Habitat-driven taxonomic and functional differentiation of microbial communities across water and sediments in a large eutrophic shallow lake deciphered by metagenomics.

Shallow lakes in arid and semi-arid regions are vulnerable to hydrological fluctuations and nutrient loading. However, the composition and functional traits of microbial communities and their roles in mediating internal nutrient cycling across the water column and sediments remain poorly understood. Here, we applied an integrated metagenomic framework to investigate microbial community structure and metabolic potential in Wuliangsuhai Lake, a typical eutrophic shallow lake in the Yellow River Basin. Read-based taxonomic profiling revealed pronounced habitat-driven community differentiation, with significantly higher microbial diversity and evenness in sediments than in water. Both habitats were dominated by Pseudomonadota, while water was enriched in Cyanobacteriota, Actinomycetota, and Bacteroidota, and sediments in Actinomycetota, Thermodesulfobacteriota, and Bacillota. Contig-based functional profiling based on a non-redundant catalog of 9.45 million genes showed clear habitat-specific divergence. Sediments were significantly enriched in pathways associated with complex carbon degradation, reductive nitrogen transformations, and sulfur redox metabolism. Genome-resolved analysis recovered 974 non-redundant metagenome-assembled genomes spanning 54 phyla, including one putative novel lineage. Metabolic reconstruction indicated community-wide dominance of heterotrophic carbon oxidation and fermentation, while methanogenic potential was largely confined to sediments. Nitrogen cycling was biased toward reductive processes, and sulfur cycling showed strong representation of both sulfite oxidation and sulfate/sulfite reduction. Metabolic weight scores further revealed a clear functional division of labor among major microbial lineages, with Pseudomonadota contributing broadly across multiple biogeochemical processes. These results indicate pronounced sediment-water functional differentiation in eutrophic shallow lakes, with sediments primarily supporting metabolic processes related to internal nutrient turnover.