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  • Review Article
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Using nanotechniques to explore microbial surfaces

Nature Reviews Microbiology volume 2, pages 451–460 (2004)Cite this article

Key Points

  • Microbial surfaces form a boundary between microbial cells and their external environment and, as well as this protective function, they actively participate in many cellular interactions. Although electron microscopy techniques have been used to study microbial surfaces to great effect, their use is limited by the fact that they cannot be used to examine specimens in aqueous solution. There was therefore a need to develop new techniques to probe the structure, properties and interactions of microbial surfaces at sub-nanometre resolution; atomic force microscopy (AFM) is one such technique.

  • Unlike conventional microscopy methods, AFM does not use an incident beam to generate an image. Instead, AFM directly measures the physical interaction between the sample and a sensitive probe, or tip. The sample can be moved in three dimensions relative to the tip by a piezoelectric system. The tip is attached to a cantilever, which functions as a small spring and the deflection of the cantilever due to the interaction between the tip and the sample is detected by a laser beam that is focused on the cantilever and reflected onto a photodiode.

  • There are several different operating modes for AFM, including contact mode and tapping mode, which is suitable for imaging 'soft' samples such as bacteria. In force spectroscopy, the forces acting on the instrument tip can be measured to piconewton sensitivity, and this mode can be used to probe the interaction forces between or within biological molecules.

  • There are many different applications for AFM imaging in microbiology research. For example, single membrane proteins can be visualized at sub-nanometre resolution and the surface of living cells can be observed directly as they grow or interact with enzymes. The use of the force spectroscopy mode opens a range of unique possibilities to probe cell-wall elasticity, map cell-surface charges, manipulate individual surface molecules and detect molecular-recognition events.

  • Since its inception in the mid-1980s, the instrumentation and methods of sample preparation for AFM have advanced greatly. The current limitations and technological issues associated with applying AFM to microbiology research are discussed.

Abstract

Our current understanding of microbial surfaces owes much to the development of electron microscopy techniques. Yet, a crucial limitation of electron microscopy is that it cannot be used to examine biological structures directly in aqueous solutions. In recent years, however, atomic force microscopy (AFM) has provided a range of new opportunities for viewing and manipulating microbial surfaces in their native environments. Examples of AFM-based analyses include visualizing conformational changes in single membrane proteins, the real-time observation of cell-surface dynamics, analysing the unfolding of cell-surface proteins and detecting individual cell-surface receptors. These analyses have contributed to our understanding of the structure–function relationships of cell surfaces and will hopefully allow new applications to be developed for AFM in medicine and biotechnology.

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Figure 1: The principles of atomic force microscopy.
Figure 2: Observing native membrane proteins at sub-nanometre resolution.
Figure 3: Visualizing conformational changes in membrane proteins.
Figure 4: Tracking cell surfaces in their native state.
Figure 5: Manipulation of single molecules.
Figure 6: Detection of molecular-recognition events at cell surfaces.

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Acknowledgements

The author is a research associate of the Belgian National Foundation for Scientific Research (FNRS). The support of the FNRS, the Université catholique de Louvain (Special Fund for Research), the Federal Office for Scientific, Technical and Cultural Affairs (Inter-university Poles of Attraction Programme) and the Research Department of Communauté Française de Belgique (Concerted Research Action) is gratefully acknowledged. He thanks nanobiotechnology researchers both in his laboratory and worldwide for sharing exciting experiments and discussions.

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  1. Unité de chimie des interfaces, Université catholique de Louvain, Croix du Sud 2/18, Louvain-la-Neuve, B-1348, Belgium

    Yves F. Dufrêne

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DATABASES

Entrez

Corynebacterium glutamicum

Deinococcus radiodurans

Dictyostelium discoideum

Escherichia coli

Halobacterium salinarium

Mycobacterium tuberculosis

Phanerochaete chrysosporium

Pseudomonas aeruginosa

Pseudomonas putida

Saccharomyces cerevisiae

Staphylococcus aureus

SwissProt

OmpF

FURTHER INFORMATION

Encyclopedia of Life Sciences

Atomic force microscopy

Scanning probe microscopy

Yves Dufrêne's laboratory

Glossary

CRYO-ELECTRON MICROSCOPY

An electron microscopy technique in which the sample is frozen to protect it during imaging.

ATOMIC FORCE MICROSCOPY

(AFM). A relatively new form of microscopy in which a sharp tip is scanned over the surface of a sample, while sensing the interaction force between the tip and the sample. Because AFM does not rely on an incident beam, as in electron or light microscopy, the specimen can be directly observed at high resolution in aqueous solution.

FORCE SPECTROSCOPY

A form of AFM in which the force acting on the tip is measured with piconewton (10−12 N) sensitivity as the tip is pushed towards the sample then retracted from it.

S-LAYERS

Two-dimensional arrays of protein or glycoprotein subunits with a molecular mass between 40,000 and 200,000 Daltons that are common constituents of bacterial cell walls.

HPI

The hexagonally packed intermediate (HPI) layer from Deinococcus radiodurans is an S-layer and was amongst the first S-layer systems to be viewed by AFM at submolecular resolution.

PORIN

A membrane protein that allows the passage of small molecules such as glucose through the membrane.

CANTILEVER

AFM tips are mounted on cantilever beams or triangles, which are typically made of silicon or silicon nitride, that behave like springs. Using Hooke's law, the magnitude of the tip–sample force is proportional to the deflection of the cantilever.

PIEZOELECTRIC CERAMICS

Materials that expand or contract when subjected to a potential difference.

MICROFABRICATION

A range of techniques that are derived from the techniques used in microelectronics to make integrated circuits and which are used to make AFM tips and cantilevers.

DEFLECTION

The vertical bending of the AFM cantilever resulting from the tip–sample interaction force.

BACTERIORHODOPSIN

A light-driven proton pump that is packed into a two-dimensional crystal lattice — known as the purple membrane — and integrated into the plasma membrane of Halobacterium salinarium.

SEPTAL ANNULUS

A structure formed during cell division that corresponds to the growth of wall material into the cytoplasm.

YOUNG'S MODULUS

Young's modulus, or the tensile elastic modulus, is a parameter that reflects the resistance of a material to elongation. The higher the Young's modulus, the larger the force needed to deform the material.

MUREIN SACCULI

Murein sacculus is the term used to refer to the net-like peptidoglycan layer that is found in the cell wall of bacteria.

BUD SCAR

The process by which S. cerevisiae proliferates is known as budding. A ring of chitin is formed between the mother cell and the daughter cell (or bud) and once the bud has been pinched off, a mark is left on the surface of the mother cell that is known as the bud scar. Chitin is the main constituent of the bud scar.

ISOELECTRIC POINT

The isoelectric point (or pI) of a protein is the pH at which the protein has an equal number of positive and negative charges.

FLOCCULATION

A process involving the aggregation of microbial cells. In beer-brewing, yeast flocculation occurs spontaneously near the end of fermentation, thereby providing an easy method to dispose of the cells.

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Dufrêne, Y. Using nanotechniques to explore microbial surfaces. Nat Rev Microbiol 2, 451–460 (2004). https://doi.org/10.1038/nrmicro905

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