Cross-shelf investigation of coral reef cryptic benthic organisms reveals diversity patterns of the hidden majority

Abstract
Coral reefs harbor diverse assemblages of organisms yet the majority of this diversity is hidden within the three dimensional structure of the reef and neglected using standard visual surveys. This study uses Autonomous Reef Monitoring Structures (ARMS) and amplicon sequencing methodologies, targeting mitochondrial cytochrome oxidase I and 18S rRNA genes, to investigate changes in the cryptic reef biodiversity. ARMS, deployed at 11 sites across a near- to off-shore gradient in the Red Sea were dominated by Porifera (sessile fraction), Arthropoda and Annelida (mobile fractions). The two primer sets detected different taxa lists, but patterns in community composition and structure were similar. While the microhabitat of the ARMS deployment affected the community structure, a clear cross-shelf gradient was observed for all fractions investigated. The partitioning of beta-diversity revealed that replacement (i.e. the substitution of species) made the highest contribution with richness playing a smaller role. Hence, different reef habitats across the shelf are relevant to regional diversity, as they harbor different communities, a result with clear implications for the design of Marine Protected Areas. ARMS can be vital tools to assess biodiversity patterns in the generally neglected but species-rich cryptic benthos, providing invaluable information for the management and conservation of hard-bottomed habitats over local and global scales.

Citation
Pearman JK, Leray M, Villalobos R, Machida RJ, Berumen ML, et al. (2018) Cross-shelf investigation of coral reef cryptic benthic organisms reveals diversity patterns of the hidden majority. Scientific Reports 8. Available: http://dx.doi.org/10.1038/s41598-018-26332-5.

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. We thank Jeffrey Hunt, Matthew Kweskin and the staff of the Laboratory of Analytical Biology at the Smithsonian National Museum of Natural History (Washington DC) who helped with logistics. The authors would also like to thank Holger Anlauf and Riaan van der Merwe who helped with the field work and sample processing along with Richard Payumo and Saskia Kürten who helped with the sample processing. We would also like to thank Ute Langner for the production of the map figures. Figure 2 was produced by Xavier Pita, scientific illustrator at King Abdullah University of Science and Technology (KAUST). Finally we would like to thank the editor and reviewers for their contribution in improving this manuscript. This work was supported by funding to SC from Saudi Aramco within the framework of the Saudi Aramco – KAUST Center for Marine Environmental Observations, KAUST baseline funding to MLB as well as the Sant Chair of the Smithsonian National Museum of Natural History.

Publisher
Springer Nature

Journal
Scientific Reports

DOI
10.1038/s41598-018-26332-5

Additional Links
https://www.nature.com/articles/s41598-018-26332-5

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