Characterization of the manganese oxide produced by pseudomonas putida strain MnB1

Manganese oxides form typically in natural aqueous environments via Mn(II) oxidation catalyzed by microorganisms, primarily bacteria, but little is known about the structure of the incipient solid-phase products. The Mn oxide produced by a Pseudomonas species representative of soils and freshwaters was characterized as to composition, average Mn oxidation number, and N₂ specific surface area. Electron microscopy, X-ray diffraction, and X-ray absorption near edge structure spectroscopy were applied to complement the physicochemical data with morphological and structural information. A series of synthetic Mn oxides also was analyzed by the same methods to gain better comparative understanding of the structure of the biogenic oxide. The latter was found to be a poorly crystalline layer type Mn(IV) oxide with hexagonal symmetry, significant negative structural charge arising from cation vacancies, and a relatively small number of randomly stacked octahedral sheets per particle. Its properties were comparable to those of δ-MnO₂ (vernadite) and a poorly crystalline hexagonal birnessite (“acid birnessite”) synthesized by reduction of permanganate with HCl, but they were very different from those of crystalline triclinic birnessite. Overall, the structure and composition of the Mn oxide produced by P. putida were similar to what has been reported for other freshly precipitated Mn oxides in natural weathering environments, yielding further support to the predominance of biological oxidation as the pathway for Mn oxide formation. Despite variations in the degree of sheet stacking and Mn(III) content, all poorly crystalline oxides studied showed hexagonal symmetry. Thus, there is a need to distinguish layer type Mn oxides with structures similar to those of natural birnessites from the synthetic triclinic variety. We propose designating the unit cell symmetry as an addition to the current nomenclature for these minerals.     

Oxidation of As^Ⅲ by Several Manganese Oxide Minerals in Absence and Presence of Goethite

Oxidation of As^Ⅲ by three types of manganese oxide minerals affected by goethite was investigated by chemical analysis, equilibrium redox, X-ray diffraction （XRD） and transmission electron microscopy （TEM）. Three synthesized Mn oxide minerals of different types, birnessite, todorokite, and hausmannite, could actively oxidize As^Ⅲ to Asv, and greatly varied in their oxidation ability. Layer structured birnessite exhibited the highest capacity of As^Ⅲ oxidation, followed by the tunnel structured todorokite. Lower oxide hansmannite possessed much low capacity of As^Ⅲ oxidation, and released more Mn^2＋ than birnessite and todorokite during the oxidation. The maximum amount of Asv produced during the oxidation of As^Ⅲ by Mn oxide minerals was in the order： birnessite （480.4 mmol/kg） 〉 todorokite （279.6 mmol/kg） 〉 hansmannite （117.9 mmol/kg）. The oxidation capacity of the Mn oxide minerals was found to be relative to the composition, crystallinity, and surface properties. In the presence of goethite oxidation of As^Ⅲ by Mn oxide minerals increased, with maximum amounts of Asv being 651.0 mmol/kg for birnessite, 332.3 mmol/kg for todorokite and 159.4 mmol/kg for hansmannite. Goethite promoted As^Ⅲ oxidation on the surface of Mn oxide minerals through adsorption of the Asv produced, incurring the decrease of Asv concentration in solutions. Thus, the combined effects of the oxidation （by Mn oxide minerals）-adsorption （by goethite） lead to rapid oxidation and immobilization of As in soils and sediments and alleviation of the As^Ⅲ toxicity in the environments.     

