京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第22665号 / 農博第2420号 / 新制||農||1080(附属図書館) / 学位論文||R2||N5296(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 栗原 達夫, 教授 小川 順, 教授 阪井 康能 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

The goal of this project is to decipher the quorum sensing (cell-to-cell signaling) abilities of Shewanella oneidensis MR-1, a Gram-negative bacterium well known for its ability to use geologic substrates, such as Fe and Mn oxides, for respiratory purposes. Overall our results show that S. oneidensis cannot utilize either an acyl-homoserine lactone (AHL) or AI-2 quorum sensing signal, despite previous work that indicated that it produced an AHL that would enhance it ability to growth in certain anaerobic environments. Using a variety of quorum sensing signal sensors, no evidence could be found that S. oneidensis has a typical AHL signal. An in silco analysis of the genome also produced little evidence that S. oneidensis has the genes to accept or relay an AHL signal. S. oneidensis can produce a luminescence response in the AI-2 reporter strain, Vibrio harveyi MM32. This luminescence response is abolished upon deletion of luxS, the gene responsible for catalyzing AI-2. Deletion of luxS also affected biofilm formation. Within 16 hours of growth in a biofilm flow-through reactor, the luxS mutant had an inhibited ability to initiate biofilm formation. After 48 hours of growth, the mutant's biofilm had developed similarly to wild-type. The addition of synthetic AI-2 did not restore the mutant's ability to initiation biofilm formation, which led to the conclusion that AI-2 is not likely used as a quorum sensing signal in S. oneidensis for this phenotype. Because of the involvement of LuxS in the activated methyl cycle (AMC) in other organisms, growth on various sulfur sources was examined. A mutation in luxS produced a reduced ability to growth with methionine as the sole sulfur source. Methionine is a key metabolite used in the AMC to produce a methyl source in the cell and homocysteine. This data suggests that LuxS is important in metabolizing methionine and the AMC in S. oneidensis. / Ph. D.

Shewanella oneidensis est une bactérie aquatique capable de chimiotactisme, c'est-à-dire d'orienter sa nage en réponse aux signaux qu'elle perçoit. Mon travail de thèse s'est focalisé sur l'étude du système chimiotactique de cette bactérie. Mon premier objectif a été d'identifier de nouveaux substrats induisant une réponse chimiotactique ainsi que les chimiorécepteurs les détectant. Une approche à haut débit utilisant une banque de substrats, couplée à une recherche de substrats plus spécifiques, a permis d'identifier de nouveaux signaux. Nous avons confirmé que S. oneidensis est attirée par les accepteurs alternatifs d'électrons ainsi que par certains métaux. Nous avons montré qu'elle est attirée par le malate et le chromate et repoussée par le nickel et le cobalt. Nous avons identifié deux MCPs potentiellement impliqués dans la détection du malate et un dans la détection du chromate.Mon second objectif a été de comprendre le rôle du système chimiotactique dans la formation d'un biofilm flottant : la pellicule. Nous avons montré que le développement de la pellicule est un processus en trois étapes déclenché par la détection de l'oxygène en condition statique, probablement par aérotactisme. Nous avons mis en évidence l'implication inattendue du chimiotactisme dans la formation de la pellicule. En effet des mutants délétés de gènes codant pour des éléments du système chimiotactique ne forment pas de pellicule normale. Le développement de la pellicule met en jeu d'autres signaux chimiotactiques, générés au sein de la pellicule, qui pourraient intervenir dans la localisation des cellules et l'homogénéisation de la pellicule au cours de sa maturation. / Shewanella oneidensis is an aquatic bacterium capable of chemotaxis, meaning that it can change its direction in response to detected signals. My thesis focused on the study of the chemotaxis system of this bacterium.The first objective of my thesis was to identify new substrates inducing a chemotactic response and the chemoreceptors involved in their detection. A high-throughput technique involving a library of solutes coupled with a search of more specific compounds allowed to identify new signals. We confirmed that S. oneidensis is attracted toward alternative electron acceptors and by several metals. We showed that S. oneidensis is attracted toward malate and also chromate. Finally, we identified two repellents, nickel and cobalt. After construction of deletion mutants, we identified two MCPs potentially involved in malate detection and one in chromate detection.The second objective of my thesis was to understand the role of the chemotaxis system in the formation of a floating biofilm: the pellicle. We first characterized the pellicle development through time, revealing that it is a three-step process. We then highlighted the unexpected role of the chemotaxis system in pellicle formation. Indeed mutants deleted of genes coding for chemotaxis elements are not able to form a pellicle or form an abnormal one. We showed that oxygen is the main signal triggering pellicle formation in static condition and that it is probably detected through aerotaxis. Pellicle development also involves other chemotactic signals produced in the pellicle which could be used in the localization of cells at the air-liquid interface but also in the homogenization of the pellicle.

