From swimming to swarming: Escherichia coli cell motility in two-dimensions

Exotic swarming dynamics of high-dimensional swarmalators

Swarmalators are oscillators that can swarm as well as sync via a dynamic balance between their spatial proximity and phase similarity. Swarmalator models employed so far in the literature comprise only one-dimensional phase variables to represent the intrinsic dynamics of the natural collectives. Nevertheless, the latter can indeed be represented more realistically by high-dimensional phase variables. For instance, the alignment of velocity vectors in a school of fish or a flock of birds can be more realistically set up in three-dimensional space, while the alignment of opinion formation in population dynamics could be multidimensional, in general. We present a generalized D-dimensional swarmalator model, which more accurately captures self-organizing behaviors of a plethora of real-world collectives by self-adaptation of high-dimensional spatial and phase variables. For a more sensible visualization and interpretation of the results, we restrict our simulations to three-dimensional spatial and phase variables. Our model provides a framework for modeling complicated processes such as flocking, schooling of fish, cell sorting during embryonic development, residential segregation, and opinion dynamics in social groups. We demonstrate its versatility by capturing the maneuvers of a school of fish, qualitatively and quantitatively, by a suitable extension of the original model to incorporate appropriate features besides a gallery of its intrinsic self-organizations for various interactions. We expect the proposed high-dimensional swarmalator model to be potentially useful in describing swarming systems and programmable and reconfigurable collectives in a wide range of disciplines, including the physics of active matter, developmental biology, sociology, and engineering.

The maps of meaning consciousness theory

In simple terms, consciousness is constituted by multiple goals for action and the continuous adjudication of such goals to implement action, which is referred to as the maps of meaning (MoM) consciousness theory. The MoM theory triangulates through three parallel corollaries: action (behavior), mechanism (morphology/pathophysiology), and goals (teleology). (1) An organism's consciousness contains fluid, nested goals. These goals are not intentionality, but intersectionality, via the Darwinian byproduct of embodiment meeting the world, i.e., Darwinian inclusive fitness or randomization and then survival of the fittest. (2) These goals are formed via a gradual descent under inclusive fitness and are the abstraction of a "match" between the evolutionary environment and the organism. (3) Human consciousness implements the brain efficiency hypothesis, genetics, epigenetics, and experience-crystallized efficiencies, not necessitating best or objective but fitness, i.e., perceived efficiency based on one's adaptive environment. These efficiencies are objectively arbitrary but determine the operation and level of one's consciousness, termed as extreme thrownness. (4) Since inclusive fitness drives efficiencies in the physiologic mechanism, morphology, and behavior (action) and originates one's goals, embodiment is necessarily entangled to human consciousness as it is at the intersection of mechanism or action (both necessitating embodiment) occurring in the world that determines fitness. (5) Perception is the operant process of consciousness and is the de facto goal adjudication process of consciousness. Goal operationalization is fundamentally efficiency-based via one's unique neuronal mapping as a byproduct of genetics, epigenetics, and experience. (6) Perception involves information intake and information discrimination, equally underpinned by efficiencies of inclusive fitness via extreme thrownness. Perception is not a 'frame rate' but Bayesian priors of efficiency based on one's extreme thrownness. (7) Consciousness and human consciousness are modular (i.e., a scalar level of richness, which builds up like building blocks) and dimensionalized (i.e., cognitive abilities become possibilities as the emergent phenomena at various modularities such as the stratified factors in factor analysis). (8) The meta dimensions of human consciousness seemingly include intelligence quotient, personality (five-factor model), richness of perception intake, and richness of perception discrimination, among other potentialities. (9) Future consciousness research should utilize factor analysis to parse modularities and dimensions of human consciousness and animal models.

Motility mediates satellite formation in confined biofilms

Bacteria have spectacular survival capabilities and can spread in many, vastly different environments. For instance, when pathogenic bacteria infect a host, they expand by proliferation and squeezing through narrow pores and elastic matrices. However, the exact role of surface structures-important for biofilm formation and motility-and matrix density in colony expansion and morphogenesis is still largely unknown. Using confocal laser-scanning microscopy, we show how satellite colonies emerge around Escherichia coli colonies embedded in semi-dense hydrogel in controlled in vitro assays. Using knock-out mutants, we tested how extra-cellular structures, (e.g., exo-polysaccharides, flagella, and fimbria) control this morphology. Moreover, we identify the extra-cellular matrix' density, where this morphology is possible. When paralleled with mathematical modelling, our results suggest that satellite formation allows bacterial communities to spread faster. We anticipate that this strategy is important to speed up expansion in various environments, while retaining the close interactions and protection provided by the community.

Swarming of P. aeruginosa: Through the lens of biophysics

Swarming is a collective flagella-dependent movement of bacteria across a surface that is observed across many species of bacteria. Due to the prevalence and diversity of this motility modality, multiple models of swarming have been proposed, but a consensus on a general mechanism for swarming is still lacking. Here, we focus on swarming by Pseudomonas aeruginosa due to the abundance of experimental data and multiple models for this species, including interpretations that are rooted in biology and biophysics. In this review, we address three outstanding questions about P. aeruginosa swarming: what drives the outward expansion of a swarm, what causes the formation of dendritic patterns (tendrils), and what are the roles of flagella? We review models that propose biologically active mechanisms including surfactant sensing as well as fluid mechanics-based models that consider swarms as thin liquid films. Finally, we reconcile recent observations of P. aeruginosa swarms with early definitions of swarming. This analysis suggests that mechanisms associated with sliding motility have a critical role in P. aeruginosa swarm formation.

