Journal articles on the topic 'Environmental DNA (eDNA)'
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1
Pomohaibo, V. M., L. D. Orlova, and N. A. Vlasenko. "Environmental DNA: ecological and genetic aspects." Ecology and Noospherology 27, no. 1-2 (March 29, 2016): 16–24. http://dx.doi.org/10.15421/031602.
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Attention to environmental DNA (eDNA) was motivated by problem of undesirable gene transfer possibility from genetically modified plants to wild bacteria and other organisms. First studies have already examined persistence of DNA from these plants in soil, and also in the samples of nearby groundwater and river for a few kilometers from the place of cultivating. In soil it persists long time enough – from a few days to a few years, and in water – from a few hours to a few days. eDNA excreted from different sources – frozen ice cores, sediments of lakes, soil, caves, water of lakes, rivers and oceans, contains genetic information about biodiversity of present and ancient organisms. Researches revealed an important fact: data of eDNA and other sources, for example pollen, macrofossils, living animals and plants, complement each other, showing more reliable information about the variety of species, than used separately. Therefore the analysis eDNA needs to be not of considered alternative method of ecological researches, but an additional to traditional methods. In the process of study of eDNA it is necessary to take into account five aspects at least: its origin, physical state, conversion, transport and technical challenges. The origin of eDNA remains studied not enough. From a few publications it is known that eDNA comes in different composition excretions, leaves, hair, peeling etc., or as a result of released plasmids and chromosomal DNA from living prokaryotes. There are also possible secondary sources of eDNA – dead bodies and excretions of predators, scavengers, detritivores and coprovores. On the amount of the genetic material, released by organisms in an environment, various ontogenetic, trophic and other factors can have considerably influence. eDNA can be presented in both intracellular and extracellular forms.. Over time intracellular eDNA releases outside by influence of different ecological factors – activity of microorganisms, presence of extracellular enzymes, mechanical destruction etc. In further extracellular eDNA can break in corpuscles of different sizes – mainly within the limits of 1–10 μm. It can be free, adsorbed by other substances or dissolved. At certain conditions the period of eDNA persistence can be very great – from a few hours (in water) to hundred thousands of years (in frozen ice cores). Ancient eDNA is very fragmented and chemically changed by various physical, chemical and biological factors of environment. Substantive eDNA amount is taken up by bacteria and protozoa. Here it quickly metabolizes, but some its fragments can be integrated in a local genome. eDNA is able to be transported to great distance (from a few meters to 10 kilometers) that can appreciably influence on the results of its research. Also the laboratory experiment has certain problems – design (equipment, sequence of operations and condition of it realization), realization of experiment, authenticity of it will depend on quality of equipment and reagents, competence and honesty of scientific personnel etc.), ability of skilled researcher to give interpretation of results. Data that given in our review testifies that the active study of eDNA only began, and further intensive efforts of environmentalists and geneticists are needed in direction of it research. The results of such researches will allow to create the effective methods of scientifically reasonable recreating nature application.
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Sengupta, Mita E., Micaela Hellström, Henry C. Kariuki, Annette Olsen, Philip F. Thomsen, Helena Mejer, Eske Willerslev, et al. "Environmental DNA for improved detection and environmental surveillance of schistosomiasis." Proceedings of the National Academy of Sciences 116, no. 18 (April 11, 2019): 8931–40. http://dx.doi.org/10.1073/pnas.1815046116.
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Schistosomiasis is a water-based, infectious disease with high morbidity and significant economic burdens affecting >250 million people globally. Disease control has, with notable success, for decades focused on drug treatment of infected human populations, but a recent paradigm shift now entails moving from control to elimination. To achieve this ambitious goal, more sensitive diagnostic tools are needed to monitor progress toward transmission interruption in the environment, especially in low-intensity infection areas. We report on the development of an environmental DNA (eDNA)-based tool to efficiently detect DNA traces of the parasite Schistosoma mansoni directly in the aquatic environment, where the nonhuman part of the parasite life cycle occurs. This is a report of the successful detection of S. mansoni in freshwater samples by using aquatic eDNA. True eDNA was detected in as few as 10 cercariae per liter of water in laboratory experiments. The field applicability of the method was tested at known transmission sites in Kenya, where comparison of schistosome detection by conventional snail surveys (snail collection and cercariae shedding) with eDNA (water samples) showed 71% agreement between the methods. The eDNA method furthermore detected schistosome presence at two additional sites where snail shedding failed, demonstrating a higher sensitivity of eDNA sampling. We conclude that eDNA provides a promising tool to substantially improve the environmental surveillance of S. mansoni. Given the proper method and guideline development, eDNA could become an essential future component of the schistosomiasis control tool box needed to achieve the goal of elimination.
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Pedersen, Mikkel Winther, Søren Overballe-Petersen, Luca Ermini, Clio Der Sarkissian, James Haile, Micaela Hellstrom, Johan Spens, et al. "Ancient and modern environmental DNA." Philosophical Transactions of the Royal Society B: Biological Sciences 370, no. 1660 (January 19, 2015): 20130383. http://dx.doi.org/10.1098/rstb.2013.0383.
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DNA obtained from environmental samples such as sediments, ice or water (environmental DNA, eDNA), represents an important source of information on past and present biodiversity. It has revealed an ancient forest in Greenland, extended by several thousand years the survival dates for mainland woolly mammoth in Alaska, and pushed back the dates for spruce survival in Scandinavian ice-free refugia during the last glaciation. More recently, eDNA was used to uncover the past 50 000 years of vegetation history in the Arctic, revealing massive vegetation turnover at the Pleistocene/Holocene transition, with implications for the extinction of megafauna. Furthermore, eDNA can reflect the biodiversity of extant flora and fauna, both qualitatively and quantitatively, allowing detection of rare species. As such, trace studies of plant and vertebrate DNA in the environment have revolutionized our knowledge of biogeography. However, the approach remains marred by biases related to DNA behaviour in environmental settings, incomplete reference databases and false positive results due to contamination. We provide a review of the field.
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Bunce, Michael, and Allan Freeth. "Looking Further and Deeper into Environmental Protection, Regulation and Policy Using Environmental DNA (eDNA)." Policy Quarterly 18, no. 4 (November 6, 2022): 33–39. http://dx.doi.org/10.26686/pq.v18i4.8013.
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DNA sequencing technologies are transforming how environments are monitored. In this article, we pose the question: is environmental DNA (eDNA) the tool that Aotearoa New Zealand needs, but does not yet realise it does? The step change with eDNA is that genetic ‘breadcrumbs’ left behind in the environment can identify every living thing, from microbes to mammals, thus providing a more nuanced and holistic lens on ecosystems. Using eDNA, we can explore the biological networks that underpin healthy environments. Here we explore whether changes in policy setting, guidance, or pathways for uptake of eDNA are needed. Can eDNA help us make better decisions, inform policy and protections, track restoration, and act as a deterrent to reduce environmental harm?
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Havermans, Charlotte, Annkathrin Dischereit, Dmitrii Pantiukhin, Madlen Friedrich, and Ayla Murray. "ENVIRONMENTAL DNA IN AN OCEAN OF CHANGE: STATUS, CHALLENGES AND PROSPECTS." Arquivos de Ciências do Mar 55, Especial (March 18, 2022): 298–337. http://dx.doi.org/10.32360/acmar.v55iespecial.78188.
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Environmental DNA (eDNA) studies have burgeoned over the last two decades and the application of eDNA has increased exponentially since 2010, albeit at a slower pace in the marine system. We provide a literature overview on marine metazoan eDNA studies and assess recent achievements in answering questions related to species distributions, biodiversity and biomass. We investigate which are the better studied taxonomic groups, geographic regions and the genetic markers used. We evaluate the use of eDNA for addressing ecological and environmental issues through food web, ecotoxicological, surveillance and management studies. Based on this state of the art, we highlight exciting prospects of eDNA for marine time series, population genetic studies, the use of natural sampler DNA, and eDNA data for building trophic networks and ecosystem models. We discuss the current limitations, in terms of marker choice and incompleteness of reference databases. We also present recent advances using experiments and modeling to better understand persistence, decay and dispersal of eDNA in coastal and oceanic systems. Finally, we explore promising avenues for marine eDNA research, including autonomous or passive eDNA sampling, as well as the combined applications of eDNA with different surveillance methods and further molecular advances.
Keywords: environmental DNA, DNA metabarcoding, marine metazoa, biodiversity, population genetics, natural sampler DNA, diet analysis.
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Chavez, Francisco, Markus Min, Kathleen Pitz, Nathan Truelove, Jacoby Baker, Diana LaScala-Grunewald, Marguerite Blum, et al. "Observing Life in the Sea Using Environmental DNA." Oceanography 34, no. 2 (June 1, 2021): 102–19. http://dx.doi.org/10.5670/oceanog.2021.218.
