生物岩石学的定义

生物岩石学是研究生物岩(即生物成因岩石)的特征、形成机制、形成环境及其与矿产资源关系的一门新兴交叉学科,其研究内容至少包括生物矿化、现代生物礁、古代生物礁、现代微生物岩石和古代微生物岩石5个方面。生物矿化作用和现代生物岩研究为古代生物岩研究提供了认识基础。由于现代生物圈和环境不同于古代,现代生物矿化作用和生物岩的研究成果并不能全部直接应用于古代生物岩研究。古代生物岩和生物矿化作用的类型比现代丰富得多,不可能全部从现代生物岩和生物矿化作用中找到参照,但可以为现代生物矿化实验研究提供设计思路。生物岩石学的相关学科包括生物学、微生物学、古生物学、古微生物学、沉积学、沉积岩石学、矿物学、地球化学、地质微生物学等。生物岩石学研究需要应用这些学科的知识,也会反哺这些学科。

Iron L-edge and sulfur K-edge XANES spectroscopy analysis of pyrite leached by Acidianus manzaensis

Iron L-edge and sulfur K-edge X-ray absorption near edge structure（XANES） spectroscopy analysis of pyrite leached by extreme thermophilic Archaea strain Acidianus manzaensis（A.manzaensis） was carried out.Leaching experiments show that the oxidation of pyrite can be accelerated by A.manzaensis.Leaching results show that with the increase of leaching time,pH value in the leaching solution gradually decreases,redox potential increases rapidly from day 0 to day 3,and then increases slowly.The SEM results show that the pyrite surfaces are corroded gradually by A.manzaensis,and the XRD results show that the leaching residues contain new compositions of jarosite and elemental sulfur（S0）.The iron L-edge XANES spectroscopy analysis of pyrite during biooxidation indicates that pyrite is gradually converted to Fe（III）-containing species.The sulfur K-edge XANES spectroscopy analysis indicates that elemental sulfur is produced during bioleaching and maintains mass fractions of 3.2%-5.9%.Sodium thiosulfate was also detected from day 2 to day 4,indicating the existence of thiosulfate during biooxidation of pyrite.

Sulfur composition on surface of chalcopyrite during its bioleaching at 50°C

The composition of passive layer of chalcopyrite was investigated by X-ray photoelectron spectroscopy（XPS）, accompanied with cyclic voltammetry（CV）. The leaching experiment shows that the extraction rates of Cu with leaching for 30 d by sterile control and microorganisms are 4.0% and 21.5%, respectively. In comparison, 3.8% and 10.5% Fe are leached by sterile control and microorganisms, respectively. The results of XPS studies suggest that Fe atoms dissolve preferentially from the chalcopyrite lattice, and disulfide（S22-）, polysulfide（Sn2-） and elemental sulfur（S0） are identified on the chalcopyrite surfaces leached by sterile control and microorganisms. Additionally, sulfate（SO42-） is detected on the chalcopyrite surfaces leached by microorganisms, and most of it probably originates from jarosite. The analysis of CV results reveals that metal-deficient sulfide（Cu1-xFe1-yS2-z, yx） and elemental sulfur（S0） passivate the surface of chalcopyrite electrode. The elemental sulfur and/or jarosite coating on the chalcopyrite surface may have impact on the leaching process; however, the disulfide, polysulfide or metal-deficient sulfide plays a more key role in the chalcopyrite leaching.

Bioleaching and electrochemical property of marmatite by Leptospirillum ferrooxidans

The effects of several variables on the bioleaching of marmatite with pure L. ferrooxidans were investigated. The results show that zinc extraction increases with the decrease of pulp density. Adjusting pH tol.6 during the bioleaching process has a positive effect to the dissolution of marmatite. External addition of Fe^3＋ ions accelerates the bioleaching, while the concentration of additional Fe^3＋ over 2.5 g/L weakens the acceleration effect due to the inhibition effect on bacteria growth and the promotion of jarosite production. The electrochemical measurements were used to make further understanding on the dissolution of marmatite with and without additional Fe^3＋ in the presence of L. ferrooxidans. The experimental data illustrate that additional Fe^3＋ ions could increase the corrosion current density, which is favorable to zinc extraction. The EIS spectra show that rate-limiting step does not change when Fe^3＋ is added.

