Biofilms: the matrix revisited

The exopolysaccharide matrix modulates the interaction between 3D architecture and virulence of a mixed-species oral biofilm

Virulent biofilms are responsible for a range of infections, including oral diseases. All biofilms harbor a microbial-derived extracellular-matrix. The exopolysaccharides (EPS) formed on tooth-pellicle and bacterial surfaces provide binding sites for microorganisms; eventually the accumulated EPS enmeshes microbial cells. The metabolic activity of the bacteria within this matrix leads to acidification of the milieu. We explored the mechanisms through which the Streptococcus mutans-produced EPS-matrix modulates the three-dimensional (3D) architecture and the population shifts during morphogenesis of biofilms on a saliva-coated-apatitic surface using a mixed-bacterial species system. Concomitantly, we examined whether the matrix influences the development of pH-microenvironments within intact-biofilms using a novel 3D in situ pH-mapping technique. Data reveal that the production of the EPS-matrix helps to create spatial heterogeneities by forming an intricate network of exopolysaccharide-enmeshed bacterial-islets (microcolonies) through localized cell-to-matrix interactions. This complex 3D architecture creates compartmentalized acidic and EPS-rich microenvironments throughout the biofilm, which triggers the dominance of pathogenic S. mutans within a mixed-species system. The establishment of a 3D-matrix and EPS-enmeshed microcolonies were largely mediated by the S. mutans gtfB/gtfC genes, expression of which was enhanced in the presence of Actinomyces naeslundii and Streptococcus oralis. Acidic pockets were found only in the interiors of bacterial-islets that are protected by EPS, which impedes rapid neutralization by buffer (pH 7.0). As a result, regions of low pH (<5.5) were detected at specific locations along the surface of attachment. Resistance to chlorhexidine was enhanced in cells within EPS-microcolony complexes compared to those outside such structures within the biofilm. Our results illustrate the critical interaction between matrix architecture and pH heterogeneity in the 3D environment. The formation of structured acidic-microenvironments in close proximity to the apatite-surface is an essential factor associated with virulence in cariogenic-biofilms. These observations may have relevance beyond the mouth, as matrix is inherent to all biofilms.

Static biofilm cultures of Gram-positive pathogens grown in a microtiter format used for anti-biofilm drug discovery

An in vitro assay is presented for culturing staphylococcal biofilms and biofilms of nonmotile Gram-positive bacteria under static conditions in microtiter assay plates, and for the quantification of biofilm growth, using a simple staining procedure that measures amounts of bacterial cells and extracellular matrix. This basic assay can be adapted readily to study several aspects of biofilm formation, for high-throughput screening to identify small molecule inhibitors of biofilm formation or biofilm-defective mutants, and for quantifying the anti-biofilm activity of biofilm inhibitors.

Type III secretion and effectors shape the survival and growth pattern of Pseudomonas syringae on leaf surfaces

The bacterium Pseudomonas syringae pv syringae B728a (PsyB728a) uses a type III secretion system (T3SS) to inject effector proteins into plant cells, a process that modulates the susceptibility of different plants to infection. Analysis of GREEN FLUORESCENT PROTEIN-expressing PsyB728a after spray inoculation without additives under moderate relative humidity conditions permitted (1) a detailed analysis of this strain's survival and growth pattern on host (Nicotiana benthamiana) and nonhost (tomato [Solanum lycopersicum]) leaf surfaces, (2) an assessment of the role of plant defenses in affecting PsyB728a leaf surface (epiphytic) growth, and (3) the contribution of the T3SS and specific effectors to PsyB728a epiphytic survival and growth. On host leaf surfaces, PsyB728a cells initially persist without growing, and show an increased population only after 48 h, unless plants are pretreated with the defense-inducing chemical benzothiazole. During the persistence period, some PsyB728a cells induce a T3SS reporter, whereas a T3SS-deficient mutant shows reduced survival. By 72 h, rare invasion by PsyB728a to the mesophyll region of host leaves occurs, but endophytic and epiphytic bacterial growths are not correlated. The effectors HopZ3 and HopAA1 delay the onset of epiphytic growth of PsyB728a on N. benthamiana, whereas they promote epiphytic survival/growth on tomato. These effectors localize to distinct sites in plant cells and likely have different mechanisms of action. HopZ3 may enzymatically modify host targets, as it requires residues important for the catalytic activity of other proteins in its family of proteases. Thus, the T3SS, HopAA1, HopZ3, and plant defenses strongly influence epiphytic survival and/or growth of PsyB728a.

Inhibition of quorum sensing regulated biofilm formation in Serratia marcescens causing nosocomial infections

Serratia marcescens is an opportunistic pathogen causing severe urinary tract infections in hospitalized individuals. Infections of S. marcescens are of great concern because of its increasing resistance towards conventional antibiotics. Quorum sensing (QS)-a cell to cell communication-system of S. marcescens acts as a global regulator of almost all the virulence factors and majorly its biofilm formation. Since, the QS system of S. marcescens directly accords to its pathogenesis, targeting QS system will provide an improved strategy to combat drug resistant pathogens. In the present study, QS system of S. marcescens has been used as target and its inhibition has been studied upon exposure to bioactives from coral associated bacteria (CAB). This study also emphasises the potential of CAB in producing bioactive agents with anti-QS and antibiofilm properties. Two CAB isolates CAB 23 and 41 have shown to inhibit biofilm formation and the production of QS dependent virulence factors like prodigiosin, protease, lipase and swarming motility. The study, on the whole explicates the potential of QS system as a target to treat drug resistant bacterial infections.

Quorum sensing modulates colony morphology through alkyl quinolones in Pseudomonas aeruginosa

BACKGROUND

Acyl-homoserine lactone (acyl-HSL) and alkyl quinolone (AQ) based quorum-sensing (QS) systems are important for Pseudomonas aeruginosa virulence and biofilm formation. The effect of QS on biofilm formation is influenced by various genetic and environmental factors. Here, we used a colony biofilm assay to study the effect of the central acyl-HSL QS regulator, LasR, on biofilm formation and structure in the representative clinical P. aeruginosa isolate ZK2870.