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The use of environmental DNA (eDNA) for studying the ecology and variability of life in the sea is reviewed here in the context of US interagency Marine Biodiversity Observation Network (MBON) projects. Much of the information in this paper comes from samples collected within US National Marine Sanctuaries. The field of eDNA is relatively new but growing rapidly, and it has the potential to disrupt current paradigms developed on the basis of existing measurement methods. After a general review of the field, we provide specific examples of the type of information that eDNA provides regarding the changing distribution of life in the sea over space (horizontally and vertically) and time. We conclude that eDNA analyses yield results that are similar to those collected using traditional observation methods, are complementary to them, and because of the breadth of information provided, have the potential to improve conservation and management practices. Moreover, through technology development and standardization of methods, eDNA offers a means to scale biological observations globally to a level similar to those currently made for ocean physics and biogeochemistry. This scaling can ultimately result in a far better understanding of global marine biodiversity and contribute to better management and sustainable use of the world ocean. Improved information management systems that track methods and associated metadata, together with international coordination, will be needed to realize a global eDNA observation network.
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Shu, Lu, Shijing Chen, Ping Li, and Zuogang Peng. "Environmental DNA Metabarcoding Reflects Fish DNA Dynamics in Lentic Ecosystems: A Case Study of Freshwater Ponds." Fishes 7, no. 5 (September 26, 2022): 257. http://dx.doi.org/10.3390/fishes7050257.
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Environmental DNA (eDNA) is a good indicator of fish diversity and distribution in aquatic environments. This study used metabarcoding to assess fish diversity and distribution in two connected ponds during two sampling periods. The eDNA analysis of surface samples displayed differences in the fish communities between the two connected ponds, while within each sampling site the species detected across the two time points were not always the same. These results revealed poor horizontal transport of eDNA between the two connected ponds alongside poor mixing of eDNA for a single pond’s stocked fish. Additionally, water temperature, pH, and total nitrogen were the key environmental factors affecting fish eDNA spatial and temporal distribution. These findings have important implications for designing eDNA sampling strategies in lentic ecosystems; for example, complete fish diversity in a lentic ecosystem cannot be detected by collecting only surface samples and in only one sampling period.
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Shu, Lu, Arne Ludwig, and Zuogang Peng. "Standards for Methods Utilizing Environmental DNA for Detection of Fish Species." Genes 11, no. 3 (March 11, 2020): 296. http://dx.doi.org/10.3390/genes11030296.
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Environmental DNA (eDNA) techniques are gaining attention as cost-effective, non-invasive strategies for acquiring information on fish and other aquatic organisms from water samples. Currently, eDNA approaches are used to detect specific fish species and determine fish community diversity. Various protocols used with eDNA methods for aquatic organism detection have been reported in different eDNA studies, but there are no general recommendations for fish detection. Herein, we reviewed 168 papers to supplement and highlight the key criteria for each step of eDNA technology in fish detection and provide general suggestions for eliminating detection errors. Although there is no unified recommendation for the application of diverse eDNA in detecting fish species, in most cases, 1 or 2 L surface water collection and eDNA capture on 0.7-μm glass fiber filters followed by extraction with a DNeasy Blood and Tissue Kit or PowerWater DNA Isolation Kit are useful for obtaining high-quality eDNA. Subsequently, species-specific quantitative polymerase chain reaction (qPCR) assays based on mitochondrial cytochrome b gene markers or eDNA metabarcoding based on both 12S and 16S rRNA markers via high-throughput sequencing can effectively detect target DNA or estimate species richness. Furthermore, detection errors can be minimized by mitigating contamination, negative control, PCR replication, and using multiple genetic markers. Our aim is to provide a useful strategy for fish eDNA technology that can be applied by researchers, advisors, and managers.
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Cristescu, Melania E., and Paul D. N. Hebert. "Uses and Misuses of Environmental DNA in Biodiversity Science and Conservation." Annual Review of Ecology, Evolution, and Systematics 49, no. 1 (November 2, 2018): 209–30. http://dx.doi.org/10.1146/annurev-ecolsys-110617-062306.
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The study of environmental DNA (eDNA) has the potential to revolutionize biodiversity science and conservation action by enabling the census of species on a global scale in near real time. To achieve this promise, technical challenges must be resolved. In this review, we explore the main uses of eDNA as well as the complexities introduced by its misuse. Current eDNA methods require refinement and improved calibration and validation along the entire workflow to lessen false positives/negatives. Moreover, there is great need for a better understanding of the “natural history” of eDNA—its origins, state, lifetime, and transportation—and for more detailed insights concerning the physical and ecological limitations of eDNA use. Although eDNA analysis can provide powerful information, particularly in freshwater and marine environments, its impact is likely to be less significant in terrestrial settings. The broad adoption of eDNA tools in conservation will largely depend on addressing current uncertainties in data interpretation.
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Hayer, Cari-Ann, Michael F. Bayless, Amy George, Nathan Thompson, Catherine A. Richter, and Duane C. Chapman. "Use of Environmental DNA to Detect Grass Carp Spawning Events." Fishes 5, no. 3 (August 27, 2020): 27. http://dx.doi.org/10.3390/fishes5030027.
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The timing and location of spawning events are important data for managers seeking to control invasive grass carp populations. Ichthyoplankton tows for grass carp eggs and larvae can be used to detect spawning events; however, these samples can be highly debris-laden, and are expensive and laborious to process. An alternative method, environmental DNA (eDNA) technology, has proven effective in determining the presence of aquatic species. The objectives of this project were to assess the use of eDNA collections and quantitative eDNA analysis to assess the potential spawning of grass carp in five reservoir tributaries, and to compare those results to the more traditional method of ichthyoplankton tows. Grass carp eDNA was detected in 56% of sampling occasions and was detected in all five rivers. Concentrations of grass carp eDNA were orders of magnitude higher in June, corresponding to elevated discharge and egg presence. Grass carp environmental DNA flux (copies/h) was lower when no eggs were present and was higher when velocities and discharge increased and eggs were present. There was a positive relationship between grass carp eDNA flux and egg flux. Our results support the further development of eDNA analysis as a method to detect the spawning events of grass carp or other rheophilic spawners.
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Kelly, Ryan P., Ramón Gallego, and Emily Jacobs-Palmer. "The effect of tides on nearshore environmental DNA." PeerJ 6 (March 19, 2018): e4521. http://dx.doi.org/10.7717/peerj.4521.
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We can recover genetic information from organisms of all kinds using environmental sampling. In recent years, sequencing this environmental DNA (eDNA) has become a tractable means of surveying many species using water, air, or soil samples. The technique is beginning to become a core tool for ecologists, environmental scientists, and biologists of many kinds, but the temporal resolution of eDNA sampling is often unclear, limiting the ecological interpretations of the resulting datasets. Here, in a temporally and spatially replicated field study using ca. 313 bp of eukaryotic COI mtDNA as a marker, we find that nearshore organismal communities are largely consistent across tides. Our findings suggest that nearshore eDNA from both benthic and planktonic taxa tends to be endogenous to the site and water mass sampled, rather than changing with each tidal cycle. However, where physiochemical water mass characteristics change, we find that the relative contributions of a broad range of organisms to eDNA communities shift in concert.
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Takahashi, Sayaka, Shingo Takada, Hiroki Yamanaka, Reiji Masuda, and Akihide Kasai. "Intraspecific genetic variability and diurnal activity affect environmental DNA detection in Japanese eel." PLOS ONE 16, no. 9 (September 16, 2021): e0255576. http://dx.doi.org/10.1371/journal.pone.0255576.
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Environmental DNA (eDNA) analysis with species-specific primer/probe sets is promising as a tool to quantify fish abundance and distribution. Nevertheless, several factors could reduce the accuracy of this method. Here, we aimed to analyze whether intraspecific variability and diel activity rhythm affect eDNA detection in Japanese eels (Anguilla japonica). For this purpose, we performed tank experiments focusing on two points. First, we assessed the effects of base pair sequences with probe region polymorphism on eDNA detection. Next, we evaluated the influences of diel rhythm, activity, and individual differences in eDNA release rate on eDNA concentration. We examined the base pair sequences of the probe regions of 20 individuals and found genetic mismatches in two of them. The eDNA concentration was estimated to be much lower in these variants than it was in the other individuals. We conducted a rearing experiment on four non-variant individuals to explore the influences of diel activity and inter-individual differences in eDNA detection. Nocturnal eel activity was reflected in the eDNA detection but the inter-individual differences remained large. The observed weak positive correlations between eDNA concentration and activity suggest that eDNA emission is highly dependent on basal metabolism. The present study suggests that consideration of polymorphic sites at the probe region and diel activity rhythms should improve the accuracy and precision of abundance estimation through eDNA. Such fine-tuning is applicable not only for eels but also for other fishes to be targeted by eDNA technology.
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Hassan, Shahnawaz, Sabreena, Peter Poczai, Bashir Ah Ganai, Waleed Hassan Almalki, Abdul Gafur, and R. Z. Sayyed. "Environmental DNA Metabarcoding: A Novel Contrivance for Documenting Terrestrial Biodiversity." Biology 11, no. 9 (August 31, 2022): 1297. http://dx.doi.org/10.3390/biology11091297.
