Doctor of Philosophy / Agronomy / Charles W. Rice / Substitution of cellulosic biofuel in place of gasoline or diesel could reduce greenhouse gas (GHG) emissions from transportation. However, emissions of nitrous oxide (N₂O) and changes in soil organic carbon (SOC) could have a large impact on the GHG balance of cellulosic biofuel, thus there is a need to quantify these responses in cellulosic biofuel crops. The objectives of this study were to: (i) measure changes in yield, SOC and microbial communities in potential cellulosic biofuel cropping systems (ii) measure and characterize the temporal variation in N₂O emissions from these systems (iii) characterize the yield and N₂O response of switchgrass to N fertilizer and to estimate the costs of production. Sweet sorghum, photoperiod-sensitive sorghum, and miscanthus yielded the highest aboveground biomass (20-32 Mg ha⁻¹). The perennial grasses sequestered SOC over 4 yrs, while SOC stocks did not change in the annual crops. Root stocks were 4-8 times higher in the perennial crops, suggesting greater belowground C inputs. Arbuscular mycorrhizal fungi (AMF) abundance and aggregate mean weight diameter were higher in the perennials. No consistent significant differences were found in N₂O emissions between crops, though miscanthus tended to have the lowest emissions. Most N₂O was emitted during large events of short duration (1-3 days) that occurred after high rainfall events with high soil NO₃₋. There was a weak relationship between IPCC Tier 1 N₂O estimates and measured emissions, and the IPCC method tended to underestimate emissions. The response of N₂O to N rate was nonlinear in 2 of 3 years. Fertilizer induced emission factor (EF) increased from 0.7% at 50 kg N ha⁻¹ to 2.6% at 150 kg N ha⁻¹. Switchgrass yields increased with N inputs up to 100-150 kg N ha⁻¹, but the critical N level for maximum yields decreased each year, suggesting N was being applied in excess at higher N rates. Yield-scaled costs of production were minimized at 100 kg N ha-1 ($70.91 Mg⁻¹). Together, these results show that crop selection and fertilizer management can have large impacts on the productivity and soil GHG emissions biofuel cropping systems.

Master of Science / Department of Biological & Agricultural Engineering / Donghai Wang / Bioprocessing is widely involved in our daily life and significantly relative to the general public because bio-products are widely used in eating, clothing, and living as well as transportation. Due to the public concern of the environmental deterioration, limited fossil fuel resources, and energy price volatility, biofuel as a clean, safe and sustainable energy needs to be developed in response to this growing concern. Sorghum, an important dryland crop, represents a renewable resource currently grown on 8 million acres throughout the United States. Due to climate variability and the continuous decline of water resources, utilization of dryland to grow sorghum and forage sorghum is critically important in order to ensure available energy resources and sustainable economic development. The objectives of this research were 1) to study the impact of deficit irrigation strategies on sorghum grain attributes and bioethanol production, and 2) to evaluate the potential fermentable sugar yield of pedigreed sorghum mutants. Results showed that average kernel weight and test weight of grain sorghum increased as irrigation capacity increased, whereas kernel hardness index decreased as irrigation capacity increased. Starch content increased as irrigation level increased and protein contents decreased as irrigation level increased. Irrigation also had a significant effect on starch properties and bioethanol yield. Sorghum mutants had a significant effect on chemical composition and physical properties such as glucan content, glucan mass yield, ash content, and high heating value, and also had a significant effect on fermentable sugars yield and enzymatic conversion efficiency.

