The Mechanism,Thermodynamic and Kinetic Characteristics of the Microbial Reduction of Goethite Mediated by Anthraquinone-2-Sulfonate

The microbial reduction process of goethite by Shewanella decolorationis S12 was evaluated. The results showed the electron shuttle, anthraquinone-2-sulfonate (AQS), could enhance the microbial reduction. The thermodynamic and kinetic characteristics of goethite reduction by microorganisms were influenced by AQS, concentrations of iron oxide, and electron donor. Transformation between oxidized and reduced species of the electron shuttle during the microbial reduction could be newly noticed. Two interactive steps, biotic and abiotic, were involved in the microbial reduction of Fe (III) oxide mediated by electron shuttle.     

The role of biomineralization in microbiologically influenced corrosion

Synthetic iron oxides (goethite, -FeO·OH; hematite, Fe₂O₃; and ferrihydrite, Fe(OH)₃) were used as model compounds to simulate the mineralogy of surface films on carbon steel. Dissolution of these oxides exposed to pure cultures of the metal-reducing bacterium, Shewanella putrefaciens, was followed by direct atomic absorption spectroscopy measurement of ferrous iron coupled with microscopic analyses using confocal laser scanning and environmental scanning electron microscopies. During an 8-day exposure the organism colonized mineral surfaces and reduced solid ferric oxides to soluble ferrous ions. Elemental composition, as monitored by energy dispersive x-ray spectroscopy, indicated mineral replacement reactions with both ferrihydrite and goethite as iron reduction occurred. When carbon steel electrodes were exposed to S. putrefaciens, microbiologically influenced corrosion was demonstrated electrochemically and microscopically.     

Effects of Phosphate,HEDTA, and Light Sources on Cr(VI) Retention by Goethite

Iron hydrous hydro(oxide) has been regarded as an important sorbent for Cr(VI) in soil systems due to its wide distribution. However, many factors, such as phosphate (P), organic ligands, and light sources, could influence Cr(VI) retention by the soil components. The existence of inorganic or organic ligands not only competes with solution Cr(VI) for surface sites, but also results in releasing sorbed Cr(VI). Although organic matter can reduce Cr(VI) to less toxic Cr(III), the reduction rate is extremely slow. The objective of this study was to evaluate the influence of P on Cr(VI) sorption by goethite. The reduction of Cr(VI) by N-hydroxyethyl-ethylenediamine-triacetic acid (HEDTA) and goethite under different intensity of light was also investigated. Competitive sorption experiment indicated that P had lower inhibition of Cr(VI) sorption when the initial Cr(VI) concentration was higher than P. Goethite suspensions could catalyze Cr(VI) reduction under growth chamber light. Goethite accompanied with light could also accelerate Cr(VI) reduction by HEDTA. This phenomenon could be evidenced by the formation of Cr(III) and decreasing desorption of retained Cr(VI) by P.     

Bacterial and Archaeal DNA Extracted from Inoculated Experiments: Implication for the Optimization of DNA Extraction from Deep-Sea Basalts

Difficulties in efficient DNA extraction from deep-sea volcanic basalt, due to high metal concentration, complex organic matter, or sometimes the low biomass, have hampered the understanding of the significant biosphere both at and below the sea floor. In order to optimize the DNA extraction from basaltic rocks, sterilized basalts with different particle sizes and chemically synthesized goethite were inoculated with an iron oxidizer Marinobacter aquaeolei and an extreme halophilic archaeon Halobaculum gomorrense respectively, and extracted with several methods. Large variations in DNA yields by different extracting methods including FastDNA® spin for soil kit, GeneClean® for ancient DNA kit, UltraClean? and traditional phenol-chloroform methods. Among the commercially available kits tested here, FAST spin kit and GeneClean® for ancient DNA kit yield 10 times more DNA than the UltraClean? kit used. In combination with FAST spin kit, skim milk greatly enhanced the archaeal DNA yields. DNA extracting efficiency was low with the cell number lower than 1 × 10⁶ cells, but reached as high as 88% with a cell number of 1 × 10⁸ cells. On these points, different strategies should be taken into consideration for the DNA extraction from basalts, depending on original biomass and cell types anticipated. FAST spin kit could provide high quality bacterial DNA for downstream PCR whilst the combination of FAST spin kit with skim milk would greatly enhance the archaeal DNA yields. GeneClean® for ancient DNA kit is also recommended for archaeal DNA extraction from deep sea basalt due to its high yield.     

A role for iron and oxygen chemistry in preserving soft tissues,cells and molecules from deep time

The persistence of original soft tissues in Mesozoic fossil bone is not explained by current chemical degradation models. We identified iron particles (goethite-αFeO(OH)) associated with soft tissues recovered from two Mesozoic dinosaurs, using transmission electron microscopy, electron energy loss spectroscopy, micro-X-ray diffraction and Fe micro-X-ray absorption near-edge structure. Iron chelators increased fossil tissue immunoreactivity to multiple antibodies dramatically, suggesting a role for iron in both preserving and masking proteins in fossil tissues. Haemoglobin (HB) increased tissue stability more than 200-fold, from approximately 3 days to more than two years at room temperature (25°C) in an ostrich blood vessel model developed to test post-mortem ‘tissue fixation’ by cross-linking or peroxidation. HB-induced solution hypoxia coupled with iron chelation enhances preservation as follows: HB + O₂ > HB − O₂ > −O₂ ≫ +O₂. The well-known O₂/haeme interactions in the chemistry of life, such as respiration and bioenergetics, are complemented by O₂/haeme interactions in the preservation of fossil soft tissues.     

