Bacterial chemotaxis, the directed movement of cells along "chemoattractant" gradients, is among the best-characterized subjects of molecular biology 1-10. Much less is known about its physiological roles 11. Commonly, it is seen as starvation response when nutrients run out, or as escape response from harmful situations 12-16. Here, we establish an alternative role of chemotaxis by systematically examining the spatiotemporal dynamics of Escherichia coli in soft agar 12,17,18 : Chemotaxis in nutrient-replete conditions promotes the expansion of bacterial populations into unoccupied territories well before nutrients run out in the current environment. We show how low levels of chemoattractants act as aroma-like cues in this process, establishing the direction and enhancing the speed of population movement along the self-generated attractant gradients. This navigated range expansion process spreads faster and yields larger population gains than unguided expansion following the canonical Fisher-Kolmogorov dynamics 19,20 and is therefore a general strategy to promote population growth in spatially extended, nutrient-replete environments.

The quality of sensing and response to external stimuli constitutes a basic element in the selective performance of living organisms. Here we consider the response of Escherichia coli to chemical stimuli. For moderate amplitudes, the bacterial response to generic profiles of sensed chemicals is reconstructed from its response function to an impulse, which then controls the efficiency of bacterial motility. We introduce a method for measuring the impulse response function based on coupling microfluidic experiments and inference methods: The response function is inferred using Bayesian methods from the observed trajectories of bacteria swimming in microfluidically controlled chemical fields. The notable advantages are that the method is based on the bacterial swimming response, it is noninvasive, without any genetic and/or mechanical preparation, and assays the behavior of the whole flagella bundle. We exploit the inference method to measure responses to aspartate and α-methylaspartate-measured previously by other methods-as well as glucose, leucine, and serine. The response to the attractant glucose is shown to be biphasic and perfectly adapted, as for aspartate. The response to the attractant serine is shown to be biphasic yet imperfectly adapted, that is, the response function has a nonzero (positive) integral. The adaptation of the response to the repellent leucine is also imperfect, with the sign of the two phases inverted with respect to serine. The diversity in the bacterial population of the response function and its dependency upon the background concentration are quantified.bacterial chemotaxis | signal transduction | statistical inference B acterial chemotaxis constitutes a paradigmatic example of a molecular signaling pathway, transducing information from the external environment to the interior of the cell. The model organism Escherichia coli senses the environmental concentration of chemicals to regulate the rotation of flagellar motors and orient its motion (1). Counterclockwise (CCW) rotation of the flagella corresponds to runs in the trajectories, whereas bacteria tumble when the flagellar bundle is destabilized by one or several flagella rotating clockwise (CW). The second messenger in the chemotaxis pathway is the protein CheY: Its phosphorylated form, CheYp, binds the flagellar motors and increases the switching rate CCW→CW. Information on the chemical concentration sensed by the receptors is relayed via the kinase CheA, whose activity is reduced by receptors' binding. Other components of the pathway include the scaffold protein CheW, the phosphatase CheZ, the methyltransferase CheR, and the methylesterase CheB, responsible for the feedback on the receptors and adaptation (see ref. 2 for a recent review). Additional features of the pathway are the clustering of receptors at the membrane (3), well-described by allosteric models (4-7), and the mutual interaction among receptors known as "assistance neighborhood" (8,9).An approach in the spirit of physiology, aimed at capturing the net effect of t...

Soaring birds often rely on ascending thermal plumes (thermals) in the atmosphere as they search for prey or migrate across large distances. The landscape of convective currents is rugged and shifts on timescales of a few minutes as thermals constantly form, disintegrate or are transported away by the wind. How soaring birds find and navigate thermals within this complex landscape is unknown. Reinforcement learning provides an appropriate framework in which to identify an effective navigational strategy as a sequence of decisions made in response to environmental cues. Here we use reinforcement learning to train a glider in the field to navigate atmospheric thermals autonomously. We equipped a glider of two-metre wingspan with a flight controller that precisely controlled the bank angle and pitch, modulating these at intervals with the aim of gaining as much lift as possible. A navigational strategy was determined solely from the glider's pooled experiences, collected over several days in the field. The strategy relies on on-board methods to accurately estimate the local vertical wind accelerations and the roll-wise torques on the glider, which serve as navigational cues. We establish the validity of our learned flight policy through field experiments, numerical simulations and estimates of the noise in measurements caused by atmospheric turbulence. Our results highlight the role of vertical wind accelerations and roll-wise torques as effective mechanosensory cues for soaring birds and provide a navigational strategy that is directly applicable to the development of autonomous soaring vehicles.

