Correlative electron and fluorescence microscopy of magnetotactic bacteria in liquid: toward in vivo imaging

Correlative SIP-FISH-Raman-SEM-NanoSIMS links identity, morphology, biochemistry, and physiology of environmental microbes

Microscopic and spectroscopic techniques are commonly applied to study microbial cells but are typically used on separate samples, resulting in population-level datasets that are integrated across different cells with little spatial resolution. To address this shortcoming, we developed a workflow that correlates several microscopic and spectroscopic techniques to generate an in-depth analysis of individual cells. By combining stable isotope probing (SIP), fluorescence in situ hybridization (FISH), scanning electron microscopy (SEM), confocal Raman microspectroscopy (Raman), and nano-scale secondary ion mass spectrometry (NanoSIMS), we illustrate how individual cells can be thoroughly interrogated to obtain information about their taxonomic identity, structure, physiology, and metabolic activity. Analysis of an artificial microbial community demonstrated that our correlative approach was able to resolve the activity of single cells using heavy water SIP in conjunction with Raman and/or NanoSIMS and establish their taxonomy and morphology using FISH and SEM. This workflow was then applied to a sample of yet uncultured multicellular magnetotactic bacteria (MMB). In addition to establishing their identity and activity, backscatter electron microscopy (BSE), NanoSIMS, and energy-dispersive X-ray spectroscopy (EDS) were employed to characterize the magnetosomes within the cells. By integrating these techniques, we demonstrate a cohesive approach to thoroughly study environmental microbes on a single-cell level.

Identification of sulfate-reducing magnetotactic bacteria via a group-specific 16S rDNA primer and correlative fluorescence and electron microscopy: strategy for culture-independent study

Magnetotactic bacteria (MTB) biomineralize intracellular magnetic nanocrystals and swim along geomagnetic field lines. While few axenic MTB cultures exist, living cells can be separated magnetically from natural environments for analysis. The bacterial universal 27F/1492R primer pair has been used widely to amplify nearly full-length 16S rRNA genes and to provide phylogenetic portraits of MTB communities. However, incomplete coverage and amplification biases inevitably prevent detection of some phylogenetically specific or non-abundant MTB. Here, we propose a new formulation of the upstream 390F primer that we combined with the downstream 1492R primer to specifically amplify 1,100-bp 16S rRNA gene sequences of sulfate-reducing MTB in freshwater sediments from Lake Weiyanghu, Xi'an, northwestern China. With correlative fluorescence in situ hybridization and scanning/transmission electron microscopy, three novel MTB strains (WYHR-2, WYHR-3, and WYHR-4) from the Desulfobacterota phylum were identified phylogenetically and structurally at the single cell level. Strain WYHR-2 produces bullet-shaped magnetosome magnetite, while the other two strains produce both cubic/prismatic greigite and bullet-shaped magnetite. Our results expand knowledge of bacterial diversity and magnetosome biomineralization of sulfate-reducing MTB. We also propose a general strategy for identifying and characterizing uncultured MTB from natural environments. This article is protected by copyright. All rights reserved.

Inactivation of Fluorescent Lipid Bilayers by Irradiation With 300 keV Electrons Using Liquid Cell Transmission Electron Microscopy

Liquid cell transmission electron microscopy allows for imaging of samples in a fully hydrated state at high resolution and has the potential for visualizing static or dynamic biological structures. However, the ionizing nature of the electron beam makes it difficult to discern real physiological dynamics from radiation induced artifacts within liquid cell samples. Electron flux thresholds for achieving high resolution structures from biological samples frozen in ice have been described extensively by the cryo-electron microscopy field, while electron flux thresholds which do not result in a functional change for biological samples within the hydrated environment of a transmission electron microscope liquid cell is less clear. Establishing these functional thresholds for biologically relevant samples is important for accurate interpretation of results from liquid cell experiments. Here we demonstrate the electron damage threshold of fluorescently tagged lipid bilayers by quantifying the change in fluorescence before and after electron exposure. We observe the reduction of fluorescent signal in bilayers by 25% after only 0.0005 e−/Å2 and a reduction of over 90% after 0.01 e−/Å2. These results indicate that the loss of function occurs at irradiation thresholds far below a typical single high resolution (scanning) transmission electron microscopy image and orders of magnitude below fluxes used for preserving structural features with cryo-electron microscopy.

A quorum-based fluorescent probe for imaging pathogenic bacteria

Imaging of bacterial infections can be used for a wide range of investigations, including diagnosis and pathogenesis of infections, and molecular probes targeting biological processes during infection have been used...

