Heavy metal mining using microbes

A direct observation of bacterial coverage and biofilm formation by Acidithiobacillus ferrooxidans on chalcopyrite and pyrite surfaces

To obtain a fundamental understanding of the population behaviour of Acidithiobacillus ferrooxidans at chalcopyrite and pyrite surfaces, the early stage attachment behaviour and biofilm formation by this bacterium on chalcopyrite (CuFeS2) and pyrite (FeS2) were studied by optical microscopy, Raman spectroscopy, time-of-flight secondary ion mass spectrometry (ToF-SIMS) and electron backscatter diffraction (EBSD). The results indicate there was no significant difference in selectivity of bacterial attachment between chalcopyrite and pyrite. However, the result of ToF-SIMS analysis suggests that the surface of the pyrite was covered more extensively by biofilm than that of the chalcopyrite, which may indicate more extracellular polymeric substances (EPS) formation by bacterial cells growing on pyrite. EBSD and optical image analysis indicated that selectivity of bacterial attachment to chalcopyrite was not significantly affected by crystal orientation. The results also suggest that the bacterial population in defective areas of chalcopyrite was significantly higher than on the polished surfaces.

Synthesis of novel palladium(0) nanocatalysts by microorganisms from heavy-metal-influenced high-alpine sites for dehalogenation of polychlorinated dioxins

In a search for new aqueous-phase systems for catalyzing reactions of environmental and industrial importance, we prepared novel biogenerated palladium (Pd) nanocatalysts using a "green" approach based on microorganisms isolated from high-alpine sites naturally impacted by heavy metals. Bacteria and fungi were enriched and isolated from serpentinite-influenced ponds (Totalp region, Parsenn, near Davos, Graubünden, Switzerland). Effects on growth dynamics were monitored using an automated assay in 96-well microtiter plates, which allowed for simultaneous cultivation and on-line analysis of Pd(II)- and Ni(II)-mediated growth inhibition. Microorganisms from Totalp ponds tolerated up to 3mM Pd(II) and bacterial isolates were selected for cultivation and reductive synthesis of Pd(0) nanocatalysts at microbial interfaces. During reduction of Pd(II) with formate as the electron donor, Pd(0) nanoparticles were formed and deposited in the cell envelope. The Pd(0) catalysts produced in the presence of Pd(II)-tolerant Alpine Pseudomonas species were catalytically active in the reductive dehalogenation of model polychlorinated dioxin congeners. This is the first report which shows that Pd(0) synthesized in the presence of microorganisms catalyzes the reductive dechlorination of polychlorinated dibenzo-p-dioxins (PCDDs). Because the "bioPd(0)" catalyzed the dechlorination reactions preferably via non-lateral chlorinated intermediates, such a pathway could potentially detoxify PCDDs via a "safe route". It remains to be determined whether the microbial formation of catalytically active metal catalysts (e.g., Zn, Ni, Fe) occurs in situ and whether processes involving such catalysts can alter the fate and transport of persistent organic pollutants (POPs) in Alpine habitats.

Presentation on mechanisms and applications of chalcopyrite and pyrite bioleaching in biohydrometallurgy - a presentation

This review outlines classic and current research, scientific documents and research achievements in bioleaching, particularly in respect of the bioleaching of chalcopyrite and pyrite. The diversity and commonality of the microbial leaching process can be easily studied through comparing the bioleaching mechanism and the application of these two metal sulfides. The crystal, electronic and surface structures of chalcopyrite and pyrite are summarized in detail in this paper. It determines the specific and complicated interaction pathways, kinetics of the atmospheric/aqueous oxidation, and the control process of bioleaching of the minerals as the precondition. Bioleaching of metal sulfides is performed by a diverse group of microorganisms and microbial communities. The species of the bacteria which have a significant effect on leaching ores are miraculously diverse. The newly identified acidophilic microorganisms with unique characteristics for efficient bioleaching of sulfidic minerals are increasing sharply. The cell-to-cell communication mechanisms, which are still implicit, elusive and intangible at present day, have gradually become a research hotspot. The different mineralogy characteristics and the acid solubility of the metal sulfides (e.g., chalcopyrite and pyrite) cause two different dissolution pathways, the thiosulfate and the polysulfide pathways. The bioleaching mechanisms are categorized by contact (an electrostatic attachment) and noncontact (planktonic) process, with emphasis on the produce of extracellular polymeric substances and formation of biofilm on the surface of the metal sulfides in this paper. The division of the direct and indirect effect are not adopted due to the redox chain, the reduction of the ferric iron and oxidation of the ferrous iron. The molecular oxygen is reduced by the electrons extracted from the specific metal sulfide, via a redox chain forming a supercomplex spanning the periplasmic space and connecting both outer and inner membrane. The passivation of the mineral surface can obviously hinder the dissolution of metal sulfides during the bioleaching process, which is significantly affected by the kinetic model, microenvironment on the surface of ore and the leach conditions, such as temperature, pH and Eh. The new development of mechanism research, enhanced and intensified technologies on the bioleaching of chalcopyrite and pyrite, are conducted and summarized from the different branches of natural science. Some are depicted and explained based on molecular level in this paper. Catalyst and catalytic mechanisms in bioleaching and biooxidation for this two sulfide minerals have been concluded and applied for several decades, the continuous emergence of the new material and technology are also gradually applied into the biohydrometallurgy. The industrial applications of the bioleaching on chalcopyrite and pyrite are totally based on the understanding of the interaction mechanism between microbes and minerals, the optimization of ore leaching conditions and the development of new material and the leaching equipment. It is not incredible and unimaginable to take a different bioleaching process and diagram to deal with the two sulfuric metals, which is vital to succeed in elevating the leaching rate of copper.

