Progress in bioleaching: part B: applications of microbial processes by the minerals industries

This review presents developments and applications in bioleaching and mineral biooxidation since publication of a previous mini review in 2003 (Olson et al. Appl Microbiol Biotechnol 63:249–257, 2003). There have been discoveries of newly identified acidophilic microorganisms that have unique characteristics for effective bioleaching of sulfidic ores and concentrates. Progress has been made in understanding and developing bioleaching of copper from primary copper sulfide minerals, chalcopyrite, covellite, and enargite. These developments point to low oxidation–reduction potential in concert with thermophilic bacteria and archaea as a potential key to the leaching of these minerals. On the commercial front, heap bioleaching of nickel has been commissioned, and the mineral biooxidation pretreatment of sulfidic-refractory gold concentrates is increasingly used on a global scale to enhance precious metal recovery. New and larger stirred-tank reactors have been constructed since the 2003 review article. One biooxidation–heap process for pretreatment of sulfidic-refractory gold ores was also commercialized. A novel reductive approach to bioleaching nickel laterite minerals has been proposed.     

Mineral leaching of non-sulphide nickel ores using heterotrophic micro-organisms

Laboratory studies were conducted on microbial leaching of non-sulphide nickel ores not amenable to conventional mineral processing operations. The results showed that extensive low-grade laterite domestic sources are generally amenable to bioleaching when micro-organisms were cultivated in the presence of the ore. Nickel recoveries were as high as 60% using hydroxycarboxylic acid producing strains of Aspergillus and Penicillium codes A3, P2. Cobalt recovery achieved was around 50%. Losses of soluble nickel in the fungal biomass were found to be 3.5–10.8%. Chemical analysis of the leach liquors showed the presence of significant amounts of citric, oxalic and other organic acids, indicating that leaching may be ascribed to the production of these metabolic products of fungal activity.     

Bioleaching of a Spanish uranium ore

Abstract: The bioleaching of a low-grade uranium ore in shaker and columns using natural, pure and mixed cultures has been studied. Initially, a chemical and microscopical characterization of the mineral was carried out. Orbital shaker experiments were performed to quickly obtain the best bacterial leaching conditions. Afterwards, small columns were used to determine other variables related to percolation leaching. Finally, an uranium ore from the F6 mine (Ciudad Rodrigo, Spain) was leached in the presence of bacteria using large columns (24 cm diameter and 275 cm height). The most important results were: (i) the ore contains sufficient pyrite in order for uranium bioleaching to take place under optimum conditions; (ii) shaker experiments showed that temperature, pH and type of inoculum are the most important variables in bioleaching; (iii) two different ores were attacked in the columns: altered and non-altered. In the first case, the extraction rate of uranium was higher. However, in both cases the final efficiency was very similar (95%).     

Optimization of staged bioleaching of low-grade chalcopyrite ore in the presence and absence of chloride in the irrigating lixiviant: ANFIS simulation

In this investigation, copper was bioleached from a low-grade chalcopyrite ore using a chloride-containing lixiviant. In this regard, firstly, the composition of the bacterial culture media was designed to control the cost in commercial application. The bacterial culture used in this process was acclimated to the presence of chloride in the lixiviant. Practically speaking, the modified culture helped the bio-heap-leaching system operate in the chloridic media. Compared to the copper recovery from the low-grade chalcopyrite by bioleaching in the absence of chloride, bioleaching in the presence of chloride resulted in improved copper recovery. The composition of the lixiviant used in this study was a modification with respect to the basal salts in 9 K medium to optimize the leaching process. When leaching the ore in columns, 76.81 % Cu (based on solid residues of bioleaching operation) was recovered by staged leaching with lixiviant containing 34.22 mM NaCl. The quantitative findings were supported by SEM/EDS observations, X-ray elemental mapping, and mineralogical analysis of the ore before and after leaching. Finally, Adaptive neuro-fuzzy inference system (ANFIS) was used to simulate the operational parameters affecting the bioleaching operation in chloride–sulfate system.     

