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Recent NMR/MRI studies of biofilm structures and dynamics
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Biofilm systems consist of complex microbial communities embedded in hydrated bio-macromolecules. These biological systems have been studied by diverse analytical techniques, among them by nuclear magnetic resonance and imaging. There are still open questions regarding structure and functionality. In this review, nuclear magnetic resonance approaches, especially in form of magnetic resonance imaging and diffusion modalities, are summarized with respect to insights into biofilm structure, diffusion and advection, i.e. mass transport. Furthermore, possibilities and limitations regarding metabolomics are recapitulated and analysed with respect to open research questions. Perspectives for biofilm research will be discussed from the point of view of current technical and methodical developments of nuclear magnetic resonance. The impact of the named nuclear magnetic resonance techniques will be reflected in the context of water treatment and biofilm development in porous media as well as in technical applications such as biofilm reactors and biofiltration.
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... Nuclear magnetic resonance (NMR) and modifications of this method are used to reveal the metabolic processes in multispecies microbial communities (Herrling et al., 2019). Enumeration of biofilm microorganisms by CFU counts, which provides highly variable results, may be successfully replaced by flow cytometry; this method, however, requires expensive equipment (Sgier et al., 2016(Sgier et al., , 2018. ...
... NMR spectroscopy is used in biofilm research to determine the metabolic properties of prokaryotic and eukaryotic cells. 1 H and 13 C NMR, specifically, allow for the direct, time-resolved, and noninvasive monitoring of metabolic pathways of living bacterial suspensions or bacterial biofilms on porous substrates [7,136]. Moreover, solid-state NMR (generally associated with imaging, MRI) method has been used to study the chemical composition [137] and molecular mobility of EPS [75], and to generate 2D and 3D maps of S. oneidensis with molecular resolution [138]. ...
Biofilms are a major cause of health and environmental issues. Bacteria organized in biofilms are much more resistant to biocides than their equivalents in the planktonic state. In this context, spectroscopic techniques have significantly contributed to a more fundamental understanding of biofilm formation, which is crucial to prevent and limit their generation, spreading, and maturation. In this review, recent progress on the main analytical approaches enabling the spectroscopic characterization of microbial biofilms is comparatively discussed. In addition, less commonly used techniques facilitating biofilm studies will be also presented. Advantages and drawbacks of each discussed technique will be underlined, thus providing an overview on spectroscopic approaches for studying biofilms.
... These techniques have dramatically advanced quantitative and qualitative characterization of microbial communities, including biofilms, as it relates to important traits such as genomics, proteomics, structure, biomechanics and biomolecular composition [165,166]. Non-invasive monitoring of biofilms in vivo is very difficult and currently limited to more expensive techniques such as Optical Coherence Tomography (OCT) [167] and Magnetic Resonance Imaging (MRI) [168]. Surface imaging methods such as Scanning Electron Microscopy (SEM) [169], Scanning Electrochemical Microscopy (SECM) [170] and Atomic Force Microscopy (AFM) [171] have become excellent tools for exploring topological structure and biochemical properties along the cell surface. ...
Biofilms form complex structures that are ubiquitous in natural environments and can cause chronic infections which are difficult to treat. While much is known about biofilms, many questions remain about how biofilms mature and respond to internal and external stimuli. To understand the phenomena that occur within the biofilm matrix, sensing techniques capable of quantitatively resolving spatial and temporal dynamics of key analytes in the biofilm are needed. Biofilm spatial and temporal heterogeneity provide unique hurdles in fully assessing these intricacies. This review provides a detailed overview of methods that have been used to sense a variety of relevant analytes in biofilms. Electrochemical, optical, and other analytical techniques each possess distinct strengths and weaknesses depending on the application showing that biofilm sensing does not have a “one-size fits all” solution. The analyte being measured, the environment it is analyzed in, and the information that is needed determine whether known approaches may be appropriate or novel methods need to be developed. This review aims to help readers understand these techniques so that they can be applied to future projects for better understanding of biofilm elements and evolving sensing approaches.
