Heavy metal mining using microbes

An astrophysical view of Earth-based metabolic biosignature gases

Microbial life on Earth uses a wide range of chemical and energetic resources from diverse habitats. An outcome of this microbial diversity is an extensive and varied list of metabolic byproducts. We review key points of Earth-based microbial metabolism that are useful to the astrophysical search for biosignature gases on exoplanets, including a list of primary and secondary metabolism gas byproducts. Beyond the canonical, unique-to-life biosignature gases on Earth (O(2), O(3), and N(2)O), the list of metabolic byproducts includes gases that might be associated with biosignature gases in appropriate exoplanetary environments. This review aims to serve as a starting point for future astrophysical biosignature gas research.

Bio-processing of solid wastes and secondary resources for metal extraction - A review

Metal containing wastes/byproducts of various industries, used consumer goods, and municipal waste are potential pollutants, if not treated properly. They may also be important secondary resources if processed in eco-friendly manner for secured supply of contained metals/materials. Bio-extraction of metals from such resources with microbes such as bacteria, fungi and archaea is being increasingly explored to meet the twin objectives of resource recycling and pollution mitigation. This review focuses on the bio-processing of solid wastes/byproducts of metallurgical and manufacturing industries, chemical/petrochemical plants, electroplating and tanning units, besides sewage sludge and fly ash of municipal incinerators, electronic wastes (e-wastes/PCBs), used batteries, etc. An assessment has been made to quantify the wastes generated and its compositions, microbes used, metal leaching efficiency etc. Processing of certain effluents and wastewaters comprising of metals is also included in brief. Future directions of research are highlighted.

Draft genome sequence of the extremely acidophilic biomining bacterium Acidithiobacillus thiooxidans ATCC 19377 provides insights into the evolution of the Acidithiobacillus genus

Acidithiobacillus thiooxidans is a mesophilic, extremely acidophilic, chemolithoautotrophic gammaproteobacterium that derives energy from the oxidation of sulfur and inorganic sulfur compounds. Here we present the draft genome sequence of A. thiooxidans ATCC 19377, which has allowed the identification of genes for survival and colonization of extremely acidic environments.

Supplementation of inorganic phosphate enhancing the removal efficiency of tannery sludge-borne Cr through bioleaching

Four inorganic mineral nutrients including NH4+, K+, Mg2+ and soluble inorganic phosphate (Pi) were investigated to reveal the potential limiting nutrients for tannery sludge bioleaching process driven by Acidithiobacillus species, and the feasibility of supplementing the limiting nutrients to accelerate tannery sludge bioleaching was studied in the present study. It was found that the concentration of Pi was lower than 3.5 mg/L throughout the whole bioleaching process, which is the most probable restricting nutrient for tannery sludge bioleaching. Further experiments revealed that the deficiency of Pi could seriously influence the growth of Acidithiobacillus thiooxidans and lower its oxidization capacity for S0, and the limiting concentration of Pi for the growth of A. thiooxidans was 6 mg/L. The low concentration of soluble Pi in sludge matrix was resulted from the extremely strong sorbing/binding capacity of tannery sludge for phosphate. The supplementation of more than 1.6 g/L KH2PO4 into tannery sludge bioleaching system could effectively stimulate the growth of Acidithiobacillus species, enhance Cr removal rate and further shorten tannery sludge bioleaching period from 10 days to 7 days. Therefore, inorganic phosphate supplementation is an effective and feasible method to accelerate tannery sludge bioleaching process, and the optimum dosage of KH2PO4 was 1.6 g/L for tannery sludge with 5.1% of total solids.

An investigation of biooxidation ability of Acidithiobacillus ferrooxidans using NMR relaxation measurement

NMR relaxation measurements can provide a simple means for understanding biological activity of cells in solution with known composition. It has the advantage that it is an in situ, non-intrusive technique, and the acquisition is fast. The iron oxidation ability of Acidithiobacillus ferrooxidans was investigated using NMR relaxation measurements. The transversal relaxation is characterized by a time constant, T₂, which is sensitive to the chemical environment. Fe³⁺ ion has more significant T₂ shortening than Fe²⁺ ion. In the presence of A. ferrooxidans in solutions containing Fe²⁺ ion, T₂ shortening was found with increasing time as the bacteria oxidize Fe²⁺ to Fe³⁺ ions. In the optimal growth medium, the bacteria concentration increased 80 times and high iron oxidation rate was found. In 10 mM K₂SO₄ medium, however, bacteria concentration remained almost unchanged and the iron oxidation rate was significantly lower.

