Biofilm formation by Bacillus subtilis: new insights into regulatory strategies and assembly mechanisms

EpsM from Bacillus subtilis 168 has UDP-2,4,6-trideoxy-2-acetamido-4-amino glucose acetyltransferase activity in vitro

Bacillus subtilis 168 EpsM (UniProt id P71063) has been electronically annotated as putative acetyltransferase in the UniProt database. The gene epsM was cloned and overexpressed in E. coli with an N-terminal GST tag. The purified fusion protein was shown by absorption spectroscopy, autoradiography and reverse phase HPLC to catalyse the conversion of UDP-2,4,6-trideoxy-2-acetamido-4-amino glucose to UDP-2,4,6-trideoxy-2,4-diacetamido glucose, commonly known as N,N'-diacetylbacillosamine, using acetyl coenzyme A as the donor substrate. His146 was shown by site-directed mutagenesis to be essential for acetyltransferase activity. It is hypothesized that EpsC (NAD⁺ dependent UDP GlcNAc 4,6-dehydratase), EpsN (PLP dependent aminotransferase) and EpsM, all of which are part of the eps operon, are involved in the biosynthesis of N,N'-diacetylbacillosamine.

Clostridium difficile Biofilm: Remodeling Metabolism and Cell Surface to Build a Sparse and Heterogeneously Aggregated Architecture

Clostridium difficile is an opportunistic entero-pathogen causing post-antibiotic and nosocomial diarrhea upon microbiota dysbiosis. Although biofilms could contribute to colonization, little is known about their development and physiology. Strain 630Δerm is able to form, in continuous-flow micro-fermentors, macro-colonies and submersed biofilms loosely adhesive to glass. According to gene expression data, in biofilm/planktonic cells, central metabolism is active and fuels fatty acid biosynthesis rather than fermentations. Consistently, succinate is consumed and butyrate production is reduced. Toxin A expression, which is coordinated to metabolism, is down-regulated, while surface proteins, like adhesins and the primary Type IV pili subunits, are over-expressed. C-di-GMP level is probably tightly controlled through the expression of both diguanylate cyclase-encoding genes, like dccA, and phosphodiesterase-encoding genes. The coordinated expression of genes controlled by c-di-GMP and encoding the putative surface adhesin CD2831 and the major Type IV pilin PilA₁, suggests that c-di-GMP could be high in biofilm cells. A Bacillus subtilis SinR-like regulator, CD2214, and/or CD2215, another regulator co-encoded in the same operon as CD2214, control many genes differentially expressed in biofilm, and in particular dccA, CD2831 and pilA₁ in a positive way. After growth in micro-titer plates and disruption, the biofilm is composed of robust aggregated structures where cells are embedded into a polymorphic material. The intact biofilm observed in situ displays a sparse, heterogeneous and high 3D architecture made of rods and micro-aggregates. The biofilm is denser in a mutant of both CD2214 and CD2215 genes, but it is not affected by the inactivation of neither CD2831 nor pilA₁. dccA, when over-expressed, not only increases the biofilm but also triggers its architecture to become homogeneous and highly aggregated, in a way independent of CD2831 and barely dependent of pilA₁. Cell micro-aggregation is shown to play a major role in biofilm formation and architecture. This thorough analysis of gene expression reprogramming and architecture remodeling in biofilm lays the foundation for a deeper understanding of this lifestyle and could lead to novel strategies to limit C. difficile spread.

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

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.

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.

The Characteristics of Growth of Bacilli Formed Fouling on Wooden Constructions

Problem of biofilm formation have a great significance for environmental microbiological research. Biospheric microorganisms can form biofilm, that provide bacteria resistance to influence of different environmental factors. Some of the most common bacteria in biosphere are bacilli, among them there are film-forming strains. Bacillus spp. ia a well-known film forming microorganisms that colonize environmental objects. The biofilm fouling of underwater elements of small wooden constructions located on the Dnieper River near the city of the Dnipro (Ukraine) was studied. It was found that biofilms from surfaces of water constructions include bacilli. It is established that the mean values of CFU in samples from running and still water were (1.81±0.52)×108 and (1.83±0.53)×108 CFU / ml respectively per area of wooden sample approximately 1 cm2, while during the laboratory cultivation of the film, formed by these cultures on the plate, the number of cells was (4.90±0.93)×107 and (4.60±1.07)×107 CFU / ml per 1 cm2 of the well’s bottom, which was an approximate limit of the content of cells of the Bacillus spp. film per unit of area.

Poultry and beef meat as potential seedbeds for antimicrobial resistant enterotoxigenic Bacillus species: a materializing epidemiological and potential severe health hazard

Although Bacillus cereus is of particular concern in food safety and public health, the role of other Bacillus species was overlooked. Therefore, we investigated the presence of eight enterotoxigenic genes, a hemolytic gene and phenotypic antibiotic resistance profiles of Bacillus species in retail meat samples. From 255 samples, 124 Bacillus isolates were recovered, 27 belonged to B. cereus and 97 were non-B. cereus species. Interestingly, the non-B. cereus isolates carried the virulence genes and exhibited phenotypic virulence characteristics as the B. cereus. However, correlation matrix analysis revealed the B. cereus group positively correlates with the presence of the genes hblA, hblC, and plc, and the detection of hemolysis (p < 0.05), while the other Bacillus sp. groups are negatively correlated. Tests for antimicrobial resistance against ten antibiotics revealed extensive drug and multi-drug resistant isolates. Statistical analyses didn't support a correlation of antibiotic resistance to tested virulence factors suggesting independence of these phenotypic markers and virulence genes. Of special interest was the isolation of Paenibacillus alvei and Geobacillus stearothermophilus from the imported meat samples being the first recorded. The isolation of non-B. cereus species carrying enterotoxigenic genes in meat within Egypt, suggests their impact on food safety and public health and should therefore not be minimised, posing an area that requires further research.

The Characteristics of Growth of Bacilli Formed Fouling on Wooden Constructions

Problem of biofilm formation have a great significance for environmental microbiological research. Biospheric microorganisms can form biofilm, that provide bacteria resistance to influence of different environmental factors. Some of the most common bacteria in biosphere are bacilli, among them there are film-forming strains.Bacillus spp.ia a well-known film forming microorganisms that colonize environmental objects. The biofilm fouling of underwater elements of small wooden constructions located on the Dnieper River near the city of the Dnipro (Ukraine) was studied. It was found that biofilms from surfaces of water constructions include bacilli. It is established that the mean values of CFU in samples from running and still water were (1.81±0.52)×108and (1.83±0.53)×108CFU / ml respectively per area of wooden sample approximately 1 cm2, while during the laboratory cultivation of the film, formed by these cultures on the plate, the number of cells was (4.90±0.93)×107and (4.60±1.07)×107CFU / ml per 1 cm2of the well’s bottom, which was an approximate limit of the content of cells of theBacillus spp.film per unit of area.

