Item talk:Q227263
From geokb
{
"@context": "http://schema.org/", "@type": "WebPage", "additionalType": "Project", "url": "https://www.usgs.gov/centers/upper-midwest-environmental-sciences-center/science/resource-managers-edna-toolbox", "headline": "Resource Manager's eDNA Toolbox", "datePublished": "September 7, 2022", "author": [ { "@type": "Person", "name": "Jon Amberg, PhD", "url": "https://www.usgs.gov/staff-profiles/jon-amberg", "identifier": { "@type": "PropertyValue", "propertyID": "orcid", "value": "0000-0002-8351-4861" } } ], "description": [ { "@type": "TextObject", "text": "15 Shu, L., Ludwig, A., Peng, Z. 2020. Standards for Methods Utilizing Environmental DNA for Detection of Fish Species. Genes. 11, 296." }, { "@type": "TextObject", "text": "Labs that are used for eDNA surveillance programs should have certain criteria needed to be properly used for eDNA purposes. There must be strict decontamination protocols in place and a dedicated space for analysis. See eDNA Best Practices for recommendations on laboratory analysis." }, { "@type": "TextObject", "text": "6 Ferrante J.A., Daniel W.M., Freedman J.A., Klymus K.E., Neilson M.E., Passamaneck Y., Rees C.B., Sepulveda A., Hunter M.E. 2022. Gaining decision-maker confidence through community consensus: developing environmental DNA standards for data display on the USGS Nonindigenous Aquatic Species database. Management of Biological Invasions 13(4): 809\u2013832." }, { "@type": "TextObject", "text": "14 Sepulveda A.J., Nelson N.M., Jerde C.L., Luikart G. 2020b. Are Environmental DNA Methods Ready for Aquatic Invasive Species Management? Trends in Ecology & Evolution 35: 668\u2013 678." }, { "@type": "TextObject", "text": "11 Langlois V.S., Allison M.J., Bergman L.C., To T.A., Helbing C.C. 2021. The need for robust qPCR\u2010based eDNA detection assays in environmental monitoring and species inventories. Environmental DNA 3: 519\u2013527." }, { "@type": "TextObject", "text": "8 Hobbs, J., Round, J. M., Allison, M. J., & Helbing, C. C. 2019. Expansion of the known distribution of the coastal tailed frog, Ascaphus truei, in British Columbia, Canada, using robust eDNA detection methods. PLoS One, 14(3)." }, { "@type": "TextObject", "text": "17 Taberlet, P., Coissac, E., Hajibabaei, M., Rieseberg, L.H. 2012. Environmental DNA. Mol. Ecol. 21, 1789\u20131793." }, { "@type": "TextObject", "text": "12 Lesperance, M. L., Allison, M. J., Bergman, L. C., Hocking, M. D., & Helbing, C. C. (2021). A statistical model for calibration and computation of detection and quantification limits for low copy number environmental DNA samples. Environmental DNA, 3, 970\u2013981." }, { "@type": "TextObject", "text": "The Resource Manager's eDNA Toolbox is a series of web pages where managers can assess the available approaches, markers, validation techniques, and communication strategies when interested in molecular tools in resource management." }, { "@type": "TextObject", "text": "5 Erickson R.A., Merkes C.M., Mize E.L. 2019. Sampling designs for landscape-level eDNA monitoring programs. Integrated Environmental Assessment and Management. 15(5): 760-771." }, { "@type": "TextObject", "text": "21 U.S. Fish and Wildlife Service. 2023. Environmental DNA (eDNA) Best Management Practices for Project Planning, Deployment, and Application. U.S. Fish and Wildlife Service. Anchorage, AK: Conservation Genetics Laboratory." }, { "@type": "TextObject", "text": "While eDNA is a powerful tool that resource managers can use for conservation efforts, biodiversity monitoring, and ecosystem management, it should not be used to replace traditional surveying methods. eDNA is used to contribute to the weight of evidence used for decision making and should be used to complement traditional methods." }, { "@type": "TextObject", "text": "Molecular tools have garnered a lot of interest in natural resource management, particularly in biosurveillance. Filling gaps in monitoring, characterizing, communicating molecular approaches, and easily accessible information will help realize the potential of molecular tools." }, { "@type": "TextObject", "text": "Learn about the communication strategies involved in eDNA studies." }, { "@type": "TextObject", "text": "13 Morisette J., Burgiel S., Brantley K., Daniel W., Darling J., Davis J., Franklin T., Gaddis K., Hunter M., Lance R., Leskey T., Passamaneck Y., Piaggio A., Rector B., Sepulveda A., Smith M., Stepien C., Wilcox T., Wm D., Stepien S. 2021. Strategic considerations for invasive species managers in the utilization of environmental DNA (eDNA): steps for incorporating this powerful surveillance tool. Management of Biological Invasions 12: 747\u2013775." }, { "@type": "TextObject", "text": "What are the costs associated with beginning an eDNA surveillance program?" }, { "@type": "TextObject", "text": "Environmental DNA sampling is a powerful surveillance tool. Instead of relying on the capture of live organisms in the environment, utilizing eDNA methods allows you to indirectly monitor species without the need to physically observe them. eDNA also enhances your ability