1
|
Charlton SG, Jana S, Chen J. Yielding behaviour of chemically treated Pseudomonas fluorescens biofilms. Biofilm 2024; 8:100209. [PMID: 39071175 PMCID: PMC11279707 DOI: 10.1016/j.bioflm.2024.100209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 06/20/2024] [Accepted: 07/02/2024] [Indexed: 07/30/2024] Open
Abstract
The mechanics of biofilms are intrinsically shaped by their physicochemical environment. By understanding the influence of the extracellular matrix composition, pH and elevated levels of cationic species on the biofilm rheology, novel living materials with tuned properties can be formulated. In this study, we examine the role of a chaotropic agent (urea), two divalent cations and distilled deionized water on the nonlinear viscoelasticity of a model biofilm Pseudomonas fluorescens. The structural breakdown of each biofilm is quantified using tools of non-linear rheology. Our findings reveal that urea induced a softening response, and displayed strain overshoots comparable to distilled deionized water, without altering the microstructural packing fraction and macroscale morphology. The absorption of divalent ferrous and calcium cations into the biofilm matrix resulted in stiffening and a reduction in normalized elastic energy dissipation, accompanied by macroscale morphological wrinkling and moderate increases in the packing fraction. Notably, ferrous ions induced a predominance of rate dependent yielding, whereas the calcium ions resulted in equal contribution from both rate and strain dependent yielding and structural breakdown of the biofilms. Together, these results indicate that strain rate increasingly becomes an important factor controlling biofilm fluidity with cation-induced biofilm stiffening. The finding can help inform effective biofilm removal protocols and in development of bio-inks for additive manufacturing of biofilm derived materials.
Collapse
Affiliation(s)
- Samuel G.V. Charlton
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zürich, Zürich, 8093, Switzerland
- Newcastle University, School of Engineering, Newcastle Upon Tyne, NE1 7RU, United Kingdom
| | - Saikat Jana
- Ulster University, School of Engineering, 2-24 York Street, Belfast, BT15 1AP, United Kingdom
- Newcastle University, School of Engineering, Newcastle Upon Tyne, NE1 7RU, United Kingdom
| | - Jinju Chen
- Newcastle University, School of Engineering, Newcastle Upon Tyne, NE1 7RU, United Kingdom
- Loughborough University, Department of Materials, Loughborough, LE11 3TU, United Kingdom
| |
Collapse
|
2
|
Voigtländer A, Houssais M, Bacik KA, Bourg IC, Burton JC, Daniels KE, Datta SS, Del Gado E, Deshpande NS, Devauchelle O, Ferdowsi B, Glade R, Goehring L, Hewitt IJ, Jerolmack D, Juanes R, Kudrolli A, Lai CY, Li W, Masteller C, Nissanka K, Rubin AM, Stone HA, Suckale J, Vriend NM, Wettlaufer JS, Yang JQ. Soft matter physics of the ground beneath our feet. SOFT MATTER 2024. [PMID: 39012310 DOI: 10.1039/d4sm00391h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
The soft part of the Earth's surface - the ground beneath our feet - constitutes the basis for life and natural resources, yet a general physical understanding of the ground is still lacking. In this critical time of climate change, cross-pollination of scientific approaches is urgently needed to better understand the behavior of our planet's surface. The major topics in current research in this area cross different disciplines, spanning geosciences, and various aspects of engineering, material sciences, physics, chemistry, and biology. Among these, soft matter physics has emerged as a fundamental nexus connecting and underpinning many research questions. This perspective article is a multi-voice effort to bring together different views and approaches, questions and insights, from researchers that work in this emerging area, the soft matter physics of the ground beneath our feet. In particular, we identify four major challenges concerned with the dynamics in and of the ground: (I) modeling from the grain scale, (II) near-criticality, (III) bridging scales, and (IV) life. For each challenge, we present a selection of topics by individual authors, providing specific context, recent advances, and open questions. Through this, we seek to provide an overview of the opportunities for the broad Soft Matter community to contribute to the fundamental understanding of the physics of the ground, strive towards a common language, and encourage new collaborations across the broad spectrum of scientists interested in the matter of the Earth's surface.
Collapse
Affiliation(s)
- Anne Voigtländer
- German Research Centre for Geosciences (GFZ), Geomorphology, Telegrafenberg, 14473 Potsdam, Germany.
