Salt–Alkali Gradient Correlates with Distinct Bacterial Communities of Salicornia europaea L. Across Soil–Root–Leaf Compartments in Guhya Salt Lake

Bacteria play a vital role in enhancing host resistance to salt–alkali stress. However, the composition and structure of bacterial communities associated with halophytes under natural high salt–alkali conditions remain poorly understood. Here, a transect comprising six sampling points (0, 9, 18, 27, 36, and 45 m) was established across a natural population of Salicornia europaea L. in Guhya Salt Lake salt–alkali soils. At each sampling site, bulk soil, rhizosphere soil, root, and leaf samples were collected for 16S rRNA gene amplicon sequencing. The pH and soil electrical conductivity (EC) significantly increased along the sampling sites establishing a distinct salt–alkali gradient. This gradient provides an ideal model for studying the ecological adaptation mechanisms of halophytes and their related microorganisms. The results showed that alpha diversity (Shannon index) of bacterial communities significantly decreased across sampling sites in bulk soil, rhizosphere soil and root, but not in leaf. Beta diversity varied significantly across sampling points in all sample types examined. Linear Discriminant Analysis Effect Size (LEfSe) identified specific microbial biomarkers (such as Halomonas spp.) for each sampling point and sample type, many of which are known salt–alkali-tolerant lineages. Random forest and correlation analysis indicated that soil chemical properties had a clear impact on these identified biomarkers. Overall, salt–alkali gradient was associated with habitat-specific microbial communities across plant compartments and certain bacterial taxa were found to be enriched in specific niches. These taxa include known salt–alkali-tolerant lineages, and may putatively contribute to host adaptation to extreme environments, which provides deeper insights into plant–microbe interactions in natural ecosystems and offers potential microbial resources for improving crop salt–alkali tolerance.