Molecular genetics of Thiobacillus ferrooxidans.

Thiobacillus ferrooxidans is a gram-negative, highly acidophilic (pH 1.5 to 2.0), autotrophic bacterium that obtains its energy through the oxidation of ferrous iron or reduced inorganic sulfur compounds. It is usually dominant in the mixed bacterial populations that are used industrially for the extraction of metals such as copper and uranium from their ores. More recently, these bacterial consortia have been used for the biooxidation of refractory gold-bearing arsenopyrite ores prior to the recovery of gold by cyanidation. The commercial use of T. ferrooxidans has led to an increasing interest in the genetics and molecular biology of the bacterium. Initial investigations were aimed at determining whether the unique physiology and specialized habitat of T. ferrooxidans had been accompanied by a high degree of genetic drift from other gram-negative bacteria. Early genetic studies were comparative in nature and concerned the isolation of genes such as nifHDK, glnA, and recA, which are widespread among bacteria. From a molecular biology viewpoint, T. ferrooxidans appears to be a typical member of the proteobacteria. In most instances, cloned gene promoters and protein products have been functional in Escherichia coli. Although T. ferrooxidans has proved difficult to transform with DNA, research on indigenous plasmids and the isolation of the T. ferrooxidans merA gene have resulted in the development of a low-efficiency electroporation system for one strain of T. ferrooxidans. The most recent studies have focused on the molecular genetics of the pathways associated with nitrogen metabolism, carbon dioxide fixation, and components of the energy-producing mechanisms.     

Strain polymorphism of the plasmid profiles in Acidithiobacillus ferrooxidans

Plasmid profiles were studied in 27 Acidithiobacillus ferrooxidans strains isolated from different geographic zones and substrates differing in the composition of the main sulfide minerals, and also in experimentally obtained strains with acquired enhanced resistance to the ions of heavy metals (Fe, Ni, Cu, Zn, As). In 16 out of 20 strains isolated from different substrates, one to four 2- to 20-kb and larger plasmids were revealed. Plasmids were found in all five strains isolated from gold-containing pyrite-arsenopyrite ores and concentrates, in nine of 11 strains isolated from the ores and concentrates containing nonferrous metals, and in two of four strains isolated from the oxidation substrates of simple composition (mine waters, pyritized coals, active sludge). Changes in the plasmid profiles in some A. ferrooxidans strains (TFZ, TFI-Fe, TFV-1-Cu) with experimentally enhanced resistance to Zn2+, Fe3+, and Cu2+, respectively, were noted as compared with the initial strains. After 30 passages on S0-containing medium, strain TFBk showed changes in the copy number of plasmids. The role of plasmids in the processes of oxidation of energy substrates and in the acquired enhanced resistance to the heavy metal ions is discussed.     

Molecular and atomic analysis of uranium complexes formed by three eco-types of Acidithiobacillus ferrooxidans

A combination of EXAFS, transmission electron microscopy and energy-dispersive X-ray was used to conduct a molecular and atomic analysis of the uranium complexes formed by Acidithiobacillus ferrooxidans. The results demonstrate that this bacterium accumulates uranium as phosphate compounds. We suggest that at toxic levels when the uranium enters the bacterial cells, A. ferrooxidans can detoxify and efflux this metal by a process in which its polyphosphate bodies are involved.     

Bacterial populations in samples of bioleached copper ore as revealed by analysis of DNA obtained before and after cultivation.

The composition of bacterial populations in copper bioleaching systems was investigated by analysis of DNA obtained either directly from ores or leaching solutions or after laboratory cultures. This analysis consisted of the characterization of the spacer regions between the 16 and 23S genes in the bacterial rRNA genetic loci after PCR amplification. The sizes of the spacer regions, amplified from DNAs obtained from samples, were compared with the sizes of those obtained from cultures of the main bacterial species isolated from bioleaching systems. This allowed a preliminary assessment of the bacterial species present in the samples. Identification of the bacteria was achieved by partial sequencing of the 16S rRNA genes adjacent to the spacer regions. The spacer regions observed in DNA from columns leached at different iron concentrations indicated the presence of a mixture of different bacteria. The spacer region corresponding to Thiobacillus ferrooxidans was the main product observed at high ferrous iron concentration. At low ferrous iron concentration, spacer regions of different lengths, corresponding to Thiobacillus thiooxidans and "Leptospirillum ferrooxidans" were observed. However, T. ferrooxidans appeared to predominate after culture of these samples in medium containing ferrous iron as energy source. Although some of these strains contained singular spacer regions, they belonged within previously described groups of T. ferrooxidans according to the nucleotide sequence of the neighbor 16S rRNA. These results illustrate the bacterial diversity in bioleaching systems and the selective pressure generated by different growth conditions.     

