Progress in bioleaching: fundamentals and mechanisms of bacterial metal sulfide oxidation—part A

A review of greener approaches for rare earth elements recovery from mineral wastes

The use of rare earth elements (REE) in many various fields, including high-tech products, increases the demand for these materials day by day. The production of REE from primary sources has expanded in response to increasing demand; however, due to its limited, a more sustainable supply is also started to offer for the REE demand by using secondary sources. The most commonly used metallurgical method for REE recovery is hydrometallurgical processes. However, it has some disadvantages, like pyrometallurgical methods. In the review, studies of the environmental impacts of REE production from primary sources and life cycle assessments of products containing REE were investigated. According to the results, it has been seen that those studies in the literature in which hydrometallurgical methods have changed to more environmentally friendly approaches have begun to increase. In this review, mine wastes, which are secondary sources, were defined, conventional methods of recovery of rare earth elements were discussed, greener approaches to the recovery of REE from these sources were comprehensively examined and studies in the literature were evaluated. Furthermore, it was stated that there are limited studies on green approaches and REE recovery from mineral wastes and that this field is developing with an emphasis on the current outlook and future perspectives.

Synthetic microbiology in sustainability applications

Microorganisms are a promising means to address many societal sustainability challenges owing to their ability to thrive in diverse environments and interface with the microscale chemical world via diverse metabolic capacities. Synthetic biology can engineer microorganisms by rewiring their regulatory networks or introducing new functionalities, enhancing their utility for target applications. In this Review, we provide a broad, high-level overview of various research efforts addressing sustainability challenges through synthetic biology, emphasizing foundational microbiological research questions that can accelerate the development of these efforts. We introduce an organizational framework that categorizes these efforts along three domains - factory, farm and field - that are defined by the extent to which the engineered microorganisms interface with the natural external environment. Different application areas within the same domain share many fundamental challenges, highlighting productive opportunities for cross-disciplinary collaborations between researchers working in historically disparate fields.

Novel insights into the kinetics and mechanism of arsenopyrite bio-dissolution enhanced by pyrite

Arsenopyrite and pyrite often coexist in metal deposits and tailings, thus simultaneous bioleaching of both sulfides has economic (as well as environmental) significance. Important targets in bio-oxidation operations are high solubilization rates and minimized accumulation of Fe(III)/As-bearing secondary products. This study investigated the role of pyrite bioleaching in the enhancement of arsenopyrite dissolution. At a pyrite to arsenopyrite mass ratio of 1:1, 93.6% of As and 93.0% of Fe were solubilized. The results show that pyrite bio-oxidation can promote arsenopyrite dissolution, enhance S0 bio-oxidation, and inhibit the formation of jarosites, tooeleite, and amorphous ferric arsenate. The dry weight of the pyrite & arsenopyrite residue was reduced by 95.1% after bioleaching, compared to the initial load, while only 5% weight loss was observed when pyrite was absent. A biofilm was formed on the arsenopyrite surface in the presence of pyrite, while a dense passivation layer was observed in the absence of pyrite. As(III) (as As2O3) was a dominant As species in the pyrite & arsenopyrite residue. Novel and detailed findings are presented on arsenopyrite bio-dissolution in the presence of pyrite, and the presented approach could contribute to the development of novel cost-effective extractive bioprocesses. ENVIRONMENTAL IMPLICATION: The oxidation of arsenopyrite presents significant environmental hazards, as it can contribute to acid mine drainage generation and arsenic mobilization from sulfidic mine wastes. Bioleaching is a proven cost-effective and environmentally friendly extractive technology, which has been applied for decades in metal recovery from minerals or tailings. In this work, efficient extraction of arsenic from arsenopyrite bioleaching was presented through coupling the process with bio-oxidation of pyrite, resulting in lowered accumulation of hazardous and metastable Fe(III)/As-bearing secondary phases. The results could help improve current biomining operations and/or contribute to the development of novel cost-effective bioprocesses for metal extraction.

Bioreactor Expansion Affects Microbial Succession of Mixotrophic Acidophiles and Bioremediation of Cadmium-Contaminated Soils

Microbial scale-up cultivation is the first step to bioremediating cadmium (Cd)-contaminated soils at the industrial scale. However, the changes in the microbial community as the bioreactor volume expands and their associations with soil Cd removal remain unclear. Herein, a six-stage scale-up cultivation process of mixotrophic acidophiles was conducted, scaling from 0.1 L to 10 m3, to remediate Cd-contaminated soils. The findings showed that bioreactor expansion led to a delay in sulfur and glucose oxidations, resulting in a reduced decline in solution pH and cell density. There were minimal differences observed in bacterial alpha-diversity and community structure as the bioreactor volume increased, except for the 10 m3 scale. However, bioreactor expansion decreased fungal alpha-diversity, changed the community structure, and simplified fungal community compositions. At the family level, Acidithiobacillaceae and Debaryomycetaceae dominated the bacterial and fungal communities throughout the scale-up process, respectively. Correlation analysis indicated that the indirect effect of mixotrophic acidophiles played a significant role in soil Cd removal. Bacterial community shifts, driven by changes in bioreactor volume, decreased the pH value through sulfur oxidation, thereby indirectly enhancing Cd removal efficiency. This study will contribute to the potential industrial application of mixotrophic acidophiles in bioremediating Cd-contaminated soils.

Comprehensive review on recent trends and perspectives of natural exo-polysaccharides: Pioneering nano-biotechnological tools

Exopolysaccharides (EPSs), originating from various microbes, and mushrooms, excel in their conventional role in bioremediation to showcase diverse applications emphasizing nanobiotechnology including nano-drug carriers, nano-excipients, medication and/or cell encapsulation, gene delivery, tissue engineering, diagnostics, and associated treatments. Acknowledged for contributions to adsorption, nutrition, and biomedicine, EPSs are emerging as appealing alternatives to traditional polymers, for biodegradability and biocompatibility. This article shifts away from the conventional utility to delve deeply into the expansive landscape of EPS applications, particularly highlighting their integration into cutting-edge nanobiotechnological methods. Exploring EPS synthesis, extraction, composition, and properties, the discussion emphasizes their structural diversity with molecular weight and heteropolymer compositions. Their role as raw materials for value-added products takes center stage, with critical insights into recent applications in nanobiotechnology. The multifaceted potential, biological relevance, and commercial applicability of EPSs in contemporary research and industry align with the nanotechnological advancements coupled with biotechnological nano-cleansing agents are highlighted. EPS-based nanostructures for biological applications have a bright future ahead of them. Providing crucial information for present and future practices, this review sheds light on how eco-friendly EPSs derived from microbial biomass of terrestrial and aquatic environments can be used to better understand contemporary nanobiotechnology for the benefit of society.

Nano-mineral assemblages in mercury- and silver-contaminated soils: records of sequestration, transformation, and release of mercury- and silver-bearing nanoparticles

Mercury-bearing nano-mineral assemblages (Hg-NMAs) are chemically and mineralogically heterogeneous, micrometer-sized aggregates of nanoparticles (NPs) found in contaminated soils and sediments. Although these NMAs control sequestration and release of Hg that is a global contaminant, our understanding is limited with respect to the conditions of different types of Hg-NMAs, the diversity of its minerals, the size distribution of its NPs and whether mineral replacement and alteration reactions in these NMAs result in the release of Hg-bearing NPs. For this purpose, Hg-NMAs in four sediment samples from the Guanajuato Mining District (GMD) in Mexico, a region that was polluted by Hg and silver (Ag) due to historical mining involving Hg amalgamation, are characterized at the micro- and nanoscale. Microscale examinations with SEM show that the majority of Hg-NMAs occurs in mineral surface coatings (MSC) and fillings in fractures within quartz grains and are enriched in Hg and sulfur (S) relative to Ag, and in S and selenium (Se) relative to chloride (Cl). Examinations at the nanoscale show that Hg-NMAs contain (a) residuals of the patio process such as amalgam phases and elemental Ag; (b) associations of Hg- and Ag-sulfide NPs with pyrite and marcasite; (c) associations of Hg- and Ag-sulfide NPs with goethite and clay minerals along the rims of the MSC. The latter minerals replaced the Fe-Si-rich matrix at high-water rock ratios most likely due to an increase in porosity during flooding of the Pastita River. Consequently, the rims are depleted in Hg-Ag-sulfide NPs relative to the unaltered Fe-Si-rich matrices indicating that changes in the physiochemical conditions of soils and sediments in the GMD can result in the release of Hg-Ag-bearing NPs. In this context, this study discusses whether release and dissolution of Hg-Ag-bearing NPs contribute to the recently observed elevated gaseous elemental Hg concentrations in the soil, interstitial air and ambient air, and to the fate and effects of Hg in local aquatic environments.

