Dissertations / Theses on the topic 'Direct interspecies electron transfer'

Master of Science
Department of Geology
Matthew Kirk
A growing body of evidence demonstrates that methanogenesis and Fe(III) reduction can occur simultaneously. However, environmental controls on interactions between each are poorly understood. In this study we considered pH as a control on interactions between Fe(III) reduction and methanogenesis in anoxic sediment bioreactors. The reactors consisted of 100mL of synthetic aqueous media, and 1 g of marsh sediment amended with goethite (1mmol). One set of reactors received acidic media (pH 6), and the other alkaline media (pH 7.5). Each set received media containing acetate (0.25 mM) to serve as an electron donor. Control reactors, deficient in acetate, were also included. We maintained a fluid residence time of 35 days by sampling and feeding the reactors every seven days. For pH 6.0 and pH 7.5 reactors, the measured pH of effluent samples averaged 6.33 and 7.37, respectively. The extent of Fe(III) reduction and methanogenesis varied considerably between each set of reactors. More Fe(III) was reduced in the pH 6 reactors (646.39 μmoles on avg.) than the pH 7.5 reactors (31.32 μmoles on avg.). Conversely, more methane formed in pH 7.5 reactors (127.5 μmoles on avg.) than the pH 6 reactors (78.9 μmoles on avg.). Alkalinity concentrations during the middle and end of the experiment averaged 9.6 meq/L and 5.2 meq/L in pH 6 and pH7.5 reactors, respectively Although much less Fe(III) reduction occurred in pH 7.5 reactors, the relative abundance of Fe(III) reducers in them decreased little from levels observed in the pH 6 reactors. Sequences classified within Geobacter, a genus of bacteria known primarily as dissimilatory metal reducers, accounted for 22% and 13.45% of the sequences in the pH 6 and pH 7.5 reactors and only 0.8% of the sequences in the marsh sediment inoculum. In contrast, sequences classified within orders of methanogens were low in abundance, making up only 0.47% and 1.04% of the sequences in the pH 6 and pH 7.5 reactors, respectively. Mass balance calculations demonstrate that the amount of electron donor consumed by each group varied considerably between the sets of reactors. Expressed as a quantity of acetate, the reactions consumed about 160μM of electron donor each in pH 6 reactors. In contrast, methanogenesis consumed over 30 times more electron donor than Fe(III) reduction in the pH 7.5 reactors. Thus, the results of our experiment indicate that the decrease in electron donor consumption by Fe(III) reduction at basic pH was nearly matched by the increase in electron donor consumption by methanogens. Results of geochemical modeling calculations indicate that more energy was available for Fe(III) reduction in the pH 6.0 reactors than the pH 7.5 reactors, matching variation in Fe(III) reduction rates, and that the density of sorbed ferrous iron was higher in pH 6 reactors than pH 7.5 reactors. Thus, the calculation results are consistent with bioenergetics, but not variation in ferrous iron sorption, as a potential mechanism driving variation in the balance between each reaction with pH.

Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第19022号
農博第2100号
新制||農||1030(附属図書館)
学位論文||H27||N4904(農学部図書室)
31973
京都大学大学院農学研究科応用生命科学専攻
(主査)教授 加納 健司, 教授 阪井 康能, 教授 小川 順
学位規則第4条第1項該当

Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第13102号
農博第1607号
新制||農||939(附属図書館)
学位論文||H19||N4228(農学部図書室)
UT51-2007-H375
京都大学大学院農学研究科応用生命科学専攻
(主査)教授 加納 健司, 教授 植田 和光, 教授 宮川 恒
学位規則第4条第1項該当

Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第21836号
農博第2349号
新制||農||1068(附属図書館)
学位論文||H31||N5208(農学部図書室)
京都大学大学院農学研究科応用生命科学専攻
(主査)教授 加納 健司, 教授 三芳 秀人, 教授 三上 文三
学位規則第4条第1項該当

Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第20426号
農博第2211号
新制||農||1048(附属図書館)
学位論文||H29||N5047(農学部図書室)
京都大学大学院農学研究科応用生命科学専攻
(主査)教授 加納 健司, 教授 植田 充美, 教授 三上 文三
学位規則第4条第1項該当

Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第20425号
農博第2210号
新制||農||1047(附属図書館)
学位論文||H29||N5046(農学部図書室)
京都大学大学院農学研究科応用生命科学専攻
(主査)教授 加納 健司, 教授 宮川 恒, 教授 三芳 秀人
学位規則第4条第1項該当

Dissertação apresentada para a obtenção do Grau de Doutor em Química Sustentável pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia
REQUIMTE ; Fundação para a Ciência e Tecnologia -(POCI/QUI/58026/2004 and SFRH/BD/28921/2006)

La corrosion induite par les micro-organismes (CIM) génère des pertes économiques mondiales chiffrées en milliards d’euros par an. Il est communément admis que les bactéries sulfato-réductrices (BSR) jouent un rôle clé dans la CIM anaérobie des aciers. Malgré cette unanimité, les essais en laboratoire peinent à reproduire la corrosion des aciers observées en milieu naturel; bien plus, ils n’expliquent pas quel est l’élément qui déclenche la corrosion, puisque les BSR présentes dans de nombreux environnements naturels n’induisent pas systématiquement de corrosion. L’objectif de ce travail est d’évaluer la pertinence dans le domaine de la CIM de nouveaux mécanismes de transferts électroniques entre aciers et protéines ou cellules microbiennes. La première partie de la thèse évalue l’effet d’une [Fe]-hydrogénase sur les processus de corrosion anaérobie des aciers au carbone. L’hypothèse d’une catalyse directe de la réduction des protons par des hydrogénases adsorbées a souvent été suggérée dans la bibliographie, elle est ici clairement démontrée. L’hydrogénase de Clostridium acetobutylicum, qu’elle soit active, désactivée ou dénaturée accélère la corrosion de l’acier au carbone. La présence de phosphate dans le milieu rend les interprétations plus complexes mais ne modifie pas le mécanisme. Une nouvelle hypothèse est avancée qui donne un rôle essentiel aux centres fer-soufre de la protéine. La catalyse de la corrosion par les hydrogénases pourrait donc être rapprochée des mécanismes bien connus de catalyse par le sulfure de fer. Dans ce cas l’état redox des centres fer-soufre serait une clé essentielle de l’apparition ou non de la corrosion. La deuxième partie élucide le rôle de Geobacter sulfurreducens sur la corrosion anaérobie de trois types de matériaux : aciers au carbone (1145), ferritique (403) et austénitiques (304L et 316L). Les résultats mettent en évidence pour la première fois que des cellules bactériennes adhérées induisent un anoblissement du potentiel libre des aciers et accélèrent la corrosion des aciers faiblement alliés par un mécanisme de transfert direct d’électrons. Suivant les concentrations d’accepteurs et de donneurs d’électrons en solution, G. sulfurreducens peut accentuer la propagation de la corrosion en catalysant directement la réduction cathodique ou, au contraire, en absence d’accepteurs et en excès de donneurs, protéger contre la corrosion. L’apparition de la corrosion ne peut donc être induite que par la conjonction défavorable de plusieurs paramètres. Ces résultats obtenus en laboratoire apportent de nouvelles voies d’investigations des phénomènes de CIM qui doivent maintenant être confrontées aux milieux naturels.

