Reference EPFL-CONF-207213View record in Web of Science Record created on 2015-04-13, modified on... more Reference EPFL-CONF-207213View record in Web of Science Record created on 2015-04-13, modified on 2016-08-09
ABSTRACT The chemical stability of bacteriogenic “UO2” is one of the seminal issues governing its... more ABSTRACT The chemical stability of bacteriogenic “UO2” is one of the seminal issues governing its success as an in-situ waste form in remediated subsurface locations. Little detail is known about the structure and reactivity of this material, but based on comparison to its closest abiotic analog, UO2+x (0 < x < 0.25), we expect that it is complex and defected, likely to exhibit non- stoichiometry, and capable of structurally incorporating common groundwater cations as well as U(VI). This complex behavior is expected to substantially impact its stability in groundwater. Our four-institution team is conducting a systematic and coordinated characterization of: (1) the atomic- and nano-scale structures of bacteriogenic UO2+x in the absence and presence of potentially important environmental cation dopants, (2) the equilibrium solubilities and dissolution rates of these materials, (3) the biogeochemical coupling of biologically mediated Mn cycling and UO2+x oxidation, and (4) the influence of these molecular scale processes on meter scale release of U(VI) in sediments. This presentation describes results from Year 1 of this project.
Proceedings of the National Academy of Sciences, 2013
Redox transitions of uranium [from U(VI) to U(IV)] in low-temperature sediments govern the mobili... more Redox transitions of uranium [from U(VI) to U(IV)] in low-temperature sediments govern the mobility of uranium in the environment and the accumulation of uranium in ore bodies, and inform our understanding of Earth’s geochemical history. The molecular-scale mechanistic pathways of these transitions determine the U(IV) products formed, thus influencing uranium isotope fractionation, reoxidation, and transport in sediments. Studies that improve our understanding of these pathways have the potential to substantially advance process understanding across a number of earth sciences disciplines. Detailed mechanistic information regarding uranium redox transitions in field sediments is largely nonexistent, owing to the difficulty of directly observing molecular-scale processes in the subsurface and the compositional/physical complexity of subsurface systems. Here, we present results from an in situ study of uranium redox transitions occurring in aquifer sediments under sulfate-reducing cond...
This report presents a thorough review of the tenure-track system at EPFL and was conducted by th... more This report presents a thorough review of the tenure-track system at EPFL and was conducted by the tenure-track assistant professors (PATTs) at this institution with emphasis on current practices in each Faculty regarding 1) clarity, transparency and implementation of the tenure promotion procedure; 2) pre-tenure evaluation procedures (annual and midterm reviews) and 3) mentoring and support of junior faculty. The focus was on the process leading to the official tenure evaluation rather than the tenure evaluation itself. Detailed polling of the PATTs was conducted and analyzed; the salient results are presented in this report. The primary objective of this exercise was to propose recommendations to improve clarity, transparency and practice where needed. The complete survey results, graphs and analyses, best practices and examples of adapted implementations for EPFL are presented in the appendices. Below is a summary of the main findings and recommendations by the PATTs. <strong&...
Reductive immobilization of uranium has been explored as a remediation strategy for the U-contami... more Reductive immobilization of uranium has been explored as a remediation strategy for the U-contaminated subsurface. Via the in-situ biostimulation of microbial processes, hexavalent U is reduced to less soluble tetravalent species which are immobilized within the sediments. Although the mineral uraninite (UO2) was initially considered the dominant product of biological reduction, non-crystalline U(IV) species (NCU(IV)) are found to be abundant in the environment, despite their greater susceptibility to oxidation and remobilization. However, it has been recently proposed that, through aging, NCU(IV) might transform into UO2, which would potentially enhance the stability of the reduced U pool. In this study, we performed column experiments to produce NCU(IV) species in a natural sediment mimicking the environmental conditions during bioremediation. Bioreduced sediments retrieved from the columns and harboring NCU(IV), were incubated in static microcosms under anoxic conditions, to allow the systematic monitoring of U coordination by X-ray absorption spectroscopy (XAS) over 12 months. XAS revealed that, under the investigated conditions, the speciation of U(IV) does not change over time. Thus, because NCU(IV) is the dominant species in the sediments, bioreduced U(IV) species remain vulnerable to oxidation and remobilization in the aqueous phase even after a 12-month aging period.
