Shifts in the Microbial Populations of Bioleach Reactors Are Determined by Carbon Sources and Temperature

In the present study, the effect of additional carbon sources (carbon dioxide and molasses) on the bio-oxidation of a pyrite-arsenopyrite concentrate at temperatures of 40-50 °C was studied, and novel data regarding the patterns of the bio-oxidation of gold-bearing sulfide concentrates and the composition of the microbial populations performing these processes were obtained. At 40 °C, additional carbon sources did not affect the bio-oxidation efficiency. At the same time, the application of additional carbon dioxide improved the bio-oxidation performance at temperatures of 45 and 50 °C and made it possible to avoid the inhibition of bio-oxidation due to an increase in the temperature. Therefore, the use of additional carbon dioxide may be proposed to prevent the negative effect of an increase in temperature on the bio-oxidation of sulfide concentrates. 16S rRNA gene profiling revealed archaea of the family Thermoplasmataceae (Acidiplasma, Ferroplasma, Cuniculiplasma, and A-plasma group) and bacteria of the genera Leptospirillum, with Sulfobacillus and Acidithiobacillus among the dominant groups in the community. Temperature influenced the composition of the communities to a greater extent than the additional sources of carbon and the mode of operation of the bioreactor. Elevating the temperature from 40 °C to 50 °C resulted in increases in the shares of Acidiplasma and Sulfobacillus and decreases in the relative abundances of Ferroplasma, Leptospirillum, and Acidithiobacillus, while Cuniculiplasma and A-plasma were more abundant at 45 °C. A metagenomic analysis of the studied population made it possible to characterize novel archaea belonging to an uncultivated, poorly-studied group of Thermoplasmatales which potentially plays an important role in the bio-oxidation process. Based on an analysis of the complete genome, we propose describing the novel species and novel genus as "Candidatus Carboxiplasma ferriphilum" gen. nov., spec. nov.

Bioleaching of Chalcopyrite Waste Rock in the Presence of the Copper Solvent Extractant LIX984N

Heap bioleaching, the solubilization of metal ions from metal sulfides by microbial oxidation, is often combined with solvent extraction (SX) and electrowinning to recover, e.g., copper from low-grade ores. After extraction, the leaching solution is recycled, but the entrained organic solvents may be toxic to the microorganisms. Here Acidithiobacillus ferrooxidans, Leptospirillum ferrooxidans, and Sulfobacillus thermosulfidooxidans were selected to perform bioleaching of chalcopyrite waste rock in the presence of the SX reagent (2.5% v/v LIX984N in kerosene). Possibly inhibitory effects have been evaluated by copper extraction, bacterial activity, number of actively Fe(II)-oxidizing cells, and biofilm formation. Microcalorimetry, most probable number determination, and atomic force microscopy combined with epifluorescence microscopy were applied. The results show that 100 and 300 mg/L SX reagent could hardly inhibit At. ferrooxidans from oxidizing Fe2+, but they seriously interfered with the biofilm formation and the oxidization of sulfur, thereby hindering bioleaching. L. ferrooxidans was sensitive to 50 mg/L SX reagent, which inhibited its bioleaching completely. Sb. thermosulfidooxidans showed different metabolic preferences, if the concentration of the SX reagent differed. With 10 mg/L LIX984N Sb. thermosulfidooxidans preferred to oxidize Fe2+ and extracted the same amount of copper as the assay without LIX984N. With 50 mg/L extractant the bioleaching stopped, since Sb. thermosulfidooxidans preferred to oxidize reduced inorganic sulfur compounds.

Carbon Sources as a Factor Determining the Activity of Microbial Oxidation of Sulfide Concentrate at Elevated Temperature

The goal of the present work was to evaluate the possibility of improving the efficiency of the stirred tank reactor biooxidation of sulfide gold-bearing concentrate by means of addition of carbon sources required for the constructive metabolism of microorganisms. Biooxidation experiments were performed on gold-bearing pyrite-arsenopyrite concentrate in continuous mode at 45 °C to determine the influence of additional carbon sources (carbon dioxide and molasses) on sulfide mineral oxidation. The use of CO2 allowed increasing the efficiency of the biooxidation and the extents of sulfide sulfur (Ss) oxidation and gold recovery were 79% and 84%, respectively. Biooxidation in a control experiment (without additional carbon sources) and when using molasses allowed achieving 39% and 66% oxidation of Ss as well as 73% and 81% of gold recovery. Analysis of the microbial populations formed in biooxidation reactors using NGS methods demonstrated that CO2 application led to an increase in the relative abundance of the genus Sulfobacillus. Thus, it was determined that application of additional carbon source makes it possible to manage the biooxidation process, affecting both sulfide mineral oxidation and microbial population composition.

