Biomineralization and Bioaccumulation of Europium by a Thermophilic Metal Resistant Bacterium

Changes in growth, lanthanide binding, and gene expression in Pseudomonas alloputida KT2440 in response to light and heavy lanthanides

Pseudomonas alloputida KT2440 is a ubiquitous, soil-dwelling bacterium that metabolizes recalcitrant and volatile carbon sources. The latter is utilized by two redundant, Ca- and lanthanide (Ln)-dependent, pyrroloquinoline quinone-dependent alcohol dehydrogenases (PQQ ADH), PedE and PedH, whose expression is regulated by Ln availability. P. alloputida KT2440 is the best-studied non-methylotroph in the context of Ln-utilization. Combined with microfluidic cultivation and single-cell elemental analysis, we studied the impact of light and heavy Ln on transcriptome-wide gene expression when growing P. alloputida KT2440 with 2-phenylethanol as the carbon and energy source. Light Ln (La, Ce, and Nd) and a mixture of light and heavy Ln (La, Ce, Nd, Dy, Ho, Er, and Yb) had a positive effect on growth, whereas supplementation with heavy Ln (Dy, Ho, Er, and Yb) exerted fitness costs. These were likely a consequence of mismetallation and non-utilizable Ln interfering with Ln sensing and signaling. The measured amounts of cell-associated Ln varied between elements. Gene expression analysis suggested that the Ln sensing and signaling machinery, the two-component system PedS2R2 and PedH, responds differently to (non-)utilizable Ln. We expanded our understanding of the lanthanide (Ln) switch in P. alloputida KT2440, demonstrating that it adjusts the levels of pedE and pedH transcripts based on the availability of Ln. We propose that the usability of Ln influences the bacterium's response to different Ln elements.IMPORTANCEThe Ln switch, the inverse regulation of Ca- and Ln-dependent PQQ ADH in response to Ln availability in organisms featuring both, is central to our understanding of Ln utilization. Although the preference of bacteria for light Ln is well known, the effect of different Ln, light and heavy, on growth and gene expression has rarely been studied. We provide evidence for a fine-tuning mechanism of Ca- and Ln-dependent PQQ ADH in P. alloputida KT2440 on the transcriptome level. The response to (non-)utilizable Ln differs depending on the element. Ln commonly co-occur in nature. Our findings underline that Ln-utilizing microbes must be able to discriminate between Ln to use them effectively. Considering the prevalence of Ln-dependent proteins in many microbial taxa, more work addressing Ln sensing and signaling is needed. Ln availability likely necessitates different adaptations regarding Ln utilization.

Unlocking nature's brilliance: using Antarctic extremophile Shewanella baltica to biosynthesize lanthanide-containing nanoparticles with optical up-conversion

Both lanthanide-containing and fluorine-containing nanomaterials present challenging targets for microbial biosynthesis because these elements are toxic to most bacteria. Here, we overcome these challenges by using an Antarctic Shewanella baltica strain that tolerates these elements and report the first biosynthesis of lanthanide-doped fluoride nanoparticles (NPs) from them. NaYF4 NPs doped with Er3+/Yb3+ are prototypical lanthanide-based upconverting nanoparticles (UCNPs) with upconverted luminescence at visible wavelengths under infrared excitation. However, their synthesis employs high precursor concentrations, organic solvents, and elevated temperatures. Microbial biosynthesis offers a greener alternative but has not been explored for these materials. Here, we harness an extremophile S. baltica strain to biosynthesize UCNPs at room temperature, based upon its high tolerance for fluoride and lanthanide ions and the observation that tolerance of lanthanides increased in the presence of fluoride. Our biosynthesis produces electron-dense nanostructures composed of Na, Y, F, Yb, and Er in the bacterial periplasm, adhered to the outer cell membrane, and dispersed extracellularly, which exhibited up-converted emission under 980 nm excitation. This suggests that extracellular or periplasmic mineralization of lanthanides as fluorides protects the bacteria from lanthanide toxicity. Subsequent heating both enhanced upconverted emission from UCNPs and allowed observation of their crystallinity in transmission electron microscopy (TEM). This work establishes the first biosynthesis of NaYF4:Yb: Er UCNPs, advancing both nanotechnology and biotechnology.

Microbial green synthesis of luminescent terbium sulfide nanoparticles using E. Coli: a rare earth element detoxification mechanism

BACKGROUND

Rare-earth sulfide nanoparticles (NPs) could harness the optical and magnetic features of rare-earth ions for applications in nanotechnology. However, reports of their synthesis are scarce and typically require high temperatures and long synthesis times.

RESULTS

Here we present a biosynthesis of terbium sulfide (TbS) NPs using microorganisms, identifying conditions that allow Escherichia coli to extracellularly produce TbS NPs in aqueous media at 37 °C by controlling cellular sulfur metabolism to produce a high concentration of sulfide ions. Electron microscopy revealed ultrasmall spherical NPs with a mean diameter of 4.1 ± 1.3 nm. Electron diffraction indicated a high degree of crystallinity, while elemental mapping confirmed colocalization of terbium and sulfur. The NPs exhibit characteristic absorbance and luminescence of terbium, with downshifting quantum yield (QY) reaching 28.3% and an emission lifetime of ~ 2 ms.

CONCLUSIONS

This high QY and long emission lifetime is unusual in a neat rare-earth compound; it is typically associated with rare-earth ions doped into another crystalline lattice to avoid non-radiative cross relaxation. This suggests a reduced role of nonradiative processes in these terbium-based NPs. This is, to our knowledge, the first report revealing the advantage of biosynthesis over chemical synthesis for Rare Earth Element (REE) based NPs, opening routes to new REE-based nanocrystals.

