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Tang Y, Tao C, Zhang Z, Liu S, Dong F, Zhang D, Zhang J, Wang X. The porous structure induced heterogeneous and localized failure of the biofilm in microfluidic channels. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2023; 88:3181-3193. [PMID: 38154803 PMCID: wst_2023_384 DOI: 10.2166/wst.2023.384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Abstract
Understanding the mechanism of biofilm distribution and detachment is very important to effectively improve water treatment and prevent blockage in porous media. The existing research is more related to the local biofilm evolving around one or few microposts and the lack of the integral biofilm evolution in a micropost array for a longer growth period. This study combines microfluidic experiments and mathematical simulations to study the distribution and detachment of biofilm in porous media. Microfluidic chips with an array of microposts with different sizes are designed to simulate the physical pore structure of soil. The research shows that the initial formation and distribution of biofilm are influenced by bacterial transport velocity gradients within the pore space. Bacteria prefer to aggregate areas with smaller microposts, leading to the development of biofilm in those regions. Consequently, impermeable blockage structures form in this area. By analyzing experimental images of biofilm structures at the later stages, as well as coupling fluid flow and porous medium, and the finite element simulation, we find that the biofilm detachment is correlated with the morphology and permeability (kb) (from 10-15 to 10-9 m2) of the biofilm. The simulations show that there are two modes of biofilm detachment, such as internal detachment and external erosion.
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Affiliation(s)
- Yangyang Tang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China E-mail:
| | - Cong Tao
- 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
| | - Song Liu
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Fulin Dong
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Duohuai Zhang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Jinchang Zhang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Xiaoling Wang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China; School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
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Hallatschek O, Datta SS, Drescher K, Dunkel J, Elgeti J, Waclaw B, Wingreen NS. Proliferating active matter. NATURE REVIEWS. PHYSICS 2023; 5:1-13. [PMID: 37360681 PMCID: PMC10230499 DOI: 10.1038/s42254-023-00593-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 05/02/2023] [Indexed: 06/28/2023]
Abstract
The fascinating patterns of collective motion created by autonomously driven particles have fuelled active-matter research for over two decades. So far, theoretical active-matter research has often focused on systems with a fixed number of particles. This constraint imposes strict limitations on what behaviours can and cannot emerge. However, a hallmark of life is the breaking of local cell number conservation by replication and death. Birth and death processes must be taken into account, for example, to predict the growth and evolution of a microbial biofilm, the expansion of a tumour, or the development from a fertilized egg into an embryo and beyond. In this Perspective, we argue that unique features emerge in these systems because proliferation represents a distinct form of activity: not only do the proliferating entities consume and dissipate energy, they also inject biomass and degrees of freedom capable of further self-proliferation, leading to myriad dynamic scenarios. Despite this complexity, a growing number of studies document common collective phenomena in various proliferating soft-matter systems. This generality leads us to propose proliferation as another direction of active-matter physics, worthy of a dedicated search for new dynamical universality classes. Conceptual challenges abound, from identifying control parameters and understanding large fluctuations and nonlinear feedback mechanisms to exploring the dynamics and limits of information flow in self-replicating systems. We believe that, by extending the rich conceptual framework developed for conventional active matter to proliferating active matter, researchers can have a profound impact on quantitative biology and reveal fascinating emergent physics along the way.
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Affiliation(s)
- Oskar Hallatschek
- Departments of Physics and Integrative Biology, University of California, Berkeley, CA US
- Peter Debye Institute for Soft Matter Physics, Leipzig University, Leipzig, Germany
| | - Sujit S. Datta
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ USA
| | | | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Jens Elgeti
- Theoretical Physics of Living Matter, Institute of Biological Information Processing, Forschungszentrum Jülich, Jülich, Germany
| | - Bartek Waclaw
- Dioscuri Centre for Physics and Chemistry of Bacteria, Institute of Physical Chemistry PAN, Warsaw, Poland
- School of Physics and Astronomy, The University of Edinburgh, JCMB, Edinburgh, UK
| | - Ned S. Wingreen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ USA
- Department of Molecular Biology, Princeton University, Princeton, NJ USA
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3
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Wei Z, Li D, Li S, Hao T, Zeng H, Zhang J. Improving mechanical stability of anammox granules with organic stress by limited filamentous bulking. BIORESOURCE TECHNOLOGY 2023; 370:128558. [PMID: 36587769 DOI: 10.1016/j.biortech.2022.128558] [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] [Received: 12/05/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
Under organic stress, the limited filamentous bulking (FB) was demonstrated to improve anammox capability by inhibiting granule disintegration and washout. The accumulation of internal stress played a more important role than the adverse physicochemical properties (low viscoelasticity and hydrophobicity) of granules in limiting granular strength by consuming the granular elastic energy. Different from the floc-forming heterotrophic bacteria (HB) that stored its growth stress as internal stress by pushing the surrounded anammox micro-colonies outwards under the spatial constraint of elastic anammox "shell", the filamentous HB grew into a uniform network structure within granules, endowed granules low internal stress and acted as the granular skeleton due to its rich amyloid substance, which was benefited from the elimination of inhomogeneous growth and the consequent expansion competition for living space. Combined with the mechanical instability and sticking-spring models, controlling FB at limited level was effective for improving granular strength without affecting sludge-water separation.
