A sustainable and low-cost system, namely a photo-bioelectrochemical system (photo-BES), based on the natural blueprint of photosynthetic microorganisms was studied. The aim of this research work is to improve the efficiency of electron transfer of the microorganisms for bioelectricity generation. The first strategy adopted was the evaluation of the exoelectrogenic activity of oxygenic photosynthetic cyanobaterium, Synechococcus elongatus PCC 7942, in biophotovoltaic (BPV) platforms through a comparative performance analysis of bioanode materials. The second approach involved improving the performance of anoxygenic photosynthetic bacterium, Rhodopseudomonas palustris ATCC® 17001™, by varying the ratio of nitrogen to carbon sources (N:C) to maximise both biohydrogen production and exoelectrogenesis for conversion into bioelectricity in photosynthetic microbial fuel cells (photoMFCs). A linear correlation was obtained between average surface roughness/surface area and maximum power density of ITO-coated and graphene/ITO-coated substrates. Graphene/ITO-coated PET bioanodes produced the highest maximum power output of 29±4 μW m-2 in a single chamber BPV device due to improved biofilm formation and improved electrochemical activity. XG Leaf®, also known as graphene paper, helped to bridge the shortcomings of carbon fibres in terms of wettability. The most hydrophilic, 240 μm thick graphene paper, produced the highest maximum power output of 393±20 μW m-2 in a membrane electrode assembly (MEA)-type BPV device, mainly due to reduced electrochemical polarisation. A proof of concept study compared the performance of screen-printed graphene onto a membrane separator against 3D-printed bioanodes coated with carbon nanotubes. One mm thick 3D-printed bioanode was better performing as its structures promoted a much denser biofilm with extensive fibrous extracellular matrix. Using a ratio of N:C=0.20 resulted in higher biohydrogen production and higher exoelectrogenic activity, generating a maximum power output of 361±157 mW m-2 and 2.39±0.13 mW m-2, respectively. This study provided additional insight in improving the electron transfer efficiency, which could be used to further optimise photo-BESs as part of future research and development for sustainable technologies.