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The dearth of cardinal data on species presence, dispersion, abundance, and habitat prerequisites, besides the threats impeded by escalating human pressure has enormously affected biodiversity conservation. The innovative concept of eDNA, has been introduced as a way of overcoming many of the difficulties of rigorous conventional investigations, and is hence becoming a prominent and novel method for assessing biodiversity. Recently the demand for eDNA in ecology and conservation has expanded exceedingly, despite the lack of coordinated development in appreciation of its strengths and limitations. Therefore it is pertinent and indispensable to evaluate the extent and significance of eDNA-based investigations in terrestrial habitats and to classify and recognize the critical considerations that need to be accounted before using such an approach. Presented here is a brief review to summarize the prospects and constraints of utilizing eDNA in terrestrial ecosystems, which has not been explored and exploited in greater depth and detail in such ecosystems. Given these obstacles, we focused primarily on compiling the most current research findings from journals accessible in eDNA analysis that discuss terrestrial ecosystems (2012–2022). In the current evaluation, we also review advancements and limitations related to the eDNA technique.
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Furlan, Elise M., and Dianne Gleeson. "Improving reliability in environmental DNA detection surveys through enhanced quality control." Marine and Freshwater Research 68, no. 2 (2017): 388. http://dx.doi.org/10.1071/mf15349.
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Species-specific environmental DNA (eDNA) surveys are increasingly being used to infer species presence in an environment. Current inadequacies in quality control increase concern for false negatives, which can have serious ramifications for both the management of invasive species and the conservation of native species. eDNA surveys involve a multi-step process to sample, capture, extract and amplify target DNA from the environment. We outline various positive control options and show that many of the commonly used controls are capable of detecting false negatives arising during the amplification stage only. We suggest a secondary, generic primer, designed to co-amplify endogenous DNA sampled during species-specific eDNA surveys, constitutes a superior positive control to monitor method success throughout all stages of eDNA analysis. We develop a species-specific European carp (Cyprinus carpio) assay and a generic fish assay for use as an endogenous control for eDNA surveys in Australian freshwater systems where fish are known to be abundant. We use these assays in a multiplex on eDNA samples that are simultaneously sampled, captured, extracted and amplified. This positive control allows us to distinguish method error from informative non-amplification results, improving reliability in eDNA surveys, which will ultimately lead to better informed conservation management decisions.
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Pilliod, David S., Caren S. Goldberg, Robert S. Arkle, and Lisette P. Waits. "Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples." Canadian Journal of Fisheries and Aquatic Sciences 70, no. 8 (August 2013): 1123–30. http://dx.doi.org/10.1139/cjfas-2013-0047.
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Environmental DNA (eDNA) methods for detecting aquatic species are advancing rapidly, but with little evaluation of field protocols or precision of resulting estimates. We compared sampling results from traditional field methods with eDNA methods for two amphibians in 13 streams in central Idaho, USA. We also evaluated three water collection protocols and the influence of sampling location, time of day, and distance from animals on eDNA concentration in the water. We found no difference in detection or amount of eDNA among water collection protocols. eDNA methods had slightly higher detection rates than traditional field methods, particularly when species occurred at low densities. eDNA concentration was positively related to field-measured density, biomass, and proportion of transects occupied. Precision of eDNA-based abundance estimates increased with the amount of eDNA in the water and the number of replicate subsamples collected. eDNA concentration did not vary significantly with sample location in the stream, time of day, or distance downstream from animals. Our results further advance the implementation of eDNA methods for monitoring aquatic vertebrates in stream habitats.
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Carraro, Luca, Hanna Hartikainen, Jukka Jokela, Enrico Bertuzzo, and Andrea Rinaldo. "Estimating species distribution and abundance in river networks using environmental DNA." Proceedings of the National Academy of Sciences 115, no. 46 (October 29, 2018): 11724–29. http://dx.doi.org/10.1073/pnas.1813843115.
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All organisms leave traces of DNA in their environment. This environmental DNA (eDNA) is often used to track occurrence patterns of target species. Applications are especially promising in rivers, where eDNA can integrate information about populations upstream. The dispersion of eDNA in rivers is modulated by complex processes of transport and decay through the dendritic river network, and we currently lack a method to extract quantitative information about the location and density of populations contributing to the eDNA signal. Here, we present a general framework to reconstruct the upstream distribution and abundance of a target species across a river network, based on observed eDNA concentrations and hydro-geomorphological features of the network. The model captures well the catchment-wide spatial biomass distribution of two target species: a sessile invertebrate (the bryozoan Fredericella sultana) and its parasite (the myxozoan Tetracapsuloides bryosalmonae). Our method is designed to easily integrate general biological and hydrological data and to enable spatially explicit estimates of the distribution of sessile and mobile species in fluvial ecosystems based on eDNA sampling.
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Brady, Sean F., Carol J. Chao, and Jon Clardy. "Long-Chain N-Acyltyrosine Synthases from Environmental DNA." Applied and Environmental Microbiology 70, no. 11 (November 2004): 6865–70. http://dx.doi.org/10.1128/aem.70.11.6865-6870.2004.
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ABSTRACT The heterologous expression of DNA extracted directly from environmental samples (environmental DNA [eDNA]) in easily cultured hosts provides access to natural products produced by previously inaccessible microorganisms. When eDNA cosmid libraries were screened in Escherichia coli for antibacterially active clones, long-chain N-acyltyrosine-producing clones were found in every eDNA library. These apparently common natural products have not been previously described from screening extracts of cultured bacteria for biologically active natural products. Of the 11 long-chain N-acyl amino acid synthases (NASs) that were characterized, 10 are unique sequences. A predicted protein of previously unknown function from Nitrosomonas europaea, a gram-negative nitrifying beta-proteobacterium, is 14 to 37% identical to eDNA NASs. When cloned into E. coli, this open reading frame confers the production of long-chain N-acyltyrosines to the host and is therefore the first NAS from a cultured bacterium to be functionally characterized. Understanding the role that long-chain N-acyl amino acids play in soil microbial communities should now be feasible with the identification of a cultured organism that has the genetic capacity to produce these compounds.
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Iwai, Noriko, Kiyomi Yasumiba, and Teruhiko Takahara. "Efficacy of environmental DNA to detect and quantify stream tadpoles of Odorrana splendida." Royal Society Open Science 6, no. 1 (January 2019): 181798. http://dx.doi.org/10.1098/rsos.181798.
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Environmental DNA (eDNA) can be used to detect and estimate the density of rare or secretive species, especially in aquatic systems. However, the efficacy of eDNA method has not been validated in lotic systems. We examined the efficacy of the eDNA method to detect and estimate abundance and biomass of a stream-dwelling frog species, Odorrana splendida . We conducted eight field surveys over 2 years and obtained 53 water samples from 10 streams with known distribution of O. splendida tadpoles. The eDNA method accurately detected the presence of O. splendida in 79.2% of survey samples. The amount of O. splendida eDNA (copies s −1 ) in the water samples fluctuated seasonally and each site showed different peaks during different seasons. The relationship between the abundance or biomass of tadpoles and the amount of eDNA was significantly positive, but was not strong, probably because of a large difference in the relationship patterns among streams. In lotic systems, water flow might prevent even distribution of eDNA and thus make it difficult to obtain eDNA reflecting its total amount in the water. Sampling a larger amount of water or higher number of subsamples might more accurately reflect the presence and absolute amount of eDNA in water.
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Lacoursière-Roussel, Anaïs, Yohann Dubois, Eric Normandeau, and Louis Bernatchez. "Improving herpetological surveys in eastern North America using the environmental DNA method." Genome 59, no. 11 (November 2016): 991–1007. http://dx.doi.org/10.1139/gen-2015-0218.
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Among vertebrates, herpetofauna has the highest proportion of declining species. Detection of environmental DNA (eDNA) is a promising method towards significantly increasing large-scale herpetological conservation efforts. However, the integration of eDNA results within a management framework requires an evaluation of the efficiency of the method in large natural environments and the calibration of eDNA surveys with the quantitative monitoring tools currently used by conservation biologists. Towards this end, we first developed species-specific primers to detect the wood turtle (Glyptemys insculpta) a species at risk in Canada, by quantitative PCR (qPCR). The rate of eDNA detection obtained by qPCR was also compared to the relative abundance of this species in nine rivers obtained by standardized visual surveys in the Province of Québec (Canada). Second, we developed multi-species primers to detect North American amphibian and reptile species using eDNA metabarcoding analysis. An occurrence index based on the distribution range and habitat type was compared with the eDNA metabarcoding dataset from samples collected in seven lakes and five rivers. Our results empirically support the effectiveness of eDNA metabarcoding to characterize herpetological species distributions. Moreover, detection rates provided similar results to standardized visual surveys currently used to develop conservation strategies for the wood turtle. We conclude that eDNA detection rates may provide an effective semiquantitative survey tool, provided that assay calibration and standardization is performed.
