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Proceedings of the Zoological Society

, Volume 72, Issue 3, pp 211–228 | Cite as

Environmental DNA (eDNA): A Promising Biological Survey Tool for Aquatic Species Detection

  • Debabrata Senapati
  • Manojit Bhattacharya
  • Avijit Kar
  • Deep Sankar Chini
  • Basanta Kumar Das
  • Bidhan Chandra PatraEmail author
Review Article
  • 442 Downloads

Abstract

Aquatic species are facing at higher risk of extinction similar to that of any other living components of diversified ecosystem in present scenario. So that, the conservation of aquatic biodiversity is much more important to know about the accurate information regarding species composition and their biological community interactions. Generally, traditional survey methods depend on physical identification and characterization of species but it has some sorts of challenging chances due to the phenotypic plasticity, sibling species, different stages of life cycle and its invasiveness. To overcome such barriers one of the significant and promising tool likewise environmental DNA (eDNA), which way the collection of genetic materials from bulk environment (i.e. soil, water, sediment etc.) circuitously from organisms has been used to monitor and analyzed the biodiversity status, invasive species along with the species of conservation category. Recently, the real application of eDNA analysis based outcomes uphold the actual emerging know how practices in support of the population and community ecology, conservation biology as well as in the superior field of taxonomical research. Such scientific appraisal will be useful in understanding the brief history of aquatic eDNA and obviously its methodological considerations, gentle sources, collection and analysis process, physical form, its persistence and proper transport in aquatic ecosystem. Moreover, the fruitful drives for summarization the discoveries of eDNA application and method over traditional technique, its recent challenges and examine the current and future frontiers along with the appropriate practices of aquatic eDNA relevancy in aquatic ecosystem.

Keywords

Biodiversity Phenotypic plasticity Sibling species Invasive species Population and Community ecology 

Notes

Acknowledgements

Authors are highly thankful to University Grants Commission (Ref. No.831 344156), Science and Engineering Research Board (Project file No Ref. No. PDF/2016/001776), Department of Science and Technology, Government of India for financial assistance to carried out the research work.

