How signals are heard during bacterial chemotaxis: protein-protein interactions in sensory signal propagation

Programming Surface Motility and Modulating Physiological Behaviors of Bacteria via Biosurfactant-Mimetic Polyurethanes

Modulating microbial motility and physiology can enhance the production of bacterial macromolecules and small molecules. Herein, a platform of water-soluble and amphiphilic peptidomimetic polyurethanes is reported as a means of regulating bacterial surface behavior and the concomitant production of extracellular polymeric substances (EPS). It is demonstrated that carboxyl (-COOH)-containing polyurethanes exhibited 17-fold and 80-fold enhancements in Pseudomonas aeruginosa (P. aeruginosa) swarming and twitching areas, respectively. Conversely, an amine (-NH2)-functionalized polyurethane reduces the P. aeruginosa swarming area by 58%. Similar influences on the surface motility of Escherichia coli (E. coli) and a nonswarming P. aeruginosa mutant strain are also observed. Notably, -COOH polyurethanes completely wet the agar hydrogel surface and promote bacterial surface proliferation, resulting in enhanced EPS and rhamnolipid production. The programming of bacterial spatial migration into designed patterns is achieved by leveraging the opposing influences of -NH2 and -COOH polyurethanes. The results highlight the potential of this synthetic polyurethane platform and potentially other polymer systems as an exciting approach to control bacterial surface behaviors and influence the production of engineered living materials.

Enhanced chemotaxis efficiency of Escherichia coli in viscoelastic solutions

Bacteria inhabit complex environments rich in macromolecular polymers that exhibit viscoelastic properties. While the influence of viscoelasticity on bacterial swimming is recognized, its impact on chemotaxis-a critical behavior for bacterial survival and colonization-remains elusive. In this study, we employed a microfluidic device to establish attractant gradients and observed the chemotactic behavior of Escherichia coli in both viscoelastic solutions containing carboxymethyl cellulose (CMC) and Newtonian buffers. Our results reveal that E. coli demonstrates markedly enhanced chemotactic efficiency in viscoelastic media. Notably, bacteria achieved faster migration velocities and higher steady-state accumulation in areas with higher attractant concentrations compared to those in Newtonian conditions. Through 3D tracking, we determined that changes in bulk motility parameters alone do not account for the observed enhancements. Further investigations through theoretical analysis and stochastic simulations suggested that the main enhancement mechanisms are mitigation of surface hydrodynamic hindrance resulting from solid surfaces commonly present in bacterial habitats, and the induction of a lifting force in viscoelastic solutions. These findings highlight the significant role of the rheological properties of bacterial habitats in shaping their chemotactic strategies, offering deeper insights into bacterial adaptive mechanisms in both natural and clinical settings.

Optimizing the placement of medical wastewater outlets in sewer systems to reduce chemical consumption at wastewater treatment plants

The severely low influent chemical oxygen demand (COD) concentration at wastewater treatment plants (WWTPs) has become a critical issue. A key factor is the excessive biodegradation of organic matter by microbial communities within sewer systems. Intense disinfection commonly adopted for medical wastewater leads to abundant residual chlorine entering sewers, likely causing significant changes in microbial communities and sewage quality in sewers, yet our understanding is limited. Through long-term sewer simulation batch tests, this study revealed the response mechanism of microbial communities to residual chlorine and its impact on organic matter concentration in sewage. Under residual chlorine stress, microbial community structure rapidly changed, and more complex microbial interactions were observed. Besides, pathways related to stress response such as two-component system were significantly enriched; pathways related to energy metabolism (such as carbon fixation in prokaryotes and citrate cycle) in microbial communities were inhibited, and carbon metabolism shifted from the Embden-Meyerhof pathway to the pentose phosphate pathway to enhance cellular reducing power, reduce oxidative stress, and consequently decrease organic matter degradation. Therefore, compared to sewers with normal disinfection, concentrations of COD and dissolved organic carbon in sewage under chlorine stress increased by 12.6 % and 7.4 %, respectively. Besides, the decay and transformation of residual chlorine in sewers were explored. These findings suggest a new approach to medical wastewater discharge management: placing the medical wastewater outlet at the upstream in sewer systems, which ensures that residual chlorine consumption reaches maximum during long-distance transportation, mitigating its harmful effects on WWTPs, and increases the influent organic matter concentration, thereby reducing the need for additional carbon sources.

Gut epithelial electrical cues drive differential localization of enterobacteria

Salmonella translocate to the gut epithelium via microfold cells lining the follicle-associated epithelium (FAE). How Salmonella localize to the FAE is not well characterized. Here we use live imaging and competitive assays between wild-type and chemotaxis-deficient mutants to show that Salmonella enterica serotype Typhimurium (S. Typhimurium) localize to the FAE independently of chemotaxis in an ex vivo mouse caecum infection model. Electrical recordings revealed polarized FAE with sustained outward current and small transepithelial potential, while the surrounding villus is depolarized with inward current and large transepithelial potential. The distinct electrical potentials attracted S. Typhimurium to the FAE while Escherichia coli (E. coli) localized to the villi, through a process called galvanotaxis. Chloride flux involving the cystic fibrosis transmembrane conductance regulator (CFTR) generated the ionic currents around the FAE. Pharmacological inhibition of CFTR decreased S. Typhimurium FAE localization but increased E. coli recruitment. Altogether, our findings demonstrate that bioelectric cues contribute to S. Typhimurium targeting of specific gut epithelial locations, with potential implications for other enteric bacterial infections.

Advancements in bacterial chemotaxis: Utilizing the navigational intelligence of bacteria and its practical applications

The fascinating world of microscopic life unveils a captivating spectacle as bacteria effortlessly maneuver through their surroundings with astonishing accuracy, guided by the intricate mechanism of chemotaxis. This review explores the complex mechanisms behind this behavior, analyzing the flagellum as the driving force and unraveling the intricate signaling pathways that govern its movement. We delve into the hidden costs and benefits of this intricate skill, analyzing its potential to propagate antibiotic resistance gene while shedding light on its vital role in plant colonization and beneficial symbiosis. We explore the realm of human intervention, considering strategies to manipulate bacterial chemotaxis for various applications, including nutrient cycling, algal bloom and biofilm formation. This review explores the wide range of applications for bacterial capabilities, from targeted drug delivery in medicine to bioremediation and disease control in the environment. Ultimately, through unraveling the intricacies of bacterial movement, we can enhance our comprehension of the intricate web of life on our planet. This knowledge opens up avenues for progress in fields such as medicine, agriculture, and environmental conservation.

Potassium-mediated bacterial chemotactic response

Bacteria in biofilms secrete potassium ions to attract free swimming cells. However, the basis of chemotaxis to potassium remains poorly understood. Here, using a microfluidic device, we found that Escherichia coli can rapidly accumulate in regions of high potassium concentration on the order of millimoles. Using a bead assay, we measured the dynamic response of individual flagellar motors to stepwise changes in potassium concentration, finding that the response resulted from the chemotaxis signaling pathway. To characterize the chemotactic response to potassium, we measured the dose-response curve and adaptation kinetics via an Förster resonance energy transfer (FRET) assay, finding that the chemotaxis pathway exhibited a sensitive response and fast adaptation to potassium. We further found that the two major chemoreceptors Tar and Tsr respond differently to potassium. Tar receptors exhibit a biphasic response, whereas Tsr receptors respond to potassium as an attractant. These different responses were consistent with the responses of the two receptors to intracellular pH changes. The sensitive response and fast adaptation allow bacteria to sense and localize small changes in potassium concentration. The differential responses of Tar and Tsr receptors to potassium suggest that cells at different growth stages respond differently to potassium and may have different requirements for potassium.

