Sulfur-reducing bacteria | EPFL Graph Search

Sulfur-reducing bacteria are microorganisms able to reduce elemental sulfur (S0) to hydrogen sulfide (H2S). These microbes use inorganic sulfur compounds as electron acceptors to sustain several activities such as respiration, conserving energy and growth, in absence of oxygen. The final product of these processes, sulfide, has a considerable influence on the chemistry of the environment and, in addition, is used as electron donor for a large variety of microbial metabolisms. Several types of bacteria and many non-methanogenic archaea can reduce sulfur. Microbial sulfur reduction was already shown in early studies, which highlighted the first proof of S0 reduction in a vibrioid bacterium from mud, with sulfur as electron acceptor and H2 as electron donor. The first pure cultured species of sulfur-reducing bacteria, Desulfuromonas acetoxidans, was discovered in 1976 and described by Pfennig Norbert and Biebel Hanno as an anaerobic sulfur-reducing and acetate-oxidizing b

Microbial metabolism in the deep subsurface

Alexandre Bagnoud

Microbes have successfully colonized the deep subsurface, thanks to their small size and their diverse metabolic activities. This part of the biosphere remains a terra incognita for microbiologists, containing innumerable unknown microbial species and processes. We depend on it for many things, i. e. water supply, oil extraction and nuclear waste disposal. In Switzerland, Opalinus Clay will be used for deep geological repositories, because of its very low permeability. This rock has been studied for 20 years, however, the potential role of microbes has long been overlooked, even though they could play a major role in controlling geochemical conditions. It was showed that they were present in pristine rock, but were not active due to the lack of space. The potential for microbial activity in disturbed rock, under repository relevant conditions, remains unexplored. This is the focus of this thesis. The first condition tested was the presence of space alone. This will occur when the rock is excavated to build the repository. The digging creates a network of large fractures in the rock zones near the galleries. This change is enough to promote microbial activity in a system, mainly composed of two species. The first one, a Peptococcaceae, oxidizes organic carbon to dioxide carbon, by reducing sulfate. The second organism is a Pseudomonas that seems to grow by fermenting organic carbon. From this model, it appears that the Peptococcaceae feeds on low molecular organic acids present in the Opalinus Clay, but also on fermentation products from Pseudomonas. What is less clear is the source of organic carbon for the latter. Is it only feeding on dead microbial cells, or is it also able to feed on reactive fossilized carbon contained in Opalinus Clay? The second case study included an additional energy source, hydrogen. This gas will be produced by anoxic steel corrosion and could damage the repository if the pressure increases significantly. However, it can be oxidized in situ by autotrophic microbial species. The dominating microbe in this system is a sulfate-reducing Desulfobulbaceae. It produces organic carbon from carbon dioxide, which can later feed heterotrophic bacteria, which are also sulfate-reducing and that release carbon dioxide. A carbon loop was thus reconstructed for the first time in the deep subsurface. It includes a fermentation step that releases the organic substrate for heterotrophic sulfate-reducing bacteria that completely oxidize simple organic carbon molecules, i.e., acetate, to carbon dioxide. In this system, hydrogen and sulfate consumption rates are 1.5 and 0.2 µmol·cm-3·day-1, respectively. This means that electrons derived from hydrogen reduce electron acceptors other than sulfate, confirming carbon fixation. These projects highlight the role that microbes can play for the safety of nuclear waste disposal. Hydrogen consumption is a beneficial process, but the overall impact of microbial activity can be negative, because it can promote corrosion and weathering of the different barriers surrounding the waste. Further work is needed in order to obtain a more complete picture of the role played by bacteria in a deep geological repository. Nonetheless, the results presented here represent a large improvement in our understanding of deep subsurface microbiology. Microbial processes were never described in this much detail in these environments, as is done here: from the metabolic pathway level, up to the ecosystem level.

