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Environmental DNA: An Emerging Tool in Ecological Assessment

  • Pengyuan Wang
  • Zhenguang YanEmail author
  • Suwen Yang
  • Shuping Wang
  • Xin Zheng
  • Juntao Fan
  • Tianxu Zhang
Focused Review

Abstract

Environmental DNA (eDNA), as a recent research hotspot in environmental science, the use of eDNA in biological monitoring has the advantages of sensitivity and time/labor saving. The eDNA technology combined with scientific advancement has been applied in investigations of target species (such as invasive species, endangered species and other rare species), biomass, and biodiversity. In addition, ecotoxicology studies and environmental pollution impact assessments based on the development of eDNA technology have gradually emerged in recent years. In this article, we summarizes the application of eDNA in ecological assessment, include species diversity assessment and chemical contamination impacts assessment, provide guiding questions for study design. We additionally discuss current challenges associated with eDNA. Finally, looking to the future, we discuss the opportunities of eDNA technology in environmental protein, environmental sample processor and ecogenomic sensors.

Keywords

Environmental DNA Ecological assessment Ecotoxicology Biodiversity 

Notes

Acknowledgements

This work was financially supported by the Fundamental Research Funds for Central Public Welfare Scientific Research Institutes of China (Grant No. 2019YSKY-007) & the Major Science and Technology Program for Water Pollution Control and Treatment (Grant No. 2017ZX07301002-01).