ARAGÃO, Janisi Sales. Aspectos ecotoxicológicos relacionados à carcinicultura marinha. 2012. 138 f. : Tese (doutorado) - Universidade Federal do Ceará, Centro de Ciências Agrárias, Departamento de Engenharia de Pesca, Fortaleza-CE, 2012 / Submitted by Nádja Goes (nmoraissoares@gmail.com) on 2016-07-26T15:05:27Z No. of bitstreams: 1 2012_tese_jsaragão.pdf: 1589132 bytes, checksum: a1ac0fd409cb94137f61baa73b6571b7 (MD5) / Approved for entry into archive by Nádja Goes (nmoraissoares@gmail.com) on 2016-07-26T15:05:39Z (GMT) No. of bitstreams: 1 2012_tese_jsaragão.pdf: 1589132 bytes, checksum: a1ac0fd409cb94137f61baa73b6571b7 (MD5) / Made available in DSpace on 2016-07-26T15:05:39Z (GMT). No. of bitstreams: 1 2012_tese_jsaragão.pdf: 1589132 bytes, checksum: a1ac0fd409cb94137f61baa73b6571b7 (MD5) Previous issue date: 2012 / Farming of shrimp is an important economic activity; however, its exponential growth has attracted attention to the potential impacts brought over the environment. Wastewater generated by this activity can contribute to the eutrophication of waters receiving these effluents, as those may bear a variety of contaminants, such as sodium metabisulfite, a sulphitant agent that removes the oxygen from water and food. Additionally, this effluent carries the phytoplankton community that proliferates in these systems, which may include toxic cyanobacteria. Therefore, the aim of the present study was to perform an ecotoxicological assessment using biological test models and biological responses to evaluate potential impacts caused by use of sodium metabisulfite and by the proliferation of cyanobacteria in shrimp farming. Phytoplankton samples were collected in three shrimp farms from the state of Ceará for quantitative and qualitative analysis and for the isolation of cyanobacteria. The microorganisms, which were identified by morphological and molecular techniques, were grown in laboratory to o btain organic extracts on which were conducted toxicity tests with mice and mysids. Sodium metabisulfite was evaluated through acutetoxicity tests using organisms at different trophic levels (microalgae, cladocerans, shrimps and fish) and by the rate of oxygen consumption and enzymatic activities (CAT,AChE and GST) in shrimps. On fish, tests evaluating the embriolarval development and enzymatic activities (AChE and GST) were performed. Qualitative and quantitative analysis of phytoplankton community showed a large number of species from nearly all classes of phytoplankton, including cyanobacteria. From this latter group, Synechococcus sp. was isolated and cultivated, and the extract generated from the living cells showed toxicity in mice, as evidenced by damage to the liver and kidneys of animals. For acute toxicity tests sodium metabisulphite showed an EC 50 of 24.29 mg/L for the microalgae and LC 50 of 34.90 mg/L and 69.65 mg/L for cladocer ans and shrimp, respectively. Regarding the consumption of oxygen and enzymatic activities, these did not show significant differences when compared to their respective controls, except for the AChE in shrimp and GST in fish. On embriolarval developing of fish, sodium metabisulfite caused different types of effects, from destruction of eggs to deformities in larvae. Thus, these results show that sodium metabisulphite and the cyanobacteria Synechococcus sp. are toxic to other organisms, evidenced by both, acute and chronic toxicity / Apesar do cultivo de camarão ser uma importante atividade econômica, o seu crescimento tem atraído a atenção para os possíveis impactos ao meio ambiente. As águas residuais geradas pelos cultivos podem contribuir para a eutrofização das águas receptoras desses efluentes, já que possuem uma ampla variedade de substâncias consideradas contaminantes potenciais, como o metabissulfito de sódio, um agente sulfitante que retira o oxigênio da água e de alimentos. Além disso, os efluentes carreiam a comunidade fitoplanctônica que prolifera nos sistemas de cultivo, incluindo cianobactérias produtoras de toxinas. Com isso o objetivo desse estudo foi uma avaliação ecotoxicológica utilizando diferentes organismos testes e respostas biológicas dos possíveis impactos causados pelo uso do metabissulfito de sódio ou pela proliferação de cianobactérias coletadas nos próprios cultivos. Amostras do fitoplâncton foram coletadas em três fazendas do estado do Ceará para análise qualitativa, quantitativa e para o isolamento das cianobactérias. Estes organismos foram identificados através de técnicas morfológicas e de biologia molecular, cultivados no laboratório para obtenção dos extratos e realizados ensaios com camundongos e misidáceos. O metabissulfito de sódio teve sua toxicidade avaliada por meio de ensaios agudos em diferentes níveis tróficos (microalgas, cladóceros, camarões e peixes), mas também pela taxa do consumo de oxigênio e das atividades enzimáticas (CAT; AChE e GST) em camarões. Para os peixes, foram realizados ainda ensaios com o desenvolvimento embriolarval e das atividades enzimáticas (AChE e GST). A análise qualitativa e quantitativa da comunidade fitoplanctônica mostrou um grande número de espécies de quase todas as classes do fitoplâncton, inclusive cianobactérias. Deste último grupo foi isolada e cultivada Synechococcus sp., para a qual o extrato e as células vivas mostraram toxicidade em camundongos evidenciada por danos observados no fígado e rins dos animais. Já na avaliação da toxicidade do metabissulfito de sódio, este apresentou toxicidade aguda para os organismos testes, apresentando uma EC50 de 24,29 mg/L para as microalgas, CL50 de 34,90 mg/L e 69,65 mg/L para cladóceros e camarões, respectivamente. Em relação ao consumo de oxigênio e atividades enzimáticas, estes não apresentaram diferenças significativas quando comparados aos controles, com exceção para a AChE nos camarões e GST nos peixes. No desenvolvimento embriolarval dos peixes, o metabissulfito de sódio causou diferentes tipos de efeitos desde a destruição dos ovos à deformidades nas larvas. Sendo assim, esses resultados mostram que o metabissulfito de sódio e a cianobactéria Synechococcus sp. são tóxicos para diferentes organismos, evidenciados tanto pela toxicidade aguda quanto pela crônica.

PipX es una proteína única de cianobacterias identificada por su habilidad para interactuar de forma excluyente con PII y NtcA, dos reguladores clave implicados en la integración de señales de nitrógeno/carbono y energía, estableciendo un vínculo mecanístico entre ambos. Sin embargo, los datos recabados indican que el papel de PipX no se limita únicamente a esto, sino que parece formar parte de una red de señalización más amplia exclusiva de cianobacterias. La formación de los complejos PII-PipX no solo permite el secuestro de PipX, impidiendo la co-activación de NtcA, sino que favorece la formación de los complejos con el regulador transcripcional cianobacteriano PlmA. Esta interacción con PII afecta a la localización dinámica de PipX en respuesta al estado energético de la célula, limitando su actividad a condiciones de alta energía. Además, PipX está funcionalmente conectado con pipY, el gen aguas abajo que codifica a un miembro de la familia de proteínas PLPBP, universalmente distribuidas e implicadas en la homeostasis de la vitamina B6 y amino ácidos y, en humanos, epilepsia dependiente de vitamina B6. No solo PipX sería capaz de controlar a nivel traduccional la expresión de PipY, sino que ambos participarían en el control de la expresión génica y vías metabólicas comunes. Por último, el análisis de genomas cianobacterianos posiciona a PipX en una red de interacción con PipY y otras 4 proteínas con las que PipX podría tener una relación funcional.

