Investigation of the magnetosome biomineralization in magnetotactic bacteria using graphene liquid cell - transmission electron microscopy

Convergence of Nanotechnology and Bacteriotherapy for Biomedical Applications

Bacteria have distinctive properties that make them ideal for biomedical applications. They can self-propel, sense their surroundings, and be externally detected. Using bacteria as medical therapeutic agents or delivery platforms opens new possibilities for advanced diagnosis and therapies. Nano-drug delivery platforms have numerous advantages over traditional ones, such as high loading capacity, controlled drug release, and adaptable functionalities. Combining bacteria and nanotechnologies to create therapeutic agents or delivery platforms has gained increasing attention in recent years and shows promise for improved diagnosis and treatment of diseases. In this review, design principles of integrating nanoparticles with bacteria, bacteria-derived nano-sized vesicles, and their applications and future in advanced diagnosis and therapeutics are summarized.

Phenomic and transcriptomic analyses reveal the sequential synthesis of Fe3O4 nanoparticles in Acidithiobacillus ferrooxidans BYM

IMPORTANCE

As the most important non-magnetotactic magnetosome-producing bacteria, Acidithiobacillus ferrooxidans only requires very mild conditions to produce Fe3O4 nanoparticles, thus conferring greater flexibility and potential application in biomagnetic nanoparticle production. However, the available information cannot explain the mechanism of Fe3O4 nanoparticle formation in A. ferrooxidans. In this study, we applied phenomic and transcriptomic analyses to reveal this mechanism. We found that different treatment condition factors notably affect the phenomic data of Fe3O4 nanoparticle in A. ferrooxidans. Using transcriptomic analyses, the gene network controlling/regulating Fe3O4 nanoparticle biogenesis in A. ferrooxidans was proposed, excavating the candidate hub genes for Fe3O4 nanoparticle formation in A. ferrooxidans. Based on this information, a sequential model for Fe3O4 nanoparticle synthesis in A. ferrooxidans was hypothesized. It lays the groundwork for further clarifying the feature of Fe3O4 nanoparticle synthesis.

Liquid Transmission Electron Microscopy for Probing Collagen Biomineralization

Collagen biomineralization is fundamental to hard tissue assembly. While studied extensively, collagen mineralization processes are not fully understood, with the majority of theories derived from electron microscopy (EM) under static, dehydrated, or frozen conditions, unlike the liquid phase environment where mineralization occurs. Herein, novel liquid transmission EM (TEM) strategies are presented, in which collagen mineralization was explored in liquid for the first time via TEM. Custom thin-film enclosures were employed to visualize the mineralization of reconstituted collagen fibrils in a calcium phosphate and polyaspartic acid solution to promote intrafibrillar mineralization. TEM highlighted that at early time points precursor mineral particles attached to collagen and progressed to crystalline mineral platelets aligned with fibrils at later time points. This aligns with observations from other techniques and validates the liquid TEM approach. This work provides a new liquid imaging approach for exploring collagen biomineralization, advancing toward understanding disease pathogenesis and remineralization strategies for hard tissues.

Real-time TEM observations of ice formation in graphene liquid cell

The study of ice nucleation and growth at the nanoscale is of utmost importance in geological and atmospheric sciences. However, existing transmission electron microscopy (TEM) approaches have been unsuccessful in imaging ice formation directly. Herein, we demonstrate how radical scavengers - such as TiO₂ - encased with water in graphene liquid cells (GLCs) facilitate the observation of ice nucleation phenomena at low temperatures. Atomic-resolution imaging reveals the nucleation and growth of cubic ice-phase crystals at close proximity to TiO₂-water nanointerfaces at low temperatures. Interestingly, both heterogeneously and homogeneously nucleated ice crystals exhibited this cubic phase. Ice crystal nuclei were observed to be more stable at the TiO₂-water nanointerface, as compared with crystals in the bulk liquid (homogeneous nucleation), suggesting the radical scavenging efficacy of TiO₂ nanoparticles mitigating the electron beam by-products. The present work demonstrates that the use of radical scavengers in GLC TEM shows great promise towards unveiling the nanoscale pathways for ice nucleation and growth dynamic events.

