The bioleaching potential of a bacterial consortium

Bioremediation of paddy soil with amphitropic mixture markedly attenuates rice cadmium: Effect of soil cadmium removal and Fe/S-cycling bacteria in rhizosphere

Cadmium (Cd) pollution in paddy soil can easily lead to excessive Cd in rice, thereby considerably threatening human health. Microbial leaching is an effective pathway for the mobilization and removal of Cd from soil. In this study, an amphitropic mixture (AM) composed of autotrophic and heterotrophic microbial strains was used to leach Cd-contaminated paddy fields. Chemical analysis showed that the AM effectively removed 52 % of the total Cd, 39 % of the available Cd, and 60 % of the exchangeable and carbonate-bound Cd from the paddy soil. After bioleaching, the Cd in the discarded AM solution was adsorbed using a metal adsorbent. Effects of remediation on the soil nutrients or secondary pollution were not significant. Microbial analysis showed that >96 % and 67 % of the indigenous bacteria and fungi, respectively, remained in the AM-remediated soil. Double-cropped rice was cultivated to evaluate the Cd removal efficiency of grains using AM remediation. The Cd in early and late brown rice decreased by 86 % and 56 %, respectively, which was higher than that found for a series of biochemical remediation materials reported in other studies. Furthermore, the AM remediation promoted the growth of iron (Fe)- and sulfur (S)-cycling bacteria in the rice rhizosphere, such as Sulfuricurvum, Desulfurivibrio and Geobacter etc., which reduced the Cd availability in the soil and rice uptake. This study shows that AM has potential applications in the remediation of Cd-contaminated paddy fields and provides a new pathway for safe rice production.

Recovery of precious metals from waste printed circuit boards though bioleaching route: A review of the recent progress and perspective

The rapid proliferation of electronic waste (e-waste), including waste printed circuit boards (WPCBs), has exerted immense pressure on the environment. The recovery of precious metals from WPCBs not only serves as an effective means of alleviating this environmental burden but also generates economic value. This review focuses on bioleaching, an environmentally friendly method for extracting precious metals from WPCBs. Under various conditions, this method has achieved leaching rates of 30%-73% for Au and 33.8%-90% for Ag. However, there is a relative scarcity of studies on the bioleaching of precious metals from WPCBs. In this paper, we provide an overview of the current status of bioleaching for precious metals from WPCBs and describe the underlying mechanisms. We also briefly outline the influence of various process factors on leaching efficiency. While this review underscores the considerable potential of bioleaching in WPCBs applications, certain limitations hinder the engineering-scale application of the technology. Consequently, this paper describes the current enhanced processes for enhancing leaching efficiency. Overall, this review can serve as a valuable reference for future research endeavors, ultimately promoting the widespread utilization of bioleaching for the recovery of precious metals from WPCBs.

Unveiling abundance-dependent metabolic phenotypes of microbial communities

IMPORTANCE

In nature, organisms live in communities and not as isolated species, and their interactions provide a source of resilience to environmental disturbances. Despite their importance in ecology, human health, and industry, understanding how organisms interact in different environments remains an open question. In this work, we provide a novel approach that, only using genomic information, studies the metabolic phenotype exhibited by communities, where the exploration of suboptimal growth flux distributions and the composition of a community allows to unveil its capacity to respond to environmental changes, shedding light of the degrees of metabolic plasticity inherent to the community.

Influence of mobile genetic elements and insertion sequences in long- and short-term adaptive processes of Acidithiobacillus ferrooxidans strains

The recent revision of the Acidithiobacillia class using genomic taxonomy methods has shown that, in addition to the existence of previously unrecognized genera and species, some species of the class harbor levels of divergence that are congruent with ongoing differentiation processes. In this study, we have performed a subspecies-level analysis of sequenced strains of Acidithiobacillus ferrooxidans to prove the existence of distinct sublineages and identify the discriminant genomic/genetic characteristics linked to these sublineages, and to shed light on the processes driving such differentiation. Differences in the genomic relatedness metrics, levels of synteny, gene content, and both integrated and episomal mobile genetic elements (MGE) repertoires support the existence of two subspecies-level taxa within A. ferrooxidans. While sublineage 2A harbors a small plasmid related to pTF5, this episomal MGE is absent in sublineage 2B strains. Likewise, clear differences in the occurrence, coverage and conservation of integrated MGEs are apparent between sublineages. Differential MGE-associated gene cargo pertained to the functional categories of energy metabolism, ion transport, cell surface modification, and defense mechanisms. Inferred functional differences have the potential to impact long-term adaptive processes and may underpin the basis of the subspecies-level differentiation uncovered within A. ferrooxidans. Genome resequencing of iron- and sulfur-adapted cultures of a selected 2A sublineage strain (CCM 4253) showed that both episomal and large integrated MGEs are conserved over twenty generations in either growth condition. In turn, active insertion sequences profoundly impact short-term adaptive processes. The ISAfe1 element was found to be highly active in sublineage 2A strain CCM 4253. Phenotypic mutations caused by the transposition of ISAfe1 into the pstC2 encoding phosphate-transport system permease protein were detected in sulfur-adapted cultures and shown to impair growth on ferrous iron upon the switch of electron donor. The phenotypic manifestation of the △pstC2 mutation, such as a loss of the ability to oxidize ferrous iron, is likely related to the inability of the mutant to secure the phosphorous availability for electron transport-linked phosphorylation coupled to iron oxidation. Depletion of the transpositional △pstC2 mutation occurred concomitantly with a shortening of the iron-oxidation lag phase at later transfers on a ferrous iron-containing medium. Therefore, the pstII operon appears to play an essential role in A. ferrooxidans when cells oxidize ferrous iron. Results highlight the influence of insertion sequences and both integrated and episomal mobile genetic elements in the short- and long-term adaptive processes of A. ferrooxidans strains under changing growth conditions.

