Applications of environmental DNA (eDNA) to detect subterranean and aquatic invasive species: A critical review on the challenges and limitations of eDNA metabarcoding

Environmental Advances - Tập 12 - Trang 100370 - 2023
Sakib Tahmid Rishan1, Richard J. Kline1,2,3, Md Saydur Rahman1,2,3
1Biochemistry and Molecular Biology Program, University of Texas Rio Grande Valley, Brownsville, Texas, USA
2School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA
3Department of Biology, University of Texas Rio Grande Valley, Brownsville, Texas, USA

Tài liệu tham khảo

Adrian-Kalchhauser, 2016, An eDNA assay to monitor a globally invasive fish species from flowing freshwater, PLoS One, 11, 10.1371/journal.pone.0147558 Agerbo Rasmussen, 2021, eDNA-based biomonitoring at an experimental German vineyard to characterize how management regimes shape ecosystem diversity, Environ. DNA, 3, 70, 10.1002/edn3.131 Aizpurua, 2017, Agriculture shapes the trophic niche of a bat preying on multiple pest arthropods across Europe: Evidence from DNA metabarcoding, Mol. Ecol., 27, 815, 10.1111/mec.14474 Alberdi, 2018, Scrutinizing key steps for reliable metabarcoding of environmental samples, Methods Ecol. Evol., 9, 134, 10.1111/2041-210X.12849 Alexander, 2020, Development of a multi-assay approach for monitoring coral diversity using eDNA metabarcoding, Coral Reefs, 39, 159, 10.1007/s00338-019-01875-9 Allen, 2023, Sampling environmental DNA from trees and soil to detect cryptic arboreal mammals, Sci. Rep., 13, 1, 10.1038/s41598-023-27512-8 Allen, 2021, Terrestrial eDNA survey outperforms conventional approach for detecting an invasive pest insect within an agricultural ecosystem, Environ. DNA, 3, 1102, 10.1002/edn3.231 Alvarez, 1996, Stability of manipulated plasmid DNA in aquatic environments, Environ. Toxicol. Water Qual., 11, 129, 10.1002/(SICI)1098-2256(1996)11:2<129::AID-TOX8>3.0.CO;2-B Amari, 2021, Potential impact of global warming on virus propagation in infected plants and agricultural productivity, Front. Plant Sci., 12, 10.3389/fpls.2021.649768 Amberg, 2015, Improving efficiency and reliability of environmental DNA analysis for silver carp, J. Great Lakes Res., 41, 367, 10.1016/j.jglr.2015.02.009 Amberg, 2019, Environmental DNA as a tool to help inform zebra mussel, Dreissena polymorpha, management in inland lakes, Manage.Biolog. Invas., 10, 96 Ando, 2020, Methodological trends and perspectives of animal dietary studies by noninvasive fecal DNA metabarcoding, Environ. DNA, 2, 391, 10.1002/edn3.117 Andres, 2021, Nuclear eDNA estimates population allele frequencies and abundance in experimental mesocosms and field samples, Mol. Ecol., 30, 685, 10.1111/mec.15765 Andruszkiewicz, 2017, Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding, PLoS One, 12, 10.1371/journal.pone.0176343 Anand, 2021, A review of the presence of SARS–CoV–2 RNA in wastewater and airborne particulates and its use for virus spreading surveillance, Environ. Res., 196, 10.1016/j.envres.2021.110929 Antognazza, 2019, Environmental DNA as a non–invasive sampling tool to detect the spawning distribution of European anadromous shads (Alosa spp.), Aquat. Conserv., 29, 148, 10.1002/aqc.3010 Antognazza, 2021, Application of eDNA metabarcoding in a fragmented lowland river: Spatial and methodological comparison of fish species composition, Environ. DNA, 3, 458, 10.1002/edn3.136 Ardura, 2017, Rapid assessment of non–indigenous species in the era of the eDNA barcoding: A Mediterranean case study, Estuarine Coastal Shelf Sci., 188, 81, 10.1016/j.ecss.2017.02.004 Ardura, 2015, eDNA and specific primers for early detection of invasive species–A case study on the bivalve Rangia cuneata, currently spreading in Europe, Mar. Environ. Res., 112, 48, 10.1016/j.marenvres.2015.09.013 Ariza, 2022, Plant biodiversity assessment through soil eDNA reflects temporal and local diversity, Methods Ecol. Evol., 14, 415, 10.1111/2041-210X.13865 Asahida, 1997, Identification of consumed stone flounder, Kareius bicoloratus (Basilewsky), from the stomach contents of sand shrimp, Crangon affinis (De Haan) using mitochondrial DNA analysis, J. Exp. Mar. Biol. Ecol., 217, 153, 10.1016/S0022-0981(97)00039-7 Ashfaq, 2016, DNA barcodes for bio–surveillance: regulated and economically important arthropod plant pests, Genome, 59, 933, 10.1139/gen-2016-0024 Balasingham, 2018, Environmental DNA detection of rare and invasive fish species in two Great Lakes tributaries, Mol. Ecol., 27, 112, 10.1111/mec.14395 Baldigo, 2017, Efficacy of environmental DNA to detect and quantify brook trout populations in headwater streams of the Adirondack Mountains, New York, Trans Am Fish Soc, 146, 99, 10.1080/00028487.2016.1243578 Barnes, 2021, Environmental conditions influence eDNA particle size distribution in aquatic systems, Environmental DNA, 3, 643, 10.1002/edn3.160 Barnes, 2016, The ecology of environmental DNA and implications for conservation genetics, Conservation Genetics, 17, 1, 10.1007/s10592-015-0775-4 Barnosky, 2011, Has the Earth's sixth mass extinction already arrived?, Nature, 471, 51, 10.1038/nature09678 Barrios, 2007, Soil biota, ecosystem services and land productivity, Ecol. Econ., 64, 269, 10.1016/j.ecolecon.2007.03.004 Bay, 2006, The relationship between population genetic structure and pelagic larval duration in coral reef fishes on the Great Barrier Reef, Mar. Biol., 149, 1247, 10.1007/s00227-006-0276-6 Beja–Pereira, 2009, Advancing ecological understandings through technological transformations in noninvasive genetics, Mol. Ecol. Resour., 9, 1279, 10.1111/j.1755-0998.2009.02699.x Beng, 2020, Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects, Biodivers. Conserv., 29, 2089, 10.1007/s10531-020-01980-0 Bessey, 2020, Maximizing fish detection with eDNA metabarcoding, Environmental DNA, 2, 493, 10.1002/edn3.74 Bessey, 2021, Passive eDNA collection enhances aquatic biodiversity analysis, Commun Biol, 4, 1 Bienert, 2012, Tracking earthworm communities from soil DNA, Mol. Ecol., 21, 2017, 10.1111/j.1365-294X.2011.05407.x Biggs, 2015, Using eDNA to develop a national citizen science–based monitoring programme for the great crested newt (Triturus cristatus), Biol. Conserv., 183, 19, 10.1016/j.biocon.2014.11.029 Billah, 2021, Impacts of anthropogenic contaminants and elevated temperature on prevalence and proliferation of Escherichia coli in the wild–caught American oyster, Crassostrea virginica in the southern Gulf of Mexico coast, Mar. Biol. Res., 17, 775, 10.1080/17451000.2022.2053161 Bista, 2017, Annual time–series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity, Nat. Commun., 8, 1, 10.1038/ncomms14087 Blanc, 2001, Introduction of pathogens in European aquatic ecosystems: Attemp of evaluation and realities, Cahiers Options Méditerranéennes (CIHEAM) Bohmann, 2014, Environmental DNA for wildlife biology and biodiversity monitoring, Trends Ecol. Evol., 29, 358, 10.1016/j.tree.2014.04.003 Bonfil, 2021, Detection of critically endangered marine species with dwindling populations in the wild using eDNA gives hope for sawfishes, Mar. Biol., 168, 1 Borrell, 2017, DNA in a bottle—Rapid metabarcoding survey for early alerts of invasive species in ports, PLoS One, 12, 10.1371/journal.pone.0183347 Boyd, 2020, Using environmental DNA methods to survey for rare groundwater fauna: Detection of an endangered endemic cave crayfish in northern Alabama, PLoS One, 15, 10.1371/journal.pone.0242741 Brunner, 2020, Pooled samples and eDNA–based detection can facilitate the “clean trade” of aquatic animals, Sci. Rep., 10, 1, 10.1038/s41598-020-66280-7 Brys, 2021, Reliable eDNA detection and quantification of the European weather loach (Misgurnus fossilis), J. Fish Biol., 98, 399, 10.1111/jfb.14315 Bylemans, 2016, Improving the containment of a freshwater invader using environmental DNA (eDNA) based monitoring, Russ. J. Biol. Invasions, 18, 3081, 10.1007/s10530-016-1203-5 Bylemans, 2019, A performance evaluation of targeted eDNA and eDNA metabarcoding analyses for freshwater fishes, Environ. DNA, 1, 402, 10.1002/edn3.41 