References

  1. Bacher, Sven. 2012. Still not enough taxonomists: Reply to Joppa, et al. Trends in Ecology & Evolution 27(2): 65–66.Google Scholar
  2. Baird, Donald J., and Mehrdad Hajibabaei. 2012. Biomonitoring 2.0: A new paradigm in ecosystem assessment made possible by next-generation DNA sequencing. Molecular Ecology 21(8): 2039–2044.Google Scholar
  3. Baldwin, C. C., B. B. Collette, L. R. Parenti, D. G. Smith, and V. G. Springer. 1996. Collecting Fishes. pp. 11-33 in: Lang, M. A. and C. C. Baldwin (eds.). Methods and Techniques of Underwater Research. Proceedings of the 16th Annual Scientific Diving Symposium, American Academy of Underwater Sciences.Google Scholar
  4. Barnes, Matthew A., Cameron R. Turner, Christopher L. Jerde, Mark A. Renshaw, W. Lindsay Chadderton, and David M. Lodge. 2014. Environmental conditions influence eDNA persistence in aquatic systems. Environmental Science and Technology 48(3): 1819–1827.Google Scholar
  5. Barnes, Matthew A., and Cameron R. Turner. 2016. The ecology of environmental DNA and implications for conservation genetics. Conservation Genetics 17(1): 1–17.Google Scholar
  6. Barnosky, Anthony D., Nicholas Matzke, Susumu Tomiya, Guinevere O.U. Wogan, Brian Swartz, Tiago B. Quental, Charles Marshall, Jenny L. McGuire, Emily L. Lindsey, and Kaitlin C. Maguire. 2011. Has the Earth’s sixth mass extinction already arrived? Nature 471(7336): 51–57.Google Scholar
  7. Beebee, Trevor J.C. 1991. Analysis, purification and quantification of extracellular DNA from aquatic environments. Freshwater Biology 25(3): 525–532.Google Scholar
  8. Biggs, Jeremy, Naomi Ewald, Alice Valentini, Coline Gaboriaud, Tony Dejean, Richard A. Griffiths, Jim Foster, John W. Wilkinson, Andy Arnell, and Peter Brotherton. 2015. Using eDNA to develop a national citizen science-based monitoring programme for the great crested newt (Triturus cristatus). Biological Conservation 183: 19–28.Google Scholar
  9. Bista, Iliana, Gary R. Carvalho, Kerry Walsh, Mathew Seymour, Mehrdad Hajibabaei, Delphine Lallias, Martin Christmas, and Simon Creer. 2017. Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity. Nature Communications 8:14087.  https://doi.org/10.1038/ncomms14087. https://www.nature.com/articles/ncomms14087#supplementary-information.
  10. Blaxter, Mark, Robin Floyd, Mark Dorris, A. Eyualem, and Paul De Ley. 2004. Utilising the new nematode phylogeny for studies of parasitism and diversity. Nematology Monographs and Perspectives (ed. R. Cook & DJ Hunt) 2: 615–632.Google Scholar
  11. Blum, Stephanie A.E., Michael G. Lorenz, and Wilfried Wackernagel. 1997. Mechanism of retarded DNA degradation and prokaryotic origin of DNases in nonsterile soils. Systematic and Applied Microbiology 20(4): 513–521.Google Scholar
  12. Bowen, Brian W., Naoki Kamezaki, Colin J. Limpus, George R. Hughes, Anne B. Meylan, and John C. Avise. 1994. Global phylogeography of the loggerhead turtle (Caretta caretta) as indicated by mitochondrial DNA haplotypes. Evolution 48(6):1820–1828.Google Scholar
  13. Braley, Michelle, Simon D. Goldsworthy, Brad Page, Mike Steer, and Jeremy J. Austin. 2010. Assessing morphological and DNA-based diet analysis techniques in a generalist predator, the arrow squid Nototodarus gouldi. Molecular Ecology Resources 10(3): 466–474.Google Scholar
  14. Brander, Keith M. 2007. Global fish production and climate change. Proceedings of the National Academy of Sciences 104(50): 19709–19714.Google Scholar
  15. Brock, Richard E. 1982. A critique of the visual census method for assessing coral reef fish populations. Bulletin of Marine Science 32(1): 269–276.Google Scholar
  16. Bunce, Michael, Marta Szulkin, Heather R.L. Lerner, Ian Barnes, Beth Shapiro, Alan Cooper, and Richard N. Holdaway. 2005. Ancient DNA provides new insights into the evolutionary history of New Zealand’s extinct giant eagle. PLoS Biology 3(1): e9.Google Scholar
  17. Butchart, Stuart H.M., Matt Walpole, Ben Collen, Arco Van Strien, Jörn P.W. Scharlemann, Rosamunde E.A. Almond, Jonathan E.M. Baillie, Bastian Bomhard, Claire Brown, and John Bruno. 2010. Global biodiversity: Indicators of recent declines. Science 328(5982): 1164–1168.Google Scholar
  18. Cannon, M.V., James Hester, Amanda Shalkhauser, Ernest R. Chan, Kyle Logue, Scott T. Small, and David Serre. 2016. In silico assessment of primers for eDNA studies using PrimerTree and application to characterize the biodiversity surrounding the Cuyahoga River. Scientific Reports 6: 22908.Google Scholar
  19. Carim, Kellie J., Kyle R. Christianson, Kevin M. McKelvey, William M. Pate, Douglas B. Silver, Brett M. Johnson, Benjamin T. Galloway, Michael K. Young, and Michael K. Schwartz. 2016a. Correction: Environmental DNA marker development with sparse biological information: A case study on opossum shrimp (Mysis diluviana). PLoS ONE 11(10):e0165573.Google Scholar
