Response of the biomining Acidithiobacillus ferrooxidans to high cadmium concentrations

Removal of toxic metal Cd (II) by Serratia bozhouensis CdIW2 using in moving bed biofilm reactor (MBBR)

The use of bioreactor technology to treat industrial wastewater containing heavy metals has created new perspectives. Cadmium metal is one of the toxic heavy metals that have harmful effects on human health and the environment. This research work presents a comprehensive approach for aqueous cadmium removal through biosorption in a moving bed biofilm reactor (MBBR). The bacterium resistant to Cd(II) (350 mg/L) CdIW2 was selected among 8 cadmium tolerant bacteria isolated from the industrial wastewater of the metal industry. 16S rRNA gene and phenotypic analysis showed that the bacterium CdIW2 is similar to Serratia bozhouensis. The highest biosorption capacity of 65.79 mg/g was acquired in optimal conditions (30 min, pH = 6, 0.5 g/L, and 35 °C). The biosorption of the CdIW2 strain was consistent with the Langmuir isotherm and the pseudo-second order kinetic and showed the process's spontaneous thermodynamic and endothermic results. The removal rate 91.74% of MBBR in batch mode was obtained in 72 h and 10 mg/L of Cd(II). Furthermore, continuous mode bioreactor analysis has shown high efficiency at intel loading rates of 6-36 mg/L. day for cadmium removal. The second order kinetic (Grau) was chosen as the suitable model for modeling the MBBR process. Although several studies have evaluated the removal of various types of heavy metals, none of the studies involved the use of a metal-resistant strain in an MBBR bioreactor.

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.

Cloning, expression, and bioinformatics analysis of heavy metal resistance-related genes fd-I and fd-II from Acidithiobacillus ferrooxidans

Five heavy metals were introduced into the bacterial heavy metal resistance tests. The results showed that apparent inhibition effects of Cd2+ and Cu2+ on the growth of Acidithiobacillus ferrooxidans BYSW1 occurred at high concentrations (>0.04 mol l-1). Significant differences (P < 0.001) were both noticed in the expression of two ferredoxin-encoding genes (fd-I and fd-II) related to heavy metal resistance in the presence of Cd2+ and Cu2+ . When exposed to 0.06 mol l-1 Cd2+, the relative expression levels of fd-I and fd-II were about 11 and 13 times as much as those of the control, respectively. Similarly, exposure to 0.04 mol l-1 Cu2+ caused approximate 8 and 4 times higher than those of the control, respectively. These two genes were cloned and expressed in Escherichia coli, and the structures, functions of two corresponding target proteins, i.e. Ferredoxin-I (Fd-I) and Ferredoxin-II (Fd-II), were predicted. The recombinant cells inserted by fd-I or fd-II were more resistant to Cd2+ and Cu2+ compared with wild-type cells. This study was the first investigation regarding the contribution of fd-I and fd-II to enhancing heavy metal resistance of this bioleaching bacterium, and laid a foundation for further elucidation of heavy metal resistance mechanisms caused by Fd.

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.

The Materials Science behind Sustainable Metals and Alloys

Production of metals stands for 40% of all industrial greenhouse gas emissions, 10% of the global energy consumption, 3.2 billion tonnes of minerals mined, and several billion tonnes of by-products every year. Therefore, metals must become more sustainable. A circular economy model does not work, because market demand exceeds the available scrap currently by about two-thirds. Even under optimal conditions, at least one-third of the metals will also in the future come from primary production, creating huge emissions. Although the influence of metals on global warming has been discussed with respect to mitigation strategies and socio-economic factors, the fundamental materials science to make the metallurgical sector more sustainable has been less addressed. This may be attributed to the fact that the field of sustainable metals describes a global challenge, but not yet a homogeneous research field. However, the sheer magnitude of this challenge and its huge environmental effects, caused by more than 2 billion tonnes of metals produced every year, make its sustainability an essential research topic not only from a technological point of view but also from a basic materials research perspective. Therefore, this paper aims to identify and discuss the most pressing scientific bottleneck questions and key mechanisms, considering metal synthesis from primary (minerals), secondary (scrap), and tertiary (re-mined) sources as well as the energy-intensive downstream processing. Focus is placed on materials science aspects, particularly on those that help reduce CO₂ emissions, and less on process engineering or economy. The paper does not describe the devastating influence of metal-related greenhouse gas emissions on climate, but scientific approaches how to solve this problem, through research that can render metallurgy fossil-free. The content is considering only direct measures to metallurgical sustainability (production) and not indirect measures that materials leverage through their properties (strength, weight, longevity, functionality).

