  Biofilms inhabit a range of environments, such as dental plaques or soil
micropores, often characterized by intricate, non-even surfaces. However, the
impact of surface irregularities on the population dynamics of biofilms remains
elusive as most biofilm experiments are conducted on flat surfaces. Here, we
show that the shape of the surface on which a biofilm grows influences genetic
drift and selection within the biofilm. We culture E. coli biofilms in
micro-wells with an undulating bottom surface and observe the emergence of
clonal sectors whose size corresponds to that of the undulations, despite no
physical barrier separating different areas of the biofilm. The sectors are
remarkably stable over time and do not invade each other; we attribute this
stability to the characteristics of the velocity field within the growing
biofilm, which hinders mixing and clonal expansion. A microscopically-detailed
computer model fully reproduces these findings and highlights the role of
mechanical (physical) interactions such as adhesion and friction in microbial
evolution. The model also predicts clonal expansion to be severely limited even
for clones with a significant growth advantage - a finding which we
subsequently confirm experimentally using a mixture of antibiotic-sensitive and
antibiotic-resistant mutants in the presence of sub-lethal concentrations of
the antibiotic rifampicin. The strong suppression of selection contrasts
sharply with the behavior seen in bacterial colonies on agar commonly used to
study range expansion and evolution in biofilms. Our results show that biofilm
population dynamics can be controlled by patterning the surface, and
demonstrate how a better understanding of the physics of bacterial growth can
pave the way for new strategies in steering microbial evolution.
