Non-genetic adaptation by collective migration.

Collective behaviors require coordination of individuals. Thus, a population must adjust its phenotypic distribution to adapt to changing environments. How can a population regulate its phenotypic distribution? One strategy is to utilize specialized networks for gene regulation and maintaining distinct phenotypic subsets. Another involves genetic mutations, which can be augmented by stress-response pathways. Here, we studied how a migrating bacterial population regulates its phenotypic distribution to traverse across diverse environments. We generated isogenic Escherichia coli populations with varying distributions of swimming behaviors and observed their phenotype distributions during migration in liquid and porous environments. Surprisingly, we found that during collective migration, the distributions of swimming phenotypes adapt to the environment without mutations or gene regulation. Instead, adaptation is caused by the dynamic and reversible enrichment of high-performing swimming phenotypes within each environment. This adaptation mechanism is supported by a recent theoretical study, which proposed that the phenotypic composition of a migrating population results from a balance between cell growth generating diversity and collective migration eliminating the phenotypes that are unable to keep up with the migrating group. Furthermore, by examining chemoreceptor abundance distributions during migration towards different attractants, we found that this mechanism acts on multiple chemotaxis-related traits simultaneously. Our findings reveal that collective migration itself can enable cell populations with continuous, multi-dimensional phenotypes to flexibly and rapidly adapt their phenotypic composition to diverse environmental conditions. Significance statement: Conventional cell adaptation mechanisms, like gene regulation and random phenotypic switching, act swiftly but are limited to a few traits, while mutation-driven adaptations unfold slowly. By quantifying phenotypic diversity during bacterial collective migration, we discovered an adaptation mechanism that rapidly and reversibly adjusts multiple traits simultaneously. By dynamically balancing the elimination of phenotypes unable to keep pace with generation of diversity through growth, this process enables populations to tune their phenotypic composition based on the environment, without the need for gene regulation or mutations. Given the prevalence of collective migration in microbes, cancers, and embryonic development, non-genetic adaptation through collective migration may be a universal mechanism for populations to navigate diverse environments, offering insights into broader applications across various fields.

Exploring the dynamics of vascular adaptation.

A combination of in toto imaging and theory suggests a new mechanism for the remodeling of veins in vascular networks.

Optimal inference of molecular interaction dynamics in FRET microscopy.

Intensity-based time-lapse fluorescence resonance energy transfer (FRET) microscopy has been a major tool for investigating cellular processes, converting otherwise unobservable molecular interactions into fluorescence time series. However, inferring the molecular interaction dynamics from the observables remains a challenging inverse problem, particularly when measurement noise and photobleaching are nonnegligible-a common situation in single-cell analysis. The conventional approach is to process the time-series data algebraically, but such methods inevitably accumulate the measurement noise and reduce the signal-to-noise ratio (SNR), limiting the scope of FRET microscopy. Here, we introduce an alternative probabilistic approach, B-FRET, generally applicable to standard 3-cube FRET-imaging data. Based on Bayesian filtering theory, B-FRET implements a statistically optimal way to infer molecular interactions and thus drastically improves the SNR. We validate B-FRET using simulated data and then apply it to real data, including the notoriously noisy in vivo FRET time series from individual bacterial cells to reveal signaling dynamics otherwise hidden in the noise.

Sensory diversity and precise adaptation enable independent bet-hedging strategies for multiple signals at the same time.

While navigating their environments, cells encounter many different signals at once. In the face of uncertain conditions, diversifying the sensitivity to different signals across the population can be useful. Previous studies established that one of the simplest sensory systems, the chemotaxis network of Escherichia coli , can switch between a high diversity bet-hedging strategy, and a low diversity tracking strategy for a ligand as that ligand becomes prevalent. Here, we combine mathematical modeling and single-cell experiments to show that populations of chemotactic bacteria make this transition for each ligand independently. That is, transitioning to tracking one ligand does not compromise the population’s ability to hedge its bets across other future ligands. Remarkably, we found that this independence holds even if those ligands compete for receptor binding sites with the background ligand being tracked. The independence of this transition between two diversity regimes is explained by a simple allosteric model of chemoreceptor clusters with negative integral feedback, which accurately predicts the observed diversity in sensitivity under various background stimulus conditions. Our mathematical analysis shows that similar transitions from bet-hedging to tracking also arise in feed-forward network architectures capable of precise adaptation, suggesting that environment-dependent modulation of diversity may occur in many cell types.