Molecular Insights into a Novel Cu(I)-Sensitive ArsR/SmtB Family Repressor in Extremophile Acidithiobacillus caldus

Acidithiobacillus caldus is a common bioleaching bacterium that is inevitably exposed to extreme copper stress in leachates. The ArsR/SmtB family of metalloregulatory repressors regulates homeostasis and resistance in bacteria by specifically responding to metals. Here, we characterized A. caldus Cu(I)-sensitive repressor (AcsR) and gained molecular insights into this new member of the ArsR/SmtB family. Transcriptional analysis indicated that the promoter (PIII) of acsR was highly active in Escherichia coli but inhibited upon AcsR binding to the PIII-acsR region. Size exclusion chromatography and circular dichroism spectra revealed that Cu^I-AcsR shared an identical assembly state with apo-AcsR, as a dimer with fewer α helices, more extended strands, and more β turns. Mutation of the cysteine site in AcsR did not affect its assembly state. Copper(I) titrations revealed that apo-AcsR bound two Cu(I) molecules per monomer in vitro with an average dissociation constant (K_D) for bicinchoninic acid competition of 2.55 × 10^-9 M. Site-directed mutation of putative Cu(I)-binding ligands in AcsR showed that replacing Cys64 with Ala reduces copper binding ability from two Cu(I) molecules per monomer to one, with an average K_D of 6.05 × 10^-9 M. Electrophoretic mobility shift assays revealed that apo-AcsR has high affinity for the 12-2-12 imperfect inverted repeats P2245 and P2270 in the acsR gene cluster and that Cu-loaded AcsR had lower affinity for DNA fragments than apo-AcsR. We developed a hypothetical working model of AcsR to better understand Cu resistance mechanisms in A. caldus. IMPORTANCE Copper (Cu) resistance among various microorganisms is attracting interest. The chemolithoautotrophic bacterium A. caldus, which can tolerate extreme copper stress (≥10 g/L Cu ions), is typically used to bioleach chalcopyrite (CuFeS₂). Understanding of Cu resistance in A. caldus is limited due to scant investigation and the absence of efficient gene manipulation tools. Here, we characterized a new member of the ArsR/SmtB family of prokaryotic metalloregulatory transcriptional proteins that repress operons linked to stress-inducing concentrations of heavy metal ions. This protein can bind two Cu(I) molecules per monomer and negatively regulate its gene cluster. Members of the ArsR/SmtB family have not been investigated in A. caldus until now. The discovery of this novel protein enriches understanding of Cu homeostasis in A. caldus.

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.

Indirect bioleaching recovery of valuable metals from electroplating sludge and optimization of various parameters using response surface methodology (RSM)

Electroplating sludge contains amounts of valuable/toxic metals as a typical hazardous solid waste, but existing technology is hard to simultaneously gain the high recovery of valuable metals and its convert into general solid waste. In this study, indirect bioleaching process was optimized by using RSM for high recovery of four valuable metals (Ni, Cu, Zn and Cr) from electroplating sludge and its shift into general waste. The results showed that the maximum leaching rate respectively was 100% for Ni, 96.5% for Cu, 100% for Zn and 76.1% for Cr at the optimal conditions. In particular, bioleaching saw a much better performance than H₂SO₄ leaching in removal of highly toxic Cr (76.1% vs. 30.2%). The extraction efficiency of Cr by H₂SO₄ leaching sharply rose to 72.6% in the presence of 9.0 g/L Fe³⁺, suggesting that Fe³⁺ played an important role in the bioleaching of Cr. Based on bioleaching dynamics analysis, it was speculated that Fe³⁺ passes through the solid shell and enter inside the sludge to attack Cr assisting by extracellular polymeric substances (EPS), leading to high extraction and low residue of Cr. Meanwhile, due to high-efficient release and removal of valuable/toxic metals by bioleaching, the bioleached residues successfully degraded into general based on TCLP test and can be reused as construction material safely.

Deciphering the extracellular and intracellular antibiotic resistance genes in multiple environments reveals the persistence of extracellular ones

The extracellular and intracellular antibiotic resistance genes (eARGs and iARGs) together constitute the entire resistome in environments. However, the systematic analysis of eARGs and iARGs was still inadequate. Three kinds of environments, i.e., livestock manure, sewage sludge, and lake sediment, were analyzed to reveal the comprehensive characteristics of eARGs and iARGs. Based on the metagenomic data, the diversities, relative abundances, and compositions of eARGs and iARGs were similar. The extracellular and intracellular integrons and insertion sequences (ISs) also did not show any significant differences. However, the degree and significance of the correlation between total relative abundances of integrons/ISs and ARGs were lower outside than inside the cells. Gene cassettes carried by class 1 integron were amplified in manure and sludge samples, and sequencing results showed that the identified ARGs extracellularly and intracellularly were distinct. By analyzing the genetic contexts, most ARGs were found located on chromosomes. Nevertheless, the proportion of ARGs carried by plasmids increased extracellularly. qPCR was employed to quantify the absolute abundances of sul1, sul2, tetO, and tetW, and their extracellular proportions were found highest in sludge samples. These findings together raised the requirements of considering eARGs and iARGs separately in terms of risk evaluation and removal management.

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.

