Utility of Environmental DNA for Monitoring Rare and Indicator Macroinvertebrate Species

Freshwater Science

Volumn 33, Issue 4, 2014, Pages 1174-1183

  MäcHler, Elvira ^a   Deiner, Kristy ^a   Steinmann, Patrick ^b   Altermatt, Florian ^a  

^a SWISS FEDERAL INSTITUTE OF AQUATIC SCIENCE AND TECHNOLOGY   (Switzerland)

^b Amt für Abfall Wasser Energie und Luft ^*  (Switzerland)

Author keywords

Amphipoda; cytochrome oxidase I; eDNA; EPT; kicknet sampling; lotic systems; water quality assessment

Indexed keywords

BIOINDICATOR; BIOMONITORING; CONSERVATION MANAGEMENT; CYTOCHROME; DNA; ENZYME ACTIVITY; FRESHWATER ECOSYSTEM; GENETIC MARKER; LOTIC ENVIRONMENT; MACROINVERTEBRATE; MOLECULAR ANALYSIS; RARITY; TAXONOMY; WATER QUALITY;

AMPHIBIA; AMPHIPODA; ANCYLUS FLUVIATILIS; ASELLUS AQUATICUS; BAETIS BUCERATUS; CRANGONYX PSEUDOGRACILIS; EPHEMEROPTERA; GAMMARUS PULEX; GASTROPODA; ISOPODA;

EID: 84908601386     PISSN: 21619549     EISSN: 21619565     Source Type: Journal    
DOI: 10.1086/678128     Document Type: Article

References (50)

