Gene expression in Pseudomonas aeruginosa: evidence of iron override effects on quorum sensing and biofilm-specific gene regulation

Studying microbially induced corrosion on glass using ToF-SIMS

Microbially induced corrosion (MIC) is an emerging topic that has huge environmental impacts, such as long-term evaluation of microbial interactions with radioactive waste glass, environmental cleanup and disposal of radioactive material, and weathering effects of microbes. Time-of-flight secondary ion mass spectrometry (ToF-SIMS), a powerful mass spectral imaging technique with high surface sensitivity, mass resolution, and mass accuracy, can be used to study biofilm effects on different substrates. Understanding how to prepare biofilms on MIC susceptible substrates is critical for proper analysis via ToF-SIMS. We present here a step-by-step protocol for preparing bacterial biofilms for ToF-SIMS analysis, comparing three biofilm preparation techniques: no desalination, centrifugal spinning (CS), and water submersion (WS). Comparisons of two desalinating methods, CS and WS, show a decrease in the media peaks up to 99% using CS and 55% using WS, respectively. Proper desalination methods also can increase biological signals by over four times for fatty acids using WS, for example. ToF-SIMS spectral results show chemical compositional changes of the glass exposed in a Paenibacillus polymyxa SCE2 biofilm, indicating its capability to probe microbiologically induced corrosion of solid surfaces. This represents the proper desalination technique to use without significantly altering biofilm structure and substrate for ToF-SIMS analysis. ToF-SIMS spectral results showed chemical compositional changes of the glass exposed by a Paenibacillus bacterial biofilm over 3-month inoculation. Possible MIC products include various phosphate phase molecules not observed in any control samples with the highest percent increases when experimental samples were compared with biofilm control samples.

RNA-Seq reveals that Pseudomonas aeruginosa mounts growth medium-dependent competitive responses when sensing diffusible cues from Burkholderia cenocepacia

Most habitats host diverse bacterial communities, offering opportunities for inter-species interactions. While competition might often dominate such interactions, little is known about whether bacteria can sense competitors and mount adequate responses. The competition sensing hypothesis proposes that bacteria can use cues such as nutrient stress and cell damage to prepare for battle. Here, we tested this hypothesis by measuring transcriptome changes in Pseudomonas aeruginosa exposed to the supernatant of its competitor Burkholderia cenocepacia. We found that P. aeruginosa exhibited significant growth-medium-dependent transcriptome changes in response to competition. In an iron-rich medium, P. aeruginosa upregulated genes encoding the type-VI secretion system and the siderophore pyoverdine, whereas genes encoding phenazine toxins and hydrogen cyanide were upregulated under iron-limited conditions. Moreover, general stress response and quorum sensing regulators were upregulated upon supernatant exposure. Altogether, our results reveal nuanced competitive responses of P. aeruginosa when confronted with B. cenocepacia supernatant, integrating both environmental and social cues.

Laser desorption rapid evaporative ionization mass spectrometry (LD-REIMS) demonstrates a direct impact of hypochlorous acid stress on PQS-mediated quorum sensing in Pseudomonas aeruginosa

To establish infections in human hosts, Pseudomonas aeruginosa must overcome innate immune-generated oxidative stress, such as the hypochlorous acid (HOCl) produced by neutrophils. We set out to find specific biomarkers of oxidative stress through the development of a protocol for the metabolic profiling of P. aeruginosa cultures grown in the presence of different oxidants using a novel ionization technique for mass spectrometry, laser desorption rapid evaporative ionization mass spectrometry (LD-REIMS). We demonstrated the ability of LD-REIMS to classify samples as untreated or treated with a specific oxidant with 100% accuracy and identified a panel of 54 metabolites with significantly altered concentrations after exposure to one or more of the oxidants. Key metabolic changes were conserved in P. aeruginosa clinical strains isolated from patients with cystic fibrosis lung infections. These data demonstrated that HOCl stress impacted the Pseudomonas quinolone signal (PQS) quorum sensing system. Ten 2-alkyl-4-quinolones (AHQs) associated with the PQS system were significantly lower in concentration in HOCl-stressed P. aeruginosa cultures, including 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS), the most active signal molecule of the PQS system. The PQS system regulates the production of virulence factors, including pyocyanin and elastase, and their levels were markedly affected by HOCl stress. No pyocyanin was detectable and elastase concentrations were reduced by more than 75% in cultures grown with sub-lethal concentrations of HOCl, suggesting that this neutrophil-derived oxidant may disrupt the ability of P. aeruginosa to establish infections through interference with production of PQS-associated virulence factors.

