Bacterial biofilms on gold grains-implications for geomicrobial transformations of gold

Toward Practical Applications of Engineered Living Materials with Advanced Fabrication Techniques

Engineered Living Materials (ELMs) are materials composed of or incorporating living cells as essential functional units. These materials can be created using bottom-up approaches, where engineered cells spontaneously form well-defined aggregates. Alternatively, top-down methods employ advanced materials science techniques to integrate cells with various kinds of materials, creating hybrids where cells and materials are intricately combined. ELMs blend synthetic biology with materials science, allowing for dynamic responses to environmental stimuli such as stress, pH, humidity, temperature, and light. These materials exhibit unique "living" properties, including self-healing, self-replication, and environmental adaptability, making them highly suitable for a wide range of applications in medicine, environmental conservation, and manufacturing. Their inherent biocompatibility and ability to undergo genetic modifications allow for customized functionalities and prolonged sustainability. This review highlights the transformative impact of ELMs over recent decades, particularly in healthcare and environmental protection. We discuss current preparation methods, including the use of endogenous and exogenous scaffolds, living assembly, 3D bioprinting, and electrospinning. Emphasis is placed on ongoing research and technological advancements necessary to enhance the safety, functionality, and practical applicability of ELMs in real-world contexts.

A gold speciation that adds a second layer to synergistic gold-copper toxicity in Cupriavidus metallidurans

The metal-resistant bacterium Cupriavidus metallidurans occurs in metal-rich environments. In auriferous soils, the bacterium is challenged by a mixture of copper ions and gold complexes, which exert synergistic toxicity. The previously used, self-made Au(III) solution caused a synergistic toxicity of copper and gold that was based on the inhibition of the CupA-mediated efflux of cytoplasmic Cu(I) by Au(I) in this cellular compartment. In this publication, the response of the bacterium to gold and copper was investigated by using a commercially available Au(III) solution instead of the self-made solution. The new solution was five times more toxic than the previously used one. Increased toxicity was accompanied by greater accumulation of gold atoms by the cells. The contribution of copper resistance determinants to the commercially available Au(III) solution and synergistic gold-copper toxicity was studied using single- and multiple-deletion mutants. The commercially available Au(III) solution inhibited periplasmic Cu(I) homeostasis, which is required for the allocation of copper ions to copper-dependent proteins in this compartment. The presence of the gene for the periplasmic Cu(I) and Au(I) oxidase, CopA, decreased the cellular copper and gold content. Transcriptional reporter gene fusions showed that up-regulation of gig, encoding a minor contributor to copper resistance, was strictly glutathione dependent. Glutathione was also required to resist synergistic gold-copper toxicity. The new data indicated a second layer of synergistic copper-gold toxicity caused by the commercial Au(III) solution, inhibition of the periplasmic copper homeostasis in addition to the cytoplasmic one.IMPORTANCEWhen living in auriferous soils, Cupriavidus metallidurans is not only confronted with synergistic toxicity of copper ions and gold complexes but also by different gold species. A previously used gold solution made by using aqua regia resulted in the formation of periplasmic gold nanoparticles, and the cells were protected against gold toxicity by the periplasmic Cu(I) and Au(I) oxidase CopA. To understand the role of different gold species in the environment, another Au(III) solution was commercially acquired. This compound was more toxic due to a higher accumulation of gold atoms by the cells and inhibition of periplasmic Cu(I) homeostasis. Thus, the geo-biochemical conditions might influence Au(III) speciation. The resulting Au(III) species may subsequently interact in different ways with C. metallidurans and its copper homeostasis system in the cytoplasm and periplasm. This study reveals that the geochemical conditions may decide whether bacteria are able to form gold nanoparticles or not.

