Life in blue: copper resistance mechanisms of bacteria and archaea used in industrial biomining of minerals

Investigating the acidophilic microbial community's adaptation for enhancement indium bioleaching from high pulp density shredded discarded LCD panels

As part of electronic waste (e-waste), the fastest growing solid waste stream in the world, discarded liquid crystal displays (LCDs) contain substantial amounts of both valuable and potentially harmful metal, offering valuable opportunities for resource extraction but posing environmental threats. The present comprehensive study is an investigation into the bioleaching of indium from discarded LCD panels, with a particular focus on high pulp density shredded (Sh-LCDs) and powdered (P-LCDs) materials. This study involved an acidophilic consortium, with two pathways, namely the mixed sulfur-iron pathways and sulfur pathways, being explored to understand the bioleaching mechanisms. Indium bioleaching efficiencies through the mixed sulfur-iron pathway were approximately 60% and 100% for Sh-LCDs and P-LCDs, respectively. Three mechanisms were involved in the extraction of indium from LCD samples: acidolysis, complexolysis, and redoxolysis. The microbial community adapted to a pulp density of 32.5 g/L was streak-plated and it was revealed that sulfur-oxizing bacteria dominated, resulting in the minimum indium extraction of 10% and 55% for both Sh-LCDs and P-LCDs samples, respectively. It was generally accepted that ferric ions as oxidants were effective for indium bioleaching from both the Sh-LCDs and P-LCDs. This implies that the cooperation or interaction within the microbial community used in the bioleaching process had a beneficial impact, enhancing the overall effectiveness of extracting indium from LCD panels. The adapted consortium utilizes a combination of microbial transformation, efflux systems, and chelation through extracellular substances to detoxify heavy metals. The adapted microbial community demonstrated better indium leaching efficiency (50%) compared to the non-adapted microbial community which achieved a maximum of 29% and 5% respectively from Sh-LCDs and P-LCDs at a pulp density of 32.5 g/L. The advantages of an adapted microbial community for indium leaching efficiency, attributing this advantage to factors such as high metabolic activity and improved tolerance to heavy metals. Additionally, the protective role of the biofilm formed by the adapted microbial community is particularly noteworthy, as it contributes to the community's resilience in the presence of inhibitory substances. This information is valuable for understanding and optimizing bioleaching processes for indium recovery, and by extension to possibly other metals.

Legacy copper/nickel mine tailings potentially harbor novel iron/sulfur cycling microorganisms within highly variable communities

The oxidation of sulfide-bearing mine tailings catalyzed by acidophilic iron and sulfur-oxidizing bacteria releases toxic metals and other contaminants into soil and groundwater as acid mine drainage. Understanding the environmental variables that control the community structure and metabolic activity of microbes indigenous to tailings (especially the abiotic stressors of low pH and high dissolved metal content) is crucial to developing sustainable bioremediation strategies. We determined the microbial community composition along two continuous vertical gradients of Cu/Ni mine tailings at each of two tailings impoundments near Sudbury, Ontario. 16S rRNA amplicon data showed high variability in community diversity and composition between locations, as well as at different depths within each location. A temporal comparison for one tailings location showed low fluctuation in microbial communities across 2 years. Differences in community composition correlated most strongly with pore-water pH, Eh, alkalinity, salinity, and the concentration of several dissolved metals (including iron, but not copper or nickel). The relative abundances of individual genera differed in their degrees of correlation with geochemical factors. Several abundant lineages present at these locations have not previously been associated with mine tailings environments, including novel species predicted to be involved in iron and sulfur cycling.IMPORTANCEMine tailings represent a significant threat to North American freshwater, with legacy tailings areas generating acid mine drainage (AMD) that contaminates rivers, lakes, and aquifers. Microbial activity accelerates AMD formation through oxidative metabolic processes but may also ameliorate acidic tailings by promoting secondary mineral precipitation and immobilizing dissolved metals. Tailings exhibit high geochemical variation within and between mine sites and may harbor many novel extremophiles adapted to high concentrations of toxic metals. Characterizing the unique microbiomes associated with tailing environments is key to identifying consortia that may be used as the foundation for innovative mine-waste bioremediation strategies. We provide an in-depth analysis of microbial diversity at four copper/nickel mine tailings impoundments, describe how communities (and individual lineages) differ based on geochemical gradients, predict organisms involved in AMD transformations, and identify taxonomically novel groups present that have not previously been observed in mine tailings.

Assessment of microbial communities from cold mine environments and subsequent enrichment, isolation and characterization of putative antimony- or copper-metabolizing microorganisms

Mining activities, even in arctic regions, create waste materials releasing metals and metalloids, which have an impact on the microorganisms inhabiting their surroundings. Some species can persist in these areas through tolerance to meta(loid)s via, e.g., metabolic transformations. Due to the interaction between microorganisms and meta(loid)s, interest in the investigation of microbial communities and their possible applications (like bioremediation or biomining) has increased. The main goal of the present study was to identify, isolate, and characterize microorganisms, from subarctic mine sites, tolerant to the metalloid antimony (Sb) and the metal copper (Cu). During both summer and winter, samples were collected from Finnish mine sites (site A and B, tailings, and site C, a water-treatment peatland) and environmental parameters were assessed. Microorganisms tolerant to Sb and Cu were successfully enriched under low temperatures (4°C), creating conditions that promoted the growth of aerobic and fermenting metal(loid) tolerating or anaerobic metal(loid) respiring organism. Microbial communities from the environment and Sb/Cu-enriched microorganisms were studied via 16S rRNA amplicon sequencing. Site C had the highest number of taxa and for all sites, an expected loss of biodiversity occurred when enriching the samples, with genera like Prauserella, Pseudomonas or Clostridium increasing their relative abundances and others like Corynebacterium or Kocuria reducing in relative abundance. From enrichments, 65 putative Sb- and Cu-metabolizing microorganisms were isolated, showing growth at 0.1 mM to 10 mM concentrations and 0°C to 40°C temperatures. 16S rRNA gene sequencing of the isolates indicated that most of the putative anaerobically Sb-respiring tolerators were related to the genus Clostridium. This study represents the first isolation, to our knowledge, of putative Sb-metabolizing cold-tolerant microorganisms and contributes to the understanding of metal (loid)-tolerant microbial communities in Arctic mine sites.

Omics technology draws a comprehensive heavy metal resistance strategy in bacteria

The rapid industrial revolution significantly increased heavy metal pollution, becoming a major global environmental concern. This pollution is considered as one of the most harmful and toxic threats to all environmental components (air, soil, water, animals, and plants until reaching to human). Therefore, scientists try to find a promising and eco-friendly technique to solve this problem i.e., bacterial bioremediation. Various heavy metal resistance mechanisms were reported. Omics technologies can significantly improve our understanding of heavy metal resistant bacteria and their communities. They are a potent tool for investigating the adaptation processes of microbes in severe conditions. These omics methods provide unique benefits for investigating metabolic alterations, microbial diversity, and mechanisms of resistance of individual strains or communities to harsh conditions. Starting with genome sequencing which provides us with complete and comprehensive insight into the resistance mechanism of heavy metal resistant bacteria. Moreover, genome sequencing facilitates the opportunities to identify specific metal resistance genes, operons, and regulatory elements in the genomes of individual bacteria, understand the genetic mechanisms and variations responsible for heavy metal resistance within and between bacterial species in addition to the transcriptome, proteome that obtain the real expressed genes. Moreover, at the community level, metagenome, meta transcriptome and meta proteome participate in understanding the microbial interactive network potentially novel metabolic pathways, enzymes and gene species can all be found using these methods. This review presents the state of the art and anticipated developments in the use of omics technologies in the investigation of microbes used for heavy metal bioremediation.

