Thèse de doctorat : Physique, chimie et biologie de l'environnement : Strasbourg 1 : 2008. / Texte en anglais. Titre provenant de l'écran-titre. Bibliogr. p. 180-192.

Despite the environmental significance of microbial manganese reduction, the molecular mechanism of microbial manganese respiration remains poorly understood. Soluble Mn(III) has been recently found to be a dominant soluble species in aquatic systems, yet little is known about the identity of microbial populations catalyzing Mn(III) reduction in the environment nor the molecular mechanism of Mn(III) respiration. In this research, a suite of Mn(III) reduction-deficient mutant strains were isolated, including Mn(III) reduction-deficient mutant strain Mn3-1 that also displayed the ability to reduce soluble organic-Fe(III), but not solid Fe(III) oxides, demonstrating for the first time that the reduction of soluble organic-Fe(III) and solid Fe(III) oxides proceed through electron transport pathways with at least one distinct component. This work also shows that the electron transport pathway for Mn(III) reduction in S. oneidensis shares many of the electron transport components of Fe(III) and Mn(IV) reduction pathways and that Mn(IV) reduction to Mn(II) proceeds step-wise through two one-electron transfer reactions with Mn(III) as a transient intermediate. Finally, sediment incubations were carried out to enrich for NH4+ oxidizing- Mn(III) reducing consortia. The Mn(III) reducing consortium was found to be dominated by an electrogenic Ochrobactrum sp. and a Shewanella sp. The isolated Shewanella strain is able to oxidize acetate with Mn(III) as electron acceptor, an activity never observed before in a metal-reducing member of the Shewanella genus.

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The electron transfer mechanisms of multiheme cytochromes were examined with scanning tunneling microscopy (STM). To simulate bacterial metal reduction mediated by proteins in direct contact with mineral surfaces, monolayers of purified decaheme cytochromes from the metal-reducing bacterium Shewanella oneidensis were prepared on Au(111) surfaces. Recombinant tetracysteine sequences were added to two outermembrane decaheme cytochromes (OmcA and MtrC) from S. oneidensis MR-1 to ensure chemical immobilization on Au(111). STM images of the cytochrome monolayers showed good coverage and their shapes/sizes matched that predicted by their respective molecular masses. Current-voltage (I-V) tunneling spectroscopy revealed that OmcA and MtrC exhibit characteristic tunneling spectra. Theoretical modeling of the single-molecule tunneling spectra revealed a distinct tunneling mechanism for each cytochrome: OmcA mediates tunneling current coherently whereas MtrC temporarily traps electrons via orbital-mediated tunneling. These mechanisms suggest a superexchange electron transfer mechanism for OmcA and a redox-specific (i.e. heme-mediated) electron transfer mechanism for MtrC at mineral surfaces during bacterial metal reduction. Additionally, a novel electrochemical STM configuration was designed to measure tunneling current from multiheme cytochromes to hematite (001) surfaces in various electrolyte solutions. Current-distance (I-s) profiles on hematite (001) reveal predictable electric double layer structure that changes with ionic strength. The addition of the small tetraheme cytochrome c (STC) from S. oneidensis on insulated Au tips resulted in modified tunneling profiles that suggest STC significantly modulates the double layer. This observation is relevant to understanding metal reduction in cases where terminal metal-reducing enzymes are unable to come in direct contact with reducible mineral surfaces. Electronic coupling to the mineral surface might therefore be mediated by a localized ion swarm specific to the mineral surface. / Ph. D.