Changes in the composition of an acid mine drainage microbial community upon successive transfers in medium containing low-grade copper sulfide

A consortium of microorganisms from acid mine drainage samples was cultured in modified 9 K medium containing low-grade copper sulfide. The culture was maintained for sixty days and then transferred to fresh medium. This process was repeated three more times and a final consortium exhibiting a copper extraction rate of 89.3% was obtained. RFLP and microarrays analysis of 16S rRNA sequences retrieved from the consortia showed that Acidithiobacilluscaldus, Leptospirillumferriphilum, Sulfobacillus sp., Acidiphilium sp., and Sulfolobus spp. were represented in higher numbers in the consortia obtained in the copper-containing medium than in the original consortium. In contrast, a decrease in Acidithiobacillus ferrooxidans, Alicyclobacillus sp., Pseudomonas sp., and Sulfobacillus thermosulfidooxidans was observed. The abundance of genes related to sulfur metabolism from At. caldus and Sulfolobus spp., iron oxidation from Leptospirillum sp. and metal resistance from most of the detected microorganisms increased as the consortium was successively transferred into fresh medium.

Global transcriptional analysis of stress-response strategies in Acidithiobacillus ferrooxidans ATCC 23270 exposed to organic extractant--Lix984n

Acidithiobacillus ferrooxidans (A. ferrooxidans) ATCC 23270 is a model bacteria for bioleaching research. Because of the use of extractant in metal extraction industry, A. ferrooxidans needs to cope with the water-organic two-phase system. To get insight into the molecular response of A. ferrooxidans to organic solvent, global gene expression pattern was examined in A. ferrooxidans ATCC 23270 cells subjected to Lix984n (an organic extractant) using the method of whole-genome DNA microarray. The data suggested that the global response of A. ferrooxidans to Lix984n stress was characterized by the up-regulation of genes involved in pentose phosphate pathway, fatty acid and glutamate biosynthesis. In further study, compared to heterotrophic bacteria in dealing with short-time stress, A. ferrooxidans has a special strategy of continuously enhancing the expression of genes encoding proteins involved in electron transport, such as petI, petII, cyo and cyd. Besides, acrAB-tolC operon encoding organic solvent efflux pump and its positive regulator gene ostR were addressed.

Genome wide identification of Acidithiobacillus ferrooxidans (ATCC 23270) transcription factors and comparative analysis of ArsR and MerR metal regulators

Acidithiobacillus ferrooxidans is a chemolithoautotrophic acidophilic bacterium that obtains its energy from the oxidation of ferrous iron, elemental sulfur, or reduced sulfur minerals. This capability makes it of great industrial importance due to its applications in biomining. During the industrial processes, A. ferrooxidans survives to stressing circumstances in its environment, such as an extremely acidic pH and high concentration of transition metals. In order to gain insight into the organization of A. ferrooxidans regulatory networks and to provide a framework for further studies in bacterial growth under extreme conditions, we applied a genome-wide annotation procedure to identify 87 A. ferrooxidans transcription factors. We classified them into 19 families that were conserved among diverse prokaryotic phyla. Our annotation procedure revealed that A. ferrooxidans genome contains several members of the ArsR and MerR families, which are involved in metal resistance and detoxification. Analysis of their sequences revealed known and potentially new mechanism to coordinate gene-expression in response to metal availability. A. ferrooxidans inhabit some of the most metal-rich environments known, thus transcription factors identified here seem to be good candidates for functional studies in order to determine their physiological roles and to place them into A. ferrooxidans transcriptional regulatory networks.

Effects of gamma-sterilization on DOC, uranium and arsenic remobilization from organic and microbial rich stream sediments

Organic-rich sediments are known to be effective accumulators for uranium and arsenic. Much is known about the capacity for metal or metalloid fixation by microbes and organic compounds as well as inorganic sediment particles. Experiments investigating the effect of microbes on the process of metal fixation in sediments require sterilized sediments as control treatment which is often realized by gamma-sterilization. Only few studies show that gamma-sterilization has an effect on the remobilization of metal and metalloids and on their physico-chemical properties. These studies deal with sediments with negligible organic content whereas almost nothing is known about organic-rich sediments including a probably high microbial activity. In view of this, we investigated the effect of gamma-sterilization of organic-rich sediments on uranium and arsenic fixation and release. After ten days within an exposure experiment we found a significant higher remobilization of uranium and arsenic in sterile compared to unsterile treatments. In line with these findings the content of dissolved organic carbon (DOC), manganese, and iron increased to even significantly higher concentration in the sterile compared to unsterile treatment. Gamma-sterilization seems to change the physico-chemical properties of organic-rich sediments. Microbial activity is effectively eliminated. From increased DOC concentrations in overlaying water it is concluded that microbes are eventually killed with leaching of cellular compounds in the overlaying water. This decreases the adsorption capacity of the sediment and leads to enhanced uranium and arsenic remobilization.