... Magnetic resonance imaging (MRI), a technique well-known from medical diagnostics, is suitable for visualization and characterization of biofilms (Gonzalez-Gil et al., 2001;Manz et al., 2003;Neu et al., 2010;Phoenix and Holmes, 2008;Ramanan et al., 2013;Ranzinger et al., 2016). For an overview on recent studies in biofilm research using MRI, a book chapter is available (Herrling et al., 2019). Existing MRI research studies on biofilms have mainly focused on biofilm structure, transport of water (i.e. ...
The use of microbial fuel cells (MFCs) for wastewater treatment fits in a circular economy context, as they can produce electricity by the removal of organic matter in the wastewater. Activated carbon (AC) granules are an attractive electrode material for bioanodes in MFCs, as they are cheap and provide electroactive bacteria with a large surface area for attachment. The characterization of biofilm growth on AC granules, however, is challenging due to their high roughness and three-dimensional structure. In this research, we show that 3D magnetic resonance imaging (MRI) can be used to visualize biofilm distribution and determine its volume on irregular-shaped single AC granules in a non-destructive way, while being combined with electrochemical and biomass analyses. Ten AC granules with electroactive biofilm (i.e. granular bioanodes) were collected at different growth stages (3 to 21 days after microbial inoculation) from a multi-anode MFC and T1-weighted 3D-MRI experiments were performed for three-dimensional biofilm visualization. With time, a more homogeneous biofilm distribution and an increased biofilm thickness could be observed in the 3D-MRI images. Biofilm volumes varied from 0.4 μL (day 4) to 2 μL (day 21) and were linearly correlated (R2 = 0.9) to the total produced electric charge and total nitrogen content of the granular bioanodes, with values of 66.4 C μL-1 and 17 μg N μL-1, respectively. In future, in situ MRI measurements could be used to monitor biofilm growth and distribution on AC granules.
The conception of mobile nuclear magnetic resonance (NMR) was nourished by the need of the petrochemical industry to characterize oil wells and optimize their yield. Compact NMR instruments rely on permanent magnets because they are smaller than electromagnets for field strengths in the range of 2 T and below. One of the earliest applications of the NMR‐MOUSE was to characterize car tires in an effort to reduce racetrack testing during tire development. Given the performance levels of the tires from driving tests, material properties can be optimized with reference to NMR relaxation‐time distributions replacing many of the expensive driving tests by more economical NMR measurements. The chapter summarizes adventures with the NMR‐MOUSE applied to heritage buildings. The acceptance of stray‐field sensors like the NMR‐MOUSE to analyze material properties has grown over the years and it has also become part of the portfolio of instruments to diagnose cultural heritage.
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies.
NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success.
We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the “why”, oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the “how”, where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
This chapter summarises recent advances in solution, HR-MAS and solid-state NMR techniques to study the structure and dynamics of soft matter. NMR enjoys widespread use in the analysis of gels, liquid crystals, polymer solutions and surfactants. Rather than focus on each class of soft matter in turn, this chapter is instead arranged in terms of the NMR techniques themselves in the hope of stimulating the translation of methodologies between the traditional branches of soft matter science. Original research articles published between January 2015 and March 2020 are discussed.
After decades of research, there are still open questions regarding biofilms' structure, molecular composition, and functionality, mainly with respect to the extracellular polymeric substances (EPS). EPS has a critical role in enmeshing the microbial cells within the biofilm matrix and in providing diffusion-limiting three-dimensional multicellular structures formed by a series of microenvironments of microbial heterogeneity. Due to its complexity, few components have been identified in even the most thoroughly characterized biofilm. Analytical methods must be boosted to explain the roles and constitution of EPS and to unravel biochemical pathways of biofilm formation and resilience. Nuclear magnetic resonance (NMR) has been applied to various biofilm systems. This chapter provides an overview on how NMR has contributed to the current knowledge about biofilms, whether in liquid and solid state, in the form of magnetic resonance imaging or diffusion modalities and when combined with chemometric tools under the umbrella of NMR-based metabolomics.
Discussions about food quality, industrial vs. biological-organic production and their environmental impact currently lead to socially constitutive questions about nutritional value, about food composition, shelf life, and economical sustainability, evidencing the need of dedicated and reliable analytics. Apart from metabolic studies based on NMR spectroscopy concerning food quality of mainly liquid foods like wine or juices, the imaging modality of NMR and its diffusion application are valuable tools in this context. An update of the technical and methodical developments with respect to characterizing foods will be given in this review. We relate this paper to our previous review, which was focusing on the methodical aspects of these magnetic resonance modalities and on processes in nature and during food processing—now we put the focus on upcoming techniques in magnetic resonance imaging and diffusion and illustrate them on examples of food-related studies.