1. Altermatt, F. 2013. Diversity in riverine metacommunities: a network perspective. Aquatic Ecology 47:365-377.
2. Altermatt, F., M. Seymour, and N. Martinez. 2013. River network properties shape ?-diversity and community similarity patterns of aquatic insect communities across major drainage basins. Journal of Biogeography 40:2249-2260
3. AWEL (Abfall, Wasser, Energie, und Luft). 2012. Zürcher Gewässer 2012: Entwicklung-Zustand-Ausblick. Amt für Abfall, Wasser, Energie und Luft, Zürich, Switzerland. (Available from: http://www.awel.zh.ch/internet/baudirektion/awel/de/wasserwirtschaft/veroeffentlichungen.html)
4. Baird, D. J., and M. Hajibabaei. 2012. Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing. Molecular Ecology 21:2039-2044.
5. Barbour, M. T., J. Gerritsen, B. D. Snyder, and J. B. Stribling. 1999. Rapid Bioassessment Protocols for use in streams and wadeable rivers: periphyton, benthic macroinvertebrates and fish. 2nd edition. EPA 841-B-99-002. Office of Water, US Environmental Protection Agency, Washington, DC.
6. Barnes, M., C. R. Turner, C. L. Jerde, M. A. Renshaw, W. L. Chadderton, and D. M. Lodge. 2014. Environmental conditions influence eDNA persistence in aquatic systems. Environmental Science and Technology 48:1819-1827.
7. Benson, D. A., I. Karsch-Mizrachi, K. Clark, D. J. Lipman, J. Ostell, and E. W. Sayers. 2012. GenBank. Nucleic Acids Research 40: D48-D53.
8. Crawley, M. J. 2012. The R book. John Wiley and Sons Ltd., Chichester, UK.
9. Deiner, K., and F. Altermatt. 2014. Transport distance of invertebrate environmental DNA in a natural river. PloS ONE 9:e88786.
10. Deiner, K., R. A. Knapp, D. M. Boiano, and B. May. 2013. Increased accuracy of species lists developed for alpine lakes using morphology and cytochrome oxidase I for identification of specimens. Molecular Ecology Resources 13:820-831.
11. Dejean, T., A. Valentini, A. Duparc, S. Pellier-Cuit, F. Pompanon, P. Taberlet, and C. Miaud. 2011. Persistence of environmental DNA in freshwater ecosystems. PLoS ONE 6:e23398.
12. Eggers, T. O., and A. Martens. 2001. Bestimmungsschlüssel der Süßwasser-Amphipoda (Crustacea) Deutschlands. Lauterbornia 42:1-68.
13. Ficetola, G. F., C. Miaud, F. Pompanon, and P. Taberlet. 2008. Species detection using environmental DNA from water samples. Biology Letters 4:423-425.
14. Fulton, T. L. 2012. Setting up an ancient DNA laboratory. Pages 1-11 in B. Shapiro and M. Hofreiter (editors). Ancient DNA: methods and protocols. Springer, Dordrecht, The Netherlands.
15. Gloër, P., and C. Meier-Brook. 1998. Süßwassermollusken. Deutscher Jugendbund für Naturbeobachtung, Hamburg, Germany.
16. Goldberg, C. S., D. S. Pilliod, R. S. Arkle, and L. P. Waits. 2011. Molecular detection of vertebrates in stream water: a demonstration using Rocky Mountain tailed frogs and Idaho giant salamanders. PLoS ONE 6:e22746.
17. Goldberg, C. S., A. Sepulveda, A. Ray, J. Baumgardt, and L. P. Waits. 2013. Environmental DNA as a new method for early detection of New Zealand mudsnails (Potamopyrgus antipodarum). Freshwater Science 32:792-800.
18. Haase, P., S. U. Pauls, K. Schindehütte, and A. Sundermann. 2010. First audit of macroinvertebrate samples from an EU Water Framework Directive monitoring program: human error greatly lowers precision of assessment results. Journal of the North American Benthological Society 29:1279-1291.
19. Hajibabaei,M., S. Shokralla, X. Zhou, G. A. Singer, and D. J. Baird. 2011. Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS ONE 6:e17497.
20. Hebert, P. D. N., S. Ratnasingham, and J. R. de Waard. 2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London Series B: Biological Sciences 270:96-99.
21. Heino, J., R. Paavola, R. Virtanen, and T. Muotka. 2005. Searching for biodiversity indicators in running waters: do bryophytes, macroinvertebrates, and fish show congruent diversity patterns? Biodiversity and Conservation 14:415-428.
22. IUCN (International Union for the Conservation of Nature). 2012. The IUCN Red List of threatened species. Version 2012.2.
23. International Union for the Conservation of Nature, Gland, Switzerland. (Available from: http://www.iucnredlist.org)
24. Jerde, C. L., A. R. Mahon, W. L. Chadderton, and D. M. Lodge. 2011. "Sight-unseen" detection of rare aquatic species using environmental DNA. Conservation Letters 4:150-157.
25. Lodge, D.M., C. R. Turner, C. L. Jerde, M.A. Barnes, L. Chadderton, S. P. Egan, J. L. Feder, A. R. Mahon, and M. E. Pfrender. 2012. Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA. Molecular Ecology 21:2555-2558.
26. Lubini, V., S. Knispel, M. Sartori, H. Vicentini, and A. Wagner. 2012. Rote Listen Eintagsfliegen, Steinfliegen, Köcherfliegen. Page 111 in Gefährdete Arten der
