Biological Samples Preparation for Speciation at Cryogenic Temperature using High-Resolution  X-Ray Absorption Spectroscopy

The study of elements with X-ray absorption spectroscopy (XAS) is of particular interest when studying the role of metals in biological systems. Sample ...

Université Grenoble Alpes

ESRF, The European Synchrotron

In regions impacted by mining and smelting activities, dredged sediments are often contaminated with metals. Phytotechnologies could be used for their management, but more knowledge on the speciation of metals in the sediment and on their fate after colonization by plant roots is needed. This work was focused on a dredged sediment from the Scarpe river (North of France), contaminated with Zn and Cd. Zn, Cd hyperaccumulating plants Arabidopsis halleri from metallicolous and non-metallicolous origin were grown on the sediment for five months in a pot experiment. The nature and extent of the modifications in Cd speciation with or without plant were determined by electron microscopy, micro X-ray fluorescence and bulk and micro X-ray absorption spectroscopy. In addition, changes in Cd exchangeable and bioavailable pools were evaluated, and Cd content in leachates was measured. Finally, Cd plant uptake and plant growth parameters were monitored. In the original sediment, Cd was present as a mixed Zn, Cd, Fe sulfide. After five months, although pots still contained reduced sulfur, Cd-bearing sulfides were totally oxidized in vegetated pots, whereas a minor fraction (8%) was still present in non-vegetated ones. Secondary species included Cd bound to O-containing groups of organic matter and Cd phosphates. Cd exchangeability and bioavailability were relatively low and did not increase during changes in Cd speciation, suggesting that Cd released by sulfide oxidation was readily taken up with strong interactions with organic matter and phosphate ligands. Thus, the composition of the sediment, the oxic conditions and the rhizospheric activity (regardless of the plant origin) created favorable conditions for Cd stabilization. However, it should be kept in mind that returning to anoxic conditions may change Cd speciation, so the species formed cannot be considered as stable on the long term. 

Fate of cadmium in the rhizosphere of Arabidopsis halleri grown in a contaminated dredged sediment.

Current models of the formation and distribution of gold deposits on Earth are based on the long-standing paradigm that hydrogen sulfide and chloride are the ligands responsible for gold mobilization and precipitation by fluids across the lithosphere. Here we challenge this view by demonstrating, using in situ X-ray absorption spectroscopy and solubility measurements, coupled with molecular dynamics and thermodynamic simulations, that sulfur radical species, such as the trisulfur ion S3(-), form very stable and soluble complexes with Au(+) in aqueous solution at elevated temperatures (>250 °C) and pressures (>100 bar). These species enable extraction, transport, and focused precipitation of gold by sulfur-rich fluids 10-100 times more efficiently than sulfide and chloride only. As a result, S3(-) exerts an important control on the source, concentration, and distribution of gold in its major economic deposits from magmatic, hydrothermal, and metamorphic settings. The growth and decay of S3(-) during the fluid generation and evolution is one of the key factors that determine the fate of gold in the lithosphere.

Sulfur radical species form gold deposits on Earth.

We have studied the local structure and valence electronic unoccupied states of thermoelectric CsBiTe and superconducting CsBiPbTe (T ∼ 3 K) by extended X-ray absorption fine structure (EXAFS) and X-ray absorption near edge structure (XANES) measurements. The Bi-L edge EXAFS reveals wide Bi-Te distance distribution for both compounds indicating complex atomic arrangements in the studied system. The mean square relative displacements (MSRDs) of the Bi-Te bond distances appear largely increased in Pb substituted system due to larger overall local disorder, however, one of the Bi-Te bonds shows a reduced disorder. On the other hand, the Bi-L edge XANES is hardly affected by Pb substitution while the Te-L edge XANES reveals increased density of unoccupied Te 5p states. This suggests that the carriers introduced by the Pb substitution in CsBiPbTe preferentially goes on Te sites. Similarly, the Cs-L edge XANES also shows small changes due to Pb-substitution and reduced local disorder indicated by the reduced width of the Cs-L edge white line. We have also shown that the X-ray photoemission spectroscopy (XPS) measurements on various electronic core levels are in a qualitative agreement with the XANES results. These findings are consistent with carrier doping and a reduced disorder in one direction to be likely factors to drive the thermoelectric CsBiTe into a bulk superconductor by Pb-substitution in CsBiPbTe.

Determination of the local structure of CsBiPbTe (x = 0, 0.5) by X-ray absorption spectroscopy.