Possible Role of CHAD Proteins in Copper Resistance

Conserved Histidine Alpha-helical Domain (CHAD) proteins attached to the surface of polyphosphate (PolyP) have been studied in some bacteria and one archaeon. However, the activity of CHAD proteins is unknown beyond their interaction with PolyP granules. By using bioinformatic analysis, we report that several species of the biomining acidophilic bacteria contain orthologs of CHAD proteins with high sequence identity. Furthermore, the gene coding for the CHAD protein is in the same genetic context of the enzyme polyphosphate kinase (PPK), which is in charge of PolyP synthesis. Particularly, the group of ppk and CHAD genes is highly conserved. Metallosphaera sedula and other acidophilic archaea used in biomining also contain CHAD proteins. These archaea show high levels of identity in genes coding for a cluster having the same organization. Amongst these genes are chad and ppx. In general, both biomining bacteria and archaea contain high PolyP levels and are highly resistant to heavy metals. Therefore, the presence of this conserved genetic organization suggests a high relevance for their metabolism. It has been formerly reported that a crystallized CHAD protein contains a copper-binding site. Based on this previous knowledge, in the present report, it was determined that all analyzed CHAD proteins are very conserved at their structural level. In addition, it was found that the lack of YgiF, an Escherichia coli CHAD-containing protein, decreases copper resistance in this bacterium. This phenotype was not only complemented by transforming E. coli with YgiF but also by expressing CHAD from Acidithiobacillus ferrooxidans in it. Interestingly, the strains in which the possible copper-binding sites were mutated were also more metal sensitive. Based on these results, we propose that CHAD proteins are involved in copper resistance in microorganisms. These findings are very interesting and may eventually improve biomining operations in the future.

Extremely thermoacidophilic archaea for metal bioleaching: What do their genomes tell Us?

Elevated temperatures favor bioleaching processes through faster kinetics, more favorable mineral chemistry, lower cooling requirements, and less surface passivation. Extremely thermoacidophilic archaea from the order Sulfolobales exhibit novel mechanisms for bioleaching metals from ores and have great potential. Genome sequences of many extreme thermoacidophiles are now available and provide new insights into their biochemistry, metabolism, physiology and ecology as these relate to metal mobilization from ores. Although there are some molecular genetic tools available for extreme thermoacidophiles, further development of these is sorely needed to advance the study and application of these archaea for bioleaching applications. The evolving landscape for bioleaching technologies at high temperatures merits a closer look through a genomic lens at what is currently possible and what lies ahead in terms of new developments and emerging opportunities. The need for critical metals and the diminishing primary deposits for copper should provide incentives for high temperature bioleaching.

From biomolecules to biogeochemistry: Exploring the interaction of an indigenous bacterium with gold

Specialised microbial communities colonise the surface of gold particles in soils/sediments, and catalyse gold dissolution and re-precipitation, thereby contributing to the environmental mobility and toxicity of this 'inert' precious metal. We assessed the proteomic and physiological response of Serratia proteamaculans, the first metabolically active bacterium enriched and isolated directly from natural gold particles, when exposed to toxic levels of soluble Au3+ (10 μM). The results were compared to a metal-free blank, and to cultures exposed to similarly toxic levels of soluble Cu2+ (0.1 mM); Cu was chosen for comparison because it is closely associated with Au in nature due to similar geochemical properties. A total of 273 proteins were detected from the cells that experienced the oxidative effects of soluble Au, of which 139 (51%) were upregulated with either sole expression (31%) or had synthesis levels greater than the Au-free control (20%). The majority (54%) of upregulated proteins were functionally different from up-regulated proteins in the bacteria-copper treatment. These proteins were related to broad functions involving metabolism and biogenesis, followed by cellular process and signalling, indicating significant specificity for Au. This proteomic study revealed that the bacterium upregulates the synthesis of various proteins related to oxidative stress response (e.g., Monothiol-Glutaredoxin, Thiol Peroxidase, etc.) and cellular damage repair, which leads to the formation of metallic gold nanoparticles less toxic than ionic gold. Therefore, indigenous bacteria may mediate the toxicity of Au through two different yet simultaneous processes: i) repairing cellular components by replenishing damaged proteins and ii) neutralising reactive oxygen species (ROS) by up-regulating the synthesis of antioxidants. By connecting the fields of molecular bacteriology and environmental biogeochemistry, this study is the first step towards the development of biotechnologies based on indigenous bacteria applied to gold bio-recovery and bioremediation of contaminated environments.

Recovery of valuable metals from spent lithium-ion batteries using microbial agents for bioleaching: a review

Spent lithium-ion batteries (LIBs) are increasingly generated due to their widespread use for various energy-related applications. Spent LIBs contain several valuable metals including cobalt (Co) and lithium (Li) whose supply cannot be sustained in the long-term in view of their increased demand. To avoid environmental pollution and recover valuable metals, recycling of spent LIBs is widely explored using different methods. Bioleaching (biohydrometallurgy), an environmentally benign process, is receiving increased attention in recent years since it utilizes suitable microorganisms for selective leaching of Co and Li from spent LIBs and is cost-effective. A comprehensive and critical analysis of recent studies on the performance of various microbial agents for the extraction of Co and Li from the solid matrix of spent LIBs would help for development of novel and practical strategies for effective extraction of precious metals from spent LIBs. Specifically, this review focuses on the current advancements in the application of microbial agents namely bacteria (e.g., Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans) and fungi (e.g., Aspergillus niger) for the recovery of Co and Li from spent LIBs. Both bacterial and fungal leaching are effective for metal dissolution from spent LIBs. Among the two valuable metals, the dissolution rate of Li is higher than Co. The key metabolites which drive the bacterial leaching include sulfuric acid, while citric acid, gluconic acid and oxalic acid are the dominant metabolites in fungal leaching. The bioleaching performance depends on both biotic (microbial agents) and abiotic factors (pH, pulp density, dissolved oxygen level and temperature). The major biochemical mechanisms which contribute to metal dissolution include acidolysis, redoxolysis and complexolysis. In most cases, the shrinking core model is suitable to describe the bioleaching kinetics. Biological-based methods (e.g., bioprecipitation) can be applied for metal recovery from the bioleaching solution. There are several potential operational challenges and knowledge gaps which should be addressed in future studies to scale-up the bioleaching process. Overall, this review is of importance from the perspective of development of highly efficient and sustainable bioleaching processes for optimum resource recovery of Co and Li from spent LIBs, and conservation of natural resources to achieve circular economy.

Responses of microbial community to geochemical parameters on vertical depth in bioheap system of low-grade copper sulfide

Monitoring of the microbial community in bioleaching system is essential for control process parameters and enhance the leaching efficiency. Due to the difficulty of sampling, microbial distribution, community succession and bioleaching activity along the vertical depth of bioleaching heaps remain unresolved. This study investigated the geochemical parameters and microbial community structure along a depth profile in a bioleaching heap and leachate. 80 ore samples at different heap depths and 9 leaching solution samples from three bioheaps of Zijin Copper Mine were collected. Microbial composition, mineral types and geochemical parameters of these samples were analyzed by 16S rRNA high-throughput sequencing and a series of chemical measurement technologies. The results revealed that the pH, Cu, Fe and the total sulfur contents were the major factors shaping the composition of the microbial communities in the bioleaching system. The extent of mineral oxidation increased as the sample depth increases, followed by the increasing of sulfur oxidizers. The abundance of sulfur and iron oxidizers including members of Acidithiobacillus, Sulfobacillus and Acidiferrobacter were significantly higher in the leaching heap than in the leaching solution, meanwhile, they showed strong positive interactions with other members within the same genera and iron oxidizer Leptospirillum and Ferroplasma. Besides, Acidithiobacillus negatively interacted with heterotrophs such as Sphingobium, Exiguobacterium, Brevundimonas and so on. On the contrast, members of Leptospirillum and unclassified Archaea were significantly abundant in the leaching solution and revealed strong interactions with members of Thermoplasmatales. The main conclusion of this study, especially the leaching potential of microorganisms prevailing in bioheaps and their relationships with geochemical factors, provides theoretical guidance for future process design such as the control of processing parameters and microbial community in heap leaching.

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.

Contrasting responses of cuticular bacteria of Pardosa pseudoannulata under cadmium stress

Although research into how spiders respond to cadmium (Cd)-induced toxicity is ongoing, little is known about the effects of Cd contamination on the exogenous microorganisms of spiders. The current study used 16 S rRNA gene sequencing to evaluate the richness and structure of external bacterial communities in the wolf spider Pardosa pseudoannulata under long- and short-term Cd stress. Our results showed that Proteobacteria and Acidibacter were the dominating bacterial phylum and genus. The alpha diversity analysis showed that the high background of Cd concentration (Cd) reduced bacterial alpha diversity, and short-term Cd (SCd) stress elevated bacterial richness and diversity. Hub bacterial genera, including Stenotrophobacter, Hymenobacter, Chitinophaga, and Bryobacter, were identified by co-occurrence network analysis and showed high connectance with other bacterial genera. Further investigation revealed 15 and 14 bacterial taxa that were classified distinctively under SCd and Cd stresses. Interestingly, functional prediction analysis showed that Cd stress enhanced some crucial pathways involved in specialized functions, including manganese oxidation and aromatic compound degradation. Random forest and correlation analyses found that the spider's molting time was the dominant driver affecting bacterial phyla (i.e., Proteobacteria and Planctomycetes) and genera (e.g., Acidibacter, Reyranella, and Haliangium). Collectively, this comprehensive analysis creates new perspectives to investigate the divergent responses of microbial communities in the spiders' external habitat under Cd stress, and provides valuable viewpoints for Cd pollution evaluation and control.