IMPORTANCE

This work demonstrates that a high-throughput ambient ionization mass spectrometry method can be used successfully to study a bacterial stress response. Its application to the opportunistic pathogen Pseudomonas aeruginosa led to the identification of specific oxidative stress biomarkers, and demonstrated that hypochlorous acid, an oxidant specifically produced by human neutrophils during infection, affects quorum sensing and reduces production of the virulence factors pyocyanin and elastase. No pyocyanin was detectable and elastase levels were reduced by more than 75% in bacteria grown in the presence of hypochlorous acid. This approach has the potential to be widely applicable to the characterization of the stress responses of bacteria.

Quorum sensing responses of r-/K-strategists Nitrospira in continuous flow and sequencing batch nitrifying biofilm reactors

A better understanding of r-/K-strategists nitrifiers will help to balance the design and operation of bioprocesses for efficient pollution removal from wastewater. The objectives of study were to investigate the nitrite oxidation biokinetics, biofilm property, microbial community and quorum sensing (QS) of nitrifying biofilm in a continuously flow reactor (CFR) and a sequencing batch reactor (SBR). Results showed that nitrite-oxidizing bacteria were estimated to have a nitrite half saturation constant of 76.23 and 224.73 μM in CFR and SBR, respectively. High-throughput and metagenomic sequencing results showed that Nitrospira and Candidatus Nitrospira defluvii were the dominated nitrite-oxidizing taxa performing nitrite oxidation in both reactors. Nitrifying biofilm developed in CFR and SBR showed obviously different properties. Biofilm in SBR had an obviously higher ratio of polysaccharide and protein in extracellular polymeric substances, and higher thickness than in CFR. Metagenomics and chemical analysis revealed various types of acyl-homoserine lactone (AHL) circuit genes (e.g., luxI, lasI, hdtS) and four types of AHL signaling substances (e.g., C₆-HSL, C₈-HSL, C₁₀-HSL and 3-oxo-C₁₀-HSL) in nitrifying biofilm. The concentrations of these AHLs in biomass and water phases were obviously higher in SBR than that in CFR. Together, AHLs-based QS might affect the formation of nitrifying biofilm and thus contribute to the different biokinetics of Nitrospira in CFR and SBR. Our insights may reveal the molecular mechanism of Nitrospira for different biokinetics, and indicate the AHL association with Nitrospira adaptation to various conditions.

Changes in fatty acid composition as a response to glyphosate toxicity in Pseudomonas fluorescens

Excessive use of herbicides decreases soil biodiversity and fertility. The literature on the xenobiotic response by microorganisms is focused on herbicide biodegradation as a selective event. Non-degradation systems independent of selection could allow the survival of tolerant bacteria in contaminated environments, impacting xenobiotic turnover and, consequently, bioremediation strategies. However, it is uncertain whether the response based on these systems requires selective pressure to be effective. The objective here was to analyze non-degradation phenotypes, enzymatic and structural response systems, of Pseudomonas fluorescens CMA-55 strain, already investigated the production pattern of quorum sensing molecules in response to glyphosate, not present at the isolation site. One mode of response was associated with decrease in membrane permeability and effective antioxidative response for 0–2.30 mM glyphosate, at the mid-log growing phase, with higher activities of Mn-SOD, KatA, and KatB, and presence of fatty acids as nonadecylic acid, margaric and lauric acid. The second response system was characterized by lower antioxidative enzymes activity, presence of KatC isoform, and pelargonic, capric, myristic, stearic, palmitoleic and palmitic acid as principal fatty acids, allowing the strain to face stressful conditions in 9.20–11.50 mM glyphosate at the stationary phase. Therefore, the bacterial strain could modify the fatty acid composition and the permeability of membranes in two response modes according to the herbicide concentration, even glyphosate was not previously selective for P. fluorescens, featuring a generalist system based on physiological plasticity.