Radionuclide release from simulated waste material after biogeochemical leaching of uraniferous mineral samples

Biogeochemical mineral dissolution is a promising method for the released of metals in low-grade host mineralization that contain sulphidic minerals. The application of biogeochemical mineral dissolution to engineered leach heap piles in the Elliot Lake region may be considered as a promising passive technology for the economic recovery of low grade Uranium-bearing ores. In the current investigation, the decrease of radiological activity of uraniferous mineral material after biogeochemical mineral dissolution is quantified by gamma spectroscopy and compared to the results from digestion/ICP-MS analysis of the ore materials to determine if gamma spectroscopy is a simple, viable alternative quantification method for heavy nuclides. The potential release of Uranium (U) and Radium-226 ((226)Ra) to the aqueous environment from samples that have been treated to represent various stages of leaching and passive closure processes are assessed. Dissolution of U from the solid phase has occurred during biogeochemical mineral dissolution in the presence of Acidithiobacillus ferrooxidans, with gamma spectroscopy indicating an 84% decrease in Uranium-235 ((235)U) content, a value in accordance with the data obtained by dissolution chemistry. Gamma spectroscopy data indicate that only 30% of the (226)Ra was removed during the biogeochemical mineral dissolution. Chemical inhibition and passivation treatments of waste materials following the biogeochemical mineral dissolution offer greater protection against residual U and (226)Ra leaching. Pacified samples resist the release of (226)Ra contained in the mineral phase and may offer more protection to the aqueous environment for the long term, compared to untreated or inhibited residues, and should be taken into account for future decommissioning.

Platinum and rhenium extraction from a spent refinery catalyst using Bacillus megaterium as a cyanogenic bacterium: statistical modeling and process optimization

The present study evaluated the potential of Bacillus megaterium as a cyanogenic bacterium to produce cyanide for solubilization of platinum and rhenium from a spent refinery catalyst. Response surface methodology was applied to study the effects and interaction between two main effective parameters including initial glycine concentration and pulp density. Maximum Pt and Re recovery was obtained 15.7% and 98%, respectively, under optimum conditions of 12.8 g/l initial glycine concentration and 4% (w/v) pulp density after 7 days. Increasing the free cyanide concentration to 3.6 mg/l, varying the pH from 6.7 to 9, and increasing the dissolved oxygen from 2 to 5mg/l demonstrated the growth characteristics of B. megaterium during bioleaching process. The modified shrinking core model was used to determine the rate limiting step of the process. It was found that diffusion through the product layer is the rate controlling step.

Getting rid of the unwanted: highlights of developments and challenges of biobeneficiation of iron ore minerals-a review

The quest for quality mineral resources has led to the development of many technologies that can be used to refine minerals. Biohydrometallurgy is becoming an increasingly acceptable technology worldwide because it is cheap and environmentally friendly. This technology has been successfully developed for some sulphidic minerals such as gold and copper. In spite of wide acceptability of this technology, there are limitations to its applications especially in the treatment of non-sulphidic minerals such as iron ore minerals. High levels of elements such as potassium (K) and phosphorus (P) in iron ore minerals are known to reduce the quality and price of these minerals. Hydrometallurgical methods that are non-biological involving the use of chemicals are usually used to deal with this problem. However, recent advances in mining technologies favour green technologies, known as biohydrometallurgy, with minimal impact on the environment. This technology can be divided into two, namely bioleaching and biobeneficiation. This review focuses on Biobeneficiation of iron ore minerals. Biobeneficiation of iron ore is very challenging due to the low price and chemical constitution of the ore. There are substantial interests in the exploration of this technology for improving the quality of iron ore minerals. In this review, current developments in the biobeneficiation of iron ore minerals are considered, and potential solutions to challenges faced in the wider adoption of this technology are proposed.

Río tinto: a geochemical and mineralogical terrestrial analogue of Mars

The geomicrobiological characterization of the water column and sediments of Río Tinto (Huelva, Southwestern Spain) have proven the importance of the iron and the sulfur cycles, not only in generating the extreme conditions of the habitat (low pH, high concentration of toxic heavy metals), but also in maintaining the high level of microbial diversity detected in the basin. It has been proven that the extreme acidic conditions of Río Tinto basin are not the product of 5000 years of mining activity in the area, but the consequence of an active underground bioreactor that obtains its energy from the massive sulfidic minerals existing in the Iberian Pyrite Belt. Two drilling projects, MARTE (Mars Astrobiology Research and Technology Experiment) (2003–2006) and IPBSL (Iberian Pyrite Belt Subsurface Life Detection) (2011–2015), were developed and carried out to provide evidence of subsurface microbial activity and the potential resources that support these activities. The reduced substrates and the oxidants that drive the system appear to come from the rock matrix. These resources need only groundwater to launch diverse microbial metabolisms. The similarities between the vast sulfate and iron oxide deposits on Mars and the main sulfide bioleaching products found in the Tinto basin have given Río Tinto the status of a geochemical and mineralogical Mars terrestrial analogue.