- Lawrence Berkeley National Laboratory (LBNL), Energy Geosciences Division, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Morgane Houssais
- Department of Physics, Clark University, 950 Main St, Worcester, MA 01610, USA
| | - Karol A Bacik
- Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Ian C Bourg
- Civil and Environmental Engineering (CEE) and High Meadows Environmental Institute (HMEI), Princeton University, E208 EQuad, Princeton, NJ 08540, USA
| | - Justin C Burton
- Department of Physics, Emory University, 400 Dowman Dr, Atlanta, GA 30033, USA
| | - Karen E Daniels
- North Carolina State University, 2401 Stinson Dr, Raleigh, NC 27607, USA
| | - Sujit S Datta
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Emanuela Del Gado
- Department of Physics, Institute for Soft Matter Synthesis and Metrology, Georgetown University, Washington, DC, USA
| | - Nakul S Deshpande
- North Carolina State University, 2401 Stinson Dr, Raleigh, NC 27607, USA
| | - Olivier Devauchelle
- Institut de Physique du Globe de Paris, Université Paris Cité, 1 rue Jussieu, CNRS, F-75005 Paris, France
| | - Behrooz Ferdowsi
- Department of Civil and Environmental Engineering, jUniversity of Houston, Houston, TX 77204, USA
| | - Rachel Glade
- Earth & Environmental Sciences Department and Mechanical Engineering Department, University of Rochester, 227 Hutchison Hall, P.O. Box 270221, Rochester, NY 14627, USA
| | - Lucas Goehring
- School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, UK
| | - Ian J Hewitt
- Mathematical Institute, University of Oxford, Woodstock Road, Oxford OX2 6GG, UK
| | - Douglas Jerolmack
- Department of Earth & Environmental Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ruben Juanes
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Arshad Kudrolli
- Department of Physics, Clark University, 950 Main St, Worcester, MA 01610, USA
| | - Ching-Yao Lai
- Department of Geophysics, Stanford University, Stanford, CA 94305, USA
| | - Wei Li
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Stony Brook University, Department of Civil Engineering, Stony Brook, NY 11794, USA
| | - Claire Masteller
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, USA
| | - Kavinda Nissanka
- Department of Physics, Emory University, 400 Dowman Dr, Atlanta, GA 30033, USA
| | - Allan M Rubin
- Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
| | - Howard A Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Jenny Suckale
- Computational and Mathematical Engineering, and Environmental Engineering, Stanford University, Stanford, CA 94305, USA
| | - Nathalie M Vriend
- Department of Mechanical Engineering, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - John S Wettlaufer
- Departments of Earth & Planetary Sciences, Mathematics and Physics, Yale University, New Haven, CT 06520, USA
- Nordic Institute for Theoretical Physics, 106 91, Stockholm, Sweden
| | - Judy Q Yang
- Saint Anthony Falls Laboratory and Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis, MN, USA
| |
Collapse
|
3
|
Ohmura T, Skinner DJ, Neuhaus K, Choi GPT, Dunkel J, Drescher K. In Vivo Microrheology Reveals Local Elastic and Plastic Responses Inside 3D Bacterial Biofilms. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2314059. [PMID: 38511867 DOI: 10.1002/adma.202314059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/08/2024] [Indexed: 03/22/2024]
Abstract
Bacterial biofilms are highly abundant 3D living materials capable of performing complex biomechanical and biochemical functions, including programmable growth, self-repair, filtration, and bioproduction. Methods to measure internal mechanical properties of biofilms in vivo with spatial resolution on the cellular scale have been lacking. Here, thousands of cells are tracked inside living 3D biofilms of the bacterium Vibrio cholerae during and after the application of shear stress, for a wide range of stress amplitudes, periods, and biofilm sizes, which revealed anisotropic elastic and plastic responses of both cell displacements and cell reorientations. Using cellular tracking to infer parameters of a general mechanical model, spatially-resolved measurements of the elastic modulus inside the biofilm are obtained, which correlate with the spatial distribution of the polysaccharides within the biofilm matrix. The noninvasive microrheology and force-inference approach introduced here provides a general framework for studying mechanical properties with high spatial resolution in living materials.