Comprehensive insights into the gallic acid assisted bioleaching process for spent LIBs: Relationships among bacterial functional genes, Co(III) reduction and metal dissolution behavior

Despite the growing demand for resource recovery from spent lithium-ion batteries (LIBs) by bioleaching, low Co leaching efficiency has hindered the development and application of this technology. Therefore, a novel process was designed, combining gallic acid (GA) and mixed culture bioleaching (MCB), to enhance the removal of metals from spent LIBs. Results indicated that the GA + MCB process achieved 98.03% Co and 98.02% Li leaching from spent LIBs, simultaneously reducing the biotoxicity, phytotoxicity and leaching toxicity of spent LIBs under optimal conditions. The results of mechanism analysis demonstrated that functional microorganisms adapted to the leaching system through various strategies, including oxidative stress reduction, DNA damage repair, heavy metal resistance and biofilm formation, maintaining normal physiological activities and the continuous production of biological acid. The biological acid erodes the surface of waste LIBs, causing some Co and a large amount of Li to be released, while also increasing the contact area between GA and Co(III). Therefore, GA is beneficial for reducing insoluble Co(III), forming soluble Co(II). Finally, biological acid can effectively promote Co(II) leaching. Collectively, the results of this study provide valuable insight into the simultaneous enhancement of metal extraction and the mitigation of environmental pollution from spent LIBs.

Advances in bioleaching of waste lithium batteries under metal ion stress

In modern societies, the accumulation of vast amounts of waste Li-ion batteries (WLIBs) is a grave concern. Bioleaching has great potential for the economic recovery of valuable metals from various electronic wastes. It has been successfully applied in mining on commercial scales. Bioleaching of WLIBs can not only recover valuable metals but also prevent environmental pollution. Many acidophilic microorganisms (APM) have been used in bioleaching of natural ores and urban mines. However, the activities of the growth and metabolism of APM are seriously inhibited by the high concentrations of heavy metal ions released by the bio-solubilization process, which slows down bioleaching over time. Only when the response mechanism of APM to harsh conditions is well understood, effective strategies to address this critical operational hurdle can be obtained. In this review, a multi-scale approach is used to summarize studies on the characteristics of bioleaching processes under metal ion stress. The response mechanisms of bacteria, including the mRNA expression levels of intracellular genes related to heavy metal ion resistance, are also reviewed. Alleviation of metal ion stress via addition of chemicals, such as spermine and glutathione is discussed. Monitoring using electrochemical characteristics of APM biofilms under metal ion stress is explored. In conclusion, effective engineering strategies can be proposed based on a deep understanding of the response mechanisms of APM to metal ion stress, which have been used to improve bioleaching efficiency effectively in lab tests. It is very important to engineer new bioleaching strains with high resistance to metal ions using gene editing and synthetic biotechnology in the near future.

Toxic heavy metal/oxyanion tolerance in haloarchaea from some saline and hypersaline ecosystems

Toxic heavy metal/oxyanion contamination has increased severely through the last decades. In this study, 169 native haloarchaeal strains were isolated from different saline and hypersaline econiches of Iran. After providing pure culture and performing morphological, physiological, and biochemical tests, haloarchaea resistance toward arsenate, selenite, chromate, cadmium, zinc, lead, copper, and mercury were surveyed using an agar dilution method. On the basis of minimum inhibitory concentrations (MICs), the least toxicities were found with selenite and arsenate, while the haloarchaeal strains revealed the highest sensitivity for mercury. On the other hand, the majority of haloarchaeal strains exhibited similar responses to chromate and zinc, whereas the resistance level of the isolates to lead, cadmium, and copper was very heterogeneous. 16 S ribosomal RNA (rRNA) gene sequence analysis revealed that most haloarchaeal strains belong to the Halorubrum and Natrinema genera. The obtained results from this study showed that among the identified isolates, Halococcus morrhuae strain 498 had an exceptional resistance toward selenite and cadmium (64 and 16 mM, respectively). Also, Halovarius luteus strain DA5 exhibited a remarkable tolerance against copper (32 mM). Moreover, strain Salt5, identified as Haloarcula sp., was the only strain that could tolerate all eight tested heavy metals/oxyanions and had a significant tolerance of mercury (1.5 mM).

Integrative chemical and omics analyses reveal copper biosorption and tolerance mechanisms of Bacillus cereus strain T6

A comprehensive understanding of the cellular response of microbes to metal stress is necessary for the rational development of microbe-based biosorbents for metal removal. The present study investigated the copper (Cu) sorption and resistance mechanism of Bacillus cereus strain T6, a newly isolated Cu-resistant bacterium, by integrative analyses of physiochemistry, genomics, transcriptomics, and metabolomics. The growth inhibition assay and biosorption determination showed that this bacterium exhibited high tolerance to Cu, with a minimum inhibitory concentration of 4.0 mM, and accumulated Cu by both extracellular adsorption and intracellular binding. SEM microscopic images and FTIR spectra showed significant cellular surface changes at the high Cu level but not at low, and the involvement of surface functional groups in the biosorption of Cu, respectively. Transcriptomic and untargeted metabolomic analyses detected 362 differentially expressed genes and 60 significantly altered metabolites, respectively. Integrative omics analyses revealed that Cu exposure dramatically induced a broad spectrum of genes involved in Cu transport and iron homeostasis, and suppressed the denitrification pathway, leading to significant accumulation of metabolites for metal transporter synthesis, membrane remolding, and antioxidant activities. The results presented here provide a new perspective on the intricate regulatory network of Cu homeostasis in bacteria.

Abundant microbial communities act as more sensitive bio-indicators for ecological evaluation of copper mine contamination than rare taxa in river sediments

Bacterial and fungal communities have been widely applied as bio-indicators for ecological evaluation of copper (Cu) mine pollution in river sediments. However, the response pattern of their abundant and rare sub-communities is still unknown, limiting the further development of biological diagnostics. Here, the alpha-diversity, community composition, environmental contribution and co-occurrence network of total, abundant and rare taxa for bacteria and fungi in the Jiaopingdu Cu Mine wastewater treatment plant (WWTP) were investigated through high-throughput sequencing. The results revealed different responses of microbial alpha-diversity for abundant and rare sub-communities. The abundant taxa were ubiquitous in all sediments, while rare taxa exhibited increases of species richness in polluted areas because of heterochthonous inputs of WWTP drainage. Nevertheless, the variations of community composition were consistent for bacterial and fungal abundant and rare taxa, all of which showed significant dissimilarity between control and polluted areas. Distance-decay relationship and canonical correlation analysis indicated that abundant taxa assemblies (r_bacteria = -0.924, r_fungi = -0.684) were more strongly driven by environmental changes than rare ones (r_bacteria = -0.626, r_fungi = -0.349), because abundant microbes had higher proportions of significant variations in abundance. Co-occurrence networks revealed more keystone species with high node degree and centrality among abundant taxa compared with rare ones. Moreover, bacterial abundant and rare taxa were more sensitive to Cu mine pollution than relevant fungal taxa owing to different Cu tolerance. In conclusion, among all microbial sub-communities, abundant bacteria had the highest environmental sensitivity, suggesting their important application in biological diagnosis of Cu mine pollution. Accordingly, the abundant taxa could act as "key reservoir" for future selection of specific indicator species, for example Thiobacillus, while rare taxa no longer need excessive in-depth analysis, which would greatly improve microbial diagnosis efficiency.

Will Vanadium-Based Electrode Materials Become the Future Choice for Metal-Ion Batteries?

