The EpsE flagellar clutch is bifunctional and synergizes with EPS biosynthesis to promote Bacillus subtilis biofilm formation

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.

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.

Biofilm-overproducing Bacillus amyloliquefaciens strain B9ΔywcC reduces cadmium uptake in lettuce by upregulating the expression of proteins associated with root surface biofilm formation and cell membrane homeostasis

In this study, Bacillus amyloliquefaciens strain B9 and its biofilm-overproducing B9ΔywcC mutant (ΔywcCM) were characterized for their effects on Cd accumulation in Italian lettuce and the underlying molecular mechanisms under hydroponic conditions. Both B9 and ΔywcCM significantly reduced Cd contents in lettuce tissues compared with the controls. Furthermore, ΔywcCM exhibited significantly decreased Cd accumulation and increased root surface biofilm biomass and biofilm-mediated Cd immobilization compared with B9. Proteomic analysis of lettuce root surface biofilms revealed that ΔywcCM significantly upregulated the expression of several proteins compared to B9. These included IolC and IolD (associated with inositol metabolism), GlpK (associated with glycerol metabolism), TyrS (associated with tRNA synthesis and transport), and LepA and PepT (associated with protein translation and modification), which are associated with biofilm formation; ArgS and AspS (associated with tRNA synthesis and transport), LepA (associated with protein translation and modification), and GcvT (associated with aminomethyltransferase), which are involved in cell membrane homeostasis. Furthermore, ΔywcCM significantly upregulated the expression of iolD, iolI, and pepT in the root surface biofilms relative to B9. These findings demonstrated that the biofilm-overproducing ΔywcCM enhances root surface biofilm formation and stability, thereby promoting Cd immobilization and reducing Cd accumulation in lettuce leaves grown in Cd-contaminated solutions.

The impact of the flagellar protein gene fliK on Helicobacter pylori biofilm formation

The biofilm structure of Helicobacter pylori is known to enhance its capabilities for antimicrobial resistance. This study aims to investigate the role of the flagellar hook length control protein gene fliK in the biofilm formation of H. pylori. Homologous recombination was employed to knock out the fliK gene in the H. pylori NCTC 11637 strain. The flagella of H. pylori were observed using transmission electron microscopy (TEM), whereas H. pylori motility and growth were examined through semi-solid agar assays and growth curve analyses, respectively. The bacterial biofilm and its constituents were visualized utilizing fluorescence confocal microscopy. Assessments of H. pylori adhesion to gastric mucosal cells, its vacuolar toxicity, and antibiotic resistance were evaluated using co-culture experiments and E-test methods. The fliK gene was successfully knocked out in H. pylori NCTC 11637. The ΔfliK mutant exhibited polyhook structures or lacked typical flagellar morphology, reduced mobility, and a slower bacterial growth rate compared with the wild-type strain. Fluorescence confocal microscopy revealed a decrease in the thickness of the biofilm formed by the ΔfliK strain, along with reductions in polysaccharide and DNA components. The deletion of fliK did not affect vacuolar toxicity or antibiotic resistance but did reduce the adhesive capacity of the bacterium to gastric mucosal cells. The deletion of the fliK gene significantly impairs H. pylori biofilm formation, leading to substantial decreases in biofilm components, bacterial growth, and adhesion capabilities. These findings underscore the importance of fliK in the pathogenicity of H. pylori.IMPORTANCEThe increasing antibiotic resistance of Helicobacter pylori has emerged as a global health concern, with biofilm formation serving as a crucial mechanism underlying this resistance. This study investigates the role of the fliK gene, which encodes the flagellar hook length control protein, in H. pylori biofilm formation. Furthermore, we examined the influence of fliK on H. pylori growth, motility, and cellular adhesion capabilities. Our findings elucidate the molecular mechanisms governing H. pylori biofilm formation and suggest potential therapeutic strategies for addressing H. pylori antibiotic resistance.

Harnessing the Farm Effect: Microbial Products for the Treatment and Prevention of Asthma Throughout Life

It has long been appreciated that farm exposure early in life protects individuals from allergic asthma. Understanding what component(s) of this exposure is responsible for this protection is crucial to understanding allergic asthma pathogenesis and developing strategies to prevent or treat allergic asthma. In this review, we introduce the concept of Farm-Friends, or specific microbes associated with both a farm environment and protection from allergic asthma. We review the mechanism(s) by which these Farm-Friends suppress allergic inflammation, with a focus on the molecule(s) produced by these Farm-Friends. Finally, we discuss the relevance of Farm-Friend administration (oral vs. inhaled) for preventing the development and severity of allergic asthma throughout childhood and adulthood. By developing a fuller understanding of which Farm-Friends modulate host immunity, a greater wealth of prophylactic and therapeutic options becomes available to counter the current allergy epidemic.

Bacterial species with different nanocolony morphologies have distinct flow-dependent colonization behaviors

Fluid flows are dominant features of many bacterial environments, and flow can often impact bacterial behaviors in unexpected ways. For example, the most common type of cardiovascular infection is heart valve colonization by gram-positive bacteria like Staphylococcus aureus and Enterococcus faecalis (endocarditis). This behavior is counterintuitive because heart valves experience high shear rates that would naively be expected to reduce colonization. To determine whether these bacteria preferentially colonize higher shear rate environments, we developed a microfluidic system to quantify the effect of flow conditions on the colonization of S. aureus and E. faecalis. We find that the preferential colonization in high flow of both species is not specific to heart valves and can be found in simple configurations lacking any host factors. This behavior enables bacteria that are outcompeted in low flow to dominate in high flow. Surprisingly, experimental and computational studies reveal that the two species achieve this behavior via distinct mechanisms. S. aureus grows in cell clusters and produces a dispersal signal whose transport is affected by shear rate. Meanwhile, E. faecalis grows in linear chains whose mechanical properties result in less dispersal in the presence of higher shear force. In addition to establishing two divergent mechanisms by which these bacteria each preferentially colonize high-flow environments, our findings highlight the importance of understanding bacterial behaviors at the level of collective interactions among cells. These results suggest that distinct multicellular nanocolony morphologies have previously unappreciated costs and benefits in different environments, like those introduced by fluid flow.