Cabodevilla, 2022, Simultaneous analysis of the intestinal parasites and diet through eDNA metabarcoding, Integr. Zool., 0, 1 Cai, 2022, Environmental DNA persistence and fish detection in captive sponges, Mol. Ecol. Resour., 22, 2956, 10.1111/1755-0998.13677 Cai, 2017, Using eDNA to detect the distribution and density of invasive crayfish in the Honghe–Hani rice terrace World Heritage site, PLoS One, 12, 10.1371/journal.pone.0177724 Caldwell, 2015, Prokaryotic diversity in the rhizosphere of organic, intensive, and transitional coffee farms in Brazil, PLoS One, 10, 10.1371/journal.pone.0106355 Cannon, 2016, In silico assessment of primers for eDNA studies using PrimerTree and application to characterize the biodiversity surrounding the Cuyahoga River, Sci. Rep., 6, 1, 10.1038/srep22908 Capo, 2020, Effects of filtration methods and water volume on the quantification of brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) eDNA concentrations via droplet digital PCR, Environ. DNA, 2, 152, 10.1002/edn3.52 Cardás, 2020, New eDNA based tool applied to the specific detection and monitoring of the endangered European eel, Biol. Conserv., 250 Carim, K. J., McKelvey, K. S., Young, M. K., Wilcox, T. M., & Schwartz, M. K. (2016). A protocol for collecting environmental DNA samples from streams. Gen. Tech. Rep. RMRS–GTR–355. Fort Collins, CO: US Department of Agriculture, Forest Service, Rocky Mountain Research Station. 18 p., 355. Carraro, 2018, Estimating species distribution and abundance in river networks using environmental DNA, Proc. Natl. Acad. Sci., 115, 11724, 10.1073/pnas.1813843115 Carraro, 2020, Environmental DNA allows upscaling spatial patterns of biodiversity in freshwater ecosystems, Nat. Commun., 11, 1, 10.1038/s41467-020-17337-8 Caswell, 2004, Spawning by lake sturgeon (Acipenser fulvescens) in the Detroit River, J. Appl. Ichthyol., 20, 1, 10.1111/j.1439-0426.2004.00499.x Ceresini, 2019, Wheat blast: from its origins in South America to its emergence as a global threat, Mol. Plant Pathol., 20, 155, 10.1111/mpp.12747 Chang, 2018, Molecular–assisted pollen grain analysis reveals spatiotemporal origin of long–distance migrants of a noctuid moth, Int. J. Mol. Sci., 19, 567, 10.3390/ijms19020567 Chen, 2011, Rapid range shifts of species associated with high levels of climate warming, Science, 333, 1024, 10.1126/science.1206432 Chen, 2021, DNA barcoding reveals the temporal community composition of drifting fish eggs in the lower Hongshui River, China, BMC Ecol. Evol., 11, 11507, 10.1002/ece3.7943 Chen, 2020, An optional low–cost method of extracting environmental DNA of macro–organisms from filter membranes in large scale eDNA surveys, Pak. J. Zool., 53, 263, 10.17582/journal.pjz/20190118100108 Closek, 2019, Marine vertebrate biodiversity and distribution within the central California current using environmental DNA (eDNA) metabarcoding and ecosystem surveys, Front. Mar. Sci., 6, 732, 10.3389/fmars.2019.00732 Coble, 2019, eDNA as a tool for identifying freshwater species in sustainable forestry: a critical review and potential future applications, Sci. Total Environ., 649, 1157, 10.1016/j.scitotenv.2018.08.370 Coghlan, 2021, Community eDNA metabarcoding as a detection tool for documenting freshwater mussel (Unionidae) species assemblages, Environ. DNA, 3, 1172, 10.1002/edn3.239 Cole, 2018, The science of food security, NPJ Sci. Food, 2, 1, 10.1038/s41538-018-0021-9 Collins, 2019, Non–specific amplification compromises environmental DNA metabarcoding with COI, Methods Ecol. Evol., 10, 1985, 10.1111/2041-210X.13276 Cooper, 2022, Practical eDNA sampling methods inferred from particle size distribution and comparison of capture techniques for a critically endangered elasmobranch, Environ. DNA, 4, 1011, 10.1002/edn3.279 Coster, 2021, The update and optimization of an eDNA assay to detect the invasive rusty crayfish (Faxonius rusticus), PLoS One, 16, 10.1371/journal.pone.0259084 Crisol–Martínez, 2016, Using next–generation sequencing to contrast the diet and explore pest–reduction services of sympatric bird species in macadamia orchards in Australia, PLoS One, 11, 10.1371/journal.pone.0150159 Cristescu, 2014, From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity, Trends Ecol. Evol., 29, 566, 10.1016/j.tree.2014.08.001 Cristescu, 2018, Uses and misuses of environmental DNA in biodiversity science and conservation, Annu. Rev. Ecol. Evol. Syst., 49, 209, 10.1146/annurev-ecolsys-110617-062306 Danielopol, 2003, Present state and future prospects for groundwater ecosystems, Environ. Conserv., 30, 104, 10.1017/S0376892903000109 Danner, 2017, Honey bee foraging ecology: season but not landscape diversity shapes the amount and diversity of collected pollen, PLoS One, 12, 10.1371/journal.pone.0183716 Danylchuk, 2011, Aggregations and offshore movements as indicators of spawning activity of bonefish (Albula vulpes) in The Bahamas, Mar. Biol., 158, 1981, 10.1007/s00227-011-1707-6 Danziger, 2022, Challenges in eDNA detection of the invasive European green crab, Carcinus maenas, Russ. J. Biol. Invasions, 24, 1881, 10.1007/s10530-022-02757-y Darling, 2021, What do you mean by false positive?, Environ. DNA, 3, 879, 10.1002/edn3.194 Darling, 2011, From molecules to management: adopting DNA–based methods for monitoring biological invasions in aquatic environments, Environ. Res., 111, 978, 10.1016/j.envres.2011.02.001 de Graaff, 2019, Effects of agricultural intensification on soil biodiversity and implications for ecosystem functioning: a meta–analysis, Adv. Agron., 155, 1, 10.1016/bs.agron.2019.01.001 Deagle, 2005, Molecular scatology as a tool to study diet: analysis of prey DNA in scats from captive Steller sea lions, Mol. Ecol., 14, 1831, 10.1111/j.1365-294X.2005.02531.x Deagle, 2007, Studying seabird diet through genetic analysis of faeces: a case study on macaroni penguins (Eudyptes chrysolophus), PLoS One, 2, e831, 10.1371/journal.pone.0000831 Deagle, 2009, Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces, Mol. Ecol., 18, 2022, 10.1111/j.1365-294X.2009.04158.x Deiner, 2017, Environmental DNA metabarcoding: Transforming how we survey animal and plant communities, Mol. Ecol., 26, 5872, 10.1111/mec.14350 Dejean, 2011, Persistence of environmental DNA in freshwater ecosystems, PLoS One, 6, e23398, 10.1371/journal.pone.0023398 Dejean, 2012, Improved detection of an alien invasive species through environmental DNA barcoding: the example of the American bullfrog Lithobates catesbeianus, J. Appl. Ecol., 49, 953, 10.1111/j.1365-2664.2012.02171.x Delgado–Baquerizo, 2017, Circular linkages between soil biodiversity, fertility and plant productivity are limited to topsoil at the continental scale, New Phytol., 215, 1186, 10.1111/nph.14634 Di Muri, 2022, Spatio–temporal monitoring of lake fish spawning activity using environmental DNA metabarcoding, Environ. DNA, 00, 1 Di Muri, 2020, Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds, Biorxiv Díaz–Abad, 2022, eDNA metabarcoding for diet analyses of green sea turtles (Chelonia mydas), Mar. Biol., 169, 1, 10.1007/s00227-021-04002-x Díaz–Ferguson, 2014, History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments, Rev. Biol. Trop., 62, 1273, 10.15517/rbt.v62i4.13231 DiBattista, 2022, The use of environmental DNA to monitor impacted coastal estuaries, Mar. Pollut. Bull., 181, 10.1016/j.marpolbul.2022.113860 Didham, 2005, Are invasive species the drivers of ecological change?, Trends Ecol. Evol., 20, 470, 10.1016/j.tree.2005.07.006 DiStefano, 2020, Preliminary investigation of the critically imperiled Caney Mountain cave crayfish Orconectes stygocaneyi (Hobbs III, 2001) (Decapoda: Cambaridae) in Missouri, USA, Freshwater Crayfish Pap. Int. Symp., 5th, 25, 47, 10.5869/fc.2020.v25-1.047 Doi, 2017, Water sampling for environmental DNA surveys by using an unmanned aerial vehicle, Limnol. Oceanogr. Methods, 15, 939, 10.1002/lom3.10214 Doi, 2017, Isopropanol precipitation method for collecting fish environmental DNA, Limnol. Oceanogr. Methods, 15, 212, 10.1002/lom3.10161 Doi, 2015, Use of droplet