Spring constants and adhesive properties of native bacterial biofilm cells measured by atomic force microscopy

Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment

With the generation of spatially resolved transcriptomics of microbial biofilms, computational tools can be used to integrate this data to elucidate the multi-scale mechanisms controlling heterogeneous biofilm metabolism. This work presents a Multi-scale model of Metabolism In Cellular Systems (MiMICS) which is a computational framework that couples a genome-scale metabolic network reconstruction (GENRE) with Hybrid Automata Library (HAL), an existing agent-based model and reaction-diffusion model platform. A key feature of MiMICS is the ability to incorporate multiple -omics-guided metabolic models, which can represent unique metabolic states that yield different metabolic parameter values passed to the extracellular models. We used MiMICS to simulate Pseudomonas aeruginosa regulation of denitrification and oxidative stress metabolism in hypoxic and nitric oxide (NO) biofilm microenvironments. Integration of P. aeruginosa PA14 biofilm spatial transcriptomic data into a P. aeruginosa PA14 GENRE generated four PA14 metabolic model states that were input into MiMICS. Characteristic of aerobic, denitrification, and oxidative stress metabolism, the four metabolic model states predicted different oxygen, nitrate, and NO exchange fluxes that were passed as inputs to update the agent's local metabolite concentrations in the extracellular reaction-diffusion model. Individual bacterial agents chose a PA14 metabolic model state based on a combination of stochastic rules, and agents sensing local oxygen and NO. Transcriptome-guided MiMICS predictions suggested microscale denitrification and oxidative stress metabolic heterogeneity emerged due to local variability in the NO biofilm microenvironment. MiMICS accurately predicted the biofilm's spatial relationships between denitrification, oxidative stress, and central carbon metabolism. As simulated cells responded to extracellular NO, MiMICS revealed dynamics of cell populations heterogeneously upregulating reactions in the denitrification pathway, which may function to maintain NO levels within non-toxic ranges. We demonstrated that MiMICS is a valuable computational tool to incorporate multiple -omics-guided metabolic models to mechanistically map heterogeneous microbial metabolic states to the biofilm microenvironment.

AFM Force Mapping Elucidates Pilus Deployment and Key Lifestyle-Dependent Surface Properties in Bdellovibrio bacteriovorus

Bdellovibrio bacteriovorus is known for predation of a wide variety of Gram-negative bacteria, making it of interest as an alternative or supplement to chemical antibiotics. However, a fraction of B. bacteriovorus follows a nonpredatory, "host-independent" (HI) life cycle. In this study, live predatory and HI B. bacteriovorus were captured on a surface and examined, in buffer, by collecting force maps using atomic force microscopy (AFM). The approach curves obtained on HI cells are similar to those on other Gram-negative cells, with a short nonlinear region followed by a linear region. In contrast, the approach curves obtained on predatory cells have a large nonlinear region, reflecting the unusual flexibility of the predatory cell. As the AFM tip is retracted, it shows virtually no adhesion to predatory B. bacteriovorus but has multiple adhesion events on HI cells and the 200-500+ nm region immediately surrounding them. Measured pull-off forces, pull-off distances, and effective spring constants are consistent with the multiple stretching events of Type IV pili, both on and especially adjacent to the cells. Exposure of the HI B. bacteriovorus to a pH-neutral 10% cranberry juice solution, which contains type A proanthocyanidins that are known to interfere with the adhesion of multiple types of pili, results in a substantial reduction in adhesion. Type IV pili are required for successful predation by B. bacteriovorus, but pili used in the predation process are located at the non-flagellated pole of the cell and can retract when not in use. Such pili are rarely observed under the conditions of this study, where the predator has not encountered a prey cell. In contrast, HI cells appear to have many pili distributed on and around the whole cell, presumably ready to be utilized for a variety of HI cell activities including attachment to surfaces.

Formation of Biofilm by Tetragenococcus halophilus Benefited Stress Tolerance and Anti-biofilm Activity Against S. aureus and S. Typhimurium

Tetragenococcus halophilus, a halophilic lactic acid bacterium (LAB), plays an important role in the production of high-salt fermented foods. Generally, formation of biofilm benefits the fitness of cells when faced with competitive and increasingly hostile fermented environments. In this work, the biofilm-forming capacity of T. halophilus was investigated. The results showed that the optimal conditions for biofilm formation by T. halophilus were at 3–9% salt content, 0–6% ethanol content, pH 7.0, 30°C, and on the surface of stainless steel. Confocal laser scanning microscopy (CLSM) analysis presented a dense and flat biofilm with a thickness of about 24 μm, and higher amounts of live cells were located near the surface of biofilm and more dead cells located at the bottom. Proteins, polysaccharides, extracellular-DNA (eDNA), and humic-like substances were all proved to take part in biofilm formation. Higher basic surface charge, greater hydrophilicity, and lower intracellular lactate dehydrogenase (LDH) activities were detected in T. halophilus grown in biofilms. Atomic force microscopy (AFM) imaging revealed that biofilm cultures of T. halophilus had stronger surface adhesion forces than planktonic cells. Cells in biofilm exhibited higher cell viability under acid stress, ethanol stress, heat stress, and oxidative stress. In addition, T. halophilus biofilms exhibited aggregation activity and anti-biofilm activity against Staphylococcus aureus and Salmonella Typhimurium. Results presented in the study may contribute to enhancing stress tolerance of T. halophilus and utilize their antagonistic activities against foodborne pathogens during the production of fermented foods.

