Resolving Bio-Nano Interactions of E. coli Bacteria-Dragonfly Wing Interface with Helium Ion and 3D-Structured Illumination Microscopy to Understand Bacterial Death on Nanotopography

Effects of Surface Topography and Cellular Biomechanics on Nanopillar-Induced Bactericidal Activity

Bacteria are mechanically resistant biological structures that can sustain physical stress. Experimental data, however, have shown that high-aspect-ratio nanopillars deform bacterial cells upon contact. If the deformation is sufficiently large, it lyses the bacterial cell wall, ultimately leading to cell death. This has prompted a novel strategy, known as mechano-bactericide technology, to fabricate antibacterial surfaces. Although adhesion forces were originally proposed as the driving force for mechano-bactericidal action, it has been recently shown that external forces, such as capillary forces arising from an air-water interface at bacterial surfaces, produce sufficient loads to rapidly kill bacteria on nanopillars. This discovery highlights the need to theoretically examine how bacteria respond to external loads and to ascertain the key factors. In this study, we developed a finite element model approximating bacteria as elastic shells filled with cytoplasmic fluid brought into contact with an individual nanopillar or nanopillar array. This model elucidates that bacterial killing caused by external forces on nanopillars is influenced by surface topography and cell biomechanical variables, including the density and arrangement of nanopillars, in addition to the cell wall thickness and elastic modulus. Considering that surface topography is an important design parameter, we performed experiments using nanopillar arrays with precisely controlled nanopillar diameters and spacing. Consistent with model predictions, these demonstrate that nanopillars with a larger spacing increase bacterial susceptibility to mechanical puncture. The results provide salient insights into mechano-bactericidal activity and identify key design parameters for implementing this technology.

Reusable mechano-bactericidal surface with echinoid-shaped hierarchical micro/nano-structure

Biofilms formed owing to the attachment of bacteria to surfaces have caused various problems in industries such as marine transportation/logistics and medicine. In response, many studies have been conducted on bactericidal surfaces, and nanostructured surfaces mimicking cicada and dragonfly wings are emerging as candidates for mechano-bactericidal surfaces. In specific circumstances involving mechano-bactericidal activity, certain nanostructured surfaces could exhibit their bactericidal effects by directly deforming the membranes of bacteria that adhere to these nanostructures. Additionally, in most cases, debris of bacterial cells may accumulate on these nanostructured surfaces. Such accumulation poses a significant challenge: it diminishes the mechano-bactericidal effectiveness of the surface, as it hinders the direct interaction between the nanostructures and any new bacteria that attach subsequently. In specific circumstances involving mechano-bactericidal activity, certain nanostructured surfaces could exhibit their bactericidal effects by directly deforming the membranes of bacteria that adhere to these nanostructures. Additionally, in most cases, debris of bacterial cells may accumulate on these nanostructured surfaces. Such accumulation poses a significant challenge: it diminishes the mechano-bactericidal effectiveness of the surface, as it hinders the direct interaction between the nanostructures and any new bacteria that attach subsequently.In other words, there is a need for strategies to remove the accumulated bacterial debris in order to sustain the mechano-bactericidal effect of the nanostructured surface. In this study, hierarchical micro/nano-structured surface (echinoid-shaped nanotextures were formed on Al micro-particle's surfaces) was fabricated using a simple pressure-less sintering method, and effective bactericidal efficiency was shown against E. coli (97 ± 3.81%) and S. aureus (80 ± 9.34%). In addition, thermal cleaning at 500 °C effectively eliminated accumulated dead bacterial debris while maintaining the intact Al2O3 nanostructure, resulting in significant mechano-bactericidal activity (E. coli: 89 ± 6.86%, S. aureus: 75 ± 8.31%). As a result, thermal cleaning maintains the intact nanostructure and allows the continuance of the mechano-bactericidal effect. This effect was consistently maintained even after five repetitive use (E. coli: 80 ± 16.26%, S. aureus: 76 ± 12.67%).

