The detection of aquatic animal species using environmental DNA - a review of eDNA as a survey tool in ecology

Journal of Applied Ecology

Volumn 51, Issue 5, 2014, Pages 1450-1459

  Rees, Helen C ^a   Maddison, Ben C ^a   Middleditch, David J ^b   Patmore, James R M ^b   Gough, Kevin C ^a  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^b ADAS BOXWORTH   (United Kingdom)

Author keywords

DNA barcoding; Ecosystem management; EDNA; Invasive species; Next generation sequencing; PCR; Rare or threatened species; Species specific detection; Water sampling

Indexed keywords

ANIMALIA;

EID: 84925340061     PISSN: 00218901     EISSN: 13652664     Source Type: Journal    
DOI: 10.1111/1365-2664.12306     Document Type: Review

References (40)

1. Barnes, M.A., Turner, C.R., Jerde, C.L., Renshaw, M.A., Chadderton, W.L. & Lodge, D.M. (2014) Environmental Conditions Influence eDNA Persistence in Aquatic Systems. Environmental Science and Technology, 48, 1819-1827.
2. Begon, M., Townsend, C.R. & Harper, J.L. (2005) Ecology: from Individuals to Ecosystems. Blackwell Science Ltd, USA.
3. Collins, R.A., Armstrong, K.F., Holyoake, A.J. & Keeling, S. (2013) Something in the water: biosecurity monitoring of ornamental fish imports using environmental DNA. Biological Invasions, 15, 1209-1215.
4. Coyne, K.J., Hutchins, D.A., Hare, C.E. & Cary, S.C. (2001) Assessing temporal and spatial variability in Pfiesteria piscicida distributions using molecular probing techniques. Aquatic Microbial Ecology, 24, 275-285.
5. Darling, J.A. & Mahon, A.R. (2011) From molecules to management: adopting DNA-based methods for monitoring biological invasions in aquatic environments. Environmental Research, 111, 978-988.
6. Dejean, T., Valentini, A., Duparc, A., Pellier-Cuit, S., Pompanon, F., Taberlet, P. & Miaud, C. (2011) Persistence of environmental DNA in freshwater ecosystems. PLoS ONE, 6, e23398.
7. Dejean, T., Valentini, A., Miquel, C., Taberlet, P., Bellemain, E. & Miaud, C. (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, 953-959.
8. Ficetola, G.F., Miaud, C., Pompanon, F. & Taberlet, P. (2008) Species detection using environmental DNA from water samples. Biology Letters, 4, 423-425.
9. Ficetola, G.F., Coissac, E., Zundel, S., Riaz, T., Shehzad, W., Bessiere, J., Taberlet, P. & Pompanon, F. (2010) An In silico approach for the evaluation of DNA barcodes. BMC Genomics, 11, 434.
10. Foote, A.D., Thomsen, P.F., Sveegaard, S., Wahlberg, M., Kielgast, J., Kyhn, L.A. et al. (2012) Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals. PLoS ONE, 7, e41781.
11. Goldberg, C.S., Pilliod, D.S., Arkle, R.S. & Waits, L.P. (2011) Molecular detection of vertebrates in stream water: a demonstration using rocky mountain tailed frogs and Idaho giant salamanders. PLoS ONE, 6, e22746.
12. Goldberg, C.S., Sepulveda, A., Ray, A., Baumgardt, J. & Waits, L.P. (2013) Environmental DNA as a new method for early detection of New Zealand mudsnails (Potamopyrgus antipodarum). Freshwater Science, 32, 792-800.
13. Hajibabaei, M., Smith, M.A., Janzen, D.H., Rodriguez, J.J., Whitfield, J.B. & Hebert, P.D.N. (2006) A minimalist barcode can identify a specimen whose DNA is degraded. Molecular Ecology Notes, 6, 959-964.
14. Hebert, P.D.N. & Gregory, T.R. (2005) The promise of DNA barcoding for taxonomy. Systematic Biology, 54, 852-859.
15. Hulme, P.E. (2006) Beyond control: wider implications for the management of biological invasions. Journal of Applied Ecology, 43, 835-847.
16. IUCNredlist (2012) IUCN Red List of Threatened Species. Version 2012.2. IUCNredlist, Webpage: http://www.iucnredlist.org, accessed 22 May 2013.
17. Jerde, C.L., Mahon, A.R., Chadderton, W.L. & Lodge, D.M. (2011) "Sight-unseen" detection of rare aquatic species using environmental DNA. Conservation Letters, 4, 150-157.
18. Jerde, C.L., Chadderton, W.L., Mahon, A.R., Renshaw, M.A., Corush, J., Budny, M.L., Mysorekar, S. & Lodge, D.M. (2013) Detection of Asian carp DNA as part of a Great Lakes basin-wide surveillance program. Canadian Journal of Fisheries and Aquatic Sciences, 70, 522-526.
19. Kelly, R.P., Port, J.A., Yamahara, K.M. & Crowder, L.B. (2014) Using environmental DNA to census marine fishes in a large mesocosm. PLoS ONE, 9, e86175.