Transition from active motion to anomalous diffusion for Bacillus subtilis confined in hydrogel matrices

We investigate the motility of B. subtilis under different degrees of confinement induced by transparent porous hydrogels. The dynamical behavior of the bacteria at short times is linked to characteristic parameters describing the hydrogel porosity. Mean squared displacements (MSDs) reveal that the run-and-tumble dynamics of unconfined B. subtilis progressively turns into sub-diffusive motion with increasing confinement. Correspondingly, the median instantaneous velocity of bacteria decreases and becomes more narrowly distributed, while the reorientation rate increases and reaches a plateau value. Analyzing single-trajectories, we show that the average dynamical behavior is the result of complex displacements, in which active, diffusive and sub-diffusive segments coexist. For small and moderate confinements, the number of active segments reduces, while the diffusive and sub-diffusive segments increase. The alternation of sub-diffusion, diffusion and active motion along the same trajectory can be described as a hopping ad trapping motion, in which hopping events correspond to displacements with an instantaneous velocity exceeding the corresponding mean value along a trajectory. Different from previous observations, escape from local trapping occurs for B. subtilis through active runs but also diffusion. Interestingly, the contribution of diffusion is maximum at intermediate confinements. At sufficiently long times transport coefficients estimated from the experimental MSDs under different degrees of confinement can be reproduced using a recently proposed hopping and trapping model. Finally, we propose a quantitative relationship linking the median velocity of confined and unconfined bacteria through the characteristic confinement length of the hydrogel matrix. Our work provides new insights for the bacterial motility in complex media that mimic natural environments and are relevant to important problems like sterilization, water purification, biofilm formation, membrane permeation and bacteria separation.

Comparative metagenomics and microbial dynamics of jute retting environment

Jute, eco-friendly natural fiber, depends on conventional water-based microbial retting process that suffers from the production of low-quality fiber, restricting its diversified applications. The efficiency of water retting of jute depends on plant polysaccharide fermenting pectinolytic microorganisms. Understanding the phase difference in retting microbial community composition is crucial to provide knowledge on the functions of each member of microbiota for the improvement of retting and fiber quality. The retting microbiota profiling of jute was commonly performed previously using only one retting phase with culture-dependent methods which has limited coverage and accuracy. Here, for the first we have analyzed jute retting water through WGS metagenome approach in three phases (pre-retting, aerobic retting, and anaerobic retting phases) and characterized the microbial communities both culturable and non-culturable along with their dynamics with the fluctuation of oxygen availability. Our analysis revealed a total of 25.99 × 104 unknown proteins (13.75%), 16.18 × 105 annotated proteins (86.08%), and 32.68 × 102 ribosomal RNA (0.17%) in the pre-retting phase, 15.12 × 104 unknown proteins (8.53%), 16.18 × 105 annotated proteins (91.25%), and 38.62 × 102 ribosomal RNA (0.22%) in the aerobic retting phase, and 22.68 × 102 ribosomal RNA and 80.14 × 104 (99.72%) annotated protein in the anaerobic retting phase. Taxonomically, we identified 53 different phylotypes in the retting environment, with Proteobacteria being the dominant taxa comprising over 60% of the population. We have identified 915 genera from Archaea, Viruses, Bacteria, and Eukaryota in the retting habitat, with anaerobic or facultative anaerobic pectinolytic microflora being enriched in the anoxic, nutrient-rich retting niche, such as Aeromonas (7%), Bacteroides (3%), Clostridium (6%), Desulfovibrio (4%), Acinetobacter (4%), Enterobacter (1%), Prevotella (2%), Acidovorax (3%), Bacillus (1%), Burkholderia (1%), Dechloromonas (2%), Caulobacter (1%) and Pseudomonas (7%). We observed an increase in the expression of 30 different KO functional level 3 pathways in the final retting stage compared to the middle and pre-retting stages. The main functional differences among the retting phases were found to be related to nutrient absorption and bacterial colonization. These findings reveal the bacterial groups that are involved in fiber retting different phases and will facilitate to develop future phase-specific microbial consortia for the improvement of jute retting process.

Tethered particle motion of the adaptation enzyme CheR in bacterial chemotaxis

Bacteria perform chemotactic adaptation by sequential modification of multiple modifiable sites on chemoreceptors through stochastic action of tethered adaptation enzymes (CheR and CheB). To study the molecular kinetics of this process, we measured the response to different concentrations of MeAsp for the Tar-only Escherichia coli strain. We found a strong dependence of the methylation rate on the methylation level and established a new mechanism of adaptation kinetics due to tethered particle motion of the methylation enzyme CheR. Experiments with various lengths of the C-terminal flexible chain in the Tar receptor further validated this mechanism. The tethered particle motion resulted in a CheR concentration gradient that ensures encounter-rate matching of the sequential modifiable sites. An analytical model of multisite catalytic reaction showed that this enables robustness of methylation to fluctuations in receptor activity or cell-to-cell variations in the expression of adaptation enzymes and reduces the variation in methylation level among individual receptors.

Perturbation of Quorum Sensing after the Acquisition of Bacteriophage Resistance Could Contribute to Novel Traits in Vibrio alginolyticus

Bacteria employ a wide range of molecular mechanisms to confer resistance to bacteriophages, and these mechanisms are continuously being discovered and characterized. However, there are instances where certain bacterial species, despite lacking these known mechanisms, can still develop bacteriophage resistance through intricate metabolic adaptation strategies, potentially involving mutations in transcriptional regulators or phage receptors. Vibrio species have been particularly useful for studying the orchestrated metabolic responses of Gram-negative marine bacteria in various challenges. In a previous study, we demonstrated that Vibrio alginolyticus downregulates the expression of specific receptors and transporters in its membrane, which may enable the bacterium to evade infection by lytic bacteriophages. In our current study, our objective was to explore how the development of bacteriophage resistance in Vibrio species disrupts the quorum-sensing cascade, subsequently affecting bacterial physiology and metabolic capacity. Using a real-time quantitative PCR (rt-QPCR) platform, we examined the expression pattern of quorum-sensing genes, auto-inducer biosynthesis genes, and cell density regulatory proteins in phage-resistant strains. Our results revealed that bacteriophage-resistant bacteria downregulate the expression of quorum-sensing regulatory proteins, such as LuxM, LuxN, and LuxP. This downregulation attenuates the normal perception of quorum-sensing peptides and subsequently diminishes the expression of cell density regulatory proteins, including LuxU, aphA, and LuxR. These findings align with the diverse phenotypic traits observed in the phage-resistant strains, such as altered biofilm formation, reduced planktonic growth, and reduced virulence. Moreover, the transcriptional depletion of aphA, the master regulator associated with low cell density, was linked to the downregulation of genes related to virulence. This phenomenon appears to be phage-specific, suggesting a finely tuned metabolic adaptation driven by phage-host interaction. These findings contribute to our understanding of the role of Vibrio species in microbial marine ecology and highlight the complex interplay between phage resistance, quorum sensing, and bacterial physiology.

Contrasting effect of ficoll on apo and holo forms of bacterial chemotaxis protein Y: Selective destabilization of the conformationally altered holo form

Chemotaxis Y (CheY), upon metal binding, displays a drastic alteration in its structure and stability. This premise prompted us to study the effect of crowding on the two conformationally distinct states of the same test protein. A comparative analysis on the structure and thermal stability in the presence and absence of the macromolecular crowder, ficoll, and its monomeric unit, sucrose, revealed a contrasting effect of ficoll on the apo and holo forms. In the presence of ficoll while the thermal stability (T_m) of the apo form is enhanced, the thermal stability of the holo form is reduced. The selective lowering of T_m for the holo form in the combined presence of ficoll and sucrose and not in sucrose alone suggests that the contrasting effect is due to the macromolecular nature of ficoll. Since metal-protein interaction remains unperturbed in the presence of ficoll and Mg²⁺ sequestration is ruled out in a systematic manner the alternative possibility for the exclusive reduction in the thermal stability of the holo form is the ficoll-induced modulation of the relative population of apo and holo forms of CheY.