Attachment of a pseudomonas sp. to Fe(III)‐(hydr)oxide surfaces

As a first step towards understanding microbial dissolution processes, our research focuses on characterizing attachment features that form between a Pseudomonas sp. bacteria and the Fe(III)‐(hydr)oxide minerals hematite and goethite. Microbial growth curves in Fe‐limited growth media indicated that the bacteria were able to obtain Fe from the Fe(III)‐(hydr)oxidesfor use in metabolic processes. A combination of scanning electron microscopy, epifluorescence, and Tapping Mode? atomic‐force microscopy showed that the bacteria colonized some fraction of mineralogical aggregates. These aggregates were covered by bacteria and were linked together by relatively open biofilms consisting of networks of fiber‐like attachment features intertwined through thin films of amorphous‐looking organic material. The biofilm material encompassed numerous individual bacteria, as well as minéralogie particles. We hypothesize that the bacteria first attached to mineral aggregates, perhaps via their flagella, forming colonies. Following initial attachment, the bacteria exuded additional attachment features in the form of fine, branching fibrils intertwined through thin films. The detailed structures of these attachment features were highlighted by Phase Imaging atomic‐force microscopy, which served as a real‐time contrast enhancement technique and showed some poorly defined sensitivity to different surface materials, most probably related to differences in stiffness or viscoelasticity. Although the mechanism of the microbially enhanced dissolution remains unknown, we hypothesize that the bacteria may have produced micro environments conducive to dissolution through the use of observed extracellular materials.     

Influence of pH on the balance between methanogenesis and iron reduction

Methanogenesis and iron reduction play major roles in determining global fluxes of greenhouse gases. Despite their importance, environmental factors that influence their interactions are poorly known. Here, we present evidence that pH significantly influences the balance between each reaction in anoxic environments that contain ferric (oxyhydr)oxide minerals. In sediment bioreactors that contained goethite as a source of ferric iron, both iron reduction and methanogenesis occurred but the balance between them varied significantly with pH. Compared to bioreactors receiving acidic media (pH 6), electron donor oxidation was 85% lower for iron reduction and 61% higher for methanogenesis in bioreactors receiving alkaline media (pH 7.5). Thus, methanogenesis displaced iron reduction considerably at alkaline pH. Geochemistry data collected from U.S. aquifers demonstrate that a similar pattern also exists on a broad spatial scale in natural settings. In contrast, in bioreactors that were not augmented with goethite, clay minerals served as the source of ferric iron and the balance between each reaction did not vary significantly with pH. We therefore conclude that pH can regulate the relative contributions of microbial iron reduction and methanogenesis to carbon fluxes from terrestrial environments. We further propose that the availability of ferric (oxyhydr)oxide minerals influences the extent to which the balance between each reaction is sensitive to pH. The results of this study advance our understanding of environmental controls on microbial methane generation and provide a basis for using pH and the occurrence of ferric minerals to refine predictions of greenhouse gas fluxes.     

抗重金属细菌与针铁矿体系吸附Cu~(2 )和Cd~(2 )的红外光谱研究

采用红外光谱技术探讨了抗重金属细菌NTG-01对针铁矿吸附Cu2 、Cd2 的影响。结果表明:①细菌细胞表面的游离羟基可以吸附Cu2 ;②加入细菌以后促进了Cu2 与针铁矿表面游离羟基(-OH)反应,使Cd2 与其表面的水合羟基(-OH2)的反应加强。     

Solubility and dissolution of iron oxides

In most soils, FeIII oxides (group name) are the common source of Fe for plant nutrition. Since this Fe has to be supplied via solution, the solubility and the dissolution rate of the Fe oxides are essential for the Fe supply. Hydrolysis constants and solubility products (K_sp) describing the effect of pH on FeIII ion concentration in solution are available for the well-known Fe oxides occurring in soils such as goethite, hematite, ferrihydrite. K_sp values are usually extremely low ((Fe³⁺)·(OH)³=10^–37–10^–44). However, for each mineral type, K_sp may increase by several orders of magnitude with decreasing crystal size and it decreases with increasing Al substitution assuming ideal solid solution between the pure end-members. Based on such calculations a poorly crystalline goethite with a crystal size of 5 nm may well reach the solubility of ferrihydrite. The variations in K_sp are of relevance for soils because crystal size and Al substitution of soil Fe oxides vary considerably and can now be determined relatively easily.The concentration of Fe²⁺ in soil solutions is often much higher than that of Fe(III) ions. Therefore, redox potential strongly influences the activity of FeII. At a given pH and E_h, the activity of FeII is higher the higher K_sp of the FeIII oxide and thus also varies with the type of Fe oxide present.Besides the solubility, it is the dissolution rate which governs the supply of soluble Fe to the plant roots. Dissolution of Fe oxides takes place either by protonation, complexation or, most important, by reduction. Numerous dissolution rate studies with various FeIII oxides were conducted in strong mineral acids (protonation) and they have shown that besides the Fe oxide species, crystal size and/or crystal order and substitution are important determinative factors. For example, in soils, small amounts of a more highly soluble meta- or instable Fe oxide such as ferrihydrite with a large specific surface (several hundred m²g^–1) may be essential for the Fe supply to the plant root. Its higher dissolution rate can also be used to quantify its amount in soils. Ferrihydrite can be an important component in soils with high amounts of organic matter and/or active redox dynamics, whereas highly aerated and strongly weathered soils are usually very low in ferrihydrite. On the other hand, dissolution rates of goethites decrease as their Al substitution increases.Much less information exists on the rate of reductive and chelative dissolution of Fe oxides which generally simulate soil conditions better than dissolution by protonation. Here again, type of oxide, crystal size and substitution are important factors. Organic anions such as oxalate, which are adsorbed at the surface, may weaken the Fe³⁺-O bonds and thereby increase reductive dissolution. As often observed in weathering, the dissolution features of the crystals appear to follow zones of weakness in the crystal.