digital PCR for estimation of fish abundance and biomass in environmental DNA surveys, PLoS One, 10, 10.1371/journal.pone.0122763 Dopheide, 2020, Rarity is a more reliable indicator of land–use impacts on soil invertebrate communities than other diversity metrics, Elife, 9, e52787, 10.7554/eLife.52787 Dougherty, 2016, Environmental DNA (eDNA) detects the invasive rusty crayfish Orconectes rusticus at low abundances, J. Appl. Ecol., 53, 722, 10.1111/1365-2664.12621 Drummond, 2015, Evaluating a multigene environmental DNA approach for biodiversity assessment, Gigascience, 4, 10.1186/s13742-015-0086-1 Dubreuil, 2022, The development of early monitoring tools to detect aquatic invasive species: eDNA assay development and the case of the armored catfish Hypostomus robinii, Environ. DNA, 4, 349, 10.1002/edn3.260 Edwards, 2014, Selective–logging and oil palm: Multitaxon impacts, biodiversity indicators, and trade–offs for conservation planning, Ecol. Appl., 24, 2029, 10.1890/14-0010.1 Eichmiller, 2016, Optimizing techniques to capture and extract environmental DNA for detection and quantification of fish, Mol. Ecol. Resour., 16, 56, 10.1111/1755-0998.12421 Elberri, 2020, DNA and eDNA–based tracking of the North African sharptooth catfish Clarias gariepinus, Mol. Cell. Probes, 51, 10.1016/j.mcp.2020.101535 Epp, 2012, New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems, Mol. Ecol., 21, 1821, 10.1111/j.1365-294X.2012.05537.x Erickson, 2016, Detecting the movement and spawning activity of bigheaded carps with environmental DNA, Mol. Ecol. Resour., 16, 957, 10.1111/1755-0998.12533 Everett, 2018, Exploring deep–water coral communities using environmental DNA, Deep Sea Res. Part II, 150, 229, 10.1016/j.dsr2.2017.09.008 Farrington, 2015, Mitochondrial genome sequencing and development of genetic markers for the detection of DNA of invasive bighead and silver carp (Hypophthalmichthys nobilis and H. molitrix) in environmental water samples from the United States, PLoS One, 10, 10.1371/journal.pone.0117803 Ficetola, 2008, Species detection using environmental DNA from water samples, Biol. Lett., 4, 423, 10.1098/rsbl.2008.0118 Ficetola, 2015, Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data, Mol. Ecol. Resour., 15, 543, 10.1111/1755-0998.12338 Foote, 2012, Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals, PLoS One, 7, e41781, 10.1371/journal.pone.0041781 Ford, 2009, Selection of candidate coding DNA barcoding regions for use on land plants, Bot. J. Linn. Soc., 159, 1, 10.1111/j.1095-8339.2008.00938.x Fouts, 2012, Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen, PLoS One, 7, e48289, 10.1371/journal.pone.0048289 Freeland, 2017, The importance of molecular markers and primer design when characterizing biodiversity from environmental DNA, Genome, 60, 358, 10.1139/gen-2016-0100 Frøslev, 2022, The biodiversity effect of reduced tillage on soil microbiota, Ambio, 51, 1022, 10.1007/s13280-021-01611-0 Fu'adil Amin, 2021, Development of a quantitative PCR assay for four salmon species inhabiting the Yangyangnamdae River using environmental DNA, Biology, 10, 899, 10.3390/biology10090899 Fukaya, 2021, Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modelling, Mol. Ecol., 30, 3057, 10.1111/mec.15530 Fuschi, 2021, Wastewater–based epidemiology for managing the COVID–19 pandemic, ACS EST Water, 1, 1352, 10.1021/acsestwater.1c00050 Furlan, 2016, Improving reliability in environmental DNA detection surveys through enhanced quality control, Mar. Freshwater Res., 68, 388, 10.1071/MF15349 Gamage, 2020, Understanding leptospirosis eco–epidemiology by environmental DNA metabarcoding of irrigation water from two agro–ecological regions of Sri Lanka, PLoS Negl. Trop. Dis., 14, 10.1371/journal.pntd.0008437 Garagnani, 2014, The three genetics (nuclear DNA, mitochondrial DNA, and gut microbiome) of longevity in humans considered as metaorganisms, Biomed. Res. Int., 2014, 10.1155/2014/560340 Gargan, 2017, Development of a sensitive detection method to survey pelagic biodiversity using eDNA and quantitative PCR: a case study of devil ray at seamounts, Mar. Biol., 164, 1, 10.1007/s00227-017-3141-x Garrett, 2023, Airborne eDNA documents a diverse and ecologically complex tropical bat and other mammal community, Environ. DNA, 10.1002/edn3.385 Gebreyes, 2014, The global one health paradigm: challenges and opportunities for tackling infectious diseases at the human, animal, and environment interface in low–resource settings, PLoS Negl. Trop. Dis., 8, e3257, 10.1371/journal.pntd.0003257 Gerlach, 2013, Terrestrial invertebrates as bioindicators: an overview of available taxonomic groups, J. Insect Conserv., 17, 831, 10.1007/s10841-013-9565-9 Ghosal, 2018, Attracting common carp to a bait site with food reveals strong positive relationships between fish density, feeding activity, environmental DNA, and sex pheromone release that could be used in invasive fish management, BMC Ecol. Evol., 8, 6714, 10.1002/ece3.4169 Gold, 2021, eDNA metabarcoding as a biomonitoring tool for marine protected areas, PLoS One, 16, 10.1371/journal.pone.0238557 Goldberg, 2011, Molecular detection of vertebrates in stream water: a demonstration using Rocky Mountain tailed frogs and Idaho giant salamanders, PLoS One, 6, e22746, 10.1371/journal.pone.0022746 Goldberg, 2013, Environmental DNA as a new method for early detection of New Zealand mudsnails (Potamopyrgus antipodarum), Freshwater Sci., 32, 792, 10.1899/13-046.1 Goldberg, 2016, Critical considerations for the application of environmental DNA methods to detect aquatic species, Methods Ecol. Evol., 7, 1299, 10.1111/2041-210X.12595 Gomes, 2017, Use of environmental DNA (eDNA) and water quality data to predict protozoan parasites outbreaks in fish farms, Aquaculture, 479, 467, 10.1016/j.aquaculture.2017.06.021 Guan, 2019, Environmental DNA (eDNA) assays for invasive populations of black carp in North America, Trans. Am. Fish Soc., 148, 1043, 10.1002/tafs.10195 Hamaguchi, 2018, Quantitative real-time polymerase chain reaction (PCR) and droplet digital PCR duplex assays for detecting Zostera marina DNA in coastal sediments, Limnol. Oceanogr. Methods, 16, 253, 10.1002/lom3.10242 Hänfling, 2016, Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods, Mol. Ecol., 25, 3101, 10.1111/mec.13660 Harper, 2019, Development and application of environmental DNA surveillance for the threatened crucian carp (Carassius carassius), Freshwater Biol., 64, 93, 10.1111/fwb.13197 Hashemzadeh Segherloo, 2022, eDNA metabarcoding as a means to assess distribution of subterranean fish communities: Iranian blind cave fishes as a case study, Environ. DNA, 4, 402, 10.1002/edn3.264 Hata, 2022, Population decline of an endangered unionid, Pronodularia japanensis, in streams is revealed by eDNA and conventional monitoring approaches, Hydrobiologia, 849, 2635, 10.1007/s10750-022-04852-6 Havis, 2015, Ramularia collo–cygni—an emerging pathogen of barley crops, Phytopathology, 105, 895, 10.1094/PHYTO-11-14-0337-FI He, 2022, Using eDNA to assess the fish diversity and spatial characteristics in the Changjiang River–Shijiu Lake connected system, Ecol. Indic., 139, 10.1016/j.ecolind.2022.108968 Hebert, 2005, The promise of DNA barcoding for taxonomy, Syst. Biol., 54, 852, 10.1080/10635150500354886 Hebsgaard, 2009, ‘The Farm Beneath the Sand’–an archaeological case study on ancient ‘dirt'DNA, Am. Antiq., 83, 430 Hernandez, 2020, 60 specific eDNA qPCR assays to detect invasive, threatened, and exploited freshwater vertebrates and invertebrates in Eastern Canada, Environ. DNA, 2, 373, 10.1002/edn3.89 Hinlo, 2018, Performance of eDNA assays to detect and quantify an elusive benthic fish in upland streams, Russ. J. Biol. Invasions, 20, 3079, 10.1007/s10530-018-1760-x Hobbs, 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, 10.1371/journal.pone.0213849 Hohenlohe, 2021, Population genomics for wildlife conservation and management, Mol. Ecol., 30, 62, 10.1111/mec.15720 Holman, 2022, How does eDNA decay affect metabarcoding experiments?, Environ. DNA, 4, 108, 