A peptide-based method for 13C Metabolic Flux Analysis in microbial communities

The study of intracellular metabolic fluxes and inter-species metabolite exchange for microbial communities is of crucial importance to understand and predict their behaviour. The most authoritative method of measuring intracellular fluxes, ¹³C Metabolic Flux Analysis (¹³C MFA), uses the labeling pattern obtained from metabolites (typically amino acids) during ¹³C labeling experiments to derive intracellular fluxes. However, these metabolite labeling patterns cannot easily be obtained for each of the members of the community. Here we propose a new type of ¹³C MFA that infers fluxes based on peptide labeling, instead of amino acid labeling. The advantage of this method resides in the fact that the peptide sequence can be used to identify the microbial species it originates from and, simultaneously, the peptide labeling can be used to infer intracellular metabolic fluxes. Peptide identity and labeling patterns can be obtained in a high-throughput manner from modern proteomics techniques. We show that, using this method, it is theoretically possible to recover intracellular metabolic fluxes in the same way as through the standard amino acid based ¹³C MFA, and quantify the amount of information lost as a consequence of using peptides instead of amino acids. We show that by using a relatively small number of peptides we can counter this information loss. We computationally tested this method with a well-characterized simple microbial community consisting of two species.

Microbial communities underlie a variety of important biochemical processes ranging from underground cave formation to gold mining or the onset of obesity. Metabolic fluxes describe how carbon and energy flow through the microbial community and therefore provide insights that are rarely captured by other techniques, such as metatranscriptomics or metaproteomics. The most authoritative method to measure fluxes for pure cultures consists of feeding the cells a labeled carbon source and deriving the fluxes from the ensuing metabolite labeling pattern (typically amino acids). Since we cannot easily separate cells of metabolite for each species in a community, this approach is not generally applicable to microbial communities. Here we present a method to derive fluxes from the labeling of peptides, instead of amino acids. This approach has the advantage that peptides can be assigned to each species in a community in a high-throughput fashion through modern proteomic methods. We show that, by using this method, it is theoretically possible to recover the same amount of information as through the standard approach, if enough peptides are used. We computationally tested this method with a well-characterized simple microbial community consisting of two species.

Bioleaching characteristics, influencing factors of Cu solubilization and survival of Herbaspirillum sp. GW103 in Cu contaminated mine soil

This study was aimed at assess the potential of diazotrophic bacteria, Herbaspirillum sp. GW103, for bioleaching of Cu in mine soil. The strain exhibited resistance to As (550mgL(-1)), Cu (350mgL(-1)), Zn (300mgL(-1)) and Pb (200mgL(-1)). The copper resistance was further confirmed by locating copA and copB genes. The survival of the isolate GW103 during bioleaching was analyzed using green fluorescent protein tagged GW103. Response surface methodology based Box-Behnken design was used to optimize the physical and chemical conditions for Cu bioleaching. Five significant variables (temperature, incubation time, CaCO3, coconut oil cake (COC), agitation rate) were selected for the optimization. Second-order polynomials were established to identify the relationship between Cu bioleaching and variables. The optimal conditions for maximum Cu bioleaching (66%) were 30°C, 60h of incubation with 1.75% of CaCO3 and 3% COC at 140rpm. The results of Cu sequential extraction studies indicated that the isolate GW103 leached Cu from ion-exchangeable, reducible, strong organic and residual fractions. Obtained results point out that the isolate GW103 could be used for bioleaching of Cu from mine soils.

Response to copper of Acidithiobacillus ferrooxidans ATCC 23270 grown in elemental sulfur

The response of Acidithiobacillus ferrooxidans ATCC 23270 to copper was analyzed in sulfur-grown cells by using quantitative proteomics. Forty-seven proteins showed altered levels in cells grown in the presence of 50 mM copper sulfate. Of these proteins, 24 were up-regulated and 23 down-regulated. As seen before in ferrous iron-grown cells, there was a notorious up-regulation of RND-type Cus systems and different RND-type efflux pumps, indicating that these proteins are very important in copper resistance. Copper also triggered the down-regulation of the major outer membrane porin of A. ferrooxidans in sulfur-grown bacteria, suggesting they respond to the metal by decreasing the influx of cations into the cell. On the contrary, copper in sulfur-grown cells caused an overexpression of putative TadA and TadB proteins known to be essential for biofilm formation in bacteria. Surprisingly, sulfur-grown microorganisms showed increased levels of proteins related with energy generation (rus and petII operons) in the presence of copper. Although rus operon is overexpressed mainly in cells grown in ferrous iron, the up-regulation of rusticyanin in sulfur indicates a possible role for this protein in copper resistance as well. Finally, copper response in A. ferrooxidans appears to be influenced by the substrate being oxidized by the microorganism.

