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Low-Field Nuclear Magnetic Resonance Characteristics of Biofilm Development Process. Microorganisms 2021; 9:microorganisms9122466. [PMID: 34946068 PMCID: PMC8707105 DOI: 10.3390/microorganisms9122466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/17/2021] [Accepted: 11/24/2021] [Indexed: 11/22/2022] Open
Abstract
To in situ and noninvasively monitor the biofilm development process by low-field nuclear magnetic resonance (NMR), experiments should be made to determine the mechanisms responsible for the T2 signals of biofilm growth. In this paper, biofilms were cultivated in both fluid media and saturated porous media. T2 relaxation for each sample was measured to investigate the contribution of the related processes to T2 relaxation signals. In addition, OD values of bacterial cell suspensions were measured to provide the relative number of bacterial cells. We also obtained SEM photos of the biofilms after vacuum freeze-drying the pure sand and the sand with biofilm formation to confirm the space within the biofilm matrix and identify the existence of biofilm formation. The T2 relaxation distribution is strongly dependent on the density of the bacterial cells suspended in the fluid and the stage of biofilm development. The peak time and the peak percentage can be used as indicators of the biofilm growth states.
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2
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Methods for Studying Bacterial–Fungal Interactions in the Microenvironments of Soil. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11199182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Due to their small size, microorganisms directly experience only a tiny portion of the environmental heterogeneity manifested in the soil. The microscale variations in soil properties constrain the distribution of fungi and bacteria, and the extent to which they can interact with each other, thereby directly influencing their behavior and ecological roles. Thus, to obtain a realistic understanding of bacterial–fungal interactions, the spatiotemporal complexity of their microenvironments must be accounted for. The objective of this review is to further raise awareness of this important aspect and to discuss an overview of possible methodologies, some of easier applicability than others, that can be implemented in the experimental design in this field of research. The experimental design can be rationalized in three different scales, namely reconstructing the physicochemical complexity of the soil matrix, identifying and locating fungi and bacteria to depict their physical interactions, and, lastly, analyzing their molecular environment to describe their activity. In the long term, only relevant experimental data at the cell-to-cell level can provide the base for any solid theory or model that may serve for accurate functional prediction at the ecosystem level. The way to this level of application is still long, but we should all start small.
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Achinas S, Yska SK, Charalampogiannis N, Krooneman J, Euverink GJW. A Technological Understanding of Biofilm Detection Techniques: A Review. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E3147. [PMID: 32679710 PMCID: PMC7412299 DOI: 10.3390/ma13143147] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/08/2020] [Accepted: 07/13/2020] [Indexed: 12/12/2022]
Abstract
Biofouling is a persistent problem in almost any water-based application in several industries. To eradicate biofouling-related problems in bioreactors, the detection of biofilms is necessary. The current literature does not provide clear supportive information on selecting biofilm detection techniques that can be applied to detect biofouling within bioreactors. Therefore, this research aims to review all available biofilm detection techniques and analyze their characteristic properties to provide a comparative assessment that researchers can use to find a suitable biofilm detection technique to investigate their biofilms. In addition, it discusses the confluence of common bioreactor fabrication materials in biofilm formation.
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Affiliation(s)
- Spyridon Achinas
- Faculty of Science and Engineering, University of Groningen, 9747 AG Groningen, The Netherlands; (S.K.Y.); (J.K.); (G.J.W.E.)
| | - Stijn Keimpe Yska
- Faculty of Science and Engineering, University of Groningen, 9747 AG Groningen, The Netherlands; (S.K.Y.); (J.K.); (G.J.W.E.)
| | | | - Janneke Krooneman
- Faculty of Science and Engineering, University of Groningen, 9747 AG Groningen, The Netherlands; (S.K.Y.); (J.K.); (G.J.W.E.)
| | - Gerrit Jan Willem Euverink
- Faculty of Science and Engineering, University of Groningen, 9747 AG Groningen, The Netherlands; (S.K.Y.); (J.K.); (G.J.W.E.)
