Nitrate-Controlled Anaerobic Oxidation of Pyrite by Thiobacillus Cultures

Nitrate-dependent pyrite oxidation is an important process as it may prevent pollution by nitrate from agriculture. Anaerobic oxidation of pyrite with nitrate as an electron acceptor was studied in cultures of Thiobacillus denitrificans and Thiobacillus thioparus. Both strains reduced nitrate, with pyrite added as sole electron donor, but T. thioparus reduced nitrate to nitrite only. Accumulation of nitrite, however, was prevented in co-cultures of T. denitrificans and T. thioparus. Furthermore, pyrite oxidation rates were dependent on pyrite pretreatment, which results in different specific surface areas of pyrite. Initial nitrate concentration or pyrite origin did not affect the pyrite oxidation rate.     

Acdidophilic thermophilic archaebacteria: Potential application for metals recovery

Abstract The acidophilic thermophilic archaebacteria Sulfolobus and Acidianus have the potential for applid use in the recovery of metal values from ores through the process of baterial leaching. These microbes readily adapt to the conditions of low pH and high concentrations of metals required for bacterial leaching. In addition, these archaebacteria can exist at high temperatures which can occur during the oxidation of metal sulfides in bioleaching reactors. The acidophilic of copper and molybdenum from chalcopyrite and molybdenite minerals, respectively. The microbes can also enhance the recovery of gold by oxidation of pyrite which occludes gold preventing recovery by standard metallurgical procedures. The ability of this group of microbes to facilitate metals recovery is yet to be developed on a commercial scale.     

Bioleaching of pyrite by acidophilic thermophile Acidianus brierleyi

The kinetics of bioleaching of pyrite (FeS(2)) by the acidophilic thermophilic bacterium Acidianus brierleyi was studied in a well-mixed batch reactor. Experiments were done at 65 degrees C and pH 1.5 on adsorption of A. brierleyi onto pyrite particles, liquid-phase oxidation of ferrous iron by A. brierleyi, and microbial leaching of pyrite. The adsorption of A. brierleyi was a fast process; equilibrium was attained within the first 30 min of exposure to pyrite. The adsorption equilibrium data were well correlated with the Langmuir isotherm. The oxidation of ferrous iron was markedly accelerated in the presence of A. brierleyi, and the growth yield on ferrous iron was determined. The bioleaching of pyrite by A. brierleyi was found to take place with a direct attack by adsorbed cells on the surface of pyrite, the chemical leaching of pyrite by ferric iron being insignificant. Rate data collected under a wide variety of operating variables were analyzed to determine kinetic and stoichiometric parameters for the microbial pyrite leaching. The specific growth rate on pyrite for A. brierleyi was about four times that for the mesophilic bacterium, Thiobacillus ferrooxidans, whereas the growth yields on pyrite for the two microbes were approximately equal to one another in magnitude. A comparison of A. brierleyi with T. ferrooxidans for pyrite leachability demonstrated the thermophile to be much more effective. (c) 1995 John Wiley & Sons, Inc.     

Intermediary sulfur compounds in pyrite oxidation: implications for bioleaching and biodepyritization of coal

Accumulation of elemental sulfur during pyrite oxidation lowers the efficiency of coal desulfurization and bioleaching. In the case of pyrite bioleaching by Leptospirillum ferrooxidans, an iron(II)-ion-oxidizing organism without sulfur-oxidizing capacity, from the pyritic sulfur moiety about 10% elemental sulfur, 2% pentathionate, and 1% tetrathionate accumulated by a recently described cyclic pyrite oxidation mechanism. In the case of pure cultures of Thiobacillus ferrooxidans and mixed cultures of L. ferrooxidans and T. thiooxidans, pyrite was nearly completely oxidized to sulfate because of the capacity of these cultures to oxidize both iron(II) ions and sulfur compounds. Pyrite oxidation in acidic solutions, mediated chemically by iron(III) ion, resulted in an accumulation of similar amounts of sulfur compounds as obtained with L. ferrooxidans. Changes of pH to values below 2 or in the iron ion concentration are not decisive for diverting the flux of sulfur compounds. The literature on pyrite bioleaching is in agreement with the findings indicating that the chemistry of direct and indirect pyrite leaching is identical. Received: 20 April 1998 / Received revision: 27 August 1998 / Accepted: 3 September 1998     

