Chairperson, Graduate Committee: Ross CarlsonHunt, Kristopher AllenJames P. Folsom, Reed L. Taffs and Ross P. Carlson were co-authors of the article, 'Complete enumeration of elementary flux modes through scalable, demand-based subnetwork definition' in the journal 'Bioinformatics' which is contained within this thesis.Ashley E. Beck was an author and Hans C. Bernstein and Ross P. Carlson were co-authors of the article, 'Interpreting and designing microbial communities for bioprocess applications, from components to interactions to emergent properties' in the journal 'Biotechnology for biofuel production and optimization' which is contained within this thesis.Ryan deM. Jennings, William P. Inskeep and Ross P. Carlson were co-authors of the article, 'Stoichiometric modeling of assimilatory and dissimilatory biomass utilization in a microbial community' in the journal 'Environmental microbiology' which is contained within this thesis.Ryan deM. Jennings, William P. Inskeep and Ross P. Carlson were co-authors of the article, 'Multiscale analysis of autotroph-heterotroph interactions in a high-temperature microbial community' submitted to the journal 'The International Society for Microbial Ecology journal' which is contained within this thesis.Natasha D. Mallette, Brent M. Peyton and Ross P. Carlson were co-authors of the article, 'Theoretical and practical limitations of hydrocarbon production for a cellulolytic, endophytic filamentous fungus' submitted to the journal 'Metabolic engineering' which is contained within this thesis.2018-07-102018-07-102016https://scholarworks.montana.edu/handle/1/14626All life requires the acquisition and transformation of nutrients and energy, driving processes from cellular nutrient flow to planetary biogeochemical cycling. However, the organisms and communities responsible for these processes are often uncultivable and too complex to observe directly and understand. Stoichiometric modeling, a systems biology approach, analyzes the reactions in an organism and incorporates data from multiple sources to extract biologically meaningful parameters, such as theoretical limits of conversion and yields of a metabolism. These limits and yields quantify relationships between organisms to establish governing principles, from resource requirements to community productivity as a function of population composition. The presented work expanded the stoichiometric modeling algorithm and identified fundamental principles that govern nutrient and energy transfer associated with heterotrophy, community composition, and intracellular compartmentalization. A scalable routine capable of analyzing complex metabolic networks by dividing them into tractable subnetworks was demonstrated for a eukaryotic diatom. The metabolic model contained approximately two billion routes through the network and established an international benchmark for elementary flux mode analysis. Additionally, a heterotrophic archaeon was examined for the resource requirements while consuming 29 different forms of biomass derived dissolved organic carbon. These resource requirements and limitations establish a basis to analyze heterotrophy with regard to the limiting nutrient in a variety of systems. The resulting resource requirements of heterotrophy were incorporated into a community where an iron oxidizing autotroph was hypothesized to be the primary source of carbon and energy. Analysis of the community model and in situ measurements of iron and oxygen utilization indicated additional electron donors were required to account for the observed acquisition of nutrients in some communities. Finally, limits and resource requirements for fungal production of hydrocarbons were identified as a function of carbon and energy partitioning using simulated genetic modifications, providing context regarding endophytic production of bioactive molecules for host resistance as well as endophyte capacity as a petroleum producing alternative.enMicroorganismsBiomass energyMetabolismStoichiometrySystems biologyDissertationCopyright 2016 by Kristopher Allen Hunt