A eletroquímica direta de enzimas redox depende da distância entre os sítios redox da proteína e a superfície do eletrodo e também da eficiência na imobilização dessas enzimas na superfície eletródica. Dessa forma, a obtenção de enzimas mais hidrofóbicas possibilita a melhora na interação entre elas e a superfície de eletrodos sólidos, como os de carbono. Neste estudo, foi desenvolvida uma rota para a obtenção da glicose oxidase oligomerizada (Ol-GOx) com o objetivo de melhorar a interação entre a enzima e a superfície de fibras de carbono, uma vez que enzimas oligomerizadas contêm suas porções hidrofóbicas expostas.Para tanto, diferentes ácidos de Brønsted foram utilizados, sendo que a enzima obtida a partir da reação com o ácido trifluorometanosulfônico (TFMS) foi a que se manteve ativa cataliticamente. A Ol-GOx se mostrou um biocatalisador promissor devido a sua hidrofobicidade e seu tamanho, os quais permitiram uma imobilização mais eficiente em superfícies de carbono. Após a caracterização estrutural, concluiu-se que a Ol-GOx é formada por um oligômero composto por 10 unidades de GOx nativa com raio hidrodinâmico de aproximadamente 96 nm. Por voltametria cíclica estudou-se a transferência direta de elétrons (TDE) entre o cofator dinucleotídeo de flavina e adenina (FAD) e a superfície das fibras de carbono, sendo observado um aumento de 7 vezes nas correntes faradaicas em relação ao obtido para a GOx nativa. Além disso, as propriedades bioeletrocatalíticas foram melhoradas em 30% quando analisada a oxidação da glicose. Concluiu-se ainda que quanto maior a quantidade de folhas-β presente na estrutura proteica, maior a TDE observada entre a enzima e a superfície das fibras de carbono.
The direct electrochemistry of redox enzymes is dependent on the distance between the active centers of the protein and the electrode surface, and also on the efficiency in the immobilization of these enzymes on the electrodic surface. Thus, the synthesis of more hydrophobic enzymes could lead to better interaction between the redox enzymes and the solid electrode surfaces, such as carbon electrodes. In this study, it was proposed a chemical route to obtain oligomerized glucose oxidase (Ol-GOx), aiming to improve the interaction between the enzyme and the surface of carbon fibers, since oligomerized proteins have their hydrophobic chains exposed. After structural characterization, it was concluded that Ol-GOx is formed by 10 dimeric units of native GOx with a hydrodynamic radius corresponding to approximately 96 nm. By cyclic voltammetry, it was studied the direct electron transfer (DET) between the flavin adenine dinucleotide (FAD) cofactor and the surface of carbon fibers, where it was observed an increase of 7-fold in the faradaic currents in comparison to that observed for native GOx. Besides, bioelectrocatalytic properties are 30% improved, when analyzed the glucose oxidation by cyclic voltammetry. It was also concluded that the greater the β-sheet content in protein structure, the higher the DET observed between the enzyme and the carbon fibers surface.

Proton-coupled electron transfer (PCET) reactions are ubiquitous throughout chemistry and biology. However, challenges arise in both the the experimental and theoretical investigation of PCET reactions; the rare-event nature of the reactions and the coupling between quantum mechanical electron- and proton-transfer with the slower classical dynamics of the surrounding environment necessitates the development of robust simulation methodology. In the following dissertation, novel path-integral based methods are developed and employed for the direct simulation of the reaction dynamics and mechanisms of condensed-phase PCET.

碩士
國立中興大學
化學系所
95
We present here a unique property of preanodized screen printed electrodes (SPCE*) that can drive direct electron transfer of glucose oxidase. When the enzyme is immobilized on the SPCE*, the enzyme is directly connected to the electrode by the oxidized functional groups which are generated by preanodization. The direct electron transfer of glucose oxidase can be applied in electroanalysis as well as energy generation. In electroanalysis, the advantage comes from the high selectivity of enzyme and the low detection potential of DET. In glucose biofuel cell application the DET of GOD in fabricating of electrode can work efficiently as anode in sugar/air battery. The application of DET of GOD is very convenient and the fabrication of electrode is cheap, it gets good sensitivity in electroanalysis and high performance in power generation. The biofuel cell generates an OCP of 0.6 V and a max. power density of ~ 150 μW/cm2.