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.

Bacillus Subtilis-Derived Exopolysaccharide Halts Depigmentation and Autoimmunity in Vitiligo

Vitiligo has a complex multifactorial etiology involving a T-cell-mediated autoimmune response to cutaneous melanocytes. Microbial dysbiosis has been assigned a contributing role in vitiligo etiology. Treating vitiligo can be a challenging task, and finding novel treatment approaches is crucial. In this study, we tested exopolysaccharides (EPSs) isolated from Bacillus subtilis as a microbiome-based therapy. Vitiligo-prone h3TA2 mice were treated by weekly intraperitoneal EPS injection for 18 weeks. Depigmentation was evaluated over time, measuring immune responses at end point. EPS treatment significantly limited the rate of depigmentation. The abundance of cutaneous T cells, specifically CD8+ cytotoxic T cells, was reduced, whereas regulatory T cells were more abundant in the skin of treated mice than in untreated mice. Moreover, EPS treatment was associated with increased numbers of splenic M2 macrophages, elevated splenic indoleamine 2,3-dioxygenase expression, and a systemic cytokine shift toward a type 2 pattern of cytokines. Importantly, splenocytes retrieved from EPS-treated mice were less responsive to cognate tyrosinase peptide, as demonstrated by limited release of IFN-γ and other inflammatory cytokines. In summary, EPS isolated from Bsubtilis interfered with T-cell-mediated depigmentation in the h3TA2 mouse model of vitiligo, suggesting that Bsubtilis EPS could serve as a novel treatment entity for vitiligo.

Chemotaxis gene of a bacterium impacts larval settlement and metamorphosis in the marine mussel Mytilus coruscus via c-di-GMP controlling extracellular protein production

Bacterial chemotaxis enhances bacterial adaptation to the environment and is important for biofilm formation. Biofilms play a key role in inducing larval settlement and metamorphosis in many marine invertebrates. However, the specific mechanisms by which bacterial chemotaxis influences larval settlement and metamorphosis in mussels remain unknown. The findings indicate that the absence of the chemotaxis gene cheW resulted in reduced motility of Pseudoalteromonas marina, accompanied by an increase in c-di-GMP content. The ΔcheW strain exhibited a higher capacity for biofilm formation compared to the wild-type strain. The extracellular protein content of the ΔcheW strain exhibited a significant 77% reduction, specifically in the flagellin content. The inducing activity of ΔcheW was reduced by 56% compared to the wild-type strain. This study highlights that the deficiency of the chemotaxis gene cheW inhibited larval settlement and metamorphosis in mussels through c-di-GMP regulation of extracellular protein production. It provides a novel ecological function of bacterial chemotaxis in regulating the larval settlement and metamorphosis of marine invertebrates.

A phosphate starvation induced small RNA promotes Bacillus biofilm formation

Currently, almost all known regulators involved in bacterial phosphorus metabolism are proteins. In this study, we identified a conserved new small regulatory RNA (sRNA), named PhoS, encoded in the 3' untranslated region (UTR) of the phoPR genes in Bacillus velezensis and B. subtilis. Expression of phoS is strongly induced upon phosphorus scarcity and stimulated by the transcription factor PhoP. Conversely, PhoS positively regulates PhoP translation by binding to the ribosome binding site (RBS) of phoP mRNA. PhoS can promote Bacillus biofilm formation through, at least in part, enhancing the expression of the matrix-related genes, such as the eps genes and the tapA-sipW-tasA operon. The positive regulation of phoP expression by PhoS contributes to the promoting effect of PhoS on biofilm formation. sRNAs regulating biofilm formation have rarely been reported in gram-positive Bacillus species. Here we highlight the significance of sRNAs involved in two important biological processes: phosphate metabolism and biofilm formation.

Bacteriophage-mediated approaches for biofilm control

Biofilms are complex microbial communities in which planktonic and dormant bacteria are enveloped in extracellular polymeric substances (EPS) such as exopolysaccharides, proteins, lipids, and DNA. These multicellular structures present resistance to conventional antimicrobial treatments, including antibiotics. The formation of biofilms raises considerable concern in healthcare settings, biofilms can exacerbate infections in patients and compromise the integrity of medical devices employed during treatment. Similarly, certain bacterial species contribute to bulking, foaming, and biofilm development in water environments such as wastewater treatment plants, water reservoirs, and aquaculture facilities. Additionally, food production facilities provide ideal conditions for establishing bacterial biofilms, which can serve as reservoirs for foodborne pathogens. Efforts to combat antibiotic resistance involve exploring various strategies, including bacteriophage therapy. Research has been conducted on the effects of phages and their individual proteins to assess their potential for biofilm removal. However, challenges persist, prompting the examination of refined approaches such as drug-phage combination therapies, phage cocktails, and genetically modified phages for clinical applications. This review aims to highlight the progress regarding bacteriophage-based approaches for biofilm eradication in different settings.

Bacillus subtilis EpsA-O: A novel exopolysaccharide structure acting as an efficient adhesive in biofilms

Extracellular polysaccharides are crucial components for biofilm development. Although Bacillus subtilis is one of the most characterized Gram-positive biofilm model system, the structure-function of its exopolysaccharide, EpsA-O, remains to be elucidated. By combining chemical analysis, NMR spectroscopy, rheology, and molecular modeling, high-resolution data of EpsA-O structure from atom to supramolecular scale was obtained. The repeating unit is composed of the trisaccharide backbone [→3)-β-D-QuipNAc4NAc-(1→3)-β-D-GalpNAc-(1→3)-α-D-GlcpNAc-(1]n, and the side chain β-D-Galp(3,4-S-Pyr)-(1→6)-β-D-Galp(3,4-S-Pyr)-(1→6)-α-D-Galp-(1→ linked to C4 of GalNAc. Close agreement between the primary structure and rheological behavior allowed us to model EpsA-O macromolecular and supramolecular solution structure, which can span the intercellular space forming a gel that leads to a complex 3D biofilm network as corroborated by a mutant strain with impaired ability to produce EpsA-O. This is a comprehensive structure-function investigation of the essential biofilm adhesive exopolysaccharide that will serve as a useful guide for future studies in biofilm architecture formation.

