bluuebunny/crossref_metadata_2025 huggingface dataset:
Microelectrode Array Fabrication by Micro-WEDM
Authors: Wang Yu Kui , Wang Zhen Long , Li Mao Sheng , Zeng Wei Liang , Weng M.H.
Published: September 2009

In the paper, in order to overcome machining limits in throughput and precision because of positioning error and tool wear of a single tool electrode, a method for the microelectrode array fabrication by micro-WEDM is described and assessed. Characteristics of the microelectrode array fabrication by micro-WEDM, such as machining open voltage, pulse peak current, discharge duration and servo feed rate so on, are investigated through a series of experiments. A 10 10 squared electrode array is machined by micro-WEDM and the width of each squared electrode is about 40µm. The microelectrode array with good quality is obtained by applying decreased open voltage and peak current, increased discharge duration and optimized machining speed. Then micro hole-array is processed by applying obtained electrode array in micro-EDM method. The diameter of each squared hole in the array is about 50 µm due to appropriate control strategy that per micro pulse energy is decreased and periodic jump-down is applied during the machining process. Experiments have demonstrated that the combination process of microelectrode array fabricated by micro-WEDM and micro-hole array done by micro-EDM is a novel method of process which makes it more feasible and efficient to fabricate microelectrode array and high-density hole-array.
Improvement of Diamond-Cutting Surface by Means of Porous Bearing Laminar Flow
Authors: He D.X. , Sheng B.H. , Zhou Zu De , Suo Q. , Li Y.F. , Liu C.Y.
Published: September 2009

Air bearings had been widely used in ultra-precision machine tools. In order to suppress the micro-vibration caused by air bearing, an effective way is keeping the air flow in laminar state. Porous bearing to control the micro-vibration was proposed in this paper, and the related experiments show that it can meet the requirement of decreasing the micro-vibration to less than 1nm, and the surface of diamond surface can be improved.
Comparison between Acid Mine Effluents, La Zarza-Perrunal and Río Tinto (Iberian Pyritic Belt)
Authors: González-Toril E. , Aguilera A. , Souza-Egipsy V. , Diez Ercilla M. , López-Pamo Enrique , Sánchez-España F.J. , Amils R.
Published: September 2009

A 1.2 km long effluent from La Zarza-Perrunal mine (Iberian Pyritic Belt, IPB) was characterized and compared with Río Tinto. In La Zarza effluent microbial oxidation of ferrous iron is responsible for the drastic increase in ferric iron, from a ratio of Fe(III)/Fetotal of 0.11 at the origin, up to 0.99 downstream. Prokaryotic and eukaryotic diversity throughout the effluent were determined. Bacteria related to the sulfur cycle as well as iron-reducing bacteria were mainly detected near the anoxic origin. Iron-oxidizing microorganisms increased along the course of the effluent following an increase in the oxygen content in the water column. Eukaryotic diversity varied drastically along the effluent. Rio Tinto (92 km length) is a natural extreme acidic environment with a rather constant acidic pH (mean pH value 2.3) and a high concentration of heavy metals. The Tinto ecosystem is under the control of iron [1]. The geomicrobiological comparisons of both habitats were performed to unravel some basic questions of biohydrometallurgical interest.
Characterisation of Oxalate-Degrading Microorganisms in Bioreactors Treating Bayer Liquor Organic Materials
Authors: Boxall Naomi J. , Plumb Jason J. , Tilbury Amanda L. , Nyeboer Hugh J. , Sumich Matt E. , Sutton D.C.
Published: September 2009

When bauxite is digested during Bayer processing, associated organic compounds and humic acids are degraded to produce sodium salts of organic acids, including sodium oxalate. If not removed from the liquor stream, sodium oxalate co-precipitates with the aluminium hydroxide resulting in poor crystallization and alumina and soda loss. Aerobic bioremediation processes have been developed as an economic and environmentally sound option for oxalate removal. Little research has been directed at characterising the microbial communities and biological processes underpinning these processes. Analysis of samples from both a moving bed biofilm reactor and bioreactor effluent using PCR-DGGE of 16S rRNA genes showed microorganisms of the genus Halomonas dominated the process. Most Probable Number (MPN) analyses also showed Halomonas spp. to be numerically dominant in all bioreactor samples.
Microbial Ecology of a Natural Extreme Acidic Environment: Lessons from Río Tinto
Authors: Amils R. , González-Toril E. , Aguilera A. , Rodríguez Nuria , Fernández-Remolar D. , Diaz E. , García-Moyano A. , Sanz Jose Luis
Published: September 2009

Rio Tinto (Iberian Pyritic Belt, SW Spain) is a natural extreme acidic environment with a rather constant acidic pH (mean pH value 2.3) and a high concentration of heavy metals. The Tinto ecosystem is under the control of iron. The geomicrobiological characterization of Río Tinto has unravelled some basic questions of biohydrometallurgical interest. The methodologies developed for this study were applied successfully to monitor different bioleaching processes of the BioMinE project.
Studying and Identifying the Biocorrosion of Water Supply Pipes in Copper Mine
Authors: Motamedi S. , Marandi R. , Mazhar S.F.
Published: September 2009

