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Borse F, Kičiatovas D, Kuosmanen T, Vidal M, Cabrera-Vives G, Cairns J, Warringer J, Mustonen V. Quantifying massively parallel microbial growth with spatially mediated interactions. PLoS Comput Biol 2024; 20:e1011585. [PMID: 39038063 PMCID: PMC11293690 DOI: 10.1371/journal.pcbi.1011585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 08/01/2024] [Accepted: 06/19/2024] [Indexed: 07/24/2024] Open
Abstract
Quantitative understanding of microbial growth is an essential prerequisite for successful control of pathogens as well as various biotechnology applications. Even though the growth of cell populations has been extensively studied, microbial growth remains poorly characterised at the spatial level. Indeed, even isogenic populations growing at different locations on solid growth medium typically show significant location-dependent variability in growth. Here we show that this variability can be attributed to the initial physiological states of the populations, the interplay between populations interacting with their local environment and the diffusion of nutrients and energy sources coupling the environments. We further show how the causes of this variability change throughout the growth of a population. We use a dual approach, first applying machine learning regression models to discover that location dominates growth variability at specific times, and, in parallel, developing explicit population growth models to describe this spatial effect. In particular, treating nutrient and energy source concentration as a latent variable allows us to develop a mechanistic resource consumer model that captures growth variability across the shared environment. As a consequence, we are able to determine intrinsic growth parameters for each local population, removing confounders common to location-dependent variability in growth. Importantly, our explicit low-parametric model for the environment paves the way for massively parallel experimentation with configurable spatial niches for testing specific eco-evolutionary hypotheses.
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Affiliation(s)
- Florian Borse
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Dovydas Kičiatovas
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Teemu Kuosmanen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Mabel Vidal
- Department of Computer Science, Universidad de Concepción, Concepción, Chile
| | - Guillermo Cabrera-Vives
- Department of Computer Science, Universidad de Concepción, Concepción, Chile
- Data Science Unit, Universidad de Concepción, Concepción, Chile
| | - Johannes Cairns
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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2
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Haudiquet M, Le Bris J, Nucci A, Bonnin RA, Domingo-Calap P, Rocha EPC, Rendueles O. Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency. Nat Commun 2024; 15:2032. [PMID: 38448399 PMCID: PMC10918111 DOI: 10.1038/s41467-024-46147-5] [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: 05/31/2023] [Accepted: 02/14/2024] [Indexed: 03/08/2024] Open
Abstract
Bacterial evolution is affected by mobile genetic elements like phages and conjugative plasmids, offering new adaptive traits while incurring fitness costs. Their infection is affected by the bacterial capsule. Yet, its importance has been difficult to quantify because of the high diversity of confounding mechanisms in bacterial genomes such as anti-viral systems and surface receptor modifications. Swapping capsule loci between Klebsiella pneumoniae strains allowed us to quantify their impact on plasmid and phage infection independently of genetic background. Capsule swaps systematically invert phage susceptibility, revealing serotypes as key determinants of phage infection. Capsule types also influence conjugation efficiency in both donor and recipient cells, a mechanism shaped by capsule volume and conjugative pilus structure. Comparative genomics confirmed that more permissive serotypes in the lab correspond to the strains acquiring more conjugative plasmids in nature. The least capsule-sensitive pili (F-like) are the most frequent in the species' plasmids, and are the only ones associated with both antibiotic resistance and virulence factors, driving the convergence between virulence and antibiotics resistance in the population. These results show how traits of cellular envelopes define slow and fast lanes of infection by mobile genetic elements, with implications for population dynamics and horizontal gene transfer.
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Affiliation(s)
- Matthieu Haudiquet
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France.
- Ecole Doctoral FIRE-Programme Bettencourt, CRI, Paris, France.
| | - Julie Le Bris
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France
- Sorbonne Université, Collège Doctoral, Ecole Doctorale Complexité du Vivant, 75005, Paris, France
| | - Amandine Nucci
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France
| | - Rémy A Bonnin
- Team Resist UMR1184 Université Paris Saclay, CEA, Inserm, Le Kremlin-Bicêtre, Paris, France
- Service de bactériologie, Hôpital Bicêtre, Université Paris Saclay, AP-HP, Le Kremlin-Bicêtre, Paris, France
- Centre National de Référence Associé de la Résistance aux Antibiotiques, Le Kremlin-Bicêtre, Paris, France
| | - Pilar Domingo-Calap
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, 46980, Paterna, Spain
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France.
| | - Olaya Rendueles
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France.
