Fig. 3

Metabolic comparison of selected functional genes. A Metabolic comparison between freshwater lakes, brackish lakes, and saline lakes on the Tibetan Plateau. The relative abundance of selected functional genes is normalized using the average TPM of 27 universal single-copy KOs and is shown using a heatmap with a color gradient. Gene functions and names are shown on the left panel, and their relative abundance in lake samples is shown using a heatmap with a blue-to-red color gradient. Gene enrichment analysis is performed between freshwater and saline lakes using STAMP, and gene enriched in freshwater and saline lake microbiomes (FDR adjusted p value < 0.01) are colored in green and blue, respectively. Genes without enrichment patterns are colored in black. The gene rbcL, amoA, amtB, dsrA, and rdsrA refer to type I/II rbcL for Calvin cycle (Fig. S8A), copper membrane monooxygenases specific for ammonia oxidation (Fig. S8B), high-affinity ammonium transporter (Fig. S8C), reductive dsrA for sulfite reduction, and oxidative dsrA for sulfide oxidation, respectively (Fig. S8D). DNRA, dissimilatory nitrate reduction to ammonium. B, C Relative contribution of different taxonomic groups in freshwater lake (B) and saline lake microbiomes (C). The proportions of relative abundance among eleven taxonomic groups are shown using a heatmap with a white-to-red color gradient. Proportions of > 5% are given with actual numbers for better visualization. Specifically, three putative amoA genes are classified as β-Proteobacteria-type amoA, while the corresponding MAGs are affiliated with γ-Proteobacteria and Firmicutes (Fig. S8B). These genes are located on short contigs with lengths of 2.3, 3.3, and 7.8 Kb, respectively, and may be sourced from binning errors. Thus, these genes are considered to belong to β-Proteobacteria in the heatmap plot