10.1002/edn3.201 Hopkins, 2002, Declines in the numbers of amateur and professional taxonomists: implications for conservation, Anim. conserv. forum, 5, 245, 10.1017/S1367943002002299 Höss, 1992, Excrement analysis by PCR, Nature, 359, 199, 10.1038/359199a0 Hossain, 2020, Agricultural land degradation: processes and problems undermining future food security, 17 Hou, 2021, Identification of eggs and spawning zones of hairtail fishes Trichiurus (Pisces: Trichiuridae) in Northern South China Sea, using DNA barcoding, Front. Environ. Sci., 9, 10.3389/fenvs.2021.703029 Huerlimann, 2020, Enhancing tropical conservation and ecology research with aquatic environmental DNA methods: an introduction for non-environmental DNA specialists, Anim. Conserv., 23, 632, 10.1111/acv.12583 Hunter, 2017, Detection limits of quantitative and digital PCR assays and their influence in presence–absence surveys of environmental DNA, Mol. Ecol. Resour., 17, 221, 10.1111/1755-0998.12619 Hunter, 2018, Surveys of environmental DNA (eDNA): a new approach to estimate occurrence in Vulnerable manatee populations, Endangered Species Res., 35, 101, 10.3354/esr00880 Hunter, 2019, Efficacy of eDNA as an early detection indicator for Burmese pythons in the ARM loxahatchee national wildlife refuge in the greater everglades ecosystem, Ecol. Indic., 102, 617, 10.1016/j.ecolind.2019.02.058 Hunter, 2015, Environmental DNA (eDNA) sampling improves occurrence and detection estimates of invasive Burmese pythons, PLoS One, 10, 10.1371/journal.pone.0121655 Hutchins, 2022, Time to get real with qPCR controls: The frequency of sample contamination and the informative power of negative controls in environmental DNA studies, Mol. Ecol. Resour., 22, 1319, 10.1111/1755-0998.13549 Innes, 2022, Wastewater–Based Epidemiology Mitigates COVID–19 Outbreaks at a Food Processing Facility near the Mexico–US Border—November 2020–March 2022, Viruses, 14, 2684, 10.3390/v14122684 Ip, 2022, Multispecies environmental DNA metabarcoding sheds light on annual coral spawning events, Mol. Ecol., 00, 1 Jafarinejad, 2021, Tracking and analysis of discourse dynamics and polarity during the early Corona pandemic in Iran, J. Biomed. Inform., 121, 10.1016/j.jbi.2021.103862 Jarman, 2004, Group–specific polymerase chain reaction for DNA–based analysis of species diversity and identity in dietary samples, Mol. Ecol., 13, 1313, 10.1111/j.1365-294X.2004.02109.x Jarman, 2002, A DNA–based method for identification of krill species and its application to analysing the diet of marine vertebrate predators, Mol. Ecol., 11, 2679, 10.1046/j.1365-294X.2002.01641.x Jerde, 2013, Detection of Asian carp DNA as part of a Great Lakes basin–wide surveillance program, Can. J. Fish. Aquat.Sci., 70, 522, 10.1139/cjfas-2012-0478 Jerde, 2011, Sight–unseen” detection of rare aquatic species using environmental DNA, Conserv. Lett., 4, 150, 10.1111/j.1755-263X.2010.00158.x Jeunen, 2023, Assessing the utility of marine filter feeders for environmental DNA (eDNA) biodiversity monitoring, Mol. Ecol. Resour., 00, 1 Jeunen, 2022, Moving environmental DNA (eDNA) technologies from benchtop to the field using passive sampling and PDQeX extraction, Environ. DNA, 4, 1420, 10.1002/edn3.356 Ji, 2013, Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding, Ecol. Lett., 16, 1245, 10.1111/ele.12162 Jiang, 2014, Latitudinal distribution of ammonia–oxidizing bacteria and archaea in the agricultural soils of eastern China, Appl. Environ. Microbiol., 80, 5593, 10.1128/AEM.01617-14 Jo, 2019, Discrimination of spatial distribution of aquatic organisms in a coastal ecosystem using eDNA, Appl. Sci., 9, 3450, 10.3390/app9173450 Jo, 2021, Complex interactions between environmental DNA (eDNA) state and water chemistries on eDNA persistence suggested by meta–analyses, Mol. Ecol. Resour., 21, 1490, 10.1111/1755-0998.13354 Johnstone, 2019, Effects of elevated temperature on gonadal functions, cellular apoptosis and oxidative stress in Atlantic sea urchin Arabacia punculata, Mar. Environ. Res., 149, 40, 10.1016/j.marenvres.2019.05.017 Jones, 2009, Plant virus emergence and evolution: origins, new encounter scenarios, factors driving emergence, effects of changing world conditions, and prospects for control, Virus Res., 141, 113, 10.1016/j.virusres.2008.07.028 Jørgensen, 2012, A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long–term vegetational stability, Mol. Ecol., 21, 1989, 10.1111/j.1365-294X.2011.05287.x Joseph, 2022, Persistence and degradation dynamics of eDNA affected by environmental factors in aquatic ecosystems, Hydrobiologia, 849, 4119, 10.1007/s10750-022-04959-w Karahan, 2017, Employing DNA barcoding as taxonomy and conservation tools for fish species censuses at the southeastern Mediterranean, a hot–spot area for biological invasion, J. Nature Conserv., 36, 1, 10.1016/j.jnc.2017.01.004 Kawato, 2021, Optimization of environmental DNA extraction and amplification methods for metabarcoding of deep–sea fish, MethodsX, 8, 10.1016/j.mex.2021.101238 Kelly, 2014, Using environmental DNA to census marine fishes in a large mesocosm, PLoS One, 9, e86175, 10.1371/journal.pone.0086175 Kelly, 2019, Understanding PCR processes to draw meaningful conclusions from environmental DNA studies, Sci. Rep., 9, 1, 10.1038/s41598-019-48546-x Keskin, 2016, Detection of rare and invasive freshwater fish species using eDNA pyrosequencing: Lake Iznik ichthyofauna revised, Biochem. Syst. Ecol., 67, 29, 10.1016/j.bse.2016.05.020 Khalsa, 2020, Identifying under–ice overwintering locations of juvenile Chinook salmon by using environmental DNA, North Am. J. Fisheries Manage., 40, 762, 10.1002/nafm.10444 Kim, 2018, Early detection of marine invasive species, Bugula neritina (Bryozoa: Cheilostomatida), using species–specific primers and environmental DNA analysis in Korea, Mar. Environ. Res., 139, 1, 10.1016/j.marenvres.2018.04.015 Klepke, 2022, Accumulation and diversity of airborne, eukaryotic environmental DNA, Environ. DNA, 4, 1323, 10.1002/edn3.340 Klymus, 2015, Quantification of eDNA shedding rates from invasive bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix, Biol. Conserv., 183, 77, 10.1016/j.biocon.2014.11.020 Klymus, 2021, Metabarcoding assays for the detection of freshwater mussels (Unionida) with environmental DNA, Environ. DNA, 3, 231, 10.1002/edn3.166 Kinoshita, 2019, Environmental DNA collected from snow tracks is useful for identification of mammalian species, Zoolog. Sci., 36, 198, 10.2108/zs180172 Knudsen, 2019, Species–specific detection and quantification of environmental DNA from marine fishes in the Baltic Sea, J. Exp. Mar. Biol. Ecol., 510, 31, 10.1016/j.jembe.2018.09.004 Ko, 2013, Evaluating the Accuracy of Morphological Identification of Larval Fishes by Applying DNA Barcoding, PLoS One, 8, e53451, 10.1371/journal.pone.0053451 Korbel, 2017, Wells provide a distorted view of life in the aquifer: implications for sampling, monitoring and assessment of groundwater ecosystems, Sci. Rep., 7, 1, 10.1038/srep40702 Krah, 2022, eDNA metabarcoding reveals high soil fungal diversity and variation in community composition among Spanish cliffs, BMC Ecol Evol, 12, e9594, 10.1002/ece3.9594 Kumar, 2020, A practical guide to sample preservation and pre–PCR processing of aquatic environmental DNA, Mol. Ecol. Resour., 20, 29, 10.1111/1755-0998.13107 Kvitrud, 2005, Pacific harbor seals (Phoca vitulina) and salmon: genetics presents hard numbers for elucidating predator–prey dynamics, Mar. Biol., 147, 1459, 10.1007/s00227-005-0047-9 Kyle, 2022, Combining surface and soil environmental DNA with artificial cover objects to improve terrestrial reptile survey detection, Conserv. Biol., 36, e13939, 10.1111/cobi.13939 Lacoursière–Roussel, 2016, Estimating fish abundance and biomass from eDNA concentrations: variability among capture methods and environmental conditions, Mol. Ecol. Resour., 16, 1401, 10.1111/1755-0998.12522 Lafferty, 2018, Detecting southern California's white sharks with environmental DNA, Front. Mar. Sci., 5, 355, 10.3389/fmars.2018.00355 Lafferty, 