Complex microbial systems across different levels of description

Complex biological systems offer a variety of interesting phenomena at the different physical scales. With increasing abstraction, details of the microscopic scales can often be extrapolated to average or typical macroscopic properties. However, emergent properties and cross-scale interactions can impede naïve abstractions and necessitate comprehensive investigations of these complex systems. In this review paper, we focus on microbial communities, and first, summarize a general hierarchy of relevant scales and description levels to understand these complex systems: (1) genetic networks, (2) single cells, (3) populations, and (4) emergent multi-cellular properties. Second, we employ two illustrating examples, microbial competition and biofilm formation, to elucidate how cross-scale interactions and emergent properties enrich the observed multi-cellular behavior in these systems. Finally, we conclude with pointing out the necessity of multi-scale investigations to understand complex biological systems and discuss recent investigations.

Exogenous N-acyl homoserine lactones facilitate microbial adhesion of high ammonia nitrogen wastewater on biocarrier surfaces

Startup of biofilm process triggered by initial adhesion of bacteria is difficult in high ammonia nitrogen wastewater treatment. In this study, the influence of two commonly used N-acyl homoserine lactones (AHLs), N-Hexanoyl-l-homoserine lactone (C6-HSL) and N-Octanoyl-l-homoserine lactone (C8-HSL), on the adhesion of soluble macromolecules and bacteria in four types of high ammonia nitrogen wastewater to surfaces of model biocarriers (i.e. polystyrene, polyamide and polyethylene terephthalate) was investigated by using a quartz crystal microbalance with dissipation (QCM-D) monitoring technology. Results showed that the adhesion was enhanced by the addition of exogenous AHLs and there was more microbial retention attributed by C8-HSL. Greater deposition amount was generally found on PS and better enhanced performances of the adhesion were found on PA surface. Furthermore, viscoelastic film formed under synchronous high-low salinity and organic content and dominant bacteria of real wastewater determined the role of exogenous AHLs. The method of adding moderate amount of exogenous AHLs into bioreactors has important implications for accelerating the startup process treating high ammonia nitrogen wastewater by biofilm process.

ResDE Two-Component Regulatory System Mediates Oxygen Limitation-Induced Biofilm Formation by Bacillus amyloliquefaciens SQR9

Efficient biofilm formation and root colonization capabilities facilitate the ability of beneficial plant rhizobacteria to promote plant growth and antagonize soilborne pathogens. Biofilm formation by plant-beneficial Bacillus strains is triggered by environmental cues, including oxygen deficiency, but the pathways that sense these environmental signals and regulate biofilm formation have not been thoroughly elucidated. In this study, we showed that the ResDE two-component regulatory system in the plant growth-promoting rhizobacterium Bacillus amyloliquefaciens strain SQR9 senses the oxygen deficiency signal and regulates biofilm formation. ResE is activated by sensing the oxygen limitation-induced reduction of the NAD⁺/NADH pool through its PAS domain, stimulating its kinase activity, and resulting in the transfer of a phosphoryl group to ResD. The phosphorylated ResD directly binds to the promoter regions of the qoxABCD and ctaCDEF operons to improve the biosynthesis of terminal oxidases, which can interact with KinB to activate biofilm formation. These results not only revealed the novel regulatory function of the ResDE two-component system but also contributed to the understanding of the complicated regulatory network governing Bacillus biofilm formation. This research may help to enhance the root colonization and the plant-beneficial efficiency of SQR9 and other Bacillus rhizobacteria used in agriculture.IMPORTANCEBacillus spp. are widely used as bioinoculants for plant growth promotion and disease suppression. The exertion of their plant-beneficial functions is largely dependent on their root colonization, which is closely related to their biofilm formation capabilities. On the other hand, Bacillus is the model bacterium for biofilm study, and the process and molecular network of biofilm formation are well characterized (B. Mielich-Süss and D. Lopez, Environ Microbiol 17:555-565, 2015, https://doi.org/10.1111/1462-2920.12527; L. S. Cairns, L. Hobley, and N. R. Stanley-Wall, Mol Microbiol 93:587-598, 2014, https://doi.org/10.1111/mmi.12697; H. Vlamakis, C. Aguilar, R. Losick, and R. Kolter, Genes Dev 22:945-953, 2008, https://doi.org/10.1101/gad.1645008; S. S. Branda, A. Vik, L. Friedman, and R. Kolter, Trends Microbiol 13:20-26, 2005, https://doi.org/10.1016/j.tim.2004.11.006; C. Aguilar, H. Vlamakis, R. Losick, and R. Kolter, Curr Opin Microbiol 10:638-643, 2007, https://doi.org/10.1016/j.mib.2007.09.006; S. S. Branda, J. E. González-Pastor, S. Ben-Yehuda, R. Losick, and R. Kolter, Proc Natl Acad Sci U S A 98:11621-11626, 2001, https://doi.org/10.1073/pnas.191384198). However, the identification and sensing of environmental signals triggering Bacillus biofilm formation need further research. Here, we report that the oxygen deficiency signal inducing Bacillus biofilm formation is sensed by the ResDE two-component regulatory system. Our results not only revealed the novel regulatory function of the ResDE two-component regulatory system but also identified the sensing system of a biofilm-triggering signal. This knowledge can help to enhance the biofilm formation and root colonization of plant-beneficial Bacillus strains and also provide new insights of bacterial biofilm formation regulation.

Antagonism of Two Plant-Growth Promoting Bacillus velezensis Isolates Against Ralstonia solanacearum and Fusarium oxysporum

Plant growth promoting rhizobacteria (PGPR) provide an effective and environmentally sustainable method to protect crops against pathogens. The spore-forming Bacilli are attractive PGPR due to their ease of storage and application. Here, we characterized two rhizosphere-associated Bacillus velezensis isolates (Y6 and F7) that possess strong antagonistic activity against Ralstonia solanacearum and Fusarium oxysporum under both laboratory and greenhouse conditions. We identified three lipopeptide (LP) compounds (surfactin, iturin and fengycin) as responsible for the antimicrobial activity of these two strains. We further dissected the contribution of LPs to various biological processes important for rhizosphere colonization. Although either iturin or fengycin is sufficient for antibacterial activity, cell motility and biofilm formation, only iturin plays a primary role in defense against the fungal pathogen F. oxysporum. Additionally, we found that LP production is significantly stimulated during interaction with R. solanacearum. These results demonstrate the different roles of LPs in the biology of B. velezensis and highlight the potential of these two isolates as biocontrol agents against phytopathogens.

Structural changes of TasA in biofilm formation of Bacillus subtilis

Understanding the formation and structure of protective bacterial biofilms will help to design and identify antimicrobial strategies. Our experiments with the secreted major biofilm protein TasA characterize on a molecular level in vivo the transition of a folded protein into protease-resistant biofilm-stabilizing fibrils. Such conformational changes from a globular state into fibrillar structures are so far not seen for other biofilm-forming proteins. In this context, TasA can serve as a model system to study functional fibril formation from a globular state.

Microorganisms form surface-attached communities, termed biofilms, which can serve as protection against host immune reactions or antibiotics. Bacillus subtilis biofilms contain TasA as major proteinaceous component in addition to exopolysaccharides. In stark contrast to the initially unfolded biofilm proteins of other bacteria, TasA is a soluble, stably folded monomer, whose structure we have determined by X-ray crystallography. Subsequently, we characterized in vitro different oligomeric forms of TasA by NMR, EM, X-ray diffraction, and analytical ultracentrifugation (AUC) experiments. However, by magic-angle spinning (MAS) NMR on live biofilms, a swift structural change toward only one of these forms, consisting of homogeneous and protease-resistant, β-sheet–rich fibrils, was observed in vivo. Thereby, we characterize a structural change from a globular state to a fibrillar form in a functional prokaryotic system on the molecular level.

