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Ma T, Rothschild J, Halabeya F, Zilman A, Milstein JN. Mechanics limits ecological diversity and promotes heterogeneity in confined bacterial communities. Proc Natl Acad Sci U S A 2024; 121:e2322321121. [PMID: 38728226 PMCID: PMC11098131 DOI: 10.1073/pnas.2322321121] [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: 12/26/2023] [Accepted: 04/06/2024] [Indexed: 05/12/2024] Open
Abstract
Multispecies bacterial populations often inhabit confined and densely packed environments where spatial competition determines the ecological diversity of the community. However, the role of mechanical interactions in shaping the ecology is still poorly understood. Here, we study a model system consisting of two populations of nonmotile Escherichia coli bacteria competing within open, monolayer microchannels. The competitive dynamics is observed to be biphasic: After seeding, either one strain rapidly fixates or both strains orient into spatially stratified, stable communities. We find that mechanical interactions with other cells and local spatial constraints influence the resulting community ecology in unexpected ways, severely limiting the overall diversity of the communities while simultaneously allowing for the establishment of stable, heterogeneous populations of bacteria displaying disparate growth rates. Surprisingly, the populations have a high probability of coexisting even when one strain has a significant growth advantage. A more coccus morphology is shown to provide a selective advantage, but agent-based simulations indicate this is due to hydrodynamic and adhesion effects within the microchannel and not from breaking of the nematic ordering. Our observations are qualitatively reproduced by a simple Pólya urn model, which suggests the generality of our findings for confined population dynamics and highlights the importance of early colonization conditions on the resulting diversity and ecology of bacterial communities. These results provide fundamental insights into the determinants of community diversity in dense confined ecosystems where spatial exclusion is central to competition as in organized biofilms or intestinal crypts.
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Affiliation(s)
- Tianyi Ma
- Department of Physics, University of Toronto, Toronto, ONM5S 3J1, Canada
- Department of Chemical and Physical Sciences, University of Toronto, Mississauga, ONL5L 1C6, Canada
| | - Jeremy Rothschild
- Department of Physics, University of Toronto, Toronto, ONM5S 3J1, Canada
| | - Faisal Halabeya
- Department of Physics, University of Toronto, Toronto, ONM5S 3J1, Canada
- Department of Chemical and Physical Sciences, University of Toronto, Mississauga, ONL5L 1C6, Canada
| | - Anton Zilman
- Department of Physics, University of Toronto, Toronto, ONM5S 3J1, Canada
| | - Joshua N. Milstein
- Department of Physics, University of Toronto, Toronto, ONM5S 3J1, Canada
- Department of Chemical and Physical Sciences, University of Toronto, Mississauga, ONL5L 1C6, Canada
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2
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Khandoori R, Mondal K, Ghosh P. Resource limitation and population fluctuation drive spatiotemporal order in microbial communities. SOFT MATTER 2024; 20:3823-3835. [PMID: 38647378 DOI: 10.1039/d4sm00066h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Microbial communities display complex spatiotemporal behaviors leading to spatially-structured and ordered organization driven by species interactions and environmental factors. Resource availability plays a pivotal role in shaping the dynamics of bacterial colonies. In this study, we delve into the intricate interplay between resource limitation and the emergent properties of a growing colony of two visually distinct bacterial strains having similar growth and mechanical properties. Employing an agent-based modeling and computer simulations, we analyze the resource-driven effect on segregation and sectoring, cell length regulation and nematic ordering within a growing colony. We introduce a dimensionless parameter referred to as the active layer thickness, derived from nutrient diffusion equations, indicating effective population participation due to local resource availability. Our results reveal that lower values of active layer thickness arising from decreased resource abundance lead to rougher colony fronts, fostering heightened population fluctuations within the colony and faster spatial genetic diversity loss. Our temporal analyses unveil the dynamics of mean cell length and fluctuations, showcasing how initial disturbances evolve as colonies are exposed to nutrients and subsequently settle. Furthermore, examining microscopic details, we find that lower resource levels yield diverse cell lengths and enhanced nematic ordering, driven by the increased prevalence of longer rod-shaped cells. Our investigation sheds light on the multifaceted relationship between resource constraints and bacterial colony dynamics, revealing insights into their spatiotemporal organization.
