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Papadopoulos C, Larue AE, Toulouze C, Mokhtari O, Lefort J, Libert E, Assémat P, Swider P, Malaquin L, Davit Y. A versatile micromodel technology to explore biofilm development in porous media flows. LAB ON A CHIP 2024; 24:254-271. [PMID: 38059908 DOI: 10.1039/d3lc00293d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Bacterial biofilms that grow in porous media are critical to ecosystem processes and applications ranging from soil bioremediation to bioreactors for treating wastewater or producing value-added products. However, understanding and engineering the complex phenomena that drive the development of biofilms in such systems remains a challenge. Here we present a novel micromodel technology to explore bacterial biofilm development in porous media flows. The technology consists of a set of modules that can be combined as required for any given experiment and conveniently tuned for specific requirements. The core module is a 3D-printed micromodel where biofilm is grown into a perfusable porous substrate. High-precision additive manufacturing, in particular stereolithography, is used to fabricate porous scaffolds with precisely controlled architectures integrating flow channels with diameters down to several hundreds of micrometers. The system is instrumented with: ultraviolet-C light-emitting diodes; on-line measurements of oxygen consumption and pressure drop across the porous medium; camera and spectrophotometric cells for the detection of biofilm detachment events at the outlet. We demonstrate how this technology can be used to study the development of Pseudomonas aeruginosa biofilm for several days within a network of flow channels. We find complex dynamics whereby oxygen consumption reaches a steady-state but not the pressure drop, which instead features a permanent regime with large fluctuations. We further use X-ray computed microtomography to image the spatial distribution of biofilms and computational fluid dynamics to link biofilm development with local flow properties. By combining the advantages of additive manufacturing for the creation of reproducible 3D porous microarchitectures with the flow control and instrumentation accuracy of microfluidics, our system provides a platform to study the dynamics of biofilm development in 3D porous media and to rapidly test new concepts in process engineering.
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Affiliation(s)
- Christos Papadopoulos
- Institut de Mécanique des Fluides (IMFT), CNRS & Université de Toulouse, 31400 Toulouse, France.
- LAAS-CNRS, CNRS & Université de Toulouse, 31400 Toulouse, France
| | - Anne Edith Larue
- Institut de Mécanique des Fluides (IMFT), CNRS & Université de Toulouse, 31400 Toulouse, France.
- Transverse Lab, 271 rue des Fontaines, 31300 Toulouse, France
| | - Clara Toulouze
- Institut de Mécanique des Fluides (IMFT), CNRS & Université de Toulouse, 31400 Toulouse, France.
| | - Omar Mokhtari
- Physikalisches Institut, Universität Bern, Gesellschaftsstrasse 6, 3012 Bern, Switzerland
| | - Julien Lefort
- Institut de Mécanique des Fluides (IMFT), CNRS & Université de Toulouse, 31400 Toulouse, France.
| | - Emmanuel Libert
- Institut de Mécanique des Fluides (IMFT), CNRS & Université de Toulouse, 31400 Toulouse, France.
| | - Pauline Assémat
- Institut de Mécanique des Fluides (IMFT), CNRS & Université de Toulouse, 31400 Toulouse, France.
| | - Pascal Swider
- Institut de Mécanique des Fluides (IMFT), CNRS & Université de Toulouse, 31400 Toulouse, France.
| | - Laurent Malaquin
- LAAS-CNRS, CNRS & Université de Toulouse, 31400 Toulouse, France
| | - Yohan Davit
- Institut de Mécanique des Fluides (IMFT), CNRS & Université de Toulouse, 31400 Toulouse, France.
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2
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Lohrmann C, Holm C. A novel model for biofilm initiation in porous media flow. SOFT MATTER 2023; 19:6920-6928. [PMID: 37664878 DOI: 10.1039/d3sm00575e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Bacteria often form biofilms in porous environments where an external flow is present, such as soil or filtration systems. To understand the initial stages of biofilm formation, one needs to study the interactions between cells, the fluid and the confining geometries. Here, we present an agent based numerical model for bacteria that takes into account the planktonic stage of motile cells as well as surface attachment and biofilm growth in a lattice Boltzmann fluid. In the planktonic stage we show the importance of the interplay between complex flow and cell motility when determining positions of surface attachment. In the growth stage we show the applicability of our model by investigating how external flow and biofilm stiffness determine qualitative colony morphologies as well as quantitative measurements of, e.g., permeability.
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Affiliation(s)
- Christoph Lohrmann
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany.
| | - Christian Holm
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany.
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3
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Tang P, Xu H, Zhang W, Zhu Y, Yang J, Zhou Y. Fluid transport in porous media based on differences in filter media morphology and biofilm growth in bioreactors. ENVIRONMENTAL RESEARCH 2023; 219:115122. [PMID: 36549494 DOI: 10.1016/j.envres.2022.115122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/15/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
To elucidate the effect of pore structure on bioclogging and seepage flow in bioreactors, we used X-ray computed tomography (X-CT) to investigate the changes in seepage flow of porous media in zeolite, gravel and ceramsite bioreactors with biofilm growth by injecting a non-ionic contrast medium iohexol. Based on the X-CT images using a ball-and-stick model, the highest average pore radius (R‾) and the average pore throat radius (r‾) in the ceramsite column were found under the initial conditions, which facilitated its permeability. The pore and throat of the gravel column were small and homogeneous relatively. Biofilm growth decreased the pore and pore throat in the columns. The total throat area of zeolite, gravel and ceramsite columns declined by 74%, 73% and 79% respectively. The zeolite column had the highest average pore throat, which contributed to its maximum conductivity subsequently after biofilm growth. Further, the fractal dimensions of the pore structure increased with biofilm growth, especially in the zeolite and ceramsite columns. The heterogeneity of the porous media was reinforced by the biofilm growth in the zeolite and ceramsite columns due to their higher heterogeneity initially. We also observed that an increase in heterogeneity of porous medium amplified the preferential flow and flow heterogeneities, especially in the zeolite and ceramsite columns.
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Affiliation(s)
- Ping Tang
- College of Material and Environment Engineering, Hangzhou Dianzi University, Hangzhou, China
| | - Henglei Xu
- Key Laboratory of Drinking Water Safety and Distribution Technology of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Wenming Zhang
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, AB T6G 2W2, Canada
| | - Yixuan Zhu
- Key Laboratory of Drinking Water Safety and Distribution Technology of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Jin Yang
- China Power Construction Group Environmental Engineering Co., Ltd, China
| | - Yongchao Zhou
- Key Laboratory of Drinking Water Safety and Distribution Technology of Zhejiang Province, Zhejiang University, Hangzhou, China.