  20. Carim, K.J., J.C.S. Dysthe, M.K. Young, K.S. McKelvey, and M.K. Schwartz. 2016b. An environmental DNA assay for detecting Arctic grayling in the upper Missouri River basin, North America. Conservation Genetics Resources 8(3): 197–199.Google Scholar
  21. Carim, K.J., T.M. Wilcox, M. Anderson, D.J. Lawrence, M.K. Young, K.S. McKelvey, and M.K. Schwartz. 2016c. An environmental DNA marker for detecting nonnative brown trout (Salmo trutta). Conservation Genetics Resources 8(3): 259–261.Google Scholar
  22. Clayton, David A. 1984. Transcription of the mammalian mitochondrial genome. Annual Review of Biochemistry 53(1): 573–594.Google Scholar
  23. Clusa, L., Ardura, A., Fernández, S., Roca, A.A. and García-Vázquez, E. 2017. An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples. PeerJ 5: 3045.Google Scholar
  24. Collins, Rupert A., Karen F. Armstrong, Andrew J. Holyoake, and Suzanne Keeling. 2013. Something in the water: Biosecurity monitoring of ornamental fish imports using environmental DNA. Biological Invasions 15(6): 1209–1215.Google Scholar
  25. Corinaldesi, Cinzia, Marco Barucca, Gian Marco Luna, and A. Dell’Anno. 2011. Preservation, origin and genetic imprint of extracellular DNA in permanently anoxic deep-sea sediments. Molecular Ecology 20(3): 642–654.Google Scholar
  26. Creer, S., Fonseca, V.G., Porazinska, D.L., Giblin Davis, R.M., Sung, W., Power, D.M., Packer, M., Carvalho, G.R., Blaxter, M.L., Lambshead, P.J.D. and Thomas, W.K. 2010. Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises. Molecular Ecology 19: 4–20.Google Scholar
  27. Daan, Niels. 2001. The IBTS database: a plea for quality control. ICES CM 2001/T:03. 19.Google Scholar
  28. Davies, Richard Gareth. 2012. Computer programming in quantitative biology. New York City: Elsevier.Google Scholar
  29. de Souza, Lesley S., James C. Godwin, Mark A. Renshaw, and Eric Larson. 2016. Environmental DNA (eDNA) detection probability is influenced by seasonal activity of organisms. PLoS ONE 11(10): e0165273.Google Scholar
  30. DeFlaun, Mary F., John H. Paul, and Dean Davis. 1986. Simplified method for dissolved DNA determination in aquatic environments. Applied and Environmental Microbiology 52(4): 654–659.Google Scholar
  31. DeFlaun, Mary F., John H. Paul, and Wade H. Jeffrey. 1987. Distribution and molecular weight of dissolved DNA in subtropical estuarine and oceanic environments. Marine Ecology-Progress Series 38(1): 65.Google Scholar
  32. Deiner, Kristy, and Florian Altermatt. 2014. Transport distance of invertebrate environmental DNA in a natural river. PLoS ONE 9(2): e88786.Google Scholar
  33. Deiner, Kristy, Emanuel A. Fronhofer, Elvira Mächler, Jean-Claude Walser, and Florian Altermatt. 2016. Environmental DNA reveals that rivers are conveyer belts of biodiversity information. Nature Communications 7: 12544.  https://doi.org/10.1038/ncomms12544.Google Scholar
  34. Dejean, Tony, Alice Valentini, Christian Miquel, Pierre Taberlet, Eva Bellemain, and Claude 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.Google Scholar
  35. Dell’Anno, Antonio, and Cinzia Corinaldesi. 2004. Degradation and turnover of extracellular DNA in marine sediments: Ecological and methodological considerations. Applied and Environmental Microbiology 70(7): 4384–4386.Google Scholar
  36. Dell’Anno, Antonio, Bompadre Stefano, and Roberto Danovaro. 2002. Quantification, base composition, and fate of extracellular DNA in marine sediments. Limnology and Oceanography 47(3): 899–905.Google Scholar
  37. Díaz, Sandra, F. Joseph Fargione, I.I.I. Stuart Chapin, and David Tilman. 2006. Biodiversity loss threatens human well-being. PLoS Biology 4(8): e277.Google Scholar
  38. Doi, H., Uchii, K., Takahara, T., Matsuhashi, S., Yamanaka, H. and Minamoto, T. 2015. Use of droplet digital PCR for estimation of fish abundance and biomass in environmental DNA surveys. PloS one 10(3): 0122763.Google Scholar
  39. Douville, M., F. Gagné, C. Blaise, and C. Andre. 2007. Occurrence and persistence of Bacillus thuringiensis (Bt) and transgenic Bt corn cry1Ab gene from an aquatic environment. Ecotoxicology and Environmental Safety 66(2): 195–203.Google Scholar
  40. Dysthe, Joseph C., Kellie J. Carim, Yvette M. Paroz, Kevin S. McKelvey, Michael K. Young, and Michael K. Schwartz. 2016. Quantitative PCR assays for detecting loach minnow (Rhinichthys cobitis) and spikedace (Meda fulgida) in the southwestern United States. PLoS ONE 11(9): e0162200.Google Scholar
  41. Ebach, Malte C., and Craig Holdrege. 2005. DNA barcoding is no substitute for taxonomy. Nature 434(7034): 697.Google Scholar
  42. Egan, Scott P., Matthew A. Barnes, Ching-Ting Hwang, Andrew R. Mahon, Jeffery L. Feder, Steven T. Ruggiero, Carol E. Tanner, and David M. Lodge. 2013. Rapid invasive species detection by combining environmental DNA with light transmission spectroscopy. Conservation Letters 6(6): 402–409.Google Scholar
