A modular atomic force microscopy approach reveals a large range of hydrophobic adhesion forces among bacterial members of the leaf microbiota

Nanovibrational Stimulation of Escherichia coli Mitigates Surface Adhesion by Altering Cell Membrane Potential

Mechanical forces shape living matter from the macro- to the microscale as both eukaryotic and prokaryotic cells are force wielders and sensors. However, whereas such forces have been used to control mechanically dependent behaviors in mammalian cells, we lack the same level of understanding in bacteria. Surface adhesion, the initial stages of biofilm formation and surface biofouling, is a mechanically dependent process, which makes it an ideal target for mechano-control. In this study, we employed nanometer surface vibrations to mechanically stimulate bacteria and investigate their effect on adhesion. We discovered that vibrational stimulation at the nanoscale consistently reduces surface adhesion by altering cell membrane potential. Our findings identify a link between bacteria electrophysiology and surface adhesion and provide evidence that the nanometric mechanical "tickling" of bacteria can inhibit surface adhesion.

A rapid and specific antimicrobial resistance detection of Escherichia coli via magnetic nanoclusters

Drinking water contamination, often caused by bacteria, leads to substantial numbers of diarrhea deaths each year, especially in developing regions. Human urine as a source of fertilizer, when handled improperly, can contaminate drinking water. One dominant bacterial pathogen in urine is Escherichia coli, which can trigger serious waterborne/foodborne diseases. Considering the prevalence of the multi-drug resistant extended-spectrum beta-lactamase (ESBL) producing E. coli, a rapid detection method for resistance is highly desired. In this work, we developed a method for quick identification of E. coli and, at the same time, capable of removal of general bacterial pathogens from human urine. A specific peptide GRHIFWRRGGGHKVAPR, reported to have a strong affinity to E. coli, was utilized to modify the PEGylated magnetic nanoclusters, resulting in a specific capture and enrichment of E. coli from the bacteria-spiked artificial urine. Subsequently, a novel luminescent probe was applied to rapidly identify the antimicrobial resistance of the collected E. coli within 30 min. These functionalized magnetic nanoclusters demonstrate a promising prospect to rapidly detect ESBL E. coli in urine and contribute to reducing drinking water contamination.

Nanomechanical changes in probiotic bacteria under antibiotics exposure: Implications on Lactobacillus biofilm formation

Recognition of the microbial cell's surface constituents' biophysical properties is an important research topic, allowing a better understanding of the cell's behaviour under different conditions. Atomic force microscopy (AFM) was employed in this study to analyse the basis of the nanomechanical changes in probiotic bacteria under nitrofurantoin, furazolidone, and nitrofurazone exposure. Recorded significant changes in the two Lactobacillus strains cells morphology, topography, and adhesion parameters resulted in the increase of the cells' longitude (up to 2.58 μm), profile height (by around 0.50 μm), and decrease in the adhesion force (up to 13.58 nN). Young's modulus and adhesion energy decreased within 96 h, however with no negative effect on the cells' morphology or loss of structural integrity. Observed modifications present the mode of action of the 5-nitrofuran derivative antibiotics on probiotic biofilm formation and suggest activation of the multilevel adaptation mechanisms to counteract unfavorable environments. A visual change in bacterial morphology such as an increased surface-to-volume ratio might be a link between molecular-level events and outcomes in individual cells and biofilms. This paper for the first time shows, that these antibiotics affect the properties of non-target microorganisms as lactobacilli, and might impair biofilm formation. However, the degree of such transformations depends on the delivered active substance.

Specific capture of Pseudomonas aeruginosa for rapid detection of antimicrobial resistance in urinary tract infections

Urinary tract infections (UTIs) are among the most predominant microbial diseases, leading to substantial healthcare burdens and threatening human well-being. UTIs can become more critical when caused by Pseudomonas aeruginosa, particularly by antimicrobial-resistant types. Thereby a rapid diagnosis and identification of the antimicrobial-resistant P. aeruginosa can support and guide an efficient medication and an effective treatment toward UTIs. Herein, we designed a platform for prompt purification, and effective identification of P. aeruginosa to combat the notorious P. aeruginosa associated UTIs. A peptide (QRKLAAKLT), specifically binding to P. aeruginosa, was grafted onto PEGylated magnetic nanoclusters and enabled a successful capture and enrichment of P. aeruginosa from artificial human urine. Rapid identification of antimicrobial resistance of the enriched P. aeruginosa can be moreover accomplished within 30 min. These functionalized magnetic nanoclusters demonstrate a prominent diagnostic potential to combat P. aeruginosa associated UTIs, which can be extended to other P. aeruginosa involved infections.