References

  1. Andersen K, Bird KL, Rasmussen M et al (2011) Meta-barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity. Mol Ecol 21:1966–1979Google Scholar
  2. Anderson-Carpenter LL, Mclachlan JS, Jackson ST et al (2011) Ancient DNA from lake sediments: bridging the gap between paleoecology and genetics. BMC Evol Biol 11:30Google Scholar
  3. Balasingham KD, Walter RP, Mandrak NE, Heath DD (2018) Environmental DNA detection of rare and invasive fish species in two Great Lakes tributaries. Mol Ecol 27:112–127Google Scholar
  4. Barnes MA, Turner CR (2016) The ecology of environmental DNA and implications for conservation genetics. Conserv Genet 17:1–17Google Scholar
  5. Barnes MA, Turner CR, Jerde CL, Renshaw MA, Chadderton WL, Lodge DM (2014) Environmental conditions influence eDNA persistence in aquatic systems. Environ Sci Technol 48:1819–1827Google Scholar
  6. Bienert R, de Danieli S, Miquel C et al (2012) Tracking earthworm communities from soil DNA. Mol Ecol 21:2017–2030Google Scholar
  7. Bista I, Carvalho GR, Walsh K et al (2017) Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity. Nat Commun 8:14087Google Scholar
  8. Bohmann K, Evans A, Gilbert TP et al (2014) Environmental DNA for wildlife biology and biodiversity monitoring. Trends Ecol Evol 29:358–367Google Scholar
  9. Butchart SH, Walpole M, Collen B et al (2010) Global biodiversity: Indicators of recent declines. Science 328(5982):1164–1168Google Scholar
  10. Carraro L, Hartikainen H, Jokela J, Bertuzzo E, Rinaldo A (2018) Estimating species distribution and abundance in river networks using environmental DNA. Proc Natl Acad Sci USA 115:11724–11729Google Scholar
  11. Cristescu ME, Hebert PD (2018) Uses and misuses of environmental DNA in biodiversity science and conservation. Annu Rev Ecol Evol S 49(1):209–230Google Scholar
  12. Currier CA, Morris TJ, Wilson CC, Freeland JR (2018) Validation of environmental DNA (eDNA) as a detection tool for at-risk freshwater pearly mussel species (Bivalvia: Unionidae). Aquat Conserv 28:545–558Google Scholar
  13. Deiner K, Fronhofer EA, Machler E, Walser J, Altermatt F (2016) Environmental DNA reveals that rivers are conveyer belts of biodiversity information. Nat Commun 7:12544Google Scholar
  14. Eichmiller JJ, Best SE, Sorensen PW (2016) Effects of temperature and trophic state on degradation of environmental DNA in lake water. Environ Sci Technol 50:1859–1867Google Scholar
  15. Ficetola GF, Miaud C, Pompanon F, Taberlet P (2008) Species detection using environmental DNA from water samples. Biol Lett 4:423–425Google Scholar
  16. Fukumoto S, Ushimaru A, Minamoto T (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. J Appl Ecol 52:358–365Google Scholar
  17. Geml J, Laursen GA, Timling I et al (2009) Molecular phylogenetic biodiversity assessment of arctic and boreal ectomycorrhizal Lactarius Pers (Russulales; Basidiomycota) in Alaska, based on soil and sporocarp DNA. Mol Ecol 18:2213–2227Google Scholar
  18. Giguet-Covex C, Pansu J, Arnaud F et al (2014) Long livestock farming history and human landscape shaping revealed by lake sediment DNA. Nat Commun 5(1):3211Google Scholar
  19. Hering D, Borja A, Jones JI et al (2018) Implementation options for DNA-based identification into ecological status assessment under the European water framework directive. Water Res 138:192–205Google Scholar
  20. Hofreiter M, Mead JI, Martin P, Poinar HN (2003) Molecular caving. Curr Biol 13:R693–R695Google Scholar
  21. Jerde CL, Mahon AR, Chadderton WL, Lodge DM (2011) “Sight-unseen” detection of rare aquatic species using environmental DNA. Conserv Lett 4:150–157Google Scholar
  22. Keeley NB, Wood SA, Pochon X (2018) Development and preliminary validation of a multi-trophic metabarcoding biotic index for monitoring benthic organic enrichment. Ecol Indic 85:1044–1057Google Scholar
  23. Laramie MB, Pilliod DS, Goldberg CS (2015) Characterizing the distribution of an endangered salmonid using environmental DNA analysis. Biol Conserv 183:29–37Google Scholar
  24. Leray M, Knowlton N (2015) DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity. Proc Natl Acad Sci USA 112:2076–2081Google Scholar
  25. Li F, Peng Y, Fang W, Altermatt F, Xie Y, Yang J, Zhang X (2018) Application of environmental DNA metabarcoding for predicting anthropogenic pollution in rivers. Environ Sci Technol 52:11708–11719Google Scholar
  26. Matisoo-Smith E, Roberts K, Welikala N et al (2008) Recovery of DNA and pollen from New Zealand lake sediments. Quat Int 184:139–149Google Scholar
  27. Miya M (2017) Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea. Sci Rep 7:40368Google Scholar
  28. Ogram A, Sayler GS, Barkay T (1987) The extraction and purification of microbial DNA from sediments. J Microbiol Methods 7:57–66Google Scholar
  29. Ottesen EA (2016) Probing the living ocean with ecogenomic sensors. Curr Opin Microbiol 31:132–139Google Scholar
  30. Rees HC, Maddison BC, Middleditch DJ et al (2014) REVIEW: The detection of aquatic animal species using environmental DNA—a review of eDNA as a survey tool in ecology. J Appl Ecol 51(5):1450–1459Google Scholar
  31. Rodgers TW, Mock KE (2015) Drinking water as a source of environmental DNA for the detection of terrestrial wildlife species. Conserv Genet Resour 7:693–696Google Scholar
  32. Seymour M (2019) Rapid progression and future of environmental DNA research. Commun Biol 2:80Google Scholar
  33. Shogren AJ, Tank JL, Andruszkiewicz E et al (2017) Controls on eDNA movement in streams: transport, retention, and resuspension. Sci Rep 7(1):5065Google Scholar
  34. Sigsgaard EE, Carl H, Moller P, Thomsen PF (2015) Monitoring the near-extinct European weather loach in Denmark based on environmental DNA from water samples. Biol Conserv 183:46–52Google Scholar
  35. Sigsgaard EE, Nielsen IB, Bach SS et al (2016) Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA. Nat Ecol Evol 1:01–04Google Scholar
  36. Simmons M, Tucker A, Chadderton WL, Jerde CL, Mahon AR (2016) Active and passive environmental DNA surveillance of aquatic invasive species. Can J Fish Aquat Sci 73:76–83Google Scholar
  37. Thomsen PF, Willerslev E (2015) Environmental DNA—an emerging tool in conservation for monitoring past and present biodiversity. Biol Conserv 183:4–18Google Scholar
  38. Ushio M, Fukuda H, Inoue T et al (2017) Environmental DNA enables detection of terrestrial mammals from forest pond water. Mol Ecol Resour 17:e63–e75Google Scholar
  39. Xie Y, Wang J, Wu Y, Ren C, Song C, Yang J, Yu H, Giesy JP, Zhang X (2016) Using in situ bacterial communities to monitor contaminants in river sediments. Environ Pollut 212:348–357Google Scholar
  40. Xie Y, Zhang X, Yang J et al (2018) eDNA-based bioassessment of coastal sediments impacted by an oil spill. Environ Pollut 238:739–748Google Scholar
  41. Yang J, Zhang X, Xie Y, Song C, Sun J, Zhang Y, Giesy JP, Yu H (2017a) Ecogenomics of zooplankton community reveals ecological threshold of ammonia nitrogen. Environ Sci Technol 51:3057–3064Google Scholar
  42. Yang J, Zhang X, Zhang W, Sun J, Xie Y, Zhang Y, Burton GA, Yu H (2017b) Indigenous species barcode database improves the identification of zooplankton. PLoS ONE.  https://doi.org/10.1371/journal.pone.0185697 CrossRefGoogle Scholar
  43. Yang J, Xie Y, Jeppe K, Long SM, Pettigrove V, Zhang X (2018) Sensitive community responses of microbiota to copper in sediment toxicity test. Environ Toxicol Chem 37:599–608Google Scholar
  44. Yang Y, Gao Y, Huang X, Ni P, Wu Y, Deng Y, Zhan A (2019a) Adaptive shifts of bacterioplankton communities in response to nitrogen enrichment in a highly polluted river. Environ Pollut 245:290–299Google Scholar
  45. Yang Y, Li S, Guo Y, Chen Y, Zhan A (2019b) Environment-driven geographical distribution of bacterial communities and identification of indicator taxa in Songhua River. Ecol Indic 101:62–70Google Scholar
  46. Yoccoz NG, Bra˚then KA, Gielly L et al (2012) DNA from soil mirrors plant taxonomic and growth form diversity. Mol Ecol 21:3647–3655Google Scholar
  47. Zhang X (2019) Environmental DNA shaping a new era of ecotoxicological research. Environ Sci Technol 53:5605–5612Google Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Pengyuan Wang
    • 1
  • Zhenguang Yan
    • 1
    Email author
  • Suwen Yang
    • 2
  • Shuping Wang
    • 1
  • Xin Zheng
    • 1
  • Juntao Fan
    • 1
  • Tianxu Zhang
    • 1
  1. 1.State Key Laboratory of Environmental Criteria and Risk AssessmentChinese Research Academy of Environmental SciencesBeijingPeople’s Republic of China
  2. 2.National Engineering Laboratory for Lake Pollution Control and Ecological RestorationChinese Research Academy of Environmental SciencesBeijingPeople’s Republic of China

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