Fig. 3

Genomic analysis of ARGs, MGEs, and biosynthetic gene clusters (BGCs) present in 208 MAGs extracted from the first soil microcosm experiment soil samples. a A phylogenetic tree of 208 bacterial MAGs was recovered from metagenomes of all samples based on a concatenated set of 120 conserved bacterial single-copy marker genes. Inner circles are colored by phylum-level taxonomy (see source legend on the left). The different circle colors from inner to outer rings represent the number of ARGs, MGEs, and BGCs in MAGs. The tree scale shows nucleotide substitutions for each site. b The genetic structure of biosynthetic gene clusters (BGC) is associated with known antibiotic production in three Streptomyces MAGs. c Zi-Pi plot exhibiting the distribution of MAGs based on topological roles in a constructed co-occurrence network. Each node represents an MAG and the position of nodes is determined by the scatter plot of within-module connectivity (Zi) and among-module connectivity (Pi). Two Streptomyces taxa were identified as the network hubs among the community in the top right corner. Module hubs were defined with Zi > 2.5 and Pi < 0.62, network hubs were defined with Pi > 0.62 and Zi > 2.5, and connectors were defined with Pi > 0.62 and Zi < 2.5