Characterization of curli A production on living bacterial surfaces by scanning probe microscopy

Genetically engineered bacterial biofilm materials enhances portable whole cell sensing

In recent years, whole-cell biosensors (WCBs) have emerged as a potent approach for environmental monitoring and on-site analyte detection. These biosensors harness the biological apparatus of microorganisms to identify specific analytes, offering advantages in sensitivity, specificity, and real-time monitoring capabilities. A critical hurdle in biosensor development lies in ensuring the robust attachment of cells to surfaces, a crucial step for practical utility. In this study, we present a comprehensive approach to tackle this challenge via engineering Escherichia coli cells for immobilization on paper through the Curli biofilm pathway. Furthermore, incorporating a cellulose-binding peptide domain to the CsgA biofilm protein enhances cell adhesion to paper surfaces, consequently boosting biosensor efficacy. To demonstrate the versatility of this platform, we developed a WCB for copper, optimized to exhibit a discernible response, even with the naked eye. To confirm its suitability for practical field use, we characterized our copper sensor under various environmental conditions-temperature, salinity, and pH-to mimic real-world scenarios. The biosensor-equipped paper discs can be freeze-dried for deployment in on-site applications, providing a practical method for long-term storage without loss of sensitivity paper discs demonstrate sustained functionality and viability even after months of storage with 5 μM limit of detection for copper with visible-to-naked-eye signal levels. Biofilm-mediated surface attachment and analyte sensing can be independently engineered, allowing for flexible utilization of this platform as required. With the implementation of copper sensing as a proof-of-concept study, we underscore the potential of WCBs as a promising avenue for the on-site detection of a multitude of analytes.

Assessment of Efficacy of a Novel Crosslinking Protocol with Intracameral Oxygen (Bubble-CXL) in Increasing the Corneal Stiffness Using Atomic Force Microscopy

The environmental oxygen level plays a critical role in corneal crosslinking (CXL), a treatment method to increase corneal biomechanical stability. In this study, we introduce a new CXL method (Bubble-CXL), in which intracameral oxygen serves as an additional oxygen source during eye treatment. The efficiency of this new method was compared with the efficiency of the standard CXL method. Three fresh porcine eye pairs were included in this study. One eye of each pair was treated with standard CXL, whereas in the partner eye, intracameral oxygen was injected prior to CXL and removed at the end of the procedure. The Young's modulus of each cornea was measured using atomic force microscopy. All analyzed corneas treated with intracameral oxygen showed significantly higher Young's modulus and thus an increased stiffness compared to the cornea of the partner eye treated with the standard protocol. Using intracameral oxygen in CXL therapy may increase crosslinking efficiency and improve biomechanical corneal properties.

Use of Atomic Force Microscopy to Characterize LPS Perturbations

Lipopolysaccharide (LPS) on Gram-negative bacterial outer membranes is the first target for antimicrobial agents, due to their spatial proximity to outer environments of microorganisms. To understand the molecular nature and their interaction with antimicrobial agents, establishing a model LPS structure is of key importance. Here, we describe procedures for following LPS layer attachment to a solid surface and provide protocols for measuring bacterial membrane morphology after adding antibiotics. Using atomic force microscopy (AFM), we show methods to characterize the effects of antibiotic polymyxin B to the LPS layers at the nanoscale.

Nanomechanical mechanisms of Lyme disease spirochete motility enhancement in extracellular matrix

As opposed to pathogens passively circulating in the body fluids of their host, pathogenic species within the Spirochetes phylum are able to actively coordinate their movement in the host to cause systemic infections. Based on the unique morphology and high motility of spirochetes, we hypothesized that their surface adhesive molecules might be suitably adapted to aid in their dissemination strategies. Designing a system that mimics natural environmental signals, which many spirochetes face during their infectious cycle, we observed that a subset of their surface proteins, particularly Decorin binding protein (Dbp) A/B, can strongly enhance the motility of spirochetes in the extracellular matrix of the host. Using single-molecule force spectroscopy, we disentangled the mechanistic details of DbpA/B and decorin/laminin interactions. Our results show that spirochetes are able to leverage a wide variety of adhesion strategies through force-tuning transient molecular binding to extracellular matrix components, which concertedly enhance spirochetal dissemination through the host.