An Overview of Bacteria-Mediated Heavy Metal Bioremediation Strategies

Contamination-free groundwater is considered a good source of potable water. Even in the twenty-first century, over 90 percent of the population is reliant on groundwater resources for their lives. Groundwater influences the economical state, industrial development, ecological system, and agricultural and global health conditions worldwide. However, different natural and artificial processes are gradually polluting groundwater and drinking water systems throughout the world. Toxic metalloids are one of the major sources that pollute the water system. In this review work, we have collected and analyzed information on metal-resistant bacteria along with their genetic information and remediation mechanisms of twenty different metal ions [arsenic (As), mercury (Hg), lead (Pb), chromium (Cr), iron (Fe), copper (Cu), cadmium (Cd), palladium (Pd), zinc (Zn), cobalt (Co), antimony (Sb), gold (Au), silver (Ag), platinum (Pt), selenium (Se), manganese (Mn), molybdenum (Mo), nickel (Ni), tungsten (W), and uranium (U)]. We have surveyed the scientific information available on bacteria-mediated bioremediation of various metals and presented the data with responsible genes and proteins that contribute to bioremediation, bioaccumulation, and biosorption mechanisms. Knowledge of the genes responsible and self-defense mechanisms of diverse metal-resistance bacteria would help us to engineer processes involving multi-metal-resistant bacteria that may reduce metal toxicity in the environment.

Understanding the Effect of Free Nitrous Acid on Biofilms

Free nitrous acid (FNA, i.e., HNO₂) has been recently applied to biofilm control in wastewater management. The mechanism triggering biofilm detachment upon exposure to FNA still remains largely unknown. In this work, we aim to prove that FNA induces biofilm dispersal via extracellular polymeric matrix breakdown and cell lysis. Biofilms formed by a model organism, Pseudomonas aeruginosa PAO1, were treated with FNA at concentrations ranging from 0.2 to 15 mg N/L for 24 h (conditions typically used in applications). The biofilms and suspended biomass were monitored both before and after FNA treatment using a range of methods including optical density measurements, viability assays, confocal laser scanning microscopy, and atomic force microscopy. It was revealed that FNA treatment caused substantial and concentration-dependent biofilm detachment. The addition of a reactive nitrogen species (RNS) scavenger, that is, 2-4-carboxyphenyl-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide, substantially reduced biofilm dispersal, suggesting that the nitrosative decomposition species of HNO₂ (i.e., RNS, e.g., •NO + •NO₂) were mainly responsible for the effects. The study provides insight into and support for the use of FNA for biofilm control in wastewater treatment.

Biomineralization of Nickel Struvite Linked to Metal Resistance in Streptomyces mirabilis

Biomineral formation is a common trait and prominent for soil Actinobacteria, including the genus Streptomyces. We investigated the formation of nickel-containing biominerals in the presence of a heavy-metal-resistant Streptomyces mirabilis P16B-1. Biomineralization was found to occur both in solid and liquid media. Minerals were identified with Raman spectroscopy and TEM-EDX to be either Mg-containing struvite produced in media containing no nickel, or Ni-struvite where Ni replaces the Mg when nickel was present in sufficient concentrations in the media. The precipitation of Ni-struvite reduced the concentration of nickel available in the medium. Therefore, Ni-struvite precipitation is an efficient mechanism for tolerance to nickel. We discuss the contribution of a plasmid-encoded nickel efflux transporter in aiding biomineralization. In the elevated local concentrations of Ni surrounding the cells carrying this plasmid, more biominerals occurred supporting this point of view. The biominerals formed have been quantified, showing that the conditions of growth do influence mineralization. This control is also visible in differences observed to biosynthetically synthesized Ni-struvites, including the use of sterile-filtered culture supernatant. The use of the wildtype S. mirabilis P16B-1 and its plasmid-free derivative, as well as a metal-sensitive recipient, S. lividans, and the same transformed with the plasmid, allowed us to access genetic factors involved in this partial control of biomineral formation.