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3
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Kehila D, Tokuriki N. Measuring differential fitness costs and interactions between genetic cassettes using fluorescent spectrophotometry. Appl Environ Microbiol 2024; 90:e0141923. [PMID: 38299817 PMCID: PMC10880626 DOI: 10.1128/aem.01419-23] [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: 08/28/2023] [Accepted: 12/10/2023] [Indexed: 02/02/2024] Open
Abstract
In this article, we present a method for designing, executing, and analyzing data from a microbial competition experiment. We use fluorescent reporters to label different competing strains and resolve individual growth curves using a fluorescent spectrophotometer. Our comprehensive data analysis pipeline integrates multiple experiments to simultaneously infer sources of variation, extract selection coefficients, and estimate the genetic contributions to fitness for various synthetic genetic cassettes (SGCs). To demonstrate the method, we employ a synthetic biological system based on Escherichia coli. Strains carry 1 of 10 different plasmids and one of three genomically integrated fluorescent markers. All strains are co-cultured to obtain real-time measurements of optical density (total population density) and fluorescence (sub-population densities). We identify challenges in calibrating between fluorescence and density and of fluorescent proteins maturing at different rates. To resolve these issues, we compare two methods of fluorescence calibration and correct for maturation by measuring in vivo maturation times. We provide evidence of genetic interactions occurring between our SGCs and further show how to use our statistical model to test some hypotheses about microbial growth and the costs of protein expression.IMPORTANCEFluorescently labeled co-cultures are becoming increasingly popular. The approach proposed here offers a high standard for experimental design and data analysis to measure selection coefficients and growth rates in competition. Measuring competitive differences is useful in many laboratory studies, allowing for fitness cost-correction of growth rates and ecological interactions and testing hypotheses in synthetic biology. Using time-resolved growth curves, rather than endpoint measurements, for competition assays allows us to construct a detailed scientific model that can be used to ask questions about fine-grained phenomena, such as bacterial growth dynamics, as well as higher-level phenomena, such as the interactions between synthetic cassette expression.
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Affiliation(s)
- Dan Kehila
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
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4
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Eriksen RS, Larsen F, Svenningsen SL, Sneppen K, Mitarai N. The dynamics of phage predation on a microcolony. Biophys J 2024; 123:147-156. [PMID: 38069473 PMCID: PMC10808037 DOI: 10.1016/j.bpj.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 10/23/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
Phage predation is an important factor for controlling the bacterial biomass. At face value, dense microbial habitats are expected to be vulnerable to phage epidemics due to the abundance of fresh hosts immediately next to any infected bacteria. Despite this, the bacterial microcolony is a common habitat for bacteria in nature. Here, we experimentally quantify the fate of microcolonies of Escherichia coli exposed to virulent phage T4. It has been proposed that the outer bacterial layers of the colony will shield the inner layers from the phage invasion and thereby constrain the phage to the colony's surface. We develop a dynamical model that incorporates this shielding mechanism and fit the results with experimental measurements to extract important phage-bacteria interaction parameters. The analysis suggests that, while the shielding mechanism delays phage attack, T4 phage are able to diffuse so deep into the dense bacterial environment that colony-level survival of the bacterial community is challenged.
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Affiliation(s)
- Rasmus Skytte Eriksen
- The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark; Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Frej Larsen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark; Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | | | - Kim Sneppen
- The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Namiko Mitarai
- The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark.
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5
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Kochanowski JA, Carroll B, Asp ME, Kaputa EC, Patteson AE. Bacteria Colonies Modify Their Shear and Compressive Mechanical Properties in Response to Different Growth Substrates. ACS APPLIED BIO MATERIALS 2024. [PMID: 38193703 DOI: 10.1021/acsabm.3c00907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Bacteria build multicellular communities termed biofilms, which are often encased in a self-secreted extracellular matrix that gives the community mechanical strength and protection against harsh chemicals. How bacteria assemble distinct multicellular structures in response to different environmental conditions remains incompletely understood. Here, we investigated the connection between bacteria colony mechanics and the colony growth substrate by measuring the oscillatory shear and compressive rheology of bacteria colonies grown on agar substrates. We found that bacteria colonies modify their own mechanical properties in response to shear and uniaxial compression in a manner that depends on the concentration of agar in their growth substrate. These findings highlight that mechanical interactions between bacteria and their microenvironments are an important element in bacteria colony development, which can aid in developing strategies to disrupt or reduce biofilm growth.