Pathways to engineering the phyllosphere microbiome for sustainable crop production

Current disease resistance breeding, which is largely dependent on the exploitation of resistance genes in host plants, faces the serious challenges of rapidly evolving phytopathogens. The phyllosphere is the largest biological surface on Earth and an untapped reservoir of functional microbiomes. The phyllosphere microbiome has the potential to defend against plant diseases. However, the mechanisms of how the microbiota assemble and function in the phyllosphere remain largely elusive, and this restricts the exploitation of the targeted beneficial microbes in the field. Here we review the endogenous and exogenous cues impacting microbiota assembly in the phyllosphere and how the phyllosphere microbiota in turn facilitate the disease resistance of host plants. We further construct a holistic framework by integrating of holo-omics, genetic manipulation, culture-dependent characterization and emerging artificial intelligence techniques, such as deep learning, to engineer the phyllosphere microbiome for sustainable crop production.

Ultrafast Determination of Antimicrobial Resistant Staphylococcus aureus Specifically Captured by Functionalized Magnetic Nanoclusters

Sepsis, the systemic response to infection, is a life-threatening situation for patients and leads to high mortality, especially when caused by antimicrobial resistant pathogens. Prompt diagnosis and identification of the pathogenic bacteria, including their antibiotic resistance, are highly desired to yield a timely decision for treatment. Here, we aim to develop a platform for rapid isolation and efficient identification of Staphylococcus aureus, the most frequently occurring pathogen in sepsis. A peptide (VPHNPGLISLQG, SA5-1), specifically binding to S. aureus, was conjugated to the PEGylated magnetic nanoclusters, successfully enabling the specific capture and enrichment of S. aureus from blood serum. Consequently, fast detection of the antimicrobial resistance of the collected S. aureus was achieved within 30 min using a novel luminescent probe. These magnetic nanoclusters manifest a promising diagnostic prospect to combat sepsis.

Robust Antibacterial Activity of Xanthan-Gum-Stabilized and Patterned CeO2-x-TiO2 Antifog Films

Increased occurrence of antimicrobial resistance leads to a huge burden on patients, the healthcare system, and society worldwide. Developing antimicrobial materials through doping rare-earth elements is a new strategy to overcome this challenge. To this end, we design antibacterial films containing CeO_2-x-TiO₂, xanthan gum, poly(acrylic acid), and hyaluronic acid. CeO_2-x-TiO₂ inks are additionally integrated into a hexagonal grid for prominent transparency. Such design yields not only an antibacterial efficacy of ∼100% toward Staphylococcus aureus and Escherichia coli but also excellent antifog performance for 72 h in a 100% humidity atmosphere. Moreover, FluidFM is employed to understand the interaction in-depth between bacteria and materials. We further reveal that reactive oxygen species (ROS) are crucial for the bactericidal activity of E. coli through fluorescent spectroscopic analysis and SEM imaging. We meanwhile confirm that Ce³⁺ ions are involved in the stripping phosphate groups, damaging the cell membrane of S. aureus. Therefore, the hexagonal mesh and xanthan-gum cross-linking chains act as a reservoir for ROS and Ce³⁺ ions, realizing a long-lasting antibacterial function. We hence develop an antibacterial and antifog dual-functional material that has the potential for a broad application in display devices, medical devices, food packaging, and wearable electronics.