Metal-ion batteries have emerged as promising candidates for energy storage system due to their unlimited resources and competitive price/performance ratio. Vanadium-based compounds have diverse oxidation states rendering various open-frameworks for ions storage. To date, some vanadium-based polyanionic compounds have shown great potential as high-performance electrode materials. However, there has been a growing concern regarding the cost and environmental risk of vanadium. In this Review, all links in the industry chain of vanadium-based electrodes were comprehensively summarized, starting with an analysis of the resources, applications, and price fluctuation of vanadium. The manufacturing processes of the vanadium extraction and recovery technologies were discussed. Moreover, the commercial potentials of some typical electrode materials were critically appraised. Finally, the environmental impact and sustainability of the industry chain were evaluated. This critical Review will provide a clear vision of the prospects and challenges of developing vanadium-based electrode materials.

Antibacterial Activity of Colloidal Copper Nanoparticles against Gram-negative (Escherichia coli and Proteus vulgaris) Bacteria

Antibacterial activities of as-synthesized nanoparticles have gained attention in past few years due to rapid phylogenesis of pathogens developing multi-drug resistance (MDR). Antibacterial activity of Copper nanoparticles (CuNPs) on surrogate pathogenic Gram-negative bacteria Escherichia coli (MTCC No. 739) and Proteus vulgaris (MTCC No. 426) was evaluated under culture conditions. Three sets of colloidal CuNPs were synthesized by chemical reduction method with per batch yield of 0.2 g, 0.3 g and 0.4 g. As-synthesized CuNPs possess identical plasmonic properties and have similar hydrodynamic particle sizes (11-14 nm). Antibacterial activities of CuNPs were evaluated by MIC (minimum inhibitory concentration) and MBC (minimum bactericidal concentration) tests, cytoplasmic leakage and ROS (reactive oxygen species) assays. MIC and MBC tests revealed dose dependence bactericidal action. Growth curves of E. coli show faster growth inhibition along with higher cytoplasmic leakage than that of P. vulgaris. This might be because of increased membrane permeability of E. coli. CuNPs - microorganism interaction induces oxidative stress generated by ROS (reactive oxygen species). Leakage of cytoplasmic components, loss of membrane permeability and ROS generation are the primary causes of CuNPs induced bacterial cell death. As-synthesized CuNPs exhibiting promising antibacterial activities and could be a promising candidate for novel antibacterial agents.

The Microbiology of Metal Mine Waste: Bioremediation Applications and Implications for Planetary Health

Mine wastes pollute the environment with metals and metalloids in toxic concentrations, causing problems for humans and wildlife. Microorganisms colonize and inhabit mine wastes, and can influence the environmental mobility of metals through metabolic activity, biogeochemical cycling and detoxification mechanisms. In this article we review the microbiology of the metals and metalloids most commonly associated with mine wastes: arsenic, cadmium, chromium, copper, lead, mercury, nickel and zinc. We discuss the molecular mechanisms by which bacteria, archaea, and fungi interact with contaminant metals and the consequences for metal fate in the environment, focusing on long-term field studies of metal-impacted mine wastes where possible. Metal contamination can decrease the efficiency of soil functioning and essential element cycling due to the need for microbes to expend energy to maintain and repair cells. However, microbial communities are able to tolerate and adapt to metal contamination, particularly when the contaminant metals are essential elements that are subject to homeostasis or have a close biochemical analog. Stimulating the development of microbially reducing conditions, for example in constructed wetlands, is beneficial for remediating many metals associated with mine wastes. It has been shown to be effective at low pH, circumneutral and high pH conditions in the laboratory and at pilot field-scale. Further demonstration of this technology at full field-scale is required, as is more research to optimize bioremediation and to investigate combined remediation strategies. Microbial activity has the potential to mitigate the impacts of metal mine wastes, and therefore lessen the impact of this pollution on planetary health.

Glutathione synthetase overexpression in Acidithiobacillus ferrooxidans improves halotolerance of iron oxidation

Acidithiobacillus ferrooxidans are well-studied iron- and sulfur-oxidizing acidophilic chemolithoautotrophs that are exploited for their ability to participate in the bioleaching of metal sulfides. Here, we overexpressed the endogenous glutamate-cysteine ligase and glutathione synthetase genes in separate strains and found that glutathione synthetase overexpression increased intracellular glutathione levels. We explored the impact of pH on the halotolerance of iron oxidation in wild type and engineered cultures. The increase in glutathione allowed the modified cells to grow under salt concentrations and pH conditions that are fully inhibitory to wild type cells. Furthermore, we found that improved iron oxidation ability in the presence of chloride also resulted in higher levels of intracellular ROS in the strain. These results indicate that glutathione overexpression can be used to increase halotolerance in A. ferrooxidans and would likely be a useful strategy on other acidophilic bacteria. Importance The use of acidophilic bacteria in the hydrometallurgical processing of sulfide ores can enable many benefits including the potential reduction of environmental impacts. The cells involved in bioleaching tend to have limited halotolerance, and increased halotolerance could enable several benefits, including a reduction in the need for the use of fresh water resources. We show that the genetic modification of A. ferrooxidans for the overproduction of glutathione is a promising strategy to enable cells to resist the oxidative stress that can occur during growth in the presence of salt.

Molecular Insights into the Copper-Sensitive Operon Repressor in Acidithiobacillus caldus

The copper-sensitive operon repressor (CsoR) family, which is the main Cu(I)-sensing family, is widely distributed and regulates regulons involved in detoxification in response to extreme copper stress (a general range of ≥3 g/liter copper ions). Here, we identified CsoR in hyper-copper-resistant Acidithiobacillus caldus (CsoR^Ac), an organism used in the bioleaching process of copper ores. CsoR^Ac possesses highly conserved Cu(I) ligands and structures within the CsoR family members. Transcriptional analysis assays indicated that the promoter (PIII) of csoR was active but weakly responsive to copper in Escherichia coli. Copper titration assays gave a stoichiometry of 0.8 mol Cu(I) per apo-CsoR^Ac monomer in vitro combined with atomic absorption spectroscopy analysis. Cu^I-CsoR^Ac and apo-CsoR^Ac share essentially identical secondary structures and assembly states, as demonstrated by circular dichroism spectra and size exclusion chromatography profiles. The average dissociation constants (K_D = 2.26 × 10^-18 M and 0.53 × 10^-15 M) and Cu(I) binding affinity of apo-CsoR^Ac were estimated by bathocuproine disulfonate (BCS) and bicinchoninic acid (BCA) competition assays, respectively. Site-directed mutations of conserved Cu(I) ligands in CsoR^Ac did not significantly alter the secondary structure or assembly state. Competition assays showed that mutants had the same order of magnitude of Cu(I) binding affinity as apo-CsoR^Ac. Moreover, apo-CsoR^Ac could bind to the DNA fragment P08430 in vitro, although with low affinity. Finally, a working model was developed to illustrate putative copper resistance mechanisms in A. caldus. IMPORTANCE Research on copper resistance among various species has attracted considerable interest. However, due to the lack of effective and reproducible genetic tools, few studies regarding copper resistance have been reported for A. caldus. Here, we characterized a major Cu(I)-sensing family protein, CsoR^Ac, which binds Cu(I) with an attomolar affinity higher than that of the Cu(I)-specific chelator bathocuproine disulfonate. In particular, CsoR family proteins were identified only in A. caldus, rather than A. ferrooxidans and A. thiooxidans, which are both used for bioleaching. Meanwhile, A. caldus harbored more copper resistance determinants and a relatively full-scale regulatory system involved in copper homeostasis. These observations suggested that A. caldus may play an essential role in the application of engineered strains with higher copper resistance in the near future.

Redox stress response and UV tolerance in the acidophilic iron-oxidizing bacteria Leptospirillum ferriphilum and Acidithiobacillus ferrooxidans

The oxidative stress response represents a sum of antioxidative mechanisms that are essential for determining the adaptation and abundance of microorganisms in the environment. Leptospirillum ferriphilum and Acidithiobacillus ferrooxidans are chemolithotrophic bacteria that obtain their energy from the oxidation of ferrous ion. Both microorganisms are important for bioleaching of sulfidic ores and both are tolerant to high levels of heavy metals and other factors that can induce oxidative stress. In this work, we compared the tolerance and response of L. ferriphilum and At. ferrooxidans to Fe³⁺, H₂O₂, K₂CrO₄, and UV-C radiation. We evaluated growth, generation of reactive oxygen species (ROS), oxidative damage to lipid membranes and DNA, and the activity of antioxidative proteins in cells exposed to these stressors. L. ferriphilum had higher cell density, lower ROS content and less lipid and DNA damage than At. ferrooxidans. Consistent with this, the activity levels of thioredoxin and superoxide dismutase in L. ferriphilum were upregulated and higher than in At. ferrooxidans. This indicated that L. ferriphilum has a higher capacity to respond to oxidative stress and to manage redox homeostasis. This capacity could largely contribute to the high abundance of this species in natural and anthropogenic sites.

