Bacillus subtilis Biofilms: a Matter of Individual Choice

ABSTRACT Bacillus subtilis has the capacity to choose between two mutually exclusive lifestyles: biofilm formation and flagellum-mediated swimming motility. Interestingly, this choice is made at the individual cell level, with bacterial cells in a population expressing genes required for biofilm formation or genes required for swimming motility but not both. A bistable switch controls the biofilm-versus-swimming decision, resulting in an evolutionarily favorable strategy known as “bet hedging” that ensures that subpopulations of bacteria continue to grow as conditions change and/or become unfavorable. In a recent issue of mBio, J. Kampf and colleagues (mBio 9:e01464-18, 2018, https://doi.org/10.1128/mBio.01464-18) reported the use of a combination of genetics and microfluidics to reveal that the interplay that occurs between the SinR and YmdB proteins underlies the B. subtilis choice between biofilm formation and swimming motility. Their report suggests that B. subtilis experiences selective pressure to form biofilms while maintaining reserve cell subpopulations with the capacity to swim away.

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In VitroAnalyses of the Effects of Heparin and Parabens on Candida albicans Biofilms and Planktonic Cells

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.05061-11 ◽

2011 ◽

Vol 56 (1) ◽

pp. 148-153 ◽

Cited By ~ 15

Author(s):

Marisa H. Miceli ◽

Stella M. Bernardo ◽

T. S. Neil Ku ◽

Carla Walraven ◽

Samuel A. Lee

Keyword(s):

Candida Albicans ◽

Metabolic Activity ◽

Biofilm Formation ◽

High Dose ◽

Dependent Manner ◽

Planktonic Cells ◽

Content Type ◽

Heparin Sodium ◽

The Individual

ABSTRACTInfections and thromboses are the most common complications associated with central venous catheters. Suggested strategies for prevention and management of these complications include the use of heparin-coated catheters, heparin locks, and antimicrobial lock therapy. However, the effects of heparin onCandida albicansbiofilms and planktonic cells have not been previously studied. Therefore, we sought to determine thein vitroeffect of a heparin sodium preparation (HP) on biofilms and planktonic cells ofC. albicans. Because HP contains two preservatives, methyl paraben (MP) and propyl paraben (PP), these compounds and heparin sodium without preservatives (Pure-H) were also tested individually. The metabolic activity of the mature biofilm after treatment was assessed using XTT [2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide] reduction and microscopy. Pure-H, MP, and PP caused up to 75, 85, and 60% reductions of metabolic activity of the mature preformedC. albicansbiofilms, respectively. Maximal efficacy against the mature biofilm was observed with HP (up to 90%) compared to the individual compounds (P< 0.0001). Pure-H, MP, and PP each inhibitedC. albicansbiofilm formation up to 90%. A complete inhibition of biofilm formation was observed with HP at 5,000 U/ml and higher. When tested against planktonic cells, each compound inhibited growth in a dose-dependent manner. These data indicated that HP, MP, PP, and Pure-H havein vitroantifungal activity againstC. albicansmature biofilms, formation of biofilms, and planktonic cells. Investigation of high-dose heparin-based strategies (e.g., heparin locks) in combination with traditional antifungal agents for the treatment and/or prevention ofC. albicansbiofilms is warranted.

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PBP4 and PBP5 are involved in regulating exopolysaccharide synthesis during Escherichia coli biofilm formation

Microbiology ◽

10.1099/mic.0.001031 ◽

2021 ◽

Vol 167 (3) ◽

Author(s):

Sathi Mallick ◽

Shanti Kiran ◽

Tapas Kumar Maiti ◽

Anindya S. Ghosh

Keyword(s):

