Métabolisme méthanogène | EPFL Graph Search

Les organismes à métabolisme méthanogène, ou simplement les méthanogènes, sont des micro-organismes qui produisent du méthane comme sous-produit métabolique de la vie en conditions anoxiques, par méthanogenèse. Le méthane est le produit final de leur respiration anaérobie. Certaines espèces peuvent néanmoins survivre un certain temps en présence de dioxygène. Ils étaient autrefois classés comme Archéobactéries ; mais celles-ci ont depuis été reclassées, les méthanogènes sont maintenant des Archées, un groupe de procaryotes distinct des bactéries. Description Les microorganismes méthanogènes sont tous des procaryotes unicellulaires. Ils présentent des formes variées, principalement coccoïdales (forme de sphère) ou en bâtonnet plus ou moins longs, à enveloppe régulière ou non, formant parfois des spirilles. Ils sont isolés ou se regroupent selon des modalités classiques (par paire, en chaînettes plus ou moins allongées, en agrégats hétérogènes ou en biofilms. Certains son

Growth and viability of microorganisms in bentonite and their potential activity in deep geological repository environments

Niels Burzan

Radioactive waste is among the most dangerous anthropogenic waste and its safe disposal is a challenging multi-generational task. Many nations have sought for the peaceful application of nuclear fission for the reliable production of electric energy to power their societies. The increasing volumes of radioactive waste generated are, however, proving an increasingly urgent problem to tackle. Deep geological disposal is deemed our best option for the safe long-term disposal of radioactive waste. Different host rocks are being considered for deep geological disposal, depending on the nation's geology. Switzerland favours the Opalinus Clay Formation due to its very low hydraulic conductivity and good radionuclide retention capabilities. Microorganisms in the deep subsurface are active and must be considered as their activity will influence a deep geological repository for radioactive waste. On one hand, the microorganism's activity represents a safety concern due to the possibility of enhanced corrosion, when considering the metallic waste canister encapsulating spent fuel from nuclear power plants. In other cases, however, they can contribute to the safety of a deep geological repository, when considering the gas balance of a Swiss low- and intermediate-level repository. Anoxic corrosion of metallic radioactive waste poses risks to the structural integrity of the host rock. Harnessing the activity of naturally occurring microorganisms at a safe distance from the waste itself can result in the net reduction of gases and thus their activity can be viewed as beneficial and worth exploring. In this thesis, both the positive and negative aspects of the microbial presence are explored. Wyoming bentonite is a back-fill material and an important engineered barrier system for spent nuclear fuel and high-level waste. Within the framework of an in-situ corrosion experiment, the presence and growth of microorganisms in Wyoming bentonite are investigated. The results show that the activity of corrosion enhancing sulfate-reducing bacteria in Wyoming bentonite is inhibited during the critical bentonite saturation phase but other microorganisms were able to grow. The second in-situ research project explores the potential implementation of a microbial gas sink, a natural biofilm composed of hydrogen-oxidizing sulfate-reducing bacteria and methanogenic archaea. Indeed, under the right conditions, a microbial gas sink can fulfil its intended design purposes and consume all hydrogen-gas evolving from the anoxic corrosion of the waste. This thesis contributes to our understanding of the near-field processes of a Swiss radioactive waste repository within the Opalinus Clay Formation through the contribution of experimental insight obtained under in-situ conditions.

EPFL2021

Methylation of arsenic by single-species and soil-derived microbial cultures

Karen Elda Viacava Romo

Arsenic (As) is simultaneously a ubiquitous and a toxic element. Arsenic is subject to bio-transformations catalyzed by microorganisms constituting the As biogeochemical cycle. The primordial Earth was devoid of oxygen, exposing life to the highly mobile and toxic arsenite. This early contact with As is imprinted in the tree of life as arsenic resistance genes, e.g. arsenite efflux by transmembrane transporters. Arsenic bio-transformations includes As methylation catalyzed by the ArsM enzyme. ArsM attaches methyl groups to inorganic As, generating organic As in the trivalent (highly toxic species) and pentavalent (relatively innocuous species) forms. Worldwide concern about exposure to As has been raised due to the high As levels in groundwater in South-East Asia used for consumption and rice cultivation. Rice plants are grown under flooded conditions which are conducive to arsenite mobilization and uptake by roots, resulting in the presence of inorganic and methylated As in grains. Compared to inorganic As, methylarsenicals are more easily accumulated in rice grains and are implicated in rice plant disorders resulting in sterility. Methylated species are not synthesized by the plant but by soil microorganisms. To date, mainly aerobic microbial species able to methylate As as an apparent detoxification strategy, have been isolated from paddies. Thus, despite the fact that methylarsenical synthesis appears to be enhanced during anoxic conditions, the drivers and the physiological role of As methylation remain unknown in the absence of oxygen. The thesis focuses on the identification of active As-methylating microorganisms as single species and as members of anaerobic microbiomes from rice paddy soils. In the first part, five bacterial strains and two methanogenic archaea, belonging to genera identified in paddy soils, were evaluated for active arsenite methylation. While aerobic bacterial strains were sensitive to increasing As concentrations, they efficiently methylated As. Conversely, anaerobic bacterial strains were resistant to increasing As concentrations but methylated poorly. Suspecting that As detoxification was occurring through As efflux and outcompeting methylation under anaerobic conditions, we proceeded with the deletion of the arsenite transmembrane transporter in the anaerobic strain Clostridium pasteurianum. The As efflux was disrupted in the mutant leading to higher intracellular concentrations, higher arsM transcription, and increase in the methylation efficiency. Based on the results, we hypothesize that under anoxic conditions, the efficient arsenite efflux systems from anaerobic microorganisms preclude efficient As methylation. In the second part, meta-omic approaches (metagenomics, metatranscriptomics and metaproteomics) were used to identify active As methylators in two soil-derived microbiomes shown to methylate arsenite. The metagenomic data was used to reconstruct the microbial genomes present as metagenome-assembled genomes (MAG). The metabolic capacity for each MAG was identified by the functional annotation of genes while active metabolisms were deciphered from mRNA transcripts (metatranscriptome) and protein expression (metaproteome). Annotation and expression of arsenic resistance genes pointed to fermenting microorganisms as the main drivers of As methylation in both microbiomes. This work is a contribution to the understanding of the linkages between microbial diversity and arsenic bio-transformation.

EPFL2020

Biomimetic Hydrogenation Catalyzed by a Manganese Model of [Fe]-Hydrogenase

Xile Hu, Huijie Pan

[Fe]‐hydrogenase is an efficient biological hydrogenation catalyst. Despite intense research, Fe complexes mimicking the active site of [Fe]‐hydrogenase have not achieved turnovers in hydrogenation reactions. Herein, we describe the design and development of a manganese(I) mimic of [Fe]‐hydrogenase. This complex exhibits the highest activity and broadest scope in catalytic hydrogenation among known mimics. Thanks to its biomimetic nature, the complex exhibits unique activity in the hydrogenation of compounds analogous to methenyl‐H4MPT+, the natural substrate of [Fe]‐hydrogenase. This activity enables asymmetric relay hydrogenation of benzoxazinones and benzoxazines, involving the hydrogenation of a chiral hydride transfer agent using our catalyst coupled to Lewis acid‐catalyzed hydride transfer from this agent to the substrates.