abstract: To date, the production of algal biofuels is not economically sustainable due to the cost of production and the low cost of conventional fuels. As a result, interest has been shifting to high value products in the algae community to make up for the low economic potential of algal biofuels. The economic potential of high-value products does not however, eliminate the need to consider the environmental impacts. The majority of the environmental impacts associated with algal biofuels overlap with algal bioproducts in general (high-energy dewatering) due to the similarities in their production pathways. Selecting appropriate product sets is a critical step in the commercialization of algal biorefineries. This thesis evaluates the potential of algae multiproduct biorefineries for the production of fuel and high-value products to be economically self-sufficient and still contribute to climate change mandates laid out by the government via the Energy Independence and Security Act (EISA) of 2007. This research demonstrates: 1) The environmental impacts of algal omega-3 fatty acid production can be lower than conventional omega-3 fatty acid production, depending on the dewatering strategy. 2) The production of high-value products can support biofuels with both products being sold at prices comparable to 2016 prices. 3) There is a tradeoff between revenue and fuel production 4) There is a tradeoff between the net energy ratio of the algal biorefinery and the economic viability due to the lower fuel production in a multi-product model that produces high-value products and diesel vs. the lower economic potential from a multi-product model that just produces diesel. This work represents the first efforts to use life cycle assessment and techno-economic analysis to assess the economic and environmental sustainability of an existing pilot-scale biorefinery tasked with the production of high-value products and biofuels. This thesis also identifies improvements for multiproduct algal biorefineries that will achieve environmentally sustainable biofuel and products while maintaining economic viability. / Dissertation/Thesis / Doctoral Dissertation Civil and Environmental Engineering 2016

abstract: ABSTRACT Sustainable global energy production is one of the grand challenges of the 21st century. Next-generation renewable energy sources include using photosynthetic microbes such as cyanobacteria for efficient production of sustainable fuels from sunlight. The cyanobacterium Synechocystis PCC 6803 (Synechocystis) is a genetically tractable model organism for plant-like photosynthesis that is used to develop microbial biofuel technologies. However, outside of photosynthetic processes, relatively little is known about the biology of microbial phototrophs such as Synechocystis, which impairs their development into market-ready technologies. My research objective was to characterize strategic aspects of Synechocystis biology related to its use in biofuel production; specifically, how the cell surface modulates the interactions between Synechocystis cells and the environment. First, I documented extensive biofouling, or unwanted biofilm formation, in a 4,000-liter roof-top photobioreactor (PBR) used to cultivate Synechocystis, and correlated this cell-binding phenotype with changes in nutrient status by developing a bench-scale assay for axenic phototrophic biofilm formation. Second, I created a library of mutants that lack cell surface structures, and used this biofilm assay to show that mutants lacking the structures pili or S-layer have a non-biofouling phenotype. Third, I analyzed the transcriptomes of cultures showing aggregation, another cell-binding phenotype, and demonstrated that the cells were undergoing stringent response, a type of conserved stress response. Finally, I used contaminant Consortia and statistical modeling to test whether Synechocystis mutants lacking cell surface structures could reduce contaminant growth in mixed cultures. In summary, I have identified genetic and environmental means of manipulating Synechocystis strains for customized adhesion phenotypes, for more economical biomass harvesting and non-biofouling methods. Additionally, I developed a modified biofilm assay and demonstrated its utility in closing a key gap in the field of microbiology related to axenic phototrophic biofilm formation assays. Also, I demonstrated that statistical modeling of contaminant Consortia predicts contaminant growth across diverse species. Collectively, these findings serve as the basis for immediately lowering the cost barrier of Synechocystis biofuels via a more economical biomass-dewatering step, and provide new research tools for improving Synechocystis strains and culture ecology management for improved biofuel production. / Dissertation/Thesis / Doctoral Dissertation Biological Design 2016