A novel acidophilic, thermophilic iron and sulfur-oxidizing archaeon isolated from a hot spring of tengchong, yunnan, China

A novel thermoacidophilic iron and sulfur-oxidizing archaeon, strain YN25, was isolated from an in situ enriched acid hot spring sample collected in Yunnan, China. Cells were irregular cocci, about 0.9–1.02 µm × 1.0–1.31 µm in the medium containing elemental sulfur and 1.5–2.22 µm × 1.8–2.54 µm in ferrous sulfate medium. The ranges of growth and pH were 50–85 (optimum 65) and pH 1.0–6.0 (optimum 1.5–2.5). The acidophile was able to grow heterotrophically on several organic substrates, including various monosaccharides, alcohols and amino acids, though the growth on single substrate required yeast extract as growth factor. Growth occurred under aerobic conditions or via anaerobic respiration using elemental sulfur as terminal electron acceptor. Results of morphology, physiology, fatty acid analysis and analysis based on 16S rRNA gene sequence indicated that the strain YN25 should be grouped in the species Acidianus manzaensis. Bioleaching experiments indicated that this strain had excellent leaching capacity, with a copper yielding ratio up to 79.16% in 24 d. The type strain YN25 was deposited in China Center for Type Culture Collection (=CCTCCZNDX0050).

Characterization of an OmpA-like outer membrane protein of the acidophilic iron-oxidizing bacterium, Acidithiobacillus ferrooxidans

An OmpA family protein (FopA) previously reported as one of the major outer membrane proteins of an acidophilic iron-oxidizing bacterium Acidithiobacillus ferrooxidans was characterized with emphasis on the modification by heat and the interaction with peptidoglycan. A 30-kDa band corresponding to the FopA protein was detected in outer membrane proteins extracted at 75°C or heated to 100°C for 10 min prior to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). However, the band was not detected in outer membrane proteins extracted at ≤40°C and without boiling prior to electrophoresis. By Western blot analysis using the polyclonal antibody against the recombinant FopA, FopA was detected as bands with apparent molecular masses of 30 and 90 kDa, suggesting that FopA existed as an oligomeric form in the outer membrane of A. ferrooxidans. Although the fopA gene with a sequence encoding the signal peptide was successfully expressed in the outer membrane of Escherichia coli, the recombinant FopA existed as a monomer in the outer membrane of E. coli. FopA was detected in peptidoglycan-associated proteins from A. ferrooxidans. The recombinant FopA also showed the peptidoglycan-binding activity.

Differential gene expression in response to copper in Acidithiobacillus ferrooxidans strains possessing dissimilar copper resistance

Locus afe_0454 from Acidithiobacillus ferrooxidans (At.ferrooxidans) is annotated as related to copper resistance in The Institute for Genomic Research database. In our study, two At.ferrooxidans strains, 26(#) and DC, with different levels of copper ion resistance were isolated from acid mine drainages at two major copper mines in China, and their copper-resistance capacity was determined. The 26(#) strain had a copper-tolerance level of 0.22 mol/L, whereas the DC strain had a lower copper-tolerance level of 0.04 mol/L. The mutant 26(#) was generated from strain 26(#), and its copper-tolerance level was 0.25 mol/L. Using real-time quantitative reverse transcription polymerase chain reaction, differential expression of the afe_0454 gene during copper ion stress of these three strains was investigated. The results showed that the expression of afe_0454 was increased under copper ion stress, indicating that the afe_0454 gene is sensitive to copper levels. Furthermore, the afe_0454 gene expression ratio varied in the different copper-resistant strains. Gene expression was highest in the highest copper-resistant strain. The deduced amino acid sequence of the afe_0454 gene was 56.87% non-polar, indicating the AFE_0454 protein was hydrophobic. Searching with the AFE_0454 protein in The Institute for Genomic Research database showed that the structure of the copper resistance protein D (CopD), which transports copper ions outside of the cell, had the highest sequence identity (46%). Bioinformatics analysis showed that the AFE_0454 protein has eight transmembrane helixes and was predicted to be localized to the plasma membrane. These results strongly suggested that the AFE_0454 protein is likely a transmembrane protein and might be directly involved in copper ion resistance.

Construction of recombinant mercury resistant Acidithiobacillus caldus

A mercury-resistant plasmid of pTMJ212 which was able to shuttle between Acidithiobacillus caldus and Escherichia coli was constructed by inserting the mercury resistant determinants, the mer operon of Acidithiobacillus ferrooxidans, into the IncQ plasmid of pJRD215. pTMJ212 was transferred from Escherichia coli into Acidithiobacillus caldus through conjugation. Furthermore, pTMJ212 was transferred back from Acidithiobacillus caldus into Escherichia coli, thereby confirming the initial transfer of pTMJ212 from Escherichia coli to Acidithiobacillus caldus. Compared to the control, the cell growth of the recombinant Acidithiobacillus caldus increased markedly under mercury (Hg(2+)) stress especially at Hg(2+) concentrations ranging from 2.0 to 4.5 μg/ml.