Yttrium immobilization through biomineralization with phosphate by the resistant strain Mesorhizobium qingshengii J19

AIMS

Yttrium (Y) holds significant industrial and economic importance, being listed as a critical element on the European list of critical elements, thus emphasizing the high priority for its recovery. Bacterial strategies play a crucial role in the biorecovery of metals, offering a promising and environmentally friendly approach. Therefore, gaining a comprehensive understanding of the underlying mechanisms behind bacterial resistance, as well as the processes of bioaccumulation and biotransformation, is of paramount importance.

METHODS AND RESULTS

A total of 207 Alphaproteobacteria strains from the University of Coimbra Bacteria Culture Collection were tested for Y-resistance. Among these, strain Mesorhizobium qingshengii J19 exhibited high resistance (up to 4 mM Y) and remarkable Y accumulation capacity, particularly in the cell membrane. Electron microscopy revealed Y-phosphate interactions, while X-ray diffraction identified Y(PO3)3·9H2O biocrystals produced by J19 cells.

CONCLUSION

This study elucidates Y immobilization through biomineralization within phosphate biocrystals using M. qingshengii J19 cells.

Recovery of terbium by Lysinibacillus sp. DW018 isolated from ionic rare earth tailings based on microbial induced calcium carbonate precipitation

Microbial induced calcium carbonate precipitation (MICP) is considered as an environmentally friendly microbial-based technique to remove heavy metals. However, its application in removal and recovery of rare earth from wastewaters remains limited and the process is still less understood. In this study, a urease-producing bacterial strain DW018 was isolated from the ionic rare earth tailings and identified as Lysinibacillus based on 16S rRNA gene sequencing. Its ability and possible mechanism to recover terbium was investigated by using X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), and fourier transform infrared spectroscopy (FTIR). The results showed that the urease activity of DW018 could meet the biomineralization requirements for the recovery of Tb3+ from wastewaters. The recovery rate was as high as 98.28% after 10 min of treatment. The optimal conditions for mineralization and recovery were determined as a bacterial concentration of OD600 = 1.0, a temperature range of 35 to 40°C, and a urea concentration of 0.5%. Notably, irrespective of CaCO3 precipitation, the strain DW018 was able to utilize MICP to promote the attachment of Tb3+ to its cell surface. Initially, Tb3+ existed in amorphous form on the bacterial surface; however, upon the addition of a calcium source, Tb3+ was encapsulated in calcite with the growth of CaCO3 at the late stage of the MICP. The recovery effect of the strain DW018 was related to the amino, hydroxyl, carboxyl, and phosphate groups on the cell surface. Overall, the MICP system is promising for the green and efficient recovery of rare earth ions from wastewaters.

Can xenobiotics support the growth of Mn(II)-oxidizing bacteria (MnOB)? A case of phenol-utilizing bacteria Pseudomonas sp. AN-1

Biogenic manganese oxides (BioMnOx) produced by Mn(II)-oxidizing bacteria (MnOB) have garnered considerable attention for their exceptional adsorption and oxidation capabilities. However, previous studies have predominantly focused on the role of BioMnOx, neglecting substantial investigation into MnOB themselves. Meanwhile, whether the xenobiotics could support the growth of MnOB as the sole carbon source remains uncertain. In this study, we isolated a strain termed Pseudomonas sp. AN-1, capable of utilizing phenol as the sole carbon source. The degradation of phenol took precedence over the accumulation of BioMnOx. In the presence of 100 mg L-1 phenol and 100 µM Mn(II), phenol was entirely degraded within 20 h, while Mn(II) was completely oxidized within 30 h. However, at the higher phenol concentration (500 mg L-1), phenol degradation reduced to 32% and Mn(II) oxidation did not appear to occur. TOC determination confirmed the ability of strain AN-1 to mineralize phenol. Based on the genomic and proteomics studies, the Mn(II) oxidation and phenol mineralization mechanism of strain AN-1 was further confirmed. Proteome analysis revealed down-regulation of proteins associated with Mn(II) oxidation, including MnxG and McoA, with increasing phenol concentration. Notably, this study observed for the first time that the expression of Mn(II) oxidation proteins is modulated by the concentration of carbon sources. This work provides new insight into the interaction between xenobiotics and MnOB, thus revealing the complexity of biogeochemical cycles of Mn and C.

Cellular Response of Adapted and Non-Adapted Tetrahymena thermophila Strains to Europium Eu(III) Compounds

Europium is one of the most reactive lanthanides and humans use it in many different applications, but we still know little about its potential toxicity and cellular response to its exposure. Two strains of the eukaryotic microorganism model Tetrahymena thermophila were adapted to high concentrations of two Eu(III) compounds (EuCl3 or Eu2O3) and compared to a control strain and cultures treated with both compounds. In this ciliate, EuCl3 is more toxic than Eu2O3. LC50 values show that this microorganism is more resistant to these Eu(III) compounds than other microorganisms. Oxidative stress originated mainly by Eu2O3 is minimized by overexpression of genes encoding important antioxidant enzymes. The overexpression of metallothionein genes under treatment with Eu(III) compounds supports the possibility that this lanthanide may interact with the -SH groups of the cysteine residues from metallothioneins and/or displace essential cations of these proteins during their homeostatic function. Both lipid metabolism (lipid droplets fusing with europium-containing vacuoles) and autophagy are involved in the cellular response to europium stress. Bioaccumulation, together with a possible biomineralization to europium phosphate, seems to be the main mechanism of Eu(III) detoxification in these cells.