Fission yeast polycystin Pkd2p promotes cell size expansion and antagonizes the Hippo-related SIN pathway

Polycystins are conserved mechanosensitive channels whose mutations lead to the common human renal disorder autosomal dominant polycystic kidney disease (ADPKD). Previously, we discovered that the plasma membrane-localized fission yeast polycystin homolog Pkd2p is an essential protein required for cytokinesis; however, its role remains unclear. Here, we isolated a novel temperature-sensitive pkd2 mutant, pkd2-B42. Among the strong growth defects of this mutant, the most striking was that many mutant cells often lost a significant portion of their volume in just 5 min followed by a gradual recovery, a process that we termed 'deflation'. Unlike cell lysis, deflation did not result in plasma membrane rupture and occurred independently of cell cycle progression. The tip extension of pkd2-B42 cells was 80% slower than that of wild-type cells, and their turgor pressure was 50% lower. Both pkd2-B42 and the hypomorphic depletion mutant pkd2-81KD partially rescued mutants of the septation initiation network (SIN), a yeast Hippo-related signaling pathway, by preventing cell lysis, enhancing septum formation and doubling the number of Sid2p and Mob1p molecules at the spindle pole bodies. We conclude that Pkd2p promotes cell size expansion during interphase by regulating turgor pressure and antagonizes the SIN during cytokinesis. This article has an associated First Person interview with the first author of the paper.

Data-driven modeling of heterogeneous viscoelastic biofilms

Biofilms are typically heterogeneous in morphology, structure, and composition, resulting in non-uniform mechanical properties. The distribution of mechanical properties, in turn, determines the biofilm behavior, such as deformation and detachment. Most biofilm models neglect biofilm heterogeneity, especially at the microscale. In this study, an image-based modeling approach was developed to transform two-dimensional optical coherence tomography (OCT) biofilm images to a pixel-scale non-Newtonian viscosity map of the biofilm. The map was calibrated using the bulk viscosity data from rheometer tests, based on assumed maximum and minimum viscosities and a relationship between OCT image intensity signals and non-Newtonian viscosity. While not quantitatively measuring biofilm viscosity for each pixel, it allows a rational spatial allocation of viscosities within the biofilm: areas with lower cell density, e.g., voids, are assigned lower viscosities, and areas with high cell densities are assigned higher viscosities. The spatial distribution of non-Newtonian viscosity was applied in an established Oldroyd-B constitutive model and implemented using the phase-field continuum approach for the deformation and stress analysis. The heterogeneous model was able to predict deformations more accurately than a homogenous one. Stress distribution in the heterogeneous biofilm displayed better characteristics than that in the homogeneous one, because it is highly dependent on the viscosity distribution. This work, using a pixel-scale, image-based approach to map the mechanical heterogeneity of biofilms for computational deformation and stress analysis, provides a novel modeling approach that allows the consideration of biofilm structural and mechanical heterogeneity. Future research should better characterize the relationship between OCT signal and viscosity, and consider other constitutive models for biofilm mechanical behavior. This article is protected by copyright. All rights reserved.

Extracellular Polymeric Substance Protects Some Cells in an Escherichia coli Biofilm from the Biomechanical Consequences of Treatment with Magainin 2

Bacterial biofilms have long been recognized as a source of persistent infections and industrial contamination with their intransigence generally attributed to their protective layer of extracellular polymeric substances (EPS). EPS, consisting of secreted nucleic acids, proteins, and polysaccharides, make it difficult to fully eliminate biofilms by conventional chemical or physical means. Since most bacteria are capable of forming biofilms, understanding how biofilms respond to new antibiotic compounds and components of the immune system has important ramifications. Antimicrobial peptides (AMPs) are both potential novel antibiotic compounds and part of the immune response in many different organisms. Here, we use atomic force microscopy to investigate the biomechanical changes that occur in individual cells when a biofilm is exposed to the AMP magainin 2 (MAG2), which acts by permeabilizing bacterial membranes. While MAG2 is able to prevent biofilm initiation, cells in an established biofilm can withstand exposure to high concentrations of MAG2. Treated cells in the biofilm are classified into two distinct populations after treatment: one population of cells is indistinguishable from untreated cells, maintaining cellular turgor pressure and a smooth outer surface, and the second population of cells are softer than untreated cells and have a rough outer surface after treatment. Notably, the latter population is similar to planktonic cells treated with MAG2. The EPS likely reduces the local MAG2 concentration around the stiffer cells since once the EPS was enzymatically removed, all cells became softer and had rough outer surfaces. Thus, while MAG2 appears to have the same mechanism of action in biofilm cells as in planktonic ones, MAG2 cannot eradicate a biofilm unless coupled with the removal of the EPS.