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4
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Simkins JW, Stewart PS, Codd SL, Seymour JD. Microbial growth rates and local external mass transfer coefficients in a porous bed biofilm system measured by 19 F magnetic resonance imaging of structure, oxygen concentration, and flow velocity. Biotechnol Bioeng 2020; 117:1458-1469. [PMID: 31956979 DOI: 10.1002/bit.27275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 01/03/2020] [Accepted: 01/16/2020] [Indexed: 11/06/2022]
Abstract
19 F nuclear magnetic resonance (NMR) oximetry and 1 H NMR velocimetry were used to noninvasively map oxygen concentrations and hydrodynamics in space and time in a model packed bed biofilm system in the presence and absence of flow. The development of a local oxygen sink associated with a single gel bead inoculated with respiring Escherichia coli was analyzed with a phenomenological model to determine the specific growth rate of the bacteria in situ, returning a value (0.66 hr-1 ) that was close to that measured independently in planktonic culture (0.62 hr-1 ). The decay of oxygen concentration in and around the microbiologically active bead was delayed and slower in experiments conducted under continuous flow in comparison to no-flow experiments. Concentration boundary layer thicknesses were determined and Sherwood numbers calculated to quantify external mass transfer resistance. Boundary layers were thicker in no-flow experiments compared to experiments with flow. Whereas the oxygen concentration profile across a reactive biofilm particle was symmetric in no-flow experiments, it was asymmetric with respect to flow direction in flow experiments with Sherwood numbers on the leading edge (Sh = 7) being larger than the trailing edge (Sh = 3.5). The magnitude of the experimental Sh was comparable to values predicted by a variety of correlations. These spatially resolved measurements of oxygen distribution in a geometrically complex model reveal in innovative detail the local coupling between microbial growth, oxygen consumption, and external mass transfer.
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Affiliation(s)
- Jeffrey W Simkins
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana.,Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana
| | - Philip S Stewart
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana.,Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana
| | - Sarah L Codd
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana.,Department of Mechanical and Industrial Engineering, Montana State University, Bozeman, Montana
| | - Joseph D Seymour
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana.,Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana
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5
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O'Neill KT, Brancato L, Stanwix PL, Fridjonsson EO, Johns ML. Two-phase oil/water flow measurement using an Earth’s field nuclear magnetic resonance flow meter. Chem Eng Sci 2019. [DOI: 10.1016/j.ces.2019.03.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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6
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Baveye PC, Otten W, Kravchenko A, Balseiro-Romero M, Beckers É, Chalhoub M, Darnault C, Eickhorst T, Garnier P, Hapca S, Kiranyaz S, Monga O, Mueller CW, Nunan N, Pot V, Schlüter S, Schmidt H, Vogel HJ. Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain. Front Microbiol 2018; 9:1929. [PMID: 30210462 PMCID: PMC6119716 DOI: 10.3389/fmicb.2018.01929] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/30/2018] [Indexed: 01/17/2023] Open
Abstract
Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the bulk, macroscopic parameters (e.g., granulometry, pH, soil organic matter, and biomass contents) commonly used to characterize soils provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gasses. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale) that is commensurate with the habitat of many microorganisms. For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. With regard to the microbial aspects, although a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because of the scarcity of relevant experimental data. For significant progress to be made, it is crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead. Fortunately, a number of these challenges may be resolved by brand new measuring equipment that will become commercially available in the very near future.