Mechanism of Bacterial Pyrite Oxidation

The oxidation by Ferrobacillus ferrooxidans of untreated pyrite (FeS(2)) as well as HCl-pretreated pyrite (from which most of the acid-soluble iron species were removed) was studied manometrically. Oxygen uptake was linear during bacterial oxidation of untreated pyrite, whereas with HCl-pretreated pyrite both a decrease in oxygen uptake at 2 hr and nonlinear oxygen consumption were observed. Ferric sulfate added to HCl-pretreated pyrite restored approximately two-thirds of the decrease in total bacterial oxygen uptake and caused oxygen uptake to revert to nearly linear kinetics. Ferric sulfate also oxidized pyrite in the absence of bacteria and O(2); recovery of ferric and ferrous ions was in excellent agreement with the reaction Fe(2)(SO(4))(3) + FeS(2) = 3FeSO(4) + 2S, but the elemental sulfur produced was negligible. Neither H(2)S nor S(2)O(3) (2-) was a product of the reaction. It is probable that two mechanisms of bacterial pyrite oxidation operate concurrently: the direct contact mechanism which requires physical contact between bacteria and pyrite particles for biological pyrite oxidation, and the indirect contact mechanism according to which the bacteria oxidize ferrous ions to the ferric state, thereby regenerating the ferric ions required for chemical oxidation of pyrite.     

Experimental Study of Microbial Pyrite Oxidation: A Suggestion for Geologically Useful Biosignatures

The oxidation of pyrite in cultures of Acidithiobacillus ferrooxidans (A.f) was studied. The experiments were performed at an initial pH of 2.5 at 28°C. The concentrations of total dissolved iron in solution and the pH were monitored during the first 36 days. Pyrite surfaces were examined by scanning electron microscopy and energy-dispersive spectrometry (SEM-EDS) after 100 days. The concentrations of total dissolved iron and hydrogen ions increased significantly in the presence of bacteria. SEM examination indicated that the crystal surfaces were subjected to two types of dissolution phenomena. Cracks were observable on the of crystal surfaces under both biotic and abiotic conditions, whereas rounded and polygonal pits appeared additionally on the surfaces under biotic conditions. The co-occurrence of the rounded and polygonal pits on the crystal surfaces and the presence of A.f at the pyrite surface suggests that A.f promotes pyrite oxidation by a contact mechanism. We propose that the rounded and polygonal pits be considered to represent a practical biosignature for tracing the evolution of microbial iron oxidation in the remote past.     

Further Readings in Geomicrobiology

Microbial biofilms preferentially colonized pyrite surfaces of black shale incubated in groundwater in the Newark Basin (northeastern United States) for 1 month. SEM observation revealed the co-occurrence of bacteria-shaped pits and secondary iron minerals on pyrite, which indicate biological involvement in pyrite weathering and secondary solid formation. Of the 24 16S rDNA sequences obtained from bacterial communities on pyrite, arsenopyrite and quartz sand, 22 belonged to the phylum proteobacteria, including 5 identified as β or ?-proteobacteria capable of oxidizing iron or sulfur, 16 identified as members of the Fe(III)-reducing Geobacteraceae in the δ-proteobacteria and one identified as the Fe(III)-reducing Ferribacterium. Results indicate that microbes play an essential role in the oxidation of iron sulfides (via direct contact and indirect pathways) and the reduction of iron oxides in pyrite-bearing substrata of a slightly acidic black shale aquifer.     

