Characterization of the core microbiome and rare bacterial biosphere in three coral species across an environmental gradient in the Mexican Caribbean, using high-throughput 16S rRNA sequencing

Introduction: The coral microbiome comprises a stable core microbiome that supports host health and homeostasis, as well as a rare biosphere that enhances the capacity to respond to environmental disturbances. Objective: To characterize the core microbiome and rare bacterial biosphere associated with Acropora palmata, Orbicella faveolata, and Porites porites from the Mexican Caribbean across sites with different levels of anthropogenic stress. Methods: The composition of the core microbiome and rare bacterial biosphere was analyzed using high-throughput sequencing of the 16S rRNA gene. Results: The core microbiome represented 9.7% of the total sequences (50 ASVs) and was dominated by Amoebophilaceae, Rhodobacteraceae, and Woeseiaceae. At the genus level, Candidatus_Amoebophilus was prevalent across all coral species, while Delftia characterized A. palmata and P. porites, and Pelagibius and Woeseia dominated in O. faveolata and P. porites. The rare biosphere was more diverse (1,585 ASVs; 11.9%), with O. faveolata showing the highest richness and dominated by Rhodobacteraceae, Kiloniellaceae, and Vibrionaceae, including Vibrio, Woeseia, Limibaculum, and Desulforhopalus. Beta diversity analyses revealed significant differences among coral species and across anthropogenic gradients, with host identity explaining most of the variation in core microbiomes. The rare biosphere also showed significant variation, although much of this variability remains unexplained. SIMPER analysis identified the ASVs that contributed most to the observed differences. In the core microbiome, the main contributing ASVs were affiliated with the genera Candidatus_Amoebophilus, Delftia, Pelagibius, and Woeseia, whereas, in the rare biosphere, the ASVs contributing most to the observed differences were affiliated with Pelagibius, Tistlia, Woeseia, Desulforhopalus, and Vibrio. Additionally, 23 putative metabolic functions were predicted, with aerobic chemoheterotrophy, fermentation, and sulfur respiration being the most common. Conclusions: These findings highlight the complementary roles of the core microbiome and rare biosphere in structuring coral microbial communities, supporting resilience, and serving as potential candidates bioindicators of environmental change in the Mexican Caribbean.