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Affiliation(s)
- Philippe C. Baveye
- UMR ECOSYS, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, rance
| | - Wilfred Otten
- School of Water, Energy and Environment, Cranfield University, Cranfield, United Kingdom
| | - Alexandra Kravchenko
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - María Balseiro-Romero
- UMR ECOSYS, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, rance
- Department of Soil Science and Agricultural Chemistry, Centre for Research in Environmental Technologies, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Éléonore Beckers
- Soil–Water–Plant Exchanges, Terra Research Centre, BIOSE, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Maha Chalhoub
- UMR ECOSYS, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - Christophe Darnault
- Laboratory of Hydrogeoscience and Biological Engineering, L.G. Rich Environmental Laboratory, Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC, United States
| | - Thilo Eickhorst
- Faculty 2 Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Patricia Garnier
- UMR ECOSYS, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - Simona Hapca
- Dundee Epidemiology and Biostatistics Unit, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Serkan Kiranyaz
- Department of Electrical Engineering, Qatar University, Doha, Qatar
| | - Olivier Monga
- Institut de Recherche pour le Développement, Bondy, France
| | - Carsten W. Mueller
- Lehrstuhl für Bodenkunde, Technical University of Munich, Freising, Germany
| | - Naoise Nunan
- Institute of Ecology and Environmental Sciences – Paris, Sorbonne Universités, CNRS, IRD, INRA, P7, UPEC, Paris, France
| | - Valérie Pot
- UMR ECOSYS, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - Steffen Schlüter
- Soil System Science, Helmholtz-Zentrum für Umweltforschung GmbH – UFZ, Leipzig, Germany
| | - Hannes Schmidt
- Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of Vienna, Vienna, Austria
| | - Hans-Jörg Vogel
- Soil System Science, Helmholtz-Zentrum für Umweltforschung GmbH – UFZ, Leipzig, Germany
- Institute of Soil Science and Plant Nutrition, Martin Luther University of Halle-Wittenberg, Halle, Germany
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7
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Simkins JW, Stewart PS, Seymour JD. Spatiotemporal mapping of oxygen in a microbially-impacted packed bed using 19F Nuclear magnetic resonance oximetry. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 293:123-133. [PMID: 29940412 PMCID: PMC6047901 DOI: 10.1016/j.jmr.2018.06.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/12/2018] [Accepted: 06/13/2018] [Indexed: 06/08/2023]
Abstract
19F magnetic resonance has been used in the medical field for quantifying oxygenation in blood, tissues, and tumors. The 19F NMR oximetry technique exploits the affinity of molecular oxygen for liquid fluorocarbon phases, and the resulting linear dependence of 19F spin-lattice relaxation rate R1 on local oxygen concentration. Bacterial biofilms, aggregates of bacteria encased in a self-secreted matrix of extracellular polymers, are important in environmental, industrial, and clinical settings and oxygen gradients represent a critical determinant of biofilm function. However, measurement of oxygen distribution in biofilms and biofouled porous media is difficult. Here the ability of 19F NMR oximetry to accurately track oxygen profile development in microbial impacted packed bed systems without impacting oxygen transport is demonstrated. Time-stable and inert fluorocarbon containing particles are designed which act as oxygen reporters in porous media systems. Particles are generated by emulsifying and entrapping perfluorooctylbromide (PFOB) into alginate gel, resulting in oxygen-sensing alginate beads that are then used as the solid matrix of the packed bed. 19F oxygenation maps, when combined with 1H velocity maps, allow for insight into the interplay between fluid dynamics and oxygen transport phenomena in these complex biofouled systems. Spatial maps of oxygen consumption rate constants are calculated. The growth characteristics of two bacteria, a non-biofilm forming Escherichia coli and Staphylococcus epidermidis, a strong biofilm-former, are used to demonstrate the novel data provided by the method.
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Affiliation(s)
- Jeffrey W Simkins
- Center for Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT 59715, United States; Department of Chemical and Biological Engineering, Montana State University, 306 Cobleigh Hall, Bozeman, MT 59715, United States.
| | - Philip S Stewart
- Center for Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT 59715, United States; Department of Chemical and Biological Engineering, Montana State University, 306 Cobleigh Hall, Bozeman, MT 59715, United States.
| | - Joseph D Seymour
- Center for Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT 59715, United States; Department of Chemical and Biological Engineering, Montana State University, 306 Cobleigh Hall, Bozeman, MT 59715, United States.
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8
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Herrling MP, Weisbrodt J, Kirkland CM, Williamson NH, Lackner S, Codd SL, Seymour JD, Guthausen G, Horn H. NMR investigation of water diffusion in different biofilm structures. Biotechnol Bioeng 2017; 114:2857-2867. [PMID: 28755486 DOI: 10.1002/bit.26392] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 06/08/2017] [Accepted: 07/23/2017] [Indexed: 01/19/2023]
Abstract
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.