Metal resistance-related genes are differently expressed in response to copper and zinc ion in six Acidithiobacillus ferrooxidans strains

Metal resistance of acidophilic bacteria is very significant during bioleaching of copper ores since high concentration of metal is harmful to the growth of microorganisms. The resistance levels of six Acidithiobacillus ferrooxidans strains to 0.15 M copper and 0.2 M zinc were investigated, and eight metal resistance-related genes (afe-0022, afe-0326, afe-0329, afe-1143, afe-0602, afe-0603, afe-0604, and afe-1788) were sequenced and analyzed. The transcriptional expression levels of eight possible metal tolerance genes in six A. ferrooxidans strains exposed to 0.15 M Cu(2+) and 0.2 M Zn(2+) were determined by real-time quantitative PCR (RT-qPCR), respectively. The copper resistance levels of six A. ferrooxidans strains declined followed by DY26, DX5, DY15, GD-B, GD-0, and YTW. The zinc tolerance levels of six A. ferrooxidans strains exposed to 0.2 M Zn(2+) from high to low were YTW > GD-B > DY26 > GD-0 > DX5 > DY15. Seven metal tolerance-related genes all presented in the genome of six strains, except afe-0604. The metal resistance-related genes showed different transcriptional expression patterns in six A. ferrooxidans strains. The expression of gene afe-0326 and afe-0022 in six A. ferrooxidans strains in response to 0.15 M Cu(2+) showed the same trend with the resistance levels. The expression levels of genes afe-0602, afe-0603, afe-0604, and afe-1788 in six strains response to 0.2 M Zn(2+) did not show a clear correlation between the zinc tolerance levels of six strains. According to the results of RT-qPCR and bioinformatics analysis, the proteins encoded by afe-0022, afe-0326, afe-0329, and afe-1143 were related to Cu(2+) transport of A. ferrooxidans strains.

Novel integration strategy for enhancing chalcopyrite bioleaching by Acidithiobacillus sp. in a 7-L fermenter

An integrated strategy (additional energy substrate-three stage pH control-fed batch) was firstly proposed for efficiently improving chalcopyrite bioleaching by Acidithiobacillus sp. in a 7-L fermenter. The strain adaptive-growing phase was greatly shortened from 8days into 4days with the supplement of additional 2g/L Fe(2+)+2g/L S(0). Jarosite passivation was effectively weakened basing on higher biomass via the three-stage pH-stat control (pH 1.3-1.0-0.7). The mineral substrate inhibition was attenuated by fed-batch fermentation. With the integrated strategy, the biochemical reaction was promoted and achieved a better balance. Meanwhile, the domination course of A. thiooxidans in the microbial community was shortened from 14days to 8days. As the results of integrated strategy, the final copper ion and productivity reached 89.1mg/L and 2.23mg/(Ld), respectively, which was improved by 52.8% compared to the uncontrolled batch bioleaching. The integrated strategy could be further exploited for industrial chalcopyrite bioleaching.

Nickel-resistance determinants in Acidiphilium sp. PM identified by genome-wide functional screening

Acidiphilium spp. are conspicuous dwellers of acidic, metal-rich environments. Indeed, they are among the most metal-resistant organisms; yet little is known about the mechanisms behind the metal tolerance in this genus. Acidiphilium sp. PM is an environmental isolate from Rio Tinto, an acidic, metal-laden river located in southwestern Spain. The characterization of its metal resistance revealed a remarkable ability to tolerate high Ni concentrations. Here we report the screening of a genomic library of Acidiphilium sp. PM to identify genes involved in Ni resistance. This approach revealed seven different genes conferring Ni resistance to E. coli, two of which form an operon encoding the ATP-dependent protease HslVU (ClpQY). This protease was found to enhance resistance to both Ni and Co in E. coli, a function not previously reported. Other Ni-resistance determinants include genes involved in lipopolysaccharide biosynthesis and the synthesis of branched amino acids. The diversity of molecular functions of the genes recovered in the screening suggests that Ni resistance in Acidiphilium sp. PM probably relies on different molecular mechanisms.

Draft Genome Sequence of the Extremophile Acidithiobacillus thiooxidans A01, Isolated from the Wastewater of a Coal Dump

The draft genome of Acidithiobacillus thiooxidans A01 contains 3,820,158 bp, with a G+C content of 53.08% and 3,660 predicted coding sequences (CDSs). The bacterium contains a series of specific genes involved in the oxidation of elemental sulfur and reduced inorganic sulfur compounds (RISCs).

Enhancing gold recovery from electronic waste via lixiviant metabolic engineering in Chromobacterium violaceum

Conventional leaching (extraction) methods for gold recovery from electronic waste involve the use of strong acids and pose considerable threat to the environment. The alternative use of bioleaching microbes for gold recovery is non-pollutive and relies on the secretion of a lixiviant or (bio)chemical such as cyanide for extraction of gold from electronic waste. However, widespread industrial use of bioleaching microbes has been constrained by the limited cyanogenic capabilities of lixiviant-producing microorganisms such as Chromobacterium violaceum. Here we show the construction of a metabolically-engineered strain of Chromobacterium violaceum that produces more (70%) cyanide lixiviant and recovers more than twice as much gold from electronic waste compared to wild-type bacteria. Comparative proteome analyses suggested the possibility of further enhancement in cyanogenesis through subsequent metabolic engineering. Our results demonstrated the utility of lixiviant metabolic engineering in the construction of enhanced bioleaching microbes for the bioleaching of precious metals from electronic waste.