27. Schweiz, Stand 2010. Bundesamt für Umwelt, Bern, und Schweizer Zentrum für die Kartographie der Fauna, Neuenburg, Switzerland. (Available from: http://www.bafu.admin.ch/publikationen/publikation/01655/index.html?lang=de)
28. Lydolph, M. C., J. Jacobsen, P. Arctander, M. T. P. Gilbert, D. A. Gilichinsky, A. J. Hansen, E. Willerslev, and L. Lange. 2005. Beringian paleoecology inferred from permafrost-preserved fungal DNA. Applied and Environmental Microbiology 71: 1012-1017.
29. MacKenzie, D. I., J. D. Nichols, N. Sutton, K. Kawanishi, and L. L. Bailey. 2005. Improving inferences in population studies of rare species that are detected imperfectly. Ecology 86:1101-1113.
30. Mahon, A. R., C. L. Jerde, M. Galaska, J. L. Bergner, W. L. Chadderton, D. M. Lodge, M. E. Hunter, and L. G. Nico. 2013. Validation of eDNA surveillance sensitivity for detection of Asian carps in controlled and field experiments. PloS ONE 8: e58316.
31. Meusnier, I., G. Singer, J.-F. Landry, D. Hickey, P. Hebert, and M. Hajibabaei. 2008. A universal DNA mini-barcode for biodiversity analysis. BMC Genomics 9:214.
32. Mills, L. S., K. L. Pilgrim, M. K. Schwartz, and K. McKelvey. 2000. Identifying lynx and other North American felids based on mtDNA analysis. Conservation Genetics 1:285-288.
33. Olson, Z. H., J. T. Briggler, and R. N. Williams. 2012. An eDNA approach to detect eastern hellbenders (Cryptobranchus a. alleganiensis) using samples of water. Wildlife Research 39:629-636.
34. Pfrender, M., C. Hawkins, M. Bagley, G. Courtney, B. Creutzburg, J. Epler, S. Fend, L. Ferrington, P. Hartzell, and S. Jackson. 2010. Assessing macroinvertebrate biodiversity in freshwater ecosystems: advances and challenges in DNAbased approaches. Quarterly Review of Biology 85:319-340.
35. Pilliod, D. S., C. S. Goldberg, R. S. Arkle, and L. P. Waits. 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.
36. Rozen, S., and H. Skaletsky. 1999. Primer3 on the WWW for general users and for biologist programmers. Pages 365-386 in S. Misener and S. A. Krawetz (editors). Bioinformatics methods and protocols. Springer, Dordrecht, The Netherlands.
37. Schmidt, B. R., M. Kéry, S. Ursenbacher, O. J. Hyman, and 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 4:646-653.
38. Stucki, P. 2010. Methoden zur Untersuchung und Beurteilung der Fliessgewässer: Makrozoobenthos-Stufe F. Bundesamt für Umwelt-Vollzug, Bern, Switzerland. (Available from: http://www.bafu.admin.ch/publikationen/publikation/00077/index.html? lang=de)
39. Studemann, D., P. Landolt, M. Sartori, D. Hefti, and I. Tomka. 1992. Ephemeroptera. Insecta Helvetica, Fauna 9. Imprimerie Mauron + Tinguely and Lachat SA, Fribourg, Switzerland.
40. Taberlet, P., E. Coissac, M. Hajibabaei, and L. H. Riesenberg. 2012. Environmental DNA. Molecular Ecology 21:1789-1793.
41. Taberlet, P., S. Griffin, B. Goossens, S. Questiau, V. Manceau, N. Escaravage, L. P. Waits, and J. Bouvet. 1996. Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Research 24:3189-3194.
42. Tachet, H., P. Richoux, M. Bournaud, and P. Usseglio-Polatera. 2000. Invertébrés d'eau douce: systématique, biologie, écologie. CNRS Editions, Paris, France.
43. Thomsen, P. F., J. O. S. Kielgast, L. L. Iversen, C. Wiuf, M. Rasmussen, M. T. P. Gilbert, L. Orlando, and E. Willerslev. 2011. Monitoring endangered freshwater biodiversity using environmental DNA. Molecular Ecology 21:2565-2573.
44. von der Ohe, P. C., A. Prüß, R. B. Schäfer, M. Liess, E. de Deckere, and W. Brack. 2007. Water quality indices across Europe - A comparison of the good ecological status of five river basins. Journal of Environmental Monitoring 9:970-978.
45. Vörösmarty, C. J., P. McIntyre, G. O. Gessner, D. Dudgeon, A. Prusevich, P. Green, S. Glidden, S. E. Bunn, C. A. Sullivan, and C. R. Liermann. 2010. Global threats to human water security and river biodiversity. Nature 467:555-561.
46. Waringer, J., and W. Graf. 1997. Atlas der österreichischen Köcherfliegenlarven. Facultas Universitätsverlag, Vienna, Austria.
47. Wilcox, T., K. McKelvey, M. Young, S. Jane, W. Lowe, and R. C. Willson. 2013. Robust detection of rare species using environmental DNA: the importance of primer specificity. PLoS ONE 8:e59520.
48. Ye, J., G. Coulouris, I. Zaretskaya, I. Cutcutache, S. Rozen, and T. L. Madden. 2012. Primer-BLAST: a tool to design targetspecific primers for polymerase chain reaction. BMC Bioinformatics 13:134.
49. Yoccoz, N. G. 2012. The future of environmental DNA in ecology. Molecular Ecology 21:2031-2038.
50. Yu, D. W., Y. Ji, B. C. Emerson, X. Wang, C. Ye, C. Yang, and Z. Ding. 2012. Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods in Ecology and Evolution 3:613-623.