FtsEX-CwlO regulates biofilm formation by a plant-beneficial rhizobacterium Bacillus velezensis SQR9

Bacillus velezensis strain SQR9 is a well-investigated rhizobacterium with an outstanding ability to colonize roots, enhance plant growth and suppress soil-borne diseases. The recognition that biofilm formation by plant-beneficial bacteria is crucial for their root colonization and function has resulted in increased interest in understanding molecular mechanisms related to biofilm formation. Here, we report that the gene ftsE, encoding the ATP-binding protein of an FtsEX ABC transporter, is required for efficient SQR9 biofilm formation. FtsEX has been reported to regulate the atolysin CwlO. We provided evidence that FtsEX-CwlO was involved in the regulation of SQR9 biofilm formation; however, this effect has little to do with CwlO autolysin activity. We propose that regulation of biofilm formation by CwlO was exerted through the spo0A pathway, since transcription of spo0A cascade genes was altered and their downstream extracellular matrix genes were downregulated in SQR9 ftsE/cwlO deletion mutants. CwlO was also shown to interact physically with KinB/KinD. CwlO may therefore interact with KinB/KinD to interfere with the spo0A pathway. This study revealed that FtsEX-CwlO plays a previously undiscovered regulatory role in biofilm formation by SQR9 that may enhance root colonization and plant-beneficial functions of SQR9 and other beneficial rhizobacteria as well.

Crystal structure of NucB, a biofilm-degrading endonuclease

Bacterial biofilms are a complex architecture of cells that grow on moist interfaces, and are held together by a molecular glue of extracellular proteins, sugars and nucleic acids. Biofilms are particularly problematic in human healthcare as they can coat medical implants and are thus a potential source of disease. The enzymatic dispersal of biofilms is increasingly being developed as a new strategy to treat this problem. Here, we have characterized NucB, a biofilm-dispersing nuclease from a marine strain of Bacillus licheniformis, and present its crystal structure together with the biochemistry and a mutational analysis required to confirm its active site. Taken together, these data support the categorization of NucB into a unique subfamily of the ββα metal-dependent non-specific endonucleases. Understanding the structure and function of NucB will facilitate its future development into an anti-biofilm therapeutic agent.

Architecture and physicochemical characterization of Bacillus biofilm as a potential enzyme immobilization factory

Biocatalysis for industrial application is based on the use of enzymes to perform complex transformations. However, these systems have some disadvantage related to the costs of the biocatalyst. In this work, an alternative strategy for producing green immobilized biocatalysts based on biofilm was developed.A study of the rheological behavior of the biofilm from Bacillus sp. Mcn4, as well as the determination of its composition, was carried out. The dynamic rheological measurements, viscosity (G") and elasticity (G') module, showed that the biofilm presents appreciable elastic components, which is a recognized property for enzymes immobilization. After the partial purification, the exopolysaccharidewas identified as a levan with a non-Newtonian behavior. Extracellular DNA with fragments between 10,000 and 1000bp was detected also in the biofilm, and amyloid protein in the extracellular matrix using a fluorescence technique was identified. Bacillus sp. Mcn4 biofilms were developed on different surfaces, being the most stable those developed on hydrophilic supports. The biofilm showed lipase activity suggesting the presence of constitutive lipases entrapped into the biofilm. Indeed, two enzymes with lipase activity were identified in native PAGE. These were used as biocatalysts, whose reuse showed a residual lipase activity after more than one cycle of catalysis. The components identified in the biofilm could be the main contributors of the rheological characteristic of this material, giving an exceptional environment to the lipase enzyme. Based on these findings, the current study proposes green and natural biopolymers matrix as support for the enzyme immobilization for industrial applications.

In Vivo Behavior of the Tandem Glycine Riboswitch in Bacillus subtilis

In many bacterial species, the glycine riboswitch is composed of two homologous ligand-binding domains (aptamers) that each bind glycine and act together to regulate the expression of glycine metabolic and transport genes. While the structure and molecular dynamics of the tandem glycine riboswitch have been the subject of numerous in vitro studies, the in vivo behavior of the riboswitch remains largely uncharacterized. To examine the proposed models of tandem glycine riboswitch function in a biologically relevant context, we characterized the regulatory activity of mutations to the riboswitch structure in Bacillus subtilis using β-galactosidase assays. To assess the impact disruptions to riboswitch function have on cell fitness, we introduced these mutations into the native locus of the tandem glycine riboswitch within the B. subtilis genome. Our results indicate that glycine does not need to bind both aptamers for regulation in vivo and mutations perturbing riboswitch tertiary structure have the most severe effect on riboswitch function and gene expression. We also find that in B. subtilis, the glycine riboswitch-regulated gcvT operon is important for glycine detoxification.IMPORTANCE The glycine riboswitch is a unique cis-acting mRNA element that contains two tandem homologous glycine-binding domains that act on a single expression platform to regulate gene expression in response to glycine. While many in vitro experiments have characterized the tandem architecture of the glycine riboswitch, little work has investigated the behavior of this riboswitch in vivo In this study, we analyzed the proposed models of tandem glycine riboswitch regulation in the context of its native locus within the Bacillus subtilis genome and examined how disruptions to glycine riboswitch function impact organismal fitness. Our work offers new insights into riboswitch function in vivo and reinforces the potential of riboswitches as novel antimicrobial targets.

Surviving Between Hosts: Sporulation and Transmission

To survive adverse conditions, some bacterial species are capable of developing into a cell type, the "spore," which exhibits minimal metabolic activity and remains viable in the presence of multiple environmental challenges. For some pathogenic bacteria, this developmental state serves as a means of survival during transmission from one host to another. Spores are the highly infectious form of these bacteria. Upon entrance into a host, specific signals facilitate germination into metabolically active replicating organisms, resulting in disease pathogenesis. In this article, we will review spore structure and function in well-studied pathogens of two genera, Bacillus and Clostridium, focusing on Bacillus anthracis and Clostridium difficile, and explore current data regarding the lifestyles of these bacteria outside the host and transmission from one host to another.

Morphologies of Bacillus subtilis communities responding to environmental variation

Bacterial communities exhibit a variety of growth morphologies in constructing robust systems under different environmental conditions. We review the diverse morphologies of Bacillus subtilis communities and their mechanisms of self-organization. B. subtilis uses different cell types to suit environmental conditions and cell density. The subpopulation of each cell type exhibits various environment-sensitive properties. Furthermore, division of labor among the subpopulations results in flexible development for the community as a whole. We review how B. subtilis community morphologies and growth strategies respond to environmental perturbations.

In situ analysis of Bacillus licheniformis biofilms: amyloid-like polymers and eDNA are involved in the adherence and aggregation of the extracellular matrix

AIMS

This study attempts to determine which of the exopolymeric substances are involved in the adherence and aggregation of a Bacillus licheniformis biofilm.