Escherichia Coli ◽

Biofilm Formation ◽

Type Species ◽

Pentose Phosphate ◽

Bacterial Cells ◽

Surface Adhesion ◽

Content Type ◽

Penicillin Binding Proteins ◽

E Coli ◽

Link Type

Escherichia coli low-molecular-mass (LMM) Penicillin-binding proteins (PBPs) help in hydrolysing the peptidoglycan fragments from their cell wall and recycling them back into the growing peptidoglycan matrix, in addition to their reported involvement in biofilm formation. Biofilms are external slime layers of extra-polymeric substances that sessile bacterial cells secrete to form a habitable niche for themselves. Here, we hypothesize the involvement of Escherichia coli LMM PBPs in regulating the nature of exopolysaccharides (EPS) prevailing in its extra-polymeric substances during biofilm formation. Therefore, this study includes the assessment of physiological characteristics of E. coli CS109 LMM PBP deletion mutants to address biofilm formation abilities, viability and surface adhesion. Finally, EPS from parent CS109 and its ΔPBP4 and ΔPBP5 mutants were purified and analysed for sugars present. Deletions of LMM PBP reduced biofilm formation, bacterial adhesion and their viability in biofilms. Deletions also diminished EPS production by ΔPBP4 and ΔPBP5 mutants, purification of which suggested an increased overall negative charge compared with their parent. Also, EPS analyses from both mutants revealed the appearance of an unusual sugar, xylose, that was absent in CS109. Accordingly, the reason for reduced biofilm formation in LMM PBP mutants may be speculated as the subsequent production of xylitol and a hindrance in the standard flow of the pentose phosphate pathway.

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Clarithromycin Exerts an Antibiofilm Effect against Salmonella enterica Serovar Typhimurium rdar Biofilm Formation and Transforms the Physiology towards an Apparent Oxygen-Depleted Energy and Carbon Metabolism

Infection and Immunity ◽

10.1128/iai.00510-20 ◽

2020 ◽

Vol 88 (11) ◽

Author(s):

Munirah Zafar ◽

Humera Jahan ◽

Sulman Shafeeq ◽

Manfred Nimtz ◽

Lothar Jänsch ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Salmonella Enterica ◽

Biofilm Formation ◽

Antibiofilm Activity ◽

Bacterial Cells ◽

Content Type ◽

Regulatory Pathways ◽

Heat Shock Stress ◽

Extracellular Matrix Components ◽

Serovar Typhimurium

ABSTRACT Upon biofilm formation, production of extracellular matrix components and alteration in physiology and metabolism allows bacteria to build up multicellular communities which can facilitate nutrient acquisition during unfavorable conditions and provide protection toward various forms of environmental stresses to individual cells. Thus, bacterial cells within biofilms become tolerant against antimicrobials and the immune system. In the present study, we evaluated the antibiofilm activity of the macrolides clarithromycin and azithromycin. Clarithromycin showed antibiofilm activity against rdar (red, dry, and rough) biofilm formation of the gastrointestinal pathogen Salmonella enterica serovar Typhimurium ATCC 14028 (Nalr) at a 1.56 μM subinhibitory concentration in standing culture and dissolved cell aggregates at 15 μM in a microaerophilic environment, suggesting that the oxygen level affects the activity of the drug. Treatment with clarithromycin significantly decreased transcription and production of the rdar biofilm activator CsgD, with biofilm genes such as csgB and adrA to be concomitantly downregulated. Although fliA and other flagellar regulon genes were upregulated, apparent motility was downregulated. RNA sequencing showed a holistic cell response upon clarithromycin exposure, whereby not only genes involved in the biofilm-related regulatory pathways but also genes that likely contribute to intrinsic antimicrobial resistance, and the heat shock stress response were differentially regulated. Most significantly, clarithromycin exposure shifted the cells toward an apparent oxygen- and energy-depleted status, whereby the metabolism that channels into oxidative phosphorylation was downregulated, and energy gain by degradation of propane 1,2-diol, ethanolamine and l-arginine catabolism, potentially also to prevent cytosolic acidification, was upregulated. This analysis will allow the subsequent identification of novel intrinsic antimicrobial resistance determinants.

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Selective Pressure for Biofilm Formation in Bacillus subtilis: Differential Effect of Mutations in the Master Regulator SinR on Bistability

mBio ◽

10.1128/mbio.01464-18 ◽

2018 ◽

Vol 9 (5) ◽

Cited By ~ 6

Author(s):

Jan Kampf ◽

Jan Gerwig ◽

Kerstin Kruse ◽

Robert Cleverley ◽

Miriam Dormeyer ◽

...