abstract: The basic scheme for photosynthesis suggests the two photosystems existing in parity with one another. However, cyanobacteria typically maintain significantly more photosystem I (PSI) than photosystem II (PSII) complexes. I set out to evaluate this disparity through development and analysis of multiple mutants of the genetically tractable cyanobacterium Synechocystis sp. PCC 6803 that exhibit a range of expression levels of the main proteins present in PSI (Chapter 2). One hypothesis was that the higher abundance of PSI in this organism is used to enable more cyclic electron flow (CEF) around PSI to contribute to greater ATP synthesis. Results of this study show that indeed CEF is enhanced by the high amount of PSI present in WT. On the other hand, mutants with less PSI and less cyclic electron flow appeared able to maintain healthy levels of ATP synthesis through other compensatory mechanisms. Reduction in PSI abundance is naturally associated with reduced chlorophyll content, and mutants with less PSI showed greater primary productivity as light intensity increased due to increased light penetration in the cultures. Another question addressed in this research project involved the effect of deletion of flavoprotein 3 (an electron sink for PSI-generated electrons) from mutant strains that produce and secrete a fatty acid (Chapter 3). Removing Flv3 increased fatty acid production, most likely due to increased abundance of reducing equivalents that are key to fatty acid biosynthesis. Additional components of my dissertation research included examination of alkane biosynthesis in Synechocystis (Chapter 4), and effects of attempting to overexpress fibrillin genes for enhancement of stored compounds (Chapter 5). Synechocystis is an excellent platform for metabolic engineering studies with its photosynthetic capability and ease of genetic alteration, and the presented research sheds light on multiple aspects of its fundamental biology. / Dissertation/Thesis / Doctoral Dissertation Biology 2017

abstract: On average, our society generates ~0.5 ton of municipal solid waste per person annually. Biomass waste can be gasified to generate synthesis gas (syngas), a gas mixture consisting predominantly of CO, CO2, and H2. Syngas, rich in carbon and electrons, can fuel the metabolism of carboxidotrophs, anaerobic microorganisms that metabolize CO (a toxic pollutant) and produce biofuels (H2, ethanol) and commodity chemicals (acetate and other fatty acids). Despite the attempts for commercialization of syngas fermentation by several companies, the metabolic processes involved in CO and syngas metabolism are not well understood. This dissertation aims to contribute to the understanding of CO and syngas fermentation by uncovering key microorganisms and understanding their metabolism. For this, microbiology and molecular biology techniques were combined with analytical chemistry analyses and deep sequencing techniques. First, environments where CO is commonly detected, including the seafloor, volcanic sand, and sewage sludge, were explored to identify potential carboxidotrophs. Since carboxidotrophs from sludge consumed CO 1000 faster than those in nature, mesophilic sludge was used as inoculum to enrich for CO- and syngas- metabolizing microbes. Two carboxidotrophs were isolated from this culture: an acetate/ethanol-producer 99% phylogenetically similar to Acetobacterium wieringae and a novel H2-producer, Pleomorphomonas carboxidotrophicus sp. nov. Comparison of CO and syngas fermentation by the CO-enriched culture and the isolates suggested mixed-culture syngas fermentation as a better alternative to ferment CO-rich gases. Advantages of mixed cultures included complete consumption of H2 and CO2 (along with CO), flexibility under different syngas compositions, functional redundancy (for acetate production) and high ethanol production after providing a continuous supply of electrons. Lastly, dilute ethanol solutions, typical of syngas fermentation processes, were upgraded to medium-chain fatty acids (MCFA), biofuel precursors, through the continuous addition of CO. In these bioreactors, methanogens were inhibited and Peptostreptococcaceae and Lachnospiraceae spp. most likely partnered with carboxidotrophs for MCFA production. These results reveal novel microorganisms capable of effectively consuming an atmospheric pollutant, shed light on the interplay between syngas components, microbial communities, and metabolites produced, and support mixed-culture syngas fermentation for the production of a wide variety of biofuels and commodity chemicals. / Dissertation/Thesis / Doctoral Dissertation Civil, Environmental and Sustainable Engineering 2017

