Exploring phylosymbiosis in the skin microbiome of coral reef fish: Synergistic effects of environmental and host-specific factors

Abstract The skin is the largest organ in vertebrates, and its microbiome plays a crucial role in immune function and host health. Coral reef fish, characterized by rapid adaptive radiation and complex functional diversity, provide an ideal model for studying the assembly of vertebrate skin microbiomes and the mechanisms that drive this process. In this study, we used 16S rRNA gene amplicon sequencing to investigate the factors influencing the skin microbiomes of coral reef fish across a broad spatial scale. We analyzed 447 skin microbiome samples from 138 fish species, collected from different regions along the latitudinal gradient in coral reef ecosystems of the South China Sea. Our results revealed significant differences in the skin microbiomes of coral reef fish between coastal and offshore habitats in terms of taxonomic composition, diversity, and predicted functional potential. The microbiome structure was influenced by a combination of environmental factors, host traits, and phylogenetic relationships. Notably, we observed a phylosymbiotic pattern in the skin microbiomes of coral reef fish, with more closely related fish exhibiting more similar microbial communities. Temperature and silicate concentration were identified as the primary environmental drivers of microbial community structure, while host-specific factors such as mobility and diet indirectly influenced microbiome assembly by shaping host-associated microenvironment and feeding habitats. Our study highlights the complex interplay between environmental and host-specific factors in shaping coral reef fish skin microbiomes and provides new insights into host-microbe interactions in coral reef ecosystems.