Multi-scale analysis of nickel ion tolerance mechanism for thermophilic Sulfobacillus thermosulfidooxidans in bioleaching

Bioleaching is intensively investigated for recovering valuable metals such as Li, Co, Ni and Cu. Nickel ion stress threatens the health of microorganisms when Ni²⁺ starts to accumulate in the leachate during the bioleaching of materials that are rich in Ni, such as spent lithium-ion batteries. The possible mechanisms underlying the response of S. thermosulfidooxidans to nickel ion stress were analyzed using a multi-scale approach. Under the condition of nickel ion stress, high concentrations of nickel ions were immobilized by extracellular polymeric substances, while concentrations of nickel ions inside the cells remained low. The intracellular adenosine triphosphate (ATP) concentration and H⁺-ATPase activity increased to maintain normal cell growth and metabolic activities. Scavenging abilities of S. thermosulfidooxidans for hydrogen peroxide and superoxide anion were enhanced to reduce oxidative damage induced by nickel ion stress. There were 734 differentially expressed genes identified by RNA-seq under nickel ion stress. Most of them were involved in oxidative phosphorylation, glutathione metabolism and genetic information processing, responsible for intracellular energy utilization, intracellular antioxidant capacity and DNA damage repair, respectively. The results of this study are of major significance for in-depth understanding of the mechanisms of acidophilic microorganisms' resistance to metal ions.

Widespread bacterial responses and their mechanism of bacterial metallogenic detoxification under high concentrations of heavy metals

Microbial mineralization is increasingly used in bioremediation of heavy metal pollution, but better mechanistic understanding of the processes involved and how they are regulated are required to improve the practical application of microorganisms in bioremediation. We used a combination of morphological (TEM) and analytical (XRD, XPS, FTIR) methods, together with novel proteomic analyses, to investigate the detoxification mechanisms, used by a range of bacteria, including the strains Bacillus velezensis LB002, Escherichia coli DH5α, B. subtilis 168, Pseudomonas putida KT2440, and B. licheniformis MT-1, exposed to elevated concentrations of Cd²⁺ and combinations of Cd²⁺, Pb²⁺, Cu²⁺, and Zn²⁺, in the presence and absence of added CaCl₂. Common features of detoxification included biomineralization, including the production of biological vaterite, up-regulation of proteins involved in flagellar movement and chemotaxis, biofilm synthesis, transmembrane transport of small molecules and organic matter decomposition. The putative roles of differentially expressed proteins in detoxification are discussed in relation to chemical and morphological data and together provide important tools to improve screening, selection, and practical application of bacterial isolates in bioremediation of polluted environments.

Genetic engineering of extremely acidophilic Acidithiobacillus species for biomining: Progress and perspectives

With global demands for mineral resources increasing and ore grades decreasing, microorganisms have been increasingly deployed in biomining applications to recover valuable metals particularly from normally considered waste, such as low-grade ores and used consumer electronics. Acidithiobacillus are a genus of chemolithoautotrophic extreme acidophiles that are commonly found in mining process waters and acid mine drainage, which have been reported in several studies to aid in metal recovery from bioremediation of metal-contaminated sites. Compared to conventional mineral processing technologies, biomining is often cited as a more sustainable and environmentally friendly process, but long leaching cycles and low extraction efficiency are main disadvantages that have hampered its industrial applications. Genetic engineering is a powerful technology that can be used to enhance the performance of microorganisms, such as Acidithiobacillus species. In this review, we compile existing data on Acidithiobacillus species' physiological traits and genomic characteristics, progresses in developing genetic tools to engineer them: plasmids, shutter vectors, transformation methods, selection markers, promoters and reporter systems developed, and genome editing techniques. We further propose genetic engineering strategies for enhancing biomining efficiency of Acidithiobacillus species and provide our perspectives on their future applications.

Nanobiotics against antimicrobial resistance: harnessing the power of nanoscale materials and technologies

Given the spasmodic increment in antimicrobial resistance (AMR), world is on the verge of “post-antibiotic era”. It is anticipated that current SARS-CoV2 pandemic would worsen the situation in future, mainly due to the lack of new/next generation of antimicrobials. In this context, nanoscale materials with antimicrobial potential have a great promise to treat deadly pathogens. These functional materials are uniquely positioned to effectively interfere with the bacterial systems and augment biofilm penetration. Most importantly, the core substance, surface chemistry, shape, and size of nanomaterials define their efficacy while avoiding the development of AMR. Here, we review the mechanisms of AMR and emerging applications of nanoscale functional materials as an excellent substitute for conventional antibiotics. We discuss the potential, promises, challenges and prospects of nanobiotics to combat AMR.

