Emergent microscale gradients give rise to metabolic cross-feeding and antibiotic tolerance in clonal bacterial populations

Bacteria often live in spatially structured groups such as biofilms. In these groups, cells can collectively generate gradients through the uptake and release of compounds. In turn, individual cells adapt their activities to the environment shaped by the whole group. Here we studied how these processes can generate phenotypic variation in clonal populations and how this variation contributes to the resilience of the population to antibiotics. We grew two-dimensional populations of Escherichia coli in microfluidic chambers where limiting amounts of glucose were supplied from one side. We found that the collective metabolic activity of cells created microscale gradients where nutrient concentration varied over a few cell lengths. As a result, growth rates and gene expression levels varied strongly between cells close in space. Furthermore, we found evidence for a metabolic cross-feeding interaction between glucose fermenting and acetate respiring subpopulations. Finally, we found that the populations were able to survive an antibiotic pulse that was lethal in well-mixed conditions, likely due to the presence of a slow growing subpopulation. Our work shows that emergent metabolic gradients can have important consequences for the functionality of bacterial populations as they create opportunities for metabolic interactions and increase the populations tolerance to environmental stressors.