Corrosion is the destructive effect of environment on metals and alloys. Corrosion is a spontaneous phenomenon which causes metal conversion from zero oxidation degree to a species with high oxidation degree. As a result of this chemical interaction due to the corrosion phenomenon, irretrievable damages are made to the equipment and installations of various industries. Biocorrosion has occurred in the water supply pipes at Sarcheshmeh copper mine(Located in South of Iran), and in order to assess the amount of biocorrosion and remove these biological interactions we decided to chemically evaluate the water sample in the water supply pipelines at this mine. In this look, the water sample exist in the water supply pipelines at Sarcheshmeh copper mine was studied, sulfur corrosive bacteria were separated and identified and their biochemical activity was researched and studied and it was found that the target species are in fact Sulfolobus bacteria which have different enzymatic activities. Due to these enzymatic activities, a considerable amount of sulfur is accumulated on the cell surface. Based on various incubation environments, as a result of sulfur accumulation, Sulfolubos bacteria were identified.
Comparative Genomics Begins to Unravel the Ecophysiology of Bioleaching
Authors: Holmes David S. , Cárdenas Juan Pablo , Valdés Jorge H. , Quatrini Raquel , Esparza M. , Osorio Hector , Duarte F. , Lefimil C. , Jedlicki Eugenia
Published: September 2009

The metabolic potential of 16 bioleaching microorganisms (Eubacteria and Archaea) has been investigated, allowing the prediction of potential inter- and intra-species physiological interactions (ecophysiology) during spatial and temporal changes that are known to occur within industrial bioleaching heaps. Genome analysis has allowed preliminary models to be built for genes and pathways involved in key processes such as nitrogen and carbon cycling, sulfur and iron uptake and homeostasis, extra-cellular polysaccharide biosynthesis, heavy metal resistance and energy metabolism. This paper will focus on the diverse ways that microorganisms obtain carbon from their environment with a particular emphasis on elucidating how these processes might be expected to vary over space and time during the lifetime of a bioleaching operation. It is anticipated that this knowledge will improve our understanding of fundamental biological processes in extremely acidic environments and it is hoped that it will capture usable knowledge that can be applied to bioleaching. Comparative genomics between two strains of Acidthiobacillus ferrooxidans highlights the importance of lateral gene transfer in increasing genetic and metabolic potential and suggests that classical molecular DNA techniques, such as rDNA typing, significantly underestimate the microbial diversity of bioleaching heaps.
Physiological and Phylogenetic Heterogeneity among Iron-Oxidizing Acidithiobacillus spp., and Characteristics of the Novel Species Acidithiobacillus Ferrivorans
Authors: Hallberg Kevin B. , Amouric A. , Brochier-Armanet C. , Bonnefoy Violaine , Johnson D. Barrie
Published: September 2009

It has long been recognized that isolates of iron- and sulfur-oxidizing acidophiles referred to as “Acidithiobacillus ferrooxidans” probably include more than one species, on the basis of differences in chromosomal GC contents and 16S rRNA gene sequences. Phylogenetic heterogeneity among these isolates was confirmed by phylogenetic analysis using the sequences of the 16S-23S intergenic spacers (ITS). Two main groups have been identified: the first includes the type strain of Acidithiobacillus ferrooxidans and a second comprises a cluster of newly isolated strains that have 98.5% 16S rRNA gene sequence identity with the type strain. Given that the new group of isolates have GC contents of 56 mol% as opposed to 58.8 mol% for At. ferrooxidansT, and that they share only 37% homologous DNA, these were given the new species name Acidithiobacillus ferrivorans. Further studies showed that, while strains of At. ferrivorans have many physiological traits in common with At. ferrooxidans, they also differ in some key characteristics. These include the ability to grow at temperatures as low as 4°C (as opposed to the lower limit of between 10 and 12°C for At. ferrooxidans) and the greater sensitivity of At. ferrivorans to low pH (minimum of 1.9 for growth as opposed to 1.3 for At. ferrooxidansT). Important genotypic differences include the fact that all strains of At. ferrivorans do not contain the archetypal rusticyanin gene (rusA), rather most contain a rusA homologue (rusB). Furthermore, the high potential iron-sulfur protein-encoding gene of all At. ferrivorans strains analyzed is more similar to the iro than to the hip gene characterized in At. ferrooxidansT. These results suggest that the iron oxidation pathways are different in At. ferrivorans and At. ferrooxidans.
Chromosomal Arsenic Resistance Genes from Sulfobacillus Thermosulfidooxidans and a Demonstration that the Genetic Diversity of arsB among the Sulfobacilli is Similar to that of their 16S rRNA Genes
Authors: van der Merwe J. Arrie , Deane Shelly M. , Rawlings Douglas E.
Published: September 2009

Arsenic resistance genes were isolated from the moderately thermophilic, Gram-positive iron and sulfur-oxidizing bacterium, Sulfobacillus thermosulfidooxidans. Only arsR and arsB genes were present and attempts to identify an arsC using degenerate PCR primers or dependent arsC genes as probes in Southern hybridization experiments were unsuccessful. Although enhanced resistance to arsenite was not detected when the ars genes were cloned in Escherichia coli, the kumamolisin-As and arsRB genes were induced by arsenite. RT-PCR experiments suggested that transcription of the cloned kumamolisin-As-like and arsRB genes is linked in Escherichia coli, but not in Sb. thermosulfidooxidans. The gene order kumamolisin-As precursor, arsR and arsB was maintained among three strains of Sb. thermosulfidooxidans isolated from three continents. Southern hybridization using a Sb. thermosulfidooxidans arsB gene fragment as a probe gave a positive hybridization signal using S. acidophilus but not with S. thermotolerans genomic DNA. Comparison of partial sequence data of the arsB and 16S rRNA genes suggested that the two types of genes have undergone a similar evolutionary history and therefore that the arsB genes were present in the ancestral Sulfobacillus before its divergence into species.
Characterization of Biofilm Formation by the Bioleaching Acidophilic Bacterium Acidithiobacillus Ferrooxidans by a Microarray Transcriptome Analysis
Authors: Vera Mario A. , Rohwerder Thore , Bellenberg Soeren , Sand Wolfgang , Denis Y. , Bonnefoy Violaine
Published: September 2009