In the field of marine microbial ecology, many questions remain unanswered with regards to the physiological trade-offs made by phytoplankton to maximize growth (e.g., nutrient acquisition) and minimize loss (e.g., predation defenses). These tradeoffs, which occur at the cellular level, have wide reaching impacts on food web dynamics and global biogeochemical cycles. In the first chapter, we explored the use of a non-canonical amino acid (NCAA) technique, bioorthogonal non-canonical amino-acid tagging (BONCAT), in phytoplankton model systems. This technique has potential to work well in natural systems by enabling isolation of only newly synthesized proteins during an incubation period with the NCAA, reducing the complexity of natural proteomics and easing the elucidation of patterns. However, in testing BONCAT across several groups of cultured phytoplankton, we discovered that the NCAA molecule induced a stress response in the globally ubiquitous marine picocyanobacteria, Synechococcus sp. Therefore, in addition to confirming the uptake of modified amino acids by phytoplankton, chapter one investigated the implications of this stress response and limitations when using this technique to study marine microbial communities. In chapter two, we addressed our initial question by exploring tradeoffs at the protein level in a simplified culture system. This approach revealed insights into metabolic tradeoffs in response to predation pressure and nutrient stress. These insights into how phytoplankton negotiate these physiological tradeoffs at the protein level could ultimately allow for targeted proteomic studies in natural systems.

En esta tesis se ha demostrado que la radiación ultravioleta induce mortalidad en comunidades de fitoplancton de diferentes áreas del Océano Atlántico, del Mar Mediterráneo y del Océano Antártico. El fitoplancton más pequeño (pico-fitoplancton) muestra mayor sensibilidad a la radiación UV respecto al fitoplancton de mayor tamaño. Este estudio identifica que el crecimiento de las poblaciones del fitoplancton antártico está controlado por la radiación ultravioleta con inhibiciones de biomasas por encima del 80-90%. Se demuestra también que la transferencia de radicales OH, generados por la radiación ultravioleta, desde la atmósfera hacia la superficie del Océano causa mortalidad en comunidades de fitoplancton de aguas tropicales, templadas y antárticas. El trabajo presentado en esta tesis muestra la importancia de la radiación ultravioleta como factor que induce mortalidad en el fitoplancton, su influencia en el balance del crecimiento neto de estas poblaciones, así como las consecuencias que se derivan en la cadena trófica.

Includes vita. / Title from PDF of title page. / Document formatted into pages; contains 329 pages. / Thesis (Ph.D.)--University of South Florida, 2003. / Includes bibliographical references. / Text (Electronic thesis) in PDF format. / ABSTRACT: River discharge leads to extensive phytoplankton blooms often observed in ocean color satellite images to extend far into the open ocean as high chlorophyll plumes. We investigated diversity, distribution and ecology of phytoplankton populations in the Mississippi River plume, both spatially and in the water column using molecular tools. A method was developed for the quantification of diatom/pelagophyte rbcL (large subunit of Ribulose-1,5-bisphosphate Carboxylase/Oxygenase) mRNA using quantitative PCR and applied to cultures and in the plume. The vertical structure of phytoplankton species in the Mississippi River plume was described by flow cytometry, pigments, rbcL mRNA and rbcL cDNA libraries. High productivity in the plume was associated with a large population of Synechococcus and elevated levels of cellular form IA rbcL mRNA. / ABSTRACT: rbcL cDNA libraries indicated two vertically separated clades of Prochlorococcus (high-light and low-light adapted) in addition to a diverse group of prymnesiophytes and a microdiverse clade of prasinophytes, which may have dominated the SCM (Subsurface Chlorophyll Maximum). In situ sampling and satellite image analysis were used to estimate that the plume accounted for 41% and 13% of all surface water column ix productivity in the oligotrophic Gulf of Mexico, while covering less than 3% of its area. Coastally the plume is dominated by diatoms, which are replaced by a bloom of Synechococcus as the plume moves offshore. Diatoms as indicated by pigments and rbcL clone libraries again dominated the offshore, least productive plume. 15N uptake measurements indicated that rapid recycling of ammonium despite higher levels of nitrate primarily drives production in the offshore plume. / ABSTRACT: rbcL mRNA levels and photosynthetic capacity displayed strong diel patters in three out of four time series sampled during the GRIST (Geochemical Rate/mRNA Integrated Study). In addition it was demonstrated that transcriptional regulation of the global nitrogen regulatory protein NtcA in Synechococcus WH7803 may involve a small cis-encoded anti-sense mRNA. Methods for the generation of large insert BAC (Bacterial Artificial Chromosome) from cultures and the environment were refined. Partial sequencing and genomic comparison of an ntcA containing BAC clone obtained from Synechococcus WH7803 indicated that ntcA is not part of a larger nitrogen assimilation operon in cyanobacteria. / System requirements: World Wide Web browser and PDF reader. / Mode of access: World Wide Web.

