Environmental DNA as a tool for biodiversity monitoring in aquatic ecosystems – a review
Article Sidebar
Main Article Content
Abstract
The monitoring of changes in aquatic ecosystems due to anthropogenic activities is of utmost importance to ensure the health of aquatic biodiversity. Eutrophication in water bodies due to anthropogenic disturbances serves as one of the major sources of nutrient efflux and consequently changes the biological productivity and community structure of these ecosystems. Habitat destruction and overexploitation of natural resources are other sources that impact the equilibrium of aquatic systems. Environmental DNA (eDNA) is a tool that can help to assess and monitor aquatic biodiversity. There has been a considerable outpour of research in this area in the recent past, particularly concerning conservation and biodiversity management. This review focuses on the application of eDNA for the detection and relative quantification of threatened, endangered, invasive and elusive species. We give a special emphasis on how this technique developed in the past few years to become a tool for understanding the impact of spatial-temporal changes on ecosystems. Incorporating eDNA based biomonitoring with advances in sequencing technologies and computational abilities had an immense role in the development of different avenues of application of this tool.
Article Details
This work is licensed under a Creative Commons Attribution 4.0 International License.
Authors own the copyright to the articles published in JoTT. This is indicated explicitly in each publication. The authors grant permission to the publisher Wildlife Information Liaison Development (WILD) Society to publish the article in the Journal of Threatened Taxa. The authors recognize WILD as the original publisher, and to sell hard copies of the Journal and article to any buyer. JoTT is registered under the Creative Commons Attribution 4.0 International License (CC BY), which allows authors to retain copyright ownership. Under this license the authors allow anyone to download, cite, use the data, modify, reprint, copy and distribute provided the authors and source of publication are credited through appropriate citations (e.g., Son et al. (2016). Bats (Mammalia: Chiroptera) of the southeastern Truong Son Mountains, Quang Ngai Province, Vietnam. Journal of Threatened Taxa 8(7): 8953–8969. https://doi.org/10.11609/jott.2785.8.7.8953-8969). Users of the data do not require specific permission from the authors or the publisher.
References
Akamatsu, Y., G. Kume, M. Gotou, T. Kono, T. Fujii, R. Inui & Y. Kurita (2020). Using environmental DNA analyses to assess the occurrence and abundance of the endangered amphidromous fish Plecoglossus altivelis ryukyuensis. Biodiversity Data Journal 8 :e39679. https://doi.org/10.3897/BDJ.8.e39679 DOI: https://doi.org/10.3897/BDJ.8.e39679
Andruszkiewicz, E.A., J.R. Koseff, O.B. Fringer, N.T. Ouellette, A.B. Lowe, C.A. Edwards & A.B. Boehm (2019). Modeling environmental DNA transport in the coastal ocean using Lagrangian particle tracking. Frontiers in Marine Science 6: 477. https://doi.org/10.3389/fmars.2019.00477 DOI: https://doi.org/10.3389/fmars.2019.00477
Baker, C.S., D. Steel, S. Nieukirk & H. Klinck (2018). Environmental DNA (eDNA) from the wake of the whales: Droplet digital PCR for detection and species identification. Frontiers in Marine Science 5: 1021. https://doi.org/10.3389/fmars.2018.00133 DOI: https://doi.org/10.3389/fmars.2018.00133
