Bacteria are not too small for spatial sensing of chemical gradients: an experimental evidence

Application of photosensitive microalgae in targeted tumor therapy

Microalgae present a novel and multifaceted approach to cancer therapy by modulating the tumor-associated microbiome (TAM) and the tumor microenvironment (TME). Through their ability to restore gut microbiota balance, reduce inflammation, and enhance immune responses, microalgae contribute to improved cancer treatment outcomes. As photosynthetic microorganisms, microalgae exhibit inherent anti-tumor, antioxidant, and immune-regulating properties, making them valuable in photodynamic therapy and tumor imaging due to their capacity to generate reactive oxygen species. Additionally, microalgae serve as effective drug delivery vehicles, leveraging their biocompatibility and unique structural properties to target the TME more precisely. Microalgae-based microrobots further expand their therapeutic potential by autonomously navigating complex biological environments, offering a promising future for precision-targeted cancer treatments. We position microalgae as a multifunctional agent capable of modulating TAM, offering novel strategies to enhance TME and improve the efficacy of cancer therapies.

Run-and-tumble like motion of a camphor-infused Marangoni swimmer

'Run-and-tumble' (RT) motion has been a subject of intense research for several decades. Many organisms, such as bacteria, perform such motion in the presence or absence of local chemical concentration gradients and it is found to be advantageous in search processes. Although there are previous reports involving the successful design of non-living self-propelled particles exhibiting such motion in the presence of external stimuli (chemical/mechanical), RT motion with 'rest' has not yet been observed for autonomous non-living active particles. We have designed a swimmer that performs motion using a combination of 'run', 'tumble', and 'rest' states with stochastic transitions. In the present scenario, it arises solely due to self-generated local surface tension gradients. We quantify the residence time statistics by analyzing the swimmer trajectories from the experimental data, which suggests that the 'rest' and 'tumble' states are more frequent than 'run'. Then, we quantify the motion properties by computing the mean squared displacement, which shows that the swimmer performs ballistic motion on a short time scale and then slows down due to tumbling and resting. To validate the observed transport properties, we introduce a minimal model of a chiral active Brownian particle, stochastically switching between three internal states. The model parameters were extracted from the experiments, which rendered a good agreement between the experiments and simulations.

Individual bacterial cells can use spatial sensing of chemical gradients to direct chemotaxis on surfaces

Swimming bacteria navigate chemical gradients using temporal sensing to detect changes in concentration over time. Here we show that surface-attached bacteria use a fundamentally different mode of sensing during chemotaxis. We combined microfluidic experiments, massively parallel cell tracking and fluorescent reporters to study how Pseudomonas aeruginosa senses chemical gradients during pili-based 'twitching' chemotaxis on surfaces. Unlike swimming cells, we found that temporal changes in concentration did not induce motility changes in twitching cells. We then quantified the chemotactic behaviour of stationary cells by following changes in the sub-cellular localization of fluorescent proteins as cells are exposed to a gradient that alternates direction. These experiments revealed that P. aeruginosa cells can directly sense differences in concentration across the lengths of their bodies, even in the presence of strong temporal fluctuations. Our work thus overturns the widely held notion that bacterial cells are too small to directly sense chemical gradients in space.

Trapping and scattering of a multiflagellated bacterium by a hard surface

Thiovulum majus, which is one of the fastest known bacteria, swims using hundreds of flagella. Unlike typical pusher cells, which swim in circular paths over hard surfaces, T. majus localize near hard boundaries by turning their flagella to exert a net force normal to the surface. To probe the torques that stabilize this hydrodynamically bound state, the trajectories of several thousand collisions between a T. majus cell and a wall of a quasi-two-dimensional microfluidic chamber are analyzed. Measuring the fraction of cells escaping the wall either to the left or to the right of the point of contact-and how this probability varies with incident angle and time spent in contact with the surface-maps the scattering dynamics onto a first passage problem. These measurements are compared to the prediction of a Fokker-Planck equation to fit the angular velocity of a cell in contact with a hard surface. This analysis reveals a bound state with a narrow basin of attraction in which cells orient their flagella normal to the surface. The escape angle predicted by matching these near field dynamics with the far-field hydrodynamics is consistent with observation. We discuss the significance of these results for the ecology of T. majus and their self-organization into active chiral crystals.

Electrochemical Energy Harvesting Using Microbial Active Matter

With the continuous growth in world population and economy, the global energy demand is increasing rapidly. Given that non-renewable energy sources will eventually deplete, there is increasing need for clean, alternative renewable energy sources, which will be inexpensive and involve minimum risk of environmental pollution. In this paper, harnessing the activity of cupric reductase NDH-2 enzyme present in Escherichia coli bacterial cells, we demonstrate a simple and efficient energy harvesting strategy within an electrochemical chamber without the requirement of any external fuels or force fields. The transduction of energy has been demonstrated with various strains of E. coli, indicating that this strategy could, in principle, be applicable for other microbial catalytic systems. We offer a simple mechanism of the energy transduction process considering the bacterial enzyme-mediated redox reaction occurring over the working electrode of the electrochemical cell. Also, the amount of energy generated has been found to be depending on the motility of bacteria within the experimental chamber, suggesting possible opportunities for developing microbial motility-controlled small scale power generators. Finally, we show that the Faradaic electrochemical energy harvested is large enough to power a commercial light emitting diode connected to an amplifier circuit. We expect the present study to generate sufficient interest within soft condensed matter and biophysics communities, and offer useful platforms for controlled energy generation at the small scales.