Nous avons cherché dans ce travail à élaborer un biofilm artificiel électroactif dans le but de promouvoir les réactions de transfert extracellulaire d’électrons (EET) en reconstituant artificiellement un biofilm en présence de matériaux exogènes. Un matériau composite auto-assemblé constitué de cellules bactériennes (Shewanella oneidensis), de nanotubes de carbone et de cytochromes c exogènes (issue de cellules de cœur de bœuf) a été tout d’abord proposé. Le processus d’auto-assemblage a été étudié par diffusion de lumière dynamique, microscopie électronique à balayage et spectroscopie Raman. Ces analyses ont mis en évidence l’importance du cytochrome exogène dans l’assemblage et l’organisation du matériau. La viabilité bactérienne a été étudiée et l’activité métabolique a été caractérisée par électrochimie. Les courants à l’anode étaient 10 et 4 fois plus importants avec ce biofilm artificiel (0,027 A m-2) qu’avec les électrodes modifiées par les bactéries seules (0,003 A m-2) ou associées au cytochrome c (0,007 A m-2). Le biofilm artificiel a été testé en substituant S. oneidensis par Pseudomonas fluorescens, produisant un courant d’oxydation lors de l’ajout de 1,5 mM de glucose. Le cytochrome c possède, outre son rôle structurant, une activité de navette à électrons. Son potentiel redox, 254 mV (vs NHE), était adapté à l’oxydation du formiate mais inadapté à la réduction du fumarate. Pour cette raison, il a été substitué par d’autres cytochromes (c3DvH, c7Da, c553DvH, c3DdN ou c3Dg) possédant des potentiels redox plus bas, de 20 mV à -400 mV. Ces cytochromes variaient aussi au niveau de leur charge à pH neutre, permettant de valider l’importance des forces électrostatiques dans l’assemblage du biocomposite. Les résultats optimaux obtenus avec c3DvH et c7Da ont montré l’importance du potentiel redox des éléments exogènes pour l’EET. Nous avons ensuite remplacé le cytochrome c par la protamine. Cette protéine non électroactive a permis l’assemblage du biocomposite tout en maintenant les transferts directs d’électrons entre les bactéries et les différents nanomatériaux testés. Les optimisations ont permis d’atteindre des courants cathodiques de plus de 12 A m-2 en présence de 50 mM de fumarate. Les expériences de stabilité ont montré la présence d’un courant biotique de 1,75 A m-2 après 24 h de réduction de 50 mM de fumarate / The aim of this PhD work was to design an artificial electroactive biofilm in order to optimize extracellular electron transfers (EET) by artificially reconstituting the biofilm in the presence of exogenous materials. A biocomposite material was proposed from the self-assembly of the bacteria Shewanella oneidensis with carbon nanotubes and cytochrome c (extract from bovine heart). The self-assembly was first studied by diffusion light scattering, scanning electron microscopy and Raman spectroscopy. These analyzes showed the importance of the cytochrome c in the assembly and organization of the biocomposite. Bacterial viability was studied and metabolic activity was characterized with the help of electrochemistry. The current at the anode was 10 and 4 times higher with the artificial biofilm (0.027 A m2) than with film composed with bacteria alone (0.003 A m2) or associated with cytochrome c (0.007 A m2). Artificial biofilm was also tested with Pseudomonas fluorescens instead of S. oneidensis, producing an oxidative current upon the addition of 1.5 mM glucose. That indicates cytochrome c has, in addition to its structuring role, an electron shuttle activity. Its redox potential, +254 mV (vs. NHE), was adapted to the oxidation of formate but was unsuitable for the reduction of fumarate. For this reason, it has been substituted by other cytochromes, c3DvH, c7Da, c553DvH, c3DdN, and c3Dg, possessing lower redox potentials, in the range of 20 mV to -400 mV. These cytochromes also varied at the level of their charge at neutral pH and allowed to validate the importance of the electrostatic forces in the assembly of the biocomposite. The optimal results obtained with c3DvH and c7Da showed the importance of the redox potential of the exogenous elements for the EET. We then replaced the cytochrome c with protamine. This non-electroactive protein allowed the assembly of the biocomposite by promoting direct electrons transfer between the bacteria and the different nanomaterials tested. The optimizations made it possible to reach cathodic currents of more than 12 A m2 in the presence of 50 mM of fumarate. The stability experiments showed the presence of a biotic current of 1.75 A m2 after 24 h of reduction of 50 mM of fumarate