Keyword(s):

Gene Expression ◽

Bacillus Subtilis ◽

Biofilm Formation ◽

Type Strain ◽

Wild Type Strain ◽

Selective Pressure ◽

Wild Type ◽

Master Regulator ◽

Form Complex ◽

Content Type

ABSTRACT Biofilm formation by Bacillus subtilis requires the expression of genes encoding enzymes for extracellular polysaccharide synthesis and for an amyloid-like protein. The master regulator SinR represses all the corresponding genes, and repression of these key biofilm genes is lifted when SinR interacts with its cognate antagonist proteins. The YmdB phosphodiesterase is a recently discovered factor that is involved in the control of SinR activity: cells lacking YmdB exhibit hyperactive SinR and are unable to relieve the repression of the biofilm genes. In this study, we have examined the dynamics of gene expression patterns in wild-type and ymdB mutant cells by microfluidic analysis coupled to time-lapse microscopy. Our results confirm the bistable expression pattern for motility and biofilm genes in the wild-type strain and the loss of biofilm gene expression in the mutant. Moreover, we demonstrated dynamic behavior in subpopulations of the wild-type strain that is characterized by switches in sets of the expressed genes. In order to gain further insights into the role of YmdB, we isolated a set of spontaneous suppressor mutants derived from ymdB mutants that had regained the ability to form complex colonies and biofilms. Interestingly, all of the mutations affected SinR. In some mutants, large genomic regions encompassing sinR were deleted, whereas others had alleles encoding SinR variants. Functional and biochemical studies with these SinR variants revealed how these proteins allowed biofilm gene expression in the ymdB mutant strains. IMPORTANCE Many bacteria are able to choose between two mutually exclusive lifestyles: biofilm formation and motility. In the model bacterium Bacillus subtilis, this choice is made by each individual cell rather than at the population level. The transcriptional repressor SinR is the master regulator in this decision-making process. The regulation of SinR activity involves complex control of its own expression and of its interaction with antagonist proteins. We show that the YmdB phosphodiesterase is required to allow the expression of SinR-repressed genes in a subpopulation of cells and that such subpopulations can switch between different SinR activity states. Suppressor analyses revealed that ymdB mutants readily acquire mutations affecting SinR, thus restoring biofilm formation. These findings suggest that B. subtilis cells experience selective pressure to form the extracellular matrix that is characteristic of biofilms and that YmdB is required for the homeostasis of SinR and/or its antagonists.

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Ribosome Reconstruction during Recovery from High-Hydrostatic-Pressure-Induced Injury in Bacillus subtilis

Applied and Environmental Microbiology ◽

10.1128/aem.01640-19 ◽

2019 ◽

Vol 86 (1) ◽

Cited By ~ 3

Author(s):

Huyen Thi Minh Nguyen ◽

Genki Akanuma ◽

Tu Thi Minh Hoa ◽

Yuji Nakai ◽

Keitarou Kimura ◽

...

Keyword(s):

