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Jin C, Sengupta A. Microbes in porous environments: from active interactions to emergent feedback. Biophys Rev 2024; 16:173-188. [PMID: 38737203 PMCID: PMC11078916 DOI: 10.1007/s12551-024-01185-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/27/2024] [Indexed: 05/14/2024] Open
Abstract
Microbes thrive in diverse porous environments-from soil and riverbeds to human lungs and cancer tissues-spanning multiple scales and conditions. Short- to long-term fluctuations in local factors induce spatio-temporal heterogeneities, often leading to physiologically stressful settings. How microbes respond and adapt to such biophysical constraints is an active field of research where considerable insight has been gained over the last decades. With a focus on bacteria, here we review recent advances in self-organization and dispersal in inorganic and organic porous settings, highlighting the role of active interactions and feedback that mediates microbial survival and fitness. We discuss open questions and opportunities for using integrative approaches to advance our understanding of the biophysical strategies which microbes employ at various scales to make porous settings habitable.
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Affiliation(s)
- Chenyu Jin
- Physics of Living Matter Group, Department of Physics and Materials Science, University of Luxembourg, 162 A, Avenue de la Faïencerie, Luxembourg City, L-1511 Luxembourg
| | - Anupam Sengupta
- Physics of Living Matter Group, Department of Physics and Materials Science, University of Luxembourg, 162 A, Avenue de la Faïencerie, Luxembourg City, L-1511 Luxembourg
- Institute for Advanced Studies, University of Luxembourg, 2 Avenue de l’Université, Esch-sur-Alzette, L-4365 Luxembourg
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Goral M, Clement E, Darnige T, Lopez-Leon T, Lindner A. Frustrated 'run and tumble' of swimming Escherichia coli bacteria in nematic liquid crystals. Interface Focus 2022; 12:20220039. [PMID: 36330319 PMCID: PMC9560793 DOI: 10.1098/rsfs.2022.0039] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 09/05/2022] [Indexed: 10/16/2023] Open
Abstract
In many situations, bacteria move in complex environments, as soils, oceans or the human gut-track, where carrier fluids show complex structures associated with non-Newtonian rheology. Many fundamental questions concerning the ability to navigate in such environments remain unsolved. Recently, it has been shown that the kinetics of bacterial motion in structured fluids as liquid crystals (LCs) is constrained by the orientational molecular order (or director field) and that novel spatio-temporal patterns arise. A question unaddressed so far is how bacteria change swimming direction in such an environment. In this work, we study the swimming mechanism of a single bacterium, Esherichia coli, constrained to move along the director field of a lyotropic chromonic liquid crystal confined to a planar cell. Here, the spontaneous 'run and tumble' motion of the bacterium gets frustrated: the elasticity of the LC prevents flagella from unbundling. Interestingly, to change direction, bacteria execute a reversal motion along the director field, driven by the relocation of a single flagellum, a 'frustrated tumble'. We characterize this phenomenon in detail experimentally, exploiting exceptional spatial and temporal resolution of bacterial and flagellar dynamics, using a two colour Lagrangian tracking technique. We suggest a possible mechanism accounting for these observations.