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Affiliation(s)
- Jakub A Kochanowski
- Physics Department and BioInspired Institute, Syracuse University, Syracuse, New York 13210, United States
| | - Bobby Carroll
- Physics Department and BioInspired Institute, Syracuse University, Syracuse, New York 13210, United States
| | - Merrill E Asp
- Physics Department and BioInspired Institute, Syracuse University, Syracuse, New York 13210, United States
| | - Emma C Kaputa
- Physics Department and BioInspired Institute, Syracuse University, Syracuse, New York 13210, United States
| | - Alison E Patteson
- Physics Department and BioInspired Institute, Syracuse University, Syracuse, New York 13210, United States
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6
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García Vázquez A, Mitarai N, Jauffred L. Genetic mixing and demixing on expanding spherical frontiers. ISME COMMUNICATIONS 2024; 4:ycae009. [PMID: 38524760 PMCID: PMC10958774 DOI: 10.1093/ismeco/ycae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 03/26/2024]
Abstract
Genetic fluctuation during range expansion is a key process driving evolution. When a bacterial population is expanding on a 2D surface, random fluctuations in the growth of the pioneers at the front line cause a strong demixing of genotypes. Even when there is no selective advantage, sectors of low genetic diversity are formed. Experimental studies of range expansions in surface-attached colonies of fluorescently labelled micro-organisms have contributed significantly to our understanding of fundamental evolutionary dynamics. However, experimental studies on genetic fluctuations in 3D range expansions have been sparse, despite their importance for tumour or biofilm development. We encapsulated populations of two fluorescent Escherichia coli strains in inoculation droplets (volumes [Formula: see text] nl). The confined ensemble of cells grew when embedded in a hydrogel-with nutrients-and developed 3D colonies with well-defined, sector-like regions. Using confocal laser scanning microscopy, we imaged the development of 3D colonies and the emergence of sectors. We characterized how cell concentration in the inoculation droplet controls sectors, growth rate, and the transition from branched colonies to quasi-spherical colonies. We further analysed how sectors on the surface change over time. We complement these experimental results with a modified 3D Eden growth model. The model in 3D spherical growth predicts a phase, where sectors are merging, followed by a steady increase (constant rate), and the experimentally analysed sectors were consistent with this prediction. Therefore, our results demonstrate qualitative differences between radial (2D) and spherical (3D) range expansions and their importance in gene fixation processes.
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Affiliation(s)
- Alba García Vázquez
- The Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, DK-2100 Copenhagen O, Denmark
| | - Namiko Mitarai
- The Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, DK-2100 Copenhagen O, Denmark
| | - Liselotte Jauffred
- The Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, DK-2100 Copenhagen O, Denmark
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7
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Cordero M, Mitarai N, Jauffred L. Motility mediates satellite formation in confined biofilms. THE ISME JOURNAL 2023; 17:1819-1827. [PMID: 37592064 PMCID: PMC10579341 DOI: 10.1038/s41396-023-01494-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/19/2023]
Abstract
Bacteria have spectacular survival capabilities and can spread in many, vastly different environments. For instance, when pathogenic bacteria infect a host, they expand by proliferation and squeezing through narrow pores and elastic matrices. However, the exact role of surface structures-important for biofilm formation and motility-and matrix density in colony expansion and morphogenesis is still largely unknown. Using confocal laser-scanning microscopy, we show how satellite colonies emerge around Escherichia coli colonies embedded in semi-dense hydrogel in controlled in vitro assays. Using knock-out mutants, we tested how extra-cellular structures, (e.g., exo-polysaccharides, flagella, and fimbria) control this morphology. Moreover, we identify the extra-cellular matrix' density, where this morphology is possible. When paralleled with mathematical modelling, our results suggest that satellite formation allows bacterial communities to spread faster. We anticipate that this strategy is important to speed up expansion in various environments, while retaining the close interactions and protection provided by the community.
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Affiliation(s)
- Mireia Cordero
- The Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, DK-2100, Copenhagen O, Denmark
| | - Namiko Mitarai
- The Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, DK-2100, Copenhagen O, Denmark.
| | - Liselotte Jauffred
- The Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, DK-2100, Copenhagen O, Denmark.
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8
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Palmer BJ, Almgren AS, Johnson CGM, Myers AT, Cannon WR. BMX: Biological modelling and interface exchange. Sci Rep 2023; 13:12235. [PMID: 37507417 PMCID: PMC10382537 DOI: 10.1038/s41598-023-39150-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
High performance computing has a great potential to provide a range of significant benefits for investigating biological systems. These systems often present large modelling problems with many coupled subsystems, such as when studying colonies of bacteria cells. The aim to understand cell colonies has generated substantial interest as they can have strong economic and societal impacts through their roles in in industrial bioreactors and complex community structures, called biofilms, found in clinical settings. Investigating these communities through realistic models can rapidly exceed the capabilities of current serial software. Here, we introduce BMX, a software system developed for the high performance modelling of large cell communities by utilising GPU acceleration. BMX builds upon the AMRex adaptive mesh refinement package to efficiently model cell colony formation under realistic laboratory conditions. Using simple test scenarios with varying nutrient availability, we show that BMX is capable of correctly reproducing observed behavior of bacterial colonies on realistic time scales demonstrating a potential application of high performance computing to colony modelling. The open source software is available from the zenodo repository https://doi.org/10.5281/zenodo.8084270 under the BSD-2-Clause licence.