Barnes, M.A. & C.R. Turner (2016). The ecology of environmental DNA and implications for conservation genetics. Conservation Genetics 17(1): 1–17. https://doi.org/10.1007/s10592-015-0775-4 DOI: https://doi.org/10.1007/s10592-015-0775-4
Barnes, M.A., C.R. Turner, C.L. Jerde, M.A Renshaw, W.L Chadderton & D.M. Lodge (2014). Environmental conditions influence eDNA persistence in aquatic systems. Environmental Science and Technology 48(3): 1819–1827. https://doi.org/10.1021/es404734p DOI: https://doi.org/10.1021/es404734p
Bianchi, T. & E. Morrison (2018). Human Activities Create Corridors of Change in Aquatic Zones. Eos 99(11): 13–15. https://doi.org/10.1029/2018eo104743 DOI: https://doi.org/10.1029/2018EO104743
Bremmer, R.H., K.G. De Bruin, M.J.C. Van Gemert,, T.G. Van Leeuwen & M.C.G Aalders (2012). Forensic quest for age determination of bloodstains. Forensic Science International 216(1–3): 1–11. https://doi.org/10.1016/j.forsciint.2011.07.027 DOI: https://doi.org/10.1016/j.forsciint.2011.07.027
Brys, R., D. Halfmaerten, S. Neyrinck, Q. Mauvisseau, J. Auwerx, M. Sweet & J. Mergeay (2021). Reliable eDNA detection and quantification of the European weather loach (Misgurnus fossilis). Journal of Fish Biology 98(2): 399–414. https://doi.org/10.1111/jfb.14315 DOI: https://doi.org/10.1111/jfb.14315
Capo, E., G. Spong, S. Norman, H. Königsson, P. Bartels & P. Byström (2019). Droplet digital PCR assays for the quantification of brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) from environmental DNA collected in the water of mountain lakes. PLoS ONE 14(12): 1–19. https://doi.org/10.1371/journal.pone.0226638 DOI: https://doi.org/10.1371/journal.pone.0226638
Carmichael, W.W. (2001). Health Effects of Toxin-Producing Cyanobacteria: “The CyanoHABs.” Human and Ecological Risk Assessment: An International Journal Human and Ecological Risk Assessment 7(5): 1393–1407. https://doi.org/10.1080/20018091095087 DOI: https://doi.org/10.1080/20018091095087
Carpenter R.S. (1981). The American Naturalist. The American Naturalist 118(3): 372–383. DOI: https://doi.org/10.1086/283829
Clark, D.E., C.A. Pilditch, J.K. Pearman, J.I. Ellis & A. Zaiko (2020). Environmental DNA metabarcoding reveals estuarine benthic community response to nutrient enrichment – Evidence from an in-situ experiment. Environmental Pollution 267: 115472. https://doi.org/10.1016/j.envpol.2020.115472 DOI: https://doi.org/10.1016/j.envpol.2020.115472
Collins, R.A., O.S. Wangensteen, E.J. O’Gorman, S. Mariani, D.W. Sims & M.J. Genner (2018). Persistence of environmental DNA in marine systems. Communications Biology 1(1): 1–11. https://doi.org/10.1038/s42003-018-0192-6 DOI: https://doi.org/10.1038/s42003-018-0192-6
Conley, D.J., H.W. Paerl, R.W. Howarth, D.F. Boesch, S.P. Seitzinger, K.E. Havens, C. Lancelot & G.E. Likens (2009). Controlling eutrophication: phosphorus and nitrogen. Science 323: 1014–1015. DOI: https://doi.org/10.1126/science.1167755
Cowart, D.A., K.G.H Breedveld, M.J. Ellis, J.M. Hull & E.R. Larson (2018). Environmental DNA (eDNA) applications for the conservation of imperiled crayfish (Decapoda: Astacidea) through monitoring of invasive species barriers and relocated populations. Journal of Crustacean Biology 38(3): 257–266. https://doi.org/10.1093/jcbiol/ruy007 DOI: https://doi.org/10.1093/jcbiol/ruy007
Craine, J., M. Cannon, A. Elmore, S. Guinn & N. Fierer (2017). DNA metabarcoding potentially reveals multi-assemblage eutrophication responses in an eastern North American river. BioRxiv 186452. https://doi.org/10.1101/186452 DOI: https://doi.org/10.1101/186452