Bioleaching of Heavy Metals from Printed Circuit Boards with an Acidophilic Iron-Oxidizing Microbial Consortium in Stirred Tank Reactors

In this study, bioleaching was carried out for the recovery of metals (copper, zinc, tin, lead, gold and silver) from printed circuit boards residues (PCBs), one of the most important wastes from electrical and electronic equipment, using an acidophilic iron-oxidizing bacterial consortium enriched with minerals from a gold mine in the Arequipa region, Peru. High-throughput sequencing and analysis of the 16S rRNA biomarker revealed that this consortium was predominantly composed of Tissierella, Acidiphilium and Leptospirillum bacteria, from which the latter is known to grow by chemolithotrophy through iron oxidation. After the enrichment process, the acidophilic iron-oxidizing consortium was first tested for its tolerance to different PCBs concentrations, showing best growth up to 10 g/L of PCBs and a tolerance index of 0.383. Based on these results, the bioleaching efficiency of the consortium was investigated for 10 g/L of PCBs in stirred tank reactors coupled to an aeration system, for 18 days. High bioleaching efficiencies were achieved for copper and zinc (69% and 91%, respectively), indicating that these two metals can be easily extracted in this leaching system. Lower extraction efficiencies were achieved for tin (16%) and gold (28%), while for lead and silver only a residual recovery (<0.25%) was detected. These results indicate that the enriched bacterial consortium originating from the Arequipa region, Peru, has a high capacity to recover different metals of economic importance.

Co-occurrence Interaction Networks of Extremophile Species Living in a Copper Mining Tailing

Copper mining tailings are characterized by high concentrations of heavy metals and an acidic pH, conditions that require an extreme adaptation for any organism. Currently, several bacterial species have been isolated and characterized from mining environments; however, very little is known about the structure of microbial communities and how their members interact with each other under the extreme conditions where they live. This work generates a co-occurrence network, representing the bacterial soil community from the Cauquenes copper tailing, which is the largest copper waste deposit worldwide. A representative sampling of six zones from the Cauquenes tailing was carried out to determine pH, heavy metal concentration, total DNA extraction, and subsequent assignment of Operational Taxonomic Units (OTUs). According to the elemental concentrations and pH, the six zones could be grouped into two sectors: (1) the "new tailing," characterized by neutral pH and low concentration of elements, and (2) the "old tailing," having extremely low pH (~3.5) and a high concentration of heavy metals (mainly copper). Even though the abundance and diversity of species were low in both sectors, the Pseudomonadaceae and Flavobacteriaceae families were over-represented. Additionally, the OTU identifications allowed us to identify a series of bacterial species with diverse biotechnological potentials, such as copper bioleaching and drought stress alleviation in plants. Using the OTU information as a template, we generated co-occurrence networks for the old and new tailings. The resulting models revealed a rearrangement between the interactions of members living in the old and new tailings, and highlighted conserved bacterial drivers as key nodes, with positive interactions in the network of the old tailings, compared to the new tailings. These results provide insights into the structure of the soil bacterial communities growing under extreme environmental conditions in mines.

Microbial recovery of critical metals from secondary sources

The continuous development of technologies involving critical metals, both in Europe and over the world, and geopolitical challenges in areas rich in critical metal sources, imposed increased research efforts to recover them from secondary sources, by eco-efficient processes. Yet, microbes-metal interactions are not sufficiently exploited to recover metals from secondary sources, although they are already used in ore extraction. This review examines and compare strategies and processes involving microorganisms for critical metals recovery, since conventional physico-chemical methods are energy-intensive and often polluting. Two groups of microbial assisted recovery processes are discussed: metal mobilization from metal bearing waste, and selective metal separation from leaching solutions by immobilization on microbial biomass. Because most of the identified microbial technologies are developed on laboratory scale, the increase of biorecovery efficiency is compulsory for enhancing scaling-up potential. Future developments focused on novel microorganisms and high-performance strategies for critical metal recovery by microbial processes are considered.

Cyanidiophyceae (Rhodophyta) Tolerance to Precious Metals: Metabolic Response to Palladium and Gold

Polyextremophilic red algae, which belong to the class Cyanidiophyceae, are adapted to live in geothermal and volcanic sites. These sites often have very high concentrations of heavy and precious metals. In this study, we assessed the capacity of three strains of Galdieria (G. maxima, G. sulphuraria, and G. phlegrea) and one strain of Cyanidiumcaldarium to tolerate different concentrations of precious metals, such as palladium (Cl4K2Pd) and gold (AuCl4K) by monitoring algal growths in cultures exposed to metals, and we investigated the algae potential oxidative stress induced by the metals. This work provides further understanding of metals responses in the Cyanidiophyceae, as this taxonomic class is developed as a biological refinement tool.

Recovery of valuable metals from waste printed circuit boards using organic acids synthesised by Aspergillus niveus

Organic acids such as citric acid, itaconic acid and oxalic acid synthesised by Aspergillus niveus were used for the bioleaching of metals from waste printed circuit boards. Bioleaching of valuable metals was performed in one‐step, two‐steps and spent medium approaches using A. niveus. In the absence of waste printed circuit boards (WPCBs), the dry cell weight of A. niveus was higher when compared with the presence of WPCBs. Variations in the dry cell weight were observed for the presence of different particle sizes. The increase in itaconic acid and oxalic acid synthesis was found at a reduced particle size (60–80 mesh) and reached the maximum titre of itaconic acid (22.35 ± 0.87 mM) and oxalic acid (12.75 ± 0.54 mM) in 12 days during the two‐step bioleaching. The maximum recovery of 75.66% Zn, 73.58% Ni and 80.25% Cu from WPCBs was achieved in 15 days in two‐step leaching with particle sizes of the mesh being 60–80.

