Environmental DNA: history of studies, current and perspective applications in fundamental and applied research

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Abstract

This review article is dedicated to a relatively young, actively developing approach to biodiversity assessment – analysis of environmental DNA (or eDNA). Current views on the nature of eDNA, a brief overview of the history of this approach and methods of eDNA analysis are presented. Major research directions, utilizing eDNA techniques, and perspectives of their application to the study of biodiversity are described. Key issues in development of eDNA approach, its advantages and drawbacks are outlined.

About the authors

Daria V. Pinakhina

Russian ITMO University

Author for correspondence.
Email: acanthodasha@gmail.com
ORCID iD: 0000-0001-9896-6556
SPIN-code: 3163-7275
Scopus Author ID: 55551638800

PhD, master’s degree program student, Faculty of Information Technologies and Programming

Russian Federation, Saint Petersburg

Elena M. Chekunova

Saint Petersburg State University

Email: elena_chekunova@mail.ru
SPIN-code: 2788-6386
Scopus Author ID: 6701797455

Dr. Sci. (Biol.), Senior Researcher

Russian Federation, Saint Petersburg

References

  1. Cristescu ME, Hebert PD. Uses and misuses of environmental DNA in biodiversity science and conservation. Annual Review of Ecology, Evolution, and Systematics. 2018;49(1): 209-230. https://doi.org/10.1146/annurev-ecolsys-110617-062306.
  2. Thomsen PF, Willerslev E. Environmental DNA – an emerging tool in conservation for monitoring past and present biodiversity. Biological Conservation. 2015;183:4-18. https://doi.org/10.1016/j.biocon.2014.11.019.
  3. Jarman SN, Berry O, Bunce M. The value of environmental DNA biobanking for long-term biomonitoring. Nat Ecol Evol. 2018;2(8): 1192-1193. https://doi.org/10.1038/s41559-018-0614-3.
  4. Barnes MA, Turner CR. The ecology of environmental DNA and implications for conservation genetics. Conserv Genet. 2016;17(1):1-17. https://doi.org/10.1007/s10592-015-0775-4.
  5. Dejean T, Valentini A, Duparc A, et al. Persistence of environmental DNA in freshwater ecosystems. PLOS ONE. 2011;6(8): e23398. https://doi.org/10.1371/journal.pone.0023398.
  6. Willerslev E, Hansen A, Binladen J, et al. Diverse plant and animal DNA from Holocene and Pleistocene sedimentary records. Science. 2003;300(5620):791-795. https://doi.org/10.1126/science.1084114.
  7. Stewart KA. Understanding the effects of biotic and abiotic factors on sources of aquatic environmental DNA. Biodivers Conserv. 2019;28(5):983-1001. https://doi.org/10.1007/s10531-019-01709-8.
  8. Pilliod DS, Goldberg CS, Arkle RS, Waits LP. Factors influencing detection of eDNA from a stream-dwelling amphibian. Mol Ecol Resour. 2014;14(1):109-116. https://doi.org/ 10.1111/1755-0998.12159.
  9. Piggott MP. Evaluating the effects of laboratory protocols on eDNA detection probability for an endangered freshwater fish. Ecol Evol. 2016;6(9):2739-2750. https://doi.org/10.1002/ece3.2083.
  10. Goldberg CS, Pilliod DS, Arkle RS, Waits LP. Molecular detection of vertebrates in stream water: a demonstration using Rocky Mountain tailed frogs and idaho giant salamanders. PLoS One. 2011;6(7): e22746. https://doi.org/10.1371/journal.pone.0022746.
  11. Thomsen PF, Kielgast J, Iversen LL, et al. Monitoring endangered freshwater biodiversity using environmental DNA. Mol Ecol. 2012;21(11):2565-2573. https://doi.org/ 10.1111/j.1365-294X.2011.05418.x.
  12. Thomsen PF, Kielgast J, Iversen LL, et al. Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS One. 2012;7(8): e41732. https://doi.org/10.1371/journal.pone.0041732.
  13. Mächler E, Deiner K, Steinmann P, Altermatt F. Utility of environmental DNA for monitoring rare and indicator macroinvertebrate species. Freshwater Science. 2014;33(4):1174-1183. https://doi.org/10.1086/678128.
  14. de Souza LS, Godwin JC, Renshaw MA, Larson E. Environmental DNA (eDNA) detection probability is influenced by seasonal activity of organisms. PLoS One. 2016;11(10): e0165273. https://doi.org/10.1371/journal.pone.0165273.
