Doctor of Philosophy (PhD)


Biological Sciences

Document Type



Cultivation of microorganisms facilitates characterization of metabolism, interspecies dependencies, virus-host interactions, and other information necessary to resolve the functions and distribution of individual taxa. However, the metabolic and physiological capacities for the majority of microbes remains unresolved because of the lack of cultivated representatives for many groups limits our ability to test cultivation-independent observations. The Northern Gulf of Mexico offers a diversity of ecosystems under the continuous threat from natural and anthropogenic disturbances, yet little is known about its native bacterioplankton community. This dissertation sought to use high-throughput cultivation over three-years at six sites to isolate important coastal bacteria to uncover their role in biogeochemical cycling and ecosystem health. During the seventeen experiments, 7820 wells were inoculated, resulting in 328 repeatedly transferable cultivars. Isolates were placed into 49 monophyletic groups based on 16SR rRNA gene sequences, and represent multiple novel Species and Genera, including the first reported cultures of the SAR11 LD12 Alphaproteobacteria, OM241 Gammaproteobacteria, and acIV Actinobacteria clades. Cultivars also contribute to the expansion of cultured diversity of numerous cosmopolitan bacterioplankton such as SAR11 subclade IIIa and SAR116 Alphaproteobacteria, and BAL58, MWH-UniP1, and OM43 Betaproteobacteria. Physiological and genomic characterization of the first cultivated LD12 representative, Candidatus Fonsibacter ubiquis strain LSUCC0530, yielded novel insights into the potential metabolic capacity related to sulfur, ecotype differentiation based on temperature, as well as key gene losses associated with osmoregulation that provide a concise hypothesis for the evolution of salinity tolerance in SAR11. Comparison between the success of isolation and the relative abundance of the cultivar in the source water revealed that relative abundance was a good predictor of cultivation success for some frequently cultured clades, while it was unreliable for rarely cultivated clades such as SAR11 subclades IIIa, LD12 Alphaproteobacteria, acIV Actinobacteria, and HIMB59-type Alphaproteobacteria. We hypothesize that taxon-specific variations in dormancy and/or phenotypic variation rates among populations may affect the cultivation reliability of that clade rather than the isolation medium alone. The insights from this dissertation provide a new look at the complexity of cultivation even when providing an organism with its nutritional requirements while showcasing the importance of cultivation for answering ecological questions like the evolution of salinity tolerance.



Committee Chair

Thrash, J. Cameron