1
|
Swartz DW, Lee H, Kardar M, Korolev KS. Interplay between morphology and competition in two-dimensional colony expansion. Phys Rev E 2023; 108:L032301. [PMID: 37849094 PMCID: PMC11149782 DOI: 10.1103/physreve.108.l032301] [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: 01/24/2023] [Accepted: 07/01/2023] [Indexed: 10/19/2023]
Abstract
In growing populations, the fate of mutations depends on their competitive ability against the ancestor and their ability to colonize new territory. Here we present a theory that integrates both aspects of mutant fitness by coupling the classic description of one-dimensional competition (Fisher equation) to the minimal model of front shape (Kardar-Parisi-Zhang equation). We solve these equations and find three regimes, which are controlled solely by the expansion rates, solely by the competitive abilities, or by both. Collectively, our results provide a simple framework to study spatial competition.
Collapse
Affiliation(s)
- Daniel W Swartz
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Hyunseok Lee
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Mehran Kardar
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Kirill S Korolev
- Department of Physics, Graduate Program in Bioinformatics and Biological Design Center, Boston University, Boston, Massachusetts 02215, USA
| |
Collapse
|
2
|
Golden A, Dukovski I, Segrè D, Korolev KS. Growth instabilities shape morphology and genetic diversity of microbial colonies. Phys Biol 2022; 19:10.1088/1478-3975/ac8514. [PMID: 35901792 PMCID: PMC11209841 DOI: 10.1088/1478-3975/ac8514] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/28/2022] [Indexed: 11/11/2022]
Abstract
Cellular populations assume an incredible variety of shapes ranging from circular molds to irregular tumors. While we understand many of the mechanisms responsible for these spatial patterns, little is known about how the shape of a population influences its ecology and evolution. Here, we investigate this relationship in the context of microbial colonies grown on hard agar plates. This a well-studied system that exhibits a transition from smooth circular disks to more irregular and rugged shapes as either the nutrient concentration or cellular motility is decreased. Starting from a mechanistic model of colony growth, we identify two dimensionless quantities that determine how morphology and genetic diversity of the population depend on the model parameters. Our simulations further reveal that population dynamics cannot be accurately described by the commonly-used surface growth models. Instead, one has to explicitly account for the emergent growth instabilities and demographic fluctuations. Overall, our work links together environmental conditions, colony morphology, and evolution. This link is essential for a rational design of concrete, biophysical perturbations to steer evolution in the desired direction.
Collapse
Affiliation(s)
- Alexander Golden
- Department of Physics, Graduate Program in Bioinformatics, and Biological Design Center, Boston University, Boston, MA 02215, United States of America
| | - Ilija Dukovski
- Graduate Program in Bioinformatics, and Biological Design Center, Boston University, Boston, MA 02215, United States of America
| | - Daniel Segrè
- Department of Physics, Department of Biology, Department of Biomedical Engineering, Graduate Program in Bioinformatics, and Biological Design Center, Boston University, Boston, MA 02215, United States of America
| | - Kirill S Korolev
- Department of Physics, Graduate Program in Bioinformatics, and Biological Design Center, Boston University, Boston, MA 02215, United States of America
| |
Collapse
|
3
|
Zhang H, Wan LQ. Cell Chirality as a Novel Measure for Cytotoxicity. Adv Biol (Weinh) 2022; 6:e2101088. [PMID: 34796704 PMCID: PMC9008805 DOI: 10.1002/adbi.202101088] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/28/2021] [Indexed: 12/25/2022]
Abstract
Cytotoxicity assessment has great importance in both research and pharmaceutical development. The mainstream in vitro cytotoxicity assays are mostly biochemical assays that evaluate a specific cellular activity such as proliferation and apoptosis. Few assays assess toxicity by characterizing overall functional outcomes in cellular physiology such as multicellular morphogenesis. The intrinsic cellular chiral bias (also known as cell chirality, left-right asymmetry, or handedness), which determines cellular polarization along the left-right axis, is demonstrated to play important roles in development and disease. This chiral property of cells gives insights not only into functions of individual cells, such as motility and polarity but also into emerging behaviors of cell clusters, such as collective cell migration. Therefore, cell chirality characterization can be potentially used as a biomarker for assessing the overall effects of pharmaceutical drugs and environmental factors on the health of the cell. In this review article, the current in vitro techniques for cell chirality characterization and their applications are discussed and the advantages and limitations of these cell chirality assays as potential tools for detecting cytotoxicity are discussed.