Historically, it is believed that crystalline uraninite, produced via the abiotic reduction of he... more Historically, it is believed that crystalline uraninite, produced via the abiotic reduction of hexavalent uranium (U(VI)) is the dominant reduced U species formed in low-temperature uranium roll-front ore deposits. Here we show that non-crystalline U(IV) generated through biologically mediated U(VI) reduction is the predominant U(IV) species in an undisturbed U roll-front ore deposit in Wyoming, USA. Characterization of U species revealed that the majority (∼58-89%) of U is bound as U(IV) to C-containing organic functional groups or inorganic carbonate, while uraninite and U(VI) represent only minor components. The uranium deposit exhibited mostly 238U-enriched isotope signatures, consistent with largely biotic reduction of U(VI) to U(IV). This finding implies that biogenic processes are more important to uranium ore genesis than previously understood. The predominance of a relatively labile form of U(IV) also provides an opportunity for a more economical and environmentally benign ...
Investigation of the enhanced mechanical response of treated soils through microbially induced ca... more Investigation of the enhanced mechanical response of treated soils through microbially induced calcite precipitation requires extensive understanding of the pore structure. Depending on the applied treatment conditions, the resultant material exhibits distinct changes in the solid phase. In this paper, the focus is on the microstructural characteristics of bio-cemented soils derived from different treatment patterns. The objective is to clarify the predominant fabric features as a function of the adopted treatment conditions. For this purpose, microstructural observations with scanning electron microscopy are used to analyse the structure during the treatment and post-treatment. Mesocrystals – that is, aggregates of single particles – are identified as a distinct form of precipitate that provides the crucial grain-to-grain contact surfaces. The cemented samples are subsequently subjected to undrained triaxial shear test to investigate the response in three typical cases of bio-cemen...
This report presents the results of a survey conducted in January 2018 by the ETH WPF. In the sur... more This report presents the results of a survey conducted in January 2018 by the ETH WPF. In the survey, all female faculty members from both EPFL and ETHZ were asked to identify issues of concern to them and to evaluate possible measures to address those issues. At the time of the survey, the statistics for 2017 showed that women constituted only 15% of the faculty at EPFL and 14% at ETHZ. At both schools, the proportion of women was lowest at the rank of Full Professor (9% at EPFL and 10% at ETHZ). An overwhelming majority of the respondents held the opinion that there are too few women faculty, not only in general (91% EPFL, 94% ETHZ) but<br> also at the full professor rank (98% EPFL, 97% ETHZ), on decision-making boards (93% EPFL, 88% ETHZ) and as institute directors (89% EPFL, 91% ETHZ). The respondents endorsed the overall target that women should constitute 35% of the faculty by 2025. In evaluating measures to address issues that adversely affect women faculty, the respond...
Uranium (U) is a ubiquitous element in the Earth’s crust at ~2 ppm. In anoxic environments, solub... more Uranium (U) is a ubiquitous element in the Earth’s crust at ~2 ppm. In anoxic environments, soluble hexavalent uranium (U(VI)) is reduced and immobilized. The underlying reduction mechanism is unknown but likely of critical importance to explain the geochemical behavior of U. Here, we tackle the mechanism of reduction of U(VI) by the mixed-valence iron oxide, magnetite. Through high-end spectroscopic and microscopic tools, we demonstrate that the reduction proceeds first through surface-associated U(VI) to form pentavalent U, U(V). U(V) persists on the surface of magnetite and is further reduced to tetravalent UO2 as nanocrystals (~1–2 nm) with random orientations inside nanowires. Through nanoparticle re-orientation and coalescence, the nanowires collapse into ordered UO2 nanoclusters. This work provides evidence for a transient U nanowire structure that may have implications for uranium isotope fractionation as well as for the molecular-scale understanding of nuclear waste tempora...
