Diversity and composition of sponge-associated microbiomes from Korean sponges revealed by full-length 16S rRNA analysis

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.

Keywords: Amplicon sequencing; Full-length 16S rRNA; Korean sponges; Microbial community composition; Sponge microbiome; Symbiotic microorganisms.

Fig. 1

Map showing the locations of the sampling sites in Chuksan Harbor. The SCUBA sampling site is marked with a red star(*). Photographs of the eight sponge species collected from these sites are also shown.

Fig. 2

Microbial community composition of eight sponge samples Halichondria dokdoensis (SP1), Mycale sp. (SP3), Geodia reniformis (SP8), Cliona celata (SP21), Halichondria sp. (SP22, SP23), Latrunculia ikematsui (SP32), Mycale neunggulensis (SP38) and seawater (SW), illustrating the distribution of the top 10 most abundant bacterial phyla and classes (a), and orders and families (b). In the legend, “p__” denotes the phylum, “c__” denotes the class, “o__” denotes the order, and “f__” denotes the family level to which the ASVs were assigned based on 16S rRNA gene sequence classification by QIIME2 with SILVA database. For taxa that could not be assigned to the order or family levels (f__ or o__;f__), the immediately higher taxonomic rank (class) is additionally indicated.

Fig. 3

Rarefaction curves showing alpha diversity metrics for each sample, generated using QIIME2’s diversity alpha-rarefaction method at a rarefaction depth of 1,845. Visualization was performed with QIIME2. Metrics include: (a) Faith’s phylogenetic diversity, (b) Shannon entropy, and (c) observed features. Colors represent individual samples or groups as indicated in the legend. Each curve illustrates how sequencing depth influences estimated alpha diversity across samples. Plateaus in the curves indicate that sequencing depth was sufficient for robust diversity estimation.

Fig. 4

Principal coordinates analysis (PCoA) plots comparing microbial community structures among eight sponge samples and seawater. (a) PCoA based on the Bray–Curtis dissimilarity and (b) the weighted UniFrac distance matrix. Each point represents an individual sample, colored and labeled by sample identity. The axes indicate the percentage of total variance explained by the first two principal coordinates (PC1 and PC2). Samples cluster according to host species and environmental origin, with clear separation observed between seawater and sponge-associated microbial communities. Beta diversity was analyzed using QIIME2 diversity core-metrics-phylogenetic with a sampling depth of 1,845. Plots were generated in R using the qiime2R, ggplot2, and ggrepel packages.

Fig. 5

Taxonomic and phylogenetic analysis of microbial communities from sponge and seawater samples. Amplicon sequence variants (ASVs) were phylogenetically aligned to construct a tree depicting evolutionary relationships among detected taxa. For visualization, a heatmap was generated to show the relative abundance of the top 35 most abundant bacterial families (family level), after normalization of feature counts across samples. Only families with the highest abundance were retained to enhance clarity, and all displayed values were derived from normalized data. Heatmap highlights the distribution patterns of dominant families across different sample groups.