Table 3 Comparison of common experimental systems
From: Disentangling the feedback loops driving spatial patterning in microbial communities
| Â | Colonies on agar plates | Biofilms in flow cells | Monolayers in growth chambers | Microcolonies on agar pads |
|---|---|---|---|---|
Scale | ||||
Cell numbera | >109 | 103–106 | 100–1000 | 10–500 |
Length scale | 1–10 mm | 10–500 μm | 10–100 μm | 5–20 μm |
Imaging resolution | Population-level | Single-cell for small biofilms | Single-cell | Single-cell |
Physical environment | ||||
Growth interface | Agar-air | Liquid-glass | Agar-liquid-glass | PDMS-liquid-glass |
Density | High | High | High | Low |
Physical constraints | None | None | Restricted in all dimensions | Restricted in z-dimension |
Dominant forces | Crowding, friction, surface tension | Crowding, shear force | Crowding, friction | Crowding, friction, surface tension |
Chemical environment | ||||
Nutrient supply | From agar, finite resources | From liquid, replenished | From liquid, replenished | From agar, finite resources |
Dominant gradients | From air & agar interface to biofilm core | From liquid interface to biofilm core | From opening to death end of chamber | From edge to center of microcolony |
Steady-state gradients? | Quasi-steady stateb | Quasi-steady stateb | Yes | No |
Diffusion within community | Through crowded biofilm & agar | Through crowded biofilm | Through crowded chamber | Through agar |
Chemical coupling between communities? | No | Yes, through flow and diffusion | No | Yes, through diffusion |
Movement of cells between communities? | No | Yes, through flow and motility | No | Yes, through surface motility |
