1
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Engelhardt IC, Patko D, Liu Y, Mimault M, de Las Heras Martinez G, George TS, MacDonald M, Ptashnyk M, Sukhodub T, Stanley-Wall NR, Holden N, Daniell TJ, Dupuy LX. Novel form of collective movement by soil bacteria. THE ISME JOURNAL 2022; 16:2337-2347. [PMID: 35798939 PMCID: PMC9478162 DOI: 10.1038/s41396-022-01277-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 06/07/2022] [Accepted: 06/17/2022] [Indexed: 04/16/2023]
Abstract
Although migrations are essential for soil microorganisms to exploit scarce and heterogeneously distributed resources, bacterial mobility in soil remains poorly studied due to experimental limitations. In this study, time-lapse images collected using live microscopy techniques captured collective and coordinated groups of B. subtilis cells exhibiting "crowd movement". Groups of B. subtilis cells moved through transparent soil (nafion polymer with particle size resembling sand) toward plant roots and re-arranged dynamically around root tips in the form of elongating and retracting "flocks" resembling collective behaviour usually associated with higher organisms (e.g., bird flocks or fish schools). Genetic analysis reveals B. subtilis flocks are likely driven by the diffusion of extracellular signalling molecules (e.g., chemotaxis, quorum sensing) and may be impacted by the physical obstacles and hydrodynamics encountered in the soil like environment. Our findings advance understanding of bacterial migration through soil matrices and expand known behaviours for coordinated bacterial movement.
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Affiliation(s)
- I C Engelhardt
- Ecological Sciences, The James Hutton Institute, Dundee, UK
- Department of Conservation of Natural Resources, Neiker, Bilbao, Spain
| | - D Patko
- Ecological Sciences, The James Hutton Institute, Dundee, UK
- Department of Conservation of Natural Resources, Neiker, Bilbao, Spain
| | - Y Liu
- Ecological Sciences, The James Hutton Institute, Dundee, UK
- ICS, The James Hutton Institute, Dundee, UK
| | - M Mimault
- ICS, The James Hutton Institute, Dundee, UK
| | | | - T S George
- Ecological Sciences, The James Hutton Institute, Dundee, UK
| | - M MacDonald
- School of Science and Engineering, University of Dundee, Dundee, UK
| | - M Ptashnyk
- School of Mathematical & Computer Sciences, Heriot-Watt University, Edinburgh, UK
| | - T Sukhodub
- School of Life Sciences, University of Dundee, Dundee, UK
| | | | - N Holden
- Ecological Sciences, The James Hutton Institute, Dundee, UK
- North Faculty, Scotland's Rural College, Aberdeen, UK
| | - T J Daniell
- Plants, Photosynthesis and Soil, School of Biosciences, The University of Sheffield, Sheffield, UK
| | - L X Dupuy
- Ecological Sciences, The James Hutton Institute, Dundee, UK.
- Department of Conservation of Natural Resources, Neiker, Bilbao, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
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2
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Li Y, Liu S, Zhang Y, Seng ZJ, Xu H, Yang L, Wu Y. Self-organized canals enable long-range directed material transport in bacterial communities. eLife 2022; 11:e79780. [PMID: 36154945 PMCID: PMC9633063 DOI: 10.7554/elife.79780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 09/23/2022] [Indexed: 11/30/2022] Open
Abstract
Long-range material transport is essential to maintain the physiological functions of multicellular organisms such as animals and plants. By contrast, material transport in bacteria is often short-ranged and limited by diffusion. Here, we report a unique form of actively regulated long-range directed material transport in structured bacterial communities. Using Pseudomonas aeruginosa colonies as a model system, we discover that a large-scale and temporally evolving open-channel system spontaneously develops in the colony via shear-induced banding. Fluid flows in the open channels support high-speed (up to 450 µm/s) transport of cells and outer membrane vesicles over centimeters, and help to eradicate colonies of a competing species Staphylococcus aureus. The open channels are reminiscent of human-made canals for cargo transport, and the channel flows are driven by interfacial tension mediated by cell-secreted biosurfactants. The spatial-temporal dynamics of fluid flows in the open channels are qualitatively described by flow profile measurement and mathematical modeling. Our findings demonstrate that mechanochemical coupling between interfacial force and biosurfactant kinetics can coordinate large-scale material transport in primitive life forms, suggesting a new principle to engineer self-organized microbial communities.
