From Laboratory towards Industrial Operation: Biomarkers for Acidophilic Metabolic Activity in Bioleaching Systems

In the actual mining scenario, copper bioleaching, mainly raw mined material known as run-of-mine (ROM) copper bioleaching, is the best alternative for the treatment of marginal resources that are not currently considered part of the profitable reserves because of the cost associated with leading technologies in copper extraction. It is foreseen that bioleaching will play a complementary role in either concentration-as it does in Minera Escondida Ltd. (MEL)-or chloride main leaching plants. In that way, it will be possible to maximize mines with installed solvent-extraction and electrowinning capacities that have not been operative since the depletion of their oxide ores. One of the main obstacles for widening bioleaching technology applications is the lack of knowledge about the key events and the attributes of the technology's critical events at the industrial level and mainly in ROM copper bioleaching industrial operations. It is relevant to assess the bed environment where the bacteria-mineral interaction occurs to learn about the limiting factors determining the leaching rate. Thus, due to inability to accurately determine in-situ key variables, their indirect assessment was evaluated by quantifying microbial metabolic-associated responses. Several candidate marker genes were selected to represent the predominant components of the microbial community inhabiting the industrial heap and the metabolisms involved in microbial responses to changes in the heap environment that affect the process performance. The microbial community's predominant components were Acidithiobacillus ferrooxidans, At. thiooxidans, Leptospirillum ferriphilum, and Sulfobacillus sp. Oxygen reduction, CO₂ and N₂ fixation/uptake, iron and sulfur oxidation, and response to osmotic stress were the metabolisms selected regarding research results previously reported in the system. After that, qPCR primers for each candidate gene were designed and validated. The expression profile of the selected genes vs. environmental key variables in pure cultures, column-leaching tests, and the industrial bioleaching heap was defined. We presented the results obtained from the industrial validation of the marker genes selected for assessing CO₂ and N₂ availability, osmotic stress response, as well as ferrous iron and sulfur oxidation activity in the bioleaching heap process of MEL. We demonstrated that molecular markers are useful for assessing limiting factors like nutrients and air supply, and the impact of the quality of recycled solutions. We also learned about the attributes of variables like CO₂, ammonium, and sulfate levels that affect the industrial ROM-scale operation.

[Phylogenetic and genetic heterogeneity of 23 Acidithiobacillus strains isolated from different geographical locations]

OBJECTIVE

To study the phylogenetic and genetic heterogeneity of 23 Acidithiobacillus strains from various geographical locations, as well as the relationship between the DNA fingerprinting classification and geographical origin of Acidithiobacillus.

METHODS

Partial 16S-23S rRNA gene intergenic spacer (ITS) was used to construct corresponding phylogenetic trees based on the sequence homology. rus gene amplification and rep-PCR assay with two different primers (BOXAIR and ERIC) were performed to analyze genetic heterogeneity of Acidithiobacillus strains from diverse environment.

RESULTS

Acidithiobacillus revealed a great genetic heterogeneity. The whole isolates were classified into five groups by ITS sequence analysis. This result was similar with that obtained by rep-PCR. Acidithiobacillus ferrooxidans strains were always divided into two groups of phylogenetic and BOXAIR fingerprinting cluster analysis. However, these were clustered one group in the ERIC dendrogram. Genotypic analysis of the rus gene suggested that different iron oxidation pathways have been evolved in these closely related bacteria. Taken together, the iron oxidation pathway of Acidithiobacillus and phylogenetic groups have no obvious correlation. ITS gene has been proven very useful in distinguishing closely related species or subspecies of Acidithiobacillus, to BOXAIR-PCR, which has been recommended as reliable tool for genetic heterogeneity analysis of Acidithiobacillus.

A Novel Uncultured Bacterium of the Family Gallionellaceae: Description and Genome Reconstruction Based on the Metagenomic Analysis of Microbial Community in Acid Mine Drainage

Drainage waters at the metal mining areas often have low pH and high content of dissolved metals due to oxidation of sulfide minerals. Extreme conditions limit microbial diversity in- such ecosystems. A drainage water microbial community (6.5'C, pH 2.65) in an open pit at the Sherlovaya Gora polymetallic open-cast mine (Transbaikal region, Eastern Siberia, Russia) was studied using metagenomic techniques. Metagenome sequencing provided information for taxonomic and functional characterization of the micro- bial community. The majority of microorganisms belonged to a single uncultured lineage representing a new Betaproteobacteria species of the genus Gallionella. While no.acidophiles are known among the cultured members of the family Gallionellaceae, similar 16S rRNA gene sequences were detected in acid mine drain- ages. Bacteria ofthe genera Thiobacillus, Acidobacterium, Acidisphaera, and Acidithiobacillus,-which are com- mon in acid mine drainage environments, were the minor components of the community. Metagenomic data were -used to determine the almost complete (-3.4 Mb) composite genome of the new bacterial. lineage desig- nated Candidatus Gallionella acididurans ShG14-8. Genome analysis revealed that Fe(II) oxidation probably involved the cytochromes localized on the outer membrane of the cell. The electron transport chain included NADH dehydrogenase, a cytochrome bc1 complex, an alternative complex III, and cytochrome oxidases of the bd, cbb3, and bo3 types. Oxidation of reduced sulfur compounds probably involved the Sox system, sul- fide-quinone oxidoreductase, adenyl sulfate reductase, and sulfate adenyltransferase. The genes required for autotrophic carbon assimilation via the Calvin cycle were present, while no pathway for nitrogen fixation was revealed. High numbers of RND metal transporters and P type ATPases were probably responsible for resis- tance to heavy metals. The new microorganism was an aerobic chemolithoautotroph of the group of psychrotolerant iron- and sulfur-oxidizing acidophiles of the family Gallionellaceae, which are common in acid mine drainages.