  15. Laramie MB, Pilliod DS, Goldberg CS. Characterizing the distribution of an endangered salmonid using environmental DNA analysis. Biological Conservation. 2015;183:29-37. https://doi.org/10.1016/j.biocon.2014.11.025.
  16. Erickson RA, Rees CB, Coulter AA, et al. Detecting the movement and spawning activity of bigheaded carps with environmental DNA. Mol Ecol Resour. 2016;16(4):957-965. https://doi.org/10.1111/1755-0998.12533.
  17. Seymour M, Durance I, Cosby BJ, et al. Acidity promotes degradation of multi-species environmental DNA in lotic mesocosms. Commun Biol. 2018;1:4. https://doi.org/10.1038/s42003-017-0005-3.
  18. Khanna M, Stotzky G. Transformation of Bacillus subtilis by DNA bound on montmorillonite and effect of DNase on the transforming ability of bound DNA. Appl Environ Microbiol. 1992;58(6): 1930-1939. https://doi.org/10.1128/AEM.58.6. 1930-1939.1992.
  19. Díaz-Ferguson EE, Moyer GR. History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments. Rev Biol Trop. 2014;62(4):1273-1284. https://doi.org/10.15517/rbt.v62i4.13231.
  20. Ficetola GF, Miaud C, Pompanon F, Taberlet P. Species detection using environmental DNA from water samples. Biology Letters. 2008;4(4): 423-425. https://doi.org/10.1098/rsbl.2008.0118.
  21. Foote AD, Thomsen PF, Sveegaard S, et al. Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals. PLoS One. 2012;7(8):e41781. https://doi.org/10.1371/journal.pone.0041781.
  22. Piaggio AJ, Engeman RM, Hopken MW, et al. 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. 2014;14(2):374-380. https://doi.org/10.1111/1755-0998.12180.
  23. Alvarez AJ, Yumet GM, Santiago CL, Toranzos GA. Stability of manipulated plasmid DNA in aquatic environments. Environmental Toxicology and Water Quality. 1996;11(2): 129-135. https://doi.org/10.1002/(SICI)1098-2256(1996)11:2<129:: AID-TOX8>3.0.CO;2-B.
  24. Zhu B. Degradation of plasmid and plant DNA in water microcosms monitored by natural transformation and real-time polymerase chain reaction (PCR). Water Research. 2006;40(17):3231-3238. https://doi.org/10.1016/j.watres.2006.06.040.
  25. Willerslev E, Cappellini E, Boomsma W, et al. Ancient biomolecules from deep ice cores reveal a forested southern greenland. Science. 2007;317(5834):111-114. https://doi.org/10. 1126/science.1141758.
  26. Ogram A, Sayler GS, Barkay T. The extraction and purification of microbial DNA from sediments. Journal of Microbiological Methods. 1987;7(2-3): 57-66. https://doi.org/10.1016/0167-7012 (87)90025-X.
  27. Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev. 2004;68(4):669-685. https://doi.org/10.1128/MMBR.68.4.669-685.2004.
  28. Bailiff MD, Karl DM. Dissolved and particulate DNA dynamics during a spring bloom in the Antarctic Peninsula region, 1986-1987. Deep Sea Research Part A Oceanographic Research Papers. 1991;38(8-9):1077-1095. https://doi.org/10.1016/0198-0149(91)90097-Y.
  29. Paget E, Lebrun M, Freyssinet G, Simonet P. The fate of recombinant plant DNA in soil. Eur J Soil Biol. 1998;34(2):81-88. https://doi.org/10.1016/S1164-5563(99)90005-5.
  30. Willerslev E, Hansen A, Christensen B, et al. Diversity of Holocene life forms in fossil glacier ice. Proc Natl Acad Sci USA. 1999;96(14): 8017-8021. https://doi.org/10.1073/pnas.96. 14.8017.
  31. Martellini A, Payment P, Villemur R. Use of eukaryotic mitochondrial DNA to differentiate human, bovine, porcine and ovine sources in fecally contaminated surface water. Water Res. 2005;39(4):541-548. https://doi.org/10.1016/j.watres.2004.11.012.
  32. Taberlet P, Coissac E, Hajibabaei M, Rieseberg LH. Environmental DNA. Mol Ecol. 2012;21(8):1789-1793. https://doi.org/10. 1111/j.1365-294X.2012.05542.x.
  33. Yoccoz NG. The future of environmental DNA in ecology. Mol Ecol. 2012;21(8):2031-2038. https://doi.org/10.1111/j.1365-294X.2012.05505.x.
  34. Lodge DM, Turner CR, Jerde CL, et al. Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA. Mol Ecol. 2012;21(11):2555-2558. https://doi.org/10.1111/j.1365-294X.2012.05600.x.