RESULTS

A lasR mutant exhibited wrinkled colony morphology at 37°C in contrast to the smooth colony morphology of the wild-type. Mutational analysis indicated that wrinkling of the lasR mutant is dependent on pel, encoding a biofilm matrix exopolysaccharide. Suppressor mutagenesis and complementation analysis implicated the AQ signaling pathway as the link between las QS and colony morphology. In this pathway, genes pqsA-D are involved in the synthesis of 4-hydroxyalkyl quinolines ("Series A congeners"), which are converted to 3,4-dihydroxyalkyl quinolines ("Series B congeners", including the well-characterized Pseudomonas Quinolone Signal, PQS) by the product of the LasR-dependent pqsH gene. Measurement of AQ in the wild-type, the lasR pqsA::Tn suppressor mutant as well as the defined lasR, pqsH, and lasR pqsH mutants showed a correlation between 4-hydroxyalkyl quinoline levels and the degree of colony wrinkling. Most importantly, the lasR pqsH double mutant displayed wrinkly morphology without producing any 3,4-dihydroxyalkyl quinolines. Constitutive expression of pqsA-D genes in a lasR pqsR::Tnmutant showed that colony wrinkling does not require the AQ receptor PqsR.

CONCLUSIONS

Taken together, these results indicate that the las QS system represses Pel and modulates colony morphology through a 4-hydroxyalkyl quinoline in a PqsR-independent manner, ascribing a novel function to an AQ other than PQS in P. aeruginosa.

Inhibition of quorum sensing in a computational biofilm simulation

Bacteria communicate through small diffusible molecules in a process known as quorum sensing. Quorum-sensing inhibitors are compounds which interfere with this, providing a potential treatment for infections associated with bacterial biofilms. We present an individual-based computational model for a developing biofilm. Cells are aggregated into particles for computational efficiency, but the quorum-sensing mechanism is modelled as a stochastic process on the level of individual cells. Simulations are used to investigate different treatment regimens. The response to the addition of inhibitor is found to depend significantly on the form of the positive feedback in the quorum-sensing model; in cases where the model exhibits bistability, the time at which treatment is initiated proves to be critical for the effective prevention of quorum sensing and hence potentially of virulence.

Growth of Mycobacterium tuberculosis biofilms

Mycobacterium tuberculosis, the etiologic agent of human tuberculosis, has an extraordinary ability to survive against environmental stresses including antibiotics. Although stress tolerance of M. tuberculosis is one of the likely contributors to the 6-month long chemotherapy of tuberculosis (1), the molecular mechanisms underlying this characteristic phenotype of the pathogen remain unclear. Many microbial species have evolved to survive in stressful environments by self-assembling in highly organized, surface attached, and matrix encapsulated structures called biofilms (2-4). Growth in communities appears to be a preferred survival strategy of microbes, and is achieved through genetic components that regulate surface attachment, intercellular communications, and synthesis of extracellular polymeric substances (EPS) (5,6). The tolerance to environmental stress is likely facilitated by EPS, and perhaps by the physiological adaptation of individual bacilli to heterogeneous microenvironments within the complex architecture of biofilms (7). In a series of recent papers we established that M. tuberculosis and Mycobacterium smegmatis have a strong propensity to grow in organized multicellular structures, called biofilms, which can tolerate more than 50 times the minimal inhibitory concentrations of the anti-tuberculosis drugs isoniazid and rifampicin (8-10). M. tuberculosis, however, intriguingly requires specific conditions to form mature biofilms, in particular 9:1 ratio of headspace: media as well as limited exchange of air with the atmosphere (9). Requirements of specialized environmental conditions could possibly be linked to the fact that M. tuberculosis is an obligate human pathogen and thus has adapted to tissue environments. In this publication we demonstrate methods for culturing M. tuberculosis biofilms in a bottle and a 12-well plate format, which is convenient for bacteriological as well as genetic studies. We have described the protocol for an attenuated strain of M. tuberculosis, mc(2)7000, with deletion in the two loci, panCD and RD1, that are critical for in vivo growth of the pathogen (9). This strain can be safely used in a BSL-2 containment for understanding the basic biology of the tuberculosis pathogen thus avoiding the requirement of an expensive BSL-3 facility. The method can be extended, with appropriate modification in media, to grow biofilm of other culturable mycobacterial species. Overall, a uniform protocol of culturing mycobacterial biofilms will help the investigators interested in studying the basic resilient characteristics of mycobacteria. In addition, a clear and concise method of growing mycobacterial biofilms will also help the clinical and pharmaceutical investigators to test the efficacy of a potential drug.

Single-cell analysis of Bacillus subtilis biofilms using fluorescence microscopy and flow cytometry

Biofilm formation is a general attribute to almost all bacteria( 1-6). When bacteria form biofilms, cells are encased in extracellular matrix that is mostly constituted by proteins and exopolysaccharides, among other factors (7-10). The microbial community encased within the biofilm often shows the differentiation of distinct subpopulation of specialized cells (11-17). These subpopulations coexist and often show spatial and temporal organization within the biofilm ( 18-21). Biofilm formation in the model organism Bacillus subtilis requires the differentiation of distinct subpopulations of specialized cells. Among them, the subpopulation of matrix producers, responsible to produce and secrete the extracellular matrix of the biofilm is essential for biofilm formation (11,19). Hence, differentiation of matrix producers is a hallmark of biofilm formation in B. subtilis. We have used fluorescent reporters to visualize and quantify the subpopulation of matrix producers in biofilms of B. subtilis (15,19,22-24). Concretely, we have observed that the subpopulation of matrix producers differentiates in response to the presence of self-produced extracellular signal surfactin (25). Interestingly, surfactin is produced by a subpopulation of specialized cells different from the subpopulation of matrix producers (15). We have detailed in this report the technical approach necessary to visualize and quantify the subpopulation of matrix producers and surfactin producers within the biofilms of B. subtilis. To do this, fluorescent reporters of genes required for matrix production and surfactin production are inserted into the chromosome of B. subtilis. Reporters are expressed only in a subpopulation of specialized cells. Then, the subpopulations can be monitored using fluorescence microscopy and flow cytometry (See Fig 1). The fact that different subpopulations of specialized cells coexist within multicellular communities of bacteria gives us a different perspective about the regulation of gene expression in prokaryotes. This protocol addresses this phenomenon experimentally and it can be easily adapted to any other working model, to elucidate the molecular mechanisms underlying phenotypic heterogeneity within a microbial community.

