Production of carbon-containing pyrite spherules induced by hyperthermophilic Thermococcales: a biosignature?

Thermococcales, a major order of hyperthermophilic archaea inhabiting iron- and sulfur-rich anaerobic parts of hydrothermal deep-sea vents, are known to induce the formation of iron phosphates, greigite (Fe3S4) and abundant quantities of pyrite (FeS2), including pyrite spherules. In the present study, we report the characterization of the sulfide and phosphate minerals produced in the presence of Thermococcales using X-ray diffraction, synchrotron-based X ray absorption spectroscopy and scanning and transmission electron microscopies. Mixed valence Fe(II)-Fe(III) phosphates are interpreted as resulting from the activity of Thermococcales controlling phosphorus-iron-sulfur dynamics. The pyrite spherules (absent in abiotic control) consist of an assemblage of ultra-small nanocrystals of a few ten nanometers in size, showing coherently diffracting domain sizes of few nanometers. The production of these spherules occurs via a sulfur redox swing from S0 to S-2 and then to S-1, involving a comproportionation of (-II) and (0) oxidation states of sulfur, as supported by S-XANES data. Importantly, these pyrite spherules sequester biogenic organic compounds in small but detectable quantities, possibly making them good biosignatures to be searched for in extreme environments.

Bioavailability of chromium, nickel, iron and manganese in relation to their speciation in coastal sediments downstream of ultramafic catchments: A case study in New Caledonia.

Coastal sediments downstream of ultramafic catchments can show Ni and Cr concentration well above sediment quality guidelines. Despite their potential ecological impact, the bioavailability of these trace metals in such sedimentary settings has been poorly investigated. In this study, we tried to fill this gap by performing kinetic EDTA-extractions across a shore-to-reef gradient in lagoon sediments downstream of an ultramafic catchment in New Caledonia and interpreting the results in regard of synchrotron-derived speciation. Measured bioavailability ranged from very low for Cr (below 1% of total Cr) to medium for Ni (below 5% of total Ni). Both trace metals showed a decreasing shore-to-reef bioavailability gradient reflecting the larger deposition of ultramafic sediments close to the shore. According to synchrotron-derived speciation data, the very low bioavailability of Cr is attributed to its major occurrence as Cr(III)-bearing Fe-(oxyhydr)oxides and phyllosilicates, with no evidence of Cr(VI). Considering the low occurrence of Fe-sulfides, the medium bioavailability of Ni is considered to arise mainly from the reductive dissolution of Ni-bearing Fe-(oxyhydr)oxides during early diagenesis. This reaction also explains the medium bioavailability of Fe (up to 15% of total Fe) and the positive correlation observed with Total Organic Carbon (TOC). In this regard, this latter parameter appears as a major driver of Ni and Fe bioavailability in coastal sediments downstream of ultramafic catchments. On the opposite, in the absence of Mn-oxides, TOC has no influence on Mn bioavailability (up to 30% of total Mn) that appears more likely driven by sediment sources. From an ecological point of view, considering the Australian and New-Zealand High Interim Sediment Quality Guidelines (ANZ-ISQG-H), Cr should not represent a significant risk towards benthic communities in coastal sediments downstream of ultramafic catchments. On the opposite, Ni, Fe and Mn might represent an ecological risk that should be further investigated in such sedimentary settings.

Climate-driven fluxes of organic-bound uranium to an alpine lake over the Holocene.