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Pinakhina, Daria V., and Elena M. Chekunova. "Environmental DNA: history of studies, current and perspective applications in fundamental and applied research." Ecological genetics 18, no. 4 (December 12, 2020): 493–509. http://dx.doi.org/10.17816/ecogen25900.
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This review article is dedicated to a relatively young, actively developing approach to biodiversity assessment analysis of environmental DNA (or eDNA). Current views on the nature of eDNA, a brief overview of the history of this approach and methods of eDNA analysis are presented. Major research directions, utilizing eDNA techniques, and perspectives of their application to the study of biodiversity are described. Key issues in development of eDNA approach, its advantages and drawbacks are outlined.
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Cornman, Robert S., James E. McKenna, Jr., and Jennifer A. Fike. "Composition and distribution of fish environmental DNA in an Adirondack watershed." PeerJ 9 (February 26, 2021): e10539. http://dx.doi.org/10.7717/peerj.10539.
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Background Environmental DNA (eDNA) surveys are appealing options for monitoring aquatic biodiversity. While factors affecting eDNA persistence, capture and amplification have been heavily studied, watershed-scale surveys of fish communities and our confidence in such need further exploration. Methods We characterized fish eDNA compositions using rapid, low-volume filtering with replicate and control samples scaled for a single Illumina MiSeq flow cell, using the mitochondrial 12S ribosomal RNA locus for taxonomic profiling. Our goals were to determine: (1) spatiotemporal variation in eDNA abundance, (2) the filtrate needed to achieve strong sequencing libraries, (3) the taxonomic resolution of 12S ribosomal sequences in the study environment, (4) the portion of the expected fish community detectable by 12S sequencing, (5) biases in species recovery, (6) correlations between eDNA compositions and catch per unit effort (CPUE) and (7) the extent that eDNA profiles reflect major watershed features. Our bioinformatic approach included (1) estimation of sequencing error from unambiguous mappings and simulation of taxonomic assignment error under various mapping criteria; (2) binning of species based on inferred assignment error rather than by taxonomic rank; and (3) visualization of mismatch distributions to facilitate discovery of distinct haplotypes attributed to the same reference. Our approach was implemented within the St. Regis River, NY, USA, which supports tribal and recreational fisheries and has been a target of restoration activities. We used a large record of St. Regis-specific observations to validate our assignments. Results We found that 300 mL drawn through 25-mm cellulose nitrate filters yielded greater than 5 ng/µL DNA at most sites in summer, which was an approximate threshold for generating strong sequencing libraries in our hands. Using inferred sequence error rates, we binned 12S references for 110 species on a state checklist into 85 single-species bins and seven multispecies bins. Of 48 bins observed by capture survey in the St. Regis, we detected eDNA consistent with 40, with an additional four detections flagged as potential contaminants. Sixteen unobserved species detected by eDNA ranged from plausible to implausible based on distributional data, whereas six observed species had no 12S reference sequence. Summed log-ratio compositions of eDNA-detected taxa correlated with log(CPUE) (Pearson’s R = 0.655, P < 0.001). Shifts in eDNA composition of several taxa and a genotypic shift in channel catfish (Ictalurus punctatus) coincided with the Hogansburg Dam, NY, USA. In summary, a simple filtering apparatus operated by field crews without prior expertise gave useful summaries of eDNA composition with minimal evidence of field contamination. 12S sequencing achieved useful taxonomic resolution despite the short marker length, and data exploration with standard bioinformatic tools clarified taxonomic uncertainty and sources of error.
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Šuláková, Martina, Jarmila Pazlarová, Rikke Louise Meyer, and Kateřina Demnerová. "Distribution of extracellular DNA in Listeria monocytogenes biofilm." Czech Journal of Food Sciences 37, No. 6 (December 31, 2019): 409–16. http://dx.doi.org/10.17221/9/2019-cjfs.
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Extracellular DNA (eDNA) is an abundant matrix component that protects biofilm from environmental stress, facilitate horizontal gene transfer, and serve as a source of nutrients. eDNA is also found in Listeria monocytogenes biofilm, but it is unknown to which extent its importance as a matrix component varies in terms of phylogenetic relatedness. This study aims to determine if these variations exist. Biofilm forming capacity of ten L. monocytogenes strains of different phylogenetic lineages and serotypes was examined using crystal violet assay at 37°C and 22°C. eDNA content was evaluated fluorometrically at 37°C and at 22°C, then the 3D structure of biofilm was studied by confocal laser scanning microscopy (CLSM). Biofilm forming capacity differed significantly between the culturing conditions and was higher at 37°C than at ambient temperature. eDNA signal distribution was found to be influenced by strain and lineage. CLSM images revealed information about spatial distribution in the biofilm. The information about the eDNA spatial organisation in the biofilm contributes to the understanding of the role of eDNA in a biofilm formation.
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Jones, Rhys Aled, Chelsea N. Davis, Dewi Llyr Jones, Fiona Tyson, Emma Davies, David Cutress, Peter M. Brophy, Michael T. Rose, Manod Williams, and Hefin Wyn Williams. "Temporal dynamics of trematode intermediate snail host environmental DNA in small water body habitats." Parasitology 148, no. 12 (June 30, 2021): 1490–96. http://dx.doi.org/10.1017/s0031182021001104.
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AbstractEnvironmental DNA (eDNA) surveying has potential to become a powerful tool for sustainable parasite control. As trematode parasites require an intermediate snail host that is often aquatic or amphibious to fulfil their lifecycle, water-based eDNA analyses can be used to screen habitats for the presence of snail hosts and identify trematode infection risk areas. The aim of this study was to identify climatic and environmental factors associated with the detection of Galba truncatula eDNA. Fourteen potential G. truncatula habitats on two farms were surveyed over a 9-month period, with eDNA detected using a filter capture, extraction and PCR protocol with data analysed using a generalized estimation equation. The probability of detecting G. truncatula eDNA increased in habitats where snails were visually detected, as temperature increased, and as water pH decreased (P < 0.05). Rainfall was positively associated with eDNA detection in watercourse habitats on farm A, but negatively associated with eDNA detection in watercourse habitats on farm B (P < 0.001), which may be explained by differences in watercourse gradient. This study is the first to identify factors associated with trematode intermediate snail host eDNA detection. These factors should be considered in standardized protocols to evaluate the results of future eDNA surveys.
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Nevers, Meredith B., Kasia Przybyla-Kelly, Dawn Shively, Charles C. Morris, Joshua Dickey, and Murulee N. Byappanahalli. "Influence of sediment and stream transport on detecting a source of environmental DNA." PLOS ONE 15, no. 12 (December 28, 2020): e0244086. http://dx.doi.org/10.1371/journal.pone.0244086.
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Environmental DNA (eDNA) can be used for early detection, population estimations, and assessment of potential spread of invasive species, but questions remain about factors that influence eDNA detection results. Efforts are being made to understand how physical, chemical, and biological factors—settling, resuspension, dispersion, eDNA stability/decay—influence eDNA estimations and potentially population abundance. In a series of field and controlled mesocosm experiments, we examined the detection and accumulation of eDNA in sediment and water and the transport of eDNA in a small stream in the Lake Michigan watershed, using the invasive round goby fish (Neogobius melanostomus) as a DNA source. Experiment 1: caged fish (average n = 44) were placed in a stream devoid of round goby; water was collected over 24 hours along 120-m of stream, including a simultaneous sampling event at 7 distances from DNA source; stream monitoring continued for 24 hours after fish were removed. Experiment 2: round goby were placed in laboratory tanks; water and sediment were collected over 14 days and for another 150 days post-fish removal to calculate eDNA shedding and decay rates for water and sediment. For samples from both experiments, DNA was extracted, and qPCR targeted a cytochrome oxidase I gene (COI) fragment specific to round goby. Results indicated that eDNA accumulated and decayed more slowly in sediment than water. In the stream, DNA shedding was markedly lower than calculated in the laboratory, but models indicate eDNA could potentially travel long distances (up to 50 km) under certain circumstances. Collectively, these findings show that the interactive effects of ambient conditions (e.g., eDNA stability and decay, hydrology, settling-resuspension) are important to consider when developing comprehensive models. Results of this study can help resource managers target representative sites downstream of potential invasion sites, thereby maximizing resource use.
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Doi, Hideyuki, Izumi Katano, Yusuke Sakata, Rio Souma, Toshihiro Kosuge, Mariko Nagano, Kousuke Ikeda, Koki Yano, and Koji Tojo. "Detection of an endangered aquatic heteropteran using environmental DNA in a wetland ecosystem." Royal Society Open Science 4, no. 7 (July 2017): 170568. http://dx.doi.org/10.1098/rsos.170568.
