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Low-Field Borehole NMR Applications in the Near-Surface Environment
(2018-01) Kirkland, Catherine M.; Codd, Sarah L.
The inherent heterogeneity of the near subsurface (<200 m below the ground surface) presents challenges for agricultural water management, hydrogeologic characterization, and engineering, among other fields. Borehole nuclear magnetic resonance (NMR) has the potential not only to describe this heterogeneity in space nondestructively but also to monitor physical and chemical changes in the subsurface with time. Nuclear magnetic resonance is sensitive to parameters of interest like porosity and permeability, saturation, fluid viscosity, and formation mineralogy. Borehole NMR tools have been used to measure soil moisture in model soils, and recent advances in lowfield borehole NMR instrumentation allow estimation of hydraulic properties of unconsolidated aquifers. We also demonstrate the potential for low-field borehole NMR tools to monitor field-relevant biogeochemical processes like biofilm accumulation and microbially induced calcite precipitation at laboratory and field scales. Finally, we address some remaining challenges and areas of future research, as well as other possible applications where borehole. NMR could provide valuable complementary data.
NMR investigation of water diffusion in different biofilm structures
(2017-09) Herrling, M. P.; Weisbrodt, Jessica; Kirkland, Catherine M.; Williamson, Nathan H.; Lackner, S.; Codd, Sarah L.; Seymour, Joseph D.; Guthausen, G.; Horn, H.
Mass transfer in biofilms is determined by diffusion. Different mostly invasive approaches have been used to measure diffusion coefficients in biofilms, however, data on heterogeneous biomass under realistic conditions is still missing. To non-invasively elucidate fluid–structure interactions in complex multispecies biofilms pulsed field gradient-nuclear magnetic resonance (PFG-NMR) was applied to measure the water diffusion in five different types of biomass aggregates: one type of sludge flocs, two types of biofilm, and two types of granules. Data analysis is an important issue when measuring heterogeneous systems and is shown to significantly influence the interpretation and understanding of water diffusion. With respect to numerical reproducibility and physico-chemical interpretation, different data processing methods were explored: (bi)-exponential data analysis and the Γ distribution model. Furthermore, the diffusion coefficient distribution in relation to relaxation was studied by D-T2 maps obtained by 2D inverse Laplace transform (2D ILT). The results show that the effective diffusion coefficients for all biofilm samples ranged from 0.36 to 0.96 relative to that of water. NMR diffusion was linked to biofilm structure (e.g., biomass density, organic and inorganic matter) as observed by magnetic resonance imaging and to traditional biofilm parameters: diffusion was most restricted in granules with compact structures, and fast diffusion was found in heterotrophic biofilms with fluffy structures. The effective diffusion coefficients in the biomass were found to be broadly distributed because of internal biomass heterogeneities, such as gas bubbles, precipitates, and locally changing biofilm densities. Thus, estimations based on biofilm bulk properties in multispecies systems can be overestimated and mean diffusion coefficients might not be sufficiently informative to describe mass transport in biofilms and the near bulk.
Peclet number dependent superdiffusive hydrodynamic dispersion in a site percolation porous media measured by NMR
(2017-04) Seymour, Joseph D.; Codd, Sarah L.; Kimmich, Rainer
The displacement time dependent hydrodynamic dispersion in a model 2D site percolation structure is measured using PGSE NMR. The data indicate superdiffusive scaling of the mean squared displacement at high Peclet numbers, where advective transport dominates, consistent with classic percolation scaling concepts. The time scaling of the mean squared displacement is shown to vary with the Peclet number demonstrating a dependence on the changing dynamics.
Anomalous fluid transport in porous media induced by biofilm growth
(2004-11) Seymour, Joseph D.; Gage, Justin P.; Codd, Sarah L.; Gerlach, Robin
Magnetic resonance measurements of the transition from normal to anomalous hydrodynamic dispersion in porous media due to biological activity are presented. Fractional advection-diffusion equations are shown to provide models for the measured impact of biofilm growth on porous media transport dynamics.
Magnetic resonance microscopy of biofilm structure and impact on transport in a capillary bioreactor
(2004-04) Seymour, Joseph D.; Codd, Sarah L.; Gjersing, Erica L.; Stewart, Philip S.
