Techn. Universiẗat, Diss., 2003--Berlin.

Outer membrane cytochromes OmcB and OmcS of Geobacter sulfurreducens are two important components of the respiratory chain for extracellular Fe(III) reduction. OmcS is a loosely bound cell surface protein involved in the reduction of insoluble Fe(III). OmcB is an outer membrane protein and required for insoluble and soluble Fe(III) reduction. The objective of this study was to understand better the mechanism of dissimilatory Fe(III) reduction, focusing on the cell surface proteins by further localization, identification of protein-protein interactions, and biochemical characterization of OmcB and OmcS. OmcB was found to be surface-exposed but embedded in the outer membrane because mild protease treatment of cells resulted in partial degradation of OmcB. Removal of surface-exposed proteins inhibited Fe(III) reduction, which is at least partially due to the degradation of OmcB. Co-immunoprecipitation studies with outer surface proteins using an antibody against OmcS revealed that OmcS interacts with several proteins, of which some are implicated in Fe(III) reduction, such as PilA, OmpJ, and OmpB, and in electricity production, such as OmcZ. Other OmcS-associated proteins, which have not been studied, include a cytochrome (GSU2887), a hypothetical and a conserved hypothetical protein, and a putative protease with a PDZ domain. The results suggest that co-immunoprecipitation with other antibodies would help to identify more elements of electron transport pathways related to extracellular Fe(III) reduction. OmcB was purified via preparative sodium dodecylsulfate polyacrylamide gel electrophoresis (SDSPAGE) and anion-exchange chromatography. The molecular mass was determined as 82 kDa, and 11.5 hemes per molecule were found. OmcB was able to transfer electrons to either soluble or insoluble Fe(III). OmcS was purified by detergent extraction. The molecular mass was 47 kDa and it contains 6 heme groups. UV-visible, EPR, and NMR spectroscopies determined that all hemes are bis-histidyl hexacoordinated and low-spin in both oxidized and reduced forms. OmcS has a –212 mV midpoint redox potential, and donates electrons to soluble and insoluble metals and quinones. Transient state kinetics showed that OmcS reduces anthroquinone-2, 6-disulfonate 10 times faster than it reduces Fe(III) citrate. This study revealed valuable further details about the mechanism of Fe(III) reduction by G. sulfurreducens by identifying the localization, protein-protein interactions and biochemical characteristics of the components of extracellular electron transport.

Geobacter species are δ-Proteobacteria and are often predominant in the Fe(III) reduction zone of sedimentary environments. Their abilities to remediate contaminated environments and to produce electricity have inspired extensive studies. Cell motility, biofilm formation, and type IV pili, which have been shown to be regulated by chemotaxis genes in other bacteria, all appear important for the growth of Geobacter species in changing environments and for electricity production. The genomes of Geobacter species show the presence of a significant number of chemotaxis gene homologs, suggesting important roles for them in the physiology of Geobacter species, although gene functions are not yet identified. In this study, we focus on identifying chemotaxis components and studying their functions in Geobacter species. We identified a large number of homologs of chemotaxis genes, which are arranged in six or more major clusters in the genomes of Geobacter sulfurreducens, Geobacter metallireducens, and Geobacter uraniireducens. Based on homology to known pathways, functions of some chemotaxis clusters were assigned; others appear to be unique to Geobacter species. We discuss the diversity of chemoreceptors and other signaling proteins as well the regulation of chemotaxis genes in Geobacter species. The functions of chemotaxis genes were studied in G. sulfurreducens, whose genome contains ~ 70 chemotaxis gene homologs, arranged in 6 major clusters. These chemotaxis clusters are also found in other Geobacter species with similar gene order and high level of gene identity, suggesting that our study in G. sulfurreducens could be extrapolated to other Geobacter species. We identified the function of the che5 cluster of G. sulfureducens as regulation of the biosynthesis of extracellular materials. We showed that G. sulfurreducens KN400 is chemotactic, and that this behavior is flagellumdependent. Our preliminary data indicated that G. sulfurreducens may use the che1 cluster, which is found exclusively in Geobacteraceae, to regulate chemotaxis. Our studies demonstrated important roles of chemotaxis genes in Geobacter physiology and their presence in large numbers could be one of the reasons why Geobacter species outcompete other species in bioremediation sites. Further studies are warranted for better understanding of the mechanisms of Che-like pathways and their potential use in optimization of conditions for applications of Geobacter species in bioremediation and electricity generation.