Bioleaching is the extraction of metals, such as copper or gold, from ore by microorganisms. Bacterial attachment increases leaching activities due to the formation of a "reaction space" between the metal sulfide surface and the cell. This process depends on abiotic characteristics such as purity and degree of crystallization of the metal sulfide, as well as biotic ones such as the capacity of the bacteria for detecting favourable attachment sites and synthesizing a suitable cell envelope (EPS), for adhesion. Planktonic and sessile cells should differ significantly in their metabolic activities and therefore in their gene expression patterns. To help to understand At. ferrooxidans biofilm formation, microarray transcript profiling was carried out to compare planktonic and sessile cells. The high contents of EPS and ferric iron of the biofilms are interfering with RNA extraction, causing inhibition of DNAse, reverse transcriptase and/or polymerase activities required to get labelled target cDNA. In order to have sufficient high quality RNA suitable for transcriptomic analysis, we have optimized the biofilm formation of At. ferrooxidans on pyrite (FeS2) and the RNA extraction from the sessile cell population. DNA microarrays have been hybridized with labelled cDNAs from sessile and planktonic cells and preliminary data suggest that some genes are differently expressed between these two subpopulations. The understanding of these differences may help us to shift populations of leaching bacteria from the planktonic state towards the sessile state in order to influence bioleaching.
A 300 kpb Genome Segment, Including a Complete Set of tRNA Genes, is Dispensable for Acidithiobacillus Ferrooxidans
Authors: Levicán Gloria J. , Katz Assaf , Valdés Jorge H. , Quatrini Raquel , Holmes David S. , Orellana O.
Published: September 2009

The genome sequences from two strains of the acidophilic, autotrophic, chemolithotrophic proteobacterium A. ferrooxidans are available from genome databases. Bioinformatic sequence comparison revealed the existence in one strain of a putative integrative conjugative element (ICE), containing an entire set of clustered tRNA genes. ICE is missing in the other strain, suggesting that this element as well as the tRNA genes cluster is dispensable for the bacterium. Bioinformatic predictions suggest that the tRNA genes cluster might mainly contribute to the translation of ICE encoded genes.
Small Regulatory RNAs in Acidithiobacillus Ferrooxidans: Case Studies of 6S RNA and Frr
Authors: Shmaryahu Amir , Lefimil C. , Jedlicki Eugenia , Holmes David S.
Published: September 2009

Bioinformatic approaches are described for the discovery of small regulatory RNAs (srRNAs) in the biomining microorganism Acidithiobacillus ferrooxidans. Intergenic regions of the annotated genome were extracted and computationally searched for srRNAs. Candidate srRNAs that were associated with predicted sigma 70 promoters and/or rho-independent terminators were chosen for further study. Experimental validation is presented for 6S srRNA and frr. srRNAs are known to control gene expression in a wide variety of microorganisms, usually at the post-transcriptional level, by acting as antisense RNAs that bind targeted mRNAs or by interacting with regulatory proteins. srRNAs are involved in the regulation of a large variety of processes. Frr is an RNA antisense to fur; the latter encodes a global regulator involved the control of a large number of genes involved in iron uptake and homeostasis. Because of the widespread occurrence and extensive repertoire of regulatory functions afforded by srRNAs, it is expected that their discovery functional analysis in biomining microorganisms will contribute to improving our understanding of the microbiology of bioleaching processes.
Gene Organization and CO2-Responsive Expression of Four cbb Operons in the Biomining Bacterium Acidithiobacillus Ferrooxidans
Authors: Esparza M. , Bowien B. , Jedlicki Eugenia , Holmes David S.
Published: September 2009

Acidithiobacillus ferrooxidans is an obligately chemolithoautotrophic, -proteobacterium that fixes CO2 by the Calvin-Benson-Bassham (CBB) reductive pentose phosphate cycle. Our objective is to identify genes potentially involved in CO2 fixation and to advance our understanding of how they might be regulated in response to environmental signals. Bioinformatic analyses, based on the complete genome sequence of the type strain ATCC 23270, identified five cbb gene clusters four of which we show experimentally to be operons. These operons are predicted to encode: (i) the components of the carboxysome and one copy of form I RubisCO (cbb1 operon), (ii) a second copy of form I RubisCO (cbb2 operon), (iii) enzymes of central carbon metabolism (cbb3 operon), (iv) a phosphoribulokinase and enzymes of sulfur metabolism (cbb4 operon) and RubisCO form II (cbb5 gene cluster). In addition, the gene for a LysR-type transcriptional regulator CbbR was identified immediately upstream and in divergent orientation to the cbb1 operon and another associated with the cbb5 gene cluster. A. ferrooxidans was grown under different concentrations of CO2 (2.5 to 20% [v/v]), and levels of mRNA and protein were evaluated by qPCR and Western blotting, respectively. CbbR binding to predicted promoter regions of operons cbb1-4 was assayed by EMSA This information permitted the formulation of models explaining how these operons might be regulated by environmental CO2 concentrations. These models were evaluated in vivo in a heterologous host, using cloned A. ferrooxidans cbbR to complement a mutant of the facultative chemoautotroph Ralstonia eutropha H16 lacking a functional cbbR. Cloned copies of A. ferrooxidans promoter regions were also introduced into R. eutropha to evaluate their ability to drive reporter gene expression. This work lays the framework for further studies that should result in a more comprehensive picture of how CO2 fixation is regulated in A. ferrooxidans.
Microbial Succession during a Heap Bioleaching Cycle of Low Grade Copper Sulphides. Does this Knowledge Mean a Real Input for Industrial Process Design and Control?
Authors: Demergasso Cecilia
Published: September 2009