Bacterial Community in Copper Sulfide Ores Inoculated and Leached with Solution from a Commercial-Scale Copper Leaching Plant

Most copper bioleaching plants operate with a high concentration of sulfate salts caused by the continuous addition of sulfuric acid and the recycling of the leaching solution. Since the bacteria involved in bioleaching have been generally isolated at low sulfate concentrations, the bacterial population in ores leached with the high-sulfate solution (1.25 M) employed in a copper production plant was investigated. The complexity of the original population was assessed by the length pattern of the spacer regions between the 16S and 23S rRNA genes, observed after PCR amplification of the DNA extracted from the leached ore. Six main spacers were distinguished by electrophoretic migration, but they could be further resolved into eight spacers by nucleotide sequence homology. The degree of homology was inferred from the electrophoretic migration of the heteroduplexes formed after hybridization. One of the spacers was indistinguishable from that found in Thiobacillus thiooxidans, four could be related to Thiobacillus ferrooxidans, and three could be related to Leptospirillum ferrooxidans. Only five of the spacers in the original sample could be recovered after culturing in media containing different inorganic energy source. Altogether, the results indicate that the bacteria in the leached ore formed a community composed of at least three species: a fairly homogeneous population of T. thiooxidans strains and two heterogeneous populations of T. ferrooxidans and L. ferrooxidans strains.     

Chemolithotrophic Bacteria in Copper Ores Leached at High Sulfuric Acid Concentration

Extensive bacterial growth was observed when copper sulfide ores were leached with 0.6 N sulfuric acid. The bacterial population developed in this condition was examined by characterization of the spacer regions between the 16S and 23S rRNA genetic loci obtained after PCR amplification of the DNA extracted from the leached ore. The spacers observed had the sizes found in strains of "Leptospirillum ferrooxidans" and Thiobacillus thiooxidans, except for a larger one, approximately 560 bp long, that was not observed in any of the strains examined, including those of Thiobacillus ferrooxidans. The bacteria with this last spacer were selected after culturing in mineral and elemental sulfur media containing 0.7 N sulfuric acid. The spacer and the 16S ribosomal DNA of this isolate were sequenced and compared with those in species commonly found in bioleaching processes. Though the nucleotide sequence of the spacer showed an extensive heterologous region with T. thiooxidans, the sequence of its 16S rDNA gene indicated a close relationship (99.85%) with this species. These results indicate that a population comprised of bacterial strains closely related to T. thiooxidans and of another strain, possibly related to "L. ferrooxidans," can develop during leaching at high sulfuric acid concentration. Iron oxidation in this condition is attributable to "L. ferrooxidans" and not T. ferrooxidans, based on the presence of spacers with the "L. ferrooxidans" size range and the absence of spacers characteristic of T. ferrooxidans.     

磁泳分离细菌新方法的研究

从酸性矿坑水中富集培养分离到的嗜酸氧化亚铁硫杆菌（Acidithiobacillus ferrooxidans,A.ferrooxidans）[1-2] 菌同趋磁细菌具有一定的相似性。通过显微镜观察发现,部分浸矿细菌在外加磁场的作用下具有微弱的趋磁性,基于菌种的这种特性,设计了磁泳分离仪,对其在磁场作用下泳动（磁泳）进行分析,经磁泳后的近磁、远磁菌的生理特性有较大的差异。从用涂布平板法获得的近磁菌纯培养A. ferrooxidans菌体中,分离得到纳米磁性颗粒,能谱分析表明,其主要成分为Fe和O元素。实验结果证明,A. ferrooxidans具有微弱趋磁性,采用磁泳分离该类菌体内含有磁性颗粒的细菌是可行的,这一分离技术的进一步完善和改进将为传统的微生物菌种分离提供一种新型分离技术,也将大大促进趋磁细菌的研究,而且它与浸矿工艺的结合将大大促进我国生物冶金的研究步伐。     