EPFL2015

Metal reduction and sporulation in Desulfotomaculum reducens

Elena Cristina Dalla Vecchia

The genera Desulfotomaculum and Clostridium, belonging to the phylum Firmicutes, comprise Gram-positive, low G+C genomic content, anaerobic, spore- forming bacteria. Desulfotomaculum is a metabolically and environmentally versatile genus capable of growing fermentatively as well as by respiring sulfate. D. reducens is also capable of metal reduction and has been reported to conserve energy from this process. In this thesis, iron (Fe(III)) reduction by D. reducens in the presence of pyruvate or lactate as electron donors was investigated. When pyruvate is present, D. reducens grows fermentatively. If Fe(III) is present, it can act as an electron sink alternative to protons and consume excess reducing equivalents accumulated during pyruvate oxidation. Electron transfer to Fe(III) by D. reducens in the presence of pyruvate is mediated by a soluble electron carrier, likely riboflavin, released by cells during fermentation. This mechanism allows the microorganism to reduce extracellular, solid phase Fe(III) even if it is not directly accessible by physical contact. In the presence of lactate, D. reducens is unable to conserve significant energy from electron donor oxidation and Fe(III) reduction. In contrast to pyruvate, during lactate oxidation, no redox-active compound is released by the cells, and extracellular, solid phase Fe(III) can only be reduced by direct contact. This implies that a surface exposed reductase must be present in D. reducens cells. The investigation of the surface proteome of this organism led to the identification of three proteins, most likely localized to the cell surface, potentially involved in Fe(III) reduction. One is a heterodisulfide reductase subunit A, a putative intermediate in the Fe(III) reduction chain. The second is a membrane-associated hydrogenase. The third protein is annotated as alkyl hydroperoxide reductase although its actual function may be thiol-disulfide oxidoreduction; several lines of evidence suggest the involvement of the latter in metal reduction by D. reducens. Clostridium species are widespread in the environment and are capable of utilizing a great variety of organic substrates for fermentative growth, while they are unable to conserve energy through respiration. However, they can reduce terminal electron acceptors to eliminate excess reducing equivalents from fermentation. Among the electron acceptors used by Clostridium spp., are metals, such as iron and uranium (U(VI)). One species whose vegetative cells are capable of U(VI) reduction is C. acetobutylicum, although little information is available on the mechanism underlying this process. In this thesis, the potential involvement of the spores of C. acetobutylicum in U(VI) reduction is probed. It was found that the spores of this species can reduce the radionuclide, and that to do so they require the presence of an unidentified soluble compound released by growing cells and H2 as the electron donor. The involvement of spores in metal reduction is very interesting because generally spores are considered not to interact directly with the surrounding environment. In fact, spores are dormant, thus metabolically inactive, cells. Spore formation is a cell differentiation process activated in response to environmental stress and conditions that are hostile to vegetative growth. Sporulation has been extensively studied and characterized in Bacillus subtilis, for which a model has been developed. Some information is also available on sporulation in the clostridia. In this thesis, a genomic investigation of sporulation in the Desulfotomaculum genus was undertaken. The B. subtilis model was used as a reference and the information on Clostridium as a comparison. Significant similarities were found in the core regulatory process across genera, while some differences were identified in the initiation of sporulation. Substantial differences were highlighted in the spore structural proteins.

EPFL2014

As release under the microbial sulfate reduction during redox oscillations in the upper Mekong delta aquifers, Vietnam: A mechanistic study

Rizlan Bernier-Latmani, Laurent Louis José Charlet, Manon Frutschi

The impact of seasonal fluctuations linked to monsoon and irrigation generates redox oscillations in the subsurface, influencing the release of arsenic (As) in aquifers. Here, the biogeochemical control on As mobility was investigated in batch experiments using redox cycling bioreactors and As- and SO42−-amended sediment. Redox potential (Eh) oscillations between anoxic (−300–0 mV) and oxic condition (0–500 mV) were implemented by automatically modulating an admixture of N2/CO2 or compressed air. A carbon source (cellobiose, a monomer of cellulose) was added at the beginning of each reducing cycle to stimulate the metabolism of the native microbial community. Results show that successive redox cycles can decrease arsenic mobility by up to 92% during reducing conditions. Anoxic conditions drive mainly the conversion of soluble As(V) to As(III) in contrast to oxic conditions. Phylogenetic analyses of 16S rRNA amplified from the sediments revealed the presence of sulfate and iron – reducing bacteria, confirming that sulfate and iron reduction are key factors for As immobilization from the aqueous phase. As and S K-edge X-ray absorption spectroscopy suggested the association of Fe-(oxyhydr)oxides and the importance of pyrite (FeS2(s)), rather than poorly ordered mackinawite (FeS(s)), for As sequestration under oxidizing and reducing conditions, respectively. Finally, these findings suggest a role for elemental sulfur in mediating aqueous thioarsenates formation in As-contaminated groundwater of the Mekong delta.

2019