Enhancing La(III) biosorption and biomineralization with Micromonospora saelicesensis: Involvement of phosphorus and formation of monazite nano-minerals

The release of rare earth elements (REEs) from mining wastes and their applications has significant environmental implications, necessitating the development of effective prevention and reclamation strategies. The mobility of REEs in groundwater due to microorganisms has garnered considerable attention. In this study, a La(III) resistant actinobacterium, Micromonospora saelicesensis KLBMP 9669, was isolated from REE enrichment soil in GuiZhou, China, and evaluated for its ability to adsorb and biomineralize La(III). The findings demonstrated that M. saelicesensis KLBMP 9669 immobilized La(III) through the physical and chemical interactions, with immobilization being influenced by the initial La(III) concentration, biomass, and pH. The adsorption kinetics followed a pseudo-second-order rate model, and the adsorption isotherm conformed to the Langmuir model. La(III) adsorption capacity of this strain was 90 mg/g, and removal rate was 94 %. Scanning electron microscope (SEM) coupled with energy dispersive X-ray spectrometer (EDS) analysis revealed the coexistence of La(III) with C, N, O, and P. Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) investigations further indicated that carboxyl, amino, carbonyl, and phosphate groups on the mycelial surface may participate in lanthanum adsorption. Transmission electron microscopy (TEM) revealed that La(III) accumulation throughout the M. saelicesensis KLBMP 9669, with some granular deposits on the mycelial surface. Selected area electron diffraction (SAED) confirmed the presence of LaPO4 crystals on the M. saelicesensis KLBMP 9669 biomass after a prolonged period of La(III) accumulation. This post-sorption nano-crystallization on the M. saelicesensis KLBMP 9669 mycelial surface is expected to play a crucial role in limiting the bioimmobilization of REEs in geological repositories.

Biomining for sustainable recovery of rare earth elements from mining waste: A comprehensive review

Rare earth elements (REEs) are essential for advanced manufacturing (e.g., renewable energy, military equipment, electric vehicles); hence, the recovery of REEs from low-grade resources has become increasingly important to address their growing demand. Depending on specific mining sites, its geological conditions, and sociodemographic backgrounds, mining waste has been identified as a source of REEs in various concentrations and abundance. Yttrium, cerium, and neodymium are the most common REEs in mining waste streams (50 to 300 μg/L). Biomining has emerged as a viable option for REEs recovery due to its reduced environmental impact, along with reduced capital investment compared to traditional recovery methods. This paper aims to review (i) the characteristics of mining waste as a low-grade REEs resource, (ii) the key operating principles of biomining technologies for REEs recovery, (iii) the effects of operating conditions and matrix on REEs recovery, and (iv) the sustainability of REEs recovery through biomining technologies. Six types of biomining will be examined in this review: bioleaching, bioweathering, biosorption, bioaccumulation, bioprecipitation and bioflotation. Based on a SWOT analyses and techno-economic assessments (TEA), biomining technologies have been found to be effective and efficient in recovering REEs from low-grade sources. Through TEA, coal ash has been shown to return the highest profit amongst mining waste streams.

Terbium Removal from Aqueous Solutions Using a In2O3 Nanoadsorbent and Arthrospira platensis Biomass

Terbium is a rare-earth element with critical importance for industry. Two adsorbents of different origin, In2O3 nanoparticles and the biological sorbent Arthrospira platensis, were applied for terbium removal from aqueous solutions. Several analytical techniques, including X-ray diffraction, Fourier-transform infrared spectroscopy, and scanning electron microscopy, were employed to characterize the adsorbents. The effect of time, pH, and terbium concentration on the adsorption efficiency was evaluated. For both adsorbents, adsorption efficiency was shown to be dependent on the time of interaction and the pH of the solution. Maximum removal of terbium by Arthrospira platensis was attained at pH 3.0 and by In2O3 at pH 4.0-7.0, both after 3 min of interaction. Several equilibrium (Langmuir, Freundlich, and Temkin) and kinetics (pseudo-first order, pseudo-second order, and Elovich) models were applied to describe the adsorption. The maximum adsorption capacity was calculated from the Langmuir model as 212 mg/g for Arthrospira platensis and 94.7 mg/g for the In2O3 nanoadsorbent. The studied adsorbents can be regarded as potential candidates for terbium recovery from wastewater.

High-affinity amide-lanthanide adsorption to gram-positive soil bacteria

The gram-positive soil bacterium, Arthrobacter nicotianae, uses multiple organic acid functional groups to adsorb lanthanides onto its cell surface. At relevant soil pH conditions of 4.0-6.0, many of these functional groups are de-protonated and available for cation sorption and metal immobilization. However, among the plethora of naturally occurring site types, A. nicotianae is shown to possess high-affinity amide and phosphate sites that disproportionately affect lanthanide adsorption to the cell wall. We quantify neodymium (Nd)-selective site types, reporting an amide-Nd stability constant of log10 K = 6.41 ± 0.23 that is comparable to sorption via phosphate-based moieties. These sites are two to three orders of magnitude more selective for Nd than the adsorption of divalent metals to ubiquitous carboxyl-based moieties. This implies the importance of lanthanide biosorption in the context of metal transport in subsurface systems despite trace concentrations of lanthanides found in the natural environment.

Will tomorrow's mineral materials be grown?