Development of a New Bead Movement-Based Computational Framework Shows that Bacterial Amyloid Curli Reduces Bead Mobility in Biofilms

Biofilms exist in complex environments, including the intestinal tract, as a part of the gastrointestinal microbiota. The interaction of planktonic bacteria with biofilms can be influenced by material properties of the biofilm. During previous confocal studies, we observed that amyloid curli-containing Salmonella enterica serotype Typhimurium and Escherichia coli biofilms appeared rigid. In these studies, Enterococcus faecalis, which lacks curli-like protein, showed more fluid movement. To better characterize the material properties of the biofilms, a four-dimensional (4D) model was designed to track the movement of 1-μm glyoxylate beads in 10- to 20-μm-thick biofilms over approximately 20 min using laser-scanning confocal microscopy. Software was developed to analyze the bead trajectories, the amount of time they could be followed (trajectory life span), the velocity of movement, the surface area covered (bounding boxes), and cellular density around each bead. Bead movement was found to be predominantly Brownian motion. Curli-containing biofilms had very little bead movement throughout the low- and high-density regions of the biofilm compared to E. faecalis and isogenic curli mutants. Curli-containing biofilms tended to have more stable bead interactions (longer trajectory life spans) than biofilms lacking curli. In biofilms lacking curli, neither the velocity of bead movement nor the bounding box volume was strictly dependent on cell density, suggesting that other material properties of the biofilms were influencing the movement of the beads and flexibility of the material. Taken together, these studies present a 4D method to analyze bead movement over time in a 3D biofilm and suggest curli confers rigidity to the extracellular matrix of biofilms.IMPORTANCE Mathematical models are necessary to understand how the material composition of biofilms can influence their physical properties. Here, we developed a 4D computational toolchain for the analysis of bead trajectories, which laid the groundwork for establishing critical parameters for mathematical models of particle movement in biofilms. Using this open-source trajectory analyzer, we determined that the presence of bacterial amyloid curli changes the material properties of a biofilm, making the biofilm matrix rigid. This software is a powerful tool to analyze treatment- and environment-induced changes in biofilm structure and cell movement in biofilms. The open-source analyzer is fully adaptable and extendable in a modular fashion using VRL-Studio to further enhance and extend its functions.

Microscopic Investigation of the Combined Use of Antibiotics and Biosurfactants on Methicillin Resistant Staphylococcus aureus

One current strategy to deal with the serious issue of antibiotic resistance is to use biosurfactants, weak antimicrobials in their own right, with antibiotics in order to extend the efficacy of antibiotics. Although an adjuvant effect has been observed, the underlying mechanisms are poorly understood. To investigate the nature of the antibiotic and biosurfactant interaction, we undertook a scanning electron microscopy (SEM) and atomic force microscopy (AFM) microscopic study of the effects of the tetracycline antibiotic, combined with sophorolipid and rhamnolipid biosurfactants, on Methicillin-resistant Staphylococcus aureus using tetracycline concentrations below and above the minimum inhibitory concentration (MIC). Control and treated bacterial samples were prepared with an immersion technique by adsorbing the bacteria onto glass substrates grafted with the poly-cationic polymer polyethyleneimine. Bacterial surface morphology, hydrophobic and hydrophilic surface characters as well as the local bacterial cell stiffness were measured following combined antibiotic and biosurfactant treatment. The sophorolipid biosurfactant stands alone insofar as, when used with the antibiotic at sub-MIC concentration, it resulted in bacterial morphological changes, larger diameters (from 758 ± 75 to 1276 ± 220 nm, p-value = 10^-4) as well as increased bacterial core stiffness (from 205 ± 46 to 396 ± 66 mN/m, p-value = 5 × 10^-5). This investigation demonstrates that such combination of microscopic analysis can give useful information which could complement biological assays to understand the mechanisms of synergy between antibiotics and bioactive molecules such as biosurfactants.