Biofilm formation during wastewater treatment: Motility and physiological response of aerobic denitrifying bacteria under ammonia stress based on surface plasmon resonance imaging

A bacterial image analysis system based on surface plasmon resonance imaging was established to investigate the effect of bacterial motility on biofilm formation under high ammonia nitrogen at the single-cell level. The results showed that the bacterial mean rotation speed and vertical motility distance decreased with the increasing concentration of ammonia nitrogen. Ammonia nitrogen inhibited the metabolic activity of the bacteria, decreasing bacterial motility. Bacterial motility was negatively correlated with the biofilm-formation ability. The biofilm formation ability of Enterobacter cloacae strain HNR exposed to ammonia nitrogen was enhanced by reducing its movement and promoting EPS secretion. Genes related to the tricarboxylic acid cycle and oxidative phosphorylation were down-regulated, indicating inhibition of microbial energy metabolism. Genes related to bacterial secretion and lipopolysaccharide synthesis were up-regulated, facilitating the formation of biofilms and enabling the bacteria to resist ammonia nitrogen stress. This study provides new insights into the biofilm formation under ammonia stress.

Multiple Adaptive Strategies of Himalayan Iodobacter sp. PCH194 to High-Altitude Stresses

Bacterial adaption to the multiple stressed environments of high-altitude niches in the Himalayas is intriguing and is of considerable interest to biotechnologists. Previously, we studied the culturable and unculturable metagenome microbial diversity from glacial and kettle lakes in the Western Himalayas. In this study, we explored the adaptive strategies of a unique Himalayan eurypsychrophile Iodobacter sp. PCH194, which can synthesize polyhydroxybutyrate (PHB) and violacein pigment. Whole-genome sequencing and analysis of Iodobacter sp. PCH194 (4.58 Mb chromosome and three plasmids) revealed genetic traits associated with adaptive strategies for cold/freeze, nutritional fluctuation, defense against UV, acidic pH, and the kettle lake's competitive environment. Differential proteome analysis suggested the adaptive role of chaperones, ribonucleases, secretion systems, and antifreeze proteins under cold stress. Antifreeze activity inhibiting the ice recrystallization at −9°C demonstrated the bacterium's survival at subzero temperature. The bacterium stores carbon in the form of PHB under stress conditions responding to nutritional fluctuations. However, violacein pigment protects the cells from UV radiation. Concisely, genomic, proteomic, and physiological studies revealed the multiple adaptive strategies of Himalayan Iodobacter to survive the high-altitude stresses.

Plant Beneficial Bacteria as Bioprotectants against Wheat and Barley Diseases

Wheat and barley are the main cereal crops cultivated worldwide and serve as staple food for a third of the world's population. However, due to enormous biotic stresses, the annual production has significantly reduced by 30-70%. Recently, the accelerated use of beneficial bacteria in the control of wheat and barley pathogens has gained prominence. In this review, we synthesized information about beneficial bacteria with demonstrated protection capacity against major barley and wheat pathogens including Fusarium graminearum, Zymoseptoria tritici and Pyrenophora teres. By summarizing the general insights into molecular factors involved in plant-pathogen interactions, we show to an extent, the means by which beneficial bacteria are implicated in plant defense against wheat and barley diseases. On wheat, many Bacillus strains predominantly reduced the disease incidence of F. graminearum and Z. tritici. In contrast, on barley, the efficacy of a few Pseudomonas, Bacillus and Paraburkholderia spp. has been established against P. teres. Although several modes of action were described for these strains, we have highlighted the role of Bacillus and Pseudomonas secondary metabolites in mediating direct antagonism and induced resistance against these pathogens. Furthermore, we advance a need to ascertain the mode of action of beneficial bacteria/molecules to enhance a solution-based crop protection strategy. Moreover, an apparent disjoint exists between numerous experiments that have demonstrated disease-suppressive effects and the translation of these successes to commercial products and applications. Clearly, the field of cereal disease protection leaves a lot to be explored and uncovered.

Unveiling the chemotactic response and mechanism of Shewanella oneidensis MR-1 to nitrobenzene

Bioreduction by electroactive bacteria (EAB) is considered as a potential and cost-effective approach for the removal of nitroaromatic compounds (NACs). However, little is known about how the widespread EAB sense and respond to slightly soluble NACs in aquatic environments. Here, the chemotactic behaviors of Shewanella oneidensis MR-1, a model EAB, toward several NACs were examined and their underlying molecular mechanism was elucidated. S. oneidensis MR-1 was found to exhibit a strong chemotactic response to nitrobenzene (NB), but not to other selected NACs under aerobic conditions. To sense NB, this bacterium requires both the histidine kinase (CheA-3)-involved chemotactic signal transduction pathway and an inner-membrane c-type cytochrome CymA. Such a chemotactic response is mediated by an energy taxis mechanism. Additionally, external riboflavin was shown to greatly enhance the Shewanella taxis toward NB, implying a feasible way to increase the bioavailability of NACs. The present study deepens our understanding of the role of microbial chemotaxis in the removal of NACs and provides more options for the bioremediation of NAC-contaminated sites.

Dioxin-like polychlorinated biphenyl 126 (PCB126) disrupts gut microbiota-host metabolic dysfunction in mice via aryl hydrocarbon receptor activation

Exposure to environmental pollutants, including dioxin-like pollutants, can cause numerous health issues. A common exposure route to pollutants is through contaminated foods, and thus the gastrointestinal system and gut microbiota are often exposed to high amounts of pollutants. Multiple studies have focused on the imbalance in intestinal microbiota composition caused by dioxin-like pollutants. Here, we examined the effects of polychlorinated biphenyl 126 (PCB126) on the composition and functions of gut microbes through metagenomic sequencing, and explored the correlations between microflora dysbiosis and aryl hydrocarbon receptor (AHR) signaling. Adult male wild-type and Ahr^-/- mice with a C57BL/6 background were weekly exposed to 50 μg/kg body weight of PCB126 for 8 weeks. Results showed that PCB126 had the opposite effect on gut microbiota composition and diversity in the wild-type and Ahr^-/- mice. Functional prediction found that PCB126 exposure mainly altered carbon metabolism and signal regulatory pathways in wild-type mice but impacted DNA replication and lipopolysaccharide biosynthesis in Ahr^-/- mice. In wild-type mice, PCB126 exposure induced liver injury, decreased serum lipid content, and delayed gastrointestinal motility, which were significantly correlated to several specific bacterial taxa, such as Helicobacter. Following AHR knockout, however, the holistic effects of PCB126 on the host were lessened or abolished. These results suggest that PCB126 may disrupt host metabolism and gut microbiota dynamics via AHR activation. Overall, our findings provide new insight into the complex interactions between host metabolism and gut microbiota, which may contribute to grouped assessment of environmental pollutants in the future.

Tailoring Escherichia coli Chemotactic Sensing towards Cadmium by Computational Redesign of Ribose-Binding Protein

Periplasmic binding proteins such as ribose-binding proteins (RBPs) are involved in the bacterial chemotaxis two-component system. RBP selectively identifies and interacts with ribose to induce a conformational change that leads to chemotaxis. Here, we report the development of an engineered Escherichia coli (E. coli) strain expressing a redesigned RBP that can effectively sense cadmium ions and regulate chemotactic movement of cells toward a cadmium ion gradient. RBP was computationally redesigned to bind cadmium ions and produce the conformational change required for chemoreceptor binding. The successful design, CdRBP1, binds to cadmium ions with a dissociation constant of 268 nM. When CdRBP1 was expressed in the periplasmic space of E. coli, the bacteria became live cadmium ion hunters with high selectivity over other divalent metal ions. This work presents an example of making cadmium ions, which are toxic for most organisms, as an attractant to regulate cells movement. Our approach also demonstrates that RBP can be precisely designed to develop metal-detecting living systems for potential applications in synthetic biology and environmental studies.

IMPORTANCE Cadmium pollution is one of the major environmental problems due to excessive release and accumulation. New technologies that can auto-detect cadmium ions with good biocompatibility are in urgent need. In this study, we engineered the bacterial chemotaxis system to positively sense cadmium ions by redesigning ribose-binding protein (RBP) to tightly bind cadmium ion and produce the right conformational change for receptor binding and signaling. Our engineered E. coli cells can auto-detect and chase cadmium ions with divalent metal ion selectivity. Many attempts have been carried out to redesign RBP at the ribose binding site with little success. Instead of the ribose binding site, we introduced the cadmium binding site in the opening of the ribose binding pocket by a specially developed computational algorithm. Our design strategy can be applied to engineer live bacteria with autonomous detection and remediation abilities for metal ions or other chemicals in the future.

