Insights into microbial diversity affected by plant cover in athalassohaline ecosystem of el-hamra lake, wadi el-natrun, Egypt.

Soda lakes are multi-extreme ecosystems where high salinity and alkalinity impose strong environmental selection on microorganisms. However, fine-scale microbial patterns across aquatic-terrestrial transitions remain poorly understood. Herein, we characterized bacterial and archaeal communities in El-Hamra soda lake (Wadi El-Natrun, Egypt) along horizontal (2, 30, and 70 m from the lakeshore) and vertical (0.2, 0.3, and 0.5 m depth) gradients, including water and soils proximal to halophytic vegetation. Using 16 S rRNA gene amplicon sequencing, physicochemical measurements, and functional predictions, we quantified environmental drivers of community composition via principal component and canonical correspondence analyses. Aquatic communities were dominated by Pseudomonadota, Bacteroidota, and Cyanobacteriota (54.1, 23.1, and 18.3%, respectively), with horizontal gradients influenced by EC, Na⁺, and Cl⁻. In terrestrial communities, vegetation acted as an ecosystem engineer, generating secondary pH and Mg²⁺/Ca²⁺ gradients that promoted fine-scale heterogeneity and stratified microbial assemblages. Soils near the shore were dominated by Actinomycetota and Pseudomonadota (31.2 and 17.1%), whereas increasing vegetation diversity shifted communities toward copiotrophic phyla (e.g., Bacillota_D and Bacteroidota). Halobacteriota was abundant across aquatic and terrestrial habitats (80.5 and 94.9%, respectively). Vertically, unvegetated soils were relatively homogeneous, whereas vegetated soils exhibited pronounced stratification linked to root-driven gradients in carbon availability and inferred redox conditions. Predicted metabolic pathways suggested potential transitions from stress-tolerant, motile, and redox-balancing processes in bare soils to enhanced ion homeostasis, proteostasis, and NAD⁺-related metabolism in vegetated soils. These findings highlight soda lake margins as hotspots of microbial diversity and biogeochemical activity and provide new insights into microbial adaptation and resilience in saline-alkaline environments.