The ISO-standardized RHIZOtest is used here for the first time to decipher how plant species, soil properties, and physical-chemical properties of the nanoparticles and their transformation regulate the phytoavailability of nanoparticles. Two plants, tomato and fescue, were exposed to two soils with contrasted properties: a sandy soil poor in organic matter and a clay soil rich in organic matter, both contaminated with 1, 15, and 50 mg·kg of dissolved Ce(SO), bare and citrate-coated CeO nanoparticles. All the results demonstrate that two antagonistic soil properties controlled Ce uptake. The clay fraction enhanced the retention of the CeO nanoparticles and hence reduced Ce uptake, whereas the organic matter content enhanced Ce uptake. Moreover, in the soil poor in organic matter, the organic citrate coating significantly enhanced the phytoavailability of the cerium by forming smaller aggregates thereby facilitating the transport of nanoparticles to the roots. By getting rid of the dissimilarities between the root systems of the different plants and the normalizing the surfaces exposed to nanoparticles, the RHIZOtest demonstrated that the species of plant did not drive the phytoavailability, and provided evidence for soil-plant transfers at concentrations lower than those usually cited in the literature and closer to predicted environmental concentrations.

Evidence that Soil Properties and Organic Coating Drive the Phytoavailability of Cerium Oxide Nanoparticles.

Sulfidation is a key process for silver nanoparticles released from consumer products in the environment. This study focuses on the impact of a model soil microorganism, Bacillus subtilis, on the fate of pristine and already sulfidized Ag-NPs. The nanoparticles were incubated with the initial growth medium, isolated secretome, and living bacteria, and characterized for their size and morphology, agglomeration state, structure, and Ag speciation. No Ag internalization or sorption on the cell wall was detected. A partial sulfidation, leading to an Ag-AgS core-shell structure, was observed in the presence of the secretome, and the rate limiting step of the reaction was the oxidation of Ag, and it was favored near the crystal dislocations. The sulfidation was complete in the presence of the living bacteria and followed an indirect pathway. Both crystalline AgS and amorphous AgS and/or Ag-thiol were identified. At the opposite, the bacteria had no impact on AgS. These results suggest that microorganisms participate in the sulfidation of Ag-NPs in aerobic systems such as unsaturated soils, and thus affect the bioavailability of Ag. It is important to take these transformations into account during exposure experiments, since they drastically change the exposure conditions. Finally, the secretome of B. subtilis might be used for the green synthesis of Ag-AgS core-shell nanoparticles.

Impact of a Model Soil Microorganism and of Its Secretome on the Fate of Silver Nanoparticles.

Mercury(II) is an unphysiological soft ion with high binding affinity for thiolate ligands. Its toxicity lies in the interactions with low molecular weight thiols including glutathione and cysteine-containing proteins that disrupt the thiol balance and alter vital functions. However, mercury can also be detoxified via interactions with Hg(II)-responsive regulatory proteins such as MerR, which coordinates Hg(II) with three cysteine residues in a trigonal planar fashion (HgS coordination). The model cyclodecapeptide P, c(GCTCSGCSRP) was designed to promote Hg(II) chelation in a HgS coordination environment through the parallel orientation of three cysteine side chains. The binding motif is derived from the dicysteine P cyclodecapeptide validated previously as a model for d metal transporters containing the binding sequence CxxC. The formation of the mononuclear HgP complex with a HgS coordination is demonstrated using electrospray ionization mass spectrometry, UV absorption, and Hg NMR. Hg L-edge extended X-ray absorption fine structure (EXAFS) spectroscopy indicates that the Hg(II) coordination environment is T-shaped with two short Hg-S distances at 2.45 Å and one longer distance at 2.60 Å. The solution structure of the HgP complex was refined based on H-H NMR constraints and EXAFS results. The cyclic peptide scaffold has a rectangular shape with the three binding cysteine side chains pointing toward Hg(II). The HgPH complex has a p K of 4.3, indicating that the HgS coordination mode is stable over a large range of pH. This low p K value suggests that the preorientation of the three cysteine groups is particularly well-achieved for Hg(II) trithiolate coordination in P.

Mercury Trithiolate Binding (HgS) to a de Novo Designed Cyclic Decapeptide with Three Preoriented Cysteine Side Chains.

