Marine & Environmental Sciences Faculty Articles

Seq’ and ARMS shall find: DNA (meta)barcoding of Autonomous Reef Monitoring Structures across the tree of life uncovers hidden cryptobiome of tropical urban coral reefs

Yin Cheong Aden Ip, National University of Singapore
Jia Jin Marc Chang, National University of Singapore
Ren Min Oh, National University of Singapore
Zheng Bin Randolph Quek, National University of Singapore
Yong Kit Samuel Chan, National University of Singapore
Andrew G. Bauman, National University of Singapore
Danwei Huang, National University of Singapore


Ip, Y. C. A., Chang, J. J. M., Oh, R. M., Quek, Z. B. R., Chan, Y. K. S., Bauman, A., Huang, D. Singapore ARMS raw sequence reads have been made available on NCBI Sequence Read Archive under BioProject PRJNA801066.


Coral reefs are among the richest marine ecosystems on Earth, but there remains much diversity hidden within cavities of complex reef structures awaiting discovery. While the abundance of corals and other macroinvertebrates are known to influence the diversity of other reef-associated organisms, much remains unknown on the drivers of cryptobenthic diversity. A combination of standardized sampling with 12 units of the Autonomous Reef Monitoring Structure (ARMS) and high-throughput sequencing was utilized to uncover reef cryptobiome diversity across the equatorial reefs in Singapore. DNA barcoding and metabarcoding of mitochondrial cytochrome c oxidase subunit I, nuclear 18S and bacterial 16S rRNA genes revealed the taxonomic composition of the reef cryptobiome, comprising 15,356 microbial ASVs from over 50 bacterial phyla, and 971 MOTUs across 15 metazoan and 19 non-metazoan eukaryote phyla. Environmental factors across different sites were tested for relationships with ARMS diversity. Differences among reefs in diversity patterns of metazoans and other eukaryotes, but not microbial communities, were associated with biotic (coral cover) and abiotic (distance, temperature and sediment) environmental variables. In particular, ARMS deployed at reefs with higher coral cover had greater metazoan diversity and encrusting plate cover, with larger-sized non-coral invertebrates influencing spatial patterns among sites. Our study showed that DNA barcoding and metabarcoding of ARMS constitute a valuable tool for quantifying cryptobenthic diversity patterns and can provide critical information for the effective management of coral reef ecosystems.