Collapse
Affiliation(s)
- Takuya Ohmura
- Biozentrum, University of Basel, Spitalstrasse 41, Basel, 4056, Switzerland
| | - Dominic J Skinner
- Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139-4307, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, 60201, USA
| | - Konstantin Neuhaus
- Biozentrum, University of Basel, Spitalstrasse 41, Basel, 4056, Switzerland
- Department of Physics, Philipps-Universität Marburg, Renthof 5, 35032, Marburg, Germany
| | - Gary P T Choi
- Department of Mathematics, The Chinese University of Hong Kong, N.T., Hong Kong
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139-4307, USA
| | - Knut Drescher
- Biozentrum, University of Basel, Spitalstrasse 41, Basel, 4056, Switzerland
| |
Collapse
|
4
|
Tang Y, Zhang Z, Tao C, Wang X. The mechanism of biofilm detachment in porous medium under flow field. BIOMICROFLUIDICS 2024; 18:034103. [PMID: 38737754 PMCID: PMC11080962 DOI: 10.1063/5.0203061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/25/2024] [Indexed: 05/14/2024]
Abstract
Biofilms are communities formed by bacteria adhering to surfaces, widely present in porous medium, and their growth can lead to clogging. Our experiment finds that under certain flow conditions, biofilms detach in pores and form a dynamically changing flow path. We define detachment that occurs far from the boundary of the flow path (with a distance greater than 200 μm) as internal detachment and detachment that occurs at the boundary of the flow path as external detachment. To understand the mechanism of biofilm detachment, we study the detachment behaviors of the Bacillus subtilis biofilm in a porous medium in a microfluidic device, where Bacillus subtilis strain is triple fluorescent labeled, which can represent three main phenotypes during the biofilm formation: motile cells, matrix-producing cells, and spores. We find that slow small-scale internal detachment occurs in regions with very few motile cells and matrix-producing cells, and bacterial movement in these areas is disordered. The increase in the number of matrix-producing cells induces clogging, and after clogging, the rapid detachment of the bulk internal biofilm occurs due to the increased pressure difference at the inlet and outlet. When both internal and external detachments occur simultaneously, the number of matrix-producing cells in the internal detachment area is 2.5 times that in the external detachment area. The results indicate that biofilm detachment occurs in areas with fewer matrix-producing cells, as matrix-producing cells can help resist detachment by secreting extracellular polymeric substances (EPSs).
Collapse
Affiliation(s)
- Yangyang Tang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Zheng Zhang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Cong Tao
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | | |
Collapse
|
5
|
Li C, Nijjer J, Feng L, Zhang Q, Yan J, Zhang S. Agent-based modeling of stress anisotropy driven nematic ordering in growing biofilms. SOFT MATTER 2024; 20:3401-3410. [PMID: 38563244 DOI: 10.1039/d3sm01535a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Living active collectives have evolved with remarkable self-patterning capabilities to adapt to the physical and biological constraints crucial for their growth and survival. However, the intricate process by which complex multicellular patterns emerge from a single founder cell remains elusive. In this study, we utilize an agent-based model, validated through single-cell microscopy imaging, to track the three-dimensional (3D) morphodynamics of cells within growing bacterial biofilms encased by agarose gels. The confined growth conditions give rise to a spatiotemporally heterogeneous stress landscape within the biofilm. In the core of the biofilm, where high hydrostatic and low shear stresses prevail, cell packing appears disordered. In contrast, near the gel-cell interface, a state of high shear stress and low hydrostatic stress emerges, driving nematic ordering, albeit with a time delay inherent to shear stress relaxation. Strikingly, we observe a robust spatiotemporal correlation between stress anisotropy and nematic ordering within these confined biofilms. This correlation suggests a mechanism whereby stress anisotropy plays a pivotal role in governing the spatial organization of cells. The reciprocity between stress anisotropy and cell ordering in confined biofilms opens new avenues for innovative 3D mechanically guided patterning techniques for living active collectives, which hold significant promise for a wide array of environmental and biomedical applications.
Collapse
Affiliation(s)
- Changhao Li
- Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA, USA.
| | - Japinder Nijjer
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
| | - Luyi Feng
- Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA, USA.
| | - Qiuting Zhang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
| | - Jing Yan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
- Quantitative Biology Institute, Yale University, New Haven, CT, USA
| | - Sulin Zhang
- Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA, USA.