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Affiliation(s)
- Ye Li
- Department of Physics and Shenzhen Research Institute, The Chinese University of Hong KongHong KongChina
| | - Shiqi Liu
- Department of Physics and Shenzhen Research Institute, The Chinese University of Hong KongHong KongChina
| | - Yingdan Zhang
- School of Medicine, Southern University of Science and TechnologyShenzhenChina
| | - Zi Jing Seng
- Singapore Center for Environmental Life Science Engineering, Nanyang Technological UniversitySingaporeSingapore
| | - Haoran Xu
- Department of Physics and Shenzhen Research Institute, The Chinese University of Hong KongHong KongChina
| | - Liang Yang
- School of Medicine, Southern University of Science and TechnologyShenzhenChina
| | - Yilin Wu
- Department of Physics and Shenzhen Research Institute, The Chinese University of Hong KongHong KongChina
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3
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Aranson IS. Bacterial active matter. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2022; 85:076601. [PMID: 35605446 DOI: 10.1088/1361-6633/ac723d] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Bacteria are among the oldest and most abundant species on Earth. Bacteria successfully colonize diverse habitats and play a significant role in the oxygen, carbon, and nitrogen cycles. They also form human and animal microbiota and may become sources of pathogens and a cause of many infectious diseases. Suspensions of motile bacteria constitute one of the most studied examples of active matter: a broad class of non-equilibrium systems converting energy from the environment (e.g., chemical energy of the nutrient) into mechanical motion. Concentrated bacterial suspensions, often termed active fluids, exhibit complex collective behavior, such as large-scale turbulent-like motion (so-called bacterial turbulence) and swarming. The activity of bacteria also affects the effective viscosity and diffusivity of the suspension. This work reports on the progress in bacterial active matter from the physics viewpoint. It covers the key experimental results, provides a critical assessment of major theoretical approaches, and addresses the effects of visco-elasticity, liquid crystallinity, and external confinement on collective behavior in bacterial suspensions.
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Affiliation(s)
- Igor S Aranson
- Departments of Biomedical Engineering, Chemistry, and Mathematics, Pennsylvania State University, University Park, PA 16802, United States of America
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4
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Berg JS, Ahmerkamp S, Pjevac P, Hausmann B, Milucka J, Kuypers MMM. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6517451. [PMID: 35094062 PMCID: PMC9075580 DOI: 10.1093/femsre/fuac006] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 12/01/2022] Open
Abstract
Oxygen (O2) is the ultimate oxidant on Earth and its respiration confers such an energetic advantage that microorganisms have evolved the capacity to scavenge O2 down to nanomolar concentrations. The respiration of O2 at extremely low levels is proving to be common to diverse microbial taxa, including organisms formerly considered strict anaerobes. Motivated by recent advances in O2 sensing and DNA/RNA sequencing technologies, we performed a systematic review of environmental metatranscriptomes revealing that microbial respiration of O2 at nanomolar concentrations is ubiquitous and drives microbial activity in seemingly anoxic aquatic habitats. These habitats were key to the early evolution of life and are projected to become more prevalent in the near future due to anthropogenic-driven environmental change. Here, we summarize our current understanding of aerobic microbial respiration under apparent anoxia, including novel processes, their underlying biochemical pathways, the involved microorganisms, and their environmental importance and evolutionary origin.
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Affiliation(s)
- Jasmine S Berg
- Corrresponding author: Géopolis, Quartier Unil-Mouline, Université de Lausanne, 1015 Lausanne, Switzerland. E-mail:
| | - Soeren Ahmerkamp
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen 2359, Germany
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna 1090, Austria
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1090, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna 1090, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna 1090, Austria
| | - Jana Milucka
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen 2359, Germany
| | - Marcel M M Kuypers
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen 2359, Germany
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5
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Sylvestre MN, Jean-Louis P, Grimonprez A, Bilas P, Collienne A, Azède C, Gros O. Candidatus Thiovulum sp. strain imperiosus: the largest free-living Epsilonproteobacteraeota Thiovulum strain lives in a marine mangrove environment. Can J Microbiol 2021; 68:1-14. [PMID: 34461021 DOI: 10.1139/cjm-2021-0101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A large (47.75 ± 3.56 µm in diameter) Thiovulum bacterial strain forming white veils is described from a marine mangrove ecosystem. High sulfide concentrations (up to 8 mM of H2S) were measured on sunken organic matter (wood/bone debris) under laboratory conditions. This sulfur-oxidizing bacterium colonized the organic matter, forming a white veil. According to conventional scanning electron microscope (SEM) observations, bacterial cells are ovoid and slightly motile by numerous small flagella present on the cell surface. Large intracytoplasmic internal sulfur granules were observed, suggesting a sulfidic-based metabolism. Observations were confirmed by elemental sulfur distribution detected by energy-dispersive X-ray spectroscopy (EDXS) analysis using an environmental scanning electron microscope (ESEM) on non-dehydrated samples. Phylogenetic analysis of the partial sequence of 16S rDNA obtained from purified fractions of this Epsilonproteobacteraeota strain indicates that this bacterium belongs to the Thiovulaceae cluster and could be one of the largest Thiovulum ever described. We propose to name this species Candidatus Thiovulum sp. strain imperiosus.