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Affiliation(s)
- Ziqing Wei
- Key Laboratory of Water Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, China
| | - Dong Li
- Key Laboratory of Water Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, China.
| | - Shuai Li
- Key Laboratory of Water Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, China
| | - Tongyao Hao
- Key Laboratory of Water Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, China
| | - Huiping Zeng
- Key Laboratory of Water Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, China
| | - Jie Zhang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
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4
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Xie S, Wang W, Li N, Wen C, Zhu S, Luo X. Effect of Drying-Rewetting cycles on the metal adsorption and tolerance of natural biofilms. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 327:116922. [PMID: 36462490 DOI: 10.1016/j.jenvman.2022.116922] [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: 07/20/2022] [Revised: 11/15/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
Drying-rewetting (D-RW) cycles can induce changes in biofilms by forcing the microbial community to tolerate and adapt to environmental pressure. Existing studies have mostly focused on the impact of D-RW cycles on the microbial community structure, and little attention has been paid to how D-RW cycles may change the biofilm tolerance and adsorption of heavy metals. We experimentally evaluated the effect of repeated D-RW cycles on the Cd2+ and Pb2+ adsorption and tolerance of biofilms. The equilibrium adsorption capacity of the biofilm decreased as the number of D-RW cycles was increased, which was attributed to a change in affinity between the biofilm and metal ions. For a binary metal system, the D-RW cycles affected the competitive adsorption of Cd2+ and Pb2+ by the biofilm. A synergistic effect was observed with one and three D-RW cycles, while an antagonistic effect was observed for the control film and five D-RW cycles. The tolerance of the biofilm to Cd2+ and Pb2+ increased with the number of D-RW cycles. The stress from the D-RW cycles may have increased the relative abundance of drought-tolerant bacteria, which altered the biofilm functions and thus indirectly affected the heavy metal adsorption capacity.
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Affiliation(s)
- Shanshan Xie
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
| | - Wenwen Wang
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
| | - Nihong Li
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
| | - Chen Wen
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
| | - Shijun Zhu
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
| | - Xia Luo
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China.
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An open-source computational tool for measuring bacterial biofilm morphology and growth kinetics upon one-sided exposure to an antimicrobial source. Sci Rep 2022; 12:16125. [PMID: 36167741 PMCID: PMC9515175 DOI: 10.1038/s41598-022-20275-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/12/2022] [Indexed: 11/28/2022] Open
Abstract
Bacillus subtilis biofilms are well known for their complex and highly adaptive morphology. Indeed, their phenotypical diversity and intra-biofilm heterogeneity make this gram-positive bacterium the subject of many scientific papers on the structure of biofilms. The “robustness” of biofilms is a term often used to describe their level of susceptibility to antimicrobial agents and various mechanical and molecular inhibition/eradication methods. In this paper, we use computational analytics to quantify Bacillus subtilis morphological response to proximity to an antimicrobial source, in the form of the antiseptic chlorhexidine. Chlorhexidine droplets, placed in proximity to Bacillus subtilis macrocolonies at different distances result in morphological changes, quantified using Python-based code, which we have made publicly available. Our results quantify peripheral and inner core deformation as well as differences in cellular viability of the two regions. The results reveal that the inner core, which is often characterized by the presence of wrinkled formations in the macrocolony, is more preserved than the periphery. Furthermore, the paper describes a crescent-shaped colony morphology which occurs when the distance from the chlorhexidine source is 0.5 cm, as well as changes observed in the growth substrate of macrocolonies exposed to chlorhexidine.
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6
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Surapaneni VA, Schindler M, Ziege R, de Faria LC, Wölfer J, Bidan CM, Mollen FH, Amini S, Hanna S, Dean MN. Groovy and Gnarly: Surface Wrinkles as a Multifunctional Motif for Terrestrial and Marine Environments. Integr Comp Biol 2022; 62:icac079. [PMID: 35675323 PMCID: PMC9703940 DOI: 10.1093/icb/icac079] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 12/12/2022] Open
Abstract
From large ventral pleats of humpback whales to nanoscale ridges on flower petals, wrinkled structures are omnipresent, multifunctional, and found at hugely diverse scales. Depending on the particulars of the biological system-its environment, morphology, and mechanical properties-wrinkles may control adhesion, friction, wetting, or drag; promote interfacial exchange; act as flow channels; or contribute to stretching, mechanical integrity, or structural color. Undulations on natural surfaces primarily arise from stress-induced instabilities of surface layers (e.g., buckling) during growth or aging. Variation in the material properties of surface layers and in the magnitude and orientation of intrinsic stresses during growth lead to a variety of wrinkling morphologies and patterns which, in turn, reflect the wide range of biophysical challenges wrinkled surfaces can solve. Therefore, investigating how surface wrinkles vary and are implemented across biological systems is key to understanding their structure-function relationships. In this work, we synthesize the literature in a metadata analysis of surface wrinkling in various terrestrial and marine organisms to review important morphological parameters and classify functional aspects of surface wrinkles in relation to the size and ecology of organisms. Building on our previous and current experimental studies, we explore case studies on nano/micro-scale wrinkles in biofilms, plant surfaces, and basking shark filter structures to compare developmental and structure-vs-function aspects of wrinkles with vastly different size scales and environmental demands. In doing this and by contrasting wrinkle development in soft and hard biological systems, we provide a template of structure-function relationships of biological surface wrinkles and an outlook for functionalized wrinkled biomimetic surfaces.