Bacillus Subtilis ◽

Hydrostatic Pressure ◽

High Hydrostatic Pressure ◽

Growth Arrest ◽

Recovery Process ◽

Dependent Manner ◽

Bacterial Cells ◽

Vegetative Cells ◽

Content Type ◽

Growth Recovery

ABSTRACT Vegetative cells of Bacillus subtilis can recover from injury after high-hydrostatic-pressure (HHP) treatment at 250 MPa. DNA microarray analysis revealed that substantial numbers of ribosomal genes and translation-related genes (e.g., translation initiation factors) were upregulated during the growth arrest phase after HHP treatment. The transcript levels of cold shock-responsive genes, whose products play key roles in efficient translation, and heat shock-responsive genes, whose products mediate correct protein folding or degrade misfolded proteins, were also upregulated. In contrast, the transcript level of hpf, whose product (Hpf) is involved in ribosome inactivation through the dimerization of 70S ribosomes, was downregulated during the growth arrest phase. Sucrose density gradient sedimentation analysis revealed that ribosomes were dissociated in a pressure-dependent manner and then reconstructed. We also found that cell growth after HHP-induced injury was apparently inhibited by the addition of Mn2+ or Zn2+ to the recovery medium. Ribosome reconstruction in the HHP-injured cells was also significantly delayed in the presence of Mn2+ or Zn2+. Moreover, Zn2+, but not Mn2+, promoted dimer formation of 70S ribosomes in the HHP-injured cells. Disruption of the hpf gene suppressed the Zn2+-dependent accumulation of ribosome dimers, partially relieving the inhibitory effect of Zn2+ on the growth recovery of HHP-treated cells. In contrast, it was likely that Mn2+ prevented ribosome reconstruction without stimulating ribosome dimerization. Our results suggested that both Mn2+ and Zn2+ can prevent ribosome reconstruction, thereby delaying the growth recovery of HHP-injured B. subtilis cells. IMPORTANCE HHP treatment is used as a nonthermal processing technology in the food industry to inactivate bacteria while retaining high quality of foods under suppressed chemical reactions. However, some populations of bacterial cells may survive the inactivation. Although the survivors are in a transient nongrowing state due to HHP-induced injury, they can recover from the injury and then start growing, depending on the postprocessing conditions. The recovery process in terms of cellular components after the injury remains unclear. Transcriptome analysis using vegetative cells of Bacillus subtilis revealed that the translational machinery can preferentially be reconstructed after HHP treatment. We found that both Mn2+ and Zn2+ prolonged the growth-arrested stage of HHP-injured cells by delaying ribosome reconstruction. It is likely that ribosome reconstruction is crucial for the recovery of growth ability in HHP-injured cells. This study provides further understanding of the recovery process in HHP-injured B. subtilis cells.

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Galactose Metabolism Plays a Crucial Role in Biofilm Formation by Bacillus subtilis

mBio ◽

10.1128/mbio.00184-12 ◽

2012 ◽

Vol 3 (4) ◽

Cited By ~ 83

Author(s):

Yunrong Chai ◽

Pascale B. Beauregard ◽

Hera Vlamakis ◽

Richard Losick ◽

Roberto Kolter

Keyword(s):

Bacillus Subtilis ◽

Biofilm Formation ◽

Carbon Sources ◽

Galactose Metabolism ◽

Content Type ◽

Leloir Pathway ◽

The Matrix ◽

Living Organisms ◽

Galactose Metabolites ◽

Biofilm Matrix

ABSTRACTGalactose is a common monosaccharide that can be utilized by all living organisms via the activities of three main enzymes that make up the Leloir pathway: GalK, GalT, and GalE. InBacillus subtilis, the absence of GalE causes sensitivity to exogenous galactose, leading to rapid cell lysis. This effect can be attributed to the accumulation of toxic galactose metabolites, since thegalEmutant is blocked in the final step of galactose catabolism. In a screen for suppressor mutants restoring viability to agalEnull mutant in the presence of galactose, we identified mutations insinR, which is the major biofilm repressor gene. These mutations caused an increase in the production of the exopolysaccharide (EPS) component of the biofilm matrix. We propose that UDP-galactose is the toxic galactose metabolite and that it is used in the synthesis of EPS. Thus, EPS production can function as a shunt mechanism for this toxic molecule. Additionally, we demonstrated that galactose metabolism genes play an essential role inB. subtilisbiofilm formation and that the expressions of both thegalandepsgenes are interrelated. Finally, we propose thatB. subtilisand other members of theBacillusgenus may have evolved to utilize naturally occurring polymers of galactose, such as galactan, as carbon sources.IMPORTANCEBacteria switch from unicellular to multicellular states by producing extracellular matrices that contain exopolysaccharides. In such aggregates, known as biofilms, bacteria are more resistant to antibiotics. This makes biofilms a serious problem in clinical settings. The resilience of biofilms makes them very useful in industrial settings. Thus, understanding the production of biofilm matrices is an important problem in microbiology. In studying the synthesis of the biofilm matrix ofBacillus subtilis, we provide further understanding of a long-standing microbiological observation that certain mutants defective in the utilization of galactose became sensitive to it. In this work, we show that the toxicity observed before was because cells were grown under conditions that were not propitious to produce the exopolysaccharide component of the matrix. When cells are grown under conditions that favor matrix production, the toxicity of galactose is relieved. This allowed us to demonstrate that galactose metabolism is essential for the synthesis of the extracellular matrix.