  43. Evans, Nathan T., Brett P. Olds, Mark A. Renshaw, Cameron R. Turner, Yiyuan Li, Christopher L. Jerde, Andrew R. Mahon, Michael E. Pfrender, Gary A. Lamberti, and David M. Lodge. 2016. Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding. Molecular Ecology Resources 16(1): 29–41.Google Scholar
  44. Ficetola, Gentile Francesco, Claude Miaud, François Pompanon, and Pierre Taberlet. 2008. Species detection using environmental DNA from water samples. Biology Letters 4(4): 423–425.Google Scholar
  45. Fonseca, V.G., Carvalho, G.R., Sung, W., Johnson, H.F., Power, D.M., Neill, S.P., Packer, M., Blaxter, M.L., Lambshead, P.J.D., Thomas, W.K. and Creer, S. 2010. Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nature communications 1: 98.Google Scholar
  46. Foote, Andrew D., Philip Francis Thomsen, Signe Sveegaard, Magnus Wahlberg, Jos Kielgast, Line A. Kyhn, Andreas B. Salling, Anders Galatius, Ludovic Orlando, M. Thomas, and P. Gilbert. 2012. Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals. PLoS ONE 7(8): e41781.Google Scholar
  47. Foppen, J.W., Orup, C., Adell, R., Poulalion, V. and Uhlenbrook, S. 2011. Using multiple artificial DNA tracers in hydrology. Hydrological Processes 25(19): 3101–3106.Google Scholar
  48. Gingera, T.D., Bajno, R., Docker, M.F. and Reist, J.D. 2017. Environmental DNA as a detection tool for zebra mussels Dreissena polymorpha (Pallas, 1771) at the forefront of an invasion event in Lake Winnipeg, Manitoba, Canada. Management of Biological Invasions 8(3): 287–300.Google Scholar
  49. Goldberg, Caren S., David S. Pilliod, Robert S. Arkle, and Lisette P. Waits. 2011. Molecular detection of vertebrates in stream water: A demonstration using Rocky Mountain tailed frogs and Idaho giant Salamanders. PLoS ONE 6(7): e22746.Google Scholar
  50. 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.Google Scholar
  51. Gotelli, Nicholas J., and Robert K. Colwell. 2011. Estimating species richness. Biological Diversity: Frontiers in Measurement and Assessment 12: 39–54.Google Scholar
  52. Group, CBOL Plant Working, Peter M. Hollingsworth, Laura L. Forrest, John L. Spouge, Mehrdad Hajibabaei, Sujeevan Ratnasingham, Michelle van der Bank, Mark W. Chase, Robyn S. Cowan, and David L. Erickson. 2009. A DNA barcode for land plants. Proceedings of the National Academy of Sciences 106(31): 12794–12797.Google Scholar
  53. Gu, Weidong, and Robert K. Swihart. 2004. Absent or undetected? Effects of non-detection of species occurrence on wildlife–habitat models. Biological Conservation 116(2): 195–203.Google Scholar
  54. Hajibabaei, Mehrdad, Shadi Shokralla, Xin Zhou, Gregory A.C. Singer, and Donald J. Baird. 2011. Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS ONE 6(4): e17497.Google Scholar
  55. Hajibabaei, Mehrdad, M. Smith, Daniel H. Janzen, Josephine J. Rodriguez, James B. Whitfield, and Paul D.N. Hebert. 2006. A minimalist barcode can identify a specimen whose DNA is degraded. Molecular Ecology Notes 6(4): 959–964.Google Scholar
  56. Hebert, Paul D.N., Sujeevan Ratnasingham, and Jeremy R. de Waard. 2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London B: Biological Sciences 270(Suppl 1): S96–S99.Google Scholar
  57. Higuchi, Russell, Cecilia H. von Beroldingen, George F. Sensabaugh, and Henry A. Erlich. 1988. DNA typing from single hairs. Nature 332(6164): 543–546.Google Scholar
  58. Hindell, Mark A., Corey J.A. Bradshaw, Michael D. Sumner, Kelvin J. Michael, and Harry R. Burton. 2003. Dispersal of female southern elephant seals and their prey consumption during the austral summer: Relevance to management and oceanographic zones. Journal of Applied Ecology 40(4): 703–715.Google Scholar
  59. Hofreiter, Michael, Matthew Collins, and John R. Stewart. 2012. Ancient biomolecules in Quaternary palaeoecology. Quaternary Science Reviews 33: 1–13.Google Scholar
  60. Hopkins, G.W., and R.P. Freckleton. 2002. Declines in the numbers of amateur and professional taxonomists: Implications for conservation. Animal Conservation 5(3): 245–249.Google Scholar
  61. Höss, Matthias, Michael Kohn, Svante Pääbo, Felix Knauer, and Wolfgang Schröder. 1992. Excrement analysis by PCR. Nature 359(6392): 199.Google Scholar
  62. Huson, Daniel H., Alexander F. Auch, Ji Qi, and Stephan C. Schuster. 2007. MEGAN analysis of metagenomic data. Genome Research 17(3): 377–386.Google Scholar
  63. Hyman, O.J. and Collins, J.P. 2012. Evaluation of a filtration-based method for detecting Batrachochytrium dendrobatidis in natural bodies of water. Diseases of Aquatic Organisms 97(3): 185–195.Google Scholar
  64. International Union for Conservation of Nature. 2012. IUCN red list of threatened species. Version 2011.1. Google Scholar
  65. Jane, Stephen F., Taylor M. Wilcox, Kevin S. McKelvey, Michael K. Young, Michael K. Schwartz, Winsor H. Lowe, Benjamin H. Letcher, and Andrew R. Whiteley. 2015. Distance, flow and PCR inhibition: eDNA dynamics in two headwater streams. Molecular Ecology Resources 15(1): 216–227.Google Scholar
