Generation of a Gluconobacter oxydans knockout collection for improved extraction of rare earth elements

Engineering Gluconbacter oxydans with efficient co-utilization of glucose and sorbitol for one-step biosynthesis of 2-keto-L-gulonic

As the highest-demand vitamin, the development of a one-step vitamin C synthesis process has been slow for a long time. In previous research, a Gluconobacter oxydans strain (GKLG9) was constructed that can directly synthesize 2-keto-L-gulonic acid (2-KLG) from glucose, but carbon source utilization remained low. Therefore, this study first identified the gene 4kas (4-keto-D-arabate synthase) to reduce the loss of extracellular carbon and inhibit the browning of fermentation broth. Then, promoter engineering was conducted to enhance the intracellular glucose transport pathway and concentrate intracellular glucose metabolism on the pentose phosphate pathway to provide more reducing power. Finally, by introducing the D-sorbitol pathway, the titer of 2-KLG was increased to 38.6 g/L within 60 h in a 5-L bioreactor, with a glucose-to-2-KLG conversion rate of about 46 %. This study is an important step in the development of single-bacterial one-step fermentation to produce 2-KLG.

Determining the functional role of the Gluconobacter oxydans GOX1969 protein as a BamB homolog

Acetic acid bacteria are used in many industrial processes such as the production of vinegar, vitamin C, the antidiabetic drug miglitol, and various artificial flavorings. These industrially important reactions are primarily carried out by an arsenal of periplasmic-facing membrane-bound dehydrogenases that incompletely oxidize their substrates and shuttle electrons directly into the respiratory chain. Among these dehydrogenases, GOX1969 in Gluconobacter oxydans was predicted to be a pyrroloquinoline quinone-dependent dehydrogenase of unknown function. However, after multiple analysis by a number of labs, no dehydrogenase activity has been detected. Reanalysis of GOX1969 sequence and structure reveals similarities to Escherichia coli BamB, which functions as a subunit of the β-barrel assembly machinery complex that is responsible for the assembly of β-barrel outer membrane proteins in Gram-negative bacteria. To test if the physiological function of GOX1969 is similar to BamB in E. coli, we introduced the gox1969 gene into an E. coli ∆bamB mutant. Growth deficiencies in the ∆bamB mutant were restored when gox1969 was expressed on the plasmid pGox1969. Furthermore, increased membrane permeability conferred by bamB deletion was restored upon gox1969 expression, which suggests a direct link between GOX1969 and a role in maintaining outer membrane stability. Together, this evidence strongly suggests that GOX1969 is functionally acting as a BamB in G. oxydans. As such, functional information on uncharacterized genes will provide new insights that will allow for more accurate modeling of acetic acid bacterial metabolism and further efforts to design rational strains for industrial use.IMPORTANCEGluconobacter oxydans is an industrially important member of the acetic acid bacteria. Experimental characterization of putative genes is necessary to identify targets for further engineering of rational acetic acid bacteria strains that can be used in the production of vitamin C, antidiabetic compounds, artificial flavorings, or novel compounds. In this study, we have identified an undefined dehydrogenase GOX1969 with no known substrate and defined structural similarities to outer membrane biogenesis protein BamB in E. coli K12. Furthermore, we demonstrate that GOX1969 is capable of complementing bamB knockout phenotypes in E. coli K12. Taken together, these findings enhance our understanding of G. oxydans physiology and expand the list of potential targets for future industrial strain design.

Synthetic microbiology in sustainability applications

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

Bioseparation of rare earth elements and high value-added biomaterials applications

Rare earth elements (REEs) are a group of critical minerals and extensively employed in new material manufacturing. However, separation of lanthanides is difficult because of their similar chemical natures. Current lanthanide leaching and separation methods require hazardous compounds, resulting in severe environmental concerns. Bioprocessing of lanthanides offers an emerging class of tools for REE separation due to mild leaching conditions and highly selective separation scenarios. In the course of biopreparation, engineered microbes not only dissolve REEs from ores but also allow for selective separation of the lanthanides. In this review, we present an overview of recent advances in microbes and proteins used for the biomanufacturing of lanthanides and discuss high value-added applications of REE-derived biomaterials. We begin by introducing the fundamental interactions between natural microbes and REEs. Then we discuss the rational design of chassis microbes for bioleaching and biosorption. We also highlight the investigations on REE binding proteins and their applications in the synthesis of high value-added biomaterials. Finally, future opportunities and challenges for the development of next generation lanthanide-binding biological systems are discussed.