Microalgae cultivation has received much research attention in recent decades due to its high photosynthetic productivity and ability to produce biofuel feedstocks as well as high value compounds for the health food, cosmetics, and agriculture markets. Microalgae are conventionally grown in open pond raceways or closed photobioreactors. Due to the high water contents of these cultivation systems, they require large energy inputs for pumping and mixing the dilute culture, as well as concentrating and dewatering the resultant biomass. The energy required to operate these systems is generally greater than the energy contained in the resultant biomass, which precludes their use in sustainable biofuel production. To address this challenge, we designed a novel photobioreactor inspired by higher plants. In this synthetic leaf system, a modified transpiration mechanism is used which delivers water and nutrients to photosynthetic cells that grow as a biofilm on a porous, wicking substrate. Nutrient medium flow through the reactor is driven by evaporation, thereby eliminating the need for a pump. This dissertation outlines the design, construction, operation, and modeling of such a synthetic leaf system for energy positive biofuel production. First, a scaled down synthetic leaf reactor was operated alongside a conventional stirred tank photobioreactor. It was demonstrated that the synthetic leaf system required only 4% the working water volume as the conventional reactor, and showed growth rates as high as four times that of the conventional reactor. However, inefficiencies in the synthetic leaf system were identified and attributed to light and nutrient limitation of growth in the biofilm. To address these issues, a modeling study was performed with the aim of balancing the fluxes of photons and nutrients in the synthetic leaf environment. The vascular nutrient medium transport system was also modeled, enabling calculation of nutrient delivery rates as a function of environmental parameters and material properties of the porous membrane. These models were validated using an experimental setup in which the nutrient delivery rate, growth rate, and photosynthetic yield were measured for single synthetic leaves. The synthetic leaf system was shown to be competitive with existing technologies in terms of biomass productivity, while requiring zero energy for nutrient and gas delivery to the microorganisms. Future studies should focus on utilizing the synthetic leaf system for passive harvesting of secreted products in addition to passive nutrient delivery. / text

Les picocyanobactéries du genre Synechococcus sont présentes dans tous les types d'environnements marins. Cette ubiquité s'explique en partie par la grande diversité pigmentaire de ces cellules, leur permettant de capturer efficacement la lumière sur une large gamme spectrale. La plupart des souches ont une composition pigmentaire fixe mais certaines sont capables d'ajuster leur pigmentation en fonction de la lumière incidente par un processus physiologique appelé acclimatation chromatique de type IV (AC4). Une approche de métagénomique ciblée originale, combinant des techniques sophistiquées, a été développée afin d'étudier la diversité et la distribution des différents types pigmentaires de Synechococcus in situ. L'intérêt de cette approche a pu être démontré après des optimisations spécifiques. La disponibilité de 25 nouveaux génomes de Synechococcus a permis de faire d'importantes avancées sur la compréhension du mécanisme d'AC4. Un cluster de 4 à 6 gènes, codant pour une phycobiline-lyase et plusieurs régulateurs transcriptionnels, est systématiquement présent chez toutes les souches capables de cette plasticité phénotypique. Deux configurations bien distinctes de ce cluster, nommées AC4-A et AC4-B, ont été découvertes et se retrouvent dans des lignées différentes de Synechococcus. Ces deux types de clusters auraient été soumis à des processus évolutifs distincts. Par ailleurs, certaines singularités phénotypiques entre les souches possédant ces deux types de clusters génomiques ont pu être démontrées. Ce travail de thèse soulève de nouvelles hypothèses sur la régulation de cette plasticité phénotypique ainsi que sur les mécanismes biochimiques associés.