N-acyl homoserine lactonase attenuates the virulence of Salmonella typhimurium and its induction of intestinal damages in broilers

This study aimed to investigate the potential mitigating effects of N-acyl homoserine lactonase (AHLase) on the virulence of Salmonella typhimurium and its induction of intestinal damages in broilers. In vitro study was firstly conducted to examine if AHLase treatment could attenuate the virulence of S. typhimurium. Then, an in vivo experiment was performed by allocating 240 broiler chicks at 1 d old into 3 groups (8 replicates per group): negative control (NC), positive control (PC), and PC supplemented with 10,000 U/kg AHLase. All chicks except those in NC were orally challenged by S. typhimurium from 8 to 10 d of age. Parameters were measured on d 11 and 21. The results showed that treatment with 1 U/mL AHLase suppressed the biofilm-forming ability (including biofilm biomass, extracellular DNA secretion and biofilm formation-related gene expression), together with swarming motility and adhesive capacity of S. typhimurium. Supplemental 10,000 U/kg AHLase counteracted S. typhimurium-induced impairments (P < 0.05) in broiler growth performance (including final body weight, average daily gain and average daily feed intake) during either 1-11 d or 12-21 d, and increases (P < 0.05) in the indexes of liver, spleen and bursa of Fabricius on d 11, together with reductions (P < 0.05) in ileal villus height and its ratio to crypt depth on both d 11 and 21. AHLase addition also normalized the increased (P < 0.05) mRNA expression of ileal occludin on both d 11 and 21 in S. typhimurium-challenged broilers. However, neither S. typhimurium challenge nor AHLase addition altered (P > 0.05) serum diamine oxidase activity of broilers. Noticeably, S. typhimurium challenge caused little change in the mRNA expression of ileal inflammatory cytokines except for an increase (P < 0.05) in interleukin-8 expression on d 11, whereas AHLase addition normalized (P < 0.05) this change. In conclusion, AHLase treatment could attenuate the virulence and pathogenicity of S. typhimurium, thus contributing to alleviate S. typhimurium-induced growth retardation and intestinal damages in broilers.

Phase transitions on a multiplex of swarmalators

Dynamics of bidirectionally coupled swarmalators subject to attractive and repulsive couplings is analyzed. The probability of two elements in different layers being connected strongly depends on a defined vision range r_{c} which appears to lead both layers in different patterns while varying its values. Particularly, the interlayer static sync π has been found and its stability is proven. First-order transitions are observed when the repulsive coupling strength σ_{r} is very small for a fixed r_{c} and, moreover, in the absence of the repulsive coupling, they also appear for sufficiently large values of r_{c}. For σ_{r}=0 and for sufficiently small values of r_{c}, both layers achieve a second-order transition in a surprising two steps that are characterized by the drop of the energy of the internal phases while increasing the value of the interlayer attractive coupling σ_{a} and later a smooth jump, up to high energy value where synchronization is achieved. During these transitions, the internal phases present rotating waves with counterclockwise and later clockwise directions until synchronization, as σ_{a} increases. These results are supported by simulations and animations added as supplemental materials.

Motility provides specific adhesion patterns and improves Listeria monocytogenes invasion into human HEp-2 cells

Listeria monocytogenes is motile at 22°C and non-motile at 37°C. In contrast, expression of L. monocytogenes virulence factors is low at 22°C and up-regulated at 37°C. Here, we studied a character of L. monocytogenes near surface swimming (NSS) motility and its effects on adhesion patterns and invasion into epithelial cells. L. monocytogenes and its saprophytic counterpart L. innocua both grown at 22°C showed similar NSS characteristics including individual velocities, trajectory lengths, residence times, and an asymmetric distribution of velocity directions. Similar NSS patterns correlated with similar adhesion patterns. Motile bacteria, including both pathogenic and saprophytic species, showed a preference for adhering to the periphery of epithelial HEp-2 cells. In contrast, non-motile bacteria were evenly distributed across the cell surface, including areas over the nucleus. However, the uneven distribution of motile bacteria did not enhance the invasion into HEp-2 cells unless virulence factor production was up-regulated by the transient shift of the culture to 37°C. Motile L. monocytogenes grown overnight at 22°C and then shifted to 37°C for 2 h expressed invasion factors at the same level and invaded human cells up to five times more efficiently comparatively with non-motile bacteria grown overnight at 37°C. Taken together, obtained results demonstrated that (i) NSS motility and correspondent peripheral location over the cell surface did not depend on L. monocytogenes virulence traits; (ii) motility improved L. monocytogenes invasion into human HEp-2 cells within a few hours after the transition from the ambient temperature to the human body temperature.

Diverse behaviors in non-uniform chiral and non-chiral swarmalators

We study the emergent behaviors of a population of swarming coupled oscillators, dubbed swarmalators. Previous work considered the simplest, idealized case: identical swarmalators with global coupling. Here we expand this work by adding more realistic features: local coupling, non-identical natural frequencies, and chirality. This more realistic model generates a variety of new behaviors including lattices of vortices, beating clusters, and interacting phase waves. Similar behaviors are found across natural and artificial micro-scale collective systems, including social slime mold, spermatozoa vortex arrays, and Quincke rollers. Our results indicate a wide range of future use cases, both to aid characterization and understanding of natural swarms, and to design complex interactions in collective systems from soft and active matter to micro-robotics.

Swarming Motility Assays in Salmonella

Salmonella enterica has six subspecies, of which the subspecies enterica is the most important for human health. The dispersal and infectivity of this species are dependent upon flagella-driven motility. Two kinds of flagella-mediated movements have been described-swimming individually in bulk liquid and swarming collectively over a surface substrate. During swarming, the bacteria acquire a distinct physiology, the most significant consequence of which is acquisition of adaptive resistance to antibiotics. Described here are protocols to cultivate, verify, and study swimming and swarming motility in S. enterica, and an additional "border-crossing" assay, where cells "primed" to swarm are presented with an environmental challenge such as antibiotics to assess their propensity to handle the challenge.