Atomic Force Microscopy Investigation of the Contributions of Listeria monocytogenes Cell-Wall Biomacromolecules to Their Adherence and Mechanics

In this work, the contributions of the pathogenic Listeria monocytogenes cell-wall biomacromolecules to the bacterial mechanics and adhesion to a model inert surface of silicon nitride in water were investigated by atomic force microscopy. Chemical ethylenediaminetetraacetic acid (EDTA) and biological enzymatic trypsin treatments of cells were performed to partially or totally remove the bacterial cell-wall proteins and carbohydrates. Removal of 48.2% proteins and 29.2% of carbohydrates from the cell-wall of the bacterium by the EDTA treatment resulted in a significant decrease in the length of the bacterial cell-wall biomacromolecules and an increase in the rigidity of the bacterial cells as predicted from fitting a model of steric repulsion to the force-distance approach data and classic Hertz model to the indentation-force data, respectively. In comparison, removal of almost all the cell-wall proteins (99.5% removal) and 8.6% of cell-wall carbohydrates by the trypsin treatment resulted in an increase in the elasticity of the bacterial cells, an increase in the extension of the cell-wall biomacromolecules, and a significant decrease in their apparent grafting densities. In addition, adhesion strength of native-untreated L. monocytogenes to silicon nitride in water decreased by 30% on average after the EDTA treatment and further decreased by 60% on average after the trypsin treatment, showing a positive correlation with the% removal of cell-wall proteins by the EDTA and trypsin treatments, respectively.

Curli production enhances clay-E. coli aggregation and sedimentation

Curli are amyloid fibrils that polymerize extracellularly from curlin, a protein that is secreted by many enteric bacteria and is important for biofilm formation. Presented here is a systematic study of the effects of curli on bacteria-clay interactions. The aggregation trends of curli-producing and curli-deficient bacteria with clay minerals were followed using gradient-sedimentation experiments, Lumisizer measurements, bright-field and electron microscopy. The results revealed that curli-producing bacteria auto-aggregated into high-density flocs (1.23 g/cm³), ranging in size from 10 to 50 μm, that settle spontaneously. In contrast, curli-deficient bacteria remained relatively stable in solution as individual cells (1-2 μm, 1.18 g/cm³), even at high ionic strength (350 mM). The stability of clay suspensions mixed with curli-deficient bacteria depended on clay type and ionic strength, the general trends being consistent with the classic DLVO theory. However, suspensions of curli-producing bacteria mixed with clays were highly unstable regardless of clay type and solution chemistry, suggesting extensive interactions between the clays and the bacteria-curli aggregates. SEM measurements revealed interesting differences in morphologies of the aggregates; montmorillonite particles coated the bacterial auto-aggregates whereas the kaolinite platelets were embedded within the larger curli-bacteria aggregates. These new observations regarding the densities, aggregation trends, and morphologies of bacteria-curli and bacteria-curli-clay complexes make it clear that production of surface appendages, such as curli, need to be considered when addressing the fate, activity and transport of bacteria - particularly in aquatic environments.

Investigation of Bacterial Curli Production and Adhesion Using AFM

Escherichia coli cells containing the amyloid curli protein CsgA bind to abiotic surfaces and the extracellular matrix protein fibronectin. Here we describe procedures for following bacterial attachment to glass surfaces and provide protocols for coupling bacterial cells to AFM tips. Using single microbial cell force spectroscopy in physiological environment, we show methods to probe mechanical parameters and the dissociation of curliated E. coli cells from fibronectin surfaces by quantifying Young's modulus, unbinding forces, and de-adhesion works.

Sensing the Ultrastructure of Bacterial Surfaces and Their Molecular Binding Forces Using AFM

In this protocol, we provide a detailed step-by-step bacterial surface imaging and molecular analysis procedure. With SPM (scanning probe microscopy)-based dynamic force microscopy (DFM) imaging, we achieved a so far unprecedented resolution of ~1 nm on the outer surface layer of Tannerella forsythia and monitored the production of curli fibers on Escherichia coli in physiological conditions. Moreover, using these immobilization methods, single-molecule force spectroscopy experiments were conducted on living bacterial cells.