METHODS AND RESULTS

The involvement of extracellular proteins and eDNA were particularly investigated using DNase and proteinase K treatment. The permeability of the biofilms increased fivefold after DNase I treatment. The quantification of the matrix components showed that, irrespective to the enzyme tested, eDNA and amyloid-like polymers were removed simultaneously. Size-exclusion chromatography analyses supported these observations and revealed the presence of associated nucleic acid and protein complexes in the biofilm lysates. These data suggest that some extracellular DNA and amyloid-like proteins were closely interlaced within the matrix. Finally, confocal laser scanning microscopy imaging gave supplementary clues about the 3D organization of the biofilms, confirming that eDNA and exoproteins were essentially layered under and around the bacterial cells, whereas the amyloid-like fractions were homogeneously distributed within the matrix.

CONCLUSION

These results confirm that some DNA-amyloid complexes play a key role in the modulation of the mechanical resistance of B. licheniformis biofilms.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study highlights the need to consider the whole structure of biofilms and to target the interactions between matrix components. A better understanding of B. licheniformis biofilm physiology and the structural organization of the matrix will strengthen strategies of biofilm control.

Characterization of the regulation of a plant polysaccharide utilization operon and its role in biofilm formation in Bacillus subtilis

The soil bacterium Bacillus subtilis is often found in association with plants in the rhizosphere. Previously, plant polysaccharides have been shown to stimulate formation of root-associated multicellular communities, or biofilms, in this bacterium, yet the underlying mechanism is not fully understood. A five-gene gan operon (ganSPQAB) in B. subtilis has recently been shown to be involved in utilization of the plant-derived polysaccharide galactan. Despite these findings, molecular details about the regulation of the operon and the role of the operon in biofilm formation remain elusive. In this study, we performed comprehensive genetic analyses on the regulation of the gan operon. We show that this operon is regulated both by a LacI-like transcription repressor (GanR), which directly binds to pairs of inverted DNA repeats in the promoter region of the operon, and by the catabolite control protein A (CcpA). Derepression can be triggered by the presence of the inducer β-1,4-galactobiose, a hydrolysis product of galactan, or in situ when B. subtilis cells are associated with plant roots. In addition to the transcriptional regulation, the encoded ß-galactosidase GanA (by ganA), which hydrolyzes ß-1,4-galactobiose into galactose, is inhibited at the enzymatic level by the catalytic product galactose. Thus, the galactan utilization pathway is under complex regulation involving both positive and negative feedback mechanisms in B. subtilis. We discuss about the biological significance of such complex regulation as well as a hypothesis of biofilm induction by galactan via multiple mechanisms.

Subcellular clustering of a putative c-di-GMP-dependent exopolysaccharide machinery affecting macro colony architecture in Bacillus subtilis

The structure of bacterial biofilms is predominantly established through the secretion of extracellular polymeric substances (EPS). They show that Bacillus subtilis contains an operon (ydaJ-N) whose induction leads to increased Congo Red staining of biofilms and strongly altered biofilm architecture, suggesting that it mediates the production of an unknown exopolysaccharide. Supporting this idea, overproduction of YdaJKLMN leads to cell clumping during exponential growth in liquid culture, and also causes colony morphology alterations in wild type cells, as well as in a mutant background lacking the major exopolysaccharide of B. subtilis. The first gene product of the operon, YdaJ, appears to modify the overproduction effects, but is not essential for cell clumping or altered colony morphology, while the presence of the c-di-GMP receptor YdaK is required, suggesting an involvement of second messenger c-di-GMP. YdaM, YdaN and YdaK colocalize to clusters predominantly at the cell poles and are statically positioned at this subcellular site, similar to other exopolysaccharide machinery components in other bacteria. Their analysis reveals that B. subtilis contains a static subcellular assembly of an EPS machinery that affects cell aggregation and biofilm formation.

Cyclic-di-GMP signalling meets extracellular polysaccharide synthesis in Bacillus subtilis

In order to resist harmful environmental conditions, many bacteria form multicellular aggregates called biofilms. In these biofilms, they protect themselves in a self-produced matrix consisting of extracellular polysaccharides, proteins and DNA. In many bacteria, biofilm formation is stimulated in the presence of the second messenger cyclic di-GMP. In this issue of Environmental Microbiology Reports, Bedrunka and Graumann have studied matrix production by the proteins encoded in the Bacillus subtilis ydaJKLMN operon. For the first time, they were able to provide a link between c-di-GMP signalling and matrix production in this bacterium. The work demonstrates that the c-di-GMP receptor protein YdaK forms a membrane-bound complex with the YdaM and YdaN proteins, and that this interaction with YdaK is required for polysaccharide production by YdaL, YdaM and YdaN.

Spermidine promotes Bacillus subtilis biofilm formation by activating expression of the matrix regulator slrR

Ubiquitous polyamine spermidine is not required for normal planktonic growth of Bacillus subtilis but is essential for robust biofilm formation. However, the structural features of spermidine required for B. subtilis biofilm formation are unknown and so are the molecular mechanisms of spermidine-stimulated biofilm development. We report here that in a spermidine-deficient B. subtilis mutant, the structural analogue norspermidine, but not homospermidine, restored biofilm formation. Intracellular biosynthesis of another spermidine analogue, aminopropylcadaverine, from exogenously supplied homoagmatine also restored biofilm formation. The differential ability of C-methylated spermidine analogues to functionally replace spermidine in biofilm formation indicated that the aminopropyl moiety of spermidine is more sensitive to C-methylation, which it is essential for biofilm formation, but that the length and symmetry of the molecule is not critical. Transcriptomic analysis of a spermidine-depleted B. subtilis speD mutant uncovered a nitrogen-, methionine-, and S-adenosylmethionine-sufficiency response, resulting in repression of gene expression related to purine catabolism, methionine and S-adenosylmethionine biosynthesis and methionine salvage, and signs of altered membrane status. Consistent with the spermidine requirement in biofilm formation, single-cell analysis of this mutant indicated reduced expression of the operons for production of the exopolysaccharide and TasA protein biofilm matrix components and SinR antagonist slrR. Deletion of sinR or ectopic expression of slrR in the spermidine-deficient ΔspeD background restored biofilm formation, indicating that spermidine is required for expression of the biofilm regulator slrR. Our results indicate that spermidine functions in biofilm development by activating transcription of the biofilm matrix exopolysaccharide and TasA operons through the regulator slrR.

Lack of the PGA exopolysaccharide in Salmonella as an adaptive trait for survival in the host

Many bacteria build biofilm matrices using a conserved exopolysaccharide named PGA or PNAG (poly-β-1,6-N-acetyl-D-glucosamine). Interestingly, while E. coli and other members of the family Enterobacteriaceae encode the pgaABCD operon responsible for PGA synthesis, Salmonella lacks it. The evolutionary force driving this difference remains to be determined. Here, we report that Salmonella lost the pgaABCD operon after the divergence of Salmonella and Citrobacter clades, and previous to the diversification of the currently sequenced Salmonella strains. Reconstitution of the PGA machinery endows Salmonella with the capacity to produce PGA in a cyclic dimeric GMP (c-di-GMP) dependent manner. Outside the host, the PGA polysaccharide does not seem to provide any significant benefit to Salmonella: resistance against chlorine treatment, ultraviolet light irradiation, heavy metal stress and phage infection remained the same as in a strain producing cellulose, the main biofilm exopolysaccharide naturally produced by Salmonella. In contrast, PGA production proved to be deleterious to Salmonella survival inside the host, since it increased susceptibility to bile salts and oxidative stress, and hindered the capacity of S. Enteritidis to survive inside macrophages and to colonize extraintestinal organs, including the gallbladder. Altogether, our observations indicate that PGA is an antivirulence factor whose loss may have been a necessary event during Salmonella speciation to permit survival inside the host.