Made available in DSpace on 2014-12-17T15:18:11Z (GMT). No. of bitstreams: 1 AmandaLSS.pdf: 2422936 bytes, checksum: d5a0f2bb2f42d87bacd7a1d2c3f5c6bc (MD5) Previous issue date: 2009-03-26 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / Bacteria trom Shewanella and Geobacter ganera are the most studied iron-reducing microorganisms particularly due to their electron transport systems and contribution to some industrial and environmental problems, including steel corrosion, bioenergy and bioremediation of petroleum-impacted sites. The present study was focused in two ways: the first is an in silico comparative ecogenomic study of Shewanella spp. with sequenced genomes, and the second is an experimental metagenomic work to detect iron-reducing Shewanella through PCR-DGGE of a metabolic gene. The in silico study resulted in positive correIation between copy number of 16S rDNA and genome size in Shewanella spp., with clusters of rrn near lhe origin of replication. This way, the genus is inferred as opportunist. There are no compact genomes and their sequences length varied, ranging from 4306142 nt in S. amazonensis SB2B to 5935403 nt in S. woodyi ATCC 51908, without correIation to temperature range characteristic of each specie. Intragenomic 16S rDNA sequences possess little divergence, but reasonable to resuIt in different phyIogenetic trees, depending on the sequence that is chosen to compare. For moIecuIar detection of iron-reducing Shewanella, it is proposed the mtrB gene as new biomarker. because it codes to a fundamental protein at Fe (III)-reduction. The specific primers were designed and evaluated in silico and resulted in a fragment of 360 pb. In the second study, these primers were tested in a genomic sample from S. oneidensis MR-1, amplifying the expected region. After this successfuI resuIt, the primer set was used as a tool to assess the iron-reducing communities of ShewaneIla genus under an environmental stress, i.e. crude oil contamination in mangrove sediment in Rio Grande do Norte State (Brazil). The primers presented high specificity and the reactions performed resulted in one single band of ampIification in the metagenomic samples. The fingerprinting obtained at DGGE reveaIed temporal variation of Shewanella spp. in analyzed samples. The resuIts presented show the detection of a biotechnological important group of microorganisms, the iron-reducing Shewanella spp. using a metabolic gane as target. It is concluded there are eight or more 16S rDNA sequences in Shewanella genus, with little divergence among them that affects the phylogeny; the pair of primers designed to ampIify mtrB sequences is a viable alternative to detect iron-reducing ShewanelIa in metagenomic approaches; such bacteria are present in the mangrove sediment anaIyzed, with temporal variations in the samples. This is the first experimental study that screened the iron-reducing Shewanella genus in a metagenomic experiment of mangrove sediments subjected to oil contamination through a key metabolic gene / Bact?rias dos g?neros Shewanella e Geobacter s?o os microrganismos redutores de ferro mais estudados. Esse interesse ocorre particularmente devido aos seus sistemas de transporte de el?trons e contribui??o em alguns problemas industriais e ambientais, tais como corros?o de oIeodutos, bioenergia e biorremedia??o de locais contaminados com petr?leo. O presente estudo foi tocado em duas partes: a primeira ? um estudo ecogen?mico comparativo de ShewanelIa