A biophysical threshold for biofilm formation

Bacteria are ubiquitous in our daily lives, either as motile planktonic cells or as immobilized surface-attached biofilms. These different phenotypic states play key roles in agriculture, environment, industry, and medicine; hence, it is critically important to be able to predict the conditions under which bacteria transition from one state to the other. Unfortunately, these transitions depend on a dizzyingly complex array of factors that are determined by the intrinsic properties of the individual cells as well as those of their surrounding environments, and are thus challenging to describe. To address this issue, here, we develop a generally-applicable biophysical model of the interplay between motility-mediated dispersal and biofilm formation under positive quorum sensing control. Using this model, we establish a universal rule predicting how the onset and extent of biofilm formation depend collectively on cell concentration and motility, nutrient diffusion and consumption, chemotactic sensing, and autoinducer production. Our work thus provides a key step toward quantitatively predicting and controlling biofilm formation in diverse and complex settings.

Bacteroides thetaiotaomicron uses a widespread extracellular DNase to promote bile-dependent biofilm formation

Biofilms are communities of surface-attached bacteria exhibiting biofilm-specific properties. Although anaerobic biofilms impact health, industry, and environment, they are mostly studied in aerobic bacterial species. Here, we studied biofilm formation in Bacteroides thetaiotaomicron, an anaerobic gut symbiont degrading diet sugars and contributing to gut maturation. Although B. thetaiotaomicron adhesion contributes to intestinal colonization, little is known about the determinants of its biofilm capacities. We identified that bile is a physiologically relevant gut signal inducing biofilm formation in B. thetaiotaomicron and other gut Bacteroidales. Moreover, we showed that, in contrast to the known scaffolding role of extracellular DNA, bile-dependent biofilm requires a DNase degrading matrix DNA, thus revealing a previously unrecognized factor contributing to the adhesion capacity of major gut symbionts.

Bacteroides thetaiotaomicron is a gut symbiont that inhabits the mucus layer and adheres to and metabolizes food particles, contributing to gut physiology and maturation. Although adhesion and biofilm formation could be key features for B. thetaiotaomicron stress resistance and gut colonization, little is known about the determinants of B. thetaiotaomicron biofilm formation. We previously showed that the B. thetaiotaomicron reference strain VPI-5482 is a poor in vitro biofilm former. Here, we demonstrated that bile, a gut-relevant environmental cue, triggers the formation of biofilm in many B. thetaiotaomicron isolates and common gut Bacteroidales species. We determined that bile-dependent biofilm formation involves the production of the DNase BT3563 or its homologs, degrading extracellular DNA (eDNA) in several B. thetaiotaomicron strains. Our study therefore shows that, although biofilm matrix eDNA provides a biofilm-promoting scaffold in many studied Firmicutes and Proteobacteria, BT3563-mediated eDNA degradation is required to form B. thetaiotaomicron biofilm in the presence of bile.

Oxidative Stress Response in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a Gram-negative environmental and human opportunistic pathogen highly adapted to many different environmental conditions. It can cause a wide range of serious infections, including wounds, lungs, the urinary tract, and systemic infections. The high versatility and pathogenicity of this bacterium is attributed to its genomic complexity, the expression of several virulence factors, and its intrinsic resistance to various antimicrobials. However, to thrive and establish infection, P. aeruginosa must overcome several barriers. One of these barriers is the presence of oxidizing agents (e.g., hydrogen peroxide, superoxide, and hypochlorous acid) produced by the host immune system or that are commonly used as disinfectants in a variety of different environments including hospitals. These agents damage several cellular molecules and can cause cell death. Therefore, bacteria adapt to these harsh conditions by altering gene expression and eliciting several stress responses to survive under oxidative stress. Here, we used PubMed to evaluate the current knowledge on the oxidative stress responses adopted by P. aeruginosa. We will describe the genes that are often differently expressed under oxidative stress conditions, the pathways and proteins employed to sense and respond to oxidative stress, and how these changes in gene expression influence pathogenicity and the virulence of P. aeruginosa. Understanding these responses and changes in gene expression is critical to controlling bacterial pathogenicity and developing new therapeutic agents.