Revealing Reactions between the Electron Beam and Nanoparticle Capping Ligands with Correlative Fluorescence and Liquid-Phase Electron Microscopy

Liquid-phase transmission electron microscopy (LP-TEM) enables real-time imaging of nanoparticle self-assembly, formation, and etching with single nanometer resolution. Despite the importance of organic nanoparticle capping ligands in these processes, the effect of electron beam irradiation on surface-bound and soluble capping ligands during LP-TEM imaging has not been investigated. Here, we use correlative LP-TEM and fluorescence microscopy (FM) to demonstrate that polymeric nanoparticle ligands undergo competing crosslinking and chain scission reactions that nonmonotonically modify ligand coverage over time. Branched polyethylenimine (BPEI)-coated silver nanoparticles were imaged with dose-controlled LP-TEM followed by labeling their primary amine groups with fluorophores to visualize the local thickness of adsorbed capping ligands. FM images showed that free ligands crosslinked in the LP-TEM image area over imaging times of tens of seconds, enhancing local capping ligand coverage on nanoparticles and silicon nitride membranes. Nanoparticle surface ligands underwent chain scission over irradiation times of minutes to tens of minutes, which depleted surface ligands from the nanoparticle and silicon nitride surface. Conversely, solutions of only soluble capping ligand underwent successive crosslinking reactions with no chain scission, suggesting that nanoparticles enhanced the chain scission reactions by acting as radiolysis hotspots. The addition of a hydroxyl radical scavenger, tert-butanol, eliminated chain scission reactions and slowed the progression of crosslinking reactions. These experiments have important implications for performing controlled and reproducible LP-TEM nanoparticle imaging as they demonstrate that the electron beam can significantly alter ligand coverage on nanoparticles in a nonintuitive manner. They emphasize the need to understand and control the electron beam radiation chemistry of a given sample to avoid significant perturbations to the nanoparticle capping ligand chemistry, which are invisible in electron micrographs.

Graphene Liquid Cell Electron Microscopy: Progress, Applications, and Perspectives

Graphene liquid cell electron microscopy (GLC-EM), a cutting-edge liquid-phase EM technique, has become a powerful tool to directly visualize wet biological samples and the microstructural dynamics of nanomaterials in liquids. GLC uses graphene sheets with a one carbon atom thickness as a viewing window and a liquid container. As a result, GLC facilitates atomic-scale observation while sustaining intact liquids inside an ultra-high-vacuum transmission electron microscopy chamber. Using GLC-EM, diverse scientific results have been recently reported in the material, colloidal, environmental, and life science fields. Here, the developments of GLC fabrications, such as first-generation veil-type cells, second-generation well-type cells, and third-generation liquid-flowing cells, are summarized. Moreover, recent GLC-EM studies on colloidal nanoparticles, battery electrodes, mineralization, and wet biological samples are also highlighted. Finally, the considerations and future opportunities associated with GLC-EM are discussed to offer broad understanding and insight on atomic-resolution imaging in liquid-state dynamics.

100th Anniversary of Macromolecular Science Viewpoint: Polymeric Materials by In Situ Liquid-Phase Transmission Electron Microscopy

A century ago, Hermann Staudinger proposed the macromolecular theory of polymers, and now, as we enter the second century of polymer science, we face a different set of opportunities and challenges for the development of functional soft matter. Indeed, many fundamental questions remain open, relating to physical structures and mechanisms of phase transformations at the molecular and nanoscale. In this Viewpoint, we describe efforts to develop a dynamic, in situ microscopy tool suited to the study of polymeric materials at the nanoscale that allows for direct observation of discrete structures and processes in solution, as a complement to light, neutron, and X-ray scattering methods. Liquid-phase transmission electron microscopy (LPTEM) is a nascent in situ imaging technique for characterizing and examining solvated nanomaterials in real time. Though still under development, LPTEM has been shown to be capable of several modes of imaging: (1) imaging static solvated materials analogous to cryo-TEM, (2) videography of nanomaterials in motion, (3) observing solutions or nanomaterials undergoing physical and chemical transformations, including synthesis, assembly, and phase transitions, and (4) observing electron beam-induced chemical-materials processes. Herein, we describe opportunities and limitations of LPTEM for polymer science. We review the basic experimental platform of LPTEM and describe the origin of electron beam effects that go hand in hand with the imaging process. These electron beam effects cause perturbation and damage to the sample and solvent that can manifest as artefacts in images and videos. We describe sample-specific experimental guidelines and outline approaches to mitigate, characterize, and quantify beam damaging effects. Altogether, we seek to provide an overview of this nascent field in the context of its potential to contribute to the advancement of polymer science.