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Department of Material Science and Engineering, Pennsylvania State University, University Park, PA, USA
| |
Collapse
|
6
|
Shen R, Borer B, Ciccarese D, Salek MM, Babbin AR. Microscale advection governs microbial growth and oxygen consumption in macroporous aggregates. mSphere 2024; 9:e0018524. [PMID: 38530018 PMCID: PMC11036798 DOI: 10.1128/msphere.00185-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 03/27/2024] Open
Abstract
Most microbial life on Earth is found in localized microenvironments that collectively exert a crucial role in maintaining ecosystem health and influencing global biogeochemical cycles. In many habitats such as biofilms in aquatic systems, bacterial flocs in activated sludge, periphyton mats, or particles sinking in the ocean, these microenvironments experience sporadic or continuous flow. Depending on their microscale structure, pores and channels through the microenvironments permit localized flow that shifts the relative importance of diffusive and advective mass transport. How this flow alters nutrient supply, facilitates waste removal, drives the emergence of different microbial niches, and impacts the overall function of the microenvironments remains unclear. Here, we quantify how pores through microenvironments that permit flow can elevate nutrient supply to the resident bacterial community using a microfluidic experimental system and gain further insights from coupled population-based and computational fluid dynamics simulations. We find that the microscale structure determines the relative contribution of advection vs diffusion, and even a modest flow through a pore in the range of 10 µm s-1 can increase the carrying capacity of a microenvironment by 10%. Recognizing the fundamental role that microbial hotspots play in the Earth system, developing frameworks that predict how their heterogeneous morphology and potential interstitial flows change microbial function and collectively alter global scale fluxes is critical.IMPORTANCEMicrobial life is a key driver of global biogeochemical cycles. Similar to the distribution of humans on Earth, they are often not homogeneously distributed in nature but occur in dense clusters that resemble microbial cities. Within and around these clusters, diffusion is often assumed as the sole mass-transfer process that dictates nutrient supply and waste removal. In many natural and engineered systems such as biofilms in aquatic environments, aggregates in bioremediation, or flocs in wastewater treatment plants, these clusters are exposed to flow that elevates mass transfer, a process that is often overlooked. In this study, we show that advective fluxes can increase the local growth of bacteria in a single microenvironment by up to 50% and shape their metabolism by disrupting localized anoxia or supplying nutrients at different rates. Collectively, advection-enhanced mass transport may thus regulate important biogeochemical transformations in both natural and engineered environments.
Collapse
Affiliation(s)
- Rachel Shen
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Benedict Borer
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Davide Ciccarese
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - M. Mehdi Salek
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Andrew R. Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| |
Collapse
|
7
|
Qi Y, Chang SS, Wang Y, Chen C, Baek KI, Hsiai T, Roper M. Hemodynamic regulation allows stable growth of microvascular networks. Proc Natl Acad Sci U S A 2024; 121:e2310993121. [PMID: 38386707 PMCID: PMC10907248 DOI: 10.1073/pnas.2310993121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 01/16/2024] [Indexed: 02/24/2024] Open
Abstract
How do vessels find optimal radii? Capillaries are known to adapt their radii to maintain the shear stress of blood flow at the vessel wall at a set point, yet models of adaptation purely based on average shear stress have not been able to produce complex loopy networks that resemble real microvascular systems. For narrow vessels where red blood cells travel in a single file, the shear stress on vessel endothelium peaks sharply when a red blood cell passes through. We show that stable shear-stress-based adaptation is possible if vessel shear stress set points are cued to the stress peaks. Model networks that respond to peak stresses alone can quantitatively reproduce the observed zebrafish trunk microcirculation, including its adaptive trajectory when hematocrit changes or parts of the network are amputated. Our work reveals the potential for mechanotransduction alone to generate stable hydraulically tuned microvascular networks.
