The severe current situation facing to minerals processing is that the most minerals are characterized by low-grade, being complex and very hard to deal with. It is necessary to find a new way to solve these questions. Nowadays, biohydrometallurgy draw more and more attention because of its simple process, low cost and kindness to environment. However, the lack of suitable bacteria and hard research on the mechanisms between the bacteria and ores or bacteria in gene level result in the low efficiency and poor yield of the target metal in bioleaching. Therefore, the understanding of the microbial community structure and function in the bioleaching systems is very important for the optimization of microbial community by controlling the operating conditions in bioleaching systems, thus enhancing the leaching rate. A review is given on the achievements and progress related to the study on microbial community structure and function in sulfide ore bioleaching systems made in our research group.

This paper reviews the current status of commercial biomining operations around the world, identifies factors that drive the selection of biomining as a processing technology, describes challenges to exploiting these innovations, and concludes with a discussion of biomining’s future. Biomining is commercially applied using engineered dumps, heaps and stirred tanks. Overcoming the technical challenges of lowering costs, processing low-grade, low-quality and complex ores and utilizing existing capital investments at mines requires better understanding of microbial activities and innovative engineering. Surmounting biomining commercial challenges entails improved mining company/biomining innovator cooperation and intellectual property control.

The microbial consortium used in continuous-flow, stirred tank processes to treat gold-bearing arsenopyrite concentrates became adapted to high concentrations of arsenic over a number of years. The dominant microorganisms, Acidithiobacillus caldus and Leptospirillum ferriphilum, were found to contain two sets of arsenic resistance genes. One set of ars genes was present in all isolates of a species irrespective of whether they were highly arsenic resistant or not. A second set of ars genes was present on Tn21-like transposons and was found in all strains tested that had been adapted to high concentrations of arsenic. The arsenic resistance transposons present in At. caldus and L. ferriphilum were closely related, but sufficiently different for them to have been acquired independently rather than having been passed from one bacterium to the other. The transposons were transpositionally active in Escherchia coli and were shown to confer higher levels of arsenic resistance than the chromosomally-located ars genes where it was possible to test this. Transposons containing arsenic resistance genes that were identical or closely related to the transposon from L. ferriphilum, originally found in South Africa, were also found in both L. ferrooxidans and L. ferriphilum isolates from South America and Europe. An arsB gene knockout of At. caldus was produced by homologous recombination that demonstrated both the ability of the chromosomal ars genes to confer low levels of arsenic resistance in At. caldus and the development of a genetic system for the creation of knock-out mutants.

Functional gene markers can provide important information about functional gene diversity and potential activity of microbial communities. Although microarray technology has been successfully applied to study gene expression for pure cultures, simple, and artificial microbial communities, adapting such a technology to analyze complex microbial communities still presents a lot of challenges in terms of design, sample preparation, and data analysis. This work is focused on the development and application of functional gene arrays (FGAs) to target key functional gene markers for microbial community studies. A few key issues specifically related to FGAs, such as oligonucleotide probe design, nucleic acid extraction and purification, data analysis, specificity, sensitivity, and quantitative capability are discussed in detail. Recent studies have demonstrated that FGAs can provide specific, sensitive, and potentially quantitative information about microbial communities from a variety of natural environments and controlled ecosystems. This technology is expected to revolutionize the analysis of microbial communities, and link microbial structure to ecosystem functioning.

Biohydrometallurgy is the offspring of the unexpected union of biotechnology and metallurgy. From specific properties of some extreme biotopes, active principles of interactions between microbial metabolisms and minerals have been extracted to be used as efficient metallurgical processes. Many profitable industrial operations based on these bioprocesses have been running to recover copper, gold, uranium or cobalt for instance and many other applications have been designed. Europe was quite active in this area in the past, but currently the leadership is in South Africa, America and Australia. BioMinE (Biotechnology of Metal-bearing material In Europe) is a large integrated project launched with the support of the European Commision. It is aimed at stimulating synergies between the most relevant universities, research and industrial organizations to develop new concepts in this technical field that allow a better exploitation of the mineral resources in the future. The European non-ferrous metals mining industry has initiated and developed the BioMinE project as they identified the need to find new processes for metal extraction from resources of today and of tomorrow.