The construction of a high-temperature reaction cell for operando X-ray absorption spectroscopy characterization is reported. A dedicated cell was designed to operate as a plug-flow reactor using powder samples requiring gas flow and thermal treatment at high temperatures. The cell was successfully used in the reaction of dry reforming of methane (DRM). We present X-ray absorption results in the fluorescence detection mode on a 0.4 wt. % Ni/ZrO catalyst under realistic conditions at 750 °C, reproducing the conditions used for a conventional dynamic microreactor for the DRM reaction. The setup includes a gas distribution system that can be fully remotely operated. The reaction cell offers the possibility of transmission and fluorescence detection modes. The complete setup dedicated to the study of catalysts is permanently installed on the Collaborating Research Groups French Absorption spectroscopy beamline in Material and Environmental sciences (CRG-FAME) and French Absorption spectroscopy beamline in Material and Environmental sciences at Ultra-High Dilution (FAME-UHD) beamlines (BM30B and BM16) at the European Synchrotron Radiation Facility in Grenoble, France.

A new high temperature reactor for operando XAS: Application for the dry reforming of methane over Ni/ZrO catalyst.

Wetlands have been proposed to naturally attenuate U transfers in the environment via U complexation by organic matter and potential U reduction. However, U mobility may depend on the identity of particulate/dissolved uranium source materials and their redox sensitivity. Here, we examined the fate of uranium in a highly contaminated wetland (up to 4500 mg·kg U) impacted by former mine water discharges. Bulk U L-EXAFS and (micro-)XANES combined with SEM-EDXS analyses of undisturbed soil cores show a sharp U redox boundary at the water table, together with a major U redistribution from U(IV)-minerals to U(VI)-organic matter complexes. Above the water table, U is fully oxidized into mono- and bidentate U(VI)-carboxyl and monodentate U(VI)-phosphoryl complexes. Minute amounts of U(VI)-phosphate minerals are also observed. Below the water table, U is fully reduced and is partitioned between U(IV)-phosphate minerals (i.e., ningyoite and a lermontovite-like phase), and bidentate U(IV)-phosphoryl and monodentate U(IV)-carboxyl complexes. Such a U redistribution from U-minerals inherited from mine water discharge deposits could result from redox cycling nearby the water table fluctuation zone. Oxidative dissolution of U(IV)-phosphate minerals could have led to U(VI)-organic matter complexation, followed by subsequent reduction into U(IV)-organic complexes. However, uranium(IV) minerals could have been preserved in permanently waterlogged soil.

Redox Fluctuations and Organic Complexation Govern Uranium Redistribution from U(IV)-Phosphate Minerals in a Mining-Polluted Wetland Soil, Brittany, France.

Nickel superoxide dismutase (NiSOD) is an enzyme that protects cells against O. While the structure of its active site is known, the mechanism of the catalytic cycle is still not elucidated. Its active site displays a square planar Ni center with two thiolates, the terminal amine and an amidate. We report here a bioinspired Ni complex built on an ATCUN-like binding motif modulated with one cysteine, which demonstrates catalytic SOD activity in water ( = 8.4(2) × 10 M s at pH = 8.1). Its reactivity with O was also studied in acetonitrile allowing trapping two different short-lived species that were characterized by electron paramagnetic resonance or spectroelectrochemistry and a combination of density functional theory (DFT) and time-dependent DFT calculations. Based on these observations, we propose that O interacts first with the complex outer sphere through a H-bond with the peptide scaffold in a [NiO] species. This first species could then evolve into a Ni hydroperoxo inner sphere species through a reaction driven by protonation that is thermodynamically highly favored according to DFT calculations.

A Bioinspired Ni Superoxide Dismutase Catalyst Designed on an ATCUN-like Binding Motif.

We present in this work a first X-ray Absorption Spectroscopy study of the interactions of Zn with human BST2/tetherin and SARS-CoV-2 orf7a proteins as well as with some of their complexes. The analysis of the XANES region of the measured spectra shows that Zn binds to BST2, as well as to orf7a, thus resulting in the formation of BST2-orf7a complexes. This structural information confirms the the conjecture, recently put forward by some of the present Authors, according to which the accessory orf7a (and possibly also orf8) viral protein are capable of interfering with the BST2 antiviral activity. Our explanation for this behavior is that, when BST2 gets in contact with Zn bound to the orf7a Cys ligand, it has the ability of displacing the metal owing to the creation of a new disulfide bridge across the two proteins. The formation of this BST2-orf7a complex destabilizes BST2 dimerization, thus impairing the antiviral activity of the latter.

Olivier Proux

OSUG,
UMS 832 CNRS,
OSUG, UMS 832 CNRS

Université Grenoble Alpes

Biological Samples Preparation for Speciation at Cryogenic Temperature using High-Resolution X-Ray Absorption Spectroscopy

Olivier Proux

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Université Grenoble Alpes

Biological Samples Preparation for Speciation at Cryogenic Temperature using High-Resolution X-Ray Absorption Spectroscopy

OSUG,
UMS 832 CNRS,
OSUG, UMS 832 CNRS