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4
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Tang P, Chen L, Zhang W, Zhou Y. Bioclogging alleviation for constructed wetland based on the interaction among biofilm growth and hydrodynamics. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:18755-18763. [PMID: 36219300 DOI: 10.1007/s11356-022-23459-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Bioclogging is the most crucial operation problem of the constructed wetlands, which reduce its removal efficiency and life span. A strategy through properly increasing hydraulic loading is proposed in this study to alleviate the bioclogging for CWs. The two-dimensional porous media flow cell (2D PMFC) test indicated that a quadratic correlation was found between local biofilms growth rate and the near-wall Reynolds number (r > 0.765, p < 0.05). The biofilm growth rate declined with the flowrate when Re exceeded about 6.0. It was also found that the higher flowrate (6 mL/min) lead to the homogeneous biofilm and velocity distribution in the PMFC. The column test indicated that the highest hydraulic loading (9.2 cm/h) produced the smallest decrease in hydraulic conductivity, which was 80 times more than that of low hydraulic load (3.0 cm/h) at the end (40 days) of experiment. Moreover, the relatively homogenized distribution of biofilm was found along the column with the highest hydraulic loading, which confirmed that the proper increase in hydraulic loading can alleviate bioclogging.
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Affiliation(s)
- Ping Tang
- College of Material and Environment Engineering, Hangzhou Dianzi University, Hangzhou, China
| | - Li Chen
- College of Material and Environment Engineering, Hangzhou Dianzi University, Hangzhou, China
| | - Wenming Zhang
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, AB, T6G 2W2, Canada
| | - Yongchao Zhou
- Key Laboratory of Drinking Water Safety and Distribution Technology of Zhejiang Province, Zhejiang University, Hangzhou, China.
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5
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Abstract
Microbial communities are complex living systems that populate the planet with diverse functions and are increasingly harnessed for practical human needs. To deepen the fundamental understanding of their organization and functioning as well as to facilitate their engineering for applications, mathematical modeling has played an increasingly important role. Agent-based models represent a class of powerful quantitative frameworks for investigating microbial communities because of their individualistic nature in describing cells, mechanistic characterization of molecular and cellular processes, and intrinsic ability to produce emergent system properties. This review presents a comprehensive overview of recent advances in agent-based modeling of microbial communities. It surveys the state-of-the-art algorithms employed to simulate intracellular biomolecular events, single-cell behaviors, intercellular interactions, and interactions between cells and their environments that collectively serve as the driving forces of community behaviors. It also highlights three lines of applications of agent-based modeling, namely, the elucidation of microbial range expansion and colony ecology, the design of synthetic gene circuits and microbial populations for desired behaviors, and the characterization of biofilm formation and dispersal. The review concludes with a discussion of existing challenges, including the computational cost of the modeling, and potential mitigation strategies.
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Affiliation(s)
- Karthik Nagarajan
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Congjian Ni
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ting Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,National Center for Supercomputing Applications, Urbana, Illinois 61801, United States
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Lattice Boltzmann Method in Modeling Biofilm Formation, Growth and Detachment. SUSTAINABILITY 2021. [DOI: 10.3390/su13147968] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Biofilms are a complex and heterogeneous aggregation of multiple populations of microorganisms linked together by their excretion of extracellular polymer substances (EPS). Biofilms can cause many serious problems, such as chronic infections, food contamination and equipment corrosion, although they can be useful for constructive purposes, such as in wastewater treatment, heavy metal removal from hazardous waste sites, biofuel production, power generation through microbial fuel cells and microbially enhanced oil recovery; however, biofilm formation and growth are complex due to interactions among physicochemical and biological processes under operational and environmental conditions. Advanced numerical modeling techniques using the lattice Boltzmann method (LBM) are enabling the prediction of biofilm formation and growth and microbial community structures. This study is the first attempt to perform a general review on major contributions to LBM-based biofilm models, ranging from pioneering efforts to more recent progress. We present our understanding of the modeling of biofilm formation, growth and detachment using LBM-based models and present the fundamental aspects of various LBM-based biofilm models. We describe how the LBM couples with cellular automata (CA) and individual-based model (IbM) approaches and discuss their applications in assessing the spatiotemporal distribution of biofilms and their associated parameters and evaluating bioconversion efficiency. Finally, we discuss the main features and drawbacks of LBM-based biofilm models from ecological and biotechnological perspectives and identify current knowledge gaps and future research priorities.
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7
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Non-Invasive Measurement, Mathematical Simulation and In Situ Detection of Biofilm Evolution in Porous Media: A Review. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11041391] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The development of biofilms and the related changes in porous media in the subsurface cannot be directly observed and evaluated. The primary reason that the mechanism of biofilm clogging in porous media cannot be clearly demonstrated is due to the opacity and structural complexity of three-dimensional pore space. Interest in exploring methods to overcome this limitation has been increasing. In the first part of this review, we introduce the underlying characteristics of biofilm in porous media. Then, we summarize two approaches, non-invasive measurement methods and mathematical simulation strategies, for studying fluid–biofilm–porous medium interaction with spatiotemporal resolution. We also discuss the advantages and limitations of these approaches. Lastly, we provide a perspective on opportunities for in situ monitoring at the field site.
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8
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Delavar MA, Wang J. Modeling coupled temperature and transport effects on biofilm growth using thermal lattice Boltzmann model. AIChE J 2021. [DOI: 10.1002/aic.17122] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | - Junye Wang
- Faculty of Science and Technology Athabasca University Athabasca Alberta Canada
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9
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Jin X, Marshall JS. Mechanics of biofilms formed of bacteria with fimbriae appendages. PLoS One 2020; 15:e0243280. [PMID: 33290393 PMCID: PMC7723297 DOI: 10.1371/journal.pone.0243280] [Citation(s) in RCA: 12] [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: 08/03/2020] [Accepted: 11/18/2020] [Indexed: 11/23/2022] Open
Abstract
Gram-negative bacteria, as well as some Gram-positive bacteria, possess hair-like appendages known as fimbriae, which play an important role in adhesion of the bacteria to surfaces or to other bacteria. Unlike the sex pili or flagellum, the fimbriae are quite numerous, with of order 1000 fimbriae appendages per bacterial cell. In this paper, a recently developed hybrid model for bacterial biofilms is used to examine the role of fimbriae tension force on the mechanics of bacterial biofilms. Each bacterial cell is represented in this model by a spherocylindrical particle, which interact with each other through collision, adhesion, lubrication force, and fimbrial force. The bacterial cells absorb water and nutrients and produce extracellular polymeric substance (EPS). The flow of water and EPS, and nutrient diffusion within these substances, is computed using a continuum model that accounts for important effects such as osmotic pressure gradient, drag force on the bacterial cells, and viscous shear. The fimbrial force is modeled using an outer spherocylinder capsule around each cell, which can transmit tensile forces to neighboring cells with which the fimbriae capsule collides. We find that the biofilm structure during the growth process is dominated by a balance between outward drag force on the cells due to the EPS flow away from the bacterial colony and the inward tensile fimbrial force acting on chains of cells connected by adhesive fimbriae appendages. The fimbrial force also introduces a large rotational motion of the cells and disrupts cell alignment caused by viscous torque imposed by the EPS flow. The current paper characterizes the competing effects of EPS drag and fimbrial force using a series of computations with different values of the ratio of EPS to bacterial cell production rate and different numbers of fimbriae per cell.