spp. com genomas seq?enciados, e a segunda ? um trabalho metagen?mico experimental para detectar Shewanella redutoras de ferro atrav?s de PCR-DGGE de um gene metab?lico. O estudo in silico resultou em correla??o positiva entre o n?mero de c?pias 16S rDNA e tamanho do genoma em ShewaneIla spp., com agrupamentos de rrn. pr?ximo ? origem de replica??o. Desta maneira, o g?nero ? inferido como oportunista. N?o existem genomas compactos e o tamanho de suas sequ?ncias variam de 4306142 nt em S. amazonensis SB2B at? 5935403 nt em S. woodyi ATCC 51908, sem correla??o com a faixa de temperatura caracter?stica de cada esp?cie. Sequ?ncias intragen?micas de 16S rDNA possuem pouca diverg?ncia. mas razo?vel para resultar em diferentes ?rvores filogen?ticas. dependendo da sequ?ncia que ? escolhida para compara??o. Para a detec??o moIecuIar de ShewanelIa redutoras de ferro, ? proposto o gene mtrB como um novo biomarcador, por ser codante de uma prote?na fundamental na redu?ao de Fe (III). Os primers espec?ficos foram desenhados e avaliados in silico e resultou em um fragmento de 360 pb. No segundo estudo, esses primers foram testados em . amostra gen?mica de S. oneidensis MR-1, amplificando a regi?o esperada. Depois desse resultado favor?vel, o par de primers foi utilizado como ferramenta para acessar as comunidades redutoras de ferro do g?nero ShewanelIa sob um stress ambiental - contamina??o com ?leo cru em sedimento de mangue, no Estado do Grande do Norte (Brasil). Os primers apresentaram alta especificidade e as rea??es resultaram em banda ?nica de amplifica??o das amostras metagen?micas. O perfil obtido no DGGE revelou varia??o temporal de ShewanelIa spp. nas amostras analisadas. Os resultados apresentados mostram a defec??o de um grupo de microrganismos biotecnologicamente importante. ShewaneIla spp. redutoras de ferro, usando um gene metab?lico como alvo. Concluiu-se que existem oito ou mais sequ?ncias 16S rDNA no g?nero ShewaneIla, com pouca diverg?ncia entre elas que afetam a filogenia; o par de primers desenhados para amplificar sequ?ncias mtrB ? uma alternativa vi?vel para detectar Shewanella redutoras de ferro em abordagens metagen?micas; tais bact?rias est?o presentes no sedimento de mangue analisado, com varia??es temporais nas amostras. Este ? o primeiro estudo experimental que examina Shewanella redutoras de ferro em um experimento metagen?mico de sedimento de mangue submetido a contamina??o por ?leo atrav?s de um gene metab?lico

Submitted by Haroudo Xavier Filho (haroudo.xavierfo@ufpe.br) on 2016-03-04T16:25:51Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Roger Dissertação Mestrado 2014_ versão Final biblioteca_ Entregue_.pdf: 1359994 bytes, checksum: ce3bbcf3906e6cb72bdfea9a7b7e7d06 (MD5) / Made available in DSpace on 2016-03-04T16:25:51Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Roger Dissertação Mestrado 2014_ versão Final biblioteca_ Entregue_.pdf: 1359994 bytes, checksum: ce3bbcf3906e6cb72bdfea9a7b7e7d06 (MD5) Previous issue date: 2014-02-20 / CAPES / CNPq / FINEP / O gênero Shewanella é um representante da classe das Gammaproteobactérias, família Shewanellaceae, compondo um grupo de bactérias gram-negativas, móveis, baciliforme, oxidase positiva, comumente encontrada em ambiente marinho e isolada do trato digestivo de animais aquáticos. Devido a suas características vem sendo amplamente testado como probiótico na carcinicultura. Estes têm sido utilizados na aquicultura para o controle biológico, aumento da taxa de conversão alimentar e sistema imune dos camarões. Este estudo teve por objetivo identificar potenciais bactérias probióticas retiradas do hepatopâncreas e estômago do camarão cultivado em sistema heterotrófico, avaliar as relações filogenéticas das cepas com o gênero Shewanella e caracteriza-las através de análisesmorfológicas, bioquímicas, produção de biofilme e antibiograma. A partir do cultivo heterotrófico de Litopenaeus vannamei, foram selecionadas as cepasIPA-S.51, IPA-S.111 e IPA-S.252para identificação através do sequenciamento parcial do gene 