Bioleaching review part B:

This review describes the historical development and current state of metals leaching and sulfide mineral biooxidation by the minerals industries. During the past 20 years commercial processes employing microorganisms for mineral recovery have progressed from rather uncontrolled copper dump leaching to mineral oxidation and leaching in designed bioheaps for oxidation of refractory gold ores and for copper recovery. Also during this period of time, stirred tank bioleaching has been commercialized for cobalt recovery and for biooxidation of refractory gold ores. Chalcopyrite bioleaching in stirred tanks is on the verge of commercialization. Commercial applications of biohydrometallurgy have advanced due to favorable process economics and, in some cases, reduced environmental problems compared to conventional metal recovery processes such as smelting. Process development has included recognition of the importance of aeration of bioheaps, and improvements in stirred tank reactor design and operation. Concurrently, knowledge of the key microorganisms involved in these processes has advanced, aided by advances in molecular biology to characterize microbial populations.     

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.     

Isolation and Characterization of Iron and Sulfur-Oxidizing Bacteria from Maiduk Copper Mine at Shahrbabk Province in Iran

Microbial oxidation of iron and sulfur are important steps in biogeochemical cycles in mining environments. The aim of this study was the enrichment and identification of two important groups of bacteria that are involved in bioleaching of copper ores. Some soil samples were collected from the Maiduk copper mine. Iron-oxidizing bacteria were enriched in 9K medium containing ferrous sulfate, and sulfur oxidizers were enriched in 9K medium containing powdered sulfur instead of ferrous sulfate as energy source. After three subcultures, autotrophic bacteria were isolated on 9K agarose medium with appropriate energy sources. The autotrophic bacteria from the enrichments were identified by amplification of 16S rRNA gene and sequencing. Bioleaching experiments were performed in 100 ml of 9K medium containing 5 g of low-grade copper ore instead of ferrous sulfate. Twelve different iron and sulfur-oxidizing bacteria were isolated from the collected soil samples of Maiduk copper mine. Molecular identification indicated that two prevalent strains in the ore enrichments could be assigned to the Acidithiobacillus ferooxidans strain HGM and the Thiobacillus thioparus strain HGE. These two strains reached their logarithmic phase of growth after 8 days of incubation in their respective media at 30°C. Of these two cultures, strain HGM leached more copper ore (300 ppm) from the Maiduk copper ore than did strain HGE (200 ppm). Application of these two strains to the Maiduk copper ore in situ and to ore heaps should improve the leaching process.     

Bioleaching and bioprecipitation of nickel and iron from laterites

Abstract: Leaching of silicate ores, particularly nickel laterites, with the aid of heterotrophic organisms has been briefly reviewed. Samples of laterite ores from Greece were characterised mineralogically and a number of microorganisms isolated from them. One of these organisms (code FI) was successfully acclimatized to 6400 ppm nickel. Samples of the high-grade Greek Kastoria nickel laterite were leached with sulphuric acid and a number of organic acids. Sulphuric and citric acids extracted over 60 and 40% of the contained nickel, respectively, but the other acids employed were less efficient leachants. Oxalic acid precipitated nickel oxalate. Roughly the same extraction of iron was observed. The main leaching parameter was confirmed to be hydrogen ion concentration, although complexation with organic anions was a contributor. Organism FI (a strain of Penicillium ) was used in comparison with organisms from various culture collections to bioleach nickel from samples of the low-grade Greek Litharakia nickel laterite. The organisms were cultivated in a mixture of a sugar-based nutrient mineral medium and finely ground ore. Several penicillia and aspergilli leached 55–60% of the contained nickel and cobalt, and 25–35% of the iron when sucrose was the carbon source, but FI was not efficient. However, in molasses medium, Fl extracted nearly 40% of the nickel. Biosorption and bioprecipitation reactions were observed. The mechanism of bioleaching or in situ leaching is discussed in terms of close physical and chemical association between the fungal hyphae and mineral phases in the ore. This accounted for the low overall hydrogen ion concentration observed during bioleaching.     