Generation of acid mine drainage around the Karaerik copper mine (Espiye, Giresun, NE Turkey): implications from the bacterial population in the Acısu effluent

The Karaerik Cu mine is a worked-out deposit with large volumes of tailings and slags which were left around the mine site without any protection. Natural feeding of these material and run-off water from the mineralised zones into the Acısu effluent causes a serious environmental degradation and creation of acid mine drainage (AMD) along its entire length. This research aims at modelling the formation of AMD with a specific attempt on the characterisation of the bacterial population in association with AMD and their role on its occurrence. Based on 16SrRNA analyses of the clones obtained from a composite water sample, the bacterial community was determined to consist of Acidithiobacillus ferrivorans, Ferrovum myxofaciens, Leptospirillum ferrooxidans and Acidithiobacillus ferrooxidans as iron-oxidising bacteria, Acidocella facilis, Acidocella aluminiidurans, Acidiphilium cryptum and Acidiphilium multivorum as iron-reducing bacteria, and Acidithiobacillus ferrivorans, Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans and Acidiphilium cryptum as sulphur-oxidising bacteria. This association of bacteria with varying roles was interpreted as evidence of a concomitant occurrence of sulphur and iron cycles during the generation of AMD along the Acısu effluent draining the Karaerik mine.

[Phylogenetic and diversity analysis of Acidithiobacillus spp. based on 16S rRNA and RubisCO genes homologues]

OBJECTIVE

The purpose of the study was to reveal geographic region-related Acidithiobacillus spp. distribution and allopatric speciation. Phylogenetic and diversity analysis was done to expand our knowledge on microbial phylogeography, diversity-maintaining mechanisms and molecular biogeography.

METHODS

We amplified 16S rRNA gene and RubisCO genes to construct corresponding phylogenetic trees based on the sequence homology and analyzed genetic diversity of Acidithiobacillus spp..

RESULTS

Thirty-five strains were isolated from three different regions in China (Yunnan, Hubei, Xinjiang). The whole isolates were classified into five groups. Four strains were identified as A. ferrivorans, six as A. ferridurans, YNTR4-15 Leptspirillum ferrooxidans and HBDY3-31 as Leptospirillum ferrodiazotrophum. The remaining strains were identified as A. ferrooxidans. Analysis of cbbL and cbbM genes sequences of representative 26 strains indicated that cbbL gene of 19 were two copies (cbbL1 and cbbL2) and 7 possessed only cbbL1. cbbM gene was single copy. In nucleotide-based trees, cbbL1 gene sequences of strains were separated into three sequence types, and the cbbL2 was similar to cbbL1 with three types. Codon bias of RubisCO genes was not obvious in Acidithiobacillus spp..

CONCLUSION

Strains isolated from three different regions in China indicated a great genetic diversity in Acidithiobacillus spp. and their 16S rRNA/RubisCO genes sequence was of significant difference. Phylogenetic tree based on 16S rRNA genes and RubisCO genes was different in Acidithiobacillus spp..

Enhanced dewaterability of anaerobically digested sewage sludge using Acidithiobacillus ferrooxidans culture as sludge conditioner

Role of Acidithiobacillus ferrooxidans culture in bioacidification and dewaterability of anaerobically digested sewage sludge (ADS) was investigated. A. ferrooxidans culture grown in 9K medium along with Fe(2+) produced iron flocculant containing, secondary iron minerals and biopolymeric substances as confirmed by FT-IR, XRD, and SEM-EDX. Bioacidification of ADS was performed using 10% (v/v) A. ferrooxidans culture, isolated cells and cell-free culture filtrate; and dewaterability was assessed using the capillary suction time (CST) and specific resistance to filtration (SRF). Isolated bacterial cells significantly (P<0.05) reduced the sludge dewaterability when supplemented with Fe(2+) while the whole culture and cell-free filtrate rapidly acidified the sludge without Fe(2+) and showed significant reduction of CST (71.3-73.5%) and SRF (84-88%). Results clearly indicated that the culture and filtrate of the A. ferrooxidans facilitated rapid sludge dewaterability while the cells supplemented with Fe(2+) also enhanced dewaterability but required 2-4 days.

