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.