A pressure-actuated flow cell for soft X-ray spectromicroscopy in liquid media

We present and fully characterize a flow cell dedicated to imaging in liquid at the nanoscale. Its use as a routine sample environment for soft X-ray spectromicroscopy is demonstrated, in particular through the spectral analysis of inorganic particles in water. The care taken in delineating the fluidic pathways and the precision associated with pressure actuation ensure the efficiency of fluid renewal under the beam, which in turn guarantees a successful utilization of this microfluidic tool for in situ kinetic studies. The assembly of the described flow cell necessitates no sophisticated microfabrication and can be easily implemented in any laboratory. Furthermore, the design principles we relied on are transposable to all microscopies involving strongly absorbed radiation (e.g. X-ray, electron), as well as to all kinds of X-ray diffraction/scattering techniques.

In situ monitoring of exopolymer-dependent Mn mineralization on bacterial surfaces

Bacterial biomineralization is a widespread process that affects cycling of metals in the environment. Functionalized bacterial cell surfaces and exopolymers are thought to initiate mineral formation, however, direct evidences are hampered by technical challenges. Here, we present a breakthrough in the use of liquid-cell scanning transmission electron microscopy to observe mineral growth on bacteria and the exopolymers they secrete. Two Escherichia coli mutants producing distinct exopolymers are investigated. We use the incident electron beam to provoke and observe the precipitation of Mn-bearing minerals. Differences in the morphology and distribution of Mn precipitates on the two strains reflect differences in nucleation site density and accessibility. Direct observation under liquid conditions highlights the critical role of bacterial cell surface charges and exopolymer types in metal mineralization. This has strong environmental implications because biofilms structured by exopolymers are widespread in nature and constitute the main form of microbial life on Earth.

Liquid-Phase Electron Microscopy for Soft Matter Science and Biology

Innovations in liquid-phase electron microscopy (LP-EM) have made it possible to perform experiments at the optimized conditions needed to examine soft matter. The main obstacle is conducting experiments in such a way that electron beam radiation can be used to obtain answers for scientific questions without changing the structure and (bio)chemical processes in the sample due to the influence of the radiation. By overcoming these experimental difficulties at least partially, LP-EM has evolved into a new microscopy method with nanometer spatial resolution and sub-second temporal resolution for analysis of soft matter in materials science and biology. Both experimental design and applications of LP-EM for soft matter materials science and biological research are reviewed, and a perspective of possible future directions is given.

Advances in Cryo-Correlative Light and Electron Microscopy: Applications for Studying Molecular and Cellular Events

Cryo-correlative light and electron microscopy (Cryo-CLEM) is materializing as a widespread approach amalgamating the advantages of both fluorescence light microscopy (FLM) as well as three dimensional (3D) cryo-electron tomography (cryo-ET) to reveal the ultrastructure of significant target molecules with specific cellular functions. Cryo-CLEM allows imaging of cells by means of fluorescence microscopy exhibiting the location of the destined molecule at high temporal and spatial resolution while cryo-ET is employed to analyze the 3D structure at a molecular resolution in close-to-physiological condition. Present review focuses upon the practical strategies for Cryo-CLEM and recent technical developments that will assist the broad implementation of this technique to investigate and answer questions pertaining to various biological events occurring in the cell.

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.

Self-assembling peptides imaged by correlated liquid cell transmission electron microscopy and MALDI-imaging mass spectrometry

We describe the observation of stimuli-induced peptide-based nanoscale assemblies by liquid cell transmission electron microscopy (LCTEM). LCTEM offers the opportunity to directly image nanoscale materials in liquid. Despite broad interest in characterizing biological phenomena, electron beam-induced damage remains a significant problem. Concurrently, methods for verifying chemical structure during or following an LCTEM experiment have been few, with key examples limited to electron diffraction or elemental analysis of crystalline materials; this strategy is not translatable to biopolymers observed in nature. In this proof-of-concept study, oligomeric peptides are biologically or chemically stimulated within the liquid cell in a TEM to assemble into nanostructures. The resulting materials are analyzed by MALDI-imaging mass spectrometry (MALDI-IMS) to verify their identity. This approach confirms whether higher-order assemblies observed by LCTEM consist of intact peptides, verifying that observations made during the in situ experiment are because of those same peptides and not aberrant electron beam damage effects.

Genome-Based Metabolic Reconstruction of a Novel Uncultivated Freshwater Magnetotactic coccus "Ca. Magnetaquicoccus inordinatus" UR-1, and Proposal of a Candidate Family "Ca. Magnetaquicoccaceae"

Magnetotactic bacteria are widely represented microorganisms that have the ability to synthesize magnetosomes. The magnetotactic cocci of the order Magnetococcales are the most frequently identified, but their classification remains unclear due to the low number of cultivated representatives. This paper reports the analysis of an uncultivated magnetotactic coccus UR-1 collected from the Uda River (in eastern Siberia). Genome analyses of this bacterium and comparison to the available Magnetococcales genomes identified a novel species called "Ca. Magnetaquicoccus inordinatus," and a delineated candidate family "Ca. Magnetaquicoccaceae" within the order Magnetococcales is proposed. We used average amino acid identity values <55-56% and <64-65% as thresholds for the separation of families and genera, respectively, within the order Magnetococcales. Analyses of the genome sequence of UR-1 revealed a potential ability for a chemolithoautotrophic lifestyle, with the oxidation of a reduced sulfur compound and carbon assimilation by rTCA. A nearly complete magnetosome genome island, containing a set of mam and mms genes, was also identified. Further comparative analyses of the magnetosome genes showed vertical inheritance as well as horizontal gene transfer as the evolutionary drivers of magnetosome biomineralization genes in strains of the order Magnetococcales.