[Isolation, identification and oxidizing characterization of an iron-sulfur oxidizing bacterium LY01 from acid mine drainage]

An acidophilic iron-sulfur oxidizing bacterium LY01 was isolated from acid mine drainage of coal in Guizhou Province, China. Strain LY01 was identified as Acidithiobacillusferrooxidans by morphological and physiological characteristics, and phylogenetic analysis of its 16S rRNA gene sequence. Strain LY01 was able to grow using ferrous ion (Fe2+), elemental sulfur (S0) and pyrite as sole energy source, respectively, but significant differences in oxidation efficiency and bacterial growth were observed when different energy source was used. When strain LY01 was cultured in 9K medium with 44.2 g x L(-1) FeSO4.7H2O as the substrate, the oxidation efficiency of Fe2+ was 100% in 30 h and the cell number of strain LY01 reached to 4.2 x 10(7) cell x mL(-1). When LY01 was cultured in 9K medium with 10 g x L(-1) S0 as the substrate, 6.7% S0 oxidation efficiency, 2001 mg x L(-1) SO4(2-) concentration and 8.9 x 10(7) cell x mL(-1) cell number were observed in 21 d respectively. When LY01 was cultured with 30 g x L(-1) pyrite as the substrate, the oxidation efficiency of pyrite, SO4(2-) concentration and cell number reached 10%, 4443 mg x L(-1) and 3.4 x 10(8) cell x mL(-1) respectively in 20 d. The effects of different heavy metals (Ni2+, Pb2+) on oxidation activity of strain LY01 cultured with pyrite were investigated. Results showed that the oxidation activity of strain LY01 was inhibited to a certain extent with the addition of Ni2+ at 10-100 mg x L(-1) to the medium, but the addition of 10-100 mg x L(-1) Pb2+ had no effect on LY01 activity.

Community genomic analysis of an extremely acidophilic sulfur-oxidizing biofilm

Highly acidic (pH 0-1) biofilms, known as 'snottites', form on the walls and ceilings of hydrogen sulfide-rich caves. We investigated the population structure, physiology and biogeochemistry of these biofilms using metagenomics, rRNA methods and lipid geochemistry. Snottites from the Frasassi cave system (Italy) are dominated (>70% of cells) by Acidithiobacillus thiooxidans, with smaller populations including an archaeon in the uncultivated 'G-plasma' clade of Thermoplasmatales (>15%) and a bacterium in the Acidimicrobiaceae family (>5%). Based on metagenomic evidence, the Acidithiobacillus population is autotrophic (ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), carboxysomes) and oxidizes sulfur by the sulfide-quinone reductase and sox pathways. No reads matching nitrogen fixation genes were detected in the metagenome, whereas multiple matches to nitrogen assimilation functions are present, consistent with geochemical evidence, that fixed nitrogen is available in the snottite environment to support autotrophic growth. Evidence for adaptations to extreme acidity include Acidithiobacillus sequences for cation transporters and hopanoid synthesis, and direct measurements of hopanoid membrane lipids. Based on combined metagenomic, molecular and geochemical evidence, we suggest that Acidithiobacillus is the snottite architect and main primary producer, and that snottite morphology and distributions in the cave environment are directly related to the supply of C, N and energy substrates from the cave atmosphere.

[Leaching of copper ore of the Udokanskoe deposit at low temperatures by an association of acidophilic chemolithotrophic microorganisms]

Pure cultures of indigenous microorganisms Acidithiobacillus ferrooxidans strain TFUd, Leptospirillum ferrooxidans strain LUd, and Sulfobacillus thermotolerans strain SUd have been isolated from the oxidation zone of sulfide copper ore of the Udokanskoe deposit. Regimes of bacterial-chemical leaching of ore have been studied over a temperature range from -10 to +20 degrees C. Effects of pH, temperature, and the presence of microorganisms on the extraction of copper have been shown. Bacterial leaching has been detected only at positive values of temperature, and has been much more active at +20 than at +4 degrees C. The process of leaching was more active when the ore contained more hydrophilic and oxidized minerals. The possibility of copper ore leaching of the Udokanskoe deposit using sulfuric acid with pH 0.4 at negative values of temperature and applying acidophilic chemolithotrophic microorganisms at positive values of temperature and low pH values was shown.

"Isolation, identification, characterization and polymetallic concentrate leaching studies of tryptic soy- and peptone-resistant thermotolerant Acidithiobacillus ferrooxidans SRDSM2"

Acidithiobacillus ferrooxidans strain SRDSM2 was isolated from silica containing soil sample collected at a Rajpardi lignite mine. The strain responded to the addition of 0.5 g/L peptone and 1.0 g/L tryptone soya broth in the ferrous sulphate tryptone soya broth (ITSB) medium with 35.3% and 29.6% increase in iron oxidation rate (IOR), but decrease in the IOR at higher peptone or tryptone soya broth levels. The presence of 4 mM of zinc as zinc sulphate in the medium increased the IOR by 24.4%. Forty percent of the inoculated cells survived even after exposure at 80 °C for 120 min and showed 30% ferrous iron oxidation. The Vmax and Ks for iron oxidation by the isolate were 344.82 mg/L/h and 32.25 g/L respectively. The isolate was able to oxidized ferrous iron even in presence of 4.06 M ionic strength of medium and leached>85% copper and zinc from the polymetallic concentrate. Thus, this isolate can be used for bioextraction of metals from polymetallic concentrate.

