Abstract

The Eboliang Hu saline lakes in the hyper-arid Qaidam Basin is a high-altitude, weakly acidic hypersaline system with strong environmental gradients and limited nitrogen availability. To resolve its microbial ecology and evolutionary context, we performed genome-resolved metagenomic sequencing across four distinct habitats, reconstructing 46 medium- to high-quality metagenome-assembled genomes (MAGs) and a comprehensive gene catalog. The community shows pronounced spatial heterogeneity and is dominated by Thermodesulfobacteriota, Pseudomonadota, Bacteroidota, and archaeal lineages. Phylogenomic placement and large-scale sequence comparisons indicate that multiple dominant taxa exhibit affinity to marine- and subsurface-associated reference lineages, consistent with long-term isolation of a marine-derived ecosystem about 10-11 million years ago. Functional reconstruction reveals a distributed metabolic system in which carbon, nitrogen, and sulfur cycling are partitioned across taxa. Notably, hydrogen oxidation and arsenite oxidation are recurrent energy-producing strategies across dominant lineages, indicating redox flexibility under oligotrophic conditions. Comparative genomics further suggests lineage-specific adaptations to osmotic stress, UV exposure, and nutrient limitation. Horizontal gene transfer and phylogenetic incongruence among key metabolic genes indicate that co-evolutionary processes and gene exchange have contributed to functional innovation. These findings provide a framework for understanding microbial persistence and evolution in isolated extreme environments and offer potential analogs for extraterrestrial habitability.