Zhou, JizhongMichael, Jonathan2024-05-222024-05-222024-05-10https://hdl.handle.net/11244/340389Microbes and microbial communities are ubiquitous in the environment and responsible for the cycling of carbon, sulfur, nitrogen, phosphorous, and more, while also being subject to variable conditions ranging from seasonal fluctuations to anthropogenic perturbations. As such, they have a huge capacity for change and adaptation in response to perturbation from the genome scale, in the form of mutation by natural selection, to the community scale, in the form of community compositional and functional alterations. In the subsurface of a field site in Oak Ridge, TN, USA, contaminated by uranium, nitrate, and other heavy metals, microbial communities are of unique interest due to said contamination and have been investigated continuously for over two decades. In this dissertation, I investigated the responses of microbial communities as well as individual populations of microbes to various types of perturbations likely to be encountered in the Oak Ridge subsurface. In chapter 1, I describe the consistent responses of microbial communities to two carbon source amendments across an eight-year time gap. I identified consistent stimulation of specific phylogenetic lineages following carbon amendment in both injections. This conserved response was apparent at coarse phylogeny, with homogeneous selection becoming more important in community assembly following the addition of carbon as a result. In chapter 2, I describe the response of the model sulfate reducer Desulfovibrio vulgaris Hildenborough to experimental evolution under acid stress for 1,000 generations, with 24 replicate populations of varying evolutionary history. I identified several trends in adaptation of these populations. All populations, regardless of evolutionary history, had shorter lag phases in acidic conditions after evolution. However, alterations to other growth characteristics such as carrying capacity or growth rates were history-dependent, with populations previously experimentally evolved already more adapted to acidic conditions and as such not adapting as much as populations with no previous history of experimental evolution. Moreover, we not only observed mutations in specific genes occurring in replicate populations, but those mutations were also influenced by previous evolutionary history. In chapter 3, I investigate the dynamics of small-cell-size lifestyles within the subsurface identified as a consequence of successive filtration of groundwater. I identified specific lineages preferentially found in the smaller or larger filters, reflecting a small-cell free living lifestyle or biofilm lifestyle, respectively. However, overall community composition was more reflective of the location sampled and therefore level of contamination rather than phylogeny. In chapter 4, I place these results in the context of the theories that drove some of these investigations but were problematic to empirically describe within the studies themselves. Ultimately, these results demonstrate the importance of evolutionary history at all scales. In the field, phylogeny was in important determinant of environmental preference and response to added EVO, while in the lab, histories of experimental evolution altered subsequent evolutionary change. These results add to the body of literature on historical contingency at numerous ecological scales.Attribution-NonCommercial-ShareAlike 4.0 InternationalEnvironmental microbiologyMicrobial ecologyMicrobial evolution