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Affiliation(s)
- Rohit Khandoori
- School of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India.
| | - Kaustav Mondal
- Center for High-Performance Computing, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India
| | - Pushpita Ghosh
- School of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India.
- Center for High-Performance Computing, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India
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3
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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.
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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.
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4
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Maleki F, Najafi A. Instabilities in a growing system of active particles: scalar and vectorial systems. SOFT MATTER 2023; 19:8157-8163. [PMID: 37850327 DOI: 10.1039/d3sm00880k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
The physics of micron-scale biological colonies usually benefits from different out-of-equilibrium sources. In bacterial colonies and cellular tissues, the growth process is among the important active sources that determine the dynamics. In this article, we study the generic dynamical instabilities associated with the growth phenomena that may arise in both scalar and vectorial systems. In vectorial systems, where the rotational degrees of particles play a role, a phenomenological growth-mediated torque can affect the rotational dynamics of individual particles. We show that such a growth-mediated torque can result in active traveling waves in the bulk of a growing system. In addition to the bulk properties, we analyze the instabilities in the shape of growing interfaces in both scalar and vectorial systems.
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Affiliation(s)
- Forouh Maleki
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
| | - Ali Najafi
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
- Research Center for Basic Sciences & Modern Technologies (RBST), Institute for Advanced Studies in Basic Sciences, Zanjan, Iran.
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5
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Isensee J, Hupe L, Golestanian R, Bittihn P. Stress anisotropy in confined populations of growing rods. J R Soc Interface 2022; 19:20220512. [PMID: 36349447 PMCID: PMC9653230 DOI: 10.1098/rsif.2022.0512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/18/2022] [Indexed: 11/10/2022] Open
Abstract
A central feature of living matter is its ability to grow and multiply. The mechanical activity associated with growth produces both macroscopic flows shaped by confinement, and striking self-organization phenomena, such as orientational order and alignment, which are particularly prominent in populations of rod-shaped bacteria due to their nematic properties. However, how active stresses, passive mechanical interactions and flow-induced effects interact to give rise to the observed global alignment patterns remains elusive. Here, we study in silico colonies of growing rod-shaped particles of different aspect ratios confined in channel-like geometries. A spatially resolved analysis of the stress tensor reveals a strong relationship between near-perfect alignment and an inversion of stress anisotropy for particles with large length-to-width ratios. We show that, in quantitative agreement with an asymptotic theory, strong alignment can lead to a decoupling of active and passive stresses parallel and perpendicular to the direction of growth, respectively. We demonstrate the robustness of these effects in a geometry that provides less restrictive confinement and introduces natural perturbations in alignment. Our results illustrate the complexity arising from the inherent coupling between nematic order and active stresses in growing active matter, which is modulated by geometric and configurational constraints due to confinement.
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Affiliation(s)
- Jonas Isensee
- Max Planck Institute for Dynamics and Self-Organization, Göttingen 37077, Germany
- Institute for the Dynamics of Complex Systems, Göttingen University, Göttingen 37077, Germany
| | - Lukas Hupe
- Max Planck Institute for Dynamics and Self-Organization, Göttingen 37077, Germany
- Institute for the Dynamics of Complex Systems, Göttingen University, Göttingen 37077, Germany
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization, Göttingen 37077, Germany
- Institute for the Dynamics of Complex Systems, Göttingen University, Göttingen 37077, Germany
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Philip Bittihn
- Max Planck Institute for Dynamics and Self-Organization, Göttingen 37077, Germany
- Institute for the Dynamics of Complex Systems, Göttingen University, Göttingen 37077, Germany
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6
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Tsai HF, Carlson DW, Koldaeva A, Pigolotti S, Shen AQ. Optimization and Fabrication of Multi-Level Microchannels for Long-Term Imaging of Bacterial Growth and Expansion. MICROMACHINES 2022; 13:mi13040576. [PMID: 35457881 PMCID: PMC9028424 DOI: 10.3390/mi13040576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 02/01/2023]
Abstract
Bacteria are unicellular organisms whose length is usually around a few micrometers. Advances in microfabrication techniques have enabled the design and implementation of microdevices to confine and observe bacterial colony growth. Microstructures hosting the bacteria and microchannels for nutrient perfusion usually require separate microfabrication procedures due to different feature size requirements. This fact increases the complexity of device integration and assembly process. Furthermore, long-term imaging of bacterial dynamics over tens of hours requires stability in the microscope focusing mechanism to ensure less than one-micron drift in the focal axis. In this work, we design and fabricate an integrated multi-level, hydrodynamically-optimized microfluidic chip to study long-term Escherichia coli population dynamics in confined microchannels. Reliable long-term microscopy imaging and analysis has been limited by focus drifting and ghost effect, probably caused by the shear viscosity changes of aging microscopy immersion oil. By selecting a microscopy immersion oil with the most stable viscosity, we demonstrate successful captures of focally stable time-lapse bacterial images for ≥72 h. Our fabrication and imaging methodology should be applicable to other single-cell studies requiring long-term imaging.