16S rRNA e comparados ao GenBank – NCBI e RDP - Seqmatch. As cepas foram alinhadas a 45 espécies do gênero Shewanella e avaliadas filogeneticamente utilizando os métodos Neighbor-Joining, Máxima Verossimilhança e Inferência Bayesiana. Quanto àsanálises morfológicas foram avaliadas parâmetros de acordo com a similaridade a padrões estabelecidos. Os testes bioquímicos foram realizados com o auxílio dos kits BACTRAY I, BACTRAY II e BACTRAY III (Labroclin®), totalizando 30 testes bioquímicos. A avaliação da capacidade de formação de biofilme foi realizada segundo Christensen e colaboradores. No antibiograma as cepas bacterianas foram submetidas a 13 antibióticos distintos segundo à técnica de Kirby e Bauer, com três repetições. O sequenciamento das cepas revelou alta similaridade a espécie Shewanella algae, utilizando o GenBank e o RDP-seqmath. A Inferência Bayesiana apresentou maior aporte estatístico e fidelidade dentre os métodos analisados. A Shewanella upenei apresentou alta similaridade as cepas estudadas, assim como a S. algae. As análises filogenéticas não descartam a hipótese de novas espécies para IPA-S.51, IPA-S.111 e IPAS. 252. As cepas estudadas foram sensíveis aos antibióticos Ampicilina/Subactan, Ofloxacina e Tetraciclina. A caracterização fenotípica fortalece a hipótese de especiação para as cepas testadas. Portanto, a capacidade de formação de biofilme, adicionada ao alto potencial enzimático e antagonismo a patógenos, característico do gênero Shewanella, tornam estas cepas potenciais probióticos para carcinicultura. / The genus Shewanella is one representant of Gammoproteobacteria class, family Shewanellaceae, being part of gram-negative bacteria group, mobile, bacilliform, oxidasepositive, commonly found on marine environments and isolated from the digestive tract of aquatic animals. Due to its characteristics, some tests as probiotics are being carried out in carciniculture. They are being used on aquaculture for biological control, augmentations on feed conversion rates and immune system of shrimps. This study has as objective identify potentials probiotics bacteria found in the hepatopancreas and stomach of shrimps cultivated on heterotrophic based system, evaluating the strain phylogenetic relationships with Shewanella genus and characterizing them through morphological and biochemical analysis, biofilm production and antibiogram. The strains IPA-S.51, IPA-S.111 e IPA-S.252 were selected from the heterotrophic cultivation of Litopenaeus vannamei, identified through partial 16S rRNA sequencing and compared to GenBank – NCBI and RDP - Seqmatch.The strains were aligned to 45 species of Shewanella genus and phylogenetically evaluated using Neighbor-Joining,Maximum-Likelihood estimation and Bayesian Inference.Regarding the morphological analysis parameters were evaluated according with established standard similarities. The biochemical tests were conducted with the assistance of BACTRAY I, BACTRAY II and BACTRAY III (Labroclin®) kits, totalizing 30 biochemical tests.The Biofilm capacity evaluation was made according Christensen et al. Regarding the antibiogram, the bacterial strains had undergone 13 distinct antibiotics according Kirby and Bauer, with three repetitions. The strains sequencing showed high similarity to Shewanella algae species, using GenBank and RDP-seqmath.The Bayesian inference displayed higher statistic contribution e fidelity among the other methods.The Shewanella upenei showed high similarity to the strains in study also as Shewanella algae.The phylogenetic analysis does not exclude the hypothesis of IPA-S.51, IPA-S.111 e IPA-S.252 being new species.The strains studied were sensitives to the antibiotics Ampicillin/Sulbactam, Ofloxacin, Tetracyclin. The phenotypic characterization of the strains supports the hypothesis of speciation. Thus, the capacity of biofilm formation plus the high enzymatic potential and antagonism interactions to pathogens, characteristics found in the Shewanella genus, make these strains potential probiotics to carciniculture.

