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Microbial diversity of sub-bottom sediment cores from a tropical reef system

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Abstract

Declining coral reef health has triggered a multitude of studies focusing on the diversity and functional roles of reef-associated microbial communities. However, comparatively little is known about the microbial communities in deeper sediment assemblages (> 1 m) below the reef substrate. Here, we present the first characterisation of microbial community structure in sub-bottom sediment of up to 3.5 m beneath the reef substrate. Cores were retrieved from three reef sites in Singapore and profiled via 16S rRNA (V4 region) gene sequencing. Despite each core containing a large number of unique ASVs, cores from the same reef showed more similar taxonomic profiles compared to cores from other reefs. We detected limited differences in diversity between either cores or sediment facies. Our results provide novel insight into microbial communities in sub-bottom reef sediment and contribute to the growing research on reef–microbial interactions.

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Data availability

Raw sequences associated with this work have been deposited at the National Center for Biotechnology Information under the BioProject ID PRJNA665104. The code for reproducing the analyses is archived at http://doi.org/10.5281/zenodo.6164090.

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Acknowledgements

Reef coring was performed under the National Parks Board permit NP/RP16-156. We thank the 2018 Reef Coring team for their help with retrieval of all reef cores, as well as members of the Reef Ecology Laboratory, National University of Singapore, for assistance and support.

Funding

This work was supported by the National Research Foundation, Prime Minister’s Office, Singapore, under its Marine Science R&D Programme (MSRDP-P03).

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Authors and Affiliations

  1. Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore

    Ren Min Oh, Zheng Bin Randolph Quek, Yong Kit Samuel Chan, Ambert Chiam Foong Ang, Danwei Huang & Benjamin J. Wainwright

  2. School of Earth Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia

    Michael J. O’Leary

  3. Centre for Nature-Based Climate Solutions, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore

    Danwei Huang

  4. Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore, 119227, Singapore

    Danwei Huang

  5. Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore, 138527, Singapore

    Zheng Bin Randolph Quek & Benjamin J. Wainwright

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  1. Ren Min Oh
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Contributions

RMO, ZBRQ, BJW and DH planned the study. RO wrote the manuscript and performed all laboratory experiments. RMO, ZBRQ, BJW and DH analysed and interpreted the findings. All authors conducted field work, read and approved the final manuscript.

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Correspondence to Zheng Bin Randolph Quek.

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Oh, R.M., Quek, Z.B.R., Chan, Y.K.S. et al. Microbial diversity of sub-bottom sediment cores from a tropical reef system. Coral Reefs 41, 397–403 (2022). https://doi.org/10.1007/s00338-022-02231-0

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