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.

Scalable and Consolidated Microbial Platform for Rare Earth Element Leaching and Recovery from Waste Sources

Chemical methods for the extraction and refinement of technologically critical rare earth elements (REEs) are energy-intensive, hazardous, and environmentally destructive. Current biobased extraction systems rely on extremophilic organisms and generate many of the same detrimental effects as chemical methodologies. The mesophilic methylotrophic bacterium Methylobacterium extorquens AM1 was previously shown to grow using electronic waste by naturally acquiring REEs to power methanol metabolism. Here we show that growth using electronic waste as a sole REE source is scalable up to 10 L with consistent metal yields without the use of harsh acids or high temperatures. The addition of organic acids increases REE leaching in a nonspecific manner. REE-specific bioleaching can be engineered through the overproduction of REE-binding ligands (called lanthanophores) and pyrroloquinoline quinone. REE bioaccumulation increases with the leachate concentration and is highly specific. REEs are stored intracellularly in polyphosphate granules, and genetic engineering to eliminate exopolyphosphatase activity increases metal accumulation, confirming the link between phosphate metabolism and biological REE use. Finally, we report the innate ability of M. extorquens to grow using other complex REE sources, including pulverized smartphones, demonstrating the flexibility and potential for use as a recovery platform for these critical metals.

Cytoprotective Metal-Phenolic Network Sporulation to Modulate Microalgal Mobility and Division

Synthetic cell exoskeletons created from abiotic materials have attracted interest in materials science and biotechnology, as they can regulate cell behavior and create new functionalities. Here, a facile strategy is reported to mimic microalgal sporulation with on-demand germination and locomotion via responsive metal-phenolic networks (MPNs). Specifically, MPNs with tunable thickness and composition are deposited on the surface of microalgae cells via one-step coordination, without any loss of cell viability or intrinsic cell photosynthetic properties. The MPN coating keeps the cells in a dormant state, but can be disassembled on-demand in response to environmental pH or chemical stimulus, thereby reviving the microalgae within 1 min. Moreover, the artificial sporulation of microalgae resulted in resistance to environmental stresses (e.g., metal ions and antibiotics) akin to the function of natural sporulation. This strategy can regulate the life cycle of complex cells, providing a synthetic strategy for designing hybrid microorganisms.

Unusual 1-3 peptidoglycan cross-links in Acetobacteraceae are made by L,D-transpeptidases with a catalytic domain distantly related to YkuD domains

Peptidoglycan is an essential component of the bacterial cell envelope that contains glycan chains substituted by short peptide stems. Peptide stems are polymerized by D,D-transpeptidases, which make bonds between the amino acid in position four of a donor stem and the third residue of an acceptor stem (4-3 cross-links). Some bacterial peptidoglycans also contain 3-3 cross-links that are formed by another class of enzymes called L,D-transpeptidases which contain a YkuD catalytic domain. In this work, we investigate the formation of unusual bacterial 1-3 peptidoglycan cross-links. We describe a version of the PGFinder software that can identify 1-3 cross-links and report the high-resolution peptidoglycan structure of Gluconobacter oxydans (a model organism within the Acetobacteraceae family). We reveal that G. oxydans peptidoglycan contains peptide stems made of a single alanine as well as several dipeptide stems with unusual amino acids at their C-terminus. Using a bioinformatics approach, we identified a G. oxydans mutant from a transposon library with a drastic reduction in 1-3 cross-links. Through complementation experiments in G. oxydans and recombinant protein production in a heterologous host, we identify an L,D-transpeptidase enzyme with a domain distantly related to the YkuD domain responsible for these non-canonical reactions. This work revisits the enzymatic capabilities of L,D-transpeptidases, a versatile family of enzymes that play a key role in bacterial peptidoglycan remodelling.