Il est reconnu, depuis des années, que la flore intestinale par son équilibre complexe et dynamique joue un rôle essentiel dans la santé humaine. Une des stratégies les plus prometteuses pour la maintenir ou l’améliorer consiste à moduler le microbiome par l’utilisation de bactéries probiotiques ou de sucres prébiotiques. C’est dans ce contexte que s’inscrivent les études structurales et fonctionnelles d’α glucosidases bactériennes développées dans cette thèse. Ces enzymes hydrolysant les liaisons α-(1,4) glucosidiques sont classées, selon la base de données CAZy, dans les familles de glycoside hydrolases (GH) 4, 13, 31, 63, 97 et 122. Ces travaux de thèse, centrés sur trois α-glucosidases issues de Lactobacillus bulgaricus (11842aglu, GH31), Lactococcus lactis (1403aglu, GH13) et Shewanella sp. ANA-3 (SHWaglu, GH97), exposent la mise au point de leurs protocoles de surexpression et de purification. Ils présentent également des études bioinformatiques de 11842aglu et de 1403aglu, ainsi qu’une caractérisation enzymatique préliminaire de cette dernière. Une analyse structurale et fonctionnelle approfondie de SHWaglu a aussi été réalisée. La résolution, par cristallographie aux rayons X, des structures de SHWaglu seule, en complexe avec différents ligands et de mutants, a participé à enrichir les connaissances, jusqu’à présent peu étendues, sur les enzymes de la famille GH97. Ainsi, un motif structural conservé au sein de cette famille a notamment été mis en évidence. Par ailleurs, ces informations structurales combinées aux études enzymatiques ont permis de révéler des déterminants moléculaires de l’activité de cette α-glucosidase et, par conséquent, d’établir les relations structure-fonction-activité de cette enzyme. Ainsi, l’ensemble des données obtenues, couplé à des études d’ingénierie protéique, contribue à ouvrir de nouvelles perspectives industrielles, notamment en suggérant d’optimiser ou de conférer des activités enzymatiques modifiées dans certaines cibles de choix afin de leur faire synthétiser des sucres de type prébiotiques / It is now generally accepted that the gut flora with its complex and dynamic nature plays a vital role in human health. One of the most promising strategies for maintaining or improving health is to modulate the microbiome by the use of probiotics and prebiotics as food supplements. The structure/function/activity relationship studies of bacterial α-glucosidases described in this thesis have been performed within this context. These α-(1,4)-glucosidic bond hydrolyzing enzymes are classified, according to the CAZy database, into glycoside hydrolases families (GH) 4, 13, 31, 63, 97 and 122. This thesis work, has focused on three α-glucosidases from Lactobacillus bulgaricus (11842aglu, GH31), Lactococcus lactis (1403aglu, GH13) and Shewanella sp. ANA-3 (SHWaglu, GH97), and the development of their overexpression and purification protocols. It also presents a bioinformatics studies of 11842aglu and 1403aglu, as well as preliminary enzymatic characterization of the latter. As for SHWaglu, detailed structural and functional studies have been carried out. The crystal structures of SHWaglu in its native state, in complex with different ligands as well as site directed mutants have contributed to increase our knowledge on enzymes from the GH97 family which to date remains relatively limited. Notably, a conserved structural motif in this family has been identified. Overall, the structural- and enzymatic studies and analyses have revealed molecular-and structural determinants governing the activity and broad substrate specificity of this α-glucosidase which is adapted to cold temperatures. Apart from the insight gained from a fundamental research point of view, data described within this work, coupled with protein engineering studies may contribute to open up new industrial perspectives, in particular by suggesting optimized or altered enzyme activities in some attractive enzyme targets with the aim of synthesizing prebiotic compounds