Imaging of soft materials using in situ liquid-cell transmission electron microscopy

This review summarizes the breakthroughs in the field of soft material characterization by in situ liquid-cell transmission electron microscopy (TEM). The focus of this review is mostly on soft biological species such as cells, bacteria, viruses, proteins and polymers. The comparison between the two main liquid-cell systems (silicon nitride membranes liquid cell and graphene liquid cell) is also discussed in terms of their spatial resolution and imaging/analytical capabilities. We have showcased how liquid-cell TEM can reveal the structural details of whole cells, enable the chemical probing of proteins, detect the structural conformation of viruses, and monitor the dynamics of polymerization. In addition, the challenges faced by decoupling electron beam effect on beam-sensitive soft materials are discussed. At the end, future perspectives of in situ liquid-cell TEM studies of soft materials are outlined.

Direct Observation of Early Stages of Growth of Multilayered DNA-Templated Au-Pd-Au Core-Shell Nanoparticles in Liquid Phase

We report here on direct observation of early stages of formation of multilayered bimetallic Au-Pd core-shell nanocubes and Au-Pd-Au core-shell nanostars in liquid phase using low-dose in situ scanning transmission electron microscopy (S/TEM) with the continuous flow fluid cell. The reduction of Pd and formation of Au-Pd core-shell is achieved through the flow of the reducing agent. Initial rapid growth of Pd on Au along <111> direction is followed by a slower rearrangement of Pd shell. We propose the mechanism for the DNA-directed shape transformation of Au-Pd core-shell nanocubes to adopt a nanostar-like morphology in the presence of T30 DNA and discuss the observed nanoparticle motion in the confined volume of the fluid cell. The growth of Au shell over Au-Pd nanocube is initiated at the vertices of the nanocubes, leading to the preferential growth of the {111} facets and resulting in formation of nanostar-like particles. While the core-shell nanostructures formed in a fluid cell in situ under the low-dose imaging conditions closely resemble those obtained in solution syntheses, the reaction kinetics in the fluid cell is affected by the radiolysis of liquid reagents induced by the electron beam, altering the rate-determining reaction steps. We discuss details of the growth processes and propose the reaction mechanism in liquid phase in situ.

New approach to electron microscopy imaging of gel nanocomposites in situ

Characterization of Au-nanocomposites is routinely done with scattering techniques where the structure and ordering of nanoparticles can be analyzed. Imaging of Poloxamer gel-based Au-nanocomposites is usually limited to cryo-TEM imaging of cryo-microtomed thin sections of the specimen. While this approach is applicable for imaging of the individual nanoparticles and gauging their size distribution, it requires altering the state of the specimen and is prone to artifacts associated with preparation protocols. Use of Scanning Transmission Electron Microscopy (S/TEM) with fluid cell in situ provides an opportunity to analysis of these complex materials in their hydrated state with nanometer resolution, yet dispensing dense gel-based samples onto electron-transparent substrates remains challenging. We show that Poloxamer gel-based Au nanocomposites exhibiting thermoreversible behavior can be imaged in a fully hydrated state using a commercially available fluid cell holder, and we describe a specimen preparation method for depositing femtoliter amounts of gel-based nanocomposites directly onto the 50 nm-thick SiN window membranes. Ultimately, fluid cell S/TEM in situ imaging approach offers a pathway to visualization of individual nanoparticles within a thick gel media while maintaining the hydrated state of the carrier polymeric matrix.

In situ graphene liquid cell-transmission electron microscopy study of insulin secretion in pancreatic islet cells

BACKGROUND

Islet cell transplantation is one of the key treatments for type 1 diabetes. Understanding the mechanisms of insulin fusion and exocytosis are of utmost importance for the improvement of the current islet cell transplantation and treatment of diabetes. These phenomena have not been fully evaluated due either to the lack of proper dynamic imaging, or the lack of proper cell preservation during imaging at nanoscales.

METHODS

By maintaining the native environment of pancreatic β-cells between two graphene monolayer sheets, we were able to monitor the subcellular events using in situ graphene liquid cell (GLC)-transmission electron microscopy (TEM) with both high temporal and high spatial resolution.