Mining and mineral processing generate a wide range of As-rich minerals, including scorodite (FeAsO4•2H2O), and arsenical ferrihydrite, which are common secondary minerals found in mine tailings. Scorodite and arsenical ferrihydrite are relatively stable under a wide range of physico-chemical conditions which makes them suitable arsenic sinks in mining environments. However, bacteria can reduce these minerals and release arsenic into the aqueous environment. Two dissimilatory iron and arsenic reducing bacteria, Shewanella sp. ANA-3 and Shewanella putrefaciens CN32, were used to investigate their effects on the reductive dissolution of scorodite and arsenical 6-line ferrihydrite in a chemically defined medium containing low phosphate concentrations representative of the natural environment. Analysis of the aqueous phase of all biotic reduced samples found mainly As(III), the more toxic form of As, while very little As(V) was reduced in the abiotic samples. Solid state analysis of the scorodite biotic post-reduction minerals identified scorodite, biogenic Fe(II)-As(III) compounds, parasymplesite and tooeleite, while in the biotic reduced arsenical six-line ferrihydrite, biogenic Fe(II)-As(III) compounds, hematite, akaganeite and unconfirmed magnetite were identified as secondary reduction products. Results from this research add to the body of literature on As and Fe biogeochemistry and provide very useful information for future assessments of the long term stability of As-rich minerals. L’activité minière et la transformation du minerai génèrent divers minéraux riches en arsenic, tels la scorodite (FeAsO4•2H2O) et la ferrihydrite riche en arsenic, lesquels sont des minéraux secondaires communs des résidus miniers. Comme la scorodite et la ferrihydrite riche en arsenic sont relativement stables sous une grande gamme de conditions physico-chimiques, ces minéraux peuvent potentiellement être utilisés pour stocker de façon permanente l’arsenic dans les environnements miniers. Cependant, certaines bactéries peuvent réduire ces minéraux, ce qui entraine la solubilisation de l’arsenic. Deux bactéries capables de réduire l’arsenic et le fer, soit Shewanella sp. ANA-3 et Shewanella putrefaciens CN32, ont été utilisées afin de déterminer leurs effets sur la réduction microbienne de la scorodite et de la ferrihydrite riche en As dans un milieu de culture contenant de faibles concentrations de phosphate. Les analyses de la phase aqueuse ont démontré que dans tous les systèmes biotiques, As(V) a été réduit en As(III), alors que dans les systèmes contrôles abiotiques, peu de As(V) a été réduit. L’analyse des minéraux secondaires présents à la fin réduction dans les systèmes biotiques contenant de la scorodite indique que la scorodite est encore présente, ainsi que des composés organiques riches en Fe(II) et As(III), de la parasymplésite et de la tooéleite, alors que dans les systèmes biotiques contenant de la ferrihydrite riche en As, des composés riches en Fe(II) et en As(III), de l’hématite, de l’akaganéite et de la magnétique ont été identifiés comme minéraux secondaires. Les résultats de cette étude enrichissent la littérature sur le cycle biogéochimique du Fe et de As et fournissent de l’information importante pour l’évaluation de la stabilité à long terme de minéraux riches en As.

Dissimilatory metal-reducing bacteria (DMRB) play an important role in the biogeochemical cycling of metals. DMRB are unique in that they possess the ability to couple metal reduction with their metabolism. Microbial Fe(III) respiration is a central component of a variety of environmentally important processes, including the biogeochemical cycling of iron and carbon in redox stratified water and sediments, the bioremediation of radionuclide-contaminated water, the degradation of toxic hazardous pollutants, and the generation of electricity in microbial fuel cells. Despite this environmental and evolutionary importance, the molecular mechanism of microbial Fe(III) respiration is poorly understood. Current models of the molecular mechanism of microbial metal respiration are based on direct enzymatic, Fe(III) solubilization, and electron shuttling pathways. Fe(III) oxides are solid at circumneutral pH and therefore unable to come into direct contact with the microbial inner membrane, these bacteria must utilize an alternative strategy for iron reduction. Reduced organic compounds such as thiols are prominent in natural environments where DMRB are found. These thiol compounds are redox reactive and are capable of abiotically reducing Fe(III) oxides at high rates S. oneidensis wild-type and ΔluxS anaerobic biofilm formation phenotypes were examined under a variety of electron donor-electron acceptor pairs, including lactate or formate as the electron donor and fumarate, thiosulfate, or Fe(III) oxide-coated silica surfaces as the terminal electron acceptor. The rates of biofilm formation under the aforementioned growth conditions as well as in the presence of exogenous thiol compounds indicate that ∆luxS formed biofilms at rates only 5-10% of the wild-type strain and ∆luxS biofilm formation rates were restored to wild-type levels by addition of a variety of exogenous compounds including cysteine, glutathione, homocysteine, methionine, serine, and homoserine. Cell adsorption isotherm analyses results indicate that wild-type is can attach to the surface of hematite particles attachment , but ΔluxS is unable to attach the hematite surfaces. These results indicate that biofilm formation is not required for Fe(III) oxide reduction by S. oneidensis ∆luxS anaerobic biofilm formation rates were restored to wild-type levels by addition of exogenous auntoinducer-2 (AI-2), a by-product of homocysteine production in the Activated Methyl Cycle. This discovery led to subsequent experiments performed to detect the production and utilization of AI-2 by wild-type and ∆luxS strains under aerobic and anaerobic conditions. AI-2 production experiments showed wild-type, but not ΔluxS, was capable of producing AI-2. The addition of exogenous S. oneidensis and Vibrio harveyi-produced AI-2 to wild-type and ∆luxS resulted in the swift depletion of AI-2 from the media. These results provide evidence that S. oneidensis can produce AI-2 and subsequently utilize its’ own AI-2 as well as AI-2 produced by other bacteria as a carbon and electron source in the absence of preferred carbon sources. S. oneidensis produces and secretes a suite of extracellular thiols under anaerobic Fe(III)-reducing and Mn(III) and Mn(IV)-reducing conditions including cysteine, homocysteine, glutathione, and cyteamine. Exogenous thiols produced by S. oneidensis are intermediates of the Activated Methyl Cycle (AMC) and Transulfurylation Pathway (TSP). Reduced and oxidized thiols were detected, indicating that the thiols are in a constant state of flux between the reduced and oxidized forms and that the concentration of reduced thiols to its’ oxidized counterpart is indicative of the state of metal reduction by the microorganisms. Respiratory phenotypes Based on Fe(III) and Mn(IV) respiratory phenotypes observed in the AMC and TSP pathway mutants (∆luxS, ∆metB, ∆metC and ∆metY) we can infer that cysteine, glutathione, and cysteamine contribute to metal reduction by serving as efficient electron shuttling molecules, while homocysteine is critical for maintenance of the AMC, propagation of thiol biosynthesis, and maintenance of cellular metabolism via the AMC intermediate SAM. Furthermore, these findings suggest that all metal-reducing bacteria require thiol formation to reduce solid metal oxides. Direct contact mechanism is not the dominant means through electrons are transferred and metals are reduced, instead electron shuttles are the maid reduction mechanism.