Quasi-two-dimensional bacterial swimming around pillars: Enhanced trapping efficiency and curvature dependence

Microswimmers exhibit more diverse behavior in quasi-two dimensions than in three dimensions. Such behavior remains elusive due to the analytical difficulty of dealing with two parallel solid boundaries. The existence of additional obstacles in quasi-two dimensional systems further complicates the analysis. Combining experiments and hydrodynamic simulations, we investigate how the spatial dimension affects the interactions between microswimmers and obstacles. We fabricated microscopic pillars in quasi-two dimensions by etching glass coverslips and observed bacterial swimming among the pillars. Bacteria got trapped around the circular pillars and the trapping efficiency increased as the quasi-two-dimensionality was increased or as the curvature of the pillars was decreased. Numerical simulations of the simplest situation of a confined squirmer showed anomalous increase of hydrodynamic attractions, establishing that the enhanced interaction is a universal property of quasi-two-dimensional microhydrodynamics. We also demonstrated that the local curvature of the obstacle controls the trapping efficiency by experiments with elliptic pillars.

Motility Increases the Numbers and Durations of Cell-Surface Engagements for Escherichia coli Flowing near Poly(ethylene glycol)-Functionalized Surfaces

Bacteria are keenly sensitive to properties of the surfaces they contact, regulating their ability to form biofilms and initiate infections. This study examines how the presence of flagella, interactions between the cell body and the surface, or motility itself guides the dynamic contact between bacterial cells and a surface in flow, potentially enabling cells to sense physicochemical and mechanical properties of surfaces. This work focuses on a poly(ethylene glycol) biomaterial coating, which does not retain cells. In a comparison of four Escherichia coli strains with different flagellar expressions and motilities, cells with substantial run-and-tumble swimming motility exhibited increased flux to the interface (3 times the calculated transport-limited rate which adequately described the non-motile cells), greater proportions of cells engaging in dynamic nanometer-scale surface associations, extended times of contact with the surface, increased probability of return to the surface after escape and, as evidenced by slow velocities during near-surface travel, closer cellular approach. All these metrics, reported here as distributions of cell populations, point to a greater ability of motile cells, compared with nonmotile cells, to interact more closely, forcefully, and for greater periods of time with interfaces in flow. With contact durations of individual cells exceeding 10 s in the window of observation and trends suggesting further interactions beyond the field of view, the dynamic contact of individual cells may approach the minute timescales reported for mechanosensing and other cell recognition pathways. Thus, despite cell translation and the dynamic nature of contact, flow past a surface, even one rendered non-cell arresting by use of an engineered coating, may produce a subpopulation of cells already upregulating virulence factors before they arrest on a downstream surface and formally initiate biofilm formation.

Surveying a Swarm: Experimental Techniques to Establish and Examine Bacterial Collective Motion

The survival and successful spread of many bacterial species hinges on their mode of motility. One of the most distinct of these is swarming, a collective form of motility where a dense consortium of bacteria employ flagella to propel themselves across a solid surface. Surface environments pose unique challenges, derived from higher surface friction/tension and insufficient hydration. Bacteria have adapted by deploying an array of mechanisms to overcome these challenges. Beyond allowing bacteria to colonize new terrain in the absence of bulk liquid, swarming also bestows faster speeds and enhanced antibiotic resistance to the collective. These crucial attributes contribute to the dissemination, and in some cases pathogenicity, of an array of bacteria. This mini-review highlights; 1) aspects of swarming motility that differentiates it from other methods of bacterial locomotion. 2) Facilitatory mechanisms deployed by diverse bacteria to overcome different surface challenges. 3) The (often difficult) approaches required to cultivate genuine swarmers. 4) The methods available to observe and assess the various facets of this collective motion, as well as the features exhibited by the population as a whole.

Surface activation of medical grade polyurethane for the covalent immobilization of an anti-adhesive biopolymeric coating

Hospital-acquired infections are still a major concern worldwide, being frequently related to bacterial biofilm formation on medical devices, and thus difficult to eradicate with conventional antimicrobial treatments. Therefore, infection-preventive solutions based on natural polymers are being investigated. Recently, a marine cyanobacterium-derived polymeric coating (CyanoCoating) has demonstrated great anti-adhesive potential when immobilized onto gold model substrates. In this work, we took this technology a step closer to an industrial application by covalently immobilizing CyanoCoating onto medical grade polyurethane (PU). This immobilization was developed through the introduction of linkable moieties onto a PU inert surface using different pre-treatments. Besides the application of the polydopamine (pDA) linker layer, other processes frequently found in industrial settings, such as atmospheric plasma (using O2 or N2 as reactive gases) and ozone surface activations, were evaluated. From all the pre-treatments tested, the ozone activation was the most promising since the obtained coating not only revealed a homogeneous distribution, but also significantly reduced the adhesion of two relevant etiological bacteria in static conditions (the Gram-positive Staphylococcus aureus and the Gram-negative Escherichia coli). Moreover, it also impaired E. coli biofilm formation under simulated urinary tract dynamic conditions, reinforcing the potential of CyanoCoating as an antibiotic-free alternative to mitigate medical device-associated infections, particularly in the urinary tract.

In vitro effects of sub-inhibitory concentrations of amoxicillin on physiological responses and virulence determinants in a commensal strain of Escherichia coli

AIMS

The goal was to study the effects of sub-minimum inhibitory concentrations (sub-MICs) of amoxicillin (AMX) on various physiological responses and virulence determinants in a commensal strain of Escherichia coli.