Electrochemical sensors for oral biofilm-biomaterials interface characterization: A review

Important processes related to the interaction of the oral microbiome with the tooth surface happen directly at the interface. For example, the chemical microenvironment that exists at the interface of microbial biofilms and the native tooth structure is directly involved in caries development. Consequentially, a critical understanding of this interface and its chemical microenvironment would provide novel avenues in caries prevention, including secondary caries that often occurs at the interface of the dental biofilm, tooth structure, and dental material. Electrochemical sensors are a unique quantitative tool and have the inherent advantages of miniaturization, stability, and selectivity. That makes the electrochemical sensors ideal tools for studying these critical biofilm microenvironments with high precision. This review highlights the development and applications of several novel electrochemical sensors such as pH, Ca2+ , and hydrogen peroxide sensors as scanning electrochemical microscope probes in addition to flexible pH wire sensors for real-time bacterial biofilm-dental surface and dental materials interface studies.

Temporal fluctuations in chemotaxis gain implement a simulated-tempering strategy for efficient navigation in complex environments

Bacterial chemotaxis is a major testing ground for systems biology, including the role of fluctuations and individual variation. Individual bacteria vary in their tumbling frequency and adaptation time. Recently, large cell-cell variation was also discovered in chemotaxis gain, which determines the sensitivity of the tumbling rate to attractant gradients. Variation in gain is puzzling, because low gain impairs chemotactic velocity. Here, we provide a functional explanation for gain variation by establishing a formal analogy between chemotaxis and algorithms for sampling probability distributions. We show that temporal fluctuations in gain implement simulated tempering, which allows sampling of attractant distributions with many local peaks. Periods of high gain allow bacteria to detect and climb gradients quickly, and periods of low gain allow them to move to new peaks. Gain fluctuations thus allow bacteria to thrive in complex environments, and more generally they may play an important functional role for organism navigation.

Establishment of GC-MS method for the determination of Pseudomonas aeruginosa biofilm and its application in metabolite enrichment analysis

PA forms a biofilm resistant to antibiotics, hindering antibiotics efficacy and preventing the eradication of PA, has attracted much attention for its biofilm. In this study, we first established and validated an efficient and sensitive gas chromatography-mass spectrometry (GC-MS) method for the quantification of metabolites in biofilm. Decanoic acid was used as the internal standard. The separation of Palmitic acid, stearic acid and Decanoic acid was conducted on an Elite-5 MS column (30 m × 0.25 mm, 0.25 μm) using gradient elution condition at a flow rate of 1 mL/min. Palmitic acid, stearic acid and Decanoic acid were determined under the positive ionization mode, respectively. The calibration curve of Palmitic acid and stearic acid were established in the range of 4 to 128 μg/mL (r² = 0.999). The recovery of palmitic acid and stearic acid were between 98.76% and 113.91%, RSD ＜ 5%. The well validated method was used to detect the metabolites of Pseudomonas aeruginosa biofilm. 54 metabolites were isolated and identified from biofilm samples, and 7 important signal pathways were identified by KEGG enrichment analysis. ABC transporters and bacterial chemotaxis signaling pathways have an important impact on the growth of PA biofilm among these metabolic pathways. This study provides valuable references for the further study of PA biofilm, especially the change of metabolite content and the search for biomarkers.

Origins of eukaryotic excitability

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'.

Learning action-oriented models through active inference

Converging theories suggest that organisms learn and exploit probabilistic models of their environment. However, it remains unclear how such models can be learned in practice. The open-ended complexity of natural environments means that it is generally infeasible for organisms to model their environment comprehensively. Alternatively, action-oriented models attempt to encode a parsimonious representation of adaptive agent-environment interactions. One approach to learning action-oriented models is to learn online in the presence of goal-directed behaviours. This constrains an agent to behaviourally relevant trajectories, reducing the diversity of the data a model need account for. Unfortunately, this approach can cause models to prematurely converge to sub-optimal solutions, through a process we refer to as a bad-bootstrap. Here, we exploit the normative framework of active inference to show that efficient action-oriented models can be learned by balancing goal-oriented and epistemic (information-seeking) behaviours in a principled manner. We illustrate our approach using a simple agent-based model of bacterial chemotaxis. We first demonstrate that learning via goal-directed behaviour indeed constrains models to behaviorally relevant aspects of the environment, but that this approach is prone to sub-optimal convergence. We then demonstrate that epistemic behaviours facilitate the construction of accurate and comprehensive models, but that these models are not tailored to any specific behavioural niche and are therefore less efficient in their use of data. Finally, we show that active inference agents learn models that are parsimonious, tailored to action, and which avoid bad bootstraps and sub-optimal convergence. Critically, our results indicate that models learned through active inference can support adaptive behaviour in spite of, and indeed because of, their departure from veridical representations of the environment. Our approach provides a principled method for learning adaptive models from limited interactions with an environment, highlighting a route to sample efficient learning algorithms.

Structured silicon for revealing transient and integrated signal transductions in microbial systems

Bacterial response to transient physical stress is critical to their homeostasis and survival in the dynamic natural environment. Because of the lack of biophysical tools capable of delivering precise and localized physical perturbations to a bacterial community, the underlying mechanism of microbial signal transduction has remained unexplored. Here, we developed multiscale and structured silicon (Si) materials as nongenetic optical transducers capable of modulating the activities of both single bacterial cells and biofilms at high spatiotemporal resolution. Upon optical stimulation, we capture a previously unidentified form of rapid, photothermal gradient-dependent, intercellular calcium signaling within the biofilm. We also found an unexpected coupling between calcium dynamics and biofilm mechanics, which could be of importance for biofilm resistance. Our results suggest that functional integration of Si materials and bacteria, and associated control of signal transduction, may lead to hybrid living matter toward future synthetic biology and adaptable materials.