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In VitroEffects of Polyphosphate against Prevotella intermedia in Planktonic Phase and Biofilm

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01861-15 ◽

2015 ◽

Vol 60 (2) ◽

pp. 818-826 ◽

Cited By ~ 4

Author(s):

Eun-Young Jang ◽

Minjung Kim ◽

Mi Hee Noh ◽

Ji-Hoi Moon ◽

Jin-Yong Lee

Keyword(s):

Biofilm Formation ◽

Sodium Tripolyphosphate ◽

Dilution Method ◽

Agar Dilution Method ◽

Prevotella Intermedia ◽

Dependent Manner ◽

Bacterial Cells ◽

Concentration Dependent Manner ◽

Content Type ◽

Planktonic Phase

ABSTRACTPolyphosphate (polyP) has gained a wide interest in the food industry due to its potential as a decontaminating agent. In this study, we examined the effect of sodium tripolyphosphate (polyP3; Na5P3O10) against planktonic and biofilm cells ofPrevotella intermedia, a major oral pathogen. The MIC of polyP3 againstP. intermediaATCC 49046 determined by agar dilution method was 0.075%, while 0.05% polyP3 was bactericidal againstP. intermediain time-kill analysis performed using liquid medium. A crystal violet binding assay for the assessment of biofilm formation byP. intermediashowed that sub-MICs of polyP3 significantly decreased biofilm formation. Under the scanning electron microscope, decreased numbers ofP. intermediacells forming the biofilms were observed when the bacterial cells were incubated with 0.025% or higher concentrations of polyP3. Assessment of biofilm viability with LIVE/DEAD staining and viable cell count methods showed that 0.05% or higher concentrations of polyP3 significantly decreased the viability of the preformed biofilms in a concentration-dependent manner. The zone sizes of alpha-hemolysis formed on horse blood agar produced byP. intermediawere decreased in the presence of polyP3. The expression of the genes encoding hemolysins and the genes of the hemin uptake (hmu) locus was downregulated by polyP3. Collectively, our results show that polyP is an effective antimicrobial agent againstP. intermediain biofilms as well as planktonic phase, interfering with the process of hemin acquisition by the bacterium.

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Engineering of Bacillus subtilis Strains To Allow Rapid Characterization of Heterologous Diguanylate Cyclases and Phosphodiesterases

Applied and Environmental Microbiology ◽

10.1128/aem.01638-14 ◽

2014 ◽

Vol 80 (19) ◽

pp. 6167-6174 ◽

Cited By ~ 20

Author(s):

Xiaohui Gao ◽

Xiao Dong ◽

Sundharraman Subramanian ◽

Paige M. Matthews ◽

Caleb A. Cooper ◽

...

Keyword(s):