Collapse
Affiliation(s)
- Yujia Qi
- Department of Mechanical Engineering, University of California, Los Angeles, CA90095
| | - Shyr-Shea Chang
- Department of Mathematics, University of California, Los Angeles, CA90095
| | - Yixuan Wang
- Department of Mathematics, University of California, Los Angeles, CA90095
| | - Cynthia Chen
- Department of Bioengineering, University of California, Los Angeles, CA90095
| | - Kyung In Baek
- Department of Bioengineering, University of California, Los Angeles, CA90095
| | - Tzung Hsiai
- Department of Bioengineering, University of California, Los Angeles, CA90095
| | - Marcus Roper
- Department of Mathematics, University of California, Los Angeles, CA90095
- Department of Computational Medicine, University of California, Los Angeles, CA90095
| |
Collapse
|
8
|
Ugolini GS, Wang M, Secchi E, Pioli R, Ackermann M, Stocker R. Microfluidic approaches in microbial ecology. LAB ON A CHIP 2024; 24:1394-1418. [PMID: 38344937 PMCID: PMC10898419 DOI: 10.1039/d3lc00784g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Microbial life is at the heart of many diverse environments and regulates most natural processes, from the functioning of animal organs to the cycling of global carbon. Yet, the study of microbial ecology is often limited by challenges in visualizing microbial processes and replicating the environmental conditions under which they unfold. Microfluidics operates at the characteristic scale at which microorganisms live and perform their functions, thus allowing for the observation and quantification of behaviors such as growth, motility, and responses to external cues, often with greater detail than classical techniques. By enabling a high degree of control in space and time of environmental conditions such as nutrient gradients, pH levels, and fluid flow patterns, microfluidics further provides the opportunity to study microbial processes in conditions that mimic the natural settings harboring microbial life. In this review, we describe how recent applications of microfluidic systems to microbial ecology have enriched our understanding of microbial life and microbial communities. We highlight discoveries enabled by microfluidic approaches ranging from single-cell behaviors to the functioning of multi-cellular communities, and we indicate potential future opportunities to use microfluidics to further advance our understanding of microbial processes and their implications.
Collapse
Affiliation(s)
- Giovanni Stefano Ugolini
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Miaoxiao Wang
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
| | - Eleonora Secchi
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Roberto Pioli
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Martin Ackermann
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
- Laboratory of Microbial Systems Ecology, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédéral de Lausanne (EPFL), Lausanne, Switzerland
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| |
Collapse
|
9
|
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: 1] [Impact Index Per Article: 1.0] [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.
Collapse
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.
| |
Collapse
|
10
|
Jung H. A pore-scale reactive transport modeling study for quorum sensing-driven biofilm dispersal in heterogeneous porous media. Math Biosci 2024; 367:109126. [PMID: 38070765 DOI: 10.1016/j.mbs.2023.109126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/26/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023]
Abstract
Microorganisms regulate the expression of energetically expensive phenotypes via a collective decision-making mechanism known as quorum sensing (QS). This study investigates the intricate dynamics of biofilm growth and QS-controlled biofilm dispersal in heterogeneous porous media, employing a pore-scale reactive transport modeling approach. Model simulations carried out under various fluid flow conditions and biofilm growth scenarios reveal that QS processes are influenced not only by the biomass density of biofilm colonies but also by a complex interplay between pore architecture, flow velocity, and the rates of biofilm growth and dispersal. This study demonstrates that pore architecture controls the initiation of QS processes and advection gives rise to oscillatory growth of biofilms. Such oscillation is suppressed if biofilm dynamics are in favor of sustaining a sufficiently high signal concentration, such as fast growth or slow dispersal rates. By establishing a mathematical framework, this study contributes to the fundamental understanding of QS-controlled biofilm dynamics in complex environments.
Collapse
Affiliation(s)
- Heewon Jung
- Department of Geological Sciences, Chungnam National University, Daejeon 34134, South Korea.
| |
Collapse
|
11
|
Zhai H, Yeo J. Controlling biofilm transport with porous metamaterials designed with Bayesian learning. J Mech Behav Biomed Mater 2023; 147:106127. [PMID: 37797554 DOI: 10.1016/j.jmbbm.2023.106127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/29/2023] [Accepted: 09/12/2023] [Indexed: 10/07/2023]
Abstract
Biofilm growth and transport in confined systems frequently occur in natural and engineered systems. Designing customizable engineered porous materials for controllable biofilm transportation properties could significantly improve the rapid utilization of biofilms as engineered living materials for applications in pollution alleviation, material self-healing, energy production, and many more. We combine Bayesian optimization (BO) and individual-based modeling to conduct design optimizations for maximizing different porous materials' (PM) biofilm transportation capability. We first characterize the acquisition function in BO for designing 2-dimensional porous membranes. We use the expected improvement acquisition function for designing lattice metamaterials (LM) and 3-dimensional porous media (3DPM). We find that BO is 92.89% more efficient than the uniform grid search method for LM and 223.04% more efficient for 3DPM. For all three types of structures, the selected characterization simulation tests are in good agreement with the design spaces approximated with Gaussian process regression. All the extracted optimal designs exhibit better biofilm growth and transportability than unconfined space without substrates. Our comparison study shows that PM stimulates biofilm growth by taking up volumetric space and pushing biofilms' upward growth, as evidenced by a 20% increase in bacteria cell numbers in unconfined space compared to porous materials, and 128% more bacteria cells in the target growth region for PM-induced biofilm growth compared with unconfined growth. Our work provides deeper insights into the design of substrates to tune biofilm growth, analyzing the optimization process and characterizing the design space, and understanding biophysical mechanisms governing the growth of biofilms.