RESULTS

For the first time, the nucleation and growth of insulin particles until the later stages of fusion were imaged at nanometer scales. The release of insulin from plasma membrane involves the degradation of plasma membrane and drastic reductions in the shorter axis of the insulin particles. Sequential exocytosis results indicated the nucleation, growth and attachment of the new insulin particles to the already anchored ones, which is thermodynamically favorable due to the reduction in total surface, further reducing the Gibbs free energy. The retraction of the already anchored insulin toward the cell is also monitored for the first time live at nanoscale resolution.

CONCLUSION

Investigation of insulin granule dynamics in β-cells can be investigated via GLC-TEM. Our findings with this technology open new realms for the development of novel drugs on pathological pancreatic β-cells, because this approach facilitates observing the effects of the stimuli on the live cells and insulin granules.

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

Understanding the biomineralization pathways in living biological species is a grand challenge owing to the difficulties in monitoring the mineralization process at sub-nanometer scales. Here, we monitored the nucleation and growth of magnetosome nanoparticles in bacteria and in real time using a transmission electron microscope (TEM). To enable biomineralization within the bacteria, we subcultured magnetotactic bacteria grown in iron-depleted medium and then mixed them with iron-rich medium within graphene liquid cells (GLCs) right before imaging the bacteria under the microscope. Using in situ electron energy loss spectroscopy (EELS), the oxidation state of iron in the biomineralized magnetosome was analysed to be magnetite with trace amount of hematite. The increase of mass density of biomineralized magnetosomes as a function of incubation time indicated that the bacteria maintained their functionality during the in situ TEM imaging. Our results underpin that GLCs enables a new platform to observe biomineralization events in living biological species at unprecedented spatial resolution. Understanding the biomineralization processes in living organisms facilitates the design of biomimetic materials, and will enable a paradigm shift in understanding the evolution of biological species.

Direct mineralogical imaging of economic ore and rock samples with multi-modal nonlinear optical microscopy

Multi-modal nonlinear optical (NLO) microscopy, including stimulated Raman scattering (SRS) and second harmonic generation (SHG), was used to directly image mineralogical features of economic ore and rock samples. In SRS/SHG imaging, ore samples generally require minimal preparation and may be rapidly imaged, even in their wet state. 3D structural details, at submicron resolution, are revealed tens of microns deep within samples. Standard mineral imaging based on scanning electron microscopy (SEM), with elemental analysis via energy dispersive X-Ray spectroscopy, was used to independently validate the mineral composition of the samples. Spatially-resolved SRS from dominant Raman-resonant bands precisely maps the locations of specific minerals contained within the samples. SHG imaging reveals locally non-centrosymmetric structures, such as quartz grains. Competing absorption and nonlinear scattering processes, however, can reduce contrast in SRS imaging. Importantly, the correlation between standard electron microscopy and multi-modal NLO optical microscopy shows that the latter offers rapid image contrast based on the mineral content of the sample.

The 2018 correlative microscopy techniques roadmap

Developments in microscopy have been instrumental to progress in the life sciences, and many new techniques have been introduced and led to new discoveries throughout the last century. A wide and diverse range of methodologies is now available, including electron microscopy, atomic force microscopy, magnetic resonance imaging, small-angle x-ray scattering and multiple super-resolution fluorescence techniques, and each of these methods provides valuable read-outs to meet the demands set by the samples under study. Yet, the investigation of cell development requires a multi-parametric approach to address both the structure and spatio-temporal organization of organelles, and also the transduction of chemical signals and forces involved in cell-cell interactions. Although the microscopy technologies for observing each of these characteristics are well developed, none of them can offer read-out of all characteristics simultaneously, which limits the information content of a measurement. For example, while electron microscopy is able to disclose the structural layout of cells and the macromolecular arrangement of proteins, it cannot directly follow dynamics in living cells. The latter can be achieved with fluorescence microscopy which, however, requires labelling and lacks spatial resolution. A remedy is to combine and correlate different readouts from the same specimen, which opens new avenues to understand structure-function relations in biomedical research. At the same time, such correlative approaches pose new challenges concerning sample preparation, instrument stability, region of interest retrieval, and data analysis. Because the field of correlative microscopy is relatively young, the capabilities of the various approaches have yet to be fully explored, and uncertainties remain when considering the best choice of strategy and workflow for the correlative experiment. With this in mind, the Journal of Physics D: Applied Physics presents a special roadmap on the correlative microscopy techniques, giving a comprehensive overview from various leading scientists in this field, via a collection of multiple short viewpoints.