Biological active matter aggregates: Inspiration for smart colloidal materials

Aggregations of social organisms exhibit a remarkable range of properties and functionalities. Multiple examples, such as fire ants or slime mold, show how a population of individuals is able to overcome an existential threat by gathering into a solid-like aggregate with emergent functionality. Surprisingly, these aggregates are driven by simple rules, and their mechanisms show great parallelism among species. At the same time, great effort has been made by the scientific community to develop active colloidal materials, such as microbubbles or Janus particles, which exhibit similar behaviors. However, a direct connection between these two realms is still not evident, and it would greatly benefit future studies. In this review, we first discuss the current understanding of living aggregates, point out the mechanisms in their formation and explore the vast range of emergent properties. Second, we review the current knowledge in aggregated colloidal systems, the methods used to achieve the aggregations and their potential functionalities. Based on this knowledge, we finally identify a set of over-arching principles commonly found in biological aggregations, and further suggest potential future directions for the creation of bio-inspired colloid aggregations.

Collective gradient sensing in fish schools

Throughout the animal kingdom, animals frequently benefit from living in groups. Models of collective behaviour show that simple local interactions are sufficient to generate group morphologies found in nature (swarms, flocks and mills). However, individuals also interact with the complex noisy environment in which they live. In this work, we experimentally investigate the group performance in navigating a noisy light gradient of two unrelated freshwater species: golden shiners (Notemigonuscrysoleucas) and rummy nose tetra (Hemigrammus bleheri). We find that tetras outperform shiners due to their innate individual ability to sense the environmental gradient. Using numerical simulations, we examine how group performance depends on the relative weight of social and environmental information. Our results highlight the importance of balancing of social and environmental information to promote optimal group morphologies and performance.

A computational model for how cells choose temporal or spatial sensing during chemotaxis

Cell size is thought to play an important role in choosing between temporal and spatial sensing in chemotaxis. Large cells are thought to use spatial sensing due to large chemical difference at its ends whereas small cells are incapable of spatial sensing due to rapid homogenization of proteins within the cell. However, small cells have been found to polarize and large cells like sperm cells undergo temporal sensing. Thus, it remains an open question what exactly governs spatial versus temporal sensing. Here, we identify the factors that determines sensing choices through mathematical modeling of chemotactic circuits. Comprehensive computational search of three-node signaling circuits has identified the negative integral feedback (NFB) and incoherent feedforward (IFF) circuits as capable of adaptation, an important property for chemotaxis. Cells are modeled as one-dimensional circular system consisting of diffusible activator, inactivator and output proteins, traveling across a chemical gradient. From our simulations, we find that sensing outcomes are similar for NFB or IFF circuits. Rather than cell size, the relevant parameters are the 1) ratio of cell speed to the product of cell diameter and rate of signaling, 2) diffusivity of the output protein and 3) ratio of the diffusivities of the activator to inactivator protein. Spatial sensing is favored when all three parameters are low. This corresponds to a cell moving slower than the time it takes for signaling to propagate across the cell diameter, has an output protein that is polarizable and has a local-excitation global-inhibition system to amplify the chemical gradient. Temporal sensing is favored otherwise. We also find that temporal sensing is more robust to noise. By performing extensive literature search, we find that our prediction agrees with observation in a wide range of species and cell types ranging from E. coli to human Fibroblast cells and propose that our result is universally applicable.

Unicellular organisms and other single cells often have to migrate towards food sources or away from predators by sensing chemicals present in the environment. There are two ways for a cell to sense these external chemicals: temporal sensing, where the cell senses the external chemical at two different time points after it has moved through a certain distance, or spatial sensing, where the cell senses the external chemical at two different locations on its cellular surface (e.g., the front and rear of the cell) simultaneously. It has been thought that small unicellular organisms employ temporal sensing as their small size prohibits sensing at two different locations on the cellular surface. Using computational modeling, we find that the choice between temporal and spatial sensing is determined by the ratio of cell velocity to the product of cell diameter and rate of signaling, as well as the diffusivities of the signaling proteins. Predictions from our model agree with experimental observations over a wide range of cells, where a fast-moving, small cell performs better comparing the chemoattractant at different times in its trajectory; whereas, a slow-moving, big cell performs better by comparing the chemoattractant concentration at its two ends.

Modelling the collective response of heterogeneous cell populations to stationary gradients and chemical signal relay

The directed motion of cell aggregates toward a chemical source occurs in many relevant biological processes. Understanding the mechanisms that control this complex behavior is of great relevance for our understanding of developmental biological processes and many diseases. In this paper, we consider a self-propelled particle model for the movement of heterogeneous subpopulations of chemically interacting cells towards an imposed stable chemical gradient. Our simulations show explicitly how self-organisation of cell populations (which could lead to engulfment or complete cell segregation) can arise from the heterogeneity of chemotactic responses alone. This new result complements current theoretical and experimental studies that emphasise the role of differential cell-cell adhesion on self-organisation and spatial structure of cellular aggregates. We also investigate how the speed of individual cell aggregations increases with the chemotactic sensitivity of the cells, and decreases with the number of cells inside the aggregates.

Light-controlled motility in prokaryotes and the problem of directional light perception

The natural light environment is important to many prokaryotes. Most obviously, phototrophic prokaryotes need to acclimate their photosynthetic apparatus to the prevailing light conditions, and such acclimation is frequently complemented by motility to enable cells to relocate in search of more favorable illumination conditions. Non-phototrophic prokaryotes may also seek to avoid light at damaging intensities and wavelengths, and many prokaryotes with diverse lifestyles could potentially exploit light signals as a rich source of information about their surroundings and a cue for acclimation and behavior. Here we discuss our current understanding of the ways in which bacteria can perceive the intensity, wavelength and direction of illumination, and the signal transduction networks that link light perception to the control of motile behavior. We discuss the problems of light perception at the prokaryotic scale, and the challenge of directional light perception in small bacterial cells. We explain the peculiarities and the common features of light-controlled motility systems in prokaryotes as diverse as cyanobacteria, purple photosynthetic bacteria, chemoheterotrophic bacteria and haloarchaea.