Extending applications of AFM to fluidic AFM in single living cell studies

In this article, a review of a series of applications of atomic force microscopy (AFM) and fluidic Atomic Force Microscopy (fluidic AFM, hereafter fluidFM) in single-cell studies is presented. AFM applications involving single-cell and extracellular vesicle (EV) studies, colloidal force spectroscopy, and single-cell adhesion measurements are discussed. FluidFM is an offshoot of AFM that combines a microfluidic cantilever with AFM and has enabled the research community to conduct biological, pathological, and pharmacological studies on cells at the single-cell level in a liquid environment. In this review, capacities of fluidFM are discussed to illustrate (1) the speed with which sequential measurements of adhesion using coated colloid beads can be done, (2) the ability to assess lateral binding forces of endothelial or epithelial cells in a confluent cell monolayer in an appropriate physiological environment, and (3) the ease of measurement of vertical binding forces of intercellular adhesion between heterogeneous cells. Furthermore, key applications of fluidFM are reviewed regarding to EV absorption, manipulation of a single living cell by intracellular injection, sampling of cellular fluid from a single living cell, patch clamping, and mass measurements of a single living cell.

Uncoupling bacterial attachment on and detachment from polydimethylsiloxane surfaces through empirical and simulation studies

Bacterial infections related to medical devices can cause severe problems, whose solution requires in-depth understanding of the interactions between bacteria and surfaces. This work investigates the influence of surface physicochemistry on bacterial attachment and detachment under flow through both empirical and simulation studies. We employed polydimethylsiloxane (PDMS) substrates having different degrees of crosslinking as the model material and the extended Derjaguin - Landau - Verwey - Overbeek model as the simulation method. Experimentally, the different PDMS materials led to similar numbers of attached bacteria, which can be rationalized by the identical energy barriers simulated between bacteria and the different materials. However, different numbers of residual bacteria after detachment were observed, which was suggested by simulation that the detachment process is determined by the interfacial physicochemistry rather than the mechanical property of a material. This finding is further supported by analyzing the bacteria detachment from PDMS substrates from which non-crosslinked polymer chains had been removed: similar numbers of residual bacteria were found on the extracted PDMS substrates. The knowledge gained in this work can facilitate the projection of bacterial colonization on a given surface.

Cell-Cell Mating Interactions: Overview and Potential of Single-Cell Force Spectroscopy

It is an understatement that mating and DNA transfer are key events for living organisms. Among the traits needed to facilitate mating, cell adhesion between gametes is a universal requirement. Thus, there should be specific properties for the adhesion proteins involved in mating. Biochemical and biophysical studies have revealed structural information about mating adhesins, as well as their specificities and affinities, leading to some ideas about these specialized adhesion proteins. Recently, single-cell force spectroscopy (SCFS) has added important findings. In SCFS, mating cells are brought into contact in an atomic force microscope (AFM), and the adhesive forces are monitored through the course of mating. The results have shown some remarkable characteristics of mating adhesins and add knowledge about the design and evolution of mating adhesins.

Adhesion heterogeneity of individual bacterial cells in an axenic culture studied by atomic force microscopy

The evaluation of bacterial adhesive properties at a single-cell level is critical for under standing the role of phenotypic heterogeneity in bacterial attachment and community formation. Bacterial population exhibits a wide variety of adhesive properties at the single-cell level, suggesting that bacterial adhesion is a rather complex process and some bacteria are prone to phenotypic heterogeneity. This heterogeneity was more pronounced for Escherichia coli, where two subpopulations were detected. Subpopulations exhibiting higher adhesion forces may be better adapted to colonize a new surface, especially during sudden changes in environmental conditions. Escherichia coli was characterized by a higher adhesion force, a stronger ability to form biofilm and larger heterogeneity index calculated in comparison with Bacillus subtilis. Higher adhesion forces are associated with a more efficient attachment of bacteria observed in an adhesion assay and might provide a basis for successful colonization, survival and multiplications in changing environment. The atomic force microscopy provides a platform for investigation of the adhesion heterogeneity of individual cells within a population, which may be expected to underpin further elucidation of the adaptive significance of phenotypic heterogeneity in a natural environment.

