1
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Luo N, Lu J, Şimşek E, Silver A, Yao Y, Ouyang X, West SA, You L. The collapse of cooperation during range expansion of Pseudomonas aeruginosa. Nat Microbiol 2024; 9:1220-1230. [PMID: 38443483 PMCID: PMC7615952 DOI: 10.1038/s41564-024-01627-8] [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: 08/12/2022] [Accepted: 01/30/2024] [Indexed: 03/07/2024]
Abstract
Cooperation is commonly believed to be favourable in spatially structured environments, as these systems promote genetic relatedness that reduces the likelihood of exploitation by cheaters. Here we show that a Pseudomonas aeruginosa population that exhibited cooperative swarming was invaded by cheaters when subjected to experimental evolution through cycles of range expansion on solid media, but not in well-mixed liquid cultures. Our results suggest that cooperation is disfavoured in a more structured environment, which is the opposite of the prevailing view. We show that spatial expansion of the population prolongs cooperative swarming, which was vulnerable to cheating. Our findings reveal a mechanism by which spatial structures can suppress cooperation through modulation of the quantitative traits of cooperation, a process that leads to population divergence towards distinct colonization strategies.
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Affiliation(s)
- Nan Luo
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jia Lu
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Emrah Şimşek
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Anita Silver
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Yi Yao
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Xiaoyi Ouyang
- School of Physics, Peking University, Beijing, China
| | - Stuart A West
- Department of Biology, University of Oxford, Oxford, UK
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Center for Quantitative Biodesign, Duke University, Durham, NC, USA.
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
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2
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Tran P, Lander SM, Prindle A. Active pH regulation facilitates Bacillus subtilis biofilm development in a minimally buffered environment. mBio 2024; 15:e0338723. [PMID: 38349175 PMCID: PMC10936434 DOI: 10.1128/mbio.03387-23] [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: 12/18/2023] [Accepted: 01/12/2024] [Indexed: 03/14/2024] Open
Abstract
Biofilms provide individual bacteria with many advantages, yet dense cellular proliferation can also create intrinsic metabolic challenges including excessive acidification. Because such pH stress can be masked in buffered laboratory media-such as MSgg commonly used to study Bacillus subtilis biofilms-it is not always clear how such biofilms cope with minimally buffered natural environments. Here, we report how B. subtilis biofilms overcome this intrinsic metabolic challenge through an active pH regulation mechanism. Specifically, we find that these biofilms can modulate their extracellular pH to the preferred neutrophile range, even when starting from acidic and alkaline initial conditions, while planktonic cells cannot. We associate this behavior with dynamic interplay between acetate and acetoin biosynthesis and show that this mechanism is required to buffer against biofilm acidification. Furthermore, we find that buffering-deficient biofilms exhibit dysregulated biofilm development when grown in minimally buffered conditions. Our findings reveal an active pH regulation mechanism in B. subtilis biofilms that could lead to new targets to control unwanted biofilm growth.IMPORTANCEpH is known to influence microbial growth and community dynamics in multiple bacterial species and environmental contexts. Furthermore, in many bacterial species, rapid cellular proliferation demands the use of overflow metabolism, which can often result in excessive acidification. However, in the case of bacterial communities known as biofilms, these acidification challenges can be masked when buffered laboratory media are employed to stabilize the pH environment for optimal growth. Our study reveals that B. subtilis biofilms use an active pH regulation mechanism to mitigate both growth-associated acidification and external pH challenges. This discovery provides new opportunities for understanding microbial communities and could lead to new methods for controlling biofilm growth outside of buffered laboratory conditions.
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Affiliation(s)
- Peter Tran
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois, USA
| | - Stephen M Lander
- Medical Scientist Training Program, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Arthur Prindle
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Chicago, Illinois, USA
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3
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Babenko I, Kröger N, Friedrich BM. Mechanism of branching morphogenesis inspired by diatom silica formation. Proc Natl Acad Sci U S A 2024; 121:e2309518121. [PMID: 38422023 DOI: 10.1073/pnas.2309518121] [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: 07/13/2023] [Accepted: 01/07/2024] [Indexed: 03/02/2024] Open
Abstract
The silica-based cell walls of diatoms are prime examples of genetically controlled, species-specific mineral architectures. The physical principles underlying morphogenesis of their hierarchically structured silica patterns are not understood, yet such insight could indicate novel routes toward synthesizing functional inorganic materials. Recent advances in imaging nascent diatom silica allow rationalizing possible mechanisms of their pattern formation. Here, we combine theory and experiments on the model diatom Thalassiosira pseudonana to put forward a minimal model of branched rib patterns-a fundamental feature of the silica cell wall. We quantitatively recapitulate the time course of rib pattern morphogenesis by accounting for silica biochemistry with autocatalytic formation of diffusible silica precursors followed by conversion into solid silica. We propose that silica deposition releases an inhibitor that slows down up-stream precursor conversion, thereby implementing a self-replicating reaction-diffusion system different from a classical Turing mechanism. The proposed mechanism highlights the role of geometrical cues for guided self-organization, rationalizing the instructive role for the single initial pattern seed known as the primary silicification site. The mechanism of branching morphogenesis that we characterize here is possibly generic and may apply also in other biological systems.
