Studying how bacterial strains diverge over time and how divergence leads to specialization to new environmental niches is important for understanding the dynamics of environmental communities. I studied these questions using a collection of 46 Shewanella baltica strains isolated over a period of 12 years from the Gotland Deep in the central Baltic Sea, which is characterized by the presence of a stable redox gradient over 140 m in depth. I used several experimental and computational methods to explore the genetic and phenotypic profiles of these strains and determined whether these profiles could be explained by the conditions at their sites of isolation. Specifically, genotyping by both single gene-based and multi-locus sequence typing (MLST) indicated specialization across the redox gradient and over time. Versatility in anaerobic respiration, for example, the ability to respire thiosulfate, was correlated with the redox gradient, while versatility in carbon source utilization was correlated with specialization over time. Comparative Genomic Hybridization (CGH) revealed a heterogeneous distribution of genes across S. baltica genomes, where genes potentially important for specialization both over the redox gradient and over time were identified. Further mechanistic investigation of their evolution provided evidence of horizontal gene transfer in the S. baltica genomes, whereas predicted recent recombination among strains from two lineages was also supported by this larger dataset. The differential fitness of S. baltica strains under particular redox conditions was determined from competition assays, where competed strains were labeled with gfp and cfp and the population dynamics during competition was measured by flow cytometry. The two competed genotypes were separated by flow cytometry and their transcriptomes analyzed by RNA-Seq which showed differential expression in response to the nitrate condition as well as to the competitor strain. By integrating these different types of information, I determined that specialization has occurred in this S. baltica population both over the redox gradient and over time, and that the genomic plasticity as well as the extensive gene exchange has facilitated the specialization process. Overall, I used S. baltica as a model to provide insights into fundamental questions about the interactions among bacterial genomics, physiology, and habitat (ecology).
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