Dunfield, PeterTran, Triet M2023-05-112022-12-07Tran, T. M. (2022). From genomic data to metabolism of an uncultured thermophilic bacterium S2R-29 and a hydrocarbon degrader Solimonas aquatica (Master thesis). University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca .http://hdl.handle.net/1880/116463https://dx.doi.org/10.11575/PRISM/dspace/41307This thesis investigated metabolic functions through in-depth analyses of two bacterial genomes from two distinct environments: an uncultured thermophilic bacterium from Dewar Creek geothermal spring in British Columbia, Canada and Solimonas aquatica from freshwater in Taiwan.Twenty-two SAGs (Single-celled amplified genomes) of S2R-29 were retrieved from the source of Dewar Creek hot springs. S2R-29 is known to have extremely low GC content (24.23%) and predicted to be a facultative anaerobic bacterium. Based on phylogenetic trees constructed from full-length 16S rRNA gene sequences, the closest relatives to S2R-29 are members of the phyla Candidatus Calescamantes and Candidatus Fervidibacter. Metabolic analysis revealed 4 hypothesized energy sources for S2R-29: Cellobiose, glycerol, proteins, and DNA. Low GC content in S2R-29 might be directly related to the DNA degradation process and immediate environment surrounding the bacteria. S2R-29 is most likely a facultative anaerobe capable of twitching motility. The optimal growth temperature of S2R-29 was predicted to be at 65 – 70oC and appears to be almost exclusively present in Dewar Creek hot springs.Copper membrane monooxygenases are usually encoded by three genes found in xmoCAB operon, which is also known as pmoCAB in methanotrophs. Four sets of primers were designed to amplify the members of two phylogenetic clusters named tailing group 1 and 3. Three out of four primer pairs successfully amplified xmoA genes. Solimonas aquatica is the only xmoA-carrying bacterium from tailing group 1 with a cultured representative. Culture-based studies were therefore performed on Solimonas aquatica, which carries two different copies of xmoCAB. Solimonas aquatica cultures were grown and monitored for 30 to 60 days under various carbon sources including glucose, methane, propane, and butane in medium 10D. Gas chromatography and optical density were able to confirm the growth of Solimonas aquatica onglucose and butane only. Optical density of Solimonas aquatica cultures did not increase when cultured using butane-related intermediates aside from 1-butanol, in which the bacteria showed almost similar trend compared to butane-grown culture. However, based on the presence of genes encoding copper membrane monooxygenases and soluble di-iron monooxygenases, the exact mechanism and the enzyme responsible for butane-related oxidation is still unknown.EnglishMicrobiologyEnvironmental microbiologyExtremophileUncultured bacteriaHydrocarbon degraderBiological Sciencesmaster thesis