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Affiliation(s)
- Maria P Herrling
- Department of Wastewater Engineering, Institute IWAR, Technische Universität Darmstadt, Darmstadt, Germany.,Department of Water Chemistry and Water Technology, Engler-Bunte-Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Jessica Weisbrodt
- Department of Water Chemistry and Water Technology, Engler-Bunte-Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Catherine M Kirkland
- Center of Biofilm Engineering, Montana State University, Bozeman, Montana.,Department of Mechanical and Industrial Engineering, Montana State University, Bozeman, Montana
| | - Nathan H Williamson
- Future Industries Institute, University of South Australia, Mawson Lakes Campus, Adelaide, Australia
| | - Susanne Lackner
- Department of Wastewater Engineering, Institute IWAR, Technische Universität Darmstadt, Darmstadt, Germany
| | - Sarah L Codd
- Center of Biofilm Engineering, Montana State University, Bozeman, Montana.,Department of Mechanical and Industrial Engineering, Montana State University, Bozeman, Montana
| | - Joseph D Seymour
- Center of Biofilm Engineering, Montana State University, Bozeman, Montana.,Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana
| | - Gisela Guthausen
- Department of Water Chemistry and Water Technology, Engler-Bunte-Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany.,Institute of Mechanical Process Engineering and Mechanics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Harald Horn
- Department of Water Chemistry and Water Technology, Engler-Bunte-Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
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9
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Carrel M, Beltran MA, Morales VL, Derlon N, Morgenroth E, Kaufmann R, Holzner M. Biofilm imaging in porous media by laboratory X-Ray tomography: Combining a non-destructive contrast agent with propagation-based phase-contrast imaging tools. PLoS One 2017; 12:e0180374. [PMID: 28732010 PMCID: PMC5521744 DOI: 10.1371/journal.pone.0180374] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 06/14/2017] [Indexed: 11/21/2022] Open
Abstract
X-ray tomography is a powerful tool giving access to the morphology of biofilms, in 3D porous media, at the mesoscale. Due to the high water content of biofilms, the attenuation coefficient of biofilms and water are very close, hindering the distinction between biofilms and water without the use of contrast agents. Until now, the use of contrast agents such as barium sulfate, silver-coated micro-particles or 1-chloronaphtalene added to the liquid phase allowed imaging the biofilm 3D morphology. However, these contrast agents are not passive and potentially interact with the biofilm when injected into the sample. Here, we use a natural inorganic compound, namely iron sulfate, as a contrast agent progressively bounded in dilute or colloidal form into the EPS matrix during biofilm growth. By combining a very long source-to-detector distance on a X-ray laboratory source with a Lorentzian filter implemented prior to tomographic reconstruction, we substantially increase the contrast between the biofilm and the surrounding liquid, which allows revealing the 3D biofilm morphology. A comparison of this new method with the method proposed by Davit et al (Davit et al., 2011), which uses barium sulfate as a contrast agent to mark the liquid phase was performed. Quantitative evaluations between the methods revealed substantial differences for the volumetric fractions obtained from both methods. Namely, contrast agent—biofilm interactions (e.g. biofilm detachment) occurring during barium sulfate injection caused a reduction of the biofilm volumetric fraction of more than 50% and displacement of biofilm patches elsewhere in the column. Two key advantages of the newly proposed method are that passive addition of iron sulfate maintains the integrity of the biofilm prior to imaging, and that the biofilm itself is marked by the contrast agent, rather than the liquid phase as in other available methods. The iron sulfate method presented can be applied to understand biofilm development and bioclogging mechanisms in porous materials and the obtained biofilm morphology could be an ideal basis for 3D numerical calculations of hydrodynamic conditions to investigate biofilm-flow coupling.
