Detection of Thiobacillus ferrooxidans in acid mine environments by indirect fluorescent antibody staining.

An indirect fluorescent antibody (FA) staining technique was developed for the rapid detection of Thiobacillus ferrooxidans. The specificity of the FA stain for T. ferrooxidans was demonstrated with both laboratory and environmental samples. Coal refuse examined by scanning electron microscopy exhibited a rough, porous surface, which was characteristically covered by water-soluble crystals. Significant numbers of T. ferrooxidans were detected in the refuse pores. A positive correlation between numbers of T. ferrooxidans and acid production in coal refuse in the laboratory was demonstrated with the FA technique.     

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.     

Ecology of Iron-Oxidizing Bacteria in Pyritic Materials Associated with Coal

A technique was developed for measuring (14)CO(2) uptake by chemolithotrophic bacteria directly in pyritic materials associated with coal and coal refuse. There was good correlation between (14)CO(2) uptake, as determined by this technique, and the most probable number of iron-oxidizing bacteria. Maximal (14)CO(2) uptake occurred in coal refuse material 2 to 3 years old, and only slight incorporation was demonstrated in fresh material or material 40 years old. Samples taken from the surface of the coal refuse pile always demonstrated maximal (14)CO(2) uptake, and in most samples, only slight activity was demonstrated at depths below 8 to 10 cm. Optimal uptake of (14)CO(2) by natural samples occurred at 20 to 30 C and at a moisture content of between 23 and 35%. In addition to chemolithotrophic bacteria, heterotrophic fungi and yeasts were also routinely isolated in high numbers from acidic coal refuse. In contrast, acidophilic, heterotrophic bacteria were either absent or present in low numbers in such acidic samples.     

Development and application of small-subunit rRNA probes for assessment of selected Thiobacillus species and members of the genus Acidiphilium

Culture-dependent studies have implicated sulfur-oxidizing bacteria as the causative agents of acid mine drainage and concrete corrosion in sewers. Thiobacillus species are considered the major representatives of the acid-producing bacteria in these environments. Small-subunit rRNA genes from all of the Thiobacillus and Acidiphilium species catalogued by the Ribosomal Database Project were identified and used to design oligonucleotide DNA probes. Two oligonucleotide probes were synthesized to complement variable regions of 16S rRNA in the following acidophilic bacteria: Thiobacillus ferrooxidans and T. thiooxidans (probe Thio820) and members of the genus Acidiphilium (probe Acdp821). Using (32)P radiolabels, probe specificity was characterized by hybridization dissociation temperature (T(d)) with membrane-immobilized RNA extracted from a suite of 21 strains representing three groups of bacteria. Fluorochrome-conjugated probes were evaluated for use with fluorescent in situ hybridization (FISH) at the experimentally determined T(d)s. FISH was used to identify and enumerate bacteria in laboratory reactors and environmental samples. Probing of laboratory reactors inoculated with a mixed culture of acidophilic bacteria validated the ability of the oligonucleotide probes to track specific cell numbers with time. Additionally, probing of sediments from an active acid mine drainage site in Colorado demonstrated the ability to identify numbers of active bacteria in natural environments that contain high concentrations of metals, associated precipitates, and other mineral debris.     

An indirect fluorescent antibody staining technique for determining population levels ofThiobacillus ferrooxidans in acid mine drainage waters

Thiobacillus ferrooxidans is believed to be responsible for the oxidation of ferrous ion at low pH, the rate-limiting step in the oxidation of pyrite ores and subsequent formation of acid mine drainage (AMD). It has been suggested that efforts to control this environmental problem include procedures that would inhibit this bacterium. At present, a most probable number (MPN) procedure requiring a minimum of 10 days is used to enumerate this microorganism in natural waters. If control of AMD through inhibition ofT. ferrooxidans is to be feasible, it will be necessary to develop a more rapid method to determine population levels to facilitate application of control measures.An indirect fluorescent antibody (FA) staining technique was developed for this purpose which provided reliable estimates within a few hours. Artificial samples containing approximated numbers ofT. ferrooxidans were analyzed using the FA and MPN procedures, and the FA technique more closely approximated expected numbers of cells. The MPN method was excessively conservative, detecting only 3% to 21% of the cells enumerated by the FA procedure.     