Bacterial Oxidation of Refractory Sulfide Ores for Gold Recovery

Abstract

The microbiological leaching of refractory sulfide ores (pyrite, arsenopyrite) for recovery of gold is reviewed in this article. The underlying physiological, biochemical, and genetic fundamentals of the bacteria involved (Thiobacillus and Sulfolobus spp.) are complex and have yet to be elucidated in depth. The chemistry of acid and biological leaching of pyrite and arsenopyrite minerals is also complex, and many of the individual reactions are not known in detail. Bacterial leaching is discussed in relation to chemical speciation at acid pH values. Attempts to develop models for a better understanding of bioleaching processes are summarized. The importance of pH, redox potential, temperature, sulfur balance, and toxic metals is evaluated for optimizing conditions for bacterial activity. Gold is finely disseminated in refractory sulfide ores, thereby decreasing Au recoveries upon conventional cyanidation for gold dissolution. In the bioleaching process, bacteria remove the sulfide minerals by oxidative dissolution and thus expose Au to extraction with cyanide solution. Stirred tank reactors appear most suited for this biological leaching process. The overall oxidation of the sulfides is an important variable for gold recovery. Pilot- and commercial-scale bioleaching processes for gold-containing pyrite and arsenopyrite ores are reviewed. This application of mineral biotechnology competes favorably with pressure leaching and roasting processes, both of which are problematic and energy-intensive alternatives for pretreatment of auriferous pyrite/arsenopyrite ores.     

Analysis of Genes and Proteins in Acidithiobacillus ferrooxidans During Growth and Attachment on Pyrite Under Different Conditions

Microbes are able to enhance the sulfide mineral decomposition, which lead to the formation of AMD. Attachment of bacterial cells to the mineral surface is an important process for pyrite oxidation by Acidithiobacillus ferrooxidans. The selective advantage of bacterial adhesion is considered to favor the surface localization of bacterial populations as nutritionally favorable. Environmental factors determine cell accumulation or dissociation of attachment. In our study, the amount of sessile cells increased rapidly during the initial stage of attachment on pyrite. Planktonic cells showed high activity leading to the accumulation of large colonies on the pyrite surface. We found three proteins to be up-regulated significantly. Additionally, by matching the sequences of the three proteins to the Pfam database, we found that they are related to adhesion, pili biosynthesis and movement. When we replaced pyrite with glass to provide an inert surface that abolished electrostatic forces, we found that cell attachment was maintained under nutrient-rich conditions but drastically reduced under conditions of limited nutrients or the presence of the inhibitor homoserinelactone. Our results are consistent with the idea that starvation may lead to inhibition of attachment by an unknown mechanism that allows bacteria to search for nutrient-rich habitats.     

Degradation of massive pyrite: Physical,chemical, and bacterial effects

Massive pyrite was shown to produce soluble iron, hydrogen, and sulfate ions on exposure to air and water. The rate of this process was directly proportional to the surface area of the mineral; it was unaffected by a drop in the pH and the presence of the ferrous and sulfate ions formed. Cupic ion had no effect but ferric ion accelerated pyrite degradation until all the ferric ion was consumed, in accordance with FeS₂ + 2Fe³⁺ —>‐3Fe²⁺ + 2S°. Thiobacillus ferrooxidans increased pyrite degradation considerably; the presence of Thiobacillus thiooxidans had no influence on pyrite degradation.     

Evidence For In Vitro and In Situ Pyrite Weathering By Microbial Communities Inhabiting Weathered Shale

Microbial pyrite oxidation is an important driver of biological weathering within shale, making a significant contribution toward biogeochemical cycling, bedrock expansion, and soil formation. These processes are of global importance, both within natural systems and in anthropogenic environments. Despite its significance, there is a lack of research that directly investigates microbe– pyrite interactions within shale. In this study, we use both field and laboratory approaches to inspect microbial pyrite oxidation in weathered shale environments within North Yorkshire, UK. Incubation of polished pyrite samples within iron-oxidizing enrichment cultures in vitro resulted in extensive colonization and surface pitting, demonstrating the weathering potential of shale microbial communities. Mineral samples were buried for 1 year within the floor of a shale rock mine, to explore pyrite bioweathering in situ. Image analysis revealed the formation of dissolution channels by microbial filaments, a novel mechanism of pyrite oxidation that broadens the taxonomic range of known microbe-pyrite interactions in weathered shale.     

