism, with associations for sedentary or resident species most likely to be detected. Combined sampling with conventional non-invasive methods is advised to improve detection of habitat associations for mobile and transient species, or for species with low eDNA concentrations.
Mouy X., Black M., Cox K., Qualley J., Dosso S., Juanes F. (2023): Identification of fish sounds in the wild using a set of portable audio‐video arrays. Methods in Ecology and Evolution.
FULL TEXT
Abstract
Associating fish sounds to specific species and behaviours is important for making passive acoustics a viable tool for monitoring fish. While recording fish sounds in tanks can sometimes be performed, many fish do not produce sounds in captivity. Consequently, there is a need to identify fish sounds in situ and characterise these sounds under a wide variety of behaviours and habitats. We designed three portable audio-video platforms capable of identifying species-specific fish sounds in the wild: a large array, a mini array and a mobile array. The large and mini arrays are static autonomous platforms than can be deployed on the seafloor and record audio and video for one to two weeks. They use multichannel acoustic recorders and low-cost video cameras mounted on PVC frames. The mobile array also uses a multichannel acoustic recorder, but mounted on a remotely operated vehicle with built-in video, which allows remote control and real-time positioning in response to observed fish presence. For all arrays, fish sounds were localised in three dimensions and matched to the fish positions in the video data. We deployed these three platforms at four locations off British Columbia, Canada. The large array provided the best localisation accuracy and, with its larger footprint, was well suited to habitats with a flat seafloor. The mini and mobile arrays had lower localisation accuracy but were easier to deploy, and well suited to rough/uneven seafloors. Using these arrays, we identified, for the first time, sounds from quillback rockfish Sebastes maliger, copper rockfish Sebastes caurinus and lingcod Ophiodon elongatus. In addition to measuring temporal and spectral characteristics of sounds for each species, we estimated mean source levels for lingcod and quillback rockfish sounds (115.4 and 113.5 dB re 1 μPa, respectively) and maximum detection ranges at two sites (between 10.5 and 33 m). All proposed array designs successfully identified fish sounds in the wild and were adapted to various budget, logistical and habitat constraints. We include here building instructions and processing scripts to help users replicate this methodology, identify more fish sounds around the world and make passive acoustics a more viable way to monitor fish.
Moyer G. R., Bartron M. L., Galbraith H. S., Grassi J., Rees C. B. (2023): Development and validation of two environmental DNA assays for American Eel (Anguilla rostrata). Environmental DNA 5: 175-190.
FULL TEXT
Abstract
We developed and validated two species-specific qPCR markers to detect American Eel environmental DNA. Marker validation included assay design, specificity and sensitivity testing, and in vivo laboratory and field experiments. Markers AME1 and AME2 targeted 116 and 129 bp fragments of the mitochondrial NADH dehydrogenase subunit 2 and cytochrome b genes, respectively. Markers were 94%–100% homologous for all 49 aligned American Eel sequences. Specificity tests, with known DNA obtained from 149 individuals spanning 81 fish species, amplified DNA derived from American Eel tissue exclusively. Each marker also had high sensitivity with LOD and LOQ values of 2.8–50 copies. For each marker, pilot testing of American Eel in aquaria at increasing densities (n = 0, 1, 5, 10 eels) showed a significant (p < 0.03) negative relationship between mean qPCR cycle threshold value and number of eels per tank. Our in situ testing of water samples collected from 35 sites on the East Coast (from as far south as Maryland to as far north as Maine) revealed that sites known to contain populations of American Eel (n = 11) were all positive for American Eel DNA, while sites where American Eel were presumed absent (n = 24) failed to amplify American Eel DNA. In three cases, our assays produced positive detections in the lower portion of a watershed but failed to detect American Eel upstream of a presumed impassible barrier in each of the same watersheds (all internal positive controls indicated no evidence of PCR inhibition in our field samples and all negative controls indicated no evidence of contamination). Our encouraging results of in vitro and in situ validation demonstrate the utility of using eDNA as a tool to aid in American Eel conservation efforts.