Modeling of active swimmer suspensions and their interactions with the environment

In this article, we review mathematical models used to study the behaviour of suspensions of micro-swimmers and the accompanying biophysical phenomena, with specific focus on stimulus response. The methods discussed encompass a range of interactions exhibited by the micro-swimmers; including passive hydrodynamic (gyrotaxis) and gravitational (gravitaxis) effects, and active responses to chemical cues (chemotaxis) and light intensities (phototaxis). We introduce the simplest models first, and then build towards more sophisticated recent developments, in the process, identifying the limitations of the former and the new results obtained by the latter. We comment on the accuracy/validity of the models adopted, based on the agreement between theoretical results and experimental observations. We conclude by identifying some of the open problems and associated challenges faced by researchers in the realm of active suspensions.

Microbial Morphology and Motility as Biosignatures for Outer Planet Missions

Meaningful motion is an unambiguous biosignature, but because life in the Solar System is most likely to be microbial, the question is whether such motion may be detected effectively on the micrometer scale. Recent results on microbial motility in various Earth environments have provided insight into the physics and biology that determine whether and how microorganisms as small as bacteria and archaea swim, under which conditions, and at which speeds. These discoveries have not yet been reviewed in an astrobiological context. This paper discusses these findings in the context of Earth analog environments and environments expected to be encountered in the outer Solar System, particularly the jovian and saturnian moons. We also review the imaging technologies capable of recording motility of submicrometer-sized organisms and discuss how an instrument would interface with several types of sample-collection strategies. Key Words: In situ measurement-Biosignatures-Microbiology-Europa-Ice. Astrobiology 16, 755-774.

Effective Dynamics of Microorganisms That Interact with Their Own Trail

Like ants, some microorganisms are known to leave trails on surfaces to communicate. We explore how trail-mediated self-interaction could affect the behavior of individual microorganisms when diffusive spreading of the trail is negligible on the time scale of the microorganism using a simple phenomenological model for an actively moving particle and a finite-width trail. The effective dynamics of each microorganism takes on the form of a stochastic integral equation with the trail interaction appearing in the form of short-term memory. For a moderate coupling strength below an emergent critical value, the dynamics exhibits effective diffusion in both orientation and position after a phase of superdiffusive reorientation. We report experimental verification of a seemingly counterintuitive perpendicular alignment mechanism that emerges from the model.

Video processing analysis for the determination and evaluation of the chemotactic response in bacterial populations

The aim of the present work was to design a methodology based on video processing to obtain indicators of bacterial population motility that allow the quantitative and qualitative analysis and comparison of the chemotactic phenomenon with different attractants in the agarose-in plug bridge method. Video image sequences were processed applying Shannon's entropy to the intensity time series of each pixel, which conducted to a final pseudo colored image resembling a map of the dynamic bacterial clusters. Processed images could discriminate perfectly between positive and negative attractant responses at different periods of time from the beginning of the assay. An index of spatial and temporal motility was proposed to quantify the bacterial response. With this index, this video processing method allowed obtaining quantitative information of the dynamic changes in space and time from a traditional qualitative assay. We conclude that this computational technique, applied to the traditional agarose-in plug assay, has demonstrated good sensitivity for identifying chemotactic regions with a broad range of motility.

Biophysical basis for convergent evolution of two veil-forming microbes

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.

Diversity of magneto-aerotactic behaviors and oxygen sensing mechanisms in cultured magnetotactic bacteria

Microorganisms living in gradient environments affect large-scale processes, including the cycling of elements such as carbon, nitrogen or sulfur, the rates and fate of primary production, and the generation of climatically active gases. Aerotaxis is a common adaptation in organisms living in the oxygen gradients of stratified environments. Magnetotactic bacteria are such gradient-inhabiting organisms that have a specific type of aerotaxis that allows them to compete at the oxic-anoxic interface. They biomineralize magnetosomes, intracellular membrane-coated magnetic nanoparticles, that comprise a permanent magnetic dipole that causes the cells to align along magnetic field lines. The magnetic alignment enables them to efficiently migrate toward an optimal oxygen concentration in microaerobic niches. This phenomenon is known as magneto-aerotaxis. Magneto-aerotaxis has only been characterized in a limited number of available cultured strains. In this work, we characterize the magneto-aerotactic behavior of 12 magnetotactic bacteria with various morphologies, phylogenies, physiologies, and flagellar apparatus. We report six different magneto-aerotactic behaviors that can be described as a combination of three distinct mechanisms, including the reported (di-)polar, axial, and a previously undescribed mechanism we named unipolar. We implement a model suggesting that the three magneto-aerotactic mechanisms are related to distinct oxygen sensing mechanisms that regulate the direction of cells' motility in an oxygen gradient.

Short-range guiding can result in the formation of circular aggregates in myxobacteria populations

Myxobacteria are social bacteria that upon starvation form multicellular fruiting bodies whose shape in different species can range from simple mounds to elaborate tree-like structures. The formation of fruiting bodies is a result of collective cell movement on a solid surface. In the course of development, groups of flexible rod-shaped cells form streams and move in circular or spiral patterns to form aggregation centers that can become sites of fruiting body formation. The mechanisms of such cell movement patterns are not well understood. It has been suggested that myxobacterial development depends on short-range contact-mediated interactions between individual cells, i.e. cell aggregation does not require long-range signaling in the population. In this study, by means of a computational mass-spring model, we investigate what types of short-range interactions between cells can result in the formation of streams and circular aggregates during myxobacterial development. We consider short-range head-to-tail guiding between individual cells, whereby movement direction of the head of one cell is affected by the nearby presence of the tail of another cell. We demonstrate that stable streams and circular aggregates can arise only when the trailing cell, in addition to being steered by the tail of the leading cell, is able to speed up to catch up with it. It is suggested that necessary head-to-tail interactions between cells can arise from physical adhesion, response to a diffusible substance or slime extruded by cells, or pulling by motility engine pili. Finally, we consider a case of long-range guiding between cells and show that circular aggregates are able to form without cells increasing speed. These findings present a possibility to discriminate between short-range and long-range guiding mechanisms in myxobacteria by experimentally measuring distribution of cell speeds in circular aggregates.