Ce mémoire est consacré au développement d'un immunocapteur impédancemétrique et de deux biopiles enzymatiques. Premièrement, le poly(pyrrole-NHS) est utilisé pour l'immobilisation successive d'un modèle de la ciprofloxacine (CF) et de l'anticorps dirigé spécifiquement contre CF. La détection est réalisée par la spectroscopie d'impédance électrochimique. Elle détecte le déplacement en solution de l'anticorps. Le seuil de détection est de 1.10-12 g.mL-1. Deuxièmement, la production énergétique est abordée suivant deux approches. La première se base sur l'apparition d'un gradient de pH produit par deux enzymes (la GOx et l'uréase) et converti en f.e.m. en utilisant un couple rédox sensible au pH. La seconde, repose sur les propriétés biocatalytiques de la GOx d'oxyder le glucose et de la polyphénol oxydase de réduire le dioxygène. Cette pile est capable de fonctionner aussi bien in vitro que in vivo. Une fois optimisée, la pile affiche une f.e.m. de 315 mV et une puissance de 27 μW. / This work is focused on the development of an impedimetric immunosensor and two enzymatic biofuel cells. Firstly, poly(pyrrole-NHS) is used to graft a model of the ciprofloxacin antibiotic (CF) and its specific antibody (Ab) in two steps. The displacement of the antibody in solution directed by a strong affinity between Ab and CF is monitored by electrochemical impedance spectroscopy. The detection limit is 10-12 g mL-1. Secondly, production of electricity is studied by two different methods. The first one is based on the creation of a pH difference driven enzymatically by glucose oxidase (GOx) and urease. This pH gradient is converted to e.m.f. by adding a pH-dependant redox couple. The second method uses glucose/O2 fu

Ce mémoire est consacré à l'optimisation de la connexion enzymatique d'enzymes pour l'oxydation du glucose et la réduction de O2 sur matrices de nanotube de carbone (CNT) dans les biopiles à glucose.Premièrement, le transfert électronique indirect de la glucose oxydase (GOx) est optimisé dans une matrice nanostructurée de CNT contenant la 1,4-naphtoquinone comme médiateur rédox. Cette bioanode a ensuite été combinée avec des biocathodes similaires à bases d'enzymes à cuivre (laccase et tyrosinase). La biopile GOx-NQ/Lac a permis d'obtenir des puissances maximales de l'ordre de 1,5 mW.cm-2. Les utilisations de cette pile en décharge courte, longue et sa stabilité dans le temps ont également été étudiées. La seconde partie présente la préparation d'une autre anode basée sur la connexion indirecte d'une glucose déshydrogènase NAD+-dépendante (GDH-NAD+) comme alternative pour l'oxydation du glucose. La GDH-NAD+ a été combinée avec un catalyseur d'oxydation de NADH par différentes méthodes. Tout d'abord, elle a été encapsulée au sein du métallopolymère rédox, puis, la modification supramoléculaire a dans un second temps permis d'immobiliser le catalyseur moléculaire et l'enzyme à la surface des CNTs. Ces deux bioanodes ont permis respectivement l'obtention de courants catalytiques d'oxydation du glucose de 1,04 et 6 mA.cm-2. La seconde bioanode a été combinée avec une biocathode à base de BOD et a permis l'obtention de densités de courants maximales de l'ordre de 140 µW.cm-2 La dernière partie concerne l'élaboration d'une biocathode bienzymatique pour la réduction de O2. Le DET de la HRP sur CNTs a dans un premier temps été optimisé par modification de la surface par différents dérivés pyrène. Ensuite, la combinaison de la GOx et de la HRP sur la même électrode a permis de réduire efficacement O2 en 2 étapes. La biocathode est capable de délivrer une densité de courant maximale de l'ordre de 200 µA.cm-2. Cette dernière, combinée avec la bioanode GDH présentée précédemment a permis d'obtenir une biopile opérationnelle en conditions physiologiques et 10 mM de NAD+, en étant capable de débiter une densité de puissance maximale de l'ordre de 57 µW.cm-2. / This work focuses on the optimization of the electrical wiring of glucose oxidizing and dioxygen reducing enzymes on carbon nanotube (CNT) matrixes for glucose biofuel cells.In the first part, glucose oxidase (GOx) mediated electron transfer (MET) is optimized in nanostructured CNTs matrixes by mechanical compression of a CNTs/GOx composite containing 1,4-naphtoquinone as redox mediator. This bioanode was then combined with MCOs (laccase and tyrosinase) based biocathodes. The GOx-NQ/Lac biofuel cell was able to deliver a maximum power density of 1.5 mW.cm-2. The use of this biofuel cell in short/long time discharge and in storage has also been studied. The second part presents the preparation of another bioanode based on the indirect wiring of a NAD+-dependant glucose dehydrogenase (GDH-NAD+) as an alternative for glucose oxidation. The GDH-NAD+ has been combined with an NADH oxidation catalyst by two different techniques. The first one involves the encapsulation of the protein in the metallopolymer redox film, whereas the second one relies on the supramolecular modification of the CNTs by the molecular catalyst and the enzyme. Both bioanodes showed good catalytic properties toward glucose oxidation in presence of NAD+ with respectively 1.04 mA cm-2 and 6 mA cm-2. The latter has been combined with a BOD based biocathode to form a biofuel cell exhibiting maximum power densities of 140 µW cm-2. The last part of this work focuses on the design of a bienzymatic biocathode for O2 reduction. The DET of horseradish peroxidase (HRP) was first investigated and optimized by modification of the CNTs with pyrenes derivatives. The combination of the HRP with the GOx on the same electrode enables an efficient reduction of O2 in a 2-step process. The biocathode could exhibit maximum currents densities of 200 µA cm-2. This cathode along with the previous GDH bioanode formed a biofuel cell functional in physiological conditions and 10 mM NAD+ showing maximum power densities of 57 µW cm-2.