Considerations for imaging thick, low contrast, and beam sensitive samples with liquid cell transmission electron microscopy

Transmission electron microscopy of whole cells is hindered by the inherently large thickness and low atomic contrast intrinsic of cellular material. Liquid cell transmission electron microscopy allows samples to remain in their native hydrated state and may permit visualizing cellular dynamics in-situ. However, imaging biological cells with this approach remains challenging and identifying an optimal imaging regime using empirical data would help foster new advancements in the field. Recent questions about the role of the electron beam inducing morphological changes or damaging cellular structure and function necessitates further investigation of electron beam-cell interactions, but such comparisons are complicated by variability in imaging techniques used across various studies currently present in literature. The necessity for using low electron fluxes while imaging biological samples requires finding an imaging strategy which produces the strongest contrast and signal to noise ratio for the electron flux used. Here, we experimentally measure and evaluate signal to noise ratios and damage mechanisms between liquid and cryogenic samples of intact cells using multiple electron imaging modalities all on the same instrument and with equivalent beam parameters to standardize the comparison. We also discuss considerations for optimal electron microscopy imaging conditions for future studies on whole cells within liquid environments.

Off-axis electron holography of bacterial cells and magnetic nanoparticles in liquid

The mapping of electrostatic potentials and magnetic fields in liquids using electron holography has been considered to be unrealistic. Here, we show that hydrated cells of Magnetospirillum magneticum strain AMB-1 and assemblies of magnetic nanoparticles can be studied using off-axis electron holography in a fluid cell specimen holder within the transmission electron microscope. Considering that the holographic object and reference wave both pass through liquid, the recorded electron holograms show sufficient interference fringe contrast to permit reconstruction of the phase shift of the electron wave and mapping of the magnetic induction from bacterial magnetite nanocrystals. We assess the challenges of performing in situ magnetization reversal experiments using a fluid cell specimen holder, discuss approaches for improving spatial resolution and specimen stability, and outline future perspectives for studying scientific phenomena, ranging from interparticle interactions in liquids and electrical double layers at solid-liquid interfaces to biomineralization and the mapping of electrostatic potentials associated with protein aggregation and folding.

The role of electron irradiation history in liquid cell transmission electron microscopy

In situ liquid cell transmission electron microscopy (LC-TEM) allows dynamic nanoscale characterization of systems in a hydrated state. Although powerful, this technique remains impaired by issues of repeatability that limit experimental fidelity and hinder the identification and control of some variables underlying observed dynamics. We detail new LC-TEM devices that improve experimental reproducibility by expanding available imaging area and providing a platform for investigating electron flux history on the sample. Irradiation history is an important factor influencing LC-TEM results that has, to this point, been largely qualitatively and not quantitatively described. We use these devices to highlight the role of cumulative electron flux history on samples from both nanoparticle growth and biological imaging experiments and demonstrate capture of time zero, low-dose images on beam-sensitive samples. In particular, the ability to capture pristine images of biological samples, where the acquired image is the first time that the cell experiences significant electron flux, allowed us to determine that nanoparticle movement compared to the cell membrane was a function of cell damage and therefore an artifact rather than visualizing cell dynamics in action. These results highlight just a subset of the new science that is accessible with LC-TEM through the new multiwindow devices with patterned focusing aides.

Monitoring the dynamics of cell-derived extracellular vesicles at the nanoscale by liquid-cell transmission electron microscopy

Cell-derived extracellular vesicles (EVs) circulating in body fluids hold promises as bioactive therapeutic agents and as biomarkers to diagnose a wide range of diseases. However nano-imaging methods are needed to characterize these complex and heterogeneous soft materials in their native wet environment. Herein, we exploit liquid-cell transmission electron microscopy (LCTEM) to characterize the morphology and dynamic behavior of EVs in physiological media with nanometer resolution. The beam-induced controlled growth of Au nanoparticles on bilayer membranes is used as an original in situ staining method to improve the contrast of EVs and artificial liposomes. LCTEM provides information about the size distribution and concentration of EVs that are consistent with Cryo-TEM and nanoparticle tracking analysis measurements. Moreover, LCTEM gives a unique insight into the dynamics of EVs depending on their liquid environment. The size-dependent morphology of EVs is sensitive to osmotic stress which tends to transform their spherical shape to ellipsoidal, stomatocyte or discocyte morphologies. In the liquid-cell, EVs exhibit a sub-diffusive motion due to strong interactions between the Au nanoparticles and the liquid-cell windows. Finally, the high-resolution monitoring of EV aggregation and fusion illustrate that LCTEM opens up a new way to study cell-membrane dynamics.

Nanofluidic chip for liquid TEM cell fabricated by parylene and silicon nitride direct bonding

Despite the importance of nanofluidic transmission electron microscope (TEM) chips, a simple fabrication method has yet to be developed due to the difficulty of wafer bonding techniques using a nanoscale thick bonding layer. We present a simple and robust wafer scale bonding technique using parylene as a bonding layer. A nanoscale thick parylene layer was deposited on a silicon nitride (SiN) wafer and patterned to construct nanofluidic channels. The patterned parylene layer was directly bonded to another SiN wafer by thermal surface activation and bonding, with a bonding strength of ∼3 MPa. Fourier transform infrared spectroscopy showed that carbon-oxygen bonds were generated by thermal activation. We demonstrated TEM imaging of gold nanoparticles suspended in liquid using the fabricated nanofluidic chip.

