Composition and migration of microbial community in the ice–water–sediment interface of saline lakes in cold and arid regions

• Microbial dynamics at ice-water–sediment interface of saline lakes were studied. • Seasonal and spatial variations were explored in the microbial species of sediments. • Microbial changes across salinity gradients using ex situ methods were revealed. • Pathogenic bacteria impacting environmental health were detected in saline lakes. Ecosystems in extreme environments, such as saline lakes in cold and arid regions, are greatly affected by high salinity, significant temperature fluctuations, and low nutrient availability, resulting in unique microbial community structures. However, the spatiotemporal dynamics and migration mechanisms of microbial communities in such environments remain unclear. Here, we investigated the composition and migration of the microbial communities at the ice–water–sediment interfaces of Daihai Lake (high salinity) and Ulansuhai Lake (low salinity) in Inner Mongolia, China. The changes in microbial communities under varying salinity conditions were analysed and potential pathogenic genera with implications for fish and other aquatic animals were identified. Ice and water were dominated by Proteobacteria and Bacteroidetes, whereas sediments mainly contained Chloroflexi and Nitrospirota. Additionally, non-parametric Kruskal–Wallis rank-sum tests and linear discriminant analysis effect size (LEfSe) analysis were conducted to detect significant differences in microbial abundance. Significant seasonal and site-specific variations in indicator genera were observed in the sediments. Sulfur-oxidising bacteria, such as Thioalkalispira-Sulfurivermis and Thiobacillus, were predominant in the summer. The indicator genus at point D1 was Thiobacillus , while the indicator genus at point D2 was Bacillus . Furthermore, the microbial migration efficiency was substantially lower in high-salinity lakes (sediment-to-water body: 9.8 %; water body-to-ice: 15.9 %) than in low-salinity lakes (sediment-to-water body: 27.1 %; water body-to-ice: 22.7 %). Seven pathogenic genera were identified in the saline lake, which could affect fish health and cause acute gastrointestinal inflammation in humans upon consumption. This study will allow us to fully understand the compositional characteristics of microbial species under different salinities and provide valuable information for subsequent saline lake management. In particular, it has important practical applications in water quality monitoring and ecological restoration.