Myxobacteria are social bacteria that upon starvation form multicellular fruiting bodies whose shape in different species can range from simple mounds to elaborate tree-like structures. The formation of fruiting bodies is a result of collective cell movement on a solid surface. Since collective cell motility during biological morphogenesis is also common in higher organisms, myxobacteria serve as a relatively simple model organism to study multicellular movement, organization and development. In the course of myxobacterial development, groups of flexible rod-shaped cells form streams and move in circular or spiral patterns to form aggregation centers that can become sites of fruiting body formation. The mechanisms of such cell movement patterns are not well understood. In this study, by means of a computational mass-spring model, we demonstrate that the formation of streams and circular aggregates during myxobacterial development can be explained by short-range head-to-tail guiding between individual cells, whereby movement direction of the head of one cell is affected by the nearby presence of the tail of another cell. We suggest that such interactions between cells can result from physical adhesion, response to a diffusible substance or slime extruded by cells, or the action of cell motility engine.

Fast-moving bacteria self-organize into active two-dimensional crystals of rotating cells

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.

Deep-water microbialites of the Mesoproterozoic Dismal Lakes Group: microbial growth, lithification, and implications for coniform stromatolites

Offshore facies of the Mesoproterozoic Sulky Formation, Dismal Lakes Group, arctic Canada, preserve microbialites with unusual morphology. These microbialites grew in water depths greater than several tens of meters and correlate with high-relief conical stromatolites of the more proximal September Lake reef complex. The gross morphology of these microbial facies consists of ridge-like vertical supports draped by concave-upward, subhorizontal elements, resulting in tent-shaped cuspate microbialites with substantial primary void space. Morphological and petrographic analyses suggest a model wherein penecontemporaneous upward growth of ridge elements and development of subhorizontal draping elements initially resulted in a buoyantly supported, unlithified microbial form. Lithification began via precipitation within organic elements during microbialite growth. Mineralization either stabilized or facilitated collapse of initially neutrally buoyant microbialite forms. Microbial structures and breccias were then further stabilized by precipitation of marine herringbone cement. During late-stage diagenesis, remaining void space was occluded by ferroan dolomite cement. Cuspate microbialites are most similar to those found in offshore facies of Neoarchean carbonate platforms and to unlithified, buoyantly supported microbial mats in modern ice-covered Antarctic lakes. We suggest that such unusual microbialite morphologies are a product of the interaction between motile and non-motile communities under nutrient-limiting conditions, followed by early lithification, which served to preserve the resultant microbial form. The presence of marine herringbone cement, commonly associated with high dissolved inorganic carbon (DIC), low O2 conditions, also suggests growth in association with reducing environments at or near the seafloor or in conjunction with a geochemical interface. Predominance of coniform stromatolite forms in the Proterozoic--across a variety of depositional environments--may thus reflect a combination of heterogeneous nutrient distribution, potentially driven by variable redox conditions, and an elevated carbonate saturation state, which permits preservation of these unusual microbialite forms.

Sudden motility reversal indicates sensing of magnetic field gradients in Magnetospirillum magneticum AMB-1 strain

Many motile unicellular organisms have evolved specialized behaviors for detecting and responding to environmental cues such as chemical gradients (chemotaxis) and oxygen gradients (aerotaxis). Magnetotaxis is found in magnetotactic bacteria and it is defined as the passive alignment of these cells to the geomagnetic field along with active swimming. Herein we show that Magnetospirillum magneticum (AMB-1) show a unique set of responses that indicates they sense and respond not only to the direction of magnetic fields by aligning and swimming, but also to changes in the magnetic field or magnetic field gradients. We present data showing that AMB-1 cells exhibit sudden motility reversals when we impose them to local magnetic field gradients. Our system employs permalloy (Ni(80)Fe(20)) islands to curve and diverge the magnetic field lines emanating from our custom-designed Helmholtz coils in the vicinity of the islands (creating a drop in the field across the islands). The three distinct movements we have observed as they approach the permalloy islands are: unidirectional, single reverse and double reverse. Our findings indicate that these reverse movements occur in response to magnetic field gradients. In addition, using a permanent magnet we found further evidence that supports this claim. Motile AMB-1 cells swim away from the north and south poles of a permanent magnet when the magnet is positioned less than ∼30 mm from the droplet of cells. All together, these results indicate previously unknown response capabilities arising from the magnetic sensing systems of AMB-1 cells. These responses could enable them to cope with magnetic disturbances that could in turn potentially inhibit their efficient search for nutrients.

Cooperative target tracking by a mobile bionanosensor network

This paper describes a mobile bionanosensor network designed for target tracking. The mobile bionanosensor network is composed of bacterium-based autonomous biosensors that coordinate their movement through the use of two types of signaling molecules, repellents and attractants. In search of a target, the bacterium-based autonomous biosensors release repellents to quickly spread over the environment, while, upon detecting a target, they release attractants to recruit other biosensors in the environment toward the location around the target. A mobility model of bacterium-based autonomous biosensors is first developed based on the rotational diffusion model of bacterial chemotaxis, and from this their collective movement to track a moving target is demonstrated. In simulation experiments, the mobile bionanosensor network is evaluated based on the mean tracking time. Simulation results show a set of parameter values that can optimize the mean tracking time, providing an insight into how bacterium-based autonomous biosensors may be designed and engineered for target tracking.