Virulence Determinants and Genetic Diversity of Yersinia Species Isolated from Retail Meat

Yersinia enterocolitica is an important foodborne pathogen, and the determination of its virulence factors and genetic diversity within the food chain could help understand the epidemiology of yersiniosis. The aim of the present study was to detect the prevalence, and characterize the virulence determinants and genetic diversity, of Yersinia species isolated from meat. A total of 330 samples of retailed beef (n = 150) and pork (n = 180) in Latvia were investigated with culture and molecular methods. Whole genome sequencing (WGS) was applied for the detection of virulence and genetic diversity. The antimicrobial resistance of pathogenic Y. enterocolitica isolates was detected in accordance with EUCAST. Yersinia species were isolated from 24% (79/330) of meats, and the prevalence of Y. enterocolitica in pork (24%, 44/180) was significantly higher (p < 0.05) than in beef (13%, 19/150). Y. enterocolitica pathogenic bioserovars 2/O:9 and 4/O:3 were isolated from pork samples (3%, 6/180). Only resistance to ampicillin was confirmed in Y. enterocolitica 4/O:3 and 2/O:9 isolates, but not in other antimicrobials. Major virulence determinants, including ail, inv, virF, ystA and myfA, were confirmed with WGS in Y. enterocolitica 2/O:9 and 4/O:3. MLST typing revealed 15 STs (sequence types) of Y. enterocolitica with ST12 and ST18, which were associated with pathogenic bioserovars. For Y. enterocolitica 1A, Y. kristensenii, Y. intermedia and Y. frederiksenii, novel STs were registered (ST680-688). The presence of virulence genes and genetic characteristics of certain Y. enterocolitica STs confirm the common knowledge that pork could be an important source of pathogenic Yersinia.

Leave or Stay: Simulating Motility and Fitness of Microorganisms in Dynamic Aquatic Ecosystems

Motility is a key adaptation factor in scarce marine environments inhabited by bacteria. The question of how a capacity for adaptive migrations influences the success of a microbial population in various conditions is a challenge addressed in this study. We employed the agent-based model of competition of motile and sedentary microbial populations in a confined aquatic environment supplied with a periodic batch nutrient source to assess the fitness of both. Such factors as nutrient concentration in a batch, batch period, mortality type and energetic costs of migration were considered to determine the conditions favouring different strategies: Nomad of a motile population and Settler of a sedentary one. The modelling results demonstrate that dynamic and nutrient-scarce environments favour motile populations, whereas nutrient-rich and stagnant environments promote sedentary microorganisms. Energetic costs of migration determine whether or not the Nomad strategy of the motile population is successful, though it also depends on such conditions as nutrient availability. Even without penalties for migration, under certain conditions, the sedentary Settler population dominates in the ecosystem. It is achieved by decreasing the local nutrient availability near the nutrient source, as motile populations relying on a local optimizing strategy tend to follow benign conditions and fail, enduring stress associated with crossing the valleys of suboptimal nutrient availability.

Chemotactic behavior of Campylobacter fetus subspecies towards cervical mucus, bovine placenta and selected substances and ion

The chemotaxis of C. fetus subsp. venerealis and C. fetus subsp. fetus was determined in the presence of bovine cervical mucus and bovine placental extract. Some reported substances and ion in those materials, such amino acids, ferrous iron, hormones, sugars and organic acids were also investigated. Bovine cervical mucus, bovine placenta extracts and some substances and ion of these materials namely L–fucose, L– aspartate, L–glutamate, L–serine, ferrous iron, fumarate, pyruvate and succinate were chemoattractants. The chemottraction was significantly larger in higher concentrations of the tested substances and ion and significant differences among tested strains were also observed. Meso-erythritol and hormones bovine placental lactogen, 17β-estradiol, and progesterone did not elicit chemotactical response. In conclusion, this chemotactic behavior may guide the C. fetus navigation in the bovine host's genital tract and be an important cofactor of tissue tropism for this bacterium.

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.

Patterns of bacterial motility in microfluidics-confining environments

Understanding the motility behavior of bacteria in confining microenvironments, in which they search for available physical space and move in response to stimuli, is important for environmental, food industry, and biomedical applications. We studied the motility of five bacterial species with various sizes and flagellar architectures (Vibrio natriegens, Magnetococcus marinus, Pseudomonas putida, Vibrio fischeri, and Escherichia coli) in microfluidic environments presenting various levels of confinement and geometrical complexity, in the absence of external flow and concentration gradients. When the confinement is moderate, such as in quasi-open spaces with only one limiting wall, and in wide channels, the motility behavior of bacteria with complex flagellar architectures approximately follows the hydrodynamics-based predictions developed for simple monotrichous bacteria. Specifically, V. natriegens and V. fischeri moved parallel to the wall and P. putida and E. coli presented a stable movement parallel to the wall but with incidental wall escape events, while M. marinus exhibited frequent flipping between wall accumulator and wall escaper regimes. Conversely, in tighter confining environments, the motility is governed by the steric interactions between bacteria and the surrounding walls. In mesoscale regions, where the impacts of hydrodynamics and steric interactions overlap, these mechanisms can either push bacteria in the same directions in linear channels, leading to smooth bacterial movement, or they could be oppositional (e.g., in mesoscale-sized meandered channels), leading to chaotic movement and subsequent bacterial trapping. The study provides a methodological template for the design of microfluidic devices for single-cell genomic screening, bacterial entrapment for diagnostics, or biocomputation.

Improved Yield of Recombinant Protein via Flagella Regulator Deletion in Escherichia coli

Protein production requires a significant amount of intracellular energy. Eliminating the flagella has been proposed to help Escherichia coli improve protein production by reducing energy consumption. In this study, the gene encoding a subunit of FlhC, a master regulator of flagella assembly, was deleted to reduce the expression of flagella-related genes. FlhC knockout in the ptsG-deleted strain triggered significant growth retardation with increased ATP levels and a higher NADPH/NADP⁺ ratio. Metabolic flux analysis using a ¹³C-labeled carbon substrate showed increased fluxes toward the pentose phosphate and tricarboxylic acid cycle pathways in the flhC- and ptsG-deleted strains. Introduction of a high copy number plasmid or overexpression of the recombinant protein in this strain restored growth rate without increasing glucose consumption. These results suggest that the metabolic burden caused by flhC deletion was resolved by recombinant protein production. The recombinant enhanced green fluorescent protein yield per glucose consumption increased 1.81-fold in the flhC mutant strain. Thus, our study demonstrates that high-yield production of the recombinant protein was achieved with reduced flagella formation.

Global transcriptomic response of Listeria monocytogenes exposed to Fingered Citron (Citrus medica L. var. sarcodactylis Swingle) essential oil

Listeria monocytogenes, which could cause severe disease of listeriosis, is one of the most concerned foodborne pathogens worldwide. Citrus medica L. var. sarcodactylis Swingle (Fingered Citron) is one of the citrus species cultivated in south China. Here, we investigated the efficacy of Fingered Citron essential oil (FCEO) against L. monocytogenes and explored the response of L. monocytogenes in the presence of FCEO using genome-wide transcriptome analysis. FCEO exhibited strong anti-listeria activity and obvious alterations of cell morphology were observed by scanning electron microscopy and transmission electron microscopy. Moreover, GO analysis demonstrated many potential cell responses, including metabolic process, cellular process, single-organism process, cell part, membrane, catalytic activity, binding, and transporter activity. KEGG analysis suggests that L. monocytogenes respond and adapt by (1) increasing motility through the enhancement of flagella rotation; (2) promoting cell tumbles and re-orientating to escape from FCEO; (3) enhancing the uptake of carbohydrates from environment to gain more energy; (4) changing the uptake of several metallic cations, including iron, zinc, cobalt, and nickel. Our research contributes to the understanding of the adaptive responses of L. monocytogenes exposed to FCEO and provides novel insights for finding new targets of anti-listeria therapy.