Production of rhodanese by bacteria present in bio-oxidation plants used to recover gold from arsenopyrite concentrates

Considerably larger quantities of cyanide are required to solubilize gold following the bio-oxidation of gold-bearing ores compared with oxidation by physical-chemical processes. A possible cause of this excessive cyanide consumption is the presence of the enzyme rhodanese. Rhodanese activities were determined for the bacteria most commonly encountered in bio-oxidation tanks. Activities of between 6.4 and 8.2 micromol SCN min(-1) mg protein(-1) were obtained for crude enzyme extracts of Thiobacillus ferrooxidans, Thiobacillus thiooxidans and Thiobacillus caldus, but no rhodanese activity was detected in Leptospirillum ferrooxidans. Rhodanese activities 2-2.5-fold higher were found in the total mixed cell mass from a bio-oxidation plant. T. ferrooxidans synthesized rhodanese irrespective of whether it was grown on iron or sulphur. With a PCR-based detection technique, only L. ferrooxidans and T. caldus cells were detected in the bio-oxidation tanks. As no rhodanese activity was associated with L. ferrooxidans, it was concluded that T. caldus was responsible for all of the rhodanese activity. Production of rhodanese by T. caldus in batch culture was growth phase-dependent and highest during early stationary phase. Although the sulphur-oxidizing bacteria were clearly able to convert cyanide to thiocyanate, it is unlikely that this rhodanese activity is responsible for the excessive cyanide wastage at the high pH values associated with the gold solubilization process.     

Heterotrophic bacteria from cultures of autotrophic Thiobacillus ferrooxidans: relationships as studied by means of deoxyribonucleic acid homology.

From several presumably pure cultures of Thiobacillus ferrooxidans, we isolated a pair of stable phenotypes. One was a strict autotroph utilizing sulfur or ferrous iron as the energy source and unable to utilize glucose; the other phenotype was an acidophilic obligate heterotroph capable of utilizing glucose but not sulfur or ferrous iron. The acidophilic obligate heterotroph not only was encountered in cultures of T. ferrooxidans, but also was isolated with glucose-mineral salts medium, pH 2.0, directly from coal refuse. By means of deoxyribonucleic acid homology, we have demonstrated that the acidophilic heterotrophs are of a different genotype from T. ferrooxidans, not closely related to this species; we have shown also that the acidophilic obligate heterotrophs, regardless of their source of isolation, are related to each other. Therefore, cultures of T. ferrooxidans reported capable of utilizing organic compounds should be carefully examined for contamination. The acidophilic heterotrophs isolated by us are different from T. acidophilis, which is also associated with T. ferrooxidans but is facultative, utilizing both glucose and elemental sulfur as energy sources. Since they are so common and tenacious in T. ferrooxidans cultures, the heterotrophs must be associated with T. ferrooxidans in the natural habitat.     

Genetics of metal resistance in acidophilic prokaryotes of acidic mine environments

Acidophilic bacteria inhabiting acidic mine regions cause natural leaching of sulphidic ores. They are now exploited in industrial operations for leaching of metals and beneficiation of low-grade and recalcitrant ores. Recent trends emphasize application of thermoacidophiles and genetic engineering of ore-leaching bacteria for greater success in this area. This requires an in-depth understanding on the molecular genetics of these bacteria and construction of cloning vectors for them. Metal resistance is considered as the most suitable phenotypic trait for cloning vectors of bio-mining chemolithoautotrophic (viz. Acidithiobacillus ferrooxidans) and heterotrophic (Acidiphilium and Acidocella species) bacteria of mine environments. These bacteria take part in ore-leaching either directly or indirectly, exhibit low to high level of resistance/tolerance to various metals under different conditions. Majority of these bacteria contain one or more plasmids--the genetic elements that usually carry metal resistant genes. But none of the At. ferrooxidans plasmids has been definitely proved to harbour metal-resistant genes which have mostly been found in the chromosome of this bacterium. Plasmids of acidophilic heterotrophs of the genera Acidiphilium and Acidocella, on the other hand, carry metal resistant genes. While genes bestowing arsenic resistance in Acidiphilium multivorum are similar to those analyzed from other sources, the metal (Cd and Zn)-resistance conferring cloned plasmid DNA fragments from Acidiphilium symbioticum KM2 and Acidocella GS19h strains were found to have no sequence similarity with the reported Cd- and Zn-resistant genes. Such observations indicate some novel aspects of metal resistance in acidophilic bacteria.     