Microbial activity has the potential to enhance the corrosion of high-level radioactive waste dis... more Microbial activity has the potential to enhance the corrosion of high-level radioactive waste disposal canisters, which, in the proposed Swiss deep geological repository, will be embedded in bentonite and placed in the Opalinus Clay (OPA) rock formation. A total of 12 stainless steel cylindrical vessels (referred to as modules) containing bentonite were deployed in an anoxic borehole in OPA for up to 5.5 years. Carbon steel coupons were embedded in the bentonite. Individual modules were retrieved after 1, 1.5, 2.5, and 5.5 years. Enumeration of aerobic and anaerobic heterotrophs and sulfate-reducing bacteria (SRB) revealed microbial growth for 1.5 years followed by a decline or stagnation in microbial viability. It was surprising to observe the growth of aerobic heterotrophs followed by their persistent viability in bentonite, despite the nominally anoxic conditions. In contrast, SRB numbers remained at very low levels. DNA-based amplicon sequencing confirmed the persistence of aero...
Microbial life is widespread in the terrestrial subsurface and present down to several kilometers... more Microbial life is widespread in the terrestrial subsurface and present down to several kilometers depth, but the energy sources that fuel metabolism in deep oligotrophic and anoxic environments remain unclear. In the deep crystalline bedrock of the Fennoscandian Shield at Olkiluoto, Finland, opposing gradients of abiotic methane and ancient seawater-derived sulfate create a terrestrial sulfate-methane transition zone (SMTZ). We used chemical and isotopic data coupled to genome-resolved metaproteogenomics to demonstrate active life and, for the first time, provide direct evidence of active anaerobic oxidation of methane (AOM) in a deep terrestrial bedrock. Proteins from Methanoperedens (formerly ANME-2d) are readily identifiable despite the low abundance (≤1%) of this genus and confirm the occurrence of AOM. This finding is supported by 13C-depleted dissolved inorganic carbon. Proteins from Desulfocapsaceae and Desulfurivibrionaceae, in addition to 34S-enriched sulfate, suggest that ...
Soil microbiomes harbor unparalleled functional and phylogenetic diversity and are sources of nov... more Soil microbiomes harbor unparalleled functional and phylogenetic diversity and are sources of novel metabolisms. However, extracting isolates with a targeted function from complex microbiomes is not straightforward, particularly if the associated phenotype does not lend itself to high-throughput screening. Here, we tackle the methylation of arsenic (As) in anoxic soils. By analogy to mercury, As methylation was proposed to be catalyzed by sulfate-reducing bacteria. However, to date, there are no anaerobic isolates capable of As methylation, whether sulfate-reducing or otherwise. The isolation of such a microorganism has been thwarted by the fact that the anaerobic bacteria harboring a functional arsenite S-adenosylmethionine methyltransferase (ArsM) tested to date did not methylate As in pure culture. Additionally, fortuitous As methylation can result from the release of non-specific methyltransferases upon lysis. Thus, we combined metagenomics, metatranscriptomics, and metaproteomi...
*S Supporting Information ABSTRACT: The reduction of soluble hexavalent uranium to tetravalent ur... more *S Supporting Information ABSTRACT: The reduction of soluble hexavalent uranium to tetravalent uranium can be catalyzed by bacteria and minerals. The end-product of this reduction is often the mineral uraninite, which was long assumed to be the only product of U(VI) reduction. However, recent studies report the formation of other species including an adsorbed U(IV) species, operationally referred to as monomeric U(IV). The discovery of monomeric U(IV) is important because the species is likely to be more labile and more susceptible to reoxidation than uraninite. Because there is a need to distinguish between these two U(IV) species, we propose here a wet chemical method of differentiating monomeric U(IV) from uraninite in environmental samples. To calibrate the method, U(IV) was extracted from known mixtures of uraninite and monomeric U(IV) and tested using X-ray absorption spectroscopy (XAS). Monomeric U(IV) was efficiently removed from biomass and Fe(II)-bearing phases by bicarbonate extraction, without affecting uraninite stability. After confirming that the method effectively separates monomeric U(IV) and uraninite, it is further evaluated for a system containing those reduced U species and adsorbed U(VI). The method provides a rapid complement, and in some cases alternative, to XAS analyses for quantifying monomeric U(IV), uraninite, and adsorbed U(VI) species in environmental samples. 1.