MATERIALS AND RESULTS

The commensal strain was passaged under various sub-MICs of AMX and its effect on bacterial growth, motility, biofilm formation, expression of outer membrane proteins (OMPs) and cell adhesion was analysed. Bacterial growth was diminished at 1/2 and 1/4 MICs of AMX with significant reduction in growth rate. Using crystal violet (CV) assays and quantification of surface polysaccharides we observed strong biofilm formation, together with reduced swimming motility in E. coli at 1/2 MIC of AMX. Differential OMP expression upon AMX sub-MIC exposure coincided with enhanced cell adhesion to HT-29 cells in vitro. The results demonstrated that sub-MICs of AMX can stimulate unpredictable changes in commensal bacterial strains which can be a potent source for the propagation of antibiotic resistance.

CONCLUSIONS

The study reports that AMX at 1/2 MIC significantly compromised bacterial growth and swimming motility, alongside inducing biofilm formation. This was also accompanied by upregulation of a single OMP which subsequently increased cell adhesion capabilities in E. coli at 1/2 MIC, thereby enhancing its colonization and survival abilities within the gut microsphere.

SIGNIFICANCE AND IMPACT OF THE STUDY

For the first time, the effects of AMX sub-MICs on a commensal E. coli strain were described. The results corroborate on how antibiotics can act as stimulatory molecules and determine the pathogenicity of commensal bacteria in vivo that can disseminate resistance to other intestinal pathogens or microbes.

Molecules involved in motility regulation in Escherichia coli cells: a review

The initial colonization of the host organism by commensal, probiotic, and pathogenic Escherichia coli strains is an important step in the development of infections and biofilms. Sensing and colonization of host cell surfaces are governed by flagellar and fimbriae/pili appendages, respectively. Biofilm formation confers great advantages on pathogenic E. coli cells such as protection against the host immune system, antimicrobial agents, and several environmental stress factors. The transition from planktonic to sessile physiological states involves several signaling cascades and factors responsible for the regulation of flagellar motility in E. coli cells. These regulatory factors have thus become important targets to control pathogenicity. Hence, attenuation of flagellar motility is considered a potential therapy against pathogenic E. coli. The present review describes signaling pathways and proteins involved in direct or indirect regulation of flagellar motility. Furthermore, application strategies for antimotility natural or synthetic compounds are discussed also.

Magnetic nanoparticles coated with carbohydrates for 3D culture of bacteria

Magnetic nanoparticles (MNPs) are a specific type of nanomaterial whose applications are widespread into several fields including biomedicine as a smart drug targeter and environmental engineering due to their interactions with contaminants. Lately, the use of MNPs has also been demonstrated in structuring three-dimensional (3D) cultures of mammalian cells. However, MNPs application to other cell types is still limited. In this sense, some planktonic microorganisms when adhered to surfaces perform the swarming phenomenon to guarantee the expansion of the colony and to guarantee more niches. Therefore, the aim of this study was to produce MNPs coated with four carbohydrates (galactose - gal, glucose - glu, sucrose - suc, and maltose - mal) aiming microorganism culture applications and also for possible 3D arrays. The results showed that carbohydrate-coated MNPs showed hydrodynamic diameters ranging from 100 to 200 nm and that their coatings influenced the chemical behavior in different ways. Indeed, when subjected to biological tests to determine their potential level of cytotoxicity, it was found that in concentrations of 1 mM, 800, 600, and 400 μM (iron equivalent), there was not any alteration on growth of model microorganisms when visually evaluated. Besides, magnetization of bacteria was promoted in different ways as well as the modulation of swarming formation in Escherichia coli when exposed to MNP-Glu. In sum, MNPs coated with carbohydrates and even uncoated were atoxic to bacteria and one of them was able to modulate E. coli swarming formation showing the potential for applications in 3D cultures of bacteria.

A transition to stable one-dimensional swimming enhances E. coli motility through narrow channels

Living organisms often display adaptive strategies that allow them to move efficiently even in strong confinement. With one single degree of freedom, the angle of a rotating bundle of flagella, bacteria provide one of the simplest examples of locomotion in the living world. Here we show that a purely physical mechanism, depending on a hydrodynamic stability condition, is responsible for a confinement induced transition between two swimming states in E. coli. While in large channels bacteria always crash onto confining walls, when the cross section falls below a threshold, they leave the walls to move swiftly on a stable swimming trajectory along the channel axis. We investigate this phenomenon for individual cells that are guided through a sequence of micro-fabricated tunnels of decreasing cross section. Our results challenge current theoretical predictions and suggest effective design principles for microrobots by showing that motility based on helical propellers provides a robust swimming strategy for exploring narrow spaces.

Investigating Flagella-Driven Motility in Escherichia coli by Applying Three Established Techniques in a Series

Motility is crucial to the survival and success of many bacterial species. Many methodologies exist to exploit motility to understand signaling pathways, to elucidate the function and assembly of flagellar parts, and to examine and understand patterns of movement. Here we demonstrate a combination of three of these methodologies. Motility in soft agar is the oldest, offering a strong selection for isolating gain-of-function suppressor mutations in motility-impaired strains, where motility is restored through a second mutation. The cell-tethering technique, first employed to demonstrate the rotary nature of the flagellar motor, can be used to assess the impact of signaling effectors on the motor speed and its ability to switch rotational direction. The "border-crossing" assay is more recent, where swimming bacteria can be primed to transition into moving collectively as a swarm. In combination, these protocols represent a systematic and powerful approach to identifying components of the motility machinery, and to characterizing their role in different facets of swimming and swarming. They can be easily adapted to study motility in other bacterial species.