Fungal biotransformation of zinc silicate and sulfide mineral ores

In this work, several fungi with geoactive properties, including Aspergillus niger, Beauveria caledonica and Serpula himantioides, were used to investigate their potential bioweathering effects on zinc silicate and zinc sulfide ores used in zinc extraction and smelting, to gain understanding of the roles that fungi may play in transformations of such minerals in the soil, and effects on metal mobility. Despite the recalcitrance of these minerals, new biominerals resulted from fungal interactions with both the silicate and the sulfide, largely resulting from organic acid excretion. Zinc oxalate dihydrate was formed through oxalate excretion by the test fungi and the mineral surfaces showed varying patterns of bioweathering and biomineral formation. In addition, calcium oxalate was formed from the calcium present in the mineral ore fractions, as well as calcite. Such metal immobilization may indicate that the significance of fungi in effecting metal mobilization from mineral ores such as zinc silicate and zinc sulfide is rather limited, especially if compared with bacterial sulfide leaching. Nevertheless, important bioweathering activities of fungi are confirmed which could be of local significance in soils polluted by such materials, as well as in the mycorrhizosphere.     

Enumeration and characterization of acidophilic microorganisms isolated from a pilot plant stirred-tank bioleaching operation

Microorganisms were enumerated and isolated on selective solid media from a pilot-scale stirred-tank bioleaching operation in which a polymetallic sulfide concentrate was subjected to biologically accelerated oxidation at 45 degrees C. Four distinct prokaryotes were isolated: three bacteria (an Acidithiobacillus caldus-like organism, a thermophilic Leptospirillum sp., and a Sulfobacillus sp.) and one archaeon (a Ferroplasma-like isolate). The relative numbers of these prokaryotes changed in the three reactors sampled, and the Ferroplasma isolate became increasingly dominant as mineral oxidation progressed, eventually accounting for >99% of plate isolates in the third of three in-line reactors. The identities of the isolates were confirmed by analyses of their 16S rRNA genes, and some key physiological traits (e.g., oxidation of iron and/or sulfur and autotrophy or heterotrophy) were examined. More detailed studies were carried out with the Leptospirillum and Ferroplasma isolates. The data presented here represent the first quantitative study of the microorganisms in a metal leaching situation and confirm that mixed cultures of iron- and sulfur-oxidizing prokaryotic acidophiles catalyze the accelerated dissolution of sulfidic minerals in industrial tank bioleaching operations. The results show that indigenous acidophilic microbial populations change as mineral dissolution becomes more extensive.     

Bioleaching of Uranium From Egyptian Rocks Using Native Actinomycete Strains

Bioleaching is an economic, novel practice for extraction of metals from their sources by microorganisms. The current study aimed to extract uranium from Egyptian ores using native strains of actinomycetes. Two types of rocks and one ore sample were collected from west-central Sinai, Egypt. Major oxides of the samples and fourteen heavy metals, including uranium, were determined. X-ray diffraction analysis proved that uranium was present in the samples in various structures. Uranium was present in different concentrations, 220, 770, and 550 mg/kg in sandstone, granite, and manganese ore, respectively. Thirty-four actinomycete isolates were recovered from the studied samples using four different isolation media. Acid production capabilities were employed to select isolates for further leaching experiments. Bioleaching experiments were carried out using sterile and non-sterile ore samples. Using sterile ore samples, the highest solubilization percentages of U₃O₈ were 44.5, 38.55, and 16.76% from sandstone, manganese ore, and granite sample, achieved by isolates UA12, UA5, and U7, respectively. Lower solubilization percentages of U₃O₈ were recorded by using non-sterile ore samples. Investigating the factors affecting the bioleaching abilities of the tested organisms revealed that 10 days of incubation with 4% pulp density were the best conditions for U₃O₈ solubilization. The most efficient isolates were identified using 16S rRNA gene sequence analysis. UA12 identified to be Streptomyces bacillaris, while UA5 could not be identified, and U7 was assigned as uncultured bacterium clone. Scanning electron microscope examination of the bioleaching experiment showed different growth intensity within the active isolates. For larger-scale extraction purposes, a kilogram of sandstone, containing 220 mg of U₃O₈, was used in the form of a truncated cone in a heap leaching experiment. After 20 cycles, 14.72 mg/l (6.7%) of U₃O₈ was leached by S. bacillaris, while 19.36 mg/l (8.8%) of U₃O₈ was leached by chemical leaching using sulfuric acid. The results of this study prove that the extraction of uranium using actinomycetes could be exploited as less polluting, more economical, and more effective than traditional chemical extraction especially from low-grade ores or mining wastes.     