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Affiliation(s)
- Xing Jin
- Department of Mechanical Engineering, University of Vermont, Burlington, VT, United States of America
| | - Jeffrey S. Marshall
- Department of Mechanical Engineering, University of Vermont, Burlington, VT, United States of America
- * E-mail:
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10
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Modeling of Biofilm Growth on Fine Spherical Particles with the Use of Cellular Automata: The Influence of Cell Death and Lysis on the Biofilm Structure. Processes (Basel) 2020. [DOI: 10.3390/pr8101234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The paper concerns the modeling of heterogeneous biofilm growth on fine spherical particles of such biofilm forms as, e.g., fluidized-bed bioreactors. Three discrete mathematical models based on cellular automata theory were proposed. The double-substrate kinetics of biomass growth, biomass displacement, internal and external mass transfer resistances, death and lysis of microbiological cells and biofilm detachment were taken into account. It was shown that there are no significant qualitative and quantitative differences between biofilm growth on flat and spherical particles of different radii. Computer simulations were compared with experimental observations. Qualitative and quantitative agreement areachieved if both cell death and lysis aretaken into consideration and a proper algorithm of biomass displacement is used. The value of the bacteria lysis rate coefficient was estimated.
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11
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Aghajani Delavar M, Wang J. Modeling Combined Effects of Temperature and Structure on Competition and Growth of Multispecies Biofilms in Microbioreactors. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.0c03102] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | - Junye Wang
- Faculty of Science and Technology, Athabasca University, Athabasca, Alberta T9S 3A3, Canada
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12
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Aghajani Delavar M, Wang J. Pore‐scale modeling of competition and cooperation of multispecies biofilms for nutrients in changing environments. AIChE J 2020. [DOI: 10.1002/aic.16919] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | - Junye Wang
- Faculty of Science and TechnologyAthabasca University Athabasca Alberta Canada
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13
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Tsompanas MA, Adamatzky A, Ieropoulos I, Phillips NW, Sirakoulis GC, Greenman J. Modelling Microbial Fuel Cells Using Lattice Boltzmann Methods. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:2035-2045. [PMID: 29994029 DOI: 10.1109/tcbb.2018.2831223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
An accurate modelling of bio-electrochemical processes that govern Microbial Fuel Cells (MFCs) and mapping their behavior according to several parameters will enhance the development of MFC technology and enable their successful implementation in well defined applications. The geometry of the electrodes is among key parameters determining efficiency of MFCs due to the formation of a biofilm of anodophilic bacteria on the anode electrode, which is a decisive factor for the functionality of the device. We simulate the bio-electrochemical processes in an MFC while taking into account the geometry of the electrodes. Namely, lattice Boltzmann methods are used to simulate the fluid dynamics and the advection-diffusion phenomena in the anode compartment. The model is verified on voltage and current outputs of a single MFC derived from laboratory experiments under continuous flow. Conclusions can be obtained from a parametric analysis of the model concerning the design of the geometry of the anode compartment, the positioning and microstructure of the anode electrode, in order to achieve more efficient overall performance of the system. An example of such a parametric analysis is presented here, taking into account the positioning of the electrode in the anode compartment.
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14
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Cattò C, Cappitelli F. Testing Anti-Biofilm Polymeric Surfaces: Where to Start? Int J Mol Sci 2019; 20:E3794. [PMID: 31382580 PMCID: PMC6696330 DOI: 10.3390/ijms20153794] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 08/02/2019] [Indexed: 12/11/2022] Open
Abstract
Present day awareness of biofilm colonization on polymeric surfaces has prompted the scientific community to develop an ever-increasing number of new materials with anti-biofilm features. However, compared to the large amount of work put into discovering potent biofilm inhibitors, only a small number of papers deal with their validation, a critical step in the translation of research into practical applications. This is due to the lack of standardized testing methods and/or of well-controlled in vivo studies that show biofilm prevention on polymeric surfaces; furthermore, there has been little correlation with the reduced incidence of material deterioration. Here an overview of the most common methods for studying biofilms and for testing the anti-biofilm properties of new surfaces is provided.
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Affiliation(s)
- Cristina Cattò
- Department of Food Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
| | - Francesca Cappitelli
- Department of Food Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy.
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15
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A network model for the biofilm growth in porous media and its effects on permeability and porosity. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s00791-019-00316-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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16
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Tian Z, Wang J. Lattice Boltzmann simulation of biofilm clogging and chemical oxygen demand removal in porous media. AIChE J 2019. [DOI: 10.1002/aic.16661] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Zhiwei Tian
- Faculty of Science and TechnologyAthabasca University Athabasca Alberta Canada
| | - Junye Wang
- Faculty of Science and TechnologyAthabasca University Athabasca Alberta Canada
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17
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Mendoza MV, Sáez RT. Modelling biofilm anaerobic reactor with effluent from hydrolytic/acidogenic reactor as substrate. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2019; 79:1534-1540. [PMID: 31169511 DOI: 10.2166/wst.2019.152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This work presents modelling of an anaerobic biofilm reactor using ceramic bricks as support. The results were compared with the experimental data. It was observed that the substrate concentration curves showed the same tendency. The methane formation curves showed significant differences. The substrate removal efficiency was 83%. In the steady state, the experimental data were higher than the model, from the result the substrate degrading bacteria grew enough to reach biofilm and that the effect of the shear stress was more significant as the biofilm increased in thickness. To the methane production, the model in steady state reached a maximum value of 0.56 m3 CH4/m3 *d and the experimental data reached 0.42 (m3 CH4/m3 * d). The biofilm thickness calculated by the model was 14 μm.