Virio- and bacterioplankton microscale distributions at the sediment-water interface

The marine sediment-water interface is an important location for microbially controlled nutrient and gas exchange processes. While microbial distributions on the sediment side of the interface are well established in many locations, the distributions of microbes on the water side of the interface are less well known. Here, we measured that distribution for marine virio- and bacterioplankton with a new two-dimensional technique. Our results revealed higher heterogeneity in sediment-water interface biomass distributions than previously reported with a greater than 45- and 2500-fold change cm(-1) found within bacterial and viral subpopulations compared to previous maxima of 1.5- and 1.4-fold cm(-1) in bacteria and viruses in the same environments. The 45-fold and 2500-fold changes were due to patches of elevated and patches of reduced viral and bacterial abundance. The bacterial and viral hotspots were found over single and multiple sample points and the two groups often coincided whilst the coldspots only occurred over single sample points and the bacterial and viral abundances showed no correlation. The total mean abundances of viruses strongly correlated with bacteria (r = 0.90, p<0.0001, n = 12) for all three microplates (n = 1350). Spatial autocorrelation analysis via Moran's I and Geary's C revealed non-random distributions in bacterial subpopulations and random distributions in viral subpopulations. The variable distributions of viral and bacterial abundance over centimetre-scale distances suggest that competition and the likelihood of viral infection are higher in the small volumes important for individual cell encounters than bulk measurements indicate. We conclude that large scale measurements are not an accurate measurement of the conditions under which microbial dynamics exist. The high variability we report indicates that few microbes experience the 'average' concentrations that are frequently measured.

Hydrodynamics and collective behavior of the tethered bacterium Thiovulum majus

The ecology and dynamics of many microbial systems, particularly in mats and soils, are shaped by how bacteria respond to evolving nutrient gradients and microenvironments. Here we show how the response of the sulfur-oxidizing bacterium Thiovulum majus to changing oxygen gradients causes cells to organize into large-scale fronts. To study this phenomenon, we develop a technique to isolate and enrich these bacteria from the environment. Using this enrichment culture, we observe the formation and dynamics of T. majus fronts in oxygen gradients. We show that these dynamics can be understood as occurring in two steps. First, chemotactic cells moving up the oxygen gradient form a front that propagates with constant velocity. We then show, through observation and mathematical analysis, that this front becomes unstable to changes in cell density. Random perturbations in cell density create oxygen gradients. The response of cells magnifies these gradients and leads to the formation of millimeter-scale fluid flows that actively pull oxygenated water through the front. We argue that this flow results from a nonlinear instability excited by stochastic fluctuations in the density of cells. Finally, we show that the dynamics by which these modes interact can be understood from the chemotactic response of cells. These results provide a mathematically tractable example of how collective phenomena in ecological systems can arise from the individual response of cells to a shared resource.

Ecology and physics of bacterial chemotaxis in the ocean

Intuitively, it may seem that from the perspective of an individual bacterium the ocean is a vast, dilute, and largely homogeneous environment. Microbial oceanographers have typically considered the ocean from this point of view. In reality, marine bacteria inhabit a chemical seascape that is highly heterogeneous down to the microscale, owing to ubiquitous nutrient patches, plumes, and gradients. Exudation and excretion of dissolved matter by larger organisms, lysis events, particles, animal surfaces, and fluxes from the sediment-water interface all contribute to create strong and pervasive heterogeneity, where chemotaxis may provide a significant fitness advantage to bacteria. The dynamic nature of the ocean imposes strong selective pressures on bacterial foraging strategies, and many marine bacteria indeed display adaptations that characterize their chemotactic motility as "high performance" compared to that of enteric model organisms. Fast swimming speeds, strongly directional responses, and effective turning and steering strategies ensure that marine bacteria can successfully use chemotaxis to very rapidly respond to chemical gradients in the ocean. These fast responses are advantageous in a broad range of ecological processes, including attaching to particles, exploiting particle plumes, retaining position close to phytoplankton cells, colonizing host animals, and hovering at a preferred height above the sediment-water interface. At larger scales, these responses can impact ocean biogeochemistry by increasing the rates of chemical transformation, influencing the flux of sinking material, and potentially altering the balance of biomass incorporation versus respiration. This review highlights the physical and ecological processes underpinning bacterial motility and chemotaxis in the ocean, describes the current state of knowledge of chemotaxis in marine bacteria, and summarizes our understanding of how these microscale dynamics scale up to affect ecosystem-scale processes in the sea.

The biophysical model for accuracy of cellular sensing spatial gradients of multiple chemoattractants

Spatial gradients of surrounding chemoattractants are the key factors in determining the directionality of eukaryotic cell movement. Thus, it is important for cells to accurately measure the spatial gradients of surrounding chemoattractants. Here, we study the precision of sensing the spatial gradients of multiple chemoattractants using cooperative receptor clusters. Cooperative receptors on cells are modeled as an Ising chain of Monod-Wyman-Changeux clusters subject to multiple chemical-gradient fields to study the physical limits of multiple chemoattractants spatial gradients sensing. We found that eukaryotic cells cannot sense each chemoattractant gradient individually. Instead, cells can only sense a weighted sum of surrounding chemical gradients. Moreover, the precision of sensing one chemical gradient is signicantly affected by coexisting chemoattractant concentrations. These findings can provide a further insight into the role of chemoattractants in immune response and help develop novel treatments for inflammatory diseases.