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Affiliation(s)
- Venkata A Surapaneni
- City University of Hong Kong, 31 To Yuen Street, Kowloon, Hong Kong
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, Potsdam, Brandenburg 14476, Germany
| | - Mike Schindler
- City University of Hong Kong, 31 To Yuen Street, Kowloon, Hong Kong
| | - Ricardo Ziege
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, Potsdam, Brandenburg 14476, Germany
| | | | - Jan Wölfer
- Humboldt University of Berlin, Unter den Linden 6, Berlin 10099, Germany
| | - Cécile M Bidan
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, Potsdam, Brandenburg 14476, Germany
| | - Frederik H Mollen
- Elasmobranch Research Belgium, Rehaegenstraat 4, 2820 Bonheiden, Belgium
| | - Shahrouz Amini
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, Potsdam, Brandenburg 14476, Germany
| | - Sean Hanna
- University College London, 14 Upper Woburn Place, London WC1H 0NN, UK
| | - Mason N Dean
- City University of Hong Kong, 31 To Yuen Street, Kowloon, Hong Kong
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, Potsdam, Brandenburg 14476, Germany
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7
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Probing the growth and mechanical properties of Bacillus subtilis biofilms through genetic mutation strategies. Synth Syst Biotechnol 2022; 7:965-971. [PMID: 35756965 PMCID: PMC9194759 DOI: 10.1016/j.synbio.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 12/02/2022] Open
Abstract
Bacterial communities form biofilms on various surfaces by synthesizing a cohesive and protective extracellular matrix, and these biofilms protect microorganisms against harsh environmental conditions. Bacillus subtilis is a widely used experimental species, and its biofilms are used as representative models of beneficial biofilms. Specifically, B. subtilis biofilms are known to be rich in extracellular polymeric substances (EPS) and other biopolymers such as DNA and proteins like the amyloid protein TasA and the hydrophobic protein BslA. These materials, which form an interconnected, cohesive, three-dimensional polymer network, provide the mechanical stability of biofilms and mediate their adherence to surfaces among other functional contributions. Here, we explored how genetically-encoded components specifically contribute to regulate the growth status, mechanical properties, and antibiotic resistance of B. subtilis biofilms, thereby establishing a solid empirical basis for understanding how various genetic engineering efforts are likely to affect the structure and function of biofilms. We noted discrete contributions to biofilm morphology, mechanical properties, and survival from major biofilm components such as EPS, TasA and BslA. For example, EPS plays an important role in maintaining the stability of the mechanical properties and the antibiotic resistance of biofilms, whereas BslA has a significant impact on the resolution that can be obtained for printing applications. This work provides a deeper understanding of the internal interactions of biofilm components through systematic genetic manipulations. It thus not only broadens the application prospects of beneficial biofilms, but also serves as the basis of future strategies for targeting and effectively removing harmful biofilms.
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8
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Role of Hfq in glucose utilization, biofilm formation and quorum sensing system in Bacillus subtilis. Biotechnol Lett 2022; 44:845-855. [PMID: 35614284 DOI: 10.1007/s10529-022-03262-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/09/2022] [Indexed: 11/02/2022]
Abstract
Hfq is an RNA-binding protein, its main function is to participate in post-transcriptional regulation of bacteria and regulate small regulatory RNA (sRNA) and messenger RNA (mRNA) stability, but the Hfq function of Bacillus subtilis (B. subtilis) has not been fully explained. In this study, we used the strains of B. subtilis168 (BS168), BS168Δhfq and BS168Δhfq-C to explore the effects of Hfq on the glucose utilization, biofilm formation and quorum sensing (QS) system of B. subtilis. The results showed that the knockout of hfq resulted in growth defects when bacteria were cultured in the Luria-Bertani (LB) medium, but we did not observe the same effects in Nitrogen medium (NM) and Inorganic Salt-free medium (ISM). We further found that the growth of strains under different glucose concentrations was also different, which was related to the expression of CcpA. Interestingly, the hfq mutant showed increased resistance to a high-glucose environment. Furthermore, the biofilm and extracellular poly saccharides (EPS) formation of BS168Δhfq decreased significantly. At the same time, changes were observed in the morphology of the biofilm, such as larger intercellular space of the biofilm and thinner edge. The qRT-PCR results confirmed that the hfq knockout caused significant up-regulation or down-regulation of gene expression in QS system, and down-regulated genes were involved in the positive regulation of biofilm formation. Taken together, we demonstrated that Hfq plays a vital role in glucose utilization, biofilm formation and QS of B. subtilis, which provides a new perspective for subsequent related research.
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9
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Systems view of Bacillus subtilis pellicle development. NPJ Biofilms Microbiomes 2022; 8:25. [PMID: 35414070 PMCID: PMC9005697 DOI: 10.1038/s41522-022-00293-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/19/2022] [Indexed: 11/08/2022] Open
Abstract
In this study, we link pellicle development at the water-air interface with the vertical distribution and viability of the individual B. subtilis PS-216 cells throughout the water column. Real-time interfacial rheology and time-lapse confocal laser scanning microscopy were combined to correlate mechanical properties with morphological changes (aggregation status, filament formation, pellicle thickness, spore formation) of the growing pellicle. Six key events were identified in B. subtilis pellicle formation that are accompanied by a major change in viscoelastic and morphology behaviour of the pellicle. The results imply that pellicle development is a multifaceted response to a changing environment induced by bacterial growth that causes population redistribution within the model system, reduction of the viable habitat to the water-air interface, cell development, and morphogenesis. The outcome is a build-up of mechanical stress supporting structure that eventually, due to nutrient deprivation, reaches the finite thickness. After prolonged incubation, the formed pellicle collapses, which correlates with the spore releasing process. The pellicle loses the ability to support mechanical stress, which marks the end of the pellicle life cycle and entry of the system into the dormant state.