Novel Chronic Wound Healing by Anti-biofilm Peptides and Protease

Chronic wounds have made a challenge in medical healthcare due to their biofilm infections, which reduce the penetrance of the antibacterial agents in the injury site. In infected wounds, the most common bacterial strains are Staphylococcus aureus and Pseudomonas aeruginosa. Biofilm disruption in chronic wounds is crucial in wound healing. Due to their broad-spectrum antibacterial properties and fewer side effects, anti-biofilm peptides, especially bacteriocins, are promising in the healing of chronic wounds by biofilm destruction. This study reviews the effects of antimicrobial and anti-biofilm agents, including bacteriocins and protease enzymes as a novel approach, on wound healing, along with analyzing the molecular docking between a bacterial protease and biofilm components. Among a large number of anti-biofilm bacteriocins identified up to now, seven types have been registered in the antimicrobial peptides (AMPs) database. Although it is believed that bacterial proteases are harmful in wound healing, it has recently been demonstrated that these proteases like the human serine protease, in combination with AMPs, can improve wound healing by biofilm destruction. In this work, docking results between metalloprotease from Paenibacillus polymyxa and proteins of S. aureus and P. aeruginosa involved in biofilm production, showed that this bacterial protease could efficiently interact with biofilm components. Infected wound healing is an important challenge in clinical trials due to biofilm production by bacterial pathogens. Therefore, simultaneous use of proteases or anti-biofilm peptides with antimicrobial agents could be a promising method for chronic wound healing.

Introducing the ArsR-Regulated Arsenic Stimulon

The microbial ars operon encodes the primary bacterial defense response to the environmental toxicant, arsenic. An important component of this operon is the arsR gene, which encodes ArsR, a member of the family of proteins categorized as DNA-binding transcriptional repressors. As currently documented, ArsR regulates its own expression as well as other genes in the same ars operon. This study examined the roles of four ArsR proteins in the well-developed model Gram-negative bacterium Agrobacterium tumefaciens 5A. RNASeq was used to compare and characterize gene expression profiles in ± arsenite-treated cells of the wild-type strain and in four different arsR mutants. We report that ArsR-controlled transcription regulation is truly global, extending well beyond the current ars operon model, and includes both repression as well as apparent activation effects. Many cellular functions are significantly influenced, including arsenic resistance, phosphate acquisition/metabolism, sugar transport, chemotaxis, copper tolerance, iron homeostasis, and many others. While there is evidence of some regulatory overlap, each ArsR exhibits its own regulatory profile. Furthermore, evidence of a regulatory hierarchy was observed; i.e. ArsR1 represses arsR4, ArsR4 activates arsR2, and ArsR2 represses arsR3. Additionally and unexpectedly, aioB (arsenite oxidase small subunit) expression was shown to be under partial positive control by ArsR2 and ArsR4. Summarizing, this study demonstrates the regulatory portfolio of arsenite-activated ArsR proteins and includes essentially all major cellular functions. The broad bandwidth of arsenic effects on microbial metabolism assists in explaining and understanding the full impact of arsenic in natural ecosystems, including the mammalian gut.

Iron metabolism in Pseudomonas aeruginosa biofilm and the involved iron-targeted anti-biofilm strategies

Pseudomonas aeruginosa is a gram-negative bacterium that exists in various ecosystems, causing severe infections in patients with AIDS or cystic fibrosis. P. aeruginosa can form biofilm on a variety of surfaces, whereby the bacteria produce defensive substances and enhance antibiotic-resistance, making themselves more adaptable to hostile environments. P. aeruginosa resistance represents one of the main causes of infection-related morbidity and mortality at a global level. Iron is required for the growth of P. aeruginosa biofilm. This review summarises how the iron metabolism contributes to develop biofilm, and more importantly, it may provide some references for the clinic to achieve novel anti-biofilm therapeutics by targeting iron activities.

