Elucidating the relationships between host-associated (intestinal and gill) and environmental (water and sand) microbial communities across water exchange rates in Babylonia areolata aquaculture

Water exchange is linked to survival in aquaculture, but its relationship with host–environment microbial interactions remains unclear. We aimed to characterize host-associated and environmental microbiota in Babylonia areolata (ivory shell) aquaculture, focusing on community relationships, environmental source contributions, associations with water quality, and host survival across water exchange rates. Ivory shells were reared for 60 days at high (100% d −1 ), medium (50% d −1 ), and low (0% d −1 ) water exchange rates. On day 60, water, sand, intestinal, and gill samples (12 samples per treatment) were profiled using 16S rRNA gene V3-V4 amplicon sequencing. The results showed that survival was lower only in the low-exchange group ( p < 0.001). Analysis of similarities (ANOSIM) showed that the host microbiota differed significantly from environmental communities (R = 0.739, p = 0.001). SourceTracker identified sand as the largest environmental contributor; its contribution declined from 48.0 to 21.0% in the intestine and from 65.7 to 30.2% in the gills as the water exchange rate decreased. Reduced water exchange rates were also associated with declines in the relative abundance of intestinal Nautella and gill-associated Ruegeria . Linear discriminant analysis effect size (LEfSe) identified Halodesulfovibrio as a shared biomarker in both tissues under low water exchange conditions. Redundancy analysis (RDA) identified NO 3 − -N and pH as the environmental variables most strongly associated with environmental microbial community structure. Exploratory genus-level correlations showed that rearing water pH was negatively associated with Halodesulfovibrio in both tissues. Collectively, these results indicate that the water exchange rate is associated with host-associated microbial community composition, environmental source contributions, and ivory shell survival. Future studies should investigate the mechanisms underlying the associations among environmental microbial communities, water quality conditions, and host survival, thereby informing microecological management in low water exchange aquaculture systems.