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10
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Li Z, Wang X, Wang J, Yuan X, Jiang X, Wang Y, Zhong C, Xu D, Gu T, Wang F. Bacterial biofilms as platforms engineered for diverse applications. Biotechnol Adv 2022; 57:107932. [DOI: 10.1016/j.biotechadv.2022.107932] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 02/22/2022] [Accepted: 02/22/2022] [Indexed: 12/23/2022]
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11
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Evstigneeva SS, Telesheva EM, Mokeev DI, Borisov IV, Petrova LP, Shelud’ko AV. Response of Bacteria to Mechanical Stimuli. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721050052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Abstract—
Bacteria adapt rapidly to changes in ambient conditions, constantly inspecting their surroundings by means of their sensor systems. These systems are often thought to respond only to signals of a chemical nature. Yet, bacteria are often affected by mechanical forces, e.g., during transition from planktonic to sessile state. Mechanical stimuli, however, have seldom been considered as the signals bacteria can sense and respond to. Nonetheless, bacteria perceive mechanical stimuli, generate signals, and develop responses. This review analyzes the information on the way bacteria respond to mechanical stimuli and outlines how bacteria convert incoming signals into appropriate responses.
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12
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Arnaouteli S, Bamford NC, Stanley-Wall NR, Kovács ÁT. Bacillus subtilis biofilm formation and social interactions. Nat Rev Microbiol 2021; 19:600-614. [PMID: 33824496 DOI: 10.1038/s41579-021-00540-9] [Citation(s) in RCA: 155] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2021] [Indexed: 02/03/2023]
Abstract
Biofilm formation is a process in which microbial cells aggregate to form collectives that are embedded in a self-produced extracellular matrix. Bacillus subtilis is a Gram-positive bacterium that is used to dissect the mechanisms controlling matrix production and the subsequent transition from a motile planktonic cell state to a sessile biofilm state. The collective nature of life in a biofilm allows emergent properties to manifest, and B. subtilis biofilms are linked with novel industrial uses as well as probiotic and biocontrol processes. In this Review, we outline the molecular details of the biofilm matrix and the regulatory pathways and external factors that control its production. We explore the beneficial outcomes associated with biofilms. Finally, we highlight major advances in our understanding of concepts of microbial evolution and community behaviour that have resulted from studies of the innate heterogeneity of biofilms.
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Affiliation(s)
- Sofia Arnaouteli
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Natalie C Bamford
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK.
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark.
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13
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Winkle JJ, Karamched BR, Bennett MR, Ott W, Josić K. Emergent spatiotemporal population dynamics with cell-length control of synthetic microbial consortia. PLoS Comput Biol 2021; 17:e1009381. [PMID: 34550968 PMCID: PMC8489724 DOI: 10.1371/journal.pcbi.1009381] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 10/04/2021] [Accepted: 08/25/2021] [Indexed: 12/04/2022] Open
Abstract
The increased complexity of synthetic microbial biocircuits highlights the need for distributed cell functionality due to concomitant increases in metabolic and regulatory burdens imposed on single-strain topologies. Distributed systems, however, introduce additional challenges since consortium composition and spatiotemporal dynamics of constituent strains must be robustly controlled to achieve desired circuit behaviors. Here, we address these challenges with a modeling-based investigation of emergent spatiotemporal population dynamics using cell-length control in monolayer, two-strain bacterial consortia. We demonstrate that with dynamic control of a strain's division length, nematic cell alignment in close-packed monolayers can be destabilized. We find that this destabilization confers an emergent, competitive advantage to smaller-length strains-but by mechanisms that differ depending on the spatial patterns of the population. We used complementary modeling approaches to elucidate underlying mechanisms: an agent-based model to simulate detailed mechanical and signaling interactions between the competing strains, and a reductive, stochastic lattice model to represent cell-cell interactions with a single rotational parameter. Our modeling suggests that spatial strain-fraction oscillations can be generated when cell-length control is coupled to quorum-sensing signaling in negative feedback topologies. Our research employs novel methods of population control and points the way to programming strain fraction dynamics in consortial synthetic biology.