Alumina inhibits pyrite oxidative dissolution by regulating solid film passivation layer and S, Fe, and Al speciation transformation

The oxidation of pyrite results in the formation of a solid film passivation layer on its surface. This layer effectively hinders the direct interaction between H2O, O2, and the pyrite surface, thereby impeding the oxidation dissolution of pyrite. There are few studies on whether alumina (Al2O3), a common aluminum-containing oxide, affects the formation of a solid film passivation layer on the surface of pyrite and inhibits the oxidation dissolution of pyrite. This research investigates the impact of Al2O3 incorporation on the speciation transformation of S, Fe, and Al on the surface of pyrite during oxygen pyrite process. The oxidation of pyrite followed the "polysulfide-thiosulfate" complex oxidation pathway. When <1.5 g/L Al2O3 was introduced, it increase pyrite oxidation, whereas ≥1.5 g/L Al2O3 prevented pyrite oxidation. The process of Al2O3 dissolution results in the consumption of H+ and the subsequent release of Al3+. This, in turn, facilitates the hydrolysis of Fe3+ and Al3+ to generate a secondary mineral layer on the pyrite surface. As a result of the accumulation of S promotes the formation of polysulfide chemical (FeSn) or iron deficiency sulfide (Fe1-xS), resulting in the formation of a solid film passivation layer composed of sulfur film and secondary mineral layer. The results demonstrated that Al2O3 can promote the formation of a solid film passivation layer on the surface of pyrite, which has significant implications for controlling the oxidation dissolution process of pyrite and offers a new perspective for the source control of acid mine drainage.

Acidithiobacillus species drive the formation of ferric-silica cemented microstructure: Insights into early hardpan development for mine site rehabilitation

Hardpan-based profiles naturally formed under semi-arid climatic conditions have substantial potential in rehabilitating sulfidic tailings, resulting from their aggregation microstructure regulated by Fe-Si cements. Nevertheless, eco-engineered approaches for accelerating the formation of complex cementation structure remain unclear. The present study aims to investigate the microbial functions of extremophiles on mineral dissolution, oxidation, and aggregation (cementation) through a microcosm experiment containing pyrites and polysilicates, of which are dominant components in typical sulfidic tailings. Microspectroscopic analysis revealed that pyrite was rapidly dissolved and massive microbial corrosion pits were displayed on pyrite surfaces. Synchrotron-based X-ray absorption spectroscopy demonstrated that approximately 30 % pyrites were oxidized to jarosite-like (ca. 14 %) and ferrihydrite-like minerals (ca. 16 %) in talc group, leading to the formation of secondary Fe precipitates. The Si ions co-dissolved from polysilicates may be embedded into secondary Fe precipitates, while these clustered Fe-Si precipitates displayed distinct morphology (e.g., "circular" shaped in the talc group, "fine-grained" shaped in the chlorite group, and "donut" shaped in the muscovite group). Moreover, the precipitates could join together and act as cementing agents aggregating mineral particles together, forming macroaggregates in talc and chlorite groups. The present findings revealed critical microbial functions on accelerating mineral dissolution, oxidation, and aggregation of pyrite and various silicates, which provided the eco-engineered feasibility of hardpan-based technology for mine site rehabilitation.

A highly efficient process to enhance the bioleaching of spent lithium-ion batteries by bifunctional pyrite combined with elemental sulfur

Bioleaching technologies have been shown to be an environmentally friendly and economically beneficial tool for extracting metals from spent lithium-ion batteries (LIBs). However, conventional bioleaching methods have exhibited low efficiency in recovering metals from spent LIBs. Therefore, relied on the sustainability principle of using waste to treat waste, this study employed pyrite (FeS2) as an energy substance with reducing properties and investigated its effects in combination with elemental sulfur (S0) or FeSO4 on metals bioleaching from spent LIBs. Results demonstrated that the bioleaching efficiency was significantly higher in the leaching system constructed with FeS2 + S0, than in the FeS2 + FeSO4 or FeS2 system. When the pulp densities of FeS2, S0 and spent LIBs were 10 g L-1, 5 g L-1 and 10 g L-1, respectively, the leaching efficiency of Li, Ni, Co and Mn all reached 100%. Mechanistic analysis reveals that in the FeS2 + S0 system, the activity and acid-producing capabilities of iron-sulfur oxidizing bacteria were enhanced, promoting the generation of Fe (Ⅱ) and reducible sulfur compounds. Simultaneously, bio-acids were shown to disrupt the structure of the LIBs, thereby increasing the contact area between Fe (Ⅱ) and sulfur compounds containing high-valence metals. This effectively promoted the reduction of high-valence metals, thereby enhancing their leaching efficiency. Overall, the FeS2 + S0 bioleaching process constructed in this study, improved the leaching efficiency of LIBs while also effectively utilizing waste, providing technical support for the comprehensive and sustainable management of solid waste.

Removal of heavy metals from mine tailings by in-situ bioleaching coupled to electrokinetics

This work utilizes a combined biological-electrochemical technique for the in-situ removal of metals from polluted mine tailings. As the main novelty point it is proposed to use electrokinetics (EK) for the in-situ activation of a bioleaching mechanism into the tailings, in order to promote biological dissolution of metal sulphides (Step 1), and for the subsequent removal of leached metals by EK transport out of the tailings (Step 2). Mine tailings were collected from an abandoned Pb/Zn mine located in central-southern Spain. EK-bioleaching experiments were performed under batch mode using a lab scale EK cell. A mixed microbial culture of autochthonous acidophilic bacteria grown from the tailings was used. Direct current with polarity reversal vs alternate current was evaluated in Step 1. In turn, different biological strategies were used: biostimulation, bioaugmentation and the abiotic reference test (EK alone). It was observed that bioleaching activation was very low during Step 1, because it was difficult to maintain acidic pH in the whole soil, but then it worked correctly during Step 2. It was confirmed that microorganisms successfully contributed to the in-situ solubilization of the metal sulphides as final metal removal rates were improved compared to the conventional abiotic EK (best increases of around 40% for Cu, 162% for Pb, 18% for Zn, 13% for Mn, 40% for Ni and 15% for Cr). Alternate current seemed to be the best option. The tailings concentrations of Fe, Al, Cu, Mn, Ni and Pb after treatment comply with regulations, but Pb, Cd and Zn concentrations exceed the maximum values. From the data obtained in this work it has been observed that EK-bioleaching could be feasible, but some upgrades and future work must be done in order to optimize experimental conditions, especially the control of soil pH in acidic values.

Research progress on bioleaching recovery technology of spent lithium-ion batteries

Bioleaching of lithium-ion batteries is a microbially catalyzed process. Under the action of redox, acid leaching and complexation in the presence of microorganisms, the valuable metals in the cathode material enter the liquid phase as ions and are subsequently recovered from the succeeding process. This technique has the advantages of being inexpensive, environmentally friendly and having simple needs. However, it is still in development and has not yet commercialized. In this paper, the technology is fully discussed based on numerous excellent studies. The contents include commonly utilized microorganisms, bioleaching mechanism, microbial stress response and metabolic activation, enhancement strategies, leaching characteristics and interfacial phenomena, process evaluation, and a critical discussion of recent research breakthroughs. They give readers with comprehensive and in-depth understanding on the bioleaching of lithium-ion batteries and help to improve the technology's industrialization. Researchers can make new explorations from the potential research directions and methods presented in this work to make biotechnology better serve resource recovery and social development.

Microbial communities from weathered outcrops of a sulfide-rich ultramafic intrusion, and implications for mine waste management

The Duluth Complex (DC) contains sulfide-rich magmatic intrusions that represent one of the largest known economic deposits of copper, nickel, and platinum group elements. Previous work showed that microbial communities associated with experimentally-weathered DC waste rock and tailings were dominated by uncultivated taxa and organisms not typically associated with mine waste. However, those experiments were designed for kinetic testing and do not necessarily represent the conditions expected for long-term environmental weathering. We used 16S rRNA gene methods to characterize the microbial communities present on the surfaces of naturally-weathered and historically disturbed outcrops of DC material. Rock surfaces were dominated by diverse uncultured Ktedonobacteria, Acetobacteria, and Actinobacteria, with abundant algae and other phototrophs. These communities were distinct from microbial assemblages from experimentally-weathered DC rocks, suggesting different energy and nutrient resources in environmental samples. Sulfide mineral incubations performed with and without algae showed that photosynthetic microorganisms could have an inhibitory effect on autotrophic populations, resulting in slightly lower sulfate release and differences in dominant microorganisms. The microbial assemblages from these weathered outcrops show how communities develop during weathering of sulfide-rich DC rocks and represent baseline data that could evaluate the effectiveness of future reclamation of waste produced by large-scale mining operations.