Effect of Carbon Sources on Pyrite-Arsenopyrite Concentrate Bio-oxidation and Growth of Microbial Population in Stirred Tank Reactors

Tank bio-oxidation is a biohydrometallurgical technology widely used for metal recovery from sulfide concentrates. Since carbon availability is one of the key factors affecting microbial communities, it may also determine the rate of sulfide concentrate bio-oxidation. The goal of the present work was to evaluate the effect of carbon sources on the bio-oxidation of the concentrate containing 56% pyrite and 14% arsenopyrite at different temperatures (40 and 50 °C) in stirred tank reactors. CO2 was supplied into the pulp of the first reactor (about 0.01 L/min) and 0.02% (w/v) molasses was added to the pulp of the second one, and no additional carbon sources were used in the control tests. At 40 °C, 77% of pyrite and 98% of arsenopyrite were oxidized in the first reactor, in the second one, 73% of pyrite and 98% of arsenopyrite were oxidized, while in the control reactor, 27% pyrite and 93% arsenopyrite were oxidized. At 50 °C, in the first reactor, 94% of pyrite and 99% of arsenopyrite were oxidized, in the second one, 21% of pyrite and 94% of arsenopyrite were oxidized, while in the control reactor, 10% pyrite and 92% arsenopyrite were oxidized. The analysis of the microbial populations in the reactors revealed differences in the total number of microorganisms and their species composition. Thus, it was shown that the use of various carbon sources made it possible to increase the intensity of the concentrate bio-oxidation, since it affected microbial populations performing the process.

Effect of inoculum history, growth substrates and yeast extract addition on inhibition of Sulfobacillus thermosulfidooxidans by NaCl

This study reports on the effect of inoculum history, growth substrates, and yeast extract on sodium chloride tolerance of Sulfobacillus thermosulfidooxidans DSM 9293^T. The concentrations of NaCl for complete inhibition of Fe²⁺ oxidation by cells initially grown with ferrous iron sulfate, or tetrathionate, or pyrite as energy sources were 525 mM, 725 mM, and 800 mM, respectively. Noticeably, regardless of NaCl concentrations, oxygen consumption rates of S. thermosulfidooxidans with 20 mM tetrathionate were higher than with 50 mM FeSO₄. NaCl concentrations of higher than 400 mM strongly inhibited the iron respiration of S. thermosulfidooxidans. In contrast, the presence of NaCl was shown to stimulate tetrathionate oxidation. This trend was especially pronounced in NaCl-adapted cells where respiration rates at 200 mM NaCl were threefold of those in the absence of NaCl. In NaCl-adapted cultures greater respiration rates for tetrathionate were observed than in non-NaCl-adapted cultures, especially at concentrations ≥ 200 mM NaCl. At concentrations of ≤ 200 mM NaCl, cell growth and iron oxidation were enhanced with the addition of increasing concentrations of yeast extract. Thus, cell numbers in cultures with 0.05% yeast extract were ∼5 times higher than without yeast extract addition. At NaCl concentration as high as 400 mM, however, iron oxidation rates improved compared to control assays without yeast extract, but there was no clear dependence on yeast extract concentrations. The initial growth of bacteria with and without yeast extract in the presence of different NaCl concentrations was shown to impact leaching of copper from chalcopyrite. Copper dissolution was enhanced in the presence of 200 mM NaCl and absence of yeast extract, while the addition of 0.02% yeast extract was shown to promote copper solubilization in the presence of 500 mM NaCl.

Soil Microbiome Dynamics During Pyritic Mine Tailing Phytostabilization: Understanding Microbial Bioindicators of Soil Acidification

Challenges to the reclamation of pyritic mine tailings arise from in situ acid generation that severely constrains the growth of natural revegetation. While acid mine drainage (AMD) microbial communities are well-studied under highly acidic conditions, fewer studies document the dynamics of microbial communities that generate acid from pyritic material under less acidic conditions that can allow establishment and support of plant growth. This research characterizes the taxonomic composition dynamics of microbial communities present during a 6-year compost-assisted phytostabilization field study in extremely acidic pyritic mine tailings. A complementary microcosm experiment was performed to identify successional community populations that enable the acidification process across a pH gradient. Taxonomic profiles of the microbial populations in both the field study and microcosms reveal shifts in microbial communities that play pivotal roles in facilitating acidification during the transition between moderately and highly acidic conditions. The potential co-occurrence of organoheterotrophic and lithoautotrophic energy metabolisms during acid generation suggests the importance of both groups in facilitating acidification. Taken together, this research suggests that key microbial populations associated with pH transitions could be used as bioindicators for either sustained future plant growth or for acid generation conditions that inhibit further plant growth.