Manganese biomining: A review

Biomining comprises of processing and extraction of metal from their ores and concentrates using microbial techniques. Currently this is used by the mining industry to extract copper, uranium and gold from low grade ores but not for low grade manganese ore in industrial scale. The study of microbial genomes, metabolites and regulatory pathways provide novel insights to the metabolism of bioleaching microorganisms and their synergistic action during bioleaching operations. This will promote understanding of the universal regulatory responses that the biomining microbial community uses to adapt to their changing environment leading to high metal recovery. Possibility exists of findings ways to imitate the entire process during industrial manganese biomining endeavor. This paper reviews the current status of manganese biomining research operations around the world, identifies factors that drive the selection of biomining as a processing technology, describes challenges in exploiting these innovations, and concludes with a discussion of Mn biomining’s future.     

Microbiological and geochemical dynamics in simulated-heap leaching of a polymetallic sulfide ore

The evolution of microbial populations involved in simulated-heap leaching of a polymetallic black schist sulfide ore (from the recently-commissioned Talvivaara mine, Finland) was monitored in aerated packed bed column reactors over a period of 40 weeks. The influence of ore particle size (2-6.5 mm and 6.5-12 mm) on changes in composition of the bioleaching microflora and mineral leaching dynamics in columns was investigated and compared to fine-grain (<2 microm) ore that was bioprocessed in shake flask cultures. Both column reactors and shake flasks were inoculated with 24 different species and strains of mineral-oxidizing and other acidophilic micro-organisms, and maintained at 37 degrees C. Mineral oxidation was most rapid in shake flask cultures, with about 80% of both manganese and nickel and 68% of zinc being leached within 6 weeks, though relatively little of the copper present in the ore was solubilised. The microbial consortium that emerged from the original inoculum was relatively simple in shake flasks, and was dominated by the iron-oxidizing autotroph Leptospirillum ferriphilum, with smaller numbers of Acidimicrobium ferrooxidans, Acidithiobacillus caldus and Leptospirillum ferrooxidans. Both metal recovery and (for the most part) total numbers of prokaryotes were greater in the column reactor containing the medium-grain than that containing the coarse-grain ore. The bioleaching communities in the columns displayed temporal changes in composition and differed radically from those in shake flask cultures. While iron-oxidizing chemoautotrophic bacteria were always the most numerically dominant bacteria in the medium-grain column bioreactor, there were major shifts in the most abundant species present, with the type strain of Acidithiobacillus ferrooxidans dominating in the early phase of the experiment and other bacteria (At. ferrooxidans NO37 and L. ferriphilum) dominating from week 4 to week 40. With the coarse-grain column bioreactor, similar transitions in populations of iron-oxidizing chemoautotrophs were observed, though heterotrophic acidophiles were often the most abundant bacteria found in mineral leach liquors. Four bacteria not included in the mixed culture used to inoculate the columns were detected by biomolecular techniques and three of these (all Alicyclobacillus-like Firmicutes) were isolated as pure cultures. The fourth bacterium, identified from a clone library, was related to the Gram-positive sulfate reducer Desulfotomaculum salinum. All four were considered to have been present as endospores on the dried ore, which was not sterilized in the column bioreactors. Two of the Alicyclobacillus-like isolates were found, transiently, in large numbers in mineral leachates. The data support the hypothesis that temporal and spatial heterogeneity in mineral heaps create conditions that favour different mineral-oxidizing microflora, and that it is therefore important that sufficient microbial diversity is present in heaps to optimize metal extraction.     