Intracellular chemical gradients: morphing principle in bacteria

Advances in computational biology allow systematic investigations to ascertain whether internal chemical gradients can be maintained in bacteria – an open question at the resolution limit of fluorescence microscopy. While it was previously believed that the small bacterial cell size and fast diffusion in the cytoplasm effectively remove any such gradient, a new computational study published in BMC Biophysics supports the emerging view that gradients can exist. The study arose from the recent observation that phosphorylated CtrA forms a gradient prior to cell division in Caulobacter crescentus, a bacterium known for its complicated cell cycle. Tropini et al. (2012) postulate that such gradients can provide an internal chemical compass, directing protein localization, cell division and cell development. More specifically, they describe biochemical and physical constraints on the formation of such gradients and explore a number of existing bacterial cell morphologies. These chemical gradients may limit in vitro analyses, and may ensure timing control and robustness to fluctuations during critical stages in cell development.

Computational and experimental study of chemotaxis of an ensemble of bacteria attached to a microbead

Micro-objects propelled by whole cell actuators, such as flagellated bacteria, are being increasingly studied and considered for a wide variety of applications. In this work we present theoretical and experimental investigations of chemotactic motility of a 10 μm diameter microbead propelled by an ensemble of attached flagellated bacteria. The stochastic model presented here encompasses the behavior of each individual bacterium attached to the microbead in a spatiotemporally varying chemoattractant field. The computational model shows that in a chemotactic environment, the ensemble of bacteria, although constrained, propel the bead in a chemotactic manner with a 67% enhancement in displacement to distance ratio (defined as directionality) compared to nonchemotactic propulsion. The simulation results are validated experimentally. Close agreement between theory and experiments demonstrates the possibility of using the presented model as a predictive tool for other similar biohybrid systems.

Modeling a self-propelled autochemotactic walker

We develop a minimal model for the stochastic dynamics of microorganisms where individuals communicate via autochemotaxis. This means that microorganisms, such as bacteria, amoebae, or cells, follow the gradient of a chemical that they produce themselves to attract or repel each other. A microorganism is represented as a self-propelled particle or walker with constant speed while its velocity direction diffuses on the unit circle. We study the autochemotactic response of a single self-propelled walker whose dynamics is non-Markovian. We show that its long-time dynamics is always diffusive by deriving analytic expressions for its diffusion coefficient in the weak- and strong-coupling case. We confirm our findings by numerical simulations.

Chemotactic predator-prey dynamics

A discrete chemotactic predator-prey model is proposed in which the prey secrets a diffusing chemical which is sensed by the predator and vice versa. Two dynamical states corresponding to catching and escaping are identified and it is shown that steady hunting is unstable. For the escape process, the predator-prey distance is diffusive for short times but exhibits a transient subdiffusive behavior which scales as a power law t¹/³ with time t and ultimately crosses over to diffusion again. This allows us to classify the motility and dynamics of various predatory microbes and phagocytes. In particular, there is a distinct region in the parameter space where they prove to be infallible predators.

A tactile response in Staphylococcus aureus

It is well established that bacteria are able to respond to temporal gradients (e.g., by chemotaxis). However, it is widely held that prokaryotes are too small to sense spatial gradients. This contradicts the common observation that the vast majority of bacteria live on the surface of a solid substrate (e.g., as a biofilm). Herein we report direct experimental evidence that the nonmotile bacterium Staphylococcus aureus possesses a tactile response, or primitive sense of touch, that allows it to respond to spatial gradients. Attached cells recognize their substrate interface and localize adhesins toward that region. Braille-like avidity maps reflect a cell's biochemical sensory response and reveal ultrastructural regions defined by the actual binding activity of specific proteins.

Lithotrophic iron-oxidizing bacteria produce organic stalks to control mineral growth: implications for biosignature formation

Neutrophilic Fe-oxidizing bacteria (FeOB) are often identified by their distinctive morphologies, such as the extracellular twisted ribbon-like stalks formed by Gallionella ferruginea or Mariprofundus ferrooxydans. Similar filaments preserved in silica are often identified as FeOB fossils in rocks. Although it is assumed that twisted iron stalks are indicative of FeOB, the stalk's metabolic role has not been established. To this end, we studied the marine FeOB M. ferrooxydans by light, X-ray and electron microscopy. Using time-lapse light microscopy, we observed cells excreting stalks during growth (averaging 2.2  μm  h(-1)). Scanning transmission X-ray microscopy and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy show that stalks are Fe(III)-rich, whereas cells are low in Fe. Transmission electron microscopy reveals that stalks are composed of several fibrils, which contain few-nanometer-sized iron oxyhydroxide crystals. Lepidocrocite crystals that nucleated on the fibril surface are much larger (∼100  nm), suggesting that mineral growth within fibrils is retarded, relative to sites surrounding fibrils. C and N 1s NEXAFS spectroscopy and fluorescence probing show that stalks primarily contain carboxyl-rich polysaccharides. On the basis of these results, we suggest a physiological model for Fe oxidation in which cells excrete oxidized Fe bound to organic polymers. These organic molecules retard mineral growth, preventing cell encrustation. This model describes an essential role for stalk formation in FeOB growth. We suggest that stalk-like morphologies observed in modern and ancient samples may be correlated confidently with the Fe-oxidizing metabolism as a robust biosignature.

Physical limits on cellular sensing of spatial gradients

Many eukaryotic cells are able to detect chemical gradients by directly measuring spatial concentration differences. The precision of such gradient sensing is limited by fluctuations in the binding of diffusing particles to specific receptors on the cell surface. Here, we explore the physical limits of the spatial sensing mechanism by modeling the chemotactic cell as an Ising spin chain subject to a spatially varying field. Our results demonstrate that the accuracy to sense the gradient direction not only increases dramatically with the cell size but also can be improved significantly by introducing receptor cooperativity. Thus, receptor coupling may open the possibility for small bacteria to perform spatial measurements of gradients, as supported by a recent experimental finding.