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

Flagella are complex, trans-envelope nanomachines that localize to species- specific cellular addresses. 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. Rare basal bodies were observed to be mobile however, and the frequency of basal body mobility 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 peptidoglycan superstructure for pores of sufficient diameter that permit rod completion. Furthermore, mutation of the rod also disrupts basal body patterning in a way that phenocopies mutation of the cytoplasmic flagellar patterning protein FlhF. We infer that conformational changes in the basal body exchange information between rod synthesis and the cytoplasmic patterning proteins to restrict assembly at certain pores established by a grid-like pattern pre-existent in the peptidoglycan itself.

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 ∼15 flagella over the length of the cell body in a grid-like pattern and lacks all proteins associated with targeted assembly in polarly flagellated bacteria. Here we show that B. subtilis basal bodies are mobile soon after assembly and become immobilized when the flagellar rod transits the peptidoglycan wall. Moreover, defects in the flagellar rod lead to an asymmetric distribution of flagella with respect to the midcell. We conclude that the patterning of flagella is different in B. subtilis , and we infer that the B. subtilis rod probes the peptidoglycan for holes that can accommodate the machine.

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.

Perception of the Biocontrol Potential and Palmitic Acid Biosynthesis Pathway of Bacillus subtilis H2 through Merging Genome Mining with Chemical Analysis

Bacillus has been widely studied for its potential to protect plants from pathogens. Here, we report the whole genome sequence of Bacillus subtilis H2, which was isolated from the tea garden soil of Guiyang Forest Park. Strain H2 showed a broad spectrum of antagonistic activities against many plant fungal pathogens and bacteria pathogens, including the rice blast fungus Magnaporthe oryzae, and showed a good field control effect against rice blast. The complete genome of B. subtilis H2 contained a 4,160,635-bp circular chromosome, with an average G + C content of 43.78%. Through the genome mining of strain H2, we identified 7 known antimicrobial compound biosynthetic gene clusters (BGCs) including sporulation killing factor, surfactin, bacillaene, fengycin, bacillibactin, subtilosin A, and bacilysin. Palmitic acid (PA), a secondary metabolite, was detected and identified in the H2 strain through genome mining analysis and gas chromatography-mass spectrometry (GC-MS). Additionally, we propose, for the first time, that the type II fatty acid synthesis (FAS) pathway in Bacillus is responsible for PA biosynthesis. This finding was confirmed by studying the antimicrobial activity of PA and conducting reverse transcription-quantitative polymerase chain reaction (RT-qPCR) experiments. We also identified numerous genes associated with plant-bacteria interactions in the H2 genome, including more than 94 colonization-related genes, more than 34 antimicrobial genes, and more than 13 plant growth-promoting genes. These findings contribute to our understanding of the biocontrol mechanisms of B. subtilis H2 and have potential applications in crop disease control.

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.

Mechanical constraints to unbound expansion of B. subtilis on semi-solid surfaces

IMPORTANCE

How bacterial cells colonize new territory is a problem of fundamental microbiological and biophysical interest and is key to the emergence of several phenomena of biological, ecological, and medical relevance. Here, we demonstrate how bacteria stuck in a colony of finite size can resume exploration of new territory by aquaplaning and how they fine tune biofilm viscoelasticity to surface material properties that allows them differential mobility. We show how changing local interfacial forces and colony viscosity results in a plethora of bacterial morphologies on surfaces with different physical and mechanical properties.

In Silico Safety Assessment of Bacillus Isolated from Polish Bee Pollen and Bee Bread as Novel Probiotic Candidates

Bacillus species isolated from Polish bee pollen (BP) and bee bread (BB) were characterized for in silico probiotic and safety attributes. A probiogenomics approach was used, and in-depth genomic analysis was performed using a wide array of bioinformatics tools to investigate the presence of virulence and antibiotic resistance properties, mobile genetic elements, and secondary metabolites. Functional annotation and Carbohydrate-Active enZYmes (CAZYme) profiling revealed the presence of genes and a repertoire of probiotics properties promoting enzymes. The isolates BB10.1, BP20.15 (isolated from bee bread), and PY2.3 (isolated from bee pollen) genome mining revealed the presence of several genes encoding acid, heat, cold, and other stress tolerance mechanisms, adhesion proteins required to survive and colonize harsh gastrointestinal environments, enzymes involved in the metabolism of dietary molecules, antioxidant activity, and genes associated with the synthesis of vitamins. In addition, genes responsible for the production of biogenic amines (BAs) and D-/L-lactate, hemolytic activity, and other toxic compounds were also analyzed. Pan-genome analyses were performed with 180 Bacillus subtilis and 204 Bacillus velezensis genomes to mine for any novel genes present in the genomes of our isolates. Moreover, all three isolates also consisted of gene clusters encoding secondary metabolites.

Exopolysaccharide-Treated Dendritic Cells Effectively Ameliorate Acute Graft-versus-Host Disease

Graft-versus-host disease (GVHD) is a primary and often lethal complication of allogenic hematopoietic stem cell transplantation (HSCT). Prophylactic regimens for GVHD are given as standard pretransplantation therapy; however, up to 50% of these patients develop acute GVHD (aGVHD) and require additional immunosuppressive intervention. Using a mouse GVHD model, we previously showed that injecting mice with exopolysaccharide (EPS) from Bacillus subtilis prior to GVHD induction significantly increased 80-day survival after transplantation of complete allogeneic major histocompatibility complex-mismatched cells. To ask whether EPS might also inhibit GVHD in humans, we used humanized NSG-HLA-A2 mice and induced GVHD by i.v. injection of A2neg human peripheral blood mononuclear cells (PBMCs). Because we could not inject human donors with EPS, we transferred EPS-pretreated dendritic cells (DCs) to inhibit aGVHD. We derived these DCs from CD34+ human cord blood cells, treated them with EPS, and then injected them together with PBMCs into the NSG-HLA-A2 mice. We found that all mice that received untreated DCs were dead by day 35, whereas 25% of mice receiving EPS-treated DCs (EPS-DCs) survived. This DC cell therapy could be readily translatable to humans, because we can generate large numbers of human EPS-DCs and use them as an "off the shelf" treatment for patients undergoing HSCT.