Collapse
Affiliation(s)
- Haokang Zhang
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Leo Q Wan
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
- Center for Modeling, Simulation, and Imaging in Medicine, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| |
Collapse
|
4
|
Karasz DC, Weaver AI, Buckley DH, Wilhelm RC. Conditional filamentation as an adaptive trait of bacteria and its ecological significance in soils. Environ Microbiol 2021; 24:1-17. [PMID: 34929753 DOI: 10.1111/1462-2920.15871] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 11/30/2022]
Abstract
Bacteria can regulate cell morphology in response to environmental conditions, altering their physiological and metabolic characteristics to improve survival. Conditional filamentation, in which cells suspend division while continuing lateral growth, is a strategy with a range of adaptive benefits. Here, we review the causes and consequences of conditional filamentation with respect to bacterial physiology, ecology and evolution. We describe four major benefits from conditional filamentation: stress tolerance, surface colonization, gradient spanning and the facilitation of biotic interactions. Adopting a filamentous growth habit involves fitness trade-offs which are also examined. We focus on the role of conditional filamentation in soil habitats, where filamentous morphotypes are highly prevalent and where environmental heterogeneity can benefit a conditional response. To illustrate the use of information presented in our review, we tested the conditions regulating filamentation by the forest soil isolate Paraburkholderia elongata 5NT . Filamentation by P. elongata was induced at elevated phosphate concentrations, and was associated with the accumulation of intracellular polyphosphate, highlighting the role of filamentation in a phosphate-solubilizing bacterium. Conditional filamentation enables bacteria to optimize their growth and metabolism in environments that are highly variable, a trait that can impact succession, symbioses, and biogeochemistry in soil environments.
Collapse
Affiliation(s)
- David C Karasz
- School of Integrative Plant Science, Bradfield Hall, Cornell University, Ithaca, New York, 14853, USA
| | - Anna I Weaver
- Department of Microbiology, Wing Hall, Cornell University, Ithaca, New York, 14853, USA.,Weill Institute for Cell and Molecular Biology, Weill Hall, Cornell University, Ithaca, New York, 14853, USA
| | - Daniel H Buckley
- School of Integrative Plant Science, Bradfield Hall, Cornell University, Ithaca, New York, 14853, USA
| | - Roland C Wilhelm
- School of Integrative Plant Science, Bradfield Hall, Cornell University, Ithaca, New York, 14853, USA
| |
Collapse
|
5
|
Bacterial Filamentation Drives Colony Chirality. mBio 2021; 12:e0154221. [PMID: 34724813 PMCID: PMC8561393 DOI: 10.1128/mbio.01542-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chirality is ubiquitous in nature, with consequences at the cellular and tissue scales. As Escherichia coli colonies expand radially, an orthogonal component of growth creates a pinwheel-like pattern that can be revealed by fluorescent markers. To elucidate the mechanistic basis of this colony chirality, we investigated its link to left-handed, single-cell twisting during E. coli elongation. While chemical and genetic manipulation of cell width altered single-cell twisting handedness, colonies ceased to be chiral rather than switching handedness, and anaerobic growth altered colony chirality without affecting single-cell twisting. Chiral angle increased with increasing temperature even when growth rate decreased. Unifying these findings, we discovered that colony chirality was associated with the propensity for cell filamentation. Inhibition of cell division accentuated chirality under aerobic growth and generated chirality under anaerobic growth. Thus, regulation of cell division is intrinsically coupled to colony chirality, providing a mechanism for tuning macroscale spatial patterning. IMPORTANCE Chiral objects, such as amino acids, are distinguishable from their mirror image. For living systems, the fundamental mechanisms relating cellular handedness to chirality at the multicellular scale remain largely mysterious. Here, we use chemical, genetic, and environmental perturbations of Escherichia coli to investigate whether pinwheel patterns in bacterial colonies are directly linked to single-cell growth behaviors. We discover that chirality can be abolished without affecting single-cell twisting; instead, the degree of chirality was linked to the proportion of highly elongated cells at the colony edge. Inhibiting cell division boosted the degree of chirality during aerobic growth and even introduced chirality to otherwise achiral colonies during anaerobic growth. These findings reveal a fascinating connection between cell division and macroscopic colony patterning.
