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Self-organization of bacterial communities against environmental pH variation: Controlled chemotactic motility arranges cell population structures in biofilms. PLoS One 2017; 12:e0173195. [PMID: 28253348 PMCID: PMC5333884 DOI: 10.1371/journal.pone.0173195] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 02/16/2017] [Indexed: 11/19/2022] Open
Abstract
As with many living organisms, bacteria often live on the surface of solids, such as foods, organisms, buildings and soil. Compared with dispersive behavior in liquid, bacteria on surface environment exhibit significantly restricted mobility. They have access to only limited resources and cannot be liberated from the changing environment. Accordingly, appropriate collective strategies are necessarily required for long-term growth and survival. However, in spite of our deepening knowledge of the structure and characteristics of individual cells, strategic self-organizing dynamics of their community is poorly understood and therefore not yet predictable. Here, we report a morphological change in Bacillus subtilis biofilms due to environmental pH variations, and present a mathematical model for the macroscopic spatio-temporal dynamics. We show that an environmental pH shift transforms colony morphology on hard agar media from notched 'volcano-like' to round and front-elevated 'crater-like'. We discover that a pH-dependent dose-response relationship between nutritional resource level and quantitative bacterial motility at the population level plays a central role in the mechanism of the spatio-temporal cell population structure design in biofilms.
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Nuñez IN, Matute TF, Del Valle ID, Kan A, Choksi A, Endy D, Haseloff J, Rudge TJ, Federici F. Artificial Symmetry-Breaking for Morphogenetic Engineering Bacterial Colonies. ACS Synth Biol 2017; 6:256-265. [PMID: 27794593 DOI: 10.1021/acssynbio.6b00149] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Morphogenetic engineering is an emerging field that explores the design and implementation of self-organized patterns, morphologies, and architectures in systems composed of multiple agents such as cells and swarm robots. Synthetic biology, on the other hand, aims to develop tools and formalisms that increase reproducibility, tractability, and efficiency in the engineering of biological systems. We seek to apply synthetic biology approaches to the engineering of morphologies in multicellular systems. Here, we describe the engineering of two mechanisms, symmetry-breaking and domain-specific cell regulation, as elementary functions for the prototyping of morphogenetic instructions in bacterial colonies. The former represents an artificial patterning mechanism based on plasmid segregation while the latter plays the role of artificial cell differentiation by spatial colocalization of ubiquitous and segregated components. This separation of patterning from actuation facilitates the design-build-test-improve engineering cycle. We created computational modules for CellModeller representing these basic functions and used it to guide the design process and explore the design space in silico. We applied these tools to encode spatially structured functions such as metabolic complementation, RNAPT7 gene expression, and CRISPRi/Cas9 regulation. Finally, as a proof of concept, we used CRISPRi/Cas technology to regulate cell growth by controlling methionine synthesis. These mechanisms start from single cells enabling the study of morphogenetic principles and the engineering of novel population scale structures from the bottom up.
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Affiliation(s)
- Isaac N. Nuñez
- Escuela
de Ingeniería, Pontificia Universidad Católica de Chile, 7820436, Santiago, Chile
- Fondo
de Desarrollo de Areas Prioritarias Center for Genome Regulation,
Millennium Nucleus Center for Plant Systems and Synthetic Biology, Pontificia Universidad Católica de Chile, 7820436, Santiago, Chile
| | - Tamara F. Matute
- Escuela
de Ingeniería, Pontificia Universidad Católica de Chile, 7820436, Santiago, Chile
- Fondo
de Desarrollo de Areas Prioritarias Center for Genome Regulation,
Millennium Nucleus Center for Plant Systems and Synthetic Biology, Pontificia Universidad Católica de Chile, 7820436, Santiago, Chile
| | - Ilenne D. Del Valle
- Departamento
de Genética Molecular y Microbiología, Facultad de Ciencias
Biológicas, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
| | - Anton Kan
- Department
of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Atri Choksi
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States,
| | - Drew Endy
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States,
| | - Jim Haseloff
- Department
of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Timothy J. Rudge
- Escuela
de Ingeniería, Pontificia Universidad Católica de Chile, 7820436, Santiago, Chile
| | - Fernan Federici
- Departamento
de Genética Molecular y Microbiología, Facultad de Ciencias
Biológicas, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
- Department
of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
- Fondo
de Desarrollo de Areas Prioritarias Center for Genome Regulation,
Millennium Nucleus Center for Plant Systems and Synthetic Biology, Pontificia Universidad Católica de Chile, 7820436, Santiago, Chile