Uranium (U) isotopic signatures and concentration in sediments are widely used as paleo-redox proxies, as the behavior of U is often controlled by bottom water oxygenation. Here, we investigated the processes controlling U accumulation in the sediments of Lake Nègre (Mediterranean Alps, South-East France) over the past 9200 years. Exceptionally high natural U concentrations (350-1250 µg·g-1) allowed the measurement of U along with other elements by high-resolution X-Ray Fluorescence core-scanning. Weathering and erosion proxies (Ti content, Zr/Al and K/Ti ratios) indicate that sedimentary inputs were controlled by Holocene climatic variations. After a period of low erosion during the Holocene Climatic Optimum, a major regime shift was recorded at 4.2 kyr BP when terrigenous fluxes consistently increased until present with high sensitivity to centennial-scale climatic events. Sedimentary organic matter (OM) inputs were dominated by terrigenous OM from the catchment soils until 2.4 kyr BP, as attested by carbon to nitrogen (C/N) and bromine to organic carbon (Br/TOC) ratios. From 2.4 kyr BP to present, lake primary production and soils equally contributed to sedimentary OM. Uranium fluxes to the sediments were well correlated to terrigenous OM fluxes from 7 kyr BP to present, showing that U supply to the lake was controlled by U scavenging in the soils of the watershed followed by transport of U bound to detrital organic particles. Higher U/OM ratios before 7 kyr BP likely reflect the development of the upstream wetland. The fluctuations of U sedimentary inputs appear to be independent of bottom water oxygenation, as estimated from constant Fe/Mn ratios and δ238U isotopic signatures, and rather controlled by the production, erosion and sedimentation of terrigenous OM. This finding confirms that the use of U (and potentially other metals with high affinity to OM) concentrations alone should be used with caution for paleo-redox reconstructions.

Diagenetic formation of uranium-silica polymers in lake sediments over 3,300 years.

The long-term fate of uranium-contaminated sediments, especially downstream former mining areas, is a widespread environmental challenge. Essential for their management is the proper understanding of uranium (U) immobilization mechanisms in reducing environments. In particular, the long-term behavior of noncrystalline U(IV) species and their possible evolution to more stable phases in subsurface conditions is poorly documented, which limits our ability to predict U long-term geochemical reactivity. Here, we report direct evidence for the evolution of U speciation over 3,300 y in naturally highly U-enriched sediments (350-760 µg ⋅ g-1 U) from Lake Nègre (Mercantour Massif, Mediterranean Alps, France) by combining U isotopic data (δ238U and (234U/238U)) with U L3 -edge X-ray absorption fine structure spectroscopy. Constant isotopic ratios over the entire sediment core indicate stable U sources and accumulation modes, allowing for determination of the impact of aging on U speciation. We demonstrate that, after sediment deposition, mononuclear U(IV) species associated with organic matter transformed into authigenic polymeric U(IV)-silica species that might have partially converted to a nanocrystalline coffinite (UIVSiO4·nH2O)-like phase. This diagenetic transformation occurred in less than 700 y and is consistent with the high silica availability of sediments in which diatoms are abundant. It also yields consistency with laboratory studies that proposed the formation of colloidal polynuclear U(IV)-silica species, as precursors for coffinite formation. However, the incomplete transformation observed here only slightly reduces the potential lability of U, which could have important implications to evaluate the long-term management of U-contaminated sediments and, by extension, of U-bearing wastes in silica-rich subsurface environments.

New Insights into Pb Isotope Fingerprinting of U-Mine Material Dissemination in the Environment: Pb Isotopes as a Memory Dissemination Tracer.

Stable Pb isotope ratios were measured and compared to U distributions in three soil cores located in a wetland highly impacted by water discharge of a former U-mine. Pb isotope ratios showed notable alignments in binary mixing plots, demonstrating the dissemination of radioactive-enriched material from the U-mine. Thanks to these alignments and to the measurement of the 204Pb isotope, a precise characterization of the Pb isotope composition of the U-ore was performed without the use of U-ore samples. The well-defined end-members with the help of a reevaluated isotope mixing model allowed the accurate determination of the radiogenic Pb percentages in the cores that were overall found to be >50%. Noncorrelated distributions of radiogenic 206Pb and U are observed in several of the wetland soil samples. They reveal postdepositional U redistribution explained by major U speciation changes due to redox cycling in the wetland. On the contrary, the radiogenic 206Pb showed no or little postdepositional mobility and thus can be considered to be a memory tracer of the dissemination of U-rich radioactive material: even after an important U loss, the radiogenic 206Pb is able to reveal past contamination by U-rich materials.

Experimental redox transformations of uranium phosphate minerals and mononuclear species in a contaminated wetland.