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Affiliation(s)
- Hsieh-Fu Tsai
- Micro/Bio/Nanofluidics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan;
- Department of Biomedical Engineering, Chang Gung University, Taoyuan 333, Taiwan
- Correspondence: (H.-F.T.); (A.Q.S.); Tel.: +886-3-2118800 (ext. 3079) (H.-F.T.)
| | - Daniel W. Carlson
- Micro/Bio/Nanofluidics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan;
| | - Anzhelika Koldaeva
- Biological Complexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan; (A.K.); (S.P.)
| | - Simone Pigolotti
- Biological Complexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan; (A.K.); (S.P.)
| | - Amy Q. Shen
- Micro/Bio/Nanofluidics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan;
- Correspondence: (H.-F.T.); (A.Q.S.); Tel.: +886-3-2118800 (ext. 3079) (H.-F.T.)
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7
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Abstract
Many microbial populations proliferate in small channels. In such environments, reproducing cells organize in parallel lanes. Reproducing cells shift these lanes, potentially expelling other cells from the channel. In this paper, we combine theory and experiments to understand how these dynamics affects the diversity of a microbial population. We theoretically predict that genetic diversity is quickly lost along lanes of cells. Our experiments confirm that a population of proliferating Escherichia coli in a microchannel organizes into lanes of genetically identical cells within a few generations. Our findings elucidate the effect of lane formation on populations evolution, with potential applications ranging from microbial ecology in soil to dynamics of epithelial tissues in higher organisms. Spatial constraints, such as rigid barriers, affect the dynamics of cell populations, potentially altering the course of natural evolution. In this paper, we investigate the population genetics of Escherichia coli proliferating in microchannels with open ends. Our analysis is based on a population model, in which reproducing cells shift entire lanes of cells toward the open ends of the channel. The model predicts that diversity is lost very rapidly within lanes but at a much slower pace among lanes. As a consequence, two mixed, neutral E. coli strains competing in a microchannel must organize into an ordered regular stripe pattern in the course of a few generations. These predictions are in quantitative agreement with our experiments. We also demonstrate that random mutations appearing in the middle of the channel are much more likely to reach fixation than those occurring elsewhere. Our results illustrate fundamental mechanisms of microbial evolution in spatially confined space.
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8
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You Z, Pearce DJG, Giomi L. Confinement-induced self-organization in growing bacterial colonies. SCIENCE ADVANCES 2021; 7:eabc8685. [PMID: 33523940 PMCID: PMC10670964 DOI: 10.1126/sciadv.abc8685] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
We investigate the emergence of global alignment in colonies of dividing rod-shaped cells under confinement. Using molecular dynamics simulations and continuous modeling, we demonstrate that geometrical anisotropies in the confining environment give rise to an imbalance in the normal stresses, which, in turn, drives a collective rearrangement of the cells. This behavior crucially relies on the colony's solid-like mechanical response at short time scales and can be recovered within the framework of active hydrodynamics upon modeling bacterial colonies as growing viscoelastic gels characterized by Maxwell-like stress relaxation.