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Affiliation(s)
- Maxence Carrel
- Institute of Environmental Engineering, ETH Zürich, Stefano Franscini-Platz 5, 8093 Zurich, Switzerland
| | - Mario A. Beltran
- Swiss Federal Laboratories for Materials Science and Technology (EMPA), Dübendorf, Switzerland
| | - Verónica L. Morales
- Institute of Environmental Engineering, ETH Zürich, Stefano Franscini-Platz 5, 8093 Zurich, Switzerland
- Department of Civil and Environmental Engineering, University of California Davis, Davis, California, United States of America
| | - Nicolas Derlon
- Institute of Environmental Engineering, ETH Zürich, Stefano Franscini-Platz 5, 8093 Zurich, Switzerland
- Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Dübendorf, Switzerland
| | - Eberhard Morgenroth
- Institute of Environmental Engineering, ETH Zürich, Stefano Franscini-Platz 5, 8093 Zurich, Switzerland
- Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Dübendorf, Switzerland
| | - Rolf Kaufmann
- Swiss Federal Laboratories for Materials Science and Technology (EMPA), Dübendorf, Switzerland
| | - Markus Holzner
- Institute of Environmental Engineering, ETH Zürich, Stefano Franscini-Platz 5, 8093 Zurich, Switzerland
- * E-mail:
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10
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Tenório RP, Barros W. Patterns in Saccharomyces cerevisiae yeast colonies via magnetic resonance imaging. Integr Biol (Camb) 2017; 9:68-75. [PMID: 27942686 DOI: 10.1039/c6ib00219f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the use of high-resolution magnetic resonance imaging methods to observe pattern formation in colonies of Saccharomyces cerevisiae. Our results indicate substantial signal loss localized in specific regions of the colony rendering useful imaging contrast. This imaging contrast is recognizable as being due to discontinuities in magnetic susceptibility (χ) between different spatial regions. At the microscopic pixel level, the local variations in the magnetic susceptibility (Δχ) induce a loss in the NMR signal, which was quantified via T2 and T2* maps, permitting estimation of Δχ values for different regions of the colony. Interestingly the typical petal/wrinkling patterns present in the colony have a high degree of correlation with the estimated susceptibility distribution. We conclude that the presence of magnetic susceptibility inclusions, together with their spatial arrangement within the colony, may be a potential cause of the susceptibility distribution and therefore the contrast observed on the images.
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Affiliation(s)
- Rômulo P Tenório
- Centro Regional de Ciências Nucleares do Nordeste, Comissão Nacional de Energia Nuclear, Av. Prof. Luiz Freire, 200, Cidade Universitária, 50740-540, Recife, Pernambuco, Brazil.
| | - Wilson Barros
- Departamento de Física, Universidade Federal de Pernambuco, Av. Prof. Luiz Freire, s/n, Cidade Universitária, 50670-901, Recife, Pernambuco, Brazil
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11
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Ranzinger F, Herrling MP, Lackner S, Grande VW, Baniodeh A, Powell AK, Horn H, Guthausen G. Direct surface visualization of biofilms with high spin coordination clusters using Magnetic Resonance Imaging. Acta Biomater 2016; 31:167-177. [PMID: 26675127 DOI: 10.1016/j.actbio.2015.12.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 12/01/2015] [Accepted: 12/03/2015] [Indexed: 01/02/2023]
Abstract
Magnetic Resonance Imaging is a powerful tool for the investigation of a biofilms' physical structure determining mass transport behavior which is of major importance in biofilm research. The entire biofilm is imaged in situ non-invasively and non-destructively on a meso-scale. In this study, different contrast agents were applied to study the biofilm's properties with the focus on mass transport, which is achieved by varying the contrast agents with respect to their NMR and interaction properties. The spatio-temporal tracking of these cluster, molecular and particulate contrast agents in biofilms was achieved by T1-, T2-weighted and proton density images during short (20h) and long (14 d) term exposures. The best biofilm surface visualization was observed when applying a new high spin coordination cluster (Fe10Gd10) showing a high affinity to the biofilm's surface and a fast immobilization within minutes. Contrarily, the small molecular contrast agents show no immobilization and fully penetrated into the biofilm. A concentration equilibrium was observed which was confirmed in back diffusion experiments. Interactions between larger nanoparticulate contrast agents and the biofilm required hours to achieve immobilization. Thus, the penetration depth into the biofilm is predominantly size-dependent. Here, it is shown that biofilm surface interactions can be observed in situ and spatio-temporarily resolved. The reported methodology demonstrates a new means to explore mass transfer of various substances in biofilms. STATEMENT OF SIGNIFICANCE In biofilm research, the investigation of the biofilms' physical structure is of high relevance for the understanding of mass transport processes. However, commonly used imaging techniques for biofilm imaging such as CLSM or electron microscopy rarely visualize the real biofilm due to their invasiveness and destructiveness. Magnetic Resonance Imaging (MRI) represents the ideal tool to image the biofilm in situ, non-invasively and non-destructively with a spatial resolution of several 10μm. To gain specific structural and functional information, a variety of MRI contrast agents (molecular and particulate) was applied with different properties for the first time. Results elucidate the interactions between the biofilms' surface and the contrast agents and open a new field for biotechnological applications by functional contrast enhancement.