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.

Bioremoval of hazardous cobalt, nickel, chromium, copper and cadmium compounds from contaminated soil by Nicotiana tabacum plants and associated microbiome

Contamination of soils with heavy metals leads to reduction of soil fertility, destruction of natural ecosystems and detrimental effects on the health of society by increasing content of metals in the food chains from microorganisms to plants, animals and humans. Bioremediation is one of the most promising and cost-effective methods of cleaning soils polluted with toxic metals. According to current researchers, microorganisms and plants have the genetic potential to remove toxic metals from contaminated sites. The method of thermodynamic prediction was used to theoretically substantiate the mechanisms of interaction of soil microorganisms and plants with heavy metals. According to the our prediction, exometabolite chelators of anaerobic microorganisms may increase the mobility of metals and thereby contribute to the active transport of metals and their accumulation in plants. Plants of Nicotiana tabacum L. of Djubek cultivar were used as plant material for the current investigation. The examined toxicants were heavy metals, namely cobalt (II), nickel (II), chromium (VI), copper (II) and cadmium (II). The aqueous solutions of metal salts were added to the boxes after two months of plants growing to the final super-high concentration – 500 mg/kg of absolutely dry weight of soil. Quantitative assessments of copper and chromium-resistant microorganisms were made by cultivation on agar nutrient medium NA with a gradient of Cu(II) and Cr(VI). The concentration of metals in soil and plant material (leaves, stems and roots) was determined by atomic absorption method. The study revealed that heavy metals inhibited the growth of the examined tobacco plants. This was expressed by the necrosis of plant tissues and, ultimately, their complete death. Despite this, all investigated heavy metals were accumulated in plant tissues during 3–7 days before death of plants. The uptake of metals was observed in all parts of plants – leaves, stems and roots. The highest concentrations of Co(II), Ni(II), Cd(II), Cr(VI) were found in the leaves, Cu(II) – in the roots. The results show that the bioremoval efficiency of the investigated metals ranged 0.60–3.65%. Given the super-high initial concentration of each of the metals (500 mg/kg), the determined removal efficiency was also high. Cadmium was the most toxic to plants. Thus, the basic points of the thermodynamic prognosis of the possibility of accumulation of heavy metals by phytomicrobial consortium were experimentally confirmed on the example of N. tabacum plants and metal-resistant microorganisms. The study demonstrated that despite the high initial metals concentration, rate of damage and death of plants, metals are accumulated inplant tissues in extremely hight concentrations. Soil microorganisms were observed to have high adaptation potencial to Cu(II) and Cr(VI). In anaerobic conditions, microorganisms presumably mobilize heavy metals, which later are absorbed by plants. The obtained results are the basis for the development of environmental biotechnologies for cleaning contaminated soils from heavy metal compounds.

Microbial Community Composition Correlates with Metal Sorption in an Ombrotrophic Boreal Bog: Implications for Radionuclide Retention

Microbial communities throughout the 6.5 m depth profile of a boreal ombrotrophic bog were characterized using amplicon sequencing of archaeal, fungal, and bacterial marker genes. Microbial populations and their relationship to oxic and anoxic batch sorption of radionuclides (using radioactive tracers of I, Se, Cs, Ni, and Ag) and the prevailing metal concentrations in the natural bog was investigated. The majority of the detected archaea belonged to the Crenarchaeota, Halobacterota, and Thermoplasmatota, whereas the fungal communities consisted of Ascomycota, Basidiomycota, and unclassified fungi. The bacterial communities consisted mostly of Acidobacteriota, Proteobacteria, and Chloroflexi. The occurrence of several microbial genera were found to statistically significantly correlate with metal concentrations as well as with Se, Cs, I, and Ag batch sorption data. We suggest that the metal concentrations of peat, gyttja, and clay layers affect the composition of the microbial populations in these nutrient-low conditions and that particularly parts of the bacterial and archaeal communities tolerate high concentrations of potentially toxic metals and may concurrently contribute to the total retention of metals and radionuclides in this ombrotrophic environment. In addition, the varying metal concentrations together with chemical, mineralogical, and physical factors may contribute to the shape of the total archaeal and bacterial populations and most probably shifts the populations for more metal resistant genera.

Recent advances in exploring the heavy metal(loid) resistant microbiome

Heavy metal(loid)s exert selective pressure on microbial communities and evolution of metal resistance determinants. Despite increasing knowledge concerning the impact of metal pollution on microbial community and ecological function, it is still a challenge to identify a consistent pattern of microbial community composition along gradients of elevated metal(loid)s in natural environments. Further, our current knowledge of the microbial metal resistome at the community level has been lagging behind compared to the state-of-the-art genetic profiling of bacterial metal resistance mechanisms in a pure culture system. This review provides an overview of the core metal resistant microbiome, development of metal resistance strategies, and potential factors driving the diversity and distribution of metal resistance determinants in natural environments. The impacts of biotic factors regulating the bacterial metal resistome are highlighted. We finally discuss the advances in multiple technologies, research challenges, and future directions to better understand the interface of the environmental microbiome with the metal resistome. This review aims to highlight the diversity and wide distribution of heavy metal(loid)s and their corresponding resistance determinants, helping to better understand the resistance strategy at the community level.

Unlocking Survival Mechanisms for Metal and Oxidative Stress in the Extremely Acidophilic, Halotolerant Acidihalobacter Genus

Microorganisms used for the biohydrometallurgical extraction of metals from minerals must be able to survive high levels of metal and oxidative stress found in bioleaching environments. The Acidihalobacter genus consists of four species of halotolerant, iron–sulfur-oxidizing acidophiles that are unique in their ability to tolerate chloride and acid stress while simultaneously bioleaching minerals. This paper uses bioinformatic tools to predict the genes and mechanisms used by Acidihalobacter members in their defense against a wide range of metals and oxidative stress. Analysis revealed the presence of multiple conserved mechanisms of metal tolerance. Ac. yilgarnensis F5^T, the only member of this genus that oxidizes the mineral chalcopyrite, contained a 39.9 Kb gene cluster consisting of 40 genes encoding mobile elements and an array of proteins with direct functions in copper resistance. The analysis also revealed multiple strategies that the Acidihalobacter members can use to tolerate high levels of oxidative stress. Three of the Acidihalobacter genomes were found to contain genes encoding catalases, which are not common to acidophilic microorganisms. Of particular interest was a rubrerythrin genomic cluster containing genes that have a polyphyletic origin of stress-related functions.

Metagenomic and Metatranscriptomic Study of Microbial Metal Resistance in an Acidic Pit Lake

Cueva de la Mora (CM) is an acidic, meromictic pit lake in the Iberian Pyrite Belt characterized by extremely high metal(loid) concentrations and strong gradients in oxygen, metal, and nutrient concentrations. We hypothesized that geochemical variations with depth would result in differences in community composition and in metal resistance strategies among active microbial populations. We also hypothesized that metal resistance gene (MRG) expression would correlate with toxicity levels for dissolved metal species in the lake. Water samples were collected in the upper oxic layer, chemocline, and deep anoxic layer of the lake for shotgun metagenomic and metatranscriptomic sequencing. Metagenomic analyses revealed dramatic differences in the composition of the microbial communities with depth, consistent with changing geochemistry. Based on relative abundance of taxa identified in each metagenome, Eukaryotes (predominantly Coccomyxa) dominated the upper layer, while Archaea (predominantly Thermoplasmatales) dominated the deep layer, and a combination of Bacteria and Eukaryotes were abundant at the chemocline. We compared metal resistance across communities using a curated list of protein-coding MRGs with KEGG Orthology identifiers (KOs) and found that there were broad differences in the metal resistance strategies (e.g., intracellular metal accumulation) expressed by Eukaryotes, Bacteria, and Archaea. Although normalized abundances of MRG and MRG expression were generally higher in the deep layer, expression of metal-specific genes was not strongly related to variations in specific metal concentrations, especially for Cu and As. We also compared MRG potential and expression in metagenome assembled genomes (MAGs) from the deep layer, where metal concentrations are highest. Consistent with previous work showing differences in metal resistance mechanisms even at the strain level, MRG expression patterns varied strongly among MAG populations from the same depth. Some MAG populations expressed very few MRG known to date, suggesting that novel metal resistance strategies remain to be discovered in uncultivated acidophiles.