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Affiliation(s)
- Bruce J Palmer
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Washington, USA
| | - Ann S Almgren
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Connah G M Johnson
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Washington, USA.
| | - Andrew T Myers
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - William R Cannon
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Washington, USA
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9
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Sugianto W, Altin-Yavuzarslan G, Tickman BI, Kiattisewee C, Yuan SF, Brooks SM, Wong J, Alper HS, Nelson A, Carothers JM. Gene expression dynamics in input-responsive engineered living materials programmed for bioproduction. Mater Today Bio 2023; 20:100677. [PMID: 37273790 PMCID: PMC10239009 DOI: 10.1016/j.mtbio.2023.100677] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/14/2023] [Accepted: 05/19/2023] [Indexed: 06/06/2023] Open
Abstract
Engineered living materials (ELMs) fabricated by encapsulating microbes in hydrogels have great potential as bioreactors for sustained bioproduction. While long-term metabolic activity has been demonstrated in these systems, the capacity and dynamics of gene expression over time is not well understood. Thus, we investigate the long-term gene expression dynamics in microbial ELMs constructed using different microbes and hydrogel matrices. Through direct gene expression measurements of engineered E. coli in F127-bisurethane methacrylate (F127-BUM) hydrogels, we show that inducible, input-responsive genetic programs in ELMs can be activated multiple times and maintained for multiple weeks. Interestingly, the encapsulated bacteria sustain inducible gene expression almost 10 times longer than free-floating, planktonic cells. These ELMs exhibit dynamic responsiveness to repeated induction cycles, with up to 97% of the initial gene expression capacity retained following a subsequent induction event. We demonstrate multi-week bioproduction cycling by implementing inducible CRISPR transcriptional activation (CRISPRa) programs that regulate the expression of enzymes in a pteridine biosynthesis pathway. ELMs fabricated from engineered S. cerevisiae in bovine serum albumin (BSA) - polyethylene glycol diacrylate (PEGDA) hydrogels were programmed to express two different proteins, each under the control of a different chemical inducer. We observed scheduled bioproduction switching between betaxanthin pigment molecules and proteinase A in S. cerevisiae ELMs over the course of 27 days under continuous cultivation. Overall, these results suggest that the capacity for long-term genetic expression may be a general property of microbial ELMs. This work establishes approaches for implementing dynamic, input-responsive genetic programs to tailor ELM functions for a wide range of advanced applications.
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Affiliation(s)
- Widianti Sugianto
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, United States
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States
- Center for Synthetic Biology, University of Washington, Seattle, WA, 98195, United States
| | - Gokce Altin-Yavuzarslan
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States
- Department of Chemistry, University of Washington, Seattle, WA, 98195, United States
| | - Benjamin I. Tickman
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, United States
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States
- Center for Synthetic Biology, University of Washington, Seattle, WA, 98195, United States
| | - Cholpisit Kiattisewee
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States
- Center for Synthetic Biology, University of Washington, Seattle, WA, 98195, United States
| | - Shuo-Fu Yuan
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, United States
| | - Sierra M. Brooks
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, United States
| | - Jitkanya Wong
- Department of Chemistry, University of Washington, Seattle, WA, 98195, United States
| | - Hal S. Alper
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, United States
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, United States
| | - Alshakim Nelson
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States
- Department of Chemistry, University of Washington, Seattle, WA, 98195, United States
| | - James M. Carothers
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, United States
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States
- Center for Synthetic Biology, University of Washington, Seattle, WA, 98195, United States
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10
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Nguyen-Le TA, Zhao X, Bachmann M, Ruelens P, de Visser JAGM, Baraban L. High-Throughput Gel Microbeads as Incubators for Bacterial Competition Study. MICROMACHINES 2023; 14:645. [PMID: 36985052 PMCID: PMC10058504 DOI: 10.3390/mi14030645] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
Bacteria primarily live in structured environments, such as colonies and biofilms, attached to surfaces or growing within soft tissues. They are engaged in local competitive and cooperative interactions impacting our health and well-being, for example, by affecting population-level drug resistance. Our knowledge of bacterial competition and cooperation within soft matrices is incomplete, partly because we lack high-throughput tools to quantitatively study their interactions. Here, we introduce a method to generate a large amount of agarose microbeads that mimic the natural culture conditions experienced by bacteria to co-encapsulate two strains of fluorescence-labeled Escherichia coli. Focusing specifically on low bacterial inoculum (1-100 cells/capsule), we demonstrate a study on the formation of colonies of both strains within these 3D scaffolds and follow their growth kinetics and interaction using fluorescence microscopy in highly replicated experiments. We confirmed that the average final colony size is inversely proportional to the inoculum size in this semi-solid environment as a result of limited available resources. Furthermore, the colony shape and fluorescence intensity per colony are distinctly different in monoculture and co-culture. The experimental observations in mono- and co-culture are compared with predictions from a simple growth model. We suggest that our high throughput and small footprint microbead system is an excellent platform for future investigation of competitive and cooperative interactions in bacterial communities under diverse conditions, including antibiotics stress.
