Host genetics structure Symbiodiniaceae and prokaryotic assemblages and their co-variation in sympatric fire coral species

Host genetic and environmental filtering are key determinants of microbiome assembly, yet their relative influence across multiple symbiotic compartments remains poorly understood. In coral holobionts, studies typically focus on either algal or bacterial symbionts and rarely account for host genetic variation below the species level. Here, we combined host microsatellite genotyping with ITS2 and 16S rRNA metabarcoding to investigate the drivers of Symbiodiniaceae and prokaryotic assemblages in three sympatric fire coral species (Millepora cf. exaesa, M. tenera, and M. cf. platyphylla) across three adjacent but environmentally contrasting reef habitats on Reunion Island. Both symbiont assemblages were structured by host identity and habitat, although host genetics consistently outweighed environmental effects on the microbiome composition. At the subspecies level, host genotypes explained up to 54% of the variation in Symbiodiniaceae assemblages compared to 20% for the prokaryotes. Symbiodiniaceae communities were dominated by Symbiodinium A16 and A3 radiations, while showing marked specificity across species and habitats. All Millepora species consistently associated with the Spirochaetaceae, Kiloniellaceae and Desulfobacteraceae bacterial families across all habitats, suggesting evolutionarily maintained core associations. Integrative analysis further demonstrated genotype-specific co-variation between algal and bacterial symbionts, with some genotypes maintaining stable and co-varying symbionts across clones, while others exhibited more flexible assemblages. Together, our results indicate that sympatric fire coral acquire symbionts from locally available pools through host genotype-dependent filtering. This study highlights host genotype as a major determinant of coral holobiont assembly, shaping the composition and co-variation of both Symbiodiniaceae and prokaryotic assemblages.