Fig. 4.

Relative abundance of strains and identity of strains in which plasmid RP4 was detected using epicPCR at the end-point of 40-day microcosm experiment. Based on the results from preliminary phenotypic screening, plasmid detection was performed separately for four replicate populations for the antibiotic treatment subtreatments (red circles) and for a pool of the four replicate populations for antibiotic-free subtreatments (red dashed line ovals). Strains are clustered in the heat map according to the phylogenetic tree on the left. The symbol size in the tree represents bootstrap values in the range 0.23–0.999. The plasmid donor strain Escherichia coli K-12 JE2571(RP4), present at low abundance, occasionally appears as negative for the plasmid; this is not taken to indicate absence of the plasmid but rather failure to exceed the conservative cutoff value used for plasmid presence in the epicPCR analysis pipeline to minimize the risk of false positives