Pili and other surface proteins influence the structure and the nanomechanical properties of Lactococcus lactis biofilms

Lactic acid bacteria, in particular Lactococcus lactis, are widely used in the food industry, for the control and/or the protection of the manufacturing processes of fermented food. While L. lactis has been reported to form compact and uniform biofilms it was recently shown that certain strains able to display pili at their surface form more complex biofilms exhibiting heterogeneous and aerial structures. As the impact of those biofilm structures on the biomechanical properties of the biofilms is poorly understood, these were investigated using AFM force spectroscopy and imaging. Three types of strains were used i.e., a control strain devoid of pili and surface mucus-binding protein, a strain displaying pili but no mucus-binding proteins and a strain displaying both pili and a mucus-binding protein. To identify potential correlations between the nanomechanical measurements and the biofilm architecture, 24-h old biofilms were characterized by confocal laser scanning microscopy. Globally the strains devoid of pili displayed smoother and stiffer biofilms (Young Modulus of 4-100 kPa) than those of piliated strains (Young Modulus around 0.04-0.1 kPa). Additional display of a mucus-binding protein did not affect the biofilm stiffness but made the biofilm smoother and more compact. Finally, we demonstrated the role of pili in the biofilm cohesiveness by monitoring the homotypic adhesion of bacteria to the biofilm surface. These results will help to understand the role of pili and mucus-binding proteins withstanding external forces.

Effect of Strain-Specific Biofilm Properties on the Retention of Colloids in Saturated Porous Media under Conditions of Stormwater Biofiltration

Filter performance can be affected by bacterial colonization of the filtration media, yet little is known about how naturally occurring bacteria modify the surface properties of filtration media to affect colloidal removal. We used sand columns and simulated stormwater conditions to study the retention of model colloidal particles, carboxyl-modified-latex (CML) beads, in porous media colonized by naturally occurring bacterial strains. Colloid retention varied substantially across identical columns colonized by different, in some cases closely related, bacterial strains in a cell density independent manner. Atomic force microscopy was applied to quantify the interaction energy between CML beads and each bacterial strain's biofilm surface. We found interaction energy between CML and each strain was significantly different, with adhesive energies between the biofilm and CML, presumed to be associated with polymer-surface bonding, a better predictor of CML retention than other strain characteristics. Overall, the findings suggest that interactions with biopolymers in naturally occurring bacterial biofilms strongly influence colloid retention in porous media. This work highlights the need for more investigation into the role of biofilm microbial community composition on colloid removal in porous media to improve biofilter design and operation.

Spatial distribution of mechanical properties in Pseudomonas aeruginosa biofilms, and their potential impacts on biofilm deformation

The mechanical properties of biofilms can be used to predict biofilm deformation under external forces, for example, under fluid flow. We used magnetic tweezers to spatially map the compliance of Pseudomonas aeruginosa biofilms at the microscale, then applied modeling to assess its effects on biofilm deformation. Biofilms were grown in capillary flow cells with Reynolds numbers (Re) ranging from 0.28 to 13.9, bulk dissolved oxygen (DO) concentrations from 1 mg/L to 8 mg/L, and bulk calcium ion (Ca²⁺ ) concentrations of 0 and 100 mg CaCl₂ /L. Higher Re numbers resulted in more uniform biofilm morphologies. The biofilm was stiffer at the center of the flow cell than near the walls. Lower bulk DO led to more stratified biofilms. Higher Ca²⁺ concentrations led to increased stiffness and more uniform mechanical properties. Using the experimental mechanical properties, fluid-structure interaction models predicted up to 64% greater deformation for heterogeneous biofilms, compared with a homogeneous biofilms with the same average properties. However, the deviation depended on the biofilm morphology and flow regime. Our results show significant spatial mechanical variability exists at the microscale, and that this variability can potentially affect biofilm deformation. The average biofilm mechanical properties, provided in many studies, should be used with caution when predicting biofilm deformation.

