Microtomography of bacterial biofilms

Post-doc project

3D X-ray tomography of a biofilms developing in a biofilter (~500 mm3)
3D X-ray tomography of a biofilms developing in a biofilter (~500 mm3)

Biofilms are made of bacteria attached to a solid surface and secreting extracellular polymers that constitute a cohesive matrix facilitating adhesion and protecting the microorganisms from external aggression. Due to their low sensitivity to antimicrobial treatments, biofilms cause serious health concerns, especially when developping in catheters for instance. However, they also represent an interesting solution in bioreactor systems, for the treatment of various organic compounds which are more and more present in industrial and urban waste effluents. In the case of biofiltration, the biofilms are fixed on a packing media, through which the liquid effluent flows and the pollutants are assimilated by the bacteria.


The interactions between the growing biofilm and the liquid flow remain poorly understood although they are suspected to play a key role in the development and the efficiency of the micro-organisms involved in the assimilation of the effluent.

In this study, we focus on the biofilm growth (shape and spatial distribution) depending on the adhesive matrix (porous medium constituted of glass or clay beads), on the concentration of the nutrient solution and especially on its hydrodynamic properties.

A protocol was recently established to visualise in detail the internal structure of the biofilter using X-ray microtomography.


This project consist in visualising the 3D structure of biofilms using X-Ray Tomography for different operating conditions and at different scales and quantifying the evolution of the structural parameters (volume fraction and shape of the biofilm). The objective is to better understand the evolution of the physical parameters (permeability, dispersion) of the porous media as a function of the biofilter's height, growths conditions and filtration time, by using an upscaling process.


  • PI: Sabine Rolland du Roscoat
  • Co-PI: Zhujun Huang, Philippe Séchet
  • Post-doc: Tomislav Ivankovic


  • 3SR
  • LEGI
  • LTHE
  • LRP






Project update



Ivankovic T, Rolland du Roscoat S, Geindreau C, Sechet P, Huang Z, Martins J.M.F. Development and evaluation of an experimental protocol for 3-D visualization and characterization of the structure of bacterial biofilms in porous media using laboratory X-ray tomography. Biofouling 32 (2016) 1235-1244.


Oral papers


Tomislav Ivankovic, Sabine Rolland du Roscoat, Christian Geindreau, Philipe Séchet, Zhujun Huang, Pascal Charier, Jean M.F. Martins. Laboratory X-Ray Microtomography as a tool for 3D visualization of biofilm in porous media made up of zeolite. Microbiology Society Annual Conference 2017, Edinburgh, UK, April 3-6. 2017.


Tomislav Ivankovic, Sabine Rolland du Roscoat, Christian Geindreau, Jean Martins, Philipe Sechet, Zhujun Huang. Visualization and quantification of biofilm in porous media by X-Ray microtomography. FEMS 2015. Congress of European Microbiologists, Maastricht, Netherlands, June 7-11. 2015.


<< back