Bio-dissolution of pyrite by Phanerochaete chrysosporium

The dissolution of pyrite was studied with Phanerochaete chrysosporium(P.chrysosporium).This fungus resulted in the dissolution of 18%iron and 33%sulfur.The oxidization layer was formed on the pyrite surface,which probably consisted of iron oxide,iron oxy-hydroxide,iron sulfate,elemental sulfur and mycelia.The electrochemical characteristics of pyrite were studied in the systems without and with P.chrysosporium.P.chrysosporium could accelerate the dissolution of pyrite by decreasing pitting potential and polarization resistance plus improving polarization current,corrosion potential and corrosion current density.The dissolution of pyrite is the combined effect of enzymes,hydrogen peroxide,ferric iron and organic acids.Enzymes attack the chemical bonds by free radicals.Organic acids dissolve pyrite by acidolysis and complexolysis.Enzymes and hydrogen peroxide play an essential role in this process.

Effect of temperature-induced phase transitions on bioleaching of chalcopyrite

The phase transformation of chalcopyrite and the effect of its phase status on bacterial leaching were studied. Under the protection of high-purity argon, different temperatures(203, 382 and 552℃) were applied to natural chalcopyrite to complete the phase change. In addition, the chalcopyrite was bioleached before and after the phase change. The results show that the chalcopyrite heated at 203 and 382℃ remained in the α phase, whereas the chalcopyrite changed from α to β phase at 552℃. The leaching rates of chalcopyrite after the phase transitions at 203, 382 and 552℃ were 32.9%, 40.5% and 60.95%, respectively. Further, the crystal lattice parameters of chalcopyrite increased and lattice energy decreased, which were the fundamental reasons for the significant increase in leaching rate. Electrochemical experiments demonstrated that with increasing annealing temperature, the polarization resistance decreased and corrosion current density increased. The higher the oxidation rate was, the higher the leaching rate was.

Microbial oxidation of refractory gold sulfide concentrate by a native consortium

A defined mesophilic consortium including an iron oxidizing bacterium and a sulfur oxidizing bacterium was constructed to evaluate its ability for bioleaching a flotation concentrate from Andacollo mine in Neuquén,Argentina.Experiments were performed in shake flasks with a pulp density of10%(w/v),using a basal salt medium containing ferrous iron at pH1.8.The leaching solutions were analyzed for pH,redox potential(using specifics electrodes),ferrous iron(by UV-Vis spectrophotometry)and metal concentrations(by atomic absorption spectroscopy).The results showed that the consortium was able to reduce the refractory behavior of the concentrate,allowing91.6%of gold recovery;at the same time,high dissolution of copper and zinc was reached.These dissolutions followed a shrinking core kinetic model.According to this model,the copper solubilization was controlled by diffusion through a product layer(mainly jarosite),while zinc dissolution did not show a defined control step.This designed consortium,composed of bacterial strains with specific physiological abilities,could be useful not only to optimize gold recovery but also to decrease the leachates metallic charge,which would be an environmental advantage.

Enhancing recovery of uranium column bioleaching by process optimization and kinetic modeling

This research aimed to enhance the column bioleaching recovery of uranium ore by Acidithiobacillus ferrooxidans.Seven factors were examined for their significance on bioleaching using a Plackett-Burman factorial design.Four significant variables([Fe2+]initial,pH,aeration rate and inoculation percent)were selected for the optimization studies.The effect of these variables on uranium bioleaching was studied using a central composite design(CCD).The optimal values of the variables for the maximum uranium bioleaching recovery(90.27±0.98)%were as follows:[Fe2+]initial=2.89g/L,aeration rate420mL/min,pH1.45and inoculation6%(v/v).[Fe2+]initial was found to be the most effective parameter.The maximum uranium recovery from the predicted models was92.01%.This value was in agreement with the actual experimental value.The analysis of bioleaching residue of uranium ore under optimum conditions confirmed the formation of K-jarosite on the surface of minerals.By using optimal conditions,uranium bioleaching recovery is increased at column and jarosite precipitation is minimized.The kinetic model showed that uranium recovery has a direct relation with ferric ion concentration.

Influence of sulfur addition/solids content ratio on removal of heavy metals from mine tailings by bioleaching

The effect of sulfur addition/solids content(SA/SC)ratio on heavy metals(e.g.copper,zinc and lead)obtained from mine tailings by indigenous sulfur-oxidizing bacteria was studied,and the changes in the chemical forms of heavy metals after bioleaching were explored.The results show that the solubilization of metals is significantly influenced by SA/SC ratio,and SA/SC ratio of 2.50 is found to be the best for bacterial activity and metal solubilization among six SA/SC ratios tested(such as 1.00,1.33,1.50,1.67,2.00 and 2.50)under the chosen experimental conditions.The pH decreases fast and the maximum solubilizations of copper and zinc are respectively 81.76% and 84.35% while that of lead only reaches 40.36%.After bioleaching,the chemical forms of heavy metals have changed.The metals remained in mine tailings are mainly found in residual fractions,which is harmless to the surrounding environment.