Cristescu, M.E. & P.D.N. Hebert (2018). Uses and misuses of environmental DNA in biodiversity science and conservation. Annual Review of Ecology, Evolution, and Systematics 49: 209–230. https://doi.org/10.1146/annurev-ecolsys-110617-062306 DOI: https://doi.org/10.1146/annurev-ecolsys-110617-062306
Deiner, K., J.C. Walser, E. Mächler & F. Altermatt (2015). Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA. Biological Conservation 183: 53–63. https://doi.org/10.1016/j.biocon.2014.11.018 DOI: https://doi.org/10.1016/j.biocon.2014.11.018
Dejean, T., A. Valentini, A. Duparc, S. Pellier-Cuit, F. Pompanon, P. Taberlet & C. Miaud (2011). Persistence of environmental DNA in freshwater ecosystems. PLoS ONE 6(8): 8–11. https://doi.org/10.1371/journal.pone.0023398 DOI: https://doi.org/10.1371/journal.pone.0023398
Dejean, T., A. Valentini, C. Miquel, P. Taberlet, E. Bellemain & C. Miaud (2012). Improved detection of an alien invasive species through environmental DNA barcoding: The example of the American bullfrog Lithobates catesbeianus. Journal of Applied Ecology 49(4): 953–959. https://doi.org/10.1111/j.1365-2664.2012.02171.x DOI: https://doi.org/10.1111/j.1365-2664.2012.02171.x
Deutschmann, B., A.K. Müller, H. Hollert & M. Brinkmann (2019). Assessing the fate of brown trout (Salmo trutta) environmental DNA in a natural stream using a sensitive and specific dual-labelled probe. Science of the Total Environment 655: 321–327. https://doi.org/10.1016/j.scitotenv.2018.11.247 DOI: https://doi.org/10.1016/j.scitotenv.2018.11.247
Díaz-Ferguson, E., J. Herod, J. Galvez & G. Moyer, G (2014). Development of molecular markers for eDNA detection of the invasive African jewelfish (Hemichromis letourneuxi): A new tool for monitoring aquatic invasive species in National Wildlife Refuges. Management of Biological Invasions 5(2): 121–131. https://doi.org/10.3391/mbi.2014.5.2.05 DOI: https://doi.org/10.3391/mbi.2014.5.2.05
Doi, H., K. Uchii, T. Takahara, S. Matsuhashi, H. Yamanaka & T. Minamoto (2015). Use of droplet digital PCR for estimation of fish abundance and biomass in environmental DNA surveys. PLoS ONE 10(3): 1–11. https://doi.org/10.1371/journal.pone.0122763 DOI: https://doi.org/10.1371/journal.pone.0122763
Doi, H., T. Watanabe, N. Nishizawa, T. Saito, H. Nagata, Y. Kameda, N. Maki, K. Ikeda & T. Fukuzawa, T (2021). On-site environmental DNA detection of species using ultrarapid mobile PCR. Molecular Ecology Resources 21(7): 2364–2368. https://doi.org/10.1111/1755-0998.13448 DOI: https://doi.org/10.1111/1755-0998.13448
Anderson, D.M., P.M. Glibert & J.M. Burkholder (2002). Harmful algal blooms and eutrophication: nutrient sources, composition, and consequences. Estuaries 25(4): 704–726. DOI: https://doi.org/10.1007/BF02804901
Dougherty, M.M., E.R. Larson, M.A. Renshaw, C.A. Gantz, S.P. Egan, D.M. Erickson & D.M. Lodge (2016). Environmental DNA (eDNA) detects the invasive rusty crayfish Orconectes rusticus at low abundances. Journal of Applied Ecology 53(3): 722–732. https://doi.org/10.1111/1365-2664.12621 DOI: https://doi.org/10.1111/1365-2664.12621
Elberri, A.I., A. Galal-Khallaf, S.E. Gibreel, S.F. El-Sakhawy, I. El-Garawani, S. El-Sayed Hassab ElNabi & K. Mohammed-Geba (2020). DNA and eDNA-based tracking of the North African sharptooth catfish Clarias gariepinus. Molecular and Cellular Probes 51: 101535. https://doi.org/10.1016/j.mcp.2020.101535 DOI: https://doi.org/10.1016/j.mcp.2020.101535
Elbrecht, V. & F. Leese (2015). Can DNA-based ecosystem assessments quantify species abundance? Testing primer bias and biomass-sequence relationships with an innovative metabarcoding protocol. PLoS ONE 10(7): 1–16. https://doi.org/10.1371/journal.pone.0130324 DOI: https://doi.org/10.1371/journal.pone.0130324