Deposition of deep-sea manganese nodules

Manganese at equilibrium in seawater occurs dominantly as Mn²⁺ and inorganic complexes at a concentration ratio of about 1:0.72; solubility decreases exponentially with increasing pH or Eh. However, the nodule oxides birnessite and todorokite are at least four orders of magnitude undersaturated relative to the Mn concentrations of seawater, and are metastable relative to hausmannite and manganite. This apparent lack of equilibrium is explicable by the mechanism of precipitation.Surfaces assist Mn precipitation by catalyzing equilibration between dissolved and reactive O₂ and simultaneously also by adsorbing ionic Mn species. The effective Eh at the surface becomes 200–400 mV above that of seawater; the oxidation rate of Mn increases about 10⁸ ×, and the activation energies for Mn oxidation decrease ~ 11.5 kcal/mole. Consequently, marine Mn nodules and crusts form by adsorption and catalytic oxidation of Mn²⁺ and ferrous ions at nucleating surfaces such as sea-floor silicates, oxyhydroxides, carbonates, phosphates and biogenic debris. The resulting ferromanganese surfaces autocatalyze further growth. In addition, Mn-fixing bacteria may also significantly accelerate accretion rates on these surfaces.Mn which accumulates in submarine sediments may be diagenetically recycled in response to steep solubility gradients causing upward migration from more acidic and reducing horizons toward the sea floor. In contrast, the concentrations of the predominant ferric complexes, Fe(OH)₃⁰ and Fe(OH)₄^?, are relatively less sensitive to the Eh's and pH's found in this environment; Fe is therefore not as readily recycled within buried sediments. Consequently, Fe is not so effectively enriched on the sea floor, although it precipitates more readily than Mn because seawater is saturated in amorphous Fe(OH)₃.The metastable, perhaps kinetically-related, Mn oxides of nodules have a characteristic distribution: birnessite predominates in oxidizing environments of low sedimentation rate and todorokite where sedimentation rates and diagenetic Mn mobility are higher. Surface adsorption and cation substitution within the disordered birnessite-todorokite structure account for the high trace element content of Mn nodules.     

Zinc sorption to biogenic hexagonal-birnessite particles within a hydrated bacterial biofilm

Biofilm-embedded Mn oxides exert important controls on trace metal cycling in aquatic and soil environments. The speciation and mobility of Zn in particular has been linked to Mn oxides found in streams, wetlands, soils, and aquifers. We investigated the mechanisms of Zn sorption to a biogenic Mn oxide within a biofilm produced by model soil and freshwater Mn^II-oxidizing bacteria Pseudomonas putida. The biogenic Mn oxide is a c-disordered birnessite with hexagonal layer symmetry. Zinc adsorption isotherm and Zn and Mn K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy experiments were conducted at pH 6.9 to characterize Zn sorption to this biogenic Mn oxide, and to determine whether the bioorganic components of the biofilm affect metal sorption properties. The EXAFS data were analyzed by spectral fitting, principal component analysis, and linear least-squares fitting with reference spectra. Zinc speciation was found to change as Zn loading to the biosorbent [bacterial cells, extracellular polymeric substances (EPS), and biogenic Mn oxide] increased. At low Zn loading (0.13 ± 0.04 mol Zn kg⁻¹ biosorbent), Zn was sorbed to crystallographically well-defined sites on the biogenic oxide layers in tetrahedral coordination to structural O atoms. The fit to the EXAFS spectrum was consistent with Zn sorption above and below the Mn^IV vacancy sites of the oxide layers. As Zn loading increased to 0.72 ± 0.04 mol Zn kg⁻¹ biosorbent, Zn was also detected in octahedral coordination to these sites. Overall, our results indicate that the biofilm did not intervene in Zn sorption by the Mn-oxide because sorption to the organic material was observed only after all Mn vacancy sites were capped by Zn. The organic functional groups present in the biofilm contributed significantly to Zn removal from solution when Zn concentrations exceeded the sorption capacity of the biooxide. At the highest Zn loading studied, 1.50 ± 0.36 mol Zn kg⁻¹ biosorbent, the proportion of total Zn sorption attributed to bioorganic material was 38 mol%. The maximum Zn loading to the biogenic oxide that we observed was 4.1 mol Zn kg⁻¹ biogenic Mn oxide, corresponding to 0.37 ± 0.02 mol Zn mol⁻¹ Mn. This loading is in excellent agreement with previous estimates of the content of cation vacancies in the biogenic oxide. The results of this study improve our knowledge of Zn speciation in natural systems and are consistent with those of Zn speciation in mineral soil fractions and ferromanganese nodules where the Mn oxides present are possibly biogenic.     

Sorption of ferric iron from ferrioxamine B to synthetic and biogenic layer type manganese oxides