Biohydrometallurgy for Nonsulfidic Minerals—A Review

Bioleaching is a technology applicable to metal extraction from low-grade ores, ore beneficiation, coal beneficiation, metal detoxification, and recovery of metals from waste materials. The technology is environmentally sound and it may lower operational cost and energy requirement. Whereas leaching of sulfidic minerals using chemolithoautotrophic bacteria is the most studied and commercially exploitable aspect of mineral biotechnology today, there is a dearth of literature on the dissolution of nonsulfidic minerals. Biohydrometallurgy of nonsulfidic minerals involves the action of heterotrophic microorganisms. Heterotrophic bacteria and fungi have the potential for producing acidic metabolites that are able to solubilize oxide, silicate, carbonate and hydroxide minerals by reduction, acidolysis and complexation mechanisms. It is an important aspect of biohydrometallugy that requires development to meet future needs.     

BBProF: An Asynchronous Application Server for Rapid Identification of Proteins Associated with Bacterial Bioleaching

Recovery of metal value, especially from low-grade ores and overburden minerals using acidophilic bacteria through the process of bioleaching is an environmentally benign and commercially scalable biotechnology. In recent years, while the “OMICS” landscape has been witnessing extensive application of computational tools to understand and interpret global biological sequence data, a dedicated bioinformatic server for analysis of bacterial information in the context of its bioleaching ability is not available. We have developed an on-line Bacterial Bioleaching Protein Finder (BBProF) System, which rapidly identifies novel proteins involved in a bacterial bioleaching process and also performs phylogenetic analysis of 16S rRNA genes. BBProF uses the features of Asynchronous Java Script and XML (AJAX) to provide an efficient and fast user experience with minimal requirement of network bandwidth. In the input module the server accepts any bacterial or archaeal complete genome sequence in RAW format and provides a list of proteins involved in the microbial leaching process. BBProF web server is integrated with the European Bioinformatics Institute (EBI) web services such as BLAST for homology search and InterProScan for functional characterization of output protein sequences. Studying evolutionary relationship of bacterial strains of interest using Muscle and ClustalW2 phylogeny web services from EBI is another key feature of our server, where 16S rRNA gene sequences are considered as input through a JQUERY interface along with the sequences present in the BBProF database library. Complete genome sequences of 24 bioleaching microorganism characterized by genomic and physiological study in the laboratory and their respective 16S rRNA gene sequences were stored in the database of the BBProF library. To our knowledge BBProF is the first integrated bioinformatic web server that demonstrates its utility in identifying potential bioleaching bacteria. We hope that the server facilitate ongoing comparative genomic studies on of bioleaching microorganisms and also assist in identification and design of novel microbial consortia that are optimally efficient bioleaching agents.     

异养微生物在金属生物淋滤技术中的应用

生物淋滤技术主要应用于低品位矿石金属选矿、煤气脱硫、废弃物中金属回收和污染介质中金属离子毒性的去除等方面。作为生物淋滤技术中的主体微生物之一,异养微生物可通过其产生的酸性代谢物还原、酸化及络合,提取或者溶解非硫化矿、固体废弃物、污水污泥及土壤中的金属,有助于解决目前的资源短缺问题,还可对污染环境治理提供技术支持,具有重要的理论意义和实践价值。应用于异养微生物淋滤技术中的常见微生物包括细菌(以假单胞菌为主)和真菌(以曲霉菌和青霉菌应用最为广泛)。淋滤过程涉及酸解、络合、还原及碱化等。目前,异养微生物淋滤技术主要应用于生物冶金、固体废弃物处理、污水处理和污染土壤修复等。本文分析了异养微生物金属淋滤过程中的问题,并提出了未来研究的发展方向。     

Bacterial oxidation of propane

Abstract Much recent work in the field of biohydrometallurgy has been directed to the study of bio-oxidation of gold ores by acidophilic iron and sulfur oxidizing microorganisms. This work has been done worldwide and has resulted in several pilot plant and commercial scale operations for gold ore bio-oxidation. Bioleaching of gold by metabolic products of microorganisms has received less attention, but also offers opportunities for industrial application, especially if future regulations restrict the use of cyanide. This paper reviews recent progress in the use of microorganisms tooxidize the sulfidic matrix in refractory gold ores (bio-oxidation) and to solubilize elemental gold (bioleaching).     