Adhesion mechanisms of curli subunit CsgA to abiotic surfaces

Curli fibers are functional amyloids that play a key role in biofilm structure and adhesion to various surfaces. Strong bioinspired adhesives comprising curli fibers have recently been created; however, the mechanisms curli uses to attach onto abiotic surfaces are still uncharacterized. Toward a materials-by-design approach for curli-based adhesives and multifunctional materials, we examine curli subunit adsorption onto graphene and silica surfaces through atomistic simulation. We find that both structural features and sequence influence adhesive strength, enabling the CsgA subunit to adhere strongly to both polar and nonpolar surfaces. Specifically, flexible regions facilitate adhesion to both surfaces, charged and polar residues (Arg, Lys, and Gln) enable strong interactions with silica, and six-carbon aromatic rings (Tyr and Phe) adsorb strongly to graphene. We find that adsorption not only lowers molecular mobility but also leads to loss of secondary structure, factors that must be well balanced for effective surface attachment. Both events appear to propagate through the CsgA structure as correlated motion between clusters of residues, often H-bonded between rows on adjacent β strands. To quantify this, we present a correlation analysis approach to detecting collective motion between residue groups. We find that certain clusters of residues have a higher impact on the stability of the rest of the protein structure, often polar and bulky groups within the helix core. These findings lend insight into bacterial adhesion mechanisms and reveal strategies for theory-driven design of engineered curli fibers that harness point mutations and conjugates for stronger adhesion.

Curli mediate bacterial adhesion to fibronectin via tensile multiple bonds

Many enteric bacteria including pathogenic Escherichia coli and Salmonella strains produce curli fibers that bind to host surfaces, leading to bacterial internalization into host cells. By using a nanomechanical force-sensing approach, we obtained real-time information about the distribution of molecular bonds involved in the adhesion of curliated bacteria to fibronectin. We found that curliated E. coli and fibronectin formed dense quantized and multiple specific bonds with high tensile strength, resulting in tight bacterial binding. Nanomechanical recognition measurements revealed that approximately 10 bonds were disrupted either sequentially or simultaneously under force load. Thus the curli formation of bacterial surfaces leads to multi-bond structural components of fibrous nature, which may explain the strong mechanical binding of curliated bacteria to host cells and unveil the functions of these proteins in bacterial internalization and invasion.

Influence of csgD and ompR on Nanomechanics, Adhesion Forces, and Curli Properties of E. coli

Curli are bacterial appendages involved in the adhesion of cells to surfaces; their synthesis is regulated by many genes such as csgD and ompR. The expression of the two curli subunits (CsgA and CsgB) in Escherichia coli (E. coli) is regulated by CsgD; at the same time, csgD transcription is under the control of OmpR. Therefore, both genes are involved in the control of curli production. In this work, we elucidated the role of these genes in the nanomechanical and adhesive properties of E. coli MG1655 (a laboratory strain not expressing significant amount of curli) and its curli-producing mutants overexpressing OmpR and CsgD, employing atomic force microscopy (AFM). Nanomechanical analysis revealed that the expression of these genes gave origin to cells with a lower Young's modulus (E) and turgidity (P0), whereas the adhesion forces were unaffected when genes involved in curli formation were expressed. AFM was also employed to study the primary structure of the curli expressed through the freely jointed chain (FJC) model for polymers. CsgD increased the number of curli on the surface more than OmpR did, and the overexpression of both genes did not result in a greater number of curli. Neither of the genes had an impact on the structure (total length of the polymer and number and length of Kuhn segments) of the curli. Our results further suggest that, despite the widely assumed role of curli in cell adhesion, cell adhesion force is also dictated by surface properties because no relation between the number of curli expressed on the surface and cell adhesion was found.

Nanoscale characteristics of antibacterial cationic polymeric brushes and single bacterium interactions probed by force microscopy

A direct probing technique was applied to PEI brushes to investigate bacteria–PEI brush interactions in a single bacterium resolution.