Ficetola, G.F., J. Pansu, A. Bonin, E. Coissac, C. Giguet-Covex, M. De Barba, L. Gielly, C.M. Lopes, F. Boyer, F. Pompanon, G. Rayé & P. Taberlet (2015). Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data. Molecular Ecology Resources 15(3): 543–556. https://doi.org/10.1111/1755-0998.12338 DOI: https://doi.org/10.1111/1755-0998.12338
Fonseca, V. G (2018). Pitfalls in relative abundance estimation using edna metabarcoding. Molecular Ecology Resources 18(5): 923–926. https://doi.org/10.1111/1755-0998.12902 DOI: https://doi.org/10.1111/1755-0998.12902
Fujiwara, A., S. Matsuhashi, H. Doi, S. Yamamoto & T. Minamoto (2016). Use of environmental DNA to survey the distribution of an invasive submerged plant in ponds. Freshwater Science 35(2): 748–754. https://doi.org/10.1086/685882 DOI: https://doi.org/10.1086/685882
Fukumoto, S., A. Ushimaru & T. Minamoto (2015). A basin-scale application of environmental DNA assessment for rare endemic species and closely related exotic species in rivers: A case study of giant salamanders in Japan. Journal of Applied Ecology 52(2): 358–365. https://doi.org/10.1111/1365-2664.12392 DOI: https://doi.org/10.1111/1365-2664.12392
Gargan, L.M., T. Morato, C.K. Pham, J.A. Finarelli, J.E.L Carlsson & J. Carlsson (2017). Development of a sensitive detection method to survey pelagic biodiversity using eDNA and quantitative PCR: a case study of devil ray at seamounts. Marine Biology 164(5): 1–9. https://doi.org/10.1007/s00227-017-3141-x DOI: https://doi.org/10.1007/s00227-017-3141-x
Garlapati, D., B.C. Kumar, C. Muthukumar, P. Madeswaran, K. Ramu & M.V.R. Murthy (2021). Assessing the in situ bacterial diversity and composition at anthropogenically active sites using the environmental DNA (eDNA). Marine Pollution Bulletin 170: 112593. https://doi.org/10.1016/j.marpolbul.2021.112593 DOI: https://doi.org/10.1016/j.marpolbul.2021.112593
Geerts, A.N., P. Boets, S. Van den Heede, P. Goethals & C. Van der heyden (2018). A search for standardized protocols to detect alien invasive crayfish based on environmental DNA (eDNA): A lab and field evaluation. Ecological Indicators 84: 564–572. https://doi.org/10.1016/j.ecolind.2017.08.068 DOI: https://doi.org/10.1016/j.ecolind.2017.08.068
Gunzburger, M.S (2007). Evaluation of seven aquatic sampling methods for amphibians and other aquatic fauna. Applied Herpetology 4(1): 47–63. https://doi.org/10.1163/157075407779766750 DOI: https://doi.org/10.1163/157075407779766750
Harper, K.J., N.P. Anucha, J.F. Turnbull, C.W. Bean & M.J. Leaver (2018). Searching for a signal: Environmental DNA (eDNA) for the detection of invasive signal crayfish, Pacifastacus leniusculus (Dana, 1852). Management of Biological Invasions 9(2): 137–148. https://doi.org/10.3391/mbi.2018.9.2.07 DOI: https://doi.org/10.3391/mbi.2018.9.2.07
Hinlo, R., D. Gleeson, M.Lintermans & E.Furlan (2017). Methods to maximise recovery of environmental DNA from water samples. PLoS ONE 12(6): 1–22. https://doi.org/10.1371/journal.pone.0179251 DOI: https://doi.org/10.1371/journal.pone.0179251
Hunter, M.E., J.A. Ferrante, G. Meigs-Friend & A. Ulmer (2019). Improving eDNA yield and inhibitor reduction through increased water volumes and multi-filter isolation techniques. Scientific Reports 9(1): 1–9. https://doi.org/10.1038/s41598-019-40977-w DOI: https://doi.org/10.1038/s41598-019-40977-w
