Biological migration is usually associated with disturbances and environmental changes that are key drivers in determining the diversity, community compositions, and function of gut microbiome. However, little is known about how gut microbiome is affected by disturbance such as salinity changes during migration from seawater to freshwater. Here, we tracked the gut microbiome succession of Chinese mitten crabs (Eriocheir sinensis) during their migrations from seawater to freshwater and afterward using 16S rDNA sequencing for 127 days, and explored the temporal patterns in microbial diversity and the underlying environmental factors. The species richness of gut microbiome showed a hump-shaped trend over time during seawater–freshwater migration. The community dissimilarities of gut microbiome increased significantly with day change. The turnover rate of gut microbiome community was higher during seawater–freshwater transition (1–5 days) than that in later freshwater conditions. Salinity was the major factor leading to the alpha diversity and community dissimilarity of gut microbiome during seawater–freshwater transition, while the host selection showed dominant effects during freshwater stage. The transitivity, connectivity, and average clustering coefficient of gut microbial co-occurrence networks showed decreased trends, while modularity increased during seawater–freshwater migration. For metabolic pathways, “Amino Acid Metabolism” and “Lipid Metabolism” were higher during seawater–freshwater transition than in freshwater. This study advances our mechanistic understanding of the assembly and succession of gut microbiota, which provides new insights into the gut ecology of other aquatic animals.

Freshwater salinization is a growing environmental issue caused by various anthropic or natural factors that lead to changes in water chemistry and physical conditions, affecting the survival and diversity of phytoplankton. In this study, we tested the physiological, morphological and interspecific competition of the freshwater cyanobacterium Microcystis aeruginosa and the green algae Scenedesmus obliquus to salinity stress. Results demonstrated that increasing salinity had a significant negative effect on the growth of M. aeruginosa and S. obliquus. M. aeruginosa showed a decline in growth rate with increasing salinity, while S. obliquus showed a lower growth rate under salinity stress but with no significant difference between the two salinity groups. In cocultures, S. obliquus outcompeted M. aeruginosa, and the displacement was accelerated with increasing salinity. The photosynthetic performance of both algae was affected by salinity, the presence of competitors, and the cultivation time. S. obliquus showed morphological variations under salinity stress and the presence of a competitor. The study suggests that salinity stress and competition can have a significant impact on the growth and performance of algae species. The findings of our study suggest that the salinization of freshwater can impact the interspecific interactions among phytoplankton, which play a crucial role in the functioning of freshwater ecosystems.