Terminal oxidase diversity and function in "Metallosphaera yellowstonensis": gene expression and protein modeling suggest mechanisms of Fe(II) oxidation in the sulfolobales

"Metallosphaera yellowstonensis" is a thermoacidophilic archaeon isolated from Yellowstone National Park that is capable of autotrophic growth using Fe(II), elemental S, or pyrite as electron donors. Analysis of the draft genome sequence from M. yellowstonensis strain MK1 revealed seven different copies of heme copper oxidases (subunit I) in a total of five different terminal oxidase complexes, including doxBCEF, foxABCDEFGHIJ, soxABC, and the soxM supercomplex, as well as a novel hypothetical two-protein doxB-like polyferredoxin complex. Other genes found in M. yellowstonensis with possible roles in S and or Fe cycling include a thiosulfate oxidase (tqoAB), a sulfite oxidase (som), a cbsA cytochrome b(558/566), several small blue copper proteins, and a novel gene sequence coding for a putative multicopper oxidase (Mco). Results from gene expression studies, including reverse transcriptase (RT) quantitative PCR (qPCR) of cultures grown autotrophically on either Fe(II), pyrite, or elemental S showed that the fox gene cluster and mco are highly expressed under conditions where Fe(II) is an electron donor. Metagenome sequence and gene expression studies of Fe-oxide mats confirmed the importance of fox genes (e.g., foxA and foxC) and mco under Fe(II)-oxidizing conditions. Protein modeling of FoxC suggests a novel lysine-lysine or lysine-arginine heme B binding domain, indicating that it is likely the cytochrome component of a heterodimer complex with foxG as a ferredoxin subunit. Analysis of mco shows that it encodes a novel multicopper blue protein with two plastocyanin type I copper domains that may play a role in the transfer of electrons within the Fox protein complex. An understanding of metabolic pathways involved in aerobic iron and sulfur oxidation in Sulfolobales has broad implications for understanding the evolution and niche diversification of these thermophiles as well as practical applications in fields such as bioleaching of trace metals from pyritic ores.

From Río Tinto to Mars: the terrestrial and extraterrestrial ecology of acidophiles

The recent geomicrobiological characterization of Río Tinto, Iberian Pyrite Belt (IPB), has proven the importance of the iron cycle, 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, both prokaryotic and eukaryotic, detected in the water column and the sediments. The extreme conditions of the Tinto basin are not the product of industrial contamination but the consequence of the presence of an underground bioreactor that obtains its energy from the massive sulfide minerals of the IPB. To test this hypothesis, a drilling project was carried out to intersect ground waters that interact with the mineral ore in order to provide evidence of subsurface microbial activities and the potential resources to support these activities. The oxidants that drive the system appear to come from the rock matrix, contradicting conventional acid mine drainage models. These resources need only groundwater to launch microbial metabolism. There are several similarities between the vast deposits of sulfates and iron oxides on Mars and the main sulfide-containing iron bioleaching products found in the Tinto. Firstly, the short-lived methane detected both in Mars' atmosphere and in the sediments and subsurface of the IPB and secondly, the abundance of iron, common to both. The physicochemical properties of iron make it a source of energy, a shield against radiation and oxidative stress as well as a natural pH controller. These similarities have led to Río Tinto's status as a Mars terrestrial analogue.

Effects of cell condition, pH, and temperature on lead, zinc, and copper sorption to Acidithiobacillus caldus strain BC13

This study describes the effects of cell condition, pH, and temperature on lead, zinc, and copper sorption to Acidithiobacillus caldus strain BC13 with a Langmuir model. Copper exhibited the highest loading capacity, 4.76 ± 0.28 mmol g(-1), to viable cells at pH 5.5. The highest k(L) (binding-site affinity) observed was 61.2 ± 3.0 L mmol(-1) to dehydrated cells at pH 4.0. The pHs that maximized loading capacities and binding-site affinities were generally between 4.0 and 5.5, where the sum of free-proton and complexed-metal concentrations was near a minimum. Of additional importance, lead, zinc, and copper sorbed to viable cells at pH values as low as 1.5. Previous studies with other acidithiobacilli did not measure viable-cell sorption below pH 4.0. In separate experiments, desorption studies showed that far less copper was recovered from viable cells than any other metal or cell condition, suggesting that uptake may play an important role in copper sorption by At. caldus strain BC13. To reflect an applied system, the sorption of metal mixtures was also studied. In these experiments, lead, zinc, and copper sorption from a tertiary mixture were 40.2 ± 4.3%, 28.7 ± 3.8%, and 91.3 ± 3.0%, respectively, of that sorbed in single-metal systems.