A mini-review of heavy metal recycling technologies for municipal solid waste incineration fly ash

This mini-review article summarizes the available technologies for the recycling of heavy metals (HMs) in municipal solid waste incineration (MSWI) fly ash (FA). Recovery technologies included thermal separation (TS), chemical extraction (CE), bioleaching, and electrochemical processes. The reaction conditions of various methods, the efficiency of recovering HMs from MSWI FA and the difficulties and solutions in the process of technical development were studied. Evaluation of each process has also been done to determine the best HM recycling method and future challenges. Results showed that while bioleaching had minimal environmental impact, the process was time-consuming. TS and CE were the most mature technologies, but the former process was not cost-effective. Overall, it has the greatest economic potential to recover metals by CE with scrubber liquid produced by a wet air pollution control system. An electrochemical process or solvent extraction could then be applied to recover HMs from the enriched leachate. Ongoing development of TS and bioleaching technologies could reduce the treatment cost or time.

Bioleaching of vanadium by Acidithiobacillus ferrooxidans from vanadium-bearing resources: Performance and mechanisms

Bioleaching is promising to meet the demand of strategic vanadium both economically and environmentally. Whereas the combination of bioleaching with traditional techniques is of great interest, little is known on bioleaching of vanadium from abundant vanadium-bearing resources utilized/produced in existing processes. This study investigated the bioleaching of vanadium from vanadium-titanium magnetite, steel slag, and clinker, which are common raw mineral and intermediates used in conventional vanadium extraction process. Clinker had greater leachability by Acidithiobacillus ferrooxidans, compared to vanadium-titanium magnetite and steel slag. Pulp density, inoculum volume, initial pH and initial Fe²⁺ concentration had influencing effects on this bioleaching process. Under optimal condition with 3% pulp density, 10% inoculum volume, initial pH at 1.8, and 3 g/L initial Fe²⁺ concentration, the bioleaching of clinker achieved the maximum vanadium leaching efficiency of 59.0%. Both X-ray fluorescence and energy dispersive spectroscopy analysis confirmed the reduction of vanadium content in the solid residues after leaching. The results of Community Bureau of Reference sequential extraction suggested that vanadium in acid-soluble and oxidizable phase was more easily leachable. This study is helpful to develop sustainable and practical techniques for vanadium extraction from abundant raw materials and step forward in combining bioleaching with traditional process.

Bioleaching and Electrochemical Behavior of Chalcopyrite by a Mixed Culture at Low Temperature

Low-temperature biohydrometallurgy is implicated in metal recovery in alpine mining areas, but bioleaching using microbial consortia at temperatures <10°C was scarcely discussed. To this end, a mixed culture was used for chalcopyrite bioleaching at 6°C. The mixed culture resulted in a higher copper leaching rate than the pure culture of Acidithiobacillus ferrivorans strain YL15. High-throughput sequencing technology showed that Acidithiobacillus spp. and Sulfobacillus spp. were the mixed culture's major lineages. Cyclic voltammograms, potentiodynamic polarization and electrochemical impedance spectroscopy unveiled that the mixed culture enhanced the dissolution reactions, decreased the corrosion potential and increased the corrosion current, and lowered the charge transfer resistance and passivation layer impedance of the chalcopyrite electrode compared with the pure culture. This study revealed the mechanisms via which the mixed culture promoted the chalcopyrite bioleaching.

Bioleaching of Copper-Containing Electroplating Sludge

The recovery of precious metals from solid waste through bioleaching has become a research hotspot in recent years. Thus, in this study, different strategies, such as chemical sulfuric acid leaching and mixed consortium bioleaching, were adopted to extract copper from Copper-Containing Electroplating Sludge. The results showed that, compared to chemical leaching, bioleaching showed a much better performance. Indeed, copper bioleaching efficiency reached 94.3% on day 7 (21.1% higher than that of chemical leaching). The results also indicated that the process of bioleaching involved more mechanisms and reactions than that of chemical leaching. The SEM and EDX tests showed that the surface morphology of the sludge changed significantly after bioleaching, and that an insignificant amount of copper remained in the leached residues. Furthermore, the leached residues passed the characteristic leaching toxic test and thus can be considered as non-hazardous raw materials for the construction industry. Hence, adopting a mixed consortium leaching process to extract copper from Copper-Containing Electroplating Sludge will not only significantly reduce environmental pollution, but will also use metal resources more efficiently.

Synthetic biology approaches to copper remediation: bioleaching, accumulation and recycling

One of the current aims of synthetic biology is the development of novel microorganisms that can mine economically important elements from the environment or remediate toxic waste compounds. Copper, in particular, is a high-priority target for bioremediation owing to its extensive use in the food, metal and electronic industries and its resulting common presence as an environmental pollutant. Even though microbe-aided copper biomining is a mature technology, its application to waste treatment and remediation of contaminated sites still requires further research and development. Crucially, any engineered copper-remediating chassis must survive in copper-rich environments and adapt to copper toxicity; they also require bespoke adaptations to specifically extract copper and safely accumulate it as a human-recoverable deposit to enable biorecycling. Here, we review current strategies in copper bioremediation, biomining and biorecycling, as well as strategies that extant bacteria use to enhance copper tolerance, accumulation and mineralization in the native environment. By describing the existing toolbox of copper homeostasis proteins from naturally occurring bacteria, we show how these modular systems can be exploited through synthetic biology to enhance the properties of engineered microbes for biotechnological copper recovery applications.