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Affiliation(s)
- Trang Anh Nguyen-Le
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), 01328 Dresden, Germany
| | - Xinne Zhao
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), 01328 Dresden, Germany
| | - Michael Bachmann
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), 01328 Dresden, Germany
- Tumor Immunology, University Cancer Center (UCC), University Hospital Carl Gustav Carus Dresden, Technische Universität Dresden, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 01309 Dresden, Germany
| | - Philip Ruelens
- Department of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - J. Arjan G. M. de Visser
- Department of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Larysa Baraban
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), 01328 Dresden, Germany
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01069 Dresden, Germany
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11
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Barauah V, Parsa S, Chowdhury N, Milner T, Rylander HG. Scattering angle resolved optical coherence tomography measures morphological changes in Bacillus subtilis colonies. JOURNAL OF BIOMEDICAL OPTICS 2022; 27:126004. [PMID: 36590979 PMCID: PMC9800589 DOI: 10.1117/1.jbo.27.12.126004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Significance An unmet need is recognized for early detection and diagnosis of neurological diseases. Many psychological markers emerge years after disease onset. Mitochondrial dysfunction and corresponding neurodegeneration occur before onset of large-scale cell and tissue pathology. Early detection of subcellular morphology changes could serve as a beacon for early detection of neurological diseases. This study is on bacterial colonies, Bacillus subtilis, which are similar in size to mitochondria. Aim This study investigates whether morphological changes can be detected in Bacillus subtilis using scattering angle resolved optical coherence tomography (SAR-OCT). Approach The SAR-OCT was applied to detect scattering angle distribution changes in Bacillus subtilis. The rod-to-coccus shape transition of the bacteria was imaged, and the backscattering angle was analyzed by recording the distribution of the ratio of low- to medium angle scattering (L/M ratio). Bacillus orientation at different locations in colonies was analytically modeled and compared with SAR-OCT results. Results Significant differences in the distribution of backscattering angle were observed in Bacillus subtilis transitioning from rod-to-coccus shapes. In Bacillus subtilis, the C -parameter of the Burr distribution of the SAR-OCT-derived L/M ratio was significantly smaller in coccus compared with rod-shaped bacteria. SAR-OCT-derived L/M ratio varied with bacterial position in the colony and is consistent with predicted orientations from previous studies. Conclusions Study results support the potential of utilizing SAR-OCT to detect bacterial morphological changes.
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Affiliation(s)
- Vikram Barauah
- The University of Texas at Austin, Biomedical Optics Lab, Department of Biomedical Imaging, Austin, Texas, United States
| | - Shyon Parsa
- UT Southwestern Medical School, Dallas, Texas, United States
| | - Naail Chowdhury
- The University of Texas at Austin, Biomedical Optics Lab, Department of Biomedical Imaging, Austin, Texas, United States
| | - Thomas Milner
- University of California Irvine, Beckman Laser Institute and Medical Clinic, Irvine, California, United States
| | - Henry Grady Rylander
- The University of Texas at Austin, Biomedical Optics Lab, Department of Biomedical Imaging, Austin, Texas, United States
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12
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Lewis DD, Gong T, Xu Y, Tan C. Frequency dependent growth of bacteria in living materials. Front Bioeng Biotechnol 2022; 10:948483. [PMID: 36159663 PMCID: PMC9493075 DOI: 10.3389/fbioe.2022.948483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
The fusion of living bacteria and man-made materials represents a new frontier in medical and biosynthetic technology. However, the principles of bacterial signal processing inside synthetic materials with three-dimensional and fluctuating environments remain elusive. Here, we study bacterial growth in a three-dimensional hydrogel. We find that bacteria expressing an antibiotic resistance module can take advantage of ambient kinetic disturbances to improve growth while encapsulated. We show that these changes in bacterial growth are specific to disturbance frequency and hydrogel density. This remarkable specificity demonstrates that periodic disturbance frequency is a new input that engineers may leverage to control bacterial growth in synthetic materials. This research provides a systematic framework for understanding and controlling bacterial information processing in three-dimensional living materials.