Ferric iron uptake genes are differentially expressed in the presence of copper sulfides in Acidithiobacillus ferrooxidans strain LR

Acidithiobacillus ferrooxidans is one of the most widely used microorganisms in bioleaching operations to recover copper from low-grade copper sulfide ores. This work aimed to investigate the relative expression of genes related to the iron uptake system when A. ferrooxidans LR was maintained in contact with chalcopyrite or bornite as the sole energy source. Real-time quantitative PCR analysis revealed that the presence of bornite had no effect on the expression of seven genes related to the siderophore-mediated Fe(III) uptake system, while in the presence of chalcopyrite the expression of the genes was up-regulated. Bioinformatic analysis of the genomic region where these genes were found revealed the existence of three new putative DNA-binding sequences for the ferric iron uptake transcriptional regulator (Fur). Electrophoretic mobility shift assays demonstrated that a purified A. ferrooxidans His-tagged Fur protein was able to bind in vitro to each of these putative Fur boxes, suggesting that Fur regulated the expression of these genes. The expression of fur and two known Fur-regulated genes, mntH and dsrK, was also investigated in the presence of chalcopyrite. While the expression of fur and mntH was up-regulated, the expression of dsrK was down-regulated. The low amount of ferrous iron in the medium was probably responsible for the up-regulation of fur and the genes related to the siderophore-mediated Fe(III) uptake system when A. ferrooxidans LR was kept in the presence of chalcopyrite. A homology model of the A. ferrooxidans Fur was constructed and revealed that the putative DNA-binding surface presents conserved positively charged residues, supporting a previously suggested mode of interaction with DNA. The up-regulation of fur and the siderophore-mediated Fe(III) uptake genes, and the down-regulation of dsrK suggest that in the presence of chalcopyrite Fur acts as a transcription inducer and repressor.

Effects of ferrous sulfate, inoculum history, and anionic form on lead, zinc, and copper toxicity to Acidithiobacillus caldus strain BC13

The current study reports the single and combined toxicities of Pb, Zn, and Cu to Acidithiobacillus caldus strain BC13. The observed half-maximal inhibitory concentrations (IC50), ± 95% confidence intervals, for Pb, Zn, and Cu were 0.9 ± 0.1 mM, 39 ± 0.5 mM, and 120 ± 8 mM, respectively. The observed minimum inhibitory concentrations (MIC) for Pb, Zn, and Cu were 7.5 mM, 75 mM, and 250 mM, respectively. When metals were presented in binary mixtures, the toxicities were less than additive. For example, when 50% of the Pb MIC and 50% of the Cu MIC were presented together, the specific growth rate was inhibited by only 59 ± 3%, rather than 100%. In addition, the presence of ferrous iron in the growth media decreased Pb and Zn toxicity to A. caldus strain BC13. The importance of inoculum history was evaluated by pre-adapting cultures through subsequent transfers in the presence of Pb, Zn, and Cu at their respective IC50s. After pre-adaptation, cultures had specific growth rates 39 ± 11, 32 ± 7, and 28 ± 12% higher in the presence of Pb, Zn, and Cu IC50s, respectively, compared with cultures that had not been pre-adapted. In addition, when cells exposed to the MICs of Pb, Zn, and Cu were harvested, washed, and re-inoculated into fresh, metal-free medium, they grew, showing that the cells remained viable with little residual toxicity. Finally, metal chlorides showed more toxicity than metal sulfates, and studies using sodium chloride or a mixture of metal sulfates and sodium chloride suggested that this was attributable to an additive combination of the metal and chloride toxicities.

Cytoplasmic membrane response to copper and nickel in Acidithiobacillus ferrooxidans

Metal tolerance has been found to vary among Acidithiobacillus ferrooxidans strains and this can impact the efficiency of biomining practices. To explain observed strain variability for differences in metal tolerance we examined the effects of Cu(2+) and Ni(2+) concentrations (1-200 mM) on cytoplasmic membrane properties of two A. ferrooxidans type strains (ATCC 23270 and 19859) and four strains isolated from AMD water around Sudbury, Ontario, Canada. Growth rate, membrane fluidity and phase, determined from the fluorescence polarization of 1,6-diphenyl-1,3,5-hexatriene (DPH), and fatty acid profiles indicated that three different modes of adaptation were present and could separate between strains showing moderate, or high metal tolerance from more sensitive strains. To compensate for the membrane ordering effects of the metals, significant remodelling of the membrane was used to either maintain homeoviscous adaptation in the moderately tolerant strains or to increase membrane fluidity in the sensitive strains. Shifts in the gel-to-liquid crystalline transition temperature in the moderately tolerant strains led to multiple phase transitions, increasing the potential for phase separation and compromised membrane integrity. The metal-tolerant strain however, was able to tolerate increases in membrane order without significant compensation via fatty acid composition. Our multivariate analyses show a common adaptive response which involves changes in the abundant 16:0 and 18:1 fatty acids. However, fatty acid composition and membrane properties showed no difference in response to either copper or nickel suggesting that adaptive response was non-specific and tolerance dependent. We demonstrate that strain variation can be evaluated using differences in membrane properties as intrinsic determinants of metal susceptibility.