Le « quorum sensing » (QS) est un moyen de communication bactérienne impliquant des petites molécules appelées auto-inducteurs qui au-delà d’un certain seuil de concentration induisent une synchronisation de l’expression génétique au sein de la communauté bactérienne. Ce mécanisme est impliqué dans plusieurs processus bactériens tels que la luminescence, la formation du biofilm, ce qui en fait une cible privilégiée pour l’inhibition du biofilm bactérien nuisible aux activités humaines. Plusieurs systèmes QS ont été identifiés ; les plus étudiés sont le système AHL (acyl homoserine lactone) et le système AI2 (auto inducteur 2). L’objectif principal de cette thèse est de caractériser le(s) système(s) QS de Shewanella woodyi, une bactérie marine luminescente capable de coloniser rapidement une surface et de former un biofilm. L’utilisation de biosenseurs de référence et des expériences de LC-MS ont montré que S. woodyi synthétise la C8-HSL et l’AI2. La mutation des gènes impliqués dans la synthèse ou la détection des HSL abolit la luminescence mais n’affecte pas la formation du biofilm. De plus, le système AI2 ne semble pas impliqué dans la luminescence et la formation de biofilm de S. woodyi. L’absence d’un récepteur d’AI2 suggère que cette molécule n’a pas un rôle régulateur et qu’elle ne serait qu’un produit secondaire du métabolisme cellulaire. Ce travail a donc permis de caractériser les 2 principaux systèmes QS de S. woodyi et pourrait permettre d’en faire un nouveau biosenseur marin. / Quorum sensing (QS) is a bacterial communication system involving small molecules called autoinducers which above a threshold concentration, induce the synchronization of genes expression within the bacterial community. This mechanism is involved in several bacterial processes such as luminescence and biofilm formation, making it a preferred target for the inhibition of bacterial biofilm harmful to human activities. Several QS systems have been identified; the most studied ones are the AHL system (acylhomoserine lactone) and the AI2 system (autoinducer 2). The main objective of this thesis is to characterize the QS system (s) of Shewanella woodyi, a luminescent marine bacterium able to rapidly colonize a surface and form a biofilm. The use of reference biosensors and LC-MS experiments have shown that S. woodyi synthesizes C8-HSL and AI2. The mutation of the genes involved in the synthesis or detection of HSL abolishes luminescence but does not affect the biofilm formation. Moreover, the AI2 system does not appear to be involved in the luminescence and biofilm formation of S. woodyi. The absence of an AI2 receptor suggests that this molecule does not have a regulatory role and that it is only a secondary product of cellular metabolism. This work has allowed the characterization of the 2 main QS systems of S. woodyi, which could make this strain a new marine biosensor.

The biogenic reduction of Mn(IV) oxides is one of the most favorable anaerobic electron transfer processes in aquatic systems and likely plays an important role in the redox cycle of both carbon and nitrogen in anaerobic environments; yet, the different pathways involved in the microbial transformation of Mn(IV) oxides remain unclear. The coupling between the reduction of Mn(IV) to Mn(II) and the oxidation of organic carbon to CO₂ is largely catalyzed by microorganisms in various environments such as redox stratified water columns and sediments. The recent discovery that soluble Mn(III) exists in natural systems and is formed during biological oxidation of Mn(II) implies the possibility that Mn(III) is formed as an intermediate during the microbial reduction of Mn(IV). In this dissertation, mutagenesis studies and kinetic analysis were combined to study the mechanism of microbial reduction of Mn(IV) by Shewanella oneidensis MR-1, one of the most studied metal-respiring prokaryotes. We show for the first time that the microbial reduction of Mn(IV) proceeds step-wise via two successive one-electron transfer reactions with soluble Mn(III) as intermediate produced in solution. The point mutant strain Mn3, generated via random chemical mutagenesis, presents a unique phenotype that reduces solid Mn(IV) to Mn(III) but not to Mn(II), suggesting that these two reduction steps proceed via different electron transport pathways. Mutagenesis studies on various in-frame deletion mutant strains demonstrate that the reduction of both solid Mn(IV) and soluble Mn(III) occurs at the outer membrane of the cell and Mn(IV) respiration involves only one of the two potential