AFM-Based Correlative Microscopy Illuminates Human Pathogens

Microbes have an arsenal of virulence factors that contribute to their pathogenicity. A number of challenges remain to fully understand disease transmission, fitness landscape, antimicrobial resistance and host heterogeneity. A variety of tools have been used to address diverse aspects of pathogenicity, from molecular host-pathogen interactions to the mechanisms of disease acquisition and transmission. Current gaps in our knowledge include a more direct understanding of host-pathogen interactions, including signaling at interfaces, and direct phenotypic confirmation of pathogenicity. Correlative microscopy has been gaining traction to address the many challenges currently faced in biomedicine, in particular the combination of optical and atomic force microscopy (AFM). AFM, generates high-resolution surface topographical images, and quantifies mechanical properties at the pN scale under physiologically relevant conditions. When combined with optical microscopy, AFM probes pathogen surfaces and their physical and molecular interaction with host cells, while the various modes of optical microscopy view internal cellular responses of the pathogen and host. Here we review the most recent advances in our understanding of pathogens, recent applications of AFM to the field, how correlative AFM-optical microspectroscopy and microscopy have been used to illuminate pathogenicity and how these methods can reach their full potential for studying host-pathogen interactions.

Tryptamine-functionalized magnetic nanoparticles for highly sensitive detection of Salmonella typhimurium

There is significant demand for the development of rapid, sensitive, and specific methods for detecting bacterial pathogens in order to identify the causes of food poisoning. Nucleic acid amplification tests (NAATs) allow for the culture-free detection of bacterial pathogens and are not as labor intensive and time consuming as culture-based detection methods. However, suitable sample preparation methods must be developed for the realization of simple, rapid, and sensitive NAATs. To resolve this problem, we developed a new sample preparation method that integrates bacterial pathogen enrichment and DNA extraction. We engineered magnetic nanoparticles (MNPs) with a physicochemical probe (tryptamine) for single-tube sample preparation with minimal sample loss. The tryptamine-functionalized MNPs (Indole@MNPs) showed inherent hydrophobicity owing to the indole side chain and a change in their zeta potential with a decrease in the pH. Because of their physicochemical characteristics, the Indole@MNPs could adsorb bacterial pathogens, thus allowing sample enrichment and DNA binding and release through weak electrostatic interactions via pH control. We successfully detected Salmonella enterica serovar Typhimurium, a common cause of bacterial food poisoning, at a concentration of 10 CFU/10 mL in milk samples using quantitative PCR. Thus, the proposed method allows for the simple and sensitive detection of Salmonella typhimurium and can be used for nontyphoidal salmonella detection to ensure food safety.

Shaping the leaf microbiota: plant-microbe-microbe interactions

The aerial portion of a plant, namely the leaf, is inhabited by pathogenic and non-pathogenic microbes. The leaf's physical and chemical properties, combined with fluctuating and often challenging environmental factors, create surfaces that require a high degree of adaptation for microbial colonization. As a consequence, specific interactive processes have evolved to establish a plant leaf niche. Little is known about the impact of the host immune system on phyllosphere colonization by non-pathogenic microbes. These organisms can trigger plant basal defenses and benefit the host by priming for enhanced resistance to pathogens. In most disease resistance responses, microbial signals are recognized by extra- or intracellular receptors. The interactions tend to be species specific and it is unclear how they shape leaf microbial communities. In natural habitats, microbe-microbe interactions are also important for shaping leaf communities. To protect resources, plant colonizers have developed direct antagonistic or host manipulation strategies to fight competitors. Phyllosphere-colonizing microbes respond to abiotic and biotic fluctuations and are therefore an important resource for adaptive and protective traits. Understanding the complex regulatory host-microbe-microbe networks is needed to transfer current knowledge to biotechnological applications such as plant-protective probiotics.

The microbial adhesive arsenal deciphered by atomic force microscopy

Microbes employ a variety of strategies to adhere to abiotic and biotic surfaces, as well as host cells. In addition to their surface physicochemical properties (e.g. charge, hydrophobic balance), microbes produce appendages (e.g. pili, fimbriae, flagella) and express adhesion proteins embedded in the cell wall or cell membrane, with adhesive domains targeting specific ligands or chemical properties. Atomic force microscopy (AFM) is perfectly suited to deciphering the adhesive properties of microbial cells. Notably, AFM imaging has revealed the cell wall topographical organization of live cells at unprecedented resolution, and AFM has a dual capability to probe adhesion at the single-cell and single-molecule levels. AFM is thus a powerful tool for unravelling the molecular mechanisms of microbial adhesion at scales ranging from individual molecular interactions to the behaviours of entire cells. In this review, we cover some of the major breakthroughs facilitated by AFM in deciphering the microbial adhesive arsenal, including the exciting development of anti-adhesive strategies.