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Affiliation(s)
- James J Winkle
- Department of Mathematics, University of Houston, Houston, Texas, United States of America
| | - Bhargav R Karamched
- Department of Mathematics, Florida State University, Tallahassee, Florida, United States of America
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, United States of America
| | - Matthew R Bennett
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
- Department of Biosciences, Rice University, Houston, Texas, United States of America
| | - William Ott
- Department of Mathematics, University of Houston, Houston, Texas, United States of America
| | - Krešimir Josić
- Department of Mathematics, University of Houston, Houston, Texas, United States of America
- Department of Biosciences, Rice University, Houston, Texas, United States of America
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
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14
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Jiao R, Cai Y, He P, Munir S, Li X, Wu Y, Wang J, Xia M, He P, Wang G, Yang H, Karunarathna SC, Xie Y, He Y. Bacillus amyloliquefaciens YN201732 Produces Lipopeptides With Promising Biocontrol Activity Against Fungal Pathogen Erysiphe cichoracearum. Front Cell Infect Microbiol 2021; 11:598999. [PMID: 34222035 PMCID: PMC8253258 DOI: 10.3389/fcimb.2021.598999] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 04/20/2021] [Indexed: 01/10/2023] Open
Abstract
Bacillus amyloliquefaciens YN201732 is an endophytic bacteria with high biocontrol efficiency and broad-spectrum antimicrobial activities. In order to clarify the main active ingredients and their antifungal mechanisms against powdery mildew of tobacco, this study is focused on lipopeptide obtained through acid precipitation and organic solvent extraction. HPLC and LCMS-IT-TOF were used to separate and identify antimicrobial lipopeptides. Findings revealed that bacillomycin D plays an important role against surrogate fungal pathogen Fusarium solani. Synthetic pathways of sfp, bacillomycin D, and fengycin were separately disrupted. The sfp gene knockout mutant B. amyloliquefaciens YN201732M1 only showed minor antagonistic activity against F. solani. While Erysiphe cichoracearum spore germination was inhibited and pot experiments displayed a significant decrease in tobacco powdery mildew. The spore inhibition rate of YN201732M1 was only 30.29%, and the pot experiment control effect was less than 37.39%, which was significantly lower than that of the wild type. The inhibitory effect of mutant YN201732M2 (deficient in the production of bacillomycin D) and mutant YN201732M3 (deficient in the production of fengycin) on the spore germination of E. cichoracearum were 50.22% and 53.06%, respectively, suggesting that both fengycin and bacillomycin D had potential effects on spore germination of powdery mildew. Interestingly, in a greenhouse assay, both B. amyloliquefaciens YN201732M2 and YN201732M3 mutants displayed less of a control effect on tobacco powdery mildew than wild type. The results from in vitro, spore germination, and greenhouse-pot studies demonstrated that antimicrobial lipopeptides especially bacillomycin D and fengycin may contribute to the prevention and control of tobacco powdery mildew. In addition, gene mutation related to lipopeptide synthesis can also affect the biofilm formation of strains.
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Affiliation(s)
- Rong Jiao
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, China.,Science and Technology Division, Yuxi Normal University, Yuxi, China
| | | | - Pengfei He
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Shahzad Munir
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Xingyu Li
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Yixin Wu
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Junwei Wang
- Hongta Tobacco (Group) Co., Ltd., Yuxi, China
| | - Mengyuan Xia
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Pengbo He
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Ge Wang
- Faculty of Tobacco Science, Yunnan Agricultural University, Kunming, China
| | - Huanwen Yang
- Faculty of Tobacco Science, Yunnan Agricultural University, Kunming, China
| | - Samantha C Karunarathna
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China
| | - Yan Xie
- Qujing Tobacco Co., Ltd., Qujing, China
| | - Yueqiu He
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, China
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15
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Gloag ES, Fabbri S, Wozniak DJ, Stoodley P. Biofilm mechanics: Implications in infection and survival. Biofilm 2020; 2:100017. [PMID: 33447803 PMCID: PMC7798440 DOI: 10.1016/j.bioflm.2019.100017] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/06/2019] [Accepted: 12/09/2019] [Indexed: 12/18/2022] Open
Abstract
It has long been recognized that biofilms are viscoelastic materials, however the importance of this attribute to the survival and persistence of these microbial communities is yet to be fully realized. Here we review work, which focuses on understanding biofilm mechanics and put this knowledge in the context of biofilm survival, particularly for biofilm-associated infections. We note that biofilm viscoelasticity may be an evolved property of these communities, and that the production of multiple extracellular polymeric slime components may be a way to ensure the development of biofilms with complex viscoelastic properties. We discuss viscoelasticity facilitating biofilm survival in the context of promoting the formation of larger and stronger biofilms when exposed to shear forces, promoting fluid-like behavior of the biofilm and subsequent biofilm expansion by viscous flow, and enabling resistance to both mechanical and chemical methods of clearance. We conclude that biofilm viscoelasticity contributes to the virulence of chronic biofilm infections.
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Affiliation(s)
- Erin S. Gloag
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, 43210, USA
| | | | - Daniel J. Wozniak
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, 43210, USA
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
| | - Paul Stoodley
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, 43210, USA
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
- Department of Orthopedics, The Ohio State University, Columbus, OH, 43210, USA
- National Biofilm Innovation Centre (NBIC) and National Centre for Advanced Tribology at Southampton (nCATS), University of Southampton, Southampton, SO17 1BJ, UK
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16
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Cont A, Rossy T, Al-Mayyah Z, Persat A. Biofilms deform soft surfaces and disrupt epithelia. eLife 2020; 9:56533. [PMID: 33025904 PMCID: PMC7556879 DOI: 10.7554/elife.56533] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 08/23/2020] [Indexed: 12/12/2022] Open
Abstract
During chronic infections and in microbiota, bacteria predominantly colonize their hosts as multicellular structures called biofilms. A common assumption is that biofilms exclusively interact with their hosts biochemically. However, the contributions of mechanics, while being central to the process of biofilm formation, have been overlooked as a factor influencing host physiology. Specifically, how biofilms form on soft, tissue-like materials remains unknown. Here, we show that biofilms of the pathogens Vibrio cholerae and Pseudomonas aeruginosa can induce large deformations of soft synthetic hydrogels. Biofilms buildup internal mechanical stress as single cells grow within the elastic matrix. By combining mechanical measurements and mutations in matrix components, we found that biofilms deform by buckling, and that adhesion transmits these forces to their substrates. Finally, we demonstrate that V. cholerae biofilms can generate sufficient mechanical stress to deform and even disrupt soft epithelial cell monolayers, suggesting a mechanical mode of infection.