Siderophores are biogenic chelating agents produced in terrestrial and marine environments that increase the bioavailability of ferric iron. Recent work has suggested that both aqueous and solid-phase Mn(III) may affect siderophore-mediated iron transport, but scant information appears to be available about the potential roles of layer type manganese oxides, which are relatively abundant in soils and the oligotrophic marine water column. To probe the effects of layer type manganese oxides on the stability of aqueous Fe-siderophore complexes, we studied the sorption of ferrioxamine B [Fe(III)HDFOB⁺, an Fe(III) chelate of the trihydroxamate siderophore desferrioxamine B (DFOB)] to two synthetic birnessites [layer type Mn(III,IV) oxides] and a biogenic birnessite produced by Pseudomonas putida GB-1. We found that all of these predominantly Mn(IV) oxides greatly reduced the aqueous concentration of Fe(III)HDFOB⁺ at pH 8. Analysis of Fe K-edge EXAFS spectra indicated that a dominant fraction of Fe(III) associated with the Mn(IV) oxides is not complexed by DFOB as in solution, but instead Fe(III) is specifically adsorbed to the mineral structure at multiple sites, thus indicating that the Mn(IV) oxides displaced Fe(III) from the siderophore complex. These results indicate that layer type manganese oxides, including biogenic minerals, may sequester iron from soluble ferric complexes. We conclude that the sorption of iron-siderophore complexes may play a significant role in the bioavailability and biogeochemical cycling of iron in marine and terrestrial environments.     

Oxidation and Mineralization of Mn2+ Ions Mediated by Pseudomonas putida: Insights from an Experimental Study

The formation of manganese oxides in nature is commonly mediated by microorganisms.In this study,the mineralization of biogenic manganese oxidation mediated by Pseudomanas putida has been experimentally investigated by employing various characterization techniques,including SEM,FESEM,TEM,XRD,and STXM-NEXAFS.The results indicate that Mn~(2+) ions can be oxidized into Mn(Ⅳ) minerals(birnessite and pyrolusite) and Mn(Ⅲ) minerals(hausmannite and feitknechtite),successively.The primary products(birnessite and pyrolusite) further transformed into hausmannite and feitknechtite under Mn~(2+) ion-enriched conditions.However,birnessite and pyrolusite are the endproducts of the continuous microbial oxidation processes.These biogenic Mn oxides are poorly crystallized,which provides them with a high potential for usage in environmental restoration of contaminated soils and waters contaminated with heavy metals.The approaches employed in this study will also enrich genesis research of biological oxidation of Mn(Ⅱ) species in nature.     

Coupled biotic-abiotic Mn(II) oxidation pathway mediates the formation and structural evolution of biogenic Mn oxides

Manganese (Mn) oxides are among the strongest oxidants and sorbents in the environment, impacting the transport and speciation of metals, cycling of carbon, and flow of electrons within soils and sediments. The oxidation of Mn(II) to Mn(III/IV) oxides has been primarily attributed to biological processes, due in part to the faster rates of bacterial Mn(II) oxidation compared to observed mineral-induced and other abiotic rates. Here we explore the reactivity of biogenic Mn oxides formed by a common marine bacterium (Roseobacter sp. AzwK-3b), which has been previously shown to oxidize Mn(II) via the production of extracellular superoxide. Oxidation of Mn(II) by superoxide results in the formation of highly reactive colloidal birnessite with hexagonal symmetry. The colloidal oxides induce the rapid oxidation of Mn(II), with dramatically accelerated rates in the presence of organics, presumably due to mineral surface-catalyzed organic radical generation. Mn(II) oxidation by the colloids is further accelerated in presence of both organics and light, implicating reactive oxygen species in aiding abiotic oxidation. Indeed, the enhancement of Mn(II) oxidation is negated when the colloids are reacted with Mn(II) in the presence of superoxide dismutase, an enzyme that scavenges the reactive oxygen species (ROS) superoxide. The reactivity of the colloidal phase is short-lived due to the rapid evolution of the birnessite from hexagonal to pseudo-orthogonal symmetry. The secondary particulate triclinic birnessite phase exhibits a distinct lack of Mn(II) oxidation and subsequent Mn oxide formation. Thus, the evolution of initial reactive hexagonal birnessite to non-reactive triclinic birnessite imposes the need for continuous production of new colloidal hexagonal particles for Mn(II) oxidation to be sustained, illustrating an intimate dependency of enzymatic and mineral-based reactions in Mn(II) oxidation. Further, the coupled enzymatic and mineral-induced pathways are linked such that enzymatic formation of Mn oxide is requisite for the mineral-induced pathway to occur. Here, we show that Mn(II) oxidation involves a complex network of abiotic and biotic processes, including enzymatically produced superoxide, mineral catalysis, organic reactions with mineral surfaces, and likely photo-production of ROS. The complexity of coupled reactions involved in Mn(II) oxidation here highlights the need for further investigations of microbially-mediated Mn oxide formation, including identifying the role of Mn oxide surfaces, organics, reactive oxygen species, and light in Mn(II) oxidation and Mn oxide phase evolution.     