Many efforts have been made to isolate native nanocrystals from raw materials in the last two decades, such as cellulose nanocrystals (CNCs), but existing methods still suffer from low yields, complicated synthesis process and non-uniform sizes of obtained CNCs. Herein, we presented a novel facile self-terminating and efficient method for the formation of uniform CNCs of high yields during the periodate oxidation process within Pickering emulsions. A biphasic system containing hexane with dissolved hexylamine and an aqueous solution of sodium periodate (NaIO4) was used as the reaction medium. Regulated by hexylamine due to its limited solubility in water, the pH value of the aqueous phase was enhanced to around 9.8, leading to the precipitation of sodium orthoperiodate (Na2H3IO6) nanoplates and thus the formation of initial Pickering emulsions. During the gradual formation of cellulose nanofibers and then CNCs, CNCs were attracted to stabilize the interface of the Pickering emulsions, which prevented further decomposition of CNCs by the oxidizing agent in aqueous suspensions. Thus, this isolation strategy secured the efficient separation of CNCs based on their own particular amphiphilic properties and achieved high yield of up to 56 wt.%.
Laplace NMR (LNMR) offers deep insights on diffusional and rotational motion of molecules. The so-called “ultrafast” approach, based on spatial data encoding, enables one to carry out a multidimensional LNMR experiment in a single scan, providing from 10 to 1000-fold acceleration of the experiment. Here, we demonstrate the feasibility of ultrafast diffusion-T2 relaxation correlation (D–T2) measurements with a mobile, low-field, relatively low-cost, single-sided NMR magnet. We show that the method can probe a broad range of diffusion coefficients (at least from 10–8 to 10–12 m² s–1) and reveal multiple components of fluids in heterogeneous materials. The single-scan approach is demonstrably compatible with nuclear spin hyperpolarization techniques because the time-consuming hyperpolarization process does not need to be repeated. Using dynamic nuclear polarization (DNP), we improved the NMR sensitivity of water molecules by a factor of 10⁵ relative to non-hyperpolarized NMR in the 0.3 T field of the single-sided magnet. This enabled us to acquire a D–T2 map in a single, 22 ms scan, despite the low field and relatively low mole fraction (0.003) of hyperpolarized water. Consequently, low-field, hyperpolarized ultrafast LNMR offers significant prospects for advanced, mobile, low-cost and high-sensitivity chemical and medical analysis.
Polymeric multichannel hollow fiber membranes were developed to reduce fiber breakage and to increase the volume-to-membrane-surface ratio and consequently the efficiency of filtration processes. These membranes are commonly used in ultrafiltration and are operated in in-out dead-end mode. However, some of the filtration details are unknown. The filtration efficiency and flow in the multichannel membranes depend on filtration time and are expected to vary along spatial coordinates. In the current work, in-situ magnetic resonance imaging was used to answer these questions. Velocities were quantified in the feed channels to obtain a detailed understanding of the filtration process. Flow and deposits were measured in each of the seven channels during filtration of sodium alginate, which is a model substance for extracellular polymeric substances occurring in water treatment. Volume flow and flow profiles were calculated from phase contrast flow images. The flow in z-direction in the center channel was higher than in the surrounding channels. Flow profiles variate depending on the concentration of Ca²⁺, which changes the filtration mechanism of aqueous solutions of sodium alginate from concentration polarization to gel layer filtration.
Seven novel dirhodium coordination polymers (Rh2-Ln) (n=1-7) are prepared by employing bitopic ligands to connect dirhodium nodes. The formation of the framework is confirmed by ATR-IR and 13C CP MAS NMR. Defect sites resulting from incomplete ligand substitution are revealed by 19F MAS NMR. The random stacking behavior of the frameworks in the obtained solid is analyzed by SEM and XRD. The Rh2/O interaction in neighboring layers is investigated by DR-UV-vis and XPS. This interaction is relevant to understand the catalytic behavior of various Rh2-Ln catalysts in the cyclopropanation of styrene with ethyl diazoacetate (EDA). In this context, the structure-reactivity relationship is discussed by taking into consideration both interlayer Rh2/O interactions and steric effects of side chains.