Antimicrobial mechanisms of nanopatterned surfaces-a developing story

Whilst it is now well recognized that some natural surfaces such as seemingly fragile insect wings possess extraordinary antimicrobial properties, a quest to engineer similar nanopatterned surfaces (NPSs) is ongoing. The stake is high as biofouling impacts critical infrastructure leading to massive social and economic burden with an antimicrobial resistance (AMR) issue at the forefront. AMR is one of the most imminent health challenges the world is facing today. Here, in the effort to find more sustainable solutions, the NPSs are proposed as highly promising technology as their antimicrobial activity arises from the topographical features, which could be realized on multiple material surfaces. To fully exploit these potentials however, it is crucial to mechanistically understand the underlying killing pathways. Thus far, several mechanisms have been proposed, yet they all have one thing in common. The antimicrobial process is initiated with bacteria contacting nanopatterns, which then imposes mechanical stress onto bacterial cell wall. Hence, the activity is called "mechano-bactericidal". From this point on, however, the suggested mechanisms start to diverge partly due to our limited understanding of force interactions at the interface. The aim of this mini review is to analyze the state-of-the-art in proposed killing mechanisms by categorizing them based on the characteristics of their driving force. We also highlight the current gaps and possible future directions in investigating the mechanisms, particularly by shifting towards quantification of forces at play and more elaborated biochemical assays, which can aid validating the current hypotheses.

Helium Ion Microscopy and Sectioning of Spider Silk

Focused ion beams have recently emerged as a powerful tool for ultrastructural imaging of biological samples. In this article, we show that helium ion microscopy (HIM), in combination with ion milling, can be used to visualize the inner structure of both major and minor ampullate silk fibers of the orb-web weaving spider Nephila madagascariensis. The internal nanofibrils were imaged in pristine silk fibers, with little or no damage to the sample structure observed. Furthermore, a method to cut/rupture the fibers using He⁺ ions combined with internal sample tension is presented. This showed that the stretching and rupturing of spider silk is a highly dynamic process with considerable material reorganization.

Death at the interface: Nanotechnology’s challenging frontier against microbial surface colonization

The emergence of antimicrobial-resistant bacterial strains has led to novel approaches for combating bacterial infections and surface contamination. More specifically, efforts in combining nanotechnology and biomimetics have led to the development of next-generation antimicrobial/antifouling nanomaterials. While nature-inspired nanoscale topographies are known for minimizing bacterial attachment through surface energy and physicochemical features, few studies have investigated the combined inhibitory effects of such features in combination with chemical alterations of these surfaces. Studies describing surface alterations, such as quaternary ammonium compounds (QACs), have also gained attention due to their broad spectrum of inhibitory activity against bacterial cells. Similarly, antimicrobial peptides (AMPs) have exhibited their capacity to reduce bacterial viability. To maximize the functionality of modified surfaces, the integration of patterned surfaces and functionalized exteriors, achieved through physical and chemical surface alterations, have recently been explored as viable alternatives. Nonetheless, these modifications are prone to challenges that can reduce their efficacy considerably in the long term. Their effectiveness against a wider array of microbial cells is still a subject of investigation. This review article will explore and discuss the emerging trends in biomimetics and other antimicrobials while raising possible concerns about their limitations and discussing future implications regarding their potential combined applications.

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The past decade has seen the advent of a new imaging technique in the life sciences that is ideal for microbiological applications: the helium ion microscope (HIM). Its lateral resolution is better than one nanometre, it has a large depth-of-field and can image non-conductive specimens which renders the tool ideal for studying microbiological objects such as microbes attached to surfaces, microbial biofilms and viruses. Here we compare HIM with electron microscopy techniques and highlight selected examples that demonstrate the new possibilities for microbiology opened up by this technique.