Biorecovery of nanogold and nanogold compounds from gold-containing ores and industrial wastes

In nature, microorganisms developed at various places and adapted to the various weather and geological conditions. Microorganisms participate in geological transformations leading to the dissolution of some minerals and conversion to others. While some microorganisms with their metabolic activity increase the mobility of metals, others cause precipitation of metals and the formation of new minerals. These biogeochemical interactions found practical application in the recovery of metals. In the article, the proposals for improvement of existing engineering commercial processes for recovery of metals are given which can enable the formation of nanogold and nanogold compounds.Key points• Amino acids in pretreatment can increase the dissolution of the layer around the gold.• Amino acids in the complexing stage can increase gold leaching.• After the complexing stage, the bionanosynthesis of gold and its compounds is possible.

Nano-enabled improvements of growth and nutritional quality in food plants driven by rhizosphere processes

With the rising global population growth and limitation of traditional agricultural technology, global crop production could not provide enough nutrients to assure adequate intake for all people. Nano-fertilizers and nano-pesticides have 20-30% higher efficacy than conventional products, which offer an effective solution to the above-mentioned problem. Rhizosphere is where plant roots, soil, and soil biota interact, and is the portal of nutrients transporting from soil into plants. The rhizosphere processes could modify the bioavailability of all nutrients and nanomaterials (NMs) before entering the food plants. However, to date, the overall rhizosphere processes regulating the behaviors and bioavailability of NMs to enhance the nutritional quality are still uncertain. In this review, a meta-analysis is conducted to quantitatively assess NMs-mediated changes in nutritional quality from food plants. Furthermore, the current knowledge and related mechanisms of the behavior and bioavailability of NMs driven by rhizosphere processes, e.g., root secretions, microbial and earthworm activities, are summarized. A series of rhizosphere processes can influence how NMs enter plants and change the biological responses, including signal transduction and nutrient absorption and transport. Moreover, future perspectives are presented to maximize the potentials of NMs applications for the enhancement of food crop production and global food security.

Metal resistant bacteria on gold particles: Implications of how anthropogenic contaminants could affect natural gold biogeochemical cycling

In Earth's near-surface environments, gold biogeochemical cycling involves gold dissolution and precipitation processes, which are partly attributed to bacteria. These biogeochemical processes as well as abrasion (via physical transport) are known to act upon gold particles, thereby resulting in particle transformation including the development of pure secondary gold and altered morphology, respectively. While previous studies have inferred gold biogeochemical cycling from gold particles obtained from natural environments, little is known about how metal contamination in an environment could impact this cycle. Therefore, this study aims to infer how potentially toxic metal contaminants could affect the structure and chemistry of gold particles and therefore the biogeochemical cycling of gold. In doing so, river sediments and gold particles from the De Kaap Valley, South Africa, were analysed using both microanalytical and molecular techniques. Of the metal contaminants detected in the sediment, mercury can chemically interact with gold particles thereby directly altering particle morphology and "erasing" textural evidence indicative of particle transformation. Other metal contaminants (including mercury) indirectly affect gold cycling by exerting a selective pressure on bacteria living on the surface of gold particles. Particles harbouring gold-tolerant bacteria with diverse metal resistant genes, such as Arthrobacter sp. and Pseudomonas sp., contained nearly two times more secondary gold relative to particles harbouring bacteria with less gold-tolerance. In conclusion, metal contaminants can have a direct or indirect effect on gold biogeochemical cycling in natural environments impacted by anthropogenic activity.

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.

Microbe-mediated sustainable bio-recovery of gold from low-grade precious solid waste: A microbiological overview

In an era of electronics, recovering the precious metal such as gold from ever increasing piles of electronic-wastes and metal-ion infested soil has become one of the prime concerns for researchers worldwide. Biological mining is an attractive, economical and non-hazardous to recover gold from the low-grade auriferous ore containing waste or soil. This review represents the recent major biological gold retrieval methods used to bio-mine gold. The biomining methods discussed in this review include, bioleaching, bio-oxidation, bio-precipitation, bio-flotation, bio-flocculation, bio-sorption, bio-reduction, bio-electrometallurgical technologies and bioaccumulation. The mechanism of gold biorecovery by microbes is explained in detail to explore its intracellular mechanistic, which help it withstand high concentrations of gold without causing any fatal consequences. Major challenges and future opportunities associated with each method and how they will dictate the fate of gold bio-metallurgy from metal wastes or metal infested soil bioremediation in the coming future are also discussed. With the help of concurrent advancements in high-throughput technologies, the gold bio-exploratory methods will speed up our ways to ensure maximum gold retrieval out of such low-grade ores containing sources, while keeping the gold mining clean and more sustainable.