Rock-magnetic characterization of early, redoxomorphic diagenesis in turbiditic sediments from the Madeira Abyssal Plain

Rock‐magnetic measurements of two sediment cores from the Madeira Abyssal Plain (MAP), north Atlantic, are used to investigate post‐depositional changes in the concentration, grain size and composition of magnetic minerals in the sediments that have occurred within organic‐rich turbidite horizons. The changes are associated with an initial stage of suboxic (reductive) diagenesis, following depletion of porewater O₂, and a later stage of oxidative diagenesis associated with the slow descent of an oxidation front through the sediment, as a result of diffusion of O₂ from the overlying sea water. The turbidites are of late Quaternary age (δ¹⁸O stages 1–3) and derive both from different sites on the NW African continental margin, and from the flanks of the Canary Islands. Thus, the turbidites are variable compositionally, especially in terms of carbonate, detrital magnetic mineral and organic carbon content. Diagenetic changes in these sediments have been identified using solid‐phase geochemical data (U, Mn, C_org and CaCO₃) reported previously in more than one study. Rock‐magnetic parameters of the sediments, when expressed on a carbonate‐free basis, reveal that significant depletion of detrital ferrimagnetic iron (Fe²⁺/Fe³⁺) oxide grains has occurred within organic‐rich turbidites during redoxomorphic diagenesis. Normalized quotients of magnetic parameters also show that reductive diagenesis is a ferrimagnetic grain size‐selective process, but it has a minimal effect on the canted‐antiferromagnetic Fe³⁺ oxides in the sediment. Such components, if present, therefore become relatively enriched in magnetic assemblages as the ferrimagnetic grains are dissolved progressively, and bulk magnetic concentration is thus depleted. There is clear evidence in both cores for the existence of ultrafine ferrimagnetic grains at depth within the suboxic zone of the organic‐rich turbidites, beneath both active and fossil oxidation fronts. These grains are most probably associated with populations of live magnetotactic bacteria, which commonly inhabit such organic‐rich horizons and play a part in the chain of bacterially mediated reactions normally associated with suboxic diagenesis. These results show that simple and rapid rock‐magnetic techniques can be used to characterize early diagenetic processes involving iron phases in deep‐sea sediments, at least as effectively as more laborious, time‐consuming and sample‐destructive geochemical measurements.     

Crystal chemistry of clay-Mn oxide associations in soils, fractures, and matrix of the Bandelier Tuff, Pajarito Mesa, New Mexico

The upper 25 m of Bandelier Tuff at Pajarito Mesa, New Mexico, include soils, shallow fractures, deeper fractures, and tuff matrices in which clays provide a record of transport and alteration. The principal pathways within this system are fractures that penetrate the tuff. Large fractures that host deep root penetration provide a setting in which clay deposits accumulate through particulate or colloidal migration from the soil zone. Clays throughout the system are predominantly expandable interstratified illite/smectites (I/S), but clays of the tuff matrix at depth are distinctly Fe-rich and are not mixed with clays transported from the surface into fractures. Chemical alteration superimposed on clay particles transported into fractures results in clays with lower Al : Si ratios, higher Na, and higher lanthanide content with increasingly negative Eu anomalies with depth. These changes are accompanied by invasion and precipitation of Mn oxides, principally birnessite, within clay bodies. Investigation of the Mn oxides by synchrotron X-ray fluorescence (SXRF) shows that Mn is associated with Ba, Ce, Ni, and Pb. In addition, synchrotron X-ray absorption near-edge structure (XANES) spectra show that Ce in Mn oxides occurs as Ce³⁺ and Ce⁴⁺, with average Ce oxidation state of ∼3.75. The Mn oxides intergrown with clays actively participate in removal of Ce from solution, accompanied by oxidation of Ce³⁺ to Ce⁴⁺. Other lanthanides are accumulated by the clays but are not concentrated along with Ce in the Mn oxides. Extraction of Ce from solution by Mn oxides is more effective than lanthanide accumulation in clay, a process that is variable and likely influenced by defects, extent of recrystallization, and particle sizes. This dichotomy in lanthanide interaction results in locally constant Ce content but either negative or positive Ce anomalies in the clay-Mn oxide system as a consequence of variability in the abundance of the other lanthanides. Nevertheless, the net lanthanide pattern for the sum of all clay-Mn oxide samples in either shallow or deep fractures has no Ce anomaly, indicating that other lanthanides segregated from Ce are not transported beyond the range of either the shallow or deep fracture systems. Evidence from Eu anomalies indicates that lanthanides accumulated in the fracture clays are acquired from the local tuff. The clay-Mn oxide assemblage is more effective than clay alone in accumulating of a wide variety of heavy metals.     