Community dynamics of attached and free cells and the effects of attached cells on chalcopyrite bioleaching by Acidithiobacillus sp

The community dynamics of attached and free cells of Acidithiobacillus sp. were investigated and compared during chalcopyrite bioleaching process. In the mixed strains system, Acidithiobacillus ferrooxidans was the dominant species at the early stage while Acidithiobacillus thiooxidans owned competitive advantage from the middle stage to the end of bioprocess. Meanwhile, compared to A. ferrooxidans, more significant effects of attached cells on free biomass with A. thiooxidans were shown in either the pure or mixed strains systems. Moreover, the effects of attached cells on key chemical parameters were also studied in different adsorption-deficient systems. Consistently, the greatest reduction of key chemical ion was shown with A. thiooxidans and the loss of bioleaching efficiency was high to 50.5%. These results all demonstrated the bioleaching function of attached cells was more efficient than the free cells, especially with A. thiooxidans. These notable results would help us to further understand the chalcopyrite bioleaching.

Bioleaching of a low-grade nickel-copper sulfide by mixture of four thermophiles

This study investigated thermophilic bioleaching of a low grade nickel-copper sulfide using mixture of four acidophilic thermophiles. Effects of 0.2g/L l-cysteine on the bioleaching process were further evaluated. It aimed at offering new alternatives for enhancing metal recoveries from nickel-copper sulfide. Results showed a recovery of 80.4% nickel and 68.2% copper in 16-day bioleaching without l-cysteine; while 83.7% nickel and 81.4% copper were recovered in the presence of l-cysteine. Moreover, nickel recovery was always higher than copper recovery. l-Cysteine was found contributing to lower pH value, faster microbial growth, higher Oxidation-Reduction Potential (ORP), higher zeta potential and absorbing on the sulfide surfaces through amino, carboxyl and sulfhydryl groups. X-ray Diffraction (XRD) patterns of leached residues showed generation of S, jarosite and ammoniojarosite. Denaturing Gradient Gel Electrophoresis (DGGE) results revealed that l-cysteine could have variant impacts on different microorganisms and changed the microbial community composition dramatically during nickel-copper sulfide bioleaching.

Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage

Macroscopic growths at geographically separated acid mine drainages (AMDs) exhibit distinct populations. Yet, local heterogeneities are poorly understood. To gain novel mechanistic insights into this, we used OMICs tools to profile microbial populations coexisting in a single pyrite gallery AMD (pH ∼2) in three distinct compartments: two from a stratified streamer (uppermost oxic and lowermost anoxic sediment-attached strata) and one from a submerged anoxic non-stratified mat biofilm. The communities colonising pyrite and those in the mature formations appear to be populated by the greatest diversity of bacteria and archaea (including ‘ARMAN' (archaeal Richmond Mine acidophilic nano-organisms)-related), as compared with the known AMD, with ∼44.9% unclassified sequences. We propose that the thick polymeric matrix may provide a safety shield against the prevailing extreme condition and also a massive carbon source, enabling non-typical acidophiles to develop more easily. Only 1 of 39 species were shared, suggesting a high metabolic heterogeneity in local microenvironments, defined by the O₂ concentration, spatial location and biofilm architecture. The suboxic mats, compositionally most similar to each other, are more diverse and active for S, CO₂, CH₄, fatty acid and lipopolysaccharide metabolism. The oxic stratum of the streamer, displaying a higher diversity of the so-called ‘ARMAN'-related Euryarchaeota, shows a higher expression level of proteins involved in signal transduction, cell growth and N, H₂, Fe, aromatic amino acids, sphingolipid and peptidoglycan metabolism. Our study is the first to highlight profound taxonomic and functional shifts in single AMD formations, as well as new microbial species and the importance of H₂ in acidic suboxic macroscopic growths.

Development and application of biotechnologies in the metal mining industry

Metal mining faces a number of significant economic and environmental challenges in the twenty-first century for which established and emerging biotechnologies may, at least in part, provide the answers. Bioprocessing of mineral ores and concentrates is already used in variously engineered formats to extract base (e.g., copper, cobalt, and nickel) and precious (gold and silver) metals in mines throughout the world, though it remains a niche technology. However, current projections of an increasing future need to use low-grade primary metal ores, to reprocess mine wastes, and to develop in situ leaching technologies to extract metals from deep-buried ore bodies, all of which are economically more amenable to bioprocessing than conventional approaches (e.g., pyrometallurgy), would suggest that biomining will become more extensively utilized in the future. Recent research has also shown that bioleaching could be used to process a far wider range of metal ores (e.g., oxidized ores) than has previously been the case. Biotechnologies are also being developed to control mine-related pollution, including securing mine wastes (rocks and tailings) by using "ecological engineering" approaches, and also to remediate and recover metals from waste waters, such as acid mine drainage. This article reviews the current status of biotechnologies within the mining sector and considers how these may be developed and applied in future years.

Bioleaching of Phosphorus from Low Grade Ores and Concentrates with Acidophilic Iron- and Sulphur-Oxidizing Bacteria

Bioleaching experiments of phosphorus from low grade fluorapatite ore containing 8.2% P2O5 and from fluorapatite concentrate containing 29.8% P2O5 were carried out in shake flasks. Elemental sulphur was supplemented as an energy source for acid generation. Mixed and pure acidophilic bacterial cultures consisting of iron-and/or sulphur-oxidizing bacteria Acidithiobacillus ferrooxidans, A. thiooxidans and Leptospirillum ferrooxidans were used in the experiments. These acidophiles are commonly used in bioleaching of sulphide minerals, but their application on phosphorus bioleaching has been limited. Phosphorus leaching was shown to be a pH-dependant phenomenon. Phosphorus leaching yields of up to 97% and 28% were obtained in 3 weeks for low grade fluorapatite ore and concentrate, respectively. These results indicate a potential for applying bioleaching for phosphorus extraction from low grade materials.