Determinants of Copper Resistance in Acidithiobacillus Ferrivorans ACH Isolated from the Chilean Altiplano

The use of microorganisms in mining processes is a technology widely employed around the world. Leaching bacteria are characterized by having resistance mechanisms for several metals found in their acidic environments, some of which have been partially described in the Acidithiobacillus genus (mainly on ferrooxidans species). However, the response to copper has not been studied in the psychrotolerant Acidithiobacillus ferrivorans strains. Therefore, we propose to elucidate the response mechanisms of A. ferrivorans ACH to high copper concentrations (0-800 mM), describing its genetic repertoire and transcriptional regulation. Our results show that A. ferrivorans ACH can grow in up to 400 mM of copper. Moreover, we found the presence of several copper-related makers, belonging to cop and cus systems, as well as rusticyanins and periplasmatic acop protein in the genome. Interestingly, the ACH strain is the only one in which we find three copies of copB and copZ genes. Moreover, transcriptional expression showed an up-regulation response (acop, copZ, cusA, rusA, and rusB) to high copper concentrations. Finally, our results support the important role of these genes in A. ferrivorans copper stress resistance, promoting the use of the ACH strain in industrial leaching under low temperatures, which could decrease the activation times of oxidation processes and the energy costs.

Understanding Stress Response to High-Arsenic Gold-Bearing Sulfide Concentrate in Extremely Metal-Resistant Acidophile Sulfobacillus thermotolerans

Biooxidation of gold-bearing arsenopyrite concentrates, using acidophilic microbial communities, is among the largest commercial biohydrometallurgical processes. However, molecular mechanisms of microbial responses to sulfide raw materials have not been widely studied. The goal of this research was to gain insight into the defense strategies of the acidophilic bacterium Sulfobacillus thermotolerans, which dominates microbial communities functioning in industrial biooxidation processes at >35 °C, against the toxic effect of the high-arsenic gold-bearing sulfide concentrate. In addition to extreme metal resistance, this acidophile proved to be one of the most As-tolerant microorganisms. Comparative proteomic analysis indicated that 30 out of 33 differentially expressed proteins were upregulated in response to the ore concentrate, while the synthesis level of the functional proteins required for cell survival was not negatively affected. Despite a high level of cellular metal(loid) accumulation, no specific metal(loid)-resistant systems were regulated. Instead, several proteins involved in the metabolic pathways and stress response, including MBL fold metallo-hydrolase, sulfide:quinone oxidoreductase, and GroEL chaperonin, may play crucial roles in resistance to the sulfide ore concentrate and arsenic, in particular. This study provides the first data on the microbial responses to sulfide ore concentrates and advances our understanding of defense mechanisms against toxic compounds in acidophiles.

High copper concentration reduces biofilm formation in Acidithiobacillus ferrooxidans by decreasing production of extracellular polymeric substances and its adherence to elemental sulfur

Acidithiobacillus ferrooxidans is an acidophilic bacterium able to grow in environments with high concentrations of metals. It is a chemolithoautotroph able to form biofilms on the surface of solid minerals to obtain its energy. The response of both planktonic and sessile cells of A. ferrooxidans ATCC 23270 grown in elemental sulfur and adapted to high copper concentration was analyzed by quantitative proteomics. It was found that 137 proteins varied their abundance when comparing both lifestyles. Copper effllux proteins, some subunits of the ATP synthase complex, porins, and proteins involved in cell wall modification increased their abundance in copper-adapted sessile lifestyle cells. On the other hand, planktonic copper-adapted cells showed increased levels of proteins such as: cupreredoxins involved in copper cell sequestration, some proteins related to sulfur metabolism, those involved in biosynthesis and transport of lipopolysaccharides, and in assembly of type IV pili. During copper adaptation a decreased formation of biofilms was measured as determined by epifluorescence microscopy. This was apparently due not only to a diminished number of sessile cells but also to their exopolysaccharides production. This is the first study showing that copper, a prevalent metal in biomining environments causes dispersion of A. ferrooxidans biofilms. SIGNIFICANCE: Copper is a metal frequently found in high concentrations at mining environments inhabitated by acidophilic microorganisms. Copper resistance determinants of A. ferrooxidans have been previously studied in planktonic cells. Although biofilms are recurrent in these types of environments, the effect of copper on their formation has not been studied so far. The results obtained indicate that high concentrations of copper reduce the capacity of A. ferrooxidans ATCC 23270 to form biofilms on sulfur. These findings may be relevant to consider for a bacterium widely used in copper bioleaching processes.

Comparative Genomic Analysis Reveals the Metabolism and Evolution of the Thermophilic Archaeal Genus Metallosphaera

Members of the genus Metallosphaera are widely found in sulfur-rich and metal-laden environments, but their physiological and ecological roles remain poorly understood. Here, we sequenced Metallosphaera tengchongensis Ric-A, a strain isolated from the Tengchong hot spring in Yunnan Province, China, and performed a comparative genome analysis with other Metallosphaera genomes. The genome of M. tengchongensis had an average nucleotide identity (ANI) of approximately 70% to that of Metallosphaera cuprina. Genes sqr, tth, sir, tqo, hdr, tst, soe, and sdo associated with sulfur oxidation, and gene clusters fox and cbs involved in iron oxidation existed in all Metallosphaera genomes. However, the adenosine-5'-phosphosulfate (APS) pathway was only detected in Metallosphaera sedula and Metallosphaera yellowstonensis, and several subunits of fox cluster were lost in M. cuprina. The complete 3-hydroxypropionate/4-hydroxybutyrate cycle and dicarboxylate/4-hydroxybutyrate cycle involved in carbon fixation were found in all Metallosphaera genomes. A large number of gene family gain events occurred in M. yellowstonensis and M. sedula, whereas gene family loss events occurred frequently in M. cuprina. Pervasive strong purifying selection was found acting on the gene families of Metallosphaera, of which transcription-related genes underwent the strongest purifying selection. In contrast, genes related to prophages, transposons, and defense mechanisms were under weaker purifying pressure. Taken together, this study expands knowledge of the genomic traits of Metallosphaera species and sheds light on their evolution.

Metal and organic pollutants bioremediation by extremophile microorganisms

Extremophiles comprise microorganisms that are able to grow and thrive in extreme environments, including in an acidic or alkaline pH, high or low temperatures, high concentrations of pollutants, and salts, among others. These organisms are promising for environmental biotechnology due to their unique physiological and enzymatic characteristics, which allow them to survive in harsh environments. Due to the stability and persistence of these microorganisms under adverse environmental conditions, they can be used for the bioremediation of environments contaminated with extremely recalcitrant pollutants. Here, we provide an overview of extremophiles and the role of "omics" in the field of bioremediation of environmental pollutants, including hydrocarbons, textile dyes and metals.

Metal Toxicity and Resistance in Plants and Microorganisms in Terrestrial Ecosystems

Metals are major abiotic stressors of many organisms, but their toxicity in plants is not as studied as in microorganisms and animals. Likewise, research in plant responses to metal contamination is sketchy. Candidate genes associated with metal resistance in plants have been recently discovered and characterized. Some mechanisms of plant adaptation to metal stressors have been now decrypted. New knowledge on microbial reaction to metal contamination and the relationship between bacterial, archaeal, and fungal resistance to metals has broadened our understanding of metal homeostasis in living organisms. Recent reviews on metal toxicity and resistance mechanisms focused only on the role of transcriptomics, proteomics, metabolomics, and ionomics. This review is a critical analysis of key findings on physiological and genetic processes in plants and microorganisms in responses to soil metal contaminations.

