Signaling events that occur when cells of Escherichia coli encounter a glass surface

A genetically encoded fluorescent biosensor for sensitive detection of cellular c-di-GMP levels in Escherichia coli

Cyclic di-guanosine monophosphate (c-di-GMP) acts as a second messenger regulating bacterial behaviors including cell cycling, biofilm formation, adhesion, and virulence. Monitoring c-di-GMP levels is crucial for understanding these processes and designing inhibitors to combat biofilm-related antibiotic resistance. Here, we developed a genetically encoded biosensor, cdiGEBS, based on the transcriptional activity of the c-di-GMP-responsive transcription factor MrkH. Notably, cdiGEBS can detect both low and high cellular c-di-GMP levels, with a high fluorescence dynamic change of 23-fold. Moreover, it can detect subtle changes in c-di-GMP concentrations due to variations in the expression of c-di-GMP synthesis or degradation enzymes and can distinguish different synthesis activities among WspR mutants. These capabilities allow us to apply cdiGEBS for identifying new diguanylate cyclases and evaluating chemicals that modulate c-di-GMP levels, highlighting its potential as a high-throughput tool for screening inhibitors of c-di-GMP synthesis enzymes. Overall, cdiGEBS enhances the study of c-di-GMP-regulated functions and holds the potential for screening antimicrobials targeting c-di-GMP or its synthesis enzymes.

An improved bacterial single-cell RNA-seq reveals biofilm heterogeneity

In contrast to mammalian cells, bacterial cells lack mRNA polyadenylated tails, presenting a hurdle in isolating mRNA amidst the prevalent rRNA during single-cell RNA-seq. This study introduces a novel method, ribosomal RNA-derived cDNA depletion (RiboD), seamlessly integrated into the PETRI-seq technique, yielding RiboD-PETRI. This innovative approach offers a cost-effective, equipment-free, and high-throughput solution for bacterial single-cell RNA sequencing (scRNA-seq). By efficiently eliminating rRNA reads and substantially enhancing mRNA detection rates (up to 92%), our method enables precise exploration of bacterial population heterogeneity. Applying RiboD-PETRI to investigate biofilm heterogeneity, distinctive subpopulations marked by unique genes within biofilms were successfully identified. Notably, PdeI, a marker for the cell-surface attachment subpopulation, was observed to elevate cyclic diguanylate (c-di-GMP) levels, promoting persister cell formation. Thus, we address a persistent challenge in bacterial single-cell RNA-seq regarding rRNA abundance, exemplifying the utility of this method in exploring biofilm heterogeneity. Our method effectively tackles a long-standing issue in bacterial scRNA-seq: the overwhelming abundance of rRNA. This advancement significantly enhances our ability to investigate the intricate heterogeneity within biofilms at unprecedented resolution.

Nanovibrational Stimulation of Escherichia coli Mitigates Surface Adhesion by Altering Cell Membrane Potential

Mechanical forces shape living matter from the macro- to the microscale as both eukaryotic and prokaryotic cells are force wielders and sensors. However, whereas such forces have been used to control mechanically dependent behaviors in mammalian cells, we lack the same level of understanding in bacteria. Surface adhesion, the initial stages of biofilm formation and surface biofouling, is a mechanically dependent process, which makes it an ideal target for mechano-control. In this study, we employed nanometer surface vibrations to mechanically stimulate bacteria and investigate their effect on adhesion. We discovered that vibrational stimulation at the nanoscale consistently reduces surface adhesion by altering cell membrane potential. Our findings identify a link between bacteria electrophysiology and surface adhesion and provide evidence that the nanometric mechanical "tickling" of bacteria can inhibit surface adhesion.

Cyclic di-GMP as an antitoxin regulates bacterial genome stability and antibiotic persistence in biofilms

Biofilms are complex bacterial communities characterized by a high persister prevalence, which contributes to chronic and relapsing infections. Historically, persister formation in biofilms has been linked to constraints imposed by their dense structures. However, we observed an elevated persister frequency accompanying the stage of cell adhesion, marking the onset of biofilm development. Subsequent mechanistic studies uncovered a comparable type of toxin-antitoxin (TA) module (TA-like system) triggered by cell adhesion, which is responsible for this elevation. In this module, the toxin HipH acts as a genotoxic deoxyribonuclease, inducing DNA double strand breaks and genome instability. While the second messenger c-di-GMP functions as the antitoxin, exerting control over HipH expression and activity. The dynamic interplay between c-di-GMP and HipH levels emerges as a crucial determinant governing genome stability and persister generation within biofilms. These findings unveil a unique TA system, where small molecules act as the antitoxin, outlining a biofilm-specific molecular mechanism influencing genome stability and antibiotic persistence, with potential implications for treating biofilm infections.