Identification of Bacillus subtilis SipW as a bifunctional signal peptidase that controls surface-adhered biofilm formation

Biofilms of microbial cells encased in an exopolymeric matrix can form on solid surfaces, but how bacteria sense a solid surface and upregulate biofilm genes is largely unknown. We investigated the role of the Bacillus subtilis signal peptidase, SipW, which has a unique role in forming biofilms on a solid surface and is not required at an air-liquid interface. Surprisingly, we found that the signal peptidase activity of SipW was not required for solid-surface biofilms. Furthermore, a SipW mutant protein was constructed that lacks the ability to form a solid-surface biofilm but still retains signal peptidase activity. Through genetic and gene expression tests, the non-signal peptidase role of SipW was found to activate biofilm matrix genes specifically when cells were on a solid surface. These data provide the first evidence that a signal peptidase is bifunctional and that SipW has a regulatory role in addition to its role as a signal peptidase.

Unraveling assembly of stream biofilm communities

Microbial biofilms assemble from cells that attach to a surface, where they develop into matrix-enclosed communities. Mechanistic insights into community assembly are crucial to better understand the functioning of natural biofilms, which drive key ecosystem processes in numerous aquatic habitats. We studied the role of the suspended microbial community as the source of the biofilm community in three streams using terminal-restriction fragment length polymorphism and 454 pyrosequencing of the 16S ribosomal RNA (rRNA) and the 16S rRNA gene (as a measure for the active and the bulk community, respectively). Diversity was consistently lower in the biofilm communities than in the suspended stream water communities. We propose that the higher diversity in the suspended communities is supported by continuous inflow from various sources within the catchment. Community composition clearly differed between biofilms and suspended communities, whereas biofilm communities were similar in all three streams. This suggests that biofilm assembly did not simply reflect differences in the source communities, but that certain microbial groups from the source community proliferate in the biofilm. We compared the biofilm communities with random samples of the respective community suspended in the stream water. This analysis confirmed that stochastic dispersal from the source community was unlikely to shape the observed community composition of the biofilms, in support of species sorting as a major biofilm assembly mechanism. Bulk and active populations generated comparable patterns of community composition in the biofilms and the suspended communities, which suggests similar assembly controls on these populations.

Osmotic spreading of Bacillus subtilis biofilms driven by an extracellular matrix

Bacterial biofilms are organized communities of cells living in association with surfaces. The hallmark of biofilm formation is the secretion of a polymeric matrix rich in sugars and proteins in the extracellular space. In Bacillus subtilis, secretion of the exopolysaccharide (EPS) component of the extracellular matrix is genetically coupled to the inhibition of flagella-mediated motility. The onset of this switch results in slow expansion of the biofilm on a substrate. Different strains have radically different capabilities in surface colonization: Flagella-null strains spread at the same rate as wild type, while both are dramatically faster than EPS mutants. Multiple functions have been attributed to the EPS, but none of these provides a physical mechanism for generating spreading. We propose that the secretion of EPS drives surface motility by generating osmotic pressure gradients in the extracellular space. A simple mathematical model based on the physics of polymer solutions shows quantitative agreement with experimental measurements of biofilm growth, thickening, and spreading. We discuss the implications of this osmotically driven type of surface motility for nutrient uptake that may elucidate the reduced fitness of the matrix-deficient mutant strains.

'Life-style' control networks in Escherichia coli: signaling by the second messenger c-di-GMP

Most bacteria can exist in either a planktonic-motile single-cell state or an adhesive multicellular state known as a biofilm. Biofilms cause medical problems and technical damage since they are resistant against antibiotics, disinfectants or the attacks of the immune system. In recent years it has become clear that most bacteria use cyclic diguanylate (c-di-GMP) as a biofilm-promoting second messenger molecule. C-di-GMP is produced by GGDEF-domain-containing diguanylate cyclases and is degraded by phosphodiesterases featuring EAL or HD-GYP domains. Many bacterial species possess multiple proteins with GGDEF and EAL domains, which actually belong to the most abundant protein families in genomic data bases. Via an unprecedented variety of effector components, which include c-di-GMP-binding proteins as well as RNAs, c-di-GMP controls a wide range of targets that down-regulate motility, stimulate adhesin and biofilm matrix formation or even control virulence gene expression. Moreover, local c-di-GMP signaling in macromolecular complexes seems to allow the independent and parallel control of different output reactions. In this review, we use Escherichia coli as a paradigm for c-di-GMP signaling. Despite the huge diversity of components and molecular processes involved in biofilm formation throughout the bacterial kingdom, c-di-GMP signaling represents a unifying principle, which suggests that the enzymes that make and break c-di-GMP may be promising targets for anti-biofilm drugs.

FHA-mediated cell-substrate and cell-cell adhesions are critical for Bordetella pertussis biofilm formation on abiotic surfaces and in the mouse nose and the trachea

Bordetella spp. form biofilms in the mouse nasopharynx, thereby providing a potential mechanism for establishing chronic infections in humans and animals. Filamentous hemagglutinin (FHA) is a major virulence factor of B. pertussis, the causative agent of the highly transmissible and infectious disease, pertussis. In this study, we dissected the role of FHA in the distinct biofilm developmental stages of B. pertussis on abiotic substrates and in the respiratory tract by employing a murine model of respiratory biofilms. Our results show that the lack of FHA reduced attachment and decreased accumulation of biofilm biomass on artificial surfaces. FHA contributes to biofilm development by promoting the formation of microcolonies. Absence of FHA from B. pertussis or antibody-mediated blockade of surface-associated FHA impaired the attachment of bacteria to the biofilm community. Exogenous addition of FHA resulted in a dose-dependent inhibitory effect on bacterial association with the biofilms. Furthermore, we show that FHA is important for the structural integrity of biofilms formed on the mouse nose and trachea. Together, these results strongly support the hypothesis that FHA promotes the formation and maintenance of biofilms by mediating cell-substrate and inter-bacterial adhesions. These discoveries highlight FHA as a key factor in establishing structured biofilm communities in the respiratory tract.