An integrated insight into bioleaching performance of chalcopyrite mediated by microbial factors: Functional types and biodiversity

Six artificial communities with different function or biodiversity were reconstructed by six typical bioleaching species for chalcopyrite leaching. Absence of sulfur oxidizers in communities significantly reduced copper extraction rates, and low diversity communities also exhibited slightly poor bioleaching performances. The variations of pH, redox potential, ferrous and copper ions indicated that the community with both sulfur oxidizers and high diversity showed fast adaptation to the environment and rapid dissolution of chalcopyrite. Integrated analysis of mineralogical and microbial parameters demonstrated that functional types of microorganisms made more contributions in mediating chalcopyrite dissolution than microbial diversity. Further correlation analysis between microbial types and chalcopyrite dissolution performances showed that sulfur oxidizers, especially Acidithiobacillus caldus, could greatly accelerate chalcopyrite dissolution by regulating solution physicochemical factors, such as redox potential and pH. This study provided a theoretical basis for improving bioleaching efficiency by balancing microbial functional types and biodiversity.

Genomic Insights into the Aquatic Fusarium spp. QHM and BWC1 and Their Application in Phenol Degradation

Fusarium species are widely distributed in ecosystems with wide pH ranges and play pivotal roles in aquatic communities through xenobiotic degradation. It is necessary to explore genomic insights for the application of Fusarium species. In this study, the aquatic Fusarium strains QHM and BWC1 were isolated from a coal mine and a subterranean river, respectively, cultured under acidic conditions and sequenced genomically. Phylogenetic analysis of the isolates was conducted based on the sequences of internal transcripts and sequences encoding β-microtubulin, translation elongation factors and the second large subunit of the RNA polymerase. Fusarium QHM demonstrates close relationships to the type strains of Fusarium ramigenum and Fusarium napiforme in Fusarium fujikuroi species complex. Fusarium BWC1 is predicted to be Fusarium subglutinans. A total of 479 and 2352 scaffolds, corresponding to 14,814 and 15,295 genes, were obtained for Fusarium spp. QHM and BWC1, respectively. Genomic analyses revealed that they harbored biodegradation pathways for aromatic compounds. Phenol stress experiments indicated that Fusarium spp. QHM and BWC1 exhibited optimal degradation at a density of 300 mg/L to achieve a phenol degradation rate of 39.91-43.65% at pH 3.5-4.0. Fusarium spp. QHM and BWC1 were applied to mock phenol-water, and an average phenol degradation rate of 51.71-65.55% indicated the feasibility of these species. The findings of this study have important implications for Fusarium spp. QHM and BWC1 applied to phenol wastewater in acidic or neutral pH environments.

Bioleaching for resource recovery from low-grade wastes like fly and bottom ashes from municipal incinerators: A SWOT analysis

Bioleaching (or microbial leaching) is a biohydrometallurgical technology that can be applied for metal recovery from anthropogenic waste streams. In particular, fly ashes and bottom ashes of municipal solid waste incineration (MSWI) can be used as a target material for biomining. Globally, approximately 46 million tonnes of MSWI ashes are produced annually. Currently landfilled or used as aggregate, these contain large amounts of marketable metals, equivalent to low-grade ores. There is opportunity to recover critical materials as the circular economy demands, using mesophile, moderately thermophile, and extremophile microorganisms for bioleaching. A Strengths, Weaknesses, Opportunities and Threats (SWOT) analysis was developed to assess the potential of this biotechnology to recover critical metals from MSWI wastes. Bioleaching has potential as a sustainable technology for resource recovery and enhanced waste management. However, stakeholders can only reap the full benefits of bioleaching by addressing both the technical engineering challenges and regulatory requirements needed to realise and integrated approach to resource use.

Dissolution of Cu and Zn-bearing ore by indigenous iron-oxidizing bacterial consortia supplemented with dried bamboo sawdust and variations in bacterial structural dynamics: A new concept in bioleaching

Disposing of low-grade ores involves numerous environmental issues. Bioleaching with acidophilic bacteria is the preferred solution to process these ores for metals recovery. In this study, indigenous iron-oxidizing bacteria Acidithiobacillus ferrooxidans, Leptospirillum ferriphilum, and Leptospirillum ferrooxidans were used in consortia supplemented with acid-treated bamboo sawdust (BSD) for copper and zinc recovery. Findings showed the extreme catalytic response of BSD with the best recovery of metals. Maximum of 92.2 ± 4.0% copper (0.35%) and 90.0 ± 5.4% zinc (0.33%) were recovered after 8 days of processing in the presence of 2 g/L BSD. Significant variations were reported in physicochemical parameters during bioleaching in the presence of a different concentration of BSD. Fourier Transform Infrared spectroscopy results of bioleached residues showed significant variations in spectral pattern and maximum variations were reported in 2.0 g/L BSD, which indicates maximum metals dissolutions. The impact of bacterial consortia and BSD on iron speciation of bioleached ores was analyzed by using Mössbauer spectroscopy and clear variations in iron speciation were reported. Furthermore, the bacterial community structure dynamics revealed significant variations in the individual bacterial proportion in each experiment. This finding shows that the dosage concentration of BSD influenced the microenvironment, which effect the bacterial abundance and these variations in the bacterial structural communities were not associated with the initial proportion of bacterial cells inoculated in the bioleaching process. Moreover, the mechanism of chemical reactions was proposed by explaining the possible role of BSD as a reductant under micro-aerophilic conditions that facilitates the bacterial reduction of ferric iron. This type of bioleaching process with indigenous iron-oxidizing bacteria and BSD has significant potential to further upscale the bioleaching process for recalcitrant ore bodies in an environment friendly and cost-effective way.

Recent advances in the recovery of metals from waste through biological processes

Wastes containing critical metals are generated in various fields, such as energy and computer manufacturing. Metal-bearing wastes are considered as secondary sources of critical metals. The conventional physicochemical methods of metals recovery are energy-intensive and cause further pollution. Low-cost and eco-friendly technologies including biosorbents, bioelectrochemical systems (BESs), bioleaching, and biomineralization, have become alternatives in the recovery of critical metals. However, a relatively low recovery rate and selectivity severely hinder their large-scale applications. Researchers have expanded their focus to exploit novel strain resources and strategies to improve the biorecovery efficiency. The mechanisms and potential applicability of modified biological techniques for improving the recovery of critical metals need more attention. Hence, this review summarize and compare the strategies that have been developed for critical metals recovery, and provides useful insights for energy-efficient recovery of critical metals in future industrial applications.

