Diversity and Interactions of Bacterial Communities in the Gills of Kumamoto Oyster (Crassostrea sikamea) and Its Culture Environment

The Kumamoto oyster (Crassostrea sikamea), an indigenous species in southern China, is ecologically and aquaculturally significant. To explore the associations between oyster-associated bacteria and their environment, we analyzed bacterial communities in oyster gills, seawater, and sediment from Techeng Island (TCCS, TCW, TCS) and Longtousha (LTSCS, LTSW, LTSS) using Illumina MiSeq sequencing of the 16S rRNA gene V3–V4 region. Alpha diversity showed the highest richness and diversity in sediments (Shannon index: 6.40–6.52), followed by seawater (4.15–4.58) and gills (2.64–2.99). Taxonomic analysis revealed 75 phyla, with Pseudomonadota (23.23–49.32%) dominant across all habitats. Habitat-specific patterns were observed: Spirochaetota was enriched in gills (45.31–46.43%), Bacteroidota in seawater (6.70–14.05%), and Thermodesulfobacteriota in sediments (0.31–0.91%). At the genus level, norank_f_Spirochaetaceae, Marinococcus, and Woeseia showed significant differences among groups (p ≤ 0.001). Venn and PCoA analyses indicated closer similarity between gill and seawater communities than between gill and sediments, likely linked to oyster filter-feeding. This study clarifies the association between oyster gill bacteria and their environment, providing a basis for understanding microbial dynamics in oyster aquaculture.