Genomic characterization of rare earth binding by Shewanella oneidensis

Rare earth elements (REE) are essential ingredients of sustainable energy technologies, but separation of individual REE is one of the hardest problems in chemistry today. Biosorption, where molecules adsorb to the surface of biological materials, offers a sustainable alternative to environmentally harmful solvent extractions currently used for separation of rare earth elements (REE). The REE-biosorption capability of some microorganisms allows for REE separations that, under specialized conditions, are already competitive with solvent extractions, suggesting that genetic engineering could allow it to leapfrog existing technologies. To identify targets for genomic improvement we screened 3,373 mutants from the whole genome knockout collection of the known REE-biosorbing microorganism Shewanella oneidensis MR-1. We found 130 genes that increased biosorption of the middle REE europium, and 112 that reduced it. We verified biosorption changes from the screen for a mixed solution of three REE (La, Eu, Yb) using Inductively Coupled Plasma Mass Spectrometry (ICP-MS) in solution conditions with a range of ionic strengths and REE concentrations. We identified 18 gene ontologies and 13 gene operons that make up key systems that affect biosorption. We found, among other things, that disruptions of a key regulatory component of the arc system (hptA), which regulates cellular response to anoxic environments and polysaccharide biosynthesis related genes (wbpQ, wbnJ, SO_3183) consistently increase biosorption across all our solution conditions. Our largest total biosorption change comes from our SO_4685, a capsular polysaccharide (CPS) synthesis gene, disruption of which results in an up to 79% increase in biosorption; and nusA, a transcriptional termination/anti-termination protein, disruption of which results in an up to 35% decrease in biosorption. Knockouts of glnA, pyrD, and SO_3183 produce small but significant increases (≈ 1%) in relative biosorption affinity for ytterbium over lanthanum in multiple solution conditions tested, while many other genes we explored have more complex binding affinity changes. Modeling suggests that while these changes to lanthanide biosorption selectivity are small, they could already reduce the length of repeated enrichment process by up to 27%. This broad exploratory study begins to elucidate how genetics affect REE-biosorption by S. oneidensis, suggests new areas of investigation for better mechanistic understanding of the membrane chemistry involved in REE binding, and offer potential targets for improving biosorption and separation of REE by genetic engineering.

Efficient production of 2-keto-L-gulonic acid from D-glucose in Gluconobacter oxydans ATCC9937 by mining key enzyme and transporter

Direct production of 2-keto-L-gulonic acid (2-KLG, the precursor of vitamin C) from D-glucose through 2,5-diketo-D-gluconic acid (2,5-DKG) is a promising alternative route. To explore the pathway of producing 2-KLG from D-glucose, Gluconobacter oxydans ATCC9937 was selected as a chassis strain. It was found that the chassis strain naturally has the ability to synthesize 2-KLG from D-glucose, and a new 2,5-DKG reductase (DKGR) was found on its genome. Several major issues limiting production were identified, including the insufficient catalytic capacity of DKGR, poor transmembrane movement of 2,5-DKG and imbalanced D-glucose consumption flux inside and outside of the host strain cells. By identifying novel DKGR and 2,5-DKG transporter, the whole 2-KLG biosynthesis pathway was systematically enhanced by balancing intracellular and extracellular D-glucose metabolic flux. The engineered strain produced 30.5 g/L 2-KLG with a conversion ratio of 39.0%. The results pave the way for a more economical large-scale fermentation process for vitamin C.

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

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

New perspectives into Gluconobacter-catalysed biotransformations

Different from other aerobic microorganisms that oxidise carbon sources to water and carbon dioxide, Gluconobacter catalyses the incomplete oxidation of various substrates with regio- and stereoselectivity. This ability, as well as its capacity to release the resulting products into the reaction media, place Gluconobacter as a privileged member of a non-model microorganism class that may boost industrial biotechnology. Knowledge of new technologies applied to Gluconobacter has been piling up in recent years. Advancements in its genetic modification, application of immobilisation tools and careful designs of the transformations, have improved productivities and stabilities of Gluconobacter strains or enabled new bioconversions for the production of valuable marketable chemicals. In this work, the latest advancements applied to Gluconobacter-catalysed biotransformations are summarised with a special focus on recent available tools to improve them. From genetic and metabolic engineering to bioreactor design, the most recent works on the topic are analysed in depth to provide a comprehensive resource not only for scientists and technologists working on/with Gluconobacter, but for the general biotechnologist.

Green Extractants in Assisting Recovery of REEs: A Case Study

The recycling of REEs from the end of life (EoL) products, such as nickel metal hydride batteries (NiMH), offers great opportunities for their supply in Europe. In the presented paper, the application of 'green' extractants such as citric (CA), metatartaric (TA), and ethylenediaminedisuccinic acid (EDDS) (also with H₂O₂ addition) for the recovery of REEs was studied. The studies were conducted considering the effects of the phase contact time, the initial concentration of CA, TA, and EDDS, as well as H₂O₂, pH, and temperature. It was found that the addition of TA to the CA solution meant that higher rates of metal ion binding and, thus, leaching was observed. The optimal conditions were obtained in the system: CA-TA and H₂O₂ for the concentration 0.6M-0.3 M-2%.