During bacterial evolution, specific traits that optimize the organism’s fitness are selected. The production of exopolysaccharides is widespread among bacteria in which they play a protective shielding role as main constituents of biofilms. In contrast to closely related siblings, Salmonella has lost the capacity to produce the exopolysaccharide PGA. Our study reveals that Salmonella lost pga genes, and that the driving force for such a loss may have been the detrimental impact that PGA has during Salmonella invasion of internal organs where it augments the susceptibility to bile salts and oxygen radicals, reducing bacterial survival inside macrophages and rendering Salmonella avirulent. These results suggest that gene-loss has played an important role during Salmonella evolution.

Agriculturally important microbial biofilms: Present status and future prospects

Microbial biofilms are a fascinating subject, due to their significant roles in the environment, industry, and health. Advances in biochemical and molecular techniques have helped in enhancing our understanding of biofilm structure and development. In the past, research on biofilms primarily focussed on health and industrial sectors; however, lately, biofilms in agriculture are gaining attention due to their immense potential in crop production, protection, and improvement. Biofilms play an important role in colonization of surfaces - soil, roots, or shoots of plants and enable proliferation in the desired niche, besides enhancing soil fertility. Although reports are available on microbial biofilms in general; scanty information is published on biofilm formation by agriculturally important microorganisms (bacteria, fungi, bacterial-fungal) and their interactions in the ecosystem. Better understanding of agriculturally important bacterial-fungal communities and their interactions can have several implications on climate change, soil quality, plant nutrition, plant protection, bioremediation, etc. Understanding the factors and genes involved in biofilm formation will help to develop more effective strategies for sustainable and environment-friendly agriculture. The present review brings together fundamental aspects of biofilms, in relation to their formation, regulatory mechanisms, genes involved, and their application in different fields, with special emphasis on agriculturally important microbial biofilms.

Lack of formylated methionyl-tRNA has pleiotropic effects on Bacillus subtilis

Bacteria initiate translation using a modified amino acid, N-formylmethionine (fMet), adapted specifically for this function. Most proteins are processed co-translationally by peptide deformylase (PDF) to remove this modification. Although PDF activity is essential in WT cells and is the target of the antibiotic actinonin, bypass mutations in the fmt gene that eliminate the formylation of Met-tRNAMet render PDF dispensable. The extent to which the emergence of fmt bypass mutations might compromise the therapeutic utility of actinonin is determined, in part, by the effects of these bypass mutations on fitness. Here, we characterize the phenotypic consequences of an fmt null mutation in the model organism Bacillus subtilis. An fmt null mutant is defective for several post-exponential phase adaptive programmes including antibiotic resistance, biofilm formation, swarming and swimming motility and sporulation. In addition, a survey of well-characterized stress responses reveals an increased sensitivity to metal ion excess and oxidative stress. These diverse phenotypes presumably reflect altered synthesis or stability of key proteins involved in these processes.

Should the biofilm mode of life be taken into consideration for microbial biocontrol agents?

Almost one‐third of crop yields are lost every year due to microbial alterations and diseases. The main control strategy to limit these losses is the use of an array of chemicals active against spoilage and unwanted pathogenic microorganisms. Their massive use has led to extensive environmental pollution, human poisoning and a variety of diseases. An emerging alternative to this chemical approach is the use of microbial biocontrol agents. Biopesticides have been used with success in several fields, but a better understanding of their mode of action is necessary to better control their activity and increase their use. Very few studies have considered that biofilms are the preferred mode of life of microorganisms in the target agricultural biotopes. Increasing evidence shows that the spatial organization of microbial communities on crop surfaces may drive important bioprotection mechanisms. The aim of this review is to summarize the evidence of biofilm formation by biocontrol agents on crops and discuss how this surface‐associated mode of life may influence their biology and interactions with other microorganisms and the host and, finally, their overall beneficial activity.

Bacillus subtilis biofilm development in the presence of soil clay minerals and iron oxides

Clay minerals and metal oxides, as important parts of the soil matrix, play crucial roles in the development of microbial communities. However, the mechanism underlying such a process, particularly on the formation of soil biofilm, remains poorly understood. Here, we investigated the effects of montmorillonite, kaolinite, and goethite on the biofilm formation of the representative soil bacteria Bacillus subtilis. The bacterial biofilm formation in goethite was found to be impaired in the initial 24 h but burst at 48 h in the liquid-air interface. Confocal laser scanning microscopy showed that the biofilm biomass in goethite was 3-16 times that of the control, montmorillonite, and kaolinite at 48 h. Live/Dead staining showed that cells had the highest death rate of 60% after 4 h of contact with goethite, followed by kaolinite and montmorillonite. Atomic force microscopy showed that the interaction between goethite and bacteria may injure bacterial cells by puncturing cell wall, leading to the swarming of bacteria toward the liquid-air interface. Additionally, the expressions of abrB and sinR, key players in regulating the biofilm formation, were upregulated at 24 h and downregulated at 48 h in goethite, indicating the initial adaptation of the cells to minerals. A model was proposed to describe the effects of goethite on the biofilm formation. Our findings may facilitate a better understanding of the roles of soil clays in biofilm development and the manipulation of bacterial compositions through controlling the biofilm in soils.

An improved protocol for harvesting Bacillus subtilis colony biofilms

Bacterial biofilms cause severe problems in medicine and industry due to the high resistance to disinfectants and environmental stress of organisms within biofilms. Addressing challenges caused by biofilms requires full understanding of the underlying mechanisms for bacterial resistance and survival in biofilms. However, such work is hampered by a relative lack of systems for biofilm cultivation that are practical and reproducible. To address this problem, we developed a readily applicable method to culture Bacillus subtilis biofilms on a membrane filter. The method results in biofilms with highly reproducible characteristics, and which can be readily analyzed by a variety of methods with little further manipulation. This biofilm preparation method simplifies routine generation of B. subtilis biofilms for molecular and cellular analysis, and could be applicable to other microbial systems.

Matrix composition determines the dimensions of Bacillus subtilis NCIB 3610 biofilm colonies grown on LB agar

Exopolymeric substances secreted by biofilm formingBacillus subtilisNCIB 3610 bacteria influence the growth and final dimensions of these biofilms.