Thiobacillus ferrooxidans, a facultative hydrogen oxidizer

The type strain (ATCC 23270) and two other strains of Thiobacillus ferrooxidans were able to grow by hydrogen oxidation, a feature not recognized before. When cultivated on H2, a hydrogenase was induced and the strains were less extremely acidophilic than during growth on sulfidic ores. Cells of T. ferrooxidans grown on H2 and on ferrous iron showed 100% DNA homology. Hydrogen oxidation was not observed in eight other species of the genus Thiobacillus and in Leptospirillum ferrooxidans.     

Thiobacillus ferrooxidans, a facultative hydrogen oxidizer.

The type strain (ATCC 23270) and two other strains of Thiobacillus ferrooxidans were able to grow by hydrogen oxidation, a feature not recognized before. When cultivated on H2, a hydrogenase was induced and the strains were less extremely acidophilic than during growth on sulfidic ores. Cells of T. ferrooxidans grown on H2 and on ferrous iron showed 100% DNA homology. Hydrogen oxidation was not observed in eight other species of the genus Thiobacillus and in Leptospirillum ferrooxidans.     

Uranium mobilization from low-grade ore by cyanobacteria

Summary Three cyanobacterial isolates (two LPP-B forms and one Anabaena or Nostoc species) from different environments could mobilize uranium from low-grade ores. After 80 days, up to 18% uranium had been extracted from coal and 51% from carbonate rock by the filamentous cyanobacterium OL3, a LPP-B form. Low growth requirements with regard to light and temperature optima make this strain a possible candidate for leaching neutral and alkaline low-grade uranium ores.     

一株嗜酸化能异养菌Acidiphilium sp.的分离鉴定及其对Fe(Ⅲ)代谢的研究

从云南省腾冲热泉酸性泥土样品中分离得到一株好氧嗜酸异养细菌Teng-A。菌株Teng-A细胞大小0.6～0.8μm×1.0～1.5μm,单生或成链状排列,革兰氏染色反应为阴性,有周生鞭毛,不产芽孢,该菌适宜的生长温度为29～33℃、pH为3.0～4.0,可以利用许多有机物生长,但不能利用Fe(Ⅱ)、S、Na2S2O3、K2S4O6等为能源生长。菌株Teng-A基因组DNA的(G C)mol%为69.6mol%,其16S rRNA基因与Acidiphilium属菌种的16S rRNA基因的最高相似性大于99%。根据形态学、生理生化特点及系统发育分析表明,菌株Teng-A是Acidiphilium属的一个新成员,崭定名为Acidiphilium sp.strainTeng-A。厌氧条件下,菌株Teng-A可以葡萄糖或H2为电子供体,将Fe(Ⅲ)还原为Fe(Ⅱ),还原速率分别为11.56mg/L.day与15.34mg/L.day。菌株Teng-A与Acidithiobacillus ferrooxidansLJ-1和Leptospirilum ferriphilum LJ-2共同培养,前3dFe2 氧化速度分别为0.44g/L.day和0.41g/L.day,比LJ-1(0.64g/L.day)和LJ-2(0.60g/L.day)单独培养时氧化Fe(Ⅱ)的速率稍慢,但当培养时间超过5d时,Fe(Ⅱ)最终被全部氧化,并且发现在共培养时,Fe(Ⅱ)氧化生成的沉淀物的形态不同于At.ferrooxidans和L.ferriphilum单独培养时产生的沉淀物的形态。最后讨论了Acidiphilium对生物浸矿和生物成矿作用的影响。     

Microbial leaching of metals from sulfide minerals

Microorganisms are important in metal recovery from ores, particularly sulfide ores. Copper, zinc, gold, etc. can be recovered from sulfide ores by microbial leaching. Mineral solubilization is achieved both by 'direct (contact) leaching' by bacteria and by 'indirect leaching' by ferric iron (Fe(3+)) that is regenerated from ferrous iron (Fe(2+)) by bacterial oxidation. Thiobacillus ferrooxidans is the most studied organism in microbial leaching, but other iron- or sulfide/sulfur-oxidizing bacteria as well as archaea are potential microbial agents for metal leaching at high temperature or low pH environment. Oxidation of iron or sulfur can be selectively controlled leading to solubilization of desired metals leaving undesired metals (e.g., Fe) behind. Microbial contribution is obvious even in electrochemistry of galvanic interactions between minerals.     

