The Maldivian Archipelago hosts valuable coral reefs largely investigated for their ecological diversities. However, the microbiome diversity in different coral morphotypes is still unexplored in this area. In this study, for the first time, the microbiota composition (both symbiont and bacteria) was investigated in various coral morphotypes sampled during May 2022 across four Maldivian atolls. A total of 26 hard coral and gorgonian specimens were collected by scuba diving at reef sites located either on the ocean-exposed reefs or in lagoon sites and at various depths. Samples of surface seawater close to coral assemblages were also collected. Metabarcoding analyses were conducted targeting the 16S rRNA gene and the Internal Transcribed Spacer 2 (ITS2) rRNA region to assess bacterial composition and microalgal endosymbiont clade diversity, respectively. The results obtained for the bacterial composition showed a strong diversity, mainly shaped by coral morphotype rather than by depth or atoll geographical location. Moreover, most of Symbiodinium belong to the genus Cladocopium-C, with some Acropora specimen containing the genus Durusdinium-D, however the variant subtypes were contrasted between coral morphotypes. Seawater samples showed higher diversity as compared to corals, without showing differences between sites, and bacterial SAR groups were observed among the most dominant bacteria genera in surface water. Overall, this study provides preliminary information useful for monitoring local corals and predicting potential impacts of changing environmental conditions.
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