In Situ Microscopic Studies on the Interaction of Multi-Principal Element Nanoparticles and Bacteria

Multi-principal element nanoparticles are an emerging class of materials with potential applications in medicine and biology. However, it is not known how such nanoparticles interact with bacteria at nanoscale. In the present work, we evaluated the interaction of multi-principal elemental alloy (FeNiCu) nanoparticles with Escherichia coli (E. coli) bacteria using the in situ graphene liquid cell (GLC) scanning transmission electron microscopy (STEM) approach. The imaging revealed the details of bacteria wall damage in the vicinity of nanoparticles. The chemical mappings of S, P, O, N, C, and Cl elements confirmed the cytoplasmic leakage of the bacteria. Our results show that there is selective release of metal ions from the nanoparticles. The release of copper ions was much higher than that for nickel while the iron release was the lowest. In addition, the binding affinity of bacterial cell membrane protein functional groups with Cu, Ni, and Fe cations is found to be the driving force behind the selective metal cations' release from the multi-principal element nanoparticles. The protein functional groups driven dissolution of multielement nanoparticles was evaluated using the density functional theory (DFT) computational method, which confirmed that the energy required to remove Cu atoms from the nanoparticle surface was the least in comparison with those for Ni and Fe atoms. The DFT results support the experimental data, indicating that the energy to dissolve metal atoms exposed to oxidation and/or the to presence of oxygen atoms at the surface of the nanoparticle catalyzes metal removal from the multielement nanoparticle. The study shows the potential of compositional design of multi-principal element nanoparticles for the controlled release of metal ions to develop antibacterial strategies. In addition, GLC-STEM is a promising approach for understanding the nanoscale interaction of metallic nanoparticles with biological structures.

Enhanced Bacterial Growth by Polyelemental Glycerolate Particles

While polyelemental alloys are shown to be promising for healthcare applications, their effectiveness in promoting bacterial growth remains unexplored. In the present work, we evaluated the interaction of polyelemental glycerolate particles (PGPs) with Escherichia coli (E. coli) bacteria. PGPs were synthesized using the solvothermal route, and nanoscale random distribution of metal cations in the glycerol matrix of PGPs was confirmed. We observed 7-fold growth of E. coli bacteria upon 4 h of interaction with quinary glycerolate (NiZnMnMgSr-Gly) particles in comparison to control E. coli bacteria. Nanoscale microscopic studies on bacteria interactions with PGPs showed the release of metal cations in the bacterium cytoplasm from PGPs. The electron microscopy imaging and chemical mapping indicated bacterial biofilm formation on PGPs without causing significant cell membrane damage. The data showed that the presence of glycerol in PGPs is effective in controlling the release of metal cations, thus preventing bacterial toxicity. The presence of multiple metal cations is expected to provide synergistic effects of nutrients needed for bacterial growth. The present work provides key microscopic insights of mechanisms by which PGPs enhance biofilm growth. This study opens the door for future applications of PGPs in areas where bacterial growth is essential including healthcare, clean energy, and the food industry.

Unveiling growth and dynamics of liposomes by graphene liquid cell-transmission electron microscopy

Liposome is a model system for biotechnological and biomedical purposes spanning from targeted drug delivery to modern vaccine research. Yet, the growth mechanism of liposomes is largely unknown. In this work, the formation and evolution of phosphatidylcholine-based liposomes are studied in real-time by graphene liquid cell-transmission electron microscopy (GLC-TEM). We reveal important steps in the growth, fusion and denaturation of phosphatidylcholine (PC) liposomes. We show that initially complex lipid aggregates resembling micelles start to form. These aggregates randomly merge while capturing water and forming small proto-liposomes. The nanoscopic containers continue sucking water until their membrane becomes convex and free of redundant phospholipids, giving stabilized PC liposomes of different sizes. In the initial stage, proto-liposomes grow at a rate of 10-15 nm s^-1, which is followed by their growth rate of 2-5 nm s^-1, limited by the lipid availability in the solution. Molecular dynamics (MD) simulations are used to understand the structure of micellar clusters, their evolution, and merging. The liposomes are also found to fuse through lipid bilayers docking followed by the formation of a hemifusion diaphragm and fusion pore opening. The liposomes denaturation can be described by initial structural destabilization and deformation of the membrane followed by the leakage of the encapsulated liquid. This study offers new insights on the formation and growth of lipid-based molecular assemblies which is applicable to a wide range of amphiphilic molecules.