Reference EPFL-CONF-207213View record in Web of Science Record created on 2015-04-13, modified on... more Reference EPFL-CONF-207213View record in Web of Science Record created on 2015-04-13, modified on 2016-08-09
ABSTRACT The chemical stability of bacteriogenic “UO2” is one of the seminal issues governing its... more ABSTRACT The chemical stability of bacteriogenic “UO2” is one of the seminal issues governing its success as an in-situ waste form in remediated subsurface locations. Little detail is known about the structure and reactivity of this material, but based on comparison to its closest abiotic analog, UO2+x (0 &lt; x &lt; 0.25), we expect that it is complex and defected, likely to exhibit non- stoichiometry, and capable of structurally incorporating common groundwater cations as well as U(VI). This complex behavior is expected to substantially impact its stability in groundwater. Our four-institution team is conducting a systematic and coordinated characterization of: (1) the atomic- and nano-scale structures of bacteriogenic UO2+x in the absence and presence of potentially important environmental cation dopants, (2) the equilibrium solubilities and dissolution rates of these materials, (3) the biogeochemical coupling of biologically mediated Mn cycling and UO2+x oxidation, and (4) the influence of these molecular scale processes on meter scale release of U(VI) in sediments. This presentation describes results from Year 1 of this project.
Proceedings of the National Academy of Sciences, 2013
Redox transitions of uranium [from U(VI) to U(IV)] in low-temperature sediments govern the mobili... more Redox transitions of uranium [from U(VI) to U(IV)] in low-temperature sediments govern the mobility of uranium in the environment and the accumulation of uranium in ore bodies, and inform our understanding of Earth’s geochemical history. The molecular-scale mechanistic pathways of these transitions determine the U(IV) products formed, thus influencing uranium isotope fractionation, reoxidation, and transport in sediments. Studies that improve our understanding of these pathways have the potential to substantially advance process understanding across a number of earth sciences disciplines. Detailed mechanistic information regarding uranium redox transitions in field sediments is largely nonexistent, owing to the difficulty of directly observing molecular-scale processes in the subsurface and the compositional/physical complexity of subsurface systems. Here, we present results from an in situ study of uranium redox transitions occurring in aquifer sediments under sulfate-reducing cond...
This report presents a thorough review of the tenure-track system at EPFL and was conducted by th... more This report presents a thorough review of the tenure-track system at EPFL and was conducted by the tenure-track assistant professors (PATTs) at this institution with emphasis on current practices in each Faculty regarding 1) clarity, transparency and implementation of the tenure promotion procedure; 2) pre-tenure evaluation procedures (annual and midterm reviews) and 3) mentoring and support of junior faculty. The focus was on the process leading to the official tenure evaluation rather than the tenure evaluation itself. Detailed polling of the PATTs was conducted and analyzed; the salient results are presented in this report. The primary objective of this exercise was to propose recommendations to improve clarity, transparency and practice where needed. The complete survey results, graphs and analyses, best practices and examples of adapted implementations for EPFL are presented in the appendices. Below is a summary of the main findings and recommendations by the PATTs. <strong&...
Reductive immobilization of uranium has been explored as a remediation strategy for the U-contami... more Reductive immobilization of uranium has been explored as a remediation strategy for the U-contaminated subsurface. Via the in-situ biostimulation of microbial processes, hexavalent U is reduced to less soluble tetravalent species which are immobilized within the sediments. Although the mineral uraninite (UO2) was initially considered the dominant product of biological reduction, non-crystalline U(IV) species (NCU(IV)) are found to be abundant in the environment, despite their greater susceptibility to oxidation and remobilization. However, it has been recently proposed that, through aging, NCU(IV) might transform into UO2, which would potentially enhance the stability of the reduced U pool. In this study, we performed column experiments to produce NCU(IV) species in a natural sediment mimicking the environmental conditions during bioremediation. Bioreduced sediments retrieved from the columns and harboring NCU(IV), were incubated in static microcosms under anoxic conditions, to allow the systematic monitoring of U coordination by X-ray absorption spectroscopy (XAS) over 12 months. XAS revealed that, under the investigated conditions, the speciation of U(IV) does not change over time. Thus, because NCU(IV) is the dominant species in the sediments, bioreduced U(IV) species remain vulnerable to oxidation and remobilization in the aqueous phase even after a 12-month aging period.