  66. Jerde, Christopher L., Andrew R. Mahon, W. Lindsay Chadderton, and David M. Lodge. 2011. “Sight-unseen” detection of rare aquatic species using environmental DNA. Conservation Letters 4(2): 150–157.Google Scholar
  67. Jones, J.B. 1992. Environmental impact of trawling on the seabed: A review. New Zealand Journal of Marine and Freshwater Research 26(1): 59–67.Google Scholar
  68. Kirshtein, J.D., Anderson, C.W., Wood, J.S., Longcore, J.E. and Voytek, M.A. 2007. Quantitative PCR detection of Batrachochytrium dendrobatidis DNA from sediments and water. Diseases of aquatic organisms 77(1): 11–15.Google Scholar
  69. Kochkina, Galina, Natalya Ivanushkina, Svetlana Ozerskaya, Nadezhda Chigineva, Oleg Vasilenko, Sergey Firsov, Elena Spirina, and David Gilichinsky. 2012. Ancient fungi in Antarctic permafrost environments. FEMS Microbiology Ecology 82(2): 501–509.Google Scholar
  70. Lacoursière-Roussel, Anaïs, Yohann Dubois, Eric Normandeau, and Louis Bernatchez. 2016a. Improving herpetological surveys in eastern North America using the environmental DNA method 1. Genome 59(11): 991–1007.Google Scholar
  71. Lacoursière-Roussel, Anaïs, Maikel Rosabal, and Louis Bernatchez. 2016b. Estimating fish abundance and biomass from eDNA concentrations: Variability among capture methods and environmental conditions. Molecular Ecology Resources 16(6): 1401–1414.Google Scholar
  72. Lance, R.F. and Carr, M.R., 2012. Detecting eDNA of Invasive Dreissenid Mussels, Report on Capital Investment Project. ERDC Aquatic Nuisance Species Research Program Technical Note ANSRP 12–2.Google Scholar
  73. Levy-Booth, David J., Rachel G. Campbell, Robert H. Gulden, Miranda M. Hart, Jeff R. Powell, John N. Klironomos, K. Peter Pauls, Clarence J. Swanton, Jack T. Trevors, and Kari E. Dunfield. 2007. Cycling of extracellular DNA in the soil environment. Soil Biology & Biochemistry 39(12): 2977–2991.Google Scholar
  74. Li, Frank, Andrew R. Mahon, Matthew A. Barnes, Jeffery Feder, David M. Lodge, Ching-Ting Hwang, Robert Schafer, Steven T. Ruggiero, and Carol E. Tanner. 2011. Quantitative and rapid DNA detection by laser transmission spectroscopy. PLoS ONE 6(12): e29224.Google Scholar
  75. Lindahl, Tomas. 1993. Instability and decay of the primary structure of DNA. Nature 362(6422): 709–715.Google Scholar
  76. Little, Damon P. 2014. A DNA mini-barcode for land plants. Molecular Ecology Resources 14(3): 437–446.Google Scholar
  77. Lodge, David M., Cameron R. Turner, Christopher L. Jerde, Matthew A. Barnes, Lindsay Chadderton, Scott P. Egan, Jeffrey L. Feder, Andrew R. Mahon, and Michael E. Pfrender. 2012. Conservation in a cup of water: Estimating biodiversity and population abundance from environmental DNA. Molecular Ecology 21(11): 2555–2558.Google Scholar
  78. MacKenzie, Darryl I., James D. Nichols, Gideon B. Lachman, J. Sam Droege, Andrew Royle, and Catherine A. Langtimm. 2002. Estimating site occupancy rates when detection probabilities are less than one. Ecology 83(8): 2248–2255.Google Scholar
  79. Mahon, Andrew R., Matthew A. Barnes, Satyajyoti Senapati, Jeffrey L. Feder, John A. Darling, Hsueh-Chia Chang, and David M. Lodge. 2011. Molecular detection of invasive species in heterogeneous mixtures using a microfluidic carbon nanotube platform. PLoS ONE 6(2): e17280.Google Scholar
  80. Mahon, Andrew R., Christopher L. Jerde, Matthew Galaska, Jennifer L. Bergner, W. Lindsay Chadderton, David M. Lodge, Margaret E. Hunter, and Leo G. Nico. 2013. Validation of eDNA surveillance sensitivity for detection of Asian carps in controlled and field experiments. PLoS ONE 8(3): e58316.Google Scholar
  81. Martellini, Anouk, Pierre Payment, and Richard Villemur. 2005. Use of eukaryotic mitochondrial DNA to differentiate human, bovine, porcine and ovine sources in fecally contaminated surface water. Water Research 39(4): 541–548.Google Scholar
  82. McKee, Anna M., Stephen F. Spear, and Todd 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.Google Scholar
  83. McKelvey, K.S., M.K. Young, W.L. Knotek, K.J. Carim, T.M. Wilcox, T.M. Padgett-Stewart, and M.K. Schwartz. 2016. Sampling large geographic areas for rare species using environmental DNA: A study of bull trout Salvelinus confluentus occupancy in western Montana. Journal of fish biology 88(3): 1215–1222.Google Scholar
  84. Meier, Petra, and Wilfried Wackernagel. 2003. Mechanisms of homology-facilitated illegitimate recombination for foreign DNA acquisition in transformable Pseudomonas stutzeri. Molecular Microbiology 48(4): 1107–1118.Google Scholar
  85. Merkes, Christopher M., S. Grace McCalla, Nathan R. Jensen, Mark P. Gaikowski, and Jon J. Amberg. 2014. Persistence of DNA in carcasses, slime and avian feces may affect interpretation of environmental DNA data. PLoS ONE 9(11): e113346.Google Scholar
