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Benzi R, Nelson DR, Shankar S, Toschi F, Zhu X. Spatial population genetics with fluid flow. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2022; 85:096601. [PMID: 35853344 DOI: 10.1088/1361-6633/ac8231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
The growth and evolution of microbial populations is often subjected to advection by fluid flows in spatially extended environments, with immediate consequences for questions of spatial population genetics in marine ecology, planktonic diversity and origin of life scenarios. Here, we review recent progress made in understanding this rich problem in the simplified setting of two competing genetic microbial strains subjected to fluid flows. As a pedagogical example we focus on antagonsim, i.e., two killer microorganism strains, each secreting toxins that impede the growth of their competitors (competitive exclusion), in the presence of stationary fluid flows. By solving two coupled reaction-diffusion equations that include advection by simple steady cellular flows composed of characteristic flow motifs in two dimensions (2D), we show how local flow shear and compressibility effects can interact with selective advantage to have a dramatic influence on genetic competition and fixation in spatially distributed populations. We analyze several 1D and 2D flow geometries including sources, sinks, vortices and saddles, and show how simple analytical models of the dynamics of the genetic interface can be used to shed light on the nucleation, coexistence and flow-driven instabilities of genetic drops. By exploiting an analogy with phase separation with nonconserved order parameters, we uncover how thesegeneticdrops harness fluid flows for novel evolutionary strategies, even in the presence of number fluctuations, as confirmed by agent-based simulations as well.
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Affiliation(s)
- Roberto Benzi
- Department of Physics and INFN, University of Rome Tor Vergata, I-00133 Rome, Italy
| | - David R Nelson
- Department of Physics, Harvard University, Cambridge, MA 02138, United States of America
| | - Suraj Shankar
- Department of Physics, Harvard University, Cambridge, MA 02138, United States of America
| | - Federico Toschi
- Department of Applied Physics, Department of Mathematics and Computer Science, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- CNR-IAC, I-00185 Rome, Italy
| | - Xiaojue Zhu
- Solar and Stellar Interiors, Max Planck Institute for Solar System Research, Justus-von-Liebig-Weg 3, Göttingen 37077, Germany
- Center of Mathematical Sciences and Applications, and School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, United States of America
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Giometto A, Nelson DR, Murray AW. Antagonism between killer yeast strains as an experimental model for biological nucleation dynamics. eLife 2021; 10:e62932. [PMID: 34866571 PMCID: PMC8730724 DOI: 10.7554/elife.62932] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/11/2021] [Indexed: 11/13/2022] Open
Abstract
Antagonistic interactions are widespread in the microbial world and affect microbial evolutionary dynamics. Natural microbial communities often display spatial structure, which affects biological interactions, but much of what we know about microbial antagonism comes from laboratory studies of well-mixed communities. To overcome this limitation, we manipulated two killer strains of the budding yeast Saccharomyces cerevisiae, expressing different toxins, to independently control the rate at which they released their toxins. We developed mathematical models that predict the experimental dynamics of competition between toxin-producing strains in both well-mixed and spatially structured populations. In both situations, we experimentally verified theory's prediction that a stronger antagonist can invade a weaker one only if the initial invading population exceeds a critical frequency or size. Finally, we found that toxin-resistant cells and weaker killers arose in spatially structured competitions between toxin-producing strains, suggesting that adaptive evolution can affect the outcome of microbial antagonism in spatial settings.
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Affiliation(s)
- Andrea Giometto
- School of Civil and Environmental Engineering, Cornell UniversityIthacaUnited States
- Department of Physics, Harvard UniversityCambridgeUnited States
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - David R Nelson
- Department of Physics, Harvard UniversityCambridgeUnited States
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
- John A Paulson School of Engineering and Applied Sciences, Harvard UniversityCambridgeUnited States
| | - Andrew W Murray
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
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Das M, Kantz H. Role of thermal fluctuations in biological copying mechanisms. Phys Rev E 2021; 103:032110. [PMID: 33862776 DOI: 10.1103/physreve.103.032110] [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: 07/22/2020] [Accepted: 02/18/2021] [Indexed: 11/07/2022]
Abstract
During transcription, translation, or self-replication of DNA or RNA, information is transferred to the newly formed species from its predecessor. These processes can be interpreted as (generalized) biological copying mechanism as the new biological entities like DNA, RNA, or proteins are representing the information of their parent bodies uniquely. The accuracy of these copying processes is essential, since errors in the copied code can reduce the functionality of the next generation. Such errors might result from perturbations on these processes. Most important in this context is the temperature of the medium, i.e., thermal noise. Although a reasonable amount of experimental studies have been carried out on this important issue, theoretical understanding is truly sparse. In the present work, we illustrate a model study which is able to focus on the effect of the temperature on the process of biological copying mechanisms, as well as on mutation. We find for our paradigmatic models that, in a quite general scenario, the copying processes are most accurate at an intermediate temperature range; i.e., there exists an optimum temperature where mutation is most unlikely. This allows us to interpret the observations for some biological species with the aid of our model study.
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Affiliation(s)
- Moupriya Das
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, 01187 Dresden, Germany
| | - Holger Kantz
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, 01187 Dresden, Germany
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Steinbach G, Crisan C, Ng SL, Hammer BK, Yunker PJ. Accumulation of dead cells from contact killing facilitates coexistence in bacterial biofilms. J R Soc Interface 2020; 17:20200486. [PMID: 33292099 PMCID: PMC7811593 DOI: 10.1098/rsif.2020.0486] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/12/2020] [Indexed: 02/06/2023] Open
Abstract
Bacterial communities are governed by a wide variety of social interactions, some of which are antagonistic with potential significance for bacterial warfare. Several antagonistic mechanisms, such as killing via the type VI secretion system (T6SS), require killer cells to directly contact target cells. The T6SS is hypothesized to be a highly potent weapon, capable of facilitating the invasion and defence of bacterial populations. However, we find that the efficacy of contact killing is severely limited by the material consequences of cell death. Through experiments with Vibrio cholerae strains that kill via the T6SS, we show that dead cell debris quickly accumulates at the interface that forms between competing strains, preventing physical contact and thus preventing killing. While previous experiments have shown that T6SS killing can reduce a population of target cells by as much as 106-fold, we find that, as a result of the formation of dead cell debris barriers, the impact of contact killing depends sensitively on the initial concentration of killer cells. Killer cells are incapable of invading or eliminating competitors on a community level. Instead, bacterial warfare itself can facilitate coexistence between nominally antagonistic strains. While a variety of defensive strategies against microbial warfare exist, the material consequences of cell death provide target cells with their first line of defence.
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Affiliation(s)
- Gabi Steinbach
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Cristian Crisan
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Siu Lung Ng
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Brian K. Hammer
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Peter J. Yunker
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
- Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
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