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Affiliation(s)
- Zhihong You
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
- Instituut-Lorentz, Universiteit Leiden, P.O. Box 9506, 2300 RA Leiden, Netherlands
| | - Daniel J G Pearce
- Department of Theoretical Physics, Université de Genève, 1205 Genève, Switzerland
| | - Luca Giomi
- Instituut-Lorentz, Universiteit Leiden, P.O. Box 9506, 2300 RA Leiden, Netherlands.
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9
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Wang H, Ceylan Koydemir H, Qiu Y, Bai B, Zhang Y, Jin Y, Tok S, Yilmaz EC, Gumustekin E, Rivenson Y, Ozcan A. Early detection and classification of live bacteria using time-lapse coherent imaging and deep learning. LIGHT, SCIENCE & APPLICATIONS 2020; 9:118. [PMID: 32685139 PMCID: PMC7351775 DOI: 10.1038/s41377-020-00358-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/20/2020] [Accepted: 06/22/2020] [Indexed: 05/06/2023]
Abstract
Early identification of pathogenic bacteria in food, water, and bodily fluids is very important and yet challenging, owing to sample complexities and large sample volumes that need to be rapidly screened. Existing screening methods based on plate counting or molecular analysis present various tradeoffs with regard to the detection time, accuracy/sensitivity, cost, and sample preparation complexity. Here, we present a computational live bacteria detection system that periodically captures coherent microscopy images of bacterial growth inside a 60-mm-diameter agar plate and analyses these time-lapsed holograms using deep neural networks for the rapid detection of bacterial growth and the classification of the corresponding species. The performance of our system was demonstrated by the rapid detection of Escherichia coli and total coliform bacteria (i.e., Klebsiella aerogenes and Klebsiella pneumoniae subsp. pneumoniae) in water samples, shortening the detection time by >12 h compared to the Environmental Protection Agency (EPA)-approved methods. Using the preincubation of samples in growth media, our system achieved a limit of detection (LOD) of ~1 colony forming unit (CFU)/L in ≤9 h of total test time. This platform is highly cost-effective (~$0.6/test) and has high-throughput with a scanning speed of 24 cm2/min over the entire plate surface, making it highly suitable for integration with the existing methods currently used for bacteria detection on agar plates. Powered by deep learning, this automated and cost-effective live bacteria detection platform can be transformative for a wide range of applications in microbiology by significantly reducing the detection time and automating the identification of colonies without labelling or the need for an expert.
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Affiliation(s)
- Hongda Wang
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA 90095 USA
- Bioengineering Department, University of California, Los Angeles, CA 90095 USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095 USA
| | - Hatice Ceylan Koydemir
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA 90095 USA
- Bioengineering Department, University of California, Los Angeles, CA 90095 USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095 USA
| | - Yunzhe Qiu
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA 90095 USA
- Bioengineering Department, University of California, Los Angeles, CA 90095 USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095 USA
| | - Bijie Bai
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA 90095 USA
- Bioengineering Department, University of California, Los Angeles, CA 90095 USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095 USA
| | - Yibo Zhang
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA 90095 USA
- Bioengineering Department, University of California, Los Angeles, CA 90095 USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095 USA
| | - Yiyin Jin
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA 90095 USA
| | - Sabiha Tok
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA 90095 USA
- Bioengineering Department, University of California, Los Angeles, CA 90095 USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095 USA
- Department of Biophysics, Istanbul Medical Faculty, Istanbul University, Istanbul, 22000 Turkey
| | - Enis Cagatay Yilmaz
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA 90095 USA
| | - Esin Gumustekin
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095 USA
| | - Yair Rivenson
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA 90095 USA
- Bioengineering Department, University of California, Los Angeles, CA 90095 USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095 USA
| | - Aydogan Ozcan
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA 90095 USA
- Bioengineering Department, University of California, Los Angeles, CA 90095 USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095 USA
- Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA 90095 USA
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10
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Quantitative Connection between Cell Size and Growth Rate by Phospholipid Metabolism. Cells 2020; 9:cells9020391. [PMID: 32046235 PMCID: PMC7072380 DOI: 10.3390/cells9020391] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 02/04/2020] [Indexed: 11/16/2022] Open
Abstract
The processes involved in cell growth are extremely complicated even for a single cell organism such as Escherichia coli, while the relationship between growth rate and cell size is simple. We aimed to reveal the systematic link between them from the aspect of the genome-scale metabolic network. Since the growth rate reflects metabolic rates of bacteria and the cell size relates to phospholipid synthesis, a part of bacterial metabolic networks, we calculated the cell length from the cardiolipin synthesis rate, where the cardiolipin synthesis reaction is able to represent the phospholipid metabolism of Escherichia coli in the exponential growth phase. Combined with the flux balance analysis, it enables us to predict cell length and to examine the quantitative relationship between cell length and growth rate. By simulating bacteria growing in various nutrient media with the flux balance analysis and calculating the corresponding cell length, we found that the increase of the synthesis rate of phospholipid, the cell width, and the protein fraction in membranes caused the increase of cell length with growth rate. Different tendencies of phospholipid synthesis rate changing with growth rate result in different relationships between cell length and growth rate. The effects of gene deletions on cell size and growth rate are also examined. Knocking out the genes, such as Δ tktA, Δ tktB, Δ yqaB, Δ pgm, and Δ cysQ, affects growth rate largely while affecting cell length slightly. Results of this method are in good agreement with experiments.
