Fig. 3: Contrasting distribution patterns for diversities of bacterial taxonomy and functional genes along a pH gradient.

Diversities shown are measured by richness (S), and diversities measured by Shannon’s index (H’) are provided in Supplementary Fig. 7. a Bacterial taxonomic diversity (S.16S) increased as soil pH changed from acid to neutral. Bacterial operational taxonomic units (OTUs) are detected by 16S rRNA gene amplicon metabarcoding sequencing. b Bacterial functional diversity (S.KO) decreased as pH changed from acid to neutral. Bacterial functions are determined from the shotgun metagenome, as annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG) Ontology (KO). c Bacterial diversity of antibiotic resistance genes (S.ARG) decreased as pH changed from acid to neutral. Bacterial antibiotic resistance genes are detected based on shotgun metagenome annotated by the Resfam database. d Bacterial diversity of carbohydrate-active enzymes (S.Cazy) genes decreased as pH changed from acid to neutral. Bacterial carbohydrate-active enzymes genes are detected based on shotgun metagenome annotated by database of CAZy. e Bacterial taxonomic richness (S.16S) negatively correlated with functional gene diversity (S.KO). f–h Bacterial average genome size (AGS) positively correlated with functional diversities as measured by f S.KO, g S.ARG and h S.Cazy. Linear regression model with two-sided test was used for the statistical analysis, and adjusted R-squared was used. n = 36 samples. The grey area around the smooth line indicates the 95% confidence interval. Source data are provided as a Source Data file.