Environmental DNA metabarcoding: Transforming how we survey animal and plant communities - PubMed

Affiliations

• PMID: 28921802
• DOI: 10.1111/mec.14350

Free article

Review

Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

Kristy Deiner et al. Mol Ecol. 2017 Nov.

Free article

Abstract

The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing ("HTS") platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed "environmental DNA" or "eDNA"). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called "eDNA metabarcoding" and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education.

Keywords: bioinformatic pipeline; biomonitoring; citizen science; conservation; eDNA; ecology; invasive species; macro-organism; species richness.

Similar articles

• Comparison of environmental DNA and bulk-sample metabarcoding using highly degenerate cytochrome c oxidase I primers.

  Macher JN, Vivancos A, Piggott JJ, Centeno FC, Matthaei CD, Leese F. Macher JN, et al. Mol Ecol Resour. 2018 Nov;18(6):1456-1468. doi: 10.1111/1755-0998.12940. Epub 2018 Sep 9. Mol Ecol Resour. 2018. PMID: 30129704

• Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding.

  Valentini A, Taberlet P, Miaud C, Civade R, Herder J, Thomsen PF, Bellemain E, Besnard A, Coissac E, Boyer F, Gaboriaud C, Jean P, Poulet N, Roset N, Copp GH, Geniez P, Pont D, Argillier C, Baudoin JM, Peroux T, Crivelli AJ, Olivier A, Acqueberge M, Le Brun M, Møller PR, Willerslev E, Dejean T. Valentini A, et al. Mol Ecol. 2016 Feb;25(4):929-42. doi: 10.1111/mec.13428. Epub 2016 Jan 18. Mol Ecol. 2016. PMID: 26479867

• Environmental DNA metabarcoding for fish community analysis in backwater lakes: A comparison of capture methods.

  Fujii K, Doi H, Matsuoka S, Nagano M, Sato H, Yamanaka H. Fujii K, et al. PLoS One. 2019 Jan 31;14(1):e0210357. doi: 10.1371/journal.pone.0210357. eCollection 2019. PLoS One. 2019. PMID: 30703107 Free PMC article.

• Bioinformatic challenges for DNA metabarcoding of plants and animals.

  Coissac E, Riaz T, Puillandre N. Coissac E, et al. Mol Ecol. 2012 Apr;21(8):1834-47. doi: 10.1111/j.1365-294X.2012.05550.x. Mol Ecol. 2012. PMID: 22486822 Review.

• Environmental DNA Metabarcoding: A Novel Method for Biodiversity Monitoring of Marine Fish Communities.

  Miya M. Miya M. Ann Rev Mar Sci. 2022 Jan 3;14:161-185. doi: 10.1146/annurev-marine-041421-082251. Epub 2021 Aug 5. Ann Rev Mar Sci. 2022. PMID: 34351788 Review.

Cited by

• Different coexistence patterns between apex carnivores and mesocarnivores based on temporal, spatial, and dietary niche partitioning analysis in Qilian Mountain National Park, China.

  Cong W, Li J, Hacker C, Li Y, Zhang Y, Jin L, Zhang Y, Li D, Xue Y, Zhang Y. Cong W, et al. Elife. 2024 Sep 11;13:RP90559. doi: 10.7554/eLife.90559. Elife. 2024. PMID: 39259595 Free PMC article.

• New 12S metabarcoding primers for enhanced Neotropical freshwater fish biodiversity assessment.

  Milan DT, Mendes IS, Damasceno JS, Teixeira DF, Sales NG, Carvalho DC. Milan DT, et al. Sci Rep. 2020 Oct 21;10(1):17966. doi: 10.1038/s41598-020-74902-3. Sci Rep. 2020. PMID: 33087755 Free PMC article.

• Fungal and fungal-like diversity in marine sediments from the maritime Antarctic assessed using DNA metabarcoding.

  da Silva MK, de Souza LMD, Vieira R, Neto AA, Lopes FAC, de Oliveira FS, Convey P, Carvalho-Silva M, Duarte AWF, Câmara PEAS, Rosa LH. da Silva MK, et al. Sci Rep. 2022 Dec 6;12(1):21044. doi: 10.1038/s41598-022-25310-2. Sci Rep. 2022. PMID: 36473886 Free PMC article.

• Coupling remote sensing and eDNA to monitor environmental impact: A pilot to quantify the environmental benefits of sustainable agriculture in the Brazilian Amazon.

  Dyson K, Nicolau AP, Tenneson K, Francesconi W, Daniels A, Andrich G, Caldas B, Castaño S, de Campos N, Dilger J, Guidotti V, Jaques I, McCullough IM, McDevitt AD, Molina L, Nekorchuk DM, Newberry T, Pereira CL, Perez J, Richards-Dimitrie T, Rivera O, Rodriguez B, Sales N, Tello J, Wespestad C, Zutta B, Saah D. Dyson K, et al. PLoS One. 2024 Feb 14;19(2):e0289437. doi: 10.1371/journal.pone.0289437. eCollection 2024. PLoS One. 2024. PMID: 38354171 Free PMC article.

• DNA metabarcoding of zooplankton communities: species diversity and seasonal variation revealed by 18S rRNA and COI.

  Zhao L, Zhang X, Xu M, Mao Y, Huang Y. Zhao L, et al. PeerJ. 2021 Mar 19;9:e11057. doi: 10.7717/peerj.11057. eCollection 2021. PeerJ. 2021. PMID: 33777533 Free PMC article.

Publication types

MeSH terms

Substances

LinkOut - more resources

• Full Text Sources

  • Wiley
  • Zurich Open Access Repository and Archive

• Other Literature Sources

  • The Lens - Patent Citations Database
  • scite Smart Citations