  35. Bohmann K, Evans A, Gilbert MT, et al. Environmental DNA for wildlife biology and biodiversity monitoring. Trends Ecol Evol. 2014;29(6): 358-367. https://doi.org/10.1016/j.tree.2014.04.003.
  36. Seymour M. Rapid progression and future of environmental DNA research. Commun Biol. 2019;2:80. https://doi.org/10.1038/s42003-019-0330-9.
  37. Ruppert K, Kline R, Rahman M. Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA. Global Ecology and Conservation. 2019;17: e00547. https://doi.org/10.1016/j.gecco.2019.e00547.
  38. Bálint M, Pfenninger M, Grossart HP, et al. Environmental DNA time series in ecology. Trends Ecol Evol. 2018;33(12):945-957. https://doi.org/10.1016/j.tree.2018.09.003.
  39. Pedersen MW, Overballe-Petersen S, Ermini L, et al. Ancient and modern environmental DNA. Philos Trans R Soc Lond B Biol Sci. 2015;370(1660):20130383. https://doi.org/ 10.1098/rstb.2013.0383.
  40. Goldberg CS, Turner CR, Deiner K, et al. Critical considerations for the application of environmental DNA methods to detect aquatic species. Methods in Ecology and Evolution. 2016;7(11):1299-1307. https://doi.org/10. 1111/2041-210X.12595.
  41. Creer S, Deiner K, Frey S, et al. The ecologist’s field guide to sequence-based identification of biodiversity. Methods in Ecology and Evolution. 2016;7(9):1008-1018. https://doi.org/10.1111/2041-210X.12574.
  42. Hinlo R, Gleeson D, Lintermans M, Furlan E. Methods to maximise recovery of environmental DNA from water samples. PLoS One. 2017;12(6): e0179251. https://doi.org/10.1371/journal.pone.0179251.
  43. Tedersoo L, Tooming-Klunderud A, Anslan S. PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives. New Phytol. 2018;217(3):1370-1385. https://doi.org/10.1111/nph.14776.
  44. Egeter B, Veríssimo J, Lopes-Lima M, et al. Speeding up the detection of invasive aquatic species using environmental DNA and nanopore sequencing. bioRxiv. 2020. https://doi.org/10.1101/2020.06.09.142521.
  45. Deiner K, Bik HM, Mächler E, et al. Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Mol Ecol. 2017;26(21):5872-5895. https://doi.org/10.1111/mec.14350.
  46. Axtner J, Crampton-Platt A, Hörig LA, et al. An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies. Gigascience. 2019;8(4): giz029. https://doi.org/10.1093/gigascience/giz029.
  47. Dufresne Y, Lejzerowicz F, Perret-Gentil LA, et al. SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data. BMC Bioinformatics. 2019;20(1):88. https://doi.org/10.1186/s12859-019-2663-2.
  48. Ficetola GF, Taberlet P, Coissac E. How to limit false positives in environmental DNA and metabarcoding? Mol Ecol Resour. 2016;16(3):604-607. https://doi.org/10.1111/1755-0998.12508.
  49. Furlan EM, Gleeson D, Wisniewski C, et al. eDNA surveys to detect species at very low densities: A case study of European carp eradication in Tasmania, Australia. J Appl Ecol. 2019;56(11):2505-2517. https://doi.org/10. 1111/1365-2664.13485.
  50. Valentini A, Taberlet P, Miaud C, et al. Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Mol Ecol. 2016;25(4):929-942. https://doi.org/10.1111/mec.13428.
  51. Brown EA, Chain FJ, Zhan A, et al. Early detection of aquatic invaders using metabarcoding reveals a high number of non-indigenous species in Canadian ports. Diversity Distributions. 2016;22(10):1045-1059. https://doi.org/10.1111/ddi.12465.
  52. Clusa L, Miralles L, Basanta A, et al. eDNA for detection of five highly invasive molluscs. A case study in urban rivers from the Iberian Peninsula. PLoS One. 2017;12(11): e0188126. https://doi.org/10.1371/journal.pone.0188126.
  53. Muha TP, Skukan R, Borrell YJ, et al. Contrasting seasonal and spatial distribution of native and invasive Codium seaweed revealed by targeting species-specific eDNA. Ecol Evol. 2019;9(15): 8567-8579. https://doi.org/10.1002/ece3.5379.
  54. Great lakes restoration initiative. Asian carp early detection. Available from: https://www.usgs.gov/centers/glri/science/asian-carp-early-detection?qt-science_center_objects=0#qt-science_center_objects.
