Supervisor's Foreword; Parts of this thesis have been published in the following journal articles:; Publications and Conferences; Journal Publications; Conference Proceedings; Acknowledgements; Declaration; Contents; Nomenclature; List of Figures; List of Tables; 1 Introduction; 1.1 Methane, a Useful Fuel; 1.1.1 Production Routes; 1.1.1.1 Industrial; 1.1.1.2 Biological; 1.2 M. maripaludis S2, an Interesting Biocatalyst; 1.3 In Silico Metabolic Modeling; 1.4 Scope of the Thesis; 1.4.1 Objectives; 1.4.2 Organization; References; 2 Literature Review; 2.1 CO2 Fixing Microbes

2.2 M. maripaludis-A CO2 Fixer2.2.1 Taxonomy, Cell Structure, and Cultivation; 2.2.2 Metabolic Processes in M. maripaludis; 2.2.2.1 Methanogenesis; 2.2.2.2 Acetyl-CoA Synthesis; 2.2.2.3 Pyruvate Synthesis; 2.2.2.4 Glycolysis/Gluconeogenesis and Glycogenolysis/Glyconeogenesis; 2.2.2.5 Tri-Carboxylic Acid (TCA) Cycle; 2.2.2.6 Pentose Phosphate Pathway (PPP); 2.2.2.7 Nitrogen Metabolism; 2.2.2.8 Amino Acid Metabolism; 2.2.2.9 Nucleotide Biosynthesis; 2.2.3 Molecular Biology Tools; 2.2.3.1 Selectable Markers; 2.2.3.2 Shuttle Vectors; 2.2.3.3 Integrative Plasmid and Gene Replacement

2.2.3.4 Markerless Mutagenesis2.2.4 Potential Applications; 2.2.4.1 Wastewater Treatment; 2.2.4.2 Carbon Capture and Conversion; 2.2.4.3 Methane from Renewable Energy; 2.2.4.4 Hydrogen Production; 2.2.4.5 Other Applications; 2.3 Genome-Scale Engineering; 2.3.1 Systems Biology Models: Kinetic Versus Stoichiometric; 2.3.1.1 Constraints-Based Modeling; 2.3.1.2 Simulation Tools; 2.3.1.3 Applications; 2.3.2 iMM518: A Genome-Scale Model; 2.4 Microbial Electrolysis Cells (MECs); References; 3 A Genome-Scale Metabolic Model of M. maripaludis S2 for CO2 Capture and Conversion to Methane

3.1 Introduction3.2 Materials and Methods; 3.2.1 Reconstructing Metabolic Network; 3.2.2 Genome-Scale Metabolic Model; 3.2.3 Experimental Data; 3.2.4 Gene Essentiality/Flux Variability Analyses; 3.3 Results and Discussion; 3.3.1 Reconstructed Metabolic Network; 3.3.2 Model Validation; 3.3.3 Minimal Media; 3.3.4 Gene Essentiality and Flux Variability Analyses; 3.3.5 Formate as Alternate Carbon and Hydrogen Substrate; 3.3.6 Effect of Nitrogen Sources; 3.3.7 Novel Strains for Enhanced Methanogenesis; 3.3.8 Comparison with Other Methanogens; 3.4 Conclusions; References

4 Flux Measurements and Maintenance Energy for CO2 Utilization by M. maripaludis4.1 Introduction; 4.2 Materials and Methods; 4.2.1 Chemicals and Gases; 4.2.2 Strain and Medium; 4.2.3 Batch Cultivation; 4.2.4 Analytical Procedures; 4.2.5 Cell Growth Measurements; 4.2.6 Calculation of Extracellular Fluxes; 4.2.7 Parameter Estimation for iMM518; 4.3 Results and Discussion; 4.3.1 Cell Growth; 4.3.2 Extracellular Fluxes; 4.3.3 GAM, NGAM, and ATP Gain; 4.3.4 Intracellular Fluxes; 4.3.5 Effects of Amino Acids and Vitamins from iMM518; 4.4 Conclusions; References