2021, At Palmyra Atoll, the fish–community environmental DNA signal changes across habitats but not with tides, J. Fish Biol., 98, 415, 10.1111/jfb.14403 Langlois, 2021, The need for robust qPCR–based eDNA detection assays in environmental monitoring and species inventories, Environ. DNA, 3, 519, 10.1002/edn3.164 Laroche, 2017, Metabarcoding monitoring analysis: the pros and cons of using co–extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities, PeerJ, 5, e3347, 10.7717/peerj.3347 Larson, 2020, From eDNA to citizen science: emerging tools for the early detection of invasive species, Front. Ecol. Environ., 18, 194, 10.1002/fee.2162 Lacy, 2022, Interactive effects of high temperature and pesticide exposure on oxidative status, apoptosis, and renin expression in kidney of goldfish: Molecular and cellular mechanisms of widespread kidney damage and renin attenuation, J. Appl. Toxicol., 42, 1787, 10.1002/jat.4357 Lacy, 2022, Potential mechanisms of Na+/K+–ATPase attenuation by heat and pesticides co–exposure in goldfish: Role of cellular apoptosis, oxidative/nitrative stress, and antioxidants in gills, Environ. Sci. Pollut. Res. Int., 29, 57376, 10.1007/s11356-022-19779-7 LeBlanc, 2020, Environmental DNA (eDNA) detection of marine aquatic invasive species (AIS) in Eastern Canada using a targeted species–specific qPCR approach, Manage. Biol. Invas., 11, 201, 10.3391/mbi.2020.11.2.03 Lesk, 2021, Decadal variability modulates trends in concurrent heat and drought over global croplands, Environ. Res. Lett., 16, 10.1088/1748-9326/abeb35 Leskey, 2012, Impact of insecticides on the invasive Halyomorpha halys (Hemiptera: Pentatomidae): analysis of insecticide lethality, J. Econ. Entomol., 105, 1726, 10.1603/EC12096 Levi, 2019, Environmental DNA for the enumeration and management of Pacific salmon, Mol. Ecol. Resour., 19, 597, 10.1111/1755-0998.12987 Li, 2022, eDNA assessment of pelagic fish diversity, distribution, and abundance in the central Pacific Ocean, Regional Stud. Marine Sci., 56, 10.1016/j.rsma.2022.102661 Li, 2021, Using optimal environmental dna method to improve the fish diversity survey—from laboratory to aquatic life reserve, Water, 13, 1468, 10.3390/w13111468 Liang, 2013, Filtration recovery of extracellular DNA from environmental water samples, Environ. Sci. Technol., 47, 9324, 10.1021/es401342b Lilja, 2023, Comparing earthworm biodiversity estimated by DNA metabarcoding and morphology–based approaches, Appl. Soil Ecol., 185, 10.1016/j.apsoil.2022.104798 Lima, 2020, Use of DNA barcode in the identification of fish eggs in tributaries of the Paranapanema River basin, Genet. Mol. Biol., 43 Lippert, 2021, Revisiting the economic valuation of agricultural losses due to large–scale changes in pollinator populations, Ecol. Econ., 180, 10.1016/j.ecolecon.2020.106860 Lisnerová, 2023, Evaluation and optimization of an eDNA metabarcoding assay for detection of freshwater myxozoan communities, Environ. DNA, 5, 312, 10.1002/edn3.380 Lodge, 2012, Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA, Mol. Ecol., 21, 2555, 10.1111/j.1365-294X.2012.05600.x Lor, 2020, Using environmental DNA (eDNA) to detect the endangered Spectaclecase mussel (Margaritifera monodonta), Freshwater Sci., 39, 837, 10.1086/711673 Lovell, 2006, The economic impacts of aquatic invasive species: a review of the literature, Agric. Resour. Econ. Rev., 35, 195, 10.1017/S1068280500010157 Macgregor, 2019, Construction, validation, and application of nocturnal pollen transport networks in an agro–ecosystem: A comparison using light microscopy and DNA metabarcoding, Ecol. Entomol., 44, 17, 10.1111/een.12674 Mahon, 2013, Validation of eDNA surveillance sensitivity for detection of Asian carps in controlled and field experiments, PLoS One, 8, e58316, 10.1371/journal.pone.0058316 Makiola, 2019, Land use is a determinant of plant pathogen alpha–but not beta–diversity, Mol. Ecol., 28, 3786, 10.1111/mec.15177 Mammola, 2019, Scientists' warning on the conservation of subterranean ecosystems, Bioscience, 69, 641, 10.1093/biosci/biz064 Mariani, 2021, Shark and ray diversity, abundance and temporal variation around an Indian Ocean Island, inferred by eDNA metabarcoding, Conserv. Sci. Pract., 3, e407, 10.1111/csp2.407 Maruyama, 2018, Environmental DNA analysis as a non–invasive quantitative tool for reproductive migration of a threatened endemic fish in rivers, BMC Ecol. Evol., 8, 11964, 10.1002/ece3.4653 Mathieu, 2020, A systematic review of sources of variability and uncertainty in eDNA data for environmental monitoring, Front. Ecol. Evol., 8, 135, 10.3389/fevo.2020.00135 Matter, 2018, A rapid–assessment method to estimate the distribution of juvenile Chinook salmon in tributary habitats using eDNA and occupancy estimation, North Am. J. Fisheries Manage., 38, 223, 10.1002/nafm.10014 Mauvisseau, 2018, Environmental DNA as an efficient tool for detecting invasive crayfishes in freshwater ponds, Hydrobiologia, 805, 163, 10.1007/s10750-017-3288-y Mauvisseau, 2019, Early detection of an emerging invasive species: eDNA monitoring of a parthenogenetic crayfish in freshwater systems, Manage. Biol. Invasions, 10, 461, 10.3391/mbi.2019.10.3.04 McClenaghan, 2020, Harnessing the power of eDNA metabarcoding for the detection of deep–sea fishes, PLoS One, 15, 10.1371/journal.pone.0236540 McKee, 2015, Assessment of environmental DNA for detecting presence of imperiled aquatic amphibian species in isolated wetlands, J. Fish Wildlife Manage., 6, 498, 10.3996/042014-JFWM-034 Meulenbroek, 2018, Species–specific fish larvae drift in anthropogenically constructed riparian zones on the Vienna impoundment of the River Danube, Austria: Species occurrence, frequencies, and seasonal patterns based on DNA barcoding, River Res. Appl., 34, 854, 10.1002/rra.3303 Mezzasalma, 2017, Grape microbiome as a reliable and persistent signature of field origin and environmental conditions in Cannonau wine production, PLoS One, 12, 10.1371/journal.pone.0184615 Michelot–Antalik, 2021, Comparison of grassland plant–pollinator networks on dairy farms in three contrasting French landscapes, Acta Oncol., 112 Milazzo, 2021, High–throughput metabarcoding characterizes fungal endophyte diversity in the Phyllosphere of a barley crop, Phytobiomes J., 5, 316, 10.1094/PBIOMES-09-20-0066-R Minamoto, 2022, Environmental DNA analysis for macro–organisms: species distribution and more, DNA Res., 10.1093/dnares/dsac018 Minamoto, 2017, Environmental DNA reflects spatial and temporal jellyfish distribution, PLoS One, 12, 10.1371/journal.pone.0173073 Minamoto, 2009, Seasonal distribution of cyprinid herpesvirus 3 in Lake Biwa, Japan, Appl. Environ. Microbiol., 75, 6900, 10.1128/AEM.01411-09 Minamoto, 2012, Surveillance of fish species composition using environmental DNA, Limnology, 13, 193, 10.1007/s10201-011-0362-4 Miralles, 2019, Development and validation of eDNA markers for the detection of Crepidula fornicata in environmental samples, Mar. Pollut. Bull., 146, 827, 10.1016/j.marpolbul.2019.07.050 Miya, 2022, Environmental DNA Metabarcoding: A novel method for biodiversity monitoring of marine fish communities, Ann. Rev. Mar. Sci., 14, 161, 10.1146/annurev-marine-041421-082251 Miya, 2020, MiFish metabarcoding: a high–throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples, Fish. Sci., 86, 939, 10.1007/s12562-020-01461-x Miya, 2015, MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species, R. Soc. Open Sci., 2, 10.1098/rsos.150088 Mizumoto, 2018, Establishing an environmental DNA method to detect and estimate the biomass of Sakhalin taimen, a critically endangered Asian salmonid, Limnology, 19, 219, 10.1007/s10201-017-0535-x Mohamed, 2020, Bovine tuberculosis at the human–livestock–wildlife interface and its control through one health approach in the Ethiopian Somali pastoralists: a review, One Health, 9, 10.1016/j.onehlt.2019.100113 Mouser, 2021, Refining sampling protocols for cavefishes and cave crayfishes to account for environmental variation, Subterranean Biol., 39, 79, 10.3897/subtbiol.39.64279 Muñoz–Colmenero, 