Motile bacteria, active biohybrids and cellular physiology

This thesis investigates bacterial motility from active matter and physiological perspectives using experiments and theoretical modelling. In the first part, I design and characterize a system made of motile Escherichia coli encapsulated in giant lipid vesicles. For slightly deflated vesicles, the bacteria extrude active membrane tubes that can propel the vesicles. I show that the propulsion arises from a physical coupling between the lipid membrane tubes and the flagella of the encapsulated bacteria and develop a simple theoretical model to estimate the propulsive force. In a second part, I present two studies using motility as a tool to gain insight into bacterial physiology. First, I study the motility of dense suspensions of Escherichia coli fermenting glucose. Using new experimental data gathered by others, I develop a semi-empirical model that quantitatively links the swimming speed of the bacteria to the concentration of protonated organic acids in anaerobic conditions. Secondly, I focus on bacterial motility during complete starvation. Combining single-cell and population-level experiments, I show that Escherichia coli maintains a motile phenotype in the early stages of starvation, but that the swimming speed and motile fraction decay over a few tens of hours. I show that the complete decay of motility in these conditions happens on a much faster timescale than cell death. Interestingly, while swimming speed and flagellar motor measurements both show that the motility fully decays in about 24 h in these conditions, they seem to return different temporal dynamics

Encapsulated bacteria deform lipid vesicles into flagellated swimmers

We study a synthetic system of motile Escherichia coli bacteria encapsulated inside giant lipid vesicles. Forces exerted by the bacteria on the inner side of the membrane are sufficient to extrude membrane tubes filled with one or several bacteria. We show that a physical coupling between the membrane tube and the flagella of the enclosed cells transforms the tube into an effective helical flagellum propelling the vesicle. We develop a simple theoretical model to estimate the propulsive force from the speed of the vesicles and demonstrate the good efficiency of this coupling mechanism. Together, these results point to design principles for conferring motility to synthetic cells

Self-organisation and convection of confined magnetotactic bacteria

Funder: Natural Sciences and Engineering Research Council of Canada; doi: http://dx.doi.org/10.13039/501100000038Funder: École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris; doi: http://dx.doi.org/10.13039/501100003068Abstract: Collective motion is found at all scales in biological and artificial systems, and extensive research is devoted to describing the interplay between interactions and external cues in collective dynamics. Magnetotactic bacteria constitute a remarkable example of living organisms for which motion can be easily controlled remotely. Here, we report a new type of collective motion where a uniform distribution of magnetotactic bacteria is rendered unstable by a magnetic field. A new state of “bacterial magneto-convection” results, wherein bacterial plumes emerge spontaneously perpendicular to an interface and develop into self-sustained flow convection cells. While there are similarities to gravity driven bioconvection and the Rayleigh–Bénard instability, these rely on a density mismatch between layers of the fluids. Remarkably, here no external forces are applied on the fluid and the magnetic field only exerts an external torque aligning magnetotactic bacteria with the field. Using a theoretical model based on hydrodynamic singularities, we capture quantitatively the instability and the observed long-time growth. Bacterial magneto-convection represents a new class of collective behaviour resulting only from the balance between hydrodynamic interactions and external alignment

Soft matter science and the COVID-19 pandemic

Much of the science underpinning the global response to the COVID-19 pandemic lies in the soft matter domain. Coronaviruses are composite particles with a core of nucleic acids complexed to proteins surrounded by a protein-studded lipid bilayer shell. A dominant route for transmission is via air-borne aerosols and droplets. Viral interaction with polymeric body fluids, particularly mucus, and cell membranes control their infectivity, while their interaction with skin and artificial surfaces underpins cleaning and disinfection and the efficacy of masks and other personal protective equipment. The global response to COVID-19 has highlighted gaps in the soft matter knowledge base. We survey these gaps, especially as pertaining to the transmission of the disease, and suggest questions that can (and need to) be tackled, both in response to COVID-19 and to better prepare for future viral pandemics.Comment: 15 page

Vaccine breakthrough hypoxemic COVID-19 pneumonia in patients with auto-Abs neutralizing type I IFNs

Life-threatening `breakthrough' cases of critical COVID-19 are attributed to poor or waning antibody response to the SARS- CoV-2 vaccine in individuals already at risk. Pre-existing autoantibodies (auto-Abs) neutralizing type I IFNs underlie at least 15% of critical COVID-19 pneumonia cases in unvaccinated individuals; however, their contribution to hypoxemic breakthrough cases in vaccinated people remains unknown. Here, we studied a cohort of 48 individuals ( age 20-86 years) who received 2 doses of an mRNA vaccine and developed a breakthrough infection with hypoxemic COVID-19 pneumonia 2 weeks to 4 months later. Antibody levels to the vaccine, neutralization of the virus, and auto- Abs to type I IFNs were measured in the plasma. Forty-two individuals had no known deficiency of B cell immunity and a normal antibody response to the vaccine. Among them, ten (24%) had auto-Abs neutralizing type I IFNs (aged 43-86 years). Eight of these ten patients had auto-Abs neutralizing both IFN-a2 and IFN-., while two neutralized IFN-omega only. No patient neutralized IFN-ss. Seven neutralized 10 ng/mL of type I IFNs, and three 100 pg/mL only. Seven patients neutralized SARS-CoV-2 D614G and the Delta variant (B.1.617.2) efficiently, while one patient neutralized Delta slightly less efficiently. Two of the three patients neutralizing only 100 pg/mL of type I IFNs neutralized both D61G and Delta less efficiently. Despite two mRNA vaccine inoculations and the presence of circulating antibodies capable of neutralizing SARS-CoV-2, auto-Abs neutralizing type I IFNs may underlie a significant proportion of hypoxemic COVID-19 pneumonia cases, highlighting the importance of this particularly vulnerable population