Microbial acceleration of aerobic pyrite oxidation at circumneutral pH

Pyrite (FeS₂) is the most abundant sulfide mineral on Earth and represents a significant reservoir of reduced iron and sulfur both today and in the geologic past. In modern environments, oxidative transformations of pyrite and other metal sulfides play a key role in terrestrial element partitioning with broad impacts to contaminant mobility and the formation of acid mine drainage systems. Although the role of aerobic micro‐organisms in pyrite oxidation under acidic‐pH conditions is well known, to date there is very little known about the capacity for aerobic micro‐organisms to oxidize pyrite at circumneutral pH. Here, we describe two enrichment cultures, obtained from pyrite‐bearing subsurface sediments, that were capable of sustained cell growth linked to pyrite oxidation and sulfate generation at neutral pH. The cultures were dominated by two Rhizobiales species (Bradyrhizobium sp. and Mesorhizobium sp.) and a Ralstonia species. Shotgun metagenomic sequencing and genome reconstruction indicated the presence of Fe and S oxidation pathways in these organisms, and the presence of a complete Calvin–Benson–Bassham CO₂ fixation system in the Bradyrhizobium sp. Oxidation of pyrite resulted in thin (30–50 nm) coatings of amorphous Fe(III) oxide on the pyrite surface, with no other secondary Fe or S phases detected by electron microscopy or X‐ray absorption spectroscopy. Rates of microbial pyrite oxidation were approximately one order of magnitude higher than abiotic rates. These results demonstrate the ability of aerobic microbial activity to accelerate pyrite oxidation and expand the potential contribution of micro‐organisms to continental sulfide mineral weathering around the time of the Great Oxidation Event to include neutral‐pH environments. In addition, our findings have direct implications for the geochemistry of modern sedimentary environments, including stimulation of the early stages of acid mine drainage formation and mobilization of pyrite‐associated metals.     

Sulphur oxidation in tidal mangrove soils of Sierra Leone

Summary Tidal mangrove soil contained about 17-mg/g (oven-dry soil) of oxidisable sulphur, of which about 9 mg was insoluble in acetone. Samples showed considerable variability and this was shown to be due to the fact that decayed wood in the soil was heavily impregnated with oxidisable sulphur, a high proportion of which was insoluble in acetone. It is suggested that this proportion was the polysulphide fraction.When the soil was dried, its pH value fell to 3.0 to 2.4 due to the activity of sulphur-oxidising bacteria. When the pH value of the soil fell below 3 a rapid decline in the number of the organisms present occurred, and it is suggested that this was due to the increase in the availability of ferric iron which also occurred below this pH value.CaCO₃ had two main effects on sulphur oxidation; one on the sulphur-oxidising bacteria, increasing or decreasing sulphur oxidation according to whether the pH value was moved into or out of their range of activity, and an inhibitory effect on pyrites oxidation. The results indicate that the pyrites fraction was not oxidised above pH 3 and that it was not involved in acid-formation. It is suggested that pyrites oxidation under the experimental conditions was a chemical reaction possibly involving ferric ions.The possible application of the results to the reclamation of saline mangrove swamps is discussed.     