Two-step biohydrometallurgical technology of copper-zinc concentrate processing as an opportunity to reduce negative impacts on the environment

Polymetallic concentrates obtained during ore beneficiation pose a significant problem for the mining and metallurgy industry due to an increase in load on subsequent comminution steps and a high loss of metals in slag during smelting. Storage of such slag can lead to pollution of groundwater due to weathering. Biohydrometallurgy is an option for the processing of sulfidic raw materials that has a low impact on the environment. Processing of sulfidic concentrates of copper-zinc ore via bioleaching techniques was studied in this paper. Three mixed microbial cultures of acidophilic microorganisms were enriched from industrial mining sites: two autotrophic mesophilic cultures containing Acidithiobacillus ferroxidans and Leptospirillum spp. (grown at 30 and 35 °C), and a mixotrophic moderate thermophilic culture containing Sulfobacillus thermotolerans, Leptospirillum ferriphilum, as well as the archaea Ferroplasma acidiphilum and Acidiplasma spp. (grown at 40 °C). The autotrophic microbial culture growing at 30 °C was used to generate an iron-containing biosolution for ferric leaching of a copper-zinc concentrate. Zinc and iron extracted into solution faster than copper during high-temperature (80 °C) ferric leaching of the concentrate due to galvanic interactions between minerals, redox conditions of the medium, and differences between mineral oxidation mechanisms. Weight loss of the leach residue was 34.0%, with relative copper content increased by 1.0%, zinc content decreased by 6.18%, and iron content decreased by 15.1%. Biooxidation of ferrous iron in the pregnant leach solution by three microbial cultures was also studied. The most effective culture was moderate thermophilic. The results of studies on the bioregeneration of leaching solutions are relevant to the development of a two-step biohydrometallurgical technology for processing of copper-zinc concentrate with a closed cycle of technological flows. The ferrous iron biooxidation rate by the moderate thermophilic culture reached 20 g L^-1 day^-1. The leach residue obtained can be considered a high-grade copper concentrate able to be processed via smelting. This bioleaching process would make it possible to reduce pollution of groundwater by some toxic metals stored in slags. An environmentally friendly technology flow sheet for copper-zinc sulfidic ore processing using two-step bioleaching treatment was proposed.

Extremophiles in Mineral Sulphide Heaps: Some Bacterial Responses to Variable Temperature, Acidity and Solution Composition

In heap bioleaching, acidophilic extremophiles contribute to enhanced metal extraction from mineral sulphides through the oxidation of Fe(II) and/or reduced inorganic sulphur compounds (RISC), such as elemental sulphur or mineral sulphides, or the degradation of organic compounds derived from the ore, biota or reagents used during mineral processing. The impacts of variable solution acidity and composition, as well as temperature on the three microbiological functions have been examined for up to four bacterial species found in mineral sulphide heaps. The results indicate that bacteria adapt to sufficiently high metal concentrations (Cu, Ni, Co, Zn, As) to allow them to function in mineral sulphide heaps and, by engaging alternative metabolic pathways, to extend the solution pH range over which growth is sustained. Fluctuating temperatures during start up in sulphide heaps pose the greatest threat to efficient bacterial colonisation. The large masses of ores in bioleaching heaps mean that high temperatures arising from sulphide oxidation are hard to control initially, when the sulphide content of the ore is greatest. During that period, mesophilic and moderately thermophilic bacteria are markedly reduced in both numbers and activity.

Microbial life associated with low-temperature alteration of ultramafic rocks in the Leka ophiolite complex