The role of grain dissolution and diagenetic mineral precipitation in the cycling of metals and phosphorus: A study of a contaminated urban freshwater sediment

This paper describes the detrital mineralogy, early diagenetic reactions and authigenic mineral precipitates for freshwater contaminated sediments deposited in an urban water body (the Salford Quays of the Manchester Ship Canal, Greater Manchester, UK). These sediments contain a mix of natural and anthropogenic detrital grains. Detrital grains are dominated by quartz and clay grains, whilst anthropogenic grains are dominated by metal-rich glass grains, concentrated at a depth of 12–17 cm in the sediment as a result of historical inputs. Sediment porewaters contain significant concentrations of Fe, Mn, Zn and phosphate. Bacterial Fe(III) and Mn(IV) reduction are hypothesised to supply Fe²⁺ and Mn²⁺ to porewaters, with phosphate released from Fe oxide reduction or organic matter oxidation. Petrographic observations indicate that the metal-rich glass grains are undergoing chemical dissolution during early diagenesis, supplying Fe and Zn to porewaters.     

Biogeochemistry of southern Australian continental slope sediments

Sediment cores from the middle to lower slope of the southern continental margin of Australia between the Great Australian Bight and western Tasmania are compared in terms of marine and terrigenous input signals during the Holocene. The mass accumulation rates of carbonate, organic carbon, biogenic Ba, and Al are corrected for lateral sediment input (focusing), using the inventory of excess ²³⁰Th in the sediment normalised to its known production rate in the water column above each site. The biogenic signal is generally higher in the eastern part of the southern margin probably due to enhanced productivity associated with seasonal upwelling off southeastern South Australia and the proximity of the Subtropical Front, which passes just south of Tasmania. The input of Al, representing the terrigenous signal, is also higher in this region reflecting the close proximity of river runoff from the mountainous catchment of southeastern Australia. The distribution pattern of Mn and authigenic U, together with pore‐water profiles of Mn⁺⁺, indicate diagenetic reactions driven by the oxidation of buried organic carbon in an oxic to suboxic environment. Whereas Mn is reduced at depth and diffuses upwards to become immobilised in a Mn‐rich surface layer, U is derived from seawater and diffuses downward into the sediment, driven by reduction and precipitation at a depth below the reduction zone of Mn. The estimated removal rate of U from seawater by this process is within the range of U removal measured in hemipelagic sediments from other areas, and supports the proposition that hemipelagic sediments are a major sink of U in the global ocean. Unlike Mn, the depth profile of sedimentary Fe appears to be little affected by diagenesis, suggesting that little of the total Fe inventory in the sediment is remobilised and redistributed as soluble Fe.     

Recent macroids on the Kikai‐jima shelf,Central Ryukyu Islands,Japan

Sandy and gravelly carbonate sediments found off Kikai‐jima, southern Japan, a coral reef‐related island shelf, represent the northernmost sub‐tropical, carbonate deposits in the Central Ryukyu Islands (Ryukyus). On the Kikai‐jima shelf, at water depths of 61 to 105 m, these sediments are characterized by macroid pavements. Since the abundance of very small and of exceptionally large macroids may indicate specific hydrodynamic controls regarding constraints on growth and taphonomy, the detailed analysis of recent and fossil macroid pavements is meaningful ecologically and environmentally. Macroids, ranging in size from ca 25 to 130 mm in diameter, are spheroidal and sub‐spheroidal in shape and consist mainly of the encrusting foraminifer Acervulina inhaerens and subordinate thin encrusting and lumpy coralline algae. Accessory components include bryozoans, serpulids and, to a lesser extent, encrusting arborescent foraminifera (Homotrema and Miniacina). Low sedimentation rates and occasional movement due to current action are indicated by sizes, shapes and growth‐forms of the studied macroids, the Entobia–Gastrochaenolites–Trypanites–Maeandropolydora ichnocoenosis and the ‘Bioerosion Index’ for coated grains (introduced herein). The deep‐water tidally induced current energy was sufficient to maintain multi‐directional growth (spheroidal shapes) of the larger macroids and to initiate macroid growth using the diverse biogenic remnants as nuclei. The asymmetrical inner arrangement suggests possible periods of stability for the macroids. The residence time of the coated grain in its original environment determines the size and morphology of the macroid and the selection of coating organisms. The composition of the coating community is mainly a consequence of component growth rates in relation to turnover time and residence time. Long‐term studies are needed to assess the spatial and temporal resolution of present‐day encrusting communities across biogeographic provinces and shelf to slope regions.     