Comparative Insights Into the Complete Genome Sequence of Highly Metal Resistant Cupriavidus metallidurans Strain BS1 Isolated From a Gold-Copper Mine

The highly heavy metal resistant strain Cupriavidus metallidurans BS1 was isolated from the Zijin gold–copper mine in China. This was of particular interest since the extensively studied, closely related strain, C. metallidurans CH34 was shown to not be only highly heavy metal resistant but also able to reduce metal complexes and biomineralizing them into metallic nanoparticles including gold nanoparticles. After isolation, C. metallidurans BS1 was characterized and complete genome sequenced using PacBio and compared to CH34. Many heavy metal resistance determinants were identified and shown to have wide-ranging similarities to those of CH34. However, both BS1 and CH34 displayed extensive genome plasticity, probably responsible for significant differences between those strains. BS1 was shown to contain three prophages, not present in CH34, that appear intact and might be responsible for shifting major heavy metal resistance determinants from plasmid to chromid (CHR2) in C. metallidurans BS1. Surprisingly, the single plasmid – pBS1 (364.4 kbp) of BS1 contains only a single heavy metal resistance determinant, the czc determinant representing RND-type efflux system conferring resistance to cobalt, zinc and cadmium, shown here to be highly similar to that determinant located on pMOL30 in C. metallidurans CH34. However, in BS1 another homologous czc determinant was identified on the chromid, most similar to the czc determinant from pMOL30 in CH34. Other heavy metal resistance determinants such as cnr and chr determinants, located on megaplasmid pMOL28 in CH34, were shown to be adjacent to the czc determinant on chromid (CHR2) in BS1. Additionally, other heavy metal resistance determinants such as pbr, cop, sil, and ars were located on the chromid (CHR2) and not on pBS1 in BS1. A diverse range of genomic rearrangements occurred in this strain, isolated from a habitat of constant exposure to high concentrations of copper, gold and other heavy metals. In contrast, the megaplasmid in BS1 contains mostly genes encoding unknown functions, thus might be more of an evolutionary playground where useful genes could be acquired by horizontal gene transfer and possibly reshuffled to help C. metallidurans BS1 withstand the intense pressure of extreme concentrations of heavy metals in its environment.

Functional capabilities of bacterial biofilms on gold particles

Gold particles contain gold and other toxic, heavy metals, making them ‘extreme’ geochemical microenvironments. To date, the functional capabilities of bacterial biofilms to deal with these conditions have been inferred from taxonomic analyses. The aims of this study are to evaluate the functional capabilities of bacterial communities on gold particles from six key locations using GeoChip 5.0 and to link functional and taxonomic data. Biofilm communities displayed a wide range of functional capabilities, with up to 53 505 gene probes detected. The capability of bacterial communities to (re)cycle carbon, nitrogen, and sulphur were detected. The cycling of major nutrients is important for maintaining the biofilm community as well as enabling the biogeochemical cycling and mobilisation of heavy and noble metals. Additionally, a multitude of stress- and heavy metal resistance capabilities were also detected, most notably from the α/β/γ-Proteobacteria and Actinobacteria. The multi-copper-oxidase gene copA, which is directly involved in gold resistance and biomineralisation, was the 15th most intense response and was detected in 246 genera. The Parker Road and Belle Brooke sites were consistently the most different from other sites, which may be a result of local physicochemical conditions (extreme nutrient poverty and sulphur-richness, respectively). In conclusion, biofilms on gold particles display wide-ranging metabolic and stress-related capabilities, which may enable them to survive in these niche environments and drive biotransformation of gold particles.