  55. Asian Carp. Environmental DNA. Available from: https://www.asiancarp.us/eDNA.html.
  56. Thomas AC, Tank S, Nguyen PL, et al. A system for rapid eDNA detection of aquatic invasive species. 2020;2(3):261-270. Environmental DNA. https://doi.org/10.1002/edn3.25.
  57. Rees HC, Bishop K, Middleditch DJ, et al. The application of eDNA for monitoring of the Great Crested Newt in the UK. Ecol Evol. 2014;4(21):4023-4032. https://doi.org/10. 1002/ece3.1272.
  58. Biggs J, Ewald N, Valentini A, et al. Analytical and methodological development for improved surveillance of the Great Crested Newt. Defra Project WC1067. Oxford: Freshwater Habitats Trust; 2014. 142 р.
  59. Adams CI, Knapp M, Gemmell NJ, et al. Beyond biodiversity: can environmental DNA (eDNA) cut it as a population genetics tool? Genes (Basel). 2019;10(3):192. https://doi.org/10. 3390/genes10030192.
  60. Reinhardt T, van Schingen M, Windisch HS, et al. Monitoring a loss: Detection of the semi-aquatic crocodile lizard (Shinisaurus crocodilurus) in inaccessible habitats via environmental DNA. Aquatic Conservation: Marine and Freshwater Ecosystems. 2019;29(3):353-360. https://doi.org/10.1002/aqc.3038.
  61. Franklin TW, McKelvey KS, Golding JD, et al. Using environmental DNA methods to improve winter surveys for rare carnivores: DNA from snow and improved noninvasive techniques. Biological Conservation. 2019;229:50-58. https://doi.org/10.1016/j.biocon.2018.11.006.
  62. Meyer RS, Curd EE, Schweizer T, et al. The California environmental DNA “CALeDNA” program. Posted Content published. 2019:503383. https://doi.org/10.1101/503383.
  63. CALeDNA. California Environmental DNA Together, we can help protect California’s biodiversity. Available from: http://ucedna.com.
  64. Hempel CA, Peinert B, Beermann AJ, et al. Using environmental DNA to monitor the reintroduction success of the Rhine sculpin (Cottus rhenanus) in a restored stream. Peer J Preprints. 2019;7: e27574v2. https://doi.org/10.7287/peerj.preprints.27574v2.
  65. Boussarie G, Bakker J, Wangensteen O, et al. Environmental DNA illuminates the dark diversity of sharks. Sci Adv. 2018;4(5): eaap9661. https://doi.org/10.1126/sciadv.aap9661.
  66. Sengupta ME, Hellström M, Kariuki HC, et al. Environmental DNA for improved detection and environmental surveillance of schistosomiasis. Proc Natl Acad Sci U S A. 2019;116(18):8931-8940. https://doi.org/10.1073/pnas.1815046116.
  67. Hall EM, Crespi EJ, Goldberg CS, Brunner JL. Evaluating environmental DNA-based quantification of ranavirus infection in wood frog populations. Mol Ecol Resour.2016;16(2):423-433. https://doi.org/10.1111/1755-0998.12461.
  68. Kamoroff C, Goldberg CS. Using environmental DNA for early detection of amphibian chytrid fungus Batrachochytrium dendrobatidis prior to a ranid die-off. Dis Aquat Org. 2017;127(1):75-79. https://doi.org/10.3354/dao03183.
  69. Gomes BG, Hutson KS, Domingos JA, et al. Use of environmental DNA (eDNA) and water quality data to predict protozoan parasites outbreaks in fish farms. Aquaculture. 2017;479:467-473. https://doi.org/10.1016/j.aquaculture.2017.06.021.
  70. Peters L, Spatharis S, Dario MA, et al. Environmental DNA: a new low-cost monitoring tool for pathogens in salmonid aquaculture. Front Microbiol. 2018;9:3009. https://doi.org/10.3389/fmicb.2018.03009.
  71. Environmental DNA Solutions. Cannabis pathogen detection. Available from: https://precisionbiomonitoring.com/environmental-dna-solutions/.
  72. Banchi E, Ametrano CG, Stanković D, et al. DNA metabarcoding uncovers fungal diversity of mixed airborne samples in Italy. PLoS One. 2018;13(3): e0194489. https://doi.org/10.1371/journal.pone.0194489.
  73. Tong X, Xu H, Zou L, et al. High diversity of airborne fungi in the hospital environment as revealed by meta-sequencing-based microbiome analysis. Sci Rep. 2017;7:39606. https://doi.org/10.1038/srep39606.