Methodologies for Studying B. subtilis Biofilms as a Model for Characterizing Small Molecule Biofilm Inhibitors

This work assesses different methodologies to study the impact of small molecule biofilm inhibitors, such as D-amino acids, on the development and resilience of Bacillus subtilis biofilms. First, methods are presented that select for small molecule inhibitors with biofilm-specific targets in order to separate the effect of the small molecule inhibitors on planktonic growth from their effect on biofilm formation. Next, we focus on how inoculation conditions affect the sensitivity of multicellular, floating B. subtilis cultures to small molecule inhibitors. The results suggest that discrepancies in the reported effects of such inhibitors such as D-amino acids are due to inconsistent pre-culture conditions. Furthermore, a recently developed protocol is described for evaluating the contribution of small molecule treatments towards biofilm resistance to antibacterial substances. Lastly, scanning electron microscopy (SEM) techniques are presented to analyze the three-dimensional spatial arrangement of cells and their surrounding extracellular matrix in a B. subtilis biofilm. SEM facilitates insight into the three-dimensional biofilm architecture and the matrix texture. A combination of the methods described here can greatly assist the study of biofilm development in the presence and absence of biofilm inhibitors, and shed light on the mechanism of action of these inhibitors.

Specific Bacillus subtilis 168 variants form biofilms on nutrient-rich medium

Bacillus subtilis is an intensively studied Gram-positive bacterium that has become one of the models for biofilm development. B. subtilis 168 is a well-known domesticated strain that has been suggested to be deficient in robust biofilm formation. Moreover, the diversity of available B. subtilis laboratory strains and their derivatives have made it difficult to compare independent studies related to biofilm formation. Here, we analysed numerous 168 stocks from multiple laboratories for their ability to develop biofilms in different set-ups and media. We report a wide variation among the biofilm-forming capabilities of diverse stocks of B. subtilis 168, both in architecturally complex colonies and liquid-air interface pellicles, as well as during plant root colonization. Some 168 variants are indeed unable to develop robust biofilm structures, while others do so as efficiently as the non-domesticated NCIB 3610 strain. In all cases studied, the addition of glucose to the medium dramatically improved biofilm development of the laboratory strains. Furthermore, the expression of biofilm matrix component operons, epsA-O and tapA-sipW-tasA, was monitored during colony biofilm formation. We found a lack of direct correlation between the expression of these genes and the complexity of wrinkles in colony biofilms. However, the presence of a single mutation in the exopolysaccharide-related gene epsC correlates with the ability of the stocks tested to form architecturally complex colonies and pellicles, and to colonize plant roots.

Biofilms 2015: Multidisciplinary Approaches Shed Light into Microbial Life on Surfaces

The 7th ASM Conference on Biofilms was held in Chicago, Illinois, from 24 to 29 October 2015. The conference provided an international forum for biofilm researchers across academic and industry platforms, and from different scientific disciplines, to present and discuss new findings and ideas. The meeting covered a wide range of topics, spanning environmental sciences, applied biology, evolution, ecology, physiology, and molecular biology of the biofilm lifestyle. This report summarizes the presentations with regard to emerging biofilm-related themes.

A phenomenological description of BslA assemblies across multiple length scales

Intrinsically interfacially active proteins have garnered considerable interest recently owing to their potential use in a range of materials applications. Notably, the fungal hydrophobins are known to form robust and well-organized surface layers with high mechanical strength. Recently, it was shown that the bacterial biofilm protein BslA also forms highly elastic surface layers at interfaces. Here we describe several self-assembled structures formed by BslA, both at interfaces and in bulk solution, over a range of length scales spanning from nanometres to millimetres. First, we observe transiently stable and highly elongated air bubbles formed in agitated BslA samples. We study their behaviour in a range of solution conditions and hypothesize that their dissipation is a consequence of the slow adsorption kinetics of BslA to an air-water interface. Second, we describe elongated tubules formed by BslA interfacial films when shear stresses are applied in both a Langmuir trough and a rheometer. These structures bear a striking resemblance, although much larger in scale, to the elongated air bubbles formed during agitation. Taken together, this knowledge will better inform the conditions and applications of how BslA can be used in the stabilization of multi-phase materials.This article is part of the themed issue 'Soft interfacial materials: from fundamentals to formulation'.

Physiological and transcriptomic analyses reveal mechanistic insight into the adaption of marine Bacillus subtilis C01 to alumina nanoparticles

An increasing number of studies have investigated the effects of nanoparticles (NPs) on microbial systems; however, few existing reports have focused on the defense mechanisms of bacteria against NPs. Whether secondary metabolism biosynthesis is a response to NP stress and contributes to the adaption of bacteria to NPs is unclear. Here, a significant induction in the surfactin production and biofilm formation were detected by adding Al2O3 NPs to the B. subtilis fermentation broth. Physiological analysis showed that Al2O3 NP stress could also affect the cell and colony morphogenesis and inhibit the motility and sporulation. Exogenously adding commercial surfactin restored the swarming motility. Additionally, a suite of toxicity assays analyzing membrane damage, cellular ROS generation, electron transport activity and membrane potential was used to determine the molecular mechanisms of toxicity of Al2O3 NPs. Furthermore, whole transcriptomic analysis was used to elucidate the mechanisms of B. subtilis adaption to Al2O3 NPs. These results revealed several mechanisms by which marine B. subtilis C01 adapt to Al2O3 NPs. Additionally, this study broadens the applications of nanomaterials and describes the important effects on secondary metabolism and multicellularity regulation by using Al2O3 NPs or other nano-products.

Bacillus cereus Biofilms-Same, Only Different

Bacillus cereus displays a high diversity of lifestyles and ecological niches and include beneficial as well as pathogenic strains. These strains are widespread in the environment, are found on inert as well as on living surfaces and contaminate persistently the production lines of the food industry. Biofilms are suspected to play a key role in this ubiquitous distribution and in this persistency. Indeed, B. cereus produces a variety of biofilms which differ in their architecture and mechanism of formation, possibly reflecting an adaptation to various environments. Depending on the strain, B. cereus has the ability to grow as immersed or floating biofilms, and to secrete within the biofilm a vast array of metabolites, surfactants, bacteriocins, enzymes, and toxins, all compounds susceptible to act on the biofilm itself and/or on its environment. Within the biofilm, B. cereus exists in different physiological states and is able to generate highly resistant and adhesive spores, which themselves will increase the resistance of the bacterium to antimicrobials or to cleaning procedures. Current researches show that, despite similarities with the regulation processes and effector molecules involved in the initiation and maturation of the extensively studied Bacillus subtilis biofilm, important differences exists between the two species. The present review summarizes the up to date knowledge on biofilms produced by B. cereus and by two closely related pathogens, Bacillus thuringiensis and Bacillus anthracis. Economic issues caused by B. cereus biofilms and management strategies implemented to control these biofilms are included in this review, which also discuss the ecological and functional roles of biofilms in the lifecycle of these bacterial species and explore future developments in this important research area.

Type III secretion systems: the bacterial flagellum and the injectisome

The flagellum and the injectisome are two of the most complex and fascinating bacterial nanomachines. At their core, they share a type III secretion system (T3SS), a transmembrane export complex that forms the extracellular appendages, the flagellar filament and the injectisome needle. Recent advances, combining structural biology, cryo-electron tomography, molecular genetics, in vivo imaging, bioinformatics and biophysics, have greatly increased our understanding of the T3SS, especially the structure of its transmembrane and cytosolic components, the transcriptional, post-transcriptional and functional regulation and the remarkable adaptivity of the system. This review aims to integrate these new findings into our current knowledge of the evolution, function, regulation and dynamics of the T3SS, and to highlight commonalities and differences between the two systems, as well as their potential applications.