Competitive adsorption of binary mixture of <Emphasis Type="Italic">Leptospirillum ferriphilum</Emphasis> and <Emphasis Type="Italic">Acidithiobacillus caldus</Emphasis> onto pyrite

Leptospirillum ferriphilum and Acidithiobacillus caldus are two important acidophilic microorganisms involved in iron and sulfur oxidation during bioleaching. Cell adsorption to mineral surfaces is important for the direct leaching or contact leaching of minerals. In this study, we report the competitive adsorption of binary mixtures of L. ferriphilum LF-104 and A. caldus MTH-04 onto pyrite surfaces. The Langmuir adsorption parameter (C_Am) indicated that these two bacteria underwent competitive adsorption to pyrite. Real-time quantitive PCR was used to quantify the relative amounts of L. ferriphilum and A. caldus adsorbed onto the surfaces of pyrite following exposure to a mixture of these two organisms. The adsorption of L. ferriphilum was not affected by A. caldus. However, adsorption of A. caldus was greatly affected by the presence of L. ferriphilum. Zeta-potential measurements and FT-IR spectroscopic studies showed that L. ferriphilum had a higher electrostatic attraction towards pyrite when compared to A. caldus. Based on the above results, we propose a competitive adsorption model to explain the mechanism by which L. ferriphilum and A. caldus compete in their adsorption to pyrite, although L. ferriphilum dominated in the competitive adsorption process. This work provides a better understanding of the adsorption behavior of mixed microbial populations onto mineral surfaces.     

流式细胞术揭示出枯草芽孢杆菌多态异质性

新近的研究发现,微生物群体异质性现象普遍存在,与微生物群体许多关键功能密切相关.微生物群体中的多种异质性状态需要单细胞水平的分析技术才能被揭示,流式细胞术是获取异质性状态精确分布的重要工具.但微生物细胞尺寸微小、生物分子含量少、常常缺乏特异性试剂等都限制着传统流式细胞技术在微生物研究领域的应用.本论文采用新型的低背景、高灵敏度和高分辨率流式细胞仪,以增强的前向散射光、侧向散射光以及紫外光激发的细菌自发荧光水平这三个无需任何荧光标记就可以检测的信号为参数,首次揭示出不同生长状态的枯草芽孢杆菌具有复杂、动态的异质性状态分布.这一方法鉴定出的枯草芽孢杆菌多种状态及其与生理功能相关的、高度关联的变化,可能对该菌的生理变化规律及其分子机理的认识提供新的机遇.本论文也讨论了这一采用新型高灵敏度、高分辨率流式细胞仪测量非标记细胞参数的方法对于广泛开展各种微生物多态性研究具有巨大潜力.     

Corrosion and Electrochemical Oxidation of a Pyrite by Thiobacillus ferrooxidans

The oxidation of a pure pyrite by Thiobacillus ferrooxidans is not really a constant phenomenon; it must be considered to be more like a succession of different steps which need characterization. Electrochemical studies using a combination of a platinum electrode and a specific pyrite electrode (packed-ground-pyrite electrode) revealed four steps in the bioleaching process. Each step can be identified by the electrochemical behavior (redox potentials) of pyrite, which in turn can be related to chemical (leachate content), bacterial (growth), and physical (corrosion patterns) parameters of the leaching process. A comparison of the oxidation rates of iron and sulfur indicated the nonstoichiometric bacterial oxidation of a pure pyrite in which superficial phenomena, aqueous oxidation, and deep crystal dissolution are successively involved.     

Moulded by humans: The domestication of blue‐veined cheese fungi

It is hard to imagine a world without food‐associated microbes. The production of bread, wine, beer, salami, coffee, chocolate, cheese and many other foods and beverages all rely on specific microbes. In cheese, myriad microbial species collaborate to yield the complex organoleptic properties that are appreciated by millions of people worldwide. In the early days of cheese making, these complex communities emerged spontaneously from the natural flora associated with the raw materials, the equipment, the production environment or craftsmen involved in the production process. However, in some cases, the microbes shifted their natural habitat to the new cheese‐associated environment. The most obvious cause of this is backslopping, where part of a fermented product is used to inoculate the next batch. In addition, some microbes may simply adhere to the tools used in the production process. These microbial communities gradually adapted to the novel man‐made niches, a process referred to as “domestication.” Domestication is associated with specific genomic and phenotypic changes and ultimately leads to lineages that are genetically and phenotypically distinct from their wild ancestors. In this issue of Molecular Ecology, Dumas et al. have investigated a prime example of cheese‐associated microbes, the fungus Penicillium roqueforti. The authors identified several hallmarks of domestication in the genome and phenome of this species, allowing them to hypothesize about the origin of blue‐veined cheese fungi domestication, and the specific evolutionary processes involved in adaptation to the cheese matrix.     