Microbial community study of the iron ore concentrate of the Sishen Iron Ore Mine, South Africa

As a result of the advancing global technologies and civilisation, there has been a progressive depletion of high-grade mineral deposits. Consequently, it has become increasingly important to process lower-grade ores. Phosphorous (P) and particular potassium (K) contained in the iron ore concentrates of the Sishen Iron Ore Mine have a detrimental effect on the steel making process, whereby these alkali’s cause cracks to form in the refractory lining of blast furnaces. It is initially essential to determine which microbes are indigenously present at the Sishen Iron Ore Mine before strategising how best to employ them to industrial advantage. Therefore, the objective of this study was to determine which microorganisms are indigenous to the iron ore and soil of the Sishen Iron Ore Mine. The bacterial 16S PCR and fungal ITS PCR revealed several bacterial and fungal species present in the mine environment. The bacterial isolates were found to be closely related to Herbaspirillum species, as well as Acidithiobacillus ferrooxidans, while the fungal isolates were closely related to Aureobasidium pullulans, Phaeosphaeria nodorum, Aspergillus fumigatus, and Candida parapsilosis. Isolating A. fumigatus from the iron ore/soil of the mine may indicate that A. niger, the most common fungi used for the production of citric acid, can adapt to the stringent mine environment. This would allow the application of A. niger for the production of citric acid, which may be used for the chemical leaching of the P and K from the iron ore concentrate of the Sishen Iron Ore Mine.     

Study on reaction mechanism of bioleaching of nickel and cobalt from lateritic chromite overburdens

Depletion of high-grade ores and presence of significant quantities of metals in low-grade oxide ores has enforced to utilize the overburdens (COB) and wastes (low-grade ores) generated during mining operations. The impact of ore mineralogy and mineral–microbe interaction during bioleaching could not be ignored. Seeking to the need, a systematic study was performed to establish the reaction mechanism involved for recovery of nickel and cobalt from chromite overburden (COB), Sukinda, Orissa using pure culture of Aspergillus niger. Mineralogical analysis reveals a complete conversion of goethite into hematite phase leading to exposure of nickel particles into the micro-pores and cracks developed in the matrix which was initially found to be intertwined in the goethite lattice. As a result, it became more susceptible to attack by the fungal bio acids which in turn accelerate the dissolution rate. Organic acids like oxalic and citric acids were detected in the culture filtrate using HPLC. TEM analysis of the leached samples shows that nickel dissolute into the solution leaving a porous space in the matrix of the hematite by forming nickel oxalate or nickel citrate. Kinetics of the nickel bioleaching was studied to support the mechanism of the reaction. It was observed that the initial rate of reaction follows the chemical control dissolution reaction where as the later part fits to shrinking core model. 18% of nickel and 37.8% of cobalt was recovered from pre-treated COB at 2.5% pulp-density with 10% (v/v) fungal inoculum at 30 °C within 25 days in shake flask while 32.5% of nickel and 86% of cobalt was recovered in bioreactor.     

Enumeration and Characterization of Acidophilic Microorganisms Isolated from a Pilot Plant Stirred-Tank Bioleaching Operation

Microorganisms were enumerated and isolated on selective solid media from a pilot-scale stirred-tank bioleaching operation in which a polymetallic sulfide concentrate was subjected to biologically accelerated oxidation at 45°C. Four distinct prokaryotes were isolated: three bacteria (an Acidithiobacillus caldus-like organism, a thermophilic Leptospirillum sp., and a Sulfobacillus sp.) and one archaeon (a Ferroplasma-like isolate). The relative numbers of these prokaryotes changed in the three reactors sampled, and the Ferroplasma isolate became increasingly dominant as mineral oxidation progressed, eventually accounting for >99% of plate isolates in the third of three in-line reactors. The identities of the isolates were confirmed by analyses of their 16S rRNA genes, and some key physiological traits (e.g., oxidation of iron and/or sulfur and autotrophy or heterotrophy) were examined. More detailed studies were carried out with the Leptospirillum and Ferroplasma isolates. The data presented here represent the first quantitative study of the microorganisms in a metal leaching situation and confirm that mixed cultures of iron- and sulfur-oxidizing prokaryotic acidophiles catalyze the accelerated dissolution of sulfidic minerals in industrial tank bioleaching operations. The results show that indigenous acidophilic microbial populations change as mineral dissolution becomes more extensive.