Integration of Biological Networks for Acidithiobacillus thiooxidans Describes a Modular Gene Regulatory Organization of Bioleaching Pathways

Acidithiobacillus thiooxidans is one of the most studied biomining species, highlighting its ability to oxidize reduced inorganic sulfur compounds, coupled with its elevated capacity to live under an elevated concentration of heavy metals. In this work, using an in silico semi-automatic genome scale approach, two biological networks for A. thiooxidans Licanantay were generated: (i) An affinity transcriptional regulatory network composed of 42 regulatory family genes and 1,501 operons (57% genome coverage) linked through 2,646 putative DNA binding sites (arcs), (ii) A metabolic network reconstruction made of 523 genes and 1,203 reactions (22 pathways related to biomining processes). Through the identification of confident connections between both networks (V-shapes), it was possible to identify a sub-network of transcriptional factor (34 regulators) regulating genes (61 operons) encoding for proteins involved in biomining-related pathways. Network analysis suggested that transcriptional regulation of biomining genes is organized into different modules. The topological parameters showed a high hierarchical organization by levels inside this network (14 layers), highlighting transcription factors CysB, LysR, and IHF as complex modules with high degree and number of controlled pathways. In addition, it was possible to identify transcription factor modules named primary regulators (not controlled by other regulators in the sub-network). Inside this group, CysB was the main module involved in gene regulation of several bioleaching processes. In particular, metabolic processes related to energy metabolism (such as sulfur metabolism) showed a complex integrated regulation, where different primary regulators controlled several genes. In contrast, pathways involved in iron homeostasis and oxidative stress damage are mainly regulated by unique primary regulators, conferring Licanantay an efficient, and specific metal resistance response. This work shows new evidence in terms of transcriptional regulation at a systems level and broadens the study of bioleaching in A. thiooxidans species.

Removal of chemical oxygen demand (COD) and heavy metals by catalytic ozonation-microbial fuel cell and Acidithiobacillus ferrooxidans leaching in flotation wastewater (FW)

A catalytic ozonation-microbial fuel cell and Acidithiobacillus ferrooxidans leaching process was used in treating flotation wastewater to remove chemical oxygen demand (COD) and heavy metals in this study. The results indicated that when adding 1 g/L of manganese/modified activated carbon catalyst and 1.5 g/min ozone flow, the COD could be degraded from 2,043.67 mg/L to 711.4 mg/L. After that, the COD could continue decreasing down to 72.56 mg/L through an air-cathode single chamber microbial fuel cell (SCMFCs), coated with 0.4 mg/cm² platinum catalyst, after 15 days. Meanwhile, the maximum voltages and the ultimate power density of the SCMFCs reached 378.96 mV and 7,608.35 mW/m², respectively. For filter residue, when 1.2 g/L Fe³⁺, 10% (m/v) filter residue, and 10% Acidithiobacillus ferrooxidans were added, the copper leaching rate could reach 92.69% after 7 days if the pH values were adjusted to 1.9. Furthermore, the other heavy metals were also decreased to a level lower than the pollution control standard (Chinese standard GB3838-2002). The leaching parameters in terms of pH, redox potential, and cyclic voltammetry showed that the addition of an appropriate concentration of Fe³⁺ to the leaching systems was beneficial to copper dissolution.

Metal biorecovery and bioremediation: Whether or not thermophilic are better than mesophilic microorganisms

Metal mobilization and immobilization catalyzed by microbial action are key processes in environmental biotechnology. Metal mobilization from ores, mining wastes, or solid residues can be used for recovering metals and/or remediating polluted environments; furthermore, immobilization reduces the migration of metals; cleans up effluents plus ground- and surface water; and, moreover, can help to concentrate and recover metals. Usually these processes provide certain advantages over traditional technologies such as more efficient economical and environmentally sustainable results. Since elevated temperatures typically increase chemical kinetics, it could be expected that bioprocesses should also be enhanced by replacing mesophiles with thermophiles or hyperthermophiles. Nevertheless, other issues like process stability, flexibility, and thermophile-versus-mesophile resistance to acidity and/or metal toxicity should be carefully considered. This review critically analyzes and compares thermophilic and mesophilic microbial performances in recent and selected representative examples of metal bioremediation and biorecovery.

Mixotrophic acidophiles increase cadmium soluble fraction and phytoextraction efficiency from cadmium contaminated soils

A profound concern in developing microbially-assisted phytoextraction is that introduced microbes not only remove heavy metals from contaminated soils but also enhance metal uptake into plant tissues from the treated soils. Cadmium (Cd) removal efficiencies were compared after leaching with deionized water (CK), acidified basal salts medium (acid control), cell-free spent medium (spent bioleaching) and mixotrophic acidophiles (two-step bioleaching). Two-step bioleaching using the mixotrophic acidophiles removed 34% of total Cd and 87% of available Cd, significantly more than CK (3% and 4%), acid control (12% and 51%) and spent bioleaching (26% and 75%). Pot experiments of water spinach growing in four treated soils were conducted to evaluate the Cd uptake performance in plants. Notably, the mixotrophic acidophiles increased Cd concentration in plant tissues by 78% compared to the CK group. More interestingly, the mixotrophic acidophiles were not colonized in soils but caused the compositional increase of indigenous microbes such as the genera of Alicyclobacillus, Clostridium sensu strict and Streptacidiphilus. Meanwhile, two-step bioleaching had little effects on soil structure and physicochemical properties determined by the spectroscopy characteristics analysis. These results implied that the mixotrophic acidophiles facilitated the development of microbially-assisted phytoextraction technology.

