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

Biofilms, the primary bacterial habitat, play a crucial role in persistent, antibiotic-resistant infections. However, the intricate evolutionary processes occurring at the individual lineage level have remained largely unexplored. To address this knowledge gap, researchers combined DNA barcoding to track lineage-specific genetic markers with spatial sampling of 100,000 E. coli lineages.

Their findings reveal distinct evolutionary phases in biofilm development. Initially, severe founder effects caused by surface colonization reduced the effective population size by nearly 1,000-fold, leading to pronounced spatial segregation. This structured environment was later disrupted by a secondary migration phase, where cells released during disturbances recolonized biofilms at a rate 1,000 times higher than their initial planktonic counterparts.

This secondary migration phase proved pivotal, as it enabled adaptive evolution through mutations tailored to specific biofilm life cycle stages. Under extreme antibiotic conditions, the active secondary migration continuously replenished lineage diversity, facilitating the simultaneous emergence of resistance traits within hundreds of independent lineages.

Once established locally, migration facilitated a rapid spatial spread of these antibiotic-resistant mutants. The study provides a comprehensive understanding of how spatial segregation and secondary migration intricately interplay to shape biofilm dynamics, bridging the gap between short-term ecological resilience and long-term adaptive potential.