Effect of Flexibility and Size of Nanofabricated Topographies on the Mechanobactericidal Efficacy of Polymeric Surfaces

Driven by the growing threat of antimicrobial resistance, the design of intrinsically bactericidal surfaces has been gaining significant attention. Proposed surface topography designs are often inspired by naturally occurring nanopatterns on insect wings that mechanically damage bacteria via membrane deformation. The stability of and the absence of chemicals in such surfaces support their facile and sustainable employment in avoiding surface-born pathogen transmission. Recently, the deflection of controllably nanofabricated pillar arrays has been shown to strongly affect bactericidal activity, with the limits of mechanical effectiveness of such structures remaining largely unexplored. Here, we examine the limits of softer, commonly used polymeric materials and investigate the interplay between pillar nanostructure sizing and flexibility for effective antibacterial functionality. A facile, scalable, UV nanoimprint lithography method was used to fabricate nanopillar array topographies of variable sizes and flexibilities. It was found that bacterial death on nanopillars in the range of diameters ≤100 nm and Young's moduli ≥1.3 GPa is increased by 3.5- to 5.6-fold, while thicker or softer pillars did not reduce bacterial viability. To further support our findings, we performed a finite element analysis of pillar deformation. It revealed that differences in the amount of stress exerted on bacterial membranes, generated from the stored elastic energy in flexible pillars, contribute to the observed bactericidal performance.

Bactericidal effect of nanostructures via lytic transglycosylases of Escherichia coli

Nanostructures exhibit a bactericidal effect owing to physical interaction with the bacterial cell envelope. Here, we aimed to identify the mechanism underlying the bactericidal effect of nanostructures based on bacterial autolysis, in contrast to previous reports focusing on structural characteristics. The time profiles of active cell ratios of the Escherichia coli strains (WT, ΔmltA, ΔmltB, Δslt70), incubation time of the wild-type (WT) strains, and autolysis inhibition of WT strains were evaluated with respect to the bactericidal effect of the applied nanostructures. Addition of Mg2+, an autolysis inhibitor, was not found to cause significant cell damage. The incubation phase was significantly associated with envelope damage. The lytic transglycosylase-lacking strain of Slt70 (Δslt70) also showed only minimal envelope damage. Our results indicate that nanostructures may act by triggering bacterial autolysis.

Resolving physical interactions between bacteria and nanotopographies with focused ion beam scanning electron microscopy

To robustly assess the antibacterial mechanisms of nanotopographies, it is critical to analyze the bacteria-nanotopography adhesion interface. Here, we utilize focused ion beam milling combined with scanning electron microscopy to generate three-dimensional reconstructions of Staphylococcus aureus or Escherichia coli interacting with nanotopographies. For the first time, 3D morphometric analysis has been exploited to quantify the intrinsic contact area between each nanostructure and the bacterial envelope, providing an objective framework from which to derive the possible antibacterial mechanisms of synthetic nanotopographies. Surfaces with nanostructure densities between 36 and 58 per μm² and tip diameters between 27 and 50 nm mediated envelope deformation and penetration, while surfaces with higher nanostructure densities (137 per μm²) induced envelope penetration and mechanical rupture, leading to marked reductions in cell volume due to cytosolic leakage. On nanotopographies with densities of 8 per μm² and tip diameters greater than 100 nm, bacteria predominantly adhered between nanostructures, resulting in cell impedance.

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Bacteria-nanotopography interactions can be quantified using FIB-SEM

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Envelope penetration and cell impedance are influenced by nanotopography density

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Low density nanotopographies (8 per μm²) mediate cell impedance

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High-density nanotopographies (36–137 per μm²) mediate deformation and penetration

Future antiviral polymers by plasma processing

Coronavirus disease 2019 (COVID-19) is largely threatening global public health, social stability, and economy. Efforts of the scientific community are turning to this global crisis and should present future preventative measures. With recent trends in polymer science that use plasma to activate and enhance the functionalities of polymer surfaces by surface etching, surface grafting, coating and activation combined with recent advances in understanding polymer-virus interactions at the nanoscale, it is promising to employ advanced plasma processing for smart antiviral applications. This trend article highlights the innovative and emerging directions and approaches in plasma-based surface engineering to create antiviral polymers. After introducing the unique features of plasma processing of polymers, novel plasma strategies that can be applied to engineer polymers with antiviral properties are presented and critically evaluated. The challenges and future perspectives of exploiting the unique plasma-specific effects to engineer smart polymers with virus-capture, virus-detection, virus-repelling, and/or virus-inactivation functionalities for biomedical applications are analysed and discussed.