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Affiliation(s)
- Marisol Vergara Mendoza
- Centro de Estudios e Investigaciones Ambientales, Universidad Industrial de Santander, Calle 9ª, Carrera 27, Apdo. Aéreo 678, Bucaramanga, Colombia E-mail:
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18
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Li W, Su X, Palazzolo A, Ahmed S. Numerical modeling of concentration polarization and inorganic fouling growth in the pressure-driven membrane filtration process. J Memb Sci 2019. [DOI: 10.1016/j.memsci.2018.10.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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19
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Carrel M, Morales VL, Beltran MA, Derlon N, Kaufmann R, Morgenroth E, Holzner M. Biofilms in 3D porous media: Delineating the influence of the pore network geometry, flow and mass transfer on biofilm development. WATER RESEARCH 2018; 134:280-291. [PMID: 29433078 DOI: 10.1016/j.watres.2018.01.059] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 01/24/2018] [Accepted: 01/25/2018] [Indexed: 06/08/2023]
Abstract
This study investigates the functional correspondence between porescale hydrodynamics, mass transfer, pore structure and biofilm morphology during progressive biofilm colonization of a porous medium. Hydrodynamics and the structure of both the porous medium and the biofilm are experimentally measured with 3D particle tracking velocimetry and micro X-ray Computed Tomography, respectively. The analysis focuses on data obtained in a clean porous medium after 36 h of biofilm growth. Registration of the particle tracking and X-ray data sets allows to delineate the interplay between porous medium geometry, hydrodynamic and mass transfer processes on the morphology of the developing biofilm. A local analysis revealed wide distributions of wall shear stresses and concentration boundary layer thicknesses. The spatial distribution of the biofilm patches uncovered that the wall shear stresses controlled the biofilm development. Neither external nor internal mass transfer limitations were noticeable in the considered system, consistent with the excess supply of nutrient and electron acceptors. The wall shear stress remained constant in the vicinity of the biofilm but increased substantially elsewhere.
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Affiliation(s)
- Maxence Carrel
- Institute of Environmental Engineering, ETH Zürich, Stefano-Franscini-Platz 5, 8093 Zürich, Switzerland
| | - Verónica L Morales
- Institute of Environmental Engineering, ETH Zürich, Stefano-Franscini-Platz 5, 8093 Zürich, Switzerland; Department of Civil and Environmental Engineering, University of California, Davis, CA, USA
| | - Mario A Beltran
- School of Science, RMIT, Melbourne, Australia; Empa, Swiss Federal Laboratories for Materials Science and Technology, Center for X-ray Analytics, Dübendorf, Switzerland
| | - Nicolas Derlon
- Institute of Environmental Engineering, ETH Zürich, Stefano-Franscini-Platz 5, 8093 Zürich, Switzerland; Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Rolf Kaufmann
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Center for X-ray Analytics, Dübendorf, Switzerland
| | - Eberhard Morgenroth
- Institute of Environmental Engineering, ETH Zürich, Stefano-Franscini-Platz 5, 8093 Zürich, Switzerland; Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Markus Holzner
- Institute of Environmental Engineering, ETH Zürich, Stefano-Franscini-Platz 5, 8093 Zürich, Switzerland.
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20
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Carrel M, Morales VL, Dentz M, Derlon N, Morgenroth E, Holzner M. Pore-Scale Hydrodynamics in a Progressively Bioclogged Three-Dimensional Porous Medium: 3-D Particle Tracking Experiments and Stochastic Transport Modeling. WATER RESOURCES RESEARCH 2018; 54:2183-2198. [PMID: 29780184 PMCID: PMC5947749 DOI: 10.1002/2017wr021726] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 02/25/2018] [Indexed: 05/30/2023]
Abstract
Biofilms are ubiquitous bacterial communities that grow in various porous media including soils, trickling, and sand filters. In these environments, they play a central role in services ranging from degradation of pollutants to water purification. Biofilms dynamically change the pore structure of the medium through selective clogging of pores, a process known as bioclogging. This affects how solutes are transported and spread through the porous matrix, but the temporal changes to transport behavior during bioclogging are not well understood. To address this uncertainty, we experimentally study the hydrodynamic changes of a transparent 3-D porous medium as it experiences progressive bioclogging. Statistical analyses of the system's hydrodynamics at four time points of bioclogging (0, 24, 36, and 48 h in the exponential growth phase) reveal exponential increases in both average and variance of the flow velocity, as well as its correlation length. Measurements for spreading, as mean-squared displacements, are found to be non-Fickian and more intensely superdiffusive with progressive bioclogging, indicating the formation of preferential flow pathways and stagnation zones. A gamma distribution describes well the Lagrangian velocity distributions and provides parameters that quantify changes to the flow, which evolves from a parallel pore arrangement under unclogged conditions, toward a more serial arrangement with increasing clogging. Exponentially evolving hydrodynamic metrics agree with an exponential bacterial growth phase and are used to parameterize a correlated continuous time random walk model with a stochastic velocity relaxation. The model accurately reproduces transport observations and can be used to resolve transport behavior at intermediate time points within the exponential growth phase considered.
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Affiliation(s)
- M. Carrel
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic EngineeringETH ZurichZurichSwitzerland
| | - V. L. Morales
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic EngineeringETH ZurichZurichSwitzerland
- Department of Civil and Environmental EngineeringUniversity of California, DavisDavisCAUSA
| | - M. Dentz
- Spanish National Research Council (IDAEA‐CSIC)BarcelonaSpain
| | - N. Derlon
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic EngineeringETH ZurichZurichSwitzerland
- EAWAGDübendorfSwitzerland
| | - E. Morgenroth
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic EngineeringETH ZurichZurichSwitzerland
- EAWAGDübendorfSwitzerland
| | - M. Holzner
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic EngineeringETH ZurichZurichSwitzerland
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21
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Modeling Microbial Communities: A Call for Collaboration between Experimentalists and Theorists. Processes (Basel) 2017. [DOI: 10.3390/pr5040053] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
With our growing understanding of the impact of microbial communities, understanding how such communities function has become a priority. The influence of microbial communities is widespread. Human-associated microbiota impacts health, environmental microbes determine ecosystem sustainability, and microbe-driven industrial processes are expanding. This broad range of applications has led to a wide range of approaches to analyze and describe microbial communities. In particular, theoretical work based on mathematical modeling has been a steady source of inspiration for explaining and predicting microbial community processes. Here, we survey some of the modeling approaches used in different contexts. We promote classifying different approaches using a unified platform, and encourage cataloging the findings in a database. We believe that the synergy emerging from a coherent collection facilitates a better understanding of important processes that determine microbial community functions. We emphasize the importance of close collaboration between theoreticians and experimentalists in formulating, classifying, and improving models of microbial communities.
