Salinity-adapted and core microbiota along the soil salinity gradients encircling the Tarim Basin

Soil salinization affects nearly one-tenth of global drylands and imposes strong environmental filters on microbial communities. The Tarim Basin in Xinjiang, China, is one of the world's largest inland basins and an extreme saline-arid ecosystem, yet a basin-scale understanding of its microbiota remains lacking. In this study, we collected 132 soil samples along a salinity gradient spanning more than 3,000 km encircling the Tarim Basin. By combining amplicon sequencing with measurements of soil physicochemical properties, we aimed to unravel the salinity-adapted microbiota and core microbial taxa characteristic of this extreme environment.

Our results showed that bacterial communities, rather than fungal communities, were strongly shaped by soil salinity. Extremely saline soils exhibited reduced bacterial diversity and were enriched in halophilic and halotolerant taxa, including Natronomonas, Salinimicrobium, Stenotrophomonas, Salinibacter, Halorussus, and Halomicrobium. In contrast, taxa such as Arthrobacter, Rubrobacter, Rubellimicrobium, and Fusarium declined with increasing salinity. Soil cation concentrations (Na⁺, K⁺, Ca²⁺, Mg²⁺), major anions (Cl^-, SO₄^2-), and electrical conductivity all increased significantly along the salinity gradient. Despite this strong environmental filtering, we identified a set of potential core microbiota consistently present across all soils, dominated by Halomonas, Salinimicrobium, Natronomonas, Rubrobacter, and members of the Palleronia-Pseudomaribius group. Their persistent occurrence across the basin suggests that these taxa play key roles in sustaining ecosystem functions within the extreme saline-arid environments of the Tarim Basin.

Our basin-scale analysis reveals that soil salinity significantly contributes to microbial community assembly in the Tarim Basin, selecting for specialized halophilic and halotolerant taxa while reducing overall bacterial diversity. The discovery of core microbiota with known salt-adaptation mechanisms highlights the presence of a stable microbial backbone across heterogeneous saline landscapes. These findings provide new ecological insights into how extreme salinity shapes microbiome structure and identify candidate microbial groups potentially contributing to ecosystem stability and plant stress resilience in arid saline environments.