The current investigation is aimed at the reconstruction and analysis of genome-scale metabolic models. Specifically, it is focused on the use of mathematical-computational simulations to predict the cellular metabolism behavior towards bio-products production. The photosynthetic cyanobacterium Synechococcus elongatus PCC7942 was studied as biological system. This prokaryotic has been used in several studies as a biological platform for the synthesis of several substances for industrial interest. These studies are based on the advantage of autotrophic systems, which basically requires light and CO2 for growth. The main objective of this thesis is the integration of different types of biological information, whose interaction can be extract applicable knowledge for economic interests. To this end, our study was addressed to the use of methods for modeling, analyzing and predicting the behavior of metabolic phenotypes of cyanobacterium. The work has been divided into chapters organized sequentially, where the starting point was the in silico metabolic reconstruction network. This process intent to join in a metabolic model of all chemical reactions codified in genome. The stoichiometric coefficients of each reactions, can be arranged into a sparse matrix (stoichiometric matrix), where the columns corresponds to reactions and rows to metabolites. As a result of this process the first model was obtained (iSyf646) than later was updated to another (iSyf714). Both were generated from data ¿omics published in databases, scientific reviews as well as textbooks. To validate them, each one of the stoichiometric matrix together with relevant constraints were used by simulation techniques based on linear programming. These reconstructions have to be flexible enough to allow autotrophic growth under which the organism grows in nature. Once the reconstructions were validated, environmental variations can be simulated and we were able to study its effects through changes in outline system parameters. Subsequently, synthetic capabilities were evaluated from the in silico models in order to design metabolic engineering strategies. To do this a genetic variation was simulated in reactions network, where the disturbed stoichiometric matrix was the object of the quadratic optimization methods. As a results sets of optimal solutions were generated to enhanced production of various metabolites of energetic interest such as: ethanol, n-butanol isomers, lipids and hydrogen, as well as lactic acid as the compound which is an interest to the industry. Furthermore, functionally coupled reactions have been studied and have been weighted to the importance in the production of metabolites. Finally, genome-scale metabolic models allow us to establish criteria to integrate different types of data to help of find important points of regulation that may be subject to genetic modification. These regulatory centers have been investigated under drastic changes of illumination and have been inferred operational principles of cyanobacterium metabolism. In general, this thesis presents the metabolic capabilities of photosynthetic cyanobacterium Synechococcus elongatus PCC7942 to produce substances of interest, being a potential biological platform for clean and sustainable production. / Triana Dopico, J. (2014). Model-based analysis and metabolic design of a cyanobacterium for bio-products synthesis [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/39351 / TESIS

River discharge leads to extensive phytoplankton blooms often observed in ocean color satellite images to extend far into the open ocean as high chlorophyll plumes. We investigated diversity, distribution and ecology of phytoplankton populations in the Mississippi River plume, both spatially and in the water column using molecular tools. A method was developed for the quantification of diatom/pelagophyte rbcL (large subunit of Ribulose-1,5-bisphosphate Carboxylase/Oxygenase) mRNA using quantitative PCR and applied to cultures and in the plume. The vertical structure of phytoplankton species in the Mississippi River plume was described by flow cytometry, pigments, rbcL mRNA and rbcL cDNA libraries. High productivity in the plume was associated with a large population of Synechococcus and elevated levels of cellular form IA rbcL mRNA. rbcL cDNA libraries indicated two vertically separated clades of Prochlorococcus (high-light and low-light adapted) in addition to a diverse group of prymnesiophytes and a microdiverse clade of prasinophytes, which may have dominated the SCM (Subsurface Chlorophyll Maximum). In situ sampling and satellite image analysis were used to estimate that the plume accounted for 41% and 13% of all surface water column ix productivity in the oligotrophic Gulf of Mexico, while covering less than 3% of its area. Coastally the plume is dominated by diatoms, which are replaced by a bloom of Synechococcus as the plume moves offshore. Diatoms as indicated by pigments and rbcL clone libraries again dominated the offshore, least productive plume. 15N uptake measurements indicated that rapid recycling of ammonium despite higher levels of nitrate primarily drives production in the offshore plume. rbcL mRNA levels and photosynthetic capacity displayed strong diel patters in three out of four time series sampled during the GRIST (Geochemical Rate/mRNA Integrated Study). In addition it was demonstrated that transcriptional regulation of the global nitrogen regulatory protein NtcA in Synechococcus WH7803 may involve a small cis-encoded anti-sense mRNA. Methods for the generation of large insert BAC (Bacterial Artificial Chromosome) from cultures and the environment were refined. Partial sequencing and genomic comparison of an ntcA containing BAC clone obtained from Synechococcus WH7803 indicated that ntcA is not part of a larger nitrogen assimilation operon in cyanobacteria.