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22
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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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23
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Oka GK, Pinder GF. Multiscale Model for Assessing Effect of Bacterial Growth on Intrinsic Permeability of Soil: Model Description. Transp Porous Media 2017. [DOI: 10.1007/s11242-017-0870-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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24
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Modeling multidimensional and multispecies biofilms in porous media. Biotechnol Bioeng 2017; 114:1679-1687. [DOI: 10.1002/bit.26292] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 03/12/2017] [Accepted: 03/15/2017] [Indexed: 11/07/2022]
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25
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Microbial competition in porous environments can select against rapid biofilm growth. Proc Natl Acad Sci U S A 2016; 114:E161-E170. [PMID: 28007984 DOI: 10.1073/pnas.1525228113] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Microbes often live in dense communities called biofilms, where competition between strains and species is fundamental to both evolution and community function. Although biofilms are commonly found in soil-like porous environments, the study of microbial interactions has largely focused on biofilms growing on flat, planar surfaces. Here, we use microfluidic experiments, mechanistic models, and game theory to study how porous media hydrodynamics can mediate competition between bacterial genotypes. Our experiments reveal a fundamental challenge faced by microbial strains that live in porous environments: cells that rapidly form biofilms tend to block their access to fluid flow and redirect resources to competitors. To understand how these dynamics influence the evolution of bacterial growth rates, we couple a model of flow-biofilm interaction with a game theory analysis. This investigation revealed that hydrodynamic interactions between competing genotypes give rise to an evolutionarily stable growth rate that stands in stark contrast with that observed in typical laboratory experiments: cells within a biofilm can outcompete other genotypes by growing more slowly. Our work reveals that hydrodynamics can profoundly affect how bacteria compete and evolve in porous environments, the habitat where most bacteria live.
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26
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27
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Qin CZ, Hassanizadeh SM. Solute Mass Exchange Between Water Phase and Biofilm for a Single Pore. Transp Porous Media 2015. [DOI: 10.1007/s11242-015-0513-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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28
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Udall YC, Deeni Y, Hapca SM, Raikes D, Spiers AJ. The evolution of biofilm-forming Wrinkly Spreaders in static microcosms and drip-fed columns selects for subtle differences in wrinkleality and fitness. FEMS Microbiol Ecol 2015; 91:fiv057. [DOI: 10.1093/femsec/fiv057] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2015] [Indexed: 12/30/2022] Open
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29
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Hossain MS, Bergstrom DJ, Chen XB. Computational modelling of the scaffold-free chondrocyte regeneration: a two-way coupling between the cell growth and local fluid flow and nutrient concentration. Biomech Model Mechanobiol 2015; 14:1217-25. [PMID: 25804699 DOI: 10.1007/s10237-015-0666-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 03/16/2015] [Indexed: 12/17/2022]
Abstract
The in vitro chondrocyte cell culture process in a perfusion bioreactor provides enhanced nutrient supply as well as the flow-induced shear stress that may have a positive influence on the cell growth. Mathematical and computational modelling of such a culture process, by solving the coupled flow, mass transfer and cell growth equations simultaneously, can provide important insight into the biomechanical environment of a bioreactor and the related cell growth process. To do this, a two-way coupling between the local flow field and cell growth is required. Notably, most of the computational and mathematical models to date have not taken into account the influence of the cell growth on the local flow field and nutrient concentration. The present research aimed at developing a mathematical model and performing a numerical simulation using the lattice Boltzmann method to predict the chondrocyte cell growth without a scaffold on a flat plate placed inside a perfusion bioreactor. The model considers the two-way coupling between the cell growth and local flow field, and the simulation has been performed for 174 culture days. To incorporate the cell growth into the model, a control-volume-based surface growth modelling approach has been adopted. The simulation results show the variation of local fluid velocity, shear stress and concentration distribution during the culture period due to the growth of the cell phase and also illustrate that the shear stress can increase the cell volume fraction to a certain extent.
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Affiliation(s)
- Md Shakhawath Hossain
- Mechanical Engineering Department, University of Saskatchewan, 57 Campus Drive, Saskatoon, SK, S7N 5A9, Canada.
| | - D J Bergstrom
- Mechanical Engineering Department, University of Saskatchewan, 57 Campus Drive, Saskatoon, SK, S7N 5A9, Canada.
| | - X B Chen
- Mechanical Engineering Department, University of Saskatchewan, 57 Campus Drive, Saskatoon, SK, S7N 5A9, Canada.
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30
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Hossain MS, Bergstrom DJ, Chen XB. Modelling and simulation of the chondrocyte cell growth, glucose consumption and lactate production within a porous tissue scaffold inside a perfusion bioreactor. ACTA ACUST UNITED AC 2014. [PMID: 28626683 PMCID: PMC5466199 DOI: 10.1016/j.btre.2014.12.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Mathematical and numerical modelling of the tissue culture process in a perfusion bioreactor is able to provide insight into the fluid flow, nutrients and wastes transport, dynamics of the pH value, and the cell growth rate. Knowing the complicated interdependence of these processes is essential for optimizing the culture process for cell growth. This paper presents a resolved scale numerical simulation, which allows one not only to characterize the supply of glucose inside a porous tissue scaffold in a perfusion bioreactor, but also to assess the overall culture condition and predict the cell growth rate. The simulation uses a simplified scaffold that consists of a repeatable unit composed of multiple strands. The simulation results explore some problematic regions inside the simplified scaffold where the concentration of glucose becomes lower than the critical value for the chondrocyte cell viability and the cell growth rate becomes significantly reduced.