[Difference in acclimation of Acidithiobacillus ferrooxidans by various substrates and its effect on coal desulfurization efficiency]

In this study, Acidithiobacillus ferrooxidans LX5 was cultured in 9K medium with pyrite and ferrous sulfate as the substrates. Results showed that the number of A. ferrooxidans LX5 acclimated by pyrite for 20 d was 3.0 x 10(7) cell/mL in the liquid, and the oxidation activity to pyrite was stronger. A. ferrooxidans LX5 cultured for 48 h was 1.0 x 10(8) cell/mL in medium with FeSO4. Extracellular polymeric substance (EPS) produced from A. ferrooxidans LX5 acclimated by pyrite was 2 395 microg/(10(10) cells) three times as much as that cultured with FeSO4. A high-sulfur coal desulfurization experiment were carried out with A. ferrooxidans LX5 domesticated respectively in medium with ferrous sulfate and pyrite. The results showed that the coal desulfurization rate was up to 72.4% after bioleaching for 13 d by A. ferrooxidans LX5 acclimated by pyrite, at the same time, the desulfurization rate was only 47.2% with A. ferrooxidans LX5 cultured with ferrous sulfate and reached 65.8% in 20 d. Therefore, the desulfurization efficiency can be improved of coal and shorten the desulfurization time when A. ferrooxidans LX5 acclimated with pyrite as the substrate.

[Separation of magnetic bacteria by using a magnetic separator]

A magnetic separator was used to separate magnetic bacteria based on their magnetotactic characteristics. Acidithiobacillus ferrooxidans, a bacterium that could synthesize intra-cellular nanometer magnetic particles, was investigated as an example. Strong magnetic and weak magnetic cells were separated and collected. On average, the number of the magnetic particles present in the strong magnetic cells is more than that of the weak magnetic cells. Moreover, semisolid-plate magnetophoresis showed that the magnetotaxis of strong magnetic cells was stronger than the weak magnetic cells. These results suggest that the magnetic separator can be used to isolate the magnetic bacteria, which will facilitate the research of magnetic bacteria.

[Isolation, identification of Acidithiobacillus sp. and its role in the removal of heavy metals from contaminated sediments]

A sulfur-oxidizing bacterium FD97 was isolated from heavy metal-contaminated river sediments. According to the morphological characteristics and sequence analysis of 16S rDNA of FD97, the strain was identified as Acidithiobacillus sp.. The effects of temperature on heavy metals bioleaching efficiencies from contaminated sediments by using Acidithiobacillus sp. FD97 were investigated in shake flask experiments. The tests were performed at four different temperatures in the range of 22-40 degrees C. The results showed that after 16 days of bioleaching, almost 70% of Zn, 90% of Cu, and 25% of Cr could be removed from the sediments, respectively. From the variations of pH reduction, sulfate production, and metals removal, the order of bioleaching efficiency at different temperatures was 34 degrees C > 28 degrees C approximately to 40 degrees C > 22 degrees C. The preferable temperature used for the future larger-scale bioleaching process is 28 degrees C. It was found that during the bioleaching process, temperature did not directly affect the metal removal process; the final level of metal removal achieved was highly correlated to sediment pH. When the pH decreased to 5.0, 3.5, and 2.5, the removal of Zn, Cu, and Cr began to increase sharply, respectively, and the maximum metal removal could be achieved when the pH decreased to below 2.0.

Characterization of arsenic resistant and arsenopyrite oxidizing Acidithiobacillus ferrooxidans from Hutti gold leachate and effluents

Four arsenic resistant ferrous oxidizers were isolated from Hutti Gold Mine Ltd. (HGML) samples. Characterization of these isolates was done using conventional microbiological, biochemical and molecular methods. The ferrous oxidation rates with these isolates were 16, 48, 34 and 34 mg L(-1)h(-1) and 15, 47, 34 and 32 mg L(-1)h(-1) in absence and presence of 20 mM of arsenite (As3+) respectively. Except isolate HGM 8, other three isolates showed 2.9-6.3% inhibition due to the presence of 20 mM arsenite. Isolate HGM 8 was able to grow in presence of 14.7 g L(-1) of arsenite, with 25.77 mg L(-1)h(-1) ferrous oxidation rate. All the four isolates were able to oxidize iron and arsenopyrite from 20 g L(-1) and 40 g L(-1) refractory gold ore and 20 g L(-1) refractory gold concentrate. Once the growth was established pH adjustment was not needed inspite of ferrous oxidation, which could be due to concurrent oxidation of pyrite. Isolate HGM 8 showed the final cell count of as high as 1.12 x 10(8) cells mL(-1) in 40 g L(-1) refractory gold ore. The isolates were grouped into one haplotypes by amplified ribosomal DNA restriction analysis (ARDRA). The phylogenetic position of HGM 8 was determined by 16S rDNA sequencing. It was identified as Acidithiobacillus ferrooxidans and strain name was given as SRHGM 1.

[Gene function and microbial community structure in sulfide minerals bioleaching system based on microarray analysis]

Biohydrometallergy technology received more and more attention because of its simple process, low cost and kind to environment, especially in dealing with low-grade and complex minerals. However, it is difficult to optimize microorganism species and process parameters in bioleaching procedure because of the lack of suitable bacteria and quantitative analysis methods at micro-level for bioleaching system. This has resulted in the low efficiency and poor yield of the target metal in bioleaching. With the development of microarray and bacteria conservation technology, solutions to the above problems were being found. This article summarizes the latest findings on genetic elucidation and the community structure of microorganisms in sulfide minerals bioleaching system, in the aim of providing a better understanding on the significance of cross-field technology of biohydrometallergy and genomics.