Octa-heme cytochrome c tetrathionate reductase (OTR) from Shewanella oneidensis MR-1 is a periplasmic protein and shows several extraordinary structural features around its active-site heme. OTR has been found able to catalyse the in vitro reduction of tetrathionate, nitrite, hydroxylamine and hydrogen peroxide. However the physiological function of this novel protein remains unknown. The subject of this thesis is the in vitro catalytic mechanism and the in vivo function of OTR. As OTR displays great similarity with bacterial penta-heme cytochrome c nitrite reductase (NrfA) in several aspects, it has been proposed that OTR might be physiologically involved in the metabolism of nitrite or other nitrogenous compounds. However kinetics assays and phenotypes studies carried out in this project suggest this is not the case. In vitro kinetic assays of the reduction of nitrite and hydroxylamine catalysed by OTR showed no significant difference in enzyme activities among the wild-type OTR and its mutant forms which have one active site residue replaced by alanine, namely OTR K153A, C64A, N61A and D150A. And the nitrite reductase activity of OTR (kcat/Km = 1.0×105 M-1•s-1) are much lower than that of NrfA (kcat/Km = ~108 M-1•s-1). These results indicate that OTR is not specifically adapted to reduce nitrite and it cannot compete for nitrite against NrfA in vivo. No phenotype difference was identified between the wild-type and the Δotr strain of Shewanella oneidensis MR-1 when nitrite or nitrate served as the sole electron acceptor. OTR appears not to be involved in the respiration or detoxification of nitrite, which is consistent with previous transcriptional and phenotype reports that involve OTR or its homologues. The in vitro tetrathionate reduction activity of OTR was unable to be reproduced in this project for unknown reasons. Although transcriptomic data from the literature suggest that OTR may be related to the metabolism of sulphur-containing compounds, kinetic and phenotype studies reveal that OTR does not directly participate in the respiration of thiosulfate, sulfite, tetrathionate, polysulfide or elemental sulphur. Cysteine 64 is a highly-conserved amino acid residue of OTR close to the active site and its side-chain sulphur atom is covalently bonded by either an oxygen or a sulphur atom as observed in the crystal structure. Such a modification is potentially important to the function of OTR. ESI mass spectroscopy results show that in native OTR the modified form is around 48 Da heavier than the unmodified form, and the MALDITOF peptide mass spectra show that the modified form could be converted into the unmodified form by reducing agent DTT. These results suggest that the modification could be a cysteine persulfide attaching an extra oxygen atom in the form of water or hydroxide anion.

Metal-respiring bacteria occupy a central position in a variety of environmentally important processes including the biogeochemical cycling of metals and carbon, biocorrosion of steel surfaces, bioremediation of radionuclide-contaminated aquifers, and electricity generation in microbial fuel cells. Metal-respiring bacteria are presented, however, with a unique physiological challenge: they are required to respire anaerobically on electron acceptors (e.g., Fe(III) oxides, elemental sulfur) that are highly insoluble at circumneutral pH and unable to enter the cell and contact inner membrane-localized respiratory systems. To overcome these physiological problems, metal-respiring bacteria are postulated to employ a variety of novel respiratory strategies not found in other bacteria, including 1) direct enzymatic reduction at the cell surface, 2) electron shuttling between the cell and metal surfaces, and 3) metal solubilization by bacterially-produced organic ligands followed by respiration of the soluble organic-metal complexes. This work highlights my latest findings on the genetic and enzymatic mechanism of metal respiration by Shewanella oneidensis, a facultative anaerobe ubiquitous to redox-stratified natural waters and sediments.

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