How fast do mobile organisms respond to stimuli? Response times from bacteria to elephants and whales

Quick responses to fast changes in the environment are crucial in animal behaviour and survival, for example to seize prey, escape predators, or negotiate obstacles. Here, we study the 'simple response time' that is the time elapsed between receptor stimulation and motor activation as typically shown in escape responses, for mobile organisms of various taxa ranging from bacteria to large vertebrates. We show that 95% of these simple response times lie within one order of magnitude of the overall geometric mean of about 25 ms, which is similar to that of a well-studied sensory time scale, the inverse of the critical flicker fusion frequency in vision, also lying within close bounds for all the organisms studied. We find that this time scale is a few times smaller than the minimum time to move by one body length, which is known to lie also within a relatively narrow range for all moving organisms. The remarkably small 10²-fold range of the simple response time among so disparate life forms varying over 10²⁰-fold in body mass suggests that it is determined by basic physicochemical constraints, independently on the structure and scale of the organism. We thus propose first-principle estimates of the simple response and sensory time scales in terms of physical constants and a few basic biological properties common to mobile organisms and constraining their responses.

Collective motion enhances chemotaxis in a two-dimensional bacterial swarm

In a dilute liquid environment in which cell-cell interaction is negligible, flagellated bacteria, such as Escherichia coli, perform chemotaxis by biased random walks alternating between run-and-tumble. In a two-dimensional crowded environment, such as a bacterial swarm, the typical behavior of run-and-tumble is absent, and this raises the question whether and how bacteria can perform chemotaxis in a swarm. Here, by examining the chemotactic behavior as a function of the cell density, we showed that chemotaxis is surprisingly enhanced because of cell crowding in a bacterial swarm, and this enhancement is correlated with increase in the degree of cell body alignment. Cells tend to form clusters that move collectively in a swarm with increased effective run length, and we showed analytically that this resulted in increased drift velocity toward attractants. We also explained the enhancement by stochastically simulating bacterial chemotaxis in a swarm. We found that cell crowding in a swarm enhances chemotaxis if the cell-cell interactions used in the simulation induce cell-cell alignment, but it impedes chemotaxis if the interactions are collisions that randomize cell moving direction. Therefore, collective motion in a bacterial swarm enhances chemotaxis.

Multi-bit Boolean model for chemotactic drift of Escherichia coli

Dynamic biological systems can be modelled to an equivalent modular structure using Boolean networks (BNs) due to their simple construction and relative ease of integration. The chemotaxis network of the bacterium Escherichia coli (E. coli) is one of the most investigated biological systems. In this study, the authors developed a multi-bit Boolean approach to model the drifting behaviour of the E. coli chemotaxis system. Their approach, which is slightly different than the conventional BNs, is designed to provide finer resolution to mimic high-level functional behaviour. Using this approach, they simulated the transient and steady-state responses of the chemoreceptor sensory module. Furthermore, they estimated the drift velocity under conditions of the exponential nutrient gradient. Their predictions on chemotactic drifting are in good agreement with the experimental measurements under similar input conditions. Taken together, by simulating chemotactic drifting, they propose that multi-bit Boolean methodology can be used for modelling complex biological networks. Application of the method towards designing bio-inspired systems such as nano-bots is discussed.

A Multi-Scale Approach to Modeling E. coli Chemotaxis

The degree to which we can understand the multi-scale organization of cellular life is tied to how well our models can represent this organization and the processes that drive its evolution. This paper uses Vivarium-an engine for composing heterogeneous computational biology models into integrated, multi-scale simulations. Vivarium's approach is demonstrated by combining several sub-models of biophysical processes into a model of chemotactic E. coli that exchange molecules with their environment, express the genes required for chemotaxis, swim, grow, and divide. This model is developed incrementally, highlighting cross-compartment mechanisms that link E. coli to its environment, with models for: (1) metabolism and transport, with transport moving nutrients across the membrane boundary and metabolism converting them to useful metabolites, (2) transcription, translation, complexation, and degradation, with stochastic mechanisms that read real gene sequence data and consume base pairs and ATP to make proteins and complexes, and (3) the activity of flagella and chemoreceptors, which together support navigation in the environment.

Allosteric Priming of E. coli CheY by the Flagellar Motor Protein FliM

Phosphorylation of Escherichia coli CheY protein transduces chemoreceptor stimulation to a highly cooperative flagellar motor response. CheY binds to the N-terminal peptide of the FliM motor protein (FliM_N). Constitutively active D13K-Y106W CheY has been an important tool for motor physiology. The crystal structures of CheY and CheY ⋅ FliM_N with and without D13K-Y106W have shown FliM_N-bound CheY contains features of both active and inactive states. We used molecular dynamics (MD) simulations to characterize the CheY conformational landscape accessed by FliM_N and D13K-Y106W. Mutual information measures identified the central features of the long-range CheY allosteric network between D57 phosphorylation site and the FliM_N interface, namely the closure of the α4-β4 hinge and inward rotation of Y- or W106 with W58. We used hydroxy-radical foot printing with mass spectroscopy (XFMS) to track the solvent accessibility of these and other side chains. The solution XFMS oxidation rate correlated with the solvent-accessible area of the crystal structures. The protection of allosteric relay side chains reported by XFMS confirmed the intermediate conformation of the native CheY ⋅ FliM_N complex, the inactive state of free D13K-Y106W CheY, and the MD-based network architecture. We extended the MD analysis to determine temporal coupling and energetics during activation. Coupled aromatic residue rotation was a graded rather than a binary switch, with Y- or W106 side-chain burial correlated with increased FliM_N affinity. Activation entrained CheY fold stabilization to FliM_N affinity. The CheY network could be partitioned into four dynamically coordinated sectors. Residue substitutions mapped to sectors around D57 or the FliM_N interface according to phenotype. FliM_N increased sector size and interactions. These sectors fused between the substituted K13-W106 residues to organize a tightly packed core and novel surfaces that may bind additional sites to explain the cooperative motor response. The community maps provide a more complete description of CheY priming than proposed thus far.

Specific Root Exudate Compounds Sensed by Dedicated Chemoreceptors Shape Azospirillum brasilense Chemotaxis in the Rhizosphere

Plant roots shape the rhizosphere community by secreting compounds that recruit diverse bacteria. Colonization of various plant roots by the motile alphaproteobacterium Azospirillum brasilens e causes increased plant growth, root volume, and crop yield. Bacterial chemotaxis in this and other motile soil bacteria is critical for competitive colonization of the root surfaces. The role of chemotaxis in root surface colonization has previously been established by endpoint analyses of bacterial colonization levels detected a few hours to days after inoculation. More recently, microfluidic devices have been used to study plant-microbe interactions, but these devices are size limited. Here, we use a novel slide-in chamber that allows real-time monitoring of plant-microbe interactions using agriculturally relevant seedlings to characterize how bacterial chemotaxis mediates plant root surface colonization during the association of A. brasilens e with Triticum aestivum (wheat) and Medicago sativa (alfalfa) seedlings. We track A. brasilense accumulation in the rhizosphere and on the root surfaces of wheat and alfalfa. A. brasilense motile cells display distinct chemotaxis behaviors in different regions of the roots, including attractant and repellent responses that ultimately drive surface colonization patterns. We also combine these observations with real-time analyses of behaviors of wild-type and mutant strains to link chemotaxis responses to distinct chemicals identified in root exudates to specific chemoreceptors that together explain the chemotactic response of motile cells in different regions of the roots. Furthermore, the bacterial second messenger c-di-GMP modulates these chemotaxis responses. Together, these findings illustrate dynamic bacterial chemotaxis responses to rhizosphere gradients that guide root surface colonization.IMPORTANCE Plant root exudates play critical roles in shaping rhizosphere microbial communities, and the ability of motile bacteria to respond to these gradients mediates competitive colonization of root surfaces. Root exudates are complex chemical mixtures that are spatially and temporally dynamic. Identifying the exact chemical(s) that mediates the recruitment of soil bacteria to specific regions of the roots is thus challenging. Here, we connect patterns of bacterial chemotaxis responses and sensing by chemoreceptors to chemicals found in root exudate gradients and identify key chemical signals that shape root surface colonization in different plants and regions of the roots.