Collapse
|
6
|
Sadiq FA, Burmølle M, Heyndrickx M, Flint S, Lu W, Chen W, Zhao J, Zhang H. Community-wide changes reflecting bacterial interspecific interactions in multispecies biofilms. Crit Rev Microbiol 2021; 47:338-358. [PMID: 33651958 DOI: 10.1080/1040841x.2021.1887079] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Existence of most bacterial species, in natural, industrial, and clinical settings in the form of surface-adhered communities or biofilms has been well acknowledged for decades. Research predominantly focusses on single-species biofilms as these are relatively easy to study. However, microbiologists are now interested in studying multispecies biofilms and revealing interspecific interactions in these communities because of the existence of a plethora of different bacterial species together in almost all natural settings. Multispecies biofilms-led emergent properties are triggered by bacterial social interactions which have huge implication for research and practical knowledge useful for the control and manipulation of these microbial communities. Here, we discuss some important bacterial interactions that take place in multispecies biofilm communities and provide insights into community-wide changes that indicate bacterial interactions and elucidate underlying mechanisms.
Collapse
Affiliation(s)
- Faizan Ahmed Sadiq
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Marc Heyndrickx
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology & Food Sciences Unit, Melle, Belgium.,Department of Pathology, Bacteriology and Poultry Diseases, Ghent University, Merelbeke, Belgium
| | - Steve Flint
- School of Food and Advanced Technology, Massey University, Palmerston North, New Zealand
| | - Wenwei Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| |
Collapse
|
7
|
Abstract
Microbes are social organisms, interacting primarily through secreted biomolecules. Many traits have evolved based solely on their effects upon other community members, yet even individually beneficial traits often create social side effects that are mediated by spatial population structure. Predicting the evolution of many microbial traits thus requires a comprehensive understanding of their social consequences. In this review, we examine the critical role of population spatial structure in microbial social evolution. We briefly review key mechanisms structuring microbial communities, focusing primarily on the universal roles of cellular death and reproduction. Finally, we explain how spatial assortment can be efficiently calculated in two-dimensional, surface-attached populations.
Collapse
|
8
|
Horowitz JM, Kardar M. Bacterial range expansions on a growing front: Roughness, fixation, and directed percolation. Phys Rev E 2019; 99:042134. [PMID: 31108639 DOI: 10.1103/physreve.99.042134] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Indexed: 06/09/2023]
Abstract
Directed percolation (DP) is a classic model for nonequilibrium phase transitions into a single absorbing state (fixation). It has been extensively studied by analytical and numerical techniques in diverse contexts. Recently, DP has appeared as a generic model for the evolutionary and ecological dynamics of competing bacterial populations. Range expansion-the stochastic reproduction of bacteria competing for space to be occupied by their progeny-leads to a fluctuating and rough growth front, which is known from experiment and simulation to affect the underlying critical behavior of the DP transition. In this work, we employ symmetry arguments to construct a pair of nonlinear stochastic partial differential equations describing the coevolution of surface roughness with the composition field of DP. Macroscopic manifestations (phenomenology) of these equations on growth patterns and genealogical tracks of range expansion are discussed; followed by a renormalization group analysis of possible scaling behaviors at the DP transition.
Collapse
Affiliation(s)
- Jordan M Horowitz
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, 400 Technology Square, Cambridge, Massachusetts 02139, USA
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Center for the Study of Complex Systems, University of Michigan, Ann Arbor, Michigan 48104, USA
| | - Mehran Kardar
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| |
Collapse
|