Imaging biofilm in porous media using X-ray computed microtomography

Yohan Davit (1, 2) , Gabriel Iltis (3) , Gerald Debenest (1) , Stéphanie Veran-Tissoires (1) , Dorthe Wildenschild (3) , Magali Gérino (2) , Michel Quintard (1)

1 IMFT - Institut de mécanique des fluides de Toulouse
2 LEFE - Laboratoire Ecologie Fonctionnelle et Environnement
3 Oregon State University - OSU (USA)

In this study, a new technique for three-dimensional imaging of biofilm within porous media using X-ray computed microtomography is presented. Due to the similarity in X-ray absorption coefficients for the porous media (plastic), biofilm and aqueous phase, an X-ray contrast agent is required to image biofilm within the experimental matrix using X-ray computed tomography. The presented technique utilizes a medical suspension of barium sulphate to differentiate between the aqueous phase and the biofilm. Potassium iodide is added to the suspension to aid in delineation between the biofilm and the experimental porous medium. The iodide readily diffuses into the biofilm while the barium sulphate suspension remains in the aqueous phase. This allows for effective differentiation of the three phases within the experimental systems utilized in this study. The behaviour of the two contrast agents, in particular of the barium sulphate, is addressed by comparing two-dimensional images of biofilm within a pore network obtained by (1) optical visualization and (2) X-ray absorption radiography. We show that the contrast mixture provides contrast between the biofilm, the aqueous-phase and the solid-phase (beads). The imaging method is then applied to two three-dimensional packed-bead columns within which biofilm was grown. Examples of reconstructed images are provided to illustrate the effectiveness of the method. Limitations and applications of the technique are discussed. A key benefit, associated with the presented method, is that it captures a substantial amount of information regarding the topology of the pore-scale transport processes. For example, the quantification of changes in porous media effective parameters, such as dispersion or permeability, induced by biofilm growth, is possible using specific upscaling techniques and numerical analysis. We emphasize that the results presented here serve as a first test of this novel approach; issues with accurate segmentation of the images, optimal concentrations of contrast agents and the potential need for use of synchrotron radiation sources need to be addressed before the method can be used for precise quantitative analysis of biofilm geometry in porous media.

Mots clés: Biofilm; Imaging; Porous media; X-ray tomography

Domaines: Imagerie; Microbiologie et Parasitologie

Yohan Davit, Gabriel Iltis, Gerald Debenest, Stéphanie Veran-Tissoires, Dorthe Wildenschild, et al.. Imaging biofilm in porous media using X-ray computed microtomography. Journal of Microscopy, 2011, 242 (1), pp.15 -25. ⟨10.1111/j.1365-2818.2010.03432.x⟩. ⟨hal-03469130⟩