Application Note: Imaging Bacteria and Biofilms with AFM
Reveal the Nanoscale Structure of Microbes — Without the Vacuum Chamber
Atomic force microscopy (AFM) is a powerful technique for visualizing and quantifying the exact structure of bacteria and biofilms at nanometre resolution—in air, without requiring staining, sectioning, coating, or vacuum conditions like for scanning or tunneling electron microscopy (SEM/TEM).
With ICSPI’s desktop On-Chip AFM systems, researchers can rapidly image live or fixed microbial samples on mica, glass, or filter paper to analyze morphology, biofilm structure, cell surface roughness, and modification-induced changes—offering a fast and accessible alternative to electron microscopy.
Why Use AFM for Bacterial Research?
AFM offers a unique combination of capabilities for microbiology:
✅ Quantitative nanoscale resolution: Capture high-resolution 3D surface topography down to sub-nanometre vertical resolution.
✅ Hydrated or dry imaging: Image microbes in near-native ambient conditions on filter paper or glass slides, reducing sample prep time and preserving delicate structures.
✅ Non-destructive scanning: Monitor structural changes in response to treatments over time, including antibiotics or peptides.
✅ Mechanical property mapping: Compare hardness versus softness of various features with phase imaging.
✅ Compatible with other techniques: Use AFM alongside electron and fluorescence microscopy for a more complete picture.
Read more about the specifications of our various AFM models and how they compare.
Case Study #1: Bacteria After Antibiotic Treatment
Dr. Christopher Reid (Bryant University) studies the mechanisms behind enzymatic cell wall thickening in bacteria to better understand how microbes develop antibiotic resistance.
Samples of Bacillus subtilis treated with masarimycin, an antibiotic that inhibits autolysin activity responsible for remodeling the peptidoglycan cell wall, were deposited and fixed on filter paper. Scans of these and control samples are taken using an ICSPI Redux AFM with the results shown below.
AFM revealed:
🦠 Longer chains of bacterial cells — Disruption of autolysin activity impaired cell division.
🦠 Lower cell density on substrates — Suggests impaired growth under sub-MIC antibiotic treatment.
🦠 Rough, irregular cell surfaces — Correlates with thickened cell walls observed in SEM, indicating disruption of peptidoglycan metabolism.
The AFM results supported findings from scanning electron microscopy but were acquired in under a morning with minimal sample prep.
Read more about how our AFMs support academic research on our Publications page.
Case Study #2: Discerning the Effects of Genetic Modification in Gram-Positive Bacterial Biofilms
Professor Joel Weadge (Wilfrid Laurier University) studies biofilms and their components for various infectious bacteria to understand how they colonize various surfaces and spread diseases.
He and his student from Wilfrid Laurier University brought in dried genetically modified and wild-type Gram-positive Clostridioides difficile colonies to scan using the Redux AFM.
Using AFM, they were able to visualize:
🧫 Control vs. mutant phenotypes in biofilm colonies and the effects of genetic modification
🧫 Spores vs. actively growing cells across hydrated filter paper
🧫 Cell surface morphology with high clarity across all samples
Applications in Microbiology
AFM is ideal for:
🔬 Studying cell wall synthesis and antibiotic mechanisms
🔬 Visualizing biofilm architecture and extracellular polymer networks
🔬 Investigating probiotics, pathogens, and microbiome interactions
See What AFM Can Reveal
Whether you’re investigating Gram-positive biofilms, antibiotic mechanisms, or bacterial nanostructures, On-Chip AFM offers a fast and powerful method to capture detailed morphology and structural changes at the nanoscale.
Example Workflow
Speak with an expert
Interested to learn more about how AFM can provide insight on your microbial samples?