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Gerbersdorf SU, Koca K, de Beer D, Chennu A, Noss C, Risse-Buhl U, Weitere M, Eiff O, Wagner M, Aberle J, Schweikert M, Terheiden K. Exploring flow-biofilm-sediment interactions: Assessment of current status and future challenges. WATER RESEARCH 2020; 185:116182. [PMID: 32763530 DOI: 10.1016/j.watres.2020.116182] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/19/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
Biofilm activities and their interactions with physical, chemical and biological processes are of great importance for a variety of ecosystem functions, impacting hydrogeomorphology, water quality and aquatic ecosystem health. Effective management of water bodies requires advancing our understanding of how flow influences biofilm-bound sediment and ecosystem processes and vice-versa. However, research on this triangle of flow-biofilm-sediment is still at its infancy. In this Review, we summarize the current state of the art and methodological approaches in the flow-biofilm-sediment research with an emphasis on biostabilization and fine sediment dynamics mainly in the benthic zone of lotic and lentic environments. Example studies of this three-way interaction across a range of spatial scales from cell (nm - µm) to patch scale (mm - dm) are highlighted in view of the urgent need for interdisciplinary approaches. As a contribution to the review, we combine a literature survey with results of a pilot experiment that was conducted in the framework of a joint workshop to explore the feasibility of asking interdisciplinary questions. Further, within this workshop various observation and measuring approaches were tested and the quality of the achieved results was evaluated individually and in combination. Accordingly, the paper concludes by highlighting the following research challenges to be considered within the forthcoming years in the triangle of flow-biofilm-sediment: i) Establish a collaborative work among hydraulic and sedimentation engineers as well as ecologists to study mutual goals with appropriate methods. Perform realistic experimental studies to test hypotheses on flow-biofilm-sediment interactions as well as structural and mechanical characteristics of the bed. ii) Consider spatially varying characteristics of flow at the sediment-water interface. Utilize combinations of microsensors and non-intrusive optical methods, such as particle image velocimetry and laser scanner to elucidate the mechanism behind biofilm growth as well as mass and momentum flux exchanges between biofilm and water. Use molecular approaches (DNA, pigments, staining, microscopy) for sophisticated community analyses. Link varying flow regimes to microbial communities (and processes) and fine sediment properties to explore the role of key microbial players and functions in enhancing sediment stability (biostabilization). iii) Link laboratory-scale observations to larger scales relevant for management of water bodies. Conduct field experiments to better understand the complex effects of variable flow and sediment regimes on biostabilization. Employ scalable and informative observation techniques (e.g., hyperspectral imaging, particle tracking) that can support predictions on the functional aspects, such as metabolic activity, bed stability, nutrient fluxes under variable regimes of flow-biofilm-sediment.
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Affiliation(s)
- Sabine Ulrike Gerbersdorf
- University of Stuttgart, Institute for Modelling Hydraulic and Environmental Systems, Pfaffenwaldring 61, 70569 Stuttgart, Germany.
| | - Kaan Koca
- University of Stuttgart, Institute for Modelling Hydraulic and Environmental Systems, Pfaffenwaldring 61, 70569 Stuttgart, Germany.
| | - Dirk de Beer
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany.
| | - Arjun Chennu
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany; Leibniz Center for Tropical Marine Research, Fahrenheitstraße 6, 28359 Bremen, Germany.
| | - Christian Noss
- University of Koblenz-Landau, Institute for Environmental Sciences, Fortstraße 7, 76829 Landau, Germany; Federal Waterways Engineering and Research Institute, Hydraulic Engineering in Inland Areas, Kußmaulstraße 17, 76187 Karlsruhe, Germany.
| | - Ute Risse-Buhl
- Helmholtz Centre for Environmental Research - UFZ, Department of River Ecology, Brückstraße 3a, 39114 Magdeburg, Germany.
| | - Markus Weitere
- Helmholtz Centre for Environmental Research - UFZ, Department of River Ecology, Brückstraße 3a, 39114 Magdeburg, Germany.
| | - Olivier Eiff
- KIT Karlsruhe Institute of Technology, Institute for Hydromechanics, Otto-Ammann Platz 1, 76131 Karlsruhe, Germany.
| | - Michael Wagner
- KIT Karlsruhe Institute of Technology, Engler-Bunte-Institute, Water Chemistry and Water Technology, Engler-Bunte-Ring 9a, 76131 Karlsruhe, Germany.
| | - Jochen Aberle
- Technische Universität Braunschweig, Leichtweiß-Institute for Hydraulic Engineering and Water Resources, Beethovenstraße 51a, 38106 Braunschweig, Germany.
| | - Michael Schweikert
- University of Stuttgart, Institute of Biomaterials and Biomolecular Systems, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
| | - Kristina Terheiden
- University of Stuttgart, Institute for Modelling Hydraulic and Environmental Systems, Pfaffenwaldring 61, 70569 Stuttgart, Germany.