Antibiotic Bacillomycin D Affects Iron Acquisition and Biofilm Formation in Bacillus velezensis through a Btr-Mediated FeuABC-Dependent Pathway

Bacillus spp. produce a wide range of secondary metabolites, including antibiotics, which have been well studied for their antibacterial properties but less so as signaling molecules. Previous results indicated that the lipopeptide bacillomycin D is a signal that promotes biofilm development of Bacillus velezensis SQR9. However, the mechanism behind this signaling is still unknown. Here, we show that bacillomycin D promotes biofilm development by promoting the acquisition of iron. Bacillomycin D promotes the transcription of the iron ABC transporter FeuABC by binding to its transcription factor, Btr. These actions increase intracellular iron concentration and activate the KinB-Spo0A-SinI-SinR-dependent synthesis of biofilm matrix components. We demonstrate that this strategy is beneficial for biofilm development and competition with the Pseudomonas fluorescens PF-5. Our results unravel an antibiotic-dependent signaling mechanism that links iron acquisition to biofilm development and ecological competition.

Under nonlimiting iron conditions pyocyanin is a major antifungal molecule, and differences between prototypic Pseudomonas aeruginosa strains

Airways of immunocompromised patients, or individuals with cystic fibrosis (CF), are common ground for Pseudomonas aeruginosa and Aspergillus fumigatus infections. Hence, in such a microenvironment both pathogens compete for resources. While under limiting iron conditions the siderophore pyoverdine is the most effective antifungal P. aeruginosa product, we now provide evidence that under nonlimiting iron conditions P. aeruginosa supernatants lack pyoverdine but still possess considerable antifungal activity. Spectrometric analyses of P. aeruginosa supernatants revealed the presence of phenazines, such as pyocyanin, only under nonlimiting iron conditions. Supernatants of quorum sensing mutants of strain PA14, defective in phenazine production, as well as supernatants of the P. aeruginosa strain PAO1, lacked pyocyanin, and were less inhibitory toward A. fumigatus biofilms under nonlimiting iron conditions. When blood as a natural source of iron was present during P. aeruginosa supernatant production, pyoverdine was absent, and phenazines, including pyocyanin, appeared, resulting in an antifungal effect on A. fumigatus biofilms. Pure pyocyanin reduced A. fumigatus biofilm metabolism. In summary, P. aeruginosa has mechanisms to compete with A. fumigatus under limiting and non-limiting iron conditions, and can switch from iron-denial-based to toxin-based antifungal activity. This has implications for the evolution of the microbiome in clinical settings where the two pathogens co-exist. Important differences in the iron response of P. aeruginosa laboratory strains PA14 and PAO1 were also uncovered.

Corrosion Behavior of AISI 1045 Steel in Seawater in the Presence of Flavobacterium sp

A systematic comparison study was carried out to investigate the effect of Flavobacterium sp. on AISI 1045 steel corrosion by weight loss, fluorescence microscopy (FM), surface analysis, cell count, pH measure, electrochemical impedance spectroscopy (EIS), and polarization curves. The impedances were considerably increased by Flavobacterium sp. between 1 and 7 day exposure and after 30 day exposure but considerably decreased by Flavobacterium sp. after 15 and 21 day exposure, which were supported by the I_corr results and the weight loss data. Furthermore, the biofilm was formed on the coupons. The pH values were considerably decreased by Flavobacterium sp. after 15 and 21 day exposure. The results proved that Flavobacterium sp. decreased the corrosion rates between 1 and 7 day exposure and after 30 day exposure and increased the corrosion rates between 15 and 21 day exposure, which could be ascribed to the protective biofilm and the secreted corrosive acid, respectively. In addition, Flavobacterium sp. considerably increased the pit numbers, the maximum pit depths, and the corresponding widths and considerably decreased the E_pit values. Importantly, the coverage and the heterogeneity of the biofilm were positively correlated with the increases in the maximum pit depths and the corresponding widths and the decreases in the E_pit values by Flavobacterium sp. The results demonstrated that Flavobacterium sp. increased the pitting corrosion, which could involve the heterogeneous biofilm cover.

Transposable temperate phages promote the evolution of divergent social strategies in Pseudomonas aeruginosa populations

Transposable temperate phages randomly insert into bacterial genomes, providing increased supply and altered spectra of mutations available to selection, thus opening alternative evolutionary trajectories. Transposable phages accelerate bacterial adaptation to new environments, but their effect on adaptation to the social environment is unclear. Using experimental evolution of Pseudomonas aeruginosa in iron-limited and iron-rich environments, where the cost of producing cooperative iron-chelating siderophores is high and low, respectively, we show that transposable phages promote divergence into extreme siderophore production phenotypes. Iron-limited populations with transposable phages evolved siderophore overproducing clones alongside siderophore non-producing cheats. Low siderophore production was associated with parallel mutations in pvd genes, encoding pyoverdine biosynthesis, and pqs genes, encoding quinolone signalling, while high siderophore production was associated with parallel mutations in phenazine-associated gene clusters. Notably, some of these parallel mutations were caused by phage insertional inactivation. These data suggest that transposable phages, which are widespread in microbial communities, can mediate the evolutionary divergence of social strategies.