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The use of environmental DNA (eDNA) has recently been employed to evaluate the distribution of various aquatic macroorganisms. Although this technique has been applied to a broad range of taxa, from vertebrates to invertebrates, its application is limited for aquatic insects such as aquatic heteropterans . Nepa hoffmanni (Heteroptera: Nepidae) is a small (approx. 23 mm) aquatic heteropteran that inhabits wetlands, can be difficult to capture and is endangered in Japan. The molecular tool eDNA was used to evaluate the species distribution of N. hoffmanni in comparison to that determined using hand-capturing methods in two regions of Japan. The eDNA of N. hoffmanni was detected at nearly all sites (10 eDNA-detected sites out of 14 sites), including sites where N. hoffmanni was not captured by hand (five eDNA-detected sites out of six captured sites). Thus, this species-specific eDNA technique can be applied to detect small, sparsely distributed heteropterans in wetland ecosystems. In conclusion, eDNA could be a valuable technique for the detection of aquatic insects inhabiting wetland habitats, and could make a significant contribution to providing distribution data necessary to species conservation.
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Simmons, Megan, Andrew Tucker, W. Lindsay Chadderton, Christopher L. Jerde, and Andrew R. Mahon. "Active and passive environmental DNA surveillance of aquatic invasive species." Canadian Journal of Fisheries and Aquatic Sciences 73, no. 1 (January 2016): 76–83. http://dx.doi.org/10.1139/cjfas-2015-0262.
Full textAbstract:
Environmental DNA (eDNA) is useful for delimiting species ranges in aquatic systems, whereby water samples are screened for the presence of DNA from a single species. However, DNA from many species is collected in every sample, and high-throughput sequencing approaches allow for more passive surveillance where a community of species is identified. In this study, we use active (targeted) and passive molecular surveillance approaches to detect species in the Muskingum River Watershed in Ohio, USA. The presence of bighead carp (Hypophthalmichthys nobilis) eDNA in the Muskingum River Watershed was confirmed with active surveillance using digital droplet polymerase chain reaction (ddPCR). The passive surveillance method detected the presence of eDNA from northern snakehead (Channa argus), which was further confirmed with active ddPCR. Whereas active surveillance may be more sensitive to detecting rare DNA, passive surveillance has the capability of detecting unexpected invasive species. Deploying both active and passive surveillance approaches with the same eDNA samples is beneficial for invasive species management.
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Ratsch, Rikki, Bruce A. Kingsbury, and Mark A. Jordan. "Exploration of Environmental DNA (eDNA) to Detect Kirtland’s Snake (Clonophis kirtlandii)." Animals 10, no. 6 (June 19, 2020): 1057. http://dx.doi.org/10.3390/ani10061057.
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Environmental DNA (eDNA) surveys utilize DNA shed by organisms into their environment in order to detect their presence. This technique has proven effective in many systems for detecting rare or cryptic species that require high survey effort. One potential candidate for eDNA surveying is Kirtland’s Snake (Clonophis kirtlandii), a small natricine endemic to the midwestern USA and threatened throughout its range. Due to its cryptic and fossorial lifestyle, it is also a notoriously difficult snake to survey, which has limited efforts to understand its ecology. Our goal was to utilize eDNA surveys for this species to increase detection probability and improve survey efficiency to assist future conservation efforts. We conducted coverboard surveys and habitat analyses to determine the spatial and temporal activity of snakes, and used this information to collect environmental samples in areas of high and low snake activity. In addition, we spiked artificial crayfish burrows with Kirtland’s Snake feces to assess the persistence of eDNA under semi-natural conditions. A quantitative PCR (qPCR) assay using a hydrolysis probe was developed to screen the environmental samples for Kirtland’s Snake eDNA that excluded closely related and co-occurring species. Our field surveys showed that snakes were found in the spring during the first of two seasons, and in areas with abundant grass, herbaceous vegetation, and shrubs. We found that eDNA declines within a week under field conditions in artificial crayfish burrows. In environmental samples of crayfish burrow water and sediment, soil, and open water, a single detection was found out of 380 samples. While there may be physicochemical and biological explanations for the low detection observed, characteristics of assay performance and sampling methodology may have also increased the potential for false negatives. We explored these outcomes in an effort to refine and advance the successful application of eDNA surveying in snakes and groundwater microhabitats.
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Clarke, Laurence J., Leonie Suter, Bruce E. Deagle, Andrea M. Polanowski, Aleks Terauds, Glenn J. Johnstone, and Jonathan S. Stark. "Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems." PeerJ 9 (November 15, 2021): e12458. http://dx.doi.org/10.7717/peerj.12458.
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Antarctic benthic ecosystems support high biodiversity but their characterization is limited to a few well-studied areas, due to the extreme environment and remoteness making access and sampling difficult. Our aim was to compare water and sediment as sources of environmental DNA (eDNA) to better characterise Antarctic benthic communities and further develop practical approaches for DNA-based biodiversity assessment in remote environments. We used a cytochrome c oxidase subunit I (COI) metabarcoding approach to characterise metazoan communities in 26 nearshore sites across 12 locations in the Vestfold Hills (East Antarctica) based on DNA extracted from either sediment cores or filtered seawater. We detected a total of 99 metazoan species from 12 phyla across 26 sites, with similar numbers of species detected in sediment and water eDNA samples. However, significantly different communities were detected in the two sample types at sites where both were collected (i.e., where paired samples were available). For example, nematodes and echinoderms were more likely to be detected exclusively in sediment and water eDNA samples, respectively. eDNA from water and sediment core samples are complementary sample types, with epifauna more likely to be detected in water column samples and infauna in sediment. More reference DNA sequences are needed for infauna/meiofauna to increase the proportion of sequences and number of taxa that can be identified. Developing a better understanding of the temporal and spatial dynamics of eDNA at low temperatures would also aid interpretation of eDNA signals from polar environments. Our results provide a preliminary scan of benthic metazoan communities in the Vestfold Hills, with additional markers required to provide a comprehensive biodiversity survey. However, our study demonstrates the choice of sample type for eDNA studies of benthic ecosystems (sediment, water or both) needs to be carefully considered in light of the research or monitoring question of interest.
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Fitzgerald, Amy, Jennifer Halliday, and Daniel Heath. "Environmental DNA as Novel Technology: Lessons in Agenda Setting and Framing in News Media." Animals 11, no. 10 (September 30, 2021): 2874. http://dx.doi.org/10.3390/ani11102874.
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Environmental DNA (eDNA) is an emerging technology used for understanding ecosystems, environmental change, and stressors. Cellular and extracellular DNA are collected from environmental samples instead of individual wildlife animals, and as such eDNA comes with associated logistical and ethical benefits. It is increasingly being used, yet to date public knowledge and perceptions of eDNA have not been explored. Given that most of the public gathers scientific information from news media sources, this is a logical first place to start. This paper reports on a framing and agenda-setting analysis of news media coverage of eDNA in Canada and the United States from 2000 to 2020. The findings indicate that eDNA is being framed as an emerging and powerful tool, although questions regarding its validity and reliability are raised vis-à-vis identifying the presence of invasive species. Less than half of the news articles analyzed address broader social or ethical issues in relation to eDNA, and the majority focus on the potential financial impacts of eDNA findings on development projects and business interests. The potential ethical advantages of non-lethal sampling methods used via eDNA sampling are not addressed, nor are the potential ethical issues raised by its potential use in bioprospecting, indicating that the current state of agenda setting regarding eDNA in these newspapers is focused on economic impacts, to the exclusion of potential ethical issues. This unfolding news coverage will likely be key to understanding public perceptions of this novel technology.
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Yu, Xue, Jiaying Zhou, Jun Wei, Bo Zhang, and Xueqiang Lu. "Temperature May Play a More Important Role in Environmental DNA Decay than Ultraviolet Radiation." Water 14, no. 19 (October 9, 2022): 3178. http://dx.doi.org/10.3390/w14193178.
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Environmental DNA (eDNA) preservation is crucial for biological monitoring using eDNA technology. The decay of eDNA over time in natural water bodies and the effects of temperature and ultraviolet (UV) radiation on the decay rate are largely unknown. In this study, the linear and exponential decay models were used to explore the relationship between residual eDNA content and decay time, respectively. It was found that the residual eDNA content treated with a higher temperature decreased by an average of 89.65% at the end of experiment, while those in the 4 °C treatment group remained stable. The higher decision coefficient (R2) of the exponential decay models indicated that they could better reflect the decay of eDNA over time than linear. The difference in the decay rates of the exponential modes was slight between the 20 °C (25.47%) and 20 °C + UV treatment groups (31.64%), but both were much higher than that of the 4 °C group (2.94%). The results suggest that water temperature significantly affected the decay rate of eDNA, while UV radiation had little effect.
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O’Donnell, James L., Ryan P. Kelly, Andrew Olaf Shelton, Jameal F. Samhouri, Natalie C. Lowell, and Gregory D. Williams. "Spatial distribution of environmental DNA in a nearshore marine habitat." PeerJ 5 (February 28, 2017): e3044. http://dx.doi.org/10.7717/peerj.3044.