Qualitative and Quantitative Changes to Escherichia coli during Treatment with Magainin 2 Observed in Native Conditions by Atomic Force Microscopy

The bacterial membrane has been suggested as a good target for future antibiotics, so it is important to understand how naturally occurring antibiotics like antimicrobial peptides (AMPs) disrupt those membranes. The interaction of the AMP magainin 2 (MAG2) with the bacterial cell membrane has been well characterized using supported lipid substrates, unilamellar vesicles, and spheroplasts created from bacterial cells. However, to fully understand how MAG2 kills bacteria, we must consider its effect on the outer membrane found in Gram-negative bacteria. Here, we use atomic force microscopy (AFM) to directly investigate MAG2 interaction with the outer membrane of Escherichia coli and characterize the biophysical consequences of MAG2 treatment under native conditions. While propidium iodide penetration indicates that MAG2 permeabilizes cells within seconds, a corresponding decrease in cellular turgor pressure is not observed until minutes after MAG2 application, suggesting that cellular homeostasis machinery may be responsible for helping the cell maintain turgor pressure despite a loss of membrane integrity. AFM imaging and force measurement modes applied in tandem reveal that the outer membrane becomes pitted, more flexible, and more adhesive after MAG2 treatment. MAG2 appears to have a highly disruptive effect on the outer membrane, extending the known mechanism of MAG2 to the Gram-negative outer membrane.

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.

Detrimental impact of silica nanoparticles on the nanomechanical properties of Escherichia coli, studied by AFM

Despite great innovative and technological promises, nanoparticles (NPs) can ultimately exert an antibacterial activity by affecting the cell envelope integrity. This envelope, by conferring the cell its rigidity and protection, is intimately related to the mechanical behavior of the bacterial surface. Depending on their size, surface chemistry, shape, NPs can induce damages to the cell morphology and structure among others, and are therefore expected to alter the overall mechanical properties of bacteria. Although Atomic Force Microscopy (AFM) stands as a powerful tool to study biological systems, with high resolution and in near physiological environment, it has rarely been applied to investigate at the same time both morphological and mechanical degradations of bacteria upon NPs treatment. Consequently, this study aims at quantifying the impact of the silica NPs (SiO₂-NPs) on the mechanical properties of E. coli cells after their exposure, and relating it to their toxic activity under a critical diameter. Cell elasticity was calculated by fitting the force curves with the Hertz model, and was correlated with the morphological study. SiO₂-NPs of 100 nm diameter did not trigger any significant change in the Young modulus of E. coli, in agreement with the bacterial intact morphology and membrane structure. On the opposite, the 4 nm diameter SiO₂-NPs did induce a significant decrease in E. coli Young modulus, mainly associated with the disorganization of lipopolysaccharides in the outer membrane and the permeation of the underlying peptidoglycan layer. The subsequent toxic behavior of these NPs is finally confirmed by the presence of membrane residues, due to cell lysis, exhibiting typical adhesion features.

The effects of extrinsic factors on the structural and mechanical properties of Pseudomonas fluorescens biofilms: A combined study of nutrient concentrations and shear conditions

The growth of biofilms on surfaces is a complicated process influenced by several environmental factors such as nutrient availability and fluid shear. In this study, combinations of growth conditions were selected for the study of Pseudomonas fluorescens biofilms including as cultivation time (24- or 48 h), nutrient levels (1:1 or 1:10 King B medium), and shear conditions (75 RPM shaking, 0.4 mL min ^-1 or 0.7 mL min ^-1). The use of Confocal Laser Scanning Microscopy (CLSM) determined biofilm structure, while liquid-phase Atomic Force Microscopy (AFM) techniques resolved the mechanical properties of biofilms. Under semi-static conditions, high nutrient environments led to more abundant biofilms with three times higher EPS content compared to biofilms grown under low nutrient conditions. AFM results revealed that biofilms formed under these conditions were less stiff, as shown by their Young's modulus values of 2.35 ± 0.08 kPa, compared to 4.98 ± 0.02 kPa for that of biofilms formed under low nutrient conditions. Under dynamic conditions, however, biofilms exposed to low nutrient conditions and high shear rates led to more developed biofilms compared to other tested dynamic conditions. These biofilms were also found to be significantly more adhesive compared to their counterparts grown at higher nutrient conditions.

Genetically-Tunable Mechanical Properties of Bacterial Functional Amyloid Nanofibers

Bacterial biofilms are highly ordered, complex, dynamic material systems including cells, carbohydrates, and proteins. They are known to be resistant against chemical, physical, and biological disturbances. These superior properties make them promising candidates for next generation biomaterials. Here we investigated the morphological and mechanical properties (in terms of Young's modulus) of genetically-engineered bacterial amyloid nanofibers of Escherichia coli (E. coli) by imaging and force spectroscopy conducted via atomic force microscopy (AFM). In particular, we tuned the expression and biochemical properties of the major and minor biofilm proteins of E. coli (CsgA and CsgB, respectively). Using appropriate mutants, amyloid nanofibers constituting biofilm backbones are formed with different combinations of CsgA and CsgB, as well as the optional addition of tagging sequences. AFM imaging and force spectroscopy are used to probe the morphology and measure the Young's moduli of biofilm protein nanofibers as a function of protein composition. The obtained results reveal that genetically-controlled secretion of biofilm protein components may lead to the rational tuning of Young's moduli of biofilms as promising candidates at the bionano interface.