The paper “Bacterial succession in bioheap leaching” [1] initiated the search for methods to analyze the microbial dynamics in bioleaching industrial processes as a key to advancing commercial bioheap applications. “Chemical and physical conditions within bioheaps change radically from the time the bioheap is stacked and inoculated until bioleaching is completed.” The results from a comprehensive monitoring program by culturing and molecular techniques in an industrial bioleaching process for Run-of-mine (ROM) low grade copper sulfide ore in Chile will be summarized. The analysis of the compiled information permits an understanding of changes in microbial substrates availability, chemical and physical conditions. The impact of other aspects on microbiology, such as the mining programme and the industrial design are also considered. The bacterial succession in bioheap leaching solutions allowed the leaching cycle stages to be describe as: i) Acid conditioning and soluble copper releasing, ii) Chalcocite Bacterial leaching (ferrous oxidation); iii) Chalcocite Bacterial leaching (ferrous and reduced sulfur compounds –RSC- oxidation); iv) Bacterial leaching of sulphide minerals with higher rest potentials (pyrite and covellite ), v) Bacterial oxidation of remnant sulfide minerals and RSC.
Protein Function in Extremely Acidic Conditions: Molecular Simulations of a Predicted Aquaporin and a Potassium Channel in Acidithiobacillus Ferrooxidans
Authors: Duarte F. , Araya-Secchi R. , González W. , Perez-Acle T. , González-Nilo D. , Holmes David S.
Published: September 2009

We wish to understand how membrane proteins function in extremely acid conditions (<pH1 - pH3) using, as initial models, a predicted aquaporin and a potassium (K+) channel from the acidophile, Acidithiobacillus ferrooxidans ATCC 23270. A fundamental question is how these proteins function when confronted by a proton concentration difference of 6 orders of magnitude across the membrane. Similarity alignments were used to find the most similar three dimensional structure for each protein from crystallized orthologs deposited in the protein database PDB and these were used as templates for molecular simulations. Proteins from A. ferrooxidans were submitted to a molecular modeling strategy and their structural and dynamic properties were determined using molecular dynamics (MD) simulations (20 ns). Aquaporins are a large family of transmembrane channel proteins that allow the passive but selective movement of water, glycerol or CO2 across cell membranes. MD calculations computed key biophysical features related to permeation parameters. K+ channels are membrane proteins that allow voltage-driven potassium flux across cellular membranes. A structural analysis of the A. ferrooxidans K+ channel predicts that it does not expose ionizable amino acids to the external surface. This would reduce protonation of residues at pH 1, permitting tertiary structure to be maintained.
Predicted CO/CO2 Fixation in Ferroplasma spp. via a Novel Chimaeric Pathway
Authors: Cárdenas Juan Pablo , Martínez Verónica , Covarrubias P. , Holmes David S. , Quatrini Raquel
Published: September 2009

Previous physiological studies of the genus Ferroplasma have indicated that these microorganisms are capable of fixing CO2 in the presence of ferrous iron and low concentrations of yeast extract. Analysis of the gene complement of Ferroplasma acidarmanus fer1 and two partial genomes of Ferroplasma type I and II derived from the Iron Mountain acid mine drainage metagenome revealed the absence of several functional marker genes encoding key enzymes of three know alternative CO2 fixation routes present in archaea, i.e. the 3-hydroxypropionate cycle, the Ljungdahl–Wood pathway and the reverse TCA cycle. It is thus intriguing how these chemoautotrophic archaeal species deal with their requirements for carbon and suggests that they might have a distinct CO2 fixation route, as yet unreported. Using comparative genomics and metabolic reconstruction strategies, a putative pathway was detected for C1 fixation consisting of four main steps: 1) conversion of carbon monoxide to carbon dioxide with gain of energy and/or 2) reduction of carbon dioxide to formate, 3) incorporation of formate to tetrahydrofolate and 4) donation of the carbon moiety of tetrahydrofolate to glycine to produce serine. Steps 1 to 3 involve enzymes that correspond to some of the Ljungdahl–Wood pathway proteins, whereas step 4 resembles the well known “serine cycle”, utilized by methylotrophic microorganisms for formaldehyde fixation. Thus, this chimaeric pathway might represent the missing carbon fixation route in Ferroplasmatales. Herein, we discuss the implications of these findings in the context of central carbon metabolism requirements for biomass production in acidic environments.
Elemental Ultrastructure of Bioleaching Bacteria and Archaea Grown on Different Energy Sources
Authors: Usher Kayley M. , Shaw Jeremy A. , Plumb Jason J. , Saunders Martin
Published: September 2009