2018, New specific molecular marker detects Ficopomatus enigmaticus from water eDNA before positive results of conventional sampling, J. Nat. Conserv., 43, 173, 10.1016/j.jnc.2017.12.004 Murakami, 2019, Dispersion and degradation of environmental DNA from caged fish in a marine environment, Fish. Sci., 85, 327, 10.1007/s12562-018-1282-6 Nardi, 2019, The expansion of exotic Chinook salmon (Oncorhynchus tshawytscha) in the extreme south of Patagonia: an environmental DNA approach, Russ. J. Biol. Invasions, 21, 1415, 10.1007/s10530-018-1908-8 Nash, 2019, Elevated temperature attenuates ovarian functions and induces apoptosis and oxidative stress in the American oyster, Crassostrea virginica: potential mechanisms and signaling pathways, Cell Stress Chaperones, 24, 957, 10.1007/s12192-019-01023-w Nathan, 2015, The use of environmental DNA in invasive species surveillance of the Great Lakes commercial bait trade, Conserv. Biol., 29, 430, 10.1111/cobi.12381 Navarro–Noya, 2021, Conversion of a high–altitude temperate forest for agriculture reduced alpha and beta diversity of the soil fungal communities as revealed by a metabarcoding analysis, Front. Microbiol., 12, 10.3389/fmicb.2021.667566 Nelson–Chorney, 2019, Environmental DNA in lake sediment reveals biogeography of native genetic diversity, Front. Ecol. Environ., 17, 313, 10.1002/fee.2073 Nester, 2020, Development and evaluation of fish eDNA metabarcoding assays facilitate the detection of cryptic seahorse taxa (family: Syngnathidae), Environ. DNA, 2, 614, 10.1002/edn3.93 Nevers, 2018, Environmental DNA (eDNA): A tool for quantifying the abundant but elusive round goby (Neogobius melanostomus), PLoS One, 13, 10.1371/journal.pone.0191720 Nichols, 2018, Minimizing polymerase biases in metabarcoding, Mol. Ecol. Resour., 18, 927, 10.1111/1755-0998.12895 Niemiller, 2018, Evaluation of eDNA for groundwater invertebrate detection and monitoring: a case study with endangered Stygobromus (Amphipoda: Crangonyctidae), Conserv. Genet. Resour., 10, 247, 10.1007/s12686-017-0785-2 O'Malley, 2022, An extraction method to quantify the fraction of extracellular and intracellular antibiotic resistance genes in aquatic environments, J. Environ. Eng., 148 Othman, 2021, A review on environmental DNA (eDNA) metabarcoding markers for wildlife monitoring research Othman, 2023, A review on next–generation wildlife monitoring using environmental DNA (eDNA) detection and next–generation sequencing in Malaysia, Sains Malays., 52, 17, 10.17576/jsm-2023-5201-02 Pardo, 2020, Worldwide importance of insect pollination in apple orchards: a review, Agric., Ecosyst. Environ., 293, 10.1016/j.agee.2020.106839 Parsons, 2005, DNA–based identification of salmonid prey species in seal faeces, J. Zool., 266, 275, 10.1017/S0952836905006904 Pecl, 2017, Biodiversity redistribution under climate change: Impacts on ecosystems and human well–being, Science, 355, eaai9214, 10.1126/science.aai9214 Piaggio, 2014, Detecting an elusive invasive species: A diagnostic PCR to detect Burmese python in Florida waters and an assessment of persistence of environmental DNA, Mol. Ecol. Resour., 14, 374, 10.1111/1755-0998.12180 Piggott, 2016, Evaluating the effects of laboratory protocols on eDNA detection probability for an endangered freshwater fish, BMC Ecol. Evol., 6, 2739, 10.1002/ece3.2083 Pilliod, 2013, Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples, Can. J. Fish. Aquat.Sci., 70, 1123, 10.1139/cjfas-2013-0047 Pilliod, 2014, Factors influencing detection of eDNA from a stream–dwelling amphibian, Mol. Ecol. Resour., 14, 109, 10.1111/1755-0998.12159 Poinar, 1998, Molecular coproscopy: dung and diet of the extinct ground sloth Nothrotheriops shastensis, Science, 281, 402, 10.1126/science.281.5375.402 Pont, 2022, Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR, Mol. Ecol. Resour., 23, 396, 10.1111/1755-0998.13715 Porco, 2022, eDNA–based detection of the invasive crayfish Pacifastacus leniusculus in streams with a LAMP assay using dependent replicates to gain higher sensitivity, Sci. Rep., 12, 1, 10.1038/s41598-022-10545-w Port, 2016, Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA, Mol. Ecol., 25, 527, 10.1111/mec.13481 Potts, 2010, Global pollinator declines: trends, impacts and drivers, Trends Ecol. Evol., 25, 345, 10.1016/j.tree.2010.01.007 Prakash, 2022, Anthropogenic activities and biodiversity threats, Int. J. Biol. Innov., IJBI, 4, 94, 10.46505/IJBI.2022.4110 Preece, 2021, Monitoring for freshwater mussel presence in rivers using environmental DNA, Environ. DNA, 3, 591, 10.1002/edn3.156 Przybyla–Kelly, 2023, Round goby detection in lakes Huron and Michigan—An evaluation of eDNA and fish catches, Fishes, 8, 41, 10.3390/fishes8010041 Qu, 2019, Evaluating monitoring options for conservation: comparing traditional and environmental DNA tools for a critically endangered mammal, Naturwissenschaften, 106, 1 Rasmussen, 2021, Dead or alive—Old empty shells do not prompt false–positive results in environmental DNA surveys targeting the freshwater pearl mussel (Margaritifera margaritifera L.), Aquat. Conserv., 31, 2506, 10.1002/aqc.3677 Ratsch, 2020, Exploration of environmental DNA (eDNA) to detect Kirtland's snake (Clonophis kirtlandii), Animals, 10, 1057, 10.3390/ani10061057 Rauf, 2019, Visual features based automated identification of fish species using deep convolutional neural networks, Comput. Electron. Agric., 167, 10.1016/j.compag.2019.105075 Redondo, 2020, Vegetation type determines spore deposition within a forest–agricultural mosaic landscape, FEMS Microbiol. Ecol., 96, fiaa082, 10.1093/femsec/fiaa082 Rees, 2014, The detection of aquatic animal species using environmental DNA–a review of eDNA as a survey tool in ecology, J. Appl. Ecol., 51, 1450, 10.1111/1365-2664.12306 Rodgers, 2017, Proper fin–clip sample collection for molecular analyses in the age of eDNA, J. Fish Biol., 91, 1265, 10.1111/jfb.13485 Roger, 2022, Airborne environmental DNA metabarcoding for the monitoring of terrestrial insects—A proof of concept from the field, Environ. DNA, 4, 790, 10.1002/edn3.290 Rolf, 2005, The metagenomics of soil, Nat. Rev. Microbiol., 3, 470, 10.1038/nrmicro1160 Rosel, 2021, A new species of baleen whale (Balaenoptera) from the Gulf of Mexico, with a review of its geographic distribution, Marine Mammal Sci., 37, 577, 10.1111/mms.12776 Rudko, 2019, Species–specific qPCR assays allow for high–resolution population assessment of four species avian schistosome that cause swimmer's itch in recreational lakes, Int. J. Parasitol. Parasites Wildl., 9, 122, 10.1016/j.ijppaw.2019.04.006 Ruppert, 2022, Development and assessment of an environmental DNA (eDNA) assay for a cryptic Siren (Amphibia: Sirenidae), Environ. Adv., 7, 10.1016/j.envadv.2021.100163 Ruppert, 2019, Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA, Glob. Ecol. Conserv., 17, e00547, 10.1016/j.gecco.2019.e00547 Saadi, 2020, The socio–economic burden of cystic echinococcosis in Morocco: a combination of estimation method, PLoS Negl.Trop. Dis., 14, 10.1371/journal.pntd.0008410 Saccò, 2022, eDNA in subterranean ecosystems: applications, technical aspects, and future prospects, Sci. Total Environ., 10.1016/j.scitotenv.2022.153223 Sahu, 2022, Environmental DNA (eDNA): Powerful Technique for Biodiversity Conservation, J. Nat. Conserv. Saito, 2021, Effect of salinity and water dilution on environmental DNA degradation in freshwater environments, Biorxiv Sakai, 2019, Discovery of an unrecorded population of Yamato salamander (Hynobius vandenburghi) by GIS and eDNA analysis, Environ. DNA, 1, 281, 10.1002/edn3.31 Sales, 2019, Influence of preservation methods, sample medium and sampling time on eDNA recovery in a neotropical river, Environ. DNA, 1 Sani, 2021, Environmental DNA (eDNA) reveals endangered narrow sawfish across Indonesian Reefs Sansom, 2017, Environmental DNA (eDNA) shedding and decay rates to model freshwater mussel eDNA transport in a river, Environ. Sci. Technol., 51, 14244, 10.1021/acs.est.7b05199 Santas, 2013, Noninvasive method for a statewide