Biomineralization, the capacity to form minerals, has evolved in a great diversity of bacterial lineages as an adaptation to different environmental conditions and biological functions. Microbial biominerals often display original properties (morphology, composition, structure, association with organics) that significantly differ from those of abiotically formed counterparts, altogether defining the 'mineral phenotype'. In principle, it should be possible to take advantage of microbial biomineralization processes to design and biomanufacture advanced mineral materials for a range of technological applications. In practice, this has rarely been done so far and only for a very limited number of biomineral types. This is mainly due to our poor understanding of the underlying molecular mechanisms controlling microbial biomineralization pathways, preventing us from developing bioengineering strategies aiming at improving biomineral properties for different applications. Another important challenge is the difficulty to upscale microbial biomineralization from the lab to industrial production. Addressing these challenges will require combining expertise from environmental microbiologists and geomicrobiologists, who have historically been working at the forefront of research on microbe-mineral interactions, alongside bioengineers and material scientists. Such interdisciplinary efforts may in the future allow the emergence of a mineral biomanufacturing industry, a critical tool towards the development more sustainable and circular bioeconomies.

The potential role of biofilms in promoting fouling formation in radioactive discharge pipelines

Nuclear facility discharge pipelines accumulate inorganic and microbial fouling and radioactive contamination, however, research investigating the mechanisms that lead to their accumulation is limited. Using the Sellafield discharge pipeline as a model system, this study utilised modified Robbins devices to investigate the potential interplay between inorganic and biological processes in supporting fouling formation and radionuclide uptake. Initial experiments showed polyelectrolytes (present in pipeline effluents), had minimal effects on fouling formation. Biofilms were, however, found to be the key component promoting fouling, leading to increased uptake of inorganic particulates and metal contaminants (Cs, Sr, Co, Eu and Ru) compared to a non-biofilm control system. Biologically-mediated uptake mechanisms were implicated in Co and Ru accumulation, with a potential bioreduced Ru species identified on the biofilm system. This research emphasised the key role of biofilms in promoting fouling in discharge pipelines, advocating for the use of biocide treatments methods.

Multi-scale modeling of natural organic matter-heavy metal cations interactions: Aggregation and stabilization mechanisms

Interaction between natural organic matters (NOM) and heavy metal cations in aqueous environment are of great significance for maintaining stability of organic carbon and restraining transport of heavy metal contaminants in (bio)geochemical processes. We systematically explore the aggregation process and complexation between NOM and heavy metal cations (Ag⁺, Cd²⁺, Pb²⁺, Zn²⁺, Eu³⁺) under different pH condition by molecular dynamics (MD) simulations, umbrella sampling method, and quantum chemistry calculations. The character of molecular structures NOM-heavy metal complexes and association are quantified. In acidic pH condition, aggregation proceeds via H-bonding and π-π interactions between NOM fragments. In neutral condition, Ag⁺, Cd²⁺, Pb²⁺, and Eu³⁺ can form inner-sphere complexes with the surface carboxylic groups and therefore reduce intermolecular charge repulsion, eventually leading to NOM aggregation, and it shows that even without direct binding, the outer-sphere adsorbed Zn²⁺ can also result in the formation of NOM assemble through H-bonding. Consequently, these heavy metals are capable of promoting NOM aggregation regardless of the complexing ways. Complexing free energy calculations characterized the dynamic processes of cations binding to the carboxylic groups of NOM fragment and the related energy landscape. This study provides quantitative insights for understanding the environmental processes of heavy metals and cycle of C in aquatic ecosystem, and contributes to developing environment-friendly strategies for controlling heavy metal contaminants.

South Africa's indigenous microbial diversity for industrial applications: A review of the current status and opportunities

The unique metagenomic, metaviromic libraries and indigenous micro diversity within Southern Africa have the potential for global beneficiation in academia and industry. Microorganisms that flourish at high temperatures, adverse pH conditions, and high salinity are likely to have enzyme systems that function efficiently under those conditions. These attributes afford researchers and industries alternative approaches that could replace existing chemical processes. Thus, a better understanding of African microbial/genetic diversity is crucial for the development of "greener" industries. A concerted drive to exploit the potential locked in biological resources has been previously seen with companies such as Diversa Incorporated and Verenium (Badische Anilin-und SodaFabrik-BASF) both building business models that pioneered the production of high-performance specialty enzymes for a variety of different industrial applications. The market potential and accompanying industry offerings have not been fully exploited in South Africa, nor in Africa at large. Utilization of the continent's indigenous microbial repositories could create long-lasting, sustainable growth in various production sectors, providing economic growth in resource-poor regions. By bolstering local manufacture of high-value bio-based products, scientific and engineering discoveries have the potential to generate new industries which in turn would provide employment avenues for many skilled and unskilled laborers. The positive implications of this could play a role in altering the face of business markets on the continent from costly import-driven markets to income-generating export markets. This review focuses on identifying microbially diverse areas located in South Africa while providing a profile for all associated microbial/genetically derived libraries in this country. A comprehensive list of all the relevant researchers and potential key players is presented, mapping out existing research networks for the facilitation of collaboration. The overall aim of this review is to facilitate a coordinated journey of exploration, one which will hopefully realize the value that South Africa's microbial diversity has to offer.