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12
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Biomechanical Analysis of Infectious Biofilms. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 915:99-114. [PMID: 27193540 DOI: 10.1007/978-3-319-32189-9_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The removal of infectious biofilms from tissues or implanted devices and their transmission through fluid transport systems depends in part of the mechanical properties of their polymeric matrix. Linking the various physical and chemical microscopic interactions to macroscopic deformation and failure modes promises to unveil design principles for novel therapeutic strategies targeting biofilm eradication, and provide a predictive capability to accelerate the development of devices, water lines, etc, that minimise microbial dispersal. Here, our current understanding of biofilm mechanics is appraised from the perspective of biophysics , with an emphasis on constitutive modelling that has been highly successful in soft matter. Fitting rheometric data to viscoelastic models has quantified linear and nonlinear stress relaxation mechanisms, how they vary between species and environments, and how candidate chemical treatments alter the mechanical response. The rich interplay between growth, mechanics and hydrodynamics is just becoming amenable to computational modelling and promises to provide unprecedented characterisation of infectious biofilms in their native state.
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13
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Kirkland CM, Herrling MP, Hiebert R, Bender AT, Grunewald E, Walsh DO, Codd SL. In Situ Detection of Subsurface Biofilm Using Low-Field NMR: A Field Study. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:11045-11052. [PMID: 26308099 DOI: 10.1021/acs.est.5b02690] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Subsurface biofilms are central to bioremediation of chemical contaminants in soil and groundwater whereby micro-organisms degrade or sequester environmental pollutants like nitrate, hydrocarbons, chlorinated solvents and heavy metals. Current methods to monitor subsurface biofilm growth in situ are indirect. Previous laboratory research conducted at MSU has indicated that low-field nuclear magnetic resonance (NMR) is sensitive to biofilm growth in porous media, where biofilm contributes a polymer gel-like phase and enhances T2 relaxation. Here we show that a small diameter NMR well logging tool can detect biofilm accumulation in the subsurface using the change in T2 relaxation behavior over time. T2 relaxation distributions were measured over an 18 day experimental period by two NMR probes, operating at approximately 275 kHz and 400 kHz, installed in 10.2 cm wells in an engineered field testing site. The mean log T2 relaxation times were reduced by 62% and 43%, respectively, while biofilm was cultivated in the soil surrounding each well. Biofilm growth was confirmed by bleaching and flushing the wells and observing the NMR signal's return to baseline. This result provides a direct and noninvasive method to spatiotemporally monitor biofilm accumulation in the subsurface.