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.

Trends in microbial degradation and bioremediation of emerging contaminants

Modernization and modern ways of living demands more improved products from pharmaceuticals, cosmetics, and food processing industries. Moreover, industries like pesticides, fertilizers, dyeing, paints, detergent etc., also needs improvised products as per demand. As the new product emerges, the pollutants from these industries also constitute new type of danger to the environment and serious health risks to the living organisms. These emerging contaminants (ECs) are from different category of sources such as personal care products (PCPs), pharmaceuticals (Phcs), endocrine disrupting chemicals (EDCs), etc. These ECs can easily escape from the conventional water treatment and eventually get discharged in to the surface water and thus enters in to the ground water, soil, sediments, and also into the oceans. When these contaminants emerge we also require progress in tremendous process for preventing these hazardous chemicals by effective removal and treatment. For the past 50 years, both developed and developing countries are working on this treatment process and found that Microbial degradation and bioremediation are very useful for effective treatment to prevent their emissions. This treatment can be designed for any sort of ECs since the microbial members are so versatile to redesign their metabolic pathways when subject to exposure. However, implementing bioremediation is not alone efficient to degrade ECs and hence, combination of bioremediation, nanotechnology and physical treatment method will also provide sustainable, potent and fast degradation process. In this Book Chapter, we discuss in detail about the ECs, sources of microbial degradation process and its usefulness in the bioremediation of these ECs.

Recent progress in the application of omics technologies in the study of bio-mining microorganisms from extreme environments

Bio-mining microorganisms are a key factor affecting the metal recovery rate of bio-leaching, which inevitably produces an extremely acidic environment. As a powerful tool for exploring the adaptive mechanisms of microorganisms in extreme environments, omics technologies can greatly aid our understanding of bio-mining microorganisms and their communities on the gene, mRNA, and protein levels. These omics technologies have their own advantages in exploring microbial diversity, adaptive evolution, changes in metabolic characteristics, and resistance mechanisms of single strains or their communities to extreme environments. These technologies can also be used to discover potential new genes, enzymes, metabolites, metabolic pathways, and species. In addition, integrated multi-omics analysis can link information at different biomolecular levels, thereby obtaining more accurate and complete global adaptation mechanisms of bio-mining microorganisms. This review introduces the current status and future trends in the application of omics technologies in the study of bio-mining microorganisms and their communities in extreme environments.

Microbial community and metabolic responses to electrical field intensity for alleviation of ammonia inhibition in an integrated bioelectrochemical system (BES)

Bioelectrochemical system (BES) is a promising solution for mitigation of ammonia inhibition in anaerobic digestion (AD) process. However, the effect of electric field intensity on microbial community changes and metabolic function prediction during the alleviation of ammonia inhibition are still missing. The results of the current study represented that the improvement of ammonia removal (20.6%) and methane production (14.6%) could both be achieved at 0.2 V while higher voltages led to reductions of methane production (more than 48.9%) compared with the control. Moreover, hydrogenotrophic methanogens (Methanobacterium) seemed to be more robust to high voltages compared with aceticlastic methanogens (Methanosaeta). Additionally, bacteria for hydrolysis and acidogenesis (Rikenellaceae and Soehngenia) were found vulnerable to external electric field intensity. Furthermore, abundances changes of metabolic pathways demonstrated that the degradation of carbohydrates, lipids and proteins during all steps (hydrolysis, acidogenesis, acetogenesis and methanogenesis) of AD process could be affected by different applied voltages.