Microrheology of growing Escherichia coli biofilms investigated by using magnetic force modulation atomic force microscopy

Microrheology of growing biofilms provides insightful information about its structural evolution and properties. In this study, the authors have investigated the microrheology of Escherichia coli (strain HCB1) biofilms at different indentation depth (δ) by using magnetic force modulation atomic force microscopy as a function of disturbing frequency (f). As δ increases, the dynamic stiffness (k_s) for the biofilms in the early stage significantly increases. However, it levels off when the biofilms are matured. The facts indicate that the biofilms change from inhomogeneous to homogeneous in structure. Moreover, k_s is scaled to f, which coincides with the rheology of soft glasses. The exponent increases with the incubation time, indicating the fluidization of biofilms. In contrast, the upper layer of the matured biofilms is solidlike in that the storage modulus is always larger than the loss modulus, and its viscoelasticity is slightly influenced by the shear stress.

Chlorhexidine-induced elastic and adhesive changes of Escherichia coli cells within a biofilm

Chlorhexidine is a widely used, commercially available cationic antiseptic. Although its mechanism of action on planktonic bacteria has been well explored, far fewer studies have examined its interaction with an established biofilm. The physical effects of chlorhexidine on a biofilm are particularly unknown. Here, the authors report the first observations of chlorhexidine-induced elastic and adhesive changes to single cells within a biofilm. The elastic changes are consistent with the proposed mechanism of action of chlorhexidine. Atomic force microscopy and force spectroscopy techniques were used to determine spring constants and adhesion energy of the individual bacteria within an Escherichia coli biofilm. Medically relevant concentrations of chlorhexidine were tested, and cells exposed to 1% (w/v) and 0.1% more than doubled in stiffness, while those exposed to 0.01% showed no change in elasticity. Adhesion to the biofilm also increased with exposure to 1% chlorhexidine, but not for the lower concentrations tested. Given the prevalence of chlorhexidine in clinical and commercial applications, these results have important ramifications on biofilm removal techniques.

AFM structural characterization of drinking water biofilm under physiological conditions

Insights into the complex morphology of multi-species drinking water biofilm using atomic force microscopy (AFM).

Films of bacteria at interfaces: three stages of behaviour

We report an investigation of the formation of films by bacteria at an oil-water interface using a combination of particle tracking and pendant drop elastometry. The films display a remarkably varied series of dynamical and mechanical properties as they evolve over the course of minutes to hours following the creation of an initially pristine interface. At the earliest stage of formation, which we interrogate using dispersions of colloidal probes, the interface is populated with motile bacteria. Interactions with the bacteria dominate the colloidal motion, and the interface displays canonical features of active matter in a quasi-two-dimensional context. This active stage gives way to a viscoelastic transition, presumably driven by the accumulation at the interface of polysaccharides and surfactants produced by the bacteria, which instill the interface with the hallmarks of soft glassy rheology that we characterize with microrheology. Eventually, the viscoelastic film becomes fully elastic with the capability to support wrinkling upon compression, and we investigate this final stage with the pendant drop measurements. We characterize quantitatively the dynamic and mechanical properties of the films during each of these three stages - active, viscoelastic, and elastic - and comment on their possible significance for the interfacial bacterial colony. This work also brings to the forefront the important role that interfacial mechanics may play in bacterial suspensions with free surfaces.

Mechanical properties of a mature biofilm from a wastewater system: from microscale to macroscale level

A fundamental understanding of biofilm mechanical stability is critical in order to describe detachment and develop biofouling control strategies. It is thus important to characterise the elastic deformation and flow behaviour of the biofilm under different modes of applied force. In this study, the mechanical properties of a mature wastewater biofilm were investigated with methods including macroscale compression and microscale indentation using atomic force microscopy (AFM). The mature biofilm was found to be mechanically isotropic at the macroscale level as its mechanical properties did not depend on the scales and modes of loading. However, the biofilm showed a tendency for mechanical inhomogeneity at the microscale level as indentation progressed deeper into the matrix. Moreover, it was observed that the adhesion force had a significant influence on the elastic properties of the biofilm at the surface, subjected to microscale tensile loading. These results are expected to inform a damage-based model for biofilm detachment.

The interplay between cell wall mechanical properties and the cell cycle in Staphylococcus aureus

The nanoscale mechanical properties of live Staphylococcus aureus cells during different phases of growth were studied by atomic force microscopy. Indentation to different depths provided access to both local cell wall mechanical properties and whole-cell properties, including a component related to cell turgor pressure. Local cell wall properties were found to change in a characteristic manner throughout the division cycle. Splitting of the cell into two daughter cells followed a local softening of the cell wall along the division circumference, with the cell wall on either side of the division circumference becoming stiffer. Once exposed, the newly formed septum was found to be stiffer than the surrounding, older cell wall. Deeper indentations, which were affected by cell turgor pressure, did not show a change in stiffness throughout the division cycle, implying that enzymatic cell wall remodeling and local variations in wall properties are responsible for the evolution of cell shape through division.