Objetivou-se neste trabalho avaliar a remoção e degradação de surfactante aniônico alquilbenzeno linear sulfonado (LAS) em esgoto sanitário do município de São Carlos – SP empregando o reator anaeróbio de leito granular expandido (EGSB - Expanded Granular Sludge Bed) em escala piloto, com TDH de 36 horas e temperatura mesofílica (±35ºC), instalado na ETE de São Carlos. Análises físico-químicas e cromatográficas foram realizadas para a caracterização do esgoto sanitário e monitoramento do reator EGSB. Foi observado no esgoto sanitário concentração de DQO bruta e LAS de 653,50 ± 169,30 mg L-1 e 6,189 ± 3,25 mg L-1, respectivamente. Em relação ao Ferro e metais potencialmente tóxicos, foram observados no esgoto sanitário os seguintes compostos: Cádmio, Chumbo, Ferro, Manganês, Níquel e Zinco. Em relação aos compostos recalcitrantes foram observados Butil Benzenosulfonamida, Ácido Hexadecanóico, Limoneno, Terpineno, Fenol, Álcool Feniletílico, Indolizina, Cafeína e Isobutil Octadecil Ftalato. O reator EGSB foi monitorado durante 314 dias e observou-se para DQO afluente e efluente, respectivamente, 265,82 ± 82,36 mg L-1 e 63,24 ± 40,67 mg L-1. Em relação ao LAS observou-se 7,35 ± 3,76 mg L-1 e 3,32 ± 3,08 mg L-1, respectivamente. Verificou-se 60,37 ± 29,84% de remoção de LAS. Observou-se durante toda operação pH próximo a neutralidade (7,26 ± 0,31), alcalinidade total efluente de 234,61 ± 64,39 mgCaCO3 L-1 e ácidos orgânicos voláteis efluente de 88,26 ± 23,68 mg L-1. Por meio do balanço de massa constatou-se que 56,2% do LAS foram removidos, compreendendo 12,8% por adsorção e 43,4% por biodegradação. Ao longo da operação do EGSB observou-se desestruturação e diminuição do tamanho médio dos grânulos, tal fato corrobora com a maior concentração efluente de sólidos totais e sólidos totais voláteis no primeiro mês e ao final da operação em comparação com a média geral de sólidos efluentes. Foram identificados por meio da plataforma Illumina MiSeq, 18 gêneros relacionados a degradação do LAS, tais como Synergistes, Syntrophorhabdus, Syntrophus, Clostridium, Geobacter e Desulfovibrio. / This study purpose was to evaluate the Anionic Surfactant Linear Alkylbenzene Sulfonate (LAS) in sanitary sewage from the city of São Carlos using an anaerobic expanded granular sludge bed reactor (EGSB), at pilot scale, with 36 hours TDH and (± 35ºC) mesophilic temperature, installed at São Carlos wastewater treatment station. Physical-chemical and chromatographic analyzes were performed for sanitary sewage characterization and EGSB reactor monitoring. It was observed an amount of 653,50 ± 169,30 mg L-1 in the raw sewage COD and an amount of 6,189 ± 3,25 mg L-1 in LAS. Regarding the potentially toxic metals, the following compounds were observed in the sanitary sewage: Cadmium, Lead, Iron, Manganese, Nickel and Zinc. Concerning recalcitrant compounds, Butyl Benzenesulfonamide, Hexadecanoic Acid, Limonene, Terpinene, Phenol, Phenylethyl Alcohol, Indolizine, Caffeine and Isobutyl Octadecyl Phthalate were observed. The EGSB reactor was monitored for 314 days and was observed for affluent and effluent COD, respectively, 265.82 ± 82.36 mg L-1 and 63.24 ± 40.67 mg L-1. In relation to LAS, were observed 7.35 ± 3.76 mg L-1 and 3.32 ± 3.08 mg L-1, respectively. There was 60.37 ± 29.84% LAS removal. It was observed, during the whole operation, pH close to neutrality (7.26 ± 0.31), total effluent alkalinity of 234.61 ± 64.39 mg.CaCO3.L-1 and volatile organic acids effluent of 88.26 ± 23, 68 mg L-1. By mass balance it was verified that 56,2% of the LAS were removed, comprising 12,8% by adsorption and 43,4% by biodegradation. During the EGSB operation, it was observed a disintegration and a decrease in the average granules size, fact that corroborates with higher total solids effluent concentration and total volatile solids in the first month and at the end of the operation compared to general effluent solids average. 18 genres related to LAS degradation were identified through the Illumina MiSeq platform, such as Synergistes, Syntrophorhabdus, Syntrophus, Clostridium, Geobacter and Desulfovibrio.

