We describe a novel inexpensive method, utilizing particle image velocimetry (PIV) and refractive index‐matching (RIM) for visualizing and quantifying the flow field within bio‐amended porous media. To date, this technique has been limited to idealized particles, whose refractive index does not match that of fresh water and thus requires specialized and often toxic or hazardous fluids. Here, we use irregularly shaped grains made of hydrogel as the solid matrix and water as the fluid. The advantage of using water is that it provides, for the first time, the opportunity to study both hydraulic and biological processes, which typically occur in soils and streambeds. By using RIM coupled with PIV (RIM‐PIV), we measured the interstitial flow field within a cell packed with granular material consisting of hydrogel grains in a size range of 1–8 mm, both in the presence and in the absence of Sinorhizobium meliloti bacteria (strain Rm8530). We also performed experiments with fluorescent tracer (fluorescein) and fluorescent microbes (Shewanella GPF MR‐1) to test the capability of visualizing solute transport and microbial movements. Results showed that the RIM‐PIV can measure the flow field for both biofilm‐free and biofilm‐covered hydrogel grains. The fluorescent tracer injection showed the ability to visualize both physical (concave surfaces and eddies) and biological (biofilms) transient storage zones, whereas the fluorescent microbe treatment showed the ability to track microbial movements within fluids. We conclude that the proposed methodology is a promising tool to visualize and quantify biofilm attachment, growth, and detachment in a system closer to natural conditions than a 2D flow cell experiment.

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Particle image velocimetry (PIV) is a non-invasive technique for measuring velocity fields. It is especially powerful when coupled with refractive index-matching (RIM) to map velocity fields around solid objects. The solid objects are typically removed from the flow field with a masking approach before performing the PIV analysis and mapping the velocity field, thus defined as an a priori method. However, applying this method, with a mask of the correct shape and at the correct location, is difficult, time consuming, and would be potentially unfeasible for packed bed of irregular shaped grains. To address this problem, we present the proof-of-concept of a novel approach to delineate highly irregular granular particles (grains) of varying size and shape and improve PIV processing for flows around grains in laboratory studies. The present technique makes use of seeding transparent RIM solids with light scattering particles during their fabrication. The RIM of the solids preserves the optical fidelity of images and the laser light sheet. Whereas the seeding in the solids can provide image contrast between solid (seeded) and fluid (non-seeded) as well as a strong zero-velocity signal in the solid. The fluid may then be seeded as well, allowing PIV spatial correlations to be performed with high confidence over the entire image. We tested the seeded RIM solid approach with both irregular individual solid pieces as well as with a volume of irregular grains. The new technique effectively obtains the fluid velocity field and solid boundary locations in both cases. Applications of the present method may range from studies of interstitial processes within a simulated sediment bed, such as those of aquifers, soils, sediments and the hyporheic zone, to near bed flow hydraulics.

Porous media are ubiquitous, a key component of the water cycle and locus of many biogeochemical transformations. Mapping media architecture and interstitial flows have been challenging because of the inherent difficulty of seeing through solids. Previous works used particle image velocimetry (PIV) coupled with refractive index‐matching (RIM) to quantify interstitial flows, but they were limited to specialized and often toxic fluids that precluded investigating biological processes. To address this limitation, we present a low‐cost and scalable method based on RIM coupled PIV (RIM‐PIV) and planar laser induced fluorescence (RIM‐PLIF) to simultaneously map both media architecture and interstitial velocities. Our method uses irregularly shaped grains made of a fluorocarbon plastic with refractive index of 1.36 and specific gravity of 1.93. This allows using a water–glycerin solution for the RIM fluid. By using RIM‐PIV, we mapped media structure with 2% accuracy, which improved to 0.2% with RIM‐PLIF because of improved image contrast.

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