Microorganisms that colonize surfaces, biofilms, are of significant importance due to their role in medical infections, subsurface contaminant remediation, and industrial processing. Spatially resolved data on the distribution of biomass within a capillary bioreactor, the heterogeneity of the biofilm itself and the impact on transport dynamics for a Staphylococcus epidermidis biofilm in the natural growth state are presented. The data demonstrate the ability of magnetic resonance microscopy to study spatially resolved processes in bacterial biofilms, thus providing a basis for future studies of spatially resolved metabolism and in vivo clinical detection.
Magnetic resonance microscopy analysis of advective transport in a biofilm reactor
(2005) Gjersing, Erica L.; Codd, Sarah L.; Seymour, Joseph D.; Stewart, Philip S.
In this article we present magnetic resonance microscopy (MRM) characterization of the advective transport in a biofilm capillary reactor. The biofilm generates non-axial flows that are up to 20% of the maximum axial velocity. The presence of secondary velocities of this magnitude alters the mass transport in the bioreactor relative to non-biofilm fouled reactors and questions the applicability of empirical mass transfer coefficient approaches. The data are discussed in the context of simulations and models of biofilm transport and conceptual aspects of transport modeling in complex flows are also discussed. The variation in the residence time distribution due to biofilm growth is calculated from the measured propagator of the motion. Dynamical systems methods applied to model fluid mixing in complex flows are indicated as a template for extending mass transport theory to quantitatively incorporate microscale data on the advection field into macroscale mass transfer models.
Magnetic resonance microscopy of biofilm and bioreactor transport
(2006-02) Codd, Sarah L.; Seymour, Joseph D.; Gjersing, Erica L.; Gage, Justin P.; Brown, Jennifer R.
Magnetic resonance microscopy of biofouling induced scale dependent transport in porous media
(2007-06) Seymour, Joseph D.; Gage, Justin P.; Codd, Sarah L.; Gerlach, Robin
Non-invasive magnetic resonance microscopy (MRM) methods are applied to study biofouling of a homogeneous model porous media. MRM of the biofilm biomass using magnetic relaxation weighting shows the heterogeneous nature of the spatial distribution of the biomass as a function of growth. Spatially resolved MRM velocity maps indicate a strong variation in the pore scale velocity as a function of biofilm growth. The hydrodynamic dispersion dynamics for flow through the porous media is quantitatively characterized using a pulsed gradient spin echo technique to measure the propagator of the motion. The propagator indicates a transition in transport dynamics from a Gaussian normal diffusion process following a normal advection diffusion equation to anomalous transport as a function of biofilm growth. Continuous time random walk models resulting in a time fractional advection diffusion equation are shown to model the transition from normal to anomalous transport in the context of a conceptual model for the biofouling. The initially homogeneous porous media is transformed into a more complex heterogeneous porous media by the biofilm growth.
Observations of cell cluster hollowing in Staphylococcus epidermidis biofilms
(2007-04) Stewart, Philip S.; Rani, Suriani A.; Gjersing, Erica L.; Codd, Sarah L.; Zheng, Zhilan; Pitts, Betsey
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 (Tolker-Nielsen et al. 2000), Pseudoalteromonas tunicate (Mai-Prochnow 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.
High-density targeting of a viral multifunctional nanoplatform to a pathogenic, biofilm-forming bacterium
(2007-04) Suci, Peter A.; Berglund, Deborah L.; Liepold, Lars Otto; Brumfield, Susan; Pitts, Betsey; Davison, William M.; Oltrogge, Luke; Hoyt, Kathryn Olivia; Codd, Sarah L.; Stewart, Philip S.; Young, Mark J.; Douglas, Trevor
Nanomedicine directed at diagnosis and treatment of infections can benefit from innovations that have substantially increased the variety of available multifunctional nanoplatforms. Here, we targeted a spherical, icosahedral viral nanoplatform to a pathogenic, biofilm-forming bacterium, Staphylococcus aureus. Density of binding mediated through specific protein-ligand interactions exceeded the density expected for a planar, hexagonally close-packed array. A multifunctionalized viral protein cage was used to load imaging agents (fluorophore and MRI contrast agent) onto cells. The fluorescence-imaging capability allowed for direct observation of penetration of the nanoplatform into an S. aureus biofilm. These results demonstrate that multifunctional nanoplatforms based on protein cage architectures have significant potential as tools for both diagnosis and targeted treatment of recalcitrant bacterial infections.

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