Impact of microbial processes on the safety of deep geological repositories for radioactive waste

To date, the increasing production of radioactive waste due to the extensive use of nuclear power is becoming a global environmental concern for society. For this reason, many countries have been considering the use of deep geological repositories (DGRs) for the safe disposal of this waste in the near future. Several DGR designs have been chemically, physically, and geologically well characterized. However, less is known about the influence of microbial processes for the safety of these disposal systems. The existence of microorganisms in many materials selected for their use as barriers for DGRs, including clay, cementitious materials, or crystalline rocks (e.g., granites), has previously been reported. The role that microbial processes could play in the metal corrosion of canisters containing radioactive waste, the transformation of clay minerals, gas production, and the mobility of the radionuclides characteristic of such residues is well known. Among the radionuclides present in radioactive waste, selenium (Se), uranium (U), and curium (Cm) are of great interest. Se and Cm are common components of the spent nuclear fuel residues, mainly as 79Se isotope (half-life 3.27 × 105 years), 247Cm (half-life: 1.6 × 107 years) and 248Cm (half-life: 3.5 × 106 years) isotopes, respectively. This review presents an up-to-date overview about how microbes occurring in the surroundings of a DGR may influence their safety, with a particular focus on the radionuclide-microbial interactions. Consequently, this paper will provide an exhaustive understanding about the influence of microorganisms in the safety of planned radioactive waste repositories, which in turn might improve their implementation and efficiency.

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).

Broad-spectrum and effective rare earth enriching via Lanmodulin-displayed Yarrowia lipolytica

The traditional mining processes of rare earth elements (REEs) are accompanied by the production of a large number of acid mine drainage rich in REEs. A wide-adaptive, low-cost and environmentally friendly biosorbent is an attractive technology to enrich and recycle REEs from the liquid wastes. To construct a broad-spectrum and efficient biosorbent, a novel REEs-binding protein Lanmodulin (LanM) is successfully displayed on the cell surface of a fungus, Yarrowia lipolytica, for the first time, and the adsorption capacities for various REEs are studied. The LanM-displayed Y. lipolytica shows significantly enhanced adsorption capacities for multiple REEs, achieving the highest reported values of 49.83 ± 2.87 mg Yb /g DCW, 50.38 ± 1.46 mg Tm /g DCW, 49.94 ± 3.61 mg Er /g DCW and 48.72 ± 3.09 mg Tb/g DCW, respectively. Moreover, the LanM-displayed Y. lipolytica possesses a high selectivity for REEs over other common metal cations and excellent suitability under acidic conditions. The kinetics and equilibrium analysis of biosorption processes agree well with the pseudo-first kinetic and Langmuir isotherm model. Based on the FTIR and SEM-EDS analysis, the chelation with phosphate/carboxylate groups dominates the Yb binding in LanM-displayed cells, and LanM enhances the adsorption performances by introducing more binding sites with high selectivity towards a wide range of REEs. Thus, the LanM-displayed Y. lipolytica investigated in this study exhibits prosperous potential for the enriching/removal of REEs from acid mine drainage.

Reversible Metal Ion/Complex Binding to Chitin Controlled by Ligand, Redox, and Photochemical Reactions and Active Movement of Chitin on Aquatic Arthropods

There is strong adsorption of metal ions and their complexes to chitin, which depends on both the oxidation and complexation states of many of the said elements (whereas others display chemical reactions detectable via electrochemical methods while being retained by chitin); thus, ad- and desorption at ambient water concentrations (often in the nMol/L range) are controlled by the presence and photochemical properties (concerning Eu and probably U and Ag) of mainly biogenic organic matter (both DOC and POC, and DON). With chitin forming the outer hull of mobile organisms (animals), this biopolymer is expected to take part in metal distribution in aquatic (limnetic and riverine) ecosystems. Having studied the attachment of many different elements to both crayfish and grafted (marine shrimp) chitin, with the highest accumulations observed in Bi, V, Ni, and LREEs, one should consider secondary biochemical transformations which take place at different water and sediment levels. After chitin had been embedded into sediment, methanogenesis (which requires Ni), Bi, and Sb biomethylations and photodesorption in the illuminated water column will occur if there are appropriate organics, causing the vertical separation of Eu from other REEs, at least during the daytime. Eutrophication will enhance both the production and especially the photooxidation rates of organics in water because phosphorylated sugars and lipids are formed quantitatively within min P, which enter water and undergo Eu-mediated photooxidation much more readily. Another biopolymer, gelatin, acts as an inert matrix-enhancing organic photooxidation product via Eu, producing chemical waves, indicating autocatalysis upon light impact. From the redox-related photodesorption of metal analytes from chitin, both sensors and devices for (light-assisted) electrochemical energy conversion are being developed by our workgroup. The electrochemical determination of adsorption thermodynamics on chitin is thus directly linked to its applications in environmental monitoring and technology.

Biosorption and Bioaccumulation Capacity of Arthospiraplatensis toward Europium Ions

Europium recovery from wastewater is determined by its high significance for industry and toxicity for living organisms. The capacity of cyanobacteria Arthospira platensis (Spirulina) to remove Eu(III) through biosorption and bioaccumulation was evaluated. In biosorption experiments, the effects of four variables pH, metal concentration, time, and temperature on metal removal were studied. In bioaccumulation experiments, the effect of Eu(III) concentrations on biomass bioaccumulation capacity and biochemical composition was assessed. The efficiency of Eu(III) uptake in both experiments was determined using ICP-AES techniques. Maximum biosorption of Eu(III) was achieved at pH 3.0. Equilibrium data fitted well with the Langmuir and Freundlich models, with maximum adsorption capacity of 89.5 mg/g. The pseudo-first-, pseudo-second-order, and Elovich models were found to correlate well with the experimental data. According to thermodynamic studies the sorption was feasible, spontaneous, and endothermic in nature. At addition of Eu(III) ions in the cultivation medium in concentrations of 10–30 mg/L, its accumulation in biomass was 9.8–29.8 mg/g (removal efficiency constituting 98–99%). Eu(III) did not affect productivity and content of carbohydrates and pigments in biomass but led to the decrease of the content of protein and an increase in the amount of MDA. The high Eu(III) biosorption and bioaccumulation efficiency of Arthrospira platensis may constitute an effective and eco-friendly strategy to recover it from contaminated environment.