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In the face of increasing threats to biodiversity, the advancement of methods for surveying biological communities is a major priority for ecologists. Recent advances in molecular biological technologies have made it possible to detect and sequence DNA from environmental samples (environmental DNA or eDNA); however, eDNA techniques have not yet seen widespread adoption as a routine method for biological surveillance primarily due to gaps in our understanding of the dynamics of eDNA in space and time. In order to identify the effective spatial scale of this approach in a dynamic marine environment, we collected marine surface water samples from transects ranging from the intertidal zone to four kilometers from shore. Using PCR primers that target a diverse assemblage of metazoans, we amplified a region of mitochondrial 16S rDNA from the samples and sequenced the products on an Illumina platform in order to detect communities and quantify their spatial patterns using a variety of statistical tools. We find evidence for multiple, discrete eDNA communities in this habitat, and show that these communities decrease in similarity as they become further apart. Offshore communities tend to be richer but less even than those inshore, though diversity was not spatially autocorrelated. Taxon-specific relative abundance coincided with our expectations of spatial distribution in taxa lacking a microscopic, pelagic life-history stage, though most of the taxa detected do not meet these criteria. Finally, we use carefully replicated laboratory procedures to show that laboratory treatments were remarkably similar in most cases, while allowing us to detect a faulty replicate, emphasizing the importance of replication to metabarcoding studies. While there is much work to be done before eDNA techniques can be confidently deployed as a standard method for ecological monitoring, this study serves as a first analysis of diversity at the fine spatial scales relevant to marine ecologists and confirms the promise of eDNA in dynamic environments.
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Hinz, Shawn, Jennifer Coston-Guarini, Michael Marnane, and Jean-Marc Guarini. "Evaluating eDNA for Use within Marine Environmental Impact Assessments." Journal of Marine Science and Engineering 10, no. 3 (March 6, 2022): 375. http://dx.doi.org/10.3390/jmse10030375.
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In this review, the use of environmental DNA (eDNA) within Environmental Impact Assessment (EIA) is evaluated. EIA documents provide information required by regulators to evaluate the potential impact of a development project. Currently eDNA is being incorporated into biodiversity assessments as a complementary method for detecting rare, endangered or invasive species. However, questions have been raised regarding the maturity of the field and the suitability of eDNA information as evidence for EIA. Several key issues are identified for eDNA information within a generic EIA framework for marine environments. First, it is challenging to define the sampling unit and optimal sampling strategy for eDNA with respect to the project area and potential impact receptor. Second, eDNA assay validation protocols are preliminary at this time. Third, there are statistical issues around the probability of obtaining both false positives (identification of taxa that are not present) and false negatives (non-detection of taxa that are present) in results. At a minimum, an EIA must quantify the uncertainty in presence/absence estimates by combining series of Bernoulli trials with ad hoc occupancy models. Finally, the fate and transport of DNA fragments is largely unknown in environmental systems. Shedding dynamics, biogeochemical and physical processes that influence DNA fragments must be better understood to be able to link an eDNA signal with the receptor’s state. The biggest challenge is that eDNA is a proxy for the receptor and not a direct measure of presence. Nonetheless, as more actors enter the field, technological solutions are likely to emerge for these issues. Environmental DNA already shows great promise for baseline descriptions of the presence of species surrounding a project and can aid in the identification of potential receptors for EIA monitoring using other methods.
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Li, Yiyuan, Nathan T. Evans, Mark A. Renshaw, Christopher L. Jerde, Brett P. Olds, Arial J. Shogren, Kristy Deiner, David M. Lodge, Gary A. Lamberti, and Michael E. Pfrender. "Estimating fish alpha- and beta-diversity along a small stream with environmental DNA metabarcoding." Metabarcoding and Metagenomics 2 (May 14, 2018): e24262. http://dx.doi.org/10.3897/mbmg.2.24262.
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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.
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Shogren, Arial J., Jennifer L. Tank, Elizabeth A. Andruszkiewicz, Brett Olds, Christopher Jerde, and Diogo Bolster. "Modelling the transport of environmental DNA through a porous substrate using continuous flow-through column experiments." Journal of The Royal Society Interface 13, no. 119 (June 2016): 20160290. http://dx.doi.org/10.1098/rsif.2016.0290.
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Detecting environmental DNA (eDNA) in water samples is a powerful tool in determining the presence of rare aquatic species. However, many open questions remain as to how biological and physical conditions in flowing waters influence eDNA. Motivated by what one might find in a stream/river benthos we conducted experiments in continuous flow columns packed with porous substrates to explore eDNA transport and ask whether substrate type and the presence of colonized biofilms plays an important role for eDNA retention. To interpret our data, and for modelling purposes, we began with the assumption that eDNA could be treated as a classical tracer. Comparing our experimental data with traditional transport models, we found that eDNA behaves anomalously, displaying characteristics of a heterogeneous, polydisperse substance with particle-like behaviour that can be filtered by the substrate. Columns were quickly flushed of suspended eDNA particles while a significant amount of particles never made it through and were retained in the column, as calculated from a mass balance. Suspended eDNA was exported through the column, regardless of biofilm colonization. Our results indicate that the variable particle size of eDNA results in stochastic retention, release and transport, which may influence the interpretation eDNA detection in biological systems.
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Banerjee, Pritam, Gobinda Dey, Caterina M. Antognazza, Raju Kumar Sharma, Jyoti Prakash Maity, Michael W. Y. Chan, Yi-Hsun Huang, et al. "Reinforcement of Environmental DNA Based Methods (Sensu Stricto) in Biodiversity Monitoring and Conservation: A Review." Biology 10, no. 12 (November 23, 2021): 1223. http://dx.doi.org/10.3390/biology10121223.
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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.
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McKee, Anna M., Daniel L. Calhoun, William J. Barichivich, Stephen F. Spear, Caren S. Goldberg, and Travis C. Glenn. "Assessment of Environmental DNA for Detecting Presence of Imperiled Aquatic Amphibian Species in Isolated Wetlands." Journal of Fish and Wildlife Management 6, no. 2 (September 1, 2015): 498–510. http://dx.doi.org/10.3996/042014-jfwm-034.
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Abstract Environmental DNA (eDNA) is an emerging tool that allows low-impact sampling for aquatic species by isolating DNA from water samples and screening for DNA sequences specific to species of interest. However, researchers have not tested this method in naturally acidic wetlands that provide breeding habitat for a number of imperiled species, including the frosted salamander (Ambystoma cingulatum), reticulated flatwoods salamanders (Ambystoma bishopi), striped newt (Notophthalmus perstriatus), and gopher frog (Lithobates capito). Our objectives for this study were to develop and optimize eDNA survey protocols and assays to complement and enhance capture-based survey methods for these amphibian species. We collected three or more water samples, dipnetted or trapped larval and adult amphibians, and conducted visual encounter surveys for egg masses for target species at 40 sites on 12 different longleaf pine (Pinus palustris) tracts. We used quantitative PCRs to screen eDNA from each site for target species presence. We detected flatwoods salamanders at three sites with eDNA but did not detect them during physical surveys. Based on the sample location we assumed these eDNA detections to indicate the presence of frosted flatwoods salamanders. We did not detect reticulated flatwoods salamanders. We detected striped newts with physical and eDNA surveys at two wetlands. We detected gopher frogs at 12 sites total, three with eDNA alone, two with physical surveys alone, and seven with physical and eDNA surveys. We detected our target species with eDNA at 9 of 11 sites where they were present as indicated from traditional surveys and at six sites where they were not detected with traditional surveys. It was, however, critical to use at least three water samples per site for eDNA. Our results demonstrate eDNA surveys can be a useful complement to traditional survey methods for detecting imperiled pond-breeding amphibians. Environmental DNA may be particularly useful in situations where detection probability using traditional survey methods is low or access by trained personnel is limited.
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Harrison, Jori B., Jennifer M. Sunday, and Sean M. Rogers. "Predicting the fate of eDNA in the environment and implications for studying biodiversity." Proceedings of the Royal Society B: Biological Sciences 286, no. 1915 (November 20, 2019): 20191409. http://dx.doi.org/10.1098/rspb.2019.1409.
Full textAbstract:
Environmental DNA (eDNA) applications are transforming the standard of characterizing aquatic biodiversity via the presence, location and abundance of DNA collected from environmental samples. As eDNA studies use DNA fragments as a proxy for the presence of organisms, the ecological properties of the complex and dynamic environments from which eDNA is sampled need to be considered for accurate biological interpretation. In this review, we discuss the role that differing environments play on the major processes that eDNA undergoes between organism and collection, including shedding, decay and transport. We focus on a mechanistic understanding of these processes and highlight how decay and transport models are being developed towards more accurate and robust predictions of the fate of eDNA. We conclude with five recommendations for eDNA researchers and practitioners, to advance current best practices, as well as to support a future model of eDNA spatio-temporal persistence.
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Li, Wen-Pan, Zi-Fang Liu, Tong Guo, He Chen, and Xin Xie. "Using Optimal Environmental DNA Method to Improve the Fish Diversity Survey—From Laboratory to Aquatic Life Reserve." Water 13, no. 11 (May 24, 2021): 1468. http://dx.doi.org/10.3390/w13111468.