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Affiliation(s)
- Iaroslav Babenko
- CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden 01307, Germany
- Cluster of Excellence 'Physics of Life', Technische Universität Dresden, Dresden 01307, Germany
| | - Nils Kröger
- CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden 01307, Germany
- Cluster of Excellence 'Physics of Life', Technische Universität Dresden, Dresden 01307, Germany
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden 01062, Germany
| | - Benjamin M Friedrich
- Cluster of Excellence 'Physics of Life', Technische Universität Dresden, Dresden 01307, Germany
- Center for Advancing Electronics Dresden, Technische Universität Dresden, Dresden 01069, Germany
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4
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Childs SK, Jones AAD. A microtiter peg lid with ziggurat geometry for medium-throughput antibiotic testing and in situ imaging of biofilms. Biofilm 2023; 6:100167. [PMID: 38078058 PMCID: PMC10700155 DOI: 10.1016/j.bioflm.2023.100167] [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: 07/26/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 01/12/2024] Open
Abstract
Bacteria biofilm responses to disinfectants and antibiotics are quantified and observed using multiple methods, though microscopy, particularly confocal laser scanning microscopy (CLSM) is preferred due to speed, a reduction in user error, and in situ analysis. CLSM can resolve biological and spatial heterogeneity of biofilms in 3D with limited throughput. The microplate peg-lid-based assay, described in ASTM E2799-22, is a medium-throughput method for testing biofilms but does not permit in situ imaging. Breaking off the peg, as recommended by the manufacturer, risks sample damage, and is limited to easily accessible pegs. Here we report modifications to the peg optimized for in situ visualization and visualization of all pegs. We report similar antibiotic challenge recovery via colony formation following the ASTM E2799-22 protocol and in situ imaging. We report novel quantifiable effects of antibiotics on biofilm morphologies, specifically biofilm streamers. The new design bridges the MBEC® assays design that selects for biofilm phenotypes with in situ imaging needs.
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Affiliation(s)
| | - A-Andrew D. Jones
- Department of Civil & Environmental Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
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Bru JL, Kasallis SJ, Zhuo Q, Høyland-Kroghsbo NM, Siryaporn A. Swarming of P. aeruginosa: Through the lens of biophysics. BIOPHYSICS REVIEWS 2023; 4:031305. [PMID: 37781002 PMCID: PMC10540860 DOI: 10.1063/5.0128140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 08/29/2023] [Indexed: 10/03/2023]
Abstract
Swarming is a collective flagella-dependent movement of bacteria across a surface that is observed across many species of bacteria. Due to the prevalence and diversity of this motility modality, multiple models of swarming have been proposed, but a consensus on a general mechanism for swarming is still lacking. Here, we focus on swarming by Pseudomonas aeruginosa due to the abundance of experimental data and multiple models for this species, including interpretations that are rooted in biology and biophysics. In this review, we address three outstanding questions about P. aeruginosa swarming: what drives the outward expansion of a swarm, what causes the formation of dendritic patterns (tendrils), and what are the roles of flagella? We review models that propose biologically active mechanisms including surfactant sensing as well as fluid mechanics-based models that consider swarms as thin liquid films. Finally, we reconcile recent observations of P. aeruginosa swarms with early definitions of swarming. This analysis suggests that mechanisms associated with sliding motility have a critical role in P. aeruginosa swarm formation.