The resilience and versatility of acidophiles that contribute to the bio-assisted extraction of metals from mineral sulphides

In this paper, a brief outline is presented on acidic ferric ion oxidation of mineral sulphides for the extraction of metals in both stirred tank reactors for mineral concentrates and heaps for low-grade ores. The identities and capabilities of the relatively few acidophiles that assist the oxidative processes are summarized and their responses to selected extremes in their growth environments described. Individually, the organisms adapt to the presence of high concentrations of heavy metals and other elements in the bioleaching environment, tolerate a wide range of acidities and can recover from prolonged exposure to temperatures significantly above their preferred temperatures for growth. However, the presence of chloride in their acidic environment presents a significant physiological challenge. Species that exhibit a chemotactic response and attachment to sulphide surfaces, where they can create their own micro-environments, would be favoured in both heap bioreactors with low availability of energy substrates and physically aggressive, agitated continuous stirred-tank reactor environments treating concentrates.

Cytoplasmic membrane fluidity and fatty acid composition of Acidithiobacillus ferrooxidans in response to pH stress

Strain variation in the acidophile Acidithiobacillus ferrooxidans was examined as a product of membrane adaptation in response to pH stress. We tested the effects of sub and supra-optimal pH in two type strains and four strains isolated from acid mine drainage water around Sudbury, Ontario, Canada. Growth rate, membrane fluidity and phase, determined from the fluorescence polarization of 1,6-diphenyl-1,3,5-hexatriene, and fatty acid profiles were compared. The effect of pH 1.5 was the most pronounced compared to the other pH values of 1.8, 3.1, and 3.5. Three different types of response to lower pH were observed, the first of which appeared to maintain cellular homeostasis more effectively. This adaptive mode included a decrease in membrane fluidity and concomitant depression of the phase transition in two distinct membrane lipid components. This was explained through the increase in saturated fatty acids (predominantly 16:0 and cyclopropane 19:0 w8c) with a concomitant decrease in 18:1 w7c fatty acid. The other strains also showed common adaptive mechanisms of specific fatty acid remodeling increasing the abundance of short-chain fatty acids. However, we suspect membrane permeability was compromised due to potential phase separation, which may interfere with energy transduction and viability at pH 1.5. We demonstrate that membrane physiology permits differentiating pH tolerance in strains of this extreme acidophile.

Recombinant tetrathionate hydrolase from Acidithiobacillus ferrooxidans requires exposure to acidic conditions for proper folding

Tetrathionate hydrolase (4THase) plays an important role in dissimilatory sulfur metabolism in the acidophilic chemolithoautotrophic iron- and sulfur-oxidizing bacterium Acidithiobacillus ferrooxidans. We have already identified the gene encoding 4THase (Af-tth) in this bacterium. The heterologous expression of Af-tth in Escherichia coli resulted in the formation of inclusion bodies of the protein in an inactive form. The recombinant protein (Af-Tth) was successfully activated after an in vitro refolding treatment. The specific activity of the refolded Af-Tth obtained was 21.0+/-9.4 U mg(-1) when the protein solubilized from inclusion bodies by 6 M guanidine hydrochloride solution was refolded in a buffer containing 10 mM beta-alanine, 2 mM dithiothreitol, 0.4 M ammonium sulfate, and 30% v/v glycerol with the pH adjusted to 4.0 by sulfuric acid for 14 h at 4 degrees C. The in vitro refolding experiments revealed that Af-Tth required exposure to an acidic environment during protein folding for activation. This property reflects a physiological characteristic of the Af-Tth localized in the outer membrane of the acidophilic A. ferrooxidans. No cofactor such as pyrroloquinoline quinone (PQQ) was required during the refolding process in spite of the similarity in the primary structure of Af-Tth to the PQQ family of proteins.

Archaeal transformation of metals in the environment

We are becoming increasingly aware of the role played by archaea in the biogeochemical cycling of the elements. Metabolism of metals is linked to fundamental metabolic functions, including nitrogen fixation, energy production, and cellular processes based on oxidoreductions. Comparative genomic analyses have shown that genes for metabolism, resistance, and detoxification of metals are widespread throughout the archaeal domain. Archaea share with other organisms strategies allowing them to utilize essential metals and maintain metal ions within a physiological range, although comparative proteomics show, in a few cases, preferences for specific genetic traits related to metals. A more in-depth understanding of the physiology of acidophilic archaea might lead to the development of new strategies for the bioremediation of metal-polluted sites and other applications, such as biomining.