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.     

Plasmid and transposon transfer to Thiobacillus ferrooxidans.

The broad-host-range IncP plasmids RP4, R68.45, RP1::Tn501, and pUB307 were transferred to acidophilic, obligately chemolithotrophic Thiobacillus ferrooxidans from Escherichia coli by conjugation. A genetic marker of kanamycin resistance was expressed in T. ferrooxidans. Plasmid RP4 was transferred back to E. coli from T. ferrooxidans. The broad-host-range IncQ vector pJRD215 was mobilized to T. ferrooxidans with the aid of plasmid RP4 integrated in the chromosome of E. coli SM10. pJRD215 was stable, and all genetic markers (kanamycin/neomycin and streptomycin resistance) were expressed in T. ferrooxidans. By the use of suicide vector pSUP1011, transposon Tn5 was introduced into T. ferrooxidans. The influence of some factors on plasmid transfer from E. coli to T. ferrooxidans was investigated. Results showed that the physiological state of donor cells might be important to the mobilization of plasmids. The transfer of plasmids from E. coli to T. ferrooxidans occurred in the absence of energy sources for both donor and recipient.     

Nucleotide sequence of the gene encoding the nitrogenase iron protein of Thiobacillus ferrooxidans.

The DNA sequence was determined for the cloned Thiobacillus ferrooxidans nifH and part of the nifD genes. A putative T. ferrooxidans nifH promoter was identified whose sequences showed perfect consensus with those of the Klebsiella pneumoniae nif promoter. Two putative consensus upstream activator sequences were also identified. The amino acid sequence was deduced from the DNA sequence. In a comparison of nifH DNA sequences from T. ferrooxidans and eight other nitrogen-fixing microbes, a Rhizobium sp. isolated from Parasponia andersonii showed the greatest homology (74%) and Clostridium pasteurianum (nifH 1) showed the least homology (54%). In a comparison of the amino acid sequences of the Fe proteins, the Rhizobium sp. and Rhizobium japonicum showed the greatest homology (both 86%) and C. pasteurianum (nifH 1 gene product) demonstrated the least homology (56%) to the T. ferrooxidans Fe protein.     

Seasonal variations in microbial populations and environmental conditions in an extreme acid mine drainage environment.

Microbial populations, their distributions, and their aquatic environments were studied over a year (1997) at an acid mine drainage (AMD) site at Iron Mountain, Calif. Populations were quantified by fluorescence in situ hybridizations with group-specific probes. Probes were used for the domains Eucarya, Bacteria, and Archaea and the two species most widely studied and implicated for their role in AMD production, Thiobacillus ferrooxidans and Leptospirillum ferrooxidans. Results show that microbial populations, in relative proportions and absolute numbers, vary spatially and seasonally and correlate with geochemical and physical conditions (pH, temperature, conductivity, and rainfall). Bacterial populations were in the highest proportion (>95%) in January. Conversely, archaeal populations were in the highest proportion in July and September ( approximately 50%) and were virtually absent in the winter. Bacterial and archaeal populations correlated with conductivity and rainfall. High concentrations of dissolved solids, as reflected by high conductivity values (up to 125 mS/cm), occurred in the summer and correlated with high archaeal populations and proportionally lower bacterial populations. Eukaryotes were not detected in January, when total microbial cell numbers were lowest (<10(5) cells/ml), but eukaryotes increased at low-pH sites ( approximately 0.5) during the remainder of the year. This correlated with decreasing water temperatures (50 to 30 degrees C; January to November) and increasing numbers of prokaryotes (10(8) to 10(9) cells/ml). T. ferrooxidans was in highest abundance (>30%) at moderate pHs and temperatures ( approximately 2.5 and 20 degrees C) in sites that were peripheral to primary acid-generating sites and lowest (0 to 5%) at low-pH sites (pH approximately 0.5) that were in contact with the ore body. L. ferrooxidans was more widely distributed with respect to geochemical conditions (pH = 0 to 3; 20 to 50 degrees C) but was more abundant at higher temperatures and lower pHs ( approximately 40 degrees C; pH approximately 0.5) than T. ferrooxidans.     