Electrical Signaling Beyond Neurons

Neural action potentials (APs) are difficult to interpret as signal encoders and/or computational primitives. Their relationships with stimuli and behaviors are obscured by the staggering complexity of nervous systems themselves. We can reduce this complexity by observing that "simpler" neuron-less organisms also transduce stimuli into transient electrical pulses that affect their behaviors. Without a complicated nervous system, APs are often easier to understand as signal/response mechanisms. We review examples of nonneural stimulus transductions in domains of life largely neglected by theoretical neuroscience: bacteria, protozoans, plants, fungi, and neuron-less animals. We report properties of those electrical signals-for example, amplitudes, durations, ionic bases, refractory periods, and particularly their ecological purposes. We compare those properties with those of neurons to infer the tasks and selection pressures that neurons satisfy. Throughout the tree of life, nonneural stimulus transductions time behavioral responses to environmental changes. Nonneural organisms represent the presence or absence of a stimulus with the presence or absence of an electrical signal. Their transductions usually exhibit high sensitivity and specificity to a stimulus, but are often slow compared to neurons. Neurons appear to be sacrificing the specificity of their stimulus transductions for sensitivity and speed. We interpret cellular stimulus transductions as a cell's assertion that it detected something important at that moment in time. In particular, we consider neural APs as fast but noisy detection assertions. We infer that a principal goal of nervous systems is to detect extremely weak signals from noisy sensory spikes under enormous time pressure. We discuss neural computation proposals that address this goal by casting neurons as devices that implement online, analog, probabilistic computations with their membrane potentials. Those proposals imply a measurable relationship between afferent neural spiking statistics and efferent neural membrane electrophysiology.

Surface conversion of the dynamics of bacteria escaping chemorepellents

Flagellar swimming hydrodynamics confers a recognized advantage for attachment on solid surfaces. Whether this motility further enables the following environmental cues was experimentally explored. Motile E. coli (OD ~ 0.1) in a 100 µm-thick channel were exposed to off-equilibrium gradients set by a chemorepellent Ni(NO3)2-source (250 mM). Single bacterial dynamics at the solid surface was analyzed by dark-field videomicroscopy at a fixed position. The number of bacteria indicated their congregation into a wave escaping from the repellent source. Besides the high velocity drift in the propagation direction within the wave, an unexpectedly high perpendicular component drift was also observed. Swimming hydrodynamics CW-bends the bacteria trajectories during their primo approach to the surface (< 2 µm), and a high enough tumbling frequency likely preserves a notable lateral drift. This comprehension substantiates a survival strategy tailored to toxic environments, which involves drifting along surfaces, promoting the inception of colonization at the most advantageous sites.

A bacterial sense of touch: T4P retraction motor as a means of surface sensing by Pseudomonas aeruginosa PA14

Most microbial cells found in nature exist in matrix-covered, surface-attached communities known as biofilms. This mode of growth is initiated by the ability of the microbe to sense a surface on which to grow. The opportunistic pathogen Pseudomonas aeruginosa (Pa) PA14 utilizes a single polar flagellum and type 4 pili (T4P) to sense surfaces. For Pa, T4P-dependent "twitching" motility is characterized by effectively pulling the cell across a surface through a complex process of cooperative binding, pulling, and unbinding. T4P retraction is powered by hexameric ATPases. Pa cells that have engaged a surface increase production of the second messenger cyclic AMP (cAMP) over multiple generations via the Pil-Chp system. This rise in cAMP allows cells and their progeny to become better adapted for surface attachment and activates virulence pathways through the cAMP-binding transcription factor Vfr. While many studies have focused on mechanisms of T4P twitching and regulation of T4P production and function by the Pil-Chp system, the mechanism by which Pa senses and relays a surface-engagement signal to the cell is still an open question. Here we review the current state of the surface sensing literature for Pa, with a focus on T4P, and propose an integrated model of surface sensing whereby the retraction motor PilT senses and relays the signal to the Pil-Chp system via PilJ to drive cAMP production and adaptation to a surface lifestyle.

Cell-autonomous diversification in bacteria arises from calcium dynamics self-organizing at a critical point

How dynamic bacterial calcium is regulated, with kinetics faster than typical mechanisms of cellular adaptation, is unknown. We discover bacterial calcium fluctuations are temporal-fractals resulting from a property known as self-organized criticality (SOC). SOC processes are poised at a phase transition separating ordered and chaotic dynamical regimes and are observed in many natural and anthropogenic systems. SOC in bacterial calcium emerges due to calcium channel coupling mediated via membrane voltage. Environmental or genetic perturbations modify calcium dynamics and the critical exponent suggesting a continuum of critical attractors. Moving along this continuum alters the collective information capacity of bacterial populations. We find that the stochastic transition from motile to sessile lifestyle is partially mediated by SOC-governed calcium fluctuations through the regulation of c-di-GMP. In summary, bacteria co-opt the physics of phase transitions to maintain dynamic calcium equilibrium, and this enables cell-autonomous population diversification during surface colonization by leveraging the stochasticity inherent at a boundary between phases.

Exopolysaccharides amylovoran and levan contribute to sliding motility in the fire blight pathogen Erwinia amylovora

Erwinia amylovora, the causative agent of fire blight, uses flagella-based motilities to translocate to host plant natural openings; however, little is known about how this bacterium migrates systemically in the apoplast. Here, we reveal a novel surface motility mechanism, defined as sliding, in E. amylovora. Deletion of flagella assembly genes did not affect this movement, whereas deletion of biosynthesis genes for the exopolysaccharides (EPSs) amylovoran and levan resulted in non-sliding phenotypes. Since EPS production generates osmotic pressure that potentially powers sliding, we validated this mechanism by demonstrating that water potential positively contributes to sliding. In addition, no sliding was observed when the water potential of the surface was lower than -0.5 MPa. Sliding is a passive motility mechanism. We further show that the force of gravity plays a critical role in directing E. amylovora sliding on unconfined surfaces but has a negligible effect when cells are sliding in confined microcapillaries, in which EPS-dependent osmotic pressure acts as the main force. Although amylovoran and levan are both required for sliding, we demonstrate that they exhibit different roles in bacterial communities. In summary, our study provides fundamental knowledge for a better understanding of mechanisms that drive bacterial sliding motility.