The carboxylate biofuels platform (CBP) involves the conversion of cellulosic biomass into carboxylate salts by a mixed microbial community. Chemical engineering approaches to convert these salts to a variety of fuels (diesel, gasoline, jet fuel) are well established. However, prior to initiation of this project, little was known about the influence of inoculum source on platform performance. The studies in this dissertation test the hypothesis that microbial communities from particular environments in nature (e.g. saline and/or thermal sediments) are pre-adapted to similar industrial process conditions and, therefore, exhibit superior performances. We screened an extensive collection of sediment samples from extreme environments across a wide geographic range to identify and characterize microbial communities with superior performances in the CBP. I sought to identify aspects of soil chemistry associated with superior CBP fermentation performance. We showed that CBP productivity was influenced by both fermentation conditions and inocula, thus is clearly reasonable to expect both can be optimized to target desired outcomes. Also, we learned that fermentation performance is not as simple as finding one soil parameter that leads to increases in all performance parameters. Rather, there are complex multivariate relationships that are likely indicative of trade-offs associated within the microbial communities. An analysis of targeted locus pyrosequence data for communities with superior performances in the fermentations provides clear associations between particular bacterial taxa and particular performance parameters. Further, I compared microbial community compositions across three different process screen technologies employed in research to understand and optimize CBP fermentations. Finally, we assembled and characterized an isolate library generated from a systematic culture approach. Based on partial 16S rRNA gene sequencing, I estimated operational taxonomic units (OTUs), and inferred a phylogeny of the OTUs. This isolate library will serve as a tool for future studies of assembled communities and bacterial adaptations useful within the CBP fermentations. Taken together the tools and results developed in this dissertation provide for refined hypotheses for optimizing inoculum identification, community composition, and process conditions for this important second generation biofuel platform.

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Of concern in this research were the ecological parameters associated with the establishment of a model invasive plant species, Imperata cylindrica, across a scale of ecological organization. Specifically, the study addressed the species’ ability to: differentially respond to abiotic and biotic constraints during seedling establishment, exhibit a novel underground competitive interference mechanism, and alter the decomposition dynamics in newly invaded ecosystems. Finally, the last portion of the research was centered around creating a predictive habitat model that will provide information on the most important variables responsible for creating habitat for this species. The population level seedling study indicated that soil characteristics and light availability play a significant role in seedling establishment. There were large trends in biomass allocation attributable to soil type with seedlings performing best in high nutrient soils representative of the Mississippi Alluvial Valley physiographic region. I. cylindrica seedlings also showed a positive response to increased seedling density during the initial stages of seedling establishment. The community level research examining a hypothesized novel interference mechanism deployed by I. cylindrica showed a significant and robust pattern of I. cylindrica damaging its own belowground tissue more often than that of its surrounding neighbors. Therefore, it is highly unlikely that I. cylindrica gains a competitive advantage by exposing the native plant assemblage to pathogen invasion (via ruptured tissue) as the plant would expose itself to these pathogens (to which it is evolutionarily naive) at much higher volumes. The ecosystem level examination of this globally important invasive species indicated that I. cylindrica invasion into native systems will significantly accelerate ambient rates of decomposition. Furthermore, fungal community composition in invaded areas was drastically altered as well as bacterial community functional activity in relation to several key enzymes responsible for the decomposition of plant tissue which were produced more abundantly in invaded areas.The landscape-scale analyses and modeling work validated decades of anecdotal evidence and indicated that anthropogenic disturbance factors associated with road maintenance and construction (soil disturbance and vegetation removal) are the principal factors responsible for creating habitat suitable for invasion by this species.