Biofilm formation in moderately halophilic bacteria is influenced by varying salinity levels

Bacteria in a biofilm have a co-dependent lifestyle resulting in a harmonized and complex coordination of the bacterial cells within an exopolysaccharide (EPS) matrix. We hypothesized that biofilm formation and EPS production in salt-tolerant bacteria are helpful for plant growth improvement in saline soil, but that they are influenced differently. To investigate this hypothesis, we tested the effect of different salinity levels on the biofilm formation of the bacterial strains PAa6 (Halomonas meridiana), HT2 (Kushneria indalinina) and ST2 (Halomonas aquamarina) on different abiotic and biotic surfaces. Maximum biofilm formation was established at 1 M salt concentration. However, EPS production was maximal at 0-1 M NaCl stress. We also studied the effect of salt stress on EPS produced by the bacterial strains and confirmed the presence of EPS on Cicer arietinum var. CM 98 roots and in soil at different salinity levels, using Alcian blue staining. Overall, the strain PAa6 was more effective in biofilm formation and EPS production. Under saline and non-saline conditions, this strain also colonized the plant roots more efficiently as compared to the other two strains. We conclude that the strain PAa6 has the potential of biofilm formation and EPS production at different salinity levels. The presence of EPS in the biofilm helped the bacterial strains to better colonize the roots.

Inhibitory effects of UV treatment and a combination of UV and dry heat against pathogens on stainless steel and polypropylene surfaces

Pathogens that contaminate the surfaces of food utensils may contribute to the occurrence of foodborne disease outbreaks. We investigated the efficacy of UV treatment combined with dry heat (50 °C) for inhibiting 5 foodborne pathogens (Escherichia coli O157:H7, Salmonella Typhimurium, Pseudomonas aeruginosa, Listeria monocytogenes, and Staphylococcus aureus) on stainless steel and polypropylene surfaces in this study. We inoculated substrates with each of the 5 foodborne pathogens cultured on agar surface and then UV treatment alone or a combination of both UV and dry heat (50 °C) was applied for 30 min, 1 h, 2 h, and 3 h. The initial populations of the 5 pathogens before treatment were 8.02 to 9.18 and 8.73 to 9.16 log₁₀ CFU/coupon on the surfaces of stainless steel and polypropylene coupons, respectively. UV treatments for 3 h significantly inhibited S. Typhimurium, L. monocytogenes, and S. aureus on the stainless steel by 3.06, 2.18, and 2.70 log₁₀ CFU/coupon, and S. aureus on the polypropylene by 3.11 log₁₀ CFU/coupon, respectively. The inhibitory effects of the combined UV and dry heat treatment (50 °C) increased as treatment time increased, yielding significant reductions in all samples treated for 3 h, with the exception of S. aureus on polypropylene. The reduction level of E. coli O157:H7 treated for 3 h on the surface of stainless steel and polypropylene treated was approximately 6.00 log₁₀ CFU/coupon. These results indicate that combined UV and dry heat (50 °C) treatments may be effective for controlling microbial contamination on utensils and cooking equipment surfaces as well as in other related environments.

[Chronic bronchial infection: the problem of Pseudomonas aeruginosa]

Pathogenic bronchopulmonary colonizations and the exacerbations produced are among the most important causes of reduced pulmonary function in patients with bronchiectasis. The most frequent pathogens in these patients are Haemophilus influenzae and Pseudomonas aeruginosa. Lesions are produced by the local inflammatory process and the vicious circle developed by antigen stimulation, the release of inflammatory mediators, the presence of neutrophils, the increase of bacterial inoculum and the release of bacterial exoproducts. P. aeruginosa has been demonstrated to affect the patients with bronchiectasis and poorest quality of life and to colonize those with the poorest pulmonary function and the highest number of antimicrobial treatments. In bronchiectasis, as in chronic obstructive pulmonary disease (COPD) or cystic fibrosis, P. aeruginosa is able to colonize the respiratory mucosa chronically. Due to the ecological niche occupied by P. aeruginosa and the multitude of cycles with antimicrobial agents to which these patients are subjected, the development of antimicrobial resistance is highly likely, encouraged by the high proportion of hypermutation variants in existence. Likewise, P. aeruginosa naturally grows in the form of biofilms on the mucosal surface, greatly contributing to its persistence. Antimicrobial treatment in patients with bronchiectasis and P. aeruginosa colonization should be based on antimicrobial agents, alone or in combination, that do not lose activity when acting on biofilms.

Analysis of the fusA2 locus encoding EFG2 in Mycobacterium smegmatis

The translation elongation factor G (EFG) is encoded by the fusA gene. Several bacteria possess a second fusA-like locus, fusA2 which encodes EFG2. A comparison of EFG and EFG2 from various bacteria reveals that EFG2 preserves domain organization and maintains significant sequence homology with EFG, suggesting that EFG2 may function as an elongation factor. However, with the single exception of a recent study on Thermus thermophilus EFG2, this class of EFG-like factors has not been investigated. Here, we have characterized EFG2 (MSMEG_6535) from Mycobacterium smegmatis. Expression of EFG2 was detected in stationary phase cultures of M. smegmatis (Msm). Our in vitro studies show that while MsmEFG2 binds guanine nucleotides, it lacks the ribosome-dependent GTPase activity characteristic of EFGs. Furthermore, unlike MsmEFG (MSMEG_1400), MsmEFG2 failed to rescue an E. coli strain harboring a temperature-sensitive allele of EFG, for its growth at the non-permissive temperature. Subsequent experiments showed that the fusA2 gene could be disrupted in M. smegmatis mc(2)155 with Kan(R) marker. The M. smegmatis fusA2::kan strain was viable and showed growth kinetics similar to that of the parent strain (wild-type for fusA2). However, in the growth competition assays, the disruption of fusA2 was found to confer a fitness disadvantage to M. smegmatis, raising the possibility that EFG2 is of some physiological relevance to mycobacteria.

Interaction of Acinetobacter baumannii 19606 and 1656-2 with Acanthamoeba castellanii

Acinetobacter baumannii is virtually avirulent for healthy people but maintains a high virulence among critically ill patients or immuno-compromised individuals. The ability of A. baumannii to adhere to cells and persist on surfaces as biofilms could be central to its pathogenicity. In the present study, we compared the virulence of the A. baumannii 1656-2 clinical strain, which is able to form a thick biofilm, with the virulence of the A. baumannii type strain (ATCC 19606(T)). Acanthamoeba castellanii, a single-celled organism, was used as the host model system to study the virulence of A. baumannii. Compared to A. baumannii ATCC 19606(T), A. baumannii 1656-2 exhibited a higher ability to adhere and invade A. castellanii cells and had a higher killing rate of A. castellanii cells. Furthermore, co-incubation of the amoeba cells and the cell-free supernatant of A. baumannii resulted in the cell death of the amoebae. Heat inactivation or proteinase K treatment of the supernatant did not eliminate its cytotoxicity, suggesting heat stable non-protein factors are responsible for its cytotoxicity to A. castellanii cells. In conclusion, this study for the first time has revealed the capacity of the A. baumannii strain and/or its metabolic products to induce cytotoxicity in A. castellanii cells.