Defining early steps in Bacillus subtilis biofilm biosynthesis

IMPORTANCE

Biofilms are the communal way of life that microbes adopt to increase survival. Key to our ability to systematically promote or ablate biofilm formation is a detailed understanding of the biofilm matrix macromolecules. Here, we identify the first two essential steps in the Bacillus subtilis biofilm matrix exopolysaccharide (EPS) synthesis pathway. Together, our studies and approaches provide the foundation for the sequential characterization of the steps in EPS biosynthesis, using prior steps to enable chemoenzymatic synthesis of the undecaprenyl diphosphate-linked glycan substrates.

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.

Advanced strategies for metabolic engineering of Bacillus to produce extracellular polymeric substances

Extracellular polymeric substances are mainly synthesized via a variety of biosynthetic pathways in bacteria. Bacilli-sourced extracellular polymeric substances, such as exopolysaccharides (EPS) and poly-γ-glutamic acid (γ-PGA), can serve as active ingredients and hydrogels, and have other important industrial applications. However, the functional diversity and widespread applications of these extracellular polymeric substances, are hampered by their low yields and high costs. Biosynthesis of extracellular polymeric substances is very complex in Bacillus, and there is no detailed elucidation of the reactions and regulations among various metabolic pathways. Therefore, a better understanding of the metabolic mechanisms is required to broaden the functions and increase the yield of extracellular polymeric substances. This review systematically summarizes the biosynthesis and metabolic mechanisms of extracellular polymeric substances in Bacillus, providing an in-depth understanding of the relationships between EPS and γ-PGA synthesis. This review provides a better clarification of Bacillus metabolic mechanisms during extracellular polymeric substance secretion and thus benefits their application and commercialization.

A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century

The vast majority of genomic sequences are automatically annotated using various software programs. The accuracy of these annotations depends heavily on the very few manual annotation efforts that combine verified experimental data with genomic sequences from model organisms. Here, we summarize the updated functional annotation of Bacillus subtilis strain 168, a quarter century after its genome sequence was first made public. Since the last such effort 5 years ago, 1168 genetic functions have been updated, allowing the construction of a new metabolic model of this organism of environmental and industrial interest. The emphasis in this review is on new metabolic insights, the role of metals in metabolism and macromolecule biosynthesis, functions involved in biofilm formation, features controlling cell growth, and finally, protein agents that allow class discrimination, thus allowing maintenance management, and accuracy of all cell processes. New 'genomic objects' and an extensive updated literature review have been included for the sequence, now available at the International Nucleotide Sequence Database Collaboration (INSDC: AccNum AL009126.4).

Defining Early Steps in B. subtilis Biofilm Biosynthesis

The Bacillus subtilis extracellular biofilm matrix includes an exopolysaccharide that is critical for the architecture and function of the community. To date, our understanding of the biosynthetic machinery and the molecular composition of the exopolysaccharide of B. subtilis remains unclear and incomplete. This report presents synergistic biochemical and genetic studies built from a foundation of comparative sequence analyses targeted at elucidating the activities of the first two membrane-committed steps in the exopolysaccharide biosynthetic pathway. By taking this approach, we determined the nucleotide sugar donor and lipid-linked acceptor substrates for the first two enzymes in the B. subtilis biofilm exopolysaccharide biosynthetic pathway. EpsL catalyzes the first phosphoglycosyl transferase step using UDP-di- N -acetyl bacillosamine as phospho-sugar donor. EpsD is a GT-B fold glycosyl transferase that facilitates the second step in the pathway that utilizes the product of EpsL as an acceptor substrate and UDP- N -acetyl glucosamine as the sugar donor. Thus, the study defines the first two monosaccharides at the reducing end of the growing exopolysaccharide unit. In doing so we provide the first evidence of the presence of bacillosamine in an exopolysaccharide synthesized by a Gram-positive bacterium.

IMPORTANCE

Biofilms are the communal way of life that microbes adopt to increase survival. Key to our ability to systematically promote or ablate biofilm formation is a detailed understanding of the biofilm matrix macromolecules. Here we identify the first two essential steps in the Bacillus subtilis biofilm matrix exopolysaccharide synthesis pathway. Together our studies and approaches provide the foundation for the sequential characterization of the steps in exopolysaccharide biosynthesis, using prior steps to enable chemoenzymatic synthesis of the undecaprenol diphosphate-linked glycan substrates.

Density and temperature controlled fluid extraction in a bacterial biofilm is determined by poly-γ-glutamic acid production

A hallmark of microbial biofilms is the self-production of an extracellular molecular matrix that encases the resident cells. The matrix provides protection from the environment, while spatial heterogeneity of gene expression influences the structural morphology and colony spreading dynamics. Bacillus subtilis is a model bacterial system used to uncover the regulatory pathways and key building blocks required for biofilm growth and development. In this work, we report on the emergence of a highly active population of bacteria during the early stages of biofilm formation, facilitated by the extraction of fluid from the underlying agar substrate. We trace the origin of this fluid extraction to the production of poly-γ-glutamic acid (PGA). The flagella-dependent activity develops behind a moving front of fluid that propagates from the boundary of the biofilm towards the interior. The extent of fluid proliferation is controlled by the presence of extracellular polysaccharides (EPS). We also find that PGA production is positively correlated with higher temperatures, resulting in high-temperature mature biofilm morphologies that are distinct from the rugose colony biofilm architecture typically associated with B. subtilis. Although previous reports have suggested that PGA production does not play a major role in biofilm morphology in the undomesticated isolate NCIB 3610, our results suggest that this strain produces distinct biofilm matrices in response to environmental conditions.