Jackson, M., C. Myrholm, C. Shaw & T. Ramsfield (2017). Using nested PCR to improve detection of earthworm eDNA in Canada. Soil Biology and Biochemistry 113: 215–218. https://doi.org/10.1016/j.soilbio.2017.06.009 DOI: https://doi.org/10.1016/j.soilbio.2017.06.009
Jiao, N.Z., D.K. Chen, Y.M. Luo, X.P. Huang, R. Zhang, H.B. Zhang, Z.J. Jiang & F. Zhang (2015). Climate change and anthropogenic impacts on marine ecosystems and countermeasures in China. Advances in Climate Change Research 6(2): 118–125. https://doi.org/10.1016/j.accre.2015.09.010 DOI: https://doi.org/10.1016/j.accre.2015.09.010
Jovel, J., J. Patterson, W. Wang, N. Hotte, S. O’Keefe, T. Mitchel, T. Perry, D. Kao, A.L. Mason, K.L. Madsen & G.K.S. Wong (2016). Characterization of the gut microbiome using 16S or shotgun metagenomics. Frontiers in Microbiology 7: 459. https://doi.org/10.3389/fmicb.2016.00459 DOI: https://doi.org/10.3389/fmicb.2016.00459
Lacoursière-Roussel, A., G. Côté, V. Leclerc & L. Bernatchez (2016a). Quantifying relative fish abundance with eDNA: a promising tool for fisheries management. Journal of Applied Ecology 53(4): 1148–1157. https://doi.org/10.1111/1365-2664.12598 DOI: https://doi.org/10.1111/1365-2664.12598
Lacoursière-Roussel, A., M. Rosabal & L. Bernatchez (2016b). Estimating fish abundance and biomass from eDNA concentrations: variability among capture methods and environmental conditions. Molecular Ecology Resources 16(6): 1401–1414. https://doi.org/10.1111/1755-0998.12522 DOI: https://doi.org/10.1111/1755-0998.12522
Lacoursière-Roussel, A., Y. Dubois, E. Normandeau & L. Bernatchez (2016c). Improving herpetological surveys in eastern North America using the environmental DNA method1. Genome 59(11): 991–1007. https://doi.org/10.1139/gen-2015-0218 DOI: https://doi.org/10.1139/gen-2015-0218
Lee, A.H., J. Lee, J. Noh, C. Lee, S. Hong, B.O. Kwon, J.J. Kim & J.S. Khim (2020). Characteristics of long-term changes in microbial communities from contaminated sediments along the west coast of South Korea: Ecological assessment with eDNA and physicochemical analyses. Marine Pollution Bulletin 160: 111592. https://doi.org/10.1016/j.marpolbul.2020.111592 DOI: https://doi.org/10.1016/j.marpolbul.2020.111592
Leray, M. & N. Knowlton (2017). Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding. PeerJ 3: 1–27. https://doi.org/10.7717/peerj.3006 DOI: https://doi.org/10.7717/peerj.3006
Li, F., Y. Peng, W. Fang,, F. Altermatt., Y. Xie, J. Yang & X. Zhang (2018). Application of Environmental DNA Metabarcoding for Predicting Anthropogenic Pollution in Rivers. Environmental Science and Technology 52(20): 11708–11719. https://doi.org/10.1021/acs.est.8b03869 DOI: https://doi.org/10.1021/acs.est.8b03869
Liang, Z. & A. Keeley (2013). Filtration recovery of extracellular DNA from environmental water samples. Environmental Science and Technology 47(16): 9324–9331. https://doi.org/10.1021/es401342b DOI: https://doi.org/10.1021/es401342b
Lor, Y., T.M. Schreier, D.L. Waller & C.M. Merkes (2020). Using environmental dna (eDNA) to detect the endangered spectaclecase mussel (margaritifera monodonta). Freshwater Science 39(4): 837–847. https://doi.org/10.1086/71167 DOI: https://doi.org/10.1086/711673
Manu, S. & G. Umapathy (2021). A Novel Metagenomic Workflow for Biomonitoring across the Tree of Life using PCR-free Ultra-deep Sequencing of Extracellular eDNA. Authorea Preprints. DOI: https://doi.org/10.22541/au.161401815.51766652/v1
Maruyama, A., K. Nakamura, H. Yamanaka, M. Kondoh & T. Minamoto (2014). The release rate of environmental DNA from juvenile and adult fish. PLoS ONE 9(12): 1–13. https://doi.org/10.1371/journal.pone.0114639 DOI: https://doi.org/10.1371/journal.pone.0114639