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Affiliation(s)
- Daniel D. Lewis
- Department of Biomedical Engineering, University of California, Davis, CA, United States
- Integrative Genetics and Genomics, University of California, Davis, CA, United States
| | - Ting Gong
- Department of Biomedical Engineering, University of California, Davis, CA, United States
| | - Yuanwei Xu
- Department of Biomedical Engineering, Peking University, Beijing, China
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California, Davis, CA, United States
- *Correspondence: Cheemeng Tan,
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13
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Spatial regulation of cell motility and its fitness effect in a surface-attached bacterial community. THE ISME JOURNAL 2022; 16:1004-1011. [PMID: 34759303 PMCID: PMC8940935 DOI: 10.1038/s41396-021-01148-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 09/12/2021] [Accepted: 10/22/2021] [Indexed: 01/12/2023]
Abstract
On a surface, microorganisms grow into a multi-cellular community. When a community becomes densely populated, cells migrate away to expand the community's territory. How microorganisms regulate surface motility to optimize expansion remains poorly understood. Here, we characterized surface motility of Proteus mirabilis. P. mirabilis is well known for its ability to expand its colony rapidly on a surface. Cursory visual inspection of an expanding colony suggests partial migration, i.e., one fraction of a population migrates while the other is sessile. Quantitative microscopic imaging shows that this migration pattern is determined by spatially inhomogeneous regulation of cell motility. Further analyses reveal that this spatial regulation is mediated by the Rcs system, which represses the expression of the motility regulator (FlhDC) in a nutrient-dependent manner. Alleviating this repression increases the colony expansion speed but results in a rapid drop in the number of viable cells, lowering population fitness. These findings collectively demonstrate how Rcs regulates cell motility dynamically to increase the fitness of an expanding bacterial population, illustrating a fundamental trade-off underlying bacterial colonization of a surface.
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14
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Eriksen RS, Mitarai N, Sneppen K. On Phage Adsorption to Bacterial Chains. Biophys J 2020; 119:1896-1904. [PMID: 33069271 PMCID: PMC7677248 DOI: 10.1016/j.bpj.2020.09.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/16/2020] [Accepted: 09/21/2020] [Indexed: 11/15/2022] Open
Abstract
Bacteria often arrange themselves in various spatial configurations, which changes how they interact with their surroundings. In this work, we investigate how the structure of the bacterial arrangements influences the adsorption of bacteriophages. We quantify how the adsorption rate scales with the number of bacteria in the arrangement and show that the adsorption rates for microcolonies (increasing with exponent ∼1/3) and bacterial chains (increasing with exponent ∼0.5-0.8) are substantially lower than for well-mixed bacteria (increasing with exponent 1). We further show that, after infection, the spatially clustered arrangements reduce the effective burst size by more than 50% and cause substantial superinfections in a very short time interval after phage lysis.
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Affiliation(s)
| | - Namiko Mitarai
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Kim Sneppen
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark.
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15
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Eriksen RS, Mitarai N, Sneppen K. Sustainability of spatially distributed bacteria-phage systems. Sci Rep 2020; 10:3154. [PMID: 32081858 PMCID: PMC7035299 DOI: 10.1038/s41598-020-59635-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 01/09/2020] [Indexed: 11/09/2022] Open
Abstract
Virulent phages can expose their bacterial hosts to devastating epidemics, in principle leading to complete elimination of their hosts. Although experiments indeed confirm a large reduction of susceptible bacteria, there are no reports of complete extinctions. We here address this phenomenon from the perspective of spatial organization of bacteria and how this can influence the final survival of them. By modelling the transient dynamics of bacteria and phages when they are introduced into an environment with finite resources, we quantify how time delayed lysis, the spatial separation of initial bacterial positions, and the self-protection of bacteria growing in spherical colonies favour bacterial survival. Our results suggest that spatial structures on the millimetre and submillimetre scale play an important role in maintaining microbial diversity.
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Affiliation(s)
| | - Namiko Mitarai
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Kim Sneppen
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark.
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16
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Morales P, Aguirre J, Troncoso M, Figueroa G. Comparison of in vitro and in situ antagonism assays as tools for the selection of bio-preservative lactic acid bacteria (LAB) in poultry meat. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2019.108846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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17
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Zhai X, Larkin JW, Kikuchi K, Redford SE, Roy U, Süel GM, Mugler A. Statistics of correlated percolation in a bacterial community. PLoS Comput Biol 2019; 15:e1007508. [PMID: 31790383 PMCID: PMC6907856 DOI: 10.1371/journal.pcbi.1007508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 12/12/2019] [Accepted: 10/22/2019] [Indexed: 01/06/2023] Open
Abstract
Signal propagation over long distances is a ubiquitous feature of multicellular communities, but cell-to-cell variability can cause propagation to be highly heterogeneous. Simple models of signal propagation in heterogenous media, such as percolation theory, can potentially provide a quantitative understanding of these processes, but it is unclear whether these simple models properly capture the complexities of multicellular systems. We recently discovered that in biofilms of the bacterium Bacillus subtilis, the propagation of an electrical signal is statistically consistent with percolation theory, and yet it is reasonable to suspect that key features of this system go beyond the simple assumptions of basic percolation theory. Indeed, we find here that the probability for a cell to signal is not independent from other cells as assumed in percolation theory, but instead is correlated with its nearby neighbors. We develop a mechanistic model, in which correlated signaling emerges from cell division, phenotypic inheritance, and cell displacement, that reproduces the experimentally observed correlations. We find that the correlations do not significantly affect the spatial statistics, which we rationalize using a renormalization argument. Moreover, the fraction of signaling cells is not constant in space, as assumed in percolation theory, but instead varies within and across biofilms. We find that this feature lowers the fraction of signaling cells at which one observes the characteristic power-law statistics of cluster sizes, consistent with our experimental results. We validate the model using a mutant biofilm whose signaling probability decays along the propagation direction. Our results reveal key statistical features of a correlated signaling process in a multicellular community. More broadly, our results identify extensions to percolation theory that do or do not alter its predictions and may be more appropriate for biological systems.