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Affiliation(s)
- Md Shakhawath Hossain
- Mechanical Engineering Department, University of Saskatchewan, 57 Campus Drive, Saskatoon, SK S7N 5A9, Canada
| | - D J Bergstrom
- Mechanical Engineering Department, University of Saskatchewan, 57 Campus Drive, Saskatoon, SK S7N 5A9, Canada
| | - X B Chen
- Mechanical Engineering Department, University of Saskatchewan, 57 Campus Drive, Saskatoon, SK S7N 5A9, Canada
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31
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Prediction of cell growth rate over scaffold strands inside a perfusion bioreactor. Biomech Model Mechanobiol 2014; 14:333-44. [PMID: 25022870 DOI: 10.1007/s10237-014-0606-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 07/01/2014] [Indexed: 12/18/2022]
Abstract
Mathematical and computational modeling of the dynamic process where tissue scaffolds are cultured in perfusion bioreactors is able to provide insight into the cell and tissue growth which can facilitate the design of tissue scaffolds and selection of optimal operating conditions. To date, a resolved-scale simulation of cell growth in the culture process, by taking account of the influences of the supply of nutrients and fluid shear stress on the cells, is not yet available in the literature. This paper presents such a simulation study specifically on cartilage tissue regeneration by numerically solving the momentum, scalar transport and cell growth equations, simultaneously, based on the lattice Boltzmann method. The simulation uses a simplified scaffold that consists of two circular strands placed in tandem inside a microchannel, with the object of identifying the effect of one strand on the other. The results indicate that the presence of the front strand can reduce the cell growth rate on the surface of the rear strand, depending on the distance between them. As such, the present study allows for investigation into the influence of the scaffold geometry on the cell growth rate within scaffolds, thus providing a means to improve the scaffold design and the culture process.
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32
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Coroneo M, Yoshihara L, Wall WA. Biofilm growth: a multi-scale and coupled fluid-structure interaction and mass transport approach. Biotechnol Bioeng 2014; 111:1385-95. [PMID: 24496713 DOI: 10.1002/bit.25191] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 01/03/2014] [Accepted: 01/06/2014] [Indexed: 11/07/2022]
Abstract
In this paper, we propose a novel approach for modelling biofilm growth. It is based on a finite element method and includes both fluid-structure interaction (FSI) as well as scalar transport effects. Due to the different time-scales of the involved phenomena, the growth of the biofilm structure is coupled with the FSI and mass transport through a multi-scale approach in time. In each hydrodynamic time step, first the non-linear FSI problem is solved followed by the scalar transport equations, using the information on velocities and deformations obtained in the FSI step. After a steady state solution is reached, information on mass fluxes and stresses are passed to the growth model. At this point, the growth is calculated for a biological time step larger than the hydrodynamic one and based on the mass flux through the interface and on normal and shear stresses on it. This type of approach can significantly contribute to the understanding of biofilm development in fluid flows, since the influence of hydrodynamic conditions and availability of nutrients is well known to have effects on biofilm development. Therefore, for the purpose of understanding biofilm macro-scale dynamics, it is essential to adopt a modeling approach, which takes into account all the relevant aspects, like fluid flow, structure deformation, mass transport and their effect on biofilm growth and erosion. First numerical examples demonstrate the suitability of the proposed model to catch the main features of a growing biofilm structure.
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Affiliation(s)
- Mirella Coroneo
- Institute for Computational Mechanics, Technische Universität München, Boltzmannstr. 15, D-85747, Garching, Germany.
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33
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Horn H, Lackner S. Modeling of biofilm systems: a review. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 146:53-76. [PMID: 25163572 DOI: 10.1007/10_2014_275] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The modeling of biochemical processes in biofilms is more complex compared to those in suspended biomass due to the existence of substrate gradients. The diffusion and reaction of substrates within the biofilms were simulated in 1D models in the 1970s. The quality of these simulation results was later improved by consideration of mass transfer at the bulk/biofilm interface and detachment of biomass from the surface. Furthermore, modeling of species distribution along the axis perpendicular to the substratum helped to simulate productivity and long-term behavior in multispecies biofilms. Multidimensional models that were able to give a realistic prediction of the surface structure of biofilms were published in the 1990s. The 2D or 3D representation of the distribution of the species in a matrix of extracellular polymeric substances (EPS) helped predict the behavior of multispecies biofilm systems. The influence of shear forces on such 2D or 3D biofilm structures was included by solving the Navier-Stokes equation for the liquid phase above the biofilm. More recently, the interaction between the fluid and biofilm structures was addressed more seriously by no longer considering the biofilm structures as being rigid. The latter approach opened a new door, enabling one to describe biofilms as viscoelastic systems that are not only able to grow and produce but also be deformed or even dislodged if external forces are applied.
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Affiliation(s)
- Harald Horn
- Engler-Bunte-Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany,
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34
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Deng W, Cardenas MB, Kirk MF, Altman SJ, Bennett PC. Effect of permeable biofilm on micro- and macro-scale flow and transport in bioclogged pores. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:11092-11098. [PMID: 23971830 DOI: 10.1021/es402596v] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Simulations of coupled flow around and inside biofilms in pores were conducted to study the effect of porous biofilm on micro- and macro-scale flow and transport. The simulations solved the Navier-Stokes equations coupled with the Brinkman equation representing flow in the pore space and biofilm, respectively, and the advection-diffusion equation. Biofilm structure and distribution were obtained from confocal microscope images. The bulk permeability (k) of bioclogged porous media depends on biofilm permeability (kbr) following a sigmoidal curve on a log-log scale. The upper and lower limits of the curve are the k of biofilm-free media and of bioclogged media with impermeable biofilms, respectively. On the basis of this, a model is developed that predicts k based solely on kbr and biofilm volume ratio. The simulations show that kbr has a significant impact on the shear stress distribution, and thus potentially affects biofilm erosion and detachment. The sensitivity of flow fields to kbr directly translated to effects on the transport fields by affecting the relative distribution of where advection and diffusion dominated. Both kbr and biofilm volume ratio affect the shape of breakthrough curves.
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Affiliation(s)
- Wen Deng
- Department of Geological Sciences, The University of Texas at Austin , Austin, Texas, United States
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35
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Martin KJ, Picioreanu C, Nerenberg R. Multidimensional modeling of biofilm development and fluid dynamics in a hydrogen-based, membrane biofilm reactor (MBfR). WATER RESEARCH 2013; 47:4739-4751. [PMID: 23774188 DOI: 10.1016/j.watres.2013.04.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 04/16/2013] [Accepted: 04/18/2013] [Indexed: 06/02/2023]
Abstract
A two-dimensional, particle-based biofilm model coupled with mass transport and computational fluid dynamics was developed to simulate autotrophic denitrification in a spiral-wound membrane biofilm reactor (MBfR), where hydrogen is supplied via hollow-fiber membrane fabric. The spiral-wound configuration consists of alternating layers of plastic spacer net and membrane fabric that create rows of flow channels, with the top and bottom walls comprised of membranes. The transversal filaments of the spacer partially obstruct the channel flow, producing complex mixing and shear patterns that require multidimensional representation. This study investigated the effect of hydrogen and nitrate concentrations, as well as spacer configuration, on biofilm development and denitrification fluxes. The model results indicate that the cavity spacer filaments, which rest on the bottom membranes, cause uneven biofilm growth. Most biofilm resided on the bottom membranes, only in the wake of the filaments where low shear zones formed. In this way, filament configuration may help achieve a desired biofilm thickness. For the conditions tested in this study, the highest nitrate fluxes were attained by minimizing the filament diameter and maximizing the filament spacing. This lowered the shear stress at the top membranes, allowing for more biofilm growth. For the scenarios studied, biomass limitation at the top membranes hindered performance more significantly than diffusion limitation in the thick biofilms at the bottom membranes. The results also highlighted the importance of two-dimensional modeling to capture uneven biofilm growth on a substratum with geometrical complexity.