Translational repression of NhaR, a novel pathway for multi-tier regulation of biofilm circuitry by CsrA

The RNA binding protein CsrA (RsmA) represses biofilm formation in several proteobacterial species. In Escherichia coli, it represses the production of the polysaccharide adhesin poly-β-1,6-N-acetyl-D-glucosamine (PGA) by binding to the pgaABCD mRNA leader, inhibiting pgaA translation, and destabilizing this transcript. In addition, CsrA represses genes responsible for the synthesis of cyclic di-GMP, an activator of PGA production. Here we determined that CsrA also represses NhaR, a LysR-type transcriptional regulator which responds to elevated [Na(+)] and alkaline pH and activates the transcription of the pgaABCD operon. Gel shift studies revealed that CsrA binds at two sites in the 5' untranslated segment of nhaR, one of which overlaps the Shine-Dalgarno sequence. An epitope-tagged NhaR protein, expressed from the nhaR chromosomal locus, and an nhaR posttranscriptional reporter fusion (PlacUV5-nhaR'-'lacZ) both showed robust repression by CsrA. Northern blotting revealed a complex transcription pattern for the nhaAR locus. Nevertheless, CsrA did not repress nhaR mRNA levels. Toeprinting assays showed that CsrA competes effectively with the ribosome for binding to the translation initiation region of nhaR. Together, these findings indicate that CsrA blocks nhaR translation. Epistasis studies with a pgaA-lacZ transcriptional fusion confirmed a model in which CsrA indirectly represses pgaABCD transcription via NhaR. We conclude that CsrA regulates the horizontally acquired pgaABCD operon and PGA biosynthesis at multiple levels. Furthermore, nhaR repression exemplifies an expanding role for CsrA as a global regulator of stress response systems.

Growth of Acinetobacter baumannii in pellicle enhanced the expression of potential virulence factors

Background

Interestingly, Acinetobacter baumannii presents an enhanced capacity to form biofilms (also named pellicles) at the air-liquid interface as compared to the other Acinetobacter species. This characteristic questions the contribution of this phenotype to an increased risk of clinical infections by this pathogen.

Methodology/Principal Findings

By a proteomic approach using 2-D gel electrophoresis-LC-MS/MS mass spectrometry, we compared the membrane protein patterns of A. baumannii 77, a pellicle-forming clinical isolate, grown in planktonic and in sessile modes. We identified 52 proteins with a differential expression, including 32 up-regulated and 20 down-regulated in the pellicle state. Several proteins, differentially expressed during pellicle development, were of particular interest. We determined the over-expression of four siderophore iron uptake systems including the acinetobactin and enterobactin receptors and confirmed that the development of this type of biofilm is promoted by ferric ions. Two over-expressed proteins, CarO and an OprD-homologue, putative carbapenem-resistance associated porins, would be involved in the transport of specific compounds, like ornithine, a biosynthesis precursor of a siderophore from the hydroxamate family. We evidenced the overexpression of a lipase and a transporter of LCFA that may be involved in the recycling of lipids inside the pellicle matrix. Finally, we demonstrated both by proteomic and by AFM studies that this particular type of biofilm required multiple pili systems to maintain this cohesive structure at the air-liquid interface; two of these systems have never been described in A. baumannii.

Conclusions/Significance

Our study demonstrated that several proteins, overexpressed at a late state of pellicle development, could be potentially involved in virulence processes. Therefore, regarding the number of potential virulence factors that are over-expressed in this growth mode, the pellicle-forming clinical isolates should be kept under survey.

Extracellular signaling and multicellularity in Bacillus subtilis

Bacillus subtilis regulates its ability to differentiate into distinct, co-existing cell types in response to extracellular signaling molecules produced either by itself, or present in its environment. The production of molecules by B. subtilis cells, as well as their response to these signals, is not uniform across the population. There is specificity and heterogeneity both within genetically identical populations as well as at the strain-level and species-level. This review will discuss how extracellular signaling compounds influence B. subtilis multicellularity with regard to matrix-producing cannibal differentiation, germination, and swarming behavior, as well as the specificity of the quorum-sensing peptides ComX and CSF. It will also highlight how imaging mass spectrometry can aid in identifying signaling compounds and contribute to our understanding of the functional relationship between such compounds and multicellular behavior.

Sensor kinase RscS induces the production of antigenically distinct outer membrane vesicles that depend on the symbiosis polysaccharide locus in Vibrio fischeri

Robust biofilm formation by Vibrio fischeri depends upon activation of the symbiosis polysaccharide (syp) locus, which is achieved by overexpressing the RscS sensor kinase (RscS(+)). Other than the Syp polysaccharide, however, little is known about V. fischeri biofilm matrix components. In other bacteria, biofilms contain polysaccharides, secreted proteins, and outer membrane vesicles (OMVs). Here, we asked whether OMVs are part of V. fischeri biofilms. Transmission electron microscopy revealed OMV-like particles between cells within colonies. In addition, OMVs could be purified from culture supernatants of both RscS(+) and control cells, with the former releasing 2- to 3-fold more OMVs. The increase depended upon the presence of an intact syp locus, as an RscS(+) strain deleted for sypK, which encodes a putative oligosaccharide translocase, exhibited reduced production of OMVs; it also showed a severe defect in biofilm formation. Western immunoblot analyses revealed that the RscS(+) strain, but not the control strain or the RscS(+) sypK mutant, produced a distinct set of nonproteinaceous molecules that could be detected in whole-cell extracts, OMV preparations, and lipopolysaccharide (LPS) extracts. Finally, deletion of degP, which in other bacteria influences OMV production, decreased OMV production and reduced the ability of the cells to form biofilms. We conclude that overexpression of RscS induces OMV production in a manner that depends on the presence of the syp locus and that OMVs produced under these conditions contain antigenically distinct molecules, possibly representing a modified form of lipopolysaccharide (LPS). Finally, our data indicate a correlation between OMV production and biofilm formation by V. fischeri.