  86. Meusnier, Isabelle, Gregory A.C. Singer, Jean-François Landry, Donal A. Hickey, Paul D.N. Hebert, and Mehrdad Hajibabaei. 2008. A universal DNA mini-barcode for biodiversity analysis. BMC Genomics 9(1): 214.Google Scholar
  87. Minamoto, Toshifumi, Hiroki Yamanaka, Teruhiko Takahara, Mie N. Honjo, and Z.I. Kawabata. 2012. Surveillance of fish species composition using environmental DNA. Limnology 13(2): 193–197.Google Scholar
  88. Moyer, Gregory R., Edgardo Diaz-Ferguson, Jeffrey E. Hill, and Colin Shea. 2014. Assessing environmental DNA detection in controlled lentic systems. PLoS ONE 9(7): e103767.Google Scholar
  89. Nichols, Ruth V., H.E.L.E.N.A. KOeNIGSSON, K. Danell, and G. Spong. 2012. Browsed twig environmental DNA: Diagnostic PCR to identify ungulate species. Molecular Ecology Resources 12(6): 983–989.Google Scholar
  90. Nielsen, Kaare M., Pål J. Johnsen, Douda Bensasson, and Daniele Daffonchio. 2007. Release and persistence of extracellular DNA in the environment. Environmental Biosafety Research 6(1–2): 37–53.Google Scholar
  91. Ogram, Andrew, Gary S. Sayler, and Tamar Barkay. 1987. The extraction and purification of microbial DNA from sediments. Journal of Microbiological Methods 7(2–3): 57–66.Google Scholar
  92. Olds, Brett P., Christopher L. Jerde, Mark A. Renshaw, Yiyuan Li, Nathan T. Evans, Cameron R. Turner, Kristy Deiner, Andrew R. Mahon, Michael A. Brueseke, and Patrick D. Shirey. 2016. Estimating species richness using environmental DNA. Ecology and Evolution 6(12): 4214–4226.Google Scholar
  93. Olson, Deanna H., David M. Aanensen, Kathryn L. Ronnenberg, Christopher I. Powell, Susan F. Walker, Jon Bielby, Trenton W.J. Garner, George Weaver, Group The Bd Mapping, and Matthew C. Fisher. 2013. Mapping the global emergence of Batrachochytrium dendrobatidis, the amphibian chytrid fungus. PLoS One 8(2): e56802.  https://doi.org/10.1371/journal.pone.0056802.
  94. Parducci, Laura, Irina Matetovici, Sonia L. Fontana, Keith D. Bennett, Yoshihisa Suyama, James Haile, Kurt H. Kjær, Nicolaj K. Larsen, Andreas D. Drouzas, and Eske Willerslev. 2013. Molecular- and pollen-based vegetation analysis in lake sediments from central Scandinavia. Molecular Ecology 22(13): 3511–3524.Google Scholar
  95. Paul, J.H., W.H. Jeffrey, and J.P. Cannon. 1990. Production of dissolved DNA, RNA, and protein by microbial populations in a Florida reservoir. Applied and Environmental Microbiology 56(10): 2957–2962.Google Scholar
  96. Paul, John H., Sunny C. Jiang, and Joan B. Rose. 1991. Concentration of viruses and dissolved DNA from aquatic environments by vortex flow filtration. Applied and Environmental Microbiology 57(8): 2197–2204.Google Scholar
  97. Pedersen, Mikkel Winther, Aurélien Ginolhac, Ludovic Orlando, Jesper Olsen, Kenneth Andersen, Jakob Holm, Svend Funder, Eske Willerslev, and Kurt H. Kjær. 2013. A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa. Quaternary Science Reviews 75: 161–168.Google Scholar
  98. Piaggio, Antoinette J., Richard M. Engeman, Matthew W. Hopken, John S. Humphrey, Kandy L. Keacher, William E. Bruce, and Michael L. Avery. 2014. 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(2): 374–380.Google Scholar
  99. Piganeau, Gwenaël, Michael Gardner, and Adam Eyre-Walker. 2004. A broad survey of recombination in animal mitochondria. Molecular Biology and Evolution 21(12): 2319–2325.Google Scholar
  100. Pilliod, David S., Caren S. Goldberg, Robert S. Arkle, and Lisette 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(8): 1123–1130.Google Scholar
  101. Pilliod, David S., Caren S. Goldberg, Robert S. Arkle, and Lisette P. Waits. 2014. Factors influencing detection of eDNA from a stream-dwelling amphibian. Molecular Ecology Resources 14(1): 109–116.Google Scholar
  102. Poinar, Hendrik N., W. Michael Hofreiter, Geoffrey Spaulding, Paul S. Martin, B. Artur Stankiewicz, Helen Bland, Richard P. Evershed, Göran Possnert, and Svante Pääbo. 1998. Molecular coproscopy: Dung and diet of the extinct ground sloth Nothrotheriops shastensis. Science 281(5375): 402–406.Google Scholar
  103. Poté, John, Rafaël Ackermann, and Walter Wildi. 2009. Plant leaf mass loss and DNA release in freshwater sediments. Ecotoxicology and Environmental Safety 72(5): 1378–1383.Google Scholar
  104. Powers, Tom. 2004. Nematode molecular diagnostics: From bands to barcodes. Annual review of Phytopathology 42: 367–383.Google Scholar
  105. Ratnasingham, Sujeevan, and Paul D.N. Hebert. 2007. bold: The barcode of life data system (http://www.barcodinglife.org). Molecular Ecology Notes 7(3):355–364.  https://doi.org/10.1111/j.1471-8286.2007.01678.x.
  106. Risser, Paul G. 1995. Biodiversity and ecosystem function. Conservation Biology 9(4): 742–746.Google Scholar
  107. Robertson, D.Ross, and William F. Smith-Vaniz. 2008. Rotenone: An essential but demonized tool for assessing marine fish diversity. BioScience 58(2): 165–170.Google Scholar