Assessment of Bioleaching Microbial Community Structure and Function Based on Next-Generation Sequencing Technologies

It is widely known that bioleaching microorganisms have to cope with the complex extreme environment in which microbial ecology relating to community structure and function varies across environmental types. However, analyses of microbial ecology of bioleaching bacteria is still a challenge. To address this challenge, numerous technologies have been developed. In recent years, high-throughput sequencing technologies enabling comprehensive sequencing analysis of cellular RNA and DNA within the reach of most laboratories have been added to the toolbox of microbial ecology. The next-generation sequencing technology allowing processing DNA sequences can produce available draft genomic sequences of more bioleaching bacteria, which provides the opportunity to predict models of genetic and metabolic potential of bioleaching bacteria and ultimately deepens our understanding of bioleaching microorganism. High-throughput sequencing that focuses on targeted phylogenetic marker 16S rRNA has been effectively applied to characterize the community diversity in an ore leaching environment. RNA-seq, another application of high-throughput sequencing to profile RNA, can be for both mapping and quantifying transcriptome and has demonstrated a high efficiency in quantifying the changing expression level of each transcript under different conditions. It has been demonstrated as a powerful tool for dissecting the relationship between genotype and phenotype, leading to interpreting functional elements of the genome and revealing molecular mechanisms of adaption. This review aims to describe the high-throughput sequencing approach for bioleaching environmental microorganisms, particularly focusing on its application associated with challenges.

Intensified bioleaching of chalcopyrite by communities with enriched ferrous or sulfur oxidizers

The chalcopyrite bioleaching by enriched ferrous or sulfur oxidizers was investigated. The bioleaching was also intensified three times by the enriched communities. The results indicated that copper recoveries extracted by the enriched ferrous and sulfur oxidizers (Fe-O and S-O) were 38.87% and 43.13%, compared with that by the original community (35.35%). The positive effects of re-introducing S-enriched community to Fe-O and S-O groups were observed with copper extraction rates up to 41.67% and 46.45%. CCA indicated that the community dynamics intensified by S-enriched community was closer to that of the no re-inoculated one, but the Fe-enriched community drove a great fluctuation. A mechanism model for S-enriched community intensifying chalcopyrite bioleaching was proposed. More sulfur oxidizers in community slowed down jarosite formation and maintained lower ORP, which was propitious to chalcopyrite dissolution. Meanwhile, they accelerated S⁰ decomposition and decreased pH, which promoted acid leaching of chalcopyrite at a low cost.

Sulfate-Reducing Bacteria as an Effective Tool for Sustainable Acid Mine Bioremediation

Mining industries produce vast waste streams that pose severe environmental pollution challenge. Conventional techniques of treatment are usually inefficient and unsustainable. Biological technique employing the use of microorganisms is a competitive alternative to treat mine wastes and recover toxic heavy metals. Microorganisms are used to detoxify, extract or sequester pollutants from mine waste. Sulfate-reducing microorganisms play a vital role in the control and treatment of mine waste, generating alkalinity and neutralizing the acidic waste. The design of engineered sulfate-reducing bacteria (SRB) consortia will be an effective tool in optimizing degradation of acid mine tailings waste in industrial processes. The understanding of the complex functions of SRB consortia vis-à-vis the metabolic and physiological properties in industrial applications and their roles in interspecies interactions are discussed.

Biomarker panels for characterizing microbial community biofilm formation as composite molecular process

Microbial consortia execute collaborative molecular processes with contributions from individual species, on such basis enabling optimized molecular function. Such collaboration and synergies benefit metabolic flux specifically in extreme environmental conditions as seen in acid mine drainage, with biofilms as relevant microenvironment. However, knowledge about community species composition is not sufficient for deducing presence and efficiency of composite molecular function. For this task molecular resolution of the consortium interactome is to be retrieved, with molecular biomarkers particularly suited for characterizing composite molecular processes involved in biofilm formation and maintenance. A microbial species set identified in 18 copper environmental sites provides a data matrix for deriving a cross-species molecular process model of biofilm formation composed of 191 protein coding genes contributed from 25 microbial species. Computing degree and stress centrality of biofilm molecular process nodes allows selection of network hubs and central connectors, with the top ranking molecular features proposed as biomarker candidates for characterizing biofilm homeostasis. Functional classes represented in the biomarker panel include quorum sensing, chemotaxis, motility and extracellular polysaccharide biosynthesis, complemented by chaperones. Abundance of biomarker candidates identified in experimental data sets monitoring different biofilm conditions provides evidence for the selected biomarkers as sensitive and specific molecular process proxies for capturing biofilm microenvironments. Topological criteria of process networks covering an aggregate function of interest support the selection of biomarker candidates independent of specific community species composition. Such panels promise efficient screening of environmental samples for presence of microbial community composite molecular function.

Advances in bioleaching for recovery of metals and bioremediation of fuel ash and sewage sludge

Bioleaching has been successfully used in commercial metal mining for decades. It uses microbes to biosolubilize metal-containing inorganic compounds such as metal oxides and sulfides. There is a growing interest in using bioleaching for bioremediation of solid wastes by removing heavy metals from ash and sewage sludge. This review presents the state of the art in bioleaching research for recovery of metals and bioremediation of solid wastes. Various process parameters such as reaction time, pH, temperature, mass transfer rate, nutrient requirement, pulp density and particle size are discussed. Selections of more effective microbes are assessed. Pretreatment methods that enhance bioleaching are also discussed. Critical issues in bioreactor scale-up are analyzed. The potential impact of advances in biofilm and microbiome is explained.