Effects of antibacterial agents and drugs monitored by atomic force microscopy

Originally invented for topographic imaging, atomic force microscopy (AFM) has evolved into a multifunctional biological toolkit, enabling to measure structural and functional details of cells and molecules. Its versatility and the large scope of information it can yield make it an invaluable tool in any biologically oriented laboratory, where researchers need to perform characterizations of living samples as well as single molecules in quasi-physiological conditions and with nanoscale resolution. In the last 20 years, AFM has revolutionized the characterization of microbial cells by allowing a better understanding of their cell wall and of the mechanism of action of drugs and by becoming itself a powerful diagnostic tool to study bacteria. Indeed, AFM is much more than a high-resolution microscopy technique. It can reconstruct force maps that can be used to explore the nanomechanical properties of microorganisms and probe at the same time the morphological and mechanical modifications induced by external stimuli. Furthermore it can be used to map chemical species or specific receptors with nanometric resolution directly on the membranes of living organisms. In summary, AFM offers new capabilities and a more in-depth insight in the structure and mechanics of biological specimens with an unrivaled spatial and force resolution. Its application to the study of bacteria is extremely significant since it has already delivered important information on the metabolism of these small microorganisms and, through new and exciting technical developments, will shed more light on the real-time interaction of antimicrobial agents and bacteria.

The significance of calcium ions on Pseudomonas fluorescens biofilms - a structural and mechanical study

The purpose of this study was to investigate the effects of calcium ions on the structural and mechanical properties of Pseudomonas fluorescens biofilms grown for 48 h. Advanced investigative techniques such as confocal laser scanning microscopy and atomic force spectroscopy were employed to characterize biofilm structure as well as biofilm mechanical properties following growth at different calcium concentrations. The presence of calcium during biofilm development led to higher surface coverage with distinct structural phenotypes in the form of a granular and heterogeneous surface, compared with the smoother and homogeneous biofilm surface in the absence of calcium. The presence of calcium also increased the adhesive nature of the biofilm, while reducing its elastic properties. These results suggest that calcium ions could have a functional role in biofilm development and have practical implications, for example, in analysis of biofouling in membrane-based water-treatment processes such as nanofiltration or reverse osmosis where elevated calcium concentrations may occur at the solid-liquid interface.

Characterizing pilus-mediated adhesion of biofilm-forming E. coli to chemically diverse surfaces using atomic force microscopy

Biofilms are complex communities of microorganisms living together at an interface. Because biofilms are often associated with contamination and infection, it is critical to understand how bacterial cells adhere to surfaces in the early stages of biofilm formation. Even harmless commensal Escherichia coli naturally forms biofilms in the human digestive tract by adhering to epithelial cells, a trait that presents major concerns in the case of pathogenic E. coli strains. The laboratory strain E. coli ZK1056 provides an intriguing model system for pathogenic E. coli strains because it forms biofilms robustly on a wide range of surfaces.E. coli ZK1056 cells spontaneously form living biofilms on polylysine-coated AFM cantilevers, allowing us to measure quantitatively by AFM the adhesion between native biofilm cells and substrates of our choice. We use these biofilm-covered cantilevers to probe E. coli ZK1056 adhesion to five substrates with distinct and well-characterized surface chemistries, including fluorinated, amine-terminated, and PEG-like monolayers, as well as unmodified silicon wafer and mica. Notably, after only 0-10 s of contact time, the biofilms adhere strongly to fluorinated and amine-terminated monolayers as well as to mica and weakly to "antifouling" PEG monolayers, despite the wide variation in hydrophobicity and charge of these substrates. In each case the AFM retraction curves display distinct adhesion profiles in terms of both force and distance, highlighting the cells' ability to adapt their adhesive properties to disparate surfaces. Specific inhibition of the pilus protein FimH by a nonhydrolyzable mannose analogue leads to diminished adhesion in all cases, demonstrating the critical role of type I pili in adhesion by this strain to surfaces bearing widely different functional groups. The strong and adaptable binding of FimH to diverse surfaces has unexpected implications for the design of antifouling surfaces and antiadhesion therapies.

Detection of Micrococcus luteus biofilm formation in microfluidic environments by pH measurement using an ion-sensitive field-effect transistor

Biofilm formation in microfluidic channels is difficult to detect because sampling volumes are too small for conventional turbidity measurements. To detect biofilm formation, we used an ion-sensitive field-effect transistor (ISFET) measurement system to measure pH changes in small volumes of bacterial suspension. Cells of Micrococcus luteus (M. luteus) were cultured in polystyrene (PS) microtubes and polymethylmethacrylate (PMMA)-based microfluidic channels laminated with polyvinylidene chloride. In microtubes, concentrations of bacteria and pH in the suspension were analyzed by measuring turbidity and using an ISFET sensor, respectively. In microfluidic channels containing 20 μL of bacterial suspension, we measured pH changes using the ISFET sensor and monitored biofilm formation using a microscope. We detected acidification and alkalinization phases of M. luteus from the ISFET sensor signals in both microtubes and microfluidic channels. In the alkalinization phase, after 2 day culture, dense biofilm formation was observed at the bottom of the microfluidic channels. In this study, we used an ISFET sensor to detect biofilm formation in clinical and industrial microfluidic environments by detecting alkalinization of the culture medium. 

