A molecular clutch disables flagella in the Bacillus subtilis biofilm

The SinR·SlrR Heteromer Attenuates Transcription of a Long Operon of Flagellar Genes in Bacillus subtilis

During growth, Bacillus subtilis differentiates into subpopulations of motile individuals and non-motile chains, associated with dispersal and biofilm formation, respectively. The two cell types are dictated by the activity of the alternative sigma factor SigD encoded as the penultimate gene of the 27-kb long fla/che flagellar operon. The frequency of SigD-ON motile cells is increased by the heteromeric transcription factor SwrA·DegU that activates the fla/che promoter. Conversely, the frequency of motile cells is decreased by the heteromeric transcription factor SinR·SlrR, but the mechanism and location of inhibition is poorly understood. Here, using ChIP-Seq analysis, we determine the binding sites of the SinR·SlrR heteromer on the genome. We identified two sites within the fla/che operon that were necessary and sufficient to attenuate transcript abundance by causing premature termination upstream of the gene that encodes SigD. Thus, cell motility and the transition to biofilm formation depend on the expression of a long operon governed by two opposing heteromeric transcription factors that operate at two different stages of the transcription cycle. More broadly, our study serves as a model for transcription factors that control transcriptional elongation and the regulation of long operons in bacteria.

Delayed biofilm formation in non-motile uropathogenic Escherichia coli strain in static and dynamic growth conditions

Urinary tract infections associated with the placement of indwelling urinary catheters are a significant concern in hospital settings, as they are linked to an increased risk of severe infections and complications due to biofilm formation. These infections are primarily caused by uropathogens such as Escherichia coli (UPEC). UPEC possesses peritrichous flagella, which facilitates its motility, adhesion to surfaces, and biofilm formation. Understanding the development of UPEC communities is essential for developing effective treatment and eradication strategies. In this study, we characterized the biofilm formation of a clinical non-motile UPEC strain under both static and dynamic culture conditions that simulate the urinary catheter environment. We developed a dynamic culture system coupled with light sheet fluorescence microscopy (LSFM) to quantify the stages of biofilm formation over time. Our results demonstrate that flagella play a crucial role in the initial phase of biofilm formation. The non-motile strain exhibited a delay in the adhesion phase compared to motile strains but ultimately formed biofilms of similar volume during subsequent stages. These findings highlight the significance of flagella in dynamic biofilm formation models and provide valuable insights for modeling the evolution of bacterial communities in nosocomial environments using LSFM.

Nascent flagellar basal bodies are immobilized by rod assembly in Bacillus subtilis

Flagella are complex, trans-envelope nanomachines that localize in species-specific patterns on the cell surface. Here, we study the localization dynamics of the earliest stage of basal body formation in Bacillus subtilis using a fluorescent fusion to the C-ring protein FliM. We find that B. subtilis basal bodies do not exhibit dynamic subunit exchange and are largely stationary at steady state, consistent with flagellar assembly through the peptidoglycan (PG). However, rare mobile basal bodies were observed, and the prevalence of mobile basal bodies is elevated both early in basal body assembly and when the rod is mutated. Thus, basal body mobility is a precursor to patterning, and we propose that rod polymerization probes the PG superstructure for pores of sufficient diameter to permit rod transit. Furthermore, mutation of the rod disrupts basal body patterning in a way that phenocopies mutation of the cytoplasmic flagellar patterning protein FlhF. We infer that rod synthesis and the cytoplasmic regulators coordinate flagellar assembly by interpreting a grid-like pattern of pores, pre-existent in the PG.

IMPORTANCE

Bacteria insert flagella in a species-specific pattern on the cell body, but how patterns are achieved is poorly understood. In bacteria with a single polar flagellum, a marker protein localizes to the cell pole and nucleates the assembly of the flagellum at that site. Bacillus subtilis assembles ~25 basal bodies over the length of the cell in a grid-like pattern and lacks proteins required for their polar targeting. Here, we show that B. subtilis basal bodies are mobile soon after assembly and become immobilized when the flagellar rod transits the peptidoglycan (PG) wall. Moreover, defects in the flagellar rod lead to a more-random distribution of flagella and an increase in polar basal bodies. We conclude that the peritrichous patterning of flagella of B. subtilis is different from the polar patterning of other bacteria, and we infer that the B. subtilis rod probes the PG for holes that can accommodate the machine.

Protein Homeostasis Impairment Alters Phenotypic Heterogeneity of Biofilm Communities

Biofilms are highly organized, cooperating communities of microorganisms encased in a self-produced extracellular matrix, providing resilience against external stress such as antimicrobial agents and host defenses. A hallmark of biofilms is their phenotypic heterogeneity, which enhances the overall growth and survival of the community. In this study, we demonstrate that removing the dnaK and tig genes encoding the core molecular chaperones DnaK (Hsp70 homolog) and Trigger factor disrupted protein homeostasis in Bacillus subtilis and resulted in the formation of an extremely mucoid biofilm with aberrant architecture, compromised structural integrity, and altered phenotypic heterogeneity. These changes include a large reduction in the motile subpopulation and an overrepresentation of matrix producers and endospores. Overproduction of poly-γ-glutamic acid contributed crucially to the mucoid phenotype and aberrant biofilm architecture. Homeostasis impairment, triggered by elevated temperatures, in wild-type cells led to mucoid and aberrant biofilm phenotypes similar to those observed in strains lacking both dnaK and tig. Our findings show that disruption of protein homeostasis, whether due to the absence of molecular chaperones or because of environmental factors, severely changes biofilm features.

Decoding Bacterial Motility: From Swimming States to Patterns and Chemotactic Strategies

The bacterial flagellum serves as a crucial propulsion apparatus for motility and chemotaxis. Bacteria employ complex swimming patterns to perform essential biological tasks. These patterns involve transitions between distinct swimming states, driven by flagellar motor rotation, filament polymorphism, and variations in flagellar arrangement and configuration. Over the past two decades, advancements in fluorescence staining technology applied to bacterial flagella have led to the discovery of diverse bacterial movement states and intricate swimming patterns. This review provides a comprehensive overview of nano-filament observation methodologies, swimming states, swimming patterns, and the physical mechanisms underlying chemotaxis. These novel insights and ongoing research have the potential to inspire the design of innovative active devices tailored for operation in low-Reynolds-number environments.

Morphogenesis of bacterial cables in polymeric environments

Many bacteria live in polymeric fluids, such as mucus, environmental polysaccharides, and extracellular polymers in biofilms. However, laboratory studies typically focus on cells in polymer-free fluids. Here, we show that interactions with polymers shape a fundamental feature of bacterial life-how they proliferate in space in multicellular colonies. Using experiments, we find that when polymer is sufficiently concentrated, cells generically and reversibly form large serpentine "cables" as they proliferate. By combining experiments with biophysical theory and simulations, we demonstrate that this distinctive form of colony morphogenesis arises from an interplay between polymer-induced entropic attraction between neighboring cells and their hindered ability to diffusely separate from each other in a viscous polymer solution. Our work thus reveals a pivotal role of polymers in sculpting proliferating bacterial colonies, with implications for how they interact with hosts and with the natural environment, and uncovers quantitative principles governing colony morphogenesis in such complex environments.