An effective method of DNA extraction for bioleaching bacteria from acid mine drainage

An effective and versatile method for microorganism lysis and direct extraction of DNA from bioleaching bacteria was developed using pure cultures and an acid mine drainage (AMD) sediment sample. In the described method, microorganisms are treated at three different incubation temperatures: boiling water incubation for 6-10 min, followed by 60 +/- 5 degrees C for 30 min, then 72 degrees C for 30 min. The extracted DNA is purified using a phenol/chloroform/alcohol mixture and precipitated in absolute alcohol. The 16S ribosomal RNA (rRNA) and gyrB genes of the pure cultures were amplified using the polymerase chain reaction (PCR) and differentiated using repetitive intergenic DNA sequences amplification (Rep-PCR). For the AMD sediment sample, the 16S rRNA and gyrB genes of the amplicons were digested with Hin6I and MspI, and the restriction fragment length polymorphism analysis patterns were used as a fingerprint to discern community diversity. The results indicated that this method is a versatile, reproducible, effective, and rapid technique for routine DNA extraction from bioleaching bacteria. The low cost of this method also makes it attractive for large-scale studies.

Bacterial oxidation of ferrous iron at low temperatures

This study comprises the first report of ferrous iron oxidation by psychrotolerant, acidophilic iron-oxidizing bacteria capable of growing at 5 degrees C. Samples of mine drainage-impacted surface soils and sediments from the Norilsk mining region (Taimyr, Siberia) and Kristineberg (Skellefte district, Sweden) were inoculated into acidic ferrous sulfate media and incubated at 5 degrees C. Iron oxidation was preceded by an approximately 3-month lag period that was reduced in subsequent cultures. Three enrichment cultures were chosen for further work and one culture designated as isolate SS3 was purified by colony isolation from a Norilsk enrichment culture for determining the kinetics of iron oxidation. The 16S rRNA based phylogeny of SS3 and two other psychrotolerant cultures, SS5 from Norilsk and SK5 from Northern Sweden, was determined. Comparative analysis of amplified 16S rRNA gene sequences showed that the psychrotolerant cultures aligned within Acidithiobacillus ferrooxidans. The rate constant of iron oxidation by growing cultures of SS3 was in the range of 0.0162-0.0104 h(-1) depending on the initial pH. The oxidation kinetics followed an exponential pattern, consistent with a first order rate expression. Parallel iron oxidation by a mesophilic reference culture of Acidithiobacillus ferrooxidans was extremely slow and linear. Precipitates harvested from the 5 degrees C culture were identified by X-ray diffraction as mixtures of schwertmannite (ideal formula Fe(8)O(8)(OH)(6)SO(4)) and jarosite (KFe(3)(SO(4))(2)(OH)(6)). Jarosite was much more dominant in precipitates produced at 30 degrees C.

Extremely acidic, pendulous cave wall biofilms from the Frasassi cave system, Italy

The sulfide-rich Frasassi cave system hosts an aphotic, subsurface microbial ecosystem including extremely acidic (pH 0-1), viscous biofilms (snottites) hanging from the cave walls. We investigated the diversity and population structure of snottites from three locations in the cave system using full cycle rRNA methods and culturing. The snottites were composed primarily of bacteria related to Acidithiobacillus species. Other populations present in the snottites included Thermoplasmata group archaea, bacteria related to Sulfobacillus, Acidimicrobium, and the proposed bacterial lineage TM6, protists, and filamentous fungi. Based on fluorescence in situ hybridization population counts, Acidithiobacillus are key members of the snottite communities, accompanied in some cases by smaller numbers of archaea related to Ferroplasma and other Thermoplasmata. Diversity estimates show that the Frasassi snottites are among the lowest-diversity natural microbial communities known, with one to six prokaryotic phylotypes observed depending on the sample. This study represents the first in-depth molecular survey of cave snottite microbial diversity and population structure, and contributes to understanding of rapid limestone dissolution and cave formation by microbially mediated sulfuric acid speleogenesis.

[Biodiversity of acidophiles in the sediment at an acid mine drainage site]

A sediment sample was collected at an acid mine drainage site in Anhui. The acidophiles composition and community structure in the sediment was studied with 16S rDNA clone library and denaturing gradient gel electrophoresis (DGGE). The results indicated that the acidophiles in the sediment were novel compared with the data in GenBank. The acidophiles affiliated with Acidobacteria, beta/gamma-Proteobacteria, delta-Proteobacteria, Nitrospira, Candidate Division TM7, low G + C Gram-positive. delta-Proteobacteria were major group in this acidic ecosystem. The research of aicdophiles community in sediment can help us develop high efficient method to treat acid mine drainage (AMD).