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11
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You Z, Pearce DJG, Sengupta A, Giomi L. Mono- to Multilayer Transition in Growing Bacterial Colonies. PHYSICAL REVIEW LETTERS 2019; 123:178001. [PMID: 31702266 DOI: 10.1103/physrevlett.123.178001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 06/20/2019] [Indexed: 06/10/2023]
Abstract
The transition from monolayers to multilayered structures in bacterial colonies is a fundamental step in biofilm development. Observed across different morphotypes and species, this transition is triggered within freely growing bacterial microcolonies comprising a few hundred cells. Using a combination of numerical simulations and analytical modeling, here we demonstrate that this transition originates from the competition between growth-induced in-plane active stresses and vertical restoring forces, due to the cell-substrate interactions. Using a simple chainlike colony of laterally confined cells, we show that the transition sets when individual cells become unstable to rotations; thus it is localized and mechanically deterministic. Asynchronous cell division renders the process stochastic, so that all the critical parameters that control the onset of the transition are continuously distributed random variables. Here we demonstrate that the occurrence of the first division in the colony can be approximated as a Poisson process in the limit of large cell numbers. This allows us to approximately calculate the probability distribution function of the position and time associated with the first extrusion. The rate of such a Poisson process can be identified as the order parameter of the transition, thus highlighting its mixed deterministic-stochastic nature.
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Affiliation(s)
- Zhihong You
- Instituut-Lorentz, Universiteit Leiden, P.O. Box 9506, 2300 RA Leiden, Netherlands
| | - Daniel J G Pearce
- Instituut-Lorentz, Universiteit Leiden, P.O. Box 9506, 2300 RA Leiden, Netherlands
| | - Anupam Sengupta
- Physics and Materials Science Research Unit, University of Luxembourg, 162 A, Avenue de la Faïencerie, Luxembourg City, L-1511 Luxembourg
| | - Luca Giomi
- Instituut-Lorentz, Universiteit Leiden, P.O. Box 9506, 2300 RA Leiden, Netherlands
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12
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Shimaya T, Takeuchi KA. Lane formation and critical coarsening in a model of bacterial competition. Phys Rev E 2019; 99:042403. [PMID: 31108589 DOI: 10.1103/physreve.99.042403] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Indexed: 11/07/2022]
Abstract
We study competition of two nonmotile bacterial strains in a three-dimensional channel numerically and analyze how their configuration evolves in space and time. We construct a lattice model that takes into account self-replication, mutation, and killing of bacteria. When mutation is not significant, the two strains segregate and form stripe patterns along the channel. The formed lanes are gradually rearranged, with increasing length scales in the two-dimensional cross-sectional plane. We characterize it in terms of coarsening and phase ordering in statistical physics. In particular, for the simple model without mutation and killing, we find logarithmically slow coarsening, which is characteristic of the two-dimensional voter model. With mutation and killing, we find a phase transition from a monopolistic phase, in which lanes are formed and coarsened until the system is eventually dominated by one of the two strains, to an equally mixed and disordered phase without lane structure. Critical behavior at the transition point is also studied and compared with the generalized voter class and the Ising class. These results are accounted for by continuum equations, obtained by applying a mean-field approximation along the channel axis. Our findings indicate relevance of critical coarsening of two-dimensional systems in the problem of bacterial competition within anisotropic three-dimensional geometry.