Biotechnologies for critical raw material recovery from primary and secondary sources: R&D priorities and future perspectives

Europe is confronted with an increasing supply risk of critical raw materials. These can be defined as materials of which the risks of supply shortage and their impacts on the economy are higher compared to most of other raw materials. Within the framework of the EU Innovation Partnership on raw materials Initiative, a list of 14 critical materials was defined, including some bulk metals, industrial minerals, the platinum group metals and rare earth elements. To tackle the supply risk challenge, innovation is required with respect to sustainable primary mining, substitution of critical metals, and urban mining. In these three categories, biometallurgy can play a crucial role. Indeed, microbe-metal interactions have been successfully applied on full scale to win materials from primary sources, but are not sufficiently explored for metal recovery or recycling. On the one hand, this article gives an overview of the microbial strategies that are currently applied on full scale for biomining; on the other hand it identifies technologies, currently developed in the laboratory, which have a perspective for large scale metal recovery and the needs and challenges on which bio-metallurgical research should focus to achieve this ambitious goal.

Archaea in biogeochemical cycles

Archaea constitute a considerable fraction of the microbial biomass on Earth. Like Bacteria they have evolved a variety of energy metabolisms using organic and/or inorganic electron donors and acceptors, and many of them are able to fix carbon from inorganic sources. Archaea thus play crucial roles in the Earth's global geochemical cycles and influence greenhouse gas emissions. Methanogenesis and anaerobic methane oxidation are important steps in the carbon cycle; both are performed exclusively by anaerobic archaea. Oxidation of ammonia to nitrite is performed by Thaumarchaeota. They represent the only archaeal group that resides in large numbers in the global aerobic terrestrial and marine environments on Earth. Sulfur-dependent archaea are confined mostly to hot environments, but metal leaching by acidophiles and reduction of sulfate by anaerobic, nonthermophilic methane oxidizers have a potential impact on the environment. The metabolisms of a large number of archaea, in particular those dominating the subsurface, remain to be explored.

Crystallization and preliminary X-ray diffraction analysis of tetrathionate hydrolase from Acidithiobacillus ferrooxidans

Tetrathionate hydrolase (4THase) from the iron- and sulfur-oxidizing bacterium Acidithiobacillus ferrooxidans catalyses the disproportionate hydrolysis of tetrathionate to elemental sulfur, thiosulfate and sulfate. The gene encoding 4THase (Af-tth) was expressed as inclusion bodies in recombinant Escherichia coli. Recombinant Af-Tth was activated by refolding under acidic conditions and was then purified to homogeneity. The recombinant protein was crystallized in 20 mM glycine buffer pH 10 containing 50 mM sodium chloride and 33%(v/v) PEG 1000 using the hanging-drop vapour-diffusion method. The crystal was a hexagonal cylinder with dimensions of 0.2 × 0.05 × 0.05 mm. X-ray crystallographic analysis showed that the crystal diffracted to 2.15 Å resolution and belongs to space group P3(1) or P3(2), with unit-cell parameters a = b = 92.1, c = 232.6 Å.

Thermophilic archaeal community succession and function change associated with the leaching rate in bioleaching of chalcopyrite

The community succession and function change of thermophilic archaea Acidianus brierleyi, Metallosphaera sedula, Acidianus manzaensis and Sulfolobus metallicus were studied by denaturing gradient gel electrophoresis (DGGE) analysis of amplifying 16S rRNA genes fragments and real-time qPCR analysis of amplifying sulfur-oxidizing soxB gene associated with chalcopyrite bioleaching rate at different temperatures and initial pH values. The analysis results of the community succession indicated that temperature and initial pH value had a significant effect on the consortium, and S. metallicus was most sensitive to the environmental change, A. brierleyi showed the best adaptability and sulfur oxidation ability and predominated in various leaching systems. Meanwhile, the leaching rate of chalcopyrite closely related to the consortium function embodied by soxB gene, which could prove a desirable way for revealing microbial sulfur oxidation difference and tracking the function change of the consortium, and for optimizing the leaching parameters and improving the recovery of valuable metals.

Biomining: metal recovery from ores with microorganisms

Biomining is an increasingly applied biotechnological procedure for processing of ores in the mining industry (biohydrometallurgy). Nowadays the production of copper from low-grade ores is the most important industrial application and a significant part of world copper production already originates from heap or dump/stockpile bioleaching. Conceptual differences exist between the industrial processes of bioleaching and biooxidation. Bioleaching is a conversion of an insoluble valuable metal into a soluble form by means of microorganisms. In biooxidation, on the other hand, gold is predominantly unlocked from refractory ores in large-scale stirred-tank biooxidation arrangements for further processing steps. In addition to copper and gold production, biomining is also used to produce cobalt, nickel, zinc, and uranium. Up to now, biomining has merely been used as a procedure in the processing of sulfide ores and uranium ore, but laboratory and pilot procedures already exist for the processing of silicate and oxide ores (e.g., laterites), for leaching of processing residues or mine waste dumps (mine tailings), as well as for the extraction of metals from industrial residues and waste (recycling). This chapter estimates the world production of copper, gold, and other metals by means of biomining and chemical leaching (bio-/hydrometallurgy) compared with metal production by pyrometallurgical procedures, and describes new developments in biomining. In addition, an overview is given about metal sulfide oxidizing microorganisms, fundamentals of biomining including bioleaching mechanisms and interface processes, as well as anaerobic bioleaching and bioleaching with heterotrophic microorganisms.