Heap leaching of ion adsorption rare earth ores and REEs recovery from leachate with lixiviant regeneration

In this work, semi-industrial scale heap leaching of 200 t ion adsorption rare earth ores (IRE-ore) and rare earth elements (REEs) recovery from lixivium was first conducted. Biosynthetic citrate/(Na)3Cit, a typical microbial metabolite, was chosen as the lixiviant to conduct heap leaching. Subsequently, an organic precipitation method was proposed, which used oxalic acid to effectively recover REEs and reduce the production cost by lixiviant regeneration. The results showed that the heap leaching efficiency of REEs reached 98 % with a lixiviant concentration of 50 mmol/L and a solid-liquid ratio of 1:2. The lixiviant can be regenerated during the precipitation process, with REE yields and impurity aluminum yields of 94.5 % and 7.4 %, respectively. The residual solution can then be cyclically used as a new lixiviant after simple adjustment. High-quality rare earth concentrates with a rare earth oxide (REO) content of 96 % can be finally obtained after roasting. This work provides an eco-friendly alternative for IRE-ore extraction to solve the environmental issues caused by traditional technology. The results proved feasibility and provided a foundation for in situ (bio)leaching processes in further industrial tests and production.

Micro-pressure promotes endogenous phosphorus release in a deep reservoir by favouring microbial phosphate mineralisation and solubilisation coupled with sulphate reduction

Deep reservoirs vary in their hydrostatic pressure owing to artificial water level control. The potential migration of phosphorus (P) in reservoir sediments raises the risk of harmful algal blooms. To ascertain the mechanisms of endogenous P release in reservoirs, we characterised aquatic microbial communities associated with coupled iron (Fe), P and sulphur (S) cycling at the sediment-water interface. The responses of microbial communities to hydrostatic pressures of 0.2-0.7 mega pascals (MPa; that is, micro-pressures) were investigated through a 30-day simulation experiment. Our findings unravelled a potential mechanism that micro-pressure enhanced the solubilisation of Fe/aluminium (Al)-bound P caused by microbially-driven sulphate reduction, leading to endogenous P release in the deep reservoir. Although the vertical distribution of labile Fe was not affected by pressure changes, we did observe Fe resupply at sediment depths of 2-5 cm. Metagenomic analysis revealed increased abundances of functional genes for P mineralisation (phoD, phoA), P solubilisation (pqqC, ppx-gppA) and sulphate reduction (cysD, cysC) in sediments subjected to micro-pressure, which contrasted with the pattern of S oxidation gene (soxB). There was a tight connection between P and S cycling-related microbial communities, based on significant positive correlations between labile element (P and S) concentrations and functional gene (phoD, cysD) abundances. This provided strong support that Fe-P-S coupling processes were governed by micro-pressure through modulation of P and S cycling-related microbial functions. Key taxa involved in P and S cycling (for example, Bradyrhizobium, Methyloceanibacter) positively responded to micro-pressure and as such, indirectly drove P release from sediments by facilitating P mineralisation and solubilisation coupled with sulphate reduction.

Mechanisms of bioleaching: iron and sulfur oxidation by acidophilic microorganisms

Bioleaching offers a low-input method of extracting valuable metals from sulfide minerals, which works by exploiting the sulfur and iron metabolisms of microorganisms to break down the ore. Bioleaching microbes generate energy by oxidising iron and/or sulfur, consequently generating oxidants that attack sulfide mineral surfaces, releasing target metals. As sulfuric acid is generated during the process, bioleaching organisms are typically acidophiles, and indeed the technique is based on natural processes that occur at acid mine drainage sites. While the overall concept of bioleaching appears straightforward, a series of enzymes is required to mediate the complex sulfur oxidation process. This review explores the mechanisms underlying bioleaching, summarising current knowledge on the enzymes driving microbial sulfur and iron oxidation in acidophiles. Up-to-date models are provided of the two mineral-defined pathways of sulfide mineral bioleaching: the thiosulfate and the polysulfide pathway.

Urban mining of municipal solid waste incineration (MSWI) residues with emphasis on bioleaching technologies: a critical review

Metals are essential in our daily lives and have a finite supply, being simultaneously contaminants of concern. The current carbon emissions and environmental impact of mining are untenable. We need to reclaim metals sustainably from secondary resources, like waste. Biotechnology can be applied in metal recovery from waste streams like fly ashes and bottom ashes of municipal solid waste incineration (MSWI). They represent substantial substance flows, with roughly 46 million tons of MSWI ashes produced annually globally, equivalent in elemental richness to low-grade ores for metal recovery. Next-generation methods for resource recovery, as in particular bioleaching, give the opportunity to recover critical materials and metals, appropriately purified for noble applications, in waste treatment chains inspired by circular economy thinking. In this critical review, we can identify three main lines of discussion: (1) MSWI material characterization and related environmental issues; (2) currently available processes for recycling and metal recovery; and (3) microbially assisted processes for potential recycling and metal recovery. Research trends are chiefly oriented to the potential exploitation of bioprocesses in the industry. Biotechnology for resource recovery shows increasing effectiveness especially downstream the production chains, i.e., in the waste management sector. Therefore, this critical discussion will help assessing the industrial potential of biotechnology for urban mining of municipal, post-combustion waste.

Removal of antimonite and antimonate in aqueous solution by mugwort biochar modified by Acidithiobacillus ferrooxidans after pyrolysis

In the research, iron oxides-biochar composites (ALBC) were prepared from pristine biochar modified by Acidithiobacillus ferrooxidans (A. ferrooxidans) and pyrolyzed at 500 °C and 700 °C in order to remove antimonite (Sb(III)) and antimonate (Sb(V)) from water. The results indicated that biochar prepared at 500 °C and 700 °C (ALBC500 and ALBC700) were loaded with Fe₂O₃ and Fe₃O₄, respectively. In bacterial modification systems, ferrous iron and total iron concentrations decreased continuously. The pH values of bacterial modification systems including ALBC500 increased first and then decreased to a stable state, while the pH values of bacterial modification systems with ALBC700 continued to decrease. The bacterial modification systems can facilitate the formation of more jarosites by A. ferrooxidans. ALBC500 had optimal adsorbing capacities for Sb(III) (18.81 mg·g^-1) and Sb(V) (14.64 mg·g^-1). The main mechanisms of Sb(III) and Sb(V) adsorption by ALBC were electrostatic interaction and pore filling.

Current overview and future perspective in fungal biorecovery of metals from secondary sources

Microorganisms are intimately involved in many biogeochemical processes that underpin the transformation of metals and cycling of related substances, such as metalloids and radionuclides. Many processes determine the mobility and bioavailability of metals, thereby influencing their transfer to the environment and living organisms. These processes are closely related to global phenomena such as soil formation and bioweathering. In addition to environmental significance, microbial metal transformations play an essential role in both in situ and ex situ bioremediation processes for solid and liquid wastes. The solubilization of heavy metals from industrial waste and soil is commonly used in bioremediation. Moreover, immobilization processes are applicable to bioremediation of metals and radionuclides from aqueous solutions. This review provides an overview of critical metal extraction and recovery from secondary sources, applied microorganisms and methods, metal-microbe interactions, as well as a detailed description of known metal recovery mechanisms.

Effective recovery of rare earth from (bio)leaching solution through precipitation of rare earth-citrate complex

Bioleaching is considered an alternative to traditional rare earth extraction technology. However, since rare earth elements exist as complexes in bioleaching lixivium, they cannot be directly precipitated by normal precipitants, which restricts their further development. This structurally stable complex is also a common challenge in various types of industrial wastewater treatment. In this work, a new method called a three-step precipitation process is first proposed to efficiently recover rare earth-citrate (RE-Cit) complexes from (bio)leaching lixivium. It consists of coordinate bond activation (carboxylation by pH adjustment), structure transformation (Ca²⁺ addition) and carbonate precipitation (soluble CO₃^2- addition). The optimization conditions are determined to adjust the lixivium pH to around 2.0, then add calcium carbonate until the n(Ca²⁺): n(Cit^3-) is more than 1.4:1 and lastly add sodium carbonate until n(CO₃^2-): n(RE³⁺) is more than 4:1. The results of precipitation experiments using imitated lixivium show that the rare earth yield is more than 96% and the impurity aluminum yield is less than 20%. Subsequently, pilot tests (1000 L) using real lixivium were successfully conducted. The precipitation mechanism is briefly discussed and proposed by thermogravimetric analysis, Fourier infrared spectroscopy, Raman spectroscopy and UV spectroscopy. This technology is promising in the industrial application of rare earth (bio)hydrometallurgy and wastewater treatment due to its advantages of high efficiency, low cost, environmental friendliness and simple operation.