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. / Microbially influenced corrosion (MIC) costs billions of euros per year. It is commonly agreed that sulphate-reducing bacteria (SRB) play a key role in anaerobic MIC of steels. In spite of this, laboratory experiments have difficulty in reproducing the corrosion of steels that is observed in natural environments. Moreover, they do not explain what triggers corrosion since SRB, ubiquitous in natural environments, do not systematically induce corrosion. The aim of this work was to evaluate the relevance of new electron transfer mechanisms between steels and proteins or microbial cells in the domain of MIC. The first part of the thesis evaluates the impact of [Fe]-hydrogenase on the anaerobic corrosion of mild steels. The direct catalysis of proton reduction by hydrogenases has often been suggested in the literature; here, it is clearly demonstrated. Hydrogenase from Clostridium acetobutylicum, whether it is active, deactivated on denatured, can accelerate the corrosion of mild steel. The presence of a phosphate medium makes the interpretations more complex without modifying the mechanism. A new hypothesis implying the crucial role of iron-sulphur clusters contained in the protein is brought to light. Corrosion catalysis by hydrogenases could be compared with well-known mechanisms of corrosion catalysis by iron sulphide. In this case, the redox state of iron-sulphur clusters would play a key role in the occurrence of corrosion. The second part elucidates the role of Geobacter sulfurreducens in anaerobic corrosion of three types of steels: mild steel (1145), ferritic (403) and austenitic steels (304L and 316L). Results show, for the first time, that adherent bacterial cells induce open circuit potential ennoblement of steels and accelerate the corrosion of slightly alloyed steels by a direct electron transfer mechanism. Depending on the concentrations of the electron acceptors and donors in the medium, G. sulfurreducens could either enhance corrosion propagation by direct catalysis of proton reduction or, in the absence of acceptors and with an excess of donors, protect against corrosion. Thus the occurrence of corrosion relies on the unfavourable conjunction of many parameters. These results obtained in laboratory conditions open new paths for investigating MIC in natural environments.

Objetivou-se neste trabalho avaliar a remoção e degradação de surfactante aniônico alquilbenzeno linear sulfonado (LAS) em esgoto sanitário do município de São Carlos – SP empregando o reator anaeróbio de leito granular expandido (EGSB - Expanded Granular Sludge Bed) em escala piloto, com TDH de 36 horas e temperatura mesofílica (±35ºC), instalado na ETE de São Carlos. Análises físico-químicas e cromatográficas foram realizadas para a caracterização do esgoto sanitário e monitoramento do reator EGSB. Foi observado no esgoto sanitário concentração de DQO bruta e LAS de 653,50 ± 169,30 mg L-1 e 6,189 ± 3,25 mg L-1, respectivamente. Em relação ao Ferro e metais potencialmente tóxicos, foram observados no esgoto sanitário os seguintes compostos: Cádmio, Chumbo, Ferro, Manganês, Níquel e Zinco. Em relação aos compostos recalcitrantes foram observados Butil Benzenosulfonamida, Ácido Hexadecanóico, Limoneno, Terpineno, Fenol, Álcool Feniletílico, Indolizina, Cafeína e Isobutil Octadecil Ftalato. O reator EGSB foi monitorado durante 314 dias e observou-se para DQO afluente e efluente, respectivamente, 265,82 ± 82,36 mg L-1 e 63,24 ± 40,67 mg L-1. Em relação ao LAS observou-se 7,35 ± 3,76 mg L-1 e 3,32 ± 3,08 mg L-1, respectivamente. Verificou-se 60,37 ± 29,84% de remoção de LAS. Observou-se durante toda operação pH próximo a neutralidade (7,26 ± 0,31), alcalinidade total efluente de 234,61 ± 64,39 mgCaCO3 L-1 e ácidos orgânicos voláteis efluente de 88,26 ± 23,68 mg L-1. Por meio do balanço de massa constatou-se que 56,2% do LAS foram removidos, compreendendo 12,8% por adsorção e 43,4% por biodegradação. Ao longo da operação do EGSB observou-se desestruturação e diminuição do tamanho médio dos grânulos, tal fato corrobora com a maior concentração efluente de sólidos totais e sólidos totais voláteis no primeiro mês e ao final da operação em comparação com a média geral de sólidos efluentes. Foram identificados por meio da plataforma Illumina MiSeq, 18 gêneros relacionados a degradação do LAS, tais como Synergistes, Syntrophorhabdus, Syntrophus, Clostridium, Geobacter e Desulfovibrio. / This study purpose was to evaluate the Anionic Surfactant Linear Alkylbenzene Sulfonate (LAS) in sanitary sewage from the city of São Carlos using an anaerobic expanded granular sludge bed reactor (EGSB), at pilot scale, with 36 hours TDH and (± 35ºC) mesophilic temperature, installed at São Carlos wastewater treatment station. Physical-chemical and chromatographic analyzes were performed for sanitary sewage characterization and EGSB reactor monitoring. It was observed an amount of 653,50 ± 169,30 mg L-1 in the raw sewage COD and an amount of 6,189 ± 3,25 mg L-1 in LAS. Regarding the potentially toxic metals, the following compounds were observed in the sanitary sewage: Cadmium, Lead, Iron, Manganese, Nickel and Zinc. Concerning recalcitrant compounds, Butyl Benzenesulfonamide, Hexadecanoic Acid, Limonene, Terpinene, Phenol, Phenylethyl Alcohol, Indolizine, Caffeine and Isobutyl Octadecyl Phthalate were observed. The EGSB reactor was monitored for 314 days and was observed for affluent and effluent COD, respectively, 265.82 ± 82.36 mg L-1 and 63.24 ± 40.67 mg L-1. In relation to LAS, were observed 7.35 ± 3.76 mg L-1 and 3.32 ± 3.08 mg L-1, respectively. There was 60.37 ± 29.84% LAS removal. It was observed, during the whole operation, pH close to neutrality (7.26 ± 0.31), total effluent alkalinity of 234.61 ± 64.39 mg.CaCO3.L-1 and volatile organic acids effluent of 88.26 ± 23, 68 mg L-1. By mass balance it was verified that 56,2% of the LAS were removed, comprising 12,8% by adsorption and 43,4% by biodegradation. During the EGSB operation, it was observed a disintegration and a decrease in the average granules size, fact that corroborates with higher total solids effluent concentration and total volatile solids in the first month and at the end of the operation compared to general effluent solids average. 18 genres related to LAS degradation were identified through the Illumina MiSeq platform, such as Synergistes, Syntrophorhabdus, Syntrophus, Clostridium, Geobacter and Desulfovibrio.