Aer Receptors Influence the Pseudomonas chlororaphis PCL1606 Lifestyle

Pseudomonas chlororaphis PCL1606 (PcPCL1606) is a rhizobacterium isolated from avocado roots, which is a favorable niche for its development. This strain extensively interacts with plant roots and surrounding microbes and is considered a biocontrol rhizobacterium. Genome sequencing has shown the presence of thirty-one potential methyl-accepting chemotaxis proteins (MCPs). Among these MCPs, two candidates are putative functional aerotaxis receptors, encoded at locus PCL1606_41090 (aer1-1) and locus PLC1606_20530 (aer1-2), that are homologous to the Aer receptor of Pseudomonas aeruginosa strain PaO1. Single- and double-deletion mutants in one or both genes have led to motility deficiencies in oxygen-rich areas, particularly reduced swimming motility compared with that of wildtype PcPCL1606. No differences in swarming tests were detected, and less adhesion by the aer double mutant was observed. However, the single and double mutants on avocado plant roots showed delayed biocontrol ability. During the first days of the biocontrol experiment, the aer-defective mutants also showed delayed root colonization. The current research characterizes the presence of aer transductors on P. chlororaphis. Thus, the functions of the PCL1606_41090 and PCL1606_20530 loci, corresponding to genes aer1-1 and aer1-2, respectively, are elucidated.

Cellular Stoichiometry of Chemotaxis Proteins in Sinorhizobium meliloti

Chemotaxis systems enable microbes to sense their immediate environment, moving toward beneficial stimuli and away from those that are harmful. In an effort to better understand the chemotaxis system of Sinorhizobium meliloti, a symbiont of the legume alfalfa, the cellular stoichiometries of all ten chemotaxis proteins in S. meliloti were determined. A combination of quantitative immunoblot and mass spectrometry revealed that the protein stoichiometries in S. meliloti varied greatly from those in Escherichia coli and Bacillus subtilis To compare protein ratios to other systems, values were normalized to the central kinase CheA. All S. meliloti chemotaxis proteins exhibited increased ratios to various degrees. The 10-fold higher molar ratio of adaptor proteins CheW1 and CheW2 to CheA might result in the formation of rings in the chemotaxis array that consist of only CheW instead of CheA and CheW in a 1:1 ratio. We hypothesize that the higher ratio of CheA to the main response regulator CheY2 is a consequence of the speed-variable motor in S. meliloti, instead of a switch-type motor. Similarly, proteins involved in signal termination are far more abundant in S. meliloti, which utilizes a phosphate sink mechanism based on CheA retrophosphorylation to inactivate the motor response regulator versus CheZ-catalyzed dephosphorylation as in E. coli and B. subtilis Finally, the abundance of CheB and CheR, which regulate chemoreceptor methylation, was increased compared to CheA, indicative of variations in the adaptation system of S. meliloti Collectively, these results mark significant differences in the composition of bacterial chemotaxis systems.IMPORTANCE The symbiotic soil bacterium Sinorhizobium meliloti contributes greatly to host-plant growth by fixing atmospheric nitrogen. The provision of nitrogen as ammonium by S. meliloti leads to increased biomass production of its legume host alfalfa and diminishes the use of environmentally harmful chemical fertilizers. To better understand the role of chemotaxis in host-microbe interaction, a comprehensive catalogue of the bacterial chemotaxis system is vital, including its composition, function, and regulation. The stoichiometry of chemotaxis proteins in S. meliloti has very few similarities to the systems in Escherichia coli and Bacillus subtilis In addition, total amounts of proteins are significantly lower. S. meliloti exhibits a chemotaxis system distinct from known models by incorporating new proteins as exemplified by the phosphate sink mechanism.

Taming the flagellar motor of pseudomonads with a nucleotide messenger

Pseudomonads rely on the flagellar motor to rotate a polar flagellum for swimming and swarming, and to sense surfaces for initiating the motile-to-sessile transition to adopt a surface-dwelling lifestyle. Deciphering the function and regulation of the flagellar motor is of paramount importance for understanding the behaviours of environmental and pathogenic pseudomonads. Recent studies disclosed the preeminent role played by the messenger c-di-GMP in controlling the real-time performance of the flagellar motor in pseudomonads. The studies revealed that c-di-GMP controls the dynamic exchange of flagellar stator units to regulate motor torque/speed and modulates the frequency of flagellar motor switching via the chemosensory signalling pathways. Apart from being a rotary motor, the flagellar motor is emerging as a mechanosensor that transduces surface-induced mechanical signals into an increase of cellular c-di-GMP concentration to initiate the cellular programs required for long-term colonization. Collectively, the studies generate long-awaited mechanistic insights into how c-di-GMP regulates bacterial motility and the motile-to-sessile transition. The new findings also raise the fundamental questions of how cellular c-di-GMP concentrations are dynamically coupled to flagellar output and the proton-motive force, and how c-di-GMP signalling is coordinated spatiotemporally to fine-tune flagellar response and the behaviour of pseudomonads in solutions and on surfaces.

Comparative Metagenome-Assembled Genome Analysis of "Candidatus Lachnocurva vaginae", Formerly Known as Bacterial Vaginosis-Associated Bacterium-1 (BVAB1)

Bacterial vaginosis-associated bacterium 1 (BVAB1) is an as-yet uncultured bacterial species found in the human vagina that belongs to the family Lachnospiraceae within the order Clostridiales. As its name suggests, this bacterium is often associated with bacterial vaginosis (BV), a common vaginal disorder that has been shown to increase a woman's risk for HIV, Chlamydia trachomatis, and Neisseria gonorrhoeae infections as well as preterm birth. BVAB1 has been further associated with the persistence of BV following metronidazole treatment, increased vaginal inflammation, and adverse obstetrics outcomes. There is no available complete genome sequence of BVAB1, which has made it difficult to mechanistically understand its role in disease. We present here a circularized metagenome-assembled genome (cMAG) of BVAB1 as well as a comparative analysis including an additional six metagenome-assembled genomes (MAGs) of this species. These sequences were derived from cervicovaginal samples of seven separate women. The cMAG was obtained from a metagenome sequenced with long-read technology on a PacBio Sequel II instrument while the others were derived from metagenomes sequenced on the Illumina HiSeq platform. The cMAG is 1.649 Mb in size and encodes 1,578 genes. We propose to rename BVAB1 to "Candidatus Lachnocurva vaginae" based on phylogenetic analyses, and provide genomic and metabolomic evidence that this candidate species may metabolize D-lactate, produce trimethylamine (one of the chemicals responsible for BV-associated odor), and be motile. The cMAG and the six MAGs are valuable resources that will further contribute to our understanding of the heterogeneous etiology of bacterial vaginosis.

Microfluidic techniques for separation of bacterial cells via taxis

The microbial environment is typically within a fluid and the key processes happen at the microscopic scale where viscosity dominates over inertial forces. Microfluidic tools are thus well suited to study microbial motility because they offer precise control of spatial structures and are ideal for the generation of laminar fluid flows with low Reynolds numbers at microbial lengthscales. These tools have been used in combination with microscopy platforms to visualise and study various microbial taxes. These include establishing concentration and temperature gradients to influence motility via chemotaxis and thermotaxis, or controlling the surrounding microenvironment to influence rheotaxis, magnetotaxis, and phototaxis. Improvements in microfluidic technology have allowed fine separation of cells based on subtle differences in motility traits and have applications in synthetic biology, directed evolution, and applied medical microbiology.

