Influence of Biofilms on Porous Media Hydrodynamics - Porous Media: Applications in Biological Systems and Biotechnology - page 182

Geesey and Mitchell reemphasizes the need for experimental systems in which
hydrodynamics and biological activity can be measured directly (Geesey and
Mitchell 2008).
5.3.1 The Challenge of Imaging Biofilms in Porous Media
Destructive (e.g., end-point) and nondestructive measurements have been used
to assess the presence, structure, and distribution of biofilms in porous media.
Such techniques include visual imaging using high-resolution photography and
microscopy, scanning or transmission electron microscopy (SEM or TEM), as
well as more recently developed methods such as x-ray tomography, nuclear
magnetic resonance (NMR) spectroscopy-, or ultrasound-based imaging
techniques.
Noninvasive low-energy techniques such as photography, brightfield or
reflective microscopy, NMR imaging, or ultrasound have the advantage of
having no or negligible effects on biofilms but often suffer a lack of resolution,
depth penetration, or selectivity.
Currently available microscopes and image analysis programs allow deter-
mining the thickness of stained or unstained biofilms. However, the applicabil-
ity of optical techniques to observe biofilms in porous media is limited as most
porous media particles are not flat (e.g., sand grains, glass beads). Porous
media surfaces are usually rather irregularly shaped, resulting in increased
background signal and image blurriness. Confocal scanning laser microscopy
(CSLM) combined with fluorescent labeling techniques, and three-dimensional
image analysis can reduce the amount of background fluorescence and thus
potentially allow for continuous and spatially resolved observation of biofilms
in porous media. However, since porous media are opaque and the working
distance of high-resolution microscopy objectives is limited, the depth of field
of observation is usually very limited.
There have been a few studies in which the refractive index of the fluid and
porous media used were chosen in a way to maximize the ability to observe
biofilm formation in situ over time (e.g., Leis et al . 2005). However, such
studies have remained rare and the choice of porous media materials is limited
if aqueous solutions are to be used to grow biofilms.
Paulsen et al . (1997) described a model system in which noninvasive micro-
scopic observation combined with measurements of local-flow velocity allowed
for estimating the influence of biofilm morphology on convective mass trans-
port. However, such detailed measurements are usually limited to specif-
ically designed experimental systems and one- or pseudo-two-dimensional
geometries.
Electron microscopy techniques such as SEM and TEM have been used
to estimate the thickness of biofilms on surfaces (Vandevivere and Baveye
1992b; Rinck-Pfeiffer et al . 2000; Hand et al . 2008), however, they cannot be
applied directly to porous media systems and can therefore suffer artifacts
due to destructive sampling, sample preparation, and the vacuum conditions