Degradation profiles of caffeine and 4-NP mesocosms (Fig. S1), relative abundance of 4-NP and caffeine degraders and degradation genes in the mesocosm from which they originated (Fig. S2), quantification of Burkholderia sp. KK1 tfdA genes in 2,4-D mesocosm I based on qPCR (Fig. S3), comparison of the tfd operons from the identified KK1 plasmid and the reference pJp4 and pM7012 plasmids (Fig. S4), complexity of 2,4-D, 4-NP and caffeine mesocosm microbial communities as assessed by Nonpareil curves (Fig. S5), shifts in microbial community composition (Fig. S6), microbial community gene content shifts (Fig. S7), comparison of microbial community compositions among 2,4-D and 4-NP and caffeine mesocosms (Fig. S8), qPCR-based 16S rRNA gene copy number counts for selected metagenomes (Fig. S9), statistics for each metagenomic data set used in this study (Table S1), statistics for each isolate genome used in this study (Table S2), OTU counts and diversity indices of 2,4-D and 4-NP and caffeine mesocosms (Table S3), qPCR primers used in the study (Table S4), and methods.
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