Construction of a mutant Bacillus subtilis strain for high purity poly-γ-glutamic acid production

OBJECTIVE

To construct a Bacillus subtilis strain for improved purity of poly-γ-glutamic acid.

RESULTS

The construction of strain GH16 was achieved by knocking out five genes encoding extracellular proteins and an operon from Bacillus subtilis G423. We then analyzed the amount of protein impurities in the γ-PGA produced by the resulting strain GH16/pHPG, which decreased from 1.48 to 1.39%. Subsequently the fla-che operon, PBSX, as well as the yrpD, ywoF and yclQ genes were knocked out successively, resulting in the mutant strains GH17, GH18 and GH19. Ultimately, the amount of protein impurities was reduced from 1.48 to 0.83%. In addition, the amount of polysaccharide impurities in the γ-PGA was also decreased from 2.21 to 1.93% after knocking out the epsA-O operon.

CONCLUSIONS

The high purity γ-PGA producer was constructed, and the resulting strain was a promising platform for the manufacture of other highly pure extracellular products and secretory proteins.

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.

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.

Profiling Signal Transduction in Global Marine Biofilms

Microbes use signal transduction systems in the processes of swarming motility, antibiotic resistance, virulence, conjugal plasmid transfer, and biofilm formation. However, the signal transduction systems in natural marine biofilms have hardly been profiled. Here we analyzed signal transduction genes in 101 marine biofilm and 91 seawater microbial metagenomes. The abundance of almost all signal transduction-related genes in biofilm microbial communities was significantly higher than that in seawater microbial communities, regardless of substrate types, locations, and durations for biofilm development. In addition, the dominant source microbes of signal transduction genes in marine biofilms were different from those in seawater samples. Co-occurrence network analysis on signal communication between microbes in marine biofilms and seawater microbial communities revealed potential inter-phyla interactions between microorganisms from marine biofilms and seawater. Moreover, phylogenetic tree construction and protein identity comparison displayed that proteins related to signal transductions from Red Sea biofilms were highly similar to those from Red Sea seawater microbial communities, revealing a possible biological basis of interspecies interactions between surface-associated and free-living microbial communities in a local marine environment. Our study revealed the special profile and enrichment of signal transduction systems in marine biofilms and suggested that marine biofilms participate in intercellular interactions of the local ecosystem where they were seeded.

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.

Bacillus subtilis biofilm formation and social interactions

Biofilm formation is a process in which microbial cells aggregate to form collectives that are embedded in a self-produced extracellular matrix. Bacillus subtilis is a Gram-positive bacterium that is used to dissect the mechanisms controlling matrix production and the subsequent transition from a motile planktonic cell state to a sessile biofilm state. The collective nature of life in a biofilm allows emergent properties to manifest, and B. subtilis biofilms are linked with novel industrial uses as well as probiotic and biocontrol processes. In this Review, we outline the molecular details of the biofilm matrix and the regulatory pathways and external factors that control its production. We explore the beneficial outcomes associated with biofilms. Finally, we highlight major advances in our understanding of concepts of microbial evolution and community behaviour that have resulted from studies of the innate heterogeneity of biofilms.

Transcriptomic and Functional Analyses Reveal Roles of AclR, a luxR-type Global Regular, in Regulating Motility and Virulence of Acidovorax citrulli

LuxR-type transcriptional regulators are essential for many physiological processes in bacteria, including pathogenesis. Acidovorax citrulli is a seedborne bacterial pathogen responsible for bacterial fruit blotch, which causes great losses in melon and watermelon worldwide. However, the LuxR-type transcriptional factors in A. citrulli have not been well studied, except for the previously reported LuxR-type regulatory protein, AcrR, involved in regulating virulence and motility. Here, we characterized a second LuxR-type regulator, AclR, in the group II strain Aac-5 of A. citrulli by mutagenesis, virulence and motility assays, and transcriptomic analysis. Deletion of aclR resulted in impaired twitching and swimming motility and flagellar formation and diminished virulence but increased biofilm formation. Transcriptomic analysis revealed that 1,379 genes were differentially expressed in the aclR mutant strain, including 29 genes involved in flagellar assembly and 3 involved in pili formation, suggesting a regulatory role for AclR in multiple important biological functions of A. citrulli. Together, our results not only indicate that AclR plays a global role in transcriptional regulation in A. citrulli influencing motility, biofilm formation, and virulence but also provide perspective regarding the regulatory network of biological functions in A. citrulli.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Surface Sensing and Adaptation in Bacteria

Bacteria thrive both in liquids and attached to surfaces. The concentration of bacteria on surfaces is generally much higher than in the surrounding environment, offering bacteria ample opportunity for mutualistic, symbiotic, and pathogenic interactions. To efficiently populate surfaces, they have evolved mechanisms to sense mechanical or chemical cues upon contact with solid substrata. This is of particular importance for pathogens that interact with host tissue surfaces. In this review we discuss how bacteria are able to sense surfaces and how they use this information to adapt their physiology and behavior to this new environment. We first survey mechanosensing and chemosensing mechanisms and outline how specific macromolecular structures can inform bacteria about surfaces. We then discuss how mechanical cues are converted to biochemical signals to activate specific cellular processes in a defined chronological order and describe the role of two key second messengers, c-di-GMP and cAMP, in this process.

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.

Bacterial extracellular matrix as a natural source of biotechnologically multivalent materials

The extracellular matrix (ECM) is an intricate megastructure made by bacterial cells to form architecturally complex biostructures called biofilms. Protection of cells, modulation of cell-to-cell signalling, cell differentiation and environmental sensing are functions of the ECM that reflect its diverse chemical composition. Proteins, polysaccharides and eDNA have specific functionalities while cooperatively interacting to sustain the architecture and biological relevance of the ECM. The accumulated evidence on the chemical heterogeneity and specific functionalities of ECM components has attracted attention because of their potential biotechnological applications, from agriculture to the water and food industries. This review compiles information on the most relevant bacterial ECM components, the biophysical and chemical features responsible for their biological roles, and their potential to be further translated into biotechnological applications.