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Affiliation(s)
- Kelly J Martin
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA.
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36
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Construction of two ureolytic model organisms for the study of microbially induced calcium carbonate precipitation. J Microbiol Methods 2013; 94:290-9. [DOI: 10.1016/j.mimet.2013.06.028] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 06/27/2013] [Accepted: 06/27/2013] [Indexed: 11/19/2022]
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37
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Ho QT, Carmeliet J, Datta AK, Defraeye T, Delele MA, Herremans E, Opara L, Ramon H, Tijskens E, van der Sman R, Van Liedekerke P, Verboven P, Nicolaï BM. Multiscale modeling in food engineering. J FOOD ENG 2013. [DOI: 10.1016/j.jfoodeng.2012.08.019] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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38
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Sen D, Sarkar S, Bhattacharjee S, Bandopadhya S, Ghosh S, Bhattacharjee C. Simulation of the Effect of Various Operating Parameters for the Effective Separation of Carbon Dioxide into an Aqueous Caustic Soda Solution in a Packed Bed Using Lattice Boltzmann Simulation. Ind Eng Chem Res 2013. [DOI: 10.1021/ie301954c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dwaipayan Sen
- Department of Chemical
Engineering, Jadavpur University, Kolkata, India
| | - Santanu Sarkar
- Department of Chemical
Engineering, Jadavpur University, Kolkata, India
| | | | | | - Sourja Ghosh
- Central Glass and Ceramic Research Institute, Kolkata, India
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39
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Bottero S, Storck T, Heimovaara TJ, van Loosdrecht MCM, Enzien MV, Picioreanu C. Biofilm development and the dynamics of preferential flow paths in porous media. BIOFOULING 2013; 29:1069-86. [PMID: 24028574 DOI: 10.1080/08927014.2013.828284] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
A two-dimensional pore-scale numerical model was developed to evaluate the dynamics of preferential flow paths in porous media caused by bioclogging. The liquid flow and solute transport through the pore network were coupled with a biofilm model including biomass attachment, growth, decay, lysis, and detachment. Blocking of all but one flow path was obtained under constant liquid inlet flow rate and biomass detachment caused by shear forces only. The stable flow path formed when biofilm detachment balances growth, even with biomass weakened by decay. However, shear forces combined with biomass lysis upon starvation could produce an intermittently shifting location of flow channels. Dynamic flow pathways may also occur when combined liquid shear and pressure forces act on the biofilm. In spite of repeated clogging and unclogging of interconnected pore spaces, the average permeability reached a quasi-constant value. Oscillations in the medium permeability were more pronounced for weaker biofilms.
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Affiliation(s)
- Simona Bottero
- a Faculty of Applied Sciences, Department of Biotechnology , Delft University of Technology , Delft , The Netherlands
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40
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Vogt SJ, Sanderlin AB, Seymour JD, Codd SL. Permeability of a growing biofilm in a porous media fluid flow analyzed by magnetic resonance displacement-relaxation correlations. Biotechnol Bioeng 2012; 110:1366-75. [DOI: 10.1002/bit.24803] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 11/21/2012] [Accepted: 11/28/2012] [Indexed: 11/11/2022]
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41
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Spencer T, Hidalgo-Bastida L, Cartmell S, Halliday I, Care C. In silico multi-scale model of transport and dynamic seeding in a bone tissue engineering perfusion bioreactor. Biotechnol Bioeng 2012; 110:1221-30. [DOI: 10.1002/bit.24777] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 10/19/2012] [Accepted: 10/22/2012] [Indexed: 01/25/2023]
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42
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Gonzo EE, Wuertz S, Rajal VB. Continuum heterogeneous biofilm model-A simple and accurate method for effectiveness factor determination. Biotechnol Bioeng 2012; 109:1779-90. [DOI: 10.1002/bit.24441] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 12/29/2011] [Accepted: 01/05/2012] [Indexed: 01/13/2023]
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43
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Pintelon TRR, Picioreanu C, Loosdrecht MCMV, Johns ML. The effect of biofilm permeability on bio-clogging of porous media. Biotechnol Bioeng 2011; 109:1031-42. [PMID: 22095039 DOI: 10.1002/bit.24381] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 11/07/2011] [Accepted: 11/11/2011] [Indexed: 11/12/2022]
Abstract
A 3D Biofilm model, appropriate for complex porous media support structures, is successfully modified such that non-zero permeability of biofilms structures is enabled. A systematic study is then conducted into the influence of biofilm permeability on overall biomass growth rate. This reveals a significant influence at large biofilm concentrations; even when the permeability of the biomass is 1.25% of that of the free pore space, biomass accumulation increased by a factor of ∼3 over 40 h. The effect is shown to be retained when allowing for biomass detachment or erosion as a consequence of adjacent velocity shear. We conclude that biofilm permeability should be included in biofilm models and that further experimental work is required to better describe the link between biofilm permeability and local microstructure.