Evolutionary insights into adaptation of Staphylococcus haemolyticus to human and non-human niches

Staphylococcus haemolyticus is a well-known member of human skin microbiome and an emerging opportunistic human pathogen. Presently, evolutionary studies are limited to human isolates even though it is reported from plants with beneficial properties and in environmental settings. In the present study, we report isolation of novel S. haemolyticus strains from surface sterilized rice seeds and compare their genome to other isolates from diverse niches available in public domain. The study showed expanding nature of pan-genome and revealed set of genes with putative functions related to its adaptability. This is seen by presence of type II lanthipeptide cluster in rice isolates, metal homeostasis genes in an isolate from copper coin and gene encoding methicillin resistance in human isolates. The present study on differential genome dynamics and role of horizontal gene transfers has provided novel insights into capability for ecological diversification of a bacterium of significance to human health.

Metabolic transcriptional analysis on copper tolerance in moderate thermophilic bioleaching microorganism Acidithiobacillus caldus

Bioleaching, an alternative environmental smelting technology, typically uses high concentrations of heavy metal ions, especially in the subsequent phase, due to metal ion accumulation from the mineral. In this study, we analyzed the overall response of the bioleaching microorganism Acidithiobacillus caldus to copper stress through physiological and transcriptomic analyses. Scanning electron microscopy results showed higher extracellular polymeric substances secretion and cell aggregation under copper stress. Intracellular levels of glutamic acid, glycine and cysteine increased, favoring the synthesis of glutathione for maintenance of the oxidation-reduction state. GSH, during copper stress conditions, the activity of GSH-PX and CAT increased, resulting in reduced oxidative damage while maintaining stable intracellular pH. Higher unsaturated and cyclopropane fatty acid levels resulted in increased membrane fluidity and compactness and decreased ATP levels to support the energy requirements for stress resistance. Initially, H⁺-ATPase activity increased to provide energy for proton output and decreased later at higher copper ion stress. From transcriptome analysis, 140 genes were differentially expressed under low copper stress (1 g/L), while 250 genes exhibited altered transcriptional levels at higher copper stress (3 g/L). These differentially expressed genes were involved primarily in metabolic pathways such as energy metabolism, two-component systems, amino acid metabolism, and signal transduction. The Sox family cluster gene cluster involved in the conversion of thiosulfate to sulfate was upregulated in the sulfur metabolism pathway. In the oxidative phosphorylation pathway, genes participating in the synthesis of NADH oxidoreductase and cytochrome c oxidase, nuoL, cyoABD (cyoA, cyoB and cyoD) and cydAB (cydA and cydB), were downregulated. The TCS element ompR, closely associated with the osmotic pressure, exhibited active response, while Cu²⁺ efflux system gene cusRS was upregulated. In the amino acid metabolism, the glnA involved in nitrogen fixation was upregulated and promoted the synthesis of glutamine synthetase for reducing excessive oxidative stress. This study provides new insights into the mechanism underlying A. caldus response to heavy-metal ion stress under harsh bioleaching conditions.

Sulfobacillus thermotolerans: new insights into resistance and metabolic capacities of acidophilic chemolithotrophs

The first complete genome of the biotechnologically important species Sulfobacillus thermotolerans has been sequenced. Its 3 317 203-bp chromosome contains an 83 269-bp plasmid-like region, which carries heavy metal resistance determinants and the rusticyanin gene. Plasmid-mediated metal resistance is unusual for acidophilic chemolithotrophs. Moreover, most of their plasmids are cryptic and do not contribute to the phenotype of the host cells. A polyphosphate-based mechanism of metal resistance, which has been previously unknown in the genus Sulfobacillus or other Gram-positive chemolithotrophs, potentially operates in two Sulfobacillus species. The methylcitrate cycle typical for pathogens and identified in the genus Sulfobacillus for the first time can fulfill the energy and/or protective function in S. thermotolerans Kr1 and two other Sulfobacillus species, which have incomplete glyoxylate cycles. It is notable that the TCA cycle, disrupted in all Sulfobacillus isolates under optimal growth conditions, proved to be complete in the cells enduring temperature stress. An efficient antioxidant defense system gives S. thermotolerans another competitive advantage in the microbial communities inhabiting acidic metal-rich environments. The genomic comparisons revealed 80 unique genes in the strain Kr1, including those involved in lactose/galactose catabolism. The results provide new insights into metabolism and resistance mechanisms in the Sulfobacillus genus and other acidophiles.

Archaeal biofilm formation

Biofilms are structured and organized communities of microorganisms that represent one of the most successful forms of life on Earth. Bacterial biofilms have been studied in great detail, and many molecular details are known about the processes that govern bacterial biofilm formation, however, archaea are ubiquitous in almost all habitats on Earth and can also form biofilms. In recent years, insights have been gained into the development of archaeal biofilms, how archaea communicate to form biofilms and how the switch from a free-living lifestyle to a sessile lifestyle is regulated. In this Review, we explore the different stages of archaeal biofilm development and highlight similarities and differences between archaea and bacteria on a molecular level. We also consider the role of archaeal biofilms in industry and their use in different industrial processes.

Biotechnological strategies for the recovery of valuable and critical raw materials from waste electrical and electronic equipment (WEEE) - A review

Critical raw materials (CRMs) are essential in the development of novel high-tech applications. They are essential in sustainable materials and green technologies, including renewable energy, emissionfree electric vehicles and energy-efficient lighting. However, the sustainable supply of CRMs is a major concern. Recycling end-of-life devices is an integral element of the CRMs supply policy of many countries. Waste electrical and electronic equipment (WEEE) is an important secondary source of CRMs. Currently, pyrometallurgical processes are used to recycle metals from WEEE. These processes are deemed imperfect, energy-intensive and non-selective towards CRMs. Biotechnologies are a promising alternative to the current industrial best available technologies (BAT). In this review, we present the current frontiers in CRMs recovery from WEEE using biotechnology, the biochemical fundamentals of these bio-based technologies and discuss recent research and development (R&D) activities. These technologies encompass biologically induced leaching (bioleaching) from various matrices,biomass-induced sorption (biosorption), and bioelectrochemical systems (BES).

Comparative Genomic Analysis Reveals the Distribution, Organization, and Evolution of Metal Resistance Genes in the Genus Acidithiobacillus

Members of the genus Acidithiobacillus, which can adapt to extremely high concentrations of heavy metals, are universally found at acid mine drainage (AMD) sites. Here, we performed a comparative genomic analysis of 37 strains within the genus Acidithiobacillus to answer the untouched questions as to the mechanisms and the evolutionary history of metal resistance genes in Acidithiobacillus spp. The results showed that the evolutionary history of metal resistance genes in Acidithiobacillus spp. involved a combination of gene gains and losses, horizontal gene transfer (HGT), and gene duplication. Phylogenetic analyses revealed that metal resistance genes in Acidithiobacillus spp. were acquired by early HGT events from species that shared habitats with Acidithiobacillus spp., such as Acidihalobacter, Thiobacillus, Acidiferrobacter, and Thiomonas species. Multicopper oxidase genes involved in copper detoxification were lost in iron-oxidizing Acidithiobacillus ferridurans, Acidithiobacillus ferrivorans, and Acidithiobacillus ferrooxidans and were replaced by rusticyanin genes during evolution. In addition, widespread purifying selection and the predicted high expression levels emphasized the indispensable roles of metal resistance genes in the ability of Acidithiobacillus spp. to adapt to harsh environments. Altogether, the results suggested that Acidithiobacillus spp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. This study sheds light on the distribution, organization, functionality, and complex evolutionary history of metal resistance genes in Acidithiobacillus spp.IMPORTANCE Horizontal gene transfer (HGT), natural selection, and gene duplication are three main engines that drive the adaptive evolution of microbial genomes. Previous studies indicated that HGT was a main adaptive mechanism in acidophiles to cope with heavy-metal-rich environments. However, evidences of HGT in Acidithiobacillus species in response to challenging metal-rich environments and the mechanisms addressing how metal resistance genes originated and evolved in Acidithiobacillus are still lacking. The findings of this study revealed a fascinating phenomenon of putative cross-phylum HGT, suggesting that Acidithiobacillus spp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. Altogether, the insights gained in this study have improved our understanding of the metal resistance strategies of Acidithiobacillus spp.

