Functional convergence despite taxonomic turnover across coral-associated microbiomes

Coral-associated microbiomes are fundamental to holobiont health and resilience, yet their community structures often demonstrate high taxonomic variability across host species. Whether such variability results in functional instability or reflects pervasive metabolic redundancy remains unclear. Here, we investigated microbial taxonomic structure, functional potential, and community assembly mechanisms across 15 coral species using 16S rRNA gene sequencing and shotgun metagenomics. These communities exhibited extreme taxonomic heterogeneity, high beta-diversity, and the absence of a universally shared core genus, indicating strong host-specific filtering that dictates microbial membership. In contrast, Kyoto Encyclopedia of Genes and Genomes pathway-based functional profiles exhibited striking convergence across hosts, revealing a conserved metabolic landscape despite extensive taxonomic turnover. Mantel and Procrustes analyses identified a weak but significant correspondence between taxonomic composition and functional potential, a pattern consistent with functional redundancy across coral-associated microbiomes. Null model-based assembly analyses further revealed a decoupling between taxonomic and functional organization. Taxonomic structure was shaped by a host-dependent balance of stochastic and deterministic processes, whereas functional profiles were predominantly assembled through stochastic processes, maintaining consistently high functional redundancy across hosts. Metagenomic profiling uncovered a two-tier functional architecture underlying this stability: a conserved, high-abundance metabolic core enriched in carbon and phosphorus cycling and stress response functions that support microbial persistence in the coral microenvironment, together with lower-abundance host-specific metabolic modules involved in nitrogen and sulfur transformations that enable niche adaptation. Thus, functional requirements primarily govern the coral-associated microbiome rather than taxonomic identity. This synergy between conserved survival traits and flexible metabolic capacities maintains holobiont homeostasis despite extensive taxonomic turnover.IMPORTANCECoral reefs rely on complex partnerships between corals and their associated microorganisms to maintain health and withstand environmental stress. However, it remains unclear whether changes in microbial communities across different coral species lead to loss of important functions. In this study, we examined microorganisms associated with 15 coral species from the South China Sea and found that coral species hosted highly different microbial communities, while maintaining similar microbial functions. Our findings reveal that different microbial groups can perform similar ecological roles, allowing coral-associated communities to remain functionally stable despite changes in microbial membership. This functional flexibility may help corals maintain biological balance under changing environmental conditions and provides new insights into how coral holobionts preserve resilience in the face of ecological disturbances.