De multiples micro-organismes ont la capacité de catalyser l’oxydation électrochimique de matières organiques en s’organisant en biofilm à la surface d’anodes. Ce processus est à la base de procédés électro-microbiens très innovants tels que les piles à combustible microbiennes ou les électrolyseurs microbiens. L’interface biofilm/électrode a été l’objet de nombreuses étudesdont les conclusions restent difficiles à démêler en partie du fait de la diversité des paramètres interfaciaux mis en jeu. L’objet de ce travail de thèse est d’exploiter les technologies microsystèmes pour focaliser l’impact de la topographie de surface des électrodes sur le développement du biofilm et sur ses performances électro-catalytiques. La formation de biofilmsélectroactifs de Geobacter sulfurreducens a été étudiée sur des électrodes d’or présentant des topographies bien contrôlées, sous la forme de rugosité, porosité, réseau de piliers, à des échellesallant du nanomètre à quelques centaines de micromètres. La présence de microrugosité a permis d’accroitre les densités de courant d’un facteur 8 par rapport à une surface lisse et son effet a étéquantifié à l’aide du paramètre Sa. Nous avons tenté de distinguer les effets des différentes échelles de rugosité sur le développement du biofilm et la vitesse des transferts électroniques.L’intérêt de la microporosité a été discuté. L’accroissement de surface active par la présence de micro-piliers s’est avéré très efficace et une approche théorique a donné des clés de compréhension et d’optimisation. Les connaissances acquises dans les conditions de culture pure ont finalement été confrontées avec la mise en oeuvre de biofilms multi-espèces issus d’un inoculum complexe provenant de sédiments marins. / Many microorganisms have the ability to catalyze the electrochemical oxidation of organic matterby self-organizing into biofilm on the surface of anodes. This process is the basis of highlyinnovative electro-microbial processes such as microbial fuel cells or microbial electrolysis cells.The biofilm/electrode interface has been the subject of numerous studies whose conclusionsremain difficult to disentangle partly because of the diversity of the interfacial parameters involved.The purpose of this thesis work is to exploit microsystem technologies to focus the impact ofelectrode surface topography on biofilm development and electro-catalytic performance. Theformation of electroactive biofilms of Geobacter sulfurreducens was studied on gold electrodespresenting well-controlled topographies, in the form of roughness, porosity, pillar networks, atscales ranging from nanometer to a few hundred micrometers. The presence of micro-roughnessincreased the current densities by a factor of 8 compared to a smooth surface and its effect wasquantified using the Sa parameter. We have tried to distinguish the effects of different roughnessscales on biofilm development and electron transfer rates. The suitability of micro-porosity wasdiscussed. The increase of active surface area by the presence of micro-pillars has proved veryeffective and a theoretical approach has given keys to understanding and optimization. Theknowledge acquired under pure culture conditions was finally confronted with the use of multispeciesbiofilms formed from a complex inoculum coming from marine sediments.