Evaluation of in situ layers for treatment of acid mine drainage: a field comparison

Reactive treatment layers, containing labile organic carbon, were evaluated to determine their ability to promote sulfate reduction and metal sulfide precipitation within a tailings impoundment, thereby treating tailings effluent prior to discharge. Organic carbon materials, including woodchips and pulp waste, were mixed with the upper meter of tailings in two separate test cells, a third control cell contained only tailings. In the woodchip cell sulfate reduction rates were 500 mg L-1a-1, (5.2 mmol L-1a-1) this was coupled with the gradual removal of 350 mg L-1 Zn (5.4 mmol L-1). Decreased delta13CDIC values from -3 per thousand to as low as -12 per thousand indicated that sulfate reduction was coupled with organic carbon oxidation. In the pulp waste cell the most dramatic change was observed near the interface between the pulp waste amended tailings and the underlying undisturbed tailings. Sulfate reduction rates were 5000 mg L-1a-1 (52 mmol L-1a-1), Fe concentrations decreased by 80-99.5% (148 mmol L-1) and Zn was consistently <5 mg L-1. Rates of sulfate reduction and metal removal decreased as the pore water migrated upward into the shallower tailings. Increased rates of sulfate reduction in the pulp waste cell were consistent with decreased delta13CDIC values, to as low as -22 per thousand, and increased populations of sulfate reducing bacteria. Lower concentrations of the nutrients, phosphorus, organic carbon and nitrogen in the woodchip material contribute to the lower sulfate reduction rates observed in the woodchip cell.

Acidophilic microbial communities catalyzing sludge bioleaching monitored by fluorescent in situ hybridization

Biological autotrophic sulfur oxidation processes have been proposed to remove heavy metals from wastewater treatment sludge by bioleaching. We made a characterization of the microbial population in batch and continuous sludge bioleaching reactors using fluorescent in situ hybridization of fluorescently-labeled oligonucleotidic probes targeting rRNA in a 'top to bottom approach'. Batch incubations of sludge with 0.2% (w/v) elemental sulfur resulted in a pH value of 5. Alpha-Proteobacteria hybridizing with probe ALF1b were dominant in this incubation. Members of the Acidophilium-group (hybridizing with probe Acdp821) of Nitrospira/Leptospirillum phylum (Ntspa712 probe) and from the archaeal domain (ARCH915) were also detected. When sludge was incubated with 1% elemental sulfur in batch or continuous reactor experiments, final pH values were always below 2. Active microbial communities consisted almost exclusively of gamma-Proteobacteria (hybridizing with probe GAM42a). However, further hybridization experiments with probe Thio820 targeting Acidithiobacillus ferroxidans and Acidithiobacillus thioxidans gave negative results. A new probe, named THIO181, encompassing all known members of the genus was designed. Hybridization perfomed with THIO181 and GAM42a showed a perfect co-localization of the hybridization signals. Further hybridization experiments with probe THIO181 and THC642, specific for the species Acidithiobacillus caldus, confirmed that this bacteria was largely responsible for the sulfur oxidation reaction in our acidophilic sludge bioleaching reactors.

Acidithiobacillus ferrooxidans fixation on mercuric surfaces and its application in stripping voltammetry

The adsorption (fixation) of bacteria Acidithiobacillus ferrooxidans on Hg and Cu metallic surfaces was qualitatively studied owing to two independent methods: frequency measurement using a quartz crystal microbalance and light absorption measuring at the Hg/bacterial culture interface. A method using a dropping mercury electrode (DME) allowed quantifying this bacterial fixation. Determining the superficial tension at Hg/bacterial culture interface led to determine bacteria adsorption on Hg through the Gibbs isotherm. A modified stripping voltammetry was proposed taking benefit of both bacterial adsorption on Hg surface and metal fixation capacity on biomass. Metal preconcentration on the biologically modified Hg electrode appeared to improve the measurement sensitivity of differential pulse anodic stripping voltammetry (DPASV). The height of the detected peaks was thus increased of 17.6% for copper, 48.4% for lead, and 132% for cadmium determinations compared to those obtained with an unmodified mercury electrode. Such augmentation depended on bulk bacteria concentration and bacteria preconcentration.

Bacterial sensors based on Acidithiobacillus ferrooxidans

The aerobic acidophilic bacterium Acidithiobacillus ferrooxidans oxidizes Fe(2+) and S(2)O(3)(2-) ions by consuming oxygen. An amperometric biosensor was designed including an oxygen probe as transducer and a recognition element immobilized by a suitable home-made membrane. This biosensor was used for the indirect amperometric determination of Cr(2)O(7)(2-) ions owing to methods based on a mediator (Fe(2+)) or titration. Using the mediator, the biosensor response versus Cr(2)O(7)(2-) was linear up to 0.4 mmol L(-1), with a response time of, respectively, 51 s (2 x 10(-5) mol L(-1) Cr(2)O(7)(2-)) and 61 s (6 x 10(-5) mol L(-1) Cr(2)O(7)(2-)). The method sensitivity was 816 microA L mol(-1). Response time and measurement sensitivity depended on membrane material and technique for biomass immobilization. For example, their values were 90 s-200 microA L mol(-1) when using a glass-felt membrane and 540 s-4.95 microA L mol(-1) with a carbon felt one to determine a concentration of 2 x 10(-5) mol L(-1) Cr(2)O(7)(2-). For the titration method, the biosensor is used to determine the equivalence point. The relative error of quantitative analysis was lower than 5%.