Microfluidic System for Observation of Bacterial Culture and Effects on Biofilm Formation at Microscale

Biofilms exist in the natural world and applied to many industries. However, due to the variety of characteristics caused by their complex components, biofilms can also lead to membrane fouling and recurrent infections which pose threats to human health. So, to make the best use of their advantages and avoid their disadvantages, knowing the best time and methods for improving or preventing biofilm formation is important. In situ observation without fluorescence labeling in microscale and according to a time scale is useful to research biofilm and confine its formation. In this study, we developed a microfluidic system for real-time observation of bacteria culture and biofilms development at microscale. We cultured E. coli ATCC 25922 on a chip at continuous flow of the velocity, which could promote bacterial formation. Biofilms formation under the condition of adding amoxicillin at different times is also discussed. In addition, the mixed strains from sludge were also cultured on chip, and possible factors in biofilm formation are discussed. Our results show that a microfluidic device could culture microorganisms in continuous flow and accelerate them to adhere to the surface, thereby promoting biofilm formation. Overall, this platform is a useful tool in research on initial biofilm formation, which can contribute to preventing biofouling and infections.

Long- and short-chain AHLs affect AOA and AOB microbial community composition and ammonia oxidation rate in activated sludge

Quorum sensing (QS) regulation of the composition of ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) communities and functions in wastewater treatment was investigated. Specifically, we explored the role of N-acyl-l-homoserine lactones (AHLs) in microbial community dynamics in activated sludge. On average, the specific ammonia-oxidising-rate increased from 1.6 to 2.8 mg NH₄⁺-N/g MLSS/hr after treatment with long-chain AHLs for 16 days, and the addition of AHLs to sludge resulted in an increased number of AOA/AOB amoA genes. Significant differences were observed in the AOA communities of control and AHL-treated cultures, but not the AOB community. Furthermore, the dominant functional AOA strains of the Crenarchaeota altered their ecological niche in response to AHL addition. These results provide evidence that AHLs play an important role in mediating AOA/AOB microbial community parameters and demonstrate the potential for application of QS to the regulation of nitrogen compound metabolism in wastewater treatment.

The role of metal ions in the virulence and viability of bacterial pathogens

Metal ions fulfil a plethora of essential roles within bacterial pathogens. In addition to acting as necessary cofactors for cellular proteins, making them indispensable for both protein structure and function, they also fulfil roles in signalling and regulation of virulence. Consequently, the maintenance of cellular metal ion homeostasis is crucial for bacterial viability and pathogenicity. It is therefore unsurprising that components of the immune response target and exploit both the essentiality of metal ions and their potential toxicity toward invading bacteria. This review provides a brief overview of the transition metal ions iron, manganese, copper and zinc during infection. These essential metal ions are discussed in the context of host modulation of bioavailability, bacterial acquisition and efflux, metal-regulated virulence factor expression and the molecular mechanisms that contribute to loss of viability and/or virulence during host-imposed metal stress.

Quorum sensing inhibitors as antipathogens: biotechnological applications

The mechanisms through which microbes communicate using signal molecules has inspired a great deal of research. Microbes use this exchange of information, known as quorum sensing (QS), to initiate and perpetuate infectious diseases in eukaryotic organisms, evading the eukaryotic defense system by multiplying and expressing their pathogenicity through QS regulation. The major issue to arise from such networks is increased bacterial resistance to antibiotics, resulting from QS-dependent mediation of the formation of biofilm, the induction of efflux pumps, and the production of antibiotics. QS inhibitors (QSIs) of diverse origins have been shown to act as potential antipathogens. In this review, we focus on the use of QSIs to counter diseases in humans as well as plants and animals of economic importance. We also discuss the challenges encountered in the potential applications of QSIs.

A