(Bio)dissolution of arsenopyrite coupled with multiple proportions of pyrite: Emphasis on the mobilization and existential state of arsenic

The formation of arsenic-bearing acid mine drainage (AMD) via the oxidation of arsenopyrite refuse ore has attracted significant attention. Pyrite, as main a concomitant mineral, is a crucial factor that affects the (bio)dissolution of arsenopyrite, but there are still some points on the detailed action mechanism under normal environmental conditions that need further study. In this study, the effect mechanism of pyrite with a systematic pyrite content (0, 10, 25, 50, 75, 90, and 100 wt %) on arsenopyrite oxidation and arsenic release in the presence of Acidithiobacillus ferrooxidans was investigated. The X-ray diffraction (XRD), scanning election microscopy (SEM), X-ray photoelectron spectroscopy (XPS) and electrochemical analyses were also carried out. Results showed that the existence of pyrite and Acidithiobacillus ferrooxidans significantly accelerated the dissolution of arsenopyrite and the oxidation of As (Ⅲ) to As (Ⅴ), resulting from the galvanic effect, an increase in the Fe³⁺/Fe²⁺ ratio and the oxidation-reduction potential (Eh) value, and a decrease in pH level. As the detected main intermediate products, element sulphur was considered as the dominating obstructive factor during arsenopyrite oxidation, while the added pyrite could accelerate its oxidation. Moreover, a close relationship between different mineral proportions and the galvanic effect was also observed and discussed. Finally, suggestions on AMD governance and source control are proposed.

Recombinant expression using the tetrathionate hydrolase promoter in Acidithiobacillus ferrooxidans

In the iron- and sulfur-oxidizing acidophilic chemolithoautotrophic bacterium, Acidithiobacillus ferrooxidans, tetrathionate hydrolase gene (Af-tth) is highly expressed during tetrathionate growth. The expression levels of Af-tth were specifically determined by quantitative reverse transcription-polymerase chain reaction and the expression ratios of S⁰/Fe²⁺ and S₄O₆^2-/Fe²⁺ were found to be 68 ± 21 and 181 ± 5, respectively. The transcriptional start site was identified by primer extension. Promoter regions of Af-tth were cloned into the expression shuttle vector pMPJC and GFP gene was under the direction of the regions. Green fluorescence was observed by UV irradiation in recombinant A. ferrooxidans harboring the plasmid colonies grown on tetrathionate. Furthermore, His-tagged Af-Tth was synthesized in the recombinant cells grown on tetrathionate. Recombinant, His-tagged Af-Tth in an active form, was rapidly purified through metal-affinity column chromatography, although recombinant Af-Tth was synthesized in the inclusion bodies of Escherichia coli and acid-refolding treatment was necessary to recover the activity. The specific activity of purified Af-Tth from recombinant A. ferrooxidans (2.2 ± 0.37 U mg^-1) was similar to that of acid-refolded Af-Tth from recombinant E. coli (2.5 ± 0.18 U mg^-1). This method can be applied not only to heterologous expression but also to homologous expression of target genes for modification or specific mutation in A. ferrooxidans cells.

Sulfoacidibacillus ferrooxidans, gen. nov., sp. nov., Sulfoacidibacillus thermotolerans, gen. nov., sp. nov., and Ferroacidibacillus organovorans, gen. nov., sp. nov.: Extremely acidophilic chemolitho-heterotrophic Firmicutes

Ten strains of extremely acidophilic bacteria, isolated from different environments form a distinct monophyletic clade within the phylum Firmicutes. Comparison of complete genomes of the proposed type strains confirm that they comprise two genera (proposed names Sulfoacidibacillus and Ferroacidibacillus), and at least three species (Sulfoacidibacillus ferrooxidans, Sulfoacidibacillus thermotolerans and Ferroacidibacillus organovorans). The bacterial strains share some physiological traits, including catalysing the dissimilatory oxidation and reduction of iron, and in being obligately heterotrophic. Both species of Sulfoacidibacillus are also able to oxidise elemental sulfur and tetrathionate. Both S. ferrooxidans and Ferroacidibacillus spp. are mesophilic, while S. thermotolerans isolates are moderate thermophiles. The isolates display different degrees of acid-tolerance: Ferroacidibacillus spp. are the most acid-sensitive while the type strain of S. ferrooxidans grows at pH 0.9. MK7 was detected as the sole menaquinone present in all three nominated type strains, and their peptidoglycans all contain meso-2,6 diaminopimelic acid type A1γ. The chromosomal DNA of the strains examined contain between 44 and 52 mol% G + C. The nominated type strains of the new species are S. ferrooxidans S⁰AB^T (= DSM 105355^T = JCM 33225^T); S. thermotolerans Y002^T (= ATCC TSD-104^T = JCM 31946^T); F. organovorans SLC66^T (= ATCC TSD-103^T = JCM 31945^T).

Coupled C, H, N, S and Fe biogeochemical cycles operating in the continental deep subsurface of the Iberian Pyrite Belt

Microbial activity is a major contributor to the biogeochemical cycles that make up the life support system of planet Earth. A 613 m deep geomicrobiological perforation and a systematic multi-analytical characterization revealed an unexpected diversity associated with the rock matrix microbiome that operates in the subsurface of the Iberian Pyrite Belt (IPB). Members of 1 class and 16 genera were deemed the most representative microorganisms of the IPB deep subsurface and selected for a deeper analysis. The use of fluorescence in situ hybridization allowed not only the identification of microorganisms but also the detection of novel activities in the subsurface such as anaerobic ammonium oxidation (ANAMMOX) and anaerobic methane oxidation, the co-occurrence of microorganisms able to maintain complementary metabolic activities and the existence of biofilms. The use of enrichment cultures sensed the presence of five different complementary metabolic activities along the length of the borehole and isolated 29 bacterial species. Genomic analysis of nine isolates identified the genes involved in the complete operation of the light-independent coupled C, H, N, S and Fe biogeochemical cycles. This study revealed the importance of nitrate reduction microorganisms in the oxidation of iron in the anoxic conditions existing in the subsurface of the IPB.

Convergent Community Assembly among Globally Separated Acidic Cave Biofilms

Acidophilic bacteria and archaea inhabit extreme geochemical "islands" that can tell us when and how geographic barriers affect the biogeography of microorganisms. Here, we describe microbial communities from extremely acidic (pH 0 to 1) biofilms, known as snottites, from hydrogen sulfide-rich caves. Given the extreme acidity and subsurface location of these biofilms, and in light of earlier work showing strong geographic patterns among snottite Acidithiobacillus populations, we investigated their structure and diversity in order to understand how geography might impact community assembly. We used 16S rRNA gene cloning and fluorescence in situ hybridization (FISH) to investigate 26 snottite samples from four sulfidic caves in Italy and Mexico. All samples had very low biodiversity and were dominated by sulfur-oxidizing bacteria in the genus Acidithiobacillus. Ferroplasma and other archaea in the Thermoplasmatales ranged from 0 to 50% of total cells, and relatives of the bacterial genera Acidimicrobium and Ferrimicrobium were up to 15% of total cells. Rare phylotypes included Sulfobacillus spp. and members of the phyla "Candidatus Dependentiae" and "Candidatus Saccharibacteria" (formerly TM6 and TM7). Although the same genera of acidophiles occurred in snottites on separate continents, most members of those genera represent substantially divergent populations, with 16S rRNA genes that are only 95 to 98% similar. Our findings are consistent with a model of community assembly where sulfidic caves are stochastically colonized by microorganisms from local sources, which are strongly filtered through environmental selection for extreme acid tolerance, and these different colonization histories are maintained by dispersal restrictions within and among caves. IMPORTANCE Microorganisms that are adapted to extremely acidic conditions, known as extreme acidophiles, are catalysts for rock weathering, metal cycling, and mineral formation in naturally acidic environments. They are also important drivers of large-scale industrial processes such as biomining and contaminant remediation. Understanding the factors that govern their ecology and distribution can help us better predict and utilize their activities in natural and engineered systems. However, extremely acidic habitats are unusual in that they are almost always isolated within circumneutral landscapes. So where did their acid-adapted inhabitants come from, and how do new colonists arrive and become established? In this study, we took advantage of a unique natural experiment in Earth's subsurface to show how isolation may have played a role in the colonization history, community assembly, and diversity of highly acidic microbial biofilms.

