Fig. 1. Mutations in a phage repressor region recurrently drives productive infection of the phage-plasmid.

a Productive switch of a phage-plasmid in Tritonibacter mobilis A3R06 was observed after ~40 generations of serial-dilution growth (red). A deletion mutation (11736: GA→G, purple bar) rapidly increased to ~50% relative genotypic frequency within one dilution cycle, before the increase slowed down in the next dilution cycle. A second mutation (11853: C→T, yellow bar) was observed in the last dilution cycle. Planktonic bacterial culture became highly clumpy after the productive switch, as indicated by the sharp decrease in OD600 (blue). For eco-evolutionary trajectories for the other 8 populations temporally-tracked with genomic sequencing, see Fig. S4 and Table S1. b Transmission electron microscope image of the phage-plasmid particle. Imaging was performed for seven times with biological triplicates, all yielding similar results. c Differential expression of phage-plasmid genes before and after observing the mutation. Genes related to phage production were significantly upregulated after the productive switch, in particular the phage structural genes and the phage lysozyme gene. Expression of genes that are housekeeping for plasmid replication and stability were only increased because of copy-number increase of genes. P values are calculated based on Wald test and are adjusted by the Benjamini-Hochberg (BH) procedure. d All 21 mutations identified in 15 independent lines of populations were within a short ~1000 bp region encoding a C1-type phage repressor (orange arrow). Most of mutations are insertions or deletions (purple diamond). Details of these mutations are listed in Table S1. Source data for Figs. 1a, 1c and 1d are provided in the Source Data file.