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Conserving aquatic ecosystems requires efficient tools to accurately assess the biodiversity of aquatic species. However, existing knowledge is insufficient in terms of the reliability and the comparability of methods measuring fish diversity. Environmental DNA (eDNA), as a promising method, was used to detect fish taxa in this study. We optimized the eDNA method in the laboratory, and applied the optimal eDNA method to survey fish diversity in a natural aquatic life reserve. We simulated necessary steps of the eDNA method in the lab to increase the confidence of the field survey. Specifically, we compared different eDNA sampling, extraction, and sequencing strategies for accurately capturing fish species of the target area. We found that 1L water samples were sufficient for sampling eDNA information of the majority taxa. The filtration was more effective than the centrifugal precipitation for the eDNA extraction. The cloning sequencing was better than the high-throughput sequencing. The field survey showed that the Shannon–Wiener diversity index of fish taxa was the highest in Huairou Reservoir. The diversity index also showed seasonal changes. The accuracy rate of detecting fish taxa was positively correlated with the eDNA concentration. This study provides a scientific reference for an application of the eDNA method in terms of surveying and estimating the biodiversity of aquatic species.
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Lock, Marcelle, Iris van Duren, Andrew K. Skidmore, and Neil Saintilan. "Harmonizing Forest Conservation Policies with Essential Biodiversity Variables Incorporating Remote Sensing and Environmental DNA Technologies." Forests 13, no. 3 (March 11, 2022): 445. http://dx.doi.org/10.3390/f13030445.
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It remains difficult to compare the state of conservation of forests of different nations. Essential Biodiversity Variables (EBVs) are a set of variables designed as a framework for harmonizing biodiversity monitoring. Methods to monitor forest biodiversity are traditional monitoring (according to conservation policy requirements), remote sensing, environmental DNA, and the information products that are derived from them (RS/eDNA biodiversity products). However, it is not clear to what extent indicators from conservation policies align with EBVs and RS/eDNA biodiversity products. This research evaluated current gaps in harmonization between EBVs, RS/eDNA biodiversity products and forest conservation indicators. We compared two sets of biodiversity variables: (1) forest conservation indicators and (2) RS/eDNA biodiversity products, within the context of the Essential Biodiversity Variables framework. Indicators derived from policy documents can mostly be categorized within the EBV ‘ecosystem vertical profile’, while ‘ecosystem function’ remains underrepresented. RS/eDNA biodiversity products, however, can provide information about ‘ecosystem function’. Integrating RS/eDNA biodiversity products that monitor ecosystem functioning into monitoring programs will lead to a more comprehensive and balanced reporting on forest biodiversity. In addition, using the same variables and similar RS/eDNA products for forest biodiversity and conservation policies is a requirement for harmonization and international policy reporting.
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Adams, Clare I. M., Michael Knapp, Neil J. Gemmell, Gert-Jan Jeunen, Michael Bunce, Miles D. Lamare, and Helen R. Taylor. "Beyond Biodiversity: Can Environmental DNA (eDNA) Cut It as a Population Genetics Tool?" Genes 10, no. 3 (March 1, 2019): 192. http://dx.doi.org/10.3390/genes10030192.
Full textAbstract:
Population genetic data underpin many studies of behavioral, ecological, and evolutionary processes in wild populations and contribute to effective conservation management. However, collecting genetic samples can be challenging when working with endangered, invasive, or cryptic species. Environmental DNA (eDNA) offers a way to sample genetic material non-invasively without requiring visual observation. While eDNA has been trialed extensively as a biodiversity and biosecurity monitoring tool with a strong taxonomic focus, it has yet to be fully explored as a means for obtaining population genetic information. Here, we review current research that employs eDNA approaches for the study of populations. We outline challenges facing eDNA-based population genetic methodologies, and suggest avenues of research for future developments. We advocate that with further optimizations, this emergent field holds great potential as part of the population genetics toolkit.
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Stoeckle, Mark Y., Jason Adolf, Jesse H. Ausubel, Zach Charlop-Powers, Keith J. Dunton, and Greg Hinks. "Current laboratory protocols for detecting fish species with environmental DNA optimize sensitivity and reproducibility, especially for more abundant populations." ICES Journal of Marine Science 79, no. 2 (January 11, 2022): 403–12. http://dx.doi.org/10.1093/icesjms/fsab273.
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Abstract Analysing environmental DNA (eDNA) in seawater can aid in monitoring marine fish populations. However, the extent to which current methods optimize fish eDNA detection from water samples is unknown. Here, we test modifications to laboratory components of an eDNA metabarcoding protocol targeting marine finfish. As compared to baseline methods, amplifying a smaller proportion of extracted DNA yielded fewer species, and, conversely, amplifying a larger proportion identified more taxa. Higher-read species were amplified more reproducibly and with less variation in read number than were lower-read species. Among pooled samples, 20-fold deeper sequencing recovered one additional fish species out of a total of 63 species. No benefit was observed with additional PCR cycles, alternative primer concentrations, or fish-selective primers. Experiments using an exogenous DNA standard to assess absolute eDNA concentration suggested that, for a given proportion of a DNA sample, current laboratory methods for metabarcoding marine fish eDNA are near to maximally sensitive. Our results support the unofficial standard collection volume of one liter for eDNA assessment of commonly encountered marine fish species. We conclude that eDNA rarity poses the main challenge to current methods.
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Curtis, Amanda N., and Eric R. Larson. "No evidence that crayfish carcasses produce detectable environmental DNA (eDNA) in a stream enclosure experiment." PeerJ 8 (June 11, 2020): e9333. http://dx.doi.org/10.7717/peerj.9333.
Full textAbstract:
Environmental DNA (eDNA) is an emerging tool for monitoring invasive and imperiled species, particularly at low densities. However, the factors that control eDNA production, transport, and persistence in aquatic systems remain poorly understood. For example, the extent to which carcasses produce detectable eDNA is unknown. If positive detections are associated with dead organisms, this could confound monitoring for imperiled or invasive species. Here, we present results from one of the first studies to examine carcass eDNA in situ by deploying carcasses of the invasive red swamp crayfish (Procambarus clarkii) in a stream enclosure experiment for 28 days. We predicted that carcasses would initially produce eDNA that would decline over time as carcasses decayed. Unsurprisingly, crayfish carcasses lost biomass over time, but at the conclusion of our experiment much of the carapace and chelae remained. However, no eDNA of P. clarkii was detected in any of our samples at the crayfish density (15 P. clarkii carcasses at ∼615 g of biomass initially), stream flow (520–20,319 L/s), or temperature (∼14–25 °C) at our site. Subsequent analyses demonstrated that these results were not the consequence of PCR inhibition in our field samples, poor performance of the eDNA assay for intraspecific genetic diversity within P. clarkii, or due to the preservation and extraction procedure used. Therefore, our results suggest that when crayfish are relatively rare, such as in cases of new invasive populations or endangered species, carcasses may not produce detectable eDNA. In such scenarios, positive detections from field studies may be more confidently attributed to the presence of live organisms. We recommend that future studies should explore how biomass, flow, and differences in system (lentic vs. lotic) influence the ability to detect eDNA from carcasses.
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Juhel, Jean-Baptiste, Rizkie S. Utama, Virginie Marques, Indra B. Vimono, Hagi Yulia Sugeha, Kadarusman, Laurent Pouyaud, Tony Dejean, David Mouillot, and Régis Hocdé. "Accumulation curves of environmental DNA sequences predict coastal fish diversity in the coral triangle." Proceedings of the Royal Society B: Biological Sciences 287, no. 1930 (July 8, 2020): 20200248. http://dx.doi.org/10.1098/rspb.2020.0248.
Full textAbstract:
Environmental DNA (eDNA) has the potential to provide more comprehensive biodiversity assessments, particularly for vertebrates in species-rich regions. However, this method requires the completeness of a reference database (i.e. a list of DNA sequences attached to each species), which is not currently achieved for many taxa and ecosystems. As an alternative, a range of operational taxonomic units (OTUs) can be extracted from eDNA metabarcoding. However, the extent to which the diversity of OTUs provided by a limited eDNA sampling effort can predict regional species diversity is unknown. Here, by modelling OTU accumulation curves of eDNA seawater samples across the Coral Triangle, we obtained an asymptote reaching 1531 fish OTUs, while 1611 fish species are recorded in the region. We also accurately predict ( R ² = 0.92) the distribution of species richness among fish families from OTU-based asymptotes. Thus, the multi-model framework of OTU accumulation curves extends the use of eDNA metabarcoding in ecology, biogeography and conservation.
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Hocking, Morgan D., Jeffrey C. MacAdams, Michael J. Allison, Lauren C. Bergman, Robert Sneiderman, Ben F. Koop, Brian M. Starzomski, Mary L. Lesperance, and Caren C. Helbing. "Establishing the Signal above the Noise: Accounting for an Environmental Background in the Detection and Quantification of Salmonid Environmental DNA." Fishes 7, no. 5 (September 29, 2022): 266. http://dx.doi.org/10.3390/fishes7050266.