Comparative transcriptome analysis of the biocontrol strain Bacillus amyloliquefaciens FZB42 as response to biofilm formation analyzed by RNA sequencing

The strain Bacillus amyloliquefaciens FZB42 is a plant growth promoting rhizobacterium (PGPR) and biocontrol agent known to keep infections of lettuce (Lactuca sativa) by the phytopathogen Rhizoctonia solani down. Several mechanisms, including the production of secondary metabolites possessing antimicrobial properties and induction of the host plant's systemic resistance (ISR), were proposed to explain the biocontrol effect of the strain. B. amyloliquefaciens FZB42 is able to form plaques (biofilm-like structures) on plant roots and this feature was discussed to be associated with its biocontrol properties. For this reason, formation of B. amyloliquefaciens biofilms was studied at the transcriptional level using high-throughput sequencing of whole transcriptome cDNA libraries from cells grown under biofilm-forming conditions vs. planktonic growth. Comparison of the transcriptional profiles of B. amyloliquefaciens FZB42 under these growth conditions revealed a common set of highly transcribed genes mostly associated with basic cellular functions. The lci gene, encoding an antimicrobial peptide (AMP), was among the most highly transcribed genes of cells under both growth conditions suggesting that AMP production may contribute to biocontrol. In contrast, gene clusters coding for synthesis of secondary metabolites with antimicrobial properties were only moderately transcribed and not induced in biofilm-forming cells. Differential gene expression revealed that 331 genes were significantly up-regulated and 230 genes were down-regulated in the transcriptome of B. amyloliquefaciens FZB42 under biofilm-forming conditions in comparison to planktonic cells. Among the most highly up-regulated genes, the yvqHI operon, coding for products involved in nisin (class I bacteriocin) resistance, was identified. In addition, an operon whose products play a role in fructosamine metabolism was enhanced in its transcription. Moreover, genes involved in the production of the extracellular biofilm matrix including exopolysaccharide genes (eps) and the yqxM-tasA-sipW operon encoding amyloid fiber synthesis were up-regulated in the B. amyloliquefaciens FZB42 biofilm. On the other hand, highly down-regulated genes in biofilms are associated with synthesis, assembly and regulation of the flagellar apparatus, the degradation of aromatic compounds and the export of copper. The obtained transcriptional profile for B. amyloliquefaciens biofilm cells uncovered genes involved in its development and enabled the assessment that synthesis of secondary metabolites among other factors may contribute to the biocontrol properties of the strain.

The impact of manganese on biofilm development of Bacillus subtilis

Bacterial biofilms are dynamic and structurally complex communities, involving cell-to-cell interactions. In recent years, various environmental signals that induce the complex biofilm development of the Gram-positive bacterium Bacillus subtilis have been identified. These signalling molecules are often media components or molecules produced by the cells themselves, as well as those of other interacting species. The responses can also be due to depletion of certain molecules in the vicinity of the cells. Extracellular manganese (Mn2+) is essential for proper biofilm development of B. subtilis. Mn2+ is also a component of practically all laboratory biofilm-promoting media used for B. subtilis. Comparison of complex colony biofilms in the presence or absence of supplemented Mn2+ using microarray analyses revealed that genes involved in biofilm formation are indeed downregulated in the absence of Mn2+. In addition, Mn2+ also affects the transcription of several other genes involved in distinct differentiation pathways of various cellular processes. The effects of Mn2+ on other biofilm-related traits like motility, antimicrobial production, stress and sporulation were followed using fluorescent reporter strains. The global transcriptome and morphology studies highlight the importance of Mn2+ during biofilm development and provide an overview on the expressional changes in colony biofilms in B. subtilis.

Aggregation of germlings is a major contributing factor towards mycelial heterogeneity of Streptomyces

Streptomycetes are filamentous bacteria that produce numerous valuable compounds, including the majority of clinically used antibiotics. At an industrial scale, most of these compounds are produced in bioreactors. Growth of streptomycetes under these conditions is characterized by the formation of complex mycelial particles, whose sizes follow a bimodal distribution. Given the correlation between specific productivity and morphology, this size heterogeneity poses a potential drawback in industry. Recent work indicates that mycelial morphology is controlled by a number of genes that encode proteins required for the synthesis of cell surface-associated glycans. Using a quantifiable system based on fluorescent markers, we here show that these glycans mediate aggregation between germlings and young mycelia, yielding mycelial particles that originate from many different individuals. We also demonstrate that at later time points aggregation between distinct particles is no longer detectable. Notably, the absence of the corresponding glycan synthases yields mycelia that are homogeneous in size, identifying mycelial aggregation as a driving factor towards size heterogeneity. Given that aggregation is widespread within streptomycetes and can also occur between different Streptomyces strains, our work paves the way to improve Streptomyces as a cell factory for the production of known metabolites, but possibly also to discover new ones.

Characterization of Bacillus subtilis Colony Biofilms via Mass Spectrometry and Fluorescence Imaging

Colony biofilms of Bacillus subtilis are a widely used model for studying cellular differentiation. Here, we applied matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) to examine cellular and molecular heterogeneity in B. subtilis colony biofilms. From B. subtilis cells cultivated on a biofilm-promoting medium, we detected two cannibalistic factors not found in previous MALDI MSI studies of the same strain under different culturing conditions. Given the importance of cannibalism in matrix formation of B. subtilis biofilms, we employed a transcriptional reporter to monitor matrix-producing cell subpopulations using fluorescence imaging. These two complementary imaging approaches were used to characterize three B. subtilis strains, the wild type isolate NCIB3610, and two mutants, Δspo0A and ΔabrB, with defective and enhanced biofilm phenotypes, respectively. Upon deletion of key transcriptional factors, correlated changes were observed in biofilm morphology, signaling, cannibalistic factor distribution, and matrix-related gene expression, providing new insights on cannibalism in biofilm development. This work underscores the advantages of using multimodal imaging to compare spatial patterns of selected molecules with the associated protein expression patterns, obtaining information on cellular heterogeneity and function not obtainable when using a single method to characterize biofilm formation.

Direct Comparison of Physical Properties of Bacillus subtilis NCIB 3610 and B-1 Biofilms

Many bacteria form surface-attached communities known as biofilms. Due to the extreme resistance of these bacterial biofilms to antibiotics and mechanical stresses, biofilms are of growing interest not only in microbiology but also in medicine and industry. Previous studies have determined the extracellular polymeric substances present in the matrix of biofilms formed by Bacillus subtilis NCIB 3610. However, studies on the physical properties of biofilms formed by this strain are just emerging. In particular, quantitative data on the contributions of biofilm matrix biopolymers to these physical properties are lacking. Here, we quantitatively investigated three physical properties of B. subtilis NCIB 3610 biofilms: the surface roughness and stiffness and the bulk viscoelasticity of these biofilms. We show how specific biomolecules constituting the biofilm matrix formed by this strain contribute to those biofilm properties. In particular, we demonstrate that the surface roughness and surface elasticity of 1-day-old NCIB 3610 biofilms are strongly affected by the surface layer protein BslA. For a second strain,B. subtilis B-1, which forms biofilms containing mainly γ-polyglutamate, we found significantly different physical biofilm properties that are also differently affected by the commonly used antibacterial agent ethanol. We show that B-1 biofilms are protected from ethanol-induced changes in the biofilm's stiffness and that this protective effect can be transferred to NCIB 3610 biofilms by the sole addition of γ-polyglutamate to growing NCIB 3610 biofilms. Together, our results demonstrate the importance of specific biofilm matrix components for the distinct physical properties of B. subtilis biofilms.

