abstract: Hydrothermal environments are important locales for carbon cycling on Earth and elsewhere in the Universe. Below its maximum temperature (~73 °C), microbial photosynthesis drives primary productivity in terrestrial hydrothermal ecosystems, which is thought to be performed by bacterial phototrophs in alkaline systems and eukaryotic algae in acidic systems, yet has received little attention at pH values intermediate to these extremes. Sequencing of 16S and 18S rRNA genes was performed at 12 hot springs with pH values 2.9-5.6 and revealed that cyanobacteria affiliated with the genus Chlorogloeopsis and algae of the order Cyanidiales coexisted at 10 of the sites. Cyanobacteria were present at pH values as low as 2.9, which challenges the paradigm of cyanobacteria being excluded below pH 4. Presence of the carotenoid β-cryptoxanthin in only 2 sites and quantitative PCR data suggest that algae were inactive at many of the sites when sampled. Spatial, but perhaps not temporal, overlap in the habitat ranges of bacterial and eukaryal microbial phototrophs indicates that the notion of a sharp transition between these lineages with respect to pH is untenable. In sedimentary basins, biosphere-derived organic carbon is subjected to abiotic transformations under hydrothermal conditions. Benzaldehyde was experimentally evaluated as a model to assess the chemistry of aldehydes under these conditions. It was first demonstrated that gold, a traditional vessel material for hydrothermal experiments, caused catalysis of benzaldehyde degradation. Experiments in silica tubes were performed at 250, 300, and 350 °C yielding time-dependent data at several starting concentrations, which confirmed second-order kinetics. Therefore, disproportionation was expected as a major reaction pathway, but unequal yields of benzoic acid and benzyl alcohol were inconsistent with that mechanism. Consideration of other products led to development of a putative reaction scheme and the time dependencies of these products were subjected to kinetic modeling. The model was able to reproduce the observed yields of benzoic acid and benzyl alcohol, indicating that secondary reactions were responsible for the observed ratios of these products. Aldehyde disproportionation could be an unappreciated step in the formation of carboxylic acids, which along with hydrocarbons are the most common organic compounds present in natural systems. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2016

BACKGROUND: Organelle retention is a form of mixotrophy that allows organisms to reap metabolic benefits similar to those of photoautotrophs through capture of algal prey and sequestration of their plastids. Mesodinium rubrum is an abundant and broadly distributed photosynthetic marine ciliate that steals organelles from cryptophyte algae, such as Geminigera cryophila. M. rubrum is unique from most other acquired phototrophs because it also steals a functional nucleus that facilitates genetic control of sequestered plastids and other organelles. We analyzed changes in G. cryophila nuclear gene expression and transcript abundance after its incorporation into the cellular architecture of M. rubrum as an initial step towards understanding this complex system. METHODS: We compared Illumina-generated transcriptomes of the cryptophyte Geminigera cryophila as a free-living cell and as a sequestered nucleus in M. rubrum to identify changes in protein abundance and gene expression. After KEGG annotation, proteins were clustered by functional categories, which were evaluated for over- or under-representation in the sequestered nucleus. Similarly, coding sequences were grouped by KEGG categories/ pathways, which were then evaluated for over- or under-expression via read count strategies. RESULTS: At the time of sampling, the global transcriptome of M. rubrum was dominated (~58-62 %) by transcription from its stolen nucleus. A comparison of transcriptomes from free-living G. cryophila cells to those of the sequestered nucleus revealed a decrease in gene expression and transcript abundance for most functional protein categories within the ciliate. However, genes coding for proteins involved in photosynthesis, oxidative stress reduction, and several other metabolic pathways revealed striking exceptions to this general decline. CONCLUSIONS: Major changes in G. cryophila transcript expression after sequestration by M. rubrum and the ciliate's success as a photoautotroph imply some level of control or gene regulation by the ciliate and at the very least reflect a degree of coordination between host and foreign organelles. Intriguingly, cryptophyte genes involved in protein transport are significantly under-expressed in M. rubrum, implicating a role for the ciliate's endomembrane system in targeting cryptophyte proteins to plastid complexes. Collectively, this initial portrait of an acquired transcriptome within a dynamic and ecologically successful ciliate highlights the remarkable cellular and metabolic chimerism of this system.