Mauvisseau, Q., E. Kalogianni, B. Zimmerman, M. Bulling, R. Brys & M. Sweet (2020). eDNA-based monitoring: Advancement in management and conservation of critically endangered killifish species. Environmental DNA 2(4): 601–613. https://doi.org/10.1002/edn3.92 DOI: https://doi.org/10.1002/edn3.92
McKee, A.M., S.F. Spear & T.W. Pierson (2015). The effect of dilution and the use of a post-extraction nucleic acid purification column on the accuracy, precision, and inhibition of environmental DNA samples. Biological Conservation 183: 70–76. https://doi.org/10.1016/j.biocon.2014.11.031 DOI: https://doi.org/10.1016/j.biocon.2014.11.031
Miralles, L., M. Parrondo, A. Hernández de Rojas, E. Garcia-Vazquez. & Y.J. Borrell (2019). Development and validation of eDNA markers for the detection of Crepidula fornicata in environmental samples. Marine Pollution Bulletin 146: 827–830. https://doi.org/10.1016/j.marpolbul.2019.07.050 DOI: https://doi.org/10.1016/j.marpolbul.2019.07.050
Morley, S.A. & B.L. Nielsen (2016). Chloroplast DNA copy number changes during plant development in organelle DNA polymerase mutants. Frontiers in Plant Science 7: 1–10. https://doi.org/10.3389/fpls.2016.00057 DOI: https://doi.org/10.3389/fpls.2016.00057
Nazari-Sharabian, M., S. Ahmad & K. Moses (2018). Climate change and groundwater : a short review Engineering, Technology and Applied Science Research 8(6): 3668–3672. https://digitalscholarship.unlv.edu/fac_articles/562 DOI: https://doi.org/10.48084/etasr.2392
Nevers, M.B., M.N. Byappanahalli, C.C. Morris, D. Shively, K. Przybyla-Kelly, A.M. Spoljaric, J. Dickey & E.F. Roseman (2018). Environmental DNA (eDNA): A tool for quantifying the abundant but elusive round goby (Neogobius melanostomus). PLoS ONE 13(1): 1–22. https://doi.org/10.1371/journal.pone.0191720 DOI: https://doi.org/10.1371/journal.pone.0191720
Niemiller, M.L., M.L. Porter, J. Keany, H. Gilbert, D.W. Fong, D.C. Culver, C.S. Hobson, K.D. Kendall, M.A. Davis & S.J. Taylor (2018). Evaluation of eDNA for groundwater invertebrate detection and monitoring: a case study with endangered Stygobromus (Amphipoda: Crangonyctidae). Conservation Genetics Resources 10(2): 247–257. https://doi.org/10.1007/s12686-017-0785-2 DOI: https://doi.org/10.1007/s12686-017-0785-2
Oberemm, A., J. Becker, G.A. Codd & C. Steinberg (1999). Effects of cyanobacterial toxins and aqueous crude extracts of cyanobacteria on the development of fish and amphibians. Environmental Toxicology 14(1): 77–88. https://doi.org/10.1002/(SICI)1522-7278(199902)14:1<77::AID-TOX11>3.0.CO;2-F DOI: https://doi.org/10.1002/(SICI)1522-7278(199902)14:1<77::AID-TOX11>3.0.CO;2-F
Ogram, A., G.S. Sayler & T. Barkay (1987). The extraction and purification of microbial DNA from sediments. Journal of Microbiological Methods 7(2–3): 57–66. https://doi.org/10.1016/0167-7012(87)90025-X DOI: https://doi.org/10.1016/0167-7012(87)90025-X
Parsons, K.M., M. Everett, M. Dahlheim & L. Park (2018). Water, water everywhere: Environmental DNA can unlock population structure in elusive marine species. Royal Society Open Science 5(8): 180537. https://doi.org/10.1098/rsos.180537 DOI: https://doi.org/10.1098/rsos.180537
Paul, J.H., W.H. Jeffrey & M.F. DeFlaun (1987). Dynamics of extracellular DNA in the marine environment. Applied and Environmental Microbiology 53(1): 170–179. https://doi.org/10.1128/aem.53.1.170-179.1987 DOI: https://doi.org/10.1128/aem.53.1.170-179.1987