Fusarium culmorum affects expression of biofilm formation key genes in Bacillus subtilis

It is known that there is correlation between biofilm formation and antagonistic activities of Bacillus subtilis strains; but, the mechanism of this correlation is not clear. So, the effect of the plant pathogen (Fusarium culmorum) on the biofilm formation in a B. subtilis strain with high antagonistic and biofilm formation activities was studied. The expression of sinR and tasA genes involved in the biofilm formation was studied in both single culture of bacterium (B) and co-culture with F. culmorum (FB) using real-time PCR. The results revealed that the expression of the sinR gene in both B and FB conditions was continuously decreased during the biofilm formation period and, after 24h (B4 and FB4), it reached 1% and 0.3% at the planktonic phase (B1), respectively, whereas the expression of the tasA was continuously increased and was 5.27 and 30 times more than that at the planktonic phase (B1) after 24h, respectively. So, the expression reduction rate for sinR (3 times) and the expression increasing rate for tasA (6 times) were significantly higher in FB conditions than the B ones. The relative expression of sinR in FB1 (planktonic phase), FB2 (8h), FB3(12h), and FB4 (24h) times was 0.65, 0.44, 0.35, and 0.29, whereas the tasA gene expression was 2.98, 3.44, 4.37, and 5.63-fold of the one at coordinate time points in B conditions, respectively. The significant expression reduction of sinR and increase of tasA confirmed that the presence of pathogen could stimulate biofilm formation in the antagonistic bacterium.

A Fluorescent Reporter for Single Cell Analysis of Gene Expression in Clostridium difficile

Genetically identical cells growing under homogeneous growth conditions often display cell-cell variation in gene expression. This variation stems from noise in gene expression and can be adaptive allowing for division of labor and bet-hedging strategies. In particular, for bacterial pathogens, the expression of phenotypes related to virulence can show cell-cell variation. Therefore, understanding virulence-related gene expression requires knowledge of gene expression patterns at the single cell level. We describe protocols for the use of fluorescence reporters for single cell analysis of gene expression in the human enteric pathogen Clostridium difficile, a strict anaerobe. The reporters are based on modified versions of the human DNA repair enzyme O ( 6)-alkylguanine-DNA alkyltransferase, called SNAP-tag and CLIP-tag. SNAP becomes covalently labeled upon reaction with O ( 6)-benzylguanine conjugated to a fluorophore, whereas CLIP is labeled by O ( 6)-benzylcytosine conjugates. SNAP and CLIP labeling is orthogonal allowing for dual labeling in the same cells. SNAP and CLIP cassettes optimized for C. difficile can be used for quantitative studies of gene expression at the single cell level. Both the SNAP and CLIP reporters can also be used for studies of protein subcellular localization in C. difficile.

Disturbance of the bacterial cell wall specifically interferes with biofilm formation

In nature, bacteria communicate via chemical cues and establish complex communities referred to as biofilms, wherein cells are held together by an extracellular matrix. Much research is focusing on small molecules that manipulate and prevent biofilm assembly by modifying cellular signalling pathways. However, the bacterial cell envelope, presenting the interface between bacterial cells and their surroundings, is largely overlooked. In our study, we identified specific targets within the biosynthesis pathways of the different cell wall components (peptidoglycan, wall teichoic acids and teichuronic acids) hampering biofilm formation and the anchoring of the extracellular matrix with a minimal effect on planktonic growth. In addition, we provide convincing evidence that biofilm hampering by transglycosylation inhibitors and D-Leucine triggers a highly specific response without changing the overall protein levels within the biofilm cells or the overall levels of the extracellular matrix components. The presented results emphasize the central role of the Gram-positive cell wall in biofilm development, resistance and sustainment.

An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network

Organisms from all domains of life use gene regulation networks to control cell growth, identity, function, and responses to environmental challenges. Although accurate global regulatory models would provide critical evolutionary and functional insights, they remain incomplete, even for the best studied organisms. Efforts to build comprehensive networks are confounded by challenges including network scale, degree of connectivity, complexity of organism–environment interactions, and difficulty of estimating the activity of regulatory factors. Taking advantage of the large number of known regulatory interactions in Bacillus subtilis and two transcriptomics datasets (including one with 38 separate experiments collected specifically for this study), we use a new combination of network component analysis and model selection to simultaneously estimate transcription factor activities and learn a substantially expanded transcriptional regulatory network for this bacterium. In total, we predict 2,258 novel regulatory interactions and recall 74% of the previously known interactions. We obtained experimental support for 391 (out of 635 evaluated) novel regulatory edges (62% accuracy), thus significantly increasing our understanding of various cell processes, such as spore formation.

Bacillus subtilis Bacteria Generate an Internal Mechanical Force within a Biofilm

A key issue in understanding why biofilms are the most prevalent mode of bacterial life is the origin of the degree of resistance and protection that bacteria gain from self-organizing into biofilm communities. Our experiments suggest that their mechanical properties are a key factor. Experiments on pellicles, or floating biofilms, of Bacillus subtilis showed that while they are multiplying and secreting extracellular substances, bacteria create an internal force (associated with a -80±25 Pa stress) within the biofilms, similar to the forces that self-equilibrate and strengthen plants, organs, and some engineered buildings. Here, we found that this force, or stress, is associated with growth-induced pressure. Our observations indicate that due to such forces, biofilms spread after any cut or ablation by up to 15-20% of their initial size. The force relaxes over very short timescales (tens of milliseconds). We conclude that this force helps bacteria to shape the biofilm, improve its mechanical resistance, and facilitate its invasion and self-repair.

The Bacterial Hydrophobin BslA is a Switchable Ellipsoidal Janus Nanocolloid

BslA is an amphiphilic protein that forms a highly hydrophobic coat around Bacillus subtilis biofilms, shielding the bacterial community from external aqueous solution. It has a unique structure featuring a distinct partition between hydrophilic and hydrophobic surfaces. This surface property is reminiscent of synthesized Janus colloids. By investigating the behavior of BslA variants at water-cyclohexane interfaces through a set of multiscale simulations informed by experimental data, we show that BslA indeed represents a biological example of an ellipsoidal Janus nanoparticle, whose surface interactions are, moreover, readily switchable. BslA contains a local conformational toggle, which controls its global affinity for, and orientation at, water-oil interfaces. This adaptability, together with single-point mutations, enables the fine-tuning of its solvent and interfacial interactions, and suggests that BslA could be a basis for biotechnological applications.