Magnetotactic bacteria in vertical sediments of volcanic lakes in NE China appear Alphaproteobacteria dominated distribution regardless of waterbody types

Magnetotactic bacteria (MTB) distribute widely in sediment habitats and play critical roles in iron cycling. Here, the vertical distribution of morphology and phylogenetic diversity of MTB in sediments (0-15 cm) of three lakes (open waterbody, Bailonghu, BL; semi-enclosed waterbody, Yaoquanhu, YQ; enclosed waterbody, Yueyapao, YY) in Wudalianchi volcanic field (China) were investigated. TEM showed the appearance of coccoid, rod-shaped, oval-shaped, and arc-shaped MTB. With the increase of BL sediment depth, the number of rod-shaped and spherical MTB decreased and increased, respectively. High-throughput sequencing indicated that Alphaproteobacterial MTB dominantly thrived in these lakes regardless of waterbody types. In BL and YY, the dominant genus was Magnetospirillum (44.99-70.80%) which showed a peak in the middle layer. In YQ, the genus Magnetospira was dominant in the upper (52.36%) and middle (66.56%) layer and Magnetococcus (69.63%) existed dominantly in the bottom layer. The vertical distribution of MTB in sediments of these lakes decreased first and then increased. Functional analysis showed that ABC transporter and two-component system of MTB changed significantly with the sediment depth. RDA indicated that the distribution of Magnetospirillum was positively associated with sulfide, pH, and TC. These findings will expand our knowledge of the vertical distribution of MTB in volcanic lakes.

New Insights for Biosensing: Lessons from Microbial Defense Systems

Microorganisms have gained defense systems during the lengthy process of evolution over millions of years. Such defense systems can protect them from being attacked by invading species (e.g., CRISPR-Cas for establishing adaptive immune systems and nanopore-forming toxins as virulence factors) or enable them to adapt to different conditions (e.g., gas vesicles for achieving buoyancy control). These microorganism defense systems (MDS) have inspired the development of biosensors that have received much attention in a wide range of fields including life science research, food safety, and medical diagnosis. This Review comprehensively analyzes biosensing platforms originating from MDS for sensing and imaging biological analytes. We first describe a basic overview of MDS and MDS-inspired biosensing platforms (e.g., CRISPR-Cas systems, nanopore-forming proteins, and gas vesicles), followed by a critical discussion of their functions and properties. We then discuss several transduction mechanisms (optical, acoustic, magnetic, and electrical) involved in MDS-inspired biosensing. We further detail the applications of the MDS-inspired biosensors to detect a variety of analytes (nucleic acids, peptides, proteins, pathogens, cells, small molecules, and metal ions). In the end, we propose the key challenges and future perspectives in seeking new and improved MDS tools that can potentially lead to breakthrough discoveries in developing a new generation of biosensors with a combination of low cost; high sensitivity, accuracy, and precision; and fast detection. Overall, this Review gives a historical review of MDS, elucidates the principles of emulating MDS to develop biosensors, and analyzes the recent advancements, current challenges, and future trends in this field. It provides a unique critical analysis of emulating MDS to develop robust biosensors and discusses the design of such biosensors using elements found in MDS, showing that emulating MDS is a promising approach to conceptually advancing the design of biosensors.

Innovative Approaches of Engineering Tumor-Targeting Bacteria with Different Therapeutic Payloads to Fight Cancer: A Smart Strategy of Disease Management

Conventional therapies for cancer eradication like surgery, radiotherapy, and chemotherapy, even though most widely used, still suffer from some disappointing outcomes. The limitations of these therapies during cancer recurrence and metastasis demonstrate the need for better alternatives. Some bacteria preferentially colonize and proliferate inside tumor mass; thus these bacteria can be used as ideal candidates to deliver antitumor therapeutic agents. The bacteria like Bacillus spp., Clostridium spp., E. coli, Listeria spp., and Salmonella spp. can be reprogrammed to produce, transport, and deliver anticancer agents, eg, cytotoxic agents, prodrug converting enzymes, immunomodulators, tumor stroma targeting agents, siRNA, and drug-loaded nanoformulations based on clinical requirements. In addition, these bacteria can be genetically modified to express various functional proteins and targeting ligands that can enhance the targeting approach and controlled drug-delivery. Low tumor-targeting and weak penetration power deep inside the tumor mass limits the use of anticancer drug-nanoformulations. By using anticancer drug nanoformulations and other therapeutic payloads in combination with antitumor bacteria, it makes a synergistic effect against cancer by overcoming the individual limitations. The tumor-targeting bacteria can be either used as a monotherapy or in addition with other anticancer therapies like photothermal therapy, photodynamic therapy, and magnetic field therapy to accomplish better clinical outcomes. The toxicity issues on normal tissues is the main concern regarding the use of engineered antitumor bacteria, which requires deeper research. In this article, the mechanism by which bacteria sense tumor microenvironment, role of some anticancer agents, and the recent advancement of engineering bacteria with different therapeutic payloads to combat cancers has been reviewed. In addition, future prospective and some clinical trials are also discussed.