Microorganisms Accelerate REE Mineralization in Supergene Environments

Exogenic deposits are an important source of rare earth elements (REEs), especially heavy REEs (HREEs). It is generally accepted that microorganisms are able to dissolve minerals and mobilize elements in supergene environments. However, little is known about the roles of microorganisms in the formation of exogenic deposits such as regolith-hosted REE deposits that are of HREE enrichment and provide over 90% of global HREE demand. In this study, we characterized the microbial community composition and diversity along a complete weathering profile drilled from a regolith-hosted REE deposit in Southeastern China and report the striking contributions of microorganisms to the enrichment of REEs and fractionation between HREEs and light REEs (LREEs). Our results provide evidence that the variations in REE contents are correlated with microbial community along the profile. Both fungi and bacteria contributed to the accumulation of REEs, whereas bacteria played a key role in the fractionation between HREEs and LREEs. Taking advantage of bacteria strains isolated from the profile, Gram-positive bacteria affiliated with Bacillus and Micrococcus preferentially adsorbed HREEs, and teichoic acids in the cell wall served as the main sites for HREE adsorption, leading to an enrichment of HREEs in the deposit. The present study provides the first database of microbial community in regolith-hosted REE deposits. These findings not only elucidate the crucial contribution of fungi and bacteria in the supergene REE mineralization but also provide insights into efficient utilization of mineral resources via a biological pathway.

IMPORTANCE Understanding the role of microorganisms in the formation of regolith-hosted rare earth element (REE) deposits is beneficial for improving the metallogenic theory and deposit exploitation, given that such deposits absolutely exist in subtropical regions with strong microbial activities. Little is known of the microbial community composition and its contribution to REE mineralization in this kind of deposit. Using a combination of high-throughput sequencing, batch adsorption experiments, and spectroscopic characterization, the functional microorganisms contributing to REE enrichment and fractionation are disclosed. For bacteria, the surface carboxyl and phosphate groups are active sites for REE adsorption, while teichoic acids in the cell walls of G⁺ bacteria lead to REE fractionation. The above-mentioned findings not only unravel the importance of microorganisms in the formation of supergene REE deposits but also provide experimental evidence for the bioutilization of REE resources.

Removal of yttrium from rare-earth wastewater by Serratia marcescens: biosorption optimization and mechanisms studies

The discharge of yttrium containing wastewater is a potential risk to human health. Although biosorption is a promising method to remove yttrium from wastewater, whereas the application of it is limited due to the lack of efficient biosorbents. In this study, the removal of yttrium from wastewater using Serratia marcescens as a biosorbent was conducted. The effects of six parameters including pH (2–5.5), initial yttrium concentration (10–110 mg/L), biosorbent dosage (0.1–0.5 g/L), biosorption time (10–700 min), stirring speed (50–300 rpm) and temperature (20–60 °C) were evaluated. The main parameters were optimized using response surface methodology. The results showed that the adsorption capacity reached 123.65 mg/g at the optimized conditions. The biosorption mechanism was revealed based on a combined analysis using field emission transmission electron microscope-energy dispersion spectrum, Fourier transform infrared spectrophotometer, and X-ray photoelectron spectroscopy. These results revealed that the hydroxyl, carboxyl, and amino groups were the adsorption functional groups for yttrium ions. Biosorption of yttrium by S. marcescens is under the combination of ion exchange, electrostatic attraction and complexation. These findings indicated that S. marcescens can be used as an efficient biosorbent to remove yttrium from wastewater. In addition, its adsorption capacity can be further improved by the enhancement of adsorption functional groups on the surface through chemical modification.

Advantages of Using Extremophilic Bacteria for the Biosynthesis of Metallic Nanoparticles and Its Potential for Rare Earth Element Recovery

The exceptional potential for application that metallic nanoparticles (MeNPs) have shown, has steadily increased their demand in many different scientific and technological areas, including the biomedical and pharmaceutical industry, bioremediation, chemical synthesis, among others. To face the current challenge for transitioning toward more sustainable and ecological production methods, bacterial biosynthesis of MeNPs, especially from extremophilic microorganisms, emerges as a suitable alternative with intrinsic added benefits like improved stability and biocompatibility. Currently, biogenic nanoparticles of different relevant metals have been successfully achieved using different bacterial strains. However, information about biogenic nanoparticles from rare earth elements (REEs) is very scarce, in spite of their great importance and potential. This mini review discusses the current understanding of metallic nanoparticle biosynthesis by extremophilic bacteria, highlighting the relevance of searching for bacterial species that are able to biosynthesize RRE nanoparticles.

Engineering Polyhistidine Tags on Surface Proteins of Acidithiobacillus ferrooxidans: Impact of Localization on the Binding and Recovery of Divalent Metal Cations

Metal processing using microorganisms has many advantages including the potential for reduced environmental impacts as compared to conventional technologies.Acidithiobacillus ferrooxidansis an iron- and sulfur-oxidizing chemolithoautotroph that is known to participate in metal bioleaching, and its metabolic capabilities have been exploited for industrial-scale copper and gold biomining. In addition to bioleaching, microorganisms could also be engineered for selective metal binding, enabling new opportunities for metal bioseparation and recovery. Here, we explored the ability of polyhistidine (polyHis) tags appended to two recombinantly expressed endogenous proteins to enhance the metal binding capacity of A. ferrooxidans. The genetically engineered cells achieved enhanced cobalt and copper binding capacities, and the Langmuir isotherm captures their interaction behavior with these divalent metals. Additionally, the cellular localization of the recombinant proteins correlated with kinetic modeling of the binding interactions, where the outer membrane-associated polyHis-tagged licanantase peptide bound the metals faster than the periplasmically expressed polyHis-tagged rusticyanin protein. The selectivity of the polyHis sequences for cobalt over copper from mixed metal solutions suggests potential utility in practical applications, and further engineering could be used to create metal-selective bioleaching microorganisms.