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Affiliation(s)
- Xiaoling Zhai
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana, United States of America
| | - Joseph W. Larkin
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Kaito Kikuchi
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Samuel E. Redford
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Ushasi Roy
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana, United States of America
| | - Gürol M. Süel
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
- San Diego Center for Systems Biology, University of California San Diego, La Jolla, California, United States of America
| | - Andrew Mugler
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
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18
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Mitarai N. How pirate phage interferes with helper phage: Comparison of the two distinct strategies. J Theor Biol 2019; 486:110096. [PMID: 31786182 DOI: 10.1016/j.jtbi.2019.110096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 11/26/2022]
Abstract
Pirate phages use the structural proteins encoded by unrelated helper phages to propagate. The best-studied example is the pirate P4 and helper P2 of coliphages, and it has been known that the Staphylococcus aureus pathogenicity islands (SaPIs) that can encode virulence factors act as pirate phages, too. When alone in the host, the pirate phages act as a prophage, but when the helper phage gene is also in the same host cell, the pirate phage has ability to exploit the helper phages structural proteins to produce pirate phage particles and spread, interfering with the helper phage production. The known helper phages in these systems are temperate phages. Interestingly, the interference of the pirate phage to the helper phage occurs in a different manner between the SaPI-helper system and the P4-P2 system. SaPIs cannot lyse a helper lysogen upon infection, while when a helper phage lyse a SaPI lysogen, most of the phage particles produced are the SaPI particles. On the contrary, in the P4-P2 system, a pirate phage P4 can lyse a helper P2 lysogen to produce mostly the P4 particles, while when P2 phage lyses a P4 lysogen, most of the produced phages are the P2 particles. Here, the consequences of these different strategies in the pirate and helper phage spreading among uninfected host is analyzed by using mathematical models. It is found that SaPI's strategy interferes with the helper phage spreading significantly more than the P4's strategy, because SaPI interferes with the helper phage's main reproduction step, while P4 interferes only by forcing the helper lysogens to lyse. However, the interference is found to be weaker in the spatially structured environment than in the well-mixed environment. This is because, in the spatial setting, the system tends to self-organize so that the helper phages take over the front of propagation due to the need of helper phage for the pirate phage spreading.
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Affiliation(s)
- Namiko Mitarai
- The Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, Copenhagen, 2100-DK, Denmark.
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19
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Mora T, Nemenman I. Physical Limit to Concentration Sensing in a Changing Environment. PHYSICAL REVIEW LETTERS 2019; 123:198101. [PMID: 31765216 DOI: 10.1103/physrevlett.123.198101] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Indexed: 06/10/2023]
Abstract
Cells adapt to changing environments by sensing ligand concentrations using specific receptors. The accuracy of sensing is ultimately limited by the finite number of ligand molecules bound by receptors. Previously derived physical limits to sensing accuracy largely have assumed that the concentration was constant and ignored its temporal fluctuations. We formulate the problem of concentration sensing in a strongly fluctuating environment as a nonlinear field-theoretic problem, for which we find an excellent approximate Gaussian solution. We derive a new physical bound on the relative error in concentration c which scales as δc/c∼(Dacτ)^{-1/4} with ligand diffusivity D, receptor cross section a, and characteristic fluctuation timescale τ, in stark contrast to the usual Berg and Purcell bound δc/c∼(DacT)^{-1/2} for a perfect receptor sensing concentration during time T. We show how the bound can be achieved by a biochemical network downstream of the receptor that adapts the kinetics of signaling as a function of the square root of the sensed concentration.
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Affiliation(s)
- Thierry Mora
- Laboratoire de physique de l'École normale supérieure (PSL University), CNRS, Sorbonne University, Université de Paris, 24 rue Lhomond, 75005 Paris, France
| | - Ilya Nemenman
- Department of Physics, Department of Biology, and Initiative in Theory and Modeling of Living Systems, Emory University, Atlanta, Georgia 30322, USA
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20
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Abstract
We present a simple growth model which was developed to explain Escherichia coli growth in batch culture. Optical density measurements are used to obtain E. coli growth curves for different inoculum sizes and nutrients concentrations. The model is described by two nonlinear mutually dependent differential equations that describe time evolution of bacteria and nutrients concentration. Introduction of the negative bacterium-bacterium interaction term is specific for the model and leads to the population decay. The proposed model describes entire experimental growth curves. The growth rate, as a function of initial nutrients concentration, follows the Monod function, whilst during the growth it decreases proportionally with the concentration of nutrients. The parameters in our equations can be related to the parameters of the logistic model. The proposed model can be applied to different E. coli strains and, because of the universality of the equations, might be applied to other bacterial strains.