Tetrachloroethene (PCE) is a major groundwater contaminant that often persists as dense, nonaqueous phase liquids (DNAPLs) in subsurface environments. Dissolved-phase PCE plumes emanate from DNAPL source zones, which act as continuous sources of contamination for decades. Removal of DNAPL source zones is crucial to achieve lasting remedy of contaminated aquifers. This research explored the contributions of the microbial reductive dechlorination process (i.e., anaerobic bioremediation) to PCE-DNAPL source zone remediation, either in isolation or as a polishing step for the removal of residual DNAPL remaining after application of surfactant enhanced aquifer remediation (SEAR), an emerging physical-chemical source zone treatment. Specific objectives of this research were to: (1) evaluate the ability of microorganisms to dechlorinate in the presence of PCE-DNAPL and at high dissolved-phase PCE concentrations expected near/in DNAPL source zones, (2) assess the distribution and activity of key dechlorinating populations during bioenhanced PCE-DNAPL dissolution in continuous-flow column experiments, (3) determine the influence of Tween 80, a biodegradable surfactant commonly used in SEAR, on the microbial reductive dechlorination process, (4) design and optimize quantitative real-time PCR (qPCR) protocols to detect and enumerate key dechlorinating populations (e.g., Geobacter lovleyi, Sulfurospirillum multivorans), and (5) explore the effects of oxygen on Dehalococcoides viability and biomarker quantification. This research demonstrated that microbial dechlorinating activity within DNAPL source zones promotes bioenhanced dissolution although many dechlorinating isolates cannot tolerate saturated PCE concentrations. Application of newly designed qPCR protocols established a direct link between dissolution enhancement and the distribution of relevant dechlorinating populations in the vicinity of PCE-DNAPL. The limited and reversible impact of Tween 80 on key dechlorinators supported the feasibility of a treatment train approach of SEAR followed by microbial reductive dechlorination to remediate PCE-DNAPL source zones. Finally, experiments with oxygen-exposed, Dehalococcoides-containing cultures suggested limitations of using Dehalococcoides DNA and RNA biomarkers for monitoring bioremediation at field sites. These findings advance the scientific understanding of the microbial reductive dechlorination process and are relevant to environmental remediation practitioners. The advantages and current shortcomings of PCE-DNAPL source zone bioremediation, as well as recommendations for future research, are discussed.

We propose a new method to integrate genome-scale metabolic models into biogeochemical reaction modeling. This method predicts rates of microbial metabolisms by combining flux balance analysis (FBA) with microbial rate laws. We applied this new hybrid method to methanogenesis by Methanosarcina barkeri. Our results show that the new method predicts well the progress of acetoclastic, methanol, and diauxic metabolism by M. barkeri. The hybrid method represents an improvement over dynamic FBA. We validated genome-scale metabolic models of Methanosarcina barkeri, Methanosarcina acetivorans, Geobacter metallireducens, Shewanella oneidensis, Shewanella putrefaciens and Shewanella sp. MR4 for application to biogeochemical modeling. FBA was used to predict the response of cell metabolism, and ATP and biomass yield. Our analysis provides improvements to these models for the purpose of applications to natural environments. / 2019-07-28

Addressing the low power generation of anodic biocatalysts is pertinent to the advancement of microbial fuel cell technology. While Propionibacterium freudenreichii ssp. shermanii has shown potential as a biocatalyst, its incomplete consumption of the anodic substrate is a persistent issue. This research aims to optimize substrate consumption to increase power generation using Propionibacterium freudenreichii ssp. shermanii as a biocatalyst. The effect of coculturing Geobacter sulfurreducens with Propionibacterium freudenreichii ssp. shermanii was investigated. The cocatalyst and pure culture performance was tested in an air-cathode microbial fuel cell. Geobacter sulfurreducens produced the highest maximum power density among the experimental cases. Power density produced by Propionibacterium freudenreichii ssp. shermanii was improved in the air-cathode design compared to previous experiments performed in an H-type design. The novel cocatalyst was shown to produce electricity, however a full characterization to elucidate the contribution to power generation by each microbe would be desirable to investigate.