The composition and distribution of elements within cells of two species of Fe and S oxidising microbes utilising S, Fe2+ or chalcopyrite (CuFeS2) as an energy source were compared to determine possible sites of oxidation and function of intracellular granules. The bacterium Acidithiobacillus ferrooxidans and the archaeon Metallosphaera hakonensis were examined using energy filtered transmission electron microscopy (EFTEM), TEM energy dispersive X-ray spectroscopy (EDS), Scanning TEM (STEM) and electron energy-loss spectroscopy (EELS). Both species have intracellular granules and we show that these store Fe, S and P. The microbes slowly lost Fe from granules when switched to an Fe-free medium. EELS showed that the Fe in the granules of both species was consistent with Fe3+. Both microbes sometimes contain Cu and Si on their walls and intracellularly. Si concentrations have been shown to affect bioleach performance, so element deposition on the microbial catalyst may be a reason for this. Bands of Fe and S were present close to, or in, the cell membrane of M. hakonensis, as might be expected for the site of oxidation, and S also occurred throughout the cytoplasm. These are the first element maps of M. hakonensis, and these early results demonstrate that advanced characterisation and microanalysis techniques can provide insights into microbial processes involved in bioleaching.
Substrate Utilisation by Sulfobacillus Thermosulfidooxidans in Mixed Ferrous Ion and Tetrathionate Growth Medium
Authors: Shiers Denis W. , Ralph D.E. , Watling Helen R.
Published: September 2009

Sulfobacillus thermosulfidooxidans cultures adapted to ferrous or tetrathionate ions were inoculated into media containing both substrates. In batch culture, cells showed a preference for oxidising ferrous ion followed by tetrathionate. Tetrathionate oxidation was slower in ferrous-adapted cells. Biomass formation exhibited an exponential growth phase during ferrous ion oxidation followed by an exponential growth phase during tetrathionate oxidation. Sequential utilisation of ferrous ion followed by tetrathionate ion was observed when equimolar amounts of substrates or electron-equivalent amounts were provided.
Kinetics of Microbial Ferrous-Iron Oxidation by Leptospirillum Ferriphilum: Effect of Ferric-Iron on Biomass Growth
Authors: Ojumu Tunde Victor , Petersen Jochen
Published: September 2009

The kinetics of microbial ferrous-iron oxidation have been well studied as it is a critical sub-process in bioleaching of sulphide minerals. Exhaustive studies in continuous culture have been carried out recently, investigating the effects of conditions relevant to heap bioleaching on the microbial ferrous-iron oxidation by Leptospirillum ferriphilum [1-3]. It was postulated that ferric-iron, which is known to be inhibitory, also acts as a stress stimulus, promoting microbial growth at higher total iron concentration. This paper investigates this phenomenon further, by comparing tests run with pure ferrous-iron feeds against those where the feed is partially oxidised to ferric at comparable concentrations. The findings clearly suggest that, contrary to reactor theory, it is indeed ferrous iron concentration in the reactor feed that determines biomass concentration and that ferric iron concentration has little effect on microbial growth. Further mathematical analysis shows that the phenomenon can be explained on the basis of the Pirt equation and the particular reaction conditions employed in the test work.
Effect of the Energy and Carbon Source Limitations and Ferric Inhibition on Metabolic Parameters of Leptospirillum Ferrooxidans Growing in Chemostat
Authors: Bastías Marcela , Gentina J.C.
Published: September 2009

L. ferrooxidans plays a significant role in bioleaching process of ores. Being a chemoautotrophic bacterium, its sources of carbon and energy are independent. In this study were measured separately in a chemostat, the effect of growth limited by each source (CO2 and Fe(II)), and under conditions of inhibition (Fe(III)) on metabolic parameters of the cell. The runs were carried out in a bioreactor with 1.25 liter of KJ culture medium at 33.5 °C, pH 1.8, agitation rate of 300 rpm and aeration rate of 2 VVM. Using only air as CO2 source, it was established that the cells suffer simultaneous limitation of carbon and energy. It was determined that these limitations are released separately when enriching the air with 4% CO2 in one case and when doubling concentration of Fe(II) in the feed stream in the other. Under double limitation maximum yield (YºX/S) and maintenance coefficient (m) were 6.0•10-3 gcel/gFe(II) and 2.48 gFe(III)/gcel•h respectively. Growth limited only by carbon source and only by energy source gave YºX/S 11.5•10-3 and 21.9•10-3 gcel/gFe(II), whereas m was 1.23 and 0.11 gFe(II)/gcel•h respectively. On the other hand, the lower specific Fe(III) production rate (qP) was obtained when cell growth was limited by the energy source and the higher value was observed during growth in presence of 15 g/L exogenous Fe(III). The qP values at D = 0.04 h-1 were 1.93 and 14.04 gFe(III)/gcel•h respectively. In general, the worse the culture conditions the highest the specific rate of Fe(III) production. The bacterium varied its metabolic parameters quite broadly depending on the growth limiting nutrient and presence of Fe(III).
Ferrous Iron and Pyrite Oxidation by “Acidithiomicrobium” Species
Authors: Davis-Belmar Carol S. , Norris Paul R.
Published: September 2009

Novel iron- and sulfur-oxidizing, moderate thermophiles were isolated from an acidic geothermal site and from a previously studied, pyrite-enrichment mixed culture (which also contained the related actinobacterium Acidimicrobium ferrooxidans). The novel species (proposed genus “Acidithiomicrobium”) grew autotrophically with ferrous iron at an optimum temperature of about 50°C, efficiently degraded pyrite at 55°C and also grew well autotrophically on sulfur. The extensive dissolution of pyrite during autotrophic growth contrasted with a requirement for yeast extract for significant growth of the related Acidimicrobium ferrooxidans.
Copper Resistance Mechanisms of Biomining Bacteria and Archaea Living under Extremely High Concentrations of Metals
Authors: Orell A. , Navarro C.A. , Jerez Carlos A.
Published: September 2009