Autoantibodies against type I IFNs in patients with life-threatening COVID-19

Interindividual clinical variability in the course of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is vast. We report that at least 101 of 987 patients with life-threatening coronavirus disease 2019 (COVID-19) pneumonia had neutralizing immunoglobulin G (IgG) autoantibodies (auto-Abs) against interferon-w (IFN-w) (13 patients), against the 13 types of IFN-a (36), or against both (52) at the onset of critical disease; a few also had auto-Abs against the other three type I IFNs. The auto-Abs neutralize the ability of the corresponding type I IFNs to block SARS-CoV-2 infection in vitro. These auto-Abs were not found in 663 individuals with asymptomatic or mild SARS-CoV-2 infection and were present in only 4 of 1227 healthy individuals. Patients with auto-Abs were aged 25 to 87 years and 95 of the 101 were men. A B cell autoimmune phenocopy of inborn errors of type I IFN immunity accounts for life-threatening COVID-19 pneumonia in at least 2.6% of women and 12.5% of men

Self-organisation and convection of confined magnetotactic bacteria.

Collective motion is found at all scales in biological and artificial systems, and extensive research is devoted to describing the interplay between interactions and external cues in collective dynamics. Magnetotactic bacteria constitute a remarkable example of living organisms for which motion can be easily controlled remotely. Here, we report a new type of collective motion where a uniform distribution of magnetotactic bacteria is rendered unstable by a magnetic field. A new state of "bacterial magneto-convection" results, wherein bacterial plumes emerge spontaneously perpendicular to an interface and develop into self-sustained flow convection cells. While there are similarities to gravity driven bioconvection and the Rayleigh-Bénard instability, these rely on a density mismatch between layers of the fluids. Remarkably, here no external forces are applied on the fluid and the magnetic field only exerts an external torque aligning magnetotactic bacteria with the field. Using a theoretical model based on hydrodynamic singularities, we capture quantitatively the instability and the observed long-time growth. Bacterial magneto-convection represents a new class of collective behaviour resulting only from the balance between hydrodynamic interactions and external alignment

Encapsulated bacteria deform lipid vesicles into flagellated swimmers

We study a synthetic system of motile Escherichia coli bacteria encapsulated inside giant lipid vesicles. Forces exerted by the bacteria on the inner side of the membrane are sufficient to extrude membrane tubes filled with one or several bacteria. We show that a physical coupling between the membrane tube and the flagella of the enclosed cells transforms the tube into an effective helical flagellum propelling the vesicle. We develop a simple theoretical model to estimate the propulsive force from the speed of the vesicles and demonstrate the good efficiency of this coupling mechanism. Together, these results point to design principles for conferring motility to synthetic cells

Self-organisation and convection of confined magnetotactic bacteria

Abstract Collective motion is found at all scales in biological and artificial systems, and extensive research is devoted to describing the interplay between interactions and external cues in collective dynamics. Magnetotactic bacteria constitute a remarkable example of living organisms for which motion can be easily controlled remotely. Here, we report a new type of collective motion where a uniform distribution of magnetotactic bacteria is rendered unstable by a magnetic field. A new state of “bacterial magneto-convection” results, wherein bacterial plumes emerge spontaneously perpendicular to an interface and develop into self-sustained flow convection cells. While there are similarities to gravity driven bioconvection and the Rayleigh–Bénard instability, these rely on a density mismatch between layers of the fluids. Remarkably, here no external forces are applied on the fluid and the magnetic field only exerts an external torque aligning magnetotactic bacteria with the field. Using a theoretical model based on hydrodynamic singularities, we capture quantitatively the instability and the observed long-time growth. Bacterial magneto-convection represents a new class of collective behaviour resulting only from the balance between hydrodynamic interactions and external alignment

Magnetite magnetosome biomineralization in Magnetospirillum magneticum strain AMB-1: A time course study

International audienceMagnetotactic bacteria are a highly studied group of diverse prokaryotes that 15 biomineralize chains of magnetosomes, single domain, single crystal magnetic nanoparticles of 16 magnetite or greigite, enclosed by a lipid bilayer membrane whose synthesis is under strict 17 control. In addition to characterizing the genetics and physicochemical properties of both 18 and uncultured environmental species, there have been a number of investigations using a time 19 course approach to determine the chemical pathway of magnetite biomineralization in these 20 organisms. In time course studies, cells of MTB are typically grown in the absence of iron so 21 cannot make magnetite, and then provided with iron in culture medium which initiates the 22 biomineralization of magnetosome chains over a subsequent time period. Results from previous 23 time course studies are not consistent with one another, differing with regard to the nature of 24 chemical intermediates and the rate of establishment of magnetosome chains. In this work we 25 report a time course study of Magnetospirillum magneticum strain AMB-1 over a 48 hour (h) 26 period, using transmission electron microscopy (TEM) and soft X-ray scanning transmission 27 X-ray microscopy (STXM) at the Fe Ledge. STXM provides capability to measure X-ray 28 absorption spectra (XAS) and map chemical species with ~25 nm spatial resolution and thus 29 detailed results on the chemistry of individual particles in single cells. An evolution of the iron 30 *Revised manuscript with no changes marked Click here to view linked Reference