Mapping of bacterial biofilm local mechanics by magnetic microparticle actuation

Most bacteria live in the form of adherent communities forming three-dimensional material anchored to artificial or biological surfaces, with profound impact on many human activities. Biofilms are recognized as complex systems but their physical properties have been mainly studied from a macroscopic perspective. To determine biofilm local mechanical properties, reveal their potential heterogeneity, and investigate their relation to molecular traits, we have developed a seemingly new microrheology approach based on magnetic particle infiltration in growing biofilms. Using magnetic tweezers, we achieved what was, to our knowledge, the first three-dimensional mapping of the viscoelastic parameters on biofilms formed by the bacterium Escherichia coli. We demonstrate that its mechanical profile may exhibit elastic compliance values spread over three orders of magnitude in a given biofilm. We also prove that heterogeneity strongly depends on external conditions such as growth shear stress. Using strains genetically engineered to produce well-characterized cell surface adhesins, we show that the mechanical profile of biofilm is exquisitely sensitive to the expression of different surface appendages such as F pilus or curli. These results provide a quantitative view of local mechanical properties within intact biofilms and open up an additional avenue for elucidating the emergence and fate of the different microenvironments within these living materials.

Impacts of hematite nanoparticle exposure on biomechanical, adhesive, and surface electrical properties of Escherichia coli cells

Despite a wealth of studies examining the toxicity of engineered nanomaterials, current knowledge on their cytotoxic mechanisms (particularly from a physical perspective) remains limited. In this work, we imaged and quantitatively characterized the biomechanical (hardness and elasticity), adhesive, and surface electrical properties of Escherichia coli cells with and without exposure to hematite nanoparticles (NPs) in an effort to advance our understanding of the cytotoxic impacts of nanomaterials. Both scanning electron microscopy (SEM) and atomic force microscopy (AFM) showed that E. coli cells had noticeable deformation with hematite treatment for 45 min with a statistical significance. The hematite-treated cells became significantly harder or stiffer than untreated ones, as evidenced by indentation and spring constant measurements. The average indentation of the hematite-treated E. coli cells was 120 nm, which is significantly lower (P < 0.01) than that of the untreated cells (approximately 400 nm). The spring constant of hematite-treated E. coli cells (0.28 ± 0.11 nN/nm) was about 20 times higher than that of untreated ones (0.01 ± 0.01 nN/nm). The zeta potential of E. coli cells, measured by dynamic light scattering (DLS), was shown to shift from -4 ± 2 mV to -27 ± 8 mV with progressive surface adsorption of hematite NPs, a finding which is consistent with the local surface potential measured by Kelvin probe force microscopy (KPFM). Overall, the reported findings quantitatively revealed the adverse impacts of nanomaterial exposure on physical properties of bacterial cells and should provide insight into the toxicity mechanisms of nanomaterials.

Characterisation of spin coated engineered Escherichia coli biofilms using atomic force microscopy

The ability of biofilms to withstand chemical and physical extremes gives them the potential to be developed as robust biocatalysts. Critical to this issue is their capacity to withstand the physical environment within a bioreactor; in order to assess this capability knowledge of their surface properties and adhesive strength is required. Novel atomic force microscopy experiments conducted under growth conditions (30°C) were used to characterise Escherichia coli biofilms, which were generated by a recently developed spin-coating method onto a poly-l-lysine coated glass substrate. High-resolution topographical images were obtained throughout the course of biofilm development, quantifying the tip-cell interaction force during the 10 day maturation process. Strikingly, the adhesion force between the Si AFM tip and the biofilm surface increased from 0.8 nN to 40 nN within 3 days. This was most likely due to the production of extracellular polymer substance (EPS), over the maturation period, which was also observed by electron microscopy. At later stages of maturation, multiple retraction events were also identified corresponding to biofilm surface features thought to be EPS components. The spin coated biofilms were shown to have stronger surface adhesion than an equivalent conventionally grown biofilm on the same glass substrate.

Atomic force microscopy of a ctpA mutant in Rhizobium leguminosarum reveals surface defects linking CtpA function to biofilm formation

Atomic force microscopy was used to investigate the surface ultrastructure, adhesive properties and biofilm formation of Rhizobium leguminosarum and a ctpA mutant strain. The surface ultrastructure of wild-type R. leguminosarum consists of tightly packed surface subunits, whereas the ctpA mutant has much larger subunits with loose lateral packing. The ctpA mutant strain is not capable of developing fully mature biofilms, consistent with its altered surface ultrastructure, greater roughness and stronger adhesion to hydrophilic surfaces. For both strains, surface roughness and adhesive forces increased as a function of calcium ion concentration, and for each, biofilms were thicker at higher calcium concentrations.