Microbial community structure and sulfur biogeochemistry in mildly-acidic sulfidic geothermal springs in Yellowstone National Park

Geothermal and hydrothermal waters often contain high concentrations of dissolved sulfide, which reacts with oxygen (abiotically or biotically) to yield elemental sulfur and other sulfur species that may support microbial metabolism. The primary goal of this study was to elucidate predominant biogeochemical processes important in sulfur biogeochemistry by identifying predominant sulfur species and describing microbial community structure within high-temperature, hypoxic, sulfur sediments ranging in pH from 4.2 to 6.1. Detailed analysis of aqueous species and solid phases present in hypoxic sulfur sediments revealed unique habitats containing high concentrations of dissolved sulfide, thiosulfate, and arsenite, as well as rhombohedral and spherical elemental sulfur and/or sulfide phases such as orpiment, stibnite, and pyrite, as well as alunite and quartz. Results from 16S rRNA gene sequencing show that these sediments are dominated by Crenarchaeota of the orders Desulfurococcales and Thermoproteales. Numerous cultivated representatives of these lineages, as well as the Thermoproteales strain (WP30) isolated in this study, require complex sources of carbon and respire elemental sulfur. We describe a new archaeal isolate (strain WP30) belonging to the order Thermoproteales (phylum Crenarchaeota, 98% identity to Pyrobaculum/Thermoproteus spp. 16S rRNA genes), which was obtained from sulfur sediments using in situ geochemical composition to design cultivation medium. This isolate produces sulfide during growth, which further promotes the formation of sulfide phases including orpiment, stibnite, or pyrite, depending on solution conditions. Geochemical, molecular, and physiological data were integrated to suggest primary factors controlling microbial community structure and function in high-temperature sulfur sediments.

Heterotrophic archaea contribute to carbon cycling in low-pH, suboxic biofilm communities

Archaea are widely distributed and yet are most often not the most abundant members of microbial communities. Here, we document a transition from Bacteria- to Archaea-dominated communities in microbial biofilms sampled from the Richmond Mine acid mine drainage (AMD) system (∼pH 1.0, ∼38°C) and in laboratory-cultivated biofilms. This transition occurs when chemoautotrophic microbial communities that develop at the air-solution interface sink to the sediment-solution interface and degrade under microaerobic and anaerobic conditions. The archaea identified in these sunken biofilms are from the class Thermoplasmata, and in some cases, the highly divergent ARMAN nanoarchaeal lineage. In several of the sunken biofilms, nanoarchaea comprise 10 to 25% of the community, based on fluorescent in situ hybridization and metagenomic analyses. Comparative community proteomic analyses show a persistence of bacterial proteins in sunken biofilms, but there is clear evidence for amino acid modifications due to acid hydrolysis. Given the low representation of bacterial cells in sunken biofilms based on microscopy, we infer that hydrolysis reflects proteins derived from lysed cells. For archaea, we detected ∼2,400 distinct proteins, including a subset involved in proteolysis and peptide uptake. Laboratory cultivation experiments using complex carbon substrates demonstrated anaerobic enrichment of Ferroplasma and Aplasma coupled to the reduction of ferric iron. These findings indicate dominance of acidophilic archaea in degrading biofilms and suggest that they play roles in anaerobic nutrient cycling at low pH.

Microbial Consortia Engineering for Cellular Factories: in vitro to in silico systems

This mini-review discusses the current state of experimental and computational microbial consortia engineering with a focus on cellular factories. A discussion of promising ecological theories central to community resource usage is presented to facilitate interpretation of consortial designs. Recent case studies exemplifying different resource usage motifs and consortial assembly templates are presented. The review also highlights in silico approaches to design and to analyze consortia with an emphasis on stoichiometric modeling methods. The discipline of microbial consortia engineering possesses a widely accepted potential to generate highly novel and effective bio-catalysts for applications from biofuels to specialty chemicals to enhanced mineral recovery.

Metal resistance and lithoautotrophy in the extreme thermoacidophile Metallosphaera sedula

Archaea such as Metallosphaera sedula are thermophilic lithoautotrophs that occupy unusually acidic and metal-rich environments. These traits are thought to underlie their industrial importance for bioleaching of base and precious metals. In this study, a genetic approach was taken to investigate the specific relationship between metal resistance and lithoautotrophy during biotransformation of the primary copper ore, chalcopyrite (CuFeS(2)). In this study, a genetic system was developed for M. sedula to investigate parameters that limit bioleaching of chalcopyrite. The functional role of the M. sedula copRTA operon was demonstrated by cross-species complementation of a copper-sensitive Sulfolobus solfataricus copR mutant. Inactivation of the gene encoding the M. sedula copper efflux protein, copA, using targeted recombination compromised metal resistance and eliminated chalcopyrite bioleaching. In contrast, a spontaneous M. sedula mutant (CuR1) with elevated metal resistance transformed chalcopyrite at an accelerated rate without affecting chemoheterotrophic growth. Proteomic analysis of CuR1 identified pleiotropic changes, including altered abundance of transport proteins having AAA-ATPase motifs. Addition of the insoluble carbonate mineral witherite (BaCO(3)) further stimulated chalcopyrite lithotrophy, indicating that carbon was a limiting factor. Since both mineral types were actively colonized, enhanced metal leaching may arise from the cooperative exchange of energy and carbon between surface-adhered populations. Genetic approaches provide a new means of improving the efficiency of metal bioleaching by enhancing the mechanistic understanding of thermophilic lithoautotrophy.