Two-way microscale interactions between immigrant bacteria and plant leaf microbiota as revealed by live imaging

The phyllosphere - the aerial parts of plants - is an important microbial habitat that is home to diverse microbial communities. The spatial organization of bacterial cells on leaf surfaces is non-random, and correlates with leaf microscopic features. Yet, the role of microscale interactions between bacterial cells therein is not well understood. Here, we ask how interactions between immigrant bacteria and resident microbiota affect the spatial organization of the combined community. By means of live imaging in a simplified in vitro system, we studied the spatial organization, at the micrometer scale, of the biocontrol agent Pseudomonas fluorescens A506 and the plant pathogen P. syringae B728a when introduced to pear and bean leaf microbiota (the corresponding native plants of these strains). We found significant co-localization of immigrant and resident microbial cells at distances of a few micrometers, for both strains. Interestingly, this co-localization was in part due to preferential attachment of microbiota cells near newly formed P. fluorescens aggregates. Our results indicate that two-way immigrant bacteria - resident microbiota interactions affect the microscale spatial organization of leaf microbiota, and possibly that of other surface-related microbial communities.

FluidFM as a tool to study adhesion forces of bacteria - Optimization of parameters and comparison to conventional bacterial probe Scanning Force Spectroscopy

The FluidFM enables the immobilization of single cells on a hollow cantilever using relative underpressure. In this study, we systematically optimize versatile measurement parameters (setpoint, z-speed, z-length, pause time, and relative underpressure) to improve the quality of force-distance curves recorded with a FluidFM. Using single bacterial cells (here the gram negative seawater bacterium Paracoccus seriniphilus and the gram positive bacterium Lactococcus lactis), we show that Single Cell Force Spectroscopy experiments with the FluidFM lead to comparable results to a conventional Single Cell Force Spectroscopy approach using polydopamine for chemical fixation of a bacterial cell on a tipless cantilever. Even for the bacterium Lactococcus lactis, which is difficult to immobilze chemically (like seen in an earlier study), immobilization and the measurement of force-distance curves are possible by using the FluidFM technology.

Biofunctionalization of Microgroove Surfaces with Antibacterial Nanocoatings

Objectives

To investigate the physical properties of the modified microgroove (MG) and antibacterial nanocoated surfaces. In addition, the biological interactions of the modified surfaces with human gingival fibroblasts (HGFs) and the antibacterial activity of the surfaces against Porphyromonas gingivalis were studied.

Methods

The titanium nitride (TiN) and silver (Ag) coatings were deposited onto the smooth and MG surfaces using magnetron sputtering. A smooth titanium surface (Ti-S) was used as the control. The physicochemical properties including surface morphology, roughness, and hydrophilicity were characterized using scanning electron microscopy, atomic force microscopy, and an optical contact angle analyzer. The "contact guidance" morphology was assessed using confocal laser scanning microscopy. Cell proliferation was analyzed using the Cell Counting Kit-8 assay. The expression level of the main focal adhesion-related structural protein vinculin was compared using quantitative reverse transcription PCR and Western blotting. The antibacterial activity against P. gingivalis was evaluated using the LIVE/DEAD BacLight™ Bacterial Viability Kit.

Results

The Ag and TiN antibacterial nanocoatings were successfully deposited onto the smooth and MG surfaces using magnetron sputtering technology. TiN coating on a grooved surface (TiN-MG) resulted in less nanoroughness and greater surface hydrophilicity than Ag coating on a smooth surface (Ag-S), which was more hydrophobic. Cell proliferation and expression of vinculin were higher on the TiN-MG surface than on the Ag-coated surfaces. Ag-coated surfaces showed the strongest antibacterial activity, followed by TiN-coated surfaces.