Historically, it is believed that crystalline uraninite, produced via the abiotic reduction of he... more Historically, it is believed that crystalline uraninite, produced via the abiotic reduction of hexavalent uranium (U(VI)) is the dominant reduced U species formed in low-temperature uranium roll-front ore deposits. Here we show that non-crystalline U(IV) generated through biologically mediated U(VI) reduction is the predominant U(IV) species in an undisturbed U roll-front ore deposit in Wyoming, USA. Characterization of U species revealed that the majority (∼58-89%) of U is bound as U(IV) to C-containing organic functional groups or inorganic carbonate, while uraninite and U(VI) represent only minor components. The uranium deposit exhibited mostly 238U-enriched isotope signatures, consistent with largely biotic reduction of U(VI) to U(IV). This finding implies that biogenic processes are more important to uranium ore genesis than previously understood. The predominance of a relatively labile form of U(IV) also provides an opportunity for a more economical and environmentally benign ...
Investigation of the enhanced mechanical response of treated soils through microbially induced ca... more Investigation of the enhanced mechanical response of treated soils through microbially induced calcite precipitation requires extensive understanding of the pore structure. Depending on the applied treatment conditions, the resultant material exhibits distinct changes in the solid phase. In this paper, the focus is on the microstructural characteristics of bio-cemented soils derived from different treatment patterns. The objective is to clarify the predominant fabric features as a function of the adopted treatment conditions. For this purpose, microstructural observations with scanning electron microscopy are used to analyse the structure during the treatment and post-treatment. Mesocrystals – that is, aggregates of single particles – are identified as a distinct form of precipitate that provides the crucial grain-to-grain contact surfaces. The cemented samples are subsequently subjected to undrained triaxial shear test to investigate the response in three typical cases of bio-cemen...
This report presents the results of a survey conducted in January 2018 by the ETH WPF. In the sur... more This report presents the results of a survey conducted in January 2018 by the ETH WPF. In the survey, all female faculty members from both EPFL and ETHZ were asked to identify issues of concern to them and to evaluate possible measures to address those issues. At the time of the survey, the statistics for 2017 showed that women constituted only 15% of the faculty at EPFL and 14% at ETHZ. At both schools, the proportion of women was lowest at the rank of Full Professor (9% at EPFL and 10% at ETHZ). An overwhelming majority of the respondents held the opinion that there are too few women faculty, not only in general (91% EPFL, 94% ETHZ) but<br> also at the full professor rank (98% EPFL, 97% ETHZ), on decision-making boards (93% EPFL, 88% ETHZ) and as institute directors (89% EPFL, 91% ETHZ). The respondents endorsed the overall target that women should constitute 35% of the faculty by 2025. In evaluating measures to address issues that adversely affect women faculty, the respond...
Uranium (U) is a ubiquitous element in the Earth’s crust at ~2 ppm. In anoxic environments, solub... more Uranium (U) is a ubiquitous element in the Earth’s crust at ~2 ppm. In anoxic environments, soluble hexavalent uranium (U(VI)) is reduced and immobilized. The underlying reduction mechanism is unknown but likely of critical importance to explain the geochemical behavior of U. Here, we tackle the mechanism of reduction of U(VI) by the mixed-valence iron oxide, magnetite. Through high-end spectroscopic and microscopic tools, we demonstrate that the reduction proceeds first through surface-associated U(VI) to form pentavalent U, U(V). U(V) persists on the surface of magnetite and is further reduced to tetravalent UO2 as nanocrystals (~1–2 nm) with random orientations inside nanowires. Through nanoparticle re-orientation and coalescence, the nanowires collapse into ordered UO2 nanoclusters. This work provides evidence for a transient U nanowire structure that may have implications for uranium isotope fractionation as well as for the molecular-scale understanding of nuclear waste tempora...