Active Microrobots for Dual Removal of Biofilms via Chemical and Physical Mechanisms

Bacterial biofilms are complex multicellular communities that adhere firmly to solid surfaces. They are widely recognized as major threats to human health, contributing to issues such as persistent infections on medical implants and severe contamination in drinking water systems. As a potential treatment for biofilms, this work proposes two strategies: (i) light-driven ZnFe2O4 (ZFO)/Pt microrobots for photodegradation of biofilms and (ii) magnetically driven ZFO microrobots for mechanical removal of biofilms from surfaces. Magnetically driven ZFO microrobots were realized by synthesizing ZFO microspheres through a low-cost and large-scale hydrothermal synthesis, followed by a calcination process. Then, a Pt layer was deposited on the surface of the ZFO microspheres to break their symmetry, resulting in self-propelled light-driven Janus ZFO/Pt microrobots. Light-driven ZFO/Pt microrobots exhibited active locomotion under UV light irradiation and controllable motion in terms of "stop and go" features. Magnetically driven ZFO microrobots were capable of maneuvering precisely when subjected to an external rotating magnetic field. These microrobots could eliminate Gram-negative Escherichia coli (E. coli) biofilms through photogenerated reactive oxygen species (ROS)-related antibacterial properties in combination with their light-powered active locomotion, accelerating the mass transfer to remove biofilms more effectively in water. Moreover, the actuation of magnetically driven ZFO microrobots allowed for the physical disruption of biofilms, which represents a reliable alternative to photocatalysis for the removal of strongly anchored biofilms in confined spaces. With their versatile characteristics, the envisioned microrobots highlight a significant potential for biofilm removal with high efficacy in both open and confined spaces, such as the pipelines of industrial plants.

Flow-induced bending of flagella controls bacterial surface behavior

Bacteria engage in surface-specific behaviors that are assumed to be driven by biological signaling. However, surface behaviors could be controlled by mechanical reorientation of bacterial appendages. Here, we use microfluidics and flagellar labeling to discover how shear force bends flagella to control surface behavior of the human pathogen Pseudomonas aeruginosa. By imaging flagellar rotation and using mutants with paralyzed flagella, we establish that flagellar rotation promotes surface departure in host-relevant shear regimes. Our single-cell experiments reveal two distinct subpopulations in flow: cells with their flagellum positioned upstream and cells with their flagellum positioned downstream. Shear force bends upstream flagella around the cell and blocks rotation. In contrast, downstream flagella can continue to rotate after surface arrival. Cells with downstream flagella depart the surface more frequently than cells with upstream flagella, indicating how flow direction can determine bacterial cell fate on surfaces. Together, our results demonstrate how the geometric relationship between flow and cell appendages can generate subpopulations and control surface behaviors.

The SinR•SlrR heteromer attenuates transcription of a long operon of flagellar genes in Bacillus subtilis

During growth, Bacillus subtilis differentiates into subpopulations of motile individuals and non-motile chains, associated with dispersal and biofilm formation respectively. The two cell types are dictated by the activity of the alternative sigma factor SigD encoded as the penultimate gene of the 27 kb long fla/che flagellar operon. The frequency of SigD-ON motile cells is increased by the heteromeric transcription factor SwrA•DegU that activates the fla/che promoter. Conversely, the frequency of motile cells is decreased by the heteromeric transcription factor SinR•SlrR, but the mechanism and location of inhibition is poorly understood. Here, using ChIP-Seq analysis, we determine the binding sites of the SinR•SlrR heteromer on the genome. We identified two sites within the fla/che operon that were both necessary and sufficient to attenuate transcript abundance by causing premature termination upstream of the gene that encodes SigD. Thus, cell motility and the transition to biofilm formation depend on the expression of a long operon governed by two opposing heteromeric transcription factors that operate at two different stages of the transcription cycle. More broadly, our study serves as a model for transcription factors that control transcriptional elongation and the regulation of long operons in bacteria.

Flagellar rotation facilitates the transfer of a bacterial conjugative plasmid

Conjugation-mediated DNA delivery is the primary mode for antibiotic resistance spread in bacteria; yet, molecular mechanisms regulating the conjugation process remain largely unexplored. While conjugative plasmids typically require bacterial attachment to solid surfaces for facilitation of donor-to-recipient proximity, the pLS20 conjugative plasmid, prevalent among Gram-positive Bacillus spp., uniquely requires fluid environments to enhance its transfer. Here, we show that pLS20, carried by Bacillus subtilis, induces multicellular clustering, which can accommodate various species, hence offering a stable platform for DNA delivery in a liquid milieu. We further discovered that induction of pLS20 promoters, governing crucial conjugative genes, is dependent on the presence of donor cell flagella, the major bacterial motility organelle. Moreover, the pLS20 regulatory circuit is controlled by a mechanosensing signal transduction pathway responsive to flagella rotation, thus activating conjugation gene expression exclusively during the host motile phase. This flagella-conjugation coupling strategy may allow the dissemination of the plasmid to remote destinations, allowing infiltration into new niches.

Harnessing microbial biofilms in soil ecosystems: Enhancing nutrient cycling, stress resilience, and sustainable agriculture

Soil ecosystems are complex networks of microorganisms that play pivotal roles in nutrient cycling, stress resilience, and the provision of ecosystem services. Among these microbial communities, soil biofilms, and complex aggregations of microorganisms embedded within extracellular polymeric substances (EPS) exert significant influence on soil health and function. This review delves into the dynamics of soil biofilms, highlighting their structural intricacies and the mechanisms by which they facilitate nutrient cycling, and discusses how biofilms enhance the degradation of pollutants through the action of extracellular enzymes and horizontal gene transfer, contributing to soil detoxification and fertility. Furthermore, the role of soil biofilms in stress resilience is underscored, as they form symbiotic relationships with plants, bolstering their growth and resistance to environmental stressors. The review also explores the ecological functions of biofilms in enhancing soil structure stability by promoting aggregate formation, which is crucial for water retention and aeration. By integrating these insights, we aim to provide a comprehensive understanding of the multifaceted benefits of biofilms in soil ecosystems. This knowledge is essential for developing strategies to manipulate soil biofilms to improve agricultural productivity and ecological sustainability. This review also identifies research gaps and emphasizes the need for practical applications of biofilms in sustainable agriculture.

Molecular mechanism of flagellar motor rotation arrest in bacterial zoospores of Actinoplanes missouriensis before germination

Zoospores of the filamentous actinomycete Actinoplanes missouriensis swim vigorously using flagella and stop swimming to initiate germination in response to nutrient exposure. However, the molecular mechanisms underlying swimming cessation remain unknown. A protein (FtgA) of unknown function encoded by a chemotaxis gene cluster (che cluster-1) was found to be required for flagellar rotation arrest; the zoospores of ftgA-knockout mutants kept swimming awkwardly after germination. An ftgA-overexpressing strain exhibited a non-flagellated phenotype. Isolation of a suppressor strain from this strain and further in vivo experiments revealed that the extended N-terminal region of FliN, a component of the C-ring of the flagellar basal body, was involved in the function of FtgA; FliN-P101S canceled the flagellar rotation arrest by FtgA, as well as the negative effect of ftgA-overexpression on flagellation. Furthermore, bacterial two-hybrid assays suggested that FtgA interacted not only with the C-terminal core region of FliN but also with chemotaxis regulatory proteins CheA1 and CheW1-2, which are encoded by che cluster-1. We propose the following working model of motility regulation in A. missouriensis zoospores: the chemotaxis sensory complex initially captures FtgA to allow zoospores to swim and then releases FtgA to stop flagellar rotation (i.e., swimming) in response to external nutrient signals.