Nanoscale imaging of the growth and division of bacterial cells on planar substrates with the atomic force microscope

With the use of the atomic force microscope (AFM), the Nanomicrobiology field has advanced drastically. Due to the complexity of imaging living bacterial processes in their natural growing environments, improvements have come to a standstill. Here we show the in situ nanoscale imaging of the growth and division of single bacterial cells on planar substrates with the atomic force microscope. To achieve this, we minimized the lateral shear forces responsible for the detachment of weakly adsorbed bacteria on planar substrates with the use of the so called dynamic jumping mode with very soft cantilever probes. With this approach, gentle imaging conditions can be maintained for long periods of time, enabling the continuous imaging of the bacterial cell growth and division, even on planar substrates. Present results offer the possibility to observe living processes of untrapped bacteria weakly attached to planar substrates.

Applications of microscopy in Salmonella research

Salmonella enterica is a Gram-negative enteropathogen that can cause localized infections, typically resulting in gastroenteritis, or systemic infection, e.g., typhoid fever, in humans and many other animals. Understanding the mechanisms by which Salmonella induces disease has been the focus of intensive research. This has revealed that Salmonella invasion requires dynamic cross-talk between the microbe and host cells, in which bacterial adherence rapidly leads to a complex sequence of cellular responses initiated by proteins translocated into the host cell by a type 3 secretion system. Once these Salmonella-induced responses have resulted in bacterial invasion, proteins translocated by a second type 3 secretion system initiate further modulation of cellular activities to enable survival and replication of the invading pathogen. Elucidation of the complex and highly dynamic pathogen-host interactions ultimately requires analysis at the level of single cells and single infection events. To achieve this goal, researchers have applied a diverse range of microscopy techniques to analyze Salmonella infection in models ranging from whole animal to isolated cells and simple eukaryotic organisms. For example, electron microscopy and high-resolution light microscopy techniques such as confocal microscopy can reveal the precise location of Salmonella and its relationship to cellular components. Widefield light microscopy is a simpler approach with which to study the interaction of bacteria with host cells and often has advantages for live cell imaging, enabling detailed analysis of the dynamics of infection and cellular responses. Here we review the use of imaging techniques in Salmonella research and compare the capabilities of different classes of microscope to address specific types of research question. We also provide protocols and notes on some microscopy techniques used routinely in our own research.

Characterizing the S-layer structure and anti-S-layer antibody recognition on intact Tannerella forsythia cells by scanning probe microscopy and small angle X-ray scattering

Tannerella forsythia is among the most potent triggers of periodontal diseases, and approaches to understand underlying mechanisms are currently intensively pursued. A ~22-nm-thick, 2D crystalline surface (S-) layer that completely covers Tannerella forsythia cells is crucially involved in the bacterium-host cross-talk. The S-layer is composed of two intercalating glycoproteins (TfsA-GP, TfsB-GP) that are aligned into a periodic lattice. To characterize this unique S-layer structure at the nanometer scale directly on intact T. forsythia cells, three complementary methods, i.e., small-angle X-ray scattering (SAXS), atomic force microscopy (AFM), and single-molecular force spectroscopy (SMFS), were applied. SAXS served as a difference method using signals from wild-type and S-layer-deficient cells for data evaluation, revealing two possible models for the assembly of the glycoproteins. Direct high-resolution imaging of the outer surface of T. forsythia wild-type cells by AFM revealed a p4 structure with a lattice constant of ~9.0 nm. In contrast, on mutant cells, no periodic lattice could be visualized. Additionally, SMFS was used to probe specific interaction forces between an anti-TfsA antibody coupled to the AFM tip and the S-layer as present on T. forsythia wild-type and mutant cells, displaying TfsA-GP alone. Unbinding forces between the antibody and wild-type cells were greater than with mutant cells. This indicated that the TfsA-GP is not so strongly attached to the mutant cell surface when the co-assembling TfsB-GP is missing. Altogether, the data gained from SAXS, AFM, and SMFS confirm the current model of the S-layer architecture with two intercalating S-layer glycoproteins and TfsA-GP being mainly outwardly oriented.