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Nasiri M, Loran E, Liebchen B. Smart active particles learn and transcend bacterial foraging strategies. Proc Natl Acad Sci U S A 2024; 121:e2317618121. [PMID: 38557193 PMCID: PMC11009669 DOI: 10.1073/pnas.2317618121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/30/2024] [Indexed: 04/04/2024] Open
Abstract
Throughout evolution, bacteria and other microorganisms have learned efficient foraging strategies that exploit characteristic properties of their unknown environment. While much research has been devoted to the exploration of statistical models describing the dynamics of foraging bacteria and other (micro-) organisms, little is known, regarding the question of how good the learned strategies actually are. This knowledge gap is largely caused by the absence of methods allowing to systematically develop alternative foraging strategies to compare with. In the present work, we use deep reinforcement learning to show that a smart run-and-tumble agent, which strives to find nutrients for its survival, learns motion patterns that are remarkably similar to the trajectories of chemotactic bacteria. Strikingly, despite this similarity, we also find interesting differences between the learned tumble rate distribution and the one that is commonly assumed for the run and tumble model. We find that these differences equip the agent with significant advantages regarding its foraging and survival capabilities. Our results uncover a generic route to use deep reinforcement learning for discovering search and collection strategies that exploit characteristic but initially unknown features of the environment. These results can be used, e.g., to program future microswimmers, nanorobots, and smart active particles for tasks like searching for cancer cells, micro-waste collection, or environmental remediation.
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Affiliation(s)
- Mahdi Nasiri
- Institute of Condensed Matter Physics, Department of Physics, Technische Universität Darmstadt, DarmstadtD-64289, Germany
| | - Edwin Loran
- Institute of Condensed Matter Physics, Department of Physics, Technische Universität Darmstadt, DarmstadtD-64289, Germany
| | - Benno Liebchen
- Institute of Condensed Matter Physics, Department of Physics, Technische Universität Darmstadt, DarmstadtD-64289, Germany
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Ugolini GS, Wang M, Secchi E, Pioli R, Ackermann M, Stocker R. Microfluidic approaches in microbial ecology. LAB ON A CHIP 2024; 24:1394-1418. [PMID: 38344937 PMCID: PMC10898419 DOI: 10.1039/d3lc00784g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Microbial life is at the heart of many diverse environments and regulates most natural processes, from the functioning of animal organs to the cycling of global carbon. Yet, the study of microbial ecology is often limited by challenges in visualizing microbial processes and replicating the environmental conditions under which they unfold. Microfluidics operates at the characteristic scale at which microorganisms live and perform their functions, thus allowing for the observation and quantification of behaviors such as growth, motility, and responses to external cues, often with greater detail than classical techniques. By enabling a high degree of control in space and time of environmental conditions such as nutrient gradients, pH levels, and fluid flow patterns, microfluidics further provides the opportunity to study microbial processes in conditions that mimic the natural settings harboring microbial life. In this review, we describe how recent applications of microfluidic systems to microbial ecology have enriched our understanding of microbial life and microbial communities. We highlight discoveries enabled by microfluidic approaches ranging from single-cell behaviors to the functioning of multi-cellular communities, and we indicate potential future opportunities to use microfluidics to further advance our understanding of microbial processes and their implications.
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Affiliation(s)
- Giovanni Stefano Ugolini
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Miaoxiao Wang
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
| | - Eleonora Secchi
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Roberto Pioli
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Martin Ackermann
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
- Laboratory of Microbial Systems Ecology, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédéral de Lausanne (EPFL), Lausanne, Switzerland
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
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Bacteria phototaxis optimizer. Neural Comput Appl 2023. [DOI: 10.1007/s00521-023-08391-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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Zhang Y, Wei D, Wang X, Wang B, Li M, Fang H, Peng Y, Fan Q, Ye F. Run-and-Tumble Dynamics and Mechanotaxis Discovered in Microglial Migration. RESEARCH (WASHINGTON, D.C.) 2023; 6:0063. [PMID: 36939442 PMCID: PMC10013966 DOI: 10.34133/research.0063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 01/09/2023] [Indexed: 01/22/2023]
Abstract
Microglia are resident macrophage cells in the central nervous system that search for pathogens or abnormal neural activities and migrate to resolve the issues. The effective search and targeted motion of macrophages mean dearly to maintaining a healthy brain, yet little is known about their migration dynamics. In this work, we study microglial motion with and without the presence of external mechanostimuli. We discover that the cells are promptly attracted by the applied forces (i.e., mechanotaxis), which is a tactic behavior as yet unconfirmed in microglia. Meanwhile, in both the explorative and the targeted migration, microglia display dynamics that is strikingly analogous to bacterial run-and-tumble motion. A closer examination reveals that microglial run-and-tumble is more sophisticated, e.g., they display a short-term memory when tumbling and rely on active steering during runs to achieve mechanotaxis, probably via the responses of mechanosensitive ion channels. These differences reflect the sharp contrast between microglia and bacteria cells (eukaryotes vs. prokaryotes) and their environments (compact tissue vs. fluid). Further analyses suggest that the reported migration dynamics has an optimal search efficiency and is shared among a subset of immune cells (human monocyte and macrophage). This work reveals a fruitful analogy between the locomotion of 2 remote systems and provides a framework for studying immune cells exploring complex environments.