Water-rock interactions in ultramafic lithosphere generate reduced chemical species such as hydrogen that can fuel subsurface microbial communities. Sampling of this environment is expensive and technically demanding. However, highly accessible, uplifted oceanic lithospheres emplaced onto continental margins (ophiolites) are potential model systems for studies of the subsurface biosphere in ultramafic rocks. Here, we describe a microbiological investigation of partially serpentinized dunite from the Leka ophiolite (Norway). We analysed samples of mineral coatings on subsurface fracture surfaces from different depths (10-160 cm) and groundwater from a 50-m-deep borehole that penetrates several major fracture zones in the rock. The samples are suggested to represent subsurface habitats ranging from highly anaerobic to aerobic conditions. Water from a surface pond was analysed for comparison. To explore the microbial diversity and to make assessments about potential metabolisms, the samples were analysed by microscopy, construction of small subunit ribosomal RNA gene clone libraries, culturing and quantitative-PCR. Different microbial communities were observed in the groundwater, the fracture-coating material and the surface water, indicating that distinct microbial ecosystems exist in the rock. Close relatives of hydrogen-oxidizing Hydrogenophaga dominated (30% of the bacterial clones) in the oxic groundwater, indicating that microbial communities in ultramafic rocks at Leka could partially be driven by H2 produced by low-temperature water-rock reactions. Heterotrophic organisms, including close relatives of hydrocarbon degraders possibly feeding on products from Fischer-Tropsch-type reactions, dominated in the fracture-coating material. Putative hydrogen-, ammonia-, manganese- and iron-oxidizers were also detected in fracture coatings and the groundwater. The microbial communities reflect the existence of different subsurface redox conditions generated by differences in fracture size and distribution, and mixing of fluids. The particularly dense microbial communities in the shallow fracture coatings seem to be fuelled by both photosynthesis and oxidation of reduced chemical species produced by water-rock reactions.

Kinetics of ferrous iron oxidation by batch and continuous cultures of thermoacidophilic Archaea at extremely low pH of 1.1-1.3

The extreme acid conditions required for scorodite (FeAsO₄·2H₂O) biomineralization (pH below 1.3) are suboptimal for growth of most thermoacidophilic Archaea. With the objective to develop a continuous process suitable for biomineral production, this research focuses on growth kinetics of thermoacidophilic Archaea at low pH conditions. Ferrous iron oxidation rates were determined in batch-cultures at pH 1.3 and a temperature of 75°C for Acidianus sulfidivorans, Metallosphaera prunea and a mixed Sulfolobus culture. Ferrous iron and CO₂ in air were added as sole energy and carbon source. The highest growth rate (0.066 h⁻¹) was found with the mixed Sulfolobus culture. Therefore, this culture was selected for further experiments. Growth was not stimulated by increase of the CO₂ concentration or by addition of sulphur as an additional energy source. In a CSTR operated at the suboptimal pH of 1.1, the maximum specific growth rate of the mixed culture was 0.022 h⁻¹, with ferrous iron oxidation rates of 1.5 g L⁻¹ d⁻¹. Compared to pH 1.3, growth rates were strongly reduced but the ferrous iron oxidation rate remained unaffected. Influent ferrous iron concentrations above 6 g L⁻¹ caused instability of Fe²⁺ oxidation, probably due to product (Fe³⁺) inhibition. Ferric-containing, nano-sized precipitates of K-jarosite were found on the cell surface. Continuous cultivation stimulated the formation of an exopolysaccharide-like substance. This indicates that biofilm formation may provide a means of biomass retention. Our findings showed that stable continuous cultivation of a mixed iron-oxidizing culture is feasible at the extreme conditions required for continuous biomineral formation.

Environmental, biogeographic, and biochemical patterns of archaea of the family Ferroplasmaceae

About 10 years ago, a new family of cell wall-deficient, iron-oxidizing archaea, Ferroplasmaceae, within the large archaeal phylum Euryarchaeota, was described. In this minireview, I summarize the research progress achieved since then and report on the current status of taxonomy, biogeography, physiological diversity, biochemistry, and other research areas involving this exciting group of acidophilic archaea.

Comparative characterization of the microbial diversities of an artificial microbialite model and a natural stromatolite

Microbialites are organosedimentary structures that result from the trapping, binding, and lithification of sediments by microbial mat communities. In this study we developed a model artificial microbialite system derived from natural stromatolites, a type of microbialite, collected from Exuma Sound, Bahamas. We demonstrated that the morphology of the artificial microbialite was consistent with that of the natural system in that there was a multilayer community with a pronounced biofilm on the surface, a concentrated layer of filamentous cyanobacteria in the top 5 mm, and a lithified layer of fused oolitic sand grains in the subsurface. The fused grain layer was comprised predominantly of the calcium carbonate polymorph aragonite, which corresponded to the composition of the Bahamian stromatolites. The microbial diversity of the artificial microbialites and that of natural stromatolites were also compared using automated ribosomal intergenic spacer analysis (ARISA) and 16S rRNA gene sequencing. The ARISA profiling indicated that the Shannon indices of the two communities were comparable and that the overall diversity was not significantly lower in the artificial microbialite model. Bacterial clone libraries generated from each of the three artificial microbialite layers and natural stromatolites indicated that the cyanobacterial and crust layers most closely resembled the ecotypes detected in the natural stromatolites and were dominated by Proteobacteria and Cyanobacteria. We propose that such model artificial microbialites can serve as experimental analogues for natural stromatolites.