Decreasing relatedness among mycorrhizal fungi in a shared plant network increases fungal network size but not plant benefit.

Theory suggests that relatives will cooperate more, and compete less, because of an increased benefit for shared genes. In symbiotic partnerships, hosts may benefit from interacting with highly related symbionts because there is less conflict among the symbionts. This has been difficult to test empirically. We used the arbuscular mycorrhizal symbiosis to study the effects of fungal relatedness on host and fungal benefits, creating fungal networks varying in relatedness between two hosts, both in soil and in-vitro. To determine how fungal relatedness affected overall transfer of nutrients, we fluorescently tagged phosphorus and quantified resource distribution between two root systems. We found that colonization by less-related fungi was associated with increased fungal growth, lower transport of nutrients across the network, and lower plant benefit - likely an outcome of increased fungal competition. More generally, we demonstrate how symbiont relatedness can mediate benefits of symbioses.

HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein.

The interplay between three-dimensional chromosome organisation and genomic processes such as replication and transcription necessitates in vivo studies of chromosome dynamics. Fluorescent organic dyes are often used for chromosome labelling in vivo. The mode of binding of these dyes to DNA cause its distortion, elongation, and partial unwinding. The structural changes induce DNA damage and interfere with the binding dynamics of chromatin-associated proteins, consequently perturbing gene expression, genome replication, and cell cycle progression. We have developed a minimally-perturbing, genetically encoded fluorescent DNA label consisting of a (photo-switchable) fluorescent protein fused to the DNA-binding domain of H-NS - a bacterial nucleoid-associated protein. We show that this DNA label, abbreviated as HI-NESS (H-NS-based indicator for nucleic acid stainings), is minimally-perturbing to genomic processes and labels chromosomes in eukaryotic cells in culture, and in zebrafish embryos with preferential binding to AT-rich chromatin.

Temporal tracking of quantum-dot apatite across in vitro mycorrhizal networks shows how host demand can influence fungal nutrient transfer strategies.

Arbuscular mycorrhizal fungi function as conduits for underground nutrient transport. While the fungal partner is dependent on the plant host for its carbon (C) needs, the amount of nutrients that the fungus allocates to hosts can vary with context. Because fungal allocation patterns to hosts can change over time, they have historically been difficult to quantify accurately. We developed a technique to tag rock phosphorus (P) apatite with fluorescent quantum-dot (QD) nanoparticles of three different colors, allowing us to study nutrient transfer in an in vitro fungal network formed between two host roots of different ages and different P demands over a 3-week period. Using confocal microscopy and raster image correlation spectroscopy, we could distinguish between P transfer from the hyphae to the roots and P retention in the hyphae. By tracking QD-apatite from its point of origin, we found that the P demands of the younger root influenced both: (1) how the fungus distributed nutrients among different root hosts and (2) the storage patterns in the fungus itself. Our work highlights that fungal trade strategies are highly dynamic over time to local conditions, and stresses the need for precise measurements of symbiotic nutrient transfer across both space and time.

Bacterial coexistence driven by motility and spatial competition.