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Affiliation(s)
- Lucija Krce
- Faculty of Science, Department of Physics, University of Split, Split, Croatia. Author to whom any correspondence should be addressed
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21
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Xu H, Dauparas J, Das D, Lauga E, Wu Y. Self-organization of swimmers drives long-range fluid transport in bacterial colonies. Nat Commun 2019; 10:1792. [PMID: 30996269 PMCID: PMC6470179 DOI: 10.1038/s41467-019-09818-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 03/28/2019] [Indexed: 01/08/2023] Open
Abstract
Motile subpopulations in microbial communities are believed to be important for dispersal, quest for food, and material transport. Here, we show that motile cells in sessile colonies of peritrichously flagellated bacteria can self-organize into two adjacent, centimeter-scale motile rings surrounding the entire colony. The motile rings arise from spontaneous segregation of a homogeneous swimmer suspension that mimics a phase separation; the process is mediated by intercellular interactions and shear-induced depletion. As a result of this self-organization, cells drive fluid flows that circulate around the colony at a constant peak speed of ~30 µm s−1, providing a stable and high-speed avenue for directed material transport at the macroscopic scale. Our findings present a unique form of bacterial self-organization that influences population structure and material distribution in colonies. Motile and non-motile subpopulations often coexist in bacterial communities. Here, Xu et al. show that motile cells in colonies of common flagellated bacteria can self-organize into two adjacent motile rings, driving stable flows of fluid and materials around the colony.
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Affiliation(s)
- Haoran Xu
- Department of Physics and Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, People's Republic of China
| | - Justas Dauparas
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, CB3 0WA, UK
| | - Debasish Das
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, CB3 0WA, UK
| | - Eric Lauga
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, CB3 0WA, UK
| | - Yilin Wu
- Department of Physics and Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, People's Republic of China.
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22
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Cheptsov VS, Tsypina SI, Minaev NV, Yusupov VI, Chichkov BN. New microorganism isolation techniques with emphasis on laser printing. Int J Bioprint 2018; 5:165. [PMID: 32596530 PMCID: PMC7294688 DOI: 10.18063/ijb.v5i1.165] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 10/16/2018] [Indexed: 01/05/2023] Open
Abstract
The study of biodiversity, growth, development, and metabolism of cultivated microorganisms is an integral part of modern microbiological, biotechnological, and medical research. Such studies require the development of new methods of isolation, cultivation, manipulation, and study of individual bacterial cells and their consortia. To this end, in recent years, there has been an active development of different isolation and three-dimensional cell positioning methods. In this review, the optical tweezers, surface heterogeneous functionalization, multiphoton lithography, microfluidic techniques, and laser printing are reviewed. Laser printing is considered as one of the most promising techniques and is discussed in detail.
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Affiliation(s)
- V S Cheptsov
- Department of Soil Science, Lomonosov Moscow State University, 11999 Moscow, Russia
| | - S I Tsypina
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, Troitsk, Moscow, Russia
| | - N V Minaev
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, Troitsk, Moscow, Russia
| | - V I Yusupov
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, Troitsk, Moscow, Russia
| | - B N Chichkov
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, Troitsk, Moscow, Russia.,Institut für Quantenoptik, Leibniz Universität Hannover, Welfengarten, 30167, Hannover
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23
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Eriksen RS, Svenningsen SL, Sneppen K, Mitarai N. A growing microcolony can survive and support persistent propagation of virulent phages. Proc Natl Acad Sci U S A 2018; 115:337-342. [PMID: 29259110 PMCID: PMC5777033 DOI: 10.1073/pnas.1708954115] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Bacteria form colonies and secrete extracellular polymeric substances that surround the individual cells. These spatial structures are often associated with collaboration and quorum sensing between the bacteria. Here we investigate the mutual protection provided by spherical growth of a monoclonal colony during exposure to phages that proliferate on its surface. As a proof of concept we exposed growing colonies of Escherichia coli to a virulent mutant of phage P1. When the colony consists of less than [Formula: see text]50,000 members it is eliminated, while larger initial colonies allow long-term survival of both phage-resistant mutants and, importantly, colonies of mostly phage-sensitive members. A mathematical model predicts that colonies formed solely by phage-sensitive bacteria can survive because the growth of bacteria throughout the colony exceeds the killing of bacteria on the surface and pinpoints how the critical colony size depends on key parameters in the phage infection cycle.
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Affiliation(s)
| | - Sine L Svenningsen
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Kim Sneppen
- Niels Bohr Institute, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Namiko Mitarai
- Niels Bohr Institute, University of Copenhagen, DK-2100 Copenhagen, Denmark;
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