New Tools and Cultivation Protocols for Autotrophic and Diazotrophic Non-model Bacteria

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dc.contributor.committeeMemberThyer, Rossen_US
dc.contributor.committeeMemberVerduzco, Rafaelen_US
dc.contributor.committeeMemberKampouri, Stavroulaen_US
dc.creatorAlameri, Abdulazizen_US
dc.date.accessioned2024-08-30T18:11:50Zen_US
dc.date.created2024-08en_US
dc.date.issued2024-07-29en_US
dc.date.submittedAugust 2024en_US
dc.date.updated2024-08-30T18:11:50Zen_US
dc.descriptionEMBARGO NOTE: This item is embargoed until 2030-08-01en_US
dc.description.abstractAnthropogenic climate change necessitates a societal shift toward sustainable manufacturing practices. The chemical and polymer industry, which accounts for a fifth of the global CO2 emissions, has been slow to adapt due to factors such as economic pressures and risk aversion. Biomanufacturing, which usually relies on microorganisms such as bacteria, offers a promising alternative by leveraging native biological pathways that can perform complex chemistry without the requirement for extremes of temperature and pressure, often needed in traditional chemical processes. Beyond the model bacterium E. coli, the diverse metabolisms of environmental bacteria can be harnessed to produce a wide range of chemicals, with some bacteria capable of directly fixing atmospheric CO2 (autotrophs) and N2 (diazotrophs) when provided with a source of reducing power. Biomolecular engineering and ‘domestication’ of these non-model bacteria is required to make sustainable biomanufacturing a reality. However, these efforts are hindered by a lack of genetic tools. Here, I present efforts to (i) address the challenges of introducing recombinant DNA into environmental Mycobacteriales, an industrially relevant yet largely genetically intractable clade of bacteria, (ii) investigate the metabolism of these bacteria under conditions of extreme nutrient limitation and isolate novel CO2 fixing species, and (iii) develop a modular DNA assembly framework for the model diazotroph Azotobacter vinelandii. From this work, we have developed a suite of new genetic tools which function in several Mycobacteriales genera, characterized a novel Gordonia species with potential autotrophic metabolism, and identified the presence of multiple restriction-modification systems as a dominant barrier to genetic manipulation and future biomolecular engineering efforts in these species.en_US
dc.embargo.lift2030-08-01en_US
dc.embargo.terms2030-08-01en_US
dc.format.mimetypeapplication/pdfen_US
dc.identifier.citationAlameri, Abdulaziz. New Tools and Cultivation Protocols for Autotrophic and Diazotrophic Non-model Bacteria. (2024). Masters thesis, Rice University. https://hdl.handle.net/1911/117810en_US
dc.identifier.urihttps://hdl.handle.net/1911/117810en_US
dc.language.isoengen_US
dc.rightsCopyright is held by the author, unless otherwise indicated. Permission to reuse, publish, or reproduce the work beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.en_US
dc.subjectMycobacterialesen_US
dc.subjectgenetic toolkiten_US
dc.subjectRhodococcusen_US
dc.subjectGordoniaen_US
dc.subjectAzotobacteren_US
dc.subjectgenetic tractabilityen_US
dc.subjectgenetic toolen_US
dc.subjectautotrophyen_US
dc.subjectdiazotrophyen_US
dc.titleNew Tools and Cultivation Protocols for Autotrophic and Diazotrophic Non-model Bacteriaen_US
dc.typeThesisen_US
dc.type.materialTexten_US
thesis.degree.departmentChemical and Biomolecular Engineeringen_US
thesis.degree.disciplineEngineeringen_US
thesis.degree.grantorRice Universityen_US
thesis.degree.levelMastersen_US
thesis.degree.nameMaster of Scienceen_US
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