Amelioration of Graft-versus-Host Disease by Exopolysaccharide from a Commensal Bacterium

Acute graft-versus-host disease (aGvHD) is a severe, often lethal, complication of hematopoietic stem cell transplantation, and although prophylactic regimens are given as standard pretransplantation therapy, up to 60% of these patients develop aGvHD, and require additional immunosuppressive intervention. We treated mice with a purified probiotic molecule, exopolysaccharide (EPS) from Bacillus subtilis, shortly before and after induction of aGvHD and found that, whereas only 10% of control mice survived to day 80, 70% of EPS-treated mice survived to 80 d. EPS treatment of donor-only mice resulted in ∼60% survival. Using a biosensor mouse model to assess inflammation in live mice during aGvHD, we found that EPS prevented the activation of alloreactive donor T cells. In vitro, EPS did not affect T cells directly but, instead, induced bone marrow-derived dendritic cells (BMDCs) that displayed characteristics of inhibitory dendritic cells (DCs). Development of these BMDCs required TLR4 signaling through both MyD88 and TRIF pathways. Using BMDCs derived from IDO knockout mice, we showed that T cell inhibition by EPS-treated BMDCs was mediated through the suppressive effects of IDO. These studies describe a bacterial molecule that modulates immune responses by inducing inhibitory DCs in a TLR4-dependent manner, and these cells have the capacity to inhibit T cell activation through IDO. We suggest that EPS or EPS-treated DCs can serve as novel agents for preventing aGvHD.

Effects of an EPS Biosynthesis Gene Cluster of Paenibacillus polymyxa WLY78 on Biofilm Formation and Nitrogen Fixation under Aerobic Conditions

Exopolysaccharides (EPS) are of high significance in bacterial biofilm formation. However, the effects of EPS cluster(s) on biofilm formation in Paenibacillus species are little known. In this study, we have shown that Paenibacillus polymyxa WLY78, a N₂-fixing bacterium, can form biofilm. EPS is the major component of the extracellular matrix. The genome of P. polymyxa WLY78 contains two putative gene clusters (designated pep-1 cluster and pep-2 cluster). The pep-1 cluster is composed of 12 putative genes (pepO-lytR) co-located in a 13 kb region. The pep-2 cluster contains 17 putative genes (pepA-pepN) organized as an operon in a 20 kb region. Mutation analysis reveals that the pep-2 cluster is involved in EPS biosynthesis and biofilm formation. Disruption of the pep-2 cluster also leads to the enhancement of motility and change of the colony morphology. In contrast, disruption of the pep-1 cluster does not affect EPS synthesis or biofilm formation. More importantly, the biofilm allowed P. polymyxa WLY78 to fix nitrogen in aerobic conditions, suggesting that biofilm may provide a microaerobic environment for nitrogenase synthesis and activity.

Role of Biofilm Formation by Bacillus pumilus HR10 in Biocontrol against Pine Seedling Damping-Off Disease Caused by Rhizoctonia solani

The biocontrol process mediated by plant growth-promoting rhizobacteria (PGPR) relies on multiple mechanisms. Biofilm formation plays an important role in the ability of PGPR to control plant diseases. Bacillus pumilus HR10, one such PGPR, promotes the growth of Pinus thunbergii. This study showed that the wild-type strain B. pumilus HR10 produces a stable and mature biofilm in vitro. Biofilm-deficient mutants of B. pumilus HR10 with different phenotypes were screened by mutagenesis. The contents of extracellular polysaccharides (EPS) and proteins produced by the mutant strains were significantly reduced, and the biofilms of the mutants were weakened to varying degrees. The swarming abilities of the wild-type and mutant strains were positively correlated with biofilm formation. A colonization assay demonstrated that B. pumilus HR10 could colonize the roots of Pinus massoniana seedlings in a large population and persist, while biofilm-deficient mutants showed weak colonization ability. Furthermore, a biocontrol assay showed that biocontrol efficacy of the mutants was reduced to a certain degree. We determined the inhibitory activity of B. pumilus HR10 and its ability to induce systemic resistance against Rhizoctonia solani of plants. The synthesis of lipopeptide antibiotics is probably involved in biofilm formation by B. pumilus HR10. These observations not only provide a reference for further research about the coordinated action between biofilm formation and the multiple biocontrol mechanisms of B. pumilus HR10 but also improve the understanding of the regulatory pathway of biofilm formation by B. pumilus HR10.

The extracellular matrix protein TasA is a developmental cue that maintains a motile subpopulation within Bacillus subtilis biofilms

In nature, bacteria form biofilms-differentiated multicellular communities attached to surfaces. Within these generally sessile biofilms, a subset of cells continues to express motility genes. We found that this subpopulation enabled Bacillus subtilis biofilms to expand on high-friction surfaces. The extracellular matrix (ECM) protein TasA was required for the expression of flagellar genes. In addition to its structural role as an adhesive fiber for cell attachment, TasA acted as a developmental signal stimulating a subset of biofilm cells to revert to a motile phenotype. Transcriptomic analysis revealed that TasA stimulated the expression of a specific subset of genes whose products promote motility and repress ECM production. Spontaneous suppressor mutations that restored motility in the absence of TasA revealed that activation of the biofilm-motility switch by the two-component system CssR/CssS antagonized the TasA-mediated reversion to motility in biofilm cells. Our results suggest that although mostly sessile, biofilms retain a degree of motility by actively maintaining a motile subpopulation.

The exopolysaccharide-eDNA interaction modulates 3D architecture of Bacillus subtilis biofilm

BACKGROUND

Bacterial biofilms are surface-adherent microbial communities in which individual cells are surrounded by a self-produced extracellular matrix of polysaccharides, extracellular DNA (eDNA) and proteins. Interactions among matrix components within biofilms are responsible for creating an adaptable structure during biofilm development. However, it is unclear how the interactions among matrix components contribute to the construction of the three-dimensional (3D) biofilm architecture.