Assessing the impact of silicon nanowires on bacterial transformation and viability of Escherichia coli

We investigated the biomaterial interface between the bacteria Escherichia coli DH5α and silicon nanowire patterned surfaces. We optimised the engineering of silicon nanowire coated surfaces using metal-assisted chemical etching. Using a combination of focussed ion beam scanning electron microscopy, and cell viability and transformation assays, we found that with increasing interfacing force, cell viability decreases, as a result of increasing cell rupture. However, despite this aggressive interfacing regime, a proportion of the bacterial cell population remains viable. We found that the silicon nanowires neither resulted in complete loss of cell viability nor partial membrane disruption and corresponding DNA plasmid transformation. Critically, assay choice was observed to be important, as a reduction-based metabolic reagent was found to yield false-positive results on the silicon nanowire substrate. We discuss the implications of these results for the future design and assessment of bacteria-nanostructure interfacing experiments.

Low-Temperature Hydrothermal Synthesis of Novel 3D Hybrid Nanostructures on Titanium Surface with Mechano-bactericidal Performance

Titanium is extensively employed in modern medicines as orthopedic and dental implants, but implant failures frequently occur because of bacterial infections. Herein, three types of 3D nanostructured titanium surfaces with nanowire clusters (NWC), nanowire/sheet clusters (NW/SC) and nanosheet clusters (NSC), were fabricated using the low-temperature hydrothermal synthesis under normal pressure, and assessed for the sterilization against two common human pathogens. The results show that the NWC and NSC surfaces merely display good bactericidal activity against Escherichia coli, whereas the NW/SC surface represents optimal bactericidal efficiency against both Escherichia coli (98.6 ± 1.23%) and Staphylococcus aureus (69.82 ± 2.79%). That is attributed to the hybrid geometric nanostructure of NW/SC, i.e., the pyramidal structures of ∼23 nm in tip diameter formed with tall clustered wires, and the sharper sheets of ∼8 nm in thickness in-between these nanopyramids. This nanostructure displays a unique mechano-bactericidal performance via the synergistic effect of capturing the bacteria cells and penetrating the cell membrane. This study proves that the low-temperature hydrothermal synthesized hybrid mechano-bactericidal titanium surfaces provide a promising solution for the construction of bactericidal biomedical implants.

Biomimetic Polymer Surfaces by High Resolution Molding of the Wings of Different Cicadas

Recent studies have shown that insect wings have evolved to have micro- and nanoscale structures on the wing surface, and biomimetic research aims to transfer such structures to application-specific materials. Herein, we describe a simple and cost-effective method of replica molding the wing topographies of four cicada species using UV-curable polymers. Different polymer blends of polyethylene glycol diacrylate and polypropylene glycol diacrylate were used as molding materials and a molding chamber was designed to precisely control the x, y, and z dimensions. Analysis by scanning electron microscopy showed that structures ranged from 148 to 854 nm in diameter, with a height range of 191–2368 nm, and wing patterns were transferred with high fidelity to the crosslinked polymer. Finally, bacterial cell studies show that the wing replicas possess the same antibacterial effect as the cicada wing from which they were molded. Overall, this work shows a quick and simple method for patterning UV-curable polymers without the use of expensive equipment, making it a highly accessible means of producing microstructured materials with biological properties.