Elasticity and physico-chemical properties during drinking water biofilm formation

Atomic force microscope techniques and multi-staining fluorescence microscopy were employed to study the steps in drinking water biofilm formation. During the formation of a conditioning layer, surface hydrophobic forces increased and the range of characteristic hydrophobic forces diversified with time, becoming progressively complex in macromolecular composition, which in return triggered irreversible cellular adhesion. AFM visualization of 1 to 8 week drinking water biofilms showed a spatially discontinuous and heterogeneous distribution comprising an extensive network of filamentous fungi in which biofilm aggregates were embedded. The elastic modulus of 40-day-old biofilms ranged from 200 to 9000 kPa, and the biofilm deposits with a height >0.5 μm had an elastic modulus <600 kPa, suggesting that the drinking water biofilms were composed of a soft top layer and a basal layer with significantly higher elastic modulus values falling in the range of fungal elasticity.

Physicochemical regulation of biofilm formation

This article reviews the physical and chemical constraints of environments on biofilm formation. We provide a perspective on how materials science and engineering can address fundamental questions and unmet technological challenges in this area of microbiology, such as biofilm prevention. Specifically, we discuss three factors that impact the development and organization of bacterial communities. (1) Physical properties of surfaces regulate cell attachment and physiology and affect early stages of biofilm formation. (2) Chemical properties influence the adhesion of cells to surfaces and their development into biofilms and communities. (3) Chemical communication between cells attenuates growth and influences the organization of communities. Mechanisms of spatial and temporal confinement control the dimensions of communities and the diffusion path length for chemical communication between biofilms, which, in turn, influences biofilm phenotypes. Armed with a detailed understanding of biofilm formation, researchers are applying the tools and techniques of materials science and engineering to revolutionize the study and control of bacterial communities growing at interfaces.

Application of AFM from microbial cell to biofilm

Atomic Force Microscopy (AFM) has proven itself over recent years as an essential tool for the analysis of microbial systems. This article will review how AFM has been used to study microbial systems to provide unique insight into their behavior and relationship with their environment. Immobilization of live cells has enabled AFM imaging and force measurement to provide understanding of the structure and function of numerous microbial cells. At the macromolecular level AFM investigation into the properties of surface macromolecules and the energies associated with their mechanical conformation and functionality has helped unravel the complex interactions of microbial cells. At the level of the whole cell AFM has provided an integrated analysis of how the microbial cell exploits its environment through its selective, adaptable interface, the cell surface. In addition to these areas of study the AFM investigation of microbial biofilms has been vital for industrial and medical process analysis. There exists a tremendous potential for the future application of AFM to microbial systems and this has been strengthened by the trend to use AFM in combination with other characterization methods, such as confocal microscopy and Raman spectroscopy, to elucidate dynamic cellular processes.

Application of AFM in microbiology: a review

Atomic force microscopy (AFM) is a powerful tool for microbiological investigation. This versatile technique cannot only image cellular surfaces at high resolution, but also measure many forms of fundamental interactions over scales ranging from molecules to cells. In this work, we review the recent development of AFM applications in the microbial area. We discuss several approaches for using AFM scanning images to investigate morphological characteristics of microbes and the use of force-distance curves to investigate interaction of microbial samples at the nanometer and cellular levels. Complementary techniques used in combination with AFM for study of microbes are also discussed.

Differential lipopolysaccharide core capping leads to quantitative and correlated modifications of mechanical and structural properties in Pseudomonas aeruginosa biofilms

Bacterial biofilms are responsible for the majority of all microbial infections and have profound impact on industrial and geochemical processes. While many studies documented phenotypic differentiation and gene regulation of biofilms, the importance of their structural and mechanical properties is poorly understood. Here we investigate how changes in lipopolysaccharide (LPS) core capping in Pseudomonas aeruginosa affect biofilm structure through modification of adhesive, cohesive, and viscoelastic properties at an early stage of biofilm development. Microbead force spectroscopy and atomic force microscopy were used to characterize P. aeruginosa biofilm interactions with either glass substrata or bacterial lawns. Using isogenic migA, wapR, and rmlC mutants with defined LPS characteristics, we observed significant changes in cell mechanical properties among these strains compared to wild-type strain PAO1. Specifically, truncation of core oligosaccharides enhanced both adhesive and cohesive forces by up to 10-fold, whereas changes in instantaneous elasticity were correlated with the presence of O antigen. Using confocal laser scanning microscopy to quantify biofilm structural changes with respect to differences in LPS core capping, we observed that textural parameters varied with adhesion or the inverse of cohesion, while areal and volumetric parameters were linked to adhesion, cohesion, or the balance between them. In conclusion, this report demonstrated for the first time that changes in LPS expression resulted in quantifiable cellular mechanical changes that were correlated with structural changes in bacterial biofilms. Thus, the interplay between architectural and functional properties may be an important contributor to bacterial community survival.