Detecting Gold Biomineralization by Delftia acidovorans Biofilms on a Quartz Crystal Microbalance

The extensive use of gold in sensing, diagnostics, and electronics has led to major concerns in solid waste management since gold and other heavy metals are nonbiodegradable and can easily accumulate in the environment. Moreover, gold ions are extremely reactive and potentially harmful for humans. Thus, there is an urgent need to develop reliable methodologies to detect and possibly neutralize ionic gold in aqueous solutions and industrial wastes. In this work, by using complementary measurement techniques such as quartz crystal microbalance (QCM), atomic force microscopy, crystal violet staining, and optical microscopy, we investigate a promising biologically induced gold biomineralization process accomplished by biofilms of bacterium Delftia acidovorans. When stressed by Au³⁺ ions, D. acidovorans is able to neutralize toxic soluble gold by excreting a nonribosomal peptide, which forms extracellular gold nanonuggets via complexation with metal ions. Specifically, QCM, a surface-sensitive transducer, is employed to quantify the production of these gold complexes directly on the D. acidovorans biofilm in real time. Detailed kinetics obtained by QCM captures the condition for maximized biomineralization yield and offers new insights underlying the biomineralization process. To the best of our knowledge, this is the first study providing an extensive characterization of the gold biomineralization process by a model bacterial biofilm. We also demonstrate QCM as a cheap, user-friendly sensing platform and alternative to standard analytical techniques for studies requiring high-resolution quantitative details, which offers promising opportunities in heavy-metal sensing, gold recovery, and industrial waste treatment.

Biogenic Cyanide Production Promotes Dissolution of Gold Nanoparticles in Soil

Gold nanoparticles (Au NPs) are often used to study the physiochemical behavior and distribution of nanomaterials in natural systems because they are assumed to be inert under environmental conditions, even though Au can be oxidized and dissolved by a common environmental compound: cyanide. We used the cyanogenic soil bacterium, Chromobacterium violaceum, to demonstrate that quorum-sensing-regulated cyanide production could lead to a high rate of oxidative dissolution of Au NPs in soil. After 7 days of incubation in a pH 7.0 soil inoculated with C. violaceum, labile Au concentration increased from 0 to 15%. There was no observable dissolution when Au NPs were incubated in abiotic soil. In the same soil adjusted to pH 7.5, labile Au concentration increased up to 29% over the same time frame. Furthermore, we demonstrated that Au dissolution required quorum-sensing-regulated cyanide production in soil by inoculating the soil with different cell densities and using a quorum-sensing-deficient mutant of C. violaceum, CV026. Au NP dissolution experiments in liquid media coupled with mass spectrometry analysis confirmed that biogenic cyanide oxidized Au NPs to soluble Au(CN)₂^-. These results demonstrate under which conditions biologically enhanced metal dissolution can contribute to the overall geochemical transformation kinetics of nanoparticle in soils, even though the materials may be inert in abiotic environments.

Gold nanoparticle biodissolution by a freshwater macrophyte and its associated microbiome

Predicting nanoparticle fate in aquatic environments requires mimicking of ecosystem complexity to observe the geochemical processes affecting their behaviour. Here, 12 nm Au nanoparticles were added weekly to large-scale freshwater wetland mesocosms. After six months, ~70% of Au was associated with the macrophyte Egeria densa, where, despite the thermodynamic stability of Au⁰ in water, the pristine Au⁰ nanoparticles were fully oxidized and complexed to cyanide, hydroxyls or thiol ligands. Extracted biofilms growing on E. densa leaves were shown to dissolve Au nanoparticles within days. The Au biodissolution rate was highest for the biofilm with the lowest prevalence of metal-resistant taxa but the highest ability to release cyanide, known to promote Au⁰ oxidation and complexation. Macrophytes and the associated microbiome thus form a biologically active system that can be a major sink for nanoparticle accumulation and transformations. Nanoparticle biotransformation in these compartments should not be ignored, even for nanoparticles commonly considered to be stable in the environment.