Flagellar point mutation causes social aggregation in laboratory-adapted Bacillus subtilis under conditions that promote swimming

Motility allows microbes to explore and maximize success in their environment; however, many laboratory bacterial strains have a reduced or altered capacity for motility. Swimming motility in Bacillus subtilis depends on peritrichous flagella and is carried out individually as cells move by biased random walks toward attractants. Previously, we adapted Bacillus subtilis strain 3610 to the laboratory for 300 generations in lysogeny broth (LB) batch culture and isolated lab-adapted strains. Strain SH2 is motility-defective and in broth culture forms large, frequently spherical aggregates of cells. A single point mutation in the flagellin gene hag that causes amino acid 259 to switch from A to T is necessary and sufficient to cause these social cell aggregates, and aggregation occurs between flagellated cells bearing this point mutation regardless of the strain background. Cells associate when bearing this mutation, but flagellar rotation is needed to pull associating cells into spherical aggregates. Using electron microscopy, we are able to show that the SH2 flagellar filament has limited polymorphism when compared to other flagellar structures. This limited polymorphism hinders the flagellum's ability to function as a motility apparatus but appears to alter its function to that of cell aggregation/adhesion. We speculate that the genotype-specific aggregation of cells producing HagA259T flagella could have increased representation in a batch-culture experiment by allowing similar cells to go through a transfer together and also that this mutation could serve as an early step to evolve sociality in the natural world.IMPORTANCEThe first life forms on this planet were prokaryotic, and the earliest environments were aquatic, and from these relatively simple starting conditions, complex communities of microbes and ultimately multicellular organisms were able to evolve. Usually, motile cells in aqueous environments swim as individuals but become social by giving up motility and secreting extracellular substances to become a biofilm. Here, we identify a single point mutation in the flagellum that is sufficient to allow cells containing this mutation to specifically form large, suspended groups of cells. The specific change in the flagellar filament protein subunits causes a unique change in the flagellar structure. This could represent a distinct way for closely related cells to associate as an early precursor to sociality.

Antibacterial effects and mechanisms of quercetin-β-cyclodextrin complex mediated photodynamic on Escherichia coli O157:H7

Quercetin is a natural flavonoid with antioxidant, anti-inflammatory, and antibacterial properties. This work aimed to formulate quercetin-cyclodextrin microcapsules (QT-β-CD) while examining their photodynamic antibacterial effects and underlying mechanisms in detail. Characterization of the QT-β-CD was conducted using Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), and thermogravimetric analysis (TGA). The bacteriostatic effects of UV-A irradiation on Escherichia coli O157:H7 (E. coli O157:H7) were investigated. The photodynamic impact of QT-β-CD was assessed by analyzing hydrogen peroxide (H₂O₂) production. The antimicrobial activity was further elucidated through examinations of cell membrane integrity, protein damage, changes in cellular motility, biofilm formation, and extracellular polysaccharide reduction. The effect of QT-β-CD on LuxS and motA gene expression in E. coli O157:H7 was investigated by RT-qPCR. The findings demonstrated that QT-β-CD exhibited potent photodynamic properties and functioned as an efficient photosensitizer, causing substantial damage to E. coli O157:H7 cells. These results underscore the potential of quercetin as an antimicrobial agent for food preservation.

Motile bacteria crossing liquid-liquid interfaces of an aqueous isotropic-nematic coexistence phase

In nature, bacteria often swim in complex fluids, but our understanding of the interactions between bacteria and complex surroundings is still evolving. In this work, rod-like Bacillus subtilis swims in a quasi-2D environment with aqueous liquid-liquid interfaces, i.e., the isotropic-nematic coexistence phase of an aqueous chromonic liquid crystal. Focusing on the bacteria motion near and at the liquid-liquid interfaces, we collect and quantify bacterial trajectories ranging across the isotropic to the nematic phase. Despite its small magnitude, the interfacial tension of the order of 10 μN m-1 at the isotropic-nematic interface justifies our observations that bacteria swimming more perpendicular to the interface have a higher probability of crossing the interface. Our force-balance model, considering the interfacial tension, further predicts how the length and speed of the bacteria affect their crossing behaviors. Investigating how a phase change affects bacterial motion, we also find, as soon as the bacteria cross the interface and enter the nematic phase, they wiggle less, but faster, and that this occurs as the flagellar bundles aggregate within the nematic phase. Given the ubiquity of multi-phases in biological environments, our findings will help to understand active transport across various phases.

The swimming defect caused by the absence of the transcriptional regulator LdtR in Sinorhizobium meliloti is restored by mutations in the motility genes motA and motS

The flagellar motor is a powerful macromolecular machine used to propel bacteria through various environments. We determined that flagellar motility of the alpha-proteobacterium Sinorhizobium meliloti is nearly abolished in the absence of the transcriptional regulator LdtR, known to influence peptidoglycan remodeling and stress response. LdtR does not regulate motility gene transcription. Remarkably, the motility defects of the ΔldtR mutant can be restored by secondary mutations in the motility gene motA or a previously uncharacterized gene in the flagellar regulon, which we named motS. MotS is not essential for S. meliloti motility and may serve an accessory role in flagellar motor function. Structural modeling predicts that MotS comprised an N-terminal transmembrane segment, a long-disordered region, and a conserved β-sandwich domain. The C terminus of MotS is localized in the periplasm. Genetics based substitution of MotA with MotAG12S also restored the ΔldtR motility defect. The MotAG12S variant protein features a local polarity shift at the periphery of the MotAB stator units. We propose that MotS may be required for optimal alignment of stators in wild-type flagellar motors but becomes detrimental in cells with altered peptidoglycan. Similarly, the polarity shift in stator units composed of MotB/MotAG12S might stabilize its interaction with altered peptidoglycan.

A magnetically powered nanomachine with a DNA clutch

Machines found in nature and human-made machines share common components, such as an engine, and an output element, such as a rotor, linked by a clutch. This clutch, as seen in biological structures such as dynein, myosin or bacterial flagellar motors, allows for temporary disengagement of the moving parts from the running engine. However, such sophistication is still challenging to achieve in artificial nanomachines. Here we present a spherical rotary nanomotor with a reversible clutch system based on precise molecular recognition of built-in DNA strands. The clutch couples and decouples the engine from the machine's rotor in response to encoded inputs such as DNA or RNA. The nanomotor comprises a porous nanocage as a spherical rotor to confine the magnetic engine particle within the nanospace (∼0.004 μm3) of the cage. Thus, the entropically driven irreversible disintegration of the magnetic engine and the spherical rotor during the disengagement process is eliminated, and an exchange of microenvironmental inputs is possible through the nanopores. Our motor is only 200 nm in size and the clutch-mediated force transmission powered by an embedded ferromagnetic nanocrystal is high enough (∼15.5 pN at 50 mT) for the in vitro mechanical activation of Notch and integrin receptors, demonstrating its potential as nano-bio machinery.

Morphogenesis of bacterial colonies in polymeric environments

Many bacteria live in polymeric fluids, such as mucus, environmental polysaccharides, and extracellular polymers in biofilms. However, lab studies typically focus on cells in polymer-free fluids. Here, we show that interactions with polymers shape a fundamental feature of bacterial life-how they proliferate in space in multicellular colonies. Using experiments, we find that when polymer is sufficiently concentrated, cells generically and reversibly form large serpentine "cables" as they proliferate. By combining experiments with biophysical theory and simulations, we demonstrate that this distinctive form of colony morphogenesis arises from an interplay between polymer-induced entropic attraction between neighboring cells and their hindered ability to diffusely separate from each other in a viscous polymer solution. Our work thus reveals a pivotal role of polymers in sculpting proliferating bacterial colonies, with implications for how they interact with hosts and with the natural environment, and uncovers quantitative principles governing colony morphogenesis in such complex environments.