Bioleaching of metals from printed wire boards by Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans and their mixture

Bioleaching processes were used to mobilize metals from printed wire boards (PWBs). The bacteria Acidithiobacillus ferrooxidans (A. ferrooxidans) and Acidithiobacillus thiooxidans (A. thiooxidans) isolated from an acidic mine drainage were grown and acclimated in presence of PWBs and then used as bioleaching bacteria to solubilize metals from PWBs. The experimental results demonstrate that all the percentages of copper, lead, zinc solubilized into the leaching solution from actual PWBs basically increased with decrease of sieve fraction of sample and decrease of PWBs concentration. The concentration of PWBs should be controlled under the range from 7.8 to 19.5 g l(-1). Under 7.8 g l(-1) of the concentration of PWBs, the percentages of copper solubilized are 99.0%, 74.9%, 99.9% at 0.5-1.0mm of sieve fraction at 9 d of leaching time by the pure culture of A. ferrooxidans, the pure culture of A. thiooxidans, and mixed culture of A. ferrooxidans and A. thiooxidans, respectively, while the percentages of copper, lead and zinc solubilized are all more than 88.9% at <0.35 mm of the sieve fractions of sample at 5d of leaching time by the above three kinds of cultures. Variation of pH and redox potential of leaching solution with time implied that Fe(3+) oxidized from Fe(2+) in the culture medium in presence of A. ferrooxidans caused the mobilization of metals. It is concluded that A. ferrooxidans and A. thiooxidans were able to grow in the presence of PWBs and the pure culture of A. ferrooxidans, and the mixed culture of A. ferrooxidans and A. thiooxidans can not only efficiently bioleach the main metal copper but also bioleach other minor metals such as lead, zinc as well.

Metals, minerals and microbes: geomicrobiology and bioremediation

Microbes play key geoactive roles in the biosphere, particularly in the areas of element biotransformations and biogeochemical cycling, metal and mineral transformations, decomposition, bioweathering, and soil and sediment formation. All kinds of microbes, including prokaryotes and eukaryotes and their symbiotic associations with each other and 'higher organisms', can contribute actively to geological phenomena, and central to many such geomicrobial processes are transformations of metals and minerals. Microbes have a variety of properties that can effect changes in metal speciation, toxicity and mobility, as well as mineral formation or mineral dissolution or deterioration. Such mechanisms are important components of natural biogeochemical cycles for metals as well as associated elements in biomass, soil, rocks and minerals, e.g. sulfur and phosphorus, and metalloids, actinides and metal radionuclides. Apart from being important in natural biosphere processes, metal and mineral transformations can have beneficial or detrimental consequences in a human context. Bioremediation is the application of biological systems to the clean-up of organic and inorganic pollution, with bacteria and fungi being the most important organisms for reclamation, immobilization or detoxification of metallic and radionuclide pollutants. Some biominerals or metallic elements deposited by microbes have catalytic and other properties in nanoparticle, crystalline or colloidal forms, and these are relevant to the development of novel biomaterials for technological and antimicrobial purposes. On the negative side, metal and mineral transformations by microbes may result in spoilage and destruction of natural and synthetic materials, rock and mineral-based building materials (e.g. concrete), acid mine drainage and associated metal pollution, biocorrosion of metals, alloys and related substances, and adverse effects on radionuclide speciation, mobility and containment, all with immense social and economic consequences. The ubiquity and importance of microbes in biosphere processes make geomicrobiology one of the most important concepts within microbiology, and one requiring an interdisciplinary approach to define environmental and applied significance and underpin exploitation in biotechnology.

Application of clone library analysis and real-time PCR for comparison of microbial communities in a low-grade copper sulfide ore bioheap leachate

The microbial communities of leachate from a bioleaching heap located in China were analyzed using the 16S rRNA gene clone library and real-time quantitative PCR. Both methods showed that Leptospirillum spp. were the dominant bacteria, and Ferroplasma acidiphilum were the only archaea detected in the leachate. Clone library results indicated that nine operational taxonomic units (OTUs) were obtained, which fell into four divisions, the Nitrospirae (74%), the gamma-Proteobacteria (14%), the Actinobacteria (6%) and the Euryarchaeota (6%). The results obtained by real-time PCR in some ways were the same as clone library analysis. Furthermore, Sulfobacillus spp., detected only by real-time PCR, suggests that real-time PCR was a reliable technology to study the microbial communities in bioleaching environments. It is a useful tool to assist clone library analysis, to further understand microbial consortia and to have comprehensive and exact microbiological information about bioleaching environments. Finally, the interactions among the microorganisms detected in the leachate were summarized according to the characteristics of these species.

Draft genome sequence of the extremely acidophilic bacterium Acidithiobacillus caldus ATCC 51756 reveals metabolic versatility in the genus Acidithiobacillus

Acidithiobacillus caldus is an extremely acidophilic, moderately thermophilic, chemolithoautotrophic gammaproteobacterium that derives energy from the oxidation of sulfur and reduced inorganic sulfur compounds. Here we present the draft genome sequence of Acidithiobacillus caldus ATCC 51756 (the type strain of the species), which has permitted the prediction of genes for survival in extremely acidic environments, including genes for sulfur oxidation and nutrient assimilation.