RESULTS

DNase I treatment significantly inhibited Bacillus subtilis biofilm formation in the early phases of biofilm development. Confocal laser scanning microscopy (CLSM) and image analysis revealed that eDNA was cooperative with exopolysaccharide (EPS) in the early stages of B. subtilis biofilm development, while EPS played a major structural role in the later stages. In addition, deletion of the EPS production gene epsG in B. subtilis SBE1 resulted in loss of the interaction between EPS and eDNA and reduced the biofilm biomass in pellicles at the air-liquid interface. The physical interaction between these two essential biofilm matrix components was confirmed by isothermal titration calorimetry (ITC).

CONCLUSIONS

Biofilm 3D structures become interconnected through surrounding eDNA and EPS. eDNA interacts with EPS in the early phases of biofilm development, while EPS mainly participates in the maturation of biofilms. The findings of this study provide a better understanding of the role of the interaction between eDNA and EPS in shaping the biofilm 3D matrix structure and biofilm formation.

TnFLX: a Third-Generation mariner-Based Transposon System for Bacillus subtilis

Random transposon mutagenesis is a powerful and unbiased genetic approach to answer fundamental biological questions. Here, we introduce an improved mariner-based transposon system with enhanced stability during propagation and versatile applications in mutagenesis. We used a low-copy-number plasmid as a transposon delivery vehicle, which affords a lower frequency of unintended recombination during vector construction and propagation in Escherichia coli We generated a variety of transposons allowing for gene disruption or artificial overexpression, each in combination with one of four different antibiotic resistance markers. In addition, we provide transposons that will report gene/protein expression due to transcriptional or translational coupling. We believe that the TnFLX system will help enhance the flexibility of future transposon modification and application in Bacillus and other organisms.IMPORTANCE The stability of transposase-encoding vectors during cloning and propagation is crucial for the reliable application of transposons. Here, we increased the stability of the mariner delivery vehicle in E. coli Moreover, the TnFLX transposon system will improve the application of forward genetic methods with an increased number of antibiotic resistance markers and the ability to generate unbiased green fluorescent protein (GFP) fusions to report on protein translation and subcellular localization.

Identification of Genes Required for Glucan Exopolysaccharide Production in Lactobacillus johnsonii Suggests a Novel Biosynthesis Mechanism

Exopolysaccharides are key components of the surfaces of their bacterial producers, contributing to protection, microbial and host interactions, and even virulence. They also have significant applications in industry, and understanding their biosynthetic mechanisms may allow improved production of novel and valuable polymers. Four categories of bacterial exopolysaccharide biosynthesis have been described in detail, but novel enzymes and glycosylation mechanisms are still being described. Our findings that a putative bactoprenol glycosyltransferase and flippase are essential to homopolysaccharide biosynthesis in Lactobacillus johnsonii FI9785 indicate that there may be an alternative mechanism of glucan biosynthesis to the glucansucrase pathway. Disturbance of this synthesis leads to a slow-growth phenotype. Further elucidation of this biosynthesis may give insight into exopolysaccharide production and its impact on the bacterial cell.

Lactobacillus johnsonii FI9785 makes two capsular exopolysaccharides—a heteropolysaccharide (EPS2) encoded by the eps operon and a branched glucan homopolysaccharide (EPS1). The homopolysaccharide is synthesized in the absence of sucrose, and there are no typical glucansucrase genes in the genome. Quantitative proteomics was used to compare the wild type to a mutant where EPS production was reduced to attempt to identify proteins associated with EPS1 biosynthesis. A putative bactoprenol glycosyltransferase, FI9785_242 (242), was less abundant in the Δeps_cluster mutant strain than in the wild type. Nuclear magnetic resonance (NMR) analysis of isolated EPS showed that deletion of the FI9785_242 gene (242) prevented the accumulation of EPS1, without affecting EPS2 synthesis, while plasmid complementation restored EPS1 production. The deletion of 242 also produced a slow-growth phenotype, which could be rescued by complementation. 242 shows amino acid homology to bactoprenol glycosyltransferase GtrB, involved in O-antigen glycosylation, while in silico analysis of the neighboring gene 241 suggested that it encodes a putative flippase with homology to the GtrA superfamily. Deletion of 241 also prevented production of EPS1 and again caused a slow-growth phenotype, while plasmid complementation reinstated EPS1 synthesis. Both genes are highly conserved in L. johnsonii strains isolated from different environments. These results suggest that there may be a novel mechanism for homopolysaccharide synthesis in the Gram-positive L. johnsonii.

IMPORTANCE Exopolysaccharides are key components of the surfaces of their bacterial producers, contributing to protection, microbial and host interactions, and even virulence. They also have significant applications in industry, and understanding their biosynthetic mechanisms may allow improved production of novel and valuable polymers. Four categories of bacterial exopolysaccharide biosynthesis have been described in detail, but novel enzymes and glycosylation mechanisms are still being described. Our findings that a putative bactoprenol glycosyltransferase and flippase are essential to homopolysaccharide biosynthesis in Lactobacillus johnsonii FI9785 indicate that there may be an alternative mechanism of glucan biosynthesis to the glucansucrase pathway. Disturbance of this synthesis leads to a slow-growth phenotype. Further elucidation of this biosynthesis may give insight into exopolysaccharide production and its impact on the bacterial cell.

The Flagellar Gene Regulates Biofilm Formation and Mussel Larval Settlement and Metamorphosis

Biofilms are critical components of most marine systems and provide biochemical cues that can significantly impact overall community composition. Although progress has been made in the bacteria–animal interaction, the molecular basis of modulation of settlement and metamorphosis in most marine animals by bacteria is poorly understood. Here, Pseudoalteromonas marina showing inducing activity on mussel settlement and metamorphosis was chosen as a model to clarify the mechanism that regulates the bacteria–mussel interaction. We constructed a flagellin synthetic protein gene fliP deletion mutant of P. marina and checked whether deficiency of fliP gene will impact inducing activity, motility, and extracellular polymeric substances of biofilms. Furthermore, we examined the effect of flagellar proteins extracted from bacteria on larval settlement and metamorphosis. The deletion of the fliP gene caused the loss of the flagella structure and motility of the ΔfliP strain. Deficiency of the fliP gene promoted the biofilm formation and changed biofilm matrix by reducing β-polysaccharides and increasing extracellular proteins and finally reduced biofilm-inducing activities. Flagellar protein extract promoted mussel metamorphosis, and ΔfliP biofilms combined with additional flagellar proteins induced similar settlement and metamorphosis rate compared to that of the wild-type strain. These findings provide novel insight on the molecular interactions between bacteria and mussels.