From isotopically labeled DNA to fluorescently labeled dynamic pili: building a mechanistic model of DNA transport to the cytoplasmic membrane

SUMMARYNatural competence, the physiological state wherein bacteria produce proteins that mediate extracellular DNA transport into the cytosol and the subsequent recombination of DNA into the genome, is conserved across the bacterial domain. DNA must successfully translocate across formidable permeability barriers during import, including the cell membrane(s) and the cell wall, that are normally impermeable to large DNA polymers. This review will examine the mechanisms underlying DNA transport from the extracellular space to the cytoplasmic membrane. First, the challenges inherent to DNA movement through the cell periphery will be discussed to provide context for DNA transport during natural competence. The following sections will trace the development of a comprehensive model for DNA translocation to the cytoplasmic membrane, highlighting the crucial studies performed over the last century that have contributed to building contemporary DNA import models. Finally, this review will conclude by reflecting on what is still unknown about the process and the possible solutions to overcome these limitations.

Abietic Acid as a Novel Agent against Ocular Biofilms: An In Vitro and Preliminary In Vivo Investigation

Biofilm-related ocular infections can lead to vision loss and are difficult to treat with antibiotics due to challenges with application and increasing microbial resistance. In turn, the design and testing of new synthetic drugs is a time- and cost-consuming process. Therefore, in this work, for the first time, we assessed the in vitro efficacy of the plant-based abietic acid molecule, both alone and when introduced to a polymeric cellulose carrier, against biofilms formed by Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans in standard laboratory settings as well as in a self-designed setting using the topologically challenging surface of the artificial eye. These analyses were performed using the standard microdilution method, the biofilm-oriented antiseptic test (BOAT), a modified disk-diffusion method, and eyeball models. Additionally, we assessed the cytotoxicity of abietic acid against eukaryotic cell lines and its anti-staphylococcal efficacy in an in vivo model using Galleria mellonella larvae. We found that abietic acid was more effective against Staphylococcus than Pseudomonas (from two to four times, depending on the test applied) and that it was generally more effective against the tested bacteria (up to four times) than against the fungus C. albicans at concentrations non-cytotoxic to the eukaryotic cell lines and to G. mellonella (256 and 512 µg/mL, respectively). In the in vivo infection model, abietic acid effectively prevented the spread of staphylococcus throughout the larvae organisms, decreasing their lethality by up to 50%. These initial results obtained indicate promising features of abietic acid, which may potentially be applied to treat ocular infections caused by pathogenic biofilms, with higher efficiency manifested against bacterial than fungal biofilms.

Viscosity-dependent determinants of Campylobacter jejuni impacting the velocity of flagellar motility

IMPORTANCE

Bacteria can adapt flagellar motor output in response to the load that the extracellular milieu imparts on the flagellar filament to enable propulsion. Bacteria can adapt flagellar motor output in response to the load that the extracellular milieu imparts on the flagellar filament to enable propulsion through diverse environments. These changes may involve increasing power and torque in high-viscosity environments or reducing power and flagellar rotation upon contact with a surface. C. jejuni swimming velocity in low-viscosity environments is comparable to other bacterial flagellates and increases significantly as external viscosity increases. In this work, we provide evidence that the mechanics of the C. jejuni flagellar motor has evolved to naturally promote high swimming velocity in high-viscosity environments. We found that C. jejuni produces VidA and VidB as auxiliary proteins to specifically affect flagellar motor activity in low viscosity to reduce swimming velocity. Our findings provide some of the first insights into different mechanisms that exist in bacteria to alter the mechanics of a flagellar motor, depending on the viscosity of extracellular environments.

The common origin and degenerative evolution of flagella in Actinobacteria

IMPORTANCE

Flagellar motility plays an important role in the environmental adaptation of bacteria and is found in more than 50% of known bacterial species. However, this important characteristic is sparsely distributed within members of the phylum Actinobacteria, which constitutes one of the largest bacterial groups. It is unclear why this important fitness organelle is absent in most actinobacterial species and the origin of flagellar genes in other species. Here, we present detailed analyses of the evolution of flagellar genes in Actinobacteria, in conjunction with the ecological distribution and cell biological features of major actinobacterial lineages, and the co-evolution of signal transduction systems. The results presented in addition to clarifying the puzzle of sporadic distribution of flagellar motility in Actinobacteria, also provide important insights into the evolution of major lineages within this phylum.

FlgV forms a flagellar motor ring that is required for optimal motility of Helicobacter pylori

Flagella-driven motility is essential for Helicobacter pylori to colonize the human stomach, where it causes a variety of diseases, including chronic gastritis, peptic ulcer disease, and gastric cancer. H. pylori has evolved a high-torque-generating flagellar motor that possesses several accessories not found in the archetypical Escherichia coli motor. FlgV was one of the first flagellar accessory proteins identified in Campylobacter jejuni, but its structure and function remain poorly understood. Here, we confirm that deletion of flgV in H. pylori B128 and a highly motile variant of H. pylori G27 (G27M) results in reduced motility in soft agar medium. Comparative analyses of in-situ flagellar motor structures of wild-type, ΔflgV, and a strain expressing FlgV-YFP showed that FlgV forms a ring-like structure closely associated with the junction of two highly conserved flagellar components: the MS and C rings. The results of our studies suggest that the FlgV ring has adapted specifically in Campylobacterota to support the assembly and efficient function of the high-torque-generating motors.

PlzD modifies Vibrio vulnificus foraging behavior and virulence in response to elevated c-di-GMP

IMPORTANCE

Many free-swimming bacteria propel themselves through liquid using rotary flagella, and mounting evidence suggests that the inhibition of flagellar rotation initiates biofilm formation, a sessile lifestyle that is a nearly universal surface colonization paradigm in bacteria. In general, motility and biofilm formation are inversely regulated by the intracellular second messenger bis-(3´-5´)-cyclic dimeric guanosine monophosphate (c-di-GMP). Here, we identify a protein, PlzD, bearing a conserved c-di-GMP binding PilZ domain that localizes to the flagellar pole in a c-di-GMP-dependent manner and alters the foraging behavior, biofilm, and virulence characteristics of the opportunistic human pathogen, Vibrio vulnificus. Our data suggest that PlzD interacts with components of the flagellar stator to decrease bacterial swimming speed and changes in swimming direction, and these activities are enhanced when cellular c-di-GMP levels are elevated. These results reveal a physical link between a second messenger (c-di-GMP) and an effector (PlzD) that promotes transition from a motile to a sessile state in V. vulnificus.

Pectic homogalacturonan sensed by Bacillus acts as host associated cue to promote establishment and persistence in the rhizosphere

Bacillus velezensis isolates are among the most promising plant-associated beneficial bacteria used as biocontrol agents. However, various aspects of the chemical communication between the plant and these beneficials, determining root colonization ability, remain poorly described. Here we investigated the molecular basis of such interkingdom interaction occurring upon contact between Bacillus velezensis and its host via the sensing of pectin backbone homogalacturonan (HG). We showed that B. velezensis stimulates key developmental traits via a dynamic process involving two conserved pectinolytic enzymes. This response integrates transcriptional changes leading to the switch from planktonic to sessile cells, a strong increase in biofilm formation, and an accelerated sporulation dynamics while conserving the potential to efficiently produce specialized secondary metabolites. As a whole, we anticipate that this response of Bacillus to cell wall-derived host cues contributes to its establishment and persistence in the competitive rhizosphere niche and ipso facto to its activity as biocontrol agent.