Elucidating elementary mechanisms that underlie bacterial diversity is central to ecology1,2 and microbiome research3. Bacteria are known to coexist by metabolic specialization4, cooperation5 and cyclic warfare6-8. Many species are also motile9, which is studied in terms of mechanism10,11, benefit12,13, strategy14,15, evolution16,17 and ecology18,19. Indeed, bacteria often compete for nutrient patches that become available periodically or by random disturbances2,20,21. However, the role of bacterial motility in coexistence remains unexplored experimentally. Here we show that-for mixed bacterial populations that colonize nutrient patches-either population outcompetes the other when low in relative abundance. This inversion of the competitive hierarchy is caused by active segregation and spatial exclusion within the patch: a small fast-moving population can outcompete a large fast-growing population by impeding its migration into the patch, while a small fast-growing population can outcompete a large fast-moving population by expelling it from the initial contact area. The resulting spatial segregation is lost for weak growth-migration trade-offs and a lack of virgin space, but is robust to population ratio, density and chemotactic ability, and is observed in both laboratory and wild strains. These findings show that motility differences and their trade-offs with growth are sufficient to promote diversity, and suggest previously undescribed roles for motility in niche formation and collective expulsion-containment strategies beyond individual search and survival.

Modelling the ballistic-to-diffusive transition in nematode motility reveals variation in exploratory behaviour across species.

A quantitative understanding of organism-level behaviour requires predictive models that can capture the richness of behavioural phenotypes, yet are simple enough to connect with underlying mechanistic processes. Here, we investigate the motile behaviour of nematodes at the level of their translational motion on surfaces driven by undulatory propulsion. We broadly sample the nematode behavioural repertoire by measuring motile trajectories of the canonical laboratory strain Caenorhabditis elegans N2 as well as wild strains and distant species. We focus on trajectory dynamics over time scales spanning the transition from ballistic (straight) to diffusive (random) movement and find that salient features of the motility statistics are captured by a random walk model with independent dynamics in the speed, bearing and reversal events. We show that the model parameters vary among species in a correlated, low-dimensional manner suggestive of a common mode of behavioural control and a trade-off between exploration and exploitation. The distribution of phenotypes along this primary mode of variation reveals that not only the mean but also the variance varies considerably across strains, suggesting that these nematode lineages employ contrasting 'bet-hedging' strategies for foraging.

Mycorrhizal Fungi Respond to Resource Inequality by Moving Phosphorus from Rich to Poor Patches across Networks.

The world's ecosystems are characterized by an unequal distribution of resources [1]. Trade partnerships between organisms of different species-mutualisms-can help individuals cope with such resource inequality [2-4]. Trade allows individuals to exchange commodities they can provide at low cost for resources that are otherwise impossible or more difficult to access [5, 6]. However, as resources become increasingly patchy in time or space, it is unknown how organisms alter their trading strategies [7, 8]. Here, we show how a symbiotic fungus mediates trade with a host root in response to different levels of resource inequality across its network. We developed a quantum-dot-tracking technique to quantify phosphorus-trading strategies of arbuscular mycorrhizal fungi simultaneously exposed to rich and poor resource patches. By following fluorescent nanoparticles of different colors across fungal networks, we determined where phosphorus was hoarded, relocated, and transferred to plant hosts. We found that increasing exposure to inequality stimulated trade. Fungi responded to high resource variation by (1) increasing the total amount of phosphorus distributed to host roots, (2) decreasing allocation to storage, and (3) differentially moving resources within the network from rich to poor patches. Using single-particle tracking and high-resolution video, we show how dynamic resource movement may help the fungus capitalize on value differences across the trade network, physically moving resources to areas of high demand to gain better returns. Such translocation strategies can help symbiotic organisms cope with exposure to resource inequality.

Cell Boundary Confinement Sets the Size and Position of the E. coli Chromosome.

Although the spatiotemporal structure of the genome is crucial to its biological function, many basic questions remain unanswered on the morphology and segregation of chromosomes. Here, we experimentally show in Escherichia coli that spatial confinement plays a dominant role in determining both the chromosome size and position. In non-dividing cells with lengths increased to 10 times normal, single chromosomes are observed to expand > 4-fold in size. Chromosomes show pronounced internal dynamics but exhibit a robust positioning where single nucleoids reside robustly at mid-cell, whereas two nucleoids self-organize at 1/4 and 3/4 positions. The cell-size-dependent expansion of the nucleoid is only modestly influenced by deletions of nucleoid-associated proteins, whereas osmotic manipulation experiments reveal a prominent role of molecular crowding. Molecular dynamics simulations with model chromosomes and crowders recapitulate the observed phenomena and highlight the role of entropic effects caused by confinement and molecular crowding in the spatial organization of the chromosome.

