Sarah L. Codd

Biopolymer and Water Dynamics in Microbial Biofilm Extracellular Polymeric Substance

Nuclear magnetic resonance (NMR) is a noninvasive and nondestructive tool able to access several observable quantities in biofilms such as chemical composition, diffusion, and macroscale structure and transport. Pulsed gradient spin echo (PGSE) NMR techniques were used to measure spectrally resolved biomacromolecular diffusion in biofilm biomass, extending previous research on spectrally resolved diffusion in biofilms. The dominant free water signal was nulled using an inversion recovery modification of the traditional PGSE technique in which the signal from free water is minimized in order to view the spectra of components such as the rotationally mobile carbohydrates, DNA, and proteins. Diffusion data for the major constituents obtained from each of these spectral peaks demonstrate that the biomass of the biofilm contains both a fast and slow diffusion component. The dependence of diffusion on antimicrobial and environmental challenges suggests the polymer molecular dynamics measured by NMR are a sensitive indicator of biofilm function.

Flow coherence in a bead pack observed using frequency domain modulated gradient nuclear magnetic resonance

We have used a new nuclear magnetic resonance (NMR) method based on periodic wave form magnetic field gradients to investigate temporal correlations for flow in porous media. The frequency domain modulated field gradient NMR technique directly yields the frequencydependent-dispersion coefficient, i.e., the spectral density of the velocity autocorrelation function. Our measurements of dispersion spectra have been carried out, in the direction transverse to the mean flow, for water flowing in a monodisperse latex bead pack (diameters 50–136 μm) and at Peclet numbers ranging from 10 to 5000. We observe spectral peaks at a frequency corresponding to the inverse time for flow around a bead, an effect we attribute to coherent meandering flow around the bead. This observation is in close agreement with the recent computer simulations of Maier et al., in which negative velocity autocorrelation function transients are seen.

Permeability of a growing biofilm in a porous media fluid flow analyzed by magnetic resonance displacement-relaxation correlations

Biofilm growth in porous media is difficult to study non‐invasively due to the opaqueness and heterogeneity of the systems. Magnetic resonance is utilized to non‐invasively study water dynamics within porous media. Displacement‐relaxation correlation experiments were performed on fluid flow during biofilm growth in a model porous media of mono‐dispersed polystyrene beads. The spin–spin T2 magnetic relaxation distinguishes between the biofilm phase and bulk fluid phase due to water–biopolymer interactions present in the biofilm, and the flow dynamics are measured using PGSE NMR experiments. By correlating these two measurements, the effects of biofilm growth on the fluid dynamics can be separated into a detailed analysis of both the biofilm phase and the fluid phase simultaneously within the same experiment. Within the displacement resolution of these experiments, no convective flow was measured through the biomass. An increased amount of longitudinal hydrodynamic dispersion indicates increased hydrodynamic mixing due to fluid channeling caused by biofilm growth. The effect of different biofilm growth conditions was measured by varying the strength of the bacterial growth medium. Biotechnol. Bioeng. 2013; 110: 1366–1375.

Observations of cell cluster hollowing in Staphylococcus epidermidis biofilms

Microbial biofilm formation appears to involve complex multicellular behaviours. For example, some bacteria exhibit extensive twitching and swarming motility after association with a surface. These forms of motility appear to be coordinated and to contribute to the spatial organization of biofilm structures (O’Toole and Kolter 1998; Klausen et al. 2003). Another intriguing phenomenon is the appearance of hollow interiors in biofilm cell clusters. Such hollowing seems to occur in the later stages of biofilm development. Hollow biofilm structures have been described for Pseudomonas aeruginosa (Sauer et al. 2002; Webb et al. 2003; Hunt et al. 2004; Parsek and Fuqua 2004; Stapper et al. 2004), Pseudomonas putida (TolkerNielsen et al. 2000), Pseudoalteromonas tunicate (MaiProchnow et al. 2004) and Actinobacillus actinomycetemcomitans (Kaplan et al. 2003) biofilms. Particularly, striking are movies in which motile cells can be seen seething in the centre of a cell cluster containing many immotile cells (Tolker-Nielsen et al. 2000; Hunt et al. 2004). Here, we report the direct microscopic observation, by a suite of techniques, of hollow cell clusters in Staphylococcus epidermidis biofilms.

A PGSE study of propane gas flow through model porous bead packs.

We present a study of the probability density for molecular displacements of gas flowing through bead packs. The three bead packs to be described are composed of polydispersed porous PVC particles, 500 microm glass spheres, and 300 microm polystyrene spheres. A range of velocities (1 cm s(-1) to 1 m s(-1)) and observation times (3-500 ms), hence transport distances, are presented. For comparison we also measure the propagators for water flow in the polystyrene sphere pack. The exchange time between the moving and the stagnant portions of the flow is a strong function of the diffusion coefficient of the fluid. Comparing the propagators between water and propane flowing in similar porous media makes this clear. The gas propagators, for flowing and diffusing molecules, consistently show a feature at the average pore diameter. This feature has previously been observed for similar Peclet number studies in smaller monodispersed bead packs using liquids, but is now demonstrated for larger beads with gas. We analyze and discuss these propagators in the physically intuitive propagator space and also in the well-understood Fourier q space. The extension of NMR PGSE experiments to gas systems allows flow and diffusion information to be obtained over a wider range of length and time scales than with liquids, and also for a new range of physical environments and systems. Interactions between stochastic and deterministic motion are fundamental to the theoretical description of transport in porous media, and the time and length scale dependences are central to an understanding of the resultant dispersive motion.