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Affiliation(s)
- Thomas R R Pintelon
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
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44
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Zhang W, Sileika TS, Chen C, Liu Y, Lee J, Packman AI. A novel planar flow cell for studies of biofilm heterogeneity and flow-biofilm interactions. Biotechnol Bioeng 2011; 108:2571-82. [PMID: 21656713 PMCID: PMC3462816 DOI: 10.1002/bit.23234] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 04/24/2011] [Accepted: 05/20/2011] [Indexed: 11/12/2022]
Abstract
Biofilms are microbial communities growing on surfaces, and are ubiquitous in nature, in bioreactors, and in human infection. Coupling between physical, chemical, and biological processes is known to regulate the development of biofilms; however, current experimental systems do not provide sufficient control of environmental conditions to enable detailed investigations of these complex interactions. We developed a novel planar flow cell that supports biofilm growth under complex two-dimensional fluid flow conditions. This device provides precise control of flow conditions and can be used to create well-defined physical and chemical gradients that significantly affect biofilm heterogeneity. Moreover, the top and bottom of the flow chamber are transparent, so biofilm growth and flow conditions are fully observable using non-invasive confocal microscopy and high-resolution video imaging. To demonstrate the capability of the device, we observed the growth of Pseudomonas aeruginosa biofilms under imposed flow gradients. We found a positive relationship between patterns of fluid velocity and biofilm biomass due to faster microbial growth under conditions of greater local nutrient influx, but this relationship eventually reversed because high hydrodynamic shear leads to the detachment of cells from the surface. These results reveal that flow gradients play a critical role in the development of biofilm communities. By providing new capability for observing biofilm growth, solute and particle transport, and net chemical transformations under user-specified environmental gradients, this new planar flow cell system has broad utility for studies of environmental biotechnology and basic biofilm microbiology, as well as applications in bioreactor design, environmental engineering, biogeochemistry, geomicrobiology, and biomedical research.
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Affiliation(s)
- Wei Zhang
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208
| | - Tadas S. Sileika
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208
| | - Cheng Chen
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208
- Fixed Income Technology Division, Nomura Securities Co., Ltd. Shanghai Representative Office, Shanghai, China
| | - Yang Liu
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, AB. Canada T6G 2W2
| | - Jisun Lee
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208
| | - Aaron I. Packman
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208
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45
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Ezeuko CC, Sen A, Grigoryan A, Gates ID. Pore-network modeling of biofilm evolution in porous media. Biotechnol Bioeng 2011; 108:2413-23. [PMID: 21520022 DOI: 10.1002/bit.23183] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 03/28/2011] [Accepted: 04/04/2011] [Indexed: 11/11/2022]
Abstract
The influence of bacterial biomass on hydraulic properties of porous media (bioclogging) has been explored as a viable means for optimizing subsurface bioremediation and microbial enhanced oil recovery. In this study, we present a pore network simulator for modeling biofilm evolution in porous media including hydrodynamics and nutrient transport based on coupling of advection transport with Fickian diffusion and a reaction term to account for nutrient consumption. Biofilm has non-zero permeability permitting liquid flow and transport through the biofilm itself. To handle simultaneous mass transfer in both liquid and biofilm in a pore element, a dual-diffusion mass transfer model is introduced. The influence of nutrient limitation on predicted results is explored. Nutrient concentration in the network is affected by diffusion coefficient for nutrient transfer across biofilm (compared to water/water diffusion coefficient) under advection dominated transport, represented by mass transport Péclet number >1. The model correctly predicts a dependence of rate of biomass accumulation on inlet concentration. Poor network connectivity shows a significantly large reduction of permeability, for a small biomass pore volume.
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Affiliation(s)
- C C Ezeuko
- Department of Chemical and Petroleum Engineering, Schulich School of Engineering, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4; telephone: 1-403-479-1254; fax: 1-403-284-4852.
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46
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Abstract
In this feature, leading researchers in the field of microbial biotechnology speculate on the technical and conceptual developments that will drive innovative research and open new vistas over the next few years.
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47
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Liu L, Sheng GP, Liu ZF, Li WW, Zeng RJ, Lee DJ, Liu JX, Yu HQ. Characterization of multiporous structure and oxygen transfer inside aerobic granules with the percolation model. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2010; 44:8535-40. [PMID: 20964290 DOI: 10.1021/es102437a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The characteristics of aerobic granules for wastewater treatment are greatly related to their complex internal structure. However, due to the limitation of characterizing methods, information about the granule internal morphology and structure is very sparse, and mechanism of mass transfer process is yet unclear. In this work, the internal structure of aerobic granules was explored using nitrogen adsorption method and confocal laser scanning microscopy technique. It was found that aerobic granules had multiporous structure with cross-linked gel matrix structure. With a consideration of the hydrodynamic regime and the porous structure of granules, a two-dimensional percolation model was established to describe the mass transfer in granules. With the approaches, interesting and useful results regarding the pore distribution and mass transfer in aerobic granules have been obtained. The results demonstrate that the intragranule convection could enhance mass transfer, hence ensure an efficient and stable operation of aerobic-granule-based reactors. Such approaches might also be applicable to characterizing the multiporous structure and mass transfer of other microbial aggregates for wastewater treatment.
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Affiliation(s)
- Li Liu
- School of Earth and Space Sciences, Department of Chemistry, and Department of Thermal Science and Energy Engineering, University of Science & Technology of China, Hefei, 230026, People's Republic of China
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48
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Salta M, Wharton JA, Stoodley P, Dennington SP, Goodes LR, Werwinski S, Mart U, Wood RJK, Stokes KR. Designing biomimetic antifouling surfaces. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2010; 368:4729-4754. [PMID: 20855318 DOI: 10.1098/rsta.2010.0195] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Marine biofouling is the accumulation of biological material on underwater surfaces, which has plagued both commercial and naval fleets. Biomimetic approaches may well provide new insights into designing and developing alternative, non-toxic, surface-active antifouling (AF) technologies. In the marine environment, all submerged surfaces are affected by the attachment of fouling organisms, such as bacteria, diatoms, algae and invertebrates, causing increased hydrodynamic drag, resulting in increased fuel consumption, and decreased speed and operational range. There are also additional expenses of dry-docking, together with increased fuel costs and corrosion, which are all important economic factors that demand the prevention of biofouling. Past solutions to AF have generally used toxic paints or coatings that have had a detrimental effect on marine life worldwide. The prohibited use of these antifoulants has led to the search for biologically inspired AF strategies. This review will explore the natural and biomimetic AF surface strategies for marine systems.
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Affiliation(s)
- Maria Salta
- National Centre for Advanced Tribology at Southampton (nCATS), School of Engineering Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, UK
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49
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DAVIT Y, ILTIS G, DEBENEST G, VERAN-TISSOIRES S, WILDENSCHILD D, GERINO M, QUINTARD M. Imaging biofilm in porous media using X-ray computed microtomography. J Microsc 2010; 242:15-25. [DOI: 10.1111/j.1365-2818.2010.03432.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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50
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Picioreanu C, van Loosdrecht MC, Curtis TP, Scott K. Model based evaluation of the effect of pH and electrode geometry on microbial fuel cell performance. Bioelectrochemistry 2010; 78:8-24. [DOI: 10.1016/j.bioelechem.2009.04.009] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 04/20/2009] [Accepted: 04/30/2009] [Indexed: 11/28/2022]
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