Substrate identity structures reef microbiomes: crustose coralline algae harbor distinctive assemblages in Palk Bay reef, India

Introduction Coral reef resilience is strongly influenced by microbial communities associated with diverse benthic substrates. However, microbiomes beyond corals remain poorly characterized in the Indian Ocean. This study provides the first cross-substrate microbial baseline from Palk Bay, southeast India. Methods We used 16S rRNA gene amplicon sequencing to characterize bacterial communities associated with corals, crustose coralline algae (CCA), rubble, sediments, and seawater. Alpha and beta diversity metrics, taxonomic composition, and genus-level co-occurrence network analyses were performed to compare microbial assemblages across substrates. Results Bacterial alpha diversity was broadly similar among substrates, whereas beta diversity showed strong compositional segregation (PERMANOVA, Bray–Curtis: F = 5.35, R² = 0.742, p = 0.001). Each substrate harbored distinct microbial 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 to produce larval settlement inducers, suggest a potential role in coral recruitment. Environmental substrates, particularly sediment and rubble, contained the highest number of unique genera, indicating their function as microbial reservoirs. Only a few generalist taxa, notably Pelagibius , were shared across all substrates. Network analysis identified CCA as a highly connected node within the benthic microbial community. Discussion These findings demonstrate that reef microbial communities are strongly substrate-specific rather than defined by a conserved core microbiome. The results establish a regional microbial baseline for Indian reefs and highlight the ecological significance of CCA-associated microbial assemblages in supporting reef resilience and potential coral recruitment processes.