Biofilm formation and microbial activity in a biofilter system in the presence of MTBE, ETBE and TAME

Emerging water contaminants derived from unleaded gasoline such as methyl tert-butyl ether (MTBE), ethyl tert-butyl ether (ETBE) and tert-amyl methyl ether (TAME), are in need of effective bioremediation technologies for restoring water resources. In order to design the conditions of a future groundwater bioremediating biofilter, this work assesses the potential use of Acinetobacter calcoaceticus M10, Rhodococcus ruber E10 and Gordonia amicalis T3 for the removal of MTBE, ETBE and TAME in consortia or as individual strains. Biofilm formation on an inert polyethylene support material was assessed with scanning electron microscopy, and consortia were also analysed with fluorescent in situ hybridisation to examine the relation between the strains. A. calcoaceticus M10 was the best coloniser, followed by G. amicalis T3, however, biofilm formation of pair consortia favoured consortium M10-E10 both in formation and activity. However, degradation batch studies determined that neither consortium exhibited higher degradation than individual strain degradation. The physiological state of the three strains was also determined through flow cytometry using propidium iodide and 3'-dihexylocarbocyanine iodide thus gathering information on their viability and activity with the three oxygenates since previous microbial counts revealed slow growth. Strain E10 was observed to have the highest physiological activity in the presence of MTBE, and strain M10 activity with TAME was only maintained for 24 h, thus we believe that biotransformation of MTBE occurs within the active periods established by the cytometry analyses. Viable cell counts and oxygenate removal were determined in the presence of the metabolites tert-butyl alcohol (TBA) and tert-amyl alcohol (TAA), resulting in TBA biotransformation by M10 and E10, and TAA by M10. Our results show that A. calcoaceticus M10 and the consortium M10-E10 could be adequate inocula in MTBE and TAME bioremediating technologies.

Resistance of bacterial biofilms to disinfectants: a review

A biofilm can be defined as a community of microorganisms adhering to a surface and surrounded by a complex matrix of extrapolymeric substances. It is now generally accepted that the biofilm growth mode induces microbial resistance to disinfection that can lead to substantial economic and health concerns. Although the precise origin of such resistance remains unclear, different studies have shown that it is a multifactorial process involving the spatial organization of the biofilm. This review will discuss the mechanisms identified as playing a role in biofilm resistance to disinfectants, as well as novel anti-biofilm strategies that have recently been explored.

N-Acetylglucosamine-dependent biofilm formation in Pectobacterium atrosepticum is cryptic and activated by elevated c-di-GMP levels

The phytopathogenic bacterium Pectobacterium atrosepticum (Pba) strain SCRI1043 does not exhibit appreciable biofilm formation under standard laboratory conditions. Here we show that a biofilm-forming phenotype in this strain could be activated from a cryptic state by increasing intracellular levels of c-di-GMP, through overexpression of a constitutively active diguanylate cyclase (PleD*) from Caulobacter crescentus. Randomly obtained Pba transposon mutants defective in the pga operon, involved in synthesis and translocation of poly-β-1,6-N-acetyl-D-glucosamine (PGA), were all impaired in this biofilm formation. The presence of the PGA-degrading enzyme dispersin B in the growth media prevented biofilm formation by Pba overexpressing PleD*, further supporting the importance of PGA for biofilm formation by Pba. Importantly, a pga mutant exhibited a reduction in root binding to the host plant under conditions of high intracellular c-di-GMP levels. A modest but consistent increase in pga transcript levels was associated with high intracellular levels of c-di-GMP. Our results indicate tight control of PGA-dependent biofilm formation by c-di-GMP in Pba.

Biofilm formation in Streptococcus pneumoniae

Biofilm‐grown bacteria are refractory to antimicrobial agents and show an increased capacity to evade the host immune system. In recent years, studies have begun on biofilm formation by Streptococcus pneumoniae, an important human pathogen, using a variety of in vitro model systems. The bacterial cells in these biofilms are held together by an extracellular matrix composed of DNA, proteins and, possibly, polysaccharide(s). Although neither the precise nature of these proteins nor the composition of the putative polysaccharide(s) is clear, it is known that choline‐binding proteins are required for successful biofilm formation. Further, many genes appear to be involved, although the role of each appears to vary when biofilms are produced in batch or continuous culture. Prophylactic and therapeutic measures need to be developed to fight S. pneumoniae biofilm formation. However, much care needs to be taken when choosing strains for such studies because different S. pneumoniae isolates can show remarkable genomic differences. Multispecies and in vivo biofilm models must also be developed to provide a more complete understanding of biofilm formation and maintenance.

The CRP/FNR family protein Bcam1349 is a c-di-GMP effector that regulates biofilm formation in the respiratory pathogen Burkholderia cenocepacia

Burkholderia cenocepacia is an opportunistic respiratory pathogen that can cause severe infections in immune-compromised individuals and is associated with poor prognosis for patients suffering from cystic fibrosis. The second messenger cyclic diguanosine monophosphate (c-di-GMP) has been shown to control a wide range of functions in bacteria, but little is known about these regulatory mechanisms in B. cenocepacia. Here we investigated the role that c-di-GMP plays in the regulation of biofilm formation and virulence in B. cenocepacia. Elevated intracellular levels of c-di-GMP promoted wrinkly colony, pellicle and biofilm formation in B. cenocepacia. A screen for transposon mutants unable to respond to elevated levels of c-di-GMP led to the identification of the mutant bcam1349 that did not display increased biofilm and pellicle formation with excessive c-di-GMP levels, and displayed a biofilm defect with physiological c-di-GMP levels. The bcam1349 gene is predicted to encode a transcriptional regulator of the CRP/FNR superfamily. Analyses of purified Bcam1349 protein and truncations demonstrated that it binds c-di-GMP in vitro. The Bcam1349 protein was shown to regulate the production of a number of components, including cellulose and fimbriae. It was demonstrated that the Bcam1349 protein binds to the promoter region of the cellulose synthase genes, and that this binding is enhanced by the presence of c-di-GMP. The bcam1349 mutant showed reduced virulence in a Galleria mellonella wax moth larvae infection model. Taken together, these findings suggest that the Bcam1349 protein is a transcriptional regulator that binds c-di-GMP and regulates biofilm formation and virulence in B. cenocepacia in response to the level of c-di-GMP.