Made available in DSpace on 2016-06-02T19:19:57Z (GMT). No. of bitstreams: 1 RODRIGUES_Flavio_2014.pdf: 3655156 bytes, checksum: bc501cb0db43c7e6e45c2a4f1a0e6042 (MD5) Previous issue date: 2014-02-19 / The search for materials and fuels from renewable sources is a widespread alternative and have been intensified over the past few years. One of the most studied material is a renewable bio-polymer from the most varied sources and more abundant in nature, called cellulose. Studies have been performed in order to extract the maximum potential of this material, which is mostly being used as structural reinforcement in thermoset panels (composite) by the automotive and aerospace industry, in the manufacture of fabrics using sisal fiber, for example, and energy source, is the in-kind form or after physicalchemical treatments. Lignocellulosic biomass consists primarily of cellulose (glucose-glucose dimer, cellobiose called), hemicellulose and lignin. As a result of the process of controlled acid hydrolysis of cellulose is obtained various products, including saccharides that can be recovered or treated to obtain fuels. The generation of energy from biofuels is a huge leap toward energy sustainability, since this energy is renewable. By suggesting solutions that are not dependent on finite capacities of our planet, we are demonstrating beyond real need for an alternative to this problem, an environmental sensitivity that until recently rarely watched the top of the list of priorities. The central objective of this work is the analysis of the chemical composition of a plant studied by our research group, the Typha domingensis, quantifying the presence of glucose after controlled acid hydrolysis process and verify its possible potential for recovery of saccharide or biofuel production from the same. Using the experimental design techniques to determine the most favorable experiments line, and two quantification methods, a novel and other traditional, obtained as a result of the identification of the presence of glucose after hydrolysis process to obtain whiskers from the young sample of macrophyte Typha domingensis. It was possible to obtain an amount of residual solution after removal of fibrils containing glucose at concentrations near 0.5 g.L-1. These results revealed a percentage of valuable products with the potential to be exploited. / A busca por materiais e combustíveis provenientes de fontes renováveis é uma alternativa amplamente difundida e que vêm sendo intensificada ao longo dos últimos anos. Um dos materiais mais estudados é um bio-polimero renovável proveniente das mais variadas fontes e mais abundante na natureza, denominado celulose. Em sua maioria está sendo utilizado como reforço estrutural em painéis termorrígidos (compósitos) pela indústria automobilística e aeroespacial, na confecção de tecidos usando a fibra de sisal, por exemplo, e fonte energética, esteja na forma in-natura ou após tratamentos físicoquímicos. A biomassa lignocelulósica é constituída basicamente por celulose (dímero glicose-glicose, denominado celobiose), hemicelulose e lignina. Como resultado do processo de hidrólise ácida controlada da celulose obtêm-se vários produtos, dentre eles sacarídeos que podem ser recuperados ou tratados para se obter combustíveis. A geração de energia a partir de biocombustíveis é um salto enorme em direção à sustentabilidade energética, uma vez que tal energia é renovável. Ao sugerir soluções que não sejam dependentes das capacidades finitas do nosso planeta, estamos demonstrando além da necessidade real de uma alternativa para esse problema, uma sensibilidade ambiental que até pouco tempo raramente observávamos no topo das listas de prioridades. O objetivo central deste trabalho é a análise da composição química de uma planta estudada pelo nosso grupo de pesquisa, a Typha domingensis, quantificar a presença de glicose após o processo de hidrólise ácida controlada e verificar sua eventual potencialidade para recuperação do sacarídeo ou produção de biocombustível a partir do mesmo. Utilizando a técnica de planejamento fatorial, para determinar a linha de experimentos mais favorável, assim como dois métodos de quantificação, um inovador e outro tradicional, obtivemos como resultado a identificação da presença de glicose após o processo de hidrólise para obtenção de whiskers, a partir da amostra jovem da macrofita Typha domingensis. Foi possível obter um montante de solução residual que após a retirada das fibrilas contém glicose em concentrações próximas de 0,5 g.L-1. Esses resultados revelaram um percentual de produtos valiosos com potencial de serem explorados.