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Microrheology of growing Escherichia coli biofilms investigated by using magnetic force modulation atomic force microscopy. Biointerphases 2016; 11:041005. [PMID: 27907987 DOI: 10.1116/1.4968809] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Microrheology of growing biofilms provides insightful information about its structural evolution and properties. In this study, the authors have investigated the microrheology of Escherichia coli (strain HCB1) biofilms at different indentation depth (δ) by using magnetic force modulation atomic force microscopy as a function of disturbing frequency (f). As δ increases, the dynamic stiffness (ks) for the biofilms in the early stage significantly increases. However, it levels off when the biofilms are matured. The facts indicate that the biofilms change from inhomogeneous to homogeneous in structure. Moreover, ks is scaled to f, which coincides with the rheology of soft glasses. The exponent increases with the incubation time, indicating the fluidization of biofilms. In contrast, the upper layer of the matured biofilms is solidlike in that the storage modulus is always larger than the loss modulus, and its viscoelasticity is slightly influenced by the shear stress.
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Daniels SL, Pressman JG, Wahman DG. AFM structural characterization of drinking water biofilm under physiological conditions. RSC Adv 2016. [DOI: 10.1039/c5ra20606e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Insights into the complex morphology of multi-species drinking water biofilm using atomic force microscopy (AFM).
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Affiliation(s)
- Stephanie L. Daniels
- Oak Ridge Institute for Science and Education
- Oak Ridge
- USA
- Water Supply and Water Resource Division
- National Risk Management Research Laboratory
| | - Jonathan G. Pressman
- Water Supply and Water Resource Division
- National Risk Management Research Laboratory
- U.S. Environmental Protection Agency
- Cincinnati
- USA
| | - David G. Wahman
- Water Supply and Water Resource Division
- National Risk Management Research Laboratory
- U.S. Environmental Protection Agency
- Cincinnati
- USA
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Jung GB, Nam SW, Choi S, Lee GJ, Park HK. Evaluation of antibiotic effects on Pseudomonas aeruginosa biofilm using Raman spectroscopy and multivariate analysis. BIOMEDICAL OPTICS EXPRESS 2014; 5:3238-51. [PMID: 25401035 PMCID: PMC4230853 DOI: 10.1364/boe.5.003238] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 06/08/2014] [Accepted: 08/19/2014] [Indexed: 05/22/2023]
Abstract
We investigate the mode of action and classification of antibiotic agents (ceftazidime, patulin, and epigallocatechin gallate; EGCG) on Pseudomonas aeruginosa (P. aeruginosa) biofilm using Raman spectroscopy with multivariate analysis, including support vector machine (SVM) and principal component analysis (PCA). This method allows for quantitative, label-free, non-invasive and rapid monitoring of biochemical changes in complex biofilm matrices with high sensitivity and specificity. In this study, the biofilms were grown and treated with various agents in the microfluidic device, and then transferred onto gold-coated substrates for Raman measurement. Here, we show changes in biochemical properties, and this technology can be used to distinguish between changes induced in P. aeruginosa biofilms using three antibiotic agents. The Raman band intensities associated with DNA and proteins were decreased, compared to control biofilms, when the biofilms were treated with antibiotics. Unlike with exposure to ceftazidime and patulin, the Raman spectrum of biofilms exposed to EGCG showed a shift in the spectral position of the CH deformation stretch band from 1313 cm(-1) to 1333 cm(-1), and there was no difference in the band intensity at 1530 cm(-1) (C = C stretching, carotenoids). The PCA-SVM analysis results show that antibiotic-treated biofilms can be detected with high sensitivity of 93.33%, a specificity of 100% and an accuracy of 98.33%. This method also discriminated the three antibiotic agents based on the cellular biochemical and structural changes induced by antibiotics with high sensitivity and specificity of 100%. This study suggests that Raman spectroscopy with PCA-SVM is potentially useful for the rapid identification and classification of clinically-relevant antibiotics of bacteria biofilm. Furthermore, this method could be a powerful approach for the development and screening of new antibiotics.