Monitoring of bacteria in acid mine environments by reverse sample genome probing

A variety of microorganisms can exist in acid mine drainage (AMD) environments, although their contribution to AMD problems is unclear. Environmental strains of Thiobacillus ferrooxidans and Thiobacillus acidophilus were purified by repeated plating and single-colony isolation on iron salts and tetrathionate media, respectively. Thiobacillus thiooxidans was enriched on sulfur-containing media. For the isolation of Leptospirillum ferrooxidans, iron salts and pyrite media were inoculated with environmental samples. However, L. ferrooxidans was never recovered on solid media. Denatured chromosomal DNAs from type and (or) isolated strains of T. ferrooxidans, T. acidophilus, T. thiooxidans, and L. ferrooxidans were spotted on a master filter for their detection in a variety of samples by reverse sample genome probing (RSGP). Analysis of enrichments of environmental samples by RSGP indicated that ferrous sulfate medium enriched T. ferrooxidans strains, whereas all thiobacilli grew in sulfur medium, T. thiooxidans strains being dominant. Enrichment in glucose medium followed by transfer to tetrathionate medium resulted in the selection of T. acidophilus strains. DNA was also extracted directly (without enrichment) from cells recovered from AMD water or sediments, and was analyzed by RSGP to describe the communities present. Strains showing homology with T. ferrooxidans and T. acidophilus were found to be major community components. Strains showing homology with T. thiooxidans were a minor community component, whereas strains showing homology with L. ferrooxidans were not detected.     

Bacterial leaching of a sulfide ore by Thiobacillus ferrooxidans and Thiobacillus thiooxidans: I. Shake flask studies

Bacterial leaching of a sulfide ore containing pyrite, chalcopyrite, and sphalerite was studied in shake flask experiments using Thiobacillus ferrooxidans and Thiobacillus thiooxidans strains isolated from mine sites. The Fe(2+)grown T. ferrooxidans isolates solubilized sphalerite preferentially over chalcopyrite leaching 7-10% Cu, 68-76% Zn, and 10-22% Fe from the ore in 18 days. The sulfur grown T. thiooxidans isolates leached Zn much more slowly and very little Fe, with a Cu-Zn extraction ratio twice the value obtained with T. ferrooxidans. The ore adapted T. ferrooxidans started solubilizing Cu and Zn without a lag period. The ore-adapted T. thiooxidans extracted Cu as well as T. ferrooxidans, but the extraction of Zn or Fe was still much slower in the low-phosphate medium, while in the high-phosphate medium it approached the value obtained with T. ferrooxidans. A high Cu-Zn extraction ratio of 0.34 was obtained with T. thiooxidans in the low phosphate medium. In the mixed-culture experiments with T. ferrooxidans and T. thiooxidans, the culture behaved as T. thiooxidans in the low-phosphate medium with a higher Cu-Zn extraction ratio and as T. ferrooxidans in the high-phosphate medium with a lower Cu-Zn extraction ratio. It is concluded that T. ferrooxidans and T. thiooxidans solubilize sulfide minerals by different mechanisms.     

Specific binding of Thiobacillus ferrooxidans RbcR to the intergenic sequence between the rbc operon and the rbcR gene.

The presence of two sets (rbcL1-rbcS1 and rbcL2-rbcS2) of rbc operons has been demonstrated in Thiobacillus ferrooxidans Fe1 (T. Kusano, T. Takeshima, C. Inoue, and K. Sugawara, J. Bacteriol. 173:7313-7323, 1991). A possible regulatory gene, rbcR, 930 bp long and possibly translated into a 309-amino-acid protein, was found upstream from the rbcL1 gene as a single copy. The gene is located divergently to rbcL1 with a 144-bp intergenic sequence. As in the cases of the Chromatium vinosum RbcR and Alcaligenes eutrophus CfxR, T. ferrooxidans RbcR is thought to be a new member of the LysR family, and these proteins share 46.5 and 42.8% identity, respectively. Gel mobility shift assays showed that T. ferrooxidans RbcR, produced in Escherichia coli, binds specifically to the intergenic sequence between rbcL1 and rbcR. Footprinting and site-directed mutagenesis experiments further demonstrated that RbcR binds to overlapping promoter elements of the rbcR and rbcL1 genes. The above data strongly support the participation of RbcR in regulation of the rbcL1-rbcS1 operon and the rbcR gene in T. ferrooxidans.     