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Affiliation(s)
- Jean-Louis Bru
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California 92697, USA
| | - Summer J. Kasallis
- Department of Physics and Astronomy, University of California Irvine, Irvine, California 92697, USA
| | - Quantum Zhuo
- Department of Physics and Astronomy, University of California Irvine, Irvine, California 92697, USA
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Deforet M. Long-range alteration of the physical environment mediates cooperation between Pseudomonas aeruginosa swarming colonies. Environ Microbiol 2023. [PMID: 36964975 DOI: 10.1111/1462-2920.16373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 03/15/2023] [Indexed: 03/27/2023]
Abstract
Pseudomonas aeruginosa makes and secretes massive amounts of rhamnolipid surfactants that enable swarming motility over biogel surfaces. But how these rhamnolipids interact with biogels to assist swarming remains unclear. Here, I use a combination of optical techniques across scales and genetically engineered strains to demonstrate that rhamnolipids can induce agar gel swelling over distances >10,000× the body size of an individual cell. The swelling front is on the micrometric scale and is easily visible using shadowgraphy. Rhamnolipid transport is not restricted to the surface of the gel but occurs through the whole thickness of the plate and, consequently, the spreading dynamics depend on the local thickness. Surprisingly, rhamnolipids can cross the whole gel and induce swelling on the opposite side of a two-face Petri dish. The swelling front delimits an area where the mechanical properties of the surface properties are modified: water wets the surface more easily, which increases the motility of individual bacteria and enables collective motility. A genetically engineered mutant unable to secrete rhamnolipids (ΔrhlA), and therefore unable to swarm, is rescued from afar with rhamnolipids produced by a remote colony. These results exemplify the remarkable capacity of bacteria to change the physical environment around them and its ecological consequences.
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Affiliation(s)
- Maxime Deforet
- Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire Jean Perrin, LJP, Paris, 75005, France
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7
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Formation of unique T-shape budding and differential impacts of low surface water on Bacillus mycoides rhizoidal colony. Arch Microbiol 2022; 204:528. [PMID: 35896814 DOI: 10.1007/s00203-022-03141-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/24/2022] [Accepted: 07/13/2022] [Indexed: 11/02/2022]
Abstract
Bacillus mycoides Ko01 strain grows rapidly and forms extensive rhizoidal colonies on hard agar despite limited surface water availability. The agar concentrations affect the handedness of the colonies as well as other colony architectures. In this study, we found that the local curvature of cell chains in the developing colonies did not vary based on the agar concentration, while concentration does affect the handedness of chirality at the macroscale. This result suggests independence between the microscale filament curvature and macroscale colony chirality. In addition, we discovered a novel microscopic property of cells that has not been observed before: T-shaped budding under extremely low surface water availability conditions. We propose that this feature gives rise to chaotic colony morphology. Together with bundling of chains, cells form a unique set of spatial arrangements under different surface water availability. These properties appear to impact the structural features of thick tendrils, and thereby the overall morphology of colonies. Our study provides additional insights as to how bacteria proliferate, spread, and develop macroscale colony architecture under water-limited conditions.
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8
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Spatial patterns in ecological systems: from microbial colonies to landscapes. Emerg Top Life Sci 2022; 6:245-258. [PMID: 35678374 DOI: 10.1042/etls20210282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 11/17/2022]
Abstract
Self-organized spatial patterns are ubiquitous in ecological systems and allow populations to adopt non-trivial spatial distributions starting from disordered configurations. These patterns form due to diverse nonlinear interactions among organisms and between organisms and their environment, and lead to the emergence of new (eco)system-level properties unique to self-organized systems. Such pattern consequences include higher resilience and resistance to environmental changes, abrupt ecosystem collapse, hysteresis loops, and reversal of competitive exclusion. Here, we review ecological systems exhibiting self-organized patterns. We establish two broad pattern categories depending on whether the self-organizing process is primarily driven by nonlinear density-dependent demographic rates or by nonlinear density-dependent movement. Using this organization, we examine a wide range of observational scales, from microbial colonies to whole ecosystems, and discuss the mechanisms hypothesized to underlie observed patterns and their system-level consequences. For each example, we review both the empirical evidence and the existing theoretical frameworks developed to identify the causes and consequences of patterning. Finally, we trace qualitative similarities across systems and propose possible ways of developing a more quantitative understanding of how self-organization operates across systems and observational scales in ecology.