Full textAbstract:
A current challenge for environmental DNA (eDNA) applications is how to account for an environmental (or false-positive) background in surveys. We performed two controlled experiments in the Goldstream Hatchery in British Columbia using a validated coho salmon (Oncorhynchus kisutch) eDNA assay (eONKI4). In the density experiment at high copy number, eDNA in 2 L water samples was measured from four 10 kL tanks containing 1 to 65 juvenile coho salmon. At these densities, we obtained a strong positive 1:1 relationship between predicted copy number/L and coho salmon biomass (g/L). The dilution experiment simulated a situation where fish leave a pool environment, and water from upstream continues to flow through at rates of 141–159 L/min. Here, three coho salmon were placed in four 10 kL tanks, removed after nine days, and the amount of remaining eDNA was measured at times coinciding with dilutions of 20, 40, 80, 160, and 1000 kL. The dilution experiment demonstrates a novel method using Binomial–Poisson distributions to detect target species eDNA at low copy number in the presence of an environmental background. This includes determination of the limit of blank with background (LOB-B) with a controlled false positive rate, and limit of detection with background (LOD-B) with a controlled false negative rate, which provides a statistically robust “Detect” or “No Detect” assessment for eDNA surveys.
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McColl-Gausden, Emily F., Andrew R. Weeks, and Reid Tingley. "A field ecologist's guide to environmental DNA sampling in freshwater environments." Australian Zoologist 40, no. 4 (January 2020): 641–51. http://dx.doi.org/10.7882/az.2019.025.
Full textAbstract:
Environmental DNA, or eDNA—DNA shed from organisms and extracted from environmental samples—is an emerging survey technique that has the potential to transform biodiversity monitoring in freshwater ecosystems. We provide a brief overview of the primary methodological aspects of eDNA sampling that ecologists should consider before taking environmental samples in the field. We outline five key methodological considerations: (i) targeting single species vs multiple species; (ii) where and when to sample; (iii) how much water to collect; (iv) how many samples to take; and (v) recognising potential sources of false positives. The need to account for false negatives and false positives in eDNA surveys, and the power of species occupancy detection models in accounting for imperfect detection, is also discussed.
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Jo, T., S. Tomita, Y. Kohmatsu, M. Osathanunkul, A. Ushimaru, and T. Minamoto. "Seasonal monitoring of Hida salamander Hynobius kimurae using environmental DNA with a genus-specific primer set." Endangered Species Research 43 (November 19, 2020): 341–52. http://dx.doi.org/10.3354/esr01073.
Full textAbstract:
The diversity and the abundance of amphibians have dramatically declined globally over the past 30 years, and the monitoring and conservation of their habitats is essential. However, traditional methods such as bait trapping and mark-recapture are costly, and morphological identification usually requires a high level of taxonomic expertise. Here, seasonal surveillances of Hida salamander Hynobius kimurae were performed by means of environmental DNA (eDNA) analysis with Hynobius-specific primers and a species-specific TaqMan probe. Water sampling and visual surveys were conducted seasonally in a stream in Kyoto Prefecture, Japan. Detection rates of eDNA were then calculated by real-time PCR, and eDNA site occupancy probability was estimated by multi-scale occupancy modeling. The eDNA-based detection rate of Hida salamander was 76.7%, whereas the visual survey-based detection rate was 23.3%, and target eDNA was detected at almost all sites where the presence of target species was visually confirmed. Moreover, factors relating to the site- and sample-level occurrence probabilities of the target eDNA differed depending on the developmental stage of the target species. Our findings support previous studies showing that eDNA analysis enables an effective assessment of amphibian distributions without damaging the organisms or their habitat, and we compare for the first time the site occupancy probability of amphibian eDNA throughout the life cycle of an amphibian species. The present study contributes to the development of eDNA analysis as a tool for understanding the distribution and seasonal activity of amphibian species and will thus aid in the planning of conservation measures and habitat restoration for these species.
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Igawa, Takeshi, Teruhiko Takahara, Quintin Lau, and Shohei Komaki. "An application of PCR-RFLP species identification assay for environmental DNA detection." PeerJ 7 (October 3, 2019): e7597. http://dx.doi.org/10.7717/peerj.7597.
Full textAbstract:
Recent advancement of environmental DNA (eDNA) methods for surveying species in aquatic ecosystems has been used for various organisms and contributed to monitoring and conservation of species and environments. Amphibians are one of the promising taxa which could be monitored efficiently by applying quantitative PCR (qPCR) or next generation sequencing to eDNA. However, the cost of eDNA detection using these approaches can be quite high and requires instruments that are not usually installed in ecology laboratories. For aiding researchers in starting eDNA studies of amphibians, especially those not specialized in molecular biology, we developed a cost efficient protocol using PCR-RFLP method. We attempted to detect eDNA of three Japanese Rana species (Rana japonica, Rana ornativentris, and Rana tagoi tagoi) in various spatial scales including an area close to the Fukushima nuclear power plant where the environment is recovering after the disaster in 2011. Our PCR-RFLP protocol was successful in detecting Rana species in static water in both laboratory and field; however, it could not detect Rana species in non-static water samples from the field. Even a more sensitive detection method (standard qPCR) was unable to detect frogs in all non-static water samples. We speculate that our new protocol is effective for frogs living in lentic habitats, but not for lotic habitats which may still require the gold standard of field observation for detection approach.
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Díaz-Ferguson, Edgardo E., and Gregory R. Moyer. "History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments." Revista de Biología Tropical 62, no. 4 (December 1, 2014): 1273. http://dx.doi.org/10.15517/rbt.v62i4.13231.
Full textAbstract:
<p>Genetic material (short DNA fragments) left behind by species in nonliving components of the environment (e.g. soil, sediment, or water) is defined as environmental DNA (eDNA). This DNA has been previously described as particulate DNA and has been used to detect and describe microbial communities in marine sediments since the mid-1980’s and phytoplankton communities in the water column since the early-1990’s. More recently, eDNA has been used to monitor invasive or endangered vertebrate and invertebrate species. While there is a steady increase in the applicability of eDNA as a monitoring tool, a variety of eDNA applications are emerging in fields such as forensics, population and community ecology, and taxonomy. This review provides scientist an understanding of the methods underlying eDNA detection as well as applications, key methodological considerations, and emerging areas of interest for its use in ecology and conservation of freshwater and marine environments.</p>
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Uchida, Noriko, Kengo Kubota, Shunsuke Aita, and So Kazama. "Aquatic insect community structure revealed by eDNA metabarcoding derives indices for environmental assessment." PeerJ 8 (June 11, 2020): e9176. http://dx.doi.org/10.7717/peerj.9176.
Full textAbstract:
Environmental DNA (eDNA) analysis provides an efficient and objective approach for monitoring and assessing ecological status; however, studies on the eDNA of aquatic insects, such as Ephemeroptera, Plecoptera, and Trichoptera (EPT), are limited despite its potential as a useful indicator of river health. Here, we investigated the community structures of aquatic insects using eDNA and evaluated the applicability of eDNA data for calculating assessment indices. Field surveys were conducted to sample river water for eDNA at six locations from upstream to downstream of two rivers in Japan in July and November 2016. Simultaneously, aquatic insects were collected using the traditional Surber net survey method. The communities of aquatic insects were revealed using eDNA by targeting the cytochrome oxidase subunit I gene in mitochondrial DNA via metabarcoding analyses. As a result, the eDNA revealed 63 families and 75 genera of aquatic insects, which was double than that detected by the Surber net survey (especially for families in Diptera and Hemiptera). The seasonal differences of communities were distinguished by both the eDNA and Surber net survey data. Furthermore, the total nitrogen concentration, a surrogate of organic pollution, showed positive correlations with biotic environmental assessment indices (i.e., EPT index and Chironomidae index) calculated using eDNA at the genus-level resolution but the indices calculated using the Surber net survey data. Our results demonstrated that eDNA analysis with higher taxonomic resolution can provide as a more sensitive environmental assessment index than the traditional method that requires biotic samples.
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Perry, Iain, Ifan B. Jâms, Roser Casas-Mulet, Josefina Hamutoko, Angela Marchbank, Selma Lendelvo, Erold Naomab, et al. "Challenges to Implementing Environmental-DNA Monitoring in Namibia." Frontiers in Environmental Science 9 (January 17, 2022). http://dx.doi.org/10.3389/fenvs.2021.773991.
Full textAbstract:
By identifying fragments of DNA in the environment, eDNA approaches present a promising tool for monitoring biodiversity in a cost-effective way. This is particularly pertinent for countries where traditional morphological monitoring has been sparse. The first step to realising the potential of eDNA is to develop methodologies that are adapted to local conditions. Here, we test field and laboratory eDNA protocols (aqueous and sediment samples) in a range of semi-arid ecosystems in Namibia. We successfully gathered eDNA data on a broad suite of organisms at multiple trophic levels (including algae, invertebrates and bacteria) but identified two key challenges to the implementation of eDNA methods in the region: 1) high turbidity requires a tailored sampling technique and 2) identification of taxa by eDNA methods is currently constrained by a lack of reference data. We hope this work will guide the deployment of eDNA biomonitoring in the arid ecosystems of Namibia and neighbouring countries.