模拟表生环境水钠锰矿亚结构转化及钙锰矿的形成

水钠锰矿是土壤与沉积物中最为常见的氧化锰矿物, 依据其MnO₆层对称特点分为六方和三斜两种亚结构类型.六方水钠锰矿在表生环境中可通过Mn2+的化学或生物氧化形成, 而环境中三斜水钠锰矿的形成及进一步转化为钙锰矿的途径尚不清楚.以两种六方水钠锰矿(酸性水钠锰矿和水羟锰矿)为前驱物, 采用X射线吸收光谱(EXAFS)、X射线衍射(XRD)、电镜(FESEM/TEM)及化学组成分析等技术方法模拟表生环境研究了水钠锰矿从六方向三斜的亚结构转化及生成钙锰矿的化学条件和矿物学机制.结果表明, 适当Mn(Ⅱ)浓度和弱碱性条件(pH≥8)可使六方水钠锰矿逐渐转化为三斜水钠锰矿, 继而经Mg2+交换、常压回流得到了长纤维状的钙锰矿, 其晶体生长以溶解-结晶为主.Mn(Ⅱ)与六方水钠锰矿MnO₆八面体层内的Mn(Ⅳ)反应生成Mn(Ⅲ)并填充层内空位, 使水钠锰矿对称型由六方向三斜转变.与酸性水钠锰矿相比, 水羟锰矿结晶弱、层状堆积混乱度高, 与Mn(Ⅱ)反应迅速, 层结构向三斜水钠锰矿转化快.pH升高, 促进六方水钠锰矿对Mn(Ⅱ)的吸附和Mn(Ⅱ)与Mn(Ⅳ)间的反应, 六方水钠锰矿转化为三斜水钠锰矿的速率加快."六方水钠锰矿→三斜水钠锰矿"可能是环境中三斜水钠锰矿的重要来源, 及进一步形成钙锰矿的重要化学生成机制.      

氧化锰矿物的生物成因及其性质的研究进展

土壤中的氧化锰矿物是原生矿物风化和成土过程的产物,是最具反应活性的一类矿物,决定着环境中许多物质的形态、迁移和转化,在元素生物地球化学循环中起着重要的作用,其形成机制和环境效应备受关注。已有的研究表明,环境中氧化锰的形成与微生物作用紧密相关,微生物作用可使自然环境中的Mn(Ⅱ)氧化速率提高105倍。参与Mn(Ⅱ)氧化的微生物在环境中广泛存在,已知的典型锰氧化细菌分布在变形菌门、放线菌门或厚壁菌门,它们均通过胞外聚合物中的多铜氧化酶来催化氧化Mn(Ⅱ)。细菌氧化Mn(II)成Mn(Ⅳ)是酶催化的两个连续的快速单电子传递过程,Mn(Ⅲ)在溶液中以与酶结合的瞬时中间态出现。生物形成氧化锰的最初形态为层状锰矿物,与δ-MnO2或酸性水钠锰矿很类似,且结晶弱,粒径小,锰氧化度高,结构中的八面体空穴多,因而比化学形成的氧化锰具有更强的吸附、氧化等表面活性。环境中Mn(Ⅱ)微生物氧化及形成的Mn(Ⅲ)中间体与碳、氮、硫等生命元素的地球化学循环的关系令人关注。     

