Please mind the gap – Visual census and cryptic biodiversity assessment at central Red Sea coral reefs

John K. Pearman, Holger Anlauf, Xabier Irigoien, Susana Carvalho

Research output: Contribution to journalArticlepeer-review

50 Scopus citations


Coral reefs harbor the most diverse assemblages in the ocean, however, a large proportion of the diversity is cryptic and, therefore, undetected by standard visual census techniques. Cryptic and exposed communities differ considerably in species composition and ecological function. This study compares three different coral reef assessment protocols: i) visual benthic reef surveys: ii) visual census of Autonomous Reef Monitoring Structures (ARMS) plates; and iii) metabarcoding techniques of the ARMS (including sessile, 106–500 μm and 500–2000 μm size fractions), that target the cryptic and exposed communities of three reefs in the central Red Sea. Visual census showed a dominance of Cnidaria (Anthozoa) and Rhodophyta on the reef substrate, while Porifera, Bryozoa and Rhodophyta were the most abundant groups on the ARMS plates. Metabarcoding, targeting the 18S rRNA gene, significantly increased estimates of the species diversity (p < 0.001); revealing that Annelida were generally the dominant phyla (in terms of reads) of all fractions and reefs. Furthermore, metabarcoding detected microbial eukaryotic groups such as Syndiniophyceae, Mamiellophyceae and Bacillariophyceae as relevant components of the sessile fraction. ANOSIM analysis showed that the three reef sites showed no differences based on the visual census data. Metabarcoding showed a higher sensitivity for identifying differences between reef communities at smaller geographic scales than standard visual census techniques as significant differences in the assemblages were observed amongst the reefs. Comparison of the techniques showed no similar patterns for the visual techniques while the metabarcoding of the ARMS showed similar patterns amongst fractions. Establishing ARMS as a standard tool in reef monitoring will not only advance our understanding of local processes and ecological community response to environmental changes, as different faunal components will provide complementary information but also improve the estimates of biodiversity in coral reef benthic communities. This study lays the foundations for further studies looking at integrating traditional reef survey methodologies with complementary approaches, such as metabarcoding, which investigate other components of the reef community.
Original languageEnglish (US)
Pages (from-to)20-30
Number of pages11
JournalMarine Environmental Research
StatePublished - Apr 28 2016

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: The authors would like to thank the skippers and crew from CMOR, KAUST who enabled the sampling to be performed. The authors are also indebted to the help given during sampling and laboratory work from Eva Aylagas Martinez and Miguel Viegas, as well as Saskia Kürten for undertaking the nutrient analysis. We would also like to thank Ute Langner for the production of the map. Furthermore, the authors would like to acknowledge the assistance provide in the improvement of this manuscript from the two reviewers. The research reported in this publication was supported by funding from King Abdullah University of Science and Technology (KAUST). This study was undertaken within the framework of the project DEVOTES (EU - ENV.2012.6.2–3 - Grant agreement 308392;

ASJC Scopus subject areas

  • Oceanography
  • Pollution
  • Aquatic Science


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