survey of eastern hellbenders Cryptobranchus alleganiensis using environmental DNA, Int. J. Zool., 2013, 10.1155/2013/174056 Sassoubre, 2016, Quantification of environmental DNA (eDNA) shedding and decay rates for three marine fish, Environ. Sci. Technol., 50, 10456, 10.1021/acs.est.6b03114 Savary, 2019, The global burden of pathogens and pests on major food crops, Nat. Ecol. Evol., 3, 430, 10.1038/s41559-018-0793-y Schabacker, 2020, Increased eDNA detection sensitivity using a novel high–volume water sampling method, Environ. DNA, 2, 244, 10.1002/edn3.63 Schmelzle, 2016, Using occupancy modelling to compare environmental DNA to traditional field methods for regional–scale monitoring of an endangered aquatic species, Mol. Ecol. Resour., 16, 895, 10.1111/1755-0998.12501 Schultz, 2015, Modeling the sensitivity of field surveys for detection of environmental DNA (eDNA), PLoS One, 10, 10.1371/journal.pone.0141503 Scribner, 1998, Microsatellites identify depredated waterfowl remains from glaucous gull stomachs, Mol. Ecol., 7, 1401, 10.1046/j.1365-294x.1998.00434.x Scriver, 2015, Development of species–specific environmental DNA (eDNA) markers for invasive aquatic plants, Aquatic Botany, 122, 27, 10.1016/j.aquabot.2015.01.003 Senapati, 2019, Environmental DNA (eDNA): A promising biological survey tool for aquatic species detection, Proc. Zool. Soc., 72, 211, 10.1007/s12595-018-0268-9 Sepulveda, 2020, The elephant in the lab (and field): Contamination in aquatic environmental DNA studies, Front. Ecol. Evolut., 8 Shaw, 2016, Using environmental (e) DNA sequencing for aquatic biodiversity surveys: a beginner's guide, Mar. Freshwater Res., 68, 20, 10.1071/MF15361 Shelton, 2019, Environmental DNA provides quantitative estimates of a threatened salmon species, Biol. Conserv., 237, 383, 10.1016/j.biocon.2019.07.003 Sigsgaard, 2020, Population–level inferences from environmental DNA—Current status and future perspectives, Evol. Appl., 13, 245, 10.1111/eva.12882 Sigsgaard, 2016, Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA, Nat. Ecol. Evol., 1, 1, 10.1038/s41559-016-0004 Smessaert, 2019, Temporal and spatial variation in bacterial communities of “Jonagold” apple (Malus x domestica Borkh.) and “Conference” pear (Pyrus communis L.) floral nectar, Microbiologyopen, 8, e918, 10.1002/mbo3.918 Sønstebø, 2010, Using next–generation sequencing for molecular reconstruction of past Arctic vegetation and climate, Mol. Ecol. Resour., 10, 1009, 10.1111/j.1755-0998.2010.02855.x Sowunmi, 2019, Environmental burden of fungicide application among cocoa farmers in Ondo state, Nigeria, Scientific Afr., 6, e00207, 10.1016/j.sciaf.2019.e00207 Spear, 2015, Using environmental DNA methods to improve detectability in a hellbender (Cryptobranchus alleganiensis) monitoring program, Biol. Conserv., 183, 38, 10.1016/j.biocon.2014.11.016 Spens, 2017, Comparison of capture and storage methods for aqueous macrobial eDNA using an optimized extraction protocol: advantage of enclosed filter, Methods Ecol. Evol., 8, 635, 10.1111/2041-210X.12683 Stat, 2019, Combined use of eDNA metabarcoding and video surveillance for the assessment of fish biodiversity, Conserv. Biol., 33, 196, 10.1111/cobi.13183 Srivastava, 2021, Metabarcoding analysis of the bacterial succession during vermicomposting of municipal solid waste employing the earthworm Eisenia fetida, Sci. Total Environ., 766, 10.1016/j.scitotenv.2020.144389 Stadhouders, 2010, The effect of primer–template mismatches on the detection and quantification of nucleic acids using the 5′ nuclease assay, J. Mol. Diagn., 12, 109, 10.2353/jmoldx.2010.090035 Steffen, 2011, The Anthropocene: conceptual and historical perspectives, Philos. Trans. R. Soc., A, 369, 842, 10.1098/rsta.2010.0327 Sternhagen, 2020, Contrasting patterns of functional diversity in coffee root fungal communities associated with organic and conventionally managed fields, Appl. Environ. Microbiol., 86, 10.1128/AEM.00052-20 Stewart, 2019, Understanding the effects of biotic and abiotic factors on sources of aquatic environmental DNA, Biodivers. Conserv., 28, 983, 10.1007/s10531-019-01709-8 Stoeckle, 2017, A systematic approach to evaluate the influence of environmental conditions on eDNA detection success in aquatic ecosystems, PLoS One, 12, 10.1371/journal.pone.0189119 Strayer, 2010, Alien species in fresh waters: ecological effects, interactions with other stressors, and prospects for the future, Freshwater Biol., 55, 152, 10.1111/j.1365-2427.2009.02380.x Strickland, 2019, Utility of eDNA and occupancy models for monitoring an endangered fish across diverse riverine habitats, Hydrobiologia, 826, 129, 10.1007/s10750-018-3723-8 Strickler, 2015, Quantifying effects of UV–B, temperature, and pH on eDNA degradation in aquatic microcosms, Biol. Conserv., 183, 85, 10.1016/j.biocon.2014.11.038 Sugawara, 2022, Application of eDNA for monitoring freshwater bivalve Nodularia nipponensis and its glochidium larvae, Environ. DNA, 4, 908, 10.1002/edn3.304 Sun, 2023, Evaluate the biomass of Fenneropenaeus chinensis from the Southern coast of Shandong Peninsula using eDNA, Water, 15, 342, 10.3390/w15020342 Sutter, 2019, Rangewide tidewater goby occupancy survey using environmental DNA, Conserv.Genetics, 20, 597, 10.1007/s10592-019-01161-9 Symondson, 2002, Molecular identification of prey in predator diets, Mol. Ecol., 11, 627, 10.1046/j.1365-294X.2002.01471.x Székely, 2021, Environmental DNA captures the genetic diversity of bowhead whales (Balaena mysticetus) in West Greenland, Environ. DNA, 3, 248, 10.1002/edn3.176 Taberlet, 2012, Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies, Mol. Ecol., 21, 1816, 10.1111/j.1365-294X.2011.05317.x Takahara, 2013, Using environmental DNA to estimate the distribution of an invasive fish species in ponds, PLoS One, 8, e56584, 10.1371/journal.pone.0056584 Takahara, 2015, Effects of sample processing on the detection rate of environmental DNA from the common carp (Cyprinus carpio), Biol. Conserv., 183, 64, 10.1016/j.biocon.2014.11.014 Takahara, 2012, Estimation of fish biomass using environmental DNA, PLoS One, 7, e35868, 10.1371/journal.pone.0035868 Thalinger, 2021, A validation scale to determine the readiness of environmental DNA assays for routine species monitoring, Environ. DNA, 3, 823, 10.1002/edn3.189 Thalinger, 2019, Monitoring spawning migrations of potamodromous fish species via eDNA, Sci. Rep., 9, 1, 10.1038/s41598-019-51398-0 Thomas, 2018, eDNA Sampler: a fully integrated environmental DNA sampling system, Methods Ecol. Evol., 9, 1379, 10.1111/2041-210X.12994 Thomas, 2019, A self–preserving, partially biodegradable eDNA filter, Methods Ecol. Evol., 10, 1136, 10.1111/2041-210X.13212 Thomas, 2020, A system for rapid eDNA detection of aquatic invasive species, Environ. DNA, 2, 261, 10.1002/edn3.25 Thomsen, 2012, Monitoring endangered freshwater biodiversity using environmental DNA, Mol. Ecol., 21, 2565, 10.1111/j.1365-294X.2011.05418.x Thomsen, 2019, Environmental DNA metabarcoding of wild flowers reveals diverse communities of terrestrial arthropods, BMC Ecol Evol, 9, 1665, 10.1002/ece3.4809 Thomsen, 2015, Environmental DNA–An emerging tool in conservation for monitoring past and present biodiversity, Biol. Conserv., 183, 4, 10.1016/j.biocon.2014.11.019 Tordoni, 2021, Integrated eDNA metabarcoding and morphological analyses assess spatio–temporal patterns of airborne fungal spores, Ecol. Indic., 121, 10.1016/j.ecolind.2020.107032 Travis, 2003, Climate change and habitat destruction: a deadly anthropogenic cocktail, Proc. R. Soc. Lond. B Biol. Sci., 270, 467, 10.1098/rspb.2002.2246 Tréguier, 2014, Environmental DNA surveillance for invertebrate species: Advantages and technical limitations to detect invasive crayfish Procambarus clarkii in freshwater ponds, J. Appl. Ecol., 51, 871, 10.1111/1365-2664.12262 Tsoi, 2020, Ctenocephalides felis (cat flea) infestation in neonatal dairy calves managed with deltamethrin pour–on in Australia, Vet. Parasitol., 279, 10.1016/j.vetpar.2020.109039 Tucker, 2016, A sensitive environmental DNA (eDNA) assay leads to new insights on Ruffe (Gymnocephalus cernua) spread in North America, Russ. J. Biol. Invasions, 18, 3205, 10.1007/s10530-016-1209-z Turner, 2014, Particle size distribution and optimal capture of aqueous macrobial eDNA, Methods Ecol. Evol., 5, 676, 10.1111/2041-210X.12206 Uchida, 2020, Aquatic insect community structure revealed by eDNA metabarcoding derives indices for environmental assessment, PeerJ, 8, e9176, 10.7717/peerj.9176 Uchii, 2017, Distinct seasonal migration patterns of Japanese native and non–native genotypes of common carp estimated by environmental DNA, BMC Ecol. Evol., 7, 8515, 10.1002/ece3.3346 UNICEF. (2020). The state of food security and nutrition in the world 2020. Utzeri, 2018, Entomological signatures in honey: an environmental DNA metabarcoding approach can disclose information on plant–sucking insects in agricultural and forest landscapes, Sci. Rep., 8, 1, 10.1038/s41598-018-27933-w Valdivia–Carrillo, 2021, Integrating eDNA metabarcoding and simultaneous underwater visual surveys to describe complex fish communities in a marine biodiversity hotspot, Mol. Ecol. Resour., 21, 1558, 10.1111/1755-0998.13375 Valentin, 2016, Real–time PCR assay to detect brown marmorated stink bug, Halyomorpha halys (Stål), in environmental DNA, Pest Manage. Sci., 72, 1854, 10.1002/ps.4217 Valentin, 2018, Early detection of invasive exotic insect infestations using eDNA from crop surfaces, Front. Ecol. Environ., 16, 265, 10.1002/fee.1811 Valentin, 2021, The state, transport, and fate of aboveground terrestrial arthropod eDNA, Environ. DNA, 3, 1081, 10.1002/edn3.229 Valentini, 2009, New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach, Mol. Ecol. Resour., 9, 51, 10.1111/j.1755-0998.2008.02352.x Valentini, 2016, Next–generation monitoring of aquatic biodiversity using environmental DNA metabarcoding, Mol. Ecol., 25, 929, 10.1111/mec.13428 Valsecchi, 2022, A species–specific qPCR assay provides novel insight into range expansion of the Mediterranean monk seal (Monachus monachus) by means of eDNA analysis, Biodivers. Conserv., 31, 1175, 10.1007/s10531-022-02382-0 Van Der Heyde, 2020, Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA metabarcoding, Mol. Ecol. Resour., 20, 732, 10.1111/1755-0998.13148 Veldhoen, 2012, Molecular profiling of marine fauna: integration of omics with environmental assessment of the world's oceans, Ecotoxicol. Environ. Saf., 76, 23, 10.1016/j.ecoenv.2011.10.005 Vörös, 2017, Surveying Europe's only cave–dwelling chordate species (Proteus anguinus) using environmental DNA, PLoS One, 12, 10.1371/journal.pone.0170945 Vörösmarty, 2010, Global threats to human water security and river biodiversity, Nature, 467, 555, 10.1038/nature09440 Wang, 2020, Soil microbial succession with soil development since costal reclamation, Catena, 187, 10.1016/j.catena.2019.104393 Wei, 2018, Effects of treated sample weight and DNA marker length on sediment eDNA based detection of a benthic invertebrate, Ecol. Indic., 93, 267, 10.1016/j.ecolind.2018.04.063 Wei, 2009, Using drift nets to capture early life stages and monitor spawning of the Yangtze River Chinese sturgeon (Acipenser sinensis), J. Appl. Ichthyol., 25, 100, 10.1111/j.1439-0426.2009.01269.x Weitemier, 2021, Estimating the genetic diversity of Pacific salmon and trout using multigene eDNA metabarcoding, Mol. Ecol., 30, 4970, 10.1111/mec.15811 Weldon, 2020, A comparison of European eel Anguilla anguilla eDNA concentrations to fyke net catches in five Irish lakes, Environ. DNA, 2, 587, 10.1002/edn3.91 Weltz, 2017, Application of environmental DNA to detect an endangered marine skate species in the wild, PLoS One, 12, 10.1371/journal.pone.0178124 West, 2022, The applicability of eDNA metabarcoding approaches for sessile benthic surveying in the Kimberley region, north–western Australia, Environ. DNA, 4, 34, 10.1002/edn3.184 West, 2020, Under the karst: detecting hidden subterranean assemblages using eDNA metabarcoding in the caves of Christmas Island, Australia, Sci. Rep., 10, 1, 10.1038/s41598-020-78525-6 White, 2020, Detection of the rare Australian endemic blind cave eel (Ophisternon candidum) with environmental DNA: implications for threatened species management in subterranean environments, Hydrobiologia, 847, 3201, 10.1007/s10750-020-04304-z Wilcox, 2013, Robust detection of rare species using environmental DNA: the importance of primer specificity, PLoS One, 8, e59520, 10.1371/journal.pone.0059520 Willerslev, 2003, Diverse plant and animal genetic records from Holocene and Pleistocene sediments, Science, 300, 791, 10.1126/science.1084114 Wintermantel, 2010, Methods for detection and differentiation of existing and new crinivirus species through multiplex and degenerate primer RT–PCR, J. Virol. Methods, 170, 106, 10.1016/j.jviromet.2010.09.008 Wong, 2020, Field application of an improved protocol for environmental DNA extraction, purification, and measurement using Sterivex filter, Sci. Rep., 10, 1, 10.1038/s41598-020-77304-7 Wu, 2018, Environmental DNA reveals nonmigratory individuals of Palaemon paucidens overwintering in Lake Biwa shallow waters, Freshwater Science, 37, 307, 10.1086/697542 Xia, 2018, Early detection of a highly invasive bivalve based on environmental DNA (eDNA), Russ. J. Biol. Invasions, 20, 437, 10.1007/s10530-017-1545-7 Yamamoto, 2017, Environmental DNA metabarcoding reveals local fish communities in a species–rich coastal sea, Sci. Rep., 7, 1, 10.1038/srep40368 Yamamoto, 2016, Environmental DNA as a ‘snapshot'of fish distribution: A case study of Japanese jack mackerel in Maizuru Bay, Sea of Japan, PLoS One, 11, 10.1371/journal.pone.0149786 Yamanaka, 2016, On–site filtration of water samples for environmental DNA analysis to avoid DNA degradation during transportation, Ecol. Res., 31, 963, 10.1007/s11284-016-1400-9 Yang, 2023, Small changes make big progress: A more efficient eDNA monitoring method for freshwater fish, Environmental DNA, 5, 363, 10.1002/edn3.387 Yao, 2022, Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward, Mol. Ecol., 31, 5132, 10.1111/mec.16659 Yoshitake, 2019, HaCeD–Seq: a novel method for reliable and easy estimation about the fish population using haplotype count from eDNA, Mar. Biotechnol., 21, 813, 10.1007/s10126-019-09926-6 Young, 2021, Biosurveillance for invasive insect pest species using an environmental DNA metabarcoding approach and a high salt trap collection fluid, BMC Ecol Evol, 11, 1558, 10.1002/ece3.7113 Yue, 2020, Sustainable food production, forest biodiversity and mineral pricing: Interconnected global issues, Resour. Policy, 65, 10.1016/j.resourpol.2020.101583 Yusishen, 2020, Development of quantitative PCR assays for the detection and quantification of lake sturgeon (Acipenser fulvescens) environmental DNA, Conserv. Genet. Resour., 12, 17, 10.1007/s12686-018-1054-8 Zarzoso–Lacoste, 2013, Improving PCR detection of prey in molecular diet studies: Importance of group–specific primer set selection and extraction protocol performances, Mol. Ecol. Resour., 13, 117, 10.1111/1755-0998.12029 Zenker, 2020, Assessing insect biodiversity with automatic light traps in Brazil: Pearls and pitfalls of metabarcoding samples in preservative ethanol, BMC Ecol Evol, 10, 2352, 10.1002/ece3.6042 Zhang, 2020, A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish, Methods Ecol. Evol., 11, 1609, 10.1111/2041-210X.13485 Zhu, 2006, Degradation of plasmid and plant DNA in water microcosms monitored by natural transformation and real–time polymerase chain reaction (PCR), Water Res., 40, 3231, 10.1016/j.watres.2006.06.040 Zhou, 2022, Combined use of eDNA metabarcoding and bottom trawling for the assessment of fish biodiversity in the Zhoushan Sea, Front. Mar. Sci., 8, 2056, 10.3389/fmars.2021.809703 Zhou, 2020, Microbiota in the rhizosphere and seed of rice from China, with reference to their transmission and biogeography, Front. Microbiol., 995, 10.3389/fmicb.2020.00995 Zinger, 2018, Body size determines soil community assembly in a tropical forest, Mol. Ecol., 28, 528, 10.1111/mec.14919