Coal Depyritization by the Thermophilic Archaeon Metallosphaera sedula

The kinetics of pyrite oxidation by Metallosphaera sedula were investigated with mineral pyrite and two coals with moderate (Pittsburgh no. 8) and high (New Brunswick, Canada) pyritic sulfur content. M. sedula oxidized mineral pyrite at a greater rate than did another thermophile, Acidianus brierleyi, or a mesophile, Thiobacillus ferrooxidans. Maximum rates of coal depyritization were also greater with M. sedula, although the magnitude of biological stimulation above abiotic rates was notably less than with mineral pyrite. Coal depyritization appears to be limited by the oxidation of pyrite with ferric ions and not by the rate of biotic oxidation of ferrous iron, as evidenced by the maintenance of a high ratio of ferric to ferrous iron in solution by M. sedula. Significant precipitation of hydronium jarosite at elevated temperature occurred only with New Brunswick coal.     

Toxicity of arsenic during high temperature bioleaching of gold-bearing arsenical pyrite

 A moderately thermophilic mixed culture, MT, and the thermophilic Sulfolobus acidocaldarius strain BC were studied for their response to arsenic in a defined medium and also in media containing a pyrite and an arsenical pyrite flotation concentrate. In defined medium, the individual constituents of the MT culture exhibited a high tolerance to arsenite and arsenate compared to S. acidocaldarius strain BC. When grown on increasing concentrations of the pyrite flotation concentrate, both cultures had similar specific leaching rates over the various concentrations of the mineral substrate. In contrast, S. acidocaldarius strain BC exhibited a decreasing specific leaching rate when grown on the arsenical pyrite while the MT culture was not affected. In addition, arsenic added to cultures of S. acidocaldarius strain BC growing with pyrite as a growth substrate inhibited further growth, while added arsenic had no effect on the MT culture growing on the pyrite. These data indicate that the moderately thermophilic, arsenic-resistant MT culture was able to leach arsenical pyrite more efficiently than was the S. acidocaldarius strain BC culture at high concentrations of the mineral. This emphasizes the fact that proper culture selection is an important parameter when developing commercial processes involving arsenic-containing minerals. Received: 21 June 1995/Received revision: 25 August 1995/Accepted: 7 September 1995     

Metal-dependent anaerobic methane oxidation in marine sediment: Insights from marine settings and other systems

Anaerobic oxidation of methane(AOM) plays a crucial role in controlling global methane emission. This is a microbial process that relies on the reduction of external electron acceptors such as sulfate, nitrate/nitrite, and transient metal ions. In marine settings, the dominant electron acceptor for AOM is sulfate, while other known electron acceptors are transient metal ions such as iron and manganese oxides. Despite the AOM process coupled with sulfate reduction being relatively well characterized,researches on metal-dependent AOM process are few, and no microorganism has to date been identified as being responsible for this reaction in natural marine environments. In this review, geochemical evidences of metal-dependent AOM from sediment cores in various marine environments are summarized. Studies have showed that iron and manganese are reduced in accordance with methane oxidation in seeps or diffusive profiles below the methanogenesis zone. The potential biochemical basis and mechanisms for metal-dependent AOM processes are here presented and discussed. Future research will shed light on the microbes involved in this process and also on the molecular basis of the electron transfer between these microbes and metals in natural marine environments.