Conclusion

Nano-Ag coating resulted in good antimicrobial activity; however, the biocompatibility was questionable. TiN nanocoating on an MG surface showed antibacterial properties with an optimal biocompatibility and maintained the "contact guidance" effects for HGFs.

How Microbes Use Force To Control Adhesion

Microbial adhesion and biofilm formation are usually studied using molecular and cellular biology assays, optical and electron microscopy, or laminar flow chamber experiments. Today, atomic force microscopy (AFM) represents a valuable addition to these approaches, enabling the measurement of forces involved in microbial adhesion at the single-molecule level. In this minireview, we discuss recent discoveries made applying state-of-the-art AFM techniques to microbial specimens in order to understand the strength and dynamics of adhesive interactions. These studies shed new light on the molecular mechanisms of adhesion and demonstrate an intimate relationship between force and function in microbial adhesins.

Using Atomic Force Microscopy To Illuminate the Biophysical Properties of Microbes

Since its invention in 1986, atomic force microscopy (AFM) has grown from a system designed for imaging inorganic surfaces to a tool used to probe the biophysical properties of living cells and tissues. AFM is a scanning probe technique and uses a pyramidal tip attached to a flexible cantilever to scan across a surface, producing a highly detailed image. While many research articles include AFM images, fewer include force-distance curves, from which several biophysical properties can be determined. In a single force-distance curve, the cantilever is lowered and raised from the surface, while the forces between the tip and the surface are monitored. Modern AFM has a wide variety of applications, but this review will focus on exploring the mechanobiology of microbes, which we believe is of particular interest to those studying biomaterials. We briefly discuss experimental design as well as different ways of extracting meaningful values related to cell surface elasticity, cell stiffness, and cell adhesion from force-distance curves. We also highlight both classic and recent experiments using AFM to illuminate microbial biophysical properties.

Spring constant and sensitivity calibration of FluidFM micropipette cantilevers for force spectroscopy measurements

The fluidic force microscope (FluidFM) can be considered as the nanofluidic extension of the atomic force microscope (AFM). This novel instrument facilitates the experimental procedure and data acquisition of force spectroscopy (FS) and is also used for the determination of single-cell adhesion forces (SCFS) and elasticity. FluidFM uses special probes with an integrated nanochannel inside the cantilevers supported by parallel rows of pillars. However, little is known about how the properties of these hollow cantilevers affect the most important parameters which directly scale the obtained spectroscopic data: the inverse optical lever sensitivity (InvOLS) and the spring constant (k). The precise determination of these parameters during calibration is essential in order to gain reliable, comparable and consistent results with SCFS. Demonstrated by our literature survey, the standard error of previously published SCFS results obtained with FluidFM ranges from 11.8% to 50%. The question arises whether this can be accounted for biological diversity or may be the consequence of improper calibration. Thus the aim of our work was to investigate the calibration accuracy of these parameters and their dependence on: (1) the aperture size (2, 4 and 8 µm) of the hollow micropipette type cantilever; (2) the position of the laser spot on the back of the cantilever; (3) the substrate used for calibration (silicon or polystyrene). It was found that both the obtained InvOLS and spring constant values depend significantly on the position of the laser spot. Apart from the theoretically expectable monotonous increase in InvOLS (from the tip to the base of the cantilever, as functions of the laser spot's position), we discerned a well-defined and reproducible fluctuation, which can be as high as ±30%, regardless of the used aperture size or substrate. The calibration of spring constant also showed an error in the range of -13/+20%, measured at the first 40 µm of the cantilever. Based on our results a calibration strategy is proposed and the optimal laser position which yields the most reliable spring constant values was determined and found to be on the first pair of pillars. Our proposed method helps in reducing the error introduced via improper calibration and thus increases the reliability of subsequent cell adhesion force or elasticity measurements with FluidFM.

Fluidic Force Microscopy Captures Amyloid Bonds between Microbial Cells

Fluidic force microscopy (FluidFM) is a recent force-controlled pipette technology that enables manipulation of single cells. FluidFM can be used for quantification of forces between single cells, and a novel mode of cell-cell adhesion was uncovered: amyloid-like interactions that mediate homophilic adhesion in the fungal pathogen Candida albicans.