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Affiliation(s)
- Catherine M Kirkland
- Center for Biofilm Engineering, Montana State University , Bozeman, Montana 59717, United States
- Department of Chemical and Biological Engineering, Montana State University , Bozeman, Montana 59717, United States
| | - Maria P Herrling
- Chair of Water Chemistry and Water Technology, Karlsruhe Institute of Technology , Karlsruhe 76131, Germany
| | - Randy Hiebert
- Center for Biofilm Engineering, Montana State University , Bozeman, Montana 59717, United States
| | - Andrew T Bender
- Center for Biofilm Engineering, Montana State University , Bozeman, Montana 59717, United States
- Department of Mechanical and Industrial Engineering, Montana State University , Bozeman, Montana 59717, United States
| | - Elliot Grunewald
- Vista Clara Inc. , 12201 Cyrus Way Ste. 104, Mukilteo, Washington 98275, United States
| | - David O Walsh
- Vista Clara Inc. , 12201 Cyrus Way Ste. 104, Mukilteo, Washington 98275, United States
| | - Sarah L Codd
- Center for Biofilm Engineering, Montana State University , Bozeman, Montana 59717, United States
- Department of Mechanical and Industrial Engineering, Montana State University , Bozeman, Montana 59717, United States
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14
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Fridjonsson E, Vogt S, Vrouwenvelder J, Johns M. Early non-destructive biofouling detection in spiral wound RO membranes using a mobile earth׳s field NMR. J Memb Sci 2015. [DOI: 10.1016/j.memsci.2015.03.088] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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15
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Fridjonsson EO, Creber SA, Vrouwenvelder JS, Johns ML. Magnetic resonance signal moment determination using the Earth's magnetic field. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 252:145-150. [PMID: 25700116 DOI: 10.1016/j.jmr.2015.01.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/14/2015] [Accepted: 01/17/2015] [Indexed: 06/04/2023]
Abstract
We demonstrate a method to manipulate magnetic resonance data such that the moments of the signal spatial distribution are readily accessible. Usually, magnetic resonance imaging relies on data acquired in so-called k-space which is subsequently Fourier transformed to render an image. Here, via analysis of the complex signal in the vicinity of the centre of k-space we are able to access the first three moments of the signal spatial distribution, ultimately in multiple directions. This is demonstrated for biofouling of a reverse osmosis (RO) membrane module, rendering unique information and an early warning of the onset of fouling. The analysis is particularly applicable for the use of mobile magnetic resonance spectrometers; here we demonstrate it using an Earth's magnetic field system.
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Affiliation(s)
- E O Fridjonsson
- School of Mechanical and Chemical Engineering, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - S A Creber
- Department of Chemistry and Chemical Engineering, Royal Military College of Canada, PO Box 17000, Station Forces, Kingston, Ontario K7K 7B4, Canada
| | - J S Vrouwenvelder
- Wetsus, European Centre of Excellence of Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands; Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands; Biological and Environmental Sciences and Engineering Division, Water Desalination and Reuse Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - M L Johns
- School of Mechanical and Chemical Engineering, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.
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16
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Herrling MP, Guthausen G, Wagner M, Lackner S, Horn H. Determining the flow regime in a biofilm carrier by means of magnetic resonance imaging. Biotechnol Bioeng 2015; 112:1023-32. [DOI: 10.1002/bit.25510] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 11/19/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Maria P. Herrling
- Chair of Water Chemistry Water Technology; Karlsruhe Institute of Technology; Engler-Bunte-Ring 1 Karlsruhe 76131 Germany
| | - Gisela Guthausen
- Pro2NMR; Institute for Biological Interfaces and Institute for Mechanical Process Engineering and Mechanics; Karlsruhe Institute of Technology; Karlsruhe Germany
| | - Michael Wagner
- Chair of Water Chemistry Water Technology; Karlsruhe Institute of Technology; Engler-Bunte-Ring 1 Karlsruhe 76131 Germany
- Institute of Functional Interfaces; Karlsruhe Institute of Technology; Eggenstein-Leopoldshafen Germany
| | - Susanne Lackner
- Chair of Water Chemistry Water Technology; Karlsruhe Institute of Technology; Engler-Bunte-Ring 1 Karlsruhe 76131 Germany
| | - Harald Horn
- Chair of Water Chemistry Water Technology; Karlsruhe Institute of Technology; Engler-Bunte-Ring 1 Karlsruhe 76131 Germany
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17
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Abstract
We present a model of biofilm growth in a long channel where the biomass is assumed to have the rheology of a viscous polymer solution. We examine the competition between growth and erosion-like surface detachment due to the flow. A particular focus of our investigation is the effect of the biofilm growth on the fluid flow in the pores, and the issue of whether biomass can grow sufficiently to shut off fluid flow through the pores, thus clogging the pore space. Net biofilm growth is coupled along the pore length via flow rate and nutrient transport in the pore flow. Our 2D model extends existing results on stability of 1D steady state biofilm thicknesses to show that, in the case of flows driven by a fixed pressure drop, full clogging of the pore can indeed happen in certain cases dependent on the functional form of the detachment term.
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