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Affiliation(s)
- Gyeong Bok Jung
- Department of Biomedical Engineering & Healthcare Industry Research Institute, College of Medicine, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, South Korea
- These authors contributed equally to this work
| | - Seong Won Nam
- Department of Biomedical Engineering & Healthcare Industry Research Institute, College of Medicine, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, South Korea
- These authors contributed equally to this work
| | - Samjin Choi
- Department of Biomedical Engineering & Healthcare Industry Research Institute, College of Medicine, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, South Korea
- Program of Medical Engineering, Kyung Hee University, Seoul 130-701, South Korea
| | - Gi-Ja Lee
- Department of Biomedical Engineering & Healthcare Industry Research Institute, College of Medicine, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, South Korea
- Program of Medical Engineering, Kyung Hee University, Seoul 130-701, South Korea
| | - Hun-Kuk Park
- Department of Biomedical Engineering & Healthcare Industry Research Institute, College of Medicine, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, South Korea
- Program of Medical Engineering, Kyung Hee University, Seoul 130-701, South Korea
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Wagner K, Friedrich S, Stang C, Bley T, Schilling N, Bieda M, Lasagni A, Boschke E. Initial phases of microbial biofilm formation on opaque, innovative anti-adhesive surfaces using a modular microfluidic system. Eng Life Sci 2013. [DOI: 10.1002/elsc.201200035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Katrin Wagner
- Institute of Food Technology and Bioprocess Engineering; Technische Universität Dresden; Dresden Germany
| | - Sandra Friedrich
- Institute of Food Technology and Bioprocess Engineering; Technische Universität Dresden; Dresden Germany
| | - Carolin Stang
- Institute of Food Technology and Bioprocess Engineering; Technische Universität Dresden; Dresden Germany
| | - Thomas Bley
- Institute of Food Technology and Bioprocess Engineering; Technische Universität Dresden; Dresden Germany
| | - Niels Schilling
- Fraunhofer Institute for Material and Beam Technology IWS; Dresden Germany
| | - Matthias Bieda
- Fraunhofer Institute for Material and Beam Technology IWS; Dresden Germany
| | - Andrés Lasagni
- Fraunhofer Institute for Material and Beam Technology IWS; Dresden Germany
| | - Elke Boschke
- Institute of Food Technology and Bioprocess Engineering; Technische Universität Dresden; Dresden Germany
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Characterisation of spin coated engineered Escherichia coli biofilms using atomic force microscopy. Colloids Surf B Biointerfaces 2011; 89:152-60. [PMID: 21955509 DOI: 10.1016/j.colsurfb.2011.09.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 08/26/2011] [Accepted: 09/06/2011] [Indexed: 10/17/2022]
Abstract
The ability of biofilms to withstand chemical and physical extremes gives them the potential to be developed as robust biocatalysts. Critical to this issue is their capacity to withstand the physical environment within a bioreactor; in order to assess this capability knowledge of their surface properties and adhesive strength is required. Novel atomic force microscopy experiments conducted under growth conditions (30°C) were used to characterise Escherichia coli biofilms, which were generated by a recently developed spin-coating method onto a poly-l-lysine coated glass substrate. High-resolution topographical images were obtained throughout the course of biofilm development, quantifying the tip-cell interaction force during the 10 day maturation process. Strikingly, the adhesion force between the Si AFM tip and the biofilm surface increased from 0.8 nN to 40 nN within 3 days. This was most likely due to the production of extracellular polymer substance (EPS), over the maturation period, which was also observed by electron microscopy. At later stages of maturation, multiple retraction events were also identified corresponding to biofilm surface features thought to be EPS components. The spin coated biofilms were shown to have stronger surface adhesion than an equivalent conventionally grown biofilm on the same glass substrate.
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Lim J, Lee KM, Kim SH, Kim Y, Kim SH, Park W, Park S. YkgM and ZinT proteins are required for maintaining intracellular zinc concentration and producing curli in enterohemorrhagic Escherichia coli (EHEC) O157:H7 under zinc deficient conditions. Int J Food Microbiol 2011; 149:159-70. [DOI: 10.1016/j.ijfoodmicro.2011.06.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 04/18/2011] [Accepted: 06/21/2011] [Indexed: 11/29/2022]
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10
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Shumi W, Lim J, Nam SW, Lee K, Kim SH, Kim MH, Cho KS, Park S. Environmental factors that affect Streptococcus mutans biofilm formation in a microfluidic device mimicking teeth. BIOCHIP JOURNAL 2010. [DOI: 10.1007/s13206-010-4401-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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