Sensing and Approaching Toxic Arsenate by Shewanella putrefaciens CN-32

Although arsenic at a high concentration imposes strong selective pressure on microbes, various microbes have been found to grow in As-rich environments. So far, little is known about how microbes can sense and move toward arsenate in the environment, and the underlying molecular mechanisms have not been revealed. Here, we report the chemotaxis response toward arsenate (As(V)) by Shewanella putrefaciens CN-32, a model dissimilatory metal-reducing bacterium (DMRB), and elucidate the mechanisms. We find that S. putrefaciens CN-32 exhibits a chemotactic behavior toward As(V) and diverse electron acceptors. To sense As(V), S. putrefaciens CN-32 requires functional arsenate respiratory reductase but does not depend on its metal-reducing-like respiratory pathway. We observe that such a sense is governed by an energy taxis mechanism and mediated by several methyl-accepting chemotaxis proteins (MCPs), rather than a specific MCP. Moreover, we reveal that the chemotactic signal transduction pathway is conserved in Shewanella, and histidine kinase and flagella-mediated motility are essential for taxis toward As(V). This work reverses the conventional view about arsenic as a chemotactic inhibitor to microbes by revealing the positive chemotaxis of Shewanella to As(V).

Regulation of the chemotaxis histidine kinase CheA: A structural perspective

Bacteria sense and respond to their environment through a highly conserved assembly of transmembrane chemoreceptors (MCPs), the histidine kinase CheA, and the coupling protein CheW, hereafter termed "the chemosensory array". In recent years, great strides have been made in understanding the architecture of the chemosensory array and how this assembly engenders sensitive and cooperative responses. Nonetheless, a central outstanding question surrounds how receptors modulate the activity of the CheA kinase, the enzymatic output of the sensory system. With a focus on recent advances, we summarize the current understanding of array structure and function to comment on the molecular mechanism by which CheA, receptors and CheW generate the high sensitivity, gain and dynamic range emblematic of bacterial chemotaxis. The complexity of the chemosensory arrays has motivated investigation with many different approaches. In particular, structural methods, genetics, cellular activity assays, nanodisc technology and cryo-electron tomography have provided advances that bridge length scales and connect molecular mechanism to cellular function. Given the high degree of component integration in the chemosensory arrays, we ultimately aim to understand how such networked molecular interactions generate a whole that is truly greater than the sum of its parts. This article is part of a Special Issue entitled: Molecular biophysics of membranes and membrane proteins.

Local applications but global implications: Can pesticides drive microorganisms to develop antimicrobial resistance?

Pesticides are an important agricultural input, and the introduction of new active ingredients with increased efficiencies drives their higher production and consumption worldwide. Inappropriate application and storage of these chemicals often contaminate plant tissues, air, water, or soil environments. The presence of pesticides can lead to developing tolerance, resistance or persistence and even the capabilities to degrade them by the microbiomes of theses environments. The pesticide-degrading microorganisms gain and employ several mechanisms for attraction (chemotaxis), membrane transport systems, efflux pumps, enzymes and genetical make-up with plasmid and chromosome encoded catabolic genes for degradation. Even the evolution and the mechanisms of inheritance for pesticide-degradation as a functional trait in several microorganisms are beginning to be understood. Because of the commonalities in the microbial responses of sensing and uptake, and adaptation due to the selection pressures of pesticides and antimicrobial substances including antibiotics, the pesticide-degraders have higher chances of possessing antimicrobial resistance as a surplus functional trait. This review critically examines the probabilities of pesticide contamination of soil and foliage, the knowledge gaps in the regulation and storage of pesticide chemicals, and the human implications of pesticide-degrading microorganisms with antimicrobial resistance in the global strategy of 'One Health'.

Run-and-tumble motion with steplike responses to a stochastic input

We study a simple run-and-tumble random walk whose switching frequencies between run mode and tumble mode depend on a stochastic signal. We consider a particularly sharp, steplike dependence, where the run-to-tumble switching probability jumps from zero to one as the signal crosses a particular value (say y_{1}) from below. Similarly, tumble-to-run switching probability also shows a jump like this as the signal crosses another value (y_{2}<y_{1}) from above. We are interested in characterizing the effect of signaling noise on the long-time behavior of the random walker. We consider two different time-evolutions of the stochastic signal. In one case, the signal dynamics is an independent stochastic process and does not depend on the run-and-tumble motion. In this case we can analytically calculate the mean value and the complete distribution function of the run duration and tumble duration. In the second case, we assume that the signal dynamics is influenced by the spatial location of the random walker. For this system, we numerically measure the steady state position distribution of the random walker. We discuss some similarities and differences between our system and Escherichia coli chemotaxis, which is another well-known run-and-tumble motion encountered in nature.

Intelligent Micro/nanomotors with Taxis

Micro/nanomotors (MNMs) are micro/nanoscale devices that can convert energy from their surroundings into autonomous motion. With this unique ability, they may revolutionize application fields ranging from active drug delivery to biological surgeries, environmental remediation, and micro/nanoengineering. To complete these applications, MNMs are required to have a vital capability to reach their destinations. Employing external fields to guide MNMs to the targets is common and effective way. However, in application scenarios where targets are generally unknown or dynamically change, MNMs must possess the capability of self-navigation or self-targeting. Taking advantage of tactic movements toward or away from signal sources, numerous intelligent MNMs with self-navigation or self-targeting have been demonstrated and attracted much attention during the past few years. In this Account, we elucidate the intelligent response mechanisms of such tactic MNMs, which are summarized as two main models. One is that local vector fields, including those of chemical concentration gradients, gravity, flows, and magnetic fields existing in systems, achieve the overall alignment of asymmetric MNMs via aligning torques, directing the MNMs to swim toward or away from the signal sources. Another is that isotropic MNMs may produce propulsion forces with direction solely determined by the local vector field regardless of their Brownian rotations. Then we discuss and highlight the recent progress in tactic MNMs, including chemotactic, phototactic, rheotactic, gravitactic, and magnetotactic motors. Artificial chemotactic MNMs can be designed with different morphologies and compositions if asymmetric reactions are associated with chemical concentration gradients. In these systems, asymmetric phoretic slip flows are induced, leading to torques that enable the anisotropic particles to align and exhibit chemotaxis. For phototactic MNMs, light irradiation establishes asymmetric fields surrounding the motors via light-induced chemical reactions or physical effects to generate phototactic motion. Shape-asymmetric MNMs reorient in natural fluid flows because of torques applied by the flows, inducing rheotactic movements. MNMs with either the centroid or magnetic components distributed asymmetrically maintain orientation under the torque triggered by gravity or magnetic forces, generating tactic motions. In the end, we envision the future development of synthetic tactic MNMs, including enhancement of the sensitivity of motors to target signals, increasing the diversity of chemical motor systems, and combining multiple mechanisms to endow the tactic motors with multiple functionality. By highlighting the current achievements and offering our perspective on tactic MNMs, we look forward to inspiring the emergence of the next generation of intelligent MNMs with taxis.

Chemotaxis by Pseudomonas putida (ATCC 17453) towards camphor involves cytochrome P450cam (CYP101A1)

The camphor-degrading microorganism, Pseudomonas putida strain ATCC 17453, is an aerobic, gram-negative soil bacterium that uses camphor as its sole carbon and energy source. The genes responsible for the catabolic degradation of camphor are encoded on the extra-chromosomal CAM plasmid. A monooxygenase, cytochrome P450_cam, mediates hydroxylation of camphor to 5-exo-hydroxycamphor as the first and committed step in the camphor degradation pathway, requiring a dioxygen molecule (O₂) from air. Under low O₂ levels, P450_cam catalyzes the production of borneol via an unusual reduction reaction. We have previously shown that borneol downregulates the expression of P450_cam. To understand the function of P450_cam and the consequences of down-regulation by borneol under low O₂ conditions, we have studied chemotaxis of camphor induced and non-induced P. putida strain ATCC 17453. We have tested camphor, borneol, oxidized camphor metabolites and known bacterial attractants (d)-glucose, (d) - and (l)-glutamic acid for their elicitation chemotactic behavior. In addition, we have used 1-phenylimidazole, a P450_cam inhibitor, to investigate if P450_cam plays a role in the chemotactic ability of P. putida in the presence of camphor. We found that camphor, a chemoattractant, became toxic and chemorepellent when P450_cam was inhibited. We have also evaluated the effect of borneol on chemotaxis and found that the bacteria chemotaxed away from camphor in the presence of borneol. This is the first report of the chemotactic behaviour of P. putida ATCC 17453 and the essential role of P450_cam in this process.