Pilliod, D.S., C.S. Goldberg, M.B. Laramie & L.P. Waits (2013a). Application of Environmental DNA for Inventory and Monitoring of Aquatic Species. United States Geological Survey, USA, 4 pp. http://www.arlis.org/docs/vol1/F/835572905.pdf DOI: https://doi.org/10.3133/fs20123146
Pilliod, D.S., C.S. Goldberg, R.S. Arkle & L.P. Waits (2013b). Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples. Canadian Journal of Fisheries and Aquatic Sciences 70(8): 1123–1130. https://doi.org/10.1139/cjfas-2013-0047 DOI: https://doi.org/10.1139/cjfas-2013-0047
Pinto, A.J. & L. Raskin (2012). PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS ONE 7(8): e43093. https://doi.org/10.1371/journal.pone.0043093 DOI: https://doi.org/10.1371/journal.pone.0043093
Pukk, L., J. Kanefsky, A.L. Heathman, E.M. Weise, L.R. Nathan, S.J. Herbst, N.M. Sard, K.T. Scribner & J.D. Robinson (2021). eDNA metabarcoding in lakes to quantify influences of landscape features and human activity on aquatic invasive species prevalence and fish community diversity. Diversity and Distributions 27(10): 2016–2031. https://doi.org/10.1111/ddi.13370 DOI: https://doi.org/10.1111/ddi.13370
Reji, L. & C.A. Francis (2020). Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage. ISME Journal 14(8): 2105–2115. https://doi.org/10.1038/s41396-020-0675-6 DOI: https://doi.org/10.1038/s41396-020-0675-6
Renshaw, M.A., B.P. Olds, C.L. Jerde, M.M. Mcveigh & D.M. Lodge (2015). The room temperature preservation of filtered environmental DNA samples and assimilation into a phenol-chloroform-isoamyl alcohol DNA extraction. Molecular Ecology Resources 15(1): 168–176. https://doi.org/10.1111/1755-0998.12281 DOI: https://doi.org/10.1111/1755-0998.12281
Sassoubre, L.M., K.M. Yamahara, L.D. Gardner, B.A. Block & A.B. Boehm (2016). Quantification of Environmental DNA (eDNA) Shedding and Decay Rates for Three Marine Fish. Environmental Science and Technology 50(19): 10456–10464. https://doi.org/10.1021/acs.est.6b03114 DOI: https://doi.org/10.1021/acs.est.6b03114
Schmelzle, M.C. & A.P. Kinziger (2016). Using occupancy modelling to compare environmental DNA to traditional field methods for regional-scale monitoring of an endangered aquatic species. Molecular Ecology Resources 16(4): 895–908. https://doi.org/10.1111/1755-0998.12501 DOI: https://doi.org/10.1111/1755-0998.12501
Schmidt, B.R., M. Kéry, S. Ursenbacher, O.J. Hyman & J.P. Collins (2013). Site occupancy models in the analysis of environmental DNA presence/absence surveys: A case study of an emerging amphibian pathogen. Methods in Ecology and Evolution 4(7): 646–653. https://doi.org/10.1111/2041-210X.12052 DOI: https://doi.org/10.1111/2041-210X.12052
Sigsgaard, E.E., I.B. Nielsen, S.S. Bach, E.D. Lorenzen, D.P. Robinson, S.W. Knudsen, M.W. Pedersen., M.Al Jaidah, L. Orlando, E. Willerslev, P.R. Møller & P.F. Thomsen (2017). Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA. Nature Ecology & Evolution 1(1): 1–4. https://doi.org/10.1038/s41559-016-0004 DOI: https://doi.org/10.1038/s41559-016-0004
Smith, V.H. (1998). Cultural Eutrophication of Inland, Estuarine, and Coastal Waters, pp. 7–49. In: Pace, M.L. & P.M. Groffman (eds.). Successes, Limitations, and Frontiers in Ecosystem Science. Springer, New York, 490 pp. https://doi.org/10.1007/978-1-4612-1724-4_2 DOI: https://doi.org/10.1007/978-1-4612-1724-4_2
Song, J. W., M.J. Small & E.A. Casman (2017). Making sense of the noise: The effect of hydrology on silver carp eDNA detection in the Chicago area waterway system. Science of the Total Environment 605: 713–720. https://doi.org/10.1016/j.scitotenv.2017.06.255 DOI: https://doi.org/10.1016/j.scitotenv.2017.06.255
