Beyond the visual: using metabarcoding to characterize the hidden reef cryptobiome

Susana Carvalho, Eva Aylagas, Rodrigo Villalobos, Yasser Kattan, Michael L. Berumen, John K. Pearman

Research output: Contribution to journalArticlepeer-review

44 Scopus citations


In an era of coral reef degradation, our knowledge of ecological patterns in reefs is biased towards large conspicuous organisms. The majority of biodiversity, however, inhabits small cryptic spaces within the framework of the reef. To assess this biodiverse community, which we term the ‘reef cryptobiome’, we deployed 87 autonomous reef monitoring structures (ARMS), on 22 reefs across 16 degrees latitude of the Red Sea. Combining ARMS with metabarcoding of the mitochondrial cytochrome oxidase I gene, we reveal a rich community, including the identification of 14 metazoan phyla within 10 416 operational taxonomic units (OTUs). While mobile and sessile subsets were similarly structured along the basin, the main environmental driver was different (particulate organic matter and sea surface temperature, respectively). Distribution patterns of OTUs showed that only 1.5% were present in all reefs, while over half were present in a single reef. On both local and regional scales, the majority of OTUs were rare. The high heterogeneity in community patterns of the reef cryptobiome has implications for reef conservation. Understanding the biodiversity patterns of this critical component of reef functioning will enable a sound knowledge of how coral reefs will respond to future anthropogenic impacts.
Original languageEnglish (US)
Pages (from-to)20182697
JournalProceedings of the Royal Society B: Biological Sciences
Issue number1896
StatePublished - Feb 13 2019

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: Funding: The research reported in this publication was supported by funding from a collaboration between KAUST and Saudi Aramco within the framework of the Saudi Aramco–KAUST Center for Marine Environmental Observations. Acknowledgements: We are grateful to the personnel from the King Abdullah University of Science and Technology (KAUST) Coastal and Marine Resources Core Lab for logistical support as well as to the crew of RV Thuwal. The authors would also like to thank Katherine Rowe, Joanne Ellis, Amr Gusti, Giuseppe Merlino, Aislinn Dunne, Florian Roth, Joao Curdia, Zahra Alsaffar, Alejandro Restrepo, Perdana Prihartato, Holger Anlauf, and members of the Red Sea Research Center summer student program 2017 for their help with the processing of the samples. We would also like to thank the editor and two reviewers who greatly contributed to improving an earlier version of this manuscript.


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