TU Delft
A FRAMEWORK FOR MULTIDIMENSIONAL MODELLING OF ACTIVITY AND STRUCTURE OF MULTIDIMENSIONAL MODELLING OF MULTISPECIES BIOFILMS

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:

The plot changes as the biofilm composition changes in time throughout the simulation, showing how the biomass components are distributed through the biofilm depth, x.

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).

Oxygen concentration in the liquid above the biofilm is represented using a shaded contour plot, with colours ranging from dark gray (high oxygen concentration) to white (local lower oxygen concentration:

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.

Download animation of the continuous feeding case: Quicktime Mov[12 Mb], Window AVI[17 Mb]

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.

It should also be noted that, in the left panel, the profile correspondent to the PHB constitution of the biofilm shows an intermittent behaviour resultant from the feast/famine cycles. PHB is accumulated in the feast phase and consumed in the famine phase.
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.
Download animation of the feast/famine case: Quicktime Mov[5 Mb], Window AVI[25 Mb]

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.

download the program [3 Mb]

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

2004 - Biofilm modelling group at the TU Delft