Population dynamics during the evolution experiment
Overall, bacterial density increased through time and differed among evolution treatments (linear mixed effect model, time, \(\chi_{1}^{2}\)= 360.563, P < 0.001; treatment, \(\chi_{4}^{2}\) = 2533.771, P < 0.001; time × treatment, \(\chi_{4}^{2}\)= 74.013, P < 0.001; Figure 2). There was a significant difference in mean population density between all pairs of treatments (multiple comparisons, Table S1). The clearest effect was that evolution lines with phages had lower bacterial population sizes than those without (Figure 2). Among the three types of microcosms with phages, those with bacteria/phage immigration (BP+IBP) had the greatest bacterial densities, and those with phage-only immigration (BP+IP) had the lowest bacterial densities. For the evolution lines without phages, immigration of bacteria led to higher bacterial densities (B+IB versus B). An increase of population sizes over time was found for every treatment (separate analysis for each treatment, Table S2). While the increase in population size over time in B microcosms indicates abiotic adaptation of bacteria, that in the other evolution treatments may also have been affected by changes in the immigrant populations, or changes in the top-down control effect due to the evolution of bacterial resistance.