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Affiliation(s)
- Alice Cont
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Tamara Rossy
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Zainebe Al-Mayyah
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alexandre Persat
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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17
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Mechanomicrobiology: how bacteria sense and respond to forces. Nat Rev Microbiol 2020; 18:227-240. [DOI: 10.1038/s41579-019-0314-2] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2019] [Indexed: 12/26/2022]
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18
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Díaz-Pascual F, Hartmann R, Lempp M, Vidakovic L, Song B, Jeckel H, Thormann KM, Yildiz FH, Dunkel J, Link H, Nadell CD, Drescher K. Breakdown of Vibrio cholerae biofilm architecture induced by antibiotics disrupts community barrier function. Nat Microbiol 2019; 4:2136-2145. [PMID: 31659297 PMCID: PMC6881181 DOI: 10.1038/s41564-019-0579-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 09/06/2019] [Indexed: 01/01/2023]
Abstract
Bacterial cells in nature are frequently exposed to changes in their chemical environment1,2. The response mechanisms of isolated cells to such stimuli have been investigated in great detail. By contrast, little is known about the emergent multicellular responses to environmental changes, such as antibiotic exposure3-7, which may hold the key to understanding the structure and functions of the most common type of bacterial communities: biofilms. Here, by monitoring all individual cells in Vibrio cholerae biofilms during exposure to antibiotics that are commonly administered for cholera infections, we found that translational inhibitors cause strong effects on cell size and shape, as well as biofilm architectural properties. We identified that single-cell-level responses result from the metabolic consequences of inhibition of protein synthesis and that the community-level responses result from an interplay of matrix composition, matrix dissociation and mechanical interactions between cells. We further observed that the antibiotic-induced changes in biofilm architecture have substantial effects on biofilm population dynamics and community assembly by enabling invasion of biofilms by bacteriophages and intruder cells of different species. These mechanistic causes and ecological consequences of biofilm exposure to antibiotics are an important step towards understanding collective bacterial responses to environmental changes, with implications for the effects of antimicrobial therapy on the ecological succession of biofilm communities.
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Affiliation(s)
| | - Raimo Hartmann
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Martin Lempp
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lucia Vidakovic
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Boya Song
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hannah Jeckel
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Kai M Thormann
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hannes Link
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Synmikro Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Carey D Nadell
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Biological Sciences, Dartmouth College, Hanover, USA
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Department of Physics, Philipps-Universität Marburg, Marburg, Germany.
- Synmikro Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany.
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19
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Charlton SGV, White MA, Jana S, Eland LE, Jayathilake PG, Burgess JG, Chen J, Wipat A, Curtis TP. Regulating, Measuring, and Modeling the Viscoelasticity of Bacterial Biofilms. J Bacteriol 2019; 201:e00101-19. [PMID: 31182499 PMCID: PMC6707926 DOI: 10.1128/jb.00101-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Biofilms occur in a broad range of environments under heterogeneous physicochemical conditions, such as in bioremediation plants, on surfaces of biomedical implants, and in the lungs of cystic fibrosis patients. In these scenarios, biofilms are subjected to shear forces, but the mechanical integrity of these aggregates often prevents their disruption or dispersal. Biofilms' physical robustness is the result of the multiple biopolymers secreted by constituent microbial cells which are also responsible for numerous biological functions. A better understanding of the role of these biopolymers and their response to dynamic forces is therefore crucial for understanding the interplay between biofilm structure and function. In this paper, we review experimental techniques in rheology, which help quantify the viscoelasticity of biofilms, and modeling approaches from soft matter physics that can assist our understanding of the rheological properties. We describe how these methods could be combined with synthetic biology approaches to control and investigate the effects of secreted polymers on the physical properties of biofilms. We argue that without an integrated approach of the three disciplines, the links between genetics, composition, and interaction of matrix biopolymers and the viscoelastic properties of biofilms will be much harder to uncover.