The roles of PARP-1 and XPD and their potential interplay in repairing bupivacaine-induced neuron oxidative DNA damage

Bupivacaine has been widely used in clinical Anesthesia, but its neurotoxicity has been frequently reported, implicating cellular oxidative DNA damage as the major underlying mechanism. However, the mechanism underlying bupivacaine-induced oxidative DNA damage is unknown. We, thus, exposed SH-SY5Y cells to 1.5mM bupivacaine to induce neurotoxicity. Then, iTRAQ proteomic analysis was used to explore the repair of neuronal oxidative DNA damage. By analyzing the STRING version 11.0 database, the bioinformatics relationship between key repair enzymes was tracked. Subsequently, immunofluorescence co-localization and immunoprecipitation were used to investigate the interaction between key repair enzymes. The iTRAQ showed that Poly [ADP-ribose] polymerase 1 (PARP-1) from the base excision repair pathway participated closely in the repair of oxidative DNA damage induced by bupivacaine, and inhibition of PARP-1 expression significantly aggravated bupivacaine-induced DNA damage and apoptosis. Interestingly, this study showed that there were interactions and co-expression between PARP-1 and XPD (xeroderma pigmentosum D), another key protein of the nucleic acid excision repair pathway. After inhibiting XPD, PARP-1 expression was significantly reduced. However, simultaneous inhibition of both XPD and PARP-1 did not further increase DNA damage. It is concluded that PARP-1 may repair bupivacaine-induced oxidative DNA damage through XPD-mediated interactions.

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.

Microorganisms and Their Metabolic Capabilities in the Context of the Biogeochemical Nitrogen Cycle at Extreme Environments

Extreme microorganisms (extremophile) are organisms that inhabit environments characterized by inhospitable parameters for most live beings (extreme temperatures and pH values, high or low ionic strength, pressure, or scarcity of nutrients). To grow optimally under these conditions, extremophiles have evolved molecular adaptations affecting their physiology, metabolism, cell signaling, etc. Due to their peculiarities in terms of physiology and metabolism, they have become good models for (i) understanding the limits of life on Earth, (ii) exploring the possible existence of extraterrestrial life (Astrobiology), or (iii) to look for potential applications in biotechnology. Recent research has revealed that extremophilic microbes play key roles in all biogeochemical cycles on Earth. Nitrogen cycle (N-cycle) is one of the most important biogeochemical cycles in nature; thanks to it, nitrogen is converted into multiple chemical forms, which circulate among atmospheric, terrestrial and aquatic ecosystems. This review summarizes recent knowledge on the role of extreme microorganisms in the N-cycle in extremophilic ecosystems, with special emphasis on members of the Archaea domain. Potential implications of these microbes in global warming and nitrogen balance, as well as their biotechnological applications are also discussed.

A genomic perspective of metal-resistant bacteria from gold particles: Possible survival mechanisms during gold biogeochemical cycling

A bacterial consortium was enriched from gold particles that ‘experienced’ ca. 80 years of biotransformation within waste-rock piles (Australia). This bacterial consortium was exposed to 10 µM AuCl3 to obtain Au-tolerant bacteria. From these isolates, Serratia sp. and Stenotrophomonas sp. were the most Au-tolerant and reduced soluble Au as pure gold nanoparticles, indicating that passive mineralisation is a mechanism for mediating the toxic effect of soluble Au produced during particle dissolution. Genome-wide analysis demonstrated that these isolates also possessed various genes that could provide cellular defence enabling survival under heavy-metal stressed condition by mediating the toxicity of heavy metals through active efflux/reduction. Diverse metal-resistant genes or genes clusters (cop, cus, czc, zntand ars) were detected, which could confer resistance to soluble Au. Comparative genome analysis revealed that the majority of detected heavy-metal resistant genes were similar (i.e. orthologous) to those genes of Cupriavidus metallidurans CH34. The detection of heavy-metal resistance, nutrient cycling and biofilm formation genes (pgaABCD, bsmAandhmpS) may have indirect yet important roles when dealing with soluble Au during particle dissolution. In conclusion, the physiological and genomic results suggest that bacteria living on gold particles would likely use various genes to ensure survival during Au-biogeochemical cycling.

Molecular Mechanisms of Bacterial Resistance to Metal and Metal Oxide Nanoparticles

The increase in bacterial resistance to one or several antibiotics has become a global health problem. Recently, nanomaterials have become a tool against multidrug-resistant bacteria. The metal and metal oxide nanoparticles are one of the most studied nanomaterials against multidrug-resistant bacteria. Several in vitro studies report that metal nanoparticles have antimicrobial properties against a broad spectrum of bacterial species. However, until recently, the bacterial resistance mechanisms to the bactericidal action of the nanoparticles had not been investigated. Some of the recently reported resistance mechanisms include electrostatic repulsion, ion efflux pumps, expression of extracellular matrices, and the adaptation of biofilms and mutations. The objective of this review is to summarize the recent findings regarding the mechanisms used by bacteria to counteract the antimicrobial effects of nanoparticles.