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Affiliation(s)
- Takuro Shimaya
- Department of Physics, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan and Department of Physics, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Kazumasa A Takeuchi
- Department of Physics, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan and Department of Physics, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
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13
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Yu S, Sheats J, Cicuta P, Sclavi B, Cosentino Lagomarsino M, Dorfman KD. Subdiffusion of loci and cytoplasmic particles are different in compressed Escherichia coli cells. Commun Biol 2018; 1:176. [PMID: 30374466 PMCID: PMC6200837 DOI: 10.1038/s42003-018-0185-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 10/03/2018] [Indexed: 12/13/2022] Open
Abstract
The complex physical nature of the bacterial intracellular environment remains largely unknown, and has relevance for key biochemical and biological processes of the cell. Although recent work has addressed the role of non-equilibrium sources of activity and crowding, the consequences of mechanical perturbations are relatively less explored. Here we use a microfabricated valve system to track both fluorescently labeled chromosomal loci and cytoplasmic particles in Escherichia coli cells shortly after applying a compressive force, observing the response on time scales that are too sudden to allow for biochemical response from the cell. Cytoplasmic diffusion slows markedly on compression but the exponent governing the growth of the ensemble-averaged mean-squared displacement of cytoplasmic particles is unaffected. In contrast, the corresponding exponent for DNA loci changes significantly. These results suggest that DNA elasticity and nucleoid organization play a more important role in loci subdiffusion than cytoplasmic viscoelasticity under such short time scales.
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Affiliation(s)
- Shi Yu
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, MN, 55455, USA
- School of Chemical Engineering and Technology, China University of Mining & Technology, Xuzhou, 221116, China
| | - Julian Sheats
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, MN, 55455, USA
| | - Pietro Cicuta
- Cavendish Laboratory, Cambridge University, Cambridge, UK
| | - Bianca Sclavi
- LBPA, UMR 8113 du CNRS, École Normale Supérieure Paris-Saclay, Cachan, France
| | - Marco Cosentino Lagomarsino
- Génophysique/Genomic Physics Group, UMR 7238 CNRS Génomique des Microorganismes, Université Pierre et Marie Curie, 4, Place Jussieu, 75005, Paris, France
- Sorbonne Universités, Université Pierre et Marie Curie, 4 Place Jussieu, Paris, France
- IFOM Institute for Molecular Oncology, Milan, Italy
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, MN, 55455, USA.
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Single-cell microscopy of suspension cultures using a microfluidics-assisted cell screening platform. Nat Protoc 2017; 13:170-194. [PMID: 29266097 DOI: 10.1038/nprot.2017.127] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Studies that rely on fluorescence imaging of nonadherent cells that are cultured in suspension, such as Escherichia coli, are often hampered by trade-offs that must be made between data throughput and imaging resolution. We developed a platform for microfluidics-assisted cell screening (MACS) that overcomes this trade-off by temporarily immobilizing suspension cells within a microfluidics chip. This enables high-throughput and automated single-cell microscopy for a wide range of cell types and sizes. As cells can be rapidly sampled directly from a suspension culture, MACS bypasses the need for sample preparation, and therefore allows measurements without perturbing the native cell physiology. The setup can also be integrated with complex growth chambers, and can be used to enrich or sort the imaged cells. Furthermore, MACS facilitates the visualization of individual cytoplasmic fluorescent proteins (FPs) in E. coli, allowing low-abundance proteins to be counted using standard total internal reflection fluorescence (TIRF) microscopy. Finally, MACS can be used to impart mechanical pressure for assessing the structural integrity of individual cells and their response to mechanical perturbations, or to make cells take up chemicals that otherwise would not pass through the membrane. This protocol describes the assembly of electronic control circuitry, the construction of liquid-handling components and the creation of the MACS microfluidics chip. The operation of MACS is described, and automation software is provided to integrate MACS control with image acquisition. Finally, we provide instructions for extending MACS using an external growth chamber (1 d) and for how to sort rare cells of interest.
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