Sulfated vizantin suppresses mucin layer penetration dependent on the flagella motility of Pseudomonas aeruginosa PAO1

Pseudomonas aeruginosa is an opportunistic pathogen that causes severe infections, such as pneumonia and bacteremia. Several studies demonstrated that flagellar motility is an important virulence factor for P. aeruginosa infection. In this study, we determined whether sulfated vizantin affects P. aeruginosa flagellar motility in the absence of direct antimicrobial activity. We found that 100 μM sulfated vizantin suppressed P. aeruginosa PAO1 from penetrating through an artificial mucin layer by affecting flagellar motility, although it did not influence growth nor bacterial protease activity. To further clarify the mechanism in which sulfated vizantin suppresses the flagellar motility of P. aeruginosa PAO1, we examined the effects of sulfated vizantin on the composition of the flagellar filament and mRNA expression of several flagella-related genes, finding that sulfated vizantin did not influence the composition of the flagellar complex (fliC, motA, and motB) in P. aeruginosa PAO1, but significantly decreased mRNA expression of the chemotaxis-related genes cheR1, cheW, and cheZ. These results indicated that sulfated vizantin is an effective inhibitor of flagellar motility in P. aeruginosa.

Optimal methylation noise for best chemotactic performance of E. coli

In response to a concentration gradient of chemoattractant, E. coli bacterium modulates the rotational bias of flagellar motors which control its run-and-tumble motion, to migrate towards regions of high chemoattractant concentration. Presence of stochastic noise in the biochemical pathway of the cell has important consequences on the switching mechanism of motor bias, which in turn affects the runs and tumbles of the cell in a significant way. We model the intracellular reaction network in terms of coupled time evolution of three stochastic variables-kinase activity, methylation level, and CheY-P protein level-and study the effect of methylation noise on the chemotactic performance of the cell. In presence of a spatially varying nutrient concentration profile, a good chemotactic performance allows the cell to climb up the concentration gradient quickly and localize in the nutrient-rich regions in the long time limit. Our simulations show that the best performance is obtained at an optimal noise strength. While it is expected that chemotaxis will be weaker for very large noise, it is counterintuitive that the performance worsens even when noise level falls below a certain value. We explain this striking result by detailed analysis of CheY-P protein level statistics for different noise strengths. We show that when the CheY-P level falls below a certain (noise-dependent) threshold the cell tends to move down the concentration gradient of the nutrient, which has a detrimental effect on its chemotactic response. This threshold value decreases as noise is increased, and this effect is responsible for noise-induced enhancement of chemotactic performance. In a harsh chemical environment, when the nutrient degrades with time, the amount of nutrient intercepted by the cell trajectory is an effective performance criterion. In this case also, depending on the nutrient lifetime, we find an optimum noise strength when the performance is at its best.

Genetic and Physiological Adaptations of Marine Bacterium Pseudomonas stutzeri 273 to Mercury Stress

Mercury-mediated toxicity remains one of the greatest barriers against microbial survival, even though bacterial resistance to mercury compounds can occur. However, the genetic and physiological adaptations of bacteria to mercury stress still remains unclear. Here, we show that the marine bacterium Pseudomonas stutzeri 273 is resistant to 50 μM Hg²⁺ and removes up to 94% Hg²⁺ from culture. Using gene homologous recombination and complementation, we show that genes encoding Hg²⁺-transport proteins MerT, MerP, the mercuric reductase MerA and the regulatory protein MerD are essential for bacterial mercuric resistance when challenged with Hg²⁺. Further, mercury stress inhibits flagellar development, motility, chemotaxis and biofilm formation of P. stutzeri 273, which are verified by transcriptomic and physiological analyses. Surprisingly, we discover that MerF, a previously reported Hg²⁺-transporter, determines flagellar development, motility and biofilm formation in P. stutzeri 273 by genetic and physiological analyses. Our results strongly indicate that MerF plays an integral role in P. stutzeri 273 to develop physiological responses to mercury stress. Notably, MerF homologs are also prevalent in different human pathogens. Using this unique target may provide novel strategies to control these pathogenic bacteria, given the role of MerF in flagella and biofilm formation. In summary, our data provide an original report on MerF in bacterial physiological development and suggest that the mer in marine bacteria has evolved through progressive, sequential recruitment of novel functions over time.

Cellular Stoichiometry of Methyl-Accepting Chemotaxis Proteins in Sinorhizobium meliloti

The chemosensory system in Sinorhizobium meliloti has several important deviations from the widely studied enterobacterial paradigm. To better understand the differences between the two systems and how they are optimally tuned, we determined the cellular stoichiometry of the methyl-accepting chemotaxis proteins (MCPs) and the histidine kinase CheA in S. meliloti Quantitative immunoblotting was used to determine the total amount of MCPs and CheA per cell in S. meliloti The MCPs are present in the cell in high abundance (McpV), low abundance (IcpA, McpU, McpX, and McpW), and very low abundance (McpY and McpZ), whereas McpT was below the detection limit. The approximate cellular ratio of these three receptor groups is 300:30:1. The chemoreceptor-to-CheA ratio is 23.5:1, highly similar to that seen in Bacillus subtilis (23:1) and about 10 times higher than that in Escherichia coli (3.4:1). Different from E. coli, the high-abundance receptors in S. meliloti are lacking the carboxy-terminal NWETF pentapeptide that binds the CheR methyltransferase and CheB methylesterase. Using transcriptional lacZ fusions, we showed that chemoreceptors are positively controlled by the master regulators of motility, VisNR and Rem. In addition, FlbT, a class IIA transcriptional regulator of flagellins, also positively regulates the expression of most chemoreceptors except for McpT and McpY, identifying chemoreceptors as class III genes. Taken together, these results demonstrate that the chemosensory complex and the adaptation system in S. meliloti deviates significantly from the established enterobacterial paradigm but shares some similarities with B. subtilisIMPORTANCE The symbiotic soil bacterium Sinorhizobium meliloti is of great agricultural importance because of its nitrogen-fixing properties, which enhances growth of its plant symbiont, alfalfa. Chemotaxis provides a competitive advantage for bacteria to sense their environment and interact with their eukaryotic hosts. For a better understanding of the role of chemotaxis in these processes, detailed knowledge on the regulation and composition of the chemosensory machinery is essential. Here, we show that chemoreceptor gene expression in S. meliloti is controlled through the main transcriptional regulators of motility. Chemoreceptor abundance is much lower in S. meliloti than in Escherichia coli and Bacillus subtilis Moreover, the chemoreceptor-to-kinase CheA ratio is different from that of E. coli but similar to that of B. subtilis.

Low-temperature chemotaxis, halotaxis and chemohalotaxis by the psychrophilic marine bacterium Colwellia psychrerythraea 34H

A variety of ecologically important processes are driven by bacterial motility and taxis, yet these basic bacterial behaviours remain understudied in cold habitats. Here, we present a series of experiments designed to test the chemotactic ability of the model marine psychrophilic bacterium Colwellia psychrerythraea 34H, when grown at optimal temperature and salinity (8°C, 35 ppt) or its original isolation conditions (-1°C, 35 ppt), towards serine and mannose at temperatures from -8°C to 27°C (above its upper growth temperature of 18°C), and at salinities of 15, 35 and 55 ppt (at 8°C and -1°C). Results indicate that C. psychrerythraea 34H is capable of chemotaxis at all temperatures tested, with strongest chemotaxis at the temperature at which it was first grown, whether 8°C or -1°C. This model marine psychrophile also showed significant halotaxis towards 15 and 55 ppt solutions, as well as strong substrate-specific chemohalotaxis. We suggest that such patterns of taxis may enable bacteria to colonize sea ice, position themselves optimally within its extremely cold, hypersaline and temporally fluctuating microenvironments, and respond to various chemical signals therein.