Modeling and Simulation of Enargite Bioleaching

A mathematical model for enargite bioleaching at 70℃ by Sulfolobus BC in shake-flasks has been constructed. The model included （1） the indirect leaching by Fe^3＋ and Fe^3＋ regeneration by suspended Sulfolobus, and （2） the direct leaching by the attached Sulfolobus. The model parameters were optimized using genetic algorithm （GA）. Simulations of the ferric leaching, and bioleaching processes were done using this model. The dynamic changes of the concentrations of Cu^2＋, As^3＋, As^5＋, Fe^3＋ and/or Fe^2＋, as well as ferric-arsenate precipitation were accurately predicted.

Annual Component Analysis of Pacific Oysters （Crassostrea gigas） and Mussels （Mytilus gallopro vincialis）

To study the change in components of Pacific oysters （Crassostrea gigas） and mussels （Mytilus galloprovincialis） over a year, their annual obesity ratio, umami components （glutamic acid and glycogen）, functional components （Zn, Mn, Cu, and vitamin B12）, and Cd and noroviruses （NoVs） contents were quantified. In oysters, the obesity ratio and chemical components showed seasonal changes depending on the spawning season. Glutamic acid content increased from November to March. In contrast, glycogen content peaked in May and November. Mineral content markedly increased during spawning. From the comparison of NoVs GI and GII strains, oyster predominately infected by the GI. A remarkable difference in NoVs contents was observed depending on the oyster farms. In mussels, glutamic acid, Zn and Cu contents were stable throughout the year. Mussels＇ Cd content was about one-fifths times lower than that found in oysters. Although the NoVs strain was affected by the collection area, mussels from both areas showed decreased NoVs contents in summer, corresponding with the consumption season of mussels in Japan. Our comparative study on the seasonal variability in the chemical components and NoVs contents in pacific oysters （C. gigas） and mussels （M. galloprovincialis） clearly showed an association with physiological and environmental factors.

Fractionation characteristics of rare earth elements(REEs) linked with secondary Fe, Mn, and Al minerals in soils

Soil secondary minerals are important scavengers of rare earth elements(REEs) in soils and thus affect geochemical behavior and occurrence of REEs. The fractionation of REEs is a common geochemical phenomenon in soils but has received little attention, especially fractionation induced by secondary minerals. In this study, REEs(La to Lu and Y) associated with soil-abundant secondary minerals Fe-, Al-, and Mn-oxides in 196 soil samples were investigated to explore the fractionation and anomalies of REEs related to the minerals. The results show right-inclined chondrite-normalized REE patterns for La–Lu in soils subjected to total soil digestion and partial soil extraction. Light REEs(LREEs) enrichment features were negatively correlated with a Eu anomaly and positively correlated with a Ce anomaly. The fractionation between LREEs and heavy REEs(HREEs) was attributed to the high adsorption affinity of LREEs to secondary minerals and the preferred activation/leaching of HREEs.The substantial fractions of REEs in soils extracted byoxalate and Dithionite-Citrate-Bicarbonate buffer solutions were labile(10 %–30 %), which were similar to the mass fraction of Fe(10 %–20 %). Furthermore, Eu was found to be more mobile than the other REEs in the soils, whereas Ce was less mobile. These results add to our understanding of the distribution and geochemical behavior of REEs in soils, and also help to deduce the conditions of soil formation from REE fractionation.

Biochar:An Emerging Panacea for Remediation of Soil Contaminants from Mining,Industry and Sewage Wastes

Mine tailings, waste rock piles, acid mine drainage, industrial wastewater, and sewage sludge have contaminated a vast area of cultivable and fallow lands, with a consequence of deterioration of soil and water quality and watercourses due to the erosion of contaminated soils for absence of vegetative cover. High concentrations of toxic elements, organic contaminants, acidic soils, and harsh climatic conditions have made it difficult to re-establish vegetation and produce crops there. Recently, a significant body of work has focussed on the suitability and potentiality of biochar as a soil remediation tool that increases seed emergence, soil and crop productivity, above ground biomass, and vegetation cover on mine tailings, waste rock piles, and industrial and sewage waste- contaminated soils by increasing soil nutrients and water-holding capacity, amelioration of soil acidity, and stimulation of microbial diversity and functions. This review addresses： i） the functional properties of biochar, and microbial cycling of nutrients in soil; ii） bioremediation, especially phytoremediation of mine railings, industrial waste, sewage sludge, and contaminated soil using biochar; iii） impact of biochar on reduction of acid production, acid mine drainage treatment, and geochemical dynamics in mine railings; and iv） treatment of metal and organic contaminants in soils using biochar, and restoration of degraded land.