Surface structures consisting of chromatin fibers in isolated barley (Hordeum vulgare) chromosomes revealed by helium ion microscopy

The chromosome compaction of chromatin fibers results in the formation of the nucleosome, which consists of a DNA unit coiled around a core of histone molecules associated with linker histone. The compaction of chromatin fibers has been a topic of controversy since the discovery of chromosomes in the 19th century. Although chromatin fibers were first identified using electron microscopy, the chromatin fibers on the surface of chromosome structures in plants remain unclear due to shrinking and breaking caused by prior chromosome isolation or preparation with alcohol and acid fixation, and critical point drying occurred into dehydration and denatured chromosomal proteins. This study aimed to develop a high-quality procedure for the isolation and preparation of plant chromosomes, maintaining the native chromosome structure, to elucidate the organization of chromatin fibers on the surface of plant chromosomes by electron microscopy. A simple technique to isolate intact barley (Hordeum vulgare) chromosomes with a high yield was developed, allowing chromosomes to be observed with a high-resolution scanning ion microscopy and helium ion microscopy (HIM) imaging technology, based on a scanning helium ion beam. HIM images from the surface chromatin fibers were analyzed to determine the size and alignment of the chromatin fibers. The unit size of the chromatin fibers was 11.6 ± 3.5 nm and was closely aligned to the chromatin network model. Our findings indicate that compacting the surface structure of barley via a chromatin network and observation via HIM are powerful tools for investigating the structure of chromatin.

Theoretical and computational investigations into mechanobactericidal activity of nanostructures at the bacteria-biomaterial interface: a critical review

Mechanobactericidal surfaces kill bacteria upon contact by posing landscapes hostile to them and have rapidly gained popularity amongst researchers over the past decade. But several fundamental aspects of the physical interactions between bacteria and nanostructures and the underlying killing mechanisms are still poorly understood. This is partly attributable to the difficulties associated with the characterization of the bacteria-nanostructure interface in a biological environment during the killing process and to the stochastic and non-linear behaviors generally associated with biological systems. However, several analytical and computational models have presented and analyzed possible killing routes and have proven useful in understanding different aspects of the phenomena. Analytical models formulate equations, often based on energy considerations, and aim to predict optimal nanostructure dimensions. They are more widely used than computational models that try to simulate the killing process and the stress or strain fields in the cell membrane through numerical methods. These models provide insights into the forces responsible for the spontaneous penetration of the cell into the nanostructures, which are still highly debated in the field. They have also helped to correlate the nanostructure dimensions with their bactericidal activity to optimize such values and facilitate the translation of this technology to physiological conditions. This review focuses on the rupture of the bacterial cell wall by nanopillars or similar high aspect ratio structures and applying these principles to the deformation of the cell membrane. Many recent interesting experimental results that either refute our current understanding or have the potential to challenge the current consensus are also discussed. Lastly, the limitations of the current strategies and opportunities to address the unresolved gaps in the field are also presented.

Bio-imaging with the helium-ion microscope: A review

Scanning helium-ion microscopy (HIM) is an imaging technique with sub-nanometre resolution and is a powerful tool to resolve some of the tiniest structures in biology. In many aspects, the HIM resembles a field-emission scanning electron microscope (FE-SEM), but the use of helium ions rather than electrons provides several advantages, including higher surface sensitivity, larger depth of field, and a straightforward charge-compensating electron flood gun, which enables imaging of non-conductive samples, rendering HIM a promising high-resolution imaging technique for biological samples. Starting with studies focused on medical research, the last decade has seen some particularly spectacular high-resolution images in studies focused on plants, microbiology, virology, and geomicrobiology. However, HIM is not just an imaging technique. The ability to use the instrument for milling biological objects as small as viruses offers unique opportunities which are not possible with more conventional focused ion beams, such as gallium. Several pioneering technical developments, such as methods to couple secondary ion mass spectrometry (SIMS) or ionoluminescence with the HIM, also offer the possibility for new and exciting research on biological materials. In this review, we present a comprehensive overview of almost all currently published literature which has demonstrated the application of HIM for imaging of biological specimens. We also discuss some technical features of this unique type of instrument and highlight some of the new advances which will likely become more widely used in the years to come.