Comparison of the virulence of exopolysaccharide-producing Prevotella intermedia to exopolysaccharide non-producing periodontopathic organisms

BACKGROUND

Evidence in the literature suggests that exopolysaccharides (EPS) produced by bacterial cells are essential for the expression of virulence in these organisms. Secreted EPSs form the framework in which microbial biofilms are built.

METHODS

This study evaluates the role of EPS in Prevotella intermedia for the expression of virulence. This evaluation was accomplished by comparing EPS-producing P. intermedia strains 17 and OD1-16 with non-producing P. intermedia ATCC 25611 and Porphyromonas gingivalis strains ATCC 33277, 381 and W83 for their ability to induce abscess formation in mice and evade phagocytosis.

RESULTS

EPS-producing P. intermedia strains 17 and OD1-16 induced highly noticeable abscess lesions in mice at 107 colony-forming units (CFU). In comparison, P. intermedia ATCC 25611 and P. gingivalis ATCC 33277, 381 and W83, which all lacked the ability to produce viscous materials, required 100-fold more bacteria (109 CFU) in order to induce detectable abscess lesions in mice. Regarding antiphagocytic activity, P. intermedia strains 17 and OD1-16 were rarely internalized by human polymorphonuclear leukocytes, but other strains were readily engulfed and detected in the phagosomes of these phagocytes.

CONCLUSIONS

These results demonstrate that the production of EPS by P. intermedia strains 17 and OD1-16 could contribute to the pathogenicity of this organism by conferring their ability to evade the host's innate defence response.

Magnesium limitation is an environmental trigger of the Pseudomonas aeruginosa biofilm lifestyle

Biofilm formation is a conserved strategy for long-term bacterial survival in nature and during infections. Biofilms are multicellular aggregates of cells enmeshed in an extracellular matrix. The RetS, GacS and LadS sensors control the switch from a planktonic to a biofilm mode of growth in Pseudomonas aeruginosa. Here we detail our approach to identify environmental triggers of biofilm formation by investigating environmental conditions that repress expression of the biofilm repressor RetS. Mg²⁺ limitation repressed the expression of retS leading to increased aggregation, exopolysaccharide (EPS) production and biofilm formation. Repression of retS expression under Mg²⁺ limitation corresponded with induced expression of the GacA-controlled small regulatory RNAs rsmZ and rsmY and the EPS biosynthesis operons pel and psl. We recently demonstrated that extracellular DNA sequesters Mg²⁺ cations and activates the cation-sensing PhoPQ two-component system, which leads to increased antimicrobial peptide resistance in biofilms. Here we show that exogenous DNA and EDTA, through their ability to chelate Mg²⁺, promoted biofilm formation. The repression of retS in low Mg²⁺ was directly controlled by PhoPQ. PhoP also directly controlled expression of rsmZ but not rsmY suggesting that PhoPQ controls the equilibrium of the small regulatory RNAs and thus fine-tunes the expression of genes in the RetS pathway. In summary, Mg²⁺ limitation is a biologically relevant environmental condition and the first bonafide environmental signal identified that results in transcriptional repression of retS and promotes P. aeruginosa biofilm formation.

Surface acoustic waves increase the susceptibility of Pseudomonas aeruginosa biofilms to antibiotic treatment

Bacterial urinary tract infections resulting from prolonged patient catheterization have become a major health problem. One of the major issues is bacterial resistance to antibiotic treatments due to biofilm formation inside the catheters, thus enhancing the search for alternative treatments. In the present study, a device containing a piezo element capable of transmitting low-frequency surface acoustic waves (SAW) onto the indwelling catheter was used. The SAW were able to eradicate biofilm-residing bacteria by >85% when applied simultaneously with an antibiotic in three clinically relevant species, viz. Escherichia coli, Staphylococcus epidermidis and Pseudomonas aeruginosa. Moreover, transcriptome analysis revealed that SAW can alter the transcription pattern of P. aeruginosa, suggesting that this signal can be specifically sensed by the bacterium.

YuaB functions synergistically with the exopolysaccharide and TasA amyloid fibers to allow biofilm formation by Bacillus subtilis

During biofilm formation by Bacillus subtilis, two extracellular matrix components are synthesized, namely, the TasA amyloid fibers and an exopolysaccharide. In addition, a small protein called YuaB has been shown to allow the biofilm to form. The regulatory protein DegU is known to initiate biofilm formation. In this report we show that the main role of DegU during biofilm formation is to indirectly drive the activation of transcription from the yuaB promoter. The N terminus of YuaB constitutes a signal peptide for the Sec transport system. Here we show that the presence of the signal peptide is required for YuaB function. In addition we demonstrate that upon export of YuaB from the cytoplasm, it localizes to the cell wall. We continue with evidence that increased production of TasA and the exopolysaccharide is not sufficient to overcome the effects of a mutation in yuaB, demonstrating the unique involvement of YuaB in forming a biofilm. In line with this, YuaB is not involved in correct synthesis, export, or polymerization of either the TasA amyloid fibers or the exopolysaccharide. Taken together, these findings identify YuaB as a protein that plays a novel role during biofilm formation. We hypothesize that YuaB functions synergistically with the known components of the biofilm matrix to facilitate the assembly of the biofilm matrix.

Cellulose accumulation and a cellulose synthase gene are responsible for cell aggregation in the cyanobacterium Thermosynechococcus vulcanus RKN

A thermophilic cyanobacterium, Thermosynechococcus vulcanus RKN, exhibits cell aggregation under low temperature illuminated conditions as a means of physiological acclimation to avoid excess light stress. The cell aggregation was dispersed with cellulase treatment. We developed a method to quantify small amounts of cellulose by partial cellulose purification followed by quantitation of liberated glucose by cellulase. Under low temperature illuminated light conditions, cellulose accumulation was induced approximately 2-fold, to 10 μg (4 × 10(9) cells)(-1), and slightly preceded aggregation. Based on sequence similarity, three candidate genes for cellulose synthase (Tvtll0007, Tvtlr1795 and Tvtlr1930-33) were cloned from T. vulcanus. Gene disruption analysis showed that only Tvtll0007 was responsible for both the light- and low temperature-induced cell aggregation and the induction of cellulose accumulation. Gene expression analysis suggested that the low temperature illuminated conditions quickly induced expression of Tvtlr1795 and Tvtlr1930-33, while the induction of Tvtll0007 was slow. These results suggest that Tvtll0007 encodes a functional cellulose synthase whose activity may not be regulated at the transcriptional level.

