Metagenomic insights into the structure and function of the soil microbiome in typical ecological regions across China

Abstract The structure and functioning of soil microbiomes in the eco-regions of China remain largely undetermined. Thus, we report on a comprehensive, continental-scale metagenomic study of topsoil samples (0–20 cm depth; n = 41 locations) collected from six eco-regions of China. A total of 54.7 million non-redundant genes were deposited in our metagenomic libraries and could be assigned to 105 taxonomic phyla, consisting of 82 bacterial, 12 archaea, 10 eukaryota phyla, and 1 virus phylum. Of these, the bacteria as represented by Actinobacteria , Proteobacteria and Acidobacteria dominated the metagenomic libraries across all samples. A total of 76 differentially abundant KEGG pathways spanning the six eco-regions could be classified into 23 classes, these chiefly concerning carbohydrate metabolism, amino acid metabolism, xenobiotics biodegradation and metabolism, energy metabolism, metabolism of cofactors and vitamins, replication and repair, and lipid metabolism. According to the KEGG database, we identified six CAZyme-encoding genes ( GHs , GTs , PLs , CEs , AAs , and CBMs ) involved in the decomposition and biosynthesis of SOC (soil organic carbon); 41 KOs of seven clusters—nitrogen (N) fixation, nitrification, denitrification, DNRA , ANRA , N transport, and organic N metabolism—encoding enzymes critical for N cycling; and 21 KOs of three clusters ( ASR , DSR , and thiosulfate oxidation) encoding enzymes crucial to sulfur (S) cycling, from all samples across the six regions. In addition, the functional gene abundance related to the cycling of SOC, N, and S were associated with the NDVI , soil properties, and climatic variables. Among these, SOC (both for SOC and S cycling) and MAP (for N cycling) as being two dominant drivers on the functional gene abundance distribution pattern. Altogether, these findings advance our understanding of the soil microbial functional characteristics of typical eco-regions across China.