Long-term positioning and polar preference of chemoreceptor clusters in E. coli.

The bacterial chemosensory arrays are a notable model for studying the basic principles of receptor clustering and cellular organization. Here, we provide a new perspective regarding the long-term dynamics of these clusters in growing E. coli cells. We demonstrate that pre-existing lateral clusters tend to avoid translocation to pole regions and, therefore, continually shuttle between the cell poles for many generations while being static relative to the local cell-wall matrix. We also show that the polar preference of clusters results fundamentally from reduced clustering efficiency in the lateral region, rather than a developmental-like progression of clusters. Furthermore, polar preference is surprisingly robust to structural alterations designed to probe preference due to curvature sorting, perturbing the cell envelope physiology affects the cluster-size distribution, and the size-dependent mobility of receptor complexes differs between polar and lateral regions. Thus, distinct envelope physiology in the polar and lateral cell regions may contribute to polar preference.

Bacterial Chemoreceptor Imaging at High Spatiotemporal Resolution Using Photoconvertible Fluorescent Proteins.

We describe two methods for high-resolution fluorescence imaging of the positioning and mobility of E. coli chemoreceptors fused to photoconvertible fluorescent proteins. Chemoreceptors such as Tar and Tsr are transmembrane proteins expressed at high levels (thousands of copies per cell). Together with their cognate cytosolic signaling proteins, they form clusters on the plasma membrane. Theoretical models imply that the size of these clusters is an important parameter for signaling, and recent PALM imaging has revealed a broad distribution of cluster sizes. We describe experimental setups and protocols for PALM imaging in fixed cells with ~10 nm spatial precision, which allows analysis of cluster-size distributions, and localized-photoactivation single-particle tracking (LPA-SPT) in live cells at ~10 ms temporal resolution, which allows for analysis of cluster mobility.

Build your own soil: exploring microfluidics to create microbial habitat structures.

Soil is likely the most complex ecosystem on earth. Despite the global importance and extraordinary diversity of soils, they have been notoriously challenging to study. We show how pioneering microfluidic techniques provide new ways of studying soil microbial ecology by allowing simulation and manipulation of chemical conditions and physical structures at the microscale in soil model habitats.

Phenotypic diversity and temporal variability in a bacterial signaling network revealed by single-cell FRET.

We present in vivo single-cell FRET measurements in the Escherichia coli chemotaxis system that reveal pervasive signaling variability, both across cells in isogenic populations and within individual cells over time. We quantify cell-to-cell variability of adaptation, ligand response, as well as steady-state output level, and analyze the role of network design in shaping this diversity from gene expression noise. In the absence of changes in gene expression, we find that single cells demonstrate strong temporal fluctuations. We provide evidence that such signaling noise can arise from at least two sources: (i) stochastic activities of adaptation enzymes, and (ii) receptor-kinase dynamics in the absence of adaptation. We demonstrate that under certain conditions, (ii) can generate giant fluctuations that drive signaling activity of the entire cell into a stochastic two-state switching regime. Our findings underscore the importance of molecular noise, arising not only in gene expression but also in protein networks.

Super-resolution imaging of light-matter interactions near single semiconductor nanowires.

Nanophotonics is becoming invaluable for an expanding range of applications, from controlling the spontaneous emission rate and the directionality of quantum emitters, to reducing material requirements of solar cells by an order of magnitude. These effects are highly dependent on the near field of the nanostructure, which constitutes the evanescent fields from propagating and resonant localized modes. Although the interactions between quantum emitters and nanophotonic structures are increasingly well understood theoretically, directly imaging these interactions experimentally remains challenging. Here we demonstrate a photoactivated localization microscopy-based technique to image emitter-nanostructure interactions. For a 75 nm diameter silicon nanowire, we directly observe a confluence of emission rate enhancement, directivity modification and guided mode excitation, with strong interaction at scales up to 13 times the nanowire diameter. Furthermore, through analytical modelling we distinguish the relative contribution of these effects, as well as their dependence on emitter orientation.