Estimation of uranium and boron contents in plants and soils by nuclear particle etch technique

Summary The nuclear particle etch technique has been utilized to estimate uranium concentration in soil and plant samples and boron contents in plant samples. The average value of uranium content in soil was found to be 11 ppm. Uranium was found to vary from 0.5 to 4.4 ppm and boron was found to vary from 10.9 to 19.2 ppm in plant (mesophyte and xerophyte groups) samples. The present technique of nuclear charged particle track analysis, simple and inexpensive, has high potentiality for boron and uranium analysis in plants and agricultural crops. It may find application in geobotany to get information about underlying deposits of ores and minerals.     

Iron Oxidation not Coupled to Growth in Thiobacillus ferrooxidans in Presence

Growth and iron oxidation by Thiobacillus ferrooxidans are affected by the presence of silver, molybdenum, uranium and copper. Growth is more sensitive to the presence of these metals than the iron oxidation system of the bacterium. Silver toxicity is much more specific than molybdenum and uranium. Iron oxidation is inhibited at only 0.1 parts/10⁶ of silver which is 300 and 5000 times less than the minimum inhibitory concentration of molybdenum and uranium, respectively. Copper and zinc at concentrations as high as 2000 and 15 000 parts/10⁶, respectively, have no influence on the iron oxidation rate. In the presence of silver, molybdenum, uranium and copper below their minimum inhibitory concentrations as well as in the absence of nitrogen, phosphorus and potassium, iron oxidation is not coupled to growth.     

Identification and discrimination of thiobacilli using ARDREA, RAPD and rep-APD

A highly reliable procedure for fast identification and taxonomical categorization of thiobacilli is presented. The procedure includes RFLP analysis of PCR amplified 16S rDNA, 23S rDNA, and intergenic spacer rDNA between the 16S and the 23S rRNA-genes (amplified ribosomal DNA restriction enzyme analysis – ARDREA), as well as genomic fingerprinting using random primers (RAPD) and repetitive primers (Rep-APD). The taxonomic and discriminatory power of these three analytical approaches is compared. It is demonstrated that the RAPD and Rep-APD methods provide taxonomic results which are in agreement with the classification based on the RFLP analysis of the highly conservative ribosomal RNA ( rrn ) operons of the strains studied. Moreover, both kinds of genomic PCR fingerprinting, due to the fact that they derive information from different parts of the whole bacterial genome which may possess different degrees of variability, are more informative than ARDREA. By them, a discrimination of closely related Thiobacillus strains is possible. In addition, they are easier to perform and faster than the ARDREA. Using the method described, it was found that one Thiobacillus isolate recovered from uranium waste heaps described in the literature as Thiobacillus ferrooxidans ATCC 33020 is taxonomically neither closely related to the type strain of the species, Thiobacillus ferrooxidans ATCC23270^T, nor to any other strain of this species analysed in the present work.     

Phenotypic characteristics of Thiobacillus ferrooxidans strains

Phenotypic polymorphism of strains of Thiobacillus ferrooxidans isolated from various ecological niches was studied. The strains differed both in rates of growth and oxidation of Fe2+, S0, FeS2, and sulfide minerals contained in concentrate. Each strain, irrespective of its original environment, required a period of adaptation to a new substrate. Strains TFN-d, TFBk, TFO, and TFL-2, isolated from ores and concentrates rich in oxidized substrates, showed an equal adaptation pace (five culture transfers) but differed in their adaptation efficiency. Strain TFV-1, isolated from base ore and showing the lowest rates of growth and oxidation of all the substrates, required five culture transfers to adapt to S0 and FeS2 and seven culture transfers to adapt to the concentrate. It is concluded that the phenotypic properties of the strains correlate with their genotypic polymorphism and the environmental conditions under which their microevolution took place.