Probing bacterial interactions: integrated approaches combining atomic force microscopy, electron microscopy and biophysical techniques

Nanomicrobiology

Recent advances in atomic force microscopy (AFM) are revolutionizing our views of microbial surfaces. While AFM imaging is very useful for visualizing the surface of hydrated cells and membranes on the nanoscale, force spectroscopy enables researchers to locally probe biomolecular forces and physical properties. These unique capabilities allow us to address a number of questions that were inaccessible before, such as how does the surface architecture of microbes change as they grow or interact with drugs, and what are the molecular forces driving their interaction with antibiotics and host cells? Here, we provide a flavor of recent achievements brought by AFM imaging and single molecule force spectroscopy in microbiology.

Surface-mediated chromate-resistant mechanism of Enterobacter cloacae bacteria investigated by atomic force microscopy

The Enterobacter cloacae CYS-25 strain isolated from a chromate plant shows a strong capability for chromate resistance instead of chromate reduction in aerobic conditions. In this study, atomic force microscopy (AFM) was used for studying the morphology characteristics of bacterial properties during the chromate resistance process. The average length of E. cloacae bacteria in the stationary phase is about 2.3 +/- 0.6 microm, while under the stimulation of 400 mg/L CrO42-, the length of bacteria increases to 3.2 +/- 0.7 microm. Height and phase images showed that, with the addition of CrO42-, the smooth surface of bacteria changed into one with discontinuous features with characteristic dimension of 40-200 nm. Analysis reveals that these compact convex patches are organic components stimulated by CrO42-. A chromate resistance mechanism relating to the overexpression of extracellular biologic components for preventing the permeability of CrO42- into the cell is proposed as the survival strategy of E. cloacae in chromate situation.

Atomic force microscopy of mechanically trapped bacterial cells

This article presents a study on the influence of the protocol used for immobilization of bacterial cells onto surfaces by mechanically trapping them into a filter. In this sense, the surface and structure of trapped cells are analyzed. Bacteria can be present solely or with extracellular polymeric substances (EPS). To test the behavior of the EPS layer duing the filtering process, different strains of a well-known EPS-producer bacteria (Staphylococcus epidermidis), which produce an extracellular matrix clearly visible in AFM images, have been used. Results show that this immobilization method can cause severe structural and mechanical deformation to the cell membrane. This altered mechanical state may possibly influence the parameters derived from AFM force curves (which are micro/nano-mechanical tests). Also, our results suggest that the EPS layer might move during the filtering process and could accumulate at the upper part of the cell, thus favoring distorted data of adhesion/pull-off forces as measured by an AFM tip, especially in the case of submicron-sized microbial cells such as bacteria.

HEPES-stabilized encapsulation of Salmonella typhimurium

Most bacteria, planktonic and sessile, are encapsulated inside loosely bound extracellular polymeric substance (EPS) in their physiological environment. Imaging a bacterium with its capsule requires lengthy sample preparation to enhance the capsular contrast. In this study, Salmonella typhimurium was investigated using atomic force microscopy for a practical means of imaging an encapsulated bacterium in air. The investigation further aimed to determine the relation between the buffers used for preparing the bacterium and the preservation of the capsular material surrounding it. It was observed that rinsing bacteria with HEPES buffer could stabilize and promote capsule formation, while rinsing with PBS, Tris, or glycine removes most of the capsular EPS. For bacteria rinsed with HEPES and air-dried, the height images showed only the contour of the capsular material, while the phase and amplitude images presented the detailed structures of the bacterial surface, including the flagella encapsulated inside the capsular EPS. The encapsulation was attributed to the cross-linking of the acidic exopolysaccharides mediated by the piperazine moiety of HEPES through electrostatic attraction. This explanation is supported by encapsulated bacteria observed for samples rinsed with N,N'-bis(2-hydroxyethyl)-piperazine solution and by the presence of entrapped HEPES within the dry capsular EPS suggested by micro-Raman spectroscopy.

Long polymeric tips of atomic force microscopy for large biological samples

We show a new atomic force microscopy technique for obtaining high-resolution topographic images of large bio-samples. To obtain high-resolution topographic images for the samples, we fabricated a long polymeric tip with a small protrusion using two-photon adsorbed photo-polymerization techniques. The obtained tip length was over 50 microm, and the tip was used directly to visualize COS-1 and 293 cells. Compared with commercial tips, the long tip made it easier to obtain topographic images of the large cells. In the magnified topographic images, the sub-100-nm resolution was confirmed with the long tips. This long probe tip is expected to broaden large sample-related studies and applications in the future.

Towards a nanoscale view of fungal surfaces

In the past years, atomic force microscopy (AFM) has offered novel possibilities for exploring the nanoscale surface properties of fungal cells. For the first time, AFM imaging enables investigators to visualize fine surface structures, such as rodlets, directly on native hydrated cells. Moreover, real-time imaging can be used to follow cell surface dynamics during cell growth and to monitor the effect of molecules such as enzymes and drugs. In fact, AFM is much more than a microscope in that when used in the force spectroscopy mode, it allows measurement of physicochemical properties such as surface energy and surface charge, to probe the elasticity of cell wall components and macromolecules, and to analyse the force and localization of molecular recognition events.