Sulfur enhancement effects for uranium bioleaching in column reactors from a refractory uranium ore

The feasibility of sulfur enhancement for uranium bioleaching in column reactors was assessed with a designed mixed Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans and Leptospirillum ferriphilum from a refractory uranium ore. The uranium extraction reached 86.2% with the sulfur enhancement (1 g/kg) in 77 days leaching process, increased by 12.6% vs. the control without sulfur addition. The kinetic analysis showed that uranium bioleaching with sulfur enhancement in columns followed an internal diffusion through the product layer-controlled model. Ore residue characteristics indicated that sulfur enhancement could strengthen the porosity of passivation layer, improving the ore permeability. Notably, bacterial community analysis showed that sulfur enhancement at 1 g/kg could make the iron-oxidizing and sulfur-oxidizing bacteria on the ore surface maintain a good balance (approx. 1:1), and thus decomposing ore more effectively. Lastly, a possible mechanism model for uranium bioleaching with sulfur enhancement was proposed.

Interesting Halophilic Sulphur-Oxidising Bacteria with Bioleaching Potential: Implications for Pollutant Mobilisation from Mine Waste

For many years, research on the microbial-dissolution of metals from ores or waste materials mainly focussed on the study of acidophilic organisms. However, most acidophilic bioleaching microorganisms have limited tolerance to high chloride concentrations, thereby requiring fresh water for bioleaching operations. There is a growing interest in the use of seawater for leaching purposes, especially in regions with less access to fresh water. Consequently, there is a need to find halophilic organisms with bioleaching potentials. This study investigated the bioleaching potentials of four moderately halophilic sulphur-oxidising bacteria: Thiomicrospira cyclica, Thiohalobacter thiocyanaticus, Thioclava electrotropha and Thioclava pacifica. Results revealed T. electrotropha and T. pacifica as the most promising for bioleaching. Pure cultures of the two Thioclava strains liberated about 30% Co, and between 8-17% Cu, Pb, Zn, K, Cd, and Mn from a mine waste rock sample from the Neves Corvo mine, Portugal. Microwave roasting of the waste rock at 400 and 500 °C improved the bioleaching efficiency of T. electrotropha for Pb (13.7 to 45.7%), Ag (5.3 to 36%) and In (0 to 27.4%). Mineralogical analysis of the bioleached residues using SEM/MLA-GXMAP showed no major difference in the mineral compositions before or after bioleaching by the Thioclava spp. Generally, the bioleaching rates of the Thioclava spp. are quite low compared to that of the conventional acidophilic bioleaching bacteria. Nevertheless, their ability to liberate potential pollutants (metal(loid)s) into solution from mine waste raises environmental concerns. This is due to their relevance in the biogeochemistry of mine waste dumps, as similar neutrophile halophilic sulphur-oxidising organisms (e.g., Halothiobacillus spp.) have been isolated from mine wastes. On the other hand, the use of competent halophilic microorganisms could be the future of bioleaching due to their high tolerance to Cl^- ions and their potential to catalyse mineral dissolution in seawater media, instead of fresh water.

In Situ Remediation Technology for Heavy Metal Contaminated Sediment: A Review

Sediment is an important part of the aquatic ecosystem, which involves material storage and energy exchange. However, heavy metal pollution in sediment is on the increase, becoming an important concern for the world. In this paper, the state-of-art in situ remediation technology for contaminated sediment was elaborated, including water diversion, capping, electrokinetic remediation, chemical amendments, bioremediation and combined remediation. The mechanisms for these techniques to reduce/immobilize heavy metals include physical, electrical, chemical and biological processes. Furthermore, application principle, efficiency and scope, advantages and disadvantages, as well as the latest research progress for each restoration technology, are systematically reviewed. This information will benefit in selecting appropriate and effective remediation techniques for heavy metal-contaminated sediment in specific scenarios.

A review on the bioleaching of toxic metal(loid)s from contaminated soil: Insight into the mechanism of action and the role of influencing factors

The anthropogenic activities in agriculture, industrialization, mining, and metallurgy combined with the natural weathering of rocks, have led to severe contamination of soils by toxic metal(loid)s. In an attempt to remediate these polluted sites, a plethora of conventional approaches such as Solidification/Stabilization (S/S), soil washing, electrokinetic remediation, and chemical oxidation/reduction have been used for the immobilization and removal of toxic metal(loid)s in the soil. However, these conventional methods are associated with certain limitations. These limitations include high operational costs, high energy demands, post-waste disposal difficulties, and secondary pollution. Bioleaching has proven to be a promising alternative to these conventional approaches in removing toxic metal(loid)s from contaminated soil as it is cost-effective, environmentally friendly, and esthetically pleasing. The bioleaching process is influenced by factors including pH, temperature, oxygen, and carbon dioxide supply, as well as nutrients in the medium. It is crucial to monitor these parameters before and throughout the reaction since a change in any, for instance, pH during the reaction, can alter the microbial activity and, therefore, the rate of metal leaching. However, research on these influencing factors and recent innovations has brought significant progress in bioleaching over the years. This critical review, therefore, presents the current approaches to bioleaching and the mechanisms involved in removing toxic metal(loid)s from contaminated soil. We further examined and discussed the fundamental principles of various influencing factors that necessitate optimization in the bioleaching process. Additionally, the future perspectives on adding omics for bioleaching as an emerging technology are discussed.

Electrochemical Characteristics of the Oxidation of Sulfur- and Iron-Containing Compounds by Acidophilic Microorganisms

The electrochemical features of the interactions of sulfur- and iron-containing compounds (ferrous sulfate, elemental sulfur, pyrite tailings, cysteine, sodium thiosulfate) with a model acidophilic consortium, including the genera Leptospirillum, Sulfobacillus, Acidithiobacillus, Ferroplasma, and Acidiplasma, were studied. The method of cyclic voltammetry recorded redox processes at the electrode/solution interface in the presence of the studied sulfur- and iron-containing compounds. In general, the modeling consortium led to the intensification of these processes. The characteristics of the diffuse layer near the electrode/solution interface were studied using electrochemical impedance spectroscopy. The introduction of microorganisms and/or substrates into the supporting electrolyte led to a decrease in the slope and can be interpreted as evidence of their effect on the diffusion part of the double layer. Its contribution decreases in favor of ion transport. All this, in general, does not contradict the assumption of cell adsorption on the electrode surface. Confocal laser scanning microscopy confirmed this assumption and showed cell adhesion to the surface. The data obtained confirm the importance of bioelectrochemical processes of the studied group of microorganisms in biotechnological processes associated with the leaching of metals from sulfide ores.

Enhancement and mechanisms of micron-pyrite driven autotrophic denitrification with different pretreatments for treating organic-limited waters

Pyrite-driven autotrophic denitrification (PAD) represents a cheap and promising way for nitrogen removal from organic-limited wastewater, which has obtained increasing attention in recent years. However, the limited denitrification rate and unclear mechanism underlying the process have hindered the engineered application of PAD. This study aims to shed light on the impacts of different pretreatments (i.e., ultrasonication, acid-washing and calcination) on micron-pyrite surface characteristics, denitrification performance and biofilm formation during PAD in batch reactors. A series of solid-phase analyses revealed that all pretreatments could significantly promote biofilm attachment on pyrite granules, but impacted the proportion, distribution and chemical oxidation state of sulfur (S) and iron (Fe) at varying degrees. Batch tests showed that ultrasonication and acid-washing could enhance the total nitrogen reduction rate by 14% and 99%, and decrease the sulfate production rate by 51% and 42%, respectively, when compared with untreated pyrite. Microbial community analysis indicated that Thiobacillus and Rhodanobacter dominated in PAD systems. Two types of indirect mechanisms (i.e., contact and non-contact) for pyrite leaching may co-occur in PAD system, resulting in ferrous iron (Fe²⁺), thiosulfate (S₂O₃^2-) and sulfide (S^2-) as the main electron donors for denitrification. A PAD mechanism model was proposed to describe the PAD electron transfer pathway with the aim to optimize the engineered application of PAD for nitrogen removal.