Forced Biomineralization: A Review

Biologically induced and controlled mineralization of metals promotes the development of protective structures to shield cells from thermal, chemical, and ultraviolet stresses. Metal biomineralization is widely considered to have been relevant for the survival of life in the environmental conditions of ancient terrestrial oceans. Similar behavior is seen among extremophilic biomineralizers today, which have evolved to inhabit a variety of industrial aqueous environments with elevated metal concentrations. As an example of extreme biomineralization, we introduce the category of "forced biomineralization", which we use to refer to the biologically mediated sequestration of dissolved metals and metalloids into minerals. We discuss forced mineralization as it is known to be carried out by a variety of organisms, including polyextremophiles in a range of psychrophilic, thermophilic, anaerobic, alkaliphilic, acidophilic, and halophilic conditions, as well as in environments with very high or toxic metal ion concentrations. While much additional work lies ahead to characterize the various pathways by which these biominerals form, forced biomineralization has been shown to provide insights for the progression of extreme biomimetics, allowing for promising new forays into creating the next generation of composites using organic-templating approaches under biologically extreme laboratory conditions relevant to a wide range of industrial conditions.

Extracellular and Intracellular Lanthanide Accumulation in the Methylotrophic Beijerinckiaceae Bacterium RH AL1

Recent work with Methylorubrum extorquens AM1 identified intracellular, cytoplasmic lanthanide storage in an organism that harnesses these metals for its metabolism. Here, we describe the extracellular and intracellular accumulation of lanthanides in the Beijerinckiaceae bacterium RH AL1, a newly isolated and recently characterized methylotroph. Using ultrathin-section transmission electron microscopy (TEM), freeze fracture TEM (FFTEM), and energy-dispersive X-ray spectroscopy, we demonstrated that strain RH AL1 accumulates lanthanides extracellularly at outer membrane vesicles (OMVs) and stores them in the periplasm. High-resolution elemental analyses of biomass samples revealed that strain RH AL1 can accumulate ions of different lanthanide species, with a preference for heavier lanthanides. Its methanol oxidation machinery is supposedly adapted to light lanthanides, and their selective uptake is mediated by dedicated uptake mechanisms. Based on transcriptome sequencing (RNA-seq) analysis, these presumably include the previously characterized TonB-ABC transport system encoded by the lut cluster but potentially also a type VI secretion system. A high level of constitutive expression of genes coding for lanthanide-dependent enzymes suggested that strain RH AL1 maintains a stable transcript pool to flexibly respond to changing lanthanide availability. Genes coding for lanthanide-dependent enzymes are broadly distributed taxonomically. Our results support the hypothesis that central aspects of lanthanide-dependent metabolism partially differ between the various taxa.

IMPORTANCE Although multiple pieces of evidence have been added to the puzzle of lanthanide-dependent metabolism, we are still far from understanding the physiological role of lanthanides. Given how widespread lanthanide-dependent enzymes are, only limited information is available with respect to how lanthanides are taken up and stored in an organism. Our research complements work with commonly studied model organisms and showed the localized storage of lanthanides in the periplasm. This storage occurred at comparably low concentrations. Strain RH AL1 is able to accumulate lanthanide ions extracellularly and to selectively utilize lighter lanthanides. The Beijerinckiaceae bacterium RH AL1 might be an attractive target for developing biorecovery strategies to obtain these economically highly demanded metals in environmentally friendly ways.

Extremophiles, a Nifty Tool to Face Environmental Pollution: From Exploitation of Metabolism to Genome Engineering

Extremophiles are microorganisms that populate habitats considered inhospitable from an anthropocentric point of view and are able to tolerate harsh conditions such as high temperatures, extreme pHs, high concentrations of salts, toxic organic substances, and/or heavy metals. These microorganisms have been broadly studied in the last 30 years and represent precious sources of biomolecules and bioprocesses for many biotechnological applications; in this context, scientific efforts have been focused on the employment of extremophilic microbes and their metabolic pathways to develop biomonitoring and bioremediation strategies to face environmental pollution, as well as to improve biorefineries for the conversion of biomasses into various chemical compounds. This review gives an overview on the peculiar metabolic features of certain extremophilic microorganisms, with a main focus on thermophiles, which make them attractive for biotechnological applications in the field of environmental remediation; moreover, it sheds light on updated genetic systems (also those based on the CRISPR-Cas tool), which expand the potentialities of these microorganisms to be genetically manipulated for various biotechnological purposes.