terminal reductases (c-type cytochrome MtrC and OmcA) involved in Fe(III) respiration. Interestingly, only the second electron transfer step is coupled to the respiration of organic carbon, which opposes the long-standing paradigm that microbial reduction of Mn(IV) proceeds via the single transfer of two electrons coupled to the mineralization of carbon substrates. The coupling between anaerobic nitrification and Mn reduction has been demonstrated to be thermodynamically favorable. However, the existence of this process in natural system is still in debate. In this dissertation, characterization of coastal marine sediments was combined with laboratory incubations of the same sediments to investigate the effect of Mn oxides on the redox cycle of nitrogen. Our slurry incubations demonstrate that anaerobic nitrification is catalyzed by Mn oxides. In addition, mass balance calculations on NH₄⁺ link the consumption of NH₄⁺ to anaerobic ammonium oxidation in the presence of Mn oxides and confirm the occurrence of Mn(IV)-catalyzed anaerobic nitrification. The activity of anaerobic nitrification is greatly affected by the initial ratio of Mn(IV) to NH₄⁺, the reactivity of Mn oxides, and the reducing potential of the system. Overall, Mn(IV)-catalyzed anaerobic nitrification may be an important source of nitrite/nitrate in anaerobic marine sediments and provide an alternative pathway for subsequent nitrogen losses in the marine nitrogen cycle.

Microbial metal reduction contributes to biogeochemical cycling, and reductive precipitation provides the basis for bioremediation strategies designed to immobilize radionuclide contaminants present in the subsurface. Facultatively anaerobic ×-proteobacteria of the genus Shewanella are present in many aquatic and terrestrial environments and are capable of respiration on a wide range of compounds as terminal electron acceptor including transition metals, uranium and transuranics. S. putrefaciens is readily cultivated in the laboratory and a genetic system was recently developed to study U(VI) reduction in this organism. U(VI) reduction-deficient S. putrefaciens point mutant Urr14 (hereafter referred to as CCMB1) was found to retain the ability to respire several alternate electron acceptors. In the present study, CCMB1 was tested on a suite of electron acceptors and found to retain growth on electron acceptors with high reduction potential (E¡¬0) [O2, Fe(III)-citrate, Mn(IV), Mn(III)-pyrophosphate, NO3-] but was impaired for anaerobic growth on electron acceptors with low E¡¬0 [NO2-, U(VI), dimethyl sulfoxide, trimethylamine N-oxide, fumarate, ×-FeOOH, SO32-, S2O32-]. Genetic complementation and sequencing analysis revealed that CCMB1 contained a point mutation (H108Y) in a CcmB homolog, an ABC transporter permease subunit required for c-type cytochrome maturation in E. coli. The periplasmic space of CCMB1 contained low levels of cytochrome c and elevated levels of free thiol equivalents (-SH), an indication that redox homeostasis was disrupted. Anaerobic growth ability, but not cytochrome c maturation activity, was restored to CCMB1 by adding exogenous disulfide bond-containing compounds (e.g., cystine) to the growth medium. To test the possibility that CcmB transports heme from the cytoplasm to the periplasm in S. putrefaciens, H108 was replaced with alanine, leucine, methionine and lysine residues via site-directed mutagenesis. Anaerobic growth, cytochrome c biosynthesis or redox homeostasis was disrupted in each of the site-directed mutants except H108M. The results of this study demonstrate, for the first time, that S. putrefaciens requires CcmB to produce c-type cytochromes under U(VI)-reducing conditions and maintain redox homeostasis during growth on electron acceptors with low E¡¬0. The present study is the first to examine CcmB activity during growth on electron acceptors with widely-ranging E¡¬0, and the results suggest that cytochrome c or free heme maintains periplasmic redox poise during growth on electron acceptors with E¡¬0 < 0.36V such as in the subsurface engineered for rapid U(VI) reduction or anoxic environments dominated by sulfate-reducing bacteria. A mechanism for CcmB heme translocation across the S. putrefaciens cytoplasmic membrane via heme coordination by H108 is proposed.