Recent Progress in the Transfer of Graphene Films and Nanostructures

The one-atom-thick graphene has excellent electronic, optical, thermal, and mechanical properties. Currently, chemical vapor deposition (CVD) graphene has received a great deal of attention because it provides access to large-area and uniform films with high-quality. This allows the fabrication of graphene based-electronics, sensors, photonics, and optoelectronics for practical applications. Zero bandgap, however, limits the application of a graphene film as electronic transistor. The most commonly used bottom-up approaches have achieved efficient tuning of the electronic bandgap by customizing well-defined graphene nanostructures. The postgrowth transfer of graphene films/nanostructures to a certain substrate is crucial in utilizing graphene in applicable devices. In this review, the basic growth mechanism of CVD graphene is first introduced. Then, recent advances in various transfer methods of as-grown graphene to target substrates are presented. The fabrication and transfer methods of graphene nanostructures are also provided, and then the transfer-related applications are summarized. At last, the challenging issues and the potential transfer-free approaches are discussed.

Bioinspired Magnetic Nanochains for Medicine

Superparamagnetic iron oxide nanoparticles (SPIONs) have been widely used for medicine, both in therapy and diagnosis. Their guided assembly into anisotropic structures, such as nanochains, has recently opened new research avenues; for instance, targeted drug delivery. Interestingly, magnetic nanochains do occur in nature, and they are thought to be involved in the navigation and geographic orientation of a variety of animals and bacteria, although many open questions on their formation and functioning remain. In this review, we will analyze what is known about the natural formation of magnetic nanochains, as well as the synthetic protocols to produce them in the laboratory, to conclude with an overview of medical applications and an outlook on future opportunities in this exciting research field.

Verification of water presence in graphene liquid cells

Graphene liquid cells (GLCs) present the thinnest possible sample enclosures for liquid phase electron microscopy. However, the actual presence of liquid within a GLC is not always guaranteed. Of key importance is to reliably test the presence of the liquid, which is most frequently water or saline. Here, the commonly used methods for verifying the presence of water were evaluated. It is shown that depending on the type of sample, applying a single criterion does not always conclusively verify the presence of water. Testing liquid filling for a specific GLC sample preparation protocol should thus be considered critically. The most reliable method is direct observation of the water exciton peak using electron energy loss spectroscopy (EELS). But if this method cannot be carried out, water filling of the GLC can be verified from a combination of higher contrast in the image, the presence of bubbles, and an oxygen signal in the EEL spectrum, which can be accomplished at a high electron dose in spot mode. Nanoparticle movement does not always occur in a GLC.

Magnetotactic Bacteria and Magnetosomes: Basic Properties and Applications

Magnetotactic bacteria (MTB) belong to several phyla. This class of microorganisms exhibits the ability of magneto-aerotaxis. MTB synthesize biominerals in organelle-like structures called magnetosomes, which contain single-domain crystals of magnetite (Fe3O4) or greigite (Fe3S4) characterized by a high degree of structural and compositional perfection. Magnetosomes from dead MTB could be preserved in sediments (called fossil magnetosomes or magnetofossils). Under certain conditions, magnetofossils are capable of retaining their remanence for millions of years. This accounts for the growing interest in MTB and magnetofossils in paleo- and rock magnetism and in a wider field of biogeoscience. At the same time, high biocompatibility of magnetosomes makes possible their potential use in biomedical applications, including magnetic resonance imaging, hyperthermia, magnetically guided drug delivery, and immunomagnetic analysis. In this review, we attempt to summarize the current state of the art in the field of MTB research and applications.

Microbial Fabricated Nanosystems: Applications in Drug Delivery and Targeting

The emergence of nanosystems for different biomedical and drug delivery applications has drawn the attention of researchers worldwide. The likeness of microorganisms including bacteria, yeast, algae, fungi, and even viruses toward metals is well-known. Higher tolerance to toxic metals has opened up new avenues of designing microbial fabricated nanomaterials. Their synthesis, characterization and applications in bioremediation, biomineralization, and as a chelating agent has been well-documented and reviewed. Further, these materials, due to their ability to get functionalized, can also be used as theranostics i.e., both therapeutic as well as diagnostic agents in a single unit. Current article attempts to focus particularly on the application of such microbially derived nanoformulations as a drug delivery and targeting agent. Besides metal-based nanoparticles, there is enough evidence wherein nanoparticles have been formulated using only the organic component of microorganisms. Enzymes, peptides, polysaccharides, polyhydroxyalkanoate (PHA), poly-(amino acids) are amongst the most used biomolecules for guiding crystal growth and as a capping/reducing agent in the fabrication of nanoparticles. This has promulgated the idea of complete green chemistry biosynthesis of nano-organics that are most sought after in terms of their biocompatibility and bioavailability.