Compact off-axis holographic slide microscope: design guidelines

Holographic microscopes are emerging as suitable tools for in situ diagnostics and environmental monitoring, providing high-throughput, label-free, quantitative imaging capabilities through small and compact devices. In-line holographic microscopes can be realized at contained costs, trading off complexity in the phase retrieval process and being limited to sparse samples. Here we present a 3D printed, cost effective and field portable off-axis holographic microscope based on the concept of holographic microfluidic slide. Our scheme removes complexity from the reconstruction process, as phase retrieval is non iterative and obtainable by hologram demodulation. The configuration we introduce ensures flexibility in the definition of the optical scheme, exploitable to realize modular devices with different features. We discuss trade-offs and design rules of thumb to follow for developing DH microscopes based on the proposed solution. Using our prototype, we image flowing marine microalgae, polystyrene beads, E.coli bacteria and microplastics. We detail the effect on the performance and costs of each parameter, design, and hardware choice, guiding readers toward the realization of optimized devices that can be employed out of the lab by non-expert users for point of care testing.

Formation of phage lysis patterns and implications on co-propagation of phages and motile host bacteria

Coexistence of bacteriophages, or phages, and their host bacteria plays an important role in maintaining the microbial communities. In natural environments with limited nutrients, motile bacteria can actively migrate towards locations of richer resources. Although phages are not motile themselves, they can infect motile bacterial hosts and spread in space via the hosts. Therefore, in a migrating microbial community coexistence of bacteria and phages implies their co-propagation in space. Here, we combine an experimental approach and mathematical modeling to explore how phages and their motile host bacteria coexist and co-propagate. When lytic phages encountered motile host bacteria in our experimental set up, a sector-shaped lysis zone formed. Our mathematical model indicates that local nutrient depletion and the resulting inhibition of proliferation and motility of bacteria and phages are the key to formation of the observed lysis pattern. The model further reveals the straight radial boundaries in the lysis pattern as a telltale sign for coexistence and co-propagation of bacteria and phages. Emergence of such a pattern, albeit insensitive to extrinsic factors, requires a balance between intrinsic biological properties of phages and bacteria, which likely results from coevolution of phages and bacteria.

Chemotactic behaviour of Escherichia coli at high cell density

At high cell density, swimming bacteria exhibit collective motility patterns, self-organized through physical interactions of a however still debated nature. Although high-density behaviours are frequent in natural situations, it remained unknown how collective motion affects chemotaxis, the main physiological function of motility, which enables bacteria to follow environmental gradients in their habitats. Here, we systematically investigate this question in the model organism Escherichia coli, varying cell density, cell length, and suspension confinement. The characteristics of the collective motion indicate that hydrodynamic interactions between swimmers made the primary contribution to its emergence. We observe that the chemotactic drift is moderately enhanced at intermediate cell densities, peaks, and is then strongly suppressed at higher densities. Numerical simulations reveal that this suppression occurs because the collective motion disturbs the choreography necessary for chemotactic sensing. We suggest that this physical hindrance imposes a fundamental constraint on high-density behaviours of motile bacteria, including swarming and the formation of multicellular aggregates and biofilms.

Long-range excitations in phospholipid membranes

We investigated the existence of long-range excitations and correlated structures in phospholipid membranes by means of grazing-incidence neutron spin echo spectroscopy, grazing-incidence small-angle neutron scattering, and corresponding theoretical calculations inspired by smectic-membrane theory. All these methods confirmed the existence of thermal excitations in the plane of the surface of the phospholipid membranes or the corresponding structures, respectively. Also, these measurements revealed a temperature dependence of these excitations. These excitations are associated with 100 nm in-plane correlations around physiological temperatures and of 75 nm at 16 °C. A single excitation has an energy around the μeV-regime. A temperature series revealed a high abundance at physiological temperatures and pronounced long-range in-plane structures, which are strongly suppressed at temperatures below 20 °C. From the length-scales and energy transfers involved we surmise that these excitations may play a role in several functions of the cell membranes such as stability and energy dissipation along the membrane. From a fundamental point of view, the observed behavior of those excitations is congruent with that of a quasi-particle (surface mode phonon, smomon) that exists in the plane of phospholipid membranes.

Efficiency of the flagellar propulsion of Escherichia coli in confined microfluidic geometries

Bacterial movement in confined spaces is routinely encountered either in a natural environment or in artificial structures. Consequently, the ability to understand and predict the behavior of motile bacterial cells in confined geometries is essential to many applications, spanning from the more classical, such as the management complex microbial networks involved in diseases, biomanufacturing, mining, and environment, to the more recent, such as single cell DNA sequencing and computation with biological agents. Fortunately, the development of this understanding can be helped by the decades-long advances in semiconductor microfabrication, which allow the design and the construction of complex confining structures used as test beds for the study of bacterial motility. To this end, here we use microfabricated channels with varying sizes to study the interaction of Escherichia coli with solid confining spaces. It is shown that an optimal channel size exists for which the hydrostatic potential allows the most efficient movement of the cells. The improved understanding of how bacteria move will result in the ability to design better microfluidic structures based on their interaction with bacterial movement.