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Affiliation(s)
- Samuel G V Charlton
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael A White
- Interdisciplinary Computing & Complex BioSystems Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Saikat Jana
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lucy E Eland
- Interdisciplinary Computing & Complex BioSystems Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - J Grant Burgess
- School of Natural & Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jinju Chen
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Anil Wipat
- Interdisciplinary Computing & Complex BioSystems Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Thomas P Curtis
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
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20
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WANG XIAOLING, WANG ZHAOCAN, SHEN XING, KONG YUHAO, ZHAO HUI, YAN XIAOQIANG. STUDYING THE INTERNAL STRESS HETEROGENEITY OF THE GROWING BIOFILM BY THE MICROPILLAR DEFORMATION OF THE GROWING SUBSTRATE. J MECH MED BIOL 2019. [DOI: 10.1142/s0219519419500702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The bacterial biofilm is a microbial community in which bacteria are embedded in the extracellular matrix and can also be used as a solid composite. It was found that internal stresses are generated during pellicle growth, which exists between the air and the liquid. But we do not know if there is the internal stress in the biofilm, which exists between the air and the solid, and how does the internal stress evolve and distribute in the growing biofilm. So, in this paper, we make the growing substrate into the micropillar array to grow biofilms, each micropillar has the deformation due to the growing heterogeneity of the biofilm around the micropillar, and we can get the internal stress by measuring each micropillar’s deformation. First, we find that the direction of the internal stress is approximately along the biofilm expansion at the early time, colonies are formed in the biofilm at the later time, which cause the internal stress locally along the expansion of the colony. Second, the internal stress is proportional to the biofilm thickness. Finally, we find that the matrix producing cells contribute more the internal stress, and the internal stress evolving is closely related to the secretion of the extracellular matrix. Form our work, we obtain the distribution of the internal stress direction, we also can use the biofilm thickness, which is easy to measure, express the internal stress approximately, by doing so, we can further study other phenomena of biofilms, such as self-healing and mechanical resistance.
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Affiliation(s)
- XIAOLING WANG
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
- School of Engineering and Applied Sciences, Harvard University, 02138 Cambridge MA, USA
| | - ZHAOCAN WANG
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - XING SHEN
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - YUHAO KONG
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - HUI ZHAO
- State Key Laboratory of Computer Science, Institute of Software, University of Chinese Academy of Sciences, Beijing 100083, P. R. China
| | - XIAOQIANG YAN
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
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21
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Zhang C, Li B, Tang JY, Wang XL, Qin Z, Feng XQ. Experimental and theoretical studies on the morphogenesis of bacterial biofilms. SOFT MATTER 2017; 13:7389-7397. [PMID: 28951912 DOI: 10.1039/c7sm01593c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Biofilm morphogenesis not only reflects the physiological state of bacteria but also serves as a strategy to sustain bacterial survival. In this paper, we take the Bacillus subtilis colony as a model system to explore the morphomechanics of growing biofilms confined in a defined geometry. We find that the growth-induced stresses may drive the occurrence of both surface wrinkling and interface delamination in the biofilm, leading to the formation of a labyrinthine network on its surface. The wrinkles are perpendicular to the boundary of the constraint region. The variation in the surface undulations is attributed to the spatial stress field, which is isotropic in the inner regime but anisotropic in the vicinity of the boundary. Our experiments show that the directional surface wrinkles can confer biofilms with anisotropic wetting properties. This study not only highlights the role of mechanics in sculpturing organisms within the morphogenetic context but also suggests a promising route toward desired surfaces at the interface between synthetic biology and materials sciences.
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Affiliation(s)
- Cheng Zhang
- Center for Nano and Micro Mechanics, Tsinghua University, Beijing, 100084, China.
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22
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Even C, Marlière C, Ghigo JM, Allain JM, Marcellan A, Raspaud E. Recent advances in studying single bacteria and biofilm mechanics. Adv Colloid Interface Sci 2017; 247:573-588. [PMID: 28754382 DOI: 10.1016/j.cis.2017.07.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/18/2017] [Accepted: 07/18/2017] [Indexed: 12/15/2022]
Abstract
Bacterial biofilms correspond to surface-associated bacterial communities embedded in hydrogel-like matrix, in which high cell density, reduced diffusion and physico-chemical heterogeneity play a protective role and induce novel behaviors. In this review, we present recent advances on the understanding of how bacterial mechanical properties, from single cell to high-cell density community, determine biofilm tri-dimensional growth and eventual dispersion and we attempt to draw a parallel between these properties and the mechanical properties of other well-studied hydrogels and living systems.
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23
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Raab N, Bachelet I. Resolving biofilm topography by native scanning electron microscopy. J Biol Methods 2017; 4:e70. [PMID: 31453228 PMCID: PMC6706123 DOI: 10.14440/jbm.2017.173] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/06/2017] [Accepted: 02/27/2017] [Indexed: 01/01/2023] Open
Abstract
Scanning electron microscopy (SEM) is a powerful tool for structural analysis, but it requires biological samples to undergo lengthy, chemically-complex multi-step preparation procedures, arguably altering some features in the sample. Here we report an ultra-rapid and chemical-free technique for visualizing bacterial biofilms at their native state. Our technique minimizes the time interval from culture to imaging to approximately 20 min, while producing high-resolution images that enable the detection of a variety of topographic features such as bacterial chains, and resolving cells from matrix. We analyzed images obtained from Bacillus subtilis biofilms, demonstrate the usefulness of this technique for multiple types of image analysis, and discuss its potential to be improved and adapted to other types of biological samples.
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Affiliation(s)
- Neta Raab
- Augmanity, Rehovot, Israel.,Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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24
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Tallawi M, Opitz M, Lieleg O. Modulation of the mechanical properties of bacterial biofilms in response to environmental challenges. Biomater Sci 2017; 5:887-900. [DOI: 10.1039/c6bm00832a] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In this review, we highlight recent research on the relationship between biofilm matrix composition, biofilm mechanics and environmental stimuli.
