IDEAS home Printed from https://ideas.repec.org/a/plo/pcbi00/1007508.html
   My bibliography  Save this article

Statistics of correlated percolation in a bacterial community

Author

Listed:
  • Xiaoling Zhai
  • Joseph W Larkin
  • Kaito Kikuchi
  • Samuel E Redford
  • Ushasi Roy
  • Gürol M Süel
  • Andrew Mugler

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.Author summary: Many multicellular systems send signals over long distances by relaying information over connected cell-to-cell paths. In physics, the statistics of connected path formation are described by percolation theory. We previously discovered that the statistics of electrical signal propagation in communities of the bacterium Bacillus subtilis are consistent with the predictions of percolation theory. However, we find experimentally that key features of this system go beyond the simple assumptions of basic percolation theory, which include site-to-site independence and spatial uniformity of the signaling probability. Why are the predictions of percolation theory still upheld? Using a computational model, we find that the cell-to-cell dependence does not change the predictions due to the universal nature of percolation theory near its critical point, and the spatial variability of the signaling probability actually expands the parameter range over which the predictions hold. We validate our findings using a mutant bacterial strain. Our work explores the robustness of percolation theory to its underlying assumptions, and the resulting consequences for long-range bacterial signaling.

Suggested Citation

  • Xiaoling Zhai & Joseph W Larkin & Kaito Kikuchi & Samuel E Redford & Ushasi Roy & Gürol M Süel & Andrew Mugler, 2019. "Statistics of correlated percolation in a bacterial community," PLOS Computational Biology, Public Library of Science, vol. 15(12), pages 1-19, December.
  • Handle: RePEc:plo:pcbi00:1007508
    DOI: 10.1371/journal.pcbi.1007508
    as

    Download full text from publisher

    File URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007508
    Download Restriction: no

    File URL: https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007508&type=printable
    Download Restriction: no

