Coral Reefs

, Volume 38, Issue 1, pp 79–92 | Cite as

Identification of newly settled Caribbean coral recruits by ITS-targeted single-step nested multiplex PCR

  • Elijah D. O’CainEmail author
  • Marc E. Frischer
  • J. Scott Harrison
  • Tina L. Walters
  • Megan E. Thompson
  • Nicole D. Fogarty
  • Rob Ruzicka
  • Daniel F. Gleason


As coral cover has declined throughout the Caribbean, interest in determining the potential for reef recovery via natural recruitment processes has increased. Studies investigating recruitment have been hampered by the difficulty of identifying early stage corals that often lack distinguishing morphological characters. In this study, the utility of targeting the noncoding ribosomal internal transcribed spacer (ITS) regions with a single-step nested multiplex (SSNM) PCR assay to identify common Caribbean coral species was investigated. To design this assay, a database of ITS sequences for 17 common Caribbean coral species was developed. Phylogenies based on the ITS region were generally consistent with current published coral taxonomy and indicated that the ITS regions provided sufficient variability to be useful for distinguishing corals to at least the genus level. Ultimately, we developed ITS-targeted single-step nested multiplex PCR assays capable of differentiating six corals to the species level, two to the genus level, and a pair of coral species that were recently separated at the genus level. This assay was used to classify coral recruits previously identified based on morphological characters. Agreement between these two approaches was low and highlighted the ability of the SSNM-PCR assay to increase the certainty and accuracy of coral recruit identifications. The coral SSNM assay shows promise as an effective method of identifying early stage corals to the genus or species level, and as a valuable tool in studies investigating reef recovery.


Caribbean Recruit Molecular Assay Single-Step Nested Multiplex PCR Internal Transcribed Spacer Region 



We would like to thank members of the Florida Fish and Wildlife Conservation Commission Coral and Collections Teams, including Leah Harper, Mike Colella, Lindsay Huebner, Vanessa Brinkhuis, Tiffany Boisvert, Ari Halperin, Ananda Ellis, Katy Cummings, Laura Wiggins, Paul Larson, Krista Austin, and Miguel Montaluo for assistance in the field. We would also like to thank the many laboratories and investigators who provided DNA samples: Andrew Baker (University of Miami), Mary Alice Coffroth (State University of New York at Buffalo), Daniel Brazeau (University of New England), and Stephanie Schopmeyer (University of Miami). This project was completed through a grant provided by the National Oceanic and Atmospheric Administration’s Coral Reef Conservation Program (Federal Award #MOA-2010-026/8081) via a sub-award with the Florida Fish and Wildlife Conservation Commission (FWC Agreement #14208). This study was supported in part by the US National Science Foundation Awards OCE 082599 and OCE 1459293 to MEF. This project was also funded in part by the PADI Foundation to EDO.

Compliance with ethical standards

Conflict of interest

On behalf of all authors, the corresponding author states that there is no conflict of interest.

Supplementary material

338_2018_1763_MOESM1_ESM.fas (156 kb)
Supplementary material 1 (FAS 155 kb)


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Copyright information

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

Authors and Affiliations

  1. 1.James H. Oliver, Jr., Institute for Coastal Plain ScienceGeorgia Southern UniversityStatesboroUSA
  2. 2.Skidaway Institute of OceanographyUniversity of GeorgiaSavannahUSA
  3. 3.Department of BiologyGeorgia Southern UniversityStatesboroUSA
  4. 4.Skidaway Institute of OceanographyUniversity of Georgia, Memorial Health University Medical CenterSavannahUSA
  5. 5.Halmos College of Natural Science and OceanographyNova Southeastern UniversityDania BeachUSA
  6. 6.Corals ProgramFlorida Fish and Wildlife Conservation CommissionSaint PetersburgUSA

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