Collapse
Affiliation(s)
- Hanfeng Zhai
- Sibley School of Mechanical and Aerospace Engineering Cornell University, Ithaca, NY 14850, USA
| | - Jingjie Yeo
- Sibley School of Mechanical and Aerospace Engineering Cornell University, Ithaca, NY 14850, USA.
| |
Collapse
|
12
|
Wei G, Yang JQ. Microfluidic investigation of the impacts of flow fluctuations on the development of Pseudomonas putida biofilms. NPJ Biofilms Microbiomes 2023; 9:73. [PMID: 37789000 PMCID: PMC10547774 DOI: 10.1038/s41522-023-00442-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/25/2023] [Indexed: 10/05/2023] Open
Abstract
Biofilms play critical roles in wastewater treatment, bioremediation, and medical-device-related infections. Understanding the dynamics of biofilm formation and growth is essential for controlling and exploiting their properties. However, the majority of current studies have focused on the impact of steady flows on biofilm growth, while flow fluctuations are common in natural and engineered systems such as water pipes and blood vessels. Here, we reveal the effects of flow fluctuations on the development of Pseudomonas putida biofilms through systematic microfluidic experiments and the development of a theoretical model. Our experimental results showed that biofilm growth under fluctuating flow conditions followed three phases: lag, exponential, and fluctuation phases. In contrast, biofilm growth under steady-flow conditions followed four phases: lag, exponential, stationary, and decline phases. Furthermore, we demonstrated that low-frequency flow fluctuations promoted biofilm growth, while high-frequency fluctuations inhibited its development. We attributed the contradictory impacts of flow fluctuations on biofilm growth to the adjustment time (T0) needed for biofilm to grow after the shear stress changed from high to low. Furthermore, we developed a theoretical model that explains the observed biofilm growth under fluctuating flow conditions. Our insights into the mechanisms underlying biofilm development under fluctuating flows can inform the design of strategies to control biofilm formation in diverse natural and engineered systems.
Collapse
Affiliation(s)
- Guanju Wei
- Saint Anthony Falls Laboratory, University of Minnesota, Minneapolis, MN, 55414, USA
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Judy Q Yang
- Saint Anthony Falls Laboratory, University of Minnesota, Minneapolis, MN, 55414, USA.
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis, MN, 55455, USA.
| |
Collapse
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
Markale I, Carrel M, Kurz DL, Morales VL, Holzner M, Jiménez-Martínez J. Internal Biofilm Heterogeneities Enhance Solute Mixing and Chemical Reactions in Porous Media. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:8065-8074. [PMID: 37205794 DOI: 10.1021/acs.est.2c09082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Bacterial biofilms can form in porous media that are of interest in industrial applications ranging from medical implants to biofilters as well as in environmental applications such as in situ groundwater remediation, where they can be critical locations for biogeochemical reactions. The presence of biofilms modifies porous media topology and hydrodynamics by clogging pores and consequently solutes transport and reactions kinetics. The interplay between highly heterogeneous flow fields found in porous media and microbial behavior, including biofilm growth, results in a spatially heterogeneous biofilm distribution in the porous media as well as internal heterogeneity across the thickness of the biofilm. Our study leverages highly resolved three-dimensional X-ray computed microtomography images of bacterial biofilms in a tubular reactor to numerically compute pore-scale fluid flow and solute transport by considering multiple equivalent stochastically generated internal permeability fields for the biofilm. We show that the internal heterogeneous permeability mainly impacts intermediate velocities when compared with homogeneous biofilm permeability. While the equivalent internal permeability fields of the biofilm do not impact fluid-fluid mixing, they significantly control a fast reaction. For biologically driven reactions such as nutrient or contaminant uptake by the biofilm, its internal permeability field controls the efficiency of the process. This study highlights the importance of considering the internal heterogeneity of biofilms to better predict reactivity in industrial and environmental bioclogged porous systems.