Mechanisms of nickel sorption by a bacteriogenic birnessite

A synergistic experimental-computational approach was used to study the molecular-scale mechanisms of Ni sorption at varying loadings and at pH 6-8 on the biogenic hexagonal birnessite produced by Pseudomonas putida GB-1. We found that Ni is scavenged effectively by bacterial biomass-birnessite assemblages. At surface excess values below 0.18 mol Ni kg⁻¹ sorbent (0.13 mol Ni mol⁻¹ Mn), the biomass component of the sorbent did not interfere with Ni sorption on mineral sites. Extended X-ray absorption fine structure (EXAFS) spectra showed two dominant coordination environments: Ni bound as a triple-corner-sharing (Ni-TCS) complex at vacancy sites and Ni incorporated (Ni-inc) into the MnO₂ sheet, with the latter form of Ni favored at high sorptive concentrations and decreased proton activity. In parallel to our spectral analysis, first-principles geometry optimizations based on density functional theory (DFT) were performed to investigate the structure of Ni surface complexes at vacancy sites. Excellent agreement was achieved between EXAFS- and DFT-derived structural parameters for Ni-TCS and Ni-inc. Reaction-path calculations revealed a pH-dependent energy barrier associated with the transition from Ni-TCS to Ni-inc. Our results are consistent with the rate-limited incorporation of Ni at vacancy sites in our sorption samples, but near-equilibrium state of Ni in birnessite phases found in nodule samples. This study thus provides direct and quantitative evidence of the factors governing the occurrence of Ni adsorption versus Ni incorporation in biogenic hexagonal birnessite, a key mineral in the terrestrial manganese cycle.     

Distribution and accumulation rate of ore elements in Holocene and Late Glacial Sediments of the Deryugin Basin,Sea of Okhotsk

Results of the study of contents and accumulation rates of Fe, Mn, and a number of trace elements in Upper Quaternary sediments of the Deryugin Basin are presented. Maps of the average contents and accumulation rates of excess Fe, Mn, Zn, Ba, Ni, Pb, Cu, and Mo in sediments of the first oxygen isotope stage (OIS) have been plotted. Anomalous contents and accumulation rates are confined to peripheral zones of the Deryugin sedimentary basin and large fracture zones. Different mechanisms of the influence of fluid-dynamic processes on the rate of hydrogenic and biogenic accumulation of ore elements are assumed.Translated from Litologiya i Poleznye Iskopaemye, No. 2, 2005, pp. 115–132.Original Russian Text Copyright © 2005 by Astakhov, Gorbarenko, Bakhareva, Gretskaya, Sattarova.     

Adsorption of Co and selected actinides by Mn and Fe oxides in soils and sediments

Iron and Mn oxides and associated radionuclides in soils and sediments from the radioactive waste burial grounds at Oak Ridge National Laboratory have been selectively extracted using wet chemical techniques. Product-moment-correlation analyses have demonstrated that ⁶⁰Co and various actinides, principally ²⁴⁴Cm, ²⁴¹Am and ²³⁸Pu are dominantly associated with Mn oxides. Correlation coefficients between these radionuclides and Fe oxides and organic C are generally very low. The important role of Mn oxides in radionuclide adsorption is attributed to their unique surface and colloidal properties. The data illustrate the importance of the Mn oxide component of soils and sediments in controlling transition metal and actinide solubility.These results suggest two major implications for the disposal of radioactive waste. First, in order to minimize future ⁶⁰Co and actinide mobilization from disposal sites, a chemical environment in which Mn oxides are least soluble should be maintained. Second, the liberal use of Mn oxides in waste management operations might improve long-term retention of these radionuclides. Deep-sea Mn modules, which may in the future be mined for their trace metal contents, could serve as a ready supply of Mn oxide for waste disposal applications.     

Structural CO2 in the Apatite of the Late Cretaceous Phosphorite Resources in Egypt: Effect on the Crystal Chemistry and Geologic Implications

Abstract: Phosphorite deposits in Egypt, known as the Duwi Formation, are a part of the Middle East to North Africa phospho‐genic province of late Cretaceous to Paleogene age. Based on the petrographical observation, the phosphatic grains in the phosphorites are classified into phosphatic mudclasts and phosphatic bioclasts. Both of them are composed of francolite. The structural CO₂ contents in the francolite range from 3.3 to 7.2 % with an average of 5.3 %. Results indicated that the substitution with CO₃^2‐ of PO₄^3‐ in the francolite decreases the unit cell volume and a‐cell dimension, and increases the c/a ratio. Effect is more obvious in the a‐cell dimension; therefore, it is more significant in distinction between the different apatite species. Lack of covariance between structural CO₂ contents in the francolite and the carbonate minerals contents may render the supposition that the phosphorites formed as a result of replacement of preexisting calcareous sediments is doubtful. Similarity in CO₂ content in both weathered and fresh samples indicates that the structural CO₂ content in the phosphorites is not affected by weathering, and reflects the conditions and CO₂ concentration of the depositional environment. Similarity in mineralogy and CO₂ contents in the different phosphatic grains and higher CO₂ content in the Egyptian phosphorites compared with the authigenic phosphates of Peru margin, which formed by the same mechanism as the Duwi phosphorites, suggest that the phosphatic grains in the Duwi Formation were francolitized during diagenesis by introducing CO₂ from the surrounding pore water and diagenesis took place at an elevated temperature. Scattered values of structural CO₂ contents suggest the reworking origin of the phosphatic grains in the late Cretaceous phosphorites in Egypt.     