Real-Time Deduction of Mechanisms and Kinetics Underlying Photocatalytic Water Disinfection: Cell Motility and Particle Tracking

The current methods used to study photocatalysis-assisted water disinfection at a laboratory scale may not lead to process scale-up for large-scale implementation. These methods do not capture the process complexity and address all the factors underlying disinfection kinetics, including the physical characteristics (e.g., shape and size) of the photocatalyst, the light intensity, the form of the catalyst (e.g., free-floating and immobilized), and the photocatalyst-microorganism interaction mode (e.g., collision mode and constant contact mode). This drawback can be overcome using in situ methods to track the interaction between the photocatalysts and the microorganisms (e.g., Escherichia coli) and thereby engineering the resulting disinfection kinetics. Contextually, this study employed microscopy and particle-tracking algorithms to quantify in situ cell motility of E. coli undergoing titanium dioxide (TiO2) nanowire-assisted photocatalysis, which was observed to correlate with cell viability closely. This experimentation also informed that the E. coli bacterium interacted with the photocatalysts through collisions (without sustained contact), which allowed for phenomenological modeling of the observed first-order kinetics of E. coli inactivation. Addition of fluorescent-tagging assays to microscopy revealed that cell membrane integrity loss is the primary mode of bacterial inactivation. This methodology is independent of the microorganism or the photocatalyst type and hence is expected to be beneficial for engineering disinfection kinetics.

Mechanobiology as a tool for addressing the genotype-to-phenotype problem in microbiology

The central hypothesis of the genotype-phenotype relationship is that the phenotype of a developing organism (i.e., its set of observable attributes) depends on its genome and the environment. However, as we learn more about the genetics and biochemistry of living systems, our understanding does not fully extend to the complex multiscale nature of how cells move, interact, and organize; this gap in understanding is referred to as the genotype-to-phenotype problem. The physics of soft matter sets the background on which living organisms evolved, and the cell environment is a strong determinant of cell phenotype. This inevitably leads to challenges as the full function of many genes, and the diversity of cellular behaviors cannot be assessed without wide screens of environmental conditions. Cellular mechanobiology is an emerging field that provides methodologies to understand how cells integrate chemical and physical environmental stress and signals, and how they are transduced to control cell function. Biofilm forming bacteria represent an attractive model because they are fast growing, genetically malleable and can display sophisticated self-organizing developmental behaviors similar to those found in higher organisms. Here, we propose mechanobiology as a new area of study in prokaryotic systems and describe its potential for unveiling new links between an organism's genome and phenome.

Spatial transcriptome uncovers rich coordination of metabolism in E. coli K12 biofilm

Microbial communities often display region-specific properties, which give rise to complex interactions and emergent behaviors that are critical to the homeostasis and stress response of the communities. However, systems-level understanding of these properties still remains elusive. In this study, we established RAINBOW-seq and profiled the transcriptome of Escherichia coli biofilm communities with high spatial resolution and high gene coverage. We uncovered three modes of community-level coordination, including cross-regional resource allocation, local cycling and feedback signaling, which were mediated by strengthened transmembrane transport and spatially specific activation of metabolism. As a consequence of such coordination, the nutrient-limited region of the community maintained an unexpectedly high level of metabolism, enabling it to express many signaling genes and functionally unknown genes with potential sociality functions. Our work provides an extended understanding of the metabolic interplay in biofilms and presents a new approach of investigating complex interactions in bacterial communities on the systems level.

Flagellar brake protein YcgR interacts with motor proteins MotA and FliG to regulate the flagellar rotation speed and direction

In E. coli and related species, flagellar brake protein YcgR responds to the elevated intracellular c-di-GMP, decreases the flagellar rotation speed, causes a CCW rotation bias, and regulates bacterial swimming. Boehm et al. suggested that c-di-GMP-activated YcgR directly interacted with the motor protein MotA to curb flagellar motor output. Paul et al. proposed that YcgR disrupted the organization of the FliG C-terminal domain to bias the flagellar rotation. The target proteins are controversial, and the role of motor proteins remains unclear in flagellar rotation speed and direction regulation by YcgR. Here we assayed the motor proteins' affinity via a modified FRET biosensor and accessed the role of those key residue via bead assays. We found that YcgR could interact with both MotA and FliG, and the affinities could be enhanced upon c-di-GMP binding. Furthermore, residue D54 of YcgR-N was needed for FliG binding. The mutation of the FliG binding residue D54 or the MotA binding ones, F117 and E232, restored flagellar rotation speed in wild-type cells and cells lacking chemotaxis response regulator CheY that switched the flagellar rotation direction and decreased the CCW ratio in wild-type cells. We propose that c-di-GMP-activated YcgR regulated the flagellar rotation speed and direction via its interaction with motor proteins MotA and FliG. Our work suggest the role of YcgR-motor proteins interaction in bacterial swimming regulation.

Bacterial Proprioception: Can a Bacterium Sense Its Movement?

The evolution of the bacterial flagellum gave rise to motility and repurposing of a signaling network, now termed the chemotaxis network, enabled biasing of cell movements. This made it possible for the bacterium to seek out favorable chemical environments. To enable chemotaxis, the chemotaxis network sensitively detects extracellular chemical stimuli and appropriately modulates flagellar functions. Additionally, the flagellar motor itself is capable of detecting mechanical stimuli and adapts its structure and function in response, likely triggering a transition from planktonic to surface-associated lifestyles. Recent work has shown a link between the flagellar motor's response to mechanical stimuli and the chemotactic output. Here, we elaborate on this link and discuss how it likely helps the cell sense and adapt to changes in its swimming speeds in different environments. We discuss the mechanism whereby the motor precisely tunes its chemotaxis output under different mechanical loads, analogous to proprioception in higher order organisms. We speculate on the roles bacterial proprioception might play in a variety of phenomena including the transition to surface-associated lifestyles such as swarming and biofilms.

Identification of Genes Required for Swarming Motility in Bacillus subtilis Using Transposon Mutagenesis and High-Throughput Sequencing (TnSeq)

Bacillus subtilis exhibits swarming motility, a flagellar-mediated form of surface motility. Here, we use transposon mutagenesis and sequencing (TnSeq) to perform a high-throughput screen for candidate genes required for swarming. The TnSeq approach identified all of the known genes required for flagellar biosynthesis and nearly all of the previously reported regulators that promote swarming. Moreover, we identified an additional 36 genes that improve swarming and validated them individually. Among these, two mutants with severe defects were recovered, including fliT, required for flagellar biosynthesis, and a gene of unknown function, yolB, whose defect could not be attributed to a lack of flagella. In addition to discovering additional genes required for B. subtilis swarming, our work validates TnSeq as a powerful approach for comprehensively identifying genes important for nonessential processes such as colony expansion on plates. IMPORTANCE In TnSeq, transposons are randomly inserted throughout the chromosome at a population level, but insertions that disrupt genes of essential function cause strains that carry them to fall out of the population and appear underrepresented at the sequence level. Here, we apply TnSeq to the nonessential phenotype of motility in B. subtilis and spatially select for cells proficient in swarming. We find that insertions in nearly all genes previously identified as required for swarming are underrepresented in TnSeq analysis, and we identify 36 additional genes that enhance swarming. We demonstrate that TnSeq is a powerful tool for the genetic analysis of motility and likely other nonlethal screens for which enrichment is strong.

