Coral Reefs

pp 1–13 | Cite as

Development of a multi-assay approach for monitoring coral diversity using eDNA metabarcoding

  • Jason B. AlexanderEmail author
  • Michael Bunce
  • Nicole White
  • Shaun P. Wilkinson
  • Arne A. S. Adam
  • Tina Berry
  • Michael Stat
  • Luke Thomas
  • Stephen J. Newman
  • Laurence Dugal
  • Zoe T. Richards


Cumulative anthropogenic pressures have triggered a global decline in the health of marine ecosystems, and coral reefs, in particular, are in crisis. With climate and population-related pressures predicted to intensify in the coming decades, it is increasingly crucial to develop cost-effective and accurate monitoring tools to document changes to these important ecosystems. Environmental DNA (eDNA) coupled with metabarcoding is a powerful tool for surveying a wide variety of biota. Here, we develop a baseline eDNA toolkit targeting scleractinian corals and validate its performance in conjunction with data derived on traditional diver-based visual surveys at the Cocos (Keeling) Islands. Three assays targeting the ITS2 and 16S barcoding regions were designed, which broadly detected diversity within Scleractinia and Porifera. Our eDNA assays recovered 78 ITS2 operational taxonomic units (OTUs) from 25 scleractinian genera which is comparable to the level of diversity recorded on visual surveys (68 species from 26 genera). There were some notable differences in the species detected using eDNA versus visual records that may relate to either misidentifications, intragenic variation, differential assay performance or cryptic species. Our data demonstrate that a multi-assay eDNA analytical approach, applied on surface water collections, represents a powerful and complementary way to survey diversity that can also reveal fine scale spatial differentiation in community composition. With further refinement and improved reference databases, we envisage eDNA to become a powerful complement to visual surveys and to play a key role in monitoring the health and diversity of complex coral reefs ecosystems.


Biodiversity Biomonitoring Coral reefs Environmental DNA Scleractinia 



We would like to thank the Department of Primary Industries and Regional Development for in-kind funding and Mr Craig Skepper for fieldwork collaboration. Thanks also go to the Cocos (Keeling) Islands office of Parks Australia for logistical support. This project was funded by ARC Linkage project (LP160101508). Coral samples were collected under Fisheries Exemption No. 3080. Bioinformatic resources were supplied by the Pawsey Supercomputing Centre, and we would like to thank all of the members of the TrEnD laboratory for their assistance during the laboratory phases of this project.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

338_2019_1875_MOESM1_ESM.pdf (628 kb)
Supplementary material 1 (PDF 627 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Jason B. Alexander
    • 1
    Email author
  • Michael Bunce
    • 1
    • 2
  • Nicole White
    • 1
  • Shaun P. Wilkinson
    • 3
  • Arne A. S. Adam
    • 1
  • Tina Berry
    • 1
  • Michael Stat
    • 1
    • 4
  • Luke Thomas
    • 5
  • Stephen J. Newman
    • 6
  • Laurence Dugal
    • 5
  • Zoe T. Richards
    • 1
    • 7
  1. 1.Coral Conservation and Research Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life SciencesCurtin UniversityBentleyAustralia
  2. 2.Environmental Protection AuthorityWellingtonNew Zealand
  3. 3.School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
  4. 4.School of Environmental and Life SciencesUniversity of NewcastleCallaghanAustralia
  5. 5.Australian Institute of Marine Science and the UWA Oceans Institute, Indian Ocean Marine Research CentreThe University of Western AustraliaCrawleyAustralia
  6. 6.Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional DevelopmentGovernment of Western AustraliaNorth BeachAustralia
  7. 7.Aquatic Zoology DepartmentWestern Australian MuseumWelshpoolAustralia

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