to detect the genetic traces of rare species that would be difficult to monitor using traditional surveying methods. This allows scientists and managers to gain a better understanding of what species live in a specific environment. Water is the most common medium sampled for eDNA but air and soil can also be sampled. There are many advantages to using eDNA. Environmental DNA techniques can be used for:" }, { "@type": "TextObject", "text": "Learn about eDNA best practices, data standards, and validation." }, { "@type": "TextObject", "text": "When deciding between eDNA and traditional sampling methods, the time requirement is a key factor. Traditional sampling could take days of sampling whereas eDNA could be hours. You must also consider the lab processing costs. For eDNA certain costs will include sample collection, lab analysis, lab personnel, supplies, and reagents. The choice between using traditional sampling methods and eDNA will rely on the study and target species." }, { "@type": "TextObject", "text": "4 Dejean T, Valentini A., Duparc A., Pellier-Cuit S., Pompanon F., Taberlet P., Miaud C. 2011. Persistence of Environmental DNA in Freshwater Ecosystems. PLoS ONE 6(8): e23398." }, { "@type": "TextObject", "text": "DNA (deoxyribonucleic acid) is a large, helical shaped biological molecule present in organisms that contains genetic information. The complete set of genetic information is referred to as the genome. The differences in the sequence or order of the DNA building blocks (base pairs) makes it possible to identify different species. An identifiable sequence at a recognized location in the genome is called a marker." }, { "@type": "TextObject", "text": "When beginning an eDNA surveillance program, you must clearly define your objectives. What is it that you hope to achieve with this program? Field and lab protocols must be developed before any sort of sampling or lab work can start. Pilot studies may be needed so that the techniques can be refined. Initial data collection may lead you to some preliminary conclusions that will cause you to alter your techniques or realize additional data collection is needed. Beginning an eDNA surveillance program takes time, commitment, and financial support for long-term planning. An effective communication plan must be established for all relevant parties, see eDNA Communication Strategies for details." }, { "@type": "TextObject", "text": "What should labs conducting eDNA studies consider?" }, { "@type": "TextObject", "text": "Environmental DNA is a promising biosurveillance tool that you can utilize to assess biodiversity and ecosystem health. There are certain advantages and limitations to using eDNA as a monitoring tool." }, { "@type": "TextObject", "text": "7 Goldberg, C.S.; Turner, C.R.; Deiner, K.; Klymus, K.E.; Thomsen, P.F.; Murphy, M.A.; Spear, S.F.; McKee, A.; Oyler-McCance, S.J.; Cornman, R.S.; et al. 2016. Critical considerations for the application of environmental DNA methods to detect aquatic species. Methods Ecol. Evol. 7, 1299\u20131307." }, { "@type": "TextObject", "text": "To detect multiple species at once, metabarcoding is a method that is commonly used. By using non-specific primers, followed by high-throughput sequencing, it's possible to find hundreds of species in a single sample. Barcoding is sequencing a section of DNA to identify a species. Metabarcoding is simultaneously sequencing millions of DNA fragments to identify species represented in a pool of DNA. This method is useful for surveying environments to learn what species may be present. The number of reads for each species can often be correlated to some degree with species abundance or biomass. However, you must consider eDNA movement (eDNA entering a habitat by other means such as sewage, feces from other animals, etc.) and degradation as well." }, { "@type": "TextObject", "text": "2630 Fanta Reed Road\nLa Crosse, WI 54603\nUnited States" }, { "@type": "TextObject", "text": "There is no hard number for the cost of eDNA surveillance programs as each program and study will be different. The costs involved in eDNA surveillance programs can vary. Some costs you must consider include the costs for beginning multiple pilot studies, funding for marker development and validation, for qPCR machines, and funding for research and development. The laboratory analysis costs are typically greater than field sampling costs." }, { "@type": "TextObject", "text": "Another method is the point of use assays, typically using either LAMP or CRISPR technologies. These assays allow for rapid on-site detection of single species or genera. They do not rely on the amplification of DNA through a PCR. Point of use assays need simple reagents and instruments for applications in the field or at port of entry." }, { "@type": "TextObject", "text": "19 Thomsen, P.F., Willerslev, E. 2015. Environmental DNA\u2014An emerging tool in conservation for monitoring past and present biodiversity. Biol. Conserv. 