In nature as in the host organism, bacteria rarely live alone. They form structured communities, such as colonies or biofilms, observed for example in certain chronic infections, on catheters or prostheses, as well as in the gut microbiota. This spatial organization creates complex, heterogeneous and stratified micro-ecosystems, where bacteria can grow, enter dormancy or die depending on local constraints.

In this study, the question was to understand how conditions within bacterial colonies promote the emergence of adaptive variants. To do this, 24 isolates, from an Escherichia coli colony developed on agar for three weeks were analyzed. Whole genome sequencing reveals a strong genetic diversification, with 34 distinct mutations, most of which correspond to insertions of mobile DNA elements.
 
The authors highlight an evolutionary convergence, with mutations mainly affecting transcription, stress response, metabolism and the cell envelope.  Notably, half of the isolates show alterations in the yobF-cspC operon,  making it a major target for adaptation in this context.

Transcriptomic analysis of representative mutants shows that the inactivation of cspC is accompanied by a profound remodeling of gene expression: thus, the pathways of central metabolism, biosynthesis and respiration are activated, while stress responses, in particular acid resistance, are repressed. These changes reflect a shift towards a more active metabolic state, better adapted to the environment of aging colonies, depleted in nutrients, rich in waste and subject to strong oxidative stress.

In such a hostile environment, bacteria usually activate a stress response, largely controlled by the transcriptional regulator RpoS. In the short term, this protective response promotes dormancy while limiting exchanges with the environment. In the longer term, it contributes to the loss of cell viability. The authors  show that this program is partially bypassed upon cspC inactivation.

Competition experiments between strains confirm the adaptive interest of this reprogramming: the loss of cspC confers a clear competitive advantage in this model of aging colonies.

Beyond this dominant adaptive trajectory, genome analysis also reveals mutations conferring gains in function of clinical interest, in particular resistance to β-lactams or rifamycins, despite the absence of antibiotic pressure.
 
Thus, bacterial colonies appear to be both hotspots of adaptive diversification and reservoirs of variants with potential medical relevance.