Experimental evolution of Bacillus subtilis on Arabidopsis thaliana roots reveals fast adaptation and improved root colonization

Bacillus subtilis is known to promote plant growth and protect plants against disease. B. subtilis rapidly adapts to Arabidopsis thaliana root colonization, as evidenced by improved root colonizers already after 12 consecutive transfers between seedlings in a hydroponic setup. Re-sequencing of single evolved isolates and endpoint populations revealed mutations in genes related to different bacterial traits, in accordance with evolved isolates displaying increased root colonization associated with robust biofilm formation in response to the plant polysaccharide xylan and impaired motility. Interestingly, evolved isolates suffered a fitness disadvantage in a non-selective environment, demonstrating an evolutionary cost of adaptation to the plant root. Finally, increased root colonization by an evolved isolate was also demonstrated in the presence of resident soil microbes. Our findings highlight how a plant growth-promoting rhizobacterium rapidly adapts to an ecologically relevant environment and reveal evolutionary consequences that are fundamental to consider when evolving strains for biocontrol purposes.

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Bacillus subtilis shows fast adaptation to Arabidopsis thaliana roots in a hydroponic setup

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Evolved isolates exhibit robust biofilms in response to xylan and impaired motility

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Adaptation to A. thaliana roots is accompanied by an evolutionary cost

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An evolved isolate shows higher root colonization in the presence of soil bacteria

Biophysical aspects underlying the swarm to biofilm transition

Bacteria organize in a variety of collective states, from swarming-rapid surface exploration, to biofilms-highly dense immobile communities attributed to stress resistance. It has been suggested that biofilm and swarming are oppositely controlled, making this transition particularly interesting for understanding the ability of bacterial colonies to adapt to challenging environments. Here, the swarm to biofilm transition is studied in Bacillus subtilis by analyzing the bacterial dynamics both on the individual and collective scales. We show that both biological and physical processes facilitate the transition. A few individual cells that initiate the biofilm program cause nucleation of large, approximately scale-free, stationary aggregates of trapped swarm cells. Around aggregates, cells continue swarming almost unobstructed, while inside, trapped cells are added to the biofilm. While our experimental findings rule out previously suggested purely physical effects as a trigger for biofilm formation, they show how physical processes, such as clustering and jamming, accelerate biofilm formation.

Putative functions of EpsK in teichuronic acid synthesis and phosphate starvation in Bacillus licheniformis

Extracellular polymeric substances (EPSs) are extracellular macromolecules in bacteria, which function in cell growth and show potential for mechanism study and biosynthesis application. However, the biosynthesis mechanism of EPS is still not clear. We herein chose Bacillus licheniformis CGMCC 2876 as a target strain to investigate the EPS biosynthesis. epsK, a member of eps cluster, the predicted polysaccharide synthesis cluster, was overexpressed and showed that the overexpression of epsK led to a 26.54% decrease in the production of EPS and resulted in slenderer cell shape. Transcriptome analysis combined with protein-protein interactions analysis and protein modeling revealed that epsK was likely responsible for the synthesis of teichuronic acid, a substitute cell wall component of teichoic acid when the strain was suffering phosphate limitation. Further cell cultivation showed that either phosphate limitation or the overexpression of teichuronic acid synthesis genes, tuaB and tuaE could similarly lead to EPS reduction. The enhanced production of teichuronic acid induced by epsK overexpression triggered the endogenous phosphate starvation, resulting in the decreased EPS synthesis and biomass, and the enhanced bacterial chemotaxis. This study presents an insight into the mechanism of EPS synthesis and offers the potential in controllable synthesis of target products.

Dynamic Hybrid Flagellar Motors-Fuel Switch and More

Flagellar motors are intricate rotating nanomachines that are powered by transmembrane ion gradients. The stator complexes are the powerhouses of the flagellar motor: They convert a transmembrane ion gradient, mainly of H⁺ or Na⁺, into rotation of the helical flagellar filament. They are thus essential for motor function. The number of stators synchronously engaged in the motor is surprisingly dynamic and depends on the load and the environmental concentration of the corresponding coupling ion. Thus, the rotor-stator interactions determine an important part of the properties of the motor. Numerous bacteria have been identified as possessing more than one set of stators, and some species have been demonstrated to use these different stators in various configurations to modify motor functions by dynamic in-flight swapping. Here, we review knowledge of the properties, the functions, and the evolution of these hybrid motors and discuss questions that remain unsolved.

The many faces of the unusual biofilm activator RemA

Biofilms can be viewed as tissue-like structures in which microorganisms are organized in a spatial and functional sophisticated manner. Biofilm formation requires the orchestration of a highly integrated network of regulatory proteins to establish cell differentiation and production of a complex extracellular matrix. Here, we discuss the role of the essential Bacillus subtilis biofilm activator RemA. Despite intense research on biofilms, RemA is a largely underappreciated regulatory protein. RemA forms donut-shaped octamers with the potential to assemble into dimeric superstructures. The presumed DNA-binding mode suggests that RemA organizes its target DNA into nucleosome-like structures, which are the basis for its role as transcriptional activator. We discuss how RemA affects gene expression in the context of biofilm formation, and its regulatory interplay with established components of the biofilm regulatory network, such as SinR, SinI, SlrR, and SlrA. We emphasize the additional role of RemA played in nitrogen metabolism and osmotic-stress adjustment.

Materials science and mechanosensitivity of living matter

Living systems are composed of molecules that are synthesized by cells that use energy sources within their surroundings to create fascinating materials that have mechanical properties optimized for their biological function. Their functionality is a ubiquitous aspect of our lives. We use wood to construct furniture, bacterial colonies to modify the texture of dairy products and other foods, intestines as violin strings, bladders in bagpipes, and so on. The mechanical properties of these biological materials differ from those of other simpler synthetic elastomers, glasses, and crystals. Reproducing their mechanical properties synthetically or from first principles is still often unattainable. The challenge is that biomaterials often exist far from equilibrium, either in a kinetically arrested state or in an energy consuming active state that is not yet possible to reproduce de novo. Also, the design principles that form biological materials often result in nonlinear responses of stress to strain, or force to displacement, and theoretical models to explain these nonlinear effects are in relatively early stages of development compared to the predictive models for rubberlike elastomers or metals. In this Review, we summarize some of the most common and striking mechanical features of biological materials and make comparisons among animal, plant, fungal, and bacterial systems. We also summarize some of the mechanisms by which living systems develop forces that shape biological matter and examine newly discovered mechanisms by which cells sense and respond to the forces they generate themselves, which are resisted by their environment, or that are exerted upon them by their environment. Within this framework, we discuss examples of how physical methods are being applied to cell biology and bioengineering.

Complete genome sequence of biocontrol strain Paenibacillus peoriae HJ-2 and further analysis of its biocontrol mechanism

Background

Paris polyphylla is a herb widely used in traditional Chinese medicine to treat various diseases. Stem rot diseases seriously affected the yield of P. polyphylla in subtropical areas of China. Therefore, cost-effective, chemical-free, eco-friendly strategies to control stem rot on P. polyphylla are valuable and urgently needed.

Results

In this paper, we reported the biocontrol efficiency of Paenibacillus peoriae HJ-2 and its complete genome sequence. Strain HJ-2 could serve as a potential biocontrol agent against stem rot on P. polyphylla in the greenhouse and field. The genome of HJ-2 consists of a single 6,001,192 bp chromosome with an average GC content of 45% and 5,237 predicted protein coding genes, 39 rRNAs and 108 tRNAs. The phylogenetic tree indicated that HJ-2 is most closely related to P. peoriae IBSD35. Functional analysis of genome revealed numerous genes/gene clusters involved in plant colonization, biofilm formation, plant growth promotion, antibiotic and resistance inducers synthesis. Moreover, metabolic pathways that potentially contribute to biocontrol mechanisms were identified.