Collapse
Affiliation(s)
- Ishaan Markale
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Dorothee L Kurz
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Verónica L Morales
- Department of Civil and Environmental Engineering, University of California Davis, Davis, California 95616-5270, United States
| | - Markus Holzner
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- WSL, Swiss Federal Institute of Forest, Snow and Landscape Research, 8903 Birmensdorf, Switzerland
| | - Joaquín Jiménez-Martínez
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland
| |
Collapse
|
15
|
Kurz DL, Secchi E, Stocker R, Jimenez-Martinez J. Morphogenesis of Biofilms in Porous Media and Control on Hydrodynamics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:5666-5677. [PMID: 36976631 DOI: 10.1021/acs.est.2c08890] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The functioning of natural and engineered porous media, like soils and filters, depends in many cases on the interplay between biochemical processes and hydrodynamics. In such complex environments, microorganisms often form surface-attached communities known as biofilms. Biofilms can take the shape of clusters, which alter the distribution of fluid flow velocities within the porous medium, subsequently influencing biofilm growth. Despite numerous experimental and numerical efforts, the control of the biofilm clustering process and the resulting heterogeneity in biofilm permeability is not well understood, limiting our predictive abilities for biofilm-porous medium systems. Here, we use a quasi-2D experimental model of a porous medium to characterize biofilm growth dynamics for different pore sizes and flow rates. We present a method to obtain the time-resolved biofilm permeability field from experimental images and use the obtained permeability field to compute the flow field through a numerical model. We observe a biofilm cluster size distribution characterized by a spectrum slope evolving in time between -2 and -1, a fundamental measure that can be used to create spatio-temporal distributions of biofilm clusters for upscaled models. We find a previously undescribed biofilm permeability distribution, which can be used to stochastically generate permeability fields within biofilms. An increase in velocity variance for a decrease in physical heterogeneity shows that the bioclogged porous medium behaves differently than expected from studies on heterogeneity in abiotic porous media.
Collapse
Affiliation(s)
- Dorothee L Kurz
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland
- Department Water Resources and Drinking Water, Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Eleonora Secchi
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland
| | - Joaquin Jimenez-Martinez
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland
- Department Water Resources and Drinking Water, Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| |
Collapse
|
16
|
Lee SH, Secchi E, Kang PK. Rapid formation of bioaggregates and morphology transition to biofilm streamers induced by pore-throat flows. Proc Natl Acad Sci U S A 2023; 120:e2204466120. [PMID: 36989304 PMCID: PMC10083537 DOI: 10.1073/pnas.2204466120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 02/28/2023] [Indexed: 03/30/2023] Open
Abstract
Bioaggregates are condensed porous materials comprising microbes, organic and inorganic matters, and water. They are commonly found in natural and engineered porous media and often cause clogging. Despite their importance, the formation mechanism of bioaggregates in porous media systems is largely unknown. Through microfluidic experiments and direct numerical simulations of fluid flow, we show that the rapid bioaggregation is driven by the interplay of the viscoelastic nature of biomass and hydrodynamic conditions at pore throats. At an early stage, unique flow structures around a pore throat promote the biomass attachment at the throat. Then, the attached biomass fluidizes when the shear stress at the partially clogged pore throat reaches a critical value. After the fluidization, the biomass is displaced and accumulated in the expansion region of throats forming bioaggregates. We further find that such criticality in shear stress triggers morphological changes in bioaggregates from rounded- to streamer-like shapes. This knowledge was used to control the clogging of throats by tuning the flow conditions: When the shear stress at the throat exceeded the critical value, clogging was prevented. The bioaggregation process did not depend on the detailed pore-throat geometry, as we reproduced the same dynamics in various pore-throat geometries. This study demonstrates that pore-throat structures, which are ubiquitous in porous media systems, induce bioaggregation and can lead to abrupt disruptions in flow.
Collapse
Affiliation(s)
- Sang Hyun Lee
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN55455
| | - Eleonora Secchi
- Institute of Environmental Engineering, ETH Zürich, Zürich8093, Switzerland
| | - Peter K. Kang
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN55455
- Saint Anthony Falls Laboratory, University of Minnesota, Minneapolis, MN55455
| |
Collapse
|