Bacterial sensors based on Acidithiobacillus ferrooxidans

An amperometric bacterial sensor with current response to Fe(2+) and S(2)O(3)(2-) ions has been designed by immobilizing an acidophilic biomass of Acidithiobacillus ferrooxidans on a multi disk flat-front oxygen probe. The bacterial layer was located between the oxygen probe and a membrane of cellulose. A filtration technique was used to yield the bacterial membranes having reproducible activity. The decrease of O(2) flow across the bacterial layer is proportional to the concentration of the dosed species. The dynamic range appeared to be linear for the Fe(2+) ions up to 2.5 mmol L(-1) with a detection limit of 9 x 10(-7) mol L(-1) and a sensitivity of 0.25 A L mol(-1). The response of the biosensor is 84 s for a determination of 2 x 10(-4) mol L(-1) Fe(2+). Optimizing the Fe(2+) determination by A. ferrooxidans sensor was carried out owing to Design of Experiments (DOE) methodology and empirical modelling. The optimal response was thus obtained for a pH of 3.4, at 35 degrees C under 290 rpm solution stirring. S(2)O(3)(2-) concentration was determined at pH 4.7, so avoiding its decomposition. The concentration range was linear up to 0.6 mmol L(-1). Sensitivity was 0.20 A L mol(-1) with a response time of 207 s for a 2 x 10(-4) mol L(-1) S(2)O(3)(2-) concentration.

Assessment of the microbial community in a constructed wetland that receives acid coal mine drainage

Constructed wetlands are used to treat acid drainage from surface or underground coal mines. However, little is known about the microbial communities in the receiving wetland cells. The purpose of this work was to characterize the microbial population present in a wetland that was receiving acid coal mine drainage (AMD). Samples were collected from the oxic sediment zone of a constructed wetland cell in southeastern Ohio that was treating acid drainage from an underground coal mine seep. Samples comprised Fe(III) precipitates and were pretreated with ammonium oxalate to remove interfering iron, and the DNA was extracted and purified by agarose gel electrophoresis prior to amplification of portions of the 16S rRNA gene. Amplified products were separated by denaturing gradient gel electrophoresis and DNA from seven distinct bands was excised from the gel and sequenced. The sequences were matched to sequences in the GenBank bacterial 16S rDNA database. The DNA in two of the bands yielded matches with Acidithiobacillus ferrooxidans and the DNA in each of the remaining five bands was consistent with one of the following microorganisms: Acidithiobacillus thiooxidans, strain TRA3-20 (a eubacterium), strain BEN-4 (an arsenite-oxidizing bacterium), an Alcaligenes sp., and a Bordetella sp. Low bacterial diversity in these samples reflects the highly inorganic nature of the oxic sediment layer where high abundance of iron- and sulfur-oxidizing bacteria would be expected. The results we obtained by molecular methods supported our findings, obtained using culture methods, that the dominant microbial species in an acid receiving, oxic wetland are A. thiooxidans and A. ferrooxidans.

Diversity of 16S ribosomal DNA-defined bacterial population in acid rock drainage from Japanese pyrite mine

Four acidophilic bacteria (YARDs1-4) were isolated from an acid rock drainage (ARD) from Yanahara mine, Okayama prefecture, Japan. The physiological and 16S rDNA sequence analyses revealed that YARD1 was closely affiliated with Acidithiobacillus ferrooxidans, YARD2 was an Acidiphilium-like bacterium, and YARD3 and YARD4 were sulfur-oxidizing bacteria with a relatively close relationship to A. ferrooxidans in the phylogenetic analysis. A molecular approach based on the construction of a 16S rDNA clone library was used to investigate the microbial population of the ARD. Small-subunit rRNA genes were PCR amplified, subsequently cloned and screened for variation by a restriction fragment length polymorphism (RFLP) analysis. A total of 284 clones were grouped into 133 operational taxonomic units (OTUs) by the RFLP analysis. Among them, an OTU showing the same RFLP pattern as those of the isolates from the ARD was not detected. The phylogenetic analysis based on the 16S rDNA sequences from 10 major OTUs and their close relatives revealed that 4 OTUs containing 32.1% of the total clones were loosely affiliated with Verrucomicrobia, 2 OTUs containing 6.6% of the total clones were loosely affiliated with Chloribi, and other OTUs were affiliated with Actinobacteria, Nitrospirae, and beta-Proteobacteria.

A simple procedure for elimination of fungal contamination for enumeration of iron-oxidizing bacteria from bioleaching matrix of sewage sludge

Enumeration of iron-oxidizing bacteria from the bioleaching matrix of sewage sludge is always confronted by fungal contamination. The objective of the present study was to find a reliable and simple method to remove fungal growth and to shorten the incubation time for facilitating enumeration of the iron-oxidizers from complex sludge samples. The results demonstrated that filtering the sludge sample through sterile No. 5 Whatman filter paper before serial dilution was effective in eliminating the fungal growth on agarose media. Both the counts and the incubation time required for enumeration were highly dependent on the medium pH, with maximum counts at pH 2.5–2.75. Medium prepared at pH values outside of this range led to lower counts and a longer lag time for colony formation. However, the introduction of heterotrophic microorganisms into the solid medium did not show further improvement in enumeration efficiency and shortening of the incubation period. By incorporating the optimal conditions obtained, the incubation time could be reduced to 7 and 10 d for pure cultures and sludge samples, respectively.Key words: Acidithiobacillus ferrooxidans, iron-based bioleaching process, growth media, sewage sludge.

