You cannot tell a book by looking at the cover: Cryptic complexity in bacterial evolution

Area of Science:

• Microbiology and Evolutionary Biology
• Bacterial Genetics and Adaptation

Background:

• Understanding how closely related organisms evolve under strong selection pressure is crucial for predicting adaptation.
• The Growth Advantage in Stationary Phase (GASP) Escherichia coli strain offers a model to study adaptation due to its unique stress response.
• Previous studies have not fully elucidated the genomic solutions employed by GASP strains under antibiotic stress.

Purpose of the Study:

• To investigate whether genetically similar bacteria converge on common resistant genotypes or diverge to unique genomic solutions under identical, strong selection.
• To explore the fitness landscape of closely related E. coli strains under antibiotic stress.

Main Methods:

• Utilized a GASP E. coli strain and subjected it to strong selection pressure using the fluoroquinolone antibiotic ciprofloxacin in a complex ecological setting.
• Monitored evolution over a short timeframe (under 20 hours).
• Analyzed genomic changes, including missense mutations and prophage activity.

Main Results:

• The GASP strain rapidly evolved a convergent missense mutation in gyrA, near the wild-type strain's mutation site, conferring resistance.
• The GASP strain did not evolve the other three resistance mutations found in the wild-type strain.
• Evolved prophage e14 excision, which completely inhibited biofilm formation in the mutant.

Conclusions:

• Under strong antibiotic selection, E. coli exhibits both convergent evolution (specific resistance mutations) and divergent evolution (prophage excision affecting other traits).
• The evolution of antibiotic resistance in E. coli is complex and depends on the specific selection pressures.
• Fitness landscapes can exhibit 'cryptic roughness,' meaning unexpected evolutionary pathways exist even in the absence of overt stress.