20. Mahon, A.R., Barnes, M.A., Senapati, S., Feder, J.L., Darling, J.A., Chang, H.C. & Lodge, D.M. (2011) Molecular detection of invasive species in heterogeneous mixtures using a microfluidic carbon nanotube platform. PLoS ONE, 6, e17280.
21. Mahon, A.R., Barnes, M.A., Li, F., Egan, S.P., Tanner, C.E., Ruggiero, S.T., Feder, J.L. & Lodge, D.M. (2012) DNA-based species detection capabilities using laser transmission spectroscopy. Journal of the Royal Society Interface, 10, 20120637.
22. Mahon, A.R., Jerde, C.L., Galaska, M., Bergner, J.L., Chadderton, W.L., Lodge, D.M., Hunter, M.E. & Nico, L.G. (2013) Validation of eDNA surveillance sensitivity for detection of asian carps in controlled and field experiments. PLoS ONE, 8, e58316.
23. Maitland, P.S. (1966) The present status of known populations of the Vendace, Coregonus vandesius Richardson in Great Britain. Nature, 210, 216-217.
24. Minamoto, T., Yamanaka, H., Takahara, T., Honjo, M.N. & Kawabata, Z.I. (2012) Surveillance of fish species composition using environmental DNA. Limnology, 13, 193-197.
25. Notomi, T., Okayama, H., Masubuchi, H., Yonekawa, T., Watanabe, K., Amino, N. & Hase, T. (2000) Loop-mediated isothermal amplification of DNA. Nucleic Acids Research, 28, E63.
26. Olson, Z.H., Briggler, J.T. & Williams, R.N. (2012) An eDNA approach to detect eastern hellbenders (Cryptobranchus a. alleganiensis) using samples of water. Wildlife Research, 39, 629-636.
27. Piaggio, A.J., Engeman, R.M., Hopken, M.W., Humphrey, J.S., Keacher, K.L., Bruce, W.E. & Avery, M.L. (2013) Detecting an elusive invasive species: a diagnostic PCR to detect Burmese python in Florida waters and an assessment of persistence of environmental DNA. Molecular Ecology Resources, 14, 374-380.
28. Piepenburg, O., Williams, C.H., Stemple, D.L. & Armes, N.A. (2006) DNA detection using recombination proteins. PLoS Biology, 4, e204.
29. Pilliod, D.S., Goldberg, C.S., Arkle, R.S. & Waits, L.P. (2013) Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples. Canadian Journal of Fisheries and Aquatic Sciences, 70, 1123-1130.
30. Pilliod, D.S., Goldberg, C.S., Arkle, R.S. & Waits, L.P. (2014) Factors influencing detection of eDNA from a stream-dwelling amphibian. Molecular Ecology Resources, 14, 109-116.
31. Rozen, S. & Skaletsky, H. (2000) Primer3 on the WWW for general users and for biologist programmers. Methods in Molecular Biology, 132, 365-386.
32. Taberlet, P., Griffin, S., Goossens, B., Questiau, S., Manceau, V., Escaravage, N., Waits, L.P. & Bouvet, J. (1996) Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Research, 24, 3189-3194.
33. Takahara, T., Minamoto, T. & Doi, H. (2013) Using environmental DNA to estimate the distribution of an invasive fish species in ponds. PLoS ONE, 8, e56584.
34. Takahara, T., Minamoto, T., Yamanaka, H., Doi, H. & Kawabata, Z.I. (2012) Estimation of fish biomass using environmental DNA. PLoS ONE, 7, e35868.
35. Thomsen, P.F., Kielgast, J., Iversen, L.L., Moller, P.R., Rasmussen, M. & Willerslev, E. (2012a) Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS ONE, 7, e41732.
36. Thomsen, P.F., Kielgast, J., Iversen, L.L., Wiuf, C., Rasmussen, M., Gilbert, M.T.P., Orlando, L. & Willerslev, E. (2012b) Monitoring endangered freshwater biodiversity using environmental DNA. Molecular Ecology, 21, 2565-2573.
37. Wilcox, T.M., McKelvey, K.S., Young, M.K., Jane, S.F., Lowe, W.H., Whiteley, A.R. & Schwartz, M.K. (2013) Robust detection of rare species using environmental DNA: the importance of primer specificity. PLoS ONE, 8, e59520.
38. Willerslev, E., Hansen, A.J. & Poinar, H.N. (2004) Isolation of nucleic acids and cultures from fossil ice and permafrost. Trends in Ecology & Evolution, 19, 141-147.
39. Willerslev, E., Hansen, A.J., Binladen, J., Brand, T.B., Gilbert, M.T.P., Shapiro, B. et al. (2003) Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science, 300, 791-795.
40. Winfield, I.J., Fletcher, J.M. & James, B.J. (2008) Assessment of the vendace population of Bassenthwaite Lake including observations on vendace spawning grounds. Final Report. Report to Environment Agency, North West Region, and Scottish Natural Heritage. LA/C03462/3, pp. 36.