Ultrafast Laplace NMR (UF-LNMR), which is based on the spatial encoding of multidimensional data, enables one to carry out 2D relaxation and diffusion measurements in a single-scan. Besides reducing the experiment time to a fraction, it significantly facilitates the use of nuclear spin hyperpolarization to boost experimental sensitivity, because the time consuming polarization step does not need to be repeated. Here we demonstrate the usability of hyperpolarized UF-LNMR in the context of cell metabolism, by investigating the conversion of pyruvate to lactate in the cultures of mouse 4T1 cancer cells. We show that ¹³C ultrafast diffusion – T2 relaxation correlation measurements, with the sensitivity enhanced by several orders of magnitude by dissolution dynamic nuclear polarization (D-DNP), allows the determination of the extra- vs. intracellular location of metabolites due to their significantly different values of diffusion coefficients and T2 relaxation times. Under the current conditions, pyruvate located predominantly in the extracellular pool, while lactate remained primarily intracellular. Contrary to the small flip angle diffusion methods reported in the literature, the UF-LNMR method does not require several scans with varying gradient strength, and it provides a combined diffusion and T2 contrast. Furthermore, the ultrafast concept can be extended to various other multidimensional LNMR experiments, which will provide detailed information about the dynamics and exchange processes of cell metabolites.
Ceria nanoparticles with rod-like (ceria-rod), octahedral (ceria-octahedron) and cubic (ceria-cube) morphologies and similar crystallite dimension have been synthesized. TEM results revealed that ceria-octahedra and ceria-cubes are well faceted, mainly enclosed with {111} and {100} facets, respectively. On the contrary, ceria-rods are not well faceted. By CO adsorption, in-situ FTIR and ¹⁷O ssNMR experiments on H2¹⁷O enriched ceria, it is shown that the adsorption behavior of CO/H2O is highly crystal plane selective. These results are well supported by surface enhanced DNP ¹⁷O ssNMR. A correlation between the formation of oxygen vacancies (isolated vacancies and vacancy clusters) with the surface properties of ceria is proposed.
The activation of C‐H bonds of alkanes remains a major challenge for chemistry. In a series of deuteration experiments with D2 in contact with bis‐(diphenylphosphino)butane (dppb) stabilized ruthenium nanoparticles (liquid substrates, 60°C, 6 bar D2) we have observed a surprisingly large reactivity of cyclopentane as compared to cyclohexane and other alkanes. DFT calculations using a ligand‐free Ru13H17 model cluster as catalyst indicate oxidative C‐H cleavage of the bound substrates as rate limiting reaction step. They also indicate similar binding and activation enthalpies of reactions of cyclopentane and cyclohexane.
The motivation of the present work was the preparation of bio-based thin film nanocomposites with improved dielectric properties using modified nanocellulose and chitosan, both materials known to derive from industrial waste. Cyanoethylation of cellulose nanocrystals (CNC) was achieved through a “green” method for the first time. Then, modified CNCs were incorporated into a chitosan (Chi) matrix, obtaining a homogeneous and flexible material with higher dielectric constant due to the high dipole moment of the nitrile functional group. The value of dielectric constant rises with the content of modified CNCs, from a value of 5.5 for pure chitosan at 25 °C and 1 kHz up to a value of 8.5 for the nanocomposite with 50 wt% at the same conditions. These bio-based nanocomposites show an improvement in their dielectric properties compared to pure chitosan and chitosan/unmodified CNC nanocomposites (for which dielectric constant decreases up to 4.5 at 25 °C and 1 kHz) and can be considered for high-temperature applications. Characterization of cyanoethylated cellulose nanocrystals (CN-CNC) and nanocomposites was carried out by infrared spectroscopy (FT-IR), attenuated total reflectance spectroscopy (ATR), atomic force microscopy (AFM), thermogravimetric analysis (TGA), X-ray diffraction (XRD), and solid-state NMR and broad band dielectric spectroscopy (BDS). Tensile tests were developed for mechanical characterization.