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Affiliation(s)
- Marie-Noëlle Sylvestre
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, BP 592 - 97159 Pointe-à-Pitre, Guadeloupe
| | - Patrick Jean-Louis
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, BP 592 - 97159 Pointe-à-Pitre, Guadeloupe
| | - Adrien Grimonprez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, BP 592 - 97159 Pointe-à-Pitre, Guadeloupe
| | - Philippe Bilas
- Centre Commun de Caractérisation des Matériaux des Antilles et de la Guyane (C3MAG), UFR des Sciences Exactes et Naturelles, Université des Antilles, BP 592 - 97159 Pointe-à-Pitre, Guadeloupe
- Groupe de Technologie des Surfaces et des Interfaces, Université des Antilles, BP 592 - 97159 Pointe-à-Pitre, Guadeloupe
| | - Amandine Collienne
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, BP 592 - 97159 Pointe-à-Pitre, Guadeloupe
| | - Catherine Azède
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, BP 592 - 97159 Pointe-à-Pitre, Guadeloupe
| | - Olivier Gros
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, BP 592 - 97159 Pointe-à-Pitre, Guadeloupe
- Centre Commun de Caractérisation des Matériaux des Antilles et de la Guyane (C3MAG), UFR des Sciences Exactes et Naturelles, Université des Antilles, BP 592 - 97159 Pointe-à-Pitre, Guadeloupe
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6
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Brosseau Q, Usabiaga FB, Lushi E, Wu Y, Ristroph L, Ward MD, Shelley MJ, Zhang J. Metallic microswimmers driven up the wall by gravity. SOFT MATTER 2021; 17:6597-6602. [PMID: 34259695 DOI: 10.1039/d1sm00554e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Experiments on autophoretic bimetallic nanorods propelling within a fuel of hydrogen peroxide show that tail-heavy swimmers preferentially orient upwards and ascend along inclined planes. We show that such gravitaxis is strongly facilitated by interactions with solid boundaries, allowing even ultraheavy microswimmers to climb nearly vertical surfaces. Theory and simulations show that the buoyancy or gravitational torque that tends to align the rods is reinforced by a fore-aft drag asymmetry induced by hydrodynamic interactions with the wall.
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Affiliation(s)
- Quentin Brosseau
- Applied Mathematics Laboratory, Courant Institute, New York University, NY, NY 10012, USA
| | | | - Enkeleida Lushi
- Department of Math. Sciences, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Yang Wu
- Department of Chemistry, New York University, NY, NY 10012, USA
| | - Leif Ristroph
- Applied Mathematics Laboratory, Courant Institute, New York University, NY, NY 10012, USA
| | - Michael D Ward
- Department of Chemistry, New York University, NY, NY 10012, USA
| | - Michael J Shelley
- Applied Mathematics Laboratory, Courant Institute, New York University, NY, NY 10012, USA and Flatiron Institute, Simons Foundation, NY, NY 10010, USA
| | - Jun Zhang
- Applied Mathematics Laboratory, Courant Institute, New York University, NY, NY 10012, USA and Department of Physics, New York University, NY, NY 10003, USA and NYU-ECNU Physics and Mathematics Research Institutes, New York University Shanghai, Shanghai 200062, China
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7
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Ophaus L, Knobloch E, Gurevich SV, Thiele U. Two-dimensional localized states in an active phase-field-crystal model. Phys Rev E 2021; 103:032601. [PMID: 33862772 DOI: 10.1103/physreve.103.032601] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/08/2021] [Indexed: 11/07/2022]
Abstract
The active phase-field-crystal (active PFC) model provides a simple microscopic mean field description of crystallization in active systems. It combines the PFC model (or conserved Swift-Hohenberg equation) of colloidal crystallization and aspects of the Toner-Tu theory for self-propelled particles. We employ the active PFC model to study the occurrence of localized and periodic active crystals in two spatial dimensions. Due to the activity, crystalline states can undergo a drift instability and start to travel while keeping their spatial structure. Based on linear stability analyses, time simulations, and numerical continuation of the fully nonlinear states, we present a detailed analysis of the bifurcation structure of resting and traveling states. We explore, for instance, how the slanted homoclinic snaking of steady localized states found for the passive PFC model is modified by activity. Morphological phase diagrams showing the regions of existence of various solution types are presented merging the results from all the analysis tools employed. We also study how activity influences the crystal structure with transitions from hexagons to rhombic and stripe patterns. This in-depth analysis of a simple PFC model for active crystals and swarm formation provides a clear general understanding of the observed multistability and associated hysteresis effects, and identifies thresholds for qualitative changes in behavior.