Signaling noise enhances chemotactic drift of E. coli.

Noise in the transduction of chemotactic stimuli to the flagellar motor of E. coli will affect the random run-and-tumble motion of the cell and the ability to perform chemotaxis. Here we use numerical simulations to show that an intermediate level of noise in the slow methylation dynamics enhances drift while not compromising localization near concentration peaks. A minimal model shows how such an optimal noise level arises from the interplay of noise and the dependence of the motor response on the network output. Our results suggest that cells can exploit noise to improve chemotactic performance.

Salmonella chemoreceptors McpB and McpC mediate a repellent response to L-cystine: a potential mechanism to avoid oxidative conditions.

Chemoreceptors McpB and McpC in Salmonella enterica have been reported to promote chemotaxis in LB motility-plate assays. Of the chemicals tested as potential effectors of these receptors, the only response was towards L-cysteine and its oxidized form, L-cystine. Although enhanced radial migration in plates suggested positive chemotaxis to both amino acids, capillary assays failed to show an attractant response to either, in cells expressing only these two chemoreceptors. In vivo fluorescence resonance energy transfer (FRET) measurements of kinase activity revealed that in wild-type bacteria, cysteine and cystine are chemoeffectors of opposing sign, the reduced form being a chemoattractant and the oxidized form a repellent. The attractant response to cysteine was mediated primarily by Tsr, as reported earlier for Escherichia coli. The repellent response to cystine was mediated by McpB/C. Adaptive recovery upon cystine exposure required the methyl-transferase/-esterase pair, CheR/CheB, but restoration of kinase activity was never complete (i.e. imperfect adaptation). We provide a plausible explanation for the attractant-like responses to both cystine and cysteine in motility plates, and speculate that the opposing signs of response to this redox pair might afford Salmonella a mechanism to gauge and avoid oxidative environments.

Response rescaling in bacterial chemotaxis.

Sensory systems rescale their response sensitivity upon adaptation according to simple strategies that recur in processes as diverse as single-cell signaling, neural network responses, and whole-organism perception. Here, we study response rescaling in Escherichia coli chemotaxis, where adaptation dynamically tunes the cells' motile response during searches for nutrients. Using in vivo fluorescence resonance energy transfer (FRET) measurements on immobilized cells, we demonstrate that the design of this prokaryotic signaling network follows the fold-change detection (FCD) strategy, responding faithfully to the shape of the input profile irrespective of its absolute intensity. Using a microfluidics-based assay for free swimming cells, we confirm intensity-independent gradient responses at the behavioral level. By theoretical analysis, we identify a set of sufficient conditions for FCD in E. coli chemotaxis, which leads to the prediction that the adaptation timescale is invariant with respect to the background input level. Additional FRET experiments confirm that the adaptation timescale is invariant over an ∼10,000-fold range of background concentrations. These observations in a highly optimized bacterial system support the concept that FCD represents a robust sensing strategy for spatial searches. To our knowledge, these experiments provide a unique demonstration of FCD in any biological sensory system.

Bacterial moving and shaking: the 11th blast meeting.

Since their inception 20 years ago, the biennial blast (Bacterial Locomotion and Signal Transduction) meetings instantly became the place to be for exchanging and sharing the latest developments in the field of bacterial motility and signalling. At the 11th edition, held last January in New Orleans, LA, researchers reported on the myriad of mechanisms involved in bacterial movement, sensing and adaptation, ranging from the molecular level to multicellular behaviour. New insights into bacterial signalling phenomena were gained, revealing previously unsuspected layers of complexity, particularly in mechanisms ensuring signal transduction fidelity and novel links to metabolic processes.