A 2400-year record of trace metal loading in lake sediments of Lagoa Vermelha, southeastern Brazil

Sediments of the Lagoa Vermelha (Red Lake), situated in the Ribeira Valley, southeastern Brazil, are made of a homogeneous, organic-rich, black clay with no visible sedimentary structures. The inorganic geochemical record (Al, As, Ba, Br, Co,Cs, Cr, Fe, Mn, Ni, Rb, Sc, Sb, V, Zn, Hg and Pb) of the lake sediments was analyzed in a core spanning 2430 years. The largest temporal changes in trace metal contents occurred approximately within the last 180 years. Recent sediments were found to be enriched in Pb, Zn, Hg, Ni, Mn, Br and Sb (more than 2-fold increase with respect to the “natural background level”). The enhanced accumulation of Br, Sb, and Mn was attributed to biogeochemical processes and diagenesis. On the other hand, the anomalous concentrations of Pb, Zn, Hg and Ni were attributed to pollution. As Lagoa Vermelha is located in a relatively pristine area, far removed from direct contamination sources, the increased metal contents of surface sediments most likely resulted from atmospheric fallout. Stable Pb isotopes provided additional evidence for anthropogenic contamination. The shift of ²⁰⁶Pb/²⁰⁷Pb ratios toward decreasing values in the increasingly younger sediments is consistent with an increasing contribution of airborne anthropogenic lead. In the uppermost sediments (0-10 cm), the lowest values of the ²⁰⁶Pb/²⁰⁷Pb ratios may reflect the influence of the less radiogenic Pb from the Ribeira Valley District ores (²⁰⁶Pb/²⁰⁷Pb between 1.04 and 1.10), emitted during the last 50 years.     

Sedimentology and geochemistry of fluvio-lacustrine tufa deposits controlled by evaporite solution subsidence in the central Ebro Depression, NE Spain

The Urrea de Jalón tufa deposits constitute the 20‐ to 50‐m‐thick caprock (0·3 km²) of an isolated mesa. They disconformably overlie horizontal strata of the Tertiary Ebro Basin (NE Spain), which contains a thick succession of lacustrine gypsum and marls, followed by limestones, marls and, locally, fluvial sandstones and mudstones. The tufa deposits show a complex, large‐scale framework of basin‐like structures with centripetal dips that decrease progressively from the base to the top of the tufa succession, and beds that thicken towards the centre of the structure (cumulative wedge‐out systems). These geometries reveal that the tufa deposits were affected by differential synsedimentary subsidence. Distinct onlapping depressions reflect time migration of the subsiding areas. The studied carbonates are composed mostly of low‐Mg calcite, with minor quartz. Some samples have anomalously high contents of Fe, Mn and Ba that may exceed 1% (goethite, haematite and barite are present). Carbonate facies are: (a) macrophyte encrustation deposits; (b) bryophyte build‐ups; (c) oncolite and coated grain rudstones; (d) non‐concentric stromatolite‐like structures; (e) massive or bioturbated biomicrites; and (f) green and grey marls. Facies a and c show a great variety of microbial‐related forms. These facies can be arranged in dm‐ to 2‐m‐thick vertical associations representing: (i) fluvial–paludal sequences with bryophyte growths; (ii) pond‐influenced fluvial sequences; and (iii) lacustrine–palustrine sequences. The Urrea de Jalón tufa deposits formed in a fluvio‐lacustrine environment that received little alluvial sediment supply. Isotope compositions (δ¹³C and δ¹⁸O) reveal meteoric signatures and accord with such a hydrologically open system of fresh waters. The Fe, Mn and Ba contents suggest an additional supply of mineralized waters that could be related to springs. These would have been discharge points in the Ebro Depression of a regional aquifer of the Iberian Ranges. Rising groundwater caused the solution of the underlying evaporites and the synsedimentary subsidence of the tufa deposits.