ORIGINAL RESEARCH article
Front. Mar. Sci.
Sec. Aquatic Microbiology
Substrate identity structures reef microbiomes in Palk Bay, India: crustose coralline algae harbour distinctive assemblages
Riana Peter 1
Meenatchi Ramu 2
Sowndarya Sivaprakasam 1
Uma Chinnaiyan 1
Sivagurunathan Paramasivam 1
Joseph Selvin 3
Thinesh Thangadurai 4
1. Annamalai University, Annamalai Nagar, India
2. SRM Institute of Science and Technology (Deemed to be University), Kattankulathur, India
3. Pondicherry University, Puducherry, India
4. Sultan Qaboos University, Seeb, Oman
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Abstract
Coral reef resilience depends on the microbial communities inhabiting diverse benthic substrates, yet non-coral microbiomes in the Indian Ocean remain poorly characterized. Here, we present the first cross-substrate microbiome baseline from Palk Bay, southeast India, using 16S rRNA gene amplicon sequencing across corals, crustose coralline algae (CCA), rubble, sediments, and seawater. Bacterial alpha diversity was broadly comparable among substrates, but beta diversity revealed strong compositional segregation (PERMANOVA Bray–Curtis: F = 5.35, R² = 0.742, p = 0.001). Each substrate hosted distinct assemblages: corals displayed host-linked signatures (e.g., Favia enriched in Ruegeria), sediments were dominated by Woeseia and Desulfovibrio, seawater by pelagic taxa (Pelagibacterales, Synechococcus), and CCA by Rhodobacteraceae members (Roseospira, Labrenzia, Ruegeria). CCA-associated Rhodobacteraceae, known for producing larval settlement inducers, underline the potential ecological role of these microbiomes in coral recruitment. Environmental samples (including sediment and rubble) harbored the highest number of unique genera, functioning as microbial reservoirs that may buffer ecosystem processes under disturbance. Only a few generalist taxa, notably Pelagibius, were shared across all substrates, indicating that microbial composition is largely substrate-specific rather than defined by a conserved core. Genus-level co-occurrence networks positioned CCA as a highly connected node within the broader benthic microbial community. These results establish a regional microbial baseline for Indian reefs and underscore the ecological relevance of CCA-associated microbial assemblages.
Summary
Keywords
Coral microbiome, Coral recruitment, Correline algae, Indian reefs, Southeastern India
Received
30 October 2025
Accepted
16 January 2026
Copyright
© 2026 Peter, Ramu, Sivaprakasam, Chinnaiyan, Paramasivam, Selvin and Thangadurai. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Thinesh Thangadurai
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