Joao B. Xavier*, Cristian Picioreanu, Mark C.M. van Loosdrecht
Department of Biotechnology, Delft University of Technology
Julianalaan 67, 2628 BC Delft, The Netherlands.
Tel: +31-(0)15-2781551, Fax: +31-(0)15-2782355
*Corresponding author. E-mail:
J.Xavier@tnw.tudelft.nl
This web page contains support material for our paper entitled "A
Framework for Multidimensional Modelling of Activity and Structure of
Multispecies Biofilms", Environ.
Microbiol.
7(8):1085-1103. The paper reports on the integration of
biofilm modelling concepts developed at the Environmental
Biotechnology Group
into a general purpose framework for multidimensional modelling of
biofilms.
The framework describes biofilms using individual based modelling (IbM)
and allows the simulation of biofilm species with any number of
bacterial and solute species, additionally integrating biomass
detachment and structured biomass. The following material may be found
here:
| Case study animations | Video files of 2D simulations performed for the case study presented in the article |
| The program | Java class library implementing the framework |
Case study animations
The article presents a case study which intends
to show the capability of the framework to model biofilm systems with
several components. Competition between two heterotrophic bacterial
species constituting a biofilm is analyzed in the context of two
feeding regimes: (1) continuous feeding regime, in which substrate is
supplied at a concentration constant in time and (2) feast/famine
regime, in which substrate is supplied in a intermittent way.
For a description in detail of the system described in the case study,
please refer to the
article in question. The material provided here provides only a
complement to the article.
Bellow are provided animations of the 2D simulations shown in the
article (Figure 5) for both the continuous feeding and feast/famine
cases. The simulation videos are available in both QuickTime
(recommended, download
the QuickTime player) and windows avi format.
The following legend describes the two panels shown in the animations:
Left panel: Biofilm biomass composition profiles
The left panel describes the composition of the biomass in the
particulate species considered in the model: active mass of bacterial
species H-EPS and H-PHB, EPS (extracellular polymeric substances), PHB
(an internal storage polymer) and inert biomass. The components are
represented by the following colors:
Right panel: Biofilm structure
The right panel shows the biofilm structure as the simulation
progresses.
Spherical particles composing the biomass as described in the article
are shown with different
colors representing the local biomass composition.
As active biomass (either H-PHB active mass or H-EPS active mass)
decays and
inert biomass is formed, particle color will also change towards a dark
gray. Also, particles
representing the H-PHB bacterial species may show colors ranging from
blue to yellow
depending on the fraction of PHB in the particle (blue means lower PHB
fraction, yellow means higher PHB fraction in cells).
Coninuous feeding case
In continuous feeding regime, H-EPS organisms become dominant thanks to the faster spreading resultant from EPS production. H-EPS organisms reach a top position in the biofilm where they profit from the higher oxygen concentration. H-PHB organism, in turn, located in the depth of the biofilm where oxygen concentrations are lower, stop growing and are eventually supplanted or wash out.
Notes:
The animation shows a simulation as presented in the paper (Figure 5).
The fast spreading of the H-EPS bacteria (shown in red) thanks to the
high of volume of EPS produced (shown in gray) as described in paper is
notable at the begining of the simulation.
By the end of the simulation, inert material accumulates at the bottom
of the biofilm, as a result of biomass decay. The H-PHB particles,
initially colored blue, turn green due to accumulation of PHB, which is
never consumed, as external substrate is permanently available. By the
end of the simulation, H-PHB is supplanted by the H-EPS species that,
placed favorably at the top of the biofilm, consumes most of the oxygen
that does not
reach the lower regions of the biofilm.
Feast/famine case
Feast/famine regimes select for PHB producing organisms. H-PHB bacteria store substrate in the form of PHB during the feast period, and consume their internal storage in the famine period thus being able to continue growing even in the famine period.
Notes:
In the feast/famine case, substrate concentration in the system is
intermittent: high during the feast phase and null in the famine phase.
A "blinking effect" of the oxygen concentration contour plot is visible
in the animation, which results from the different oxygen limitation
regimes verified in the feast and famine phases. In feast phase
external substrate is available, and oxygen concentration becomes
limiting. This is observable from the gradient in oxygen concentration
shown. In the famine phase, in turn, only H-PHB organisms are able to
grow, albeit slower, thanks to internally stored PHB. Overall oxygen
consumption is then much lower, and growth is no longer limited by
oxygen. This results in an increased oxygen penetration in the biofilm
depth.
Applied detachment is the same for both the continuous case shown above and this feast/famine case. However, due to overall lower growth rates in the feast/famine feeding regime, the biofilm achieved at the end of the simulation (day 62) is much thinner.
The biofilm modelling framework program
The program implementing the biofilm modelling framework is available here for download in the form of a compiled library of Java classes.
In addition to the Java compiled classes, this package also contains the source code for example applications (subdirectory nl/tudelft/bt/model/examples in the package) and javadoc documentation for the compiled code (subdirectory doc). For a quick-start refer to our guide on how to use the program with Eclipse.
The zip package contains everything necessary to run biofilm models using the framework. As described in the article, the program has many features and its use requires knowledge of the Java programming language. For those whishing use the framework it would be best to check the implementation of the biofilm system introduced in the case study. Source code for the case study model is contained also in the zip package (nl/tudelft/bt/model/examples/CaseStudyPHBvsEPS.java).
To learn more about the structure of the program, read a short description of structure of the framework's program.
To allow the users less familiar with the Java programming language to also try out the program, we have set up a web page showing a java applet that directly uses the framework.zip package. The applet can be accessed through the following link.
Run a monospecies 2D biofilm model
The applet shows a simple monospecies biofilm growing in the presence of detachment forces. Several model parameters may be changed in real-time and their effect in the biofilm growth directly observed in the ongoing simulation
Additional links
More material from our research group
| Electronic Poster | Electronic verision of a poster introducing the framework. Contains additional animations of simulations carried out using the framework |