Cellular strategies against metal exposure and metal localization patterns linked to phosphorus pathways in Ochrobactrum anthropi DE2010

Cytotoxic, chemical, biochemical, compositional, and morphometric responses were analyzed against heavy metal exposure in Ochrobactrum anthropi DE2010, an heterotrophic bacterium isolated from Ebro Delta microbial mats (Tarragona, NE Spain). Several parameters of effect and exposure were evaluated to determine tolerance to a range of cadmium (Cd), lead (Pb(II)), copper (Cu(II)), chromium (Cr(III)), and zinc (Zn) concentrations. Additionally, removal efficiency, polyphosphate production and metal localization patterns were also analyzed. O. anthropi DE2010 showed high resistance to the tested metals, supporting concentrations of up to 20 mM for Zn and 10 mM for the rest of the elements. The bacterium also demonstrated a high removal capacity of metals-up to 90 % and 40 % for Pb(II) and Cr(III), respectively. Moreover, polyphosphate production was strongly correlated with heavy metal concentration, and three clear cell localization patterns of metals were evidenced using compositional and imaging techniques: (i) extracellular in polyphosphate granules for Cu(II); (ii) in periplasmic space forming crystals with phosphorus for Pb(II); and (iii) intracytoplasmic in polyphosphate inclusions for Pb(II), Cr(III), and Zn. The high resistance and metal sequestration capacity of O. anthropi DE2010 both highlight its great potential for bioremediation strategies, especially in Pb and Cr polluted areas.

Biological, biomolecular, and bio-inspired strategies for detection, extraction, and separations of lanthanides and actinides

Lanthanides and actinides are elements of ever-increasing technological importance in the modern world. However, the similar chemical and physical properties within these groups make purification of individual elements a challenge. Current industrial standards for the extraction, separation, and purification of these metals from natural sources, recycled materials, and industrial waste are inefficient, relying upon harsh conditions, repetitive steps, and ligands with only modest selectivity. Biological, biomolecular, and bio-inspired strategies towards improving these separations and making them more environmentally sustainable have been researched for many years; however, these methods often have insufficient selectivity for practical application. Recent developments in the understanding of how lanthanides are selectively acquired and used by certain bacteria offer the opportunity for a newer, more efficient take on these designs, as well as the possibility for fundamentally new designs and strategies. Herein, we review current cell-based and biomolecular (primarily small-molecule and protein-based) methods for detection, extraction, and separations of f-block elements. We discuss how the increasing knowledge regarding the selective recognition, uptake, trafficking, and storage of these elements in biological systems has informed and will continue to promote development of novel approaches to achieve these ends.

Gene products and processes contributing to lanthanide homeostasis and methanol metabolism in Methylorubrum extorquens AM1

Lanthanide elements have been recently recognized as "new life metals" yet much remains unknown regarding lanthanide acquisition and homeostasis. In Methylorubrum extorquens AM1, the periplasmic lanthanide-dependent methanol dehydrogenase XoxF1 produces formaldehyde, which is lethal if allowed to accumulate. This property enabled a transposon mutagenesis study and growth studies to confirm novel gene products required for XoxF1 function. The identified genes encode an MxaD homolog, an ABC-type transporter, an aminopeptidase, a putative homospermidine synthase, and two genes of unknown function annotated as orf6 and orf7. Lanthanide transport and trafficking genes were also identified. Growth and lanthanide uptake were measured using strains lacking individual lanthanide transport cluster genes, and transmission electron microscopy was used to visualize lanthanide localization. We corroborated previous reports that a TonB-ABC transport system is required for lanthanide incorporation to the cytoplasm. However, cells were able to acclimate over time and bypass the requirement for the TonB outer membrane transporter to allow expression of xoxF1 and growth. Transcriptional reporter fusions show that excess lanthanides repress the gene encoding the TonB-receptor. Using growth studies along with energy dispersive X-ray spectroscopy and transmission electron microscopy, we demonstrate that lanthanides are stored as cytoplasmic inclusions that resemble polyphosphate granules.

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

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

Aluminium removal and recovery from wastewater and soil using isolated indigenous bacteria

This paper elucidates the capability of isolated indigenous bacteria to remove aluminium from wastewater and soil. Two indigenous species of Brochothrix thermosphacta and Vibrio alginolyticus were isolated from an aluminium-contaminated site. These two species were used to treat aluminium-containing wastewater and contaminated soil using the bioaugmentation method. B. thermosphacta showed the highest aluminium removal of 57.87 ± 0.45% while V. alginolyticus can remove aluminium up to 59.72 ± 0.33% from wastewater. For aluminium-contaminated soil, B. thermosphacta and V. alginolyticus, showed a highest removal of only 4.58 ± 0.44% and 5.48 ± 0.58%, respectively. The bioaugmentation method is more suitable to be used to treat aluminium in wastewater compared to contaminated soil. The produced biomass separation after wastewater treatment was so much easier and applicable, compared to the produced biomass handling from contaminated soil treatment. A 48.55 ± 2.45% and 40.12 ± 4.55% of aluminium can be recovered from B. thermosphacta and V. alginolyticus biomass, respectively, with 100 mg/L initial aluminium concentration in wastewater.

Anaerobic reduction of europium by a Clostridium strain as a strategy for rare earth biorecovery

The biorecovery of europium (Eu) from primary (mineral deposits) and secondary (mining wastes) resources is of interest due to its remarkable luminescence properties, important for modern technological applications. In this study, we explored the tolerance levels, reduction and intracellular bioaccumulation of Eu by a site-specific bacterium, Clostridium sp. 2611 isolated from Phalaborwa carbonatite complex. Clostridium sp. 2611 was able to grow in minimal medium containing 0.5 mM Eu³⁺. SEM-EDX analysis confirmed an association between Eu precipitates and the bacterium, while TEM-EDX analysis indicated intracellular accumulation of Eu. According to the HR-XPS analysis, the bacterium was able to reduce Eu³⁺ to Eu²⁺ under growth and non-growth conditions. Preliminary protein characterization seems to indicate that a cytoplasmic pyruvate oxidoreductase is responsible for Eu bioreduction. These findings suggest the bioreduction of Eu³⁺ by Clostridium sp. as a resistance mechanism, can be exploited for the biorecovery of this metal.