  108. Robson, Heather L.A., Tansyn H. Noble, Richard J. Saunders, Simon K.A. Robson, Damien W. Burrows, and Dean R. Jerry. 2016. Fine-tuning for the tropics: Application of eDNA technology for invasive fish detection in tropical freshwater ecosystems. Molecular Ecology Resources 16(4): 922–932.Google Scholar
  109. Roussel, Jean-Marc, Jean-Marc Paillisson, Anne Treguier, and Eric Petit. 2015. The downside of eDNA as a survey tool in water bodies. Journal of Applied Ecology 52(4): 823–826.Google Scholar
  110. Schoch, Conrad L., Keith A. Seifert, Sabine Huhndorf, Vincent Robert, John L. Spouge, C. André Levesque, Wen Chen, Elena Bolchacova, Kerstin Voigt, and Pedro W. Crous. 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences 109(16): 6241–6246.Google Scholar
  111. Scholin, Christopher A. 2010. What are “ ecogenomic sensors?” A review and thoughts for the future. Ocean Science 6(1): 51–60.Google Scholar
  112. Schuster, Stephan C. 2008. Next-generation sequencing transforms today’s biology. Nature Methods 5(1): 16.Google Scholar
  113. Sheppard, S.K., and J.D. Harwood. 2005. Advances in molecular ecology: Tracking trophic links through predator–prey food-webs. Functional Ecology 19(5): 751–762.Google Scholar
  114. Shokralla, Shadi, Jennifer L. Spall, Joel F. Gibson, and Mehrdad Hajibabaei. 2012. Next-generation sequencing technologies for environmental DNA research. Molecular Ecology 21(8): 1794–1805.Google Scholar
  115. Sigsgaard, Eva Egelyng, Ida Broman Nielsen, Steffen Sanvig Bach, Eline D. Lorenzen, David Philip Robinson, Steen Wilhelm Knudsen, Mikkel Winther Pedersen, Mohammed Al Jaidah, Ludovic Orlando, and Eske Willerslev. 2016. Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA. Nature Ecology & Evolution 1: 0004.Google Scholar
  116. Siuda, W., and H. Güde. 1996. Determination of dissolved deoxyribonucleic acid concentration in lake water. Aquatic Microbial Ecology 11(2): 193–202.Google Scholar
  117. Stoeckle, M.Y., Soboleva, L. and Charlop-Powers, Z. 2017. Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary. PloS one 12(4): 0175186.Google Scholar
  118. Strausberger, B.M., and Mary V. Ashley. 2001. Eggs yield nuclear DNA from egg-laying female cowbirds, their embryos and offspring. Conservation Genetics 2(4): 385–390.Google Scholar
  119. Strickler, Katherine M., Alexander K. Fremier, and Caren S. Goldberg. 2015. Quantifying effects of UV-B, temperature, and pH on eDNA degradation in aquatic microcosms. Biological Conservation 183: 85–92.Google Scholar
  120. Stuart, Simon N., Janice S. Chanson, Neil A. Cox, Bruce E. Young, Ana S.L. Rodrigues, Debra L. Fischman, and Robert W. Waller. 2004. Status and trends of amphibian declines and extinctions worldwide. Science 306(5702): 1783–1786.Google Scholar
  121. Symondson, W.O.C. 2002. Molecular identification of prey in predator diets. Molecular Ecology 11(4): 627–641.Google Scholar
  122. Taberlet, Pierre, and Jean Bouvet. 1991. A single plucked feather as a source of DNA for bird genetic studies. Auk 108(4): 959–960.Google Scholar
  123. Taberlet, Pierre, and Luca Fumagalli. 1996. Owl pellets as a source of DNA for genetic studies of small mammals. Molecular Ecology 5(2): 301–305.Google Scholar
  124. Taberlet, Pierre, Eric Coissac, Mehrdad Hajibabaei, and Loren H. Rieseberg. 2012a. Environmental DNA. Molecular Ecology 21(8): 1789–1793.  https://doi.org/10.1111/j.1365-294X.2012.05542.x.Google Scholar
  125. Taberlet, Pierre, Eric Coissac, Francois Pompanon, Christian Brochmann, and Eske Willerslev. 2012b. Towards next-generation biodiversity assessment using DNA metabarcoding. Molecular Ecology 21(8): 2045–2050.Google Scholar
  126. Takahara, Teruhiko, Toshifumi Minamoto, Hiroki Yamanaka, Hideyuki Doi, and Zen’ichiro Kawabata. 2012. Estimation of fish biomass using environmental DNA. PLoS ONE 7(4): e35868.Google Scholar
  127. Takahara, Teruhiko, Toshifumi Minamoto, and Hideyuki Doi. 2013. Using environmental DNA to estimate the distribution of an invasive fish species in ponds. PLoS ONE 8(2): e56584.Google Scholar
  128. Takahara, Teruhiko, Toshifumi Minamoto, and Hideyuki Doi. 2015. Effects of sample processing on the detection rate of environmental DNA from the Common Carp (Cyprinus carpio). Biological Conservation 183: 64–69.Google Scholar
  129. Thomsen, Philip Francis, Jos Kielgast, Lars Lønsmann Iversen, Peter Rask Møller, Morten Rasmussen, and Eske Willerslev. 2012a. Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS ONE 7(8): e41732.Google Scholar
  130. Thomsen, Philip, Jos Kielgast, Lars L. Iversen, Carsten Wiuf, M. Morten Rasmussen, Thomas P. Gilbert, Ludovic Orlando, and Eske Willerslev. 2012b. Monitoring endangered freshwater biodiversity using environmental DNA. Molecular Ecology 21(11): 2565–2573.Google Scholar
  131. Trevors, Jack T. 1996. Nucleic acids in the environment. Current Opinion in Biotechnology 7(3): 331–336.Google Scholar