Conclusions

This study revealed that P. peoriae HJ-2 could serve as a potential BCA against stem rot on P. polyphylla. Based on genome analysis, the genome of HJ-2 contains more than 70 genes and 12 putative gene clusters related to secondary metabolites, which have previously been described as being involved in chemotaxis motility, biofilm formation, growth promotion, antifungal activity and resistance inducers biosynthesis. Compared with other strains, variation in the genes/gene clusters may lead to different antimicrobial spectra and biocontrol efficacies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08330-0.

Motor-independent retraction of type IV pili is governed by an inherent property of the pilus filament

Type IV pili (T4P) are dynamic surface appendages that promote virulence, biofilm formation, horizontal gene transfer, and motility in diverse bacterial species. Pilus dynamic activity is best characterized in T4P that use distinct ATPase motors for pilus extension and retraction. Many T4P systems, however, lack a dedicated retraction motor, and the mechanism underlying this motor-independent retraction remains a mystery. Using the Vibrio cholerae competence pilus as a model system, we identify mutations in the major pilin gene that enhance motor-independent retraction. These mutants likely diminish pilin-pilin interactions within the filament to produce less-stable pili. One mutation adds a bulky residue to α1C, a universally conserved feature of T4P. We found that inserting a bulky residue into α1C of the retraction motor-dependent Acinetobacter baylyi competence T4P enhances motor-independent retraction. Conversely, removing bulky residues from α1C of the retraction motor-independent, V. cholerae toxin-coregulated T4P stabilizes the filament and diminishes pilus retraction. Furthermore, alignment of pilins from the broader type IV filament (T4F) family indicated that retraction motor-independent T4P, gram-positive Com pili, and type II secretion systems generally encode larger residues within α1C oriented toward the pilus core compared to retraction motor-dependent T4P. Together, our data demonstrate that motor-independent retraction relies, in part, on the inherent instability of the pilus filament, which may be a conserved feature of diverse T4Fs. This provides evidence for a long-standing yet previously untested model in which pili retract in the absence of a motor by spontaneous depolymerization.

Structural and functional characterization of the bacterial biofilm activator RemA

Bacillus subtilis can form structurally complex biofilms on solid or liquid surfaces, which requires expression of genes for matrix production. The transcription of these genes is activated by regulatory protein RemA, which binds to poorly conserved, repetitive DNA regions but lacks obvious DNA-binding motifs or domains. Here, we present the structure of the RemA homologue from Geobacillus thermodenitrificans, showing a unique octameric ring with the potential to form a 16-meric superstructure. These results, together with further biochemical and in vivo characterization of B. subtilis RemA, suggests that the protein can wrap DNA around its ring-like structure through a LytTR-related domain.

Biofilm formation in Bacillus subtilis requires expression of matrix production genes, which are upregulated by transcriptional activator RemA. Here, the authors show that RemA forms octameric rings with the potential to form a 16-meric superstructure, suggesting that the protein can wrap DNA through a LytTR-related domain.

Diversification of Bacillus subtilis during experimental evolution on Arabidopsis thaliana and the complementarity in root colonization of evolved subpopulations

The soil bacterium Bacillus subtilis is known to suppress pathogens as well as promote plant growth. However, in order to fully exploit the potential as natural fertilizer, we need a better understanding of the interactions between B. subtilis and plants. Here, B. subtilis was examined for root colonization through experimental evolution on Arabidopsis thaliana. The populations evolved rapidly, improved in root colonization and diversified into three distinct morphotypes. In order to better understand the adaptation that had taken place, single evolved isolates from the final transfer were randomly selected for further characterization, revealing changes in growth and pellicle formation in medium supplemented with plant polysaccharides. Intriguingly, certain evolved isolates showed improved root colonization only on the plant species they evolved on, but not on another plant species, namely tomato, suggesting A. thaliana specific adaption paths. Finally, the mix performed better than the sum of its constituents in monoculture, which was demonstrated to be caused by complementarity effects. Our results suggest that genetic diversification occurs in an ecological relevant setting on plant roots and proves to be a stable strategy for root colonization.

Effect of lon Protease Overexpression on Endotoxin Production and Stress Resistance in Bacillus thuringiensis

Lon protease, an intracellular protease, plays a key role in cell homeostasis in bacteria and is involved in numerous physiological processes. In this work, we aimed to study the impact of Lon on the production of endotoxins and stress response in Bacillus thuringiensis, which is an important bioinsecticide alternative for toxic chemicals. For this purpose, lon gene was cloned into a multi-copy vector with its original promoter and transcriptional terminator and expressed in B. thuringiensis serovar israelensis ATCC 35,646. Our results showed that the recombinant lon gene transcribed and translated efficiently and the resulting protein was active. Although the sporulation efficiency of the recombinant strain was found to be reduced and its mobility impaired, overexpression of the lon gene triggered the production of endotoxin. Together with increased biofilm formation, recombinant strain exhibited significantly better adaptation to osmotic and heat shock stresses and UV exposure compared to wild type and the control strain with empty plasmid. This study suggested a possible link between Lon protease and the production of insecticide and stress response in B. thuringiensis and provides a platform for future studies focusing on enhancing bio-insecticidal production using this bacterium.

Physicochemical Properties of Extracellular Polymeric Substances Produced by Three Bacterial Isolates From Biofouled Reverse Osmosis Membranes

This work describes the chemical composition of extracellular polymeric substances (EPS) produced by three bacteria (RO1, RO2, and RO3) isolated from a biofouled reverse osmosis (RO) membrane. We isolated pure cultures of three bacterial strains from a 7-year-old biofouled RO module that was used in a full-scale seawater treatment plant. All the bacterial strains showed similar growth rates, biofilm formation, and produced similar quantities of proteins and polysaccharides. The gel permeation chromatography showed that the EPS produced by all the strains has a high molecular weight; however, the EPS produced by strains RO1 and RO3 showed the highest molecular weight. Fourier Transform Infrared Spectroscopy (FTIR), Proton Nuclear Magnetic Resonance (¹H NMR), and Carbon NMR (¹³C NMR) were used for a detailed characterization of the EPS. These physicochemical analyses allowed us to identify features of EPS that are important for biofilm formation. FTIR analysis indicated the presence of α-1,4 glycosidic linkages (920 cm^-1) and amide II (1,550 cm^-1) in the EPS, the presence of which has been correlated with the fouling potential of bacteria. The presence of α-glycoside linkages was further confirmed by ¹³C NMR analysis. The ¹³C NMR analysis also showed that the EPS produced by these bacteria is chemically similar to foulants obtained from biofouled RO membranes in previous studies. Therefore, our results support the hypothesis that the majority of substances that cause fouling on RO membranes originate from bacteria. Investigation using ¹H NMR showed that the EPS contained a high abundance of hydrophobic compounds, and these compounds can lead to flux decline in the membrane processes. Genome sequencing of the isolates showed that they represent novel species of bacteria belonging to the genus Bacillus. Examination of genomes showed that these bacteria carry carbohydrates-active enzymes that play a role in the production of polysaccharides. Further genomic studies allowed us to identify proteins involved in the biosynthesis of EPS and flagella involved in biofilm formation. These analyses provide a glimpse into the physicochemical properties of EPS found on the RO membrane. This knowledge can be useful in the rational design of biofilm control treatments for the RO membrane.

