Low Salinity Elevated Ecological Risks for Shrimp Rearing by Promoting Stochastic Processes and Dispersion of Vibrionaceae Taxa

Inland shrimp rearing at low salinity has become widespread in recent years, yet how severe low salinity affects the microbial community and ultimately drives shrimp culture performance remains unclear. Here, we assessed the impact of salinity decline on the microbial community by diversity, community structure, assembly processes, and interspecies interactions. Water quality, enzyme activities, and shrimp culture performance were also assessed, and the complex relationship between the microbial community and environmental parameters was systematically evaluated. Our study revealed that low salinity significantly impacted community diversity. A decline in both community Richness and Evenness was observed compared to normal-salinity groups (p < 0.01). It caused drastic demographic changes in community structure, surpassing the initial difference between water and gut, and created further dissimilarity between them (p < 0.05). A drastic shift in microbial community assembly process was also observed, where large proportions of deterministic processes were replaced by stochastic processes (70.88% and 80.49% for rearing waters and shrimp gut, respectively). The number of shared microbial community members between rearing waters and shrimp gut showed an over 60-fold reduction, reflecting the reduced migration of microbes from rearing waters to shrimp gut. A drastic reduction in the number of nodes and edges in co-occurrence networks was also observed, indicating weakened interspecies interactions between microbes. Lastly, severe low salinity correlated with the dominance of Vibrionaceae, which rapidly accumulated in group S3G and may have contributed to lowered shrimp survival rate. Overall, our work systematically evaluated the responses of microbial communities in both shrimp gut and rearing waters to salinity decline, which sheds light on the importance of complex host–microbiome interactions and provides a new perspective on how salinity drives shrimp culture performance.