Dissertação de mestrado em Bioengenharia
Biogas is an alternative to substitute fossil fuels and is mostly composed by methane, a gas component that is produced by microorganisms called methanogens that use compounds such as acetate, hydrogen and carbon dioxide as substrates. In syntrophic communities, methanogens and bacteria exchange electrons for energetic purposes, normally through the use of soluble small chemical compounds that act as shuttles, such as hydrogen or formate. However, it has been recently suggested that in some cases this electron exchange can be performed directly or with the aid of conductive materials, which can potentially be a more energy conserving approach, thus improving the efficiency of methanogenesis. This project addressed the study of the effect of carbon nanotubes (CNT) in methane production by methanogenic communities, in two distinct studies. In the first study, assays were performed in batch with pure cultures of hydrogenotrophic, Methanobacterium formicicum and Methanospirillum hungatei, and acetoclastic methanogens, Methanosaeta concilii and Methanosarcina mazei, in the presence of CNT. Also, growth of pure cultures of M. formicicum was tested in the absence of a reducing agent. The results showed that CNT presence in pure cultures of the hydrogenotrophic methanogens resulted in an increased methane production and reduced lag phases. Although CNT also accelerated methane production by the acetoclastic pure cultures at 1 g/L CNT, a higher concentration of 5 g/L CNT, inhibited the methane production and induced longer lag phases. In the second study, co-cultures of butyrate-degrading bacteria Syntrophomonas wolfei and M. hungatei were grown with and without CNT, in order to determine the effect of CNT in butyrate-oxidizing syntrophic communities. The presence of CNT accelerated methane production by this co-culture, with methane production rate reaching a value of 1.03±0.03 mM/d for co-cultures incubated with 5 g/L CNT, while co-cultures in the absence of CNT only registered a rate of 0.72±0.01 mM/d. Adaptation of sludge in anaerobic bioreactors was also performed with the long-term objective of adding CNT, in order to assess its effect in complex microbial communities. By analysing the results obtained in this work, it was concluded that CNT improved hydrogen and acetate conversion to methane by pure cultures of methanogens and by syntrophic co-cultures of S. wolfei and M. hungatei. However, future studies with CNT are encouraged in order to understand the mechanisms by which CNT influences the methanogenic activity and in which cases it can be involved in interspecies electron transfer, since with the results obtained it remains unclear if they have a role in electron exchange between different species.
O biogás, que é composto maioritariamente por metano, é um componente gasoso produzido por microorganismos que usam como substrato moléculas simples, como o acetato, o hidrogénio ou o dióxido carbono, é uma conhecida alternativa aos combustíveis fósseis como fonte de energia. Em comunidades sintróficas, os organismos metanogénicos e as bactérias presentes trocam eletrões entre si com o objetivo de obtenção de energia para o seu crescimento, através de pequenos compostos químicos solúveis que servem de transporte, como o hidrogénio e o formato. Estudos recentes indicam que em alguns casos, estas trocas de eletrões podem ser realizadas diretamente ou por meio de materiais condutores, sendo esta uma abordagem que poderá ser mais favorável de um ponto de visto energético, aumentando assim a eficiência da metanogénese. Este projeto visou o estudo do efeito de nanotubos de carvão (NTC) nos mecanismos que envolvem a produção de metano em comunidades metanogénicas, através de dois diferentes estudos. No primeiro estudo, foram realizados ensaios em batch com culturas puras dos organismos metanogénicos hidrogenotróficos, Methanobacterium formicicum e Methanospirillum hungatei, e acetoclásticos, Methanosaeta concilii e Methanosarcina mazei, na presença de NTC. Além disso, também foram testadas culturas puras de M. formicicum na presença de NTC, mas sem adição de um agente redutor. Pelos resultados obtidos, verificou-se que os NTC provocaram um aumento na produção de metano e redução da fase de latência nas culturas puras dos metanogénicos hidrogenotróficos. Apesar de a presença dos NTC também ter acelerado a produção de metano nas culturas dos acetoclásticos com 1 g/L de NTC, numa maior concentração de 5 g/L de NTC, foi registada uma inibição na produção de metano e um aumento na duração das fases de latência. Num segundo estudo foram inoculadas culturas mistas contendo Syntrophomonas wolfei, uma bactéria que metaboliza butirato, e M. hungatei. Os resultados obtidos mostraram que a produção de metano também foi acelerada nas culturas mistas inoculadas com NTC, atingindo uma taxa de produção de metano de 1.03 ± 0.03 mM/d para as culturas incubadas com 5 g/L NTC, enquanto que na ausência de NTC, a taxa obtida foi de apenas 0.72 ± 0.01 mM/d. No âmbito deste trabalho, também foi realizada uma adaptação de biomassa em reatores anaeróbios, com o objetivo a longo prazo de adicionar os NTC para estudar o seu efeito em comunidades microbianas complexas. Por último, a análise dos resultados obtidos neste trabalho permitiu concluir que os NTC têm um efeito benéfico na conversão dos substratos a metano pelos microorganismos metanogénicos e pelas co-culturas sintróficas de S. wolfei e M. hungatei. Contudo, serão necessários mais estudos com os NTC para compreender melhor de que forma estes poderão estar envolvidos nos mecanismos de transferência de eletrões entre espécies, pois a sua influência neste processo continua por determinar.