Reducing conditions and high organic carbon content make wetlands favorable to uranium (U) sequestration. However, such environments are subjected to water-table fluctuations that could impact the redox behavior of U and its mobility. Our previous study on U speciation in a contaminated wetland has suggested a major role of water-table redox fluctuations in the redistribution of U from U(IV)-phosphate minerals to organic U(VI) and U(IV) mononuclear species. Here, we investigate the mechanisms of these putative processes by mimicking drying or flooding periods via laboratory incubations of wetland samples. LCF-XANES and EXAFS analyses show the total oxidation/reduction of U(IV)/U(VI)-mononuclear species after 20 days of oxic/anoxic incubation, whereas U-phosphate minerals are partly oxidized/reduced. SEM-EDXS combined with µ-XRF and µ-XANES analyses suggest that autunite Ca(UO2)2(PO4)2⋅11H2O is reduced into lermontovite U(PO4)(OH)⋅H2O, whereas oxidized ningyoite CaU(PO4)2⋅2H2O is locally dissolved. The release of U from this latter process is observed to be limited by U(VI) adsorption to the soil matrix and further re-reduction into mononuclear U(IV) upon anoxic cycling. Analysis of incubation waters show, however, that dissolved organic carbon enhances U solubilization even under anoxic conditions. This study brings important information that help to assess the long-term stability of U in seasonally saturated organic-rich contaminated environments.

Microbially Mediated Release of As from Mekong Delta Peat Sediments.

Peat layers within alluvial sediments are considered effective arsenic (As) sinks under reducing conditions due to the binding of As(III) to thiol groups in natural organic matter (NOM) and the formation of As-bearing sulfide phases. However, their possible role as sources of As for anoxic groundwaters remains unexplored. Here, we perform laboratory experiments to provide evidence for the role of a sediment peat layer in releasing As. Our results show that the peat layer, deposited about 8,000 years ago in a paleomangrove environment in the nascent Mekong Delta, could be a source of As to porewater under reducing conditions. X-ray absorption spectroscopy (XAS) analysis of the peat confirmed that As was bound to NOM thiol groups and incorporated into pyrite. Nitrate was detected in peat layer porewater, and flow-through and batch experiments evidenced the release of As from NOM and pyrite in the presence of nitrate. Based on poisoning experiments, we propose that the microbially mediated oxidation of arsenic-rich pyrite and organic matter coupled to nitrate reduction releases arsenic from this peat. Although peat layers have been proposed as As sinks in earlier studies, we show here their potential to release depositional- and/or diagenetically-accumulated As.

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

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.

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

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-1 U) impacted by former mine water discharges. Bulk U LIII-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.

Hydraulic retention time affects bacterial community structure in an As-rich acid mine drainage (AMD) biotreatment process.

Arsenic removal consecutive to biological iron oxidation and precipitation is an effective process for treating As-rich acid mine drainage (AMD). We studied the effect of hydraulic retention time (HRT)-from 74 to 456 min-in a bench-scale bioreactor exploiting such process. The treatment efficiency was monitored during 19 days, and the final mineralogy and bacterial communities of the biogenic precipitates were characterized by X-ray absorption spectroscopy and high-throughput 16S rRNA gene sequencing. The percentage of Fe(II) oxidation (10-47%) and As removal (19-37%) increased with increasing HRT. Arsenic was trapped in the biogenic precipitates as As(III)-bearing schwertmannite and amorphous ferric arsenate, with a decrease of As/Fe ratio with increasing HRT. The bacterial community in the biogenic precipitate was dominated by Fe-oxidizing bacteria whatever the HRT. The proportion of Gallionella and Ferrovum genera shifted from respectively 65 and 12% at low HRT to 23 and 51% at high HRT, in relation with physicochemical changes in the treated water. aioA genes and Thiomonas genus were detected at all HRT although As(III) oxidation was not evidenced. To our knowledge, this is the first evidence of the role of HRT as a driver of bacterial community structure in bioreactors exploiting microbial Fe(II) oxidation for AMD treatment.