Single-Cell Resolution of Uncultured Magnetotactic Bacteria via Fluorescence-Coupled Electron Microscopy

Magnetotactic bacteria (MTB) form intracellular chain-assembled nanocrystals of magnetite or greigite termed magnetosomes. The characterization of magnetosome crystals requires electron microscopy due to their nanoscopic sizes. However, electron microscopy does not provide phylogenetic information for MTB. We have developed a strategy for the simultaneous and rapid phylogenetic and biomineralogical characterization of uncultured MTB at the single-cell level. It consists of four steps: (i) enrichment of MTB cells from an environmental sample, (ii) 16S rRNA gene sequencing of MTB, and (iii) fluorescence in situ hybridization analyses coordinated with (iv) transmission or scanning electron microscopy of the probe-hybridized cells. The application of this strategy identified a magnetotactic Gammaproteobacteria strain, SHHR-1, from brackish sediments collected from the Shihe River estuary in Qinhuangdao City, China. SHHR-1 magnetosomes are elongated prismatic magnetites which can be idealized as hexagonal prisms. Taxonomic groups of uncultured MTB were also identified in freshwater sediments from Lake Miyun in northern Beijing via this novel coordinated fluorescence and scanning electron microscopy method based on four group-specific rRNA-targeted probes. Our analyses revealed that major magnetotactic taxonomic groups can be accurately determined only with coordinated scanning electron microscopy observations on fluorescently labeled single cells due to limited group coverage and specificity for existing group-specific MTB fluorescence in situ hybridization (FISH) probes. Our reported strategy is simple and efficient, offers great promise toward investigating the diversity and biomineralization of MTB, and may also be applied to other functional groups of microorganisms.

IMPORTANCE Magnetotactic bacteria (MTB) are phylogenetically diverse and biomineralize morphologically diverse magnetic nanocrystals of magnetite or greigite in intracellular structures termed magnetosomes. However, many uncultured MTB strains have not been phylogenetically identified or structurally investigated at the single-cell level, which limits our comprehensive understanding of the diversity of MTB and their role in biomineralization. We developed a fluorescence-coupled electron microscopy method for the rapid phylogenetic and biomineralogical characterization of uncultured MTB at the single-cell level. Using this novel method, we successfully identified taxonomic groups of several uncultured MTB and one novel magnetotactic Gammaproteobacteria strain, SHHR-1, from natural environments. Our analyses further indicate that strain SHHR-1 forms elongated prismatic magnetites. Our findings provide a promising strategy for the rapid characterization of phylogenetic and biomineralogical properties of uncultured MTB at the single-cell level. Furthermore, due to its simplicity and generalized methodology, this strategy can also be useful in the study of the diversity and biomineralization properties of microbial taxa involved in other mineralization processes.

CLAFEM: Correlative light atomic force electron microscopy

Atomic force microscopy (AFM) is becoming increasingly used in the biology field. It can give highly accurate topography and biomechanical quantitative data, such as adhesion, elasticity, and viscosity, on living samples. Nowadays, correlative light electron microscopy is a must-have tool in the biology field that combines different microscopy techniques to spatially and temporally analyze the structure and function of a single sample. Here, we describe the combination of AFM with superresolution light microscopy and electron microscopy. We named this technique correlative light atomic force electron microscopy (CLAFEM) in which AFM can be used on fixed and living cells in association with superresolution light microscopy and further processed for transmission or scanning electron microscopy. We herein illustrate this approach to observe cellular bacterial infection and cytoskeleton. We show that CLAFEM brings complementary information at the cellular level, from on the one hand protein distribution and topography at the nanometer scale and on the other hand elasticity at the piconewton scales to fine ultrastructural details.

High-resolution imaging of living mammalian cells bound by nanobeads-connected antibodies in a medium using scanning electron-assisted dielectric microscopy

Nanometre-scale-resolution imaging technologies for liquid-phase specimens are indispensable tools in various scientific fields. In biology, observing untreated living cells in a medium is essential for analysing cellular functions. However, nanoparticles that bind living cells in a medium are hard to detect directly using traditional optical or electron microscopy. Therefore, we previously developed a novel scanning electron-assisted dielectric microscope (SE-ADM) capable of nanoscale observations. This method enables observation of intact cells in aqueous conditions. Here, we use this SE-ADM system to clearly observe antibody-binding nanobeads in liquid-phase. We also report the successful direct detection of streptavidin-conjugated nanobeads binding to untreated cells in a medium via a biotin-conjugated anti-CD44 antibody. Our system is capable of obtaining clear images of cellular organelles and beads on the cells at the same time. The direct observation of living cells with nanoparticles in a medium allowed by our system may contribute the development of carriers for drug delivery systems (DDS).