Reduced efficiency of magnetotaxis in magnetotactic coccoid bacteria in higher than geomagnetic fields

Magnetotactic bacteria are microorganisms that orient and migrate along magnetic field lines. The classical model of polar magnetotaxis predicts that the field-parallel migration velocity of magnetotactic bacteria increases monotonically with the strength of an applied magnetic field. We here test this model experimentally on magnetotactic coccoid bacteria that swim along helical trajectories. It turns out that the contribution of the field-parallel migration velocity decreases with increasing field strength from 0.1 to 1.5 mT. This unexpected observation can be explained and reproduced in a mathematical model under the assumption that the magnetosome chain is inclined with respect to the flagellar propulsion axis. The magnetic disadvantage, however, becomes apparent only in stronger than geomagnetic fields, which suggests that magnetotaxis is optimized under geomagnetic field conditions. It is therefore not beneficial for these bacteria to increase their intracellular magnetic dipole moment beyond the value needed to overcome Brownian motion in geomagnetic field conditions.

"Candidatus Ovobacter propellens": a large conspicuous prokaryote with an unusual motility behaviour

A new type of bacterium "Candidatus Ovobacter propellens" is described. It is a large ovoid species with a number of unusual features including special intracellular membrane systems and a huge flagellar tuft consisting of about 400 flagella. "Ovobacter" lives in oxygen gradients in the surface layer of sulphidic marine sediments at an O(2)-tension of about 0.5% atmospheric saturation. It swims continuously and very fast (up to 1 mm s(-1)). Its mode of swimming and its chemosensory behaviour towards O(2) are described in detail.

Accuracy of direct gradient sensing by cell-surface receptors

Chemotactic cells of eukaryotic organisms are able to accurately sense shallow chemical concentration gradients using cell-surface receptors. This sensing ability is remarkable as cells must be able to spatially resolve small fractional differences in the numbers of particles randomly arriving at cell-surface receptors by diffusion. An additional challenge and source of uncertainty is that particles, once bound and released, may rebind the same or a different receptor, which adds to noise without providing any new information about the environment. We recently derived the fundamental physical limits of gradient sensing using a simple spherical-cell model, but not including explicit particle-receptor kinetics. Here, we use a method based on the fluctuation-dissipation theorem (FDT) to calculate the accuracy of gradient sensing by realistic receptors. We derive analytical results for two receptors, as well as two coaxial rings of receptors, e.g. one at each cell pole. For realistic receptors, we find that particle rebinding lowers the accuracy of gradient sensing, in line with our previous results.

Bacterial tracking of motile algae assisted by algal cell's vorticity field

Previously published experimental work by other authors has shown that certain motile marine bacteria are able to track free-swimming algae by executing a zigzag path and steering toward the algae at each turn. Here, we propose that the apparent steering behaviour could be a hydrodynamic effect, whereby an algal cell's vorticity and strain-rate fields rotate a pursuing bacterial cell in the appropriate direction. Using simplified models for the bacterial and algal cells, we numerically compute the trajectory of a bacterial cell and demonstrate the plausibility of this hypothesis.

Diversity in bacterial chemotactic responses and niche adaptation

The ability of microbes to rapidly sense and adapt to environmental changes plays a major role in structuring microbial communities, in affecting microbial activities, as well as in influencing various microbial interactions with the surroundings. The bacterial chemotaxis signal transduction system is the sensory perception system that allows motile cells to respond optimally to changes in environmental conditions by allowing cells to navigate in gradients of diverse physicochemical parameters that can affect their metabolism. The analysis of complete genome sequences from microorganisms that occupy diverse ecological niches reveal the presence of multiple chemotaxis pathways and a great diversity of chemoreceptors with novel sensory specificities. Owing to its role in mediating rapid responses of bacteria to changes in the surroundings, bacterial chemotaxis is a behavior of interest in applied microbiology as it offers a unique opportunity for understanding the environmental cues that contribute to the survival of bacteria. This chapter explores the diversity of bacterial chemotaxis and suggests how gaining further insights into such diversity may potentially impact future drug and pesticides development and could inform bioremediation strategies.

Run and tumble chemotaxis in a shear flow: the effect of temporal comparisons, persistence, rotational diffusion, and cell shape

Escherichia coli is a motile bacterium that moves up a chemoattractant gradient by performing a biased random walk composed of alternating runs and tumbles. This paper presents calculations of the chemotactic drift velocity v (d) (the mean velocity up the chemoattractant gradient) of an E. coli cell performing chemotaxis in a uniform, steady shear flow, with a weak chemoattractant gradient at right angles to the flow. Extending earlier models, a combined analytic and numerical approach is used to assess the effect of several complications, namely (i) a cell cannot detect a chemoattractant gradient directly but rather makes temporal comparisons of chemoattractant concentration, (ii) the tumbles exhibit persistence of direction, meaning that the swimming directions before and after a tumble are correlated, (iii) the cell suffers random re-orientations due to rotational Brownian motion, and (iv) the non-spherical shape of the cell affects the way that it is rotated by the shear flow. These complications influence the dependence of v(d) on the shear rate gamma. When they are all included, it is found that (a) shear disrupts chemotaxis and shear rates beyond gamma approximately 2 s(-1) render chemotaxis ineffective, (b) in terms of maximizing drift velocity, persistence of direction is advantageous in a quiescent fluid but disadvantageous in a shear flow, and (c) a more elongated body shape is advantageous in performing chemotaxis in a shear flow.