Existence of an iron-oxidizing bacterium Acidithiobacillus ferrooxidans resistant to organomercurial compounds

Acidithiobacillus ferrooxidans MON-1 which is highly resistant to Hg2+ could grow in a ferrous sulfate medium (pH 2.5) with 0.1 microM p-chloromercuribenzoic acid (PCMB) with a lag time of 2 d. In contrast, A. ferrooxidans AP19-3 which is sensitive to Hg2+ did not grow in the medium. Nine strains of A. ferrooxidans, including seven strains of the American Type Culture Collection grew in the medium with a lag time ranging from 5 to 12 d. The resting cells of MON-1, which has NADPH-dependent mercuric reductase activity, could volatilize Hg0 when incubated in acidic water (pH 3.0) containing 0.1 microM PCMB. However, the resting cells of AP19-3, which has a similar level of NADPH-dependent mercuric reductase activity compared with MON-1, did not volatilize Hg0 from the reaction mixture with 0.1 microM PCMB. The activity level of the 11 strains of A. ferrooxidans to volatilize Hg0 from PCMB corresponded well with the level of growth inhibition by PCMB observed in the growth experiments. The resting cells of MON-1 volatilized Hg0 from phenylmercury acetate (PMA) and methylmercury chloride (MMC) as well as PCMB. The cytosol prepared from MON-1 could volatilize Hg0 from PCMB (0.015 nmol mg(-1) h(-1)), PMA (0.33 nmol mg(-1) h(-1)) and MMC (0.005 nmol mg(-1) h(-1)) in the presence of NADPH and beta-mercaptoethanol.

Detection of Acidithiobacillus ferrooxidans in acid mine drainage environments using fluorescent in situ hybridization (FISH)

An important microorganism of acid mine drainage (AMD) and bioleaching environments is Acidithiobacillus ferrooxidans which oxidizes ferrous iron and generates ferric iron, an oxidant. Most investigations to understand microbial aspects of sulfide mineral dissolution have focused on understanding physiological, metabolic, and genetic characteristics of A. ferrooxidans. In this study, a 16S rRNA oligonucleotide probe designated S-S-T.ferr-0584-a-A-18, and labeled at the 5'-end with indocarbocyanine dye (CY3), was used in a fluorescent in situ hybridization (FISH) procedure on pure cultures of nine isolates of A. ferrooxidans. These isolates were recovered from acid mine drainage and mining environments. The probe was also used to detect cells of A. ferrooxidans, recovered from AMD samples, growing on FeTSB and FeSo solid media in a FISH procedure. In addition, the presence of cells of A. ferrooxidans in an environmental water sample from an AMD site in Copper Cliff, Ontario, Canada was analyzed using the FISH technique. Probe specificity was first confirmed with A. ferrooxidans ATCC 19859 (positive control) and Acidithiobacillus thiooxidans ATCC 19377, Acidiphilium acidophilum ATCC 27807, and Lactobacillus plantarum ATCC 8014 (negative controls). Positive and negative control cells were also used to determine optimal stringency conditions for hybridizations with the probe. Cells of the nine isolates of A. ferrooxidans stained positive, although the fluorescent signal varied in intensity from isolate to isolate. Colonies of A. ferrooxidans from the environmental water sample of the AMD site were recovered only on FeTSB solid medium after 22 days of incubation. The probe was able to detect cells of A. ferrooxidans in a FISH procedure. However, no cells of A. ferrooxidans were detected in the AMD water sample without cultivation. Thus, probe S-S-T.ferr-0584-a-A-18 hybridized effectively with cells of A. ferrooxidans recovered from pure cultures but failed to directly detect cells of A. ferrooxidans in the AMD site.

[Isolation of heterotrophic microorganism and its role in bioleaching of heavy metals from tannery sludge]

A heterotrophic microorganism was isolated from sewage sludge, it was identified as Rhodotorula sp. R30. Its optimum pH for growth was 3-7, but it can stand the acidity of pH 2.5-1.5. The optimum temperature was 28 degrees C. When R30 was inoculated in the medium containing dissolved organic matter derived from sewage sludge and incubated for 96 h, dissolved organic carbon in the medium declined from 1485 mg/L to 345 mg/L, and the yeast number was 4.8 x 10(7) mL(-1). It was found through the batch trial that the period of bioleaching could be apparently shorted to 4 days if R30 was inoculated in the bioleaching system. Furthermore, the removal efficiency of Cr in sewage sludge could be enhanced by 39% with compared to the control without inoculating R30.

Selective separation of pyrite and chalcopyrite by biomodulation

Selective separation of pyrite from other associated ferrous sulphides at acidic and neutral pH has been a challenging problem. This paper discusses the utility of Acidithiobacillus ferrooxidans for the selective flotation of chalcopyrite from pyrite. Consequent to interaction with bacterial cells, pyrite remained depressed even in the presence of potassium isopropyl xanthate collector while chalcopyrite exhibited significant flotability. However, when the minerals were conditioned together, the selectivity achieved was poor due to the activation of pyrite surface by the copper ions in solution. The selectivity was improved when the sequence of conditioning with bacterial cells and collector was reversed, since the bacterial cells were able to depress collector interacted pyrite effectively, while having negligible effect on chalcopyrite. The observed behaviour is analysed and discussed in detail. The separation obtained was significant both at acidic and alkaline pH. This selectivity achieved was retained when the minerals were interacted with both bacterial cells and collector simultaneously.