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Affiliation(s)
- Yiyu Zhang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,
Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences,
University of Chinese Academy of Sciences, Beijing 100049, China
| | - Da Wei
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,
Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaochen Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,
Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences,
University of Chinese Academy of Sciences, Beijing 100049, China
- Wenzhou Institute,
University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Boyi Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,
Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences,
University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,
Chinese Academy of Sciences, Beijing 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Haiping Fang
- Wenzhou Institute,
University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- School of Science,
East China University of Science and Technology, Shanghai 200237, China
| | - Yi Peng
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,
Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences,
University of Chinese Academy of Sciences, Beijing 100049, China
- Address correspondence to: (F.Y.); (Y.P.); (Q.F.)
| | - Qihui Fan
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,
Chinese Academy of Sciences, Beijing 100190, China
- Address correspondence to: (F.Y.); (Y.P.); (Q.F.)
| | - Fangfu Ye
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,
Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences,
University of Chinese Academy of Sciences, Beijing 100049, China
- Wenzhou Institute,
University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang 325000, China
- Address correspondence to: (F.Y.); (Y.P.); (Q.F.)
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Jiang L, Mo H, Tian P. An adaptive decentralized control strategy for deployment and aggregation of swarm robots based on bacterial chemotaxis. APPL INTELL 2022. [DOI: 10.1007/s10489-022-04128-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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6
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Marthaler PG, Class AG. Weak curvature asymptotics for Debye layers as electrohydrodynamic discontinuities. Phys Rev E 2022; 105:035106. [PMID: 35428041 DOI: 10.1103/physreve.105.035106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Important microfluidic phenomena, such as droplet deformation and cell motion, are impacted by the formation of Debye layers at charged interfaces. Previous studies examined interface problems with leaky dielectrics or the formation of diffuse charge layers. In most cases, the results are derived for weakly curved spherical geometries. Moreover, many studies of streaming-potential phenomena at fluid-solid interfaces lack a macroscale description of effects that are higher than first order. An asymptotic methodology capturing both complex surface geometries and an accurate description of higher-order phenomena is presented in this study. For this purpose, we consider a generic streaming-potential problem. As a result, the complex three-dimensional electrohydrodynamics in the Debye layer are entailed in two-dimensional discontinuity conditions. The latter contain a free parameter, the layer thickness, which mathematically represents the discontinuity position within the Debye layer. It can be used to derive an alternative definition of the Debye thickness capturing the influence of the ζ potential. We introduce a virtual particle whose outer boundary envelopes the solid particle plus a fraction of the Debye layer. It interacts with the macroscopic flow while incorporating the detailed electrohydrodynamics inside the layer.
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Affiliation(s)
- Philipp G Marthaler
- Institute for Thermal Energy Technology and Safety, Karlsruhe Institute of Technology, 76131 Karlsruhe, Baden-Württemberg, Germany
| | - Andreas G Class
- Institute for Thermal Energy Technology and Safety, Karlsruhe Institute of Technology, 76131 Karlsruhe, Baden-Württemberg, Germany
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Arellano-Caicedo C, Ohlsson P, Bengtsson M, Beech JP, Hammer EC. Habitat geometry in artificial microstructure affects bacterial and fungal growth, interactions, and substrate degradation. Commun Biol 2021; 4:1226. [PMID: 34702996 PMCID: PMC8548513 DOI: 10.1038/s42003-021-02736-4] [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: 12/11/2020] [Accepted: 10/01/2021] [Indexed: 11/25/2022] Open
Abstract
Microhabitat conditions determine the magnitude and speed of microbial processes but have been challenging to investigate. In this study we used microfluidic devices to determine the effect of the spatial distortion of a pore space on fungal and bacterial growth, interactions, and substrate degradation. The devices contained channels differing in bending angles and order. Sharper angles reduced fungal and bacterial biomass, especially when angles were repeated in the same direction. Substrate degradation was only decreased by sharper angles when fungi and bacteria were grown together. Investigation at the cellular scale suggests that this was caused by fungal habitat modification, since hyphae branched in sharp and repeated turns, blocking the dispersal of bacteria and the substrate. Our results demonstrate how the geometry of microstructures can influence microbial activity. This can be transferable to soil pore spaces, where spatial occlusion and microbial feedback on microstructures is thought to explain organic matter stabilization.
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Affiliation(s)
| | - Pelle Ohlsson
- Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Martin Bengtsson
- Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Jason P Beech
- Division of Solid State Physics, Lund University, Lund, Sweden
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E. coli takes every hurdle in stride. Nat Rev Microbiol 2019; 17:462-463. [DOI: 10.1038/s41579-019-0224-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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