The comparative study on adsorptions of Pb(Ⅱ) and Cr(Ⅵ) ions by free cells and immobilized cells of Synechococcus sp. was performed, in which different aspects including Zeta potential of the cells, the influence of pH, temperature and initial concentration of metal ions, as well as adsorption kinetics and mechanism were referred. The lyophilized free cells have a surface isoelectric point at pH 3, and the correlative experiment indicates that there is an electrostatic adsorption feature of Cr(Ⅵ) and Pb(Ⅱ). The immobilization of the free cells by Ca-alginate does not significantly modify the adsorption features of the biosorbent. The absorption processes of Cr(Ⅵ) and Pb(Ⅱ) on both free and immobilized cells are apparently affected by pH and the initial concentration of metal ions in the bulk solution, but are much weakly affected by temperature in the test range of 10−50 ℃. The slow course of biosorption follows the first order kinetic model, the adsorption of Pb(Ⅱ) obeys both Langmuir and Freundlich isotherm models, while the adsorption of Cr(Ⅵ) obeys only Freundlich model. FT-IR results indicate that carboxylic, alcoholic, amide and amino groups are responsible for the binding of the metal ions, and reduction of Cr(Ⅵ) to Cr(Ⅲ) takes place after Cr(Ⅵ) adsorbs electrostatically onto the surface of the biosorbents.

To effectively monitor the characteristic of Acidithiobacillus ferrooxidans ATCC 23270 at the whole-genomic level, a whole-genome 50-mer-based oligonucleotide microarray was developed based on the 3 217 ORFs of A. ferrooxidans ATCC 23270 genome. Based on artificial oligonucleotide probes, the results showed that the optimal hybridization temperature was 45 ℃. Specificity tests with the purified PCR amplifications of 5 genes (Sulfide-quinone reductase, Cytochrome C, Iron oxidase, Mercuric resistance protein, Nitrogenase iron protein) of A. ferrooxidans ATCC 23270 indicated that the probes on the arrays appeared to be specific to their corresponding target genes. Based on the WGA hybridization to global transcriptional difference of A. ferrooxidans ATCC 23270 strains cultured with Fe(Ⅱ) and S(0), the developed 50-mer WGA could be used for global transcriptome analysis of A. ferrooxidans ATCC 23270. The detection limit was estimated to be approximately 5 ng with the genomic DNA, and at 100 ng of the DNA concentration, all of the signals reached the saturation. In addition, strong linear relationships were observed between hybridization signal intensity and the target DNA concentrations (r²=0.977 and 0.992). The results indicated that this technology had potential as a specific, sensitive and quantitative tool for detection and identification of the strain A. ferrooxidans ATCC 23270 at the whole-genome level.

The role of chemolithotrophs such as Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans and Leptospirillum ferrooxidans which were isolated from some abandoned mines and processed waste tailings in the generation of acid mine drainage and toxic metal dissolution was discussed. Mechanisms of acid formation and dissolution of copper, zinc, iron and arsenic from copper, lead-zinc and arsenopyrite-bearing sulfide ores and tailings were established in the presence of Acidithiobacillus group of bacteria. Sulphate Reducing Bacteria(SRB) isolated from the above mine sites could be used to precipitate dissolved metals such as copper, zinc, iron and arsenic. Arsenic bioremediation was demonstrated through the use of native microorganisms such Thiomonas spp. which could oxidize arsenite to arsenate. Bioremoval of arsenic through the use of jarosite precipitates generated by Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans was also found to be very effective. Biotechnological processes  hold great promise in the remediation of acid mine drainage and efficient removal of toxic metal ions such as copper, zinc and arsenic.

The superoxide dismutase(SOD) from Acidithiobacillus ferrooxidans may play an important role in its tolerance to the extremely toxic and oxidative environment of bioleaching. This gene was cloned and then successfully expressed in Escherichia coli. The expressed protein was finally purified by one-step affinity chromatography to homogeneity and observed to be dimer according to SDS-PAGE and MALDI-TOF-MS. The metal content determination and optical spectra results of the recombinant protein confirmed that the protein was an iron-containing superoxide dismutase. Molecular modeling for the protein revealed that the iron atom was ligated by His26, His75, Asp158 and His162.

Mining companies have become increasingly aware of the potential of microbiological approaches for recovering base and precious metals from low-grade ores, and for remediating acidic, metal-rich wastewaters that drain from both operating and abandoned mine sites. Biological systems offer a number of environmental and (sometimes) economical advantages over conventional approaches, such as pyrometallurgy, though their application is not appropriate in every situation. Mineral processing using micro-organisms has been exploited for extracting gold, copper, uranium and cobalt, and current developments are targeting other base metals. Recently, there has been a great increase in our knowledge and understanding of both the diversity of the microbiology of biomining environments, and of how the microorganisms interact with each other. The results from laboratory experiments which have simulated both stirred tank and heap bioreactor systems have shown that microbial consortia are more robust than pure cultures of mineral-oxidizing acidophiles, and also tend to be more effective at bioleaching and bio-oxidizing ores and concentrates. The paper presented a concise review of the nature and interactions of microbial consortia that are involved in the oxidation of sulfide minerals, and how these might be adapted to meet future challenges in biomining operations.

