Abstract
Marine sponges host diverse and specialized microbial communities that serve essential functions in nutrient cycling, ecosystem stability, and biotechnological applications. This study investigates the diversity and composition of sponge-associated microbiomes from eight sponge species collected in Chuksan Harbor, South Korea, using full-length 16S rRNA sequencing and amplicon sequence variant (ASV)-based methods. Our results demonstrate that each sponge species harbors distinct and highly structured microbial communities. Proteobacteria, and especially Alpha- and Gammaproteobacteria, were generally dominant; however, unique dominance patterns, such as the near-exclusive presence of an uncharacterized Gammaproteobacterial lineage in Cliona celata, suggest strong host-symbiont specificity and possible coevolution. Notably, no ASVs were shared between seawater and sponge samples, confirming that sponge hosts select and maintain unique sets of microbial partners. In several Halichondria species, we detected the presence of Entotheonella, a symbiont with high biosynthetic gene cluster diversity that may contribute to host chemical defense and metabolic versatility. Depth-driven differences in microbial community composition were exemplified by Geodia reniformis, whose microbiome was dominated by deep-sea adapted and metabolically versatile lineages such as SAR202, PAUC34f, and Dadabacteriales. This study establishes a new baseline for understanding sponge-microbe partnerships in Korean marine environments. Our integrative, high-resolution approach not only uncovers remarkable taxonomic and functional diversity, but also provides a valuable genetic resource for future marine natural-product discovery and advances ecological restoration efforts.