Structural insights into the mechanism of c-di-GMP-bound YcgR regulating flagellar motility in Escherichia coli

The motile-sessile transition is critical for bacterial survival and growth. Cyclic-di-GMP (c-di-GMP) plays a central role in controlling this transition and regulating biofilm formation via various effectors. As an effector of c-di-GMP in Escherichia coli and related species, the PilZ domain-containing protein YcgR responds to elevated c-di-GMP concentrations and acts on the flagellar motor to suppress bacterial motility in a brakelike fashion, which promotes bacterial surface attachment. To date, several target proteins within the motor, MotA, FliG, and FliM, along with different regulatory mechanisms have been reported. However, how YcgR acts on these components remains unclear. Here, we report that activated YcgR stably binds to MotA at the MotA-FliG interface and thereby regulates bacterial swimming. Biochemical and structural analyses revealed that c-di-GMP rearranges the PilZ domain configuration, resulting in the formation of a MotA-binding patch consisting of an RXXXR motif and the C-tail helix α3. Moreover, we noted that a conserved region in the YcgR-N domain, which is independent of MotA interaction, is necessary for motility regulation. On the basis of these findings, we infer that the YcgR-N domain is required for activity on other motor proteins. We propose that activated YcgR appends to MotA via its PilZ domain and thereby interrupts the MotA-FliG interaction and simultaneously interacts with other motor proteins via its YcgR-N domain to inhibit flagellar motility. Our findings suggest that the mode of interaction between YcgR and motor proteins may be shared by other PilZ family proteins.

Zn(II) suppresses biofilm formation in Bacillus amyloliquefaciens by inactivation of the Mn(II) uptake

Biofilms are architecturally complex communities of microbial cells held together by a self-produced extracellular matrix. Considerable research has focused on the environmental signals that trigger or inhibit biofilm formation by affecting cellular signalling pathways; however, response to soil cues in plant-associated Bacillus has remained largely unaddressed. Therefore, we aimed to investigate the effect of Zn(II) ions in biofilm formation of Bacillus amyloliquefaciens FZB42. We demonstrated that the biofilm formation of B. amyloliquefaciens FZB42 was abolished by Zn(II) at non-deleterious concentrations. Moreover, Zn(II) blocked matrix exopolysaccharide and TasA accumulations. Furthermore, the presence of Zn(II) suppressed expression of the response regulator Spo0F but not of sensor histidine kinases KinA-D. Suppression of phosphorelay by excess Zn interferes with sinI induction under biofilm-inducing conditions, leading to repression of transcription of operons epsA-O and tapA-sigW-tasA. Addition of Zn(II) decreased the intracellular Mn(II) level by competing for binding to the solute-binding protein MntA during Mn(II) uptake. These results suggest that the metal ion Zn(II) has a negative effect on biofilm formation in the plant growth promoting and biocontrol bacterium B. amyloliquefaciens FZB42.

Modulation of flagellar rotation in surface-attached bacteria: A pathway for rapid surface-sensing after flagellar attachment

Attachment is a necessary first step in bacterial commitment to surface-associated behaviors that include colonization, biofilm formation, and host-directed virulence. The Gram-negative opportunistic pathogen Pseudomonas aeruginosa can initially attach to surfaces via its single polar flagellum. Although many bacteria quickly detach, some become irreversibly attached and express surface-associated structures, such as Type IV pili, and behaviors, including twitching motility and biofilm initiation. P. aeruginosa that lack the GTPase FlhF assemble a randomly placed flagellum that is motile; however, we observed that these mutant bacteria show defects in biofilm formation comparable to those seen for non-motile, aflagellate bacteria. This phenotype was associated with altered behavior of ΔflhF bacteria immediately following surface-attachment. Forward and reverse genetic screens led to the discovery that FlhF interacts with FimV to control flagellar rotation at a surface, and implicated cAMP signaling in this pathway. Although cAMP controls many transcriptional programs in P. aeruginosa, known targets of this second messenger were not required to modulate flagellar rotation in surface-attached bacteria. Instead, alterations in switching behavior of the motor appeared to result from direct or indirect effects of cAMP on switch complex proteins and/or the stators associated with them.

Not Just Going with the Flow: The Effects of Fluid Flow on Bacteria and Plankton

Microorganisms often live in habitats characterized by fluid flow, from lakes and oceans to soil and the human body. Bacteria and plankton experience a broad range of flows, from the chaotic motion characteristic of turbulence to smooth flows at boundaries and in confined environments. Flow creates forces and torques that affect the movement, behavior, and spatial distribution of microorganisms and shapes the chemical landscape on which they rely for nutrient acquisition and communication. Methodological advances and closer interactions between physicists and biologists have begun to reveal the importance of flow-microorganism interactions and the adaptations of microorganisms to flow. Here we review selected examples of such interactions from bacteria, phytoplankton, larvae, and zooplankton. We hope that this article will serve as a blueprint for a more in-depth consideration of the effects of flow in the biology of microorganisms and that this discussion will stimulate further multidisciplinary effort in understanding this important component of microorganism habitats.

Functional Regulators of Bacterial Flagella

Bacteria move by a variety of mechanisms, but the best understood types of motility are powered by flagella (72). Flagella are complex machines embedded in the cell envelope that rotate a long extracellular helical filament like a propeller to push cells through the environment. The flagellum is one of relatively few biological machines that experience continuous 360° rotation, and it is driven by one of the most powerful motors, relative to its size, on earth. The rotational force (torque) generated at the base of the flagellum is essential for motility, niche colonization, and pathogenesis. This review describes regulatory proteins that control motility at the level of torque generation.