NMR measurement of hydrodynamic dispersion in porous media subject to biofilm mediated precipitation reactions.

Noninvasive measurements of hydrodynamic dispersion by nuclear magnetic resonance (NMR) are made in a model porous system before and after a biologically mediated precipitation reaction. Traditional magnetic resonance imaging (MRI) was unable to detect the small scale changes in pore structure visualized during light microscopy analysis after destructive sampling of the porous medium. However, pulse gradient spin echo nuclear magnetic resonance (PGSE NMR) measurements clearly indicated a change in hydrodynamics including increased pore scale mixing. These changes were detected through time-dependent measurement of the propagator by PGSE NMR. The dynamics indicate an increased pore scale mixing which alters the preasymptotic approach to asymptotic Gaussian dynamics governed by the advection diffusion equation. The methods described here can be used in the future to directly measure the transport of solutes in biomineral-affected porous media and contribute towards reactive transport models, which take into account the influence of pore scale changes in hydrodynamics.

Nuclear magnetic resonance measurement of shear-induced particle migration in Brownian suspensions

The shear-induced migration of colloidal particles in capillary flow has been investigated using nuclear magnetic resonance. Nuclear magnetic resonance methods have the ability to measure spatially resolved velocity and probability distributions of displacement within a multiphase colloidal system. For a suspension of ∼2.49 μm Brownian model hard spheres under shear flow in a 1 mm diameter glass capillary, particle migration inward to the capillary center was found using spectrally resolved pulsed gradient spin echo techniques for a range of volume fractions. Particle migration was detected even in the dilute regime, down to ϕ<0.04. While particle migration has been measured and is expected in concentrated and noncolloidal suspensions, it has only recently been unequivocally detected in dilute Brownian suspensions.

Secondary flow mixing due to biofilm growth in capillaries of varying dimensions

Using a magnetic resonance microscopy (MRM) technique, velocity perturbations due to biofouling in capillaries were detected in 3D velocity maps. The velocity images in each of the three square capillary sizes (2, 0.9, and 0.5 mm i.d.) tested indicate secondary flow in both the x‐ and y‐directions for the biofouled capillaries. Similar flow maps generated in a clean square capillary show only an axial component. Investigation of these secondary flows and their geometric and dynamic similarity is the focus of this study. The results showed significant secondary flows present in the 0.9 mm i.d. capillary, on the scale of 20% of the bulk fluid flow. Since this is the “standard 1 mm” size capillary used in confocal microscopy laboratory bioreactors to investigate biofilm properties, it is important to understand how these enhanced flows impact bioreactor transport. Biotechnol. Bioeng. 2009;103: 353–360.

Simultaneous Gaussian and exponential inversion for improved analysis of shales by NMR relaxometry

Nuclear magnetic resonance (NMR) relaxometry is commonly used to provide lithology-independent porosity and pore-size estimates for petroleum resource evaluation based on fluid-phase signals. However in shales, substantial hydrogen content is associated with solid and fluid signals and both may be detected. Depending on the motional regime, the signal from the solids may be best described using either exponential or Gaussian decay functions. When the inverse Laplace transform, the standard method for analysis of NMR relaxometry results, is applied to data containing Gaussian decays, this can lead to physically unrealistic responses such as signal or porosity overcall and relaxation times that are too short to be determined using the applied instrument settings. We apply a new simultaneous Gaussian-Exponential (SGE) inversion method to simulated data and measured results obtained on a variety of oil shale samples. The SGE inversion produces more physically realistic results than the inverse Laplace transform and displays more consistent relaxation behavior at high magnetic field strengths. Residuals for the SGE inversion are consistently lower than for the inverse Laplace method and signal overcall at short T2 times is mitigated. Beyond geological samples, the method can also be applied in other fields where the sample relaxation consists of both Gaussian and exponential decays, for example in material, medical and food sciences.

Magnetic resonance diffusion and relaxation characterization of water in the unfrozen vein network in polycrystalline ice and its response to microbial metabolic products

Polycrystalline ice, as found in glaciers and the ice sheets of Antarctica, is a low porosity porous media consisting of a complicated and dynamic pore structure of liquid-filled intercrystalline veins within a solid ice matrix. In this work, Nuclear Magnetic Resonance measurements of relaxation rates and molecular diffusion, useful for probing pore structure and transport dynamics in porous systems, were used to physically characterize the unfrozen vein network structure in ice and its response to the presence of metabolic products produced by V3519-10, a cold tolerant microorganism isolated from the Vostok ice core. Recent research has found microorganisms that can remain viable and even metabolically active within icy environments at sub-zero temperatures. One potential mechanism of survival for V3519-10 is secretion of an extracellular ice binding protein that binds to the prism face of ice crystals and inhibits ice recrystallization, a coarsening process resulting in crystal growth with ice aging. Understanding the impact of ice binding activity on the bulk vein network structure in ice is important to modeling of frozen geophysical systems and in development of ice interacting proteins for biotechnology applications, such as cryopreservation of cell lines, and manufacturing processes in food sciences. Here, we present the first observations of recrystallization inhibition in low porosity ice containing V3519-10 extracellular protein extract as measured with Nuclear Magnetic Resonance and Magnetic Resonance Imaging.