Bacillus Subtilis ◽

Biofilm Formation ◽

Fluorescent Protein ◽

Threshold Level ◽

Metabolic Enzymes ◽

Guanosine Monophosphate ◽

Content Type ◽

Diguanylate Cyclases ◽

Rapid Characterization ◽

Green Fluorescent

ABSTRACTMicrobial processes, including biofilm formation, motility, and virulence, are often regulated by changes in the available concentration of cyclic dimeric guanosine monophosphate (c-di-GMP). Generally, high c-di-GMP concentrations are correlated with decreased motility and increased biofilm formation and low c-di-GMP concentrations are correlated with an increase in motility and activation of virulence pathways. The study of c-di-GMP is complicated, however, by the fact that organisms often encode dozens of redundant enzymes that synthesize and hydrolyze c-di-GMP, diguanylate cyclases (DGCs), and c-di-GMP phosphodiesterases (PDEs); thus, determining the contribution of any one particular enzyme is challenging. In an effort to develop a facile system to study c-di-GMP metabolic enzymes, we have engineered a suite ofBacillus subtilisstrains to assess the effect of individual heterologously expressed proteins on c-di-GMP levels. As a proof of principle, we characterized all 37 known genes encoding predicted DGCs and PDEs inClostridium difficileusing parallel readouts of swarming motility and fluorescence from green fluorescent protein (GFP) expressed under the control of a c-di-GMP-controlled riboswitch. We found that 27 of the 37 putativeC. difficile630 c-di-GMP metabolic enzymes had either active cyclase or phosphodiesterase activity, with agreement between our motility phenotypes and fluorescence-based c-di-GMP reporter. Finally, we show that there appears to be a threshold level of c-di-GMP needed to inhibit motility inBacillus subtilis.

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Exposure of Bacillus subtilis to Low Pressure (5 Kilopascals) Induces Several Global Regulons, Including Those Involved in the SigB-Mediated General Stress Response

Applied and Environmental Microbiology ◽

10.1128/aem.00885-14 ◽

2014 ◽

Vol 80 (16) ◽

pp. 4788-4794 ◽

Cited By ~ 12

Author(s):

Samantha M. Waters ◽

José A. Robles-Martínez ◽

Wayne L. Nicholson

Keyword(s):

Bacillus Subtilis ◽

Stress Response ◽

High Pressures ◽

Low Pressure ◽

Bacterial Cells ◽

Content Type ◽

General Stress Response ◽

Cellular Processes ◽

General Stress ◽

Microbial Responses

ABSTRACTStudies of how microorganisms respond to pressure have been limited mostly to the extreme high pressures of the deep sea (i.e., the piezosphere). In contrast, despite the fact that the growth of most bacteria is inhibited at pressures below ∼2.5 kPa, little is known of microbial responses to low pressure (LP). To study the global LP response, we performed transcription microarrays onBacillus subtiliscells grown under normal atmospheric pressure (∼101 kPa) and a nearly inhibitory LP (5 kPa), equivalent to the pressure found at an altitude of ∼20 km. Microarray analysis revealed altered levels of 363 transcripts belonging to several global regulons (AbrB, CcpA, CodY, Fur, IolR, ResD, Rok, SigH, Spo0A). Notably, the highest number of upregulated genes, 86, belonged to the SigB-mediated general stress response (GSR) regulon. Upregulation of the GSR by LP was confirmed by monitoring the expression of the SigB-dependentctc-lacZreporter fusion. Measuring transcriptome changes resulting from exposure of bacterial cells to LP reveals insights into cellular processes that may respond to LP exposure.

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Tryptophan Inhibits Biofilm Formation by Pseudomonas aeruginosa

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00007-13 ◽

2013 ◽

Vol 57 (4) ◽

pp. 1921-1925 ◽

Cited By ~ 39

Author(s):

Kenneth S. Brandenburg ◽

Karien J. Rodriguez ◽

Jonathan F. McAnulty ◽

Christopher J. Murphy ◽

Nicholas L. Abbott ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Tissue Culture ◽

Biofilm Formation ◽

Chronic Wounds ◽

Inhibitory Effect ◽

Equimolar Ratio ◽

Biofilm Growth ◽

Content Type ◽

Swimming Motility

ABSTRACTBiofilm formation byPseudomonas aeruginosahas been implicated in the pathology of chronic wounds. Both thedandlisoforms of tryptophan inhibitedP. aeruginosabiofilm formation on tissue culture plates, with an equimolar ratio ofdandlisoforms producing the greatest inhibitory effect. Addition ofd-/l-tryptophan to existing biofilms inhibited further biofilm growth and caused partial biofilm disassembly. Tryptophan significantly increased swimming motility, which may be responsible in part for diminished biofilm formation byP. aeruginosa.

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