Enhanced removal of sulfur-containing organic pollutants from actual wastewater by biofilm reactor: Insights of sulfur transformation and bacterial metabolic traits

Sulfur-containing organic pollutants in wastewater could threaten human health due to their high malodor and toxicity, and their conversion processes are more complex than inorganic sulfur compounds. Membrane aerated biofilm reactor (MABR), as a novel and environmentally-friendly biofilm-based technology, is able to remove inorganic sulfur in synthetic wastewater. However, it is unknown how sulfur-containing organic pollutants in actual wastewater are transformed in MABR system. This work demonstrated the feasibility of MABR to eliminate sulfur-containing organic pollutants in actual wastewater, and the removal efficiency could be reached at approximately 100%. Meanwhile, over 70% of sulfur-containing organic contaminants were transformed to SO₄^2- during the long-term operation. Further analysis indicated that the functional bacteria that participated in sulfur transformation and carbohydrates degradation (e.g., Chujaibacter, Microscillaceaesp., and Thiobacillus) were evidently enriched when treating actual wastewater. Moreover, the critical metabolic pathways (e.g., sulfur metabolism, glycolysis metabolism, and pyruvate metabolism), and the corresponding genetic expressions (e.g., nrrA, tauA, tauC, sorA, and SUOX) were evidently up-regulated during long-term operation, which was beneficial for the transformation of sulfur-containing organic pollutants in actual wastewater by MABR. This work would expand the application of MABR for treating the actual sulfur-containing organic wastewater and provide an in-depth understanding of the organic sulfur transformation in MABR.

Progress in bioleaching: fundamentals and mechanisms of microbial metal sulfide oxidation - part A

Abstract

Bioleaching of metal sulfides is performed by diverse microorganisms. The dissolution of metal sulfides occurs via two chemical pathways, either the thiosulfate or the polysulfide pathway. These are determined by the metal sulfides’ mineralogy and their acid solubility. The microbial cell enables metal sulfide dissolution via oxidation of iron(II) ions and inorganic sulfur compounds. Thereby, the metal sulfide attacking agents iron(III) ions and protons are generated. Cells are active either in a planktonic state or attached to the mineral surface, forming biofilms. This review, as an update of the previous one (Vera et al., 2013a), summarizes some recent discoveries relevant to bioleaching microorganisms, contributing to a better understanding of their lifestyle. These comprise phylogeny, chemical pathways, surface science, biochemistry of iron and sulfur metabolism, anaerobic metabolism, cell–cell communication, molecular biology, and biofilm lifestyle. Recent advances from genetic engineering applied to bioleaching microorganisms will allow in the future to better understand important aspects of their physiology, as well as to open new possibilities for synthetic biology applications of leaching microbial consortia.

Key points

• Leaching of metal sulfides is strongly enhanced by microorganisms

• Biofilm formation and extracellular polymer production influences bioleaching

• Cell interactions in mixed bioleaching cultures are key for process optimization

Sticky bacteria: Combined effect of galactose and high ferric iron concentration on extracellular polymeric substances production and the attachment of Acidithiobacillus ferrooxidans on a polymetallic sulfide ore surface

Adaptation and microbial attachment mechanisms for the degradation of sulfide ores are mediated by the production of extracellular polymeric substances (EPS) and their role in biofilm formation. EPS production responds to induction mechanisms associated with environmental conditions. In this study, the double induction of EPS with galactose and high ferric iron concentrations in planktonic cells of Acidithiobacillus ferrooxidans, and their attachment on the surface of a polymetallic sulfide ore from Bella Rica-Azuay in Ecuador were evaluated. A. ferrooxidans cells were previously adapted to different concentrations of galactose [0, 0.15, and 0.25% (w/v)], using two ferrous iron concentrations as an energy source (9 and 18 g L^–1) in a 9K culture medium. EPS production and its effect on mineral attachment were determined at the time point of maximal growth. The results obtained show a maximum cell attachment of 94.1% within 2 h at 0.15% of galactose and 18 g^⋅L^–1 of ferric iron concentration, compared to 71.4% without galactose and 9 g^⋅L^–1 of ferric iron. The maximum concentration of EPS was obtained with a 0.25% galactose concentration; however, it did not result in greater attachment compared to 0.15% galactose concentration. Through the combined induction of low galactose concentration and high ferric iron concentration, the percentage of bacterial attachment can be increased and, therefore, a possible increase in the rate of biooxidation and bioleaching could be obtained.

Efficient dealkalization of red mud and recovery of valuable metals by a sulfur-oxidizing bacterium

Red mud (RM) is a highly alkaline polymetallic waste generated via the Bayer process during alumina production. It contains metals that are critical for a sustainable development of modern society. Due to a shortage of global resources of many metals, efficient large-scale processing of RM has been receiving increasing attention from both researchers and industry. This study investigated the solubilization of metals from RM, together with RM dealkalization, via sulfur (S0) oxidation catalyzed by the moderately thermophilic bacterium Sulfobacillus thermosulfidooxidans. Optimization of the bioleaching process was conducted in shake flasks and 5-L bioreactors, with varying S0:RM mass ratios and aeration rates. The ICP analysis was used to monitor the concentrations of dissolved elements from RM, and solid residues were analyzed for surface morphology, phase composition, and Na distribution using the SEM, XRD, and STXM techniques, respectively. The results show that highest metal recoveries (89% of Al, 84% of Ce, and 91% of Y) were achieved with the S0:RM mass ratio of 2:1 and aeration rate of 1 L/min. Additionally, effective dealkalization of RM was achieved under the above conditions, based on the high rates (&gt;95%) of Na, K, and Ca dissolution. This study proves the feasibility of using bacterially catalyzed S0 oxidation to simultaneously dealkalize RM and efficiently extract valuable metals from the amassing industrial waste.

Characterization and genomic analysis of two novel psychrotolerant Acidithiobacillus ferrooxidans strains from polar and subpolar environments

The bioleaching process is carried out by aerobic acidophilic iron-oxidizing bacteria that are mainly mesophilic or moderately thermophilic. However, many mining sites are located in areas where the mean temperature is lower than the optimal growth temperature of these microorganisms. In this work, we report the obtaining and characterization of two psychrotolerant bioleaching bacterial strains from low-temperature sites that included an abandoned mine site in Chilean Patagonia (PG05) and an acid rock drainage in Marian Cove, King George Island in Antarctic (MC2.2). The PG05 and MC2.2 strains showed significant iron-oxidation activity and grew optimally at 20°C. Genome sequence analyses showed chromosomes of 2.76 and 2.84 Mbp for PG05 and MC2.2, respectively, and an average nucleotide identity estimation indicated that both strains clustered with the acidophilic iron-oxidizing bacterium Acidithiobacillus ferrooxidans. The Patagonian PG05 strain had a high content of genes coding for tolerance to metals such as lead, zinc, and copper. Concordantly, electron microscopy revealed the intracellular presence of polyphosphate-like granules, likely involved in tolerance to metals and other stress conditions. The Antarctic MC2.2 strain showed a high dosage of genes for mercury resistance and low temperature adaptation. This report of cold-adapted cultures of the At. ferrooxidans species opens novel perspectives to satisfy the current challenges of the metal bioleaching industry.

In situ, high-resolution evidence of metals at the sediment-water interface under ice cover in a seasonal freezing lake

The ice cover in winter as a physical barrier and duration would profoundly impact on changes in endogenous metal loading, migration, and transformation. Although a gradual reduction in duration and occurrence of lake ice cover in boreal lake ecosystems has been confirmed, little attention to the ice-covered period is received compared to open water studies. In this study, novel-developed diffusive gradients in thin films (DGT, ZrO-Chelex) probes were deployed to obtain the in-situ and high-resolution information on metals (Cu, Zn, Pb, Mn, Cd, Cr, and As) at the sediment-water interface (SWI) in a seasonal ice-covered lake, Chagan Lake. In addition, “source-sink” characteristics of each metal related to their endogenous release were determined based on Fick’s first law. Concentrations of labile metals at the SWI demonstrated significant spatial heterogeneity, peaking exactly below the SWI. Compared with other similar studies, concentrations of Pb (0.55 μg/L), Cr (0.58 μg/L), and As (2.4 μg/L) were a little higher even under-ice than that in other freshwater rivers and lakes, indicating potential pollution due to the agricultural intensification and petroleum extraction. The apparent diffusive fluxes suggested that sediments acted as a sink for Pb (−0.01 mg m–2 day–1), Cr (−2.37 mg m–2 day–1), and Cd (−0.1 mg m–2 day–1), diffusing from the overlying water into the sediment, while Cu (0.12 mg m–2 day–1), Zn (0.75 mg m–2 day–1), Mn (15.89 mg m–2 day–1), and As (2.12 mg m–2 day–1) as a source from sediments into the overlying water. Dissolved oxygen was the principal factor (79.5%, P = 0.032), determining the variation of the available metals at the SWI. As the urgent need for research focused on under-ice ecosystem dynamics, this study addressed the previously unknown behavior of the labile metals at the SWI and provided a unique perspective for the lake management during the ice-cover periods when external nutrient input was cut off.