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Affiliation(s)
- Lukas Ophaus
- Institut für Theoretische Physik, Westfälische Wilhelms-Universität Münster, Wilhelm-Klemm-Strasse 9, 48149 Münster, Germany.,Center of Nonlinear Science (CeNoS), Westfälische Wilhelms-Universität Münster, Corrensstrasse 2, 48149 Münster, Germany
| | - Edgar Knobloch
- Department of Physics, University of California, Berkeley, California 94720, USA
| | - Svetlana V Gurevich
- Institut für Theoretische Physik, Westfälische Wilhelms-Universität Münster, Wilhelm-Klemm-Strasse 9, 48149 Münster, Germany.,Center of Nonlinear Science (CeNoS), Westfälische Wilhelms-Universität Münster, Corrensstrasse 2, 48149 Münster, Germany
| | - Uwe Thiele
- Institut für Theoretische Physik, Westfälische Wilhelms-Universität Münster, Wilhelm-Klemm-Strasse 9, 48149 Münster, Germany.,Center of Nonlinear Science (CeNoS), Westfälische Wilhelms-Universität Münster, Corrensstrasse 2, 48149 Münster, Germany
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8
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Abstract
All living cells interact dynamically with a constantly changing world. Eukaryotes, in particular, evolved radically new ways to sense and react to their environment. These advances enabled new and more complex forms of cellular behaviour in eukaryotes, including directional movement, active feeding, mating, and responses to predation. But what are the key events and innovations during eukaryogenesis that made all of this possible? Here we describe the ancestral repertoire of eukaryotic excitability and discuss five major cellular innovations that enabled its evolutionary origin. The innovations include a vastly expanded repertoire of ion channels, the emergence of cilia and pseudopodia, endomembranes as intracellular capacitors, a flexible plasma membrane and the relocation of chemiosmotic ATP synthesis to mitochondria, which liberated the plasma membrane for more complex electrical signalling involved in sensing and reacting. We conjecture that together with an increase in cell size, these new forms of excitability greatly amplified the degrees of freedom associated with cellular responses, allowing eukaryotes to vastly outperform prokaryotes in terms of both speed and accuracy. This comprehensive new perspective on the evolution of excitability enriches our view of eukaryogenesis and emphasizes behaviour and sensing as major contributors to the success of eukaryotes. This article is part of the theme issue 'Basal cognition: conceptual tools and the view from the single cell'.
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Affiliation(s)
- Kirsty Y. Wan
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Gáspár Jékely
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
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9
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Shelton DS, Shelton SG, Daniel DK, Raja M, Bhat A, Tanguay RL, Higgs DM, Martins EP. Collective Behavior in Wild Zebrafish. Zebrafish 2020; 17:243-252. [PMID: 32513074 DOI: 10.1089/zeb.2019.1851] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Anthropogenic change is expected to alter environments at alarming rates. To predict the impact of modified environments on social behavior, we must study the relationship between environmental features and collective behavior in a genetically tractable model, zebrafish (Danio rerio). Here, we conducted a field study to examine the relationship between salient environmental features and collective behavior in four populations of zebrafish. We found zebrafish in flowing water formed volatile groups, whereas those in still water had more consistent membership and leadership. Groups in fast-flowing water were large (up to 2000 fish) and tightly knit with short nearest neighbor distances, whereas group sizes were smaller (11 fish/group) with more space between individual fish in still and slow-flowing water. These observations point to a possible profound role of water flow in influencing collective behavior in wild zebrafish.