Stepien, C.A., M.R. Snyder & A.E. Elz (2019). Invasion genetics of the silver carp Hypophthalmichthys molitrix across North America: Differentiation of fronts, introgression, and eDNA metabarcode detection. PLoS One 14(3): e0203012. DOI: https://doi.org/10.1371/journal.pone.0203012
Sutter, M. & A.P. Kinziger (2019). Rangewide tidewater goby occupancy survey using environmental DNA. Conservation Genetics 20(3): 597–613. https://doi.org/10.1007/s10592-019-01161-9 DOI: https://doi.org/10.1007/s10592-019-01161-9
Tillotson, M.D., R.P. Kelly, J.J. Duda, M. Hoy, J. Kralj & T.P. Quinn (2018). Concentrations of environmental DNA (eDNA) reflect spawning salmon abundance at fine spatial and temporal scales. Biological Conservation 220: 1–11. https://doi.org/10.1016/j.biocon.2018.01.030 DOI: https://doi.org/10.1016/j.biocon.2018.01.030
Petty, J.T., J.L. Hansbarger, B.M. Huntsman & P.M. Mazik (2012). Brook trout movement in response to temperature, flow, and thermal refugia within a complex Appalachian riverscape. Transactions of the American Fisheries Society 141(4): 1060–1073. https://doi.org/10.1080/00028487.2012.681102 DOI: https://doi.org/10.1080/00028487.2012.681102
Tran, P.Q., S.C. Bachand, P.B. McIntyre, B.M. Kraemer, Y. Vadeboncoeur, I.A. Kimirei, R. Tamatamah, K.D. McMahon & K. Anantharaman (2021). Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika. ISME Journal 1971–1986. https://doi.org/10.1038/s41396-021-00898-x DOI: https://doi.org/10.1038/s41396-021-00898-x
Wilcox, T.M., K.S. McKelvey, M.K. Young, S.F. Jane, W.H. Lowe, A.R. Whiteley & M.K. Schwartz (2013). Robust Detection of Rare Species Using Environmental DNA: The Importance of Primer Specificity. PLoS ONE 8(3): e59520. https://doi.org/10.1371/journal.pone.0059520 DOI: https://doi.org/10.1371/journal.pone.0059520
Wilcox, T.M., K.S. McKelvey, M.K. Young, W.H. Lowe & M.K. Schwartz (2015). Environmental DNA particle size distribution from Brook Trout (Salvelinus fontinalis). Conservation Genetics Resources 7(3): 639–641. https://doi.org/10.1007/s12686-015-0465-z DOI: https://doi.org/10.1007/s12686-015-0465-z
Williams, K.E., K.P. Huyvaert & A.J. Piaggio (2016). No filters, no fridges: A method for preservation of water samples for eDNA analysis. BMC Research Notes 9(1): 1–5. https://doi.org/10.1186/s13104-016-2104-5 DOI: https://doi.org/10.1186/s13104-016-2104-5
Xie, Y., X. Zhang, J. Yang, S. Kim, S. Hong, J.P. Giesy, U.H. Yim, W.J. Shim, H. Yu & J.S. Khim (2018). eDNA-based bioassessment of coastal sediments impacted by an oil spill. Environmental Pollution 238: 739–748. https://doi.org/10.1016/j.envpol.2018.02.081 DOI: https://doi.org/10.1016/j.envpol.2018.02.081
Xu, C.L., B.H. Letcher & K.H. Nislow (2010). Size-dependent survival of brook trout Salvelinus fontinalis in summer: Effects of water temperature and stream flow. Journal of Fish Biology 76(10): 2342–2369. https://doi.org/10.1111/j.1095-8649.2010.02619.x DOI: https://doi.org/10.1111/j.1095-8649.2010.02619.x
Yang, J. & X. Zhang (2020). eDNA metabarcoding in zooplankton improves the ecological status assessment of aquatic ecosystems. Environment International 134: 105230. https://doi.org/10.1016/j.envint.2019.105230 DOI: https://doi.org/10.1016/j.envint.2019.105230
Yoshitake, K., T. Yoshinaga, C. Tanaka, N. Mizusawa, M. Reza, A. Tsujimoto, T. Kobayashi & S. Watabe (2019). HaCeD-Seq: a novel method for reliable and easy estimation about the fish population using haplotype count from eDNA. Marine Biotechnology 21(6): 813–820. https://doi.org/10.1007/s10126-019-09926-6 DOI: https://doi.org/10.1007/s10126-019-09926-6