Biofilms with Extracellular Polymeric Substances
This section marks the latest completed step of BacSim development, the inclusion of Extracellular Polymeric Substances (EPS) formation in the model.
The structure of the biofilm was dramatically influenced by EPS production. All effects of EPS formation on the growth of producing and non-producing strains could be understood in terms of the energy cost of EPS production. By the same token, EPS accumulation can fall as its rate of production increases. Further, the effect of introducing binding forces between cells was investigated.
Please read this paper for a detailed description of the biofilm model with EPS production. You can also download the source of the model, or run the simulation in your web browser, see the section on BacSim.
Have a look at images producing EPS or capsules at various rates. The images show biofilms at the end of the simulated time interval (3 weeks), with oxygen contours demonstrating the oxygen limitation in the biofilm.
No EPS production (control)
Biofilm, aged 30,000 min (3 weeks). The contour lines show the oxygen concentration in mg/l. The image was rendered with POV-Ray, showing each cell as a sphere. The ammonia oxidisers ("Nitroso") are blue; the nitrite oxidisers ("Nitro") are red. See the reaction scheme below. The grey box at the bottom is the inert substratum. Note the wrapped around boundaries in the horizontal direction. Scale: total width of the system = 200 µm.
Without EPS production, the biofilm is dense throughout and oxygen penetration is very limited.
EPS production by ammonia oxidisers at a high rate
Biofilm, aged 30,000 min (3 weeks). The contour lines show the oxygen concentration in mg/l. The image was rendered with POV-Ray, showing each cell as a sphere. The ammonia oxidisers ("Nitroso") are blue, and the EPS they produce is bluish (cyan); the nitrite oxidisers ("Nitro") are red. See the reaction scheme below. The grey box at the bottom is the inert substratum. Note the wrapped around boundaries in the horizontal direction. Scale: total width of the system = 200 µm.
At this high rate of EPS production, the producing cells spend more energy on EPS synthesis than they can gain from ammonia oxidation further down in the biofilm where they are oxygen limited. Hence, they begin to shrink and eventually die when they have shrunk below a minimum size. The EPS itself is assumed not to decay in the simulation shown here. Note how the red cells are dragged along with the stream of slime produced by the blue cells while the EPS hardly mixes with the clusters of red cells.
EPS production by ammonia oxidisers at a low rate
Biofilm, aged 30,000 min (3 weeks). The contour lines show the oxygen concentration in mg/l. The image was rendered with POV-Ray, showing each cell as a sphere. The ammonia oxidisers ("Nitroso") are blue, and the EPS they produce is bluish (cyan); the nitrite oxidisers ("Nitro") are red. See the reaction scheme below. The grey box at the bottom is the inert substratum. Note the wrapped around boundaries in the horizontal direction. Scale: total width of the system = 200 µm.
At this lower rate of EPS production, the producing cells spend less energy on EPS synthesis and are thus able to survive. The EPS itself is assumed not to decay in the simulation shown here.
EPS production by ammonia oxidisers at a low rate, cells sticky
Biofilm, aged 30,000 min (3 weeks). The contour lines show the oxygen concentration in mg/l. The image was rendered with POV-Ray, showing each cell as a sphere. The ammonia oxidisers ("Nitroso") are blue, and the EPS they produce is bluish (cyan); the nitrite oxidisers ("Nitro") are red. See the reaction scheme below. The grey box at the bottom is the inert substratum. Note the wrapped around boundaries in the horizontal direction. Scale: total width of the system = 200 µm.
The EPS producing cells usually become separated from each other with time due to the flow of EPS they create. In this simulation, the producing cells stick to each other by means of weak attractive forces of short range, modelling surface-bound adhesive molecules or pili. Larger clusters of blue cells and correspondingly larger patches of EPS devoid of cells are formed compared with the previous movie with non-sticky cells.
Capsule formation by ammonia oxidisers at a high rate
Biofilm, aged 30,000 min (3 weeks). The contour lines show the oxygen concentration in mg/l. The image was rendered with POV-Ray, showing each cell as a sphere. The ammonia oxidisers ("Nitroso") are blue, and the capsules surrounding them are bluish (cyan); the nitrite oxidisers ("Nitro") are red. See the reaction scheme below. The grey box at the bottom is the inert substratum. Note the wrapped around boundaries in the horizontal direction. Scale: total width of the system = 200 µm.
As with EPS production at a high rate, producing cells shrink and eventually die in the deep end of the biofilm where not enough oxygen penetrates to sustain the energy expenditure of EPS production. Since capsules are EPS material that stays attached to the cells, cells become more evenly separated from each other compared with EPS production.
Capsule formation by ammonia oxidisers at a low rate
Biofilm, aged 30,000 min (3 weeks). The contour lines show the oxygen concentration in mg/l. The image was rendered with POV-Ray, showing each cell as a sphere. The ammonia oxidisers ("Nitroso") are blue, and the capsules surrounding them are bluish (cyan); the nitrite oxidisers ("Nitro") are red. See the reaction scheme below. The grey box at the bottom is the inert substratum. Note the wrapped around boundaries in the horizontal direction. Scale: total width of the system = 200 µm.
As with EPS production at a low rate, no death occurs since cells don't waste too much energy on capsule formation. Cells here are very evenly spaced and just not that dense as without EPS production or capsule formation.