Codon usage bias reveals genomic adaptations to environmental conditions in an acidophilic consortium

The analysis of codon usage bias has been widely used to characterize different communities of microorganisms. In this context, the aim of this work was to study the codon usage bias in a natural consortium of five acidophilic bacteria used for biomining. The codon usage bias of the consortium was contrasted with genes from an alternative collection of acidophilic reference strains and metagenome samples. Results indicate that acidophilic bacteria preferentially have low codon usage bias, consistent with both their capacity to live in a wide range of habitats and their slow growth rate, a characteristic probably acquired independently from their phylogenetic relationships. In addition, the analysis showed significant differences in the unique sets of genes from the autotrophic species of the consortium in relation to other acidophilic organisms, principally in genes which code for proteins involved in metal and oxidative stress resistance. The lower values of codon usage bias obtained in this unique set of genes suggest higher transcriptional adaptation to living in extreme conditions, which was probably acquired as a measure for resisting the elevated metal conditions present in the mine.

Enhancement of Metallosphaera sedula Bioleaching by Targeted Recombination and Adaptive Laboratory Evolution

Thermophilic and lithoautotrophic archaea such as Metallosphaera sedula occupy acidic, metal-rich environments and are used in biomining processes. Biotechnological approaches could accelerate these processes and improve metal recovery by biomining organisms, but systems for genetic manipulation in these organisms are currently lacking. To gain a better understanding of the interplay between metal resistance, autotrophy, and lithotrophic metabolism, a genetic system was developed for M. sedula and used to evaluate parameters governing the efficiency of copper bioleaching. Additionally, adaptive laboratory evolution was used to select for naturally evolved M. sedula cell lines with desirable phenotypes for biomining, and these adapted cell lines were shown to have increased bioleaching capacity and efficiency. Genomic methods were used to analyze mutations that led to resistance in the experimentally evolved cell lines, while transcriptomics was used to examine changes in stress-inducible gene expression specific to the environmental conditions.

Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models

Genome-scale metabolic models have become the tool of choice for the global analysis of microorganism metabolism, and their reconstruction has attained high standards of quality and reliability. Improvements in this area have been accompanied by the development of some major platforms and databases, and an explosion of individual bioinformatics methods. Consequently, many recent models result from "à la carte" pipelines, combining the use of platforms, individual tools and biological expertise to enhance the quality of the reconstruction. Although very useful, introducing heterogeneous tools, that hardly interact with each other, causes loss of traceability and reproducibility in the reconstruction process. This represents a real obstacle, especially when considering less studied species whose metabolic reconstruction can greatly benefit from the comparison to good quality models of related organisms. This work proposes an adaptable workspace, AuReMe, for sustainable reconstructions or improvements of genome-scale metabolic models involving personalized pipelines. At each step, relevant information related to the modifications brought to the model by a method is stored. This ensures that the process is reproducible and documented regardless of the combination of tools used. Additionally, the workspace establishes a way to browse metabolic models and their metadata through the automatic generation of ad-hoc local wikis dedicated to monitoring and facilitating the process of reconstruction. AuReMe supports exploration and semantic query based on RDF databases. We illustrate how this workspace allowed handling, in an integrated way, the metabolic reconstructions of non-model organisms such as an extremophile bacterium or eukaryote algae. Among relevant applications, the latter reconstruction led to putative evolutionary insights of a metabolic pathway.

Evolution of copper arsenate resistance for enhanced enargite bioleaching using the extreme thermoacidophile Metallosphaera sedula

Adaptive laboratory evolution (ALE) was employed to isolate arsenate and copper cross-resistant strains, from the copper-resistant M. sedula CuR1. The evolved strains, M. sedula ARS50-1 and M. sedula ARS50-2, contained 12 and 13 additional mutations, respectively, relative to M. sedula CuR1. Bioleaching capacity of a defined consortium (consisting of a naturally occurring strain and a genetically engineered copper sensitive strain) was increased by introduction of M. sedula ARS50-2, with 5.31 and 26.29% more copper recovered from enargite at a pulp density (PD) of 1 and 3% (w/v), respectively. M. sedula ARS50-2 arose as the predominant species and modulated the proportions of the other two strains after it had been introduced. Collectively, the higher Cu2+ resistance trait of M. sedula ARS50-2 resulted in a modulated microbial community structure, and consolidating enargite bioleaching especially at elevated PD.

Characterization of Rhodococcus sp. A5wh isolated from a high altitude Andean lake to unravel the survival strategy under lithium stress

Lithium (Li) is widely distributed in nature and has several industrial applications. The largest reserves of Li (over 85%) are in the so-called "triangle of lithium" that includes the Salar de Atacama in Chile, Salar de Uyuni in Bolivia and Salar del Hombre Muerto in Argentina. Recently, the use of microorganisms in metal recovery such as copper has increased; however, there is little information about the recovery of lithium. The strain Rhodococcus sp. A5_wh used in this work was previously isolated from Laguna Azul. The assays revealed that this strain was able to accumulate Li (39.52% of Li/g microbial cells in 180min) and that it was able to grow in its presence up to 1M. In order to understand the mechanisms implicated in Li tolerance, a proteomic approach was conducted. Comparative proteomic analyses of strain A5_wh exposed and unexposed to Li reveal that 17 spots were differentially expressed. The identification of proteins was performed by MALDI-TOF/MS, and the obtained results showed that proteins involved in stress response, transcription, translations, and metabolism were expressed under Li stress. This knowledge constitutes the first proteomic approach to elucidate the strategy followed by Rhodococcus to adapt to Li.