Nanoscale exploration of microbial surfaces using the atomic force microscope

Atomic force microscopy (AFM) has recently opened a variety of novel possibilities for imaging and manipulating microbial surfaces in their native environment. While AFM imaging offers a means to visualize surface structures at high resolution and in physiological conditions, AFM force spectroscopy enables researchers to probe a variety of properties, including the unfolding pathways of single-membrane proteins, the elasticity of cell walls and surface macromolecules, and the molecular forces responsible for cell–cell and cell–solid interactions. These nanoscale analyses enable us to answer a number of questions that were difficult to address previously, such as: how does the surface architecture of microbes change as they grow or interact with antibiotics; what is the force required to unfold and extract a single membrane protein; and what are the molecular forces driving the interaction between a pathogen and a host or biomaterial surface? This review will expand on these issues.

The effect of solvent polarity on the molecular surface properties and adhesion of Escherichia coli

The elasticity and molecular surface characteristics of Escherichia coli JM109 were investigated via atomic force microscopy (AFM) in solvents expressing different polarities. The nature of bacterial adhesion and surface characteristics was probed in formamide, water, and methanol, with dielectric constants of 111, 80, and 33, respectively. Solvent polarity affected the elasticity of the bacterium, the conformation of the cell surface biopolymers, the height of the surface biopolymers, and measured adhesion forces between the bacterium and silicon nitride. By applying the Hertz model to force-indentation data, we determined that the Young's modulus was greatest in the least polar solvent, with values of 182 +/- 34.6, 12.8 +/- 0.1, and 0.8 +/- 0.3 MPa in methanol, water, and formamide, respectively. The thickness of the biopolymer brush layer on the bacterial surface was quantified using a steric model, and these values increased as polarity increased, with values of 27, 93, and 257 nm in methanol, water, and formamide, respectively. The latter results suggest that highly polar conditions favor extension of the biopolymer brush layer. Cross-sectional analysis performed on tapping mode images of the bacterial cells in methanol, water, and formamide further supported this hypothesis. The image height values are larger, since the image analysis measures the height of the bacterium and the polymer layer, but the trend with respect to solvent polarity was the same as was obtained from the steric model of the brush length. Measured adhesion forces scaled inversely with solvent polarity, with greatest adhesion observed in the least polar solvent, methanol. The combined conformational changes to the bacterial surface and biopolymer layer result in different presentations of macromolecules to a substrate surface, and therefore affect the adhesion forces between the bacterial molecules and the substrate. These results suggest that polarity of the solvent environment can be manipulated as a design parameter to control or modify the bacterial adhesion process.

Influence of fermentation medium composition on physicochemical surface properties of Lactobacillus acidophilus

The effect of the simple and complex basic components of a fermentation medium on the surface properties of Lactobacillus acidophilus NCC2628 is studied by physicochemical methods, such as electrophoresis, interfacial adhesion, and X-ray photonelectron spectroscopy, and by transmission electron microscopy. Starting from an optimized complete medium, the effect of carbohydrates, peptones, and yeast extracts on the physicochemical properties of the cell wall is systematically investigated by consecutively omitting one of the principal components from the fermentation medium at the time. The physicochemical properties and structure of the bacterial cell wall remain largely unchanged if the carbohydrate content of the fermentation medium is strongly reduced, although the concentration of surface proteins increases slightly. Both peptone and yeast extract have a considerable influence on the bacterial cell wall, as witnessed by changes in surface charge, hydrophobicity, and the nitrogen-to-carbon ratio. Both zeta potential and the cell wall hydrophobicity show a positive correlation with the nitrogen-to-carbon ratio of the bacterial surfaces, indicative of the important role of surface proteins in the overall surface physical chemistry. The hydrophobicity of the cell wall, which is low for the cultures grown in the complete medium and in the absence of carbohydrates, becomes fairly high for the cultures grown in the medium without peptones and the medium without yeast extract. UV spectrophotometry and sodium dodecyl sulfate-polyacrylamide gel electrophoresis combined with liquid chromatography-tandem mass spectrometry are used to analyze the effect of medium composition on LiCl-extractable cell wall proteins, confirming the major change in protein composition of the cell wall for the culture fermented in the medium without peptones. In particular, it is found that expression of the S-layer protein is dependent on the protein source of the fermentation medium.

Plasmid donor affects host range of promiscuous IncP-1beta plasmid pB10 in an activated-sludge microbial community

Horizontal transfer of multiresistance plasmids in the environment contributes to the growing problem of drug-resistant pathogens. Even though the plasmid host cell is the primary environment in which the plasmid functions, possible effects of the plasmid donor on the range of bacteria to which plasmids spread in microbial communities have not been investigated. In this study we show that the host range of a broad-host-range plasmid within an activated-sludge microbial community was influenced by the donor strain and that various mating conditions and isolation strategies increased the diversity of transconjugants detected. To detect transconjugants, the plasmid pB10 was marked with lacp-rfp, while rfp expression was repressed in the donors by chromosomal lacI(q). The phylogeny of 306 transconjugants obtained was determined by analysis of partial 16S rRNA gene sequences. The transconjugants belonged to 15 genera of the alpha- and gamma-Proteobacteria. The phylogenetic diversity of transconjugants obtained in separate matings with donors Pseudomonas putida SM1443, Ralstonia eutropha JMP228, and Sinorhizobium meliloti RM1021 was significantly different. For example, the transconjugants obtained after matings in sludge with S. meliloti RM1021 included eight genera that were not represented among the transconjugants obtained with the other two donors. Our results indicate that the spectrum of hosts to which a promiscuous plasmid transfers in a microbial community can be strongly influenced by the donor from which it transfers.