The ability to block gene expression in bacteria with the catalytically inactive mutant of Cas9, known as dCas9, is quickly becoming a standard methodology to probe gene function, perform high-throughput screens, and engineer cells for desired purposes. Yet, we still lack a good understanding of the design rules that determine on-target activity for dCas9. Taking advantage of high-throughput screening data, we fit a model to predict the ability of dCas9 to block the RNA polymerase based on the target sequence, and validate its performance on independently generated datasets. We further design a novel genome wide guide RNA library for E. coli MG1655, EcoWG1, using our model to choose guides with high activity while avoiding guides which might be toxic or have off-target effects. A screen performed using the EcoWG1 library during growth in rich medium improved upon previously published screens, demonstrating that very good performances can be attained using only a small number of well designed guides. Being able to design effective, smaller libraries will help make CRISPRi screens even easier to perform and more cost-effective. Our model and materials are available to the community through crispr.pasteur.fr and Addgene.

Plasmids are extra chromosomal DNA that can confer to their hosts' supplementary characteristics such as antibiotic resistance. Plasmids code for their copy number through their own replication frequency. Even though the biochemical networks underlying the plasmid copy number (PCN) regulation processes have been studied and modeled, no measurement of the heterogeneity in PCN within a whole population has been done. We have developed a fluorescent-based measurement system, which enables determination of the mean and noise in PCN within a monoclonal population of bacteria. Two different fluorescent protein reporters were inserted: one on the chromosome and the other on the plasmid. The fluorescence of these bacteria was measured with a microfluidic flow cytometry device. We show that our measurements are consistent with known plasmid characteristics. We find that the partitioning system lowers the PCN mean and standard deviation. Finally, bacterial populations were allowed to grow without selective pressure. In this case, we were able to determine the plasmid loss rate and growth inhibition effect.

Evolution of biological sensory systems is driven by the need for efficient responses to environmental stimuli. A paradigm among prokaryotes is the chemotaxis system, which allows bacteria to navigate gradients of chemoattractants by biasing their run-and-tumble motion. A notable feature of chemotaxis is adaptation: after the application of a step stimulus, the bacterial running time relaxes to its pre-stimulus level. The response to the amino acid aspartate is precisely adapted whilst the response to serine is not, in spite of the same pathway processing the signals preferentially sensed by the two receptors Tar and Tsr, respectively. While the chemotaxis pathway in E. coli is well characterized, the role of adaptation, its functional significance and the ecological conditions where chemotaxis is selected, are largely unknown. Here, we investigate the role of adaptation in the climbing of gradients by E. coli. We first present theoretical arguments that highlight the mechanisms that control the efficiency of the chemotactic up-gradient motion. We discuss then the limitations of linear response theory, which motivate our subsequent experimental investigation of E. coli speed races in gradients of aspartate, serine and combinations thereof. By using microfluidic techniques, we engineer controlled gradients and demonstrate that bacterial fronts progress faster in equal-magnitude gradients of serine than aspartate. The effect is observed over an extended range of concentrations and is not due to differences in swimming velocities. We then show that adding a constant background of serine to gradients of aspartate breaks the adaptation to aspartate, which results in a sped-up progression of the fronts and directly illustrate the role of adaptation in chemotactic gradient-climbing.

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Chemotaxis may have an important role in the infection process of pathogenic Leptospira spp.; however, little is known about the regulation of flagellar-based motility in these atypical bacteria. We generated a library of random transposon mutants of the pathogen L. interrogans, which included a mutant with insertion in the first gene of an operon containing the chemotaxis genes cheA, cheW, cheD, cheB, cheY and mcp. The disrupted gene encodes a putative histidine kinase (HK). The HK mutant was motile and virulent, but swarm plate and capillary assays suggested that chemotaxis was reduced in this mutant. Further analysis of bacterial trajectories by videomicroscopy showed that the ability of this mutant to reverse was significantly impaired in comparison to wild-type strain. Our data therefore show that this operon is required for full chemotaxis of Leptospira spp.