Bioleaching of rare earths elements from phosphate rock using Acidothiobacillus ferrooxidans

Phosphate rock containing rare earth elements (REEs) is considered one of the most promising potential secondary sources of REEs, as evidenced by large tonnages of phosphate rock mined annually. The bioleaching of REEs from phosphate rock using A. ferrooxidans was done for the first time in this study, and it was found to be greater than abiotic leaching and was more environmentally friendly. The result showed that the total leaching rate of REEs in phosphate rock was 28.46% under the condition of 1% pulp concentration and pH=2, and the leaching rates of four key rare earths, Y, La, Ce, and Nd, were 35.7%, 37.03%, 27.92%, and 32.53%, respectively. The bioleaching process was found to be accomplished by bacterial contact and Fe²⁺ oxidation. The blank control group which contained Fe²⁺ was able to leach some of the rare earths, indicating that the oxidation of Fe²⁺ may affect the leaching of rare earths. X-Ray Diffraction (XRD)analysis showed that the minerals were significantly altered and the intensity of the diffraction peaks of dolomite and apatite decreased significantly after microbial action compared to the blank control, and it was observed that bacteria adhere to the mineral surface and the minerals become smooth and angular after bioleaching by Scanning electron microscope (SEM), indicating that bacteria have a further effect on the rock based on Fe²⁺ oxidation.Finally.Fourier Transform infrared spectroscopy (FTIR) and three-dimensional excitation-emission matrix (3DEEM) fluorescence spectra analysis showed that extracellular polymeric substances (EPS) participate in the bioleaching process.

Accessing Metals from Low-Grade Ores and the Environmental Impact Considerations: A Review of the Perspectives of Conventional versus Bioleaching Strategies

Mining has advanced primarily through the use of two strategies: pyrometallurgy and hydrometallurgy. Both have been used successfully to extract valuable metals from ore deposits. These strategies, without a doubt, harm the environment. Furthermore, due to decades of excessive mining, there has been a global decline in high-grade ores. This has resulted in a decrease in valuable metal supply, which has prompted a reconsideration of these traditional strategies, as the industry faces the current challenge of accessing the highly sought-after valuable metals from low-grade ores. This review outlines these challenges in detail, provides insights into metal recovery issues, and describes technological advances being made to address the issues associated with dealing with low-grade metals. It also discusses the pragmatic paradigm shift that necessitates the use of biotechnological solutions provided by bioleaching, particularly its environmental friendliness. However, it goes on to criticize the shortcomings of bioleaching while highlighting the potential solutions provided by a bespoke approach that integrates research applications from omics technologies and their applications in the adaptation of bioleaching microorganisms and their interaction with the harsh environments associated with metal ore degradation.

Potential threat of antibiotics resistance genes in bioleaching of heavy metals from sediment

Bioleaching is considered a promising technology for remediating heavy metals pollution in sediments. During bioleaching, the pressure from the metals bioleached is more likely to cause the spread of antibiotic resistance genes (ARGs). The changes in abundance of ARGs in two typical heavy metal bioleaching treatments using indigenous bacteria or functional bacteria agent were compared in this study. Results showed that both treatments successfully bioleached heavy metals, with a higher removal ratio of Cu with functional bacteria agent. The absolute abundances of most ARGs decreased by one log unit after bioleaching, particularly tetR (p = 0.02) and tetX (p = 0.04), and intI1 decreased from 10⁶ to 10⁴ copies/g. As for the relative abundance, ARGs in the non-agent treatment increased from 3.90 × 10^-4 to 1.67 × 10^-3 copies/16S rRNA gene copies (p = 0.01), and in the treatment with agent, it reached 6.65 × 10^-2 copies/16S rRNA gene copies, and intI1 relative abundance was maintained at 10^-3 copies/16S rRNA gene copies. The relative abundance of ARGs associated with efflux pump mechanism and ribosomal protection mechanism increased the most. The co-occurrence network indicated that Cu bioleached was the environmental factor determining the distribution of ARGs, Firmicutes might be the potential hosts of ARGs. Compared to bioleaching with indigenous bacteria, the addition of functional bacteria agent engendered a decrease in microbial alpha diversity and an increase in the amount of Cu bioleached, resulting in a higher relative abundance of ARGs. Heavy metal pollution can be effectively removed from sediments using the two bioleaching treatments, however, the risk of ARGs propagation posed by those procedures should be considered, especially the treatment with functional bacteria agents. In the future, an economical and efficient green technology that simultaneously reduces both the absolute abundance and relative abundance of ARGs should be developed.

Dredging and deposition of metal sulfide rich river sediments results in rapid conversion to acid sulfate soil materials

Sediments along the Baltic Sea coast can contain considerable amounts of metal sulfides that if dredged and the spoils deposited such that they are exposed to air, can release high concentrations of acid and toxic metals into recipient water bodies. Two river estuaries in western Finland were dredged from 2013 to 2018 and the dredge spoils were deposited on land previously covered with agricultural limestone to buffer the pH and mitigate acid and metal release. In this study, the geochemistry and 16S rRNA gene amplicon based bacterial communities were investigated over time to explore whether the application of lime prevented a conversion of the dredge spoils into acid producing and metal releasing soil. The pH of the dredge spoils decreased with time indicating metal sulfide oxidation and resulted in elevated sulfate concentrations along with a concomitant release of metals. However, calculations indicated only approximately 5% of the added lime had been dissolved. The bacterial communities decreased in diversity with the lowering of the pH as taxa most similar to extremely acidophilic sulfur, and in some cases iron, oxidizing Acidithiobacillus species became the dominant characterized genus in the deposited dredge spoils as the oxidation front moved deeper. In addition, other taxa characterized as involved in oxidation of iron or sulfur were identified including Gallionella, Sulfuricurvum, and Sulfurimonas. These data suggest there was a rapid conversion of the dredge spoils to severely acidic soil similar to actual acid sulfate soil and that the lime placed on the land prior to deposition of the spoils, and later ploughed into the dry dredge spoils, was insufficient to halt this process. Hence, future dredging and deposition of dredge spoils containing metal sulfides should not only take into account the amount of lime used for buffering but also its grain size and mixing into the soil.

Effects of Extracellular Polymeric Substances and Specific Compositions on Enhancement of Copper Bioleaching Efficiency from Waste Printed Circuit Boards

Bioleaching has been proven to be an efficient and environment-friendly method for processing metalliferous ore and waste printed circuit boards (PCBs), a type of urban mine waste. Extracellular polymeric substances (EPS) play a major role in the attachment of bacteria to the surface of sulfide minerals. However, there are few reports on the effects of EPS components on the bioleaching of metals from PCBs. In this study, synthetic EPS were used to investigate the effects of the composition of exo-polymers on the bioleaching of copper from waste PCBs, including the process efficiency. The copper extraction rate in bioleaching assays with synthetic EPS was 11.7% greater than in those without synthetic EPS. Moreover, the composition of EPS was proven to be a crucial factor affecting the efficiency of copper bioleaching, with EPS containing arginine yielding the highest recovery (95.2% copper). Under the condition of 0.5 g/L synthetic EPS added at the early stage of log phase, the copper leaching efficiency from waste PCBs was highly improved. This study provides important insights into how to analyze the working mechanisms of EPS for a better recovery efficiency.

Efficient nitrite accumulation and elemental sulfur recovery in partial sulfide autotrophic denitrification system: Insights of seeding sludge, S/N ratio and flocculation strategy

Partial sulfide autotrophic denitrification (PSAD) has been proposed as a promising process to achieve elemental sulfur recovery and nitrite accumulation, which is required for anaerobic ammonium oxidation reaction. This study investigated the effect of seeding sludge on the start-up performance of PSAD process, with different sludge taken from the oxidation zone (S-o) of wastewater treatment plants, partial denitrification reactor (S-_PD), and anoxic/oxic reactor (S-_A/O). The results showed that the PSAD process could be achieved rapidly in three systems on day 22, 29 and 26, respectively. In particular, the S-_O system completed the start-up in the shortest time of 22 d, with NO₃^--N and S^2- removal efficiency of 85.3% and 99.3%, respectively. Selected the S-_O system to operate long term, the nitrite (NO₂^--N) and biological elemental sulfur (S⁰) accumulation efficiencies were systematically investigated under different S/N ratios (in a range of 0.71-1.2). The maximum NO₂^--N and S⁰ accumulation efficiencies were 85.2% and 73.5%, respectively, at the S/N ratio of 1.1. In addition, the separation and recovery of S⁰ in effluent was achieved by employing polyaluminum chloride (PAC) as a flocculant. Using 2D Gaussian function as quadratic model for the maximizing of S⁰ flocculant efficiency (SFR), an optimal condition of PAC dosage 7.92 mL/L and pH 5.14 was obtained, and the SFR reached 94.1%, under such conditions. The findings offered useful information to facilitate the application of the PSAD process.