Revealing the roles of y4wF and tidC genes in Rhizobium tropici CIAT 899: biosynthesis of indolic compounds and impact on symbiotic properties

Rhizobium tropici CIAT 899 is a strain known by its ability to nodulate a broad range of legume species, to synthesize a variety of Nod factors, its tolerance of abiotic stresses, and its high capacity to fix atmospheric N₂, especially in symbiosis with common bean (Phaseolus vulgaris L.). Genes putatively related to the synthesis of indole acetic acid (IAA) have been found in the symbiotic plasmid of CIAT 899, in the vicinity of the regulatory nodulation gene nodD5, and, in this study, we obtained mutants for two of these genes, y4wF and tidC (R. tropiciindole-3-pyruvic acid decarboxylase), and investigated their expression in the absence and presence of tryptophan (TRP) and apigenin (API). In general, mutations of both genes increased exopolysaccharide (EPS) synthesis and did not affect swimming or surface motility; mutations also delayed nodule formation, but increased competitiveness. We found that the indole-3-acetamide (IAM) pathway was active in CIAT 899 and not affected by the mutations, and-noteworthy-that API was required to activate the tryptamine (TAM) and the indol-3-pyruvic acid (IPyA) pathways in all strains, particularly in the mutants. High up-regulation of y4wF and tidC genes was observed in both the wild-type and the mutant strains in the presence of API. The results obtained revealed an intriguing relationship between IAA metabolism and nod-gene-inducing activity in R. tropici CIAT 899. We discuss the IAA pathways, and, based on our results, we attribute functions to the y4wF and tidC genes of R. tropici.

Bacterial Biohybrid Microswimmers

Over millions of years, Nature has optimized the motion of biological systems at the micro and nanoscales. Motor proteins to motile single cells have managed to overcome Brownian motion and solve several challenges that arise at low Reynolds numbers. In this review, we will briefly describe naturally motile systems and their strategies to move, starting with a general introduction that surveys a broad range of developments, followed by an overview about the physical laws and parameters that govern and limit motion at the microscale. We characterize some of the classes of biological microswimmers that have arisen in the course of evolution, as well as the hybrid structures that have been constructed based on these, ranging from Montemagno's ATPase motor to the SpermBot. Thereafter, we maintain our focus on bacteria and their biohybrids. We introduce the inherent properties of bacteria as a natural microswimmer and explain the different principles bacteria use for their motion. We then elucidate different strategies that have been employed for the coupling of a variety of artificial microobjects to the bacterial surface, and evaluate the different effects the coupled objects have on the motion of the "biohybrid." Concluding, we give a short overview and a realistic evaluation of proposed applications in the field.

Genetic and Phenotypic Characterization of Indole-Producing Isolates of Pseudomonas syringae pv. actinidiae Obtained From Chilean Kiwifruit Orchards

In recent years, Chilean kiwifruit production has been affected by the phytopathogen Pseudomonas syringae pv. actinidiae (Psa), which has caused losses to the industry. In this study, we report the genotypic and phenotypic characterization of 18 Psa isolates obtained from Chilean kiwifruits orchards between 2012 and 2016 from different geographic origins. Genetic analysis by multilocus sequence analysis (MLSA) using four housekeeping genes (gyrB, rpoD, gltA, and gapA) and the identification of type III effector genes suggest that the Chilean Psa isolates belong to the Psa Biovar 3 cluster. All of the isolates were highly homogenous in regard to their phenotypic characteristics. None of the isolates were able to form biofilms over solid plastic surfaces. However, all of the isolates formed cellular aggregates in the air-liquid interface. All of the isolates, except for Psa 889, demonstrated swimming motility, while only isolate Psa 510 demonstrated swarming motility. The biochemical profiles of the isolates revealed differences in 22% of the tests in at least one Psa isolate when analyzed with the BIOLOG system. Interestingly, all of the isolates were able to produce indole using a tryptophan-dependent pathway. PCR analysis revealed the presence of the genes aldA/aldB and iaaL/matE, which are associated with the production of indole-3-acetic acid (IAA) and indole-3-acetyl-3-L-lysine (IAA-Lys), respectively, in P. syringae. In addition, IAA was detected in the cell free supernatant of a representative Chilean Psa strain. This work represents the most extensive analysis in terms of the time and geographic origin of Chilean Psa isolates. To our knowledge, this is the first report of Psa being able to produce IAA. Further studies are needed to determine the potential role of IAA in the virulence of Psa during kiwifruit infections and whether this feature is observed in other Psa biovars.

Phylogenetic relationships, biofilm formation, motility, antibiotic resistance and extended virulence genotypes among Escherichia coli strains from women with community-onset primitive acute pyelonephritis

The present work set out to search for a virulence repertoire distinctive for Escherichia coli causing primitive acute pyelonephritis (APN). To this end, the virulence potential of 18 E. coli APN strains was genotypically and phenotypically assessed, comparatively with 19 strains causing recurrent cystitis (RC), and 16 clinically not significant (control, CO) strains. Most of the strains belong to phylogenetic group B1 (69.8%; p<0.01), and APN strains showed unique features, which are the presence of phylogroup A, and the absence of phylogroup B2 and non-typeable strains. Overall, the most dominant virulence factor genes (VFGs) were ecpA and fyuA (92.4 and 86.7%, respectively; p<0.05), and the mean number of VFGs was significantly higher in uropathogenic strains. Particularly, papAH and malX were exclusive for uropathogenic strains. APN and RC strains showed a significantly higher prevalence of fyuA, usp, and malX than of CO strains. Compared to RC strains, APN ones showed a higher prevalence of iha, but a lower prevalence of iroN, cnf1, and kpsMT-II. Hierarchical cluster analysis showed a higher proportion of two gene clusters (malX and usp, and fyuA and ecpA) were detected in the APN and RC groups than in CO, whereas iutA and iha clusters were detected more frequently in APN strains. The motility level did not differ among the study-groups and phylogroups considered, although a higher proportion of swarming strains was observed in APN strains. Antibiotic-resistance rates were generally low except for ampicillin (37.7%), and were not associated with specific study- or phylogenetic groups. APN and RC strains produced more biofilm than CO strains. In APN strains, iha was associated with higher biofilm biomass formation, whereas iroN and KpSMT-K1 were associated with a lower amount of biofilm biomass. Further work is needed to grasp the virulence and fitness mechanisms adopted by E. coli causing APN, and hence develop new therapeutic and prophylactic approaches.

