Measurement of bacterial resistance
The resistance of bacteria to phages was measured for the coevolution lines (BP, BP+IP, and BP+IBP) from transfer 8 and 20. Bacterial resistance to within-microcosm phages was determined by streaking 20 independent bacterial colonies across a line of 20 µL phages pre-streaked on agar plates. Specifically, bacterial colonies were isolated by plating dilutions on KB agar plate and incubating for 48 h, grown in 96-well plates at 28°C for 48 h, and then reconditioned at 10°C for 48 h before streaking. Phage samples were extracted using chloroform as described above. A bacterial colony was scored as resistant if there was no inhibition of growth after incubated at 10°C for 72 h and population-level bacterial resistance was calculated as proportions of resistant bacterial colonies. We also measured resistance of bacterial populations from those microcosms against phages from the source habitats (SBP), where each source-habitat phage population was paired with one bacterial population from each of the following evolution regime: BP, BP+IP, BP+IBP.