High-resolution lineage tracking maps the multi-phase evolution and adaptive potential of biofilms

Abstract

Although biofilms represent the dominant bacterial lifestyle and are major contributors to recalcitrant, treatment-resistant infections, their evolutionary dynamics at the individual lineage resolution remain poorly understood. We combine DNA barcoding-mediated lineage tracking and spatial sampling of > 100,000 lineages of Escherichia coli to characterize sequential phases of biofilm evolution quantitatively. Severe founder effects during surface colonization initially reduce the effective population size by nearly three orders of magnitude, establishing significant spatial segregation. This structure is subsequently eroded by a previously underappreciated secondary migration phase, during which cells released upon perturbation recolonize biofilms with a rate 103-fold higher than naive planktonic cells. Adaptive evolution subsequently drives specialization through mutations targeting these distinct stages of the biofilm life cycle. Under severe antibiotic bottlenecks, active secondary migration continuously resuscitates local lineage diversity, enabling the parallel emergence of resistance across hundreds of independent lineages. Once locally established, migration drives a rapid spatial spread of resistant mutants. Together, these findings reveal how spatial segregation and secondary migration shape biofilm dynamics, coupling short-term ecological resilience with long-term adaptive potential.