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Affiliation(s)
- Martyna Goral
- Laboratoire de Physique et Mécanique des Milieux Hétérogènes, UMR 7636, CNRS, ESPCI Paris-PSL, Sorbonne Université, Université Paris Cité, 75005 Paris, France
- Laboratoire Gulliver, UMR 7083, CNRS, ESPCI Paris-PSL, 75005 Paris, France
| | - Eric Clement
- Laboratoire de Physique et Mécanique des Milieux Hétérogènes, UMR 7636, CNRS, ESPCI Paris-PSL, Sorbonne Université, Université Paris Cité, 75005 Paris, France
- Institut Universitaire de France (IUF), Paris, France
| | - Thierry Darnige
- Laboratoire de Physique et Mécanique des Milieux Hétérogènes, UMR 7636, CNRS, ESPCI Paris-PSL, Sorbonne Université, Université Paris Cité, 75005 Paris, France
| | - Teresa Lopez-Leon
- Laboratoire Gulliver, UMR 7083, CNRS, ESPCI Paris-PSL, 75005 Paris, France
| | - Anke Lindner
- Laboratoire de Physique et Mécanique des Milieux Hétérogènes, UMR 7636, CNRS, ESPCI Paris-PSL, Sorbonne Université, Université Paris Cité, 75005 Paris, France
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Bhat AV, Basha RA, Chikkaiah MD, Ananthamurthy S. Flagellar rotational features of an optically confined bacterium at high frequency and temporal resolution reveal the microorganism's response to changes in the fluid environment. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2022; 51:225-239. [PMID: 35157113 DOI: 10.1007/s00249-022-01590-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 12/23/2021] [Accepted: 01/22/2022] [Indexed: 01/17/2023]
Abstract
Rotations of the flagella control the movement of a peritrichous (multiflagellar) bacterium in fluids, the run and tumble events being caused through modulations in the flagella's collective rotation speed and pattern. Observing such modulations is a challenge in free swimming bacteria. In this work, we present a setup to measure the collective flagellar rotational features of an optically confined Bacillus subtilis bacterium. We adopt a Continuous Wavelet Technique (CWT) while monitoring the rotational patterns in frequency and time, thus achieving optimal resolution in both the domains. This enables in marking the events wherein subtle changes in the flagellar rotational pattern occur. These studies unravel a fact, hitherto unknown, that variations in swimming speed that are seen in pure run sequences are also caused by modulations in the rotating flagella. Further, we have monitored the flagellar rotation for durations over a minute and observe a gradual slowing down of the rotation before ceasing completely due to the trapping laser induced photodamage. We have observed a significant alteration in the rate of rotational fall off in real time with changes in pH or the nutrient concentration in the fluid. This work serves to demonstrate the advantage of optical confinement of a bacterium in its pristine form for carrying out such studies and can serve as a marker for work that assesses membrane photodamage in active matter. Details on the role of flagella in propulsion and on other factors influencing the rotations, can be of significance in the design of artificial microswimmers.
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Affiliation(s)
| | - Roshan Akbar Basha
- Department of Microbiology and Biotechnology, Bangalore University, Bangalore, 560056, India
| | | | - Sharath Ananthamurthy
- Department of Physics, Bangalore University, Bangalore, 560056, India. .,School of Physics, University of Hyderabad, Hyderabad, 500046, India.
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Clopés J, Winkler RG. Flagellar arrangements in elongated peritrichous bacteria: bundle formation and swimming properties. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:17. [PMID: 33683543 PMCID: PMC7940165 DOI: 10.1140/epje/s10189-021-00027-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/25/2021] [Indexed: 05/26/2023]
Abstract
The surface distribution of flagella in peritrichous bacterial cells has been traditionally assumed to be random. Recently, the presence of a regular grid-like pattern of basal bodies has been suggested. Experimentally, the manipulation of the anchoring points of flagella in the cell membrane is difficult, and thus, elucidation of the consequences of a particular pattern on bacterial locomotion is challenging. We analyze the bundle formation process and swimming properties of Bacillus subtilis-like cells considering random, helical, and ring-like arrangements of flagella by means of mesoscale hydrodynamics simulations. Helical and ring patterns preferentially yield configurations with a single bundle, whereas configurations with no clear bundles are most likely for random anchoring. For any type of pattern, there is an almost equally low probability to form V-shaped bundle configurations with at least two bundles. Variation of the flagellum length yields a clear preference for a single major bundle in helical and ring patterns as soon as the flagellum length exceeds the body length. The average swimming speed of cells with a single or two bundles is rather similar, and approximately [Formula: see text] larger than that of cells of other types of flagellar organization. Considering the various anchoring patterns, rings yield the smallest average swimming speed independent of the type of bundle, followed by helical arrangements, and largest speeds are observed for random anchoring. Hence, a regular pattern provides no advantage in terms of swimming speed compared to random anchoring of flagella, but yields more likely single-bundle configurations.
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Affiliation(s)
- Judit Clopés
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich and JARA, 52425, Jülich, Germany
- Institute for Theoretical Physics, RWTH Aachen University, 52074, Aachen, Germany
| | - Roland G Winkler
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich and JARA, 52425, Jülich, Germany.
- Institute for Theoretical Physics, RWTH Aachen University, 52074, Aachen, Germany.
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