183, 4\u201318." }, { "@type": "TextObject", "text": "20 Ulibarri R.M., Bonar S.A., Rees C.B., Amberg J.J., Ladell B., Jackson C. 2017.Comparing Efficiency of American Fisheries Society Standard Snorkeling Techniques to Environmental DNA Sampling Techniques. North American Journal of Fisheries Management. 37, 644-651." }, { "@type": "TextObject", "text": "2 Bohmann, K.; Evans, A.; Gilbert, M.T.; Carvalho, G.R.; Creer, S.; Knapp, M.; Yu, D.W.; de Bruyn, M. 2014. Environmental DNA for wildlife biology and biodiversity monitoring. Trends Ecol. Evol. 29, 358\u2013367." }, { "@type": "TextObject", "text": "10 Klymus K.E., Merkes C.M., Allison M.J., Goldberg C.S., Helbing C.C., Hunter M.E., Jackson C.A., Lance R.F., Mangan A.M., Monroe E.M., Piaggio A.J., Stokdyk J.P., Wilson C.C., Richter C.A. 2020. Reporting the limits of detection and quantification for environmental DNA assays. Environmental DNA 2: 271\u2013282." }, { "@type": "TextObject", "text": "Droplet digital PCR is a technology that can be used for eDNA analysis. ddPCR works using water-in-oil emulsions, separating the sample into thousands of droplets, each as small as 1 nanoliter. These droplets are run through a PCR cycle like any other probe-based method. The fluorescence is measured in each individual droplet after amplification and the positive number of droplets is calculated. ddPCR is highly sensitive and precise, making it an acceptable method for eDNA. However, it tends to be more expensive than qPCR." }, { "@type": "TextObject", "text": "Where do I begin when starting an eDNA surveillance program?" }, { "@type": "TextObject", "text": "3 Bustin S.A., Benes V., Garson J.A., Hellemans J., Huggett J., Kubista M., Mueller R., Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT. 2009. The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments. Clinical Chemistry 55: 611\u2013622." }, { "@type": "TextObject", "text": "1 Abbott C., Coulson M., Gagn\u00e9 N., Lacoursi\u00e8re\u2010Roussel A., Parent G.J., Bajno R., Dietrich C., May\u0002McNally S. 2021. Guidance on the Use of Targeted Environmental DNA (eDNA) Analysis for the Management of Aquatic Invasive Species and Species at Risk. Fisheries and Oceans Canada, Ottawa, ON, Canada, Canadian Science Advisory Secretariat, 2021/019: iv+42 pp." }, { "@type": "TextObject", "text": "You must also decide on what happens after a positive detection. Do you begin physical sampling? Is your work done? Does your partner take over? There must be a clear plan in place once a positive detection occurs that defines what your next steps are." }, { "@type": "TextObject", "text": "18 Thalinger, B., Deiner, K., Harper, L. R., Rees, H. C., Blackman, R. C., Sint, D., Traugott, M., Goldberg, C. S., & Bruce, K. 2021. A validation scale to determine the readiness of environmental DNA assays for routine species monitoring. Environmental DNA, 3(4), 823\u2013 836." }, { "@type": "TextObject", "text": "Environmental DNA (eDNA) is DNA present in various aquatic or terrestrial environments (water, soil, sediment). It's defined as \u201cgenetic material obtained directly from environmental samples without any obvious signs of biological source material.\"[19] eDNA originates from cellular material shed by organisms (such as skin, hair, excrement, etc.), and it can be extracted from complex environmental samples and analyzed using molecular techniques." }, { "@type": "TextObject", "text": "16 Stein, E. D., Jerde, C.L., Allan, E.A., Sepulveda, A., Abbott, C.L., Baerwald, M.R., Darling, J., Goodwin, K.D., Meyer, R.S., Timmers, M.A., & Thielen, P.M. 2023. Critical considerations for communicating environmental DNA science. Environmental DNA, 00, 1-12." }, { "@type": "TextObject", "text": "The technique most often used to detect eDNA from complex environmental samples is polymerase chain reaction (PCR). Targeted methods (single species or genera) eDNA assays exclude all related species or co-occurring species in the sample. PCR works by quickly replicating millions or billions of copies of a short fragment of specific DNA sequence (a marker). Quantitative PCR is often used because of its high specificity due to carefully designed forward and reverse primers and probe. Combined with its high sensitivity, this makes qPCR an ideal method for single species detection." }, { "@type": "TextObject", "text": "9 Hoorfar J., Malorny B., Abdulmawjood A., Cook N., Wagerner M., Fach P. 2004. Practical considerations in design of internal amplification controls for diagnostic PCR assays. J. Clin. Microbiol. 42(5), 1863-1868." } ], "funder": { "@type": "Organization", "name": "Upper Midwest Environmental Sciences Center", "url": "https://www.usgs.gov/centers/upper-midwest-environmental-sciences-center" }, "about": [ { "@type": "Thing", "name": "Science Technology" }, { "@type": "Thing", "name": "Biology" }, { "@type": "Thing", "name": "Information Systems" }, { "@type": "Thing", "name": "Geology" }, { "@type": "Thing", "name": "Environmental Health" }, { "@type": "Thing", "name": "Water" }, { "@type": "Thing", "name": "Methods and Analysis" }, { "@type": "Thing", "name": "Energy" }, { "@type": "Thing", "name": "Aquatic Ecosystem Health" }, { "@type": "Thing", "name": "eDNA" } ]
}