  132. Tsaousis, Anastasios D., D.P. Martin, E.D. Ladoukakis, D. Posada, and E. Zouros. 2005. Widespread recombination in published animal mtDNA sequences. Molecular Biology and Evolution 22(4): 925–933.Google Scholar
  133. Turner, Cameron R., Matthew A. Barnes, Charles C.Y. Xu, Stuart E. Jones, Christopher L. Jerde, and David M. Lodge. 2014. Particle size distribution and optimal capture of aqueous macrobial eDNA. Methods in Ecology and Evolution 5(7): 676–684.Google Scholar
  134. Turner, Cameron R., Karen L. Uy, and Robert C. Everhart. 2015. Fish environmental DNA is more concentrated in aquatic sediments than surface water. Biological Conservation 183: 93–102.Google Scholar
  135. US Fish and Wildlife Service. 1999. Endangered and threatened wildlife and plants; determination of threatened status for bull trout in the coterminous United States. Federal Register 64(210): 58909–58933.Google Scholar
  136. Valentini, Alice, Christian Miquel, Muhammad Ali Nawaz, E.V.A. Bellemain, Eric Coissac, FranCOis Pompanon, Ludovic Gielly, Corinne Cruaud, Giuseppe Nascetti, and Patrick Wincker. 2009. New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: The trnL approach. Molecular Ecology Resources 9(1): 51–60.Google Scholar
  137. Valentini, Alice, Pierre Taberlet, Claude Miaud, Raphaël Civade, Jelger Herder, Philip Francis Thomsen, Eva Bellemain, Aurélien Besnard, Eric Coissac, and Frédéric Boyer. 2016. Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology 25(4): 929–942.Google Scholar
  138. Valiere, Nathaniel, and Pierre Taberlet. 2000. Urine collected in the field as a source of DNA for species and individual identification. Molecular Ecology 9(12): 2150–2152.Google Scholar
  139. Warning, United Nations Environment Programme. Division of Early, and Assessment. 2011. UNEP year book: Emerging issues in our global environment. Nairobi: UNEP/Earthprint.Google Scholar
  140. Wilcox, T.M., McKelvey, K.S., Young, M.K., Jane, S.F., Lowe, W.H., Whiteley, A.R. and Schwartz, M.K. 2013. Robust detection of rare species using environmental DNA: the importance of primer specificity. PloS one 8(3): 59520.Google Scholar
  141. Wilcox, Taylor M., Kellie J. Carim, Kevin S. McKelvey, Michael K. Young, and Michael K. Schwartz. 2015a. The Dual Challenges of Generality and Specificity When Developing Environmental DNA Markers for Species and Subspecies of Oncorhynchus. PLoS ONE 10(11): e0142008.Google Scholar
  142. Wilcox, Taylor M., Kevin S. McKelvey, Michael K. Young, Winsor H. Lowe, and Michael K. Schwartz. 2015b. Environmental DNA particle size distribution from Brook Trout (Salvelinus fontinalis). Conservation Genetics Resources 7(3): 639–641.Google Scholar
  143. Wilcox, Taylor M., Kevin S. McKelvey, Michael K. Young, Adam J. Sepulveda, Bradley B. Shepard, Stephen F. Jane, Andrew R. Whiteley, Winsor H. Lowe, and Michael K. Schwartz. 2016. Understanding environmental DNA detection probabilities: A case study using a stream-dwelling char Salvelinus fontinalis. Biological Conservation 194: 209–216.Google Scholar
  144. Willerslev, Eske, Anders J. Hansen, Jonas Binladen, Tina B. Brand, M. Thomas, P. Gilbert, Beth Shapiro, Michael Bunce, Carsten Wiuf, David A. Gilichinsky, and Alan Cooper. 2003. Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science 300(5620): 791–795.Google Scholar
  145. Williams, Kelly E., Kathryn P. Huyvaert, and Antoinette J. Piaggio. 2016. No filters, no fridges: A method for preservation of water samples for eDNA analysis. BMC Research Notes 9(1): 298.Google Scholar
  146. Wilson, Allan C., Rebecca L. Cann, Steven M. Carr, Matthew George, Ulf B. Gyllensten, Kathleen M. Helm-Bychowski, Russell G. Higuchi, Stephen R. Palumbi, Ellen M. Prager, and Richard D. Sage. 1985. Mitochondrial DNA and two perspectives on evolutionary genetics. Biological Journal of the Linnean Society 26(4): 375–400.Google Scholar
  147. Yoccoz, Nigel G. 2012. The future of environmental DNA in ecology. Molecular Ecology 21(8): 2031–2038.Google Scholar
  148. Zhan, A., Hulák, M., Sylvester, F., Huang, X., Adebayo, A.A., Abbott, C.L., Adamowicz, S.J., Heath, D.D., Cristescu, M.E. and MacIsaac, H.J. 2013. High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities. Methods in Ecology and Evolution 4(6): 558–565.Google Scholar

Copyright information

© Zoological Society, Kolkata, India 2018

Authors and Affiliations

  • Debabrata Senapati
    • 1
  • Manojit Bhattacharya
    • 2
  • Avijit Kar
    • 1
  • Deep Sankar Chini
    • 1
  • Basanta Kumar Das
    • 2
  • Bidhan Chandra Patra
    • 1
    Email author
  1. 1.Department of Aquaculture Management and Technology, Centre For Aquaculture Research, Extension and LivelihoodVidyasagar UniversityMidnaporeIndia
  2. 2.ICAR-Central Inland Fisheries Research InstituteBarrackpore, KolkataIndia

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