Extremophiles such as the acidophilic Sulfolobus metallicus (Archaea) and Acidithiobacillus ferrooxidans (Bacteria) can resist Cu (CuSO4) concentrations of 200 mM and 800 mM respectively. These microorganisms are important in biomining processes to extract copper and other metals. A. ferrooxidans grown at low Cu concentrations (5 mM) expressed genes coding for ATPases most likely involved in pumping the metal from the cytoplasm to the periplasm of the bacterium. At 100 mM Cu the previous systems were repressed and there was a great induction in the expression of efflux systems known to use the proton motive force energy to export the metal outside the cell. These Cu-resistance determinants from A. ferrooxidans were found to be functional since when expressed in Escherichia coli they conferred higher Cu tolerance to it. Novel Cu-resistance determinants for A. ferrooxidans were found and characterized. S. metallicus possessed at least 2 CopM metallochaperones and 2 CopA ATPases whose expressions were induced by Cu (5 to 50 mM). Furthermore, we previously reported that both microorganisms accumulate high levels of inorganic polyphosphate (PolyP) and that intracellular Cu concentration stimulates polyP hydrolysis. The resulting Pi would then be transported out of the cell as a metal-Pi complex to detoxify the cells. In addition, our results suggest that at high Cu concentrations polyP could also provide energy for the metal efflux. All the data suggest that both biomining microorganisms use different systems to respond to Cu depending on the extracellular concentrations of the metal and suggest that the presence of different additional systems to respond to Cu may explain the extremely high metal resistance of these extremophiles.
Reductive Action of Activated Carbon on Ferric Iron Interferes on the Determination of the Oxidative Activity of Acidithiobacillus Ferrooxidans on Ferrous Iron
Authors: Vargas T. , Diáz P. , Escobar B.
Published: September 2009

Ferrous iron oxidation studies in the presence of activated carbon were conducted at 30 °C in basal medium at pH 1.6 with a pure strain of Acidithiobacillus ferrooxidans. Two-chamber modified shake flasks were used in these experiments, which prevented direct contact between the microorganisms and the carbon contained in the flasks. This design permitted an accurate determination of bacterial population during the experiment and enabled the involvement of ferric iron reduction with carbon to be evidenced. Notably, iron was initially added as ferric iron in a concentration of 3 g/L. It could be observed that bacteria could grow in this condition evidencing that bacteria was in fact oxidizing ferrous ion produced from reduction of ferric by carbon. From complementary experiments in which activated carbon was contacted with abiotic solutions containing ferric ion in the concentration range 0.1 – 1.2 g/l, the chemical reductive action of carbon of ferric iron was confirmed and a kinetic expression for this reaction was determined. A mathematical model was developed which incorporated expressions for the kinetic of bacterial oxidation of ferrous ion and the chemical reduction of ferric ion. This model enabled the prediction of the rate of bacterial growth and ferrous ion oxidation in a bioreactor as a function of the initial concentrations of iron, activated carbon and bacterial population.
Results in this work imply that the observed variations in activity observed by other authors during bacterial oxidation of ferrous iron with A. ferrooxidans adsorbed on carbon can be in fact related to bacterial utilization of supplementary ferrous iron produced by the chemical action of carbon, phenomenon which is not explicitly accounted for.
Mechanisms of Bioleaching and the Visualization of these by Combined AFM & EFM
Authors: Sand Wolfgang , Florian Bianca M. , Noël Nanni
Published: September 2009

The understanding of mechanisms, by which microorganisms are effecting the dissolution of metal sulfides, what in general is called bioleaching, has progressed largely during the last 15 years. Whereas in the beginning of the nineties of the last century the direct and the indirect mechanisms were state of the knowledge, nowadays it is generally accepted that contact and non-contact mechanisms besides ferric iron, perhaps with some organic sulfhydryl groups, are the relevant players [1]. Consequently, since the introduction of these ideas/hypotheses, research in this field has been revived considerably, as is obvious from the literature[2]. Also molecular biology has started to contribute to the understanding of these processes due to the clarification of the basic reactions [3, 4, 5]. Summarizing the main elements of the contact and non-contact mechanisms, we know now that in case of the contact mechanism bacteria need to attach to metal sulfide surfaces by means of their extracellular, polymeric substances (EPS) due to a primary electrostatic interaction between iron(II)ions complexed by uronic acid residues. This first interaction is followed by hydrophobic interactions (more than half of the EPS of A. ferrooxidans are lipids) and perhaps covalent bonding (speculative). These forces are active in the Angstrom range (Å). Consequently, the space between bacterial outer membrane and the surface of a metal sulfide, which is filled by EPS, ranges between 10 and 50 nm only. In this space the dissolution reactions occur.
Comparative Study of Planktonic and Sessile Cells from Pure and Mixed Cultures of Acidithiobacillus Ferrooxidans and Acidiphilium Cryptum Growing on Pyrite
Authors: Bellenberg Soeren , Florian Bianca M. , Vera Mario A. , Rohwerder Thore , Sand Wolfgang
Published: September 2009