Identification of Thiobacillus ferrooxidans strains based on restriction fragment length polymorphism analysis of 16S rDNA.

The 16S rDNA sequences from ten strains of Thiobacillus ferrooxidans were amplified by PCR. The products were compared by performing restriction fragment length polymorphism (RFLP) analysis with restriction endonucleases Alu I, Hap II, Hha I, and Hae III. The RFLP patterns revealed that T. ferrooxidans could be distinguished from other iron- or sulphur-oxidizing bacteria such as T. thiooxidans NB1-3, T. caldus GO-1, Leptospirillum ferrooxidans and the marine iron-oxidizing bacterium strain KU2-11. The RFLP patterns obtained with Alu I, Hap II, and Hae III were the same for nine strains of T. ferrooxidans except for strain ATCC 13661. The RFLP patterns for strains NASF-1 and ATCC 13661 with Hha I were distinct from those for other T. ferrooxidans strains. The 16S rDNA sequence of T. ferrooxidans NASF-1 possessed an additional restriction site for Hha I. These results show that iron-oxidizing bacteria isolated from natural environments were rapidly identified as T. ferrooxidans by the method combining RFLP analysis with physiological analysis.     

Isolation and nucleotide sequence of the Thiobacillus ferrooxidans genes for the small and large subunits of ribulose 1,5-bisphosphate carboxylase/oxygenase

The genes encoding for the large (rbcL) and small (rbcS) subunits of ribulose-1,5-bisphosphate carboxylase (RuBisCO) were cloned from the obligate autotroph Thiobacillus ferrooxidans, a bacterium involved in the bioleaching of minerals. Nucleotide sequence analysis of the cloned DNA showed that the two coding regions are separated by a 30-bp intergenic region, the smallest described for the RuBisCO genes. The rbcL and rbcS genes encode polypeptides of 473 and 118 amino acids, respectively. Comparison of the nucleotide and amino acid sequences with those of the genes for rbcL and rbcS found in other species demonstrated that the T. ferrooxidans genes have the closest degree of identity with those of Chromatium vinosum and of Alvinoconcha hessleri endosymbiont. Both T. ferrooxidans enzyme subunits contain all the conserved amino acids that are known to participate in the catalytic process or in holoenzyme assembly.     

Genetic improvement of acidophilic bacteria for biohydrometallurgical applications

Abstract

Recent success in introducing foreign genetic information into Acidiphilium and Thiobacillus ferrooxidans have opened the possibility of the improvement of the bioleaching properties of acidophilic bacteria through genetic means. The use of electroporation to transform acidophilic bacteria, while effective for diverse genera of bacteria, is potentially limited by observed strain dependence within a given species. Bacterial mating or conjugation may prove more widely applicable, but has not yet been demonstrated in T. ferrooxidans. An arsenic‐resistant, broad‐host‐range plasmid has been constructed and introduced by conjugation into Acidiphilium. This recombinant organism is being examined to assess whether it might lead to improved arsenopyrite leaching rates in mixed cultures with chemolithotrophs such as T. ferrooxidans and Leptospirillum ferrooxidans.     

Pyruvate Inhibition of Ferrobacillus ferrooxidans Reversed by Rhodotorula Yeast

Ferrobacillus ferrooxidans was isolated in this laboratory from uranium ores mined at Jaduguda, Bihar. Investigations on a laboratory scale indicated that this organism could leach uranium from ores. Pyruvic acid (10^-4 M) was found to inhibit growth of F. ferrooxidans as well as leaching of uranium ore by F. ferrooxidans . However, in the presence of a red pigmented Rhodotorula yeast isolated from the same ores, the pyruvate inhibition was found to be reversed.     

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, T?, which is sensitive to the chemical environment. Fe3? ion has more significant T? shortening than Fe2? ion. In the presence of A. ferrooxidans in solutions containing Fe2? ion, T? 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 K?SO? medium, however, bacteria concentration remained almost unchanged and the iron oxidation rate was significantly lower.     

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.     

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.