Made available in DSpace on 2014-06-11T19:24:43Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-09-01Bitstream added on 2014-06-13T19:52:22Z : No. of bitstreams: 1 bonometo_rp_me_botfca.pdf: 282254 bytes, checksum: a2dad01e970c5bd5c29c202bdf98cbdf (MD5) / Atualmente há uma grande preocupação mundial com o esgotamento e o alto custo de exploração das reservas de combustíveis fósseis e, portanto, mais do que nunca, é necessário o aprofundamento do estudo e aproveitamento de fontes alternativas que possam ser utilizadas com eficiência energética, preços adequados e com baixo impacto ambiental. De acordo com estas premissas, o biodiesel é um combustível com boas perspectivas de atender uma demanda crescente, pois além de substituir o óleo diesel, pode ser obtido a partir de várias fontes primárias de origem animal e vegetal. O Brasil se destaca na utilização das fontes alternativas de energia com o uso do etanol e, nos últimos anos vem incentivando a ampliação de sua matriz energética a partir das fontes alternativas, na qual o biodiesel passa a ter uma importância estratégica dentro da área de agronegócios. O biodiesel é um combustível que pode substituir o diesel, que é um derivado do petróleo; é um éster produzido na reação de transesterificação de óleos vegetais, goduras animais que, na presença de um álcool, metanol ou etanol, e um catalisador, são convertidos em ácidos graxos e, resultam, em ésteres com glicerol como subproduto. Com o avanço da utilização destes biocombustíveis são necessárias pesquisas que visam melhorar a qualidade e viabilidade técnica dos mesmos, sendo que, o balanço energético é um dos parâmetros mais adequado para definir a viabilidade técnica, pois estabelece a relação entre o total de energia contida no combustível e aquela investida em todo o processo de produção. O objetivo deste trabalho foi analisar energeticamente o processo de produção de biodiesel a partir do óleo dos resíduos descartados na produção de frango. Para a estimativa deste balanço de energia quantificou-se o poder calorífico de alguns... / Nowadays there is a great global concern with the depletion and the high cost of fossil fuel reserves exploitation, more than ever, it is necessary to make a profound study and take advantage of alternative sources that can be used with energy efficiency with an appropriate pricing and with low environmental impact. Under these assumptions, biodiesel is a fuel with good prospects of meeting a growing demand, as well as being a replacement of diesel oil, can be obtained from several primary sources of animal and plant origin. Brazil, which has highlighted in use of alternative energy sources with the use of ethanol and, in recent years, has been encouraging the expansion of its energy matrix in which the biodiesel will have a strategic importance within the agrobusiness area. Biodiesel is a fuel that can replace the diesel,that is a petroleum derivative. It is an ester, produced in the transesterification reaction of vegetable oils and animal greases, that in the presence of an alcohol like methanol or ethanol with an additional catalyst, are converted into fatty acids and result in esters with glycerol as subproducts. The advancement in use of biofuels, some researchs needed improve the quality and feasibility and that energetic balance is one of the most appropriate parameters to define the technical feasibility, since settle the same relationship between of total energy in the biofuel and the total energy invested in the whole production process. The objective of this study was to estimate the final energy balance for the process biodiesel production from oil chicken waste. The energy balance estimation was quantified in calorific value according the energy expenditure by calorimetric bomb method. The study was conducted in CEDETEC - Center for Development and Dissemination of Technology, Department of Agronomy... (Complete abstract click electronic access below)