Vertical distribution of the toxic metal(loid)s chemical fraction and microbial community in waste heap at a nonferrous metal mining site

Over the past few decades, nonferrous mining has produced numerous waste rock and part of the waste that has not been properly treated was generally dumped at roadsides and hill slopes. However, the vertical distributions of toxic metal(loid)s and composition of microbial communities in waste heap and the under-laid pristine soil are rarely studied. In this work, the fraction-related distributions of toxic metal(loid)s were investigated at a waste heap profile and the indigenous microbial assemblages were also analyzed by Illumina sequencing of 16 s rRNA genes. Results showed that compared to the under-laid pristine soil, content of toxic metal(loid)s, especially Cd, As and Pb, in waste rock layer were higher. Most of As in subsoil existed as non-specifically sorbed and specifically-sorbed fractions, which could be ascribed to the migration from the upper layer. The mobility was significantly correlated with Eh, EC, clay content, CEC and the total content of metal(loid)s. Phyla Proteobacteria, Acidobacteria and Firmicutes dominated the microbial communities. The microbial community compositions at the genus level were similar, but their relative abundances were mainly influenced by pH, CEC, Eh, SOM, and bioavailability content of toxic metal(loid)s. Besides, microbial functions of elements (S, Fe, Mn and As) oxidation/reduction and metabolites (siderophore, biosurfactant, organic acid, phosphatase and urease) potentially were used for pollutants bioremediation.

A review on the recycling of spent lithium-ion batteries (LIBs) by the bioleaching approach

This review discusses the latest trend in recovering valuable metals from spent lithium-ion batteries (LIBs) to meet the technological world's critical metal demands. Spent LIBs are a secondary source of valuable metals such as Li (5%-7%), Ni (5%-10%), Co (5%-25%), Mn (5-11%), and non-metal graphite. Recycling is essential for the battery industry to extract valuable critical metals from secondary sources to develop new and novel high-tech LIBs for various applications such as eco-friendly technologies, renewable energy, emission-free electric vehicles, and energy-saving lightings. LIB waste is currently undergoing high-temperature pyrometallurgical or hydrometallurgical processes to recover valuable metals, and these processes have proven to be successful and feasible. These methods, however, are not preferable due to the difficulties in controlling the process, secondary waste produced, high operational cost, and high risk of scaling up. Biotechnological approaches can be promising alternatives to pyrometallurgical and hydrometallurgical technologies in metal recovery from LIB waste. Microbiological metal dissolution or bioleaching has gained popularity for metal extraction from ores, concentrates, and recycled or residual materials in recent years. This technology is eco-friendly, safe to handle, and reduces operating costs and energy demands. The pre-treatment process (material preparation), microorganisms used in the bioleaching of LIBs, factors influencing the bioleaching process, methods of enhancing the leaching efficiency, regeneration of electrode materials, and future aspects have been discussed in detail.

Bioleaching for environmental remediation of toxic metals and metalloids: A review on soils, sediments, and mine tailings

Owing to industrial evolution, a huge mass of toxic metals, including Co, Cu, Cr, Mn, Ni, Pb, and Zn, and metalloids, such as As and Sb, has inevitably been released into the natural environment and accumulated in soils or sediments. Along with modern industrialization, many mineral mines have been explored and exploited to provide materials for industries. Mining industries also generate a vast amount of waste, such as mine tailings, which contain a high concentration of toxic metals and metalloids. Due to the low economic status, a majority of mine tailings are simply disposed into the surrounding environments, without any treatment. The mobilization and migration of toxic metals and metalloids from soils, sediments, and mining wastes to water systems via natural weathering processes put both the ecological system and human health at high risk. Considering both economic and environmental aspects, bioleaching is a preferable option for removing the toxic metals and metalloids because of its low cost and environmental safety. This chapter reviews the recent approaches of bioleaching for removing toxic metals and metalloids from soils, sediments, and mining wastes. The comparison between bioleaching and chemical leaching of various waste sources is also discussed in terms of efficiency and environmental safety. Additionally, the advanced perspectives of bioleaching for environmental remediation with consideration of other influencing factors are reviewed for future studies and applications.

Sticky Bacteria: Understanding the Behavior of a D-Galactose Adapted Consortium of Acidophilic Chemolithotroph Bacteria and Their Attachment on a Concentrate of Polymetallic Mineral

Various strategies to accelerate the formation of biofilms on minerals have been studied, and one of them is the use of D-galactose as an inducer of EPS production in planktonic cells of biooxidant bacteria. With the aim to evaluate the influence on the attachment and the effect over the solubilization of a polymetallic mineral concentrate, the behavior of a microbial consortium formed by Acidithiobacillus thiooxidans DSM 14887T and Leptospirillum ferrooxidans DSM 2705T previously induced with D-galactose for the early formation of EPS was studied. These microorganisms were previously adapted to 0.15 and 0.25% of D-galactose, respectively; afterward, different proportions of both strains were put in contact with the particle surface of a concentrate of polymetallic mineral. Also, to evaluate the affinity of each bacterium to the mineral, attachment tests were carried out with one of these species acting as a pre-colonizer. The same consortia were used to evaluate the solubilization of the polymetallic mineral. The results obtained show that the induction by D-galactose increases the microbial attachment percentage to the mineral by at least 10% with respect to the control of non-adapted consortia. On the other hand, the tests carried out with pre-colonization show that the order of inoculation also affects the microbial attachment percentage. From the different proportions tested, it was determined that the use of a consortium with a proportion of 50% of each species previously adapted to D-galactose and inoculated simultaneously, present a microbial attachment percentage to the mineral greater than 95% and better solubilization of a polymetallic mineral, reaching values of 9.7 and 11.7mgL-1 h-1 of Fe3+ and SO4 2-, respectively. Therefore, the use of D-galactose in small concentrations as inducer of EPS in acidophilic cells and the selection of an adequate strategy of inoculation can be beneficial to improve biooxidation since it would allow this process to develop in a shorter time by achieving a greater number of attached cells in a shorter time accelerating the solubilization of a sulfide mineral. Graphical AbstractEPS production using D-galactose as inducer and its influence in the attachment of consortia formed by differents proportions of A. thiooxidans and L. ferrooxidans inoculated at the same time and when one of them acting as a pre-colonizer.

Phylogenetically divergent bacteria consortium from neutral activated sludge showed heightened potential on bioleaching spent lithium-ion batteries

Recycling of spent lithium-ion batteries (LIBs) has become a global issue because of the potential environment risks raised by spent LIBs as well as high valuable metal content remaining in them. Although bioleaching is an environmentally friendly method to recover metals from spent LIBs, the commonly utilized bioleaching bacterial consortia or strains enriched/isolated from acidic environments cannot be applied at large scales owing to their long leaching cycle and poor tolerance to organic compounds. Here, two bioleaching consortia were enriched in 60 days from neutral activated sludge and were identified phylogenetically divergent from the documented bioleaching bacteria. The results showed that the novel consortia shortened the leaching cycle almost by half when compared to the previous reported consortia or strains, of which one consortium dominated by Acidithiobacillus ferrooxidans displayed high bioleaching efficiency on LiMn₂O₄, as 69.46% lithium (Li) and 67.60% manganese (Mn) were leached out in seven days. This consortium was further domesticated using cathodic materials for 100 days and proved consisted of three mixotrophs and two chemoautotrophs, three of which were novel species from the genera Sulfobacillus and Leptospirillum. More genes coding for proteins that utilize organic compounds were annotated in the metagenomic assembled genomes (MAGs) than previously reported. A mutualistic relationship between mixotrophs and chemoautotrophs was suggested to help the consortium surviving under either organic- rich or shortage environments. The results discovered that novel bioleaching bacteria with shorter leaching cycle and higher tolerance to organics could be enriched from non-acidic environments, which showed high potential for the metal recovering from spent LIBs or other organic-rich environments.