Induced clustering of Escherichia coli by acoustic fields

Brownian or self-propelled particles in aqueous suspensions can be trapped by acoustic fields generated by piezoelectric transducers usually at frequencies in the megahertz. The obtained confinement allows the study of rich collective behaviours like clustering or spreading dynamics in microgravity-like conditions. The acoustic field induces the levitation of self-propelled particles and provides secondary lateral forces to capture them at nodal planes. Here, we give a step forward in the field of confined active matter, reporting levitation experiments of bacterial suspensions of Escherichia coli. Clustering of living bacteria is monitored as a function of time, where different behaviours are clearly distinguished. Upon the removal of the acoustic signal, bacteria rapidly spread, impelled by their own swimming. Nevertheless, long periods of confinement result in irreversible bacteria entanglements that could act as seeds for levitating bacterial aggregates.

Controllable Swarming and Assembly of Micro/Nanomachines

Motion is a common phenomenon in biological processes. Major advances have been made in designing various self-propelled micromachines that harvest different types of energies into mechanical movement to achieve biomedicine and biological applications. Inspired by fascinating self-organization motion of natural creatures, the swarming or assembly of synthetic micro/nanomachines (often referred to micro/nanoswimmers, micro/nanorobots, micro/nanomachines, or micro/nanomotors), are able to mimic these amazing natural systems to help humanity accomplishing complex biological tasks. This review described the fuel induced methods (enzyme, hydrogen peroxide, hydrazine, et al.) and fuel-free induced approaches (electric, ultrasound, light, and magnetic) that led to control the assembly and swarming of synthetic micro/nanomachines. Such behavior is of fundamental importance in improving our understanding of self-assembly processes that are occurring on molecular to macroscopic length scales.

Role of tumbling in bacterial swarming

Typical wild-type bacteria swimming in sparse suspensions exhibit a movement pattern called "run and tumble," characterized by straight trajectories (runs) interspersed by shorter, random reorientation (tumbles). This is achieved by rotating their flagella counterclockwise, or clockwise, respectively. The chemotaxis signaling network operates in controlling the frequency of tumbles, enabling navigation toward or away from desired regions in the medium. In contrast, while in dense populations, flagellated bacteria exhibit collective motion and form large dynamic clusters, whirls, and jets, with intricate dynamics that is fundamentally different than trajectories of sparsely swimming cells. Although collectively swarming cells do change direction at the level of the individual cell, often exhibiting reversals, it has been suggested that chemotaxis does not play a role in multicellular colony expansion, but the change in direction stems from clockwise flagellar rotation. In this paper, the effects of cell rotor switching (i.e., the ability to tumble) and chemotaxis on the collective statistics of swarming bacteria are studied experimentally in wild-type Bacillus subtilis and two mutants-one that does not tumble and one that tumbles independently of the chemotaxis system. We show that while several of the parameters examined are similar between the strains, other collective and individual characteristics are significantly different. The results demonstrate that tumbling and/or flagellar directional rotor switching has an important role on the dynamics of swarming, and imply that swarming models of self-propelled rods that do not take tumbling and/or rotor switching into account may be oversimplified.

Noncontact Cohesive Swimming of Bacteria in Two-Dimensional Liquid Films

Bacterial swimming in confined two-dimensional environments is ubiquitous in nature and in clinical settings. Characterizing individual interactions between swimming bacteria in 2D confinement will help to understand diverse microbial processes, such as bacterial swarming and biofilm formation. Here we report a novel motion pattern displayed by flagellated bacteria in 2D confinement: When two nearby cells align their moving directions, they tend to engage in cohesive swimming without direct cell body contact, as a result of hydrodynamic interaction but not flagellar intertwining. We further found that cells in cohesive swimming move with higher directional persistence, which can increase the effective diffusivity of cells by ∼3 times as predicted by computational modeling. As a conserved behavior for peritrichously flagellated bacteria, cohesive swimming in 2D confinement may be key to collective motion and self-organization in bacterial swarms; it may also promote bacterial dispersal in unsaturated soils and in interstitial space during infections.

Effect of Cell Aspect Ratio on Swarming Bacteria

Swarming bacteria collectively migrate on surfaces using flagella, forming dynamic whirls and jets that consist of millions of individuals. Because some swarming bacteria elongate prior to actual motion, cell aspect ratio may play a significant role in the collective dynamics. Extensive research on self-propelled rodlike particles confirms that elongation promotes alignment, strongly affecting the dynamics. Here, we study experimentally the collective dynamics of variants of swarming Bacillus subtilis that differ in length. We show that the swarming statistics depends on the aspect ratio in a critical, fundamental fashion not predicted by theory. The fastest motion was obtained for the wild-type and variants that are similar in length. However, shorter and longer cells exhibit anomalous, non-Gaussian statistics and nonexponential decay of the autocorrelation function, indicating lower collective motility. These results suggest that the robust mechanisms to maintain aspect ratios may be important for efficient swarming motility. Wild-type cells are optimal in this sense.

Long-range nematic order and anomalous fluctuations in suspensions of swimming filamentous bacteria

We study the collective dynamics of elongated swimmers in a very thin fluid layer by devising long filamentous nontumbling bacteria. The strong confinement induces weak nematic alignment upon collision, which, for large enough density of cells, gives rise to global nematic order. This homogeneous but fluctuating phase, observed on the largest experimentally accessible scale of millimeters, exhibits the properties predicted by standard models for flocking, such as the Vicsek-style model of polar particles with nematic alignment: true long-range nematic order and nontrivial giant number fluctuations.