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Affiliation(s)
- Delia S Shelton
- Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, Oregon, USA.,Leibniz Institute for Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Department of Biological Sciences, University of Windsor, Windsor, Canada
| | | | - Danita K Daniel
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, India
| | - Manickam Raja
- Department of Biomedical Engineering, The Kavery College of Engineering, Salem, India
| | - Anuradha Bhat
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, India
| | - Robyn L Tanguay
- Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, Oregon, USA
| | - Dennis M Higgs
- Department of Biological Sciences, University of Windsor, Windsor, Canada
| | - Emília P Martins
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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10
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Xu H, Dauparas J, Das D, Lauga E, Wu Y. Self-organization of swimmers drives long-range fluid transport in bacterial colonies. Nat Commun 2019; 10:1792. [PMID: 30996269 PMCID: PMC6470179 DOI: 10.1038/s41467-019-09818-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 03/28/2019] [Indexed: 01/08/2023] Open
Abstract
Motile subpopulations in microbial communities are believed to be important for dispersal, quest for food, and material transport. Here, we show that motile cells in sessile colonies of peritrichously flagellated bacteria can self-organize into two adjacent, centimeter-scale motile rings surrounding the entire colony. The motile rings arise from spontaneous segregation of a homogeneous swimmer suspension that mimics a phase separation; the process is mediated by intercellular interactions and shear-induced depletion. As a result of this self-organization, cells drive fluid flows that circulate around the colony at a constant peak speed of ~30 µm s−1, providing a stable and high-speed avenue for directed material transport at the macroscopic scale. Our findings present a unique form of bacterial self-organization that influences population structure and material distribution in colonies. Motile and non-motile subpopulations often coexist in bacterial communities. Here, Xu et al. show that motile cells in colonies of common flagellated bacteria can self-organize into two adjacent motile rings, driving stable flows of fluid and materials around the colony.
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Affiliation(s)
- Haoran Xu
- Department of Physics and Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, People's Republic of China
| | - Justas Dauparas
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, CB3 0WA, UK
| | - Debasish Das
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, CB3 0WA, UK
| | - Eric Lauga
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, CB3 0WA, UK
| | - Yilin Wu
- Department of Physics and Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, People's Republic of China.
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11
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Danchin A, Ouzounis C, Tokuyasu T, Zucker JD. No wisdom in the crowd: genome annotation in the era of big data - current status and future prospects. Microb Biotechnol 2018; 11:588-605. [PMID: 29806194 PMCID: PMC6011933 DOI: 10.1111/1751-7915.13284] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Science and engineering rely on the accumulation and dissemination of knowledge to make discoveries and create new designs. Discovery-driven genome research rests on knowledge passed on via gene annotations. In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules. We argue this hinders progress through the generation and propagation of errors, leading investigators into blind alleys. More subtly, this inductive process discourages the discovery of novelty, which remains essential in biological research and reflects the nature of biology itself. Annotation systems, rather than being repositories of facts, should be tools that support multiple modes of inference. By combining deduction, induction and abduction, investigators can generate hypotheses when accurate knowledge is extracted from model databases. A key stance is to depart from 'the sequence tells the structure tells the function' fallacy, placing function first. We illustrate our approach with examples of critical or unexpected pathways, using MicroScope to demonstrate how tools can be implemented following the principles we advocate. We end with a challenge to the reader.