Metatranscriptome analysis of the intestinal microorganisms in Pardosa pseudoannulata in response to cadmium stress

Cadmium (Cd) generates a variety of physiological and ecological toxicity to spiders. However, little is known about the effects of Cd on symbiotic bacteria of spiders. Metatranscriptomics is increasing our knowledge of microorganisms in environment. To better understand the impact of Cd on the symbiotic bacteria of spiders, we generated and compared the metatranscriptomes of the intestinal microorganisms of Pardosa pseudoannulata with and without Cd stress. The community structure of intestinal microorganisms in P. pseudoannulata was composed of 4 kingdoms, namely bacteria, viruses, eukaryotes and archaea, including 46 phyla, 97 classes, 184 orders, 339 families, 470 genera, and 598 species. The abundance of eukaryotes, bacteria and viruses was decreased by 0.14%, 1.22% and 2.52% respectively while the archaea was increased by 99.16% when under Cd stress. We identified 1519 differentially expressed genes (DEGs), including 770 up-regulated and 749 down-regulated genes. The results of KEGG annotation revealed that the expression of genes that are involved in the carbon metabolism, protein and amino acid metabolism and synthesis, glucose metabolism, oxidative phosphorylation, and glutathione metabolism were influenced by Cd. Collectively, these findings showed that Cd significantly impacted the community structure and expression of related functional genes of intestinal microorganisms in P. pseudoannulata.

Enhancement of copper, nickel, and gallium recovery from LED waste by adaptation of Acidithiobacillus ferrooxidans

This paper is the first study on the extraction of Cu, Ni, and Ga from Light Emitting Diode (LED) waste by bio-hydrometallurgy technology. LEDs have a high concentration of metals and various types of brominated flame retardants (BFRs). This study demonstrates the need for strains with resistance to high concentrations of LED powder. The adaptation of Acidithiobacillus ferrooxidans to LED powder was done through a serial acclimatisation procedure in five steps of 5, 10, 15, 20, and 25 g/l. The results indicated that the heavy metals tolerance of Acidithiobacillus ferrooxidans decreased as the pulp density increased from 5 to 20 g/l. The pulp density > 20 g/l of LED powder caused a toxic response resulting in an evident inhibitory effect on bacterial activity. In the presence of 20 g/l of LED powder, adapted Acidithiobacillus ferrooxidans exhibits higher Fe³⁺ level, cell amount, ORP, and lower pH than the non-adapted cells. The recovery of copper, nickel, and gallium were higher by adapted bacteria compared to non-adapted bacteria. The adapted A. ferrooxidans leached approximately 84%, 96%, and 60%, copper, nickel, and gallium, respectively. It could be concluded that adaptation can be an effective tool for enhancement of copper, nickel, and gallium bioleaching from LED powder and adapted Acidithiobacillus ferrooxidans would be a suitable strain in LED waste bioleaching.

Possible Role of Envelope Components in the Extreme Copper Resistance of the Biomining Acidithiobacillus ferrooxidans

Acidithiobacillus ferrooxidans resists extremely high concentrations of copper. Strain ATCC 53993 is much more resistant to the metal compared with strain ATCC 23270, possibly due to the presence of a genomic island in the former one. The global response of strain ATCC 53993 to copper was analyzed using iTRAQ (isobaric tag for relative and absolute quantitation) quantitative proteomics. Sixty-seven proteins changed their levels of synthesis in the presence of the metal. On addition of CusCBA efflux system proteins, increased levels of other envelope proteins, such as a putative periplasmic glucan biosynthesis protein (MdoG) involved in the osmoregulated synthesis of glucans and a putative antigen O polymerase (Wzy), were seen in the presence of copper. The expression of A. ferrooxidansmdoG or wzy genes in a copper sensitive Escherichia coli conferred it a higher metal resistance, suggesting the possible role of these components in copper resistance of A. ferrooxidans. Transcriptional levels of genes wzy, rfaE and wzz also increased in strain ATCC 23270 grown in the presence of copper, but not in strain ATCC 53993. Additionally, in the absence of this metal, lipopolysaccharide (LPS) amounts were 3-fold higher in A. ferrooxidans ATCC 53993 compared with strain 23270. Nevertheless, both strains grown in the presence of copper contained similar LPS quantities, suggesting that strain 23270 synthesizes higher amounts of LPS to resist the metal. On the other hand, several porins diminished their levels in the presence of copper. The data presented here point to an essential role for several envelope components in the extreme copper resistance by this industrially important acidophilic bacterium.

Extremophilic Microfactories: Applications in Metal and Radionuclide Bioremediation

Metals and radionuclides (M&Rs) are a worldwide concern claiming for resilient, efficient, and sustainable clean-up measures aligned with environmental protection goals and global change constraints. The unique defense mechanisms of extremophilic bacteria and archaea have been proving usefulness towards M&Rs bioremediation. Hence, extremophiles can be viewed as microfactories capable of providing specific and controlled services (i.e., genetic/metabolic mechanisms) and/or products (e.g., biomolecules) for that purpose. However, the natural physiological plasticity of such extremophilic microfactories can be further explored to nourish different hallmarks of M&R bioremediation, which are scantly approached in the literature and were never integrated. Therefore, this review not only briefly describes major valuable extremophilic pathways for M&R bioremediation, as it highlights the advances, challenges and gaps from the interplay of ‘omics’ and biological engineering to improve extremophilic microfactories performance for M&R clean-up. Microfactories’ potentialities are also envisaged to close the M&R bioremediation processes and shift the classical idea of never ‘getting rid’ of M&Rs into making them ‘the belle of the ball’ through bio-recycling and bio-recovering techniques.

Metagenomic insights into the microbial diversity in manganese-contaminated mine tailings and their role in biogeochemical cycling of manganese

To extend the knowledge on the microbial diversity of manganese rich environments, we performed a clone library based study using metagenomic approach. Pyrosequencing based analysis of 16S rRNA genes were carried out on an Illumina platform to gain insights into the bacterial community inhabiting in a manganese mining site and the taxonomic profiles were correlated with the inherent capacities of these strains to solubilise manganese. The application of shot gun sequencing in this study yielded results which revealed the highest prevalence of Proteobacteria (42.47%), followed by Actinobacteria (23.99%) in the area of study. Cluster of orthologous group (COG) functional category has 85,066 predicted functions. Out of which 11% are involved in metabolism of amino acid, 9% are involved in production and conversion of energy while Keto Encyclopedia of Gene and Genomes (KEGG) functional category has 107,388 predicted functions, out of which 55% are involved in cellular metabolism, 15% are environmental and information processing and 12% are genetic information processing in nature. The isolated microbial consortia demonstrated visible growth in presence of high concentrations of Mn. Solubilisation studies resulted in 86% of manganese recovery after 20 days. The result presented in this study has important implications in understanding the microbial diversity in manganese contaminated mine tailings and their role in natural geochemical cycling of Mn.

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.

Global effect of the lack of inorganic polyphosphate in the extremophilic archaeon Sulfolobus solfataricus: A proteomic approach

Inorganic polyphosphates (polyP) are present in all living cells and several important functions have been described for them. They are involved in the response to stress conditions, such as nutrient depletion, oxidative stress and toxic metals amongst others. A recombinant strain of Sulfolobus solfataricus unable to accumulate polyP was designed by the overexpression of its endogenous ppx gene. The overall impact of the lack of polyP on this S. solfataricus polyP (-) strain was analyzed by using quantitative proteomics (isotope-coded protein label, ICPL). Stress-related proteins, such as peroxiredoxins and heat shock proteins, proteins involved in metabolism and several others were produced at higher levels in the ppx expression strain. The polyP deficient strain showed an increased copper sensitivity and an earlier transcriptional up-regulation of copA gene coding for the P-type copper-exporting ATPase. This implies a complementary function of both copper resistance systems. These results strongly suggests that the lack of polyP makes this hyperthermophilic archaeon more sensitive to toxic conditions, such as an exposure to metals or other harmful stimuli, emphasizing the importance of this inorganic phosphate polymers in the adaptations to live in the environmental conditions in which thermoacidophilic archaea thrive. SIGNIFICANCE: Inorganic polyphosphate (polyP) are ubiquitous molecules with many functions in living organisms. Few studies related to these polymers have been made in archaea. The construction of a polyP deficient recombinant strain of Sulfolobus solfataricus allowed the study of the global changes in the proteome of this thermoacidophilic archaeon in the absence of polyP compared with the wild type strain. The results obtained using quantitative proteomics suggest an important participation of polyP in the oxidative stress response of the cells and as having a possible metabolic role in the cell, as previously described in bacteria. The polyP deficient strain also showed an increased copper sensitivity and an earlier transcriptional up-regulation of copA, implying a complementary role of both copper resistance systems.