Bacterial swarmer cells in confinement: a mesoscale hydrodynamic simulation study

A wide spectrum of Peritrichous bacteria undergo considerable physiological changes when they are inoculated onto nutrition-rich surfaces and exhibit a rapid and collective migration denoted as swarming. Thereby, the length of such swarmer cells and their number of flagella increases substantially. In this article, we investigated the properties of individual E. coli-type swarmer cells confined between two parallel walls via mesoscale hydrodynamic simulations, combining molecular dynamics simulations of the swarmer cell with the multiparticle particle collision dynamics approach for the embedding fluid. E. coli-type swarmer cells are three-times longer than their planktonic counter parts, but their flagella density is comparable. By varying the wall separation, we analyze the confinement effect on the flagella arrangement, on the distribution of cells in the gap between the walls, and on the cell dynamics. We find only a weak dependence of confinement on the bundle structure and dynamics. The distribution of cells in the gap changes from a geometry-dominated behavior for very narrow to fluid-dominated behavior for wider gaps, where cells are preferentially located in the gap center for narrower gaps and stay preferentially next to one of the walls for wider gaps. Dynamically, the cells exhibit a wide spectrum of migration behaviors, depending on their flagella bundle arrangement, and ranges from straight swimming to wall rolling.

Feedback control of Campylobacter jejuni flagellin levels through reciprocal binding of FliW to flagellin and the global regulator CsrA

Bacterial flagella assembly is tightly regulated to ensure a timely and sequential production of the various flagellum constituents. In the pathogen Campylobacter jejuni the hierarchy in flagella biosynthesis is largely determined at the transcriptional level through the activity of the alternative sigma factors sigma⁵⁴ and sigma²⁸ . Here, we report that C. jejuni flagellin levels are also controlled at the post-transcriptional level via the thus far poorly-characterized flagellar assembly factor FliW. Analysis of flagellin synthesis in C. jejuni 81116 and a ΔfliW knock-out mutant showed reduced flagellin protein levels in the mutant strain while ectopic expression of FliW resulted in enhanced levels. Real-time RT-PCR revealed relatively minor changes in flaA and flaB mRNA levels for the recombinant and parent strain consistent with post-transcriptional regulation. Purified FliW was found to bind to FlaA and FlaB flagellin as well as to the global post-transcriptional regulator CsrA. Inactivation of CsrA resulted in increased levels of flagellin translation. An in vitro translation assay confirmed the regulatory role of CsrA in flagellin biosynthesis. We propose that competitive reciprocal binding of FliW to flagellins and the RNA binding protein CsrA serves as a feedback mechanism to control the number of cytosolic flagellin copies at the protein level.

Shelter in a Swarm

Flagella propel bacteria during both swimming and swarming, dispersing them widely. However, while swimming bacteria use chemotaxis to find nutrients and avoid toxic environments, swarming bacteria appear to suppress chemotaxis and to use the dynamics of their collective motion to continuously expand and acquire new territory, barrel through lethal chemicals in their path, carry along bacterial and fungal cargo that assists in exploration of new niches, and engage in group warfare for niche dominance. Here, we focus on two aspects of swarming, which, if understood, hold the promise of revealing new insights into microbial signaling and behavior, with ramifications beyond bacterial swarming. These are as follows: how bacteria sense they are on a surface and turn on programs that promote movement and how they override scarcity and adversity as dense packs.

Hydrodynamic analysis of flagellated bacteria swimming near one and between two no-slip plane boundaries

The motility of swimming bacteria near solid surfaces has implications in a wide range of scenarios, including water treatment facilities, microfluidics, and biomedical implants. Using the boundary element method to numerically solve the equations of low Reynolds number fluid flow, we investigate the dynamics of a model swimmer propelled by rotating a single helical flagellum. Building on previous simulation results for swimmers near a single plane boundary, we introduce a second, parallel boundary and show that the bacterial trajectories change as the two plates are brought closer together. Analysis of this dynamical system shows that the configuration in the center of the channel and parallel to the walls is an unstable equilibrium state for large plate separations, but it becomes the only stable position for swimmers when the plate separation is reduced to three to four times the cell width. Our model also predicts that transient trajectories, i.e., those not at steady states, can exhibit curvature in the opposite sense to that expected from the well-known explanation for circular bacterial paths near a single wall.

Locomotion and transport in a hexatic liquid crystal

The swimming behavior of bacteria and other microorganisms is sensitive to the physical properties of the fluid in which they swim. Mucus, biofilms, and artificial liquid-crystalline solutions are all examples of fluids with some degree of anisotropy that are also commonly encountered by bacteria. In this article, we study how liquid-crystalline order affects the swimming behavior of a model swimmer. The swimmer is a one-dimensional version of G. I. Taylor's swimming sheet: an infinite line undulating with small-amplitude transverse or longitudinal traveling waves. The fluid is a two-dimensional hexatic liquid-crystalline film. We calculate the power dissipated, swimming speed, and flux of fluid entrained as a function of the swimmer's wave form as well as properties of the hexatic film, such as the rotational and shear viscosity, the Frank elastic constant, and the anchoring strength. The departure from isotropic behavior is greatest for large rotational viscosity and weak anchoring boundary conditions on the orientational order at the swimmer surface. We even find that if the rotational viscosity is large enough, the transverse-wave swimmer moves in the opposite direction relative to a swimmer in an isotropic fluid.