The aim of this study was to investigate interspecies interaction by quantifying pyrite dissolution and to visualize the colonization of metal sulfides in pure and mixed cultures of leaching bacteria. Strains, such as chemolithoautotrophic Acidithiobacillus ferrooxidans ATCC 23270 (type strain) and chemoorganoheterotrophic Acidiphilium cryptum JF-5, were used. Sessile, pyrite-detached and planktonic cells were visualized by epifluorescence microscopy using DAPI staining and FISH. Additionally, atomic force microscopy was used for investigations on cell morphology, bacterial distribution on pyrite and mineral surface topography. In pure At. ferrooxidans cultures and in mixed cultures with Ap. cryptum JF-5, it could be shown that the bacterial morphology of sessile cells differed significantly from those of planktonic cells by decreased cell sizes and enhanced production of extracellular polymeric substances in case of sessile cells. Interspecies interaction in mixed cultures resulted in increased pyrite leaching and production of extracellular polymeric substances and consequently, enhanced biofilm formation.
Visualisation of Bacterial Behaviour Using Tapping-Mode Atomic Force Microscopy
Authors: Gorham N. , Becker T. , Shiers Denis W. , Watling Helen R.
Published: September 2009

Ex-situ and in-situ Tapping Mode AFM were used to investigate responses of attached bacteria to stressful conditions. For ex-situ measurements, the AFM was equipped with a customised re-positioning stage and sample mount to permit re-examination of the same surface area. For in-situ measurements, the inoculated pyrite coupon was immersed in solution in a flow through cell. Initial experiments using Sulfobacillus thermosulfidooxidans indicated that increased acidity promoted EPS production but increased salinity resulted in cell detachment.
Investigation and Visualisation of Microbial Attachment Trends to Sulphide Minerals in a Bioleach Environment
Authors: Africa C.J. , van Hille Robert P. , Harrison Susan T.L.
Published: September 2009

Two novel experimental approaches have been developed to investigate the attachment of microorganisms to sulphide minerals as a function of the mineral and microbial phase in a joint project with BHP Billiton, conceptualised in 2005 and initiated in 2006. In the first approach, selective attachment of pure cultures to minerals was studied in the “particle coated column reactor” using A. ferrooxidans and L. ferriphilum. The saturated reactor containing glass beads coated with fine mineral concentrates provided a quantifiable surface area of mineral concentrate and maintained good fluid flow. Results are reported for chalcopyrite and pyrite concentrates, a low grade chalcopyrite ore and quartzite. The latter, representing typical gangue material, is used as a control. A. ferrooxidans displayed greater attachment to pyrite, and selective attachment to sulfide minerals over quartz. Similar attachment behaviour trends resulted for Leptospirillum spp. In the second approach, a novel technique was developed to investigate microbial ecology of microbe-mineral attachment, site and mineral specific associations of microorganisms and spatial organisation of microbial communities present. Qualitative assessment and visualisation of microorganisms associated with the mineral surface and subsequent biofilm development was shown in the biofilm reactor, using microscopy techniques and fluorochromes. FISH analyses of A. ferrooxidans and L. ferriphilum on massive chalcopyrite sections are presented. The consequence of the observed attachment on heap bioleach performance is discussed.
Sulfide Mineral Induced Oxidative Stress as a Limiting Factor in Tank Bioleaching Performance
Authors: Jones Gavin , van Hille Robert P. , Harrison Susan T.L.
Published: September 2009

In tank bioleaching, decreasing particle size of milled concentrates has been shown to improve leaching performance owing to increased mineral surface area and mechanical activation effects of fine mineral particles. However, evidence suggests a critical lower limit of particle size distribution exists below which the performance of the thermophilic iron and sulfur oxidizer Sulfolobus metallicus is compromised and complete culture death may result. This paper proposes an explanation for these observations at fine fractions through identifying a relationship between mineral composition of six sulfide concentrates, their extent of milling and the generation of the reactive oxygen species (ROS) hydrogen peroxide (H2O2) and hydroxyl radicals (•OH) in slurries. The effect of oxidative stress induced in the absence of minerals on growth and bioleaching performance of S. metallicus is studied.
Changes in an Ore Dump during a 40-Year Period of Commercial-Scale and Spontaneous Natural Bioleaching
Authors: Groudeva V.I. , Vasilev D.V. , Karavaiko G.I. , Groudev Stoyan N.
Published: September 2009

A dump located in the proximity of the Vlaikov Vrah mine, Bulgaria, and containing about 120 000 tons of run-of-mine mining wastes (low-grade ores and rock mass), since 1968 was subjected initially to spontaneous natural bioleaching based on the rains as irrigating leach solutions, then from 1972 to 2003 to commercial-scale bioleaching by means of irrigation with acidified leach solutions, and since 2004- again to spontaneous natural bioleaching. The monitoring of these processes during this 40-year period revealed considerable changes in the composition, geotechnical and acid-base properties of the dump material, as well as in the diversity, number and activity of its microflora.The data obtained during this study were used to stimulate the bioleaching process in the huge commercial-scale copper dump leaching operation at Vlaikov Vrah mine in which about forty million tons of such mining wastes were treated.
Investigations of Attached and Unattached Cells during Bioleaching of Chalcopyrite with Acidianus Manzaensis at 65°C
Authors: Zhou H. , Zhang L. , Guo Y. , Peng J. , Wei M. , Ding J. , Gu G. , Qiu Guan Zhou
Published: September 2009