    File URL: https://libkey.io/10.1371/journal.pcbi.1007508?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Avigdor Eldar & Michael B. Elowitz, 2010. "Functional roles for noise in genetic circuits," Nature, Nature, vol. 467(7312), pages 167-173, September.
    2. Arthur Prindle & Jintao Liu & Munehiro Asally & San Ly & Jordi Garcia-Ojalvo & Gürol M. Süel, 2015. "Ion channels enable electrical communication in bacterial communities," Nature, Nature, vol. 527(7576), pages 59-63, November.
    3. Xinxian Shao & Andrew Mugler & Justin Kim & Ha Jun Jeong & Bruce R Levin & Ilya Nemenman, 2017. "Growth of bacteria in 3-d colonies," PLOS Computational Biology, Public Library of Science, vol. 13(7), pages 1-19, July.
    4. Jintao Liu & Arthur Prindle & Jacqueline Humphries & Marçal Gabalda-Sagarra & Munehiro Asally & Dong-yeon D. Lee & San Ly & Jordi Garcia-Ojalvo & Gürol M. Süel, 2015. "Metabolic co-dependence gives rise to collective oscillations within biofilms," Nature, Nature, vol. 523(7562), pages 550-554, July.
    5. Thomas M. Norman & Nathan D. Lord & Johan Paulsson & Richard Losick, 2013. "Memory and modularity in cell-fate decision making," Nature, Nature, vol. 503(7477), pages 481-486, November.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Yan, Xuejun & Lee, Hyung-Sool & Li, Nan & Wang, Xin, 2020. "The micro-niche of exoelectrogens influences bioelectricity generation in bioelectrochemical systems," Renewable and Sustainable Energy Reviews, Elsevier, vol. 134(C).
    2. Mohammad Soltani & Cesar A Vargas-Garcia & Duarte Antunes & Abhyudai Singh, 2016. "Intercellular Variability in Protein Levels from Stochastic Expression and Noisy Cell Cycle Processes," PLOS Computational Biology, Public Library of Science, vol. 12(8), pages 1-23, August.
    3. Kazunari Iwamoto & Yuki Shindo & Koichi Takahashi, 2016. "Modeling Cellular Noise Underlying Heterogeneous Cell Responses in the Epidermal Growth Factor Signaling Pathway," PLOS Computational Biology, Public Library of Science, vol. 12(11), pages 1-18, November.
    4. Ankit Gupta & Mustafa Khammash, 2022. "Frequency spectra and the color of cellular noise," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    5. Michael F. Fuss & Jan-Philip Wieferig & Robin A. Corey & Yvonne Hellmich & Igor Tascón & Joana S. Sousa & Phillip J. Stansfeld & Janet Vonck & Inga Hänelt, 2023. "Cyclic di-AMP traps proton-coupled K+ transporters of the KUP family in an inward-occluded conformation," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    6. Lee, Julian, 2023. "Poisson distributions in stochastic dynamics of gene expression: What events do they count?," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 630(C).
    7. John C. Boik, 2016. "Optimality of Social Choice Systems: Complexity, Wisdom, and Wellbeing Centrality," Working Paper 0005, Principled Societies Project, revised Mar 2017.
    8. Georg Fritz & Judith A Megerle & Sonja A Westermayer & Delia Brick & Ralf Heermann & Kirsten Jung & Joachim O Rädler & Ulrich Gerland, 2014. "Single Cell Kinetics of Phenotypic Switching in the Arabinose Utilization System of E. coli," PLOS ONE, Public Library of Science, vol. 9(2), pages 1-12, February.
    9. Laura Corrales-Guerrero & Asaf Tal & Rinat Arbel-Goren & Vicente Mariscal & Enrique Flores & Antonia Herrero & Joel Stavans, 2015. "Spatial Fluctuations in Expression of the Heterocyst Differentiation Regulatory Gene hetR in Anabaena Filaments," PLOS Genetics, Public Library of Science, vol. 11(4), pages 1-21, April.
    10. Singh, Abhyudai & Vahdat, Zahra & Xu, Zikai, 2019. "Time-triggered stochastic hybrid systems with two timer-dependent resets," OSF Preprints u8fzg, Center for Open Science.
    11. Ming Ni & Antoine L Decrulle & Fanette Fontaine & Alice Demarez & Francois Taddei & Ariel B Lindner, 2012. "Pre-Disposition and Epigenetics Govern Variation in Bacterial Survival upon Stress," PLOS Genetics, Public Library of Science, vol. 8(12), pages 1-11, December.
    12. Jan Hasenauer & Christine Hasenauer & Tim Hucho & Fabian J Theis, 2014. "ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics," PLOS Computational Biology, Public Library of Science, vol. 10(7), pages 1-17, July.
    13. Martiny, Emil S. & Jensen, Mogens H. & Heltberg, Mathias S., 2022. "Detecting limit cycles in stochastic time series," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 605(C).
    14. Ziya Kalay & Takahiro K Fujiwara & Akihiro Kusumi, 2012. "Confining Domains Lead to Reaction Bursts: Reaction Kinetics in the Plasma Membrane," PLOS ONE, Public Library of Science, vol. 7(3), pages 1-8, March.
    15. Margaritis Voliotis & Philipp Thomas & Ramon Grima & Clive G Bowsher, 2016. "Stochastic Simulation of Biomolecular Networks in Dynamic Environments," PLOS Computational Biology, Public Library of Science, vol. 12(6), pages 1-18, June.
    16. Vera Bettenworth & Simon Vliet & Bartosz Turkowyd & Annika Bamberger & Heiko Wendt & Matthew McIntosh & Wieland Steinchen & Ulrike Endesfelder & Anke Becker, 2022. "Frequency modulation of a bacterial quorum sensing response," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    17. Gabriele Micali & Gerardo Aquino & David M Richards & Robert G Endres, 2015. "Accurate Encoding and Decoding by Single Cells: Amplitude Versus Frequency Modulation," PLOS Computational Biology, Public Library of Science, vol. 11(6), pages 1-21, June.
    18. Jessica A Lee & Siavash Riazi & Shahla Nemati & Jannell V Bazurto & Andreas E Vasdekis & Benjamin J Ridenhour & Christopher H Remien & Christopher J Marx, 2019. "Microbial phenotypic heterogeneity in response to a metabolic toxin: Continuous, dynamically shifting distribution of formaldehyde tolerance in Methylobacterium extorquens populations," PLOS Genetics, Public Library of Science, vol. 15(11), pages 1-38, November.
    19. Chen, Aimin & Tian, Tianhai & Chen, Yiren & Zhou, Tianshou, 2022. "Stochastic analysis of a complex gene-expression model," Chaos, Solitons & Fractals, Elsevier, vol. 160(C).
    20. Abhyudai Singh & Mohammad Soltani, 2013. "Quantifying Intrinsic and Extrinsic Variability in Stochastic Gene Expression Models," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-12, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pcbi00:1007508. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: ploscompbiol (email available below). General contact details of provider: https://journals.plos.org/ploscompbiol/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.