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Affiliation(s)
- Marwa Tallawi
- Department of Mechanical Engineering and Munich School of Bioengineering
- Technische Universität München
- Garching
- Germany
| | - Madeleine Opitz
- Center for NanoScience
- Faculty of Physics
- Ludwig-Maximilians-Universität München
- Munich
- Germany
| | - Oliver Lieleg
- Department of Mechanical Engineering and Munich School of Bioengineering
- Technische Universität München
- Garching
- Germany
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25
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Koo H, Yamada KM. Dynamic cell-matrix interactions modulate microbial biofilm and tissue 3D microenvironments. Curr Opin Cell Biol 2016; 42:102-112. [PMID: 27257751 PMCID: PMC5064909 DOI: 10.1016/j.ceb.2016.05.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 05/07/2016] [Accepted: 05/10/2016] [Indexed: 01/22/2023]
Abstract
Microbial biofilms and most eukaryotic tissues consist of cells embedded in a three-dimensional extracellular matrix. This matrix serves as a scaffold for cell adhesion and a dynamic milieu that provides varying chemical and physical signals to the cells. Besides a vast array of specific molecular components, an extracellular matrix can provide locally heterogeneous microenvironments differing in porosity/diffusion, stiffness, pH, oxygen and metabolites or nutrient levels. Mechanisms of matrix formation, mechanosensing, matrix remodeling, and modulation of cell-cell or cell-matrix interactions and dispersal are being revealed. This perspective article aims to identify such concepts from the fields of biofilm or eukaryotic matrix biology relevant to the other field to help stimulate new questions, approaches, and insights.
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Affiliation(s)
- Hyun Koo
- Biofilm Research Labs, Levy Center for Oral Health, Department of Orthodontics and Divisions of Pediatric Dentistry & Community Oral Health, School of Dental Medicine, University of Pennsylvania, PA 19104, USA.
| | - Kenneth M Yamada
- Laboratory of Cell and Developmental Biology, Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
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26
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Chew SC, Kundukad B, Teh WK, Doyle P, Yang L, Rice SA, Kjelleberg S. Mechanical signatures of microbial biofilms in micropillar-embedded growth chambers. SOFT MATTER 2016; 12:5224-5232. [PMID: 27191395 DOI: 10.1039/c5sm02755a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Biofilms are surface-attached communities of microorganisms embedded in an extracellular matrix and are essential for the cycling of organic matter in natural and engineered environments. They are also the leading cause of many infections, for example, those associated with chronic wounds and implanted medical devices. The extracellular matrix is a key biofilm component that determines its architecture and defines its physical properties. Herein, we used growth chambers embedded with micropillars to study the net mechanical forces (differential pressure) exerted during biofilm formation in situ. Pressure from the biofilm is transferred to the micropillars via the extracellular matrix, and reduction of major matrix components decreases the magnitude of micropillar deflections. The spatial arrangement of micropillar deflections caused by pressure differences in the different biofilm strains may potentially be used as mechanical signatures for biofilm characterization. Hence, we submit that micropillar-embedded growth chambers provide insights into the mechanical properties and dynamics of the biofilm and its matrix.
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Affiliation(s)
- S C Chew
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore.
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27
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Hollenbeck EC, Douarche C, Allain JM, Roger P, Regeard C, Cegelski L, Fuller GG, Raspaud E. Mechanical Behavior of a Bacillus subtilis Pellicle. J Phys Chem B 2016; 120:6080-8. [PMID: 27046510 DOI: 10.1021/acs.jpcb.6b02074] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Bacterial biofilms consist of a complex network of biopolymers embedded with microorganisms, and together these components form a physically robust structure that enables bacteria to grow in a protected environment. This structure can help unwanted biofilms persist in situations ranging from chronic infection to the biofouling of industrial equipment, but under certain circumstances it can allow the biofilm to disperse and colonize new niches. Mechanical properties are therefore a key aspect of biofilm life. In light of the recently discovered growth-induced compressive stress present within a biofilm, we studied the mechanical behavior of Bacillus subtilis pellicles, or biofilms at the air-liquid interface, and tracked simultaneously the force response and macroscopic structural changes during elongational deformations. We observed that pellicles behaved viscoelastically in response to small deformations, such that the growth-induced compressive stress was still present, and viscoplastically at large deformations, when the pellicles were under tension. In addition, by using particle imaging velocimetry we found that the pellicle deformations were nonaffine, indicating heterogeneous mechanical properties with the pellicle being more pliable near attachment surfaces. Overall, our results indicate that we must consider not only the viscoelastic but also the viscoplastic and mechanically heterogeneous nature of these structures to understand biofilm dispersal and removal.
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Affiliation(s)
- Emily C Hollenbeck
- Department of Chemical Engineering, Stanford University , Stanford, California 94305, United States
| | - Carine Douarche
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris-Saclay , Orsay, France
| | - Jean-Marc Allain
- Laboratoire de Mécanique des Solides, École Polytechnique, CNRS, Université Paris-Saclay , Palaiseau, France
| | - Philippe Roger
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS, Université Paris-Sud, Université Paris-Saclay , Orsay, France
| | - Christophe Regeard
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay , Gif sur Yvette, France
| | - Lynette Cegelski
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Gerald G Fuller
- Department of Chemical Engineering, Stanford University , Stanford, California 94305, United States
| | - Eric Raspaud
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris-Saclay , Orsay, France
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