Survival of the fittest: overcoming oxidative stress at the extremes of Acid, heat and metal

The habitat of metal respiring acidothermophilic lithoautotrophs is perhaps the most oxidizing environment yet identified. Geothermal heat, sulfuric acid and transition metals contribute both individually and synergistically under aerobic conditions to create this niche. Sulfuric acid and metals originating from sulfidic ores catalyze oxidative reactions attacking microbial cell surfaces including lipids, proteins and glycosyl groups. Sulfuric acid also promotes hydrocarbon dehydration contributing to the formation of black “burnt” carbon. Oxidative reactions leading to abstraction of electrons is further impacted by heat through an increase in the proportion of reactant molecules with sufficient energy to react. Collectively these factors and particularly those related to metals must be overcome by thermoacidophilic lithoautotrophs in order for them to survive and proliferate. The necessary mechanisms to achieve this goal are largely unknown however mechanistics insights have been gained through genomic studies. This review focuses on the specific role of metals in this extreme environment with an emphasis on resistance mechanisms in Archaea.

AHL signaling molecules with a large acyl chain enhance biofilm formation on sulfur and metal sulfides by the bioleaching bacterium Acidithiobacillus ferrooxidans

Biofilm formation plays a pivotal role in bioleaching activities of bacteria in both industrial and natural environments. Here, by visualizing attached bacterial cells on energetic substrates with different microscopy techniques, we obtained the first direct evidence that it is possible to positively modulate biofilm formation of the extremophilic bacterium Acidithiobacillus ferrooxidans on sulfur and pyrite surfaces by using Quorum Sensing molecules of the N-acylhomoserine lactone type (AHLs). Our results revealed that AHL-signaling molecules with a long acyl chain (12 or 14 carbons) increased the adhesion of A. ferrooxidans cells to these substrates. In addition, Card-Fish experiments demonstrated that C14-AHL improved the adhesion of indigenous A. ferrooxidans cells from a mixed bioleaching community to pyrite. Finally, we demonstrated that this improvement of cell adhesion is correlated with an increased production of extracellular polymeric substances. Our results open up a promising means to develop new strategies for the improvement of bioleaching efficiency and metal recovery, which could also be used to control environmental damage caused by acid mine/rock drainage.

Engineering microbial consortia to enhance biomining and bioremediation

In natural environments microorganisms commonly exist as communities of multiple species that are capable of performing more varied and complicated tasks than clonal populations. Synthetic biologists have engineered clonal populations with characteristics such as differentiation, memory, and pattern formation, which are usually associated with more complex multicellular organisms. The prospect of designing microbial communities has alluring possibilities for environmental, biomedical, and energy applications, and is likely to reveal insight into how natural microbial consortia function. Cell signaling and communication pathways between different species are likely to be key processes for designing novel functions in synthetic and natural consortia. Recent efforts to engineer synthetic microbial interactions will be reviewed here, with particular emphasis given to research with significance for industrial applications in the field of biomining and bioremediation of acid mine drainage.

Redox Transformations of Iron at Extremely Low pH: Fundamental and Applied Aspects

Many different species of acidophilic prokaryotes, widely distributed within the domains Bacteria and Archaea, can catalyze the dissimilatory oxidation of ferrous iron or reduction of ferric iron, or can do both. Microbially mediated cycling of iron in extremely acidic environments (pH < 3) is strongly influenced by the enhanced chemical stability of ferrous iron and far greater solubility of ferric iron under such conditions. Cycling of iron has been demonstrated in vitro using both pure and mixed cultures of acidophiles, and there is considerable evidence that active cycling of iron occurs in acid mine drainage streams, pit lakes, and iron-rich acidic rivers, such as the Rio Tinto. Measurements of specific rates of iron oxidation and reduction by acidophilic microorganisms show that different species vary in their capacities for iron oxido-reduction, and that this is influenced by the electron donor provided and growth conditions used. These measurements, and comparison with corresponding data for oxidation of reduced sulfur compounds, also help explain why ferrous iron is usually used preferentially as an electron donor by acidophiles that can oxidize both iron and sulfur, even though the energy yield from oxidizing iron is much smaller than that available from sulfur oxidation. Iron-oxidizing acidophiles have been used in biomining (a technology that harness their abilities to accelerate the oxidative dissolution of sulfidic minerals and thereby facilitate the extraction of precious and base metals) for several decades. More recently they have also been used to simultaneously remediate iron-contaminated surface and ground waters and produce a useful mineral by-product (schwertmannite). Bioprocessing of oxidized mineral ores using acidophiles that catalyze the reductive dissolution of ferric iron minerals such as goethite has also recently been demonstrated, and new biomining technologies based on this approach are being developed.