SummaryIn 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 aqueousphase 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 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.

Please cite this article as: Malgorzata Peszynska, Anna Trykozko, Gabriel Iltis, Steffen Schlueter, Dorthe Wildenschild, Biofilm growth in porous media: experiments, computational modeling at the porescale, and upscaling, Advances in Water Resources (2015), Highlights 1 • We use 3D imaging with a barium-based contrasting agent to obtain 2 porescale geometries filled with biofilm 3 • We simulate the flow in the porescale geometries with and without 4 biofilm, and upscale the results to the conductivities which compare 5 • well with the experimental values, and which show the dependence of 6 the degree of bioclogging on the flow rates 7 • We simulate biomass growth and transport coupled to the flow and 8 obtain morphologies similar to those in the experiment 9 • We show several reduced models for conductivities and their depen-10 dence on the biofilm growth Abstract 21 Biofilm growth changes many physical properties of porous media such 22 as porosity, permeability and mass transport parameters. The growth de-23 pends on various environmental conditions, and in particular, on flow rates. 24 Modeling the evolution of such properties is difficult both at the porescale 25 where the phase morphology can be distinguished, as well as during up-26 scaling to the corescale effective properties. Experimental data on biofilm 27 growth is also limited because its collection can interfere with the growth, 28 while imaging itself presents challenges. 29 In this paper we combine insight from imaging, experiments, and nu-30 merical simulations and visualization. The experimental dataset is based on 31 glass beads domain inoculated by biomass which is subjected to various flow 32 conditions promoting the growth of biomass and the appearance of a biofilm 33 phase. The domain is imaged and the imaging data is used directly by a 34 computational model for flow and transport. The results of the computa-35 tional flow model are upscaled to produce conductivities which compare well 36 with the experimentally obtained hydraulic properties of the medium. The 37 flow model is also coupled to a newly developed biomass-nutrient growth 38 model, and the model reproduces morphologies qualitatively similar to those 39 observed in the experiment.40 Keywords: 41 porescale modeling, imaging porous media, microtomography, reactive 42 transport, biomass and biofilm growth, parabolic variational inequality, 43 Lagrange multipliers, coupled nonlinear system, multicomponent 44 multiphase flow and transport in porous media 45 2

A new method to resolve biofilms in three dimensions in porous media using high‐resolution synchrotron‐based X‐ray computed microtomography (CMT) has been developed. Imaging biofilms in porous media without disturbing the natural spatial arrangement of the porous medium and associated biofilm has been a challenging task, primarily because porous media generally preclude conventional imaging via optical microscopy; X‐ray tomography offers a potential alternative. Using silver‐coated microspheres for contrast, we were able to differentiate between the biomass and fluid‐filled pore spaces. The method was validated using a two‐dimensional micromodel flow cell where both light microscopy and CMT imaging were used to image the biofilm.

This paper describes the use of single-well tracer dilution techniques to resolve the rate of light nonaqueous phase liquid (LNAPL) flow through wells and the adjacent geologic formation. Laboratory studies are presented in which a fluorescing tracer is added to LNAPL in wells. An in-well mixer keeps the tracer well mixed in the LNAPL. Tracer concentrations in LNAPL are measured through time using a fiber optic cable and a spectrometer. Results indicate that the rate of tracer depletion is proportional to the rate of LNAPL flow through the well and the adjacent formation. Tracer dilution methods are demonstrated for vertically averaged LNAPL Darcy velocities of 0.00048 to 0.11 m/d and LNAPL thicknesses of 9 to 24 cm. Over the range of conditions studied, results agree closely with steady-state LNAPL flow rates imposed by pumping. A key parameter for estimating LNAPL flow rates in the formation is the flow convergence factor alpha. Measured convergence factors for 0.030-inch wire wrap, 0.030-inch-slotted polyvinyl chloride (PVC), and 0.010-inch-slotted PVC are 1.7, 0.91, and 0.79, respectively. In addition, methods for using tracer dilution data to determine formation transmissivity to LNAPL are presented. Results suggest that single-well tracer dilution techniques are a viable approach for measuring in situ LNAPL flow and formation transmissivity to LNAPL.

OATAO is an open access repository that collects the work of Toulouse researchers and makes it freely available over the web where possible. Abbreviations: ALS, Advanced Light Source; APS, Advanced Photon Source; CAMD, Center for Advanced Microstructure and Devices; CCD, charge-coupled device; CLSM, confocal laser scanning microscopy; CMT, computed microtomography; CT, computed tomography; ESEM, environmental scanning electron microscopy; ESRF, European Synchrotron Radiation Facility; GSECARS, GeoSoilEnviroCARS; HASYLAB, Hamburger Synchrotronstrahlungslabor; ISA, ASTRID, Institute for Storage Ring Facilities; LuAG, lutetium-aluminum-garnet; MRM, magnetic resonance microscopy; NAPL, nonaqueous phase liquid; NSLS, National Synchrotron Light Source; REV, representative elementary volume; SLS, Swiss Light Source; S/N, signal-to-noise ratio. AbstractDespite very rapid development in commercial X-ray tomography technology, synchrotron-based tomography facilities still have a number of advantages over conventional systems. The high photon flux inherent of synchrotron radiation sources allows for (i) high resolution to micro-or nanometer scales depending on the individual beam-line, (ii) rapid acquisition times that allow for collection of sufficient data for statistically significant results in a short amount of time as well as prevention of temporal changes that would take place during longer scan times, and (iii) optimal implementation of contrast agents that allow us to resolve features that would not be decipherable in scans obtained with a polychromatic radiation source. This chapter highlights recent advances in capabilities at synchrotron sources, as well as implementation of synchrotron-based computed microtomography (CMT) to two topics of interest to researchers in the soil science, hydrology, and environmental engineering fields, namely multiphase flow in porous media and characterization of biofilm architecture in porous media. In both examples, we make use of contrast agents and photoelectric edge-specific scanning (single-or dual-energy type), in combination with advanced image processing techniques.