Crash landing of Vibrio cholerae by MSHA pili-assisted braking and anchoring in a viscoelastic environment

Mannose-sensitive hemagglutinin (MSHA) pili and flagellum are critical for the surface attachment of Vibrio cholerae, the first step of V. cholerae colonization on host surfaces. However, the cell landing mechanism remains largely unknown, particularly in viscoelastic environments such as the mucus layers of intestines. Here, combining the cysteine-substitution-based labeling method with single-cell tracking techniques, we quantitatively characterized the landing of V. cholerae by directly observing both pili and flagellum of cells in a viscoelastic non-Newtonian solution consisting of 2% Luria-Bertani and 1% methylcellulose (LB+MC). The results show that MSHA pili are evenly distributed along the cell length and can stick to surfaces at any point along the filament. With such properties, MSHA pili are observed to act as a brake and anchor during cell landing which includes three phases: running, lingering, and attaching. Importantly, loss of MSHA pili results in a more dramatic increase in mean path length in LB+MC than in 2% LB only or in 20% Ficoll solutions, indicating that the role of MSHA pili during cell landing is more apparent in viscoelastic non-Newtonian fluids than viscous Newtonian ones. Our work provides a detailed picture of the landing dynamics of V. cholerae under viscoelastic conditions, which can provide insights into ways to better control V. cholerae infections in a real mucus-like environment.

Fresh Extension of Vibrio cholerae Competence Type IV Pili Predisposes Them for Motor-Independent Retraction

Bacteria utilize dynamic appendages, called type IV pili (T4P), to interact with their environment and mediate a wide variety of functions. Pilus extension is mediated by an extension ATPase motor, commonly called PilB, in all T4P. Pilus retraction, however, can occur with the aid of an ATPase motor or in the absence of a retraction motor. While much effort has been devoted to studying motor-dependent retraction, the mechanism and regulation of motor-independent retraction remain poorly characterized. We have previously demonstrated that Vibrio cholerae competence T4P undergo motor-independent retraction in the absence of the dedicated retraction ATPases PilT and PilU. Here, we utilize this model system to characterize the factors that influence motor-independent retraction. We find that freshly extended pili frequently undergo motor-independent retraction, but if these pili fail to retract immediately, they remain statically extended on the cell surface. Importantly, we show that these static pili can still undergo motor-dependent retraction via tightly regulated ectopic expression of PilT, suggesting that these T4P are not broken but simply cannot undergo motor-independent retraction. Through additional genetic and biophysical characterization of pili, we suggest that pilus filaments undergo conformational changes during dynamic extension and retraction. We propose that only some conformations, like those adopted by freshly extended pili, are capable of undergoing motor-independent retraction. Together, these data highlight the versatile mechanisms that regulate T4P dynamic activity and provide additional support for the long-standing hypothesis that motor-independent retraction occurs via spontaneous depolymerization. IMPORTANCE Extracellular pilus fibers are critical to the virulence and persistence of many pathogenic bacteria. A crucial function for most pili is the dynamic ability to extend and retract from the cell surface. Inhibiting this dynamic pilus activity represents an attractive approach for therapeutic interventions; however, a detailed mechanistic understanding of this process is currently lacking. Here, we use the competence pilus of Vibrio cholerae to study how pili retract in the absence of dedicated retraction motors. Our results reveal a novel regulatory mechanism of pilus retraction that is an inherent property of the pilus filament. Thus, understanding the conformational changes that pili adopt under different conditions may be critical for the development of novel therapeutics that aim to target the dynamic activity of these structures.

Zetaproteobacteria Pan-Genome Reveals Candidate Gene Cluster for Twisted Stalk Biosynthesis and Export

Twisted stalks are morphologically unique bacterial extracellular organo-metallic structures containing Fe(III) oxyhydroxides that are produced by microaerophilic Fe(II)-oxidizers belonging to the Betaproteobacteria and Zetaproteobacteria. Understanding the underlying genetic and physiological mechanisms of stalk formation is of great interest based on their potential as novel biogenic nanomaterials and their relevance as putative biomarkers for microbial Fe(II) oxidation on ancient Earth. Despite the recognition of these special biominerals for over 150 years, the genetic foundation for the stalk phenotype has remained unresolved. Here we present a candidate gene cluster for the biosynthesis and secretion of the stalk organic matrix that we identified with a trait-based analyses of a pan-genome comprising 16 Zetaproteobacteria isolate genomes. The “stalk formation in Zetaproteobacteria” (sfz) cluster comprises six genes (sfz1-sfz6), of which sfz1 and sfz2 were predicted with functions in exopolysaccharide synthesis, regulation, and export, sfz4 and sfz6 with functions in cell wall synthesis manipulation and carbohydrate hydrolysis, and sfz3 and sfz5 with unknown functions. The stalk-forming Betaproteobacteria Ferriphaselus R-1 and OYT-1, as well as dread-forming Zetaproteobacteria Mariprofundus aestuarium CP-5 and Mariprofundus ferrinatatus CP-8 contain distant sfz gene homologs, whereas stalk-less Zetaproteobacteria and Betaproteobacteria lack the entire gene cluster. Our pan-genome analysis further revealed a significant enrichment of clusters of orthologous groups (COGs) across all Zetaproteobacteria isolate genomes that are associated with the regulation of a switch between sessile and motile growth controlled by the intracellular signaling molecule c-di-GMP. Potential interactions between stalk-former unique transcription factor genes, sfz genes, and c-di-GMP point toward a c-di-GMP regulated surface attachment function of stalks during sessile growth.

An inside look at a biofilm: Pseudomonas aeruginosa flagella biotracking

The opportunistic pathogen, Pseudomonas aeruginosa, a flagellated bacterium, is one of the top model organisms for biofilm studies. To elucidate the location of bacterial flagella throughout the biofilm life cycle, we developed a new flagella biotracking tool. Bacterial flagella were site-specifically labeled via genetic code expansion. This enabled us to track bacterial flagella during biofilm maturation. Live flagella imaging revealed the presence and synthesis of flagella throughout the biofilm life cycle. To study the possible role of flagella in a biofilm, we produced a flagella knockout strain and compared its biofilm to that of the wild-type strain. Results showed a one order of magnitude stronger biofilm structure in the wild type in comparison with the flagella knockout strain. This suggests a possible structural role for flagella in a biofilm, conceivably as a scaffold. Our findings suggest a new model for biofilm maturation dynamic which underscores the importance of direct evidence from within the biofilm.

CdgL is a degenerate nucleotide cyclase domain protein affecting flagellin synthesis and motility in Bacillus thuringiensis

In Bacillus subtilis, motility genes are expressed in a hierarchical pattern - governed by the σ^D transcription factor and other proteins such as the EpsE molecular clutch and SlrA/SlrR regulator proteins. In contrast, motile species in the Bacillus cereus group seem to express their motility genes in a non-hierarchical pattern, and less is known about their regulation, also given that no orthologs to σ^D, EpsE, SlrA or SlrR are found in B. cereus group genomes. Here we show that deletion of cdgL (BTB_RS26690/BTB_c54300) in Bacillus thuringiensis 407 (cry-) resulted in a six-to ten-fold downregulation of the entire motility locus, and loss of flagellar structures and swimming motility. cdgL is unique to the B. cereus group and is found in all phylogenetic clusters in the population except for group I, which comprises isolates of non-motile Bacillus pseudomycoides. Analysis of RNA-Seq data revealed cdgL to be expressed in a three-gene operon with a NupC like nucleoside transporter, and a putative glycosyl transferase for which transposon-based gene inactivation was previously shown to produce a similar phenotype to cdgL deletion. Interestingly, all three proteins were predicted to be membrane-bound and may provide a concerted function in the regulation of B. cereus group motility.