For the purpose of investigations of the different situations when the cells of Acidianus manzaensis can or can not attach the surface of the chalcopyrite. Three experiments were carried out in the modified shake flasks, and in one of the experiments the cells could not attach the surface of the chalcopyrite, but could participate in the solution chemistry of the process. The redox potential, pH, cell density, copper, ion and thiosulfate concentration in the solution were monitored in the experiments, and the morphological feature and chemical composition of the leached residues were analyzed by SEM and XRD.
The most leach effiency of Cu and Fe was reached in the experiment that the Acidianus manzaensis could attach the surface of the chalcopyrite. However, the unattached Acidianus manzaensis could also leach the chalcopyrite, but it was less actively than attached cells. There was no precipitation of jarosite in the leached residues of the three experiments, but there was sulfur in the leached residues when the cells could not attach the chalcopyrite. So the surface passivating layer of sulfur can be removed only when the Acidianus manzaensis can attach the surface of the chalcopyrite. From these results it become apparent that the leach of the chalcopyrite is the cooperative action of the attached and unattached Acidianus manzaensis.
An Experimental Approach for Studying Chalcopyrite Leaching and Passivation in Column Bioleaching
Authors: van der Meer Tuomas , Liipo Jussi , Leppinen Jaakko
Published: September 2009

The effect of different microbial consortia on the leaching of chalcopyrite was studied at different temperatures and solution compositions with Boliden’s Aitik ore in column reactors simulating heap bioleaching. The columns were equipped with sampling chambers and chalcopyrite mineral electrodes in order to investigate the passivation of chalcopyrite. The sampling chambers were filled with agglomerated ore and pieces of chalcopyrite-rich ore. In addition to chemical analysis of the leaching solution and solids the progress of leaching of chalcopyrite was studied by continuous potential measurements with chalcopyrite electrodes. The occurrence and composition of potentially passivating layers on the surfaces of the electrodes and the samples taken from sample chambers were examined by optical and scanning electron microscopy.
Rietveld Refinement of X-Ray Diffractograms Evidences Surface Texturization in Chemical and Biological Leaching of Chalcopyrite at 70°C
Authors: Oyarzun P. , Gautier V. , Reich M. , Vargas T.
Published: September 2009

In the present work the occurrence of surface transformations triggered during chemical and biological leaching of chalcopyrite at 70 °C in basal medium were investigated with the aid of the Rietveld technique. Leaching experiments were conducted in 250 ml shake flasks at 150 rpm, contacting 1 g of a -80 # + 120# chalcopyrite concentrate with 100 ml of iron-free basal medium at pH 1.5 at 70°C. Three different conditions were used: experiment (a) in aerated conditions with basal medium inoculated with Sulfolobus metallicus (4x108 cells/ml); experiment (b) in aerated abiotic conditions; experiment (c) in abiotic conditions under N2 atmosphere. Copper and iron dissolved in solution was analyzed with atomic absorption. Samples of the initial chalcopyrite and the treated samples obtained after 16 days under the various experimental conditions were analyzed by Grazing-Incident X-ray diffraction (GID). The obtained x-ray spectra were then analyzed with the Rietveld refinement technique using the Topas software.
Results showed that the initial concentrate consisted mainly of tetragonal chalcopyrite (JCPDS : 37-0471). Chalcopyrite leached under abiotic-anaerobic conditions was crystallographically unaffected. In chalcopyrite leached under aerated abiotic conditions there was evidence of surface texturization showed as preferential orientation to the crystallographical planes ( 3 1 2 ) and (1 1 6). Finally, surface texturization was also observed in chalcopyrite leached under inoculated conditions, but in this case showed as preferential orientation to the crystallographical planes ( 0 2 4 ) and ( 2 2 0). These results give a first evidence of surface texturization phenomena during dissolution of chalcopyrite at 70 °C. They suggest that chalcopyrite dissolution occurs via selective leaching of specific crystallographic planes, and this selectivity is influenced by both the chemical action of oxygen and the microorganism actvity.
Control of the Redox Potential by Oxygen Limitation Inhibits Bioleaching of Pyrite
Authors: Wu Biao , Wen Jian Kang , Zhou Gui Ying , Ruan Ren Man
Published: September 2009

Based on the bioleaching mechanism and electrochemical studies of metal sulfides, the dissolution rate of secondary copper sulfides and pyrite are controlled by redox potentials. Experiment on the bioleaching of the secondary copper sulfides under constant potential by sparging with nitrogen gas demonstrated, by analyzing Cu and Fe content of the bioleaching solution and residues, the pyrite and secondary cooper sulfides dissolution rates have large difference in various redox potential. The pyrite and secondary cooper sulfides have good selection when the redox potential controlled between 700mV and 760mV, we can realize the secondary copper sulfides bioleaching process be controlled, then supply theoretical guide for the iron-acid balance during copper bioleaching process.
Bioleaching of Low-Grade Copper Sulfide Ore Using a Colum Reactor
Authors: Qin Wen Qing , Zhang Yan Sheng , Zhen Shi Jie , Wang Jun , Zhang Jian Wen , Qiu Guan Zhou
Published: September 2009

The effects of several variables on the column bioleaching of copper sulphide ore have been investigated. The copper ore contained chalcopyrite as the main sulfide minerals and bornite and chalcocite as the minor minerals. The experiment was carried out using bench-scale column leach reactors designed in Key Lab of Biometallurgy of Ministry of Education, which were inoculated with the pure mesophile bacteria (Acidithiobacillus ferrooxidans) and thermophile bacteria (Sulfobacillus), respectively, and the mixed bacteria which contain both iron- and sulfur-oxidizing bacteria. The results show that the mixed cultures were more efficient than the pure cultures alone and the maximum copper recovery 53.64% was achieved using the mixed cultures after 85 days. The leaching rate of chalcopyrite tended to increase with the increased dissolved ferric iron concentration. The effect of particle size on the rate of the copper leaching was also investigated, and it was shown that the copper bioleaching rate decreases as the amount of fines increase, which limits the permeability, thus decreases leaching rate. Jarosite and elemental sulphur formed in the column were characterized by the X-ray and EDS.