Host Mucosal Niche and Rearing Environment Are Associated with Distinct Gut and Gill Microbiota of L. crocea (Larimichthys crocea)

Microbial communities associated with fish mucosal tissues play important roles in host health and environmental adaptation. However, the effects of contrasting aquaculture conditions on the microorganisms of the large yellow croaker (Larimichthys crocea, L. crocea) remain poorly understood. In this study, 16S rRNA gene sequencing was used to compare the gut and gill microbiota of L. crocea cultured in a marine system and a saline–alkaline system, together with the corresponding surrounding water samples. The results showed that both host tissue type and rearing environment significantly influenced microbial community structure. Water samples generally exhibited higher alpha diversity than host-associated samples, whereas the gut and gill communities were clearly separated from the surrounding water microbial community. The intestine showed stronger culture system differentiation than the gill, suggesting greater niche selectivity, while the gill retained a closer association with the rearing water. Across multiple taxonomic levels, microbial composition differed markedly among water, gut, and gill samples, and the divergence between the marine culture and saline–alkaline culture system became more pronounced at finer taxonomic resolution. Differentially enriched taxa further revealed clear tissue- and habitat-associated microbial patterns. In addition, several dominant taxa were significantly correlated with environmental variables, especially salinity and nutrient-related factors, indicating that physicochemical heterogeneity contributed substantially to microbial community assembly. Overall, this study shows that host mucosal niche and rearing environment are associated with distinct gut and gill microbiota patterns in L. crocea and provides preliminary ecological information for future microbiome-informed aquaculture management, functional validation of candidate taxa, and the development of land-based culture systems for marine fish.