The Use of Graphene and Its Derivatives for Liquid-Phase Transmission Electron Microscopy of Radiation-Sensitive Specimens

One of the key challenges facing liquid-phase transmission electron microscopy (TEM) of biological specimens has been the damaging effects of electron beam irradiation. The strongly ionizing electron beam is known to induce radiolysis of surrounding water molecules, leading to the formation of reactive radical species. In this study, we employ DNA-assembled Au nanoparticle superlattices (DNA-AuNP superlattices) as a model system to demonstrate that graphene and its derivatives can be used to mitigate electron beam-induced damage. We can image DNA-AuNP superlattices in their native saline environment when the liquid cell window material is graphene, but not when it is silicon nitride. In the latter case, initial dissociation of assembled AuNPs was followed by their random aggregation and etching. Using graphene-coated silicon nitride windows, we were able to replicate the observation of stable DNA-AuNP superlattices achieved with graphene liquid cells. We then carried out a correlative Raman spectroscopy and TEM study to compare the effect of electron beam irradiation on graphene with and without the presence of water and found that graphene reacts with the products of water radiolysis. We attribute the protective effect of graphene to its ability to efficiently scavenge reactive radical species, especially the hydroxyl radicals which are known to cause DNA strand breaks. We confirmed this by showing that stable DNA-AuNP assemblies can be imaged in silicon nitride liquid cells when graphene oxide and graphene quantum dots, which have also recently been reported as efficient radical scavengers, are added directly to the solution. We anticipate that our study will open up more opportunities for studying biological specimens using liquid-phase TEM with the use of graphene and its derivatives as biocompatible radical scavengers to alleviate the effects of radiation damage.

Live Cell Electron Microscopy Is Probably Impossible

Electron microscopy of biological cells in liquid provides unique nanoscale information. A highly attractive idea is the capability to also study physiological processes of live cells with electron microscopy. However, this idea seems unrealistic because the minimal needed electron dose to obtain contrast is already many orders of magnitude above the lethal dose known to cause reproductive-cell death. We show here that claims of electron microscopy of viable cells in recent reports are based on a questionable interpretation of the used fluorescence live/dead assay. A practical alternative to study biological processes is correlative light and electron microscopy.

Bioinspired synthesis of magnetite nanoparticles

Magnetite (Fe3O4) is a widespread magnetic iron oxide encountered in many biological and geological systems, and also in many technological applications. The magnetic properties of magnetite crystals depend strongly on the size and shape of its crystals. Hence, engineering magnetite nanoparticles with specific shapes and sizes allows tuning their properties to specific applications in a wide variety of fields, including catalysis, magnetic storage, targeted drug delivery, cancer diagnostics and magnetic resonance imaging (MRI). However, synthesis of magnetite with a specific size, shape and a narrow crystal size distribution is notoriously difficult without using high temperatures and non-aqueous media. Nevertheless, living organisms such as chitons and magnetotactic bacteria are able to form magnetite crystals with well controlled sizes and shapes under ambient conditions and in aqueous media. In these biomineralization processes the organisms use a twofold strategy to control magnetite formation: the mineral is formed from a poorly crystalline precursor phase, and nucleation and growth are controlled through the interaction of the mineral with biomolecular templates and additives. Taking inspiration from this biological strategy is a promising route to achieve control over the kinetics of magnetite crystallization under ambient conditions and in aqueous media. In this review we first summarize the main characteristics of magnetite and what is known about the mechanisms of magnetite biomineralization. We then describe the most common routes to synthesize magnetite and subsequently will introduce recent efforts in bioinspired magnetite synthesis. We describe how the use of poorly ordered, more soluble precursors such as ferrihydrite (FeH) or white rust (Fe(OH)2) can be employed to control the solution supersaturation, setting the conditions for continued growth. Further, we show how the use of various organic additives such as proteins, peptides and polymers allows for either the promotion or inhibition of magnetite nucleation and growth processes. At last we discuss how the formation of magnetite-based organic-inorganic hybrids leads to new functional nanomaterials.

Opportunities and challenges in liquid cell electron microscopy

Transmission electron microscopy offers structural and compositional information with atomic resolution, but its use is restricted to thin, solid samples. Liquid samples, particularly those involving water, have been challenging because of the need to form a thin liquid layer that is stable within the microscope vacuum. Liquid cell electron microscopy is a developing technique that allows us to apply the powerful capabilities of the electron microscope to imaging and analysis of liquid specimens. We describe its impact in materials science and biology. We discuss how its applications have expanded via improvements in equipment and experimental techniques, enabling new capabilities and stimuli for samples in liquids, and offering the potential to solve grand challenge problems.