The growth and surface properties of new thermoacidophilic Archaea strain Acidianus manzaensis YN-25 isolated from an acid hot spring in Tengchong, Yunnan Province, China were investigated cultured on different substrates including soluble substrate ferrous sulfate and nonsoluble solid substrates S⁰, pyrite and chalcopyrite. The growth characteristics of the cells in each substrate were characterized with the changes in cell number, pH, E_h, and concentrations of Fe²⁺ or SO₄²⁻, or ratios of [Fe²⁺] to [Fe³⁺], and the surface properties were characterized and analyzed in terms of Zeta-potential, hydrophobicity, and surface FT-IR spectra of the cells. The results show that the cells grown on solid substrates have higher value of isoelectric points. They are more hydrophobic and express more surface proteins than ferrous sulfate grown cells.

The whole genome of strain Acidithiobacillus ferrooxidans ATCC 23270 was analyzed by bioinformatics and some homolog genes of functional ones in magnetotactic bacteria were available. To obtain further knowledge of the magnetosomes formation mechanisms of Acidithiobacillus ferrooxidans in response to different Fe sources and concentrations, temporal gene expression profiles of mpsA, magA, mamB and thy were examined by using Real-time quantitative reverse transcription-PCR. The microbial formation of magnetosomes and magnetotaxis was also studied under different Fe²⁺ concentration. The results indicated that ORF numbers of 1622, 0276, 1124 and 2572 of the ATCC 23270 were homologous with mpsA, thy, magA and mamB genes in magnetotactic bacteria. The expression levels of mpsA, magA and mamB were directly related to ferrous concentration, and the highest expression level at 150−200 mmol/L ferrous was gained. The number of magnetosomes in ATCC 23270 and the magnetotaxis of cells were significantly related to the expression level of these three genes, suggesting that these genes were related with the iron transport during the process of magnetosome formation in A. ferrooxidans.

Three kinds of autotrophic bioleaching bacteria strains, including mesophilic and acidophilic ferrous ion-oxidizing bacteria Acidithiobacillus ferrooxidans (A. ferrooxidans), mesophilic and acidophilic sulfur-oxidizing bacteria Acidithiobacillus thiooxidans (A. thiooxidans), and moderately thermophilic sulfur-oxidizing bacteria Acidianus brierleyi, were cryopreserved in liquid nitrogen and their ferrous ion- or sulfur-oxidizing activities were investigated and compared with the original ones. The results revealed that ferrous ion/sulfur oxidation activities of the strains were almost equal before and after cryopreservation. Glycerin was used as cryoprotective agent. In conclusion, liquid-nitrogen cryopreservation is a simple and effective method for autotrophic bioleaching microorganisms.

To study the diversity of bacteria strains newly isolated from several acid mine drainage(AMD) sites in China, repetitive sequence based polymerase chain reaction (rep-PCR), a well established technology for diversity analysis of closely related bacteria strains, was conducted on 30 strains of bacteria Leptospirillum ferriphilium, 8 strains of bacteria Acidithiobacillus ferrooxidans, as well as the Acidithiobacillus ferrooxidans type strain ATCC (American Type Culture Collection) 23270. The results showed that, using ERIC and BOX primer sets, rep-PCR produced highly discriminatory banding patterns. Phylogenetic analysis based on ERIC-PCR banding types was made and the results indicated that rep-PCR could be used as a rapid and highly discriminatory screening technique in studying bacterial diversity, especially in differentiating bacteria within one species in AMD.

The fractions of the extracellular proteins of Acidithiobacillus ferrooxidans grown on two different energy substrates, elemental sulfur and ferrous sulfate, were selectively prepared with hot water treatment and distinctly shown by two-dimensional gel electrophoresis. Some protein spots with apparently higher abundance in sulfur energy substrate than in ferrous sulfate energy substrate were identified by using MALDI-TOF/TOF. Based on peptide mass fingerprints and bioinformatical analysis, the extracellular proteins were classified according to their functions as conjugal transfer protein, pilin, vacJ lipoprotein, polysaccharide deacetylase family protein, Ser/Thr protein phosphatase family protein and hypothetical proteins. Several extracellular proteins were found abundant in thiol groups and with CXXC functional motif, these proteins may be directly involved in the sulfur activation by use of their thiol group (Pr-SH) to bond the elemental sulfur.