Arsenic Speciation in Mekong Delta Sediments Depends on Their Depositional Environment.

Arsenic contamination in groundwater is pervasive throughout deltaic regions of Southeast Asia and threatens the health of millions. The speciation of As in sediments overlying contaminated aquifers is poorly constrained. Here, we investigate the chemical and mineralogical compositions of sediment cores collected from the Mekong Delta in Vietnam, elucidate the speciation of iron and arsenic, and relate them to the sediment depositional environment. Gradual dissolution of ferric (oxyhydr)oxides with depth is observed down to 7 m, corresponding to the establishment of reducing conditions. Within the reduced sediment, layers originating from marine, coastal or alluvial depositional environments are identified and their age is consistent with a late Holocene transgression in the Mekong Delta. In the organic matter- and sulfur-rich layers, arsenic is present in association with organic matter through thiol-bonding and in the form of arsenian pyrite. The highest arsenic concentration (34-69 ppm) is found in the peat layer at 16 m and suggests the accumulation of arsenic due to the formation of thiol-bound trivalent arsenic (40-55%) and arsenian pyrite (15-30%) in a paleo-mangrove depositional environment (∼8079 yr BP). Where sulfur is limited, siderite is identified, and oxygen- and thiol-bound trivalent arsenic are the predominant forms. It is also worth noting that pentavalent arsenic coordinated to oxygen is ubiquitous in the sediment profile, even in reduced sediment layers. But the identity of the oxygen-bound arsenic species remains unknown. This work shows direct evidence of thiol-bound trivalent arsenic in the Mekong Delta sediments and provides insight to refine the current model of the origin, deposition, and release of arsenic in the alluvial aquifers of the Mekong Delta.

Complete removal of arsenic and zinc from a heavily contaminated acid mine drainage via an indigenous SRB consortium.

Acid mine drainages (AMD) are major sources of pollution to the environment. Passive bio-remediation technologies involving sulfate-reducing bacteria (SRB) are promising for treating arsenic contaminated waters. However, mechanisms of biogenic As-sulfide formation need to be better understood to decontaminate AMDs in acidic conditions. Here, we show that a high-As AMD effluent can be decontaminated by an indigenous SRB consortium. AMD water from the Carnoulès mine (Gard, France) was incubated with the consortium under anoxic conditions and As, Zn and Fe concentrations, pH and microbial activity were monitored during 94days. Precipitated solids were analyzed using electron microscopy (SEM/TEM-EDXS), and Extended X-Ray Absorption Fine Structure (EXAFS) spectroscopy at the As K-edge. Total removal of arsenic and zinc from solution (1.06 and 0.23mmol/L, respectively) was observed in two of the triplicates. While Zn precipitated as ZnS nanoparticles, As precipitated as amorphous orpiment (am-AsIII2S3) (33-73%), and realgar (AsIIS) (0-34%), the latter phase exhibiting a particular nanowire morphology. A minor fraction of As is also found as thiol-bound AsIII (14-23%). We propose that the formation of the AsIIS nanowires results from AsIII2S3 reduction by biogenic H2S, enhancing the efficiency of As removal. The present description of As immobilization may help to set the basis for bioremediation strategies using SRB.

Arsenic Incorporation in Pyrite at Ambient Temperature at Both Tetrahedral S-I and Octahedral FeII Sites: Evidence from EXAFS-DFT Analysis.