Harnessing synthetic biology for sustainable biomining with Fe/S-oxidizing microbes

Biomining is a biotechnological approach where microorganisms are used to recover metals from ores and waste materials. While biomining applications are motivated by critical issues related to the climate crisis (e.g., habitat destruction due to mine effluent pollution, metal supply chains, increasing demands for cleantech-critical metals), its drawbacks hinder its widespread commercial applications: lengthy processing times, low recovery, and metal selectivity. Advances in synthetic biology provide an opportunity to engineer iron/sulfur-oxidizing microbes to address these limitations. In this forum, we review recent progress in synthetic biology-enhanced biomining with iron/sulfur-oxidizing microbes and delineate future research avenues.

Efficient Production of 2,5-Diketo-D-gluconic Acid by Reducing Browning Levels During Gluconobacter oxydans ATCC 9937 Fermentation

D-Glucose directly generates 2-keto-L-gulonic acid (2-KLG, precursor of vitamin C) through the 2,5-diketo-D-gluconic acid (2,5-DKG) pathway. 2,5-DKG is the main rate-limiting factor of the reaction, and there are few relevant studies on it. In this study, a more accurate quantitative method of 2,5-DKG was developed and used to screen G. oxydans ATCC9937 as the chassis strain for the production of 2,5-DKG. Combining the metabolite profile analysis and knockout and overexpression of production strain, the non-enzymatic browning of 2,5-DKG was identified as the main factor leading to low yield of the target compound. By optimizing the fermentation process, the fermentation time was reduced to 48 h, and 2,5-DKG production peaked at 50.9 g/L, which was 139.02% higher than in the control group. Effectively eliminating browning and reducing the degradation of 2,5-DKG will help increase the conversion of 2,5-DKG to 2-KLG, and finally, establish a one-step D-glucose to 2-KLG fermentation pathway.

Practical and Thermodynamic Constraints on Electromicrobially-Accelerated CO2 Mineralization

By the end of the century, tens of gigatonnes of CO₂ will need to be removed from the atmosphere every year to maintain global temperatures. Natural weathering of ultramafic rocks and subsequent mineralization reactions can convert CO₂ into ultra-stable carbonates. Although this will draw down all excess CO₂, it will take thousands of years. CO₂ mineralization could be accelerated by weathering ultramafic rocks with biodegradable lixiviants. We show that if these lixiviants come from cellulosic biomass, this demand could monopolize the world’s biomass supply. We demonstrate that electromicrobial production technologies (EMP) that combine renewable electricity and microbial metabolism could produce lixiviants for as little as $200 to $400 per tonne at solar electricity prices achievable within the decade. We demonstrate that EMP could make enough lixiviants to sequester a tonne of CO₂ for less than $100. This work highlights the potential of this approach and the need for extensive R&D.

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Bio-production of acids to sequester 20 GtCO₂ yr⁻¹ could monopolize global agriculture

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Electromicrobial production could produce acids for as little as $200 to $400 per tonne

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Electromicrobial production could make acids to sequester 1 tonne CO₂ for under $100

Extraction of REEs from Blast Furnace Slag by Gluconobacter oxydans

Granulated blast furnace slag (GGBFS) is a potential resource of rare earth elements (REEs), and due to the complex mineralogy, extraction by conventional hydrometallurgical process makes it an acid-consuming method. Bioleaching is thus investigated using a chemo-organotrophic bacterium Gluconobacter oxydans (DSMZ 46616) for REE extraction from GGBFS containing 157 ppm Ce, 90 ppm La, 71 ppm Nd and 40 ppm Er, hosted in a Ca-Al-Si matrix. The gluconic acid generation by G. oxydans was assessed for its role in REE extraction from GGBFS. With 5% (w/v) GGBFS using a mixture of a non-adapted and a GGBFS-adapted culture, a maximum solubilization of 67% and 88% Nd was observed after 12 and 40 days of incubation, respectively. The total amount of gluconic acid excreted by the bacteria increased with leaching duration, which contributed to a rise in metal extraction. Scanning electron microscope-energy dispersive analysis (SEM-EDAX) analysis of the solid residue showed bacterial cells in corrosion pits, and thereby assisting in metal solubilization.