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Affiliation(s)
- Antoine Danchin
- Integromics, Institute of Cardiometabolism and Nutrition, Hôpital de la Pitié-Salpêtrière, 47 Boulevard de l'Hôpital, 75013, Paris, France
- School of Biomedical Sciences, Li KaShing Faculty of Medicine, Hong Kong University, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Christos Ouzounis
- Biological Computation and Process Laboratory, Centre for Research and Technology Hellas, Chemical Process and Energy Resources Institute, Thessalonica, 57001, Greece
| | - Taku Tokuyasu
- Shenzhen Institutes of Advanced Technology, Institute of Synthetic Biology, Shenzhen University Town, 1068 Xueyuan Avenue, Shenzhen, China
| | - Jean-Daniel Zucker
- Integromics, Institute of Cardiometabolism and Nutrition, Hôpital de la Pitié-Salpêtrière, 47 Boulevard de l'Hôpital, 75013, Paris, France
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12
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Gros O. First description of a new uncultured epsilon sulfur bacterium colonizing marine mangrove sediment in the Caribbean: Thiovulum sp. strain karukerense. FEMS Microbiol Lett 2017; 364:4067810. [DOI: 10.1093/femsle/fnx172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 08/04/2017] [Indexed: 01/06/2023] Open
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13
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Affiliation(s)
- Corina P D Brussaard
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute of Sea Research and University of Utrecht, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - Kay D Bidle
- Department of Marine and Coastal Sciences, Rutgers University, 71 Dudley Road, New Brunswick, New Jersey 08901, USA
| | - Carlos Pedrós-Alió
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Catherine Legrand
- Department of Biology and Environmental Science, Center of Ecology and Evolution in Microbial model Systems (EEMiS), Linnæeus University, 39182 Kalmar, Sweden
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14
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Petroff AP, Pasulka AL, Soplop N, Wu XL, Libchaber A. Biophysical basis for convergent evolution of two veil-forming microbes. ROYAL SOCIETY OPEN SCIENCE 2015; 2:150437. [PMID: 26716000 PMCID: PMC4680615 DOI: 10.1098/rsos.150437] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/16/2015] [Indexed: 06/05/2023]
Abstract
Microbes living in stagnant water typically rely on chemical diffusion to draw nutrients from their environment. The sulfur-oxidizing bacterium Thiovulum majus and the ciliate Uronemella have independently evolved the ability to form a 'veil', a centimetre-scale mucous sheet on which cells organize to produce a macroscopic flow. This flow pulls nutrients through the community an order of magnitude faster than diffusion. To understand how natural selection led these microbes to evolve this collective behaviour, we connect the physical limitations acting on individual cells to the cell traits. We show how diffusion limitation and viscous dissipation have led individual T. majus and Uronemella cells to display two similar characteristics. Both of these cells exert a force of approximately 40 pN on the water and attach to boundaries by means of a mucous stalk. We show how the diffusion coefficient of oxygen in water and the viscosity of water define the force the cells must exert. We then show how the hydrodynamics of filter-feeding orient a microbe normal to the surface to which it attaches. Finally, we combine these results with new observations of veil formation and a review of veil dynamics to compare the collective dynamics of these microbes. We conclude that this convergent evolution is a reflection of similar physical limitations imposed by diffusion and viscosity acting on individual cells.
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Affiliation(s)
- Alexander P. Petroff
- Laboratory of Experimental Condensed Matter Physics, The Rockefeller University, New York City, NY 10065, USA
| | - Alexis L. Pasulka
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Nadine Soplop
- Electron Microscopy Resource Center, The Rockefeller University, New York City, NY 10065, USA
| | - Xiao-Lun Wu
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Albert Libchaber
- Laboratory of Experimental Condensed Matter Physics, The Rockefeller University, New York City, NY 10065, USA
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Petroff AP, Wu XL, Libchaber A. Fast-moving bacteria self-organize into active two-dimensional crystals of rotating cells. PHYSICAL REVIEW LETTERS 2015; 114:158102. [PMID: 25933342 DOI: 10.1103/physrevlett.114.158102] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Indexed: 06/04/2023]
Abstract
We investigate a new form of collective dynamics displayed by Thiovulum majus, one of the fastest-swimming bacteria known. Cells spontaneously organize on a surface into a visually striking two-dimensional hexagonal lattice of rotating cells. As each constituent cell rotates its flagella, it creates a tornadolike flow that pulls neighboring cells towards and around it. As cells rotate against their neighbors, they exert forces on one another, causing the crystal to rotate and cells to reorganize. We show how these dynamics arise from hydrodynamic and steric interactions between cells. We derive the equations of motion for a crystal, show that this model explains several aspects of the observed dynamics, and discuss the stability of these active crystals.
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Affiliation(s)
- Alexander P Petroff
- Laboratory of Experimental Condensed Matter Physics, The Rockefeller University, New York, New York 10065, USA
| | - Xiao-Lun Wu
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Albert Libchaber
- Laboratory of Experimental Condensed Matter Physics, The Rockefeller University, New York, New York 10065, USA
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