Pyrite is a ubiquitous mineral in reducing environments and is well-known to incorporate trace elements such as Co, Ni, Se, Au, and commonly As. Indeed, As-bearing pyrite is observed in a wide variety of sedimentary environments, making it a major sink for this toxic metalloid. Based on the observation of natural hydrothermal pyrites, As-I is usually assigned to the occupation of tetrahedral S-I sites, with the same oxidation state as in arsenopyrite (FeAsS), although rare occurrences of AsIII and AsII have been reported. However, the modes of As incorporation into pyrite during its crystallization under low-temperature diagenetic conditions have not yet been elucidated because arsenic acts as an inhibitor for pyrite nucleation at ambient temperature. Here, we provide evidence from X-ray absorption spectroscopy for AsII,III incorporation into pyrite at octahedral FeII sites and for As-I at tetrahedral S-I sites during crystallization at ambient temperature. Extended X-ray absorption fine structure (EXAFS) spectra of these As-bearing pyrites are explained by local structure models obtained using density functional theory (DFT), assuming incorporation of As at the Fe and S sites, as well as local clustering of arsenic. Such observations of As-I incorporation at ambient temperature can aid in the understanding of the early formation of authigenic arsenian pyrite in subsurface sediments. Moreover, evidence for substitution of AsII,III for Fe in our synthetic samples raises questions about both the possible occurrence and the geochemical reactivity of such As-bearing pyrites in low-temperature subsurface environments.

Zinc speciation in the suspended particulate matter of an urban river (Orge, France): influence of seasonality and urbanization gradient.

Among trace metal pollutants, zinc is the major one in the rivers from the Paris urban area, such as the Orge River, where Zn concentration in the suspended particulate matter (SPM) can reach 2000 mg/kg in the most urbanized areas. In order to better understand Zn cycling in such urban rivers, we have determined Zn speciation in SPM as a function of both the seasonal water flow variations and the urbanization gradient along the Orge River. Using TEM/SEM-EDX and linear combination fitting (LCF) of EXAFS data at the Zn K-edge, we show that Zn mainly occurs as tetrahedrally coordinated Zn(2+) sorbed to ferrihydrite (37-46%), calcite (0-37%), amorphous SiO2 (0-21%), and organic-P (0-30%) and as octahedrally coordinated Zn(2+) in the octahedral layer of phyllosilicates (18-25%). Moreover, the Zn speciation pattern depends on the river flow rate. At low water flow, Zn speciation changes along the urbanization gradient: geogenic forms of Zn inherited from soil erosion decrease relative to Zn bound to organic-phosphates and amorphous SiO2. At high water flow, Zn speciation is dominated by soil-borne forms of Zn regardless the degree of urbanization, indicating that erosion of Zn-bearing minerals dominates the Zn contribution to SPM under such conditions.

X-ray absorption fine structure evidence for amorphous zinc sulfide as a major zinc species in suspended matter from the Seine River downstream of Paris, Ile-de-France, France.

Zinc is one of the most widespread trace metals (TMs) in Earth surface environments and is the most concentrated TM in the downstream section of the Seine River (France) due to significant anthropogenic input from the Paris conurbation. In order to better identify the sources and cycling processes of Zn in this River basin, we investigated seasonal and spatial variations of Zn speciation in suspended particulate matter (SPM) in the oxic water column of the Seine River from upstream to downstream of Paris using synchrotron-based extend X-ray absorption fine structure (EXAFS) spectroscopy at the Zn K-edge. First-neighbor contributions to the EXAFS were analyzed in SPM samples, dried and stored under a dry nitrogen atmosphere or under an ambient oxygenated atmosphere. We found a sulfur first coordination environment around Zn (in the form of amorphous zinc sulfide) in the raw SPM samples stored under dry nitrogen vs an oxygen first coordination environment around Zn in the samples stored in an oxygenated atmosphere. These findings are supported by scanning electron microscopy and energy dispersive X-ray spectrometry observations. Linear combination fitting of the EXAFS data for SPM samples, using a large set of EXAFS spectra of Zn model compounds, indicates dramatic changes in the Zn speciation from upstream to downstream of Paris, with amorphous ZnS particles becoming dominant dowstream. In contrast, Zn species associated with calcite (either adsorbed or incorporated in the structure) are dominant upstream. Other Zn species representing about half of the Zn pool in the SPM consist of Zn-sorbed on iron oxyhydroxides (ferrihydrite and goethite) and, to a lesser extent, Zn-Al layered double hydroxides, Zn incorporated in dioctahedral layers of clay minerals and Zn sorbed to amorphous silica. Our results highlight the importance of preserving the oxidation state in TM speciation studies when sampling suspended matter, even in an oxic water column.