Reflecting on Gold Geomicrobiology Research: Thoughts and Considerations for Future Endeavors

Research in gold (Au) geomicrobiology has developed extensively over the last ten years, as more Au-bearing materials from around the world point towards a consistent story: That microbes interact with Au. In weathering environments, Au is mobile, taking the form of oxidized, soluble complexes or reduced, elemental Au nanoparticles. The transition of Au between aqueous and solid states is attributed to varying geochemical conditions, catalyzed in part by the biosphere. Hence, a global Au-biogeochemical-cycle was proposed. The primary focus of this mini-review is to reflect upon the biogeochemical processes that contribute to what we currently know about Au cycling. In general, the global Au-biogeochemical-cycle begins with the liberation of gold-silver particles from a primary host rock, by physical weathering. Through oxidative-complexation, inorganic and organic soluble-Au complexes are produced. However, in the presence of microbes or other reductants—e.g., clays and Fe-oxides—these Au complexes can be destabilized. The reduction of soluble Au ultimately leads to the bioprecipitation and biomineralization of Au, the product of which can aggregate into larger structures, thereby completing the Au cycle. Evidence of these processes have been “recorded” in the preservation of secondary Au structures that have been observed on Au particles from around the world. These structures—i.e., nanometer-size to micrometer-size Au dissolution and reprecipitation features—are “snap shots” of biogeochemical influences on Au, during its journey in Earth-surface environments. Therefore, microbes can have a profound effect on the occurrence of Au in natural environments, given the nutrients necessary for microbial metabolism are sustained and Au is in the system.

Synergistic gold–copper detoxification at the core of gold biomineralisation inCupriavidus metallidurans

Cupriavidus metalliduransescapes synergistic Cu/Au toxicity by re-oxidation of Au(i) back to Au(iii) using the periplasmic oxidase CopA.

Synergistic Toxicity of Copper and Gold Compounds in Cupriavidus metallidurans

The bacterium Cupriavidus metallidurans can reduce toxic gold(I/III) complexes and biomineralize them into metallic gold (Au) nanoparticles, thereby mediating the (trans)formation of Au nuggets. In Au-rich soils, most transition metals do not interfere with the resistance of this bacterium to toxic mobile Au complexes and can be removed from the cell by plasmid-encoded metal efflux systems. Copper is a noticeable exception: the presence of Au complexes and Cu ions results in synergistic toxicity, which is accompanied by an increased cytoplasmic Cu content and formation of Au nanoparticles in the periplasm. The periplasmic Cu-oxidase CopA was not essential for formation of the periplasmic Au nanoparticles. As shown with the purified and reconstituted Cu efflux system CupA, Au complexes block Cu-dependent release of phosphate from ATP by CupA, indicating inhibition of Cu transport. Moreover, Cu resistance of Au-inhibited cells was similar to that of mutants carrying deletions in the genes for the Cu-exporting P_IB1-type ATPases. Consequently, Au complexes inhibit export of cytoplasmic Cu ions, leading to an increased cellular Cu content and decreased Cu and Au resistance. Uncovering the biochemical mechanisms of synergistic Au and Cu toxicity in C. metallidurans explains the issues this bacterium has to face in auriferous environments, where it is an important contributor to the environmental Au cycle.IMPORTANCE C. metallidurans lives in metal-rich environments, including auriferous soils that contain a mixture of toxic transition metal cations. We demonstrate here that copper ions and gold complexes exert synergistic toxicity because gold ions inhibit the copper-exporting P-type ATPase CupA, which is central to copper resistance in this bacterium. Such a situation should occur in soils overlying Au deposits, in which Cu/Au ratios usually are ≫1. Appreciating how C. metallidurans solves the problem of living in environments that contain both Au and Cu is a prerequisite to understand the molecular mechanisms underlying gold cycling in the environment, and the significance and opportunities of microbiota for specific targeting to Au in mineral exploration and ore processing.