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Jayathilake PG, Gupta P, Li B, Madsen C, Oyebamiji O, González-Cabaleiro R, Rushton S, Bridgens B, Swailes D, Allen B, McGough AS, Zuliani P, Ofiteru ID, Wilkinson D, Chen J, Curtis T. A mechanistic Individual-based Model of microbial communities. PLoS One 2017. [PMID: 28771505 DOI: 10.1371/jou0181965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Accurate predictive modelling of the growth of microbial communities requires the credible representation of the interactions of biological, chemical and mechanical processes. However, although biological and chemical processes are represented in a number of Individual-based Models (IbMs) the interaction of growth and mechanics is limited. Conversely, there are mechanically sophisticated IbMs with only elementary biology and chemistry. This study focuses on addressing these limitations by developing a flexible IbM that can robustly combine the biological, chemical and physical processes that dictate the emergent properties of a wide range of bacterial communities. This IbM is developed by creating a microbiological adaptation of the open source Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). This innovation should provide the basis for "bottom up" prediction of the emergent behaviour of entire microbial systems. In the model presented here, bacterial growth, division, decay, mechanical contact among bacterial cells, and adhesion between the bacteria and extracellular polymeric substances are incorporated. In addition, fluid-bacteria interaction is implemented to simulate biofilm deformation and erosion. The model predicts that the surface morphology of biofilms becomes smoother with increased nutrient concentration, which agrees well with previous literature. In addition, the results show that increased shear rate results in smoother and more compact biofilms. The model can also predict shear rate dependent biofilm deformation, erosion, streamer formation and breakup.
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Affiliation(s)
- Pahala Gedara Jayathilake
- School of Mechanical & Systems Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Prashant Gupta
- School of Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Bowen Li
- School of Computing Science, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Curtis Madsen
- School of Computing Science, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Oluwole Oyebamiji
- School of Mathematics & Statistics, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Rebeca González-Cabaleiro
- School of Chemical Engineering and Advanced Materials, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Steve Rushton
- School of Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ben Bridgens
- School of Civil Engineering & Geosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - David Swailes
- School of Mechanical & Systems Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ben Allen
- School of Civil Engineering & Geosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - A Stephen McGough
- School of Computing Science, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Paolo Zuliani
- School of Computing Science, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Irina Dana Ofiteru
- School of Chemical Engineering and Advanced Materials, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Darren Wilkinson
- School of Mathematics & Statistics, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jinju Chen
- School of Mechanical & Systems Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Tom Curtis
- School of Civil Engineering & Geosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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55
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Mao J, Lu T. Population-Dynamic Modeling of Bacterial Horizontal Gene Transfer by Natural Transformation. Biophys J 2016; 110:258-68. [PMID: 26745428 PMCID: PMC4806214 DOI: 10.1016/j.bpj.2015.11.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 11/07/2015] [Accepted: 11/24/2015] [Indexed: 11/18/2022] Open
Abstract
Natural transformation is a major mechanism of horizontal gene transfer (HGT) and plays an essential role in bacterial adaptation, evolution, and speciation. Although its molecular underpinnings have been increasingly revealed, natural transformation is not well characterized in terms of its quantitative ecological roles. Here, by using Neisseria gonorrhoeae as an example, we developed a population-dynamic model for natural transformation and analyzed its dynamic characteristics with nonlinear tools and simulations. Our study showed that bacteria capable of natural transformation can display distinct population behaviors ranging from extinction to coexistence and to bistability, depending on their HGT rate and selection coefficient. With the model, we also illustrated the roles of environmental DNA sources-active secretion and passive release-in impacting population dynamics. Additionally, by constructing and utilizing a stochastic version of the model, we examined how noise shapes the steady and dynamic behaviors of the system. Notably, we found that distinct waiting time statistics for HGT events, namely a power-law distribution, an exponential distribution, and a mix of the both, are associated with the dynamics in the regimes of extinction, coexistence, and bistability accordingly. This work offers a quantitative illustration of natural transformation by revealing its complex population dynamics and associated characteristics, therefore advancing our ecological understanding of natural transformation as well as HGT in general.
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Affiliation(s)
- Junwen Mao
- Department of Physics, Huzhou University, Zhejiang, China; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Ting Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.
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