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Lu J, Şimşek E, Silver A, You L. Advances and challenges in programming pattern formation using living cells. Curr Opin Chem Biol 2022; 68:102147. [DOI: 10.1016/j.cbpa.2022.102147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 11/29/2022]
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10
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Bryant AS, Lavrentovich MO. Survival in branching cellular populations. Theor Popul Biol 2022; 144:13-23. [PMID: 35093390 DOI: 10.1016/j.tpb.2022.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 01/15/2022] [Accepted: 01/15/2022] [Indexed: 10/19/2022]
Abstract
We analyze evolutionary dynamics in a confluent, branching cellular population, such as in a growing duct, vasculature, or in a branching microbial colony. We focus on the coarse-grained features of the evolution and build a statistical model that captures the essential features of the dynamics. Using simulations and analytic approaches, we show that the survival probability of strains within the growing population is sensitive to the branching geometry: Branch bifurcations enhance survival probability due to an overall population growth (i.e., "inflation"), while branch termination and the small effective population size at the growing branch tips increase the probability of strain extinction. We show that the evolutionary dynamics may be captured on a wide range of branch geometries parameterized just by the branch diameter N0 and branching rate b. We find that the survival probability of neutral cell strains is largest at an "optimal" branching rate, which balances the effects of inflation and branch termination. We find that increasing the selective advantage s of the cell strain mitigates the inflationary effect by decreasing the average time at which the mutant cell fate is determined. For sufficiently large selective advantages, the survival probability of the advantageous mutant decreases monotonically with the branching rate.
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Affiliation(s)
- Adam S Bryant
- Department of Physics & Astronomy, University of Tennessee, Knoxville, TN 37966, USA
| | - Maxim O Lavrentovich
- Department of Physics & Astronomy, University of Tennessee, Knoxville, TN 37966, USA.
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11
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Wang T, You L. Bringing cells to the edge. eLife 2022; 11:83789. [PMID: 36322127 PMCID: PMC9629828 DOI: 10.7554/elife.83789] [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: 11/07/2022] Open
Abstract
A network of open channels allows cells and molecular cargo to travel from the center to the periphery of lab-grown colonies of Pseudomonas aeruginosa, helping to eradicate competing species.
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Affiliation(s)
- Teng Wang
- Department of Biomedical Engineering and the Center for Quantitative Biodesign, Duke UniversityDurhamUnited States
| | - Lingchong You
- Department of Biomedical Engineering and the Center for Quantitative Biodesign, Duke UniversityDurhamUnited States
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12
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Capponi S, Wang S, Navarro EJ, Bianco S. AI-driven prediction of SARS-CoV-2 variant binding trends from atomistic simulations. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:123. [PMID: 34613523 PMCID: PMC8493367 DOI: 10.1140/epje/s10189-021-00119-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 08/24/2021] [Indexed: 05/02/2023]
Abstract
We present a novel technique to predict binding affinity trends between two molecules from atomistic molecular dynamics simulations. The technique uses a neural network algorithm applied to a series of images encoding the distance between two molecules in time. We demonstrate that our algorithm is capable of separating with high accuracy non-hydrophobic mutations with low binding affinity from those with high binding affinity. Moreover, we show high accuracy in prediction using a small subset of the simulation, therefore requiring a much shorter simulation time. We apply our algorithm to the binding between several variants of the SARS-CoV-2 spike protein and the human receptor ACE2.
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Affiliation(s)
- Sara Capponi
- IBM Almaden Research Center, 650 Harry Rd, San Jose, CA, 95120, USA
- Center for Cellular Construction, San Francisco, CA, 94158, USA
| | - Shangying Wang
- IBM Almaden Research Center, 650 Harry Rd, San Jose, CA, 95120, USA
- Center for Cellular Construction, San Francisco, CA, 94158, USA
| | - Erik J Navarro
- IBM Almaden Research Center, 650 Harry Rd, San Jose, CA, 95120, USA
- Center for Cellular Construction, San Francisco, CA, 94158, USA
- Graduate Program in Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Simone Bianco
- IBM Almaden Research Center, 650 Harry Rd, San Jose, CA, 95120, USA.
- Center for Cellular Construction, San Francisco, CA, 94158, USA.
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The spatial organization of microbial communities during range expansion. Curr Opin Microbiol 2021; 63:109-116. [PMID: 34329942 DOI: 10.1016/j.mib.2021.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/26/2021] [Accepted: 07/05/2021] [Indexed: 12/28/2022]
Abstract
Microbes in nature often live in dense and diverse communities exhibiting a variety of spatial structures. Microbial range expansion is a universal ecological process that enables populations to form spatial patterns. It can be driven by both passive and active processes, for example, mechanical forces from cell growth and bacterial motility. In this review, we provide a taste of recent creative and sophisticated efforts being made to address basic questions in spatial ecology and pattern formation during range expansion. We especially highlight the role of motility to shape community structures, and discuss the research challenges and future directions.
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