Microbial activity has the potential to enhance the corrosion of high-level radioactive waste dis... more Microbial activity has the potential to enhance the corrosion of high-level radioactive waste disposal canisters, which, in the proposed Swiss deep geological repository, will be embedded in bentonite and placed in the Opalinus Clay (OPA) rock formation. A total of 12 stainless steel cylindrical vessels (referred to as modules) containing bentonite were deployed in an anoxic borehole in OPA for up to 5.5 years. Carbon steel coupons were embedded in the bentonite. Individual modules were retrieved after 1, 1.5, 2.5, and 5.5 years. Enumeration of aerobic and anaerobic heterotrophs and sulfate-reducing bacteria (SRB) revealed microbial growth for 1.5 years followed by a decline or stagnation in microbial viability. It was surprising to observe the growth of aerobic heterotrophs followed by their persistent viability in bentonite, despite the nominally anoxic conditions. In contrast, SRB numbers remained at very low levels. DNA-based amplicon sequencing confirmed the persistence of aero...
Microbial life is widespread in the terrestrial subsurface and present down to several kilometers... more Microbial life is widespread in the terrestrial subsurface and present down to several kilometers depth, but the energy sources that fuel metabolism in deep oligotrophic and anoxic environments remain unclear. In the deep crystalline bedrock of the Fennoscandian Shield at Olkiluoto, Finland, opposing gradients of abiotic methane and ancient seawater-derived sulfate create a terrestrial sulfate-methane transition zone (SMTZ). We used chemical and isotopic data coupled to genome-resolved metaproteogenomics to demonstrate active life and, for the first time, provide direct evidence of active anaerobic oxidation of methane (AOM) in a deep terrestrial bedrock. Proteins from Methanoperedens (formerly ANME-2d) are readily identifiable despite the low abundance (≤1%) of this genus and confirm the occurrence of AOM. This finding is supported by 13C-depleted dissolved inorganic carbon. Proteins from Desulfocapsaceae and Desulfurivibrionaceae, in addition to 34S-enriched sulfate, suggest that ...
Soil microbiomes harbor unparalleled functional and phylogenetic diversity and are sources of nov... more Soil microbiomes harbor unparalleled functional and phylogenetic diversity and are sources of novel metabolisms. However, extracting isolates with a targeted function from complex microbiomes is not straightforward, particularly if the associated phenotype does not lend itself to high-throughput screening. Here, we tackle the methylation of arsenic (As) in anoxic soils. By analogy to mercury, As methylation was proposed to be catalyzed by sulfate-reducing bacteria. However, to date, there are no anaerobic isolates capable of As methylation, whether sulfate-reducing or otherwise. The isolation of such a microorganism has been thwarted by the fact that the anaerobic bacteria harboring a functional arsenite S-adenosylmethionine methyltransferase (ArsM) tested to date did not methylate As in pure culture. Additionally, fortuitous As methylation can result from the release of non-specific methyltransferases upon lysis. Thus, we combined metagenomics, metatranscriptomics, and metaproteomi...
*S Supporting Information ABSTRACT: The reduction of soluble hexavalent uranium to tetravalent ur... more *S Supporting Information ABSTRACT: The reduction of soluble hexavalent uranium to tetravalent uranium can be catalyzed by bacteria and minerals. The end-product of this reduction is often the mineral uraninite, which was long assumed to be the only product of U(VI) reduction. However, recent studies report the formation of other species including an adsorbed U(IV) species, operationally referred to as monomeric U(IV). The discovery of monomeric U(IV) is important because the species is likely to be more labile and more susceptible to reoxidation than uraninite. Because there is a need to distinguish between these two U(IV) species, we propose here a wet chemical method of differentiating monomeric U(IV) from uraninite in environmental samples. To calibrate the method, U(IV) was extracted from known mixtures of uraninite and monomeric U(IV) and tested using X-ray absorption spectroscopy (XAS). Monomeric U(IV) was efficiently removed from biomass and Fe(II)-bearing phases by bicarbonate extraction, without affecting uraninite stability. After confirming that the method effectively separates monomeric U(IV) and uraninite, it is further evaluated for a system containing those reduced U species and adsorbed U(VI). The method provides a rapid complement, and in some cases alternative, to XAS analyses for quantifying monomeric U(IV), uraninite, and adsorbed U(VI) species in environmental samples. 1.
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