Diversity Generation in Evolving Microbial Populations

Organisms have evolved and diversified since the beginning of life. Although, generation and maintenance of diversity within ecosystems has been a central concern in ecology and evolutionary biology, little is known of the evolutionary processes driving diversification. Especially, diversification in relation to chronic infection is a major concern as high population diversity has been predicted to result in survival and persistence of the infecting microbe.
Therefore, understanding within-host dynamics and population diversification is necessary for optimal diagnosis and therapeutic treatment.
Chronic Pseudomonas aeruginosa infections in the airways of patients with cystic fibrosis (CF) offer opportunities to study bacterial evolution and adaptation in natural environments. Significantly phenotypic and genomic changes of P. aeruginosa have been observed during chronic infection. While P. aeruginosa diversity has been documented in contemporary respiratory specimens, it is less clear to what extent within-patient diversity contributes to the overall population structure and whether the population is geographically or homogeneously distributed throughout the airways.
The focus of this thesis has been to get a better understanding of how bacterial populations adapt to new, complex and heterogeneous environments with multiple selective pressures over long periods, and to analyse diversification during this adaptation. Using the P. aeruginosa chronic infection as a model system, and by combining bacterial genome sequencing, phenotypic profiling and unique sampling materials which included clonal bacterial isolates sampled for more than 4 decades from chronically infected CF patients, we were able to investigate the diversity generation of the clinical important and highly successful P. aeruginosa DK1 clone type during chronic airway infection in CF patients.
We show here that diversification of P. aeruginosa DK1 occurs through the emergence of coexisting subpopulations with distinct phenotypic and genomic features and demonstrate that this diversification was a result of niche specialization as each subpopulation colonized separate geographical niches. This highly complex population diversity was observed to be stably maintained during long-term evolution. Before diversification of the DK1 clone, a regulatory mutation was found to be fixed in the population causing alteration of multiple phenotypes representing the chronic stage phenotype.
Often chronic CF infections are polyclonal and therefore we investigated the population dynamics in a patient polyclonal infected with both DK1 and DK2. We demonstrated that diversification was affected by the presence of other clones; interaction between the two clones resulted in horizontal DNA transfer that contributed to the observed population diversity by creating a novel strain DK1/2 found to persist in the CF airways.
These data indicate that spatial compartmentalization and transfer of DNA between infecting microbes can cause generation and maintenance of population diversity of infecting pathogens. Furthermore, fine-tuning of global regulatory networks by modification of transcriptional regulators has fundamental roles in successful adaptation of P. aeruginosa to the CF environment.