  74. Valentini A, Miquel C, Taberlet P. DNA barcoding for honey biodiversity. Diversity. 2010;2(4): 610-617. https://doi.org/10.3390/d2040610.
  75. De Vere N, Jones LE, Gilmore T, et al. Using DNA metabarcoding to investigate honey bee foraging reveals limited flower use despite high floral availability. Sci Rep. 2017;7:42838. https://doi.org/10.1038/srep42838.
  76. Pornon A, Escaravage N, Burrus M, et al. Using metabarcoding to reveal and quantify plant-pollinator interactions. Sci Rep. 2016;6:27282. https://doi.org/10.1038/srep27282.
  77. Lucas A, Bodger O, Brosi BJ, et al. Generalisation and specialisation in hoverfly (Syrphidae) grassland pollen transport networks revealed by DNA metabarcoding. J Anim Ecol. 2018;87(4):1008-1021. https://doi.org/10. 1111/1365-2656.12828.
  78. Suchan T, Talavera G, Sáez L, et al. Pollen metabarcoding as a tool for tracking long-distance insect migrations. Mol Ecol Resour. 2019;19(1): 149-162. https://doi.org/10.1111/1755-0998. 12948.
  79. Li F, Peng Y, Fang W, et al. Application of environmental dna metabarcoding for predicting anthropogenic pollution in rivers. Environ Sci Technol. 2018;52(20):11708-11719. https://doi.org/10.1021/acs.est.8b03869.
  80. Tromas N, Fortin N, Bedrani L, et al. Characterising and predicting cyanobacterial blooms in an 8-year amplicon sequencing time course. ISME J. 2017;11(8):1746-1763. https://doi.org/10.1038/ismej.2017.58.
  81. Sigsgaard EE, Carl H, Møller PR, Thomsen PF. Monitoring the near-extinct European weather loach in Denmark based on environmental DNA from water samples. Biological Conservation. 2015;183:46-52. https://doi.org/10.1016/j.biocon.2014.11.023.
  82. Parsons KM, Everett M, Dahlheim M, Park L. Water, water everywhere: environmental DNA can unlock population structure in elusive marine species. R Soc Open Sci. 2018;5(8):180537. https://doi.org/10.1098/rsos.180537.
  83. Elbrecht V, Vamos EE, Steinke D, Leese F. Estimating intraspecific genetic diversity from community DNA metabarcoding data. Peer J. 2018;6: e4644. https://doi.org/10.7717/peerj.4644.
  84. Pont D, Rocle M, Valentini A, et al. Environmental DNA reveals quantitative patterns of fish biodiversity in large rivers despite its downstream transportation. Sci Rep. 2018;8(1):10361. https://doi.org/10.1038/s41598-018-28424-8.
  85. Lacoursière-Roussel A, Howland K, Normandeau E, et al. eDNA metabarcoding as a new surveillance approach for coastal Arctic biodiversity. Ecol Evol. 2018;8(16):7763-7777. https://doi.org/10.1002/ece3.4213.
  86. Cowart DA, Murphy KR, Cheng C-HC. Metagenomic sequencing of environmental DNA reveals marine faunal assemblages from the West Antarctic Peninsula. Mar Genomics. 2018;37:148-160. https://doi.org/10.1016/j.margen.2017.11.003.
  87. Woods Hole Oceanographic Institution. New eyes in the twilight zone. Using E-DNA to discover what lives in the deep. Available from: https://www.whoi.edu/multimedia/new-eyes-twilight-zone/.
  88. Pansu J, Giguet-Covex C, Ficetola GF, et al. Reconstructing long-term human impacts on plant communities: an ecological approach based on lake sediment DNA. Mol Ecol. 2015;24(7): 1485-1498. https://doi.org/10.1111/mec.13136.
  89. Pedersen MW, Ruter A, Schweger C, et al. Postglacial viability and colonization in North America’s ice-free corridor. Nature. 2016;537(7618): 45-49. https://doi.org/10.1038/nature19085.
  90. Garlapati D, Charankumar B, Ramu K, et al. A review of the applications and recent advances in environmental DNA (eDNA) metagenomics. Reviews in Environmantal Science and Bio/Tachnology. 2019;18(3):389-411. https://doi.org/10.1007/s11157-019-09501-4.

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2. Figure: 1. The main general steps of environmental DNA analysis

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3. Figure: 2. The main areas in which DNA analysis of the environment is used, and links to examples of research in these areas

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Copyright (c) 2021 Pinakhina D., Chekunova E.M.

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