Rivera S. F., Vasselon V., Bouchez A., Rimet F. (2023): eDNA metabarcoding from aquatic biofilms allows studying spatial and temporal fluctuations of fish communities from Lake Geneva. Environmental DNA 5: 570-581.
FULL TEXT
Abstract
Fish communities are now studied non-invasively using environmental DNA (eDNA) recovered from water samples. The objective of this study is to evaluate the possibility of surveying these communities using fish eDNA passively “captured” by aquatic biofilms. To this end, biofilm samples developing on natural and artificial substrates were collected every 2 weeks for a year and a half in a large lake (Lake Geneva). DNA was extracted from biofilms and fish communities were targeted using a standard 12S barcode with a metabarcoding approach. The fish eDNA signal recovered from biofilms revealed temporal and spatial changes in fish communities. These changes were linked to fish habitat preferences and spawning season. Peaks in the eDNA signal of some taxa fitted with their spawning period reported in the literature. We evidenced that the nature of the biofilm’s substrate (natural or artificial) does not affect the image obtained of the fish community composition. Furthermore, by using biofilms grown on artificial substrates, the studied temporal window of the eDNA signal can be controlled. With biofilms acting as environmental passive samplers, our results open up the possibility to accurately monitor fish communities and their temporal and spatial changes with eDNA in a faster and less expensive way than with the classical water filtration approach.
Williams M. A., de Eyto E., Caestecker S., Regan F., Parle‐McDermott A. (2023): Development and field validation of RPA‐CRISPR‐Cas environmental DNA assays for the detection of brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus). Environmental DNA 5: 240-250.
FULL TEXT
Abstract
Molecular methods are rapidly evolving to enable nucleic acid diagnostics outside a laboratory setting. Such techniques are primarily utilizing isothermal amplification such as Recombinase Polymerase Amplification (RPA) and Loop-Mediated Isothermal Amplification (LAMP) but are yet to be fully explored for monitoring using environmental DNA (eDNA). We previously presented an RPA-CRISPR-Cas approach for detection of Atlantic salmon in Ireland and Canada and in this manuscript we present a further application of this technique for monitoring of brown trout and Arctic char in the Burrishoole Catchment, Co. Mayo, Ireland. In developing these assays, we offer an alternative approach to the PCR-based assays previously published and have evolved a streamlined approach to single-species monitoring using RPA-CRISPR-Cas, reducing the fluorescence acquisition time from 2 h to 30 min. This demonstrates the applicability of using RPA-CRISPR-Cas assays for eDNA-based detection beyond Atlantic salmon with the added benefit of a faster assay time without compromising detection sensitivity.
Yang J., Zhang L., Mu Y., Zhang X. (2023): Small changes make big progress: A more efficient eDNA monitoring method for freshwater fish. Environmental DNA 5: 363– 374.
FULL TEXT
Abstract
Comprehensive and accurate assessments of fish composition and diversity are essential for understanding fish ecology and resource management. Traditional fish surveys generally involve capturing organisms, which is invasive for the biological community under study and conflicts with the original intention of biodiversity conservation. Environmental DNA (eDNA) metabarcoding has become an integrated method for monitoring fish species without disturbing ecosystems. However, due to the serious nonspecific amplification of primers in eDNA-based monitoring, many non-fish sequences, usually human sequences, are also amplified, which results in serious data wastage and an increase in monitoring costs. We designed new universal primers for freshwater fish by analyzing the whole mitochondrial genome of Chinese freshwater fish. The performance of the primers was compared using an in silico polymerase chain reaction, followed by an in vitro metabarcoding analysis using eDNA from the Yangtze River, which is the third largest river in the world and harbors many freshwater fish species. We found that the mitochondrial 12S region is the most suitable metabarcoding gene marker for both Chinese and other freshwater fish. The minor change at the 3′-end of the primer can greatly reduce the nonspecific amplification and improve the effectiveness of eDNA metabarcoding. Even small changes in primers may have qualitative and quantitative effects on the detected biodiversity, which should be considered in experimental design and data interpretation. These results will help with primer design and selection for eDNA-based fish surveys, and consequently support the conservation of freshwater biodiversity.