Fig. 4: Functional enrichment and depletion along the pH gradient.

a Network analysis of KOs detected two dominant modules, Neutral pH Module, M1 (blue), containing 2777 vertices, and Acid pH module, M2 (red), containing 4309 vertices. b, c M1 correlates positively and M2 correlates negatively with soil pH. Linear mixed-effects models with two-sided test were used for the statistical analysis. The grey lines are regression lines for each KO, and the colored line are regression line for the average of all KOs. b Neutral pH module (M1, blue), showing that soil pH is significantly, positively correlated with M1 and c Acid pH module (M2, red), showing that soil pH is significantly, negatively correlated with M2. d, e Enrichments of genes in KEGG pathways for Neutral pH (M1, Blue) and Acid pH (M2, Red) modules. Differential expression analysis with two-sided test were used for the statistical analysis. M1 functions were enriched for energy metabolism, membrane transport, citrate cycle, and glyoxylate, dicarboxylate and amino acid metabolism. M2 functions were enriched for bacterial secretion system, cell motility, xenobiotics biodegradation and metabolism, two component systems, metabolism of terpenoids and polyketides, glycan biosynthesis and metabolism, starch and sucrose metabolism, porphyrin metabolism, siderophore and lipopolysaccharide synthesis. f Association between environmental variables and specific genes involved in essential functions drawn from functional pathways (n = 36). In general, soil pH positively correlates with genes in the functions enriched in M1, and negatively correlated with that in M2. Note that associations between environmental variables and genes in specific functions are detailed in Supplementary Figs. 12–18. Source data are provided as a Source Data file.