Synthesis, biological studies of linear and branched arabinofuranoside-containing glycolipids and their interaction with surfactant protein A

Oligoarabinofuranoside-containing glycolipids relevant to mycobacterial cell wall components were synthesized in order to understand the functional roles of such glycolipids. A series of linear tetra-, hexa-, octa- and a branched heptasaccharide oligoarabinofuranosides, with 1 → 2 and 1 → 5 α-linkages between the furanoside residues, were synthesized by chemical methods from readily available monomer building blocks. Upon the synthesis of glycolipids, constituted with a double alkyl chain-substituted sn-glycerol core and oligosaccharide fragments, biological studies were performed to identify the effect of synthetic glycolipids on the biofilm formation and sliding motilities of Mycobacterium smegmatis. Synthetic glycolipids and arabinofuranosides displayed an inhibitory effect on the growth profile, but mostly on the biofilm formation and maturation. Similarly, synthetic compounds also influenced the sliding motility of the bacteria. Further, biophysical studies were undertaken, so as to identify the interactions of the glycolipids with a pulmonary surfactant protein, namely surfactant protein A (SP-A), with the aid of the surface plasmon resonance technique. Specificities of each glycolipid interacting with SP-A were thus evaluated. From this study, glycolipids were found to exhibit higher apparent association constants than the corresponding oligosaccharide portion alone, without the double alkyl group-substituted glycerol core.

Energy-dependent stability of Shewanella oneidensis MR-1 biofilms

Stability and resistance to dissolution are key features of microbial biofilms. How these macroscopic properties are determined by the physiological state of individual biofilm cells in their local physical-chemical and cellular environment is largely unknown. In order to obtain molecular and energetic insight into biofilm stability, we investigated whether maintenance of biofilm stability is an energy-dependent process and whether transcription and/or translation is required for biofilm dissolution. We found that in 12-hour-old Shewanella oneidensis MR-1 biofilms, a reduction in cellular ATP concentration, induced either by oxygen deprivation or by addition of the inhibitor of oxidative phosphorylation carbonyl cyanide m-chlorophenylhydrazone (CCCP), dinitrophenol (DNP), or CN(-), resulted in massive dissolution. In 60-hour-old biofilms, the extent of uncoupler-induced cell loss was strongly attenuated, indicating that the integrity of older biofilms is maintained by means other than those operating in younger biofilms. In experiments with 12-hour-old biofilms, the transcriptional and translational inhibitors rifampin, tetracycline, and erythromycin were found to be ineffective in preventing energy starvation-induced detachment, suggesting that neither transcription nor translation is required for this process. Biofilms of Vibrio cholerae were also induced to dissolve upon CCCP addition to an extent similar to that in S. oneidensis. However, Pseudomonas aeruginosa and P. putida biofilms remained insensitive to CCCP addition. Collectively, our data show that metabolic energy is directly or indirectly required for maintaining cell attachment, and this may represent a common but not ubiquitous mechanism for stability of microbial biofilms.

Key two-component regulatory systems that control biofilm formation in Pseudomonas aeruginosa

Biofilm formation in P. aeruginosa is a highly regulated process that proceeds through a number of distinct stages. This development is controlled by a wide range of factors, of which two-component systems (TCSs) play a key role. In this review, we focus on some of the TCSs that regulate the switch from a motile to a sessile bacterial lifestyle, either via the production of extracellular appendages or by the production of exopolysaccharides. Extracellular appendages, such as flagella, type IV pili and Cup fimbriae are often involved in the initial attachment of bacteria to a surface. In P. aeruginosa, many of these surface structures are regulated by TCSs, and some systems regulate more than one type of appendage. Furthermore, the production of exopolysaccharides, such as Pel and Psl, is required for P. aeruginosa biofilm formation. The regulation of Pel and Psl is post-transcriptionally repressed by RsmA, the activity of which is controlled by a complex regulatory system involving several sensor kinases and accessory components. Furthermore, the Rsm system is a major control system that inversely regulates factors involved in motility and acute infection on one hand, and factors involved in biofilm formation and chronic infection on the other hand. Finally, a series of TCSs has recently been discovered that regulates biofilm development in a stage-specific manner. Taken together, these complex regulatory networks allow the bacterium to respond appropriately to diverse environmental stimuli, and increased knowledge of their mechanisms and signals could be of great importance in the design of novel antibacterial strategies.

An analogy between the evolution of drug resistance in bacterial communities and malignant tissues

Cancer cells rapidly evolve drug resistance through somatic evolution and, in order to continue growth in the metastatic phase, violate the organism-wide consensus of regulated growth and beneficial communal interactions. We suggest that there is a fundamental mechanistic connection between the rapid evolution of resistance to chemotherapy in cellular communities within malignant tissues and the rapid evolution of antibiotic resistance in bacterial communities. We propose that this evolution is the result of a programmed and collective stress response performed by interacting cells, and that, given this fundamental connection, studying bacterial communities can provide deeper insights into the dynamics of adaptation and the evolution of cells within tumours.

Resonance energy-transfer studies of the conformational change on the adsorption of oligonucleotides to a silica interface

Time-resolved evanescent wave-induced fluorescence studies have been carried out on a series of fluorescently labeled oligonucleotide sequences adsorbed to a silica surface from solution. The fluorescence decay profiles of a fluorescent energy donor group undergoing resonance energy transfer to a nonemissive energy-acceptor molecule have been analyzed in terms of a distribution of donor-acceptor distances to reveal the conformational changes that occur in these oligonucleotides upon adsorption. Evanescent wave-induced time-resolved Förster resonance energy-transfer (EW-TRFRET) measurements indicate that at a high electrolyte concentration, there is localized separation of the oligonucleotide strands, and the helical structure adopts an "unraveled" conformation as a result of adsorption. This is attributed to the flexibility within the oligonucleotide at high electrolyte concentration allowing multiple segments of the oligonucleotide to have direct surface interaction. In contrast, the EW-TRFRET measurements at a lower electrolyte concentration reveal that the oligonucleotide retains its helical conformation in a localized extended state. This behavior implies that the rigidity of the oligonucleotide at this electrolyte concentration restricts direct interaction with the silica to a few segments, which correspondingly introduces kinks in the double helix conformation and results in significant oligonucleotide segmental extension into solution.