Biological materials formed by Acidithiobacillus ferrooxidans and their potential applications

A variety of biological materials including schwertmannite, jarosite, iron-sulfur cluster (ISC) and magnetosomes can be produced by Acidithiobacillus ferrooxidans (A. ferrooxidans). Their possible formation mechanisms involved in iron transformation, iron transport, and electron transfer were proposed. The schwertmannite formation usually occurs under the pH of 2.0-3.51, and a lower or higher pH will promote jarosite to be produced. Available Fe2+ in the environment and the carrier proteins that can transport Fe2+ to the intracellular membranes of A. ferrooxidans play a critical role in the synthesis of magnetosomes and ISC. The potential applications of these biological materials were reviewed, including removal of heavy metal by schwertmannite, detoxification of toxic species by jarosite, the transference of electron and ripening the iron sulfur protein by ISC, and biomedical application of magnetosomes. Additionally, some perspectives for the molecular mechanisms of synthesis and regulation of these biomaterials were briefly described.

Microbe-Mediated Extracellular and Intracellular Mineralization: Environmental, Industrial, and Biotechnological Applications

Microbe-mediated mineralization is ubiquitous in nature, involving bacteria, fungi, viruses, and algae. These mineralization processes comprise calcification, silicification, and iron mineralization. The mechanisms for mineral formation include extracellular and intracellular biomineralization. The mineral precipitating capability of microbes is often harnessed for green synthesis of metal nanoparticles, which are relatively less toxic compared with those synthesized through physical or chemical methods. Microbe-mediated mineralization has important applications ranging from pollutant removal and nonreactive carriers, to other industrial and biomedical applications. Herein, the different types of microbe-mediated biomineralization that occur in nature, their mechanisms, as well as their applications are elucidated to create a backdrop for future research.

In Situ Visualization of Ferritin Biomineralization via Graphene Liquid Cell-Transmission Electron Microscopy

Ferritin biomineralization is essential to regulate the toxic Fe²⁺ iron ions in the human body. Unravelling the mechanism of biomineralization in ferritin facilitates our understanding of the causes underlying many iron disorder-related diseases. Until now, no report of in situ visualization of ferritin biomineralization events at nanoscale exists due to the requirement for high-resolution imaging of nanometer-sized ferritin proteins in their hydrated states. Herein, for the first time, we show that the biomineralization processes within individual ferritin proteins can be visualized by means of graphene liquid cell-transmission electron microscopy (GLC-TEM). The increase in the ratio of Fe³⁺/Fe²⁺ ions over time monitored via electron energy loss spectroscopy (EELS) reveals the change in oxidation state of iron oxide phases with time. This study lays a foundation for future investigations on iron regulation mechanisms in healthy and dysfunctional ferritins.

Correlative ex situ and Liquid-Cell TEM Observation of Bacterial Cell Membrane Damage Induced by Rough Surface Topology

BACKGROUND

Nanoscale surface roughness has been suggested to have antibacterial and antifouling properties. Several existing models have attempted to explain the antibacterial mechanism of nanoscale rough surfaces without direct observation. Here, conventional and liquid-cell TEM are implemented to observe nanoscale bacteria/surface roughness interaction. The visualization of such interactions enables the inference of possible antibacterial mechanisms.

METHODS AND RESULTS

Nanotextures are synthesized on biocompatible polymer microparticles (MPs) via plasma etching. Both conventional and liquid-phase transmission electron microscopy observations suggest that these MPs may cause cell lysis via bacterial binding to a single protrusion of the nanotexture. The bacterium/protrusion interaction locally compromises the cell wall, thus causing bacterial death. This study suggests that local mechanical damage and leakage of the cytosol kill the bacteria first, with subsequent degradation of the cell envelope.

CONCLUSION

Nanoscale surface roughness may act via a penetrative bactericidal mechanism. This insight suggests that future research may focus on optimizing bacterial binding to individual nanoscale projections in addition to stretching bacteria between nanopillars. Further, antibacterial nanotextures may find use in novel applications employing particles in addition to nanotextures on fibers or films.