Bacterial adaptive radiation in structured environment – bactadapt

The formidable evolutionary success of bacteria is illustrated by the fact that they inhabit almost all environmental niches on Earth. The new ecological niche is usually colonized by very small number of bacterial cells. When adaptive variants are not present among them, bacterial population will be eliminated by the natural selection. However, when the purifying selection is not very strong, population size could increase and adaptive variants can be generated thus allowing survival of the bacterial population. But adaptation is never permanent. Environments are heterogeneous in many dimensions: temporally and spatially, due to variations in the abiotic and biotic factors. Bacteria themselves constantly change their environments. One of the solutions to cope with such uncertainty is permanent multidirectional exploration of the fitness space. This evolutionary 'strategy' increases the probability of survival and of successful evolution of the bacterial populations. Causes and consequences of bacterial diversification were previously investigated in many studies. However, all these studies concerned only bacteria in the liquid environments, agitated or non-agitated, in batch cultures or in chemostats. In their natural environments, bacteria are found in structured, highly organized multicellular super-structures, such as colonies and biofilms. One prominent feature of the structured environments relative to the liquid cultures is attenuation of the clonal interference, which renders nearly impossible selective sweeps. This results in generation of much higher genetic and phenotypic diversity in structured environments. We propose to study the molecular determinants of the adaptive radiation in aging E. coli colonies. We will study spatio/temporal changes in morphology, physiology and gene expression patterns of bacterial cells inside colony using microscopy tools and flow cytometry. We intend also to sequence genomes of the interesting mutants, which will allow us to simultaneously perform genomic, transcriptomic and phenotypic analysis. This robust integrative approach will allow us to investigate the genetic basis of adaptive radiation and reconstruct its history during aging of the bacterial colony. We will also test the nature of the interaction between different mutants isolated from the same colony. Different mutants can compete for the same resources, but also some mutants can create conditions for the survival of the others. Hence, some bacteria may scavenge toxins or provide nutrients for other bacteria. This may result in the symbiotic interactions as it was described in biofilms. For this, we will reconstruct colonies using combination of different mutants derived from the same colony. If we find many mutations per genome, the identified mutations will be sequentially introduced in ancestral genome and relevant phenotypes will be studied. This will allow us to establish the nature of the epistatic interactions between different mutations. Epistasis is an important and poorly understood aspect of mutations that strongly influences the evolutionary impact of genetic variation on adaptation and fitness. Particularly important are compensatory mutations that attenuate fitness loss caused by another mutation. This biological phenomenon has important implications because it allows mutant cell to reach adaptation peak that is not accessible to the ancestral genotype. After characterization of the genetic basis of adaptive radiation in laboratory strain, we will study presence of these mutations in E. coli commensal and pathogenic strains isolated from different ecological niches. For this, we posses a large collection of E. coli natural isolates. In addition, we will test how different genotypes constrain adaptive radiation using E. coli natural isolates, whose genomes have been sequenced. These questions are of general interest to evolutionary biology, because it lends insight into the relative importance of chance, historical contingency, and natural selection in shaping the genetic outcome of adaptation. The simplicity with which both bacteria and environments can be manipulated in the laboratory allows for explicit tests of all above-mentioned hypotheses.