Dynamic of active microorganisms inhabiting a bioleaching industrial heap of low-grade copper sulfide ore monitored by real-time PCR and oligonucleotide prokaryotic acidophile microarray

The bioleaching of metal sulfide has developed into a very important industrial process and understanding the microbial dynamic is key to advancing commercial bioleaching operations. Here we report the first quantitative description of the dynamic of active communities in an industrial bioleaching heap. Acidithiobacillus ferrooxidans was the most abundant during the first part of the leaching cycle, while the abundance of Leptospirillum ferriphilum and Ferroplasma acidiphilum increased with age of the heap. Acidithiobacillus thiooxidans kept constant throughout the leaching cycle, and Firmicutes group showed a low and a patchy distribution in the heap. The Acidiphilium‐like bacteria reached their highest abundance corresponding to the amount of autotrophs. The active microorganisms in the leaching system were determined using two RNA‐based sensitive techniques. In most cases, the 16S rRNA copy numbers of At. ferrooxidans, L. ferriphilum, At. thiooxidans and F. acidiphilum, was concomitant with the DNA copy numbers, whereas Acidiphilium‐like bacteria and some Firmicutes members did not show a clear correlation between 16S rRNA accumulation and DNA copy numbers. However, the prokaryotic acidophile microarray (PAM) analysis showed active members of Alphaproteobacteria in all samples and of Sulfobacillus genus in older ones. Also, new active groups such as Actinobacteria and Acidobacterium genus were detected by PAM. The results suggest that changes during the leaching cycle in chemical and physical conditions, such as pH and Fe³⁺/Fe²⁺ ion rate, are primary factors shaping the microbial dynamic in the heap.

Differential Gene Expression of Industrial Bioleaching Transcriptomes by Leptospirillum Ferrooxidans DNA Microarray

Heap bioleaching is presently the most successful technology for copper extraction from low-grade sulfide ores. Metabolic behaviors and adaptation mechanisms of microbial communities to this system remain unknown. A combination of molecular approaches has been used to determine the key microorganisms in the Escondida Sulphide Heap. This work reports the global gene expression in industrial bioleaching samples by using a specific DNA microarray of Leptospirillum ferrooxidans to better understand the metabolic functions displayed by Leptospirillum spp. iron oxidizers as mineral leaching proceeds. Quantitative real-time PCR analysis showed low cell numbers of Leptospirillum species during the first part of the irrigation period, however, it became the most abundant and active in the second part of the cycle. Transcriptome analysis by DNA microarray could provide specifics transcription patterns in the different stages of the industrial process. We studied the gene expression from bioleaching heap samples with variable Leptospirillum cell numbers, operation times and with different chemical and physical conditions. The results showed induction of genes involved in energetic metabolism, electron transport, ribosomal proteins, DNA repair and response to heavy metals when Leptospirillum species were most abundant and active. We suggest that up- and down-regulation of specifics genes could be used as indicators of physiological responses to operational conditions in the bioleaching systems.

Sulfur Oxygenase Reductase in Different Acidithiobacillus Caldus-Like Strains

The elemental sulfur oxidising enzyme Sulfur Oxygenase Reductase (SOR) is very well investigated in acidothermophilic archaea, such as Acidianus brierleyi and Sulfolobus metallicus. In contrast, not much is known about the biochemistry of elemental sulfur oxidation in acidophilic bacteria. Recently, however, the SOR-encoding gene has been found also in a bacterial strain closely related to the moderate thermophile Acidithiobacillus caldus. Confusingly, for the latter species, also the involvement of the SOX system as well as thiosulfate:quinone oxidoreductase (TQO) and tetrathionate hydrolase (TTH) in sulfur compound oxidation has been proposed based on genome analysis. In this study, we have detected the sor-gene in other Acidithiobacillus caldus-like strains, isolated from various bioleaching habitats, indicating that SOR plays an important role in sulfur oxidation in this species. Based on sequence comparison, the new bacterial sor-genes are closely related and distant from the known archaeal sequences as well as from the SOR found in the neutrophilic bacterium Aquifex aeolicus. In addition, SOR activity has been detected in crude cell extracts from all Acidithiobacillus caldus-like strains tested. The enzyme is truly thermophilic as highest activities were achieved at 65 °C, which is far beyond the growth optimum of Acidithiobacillus caldus. This finding may give rise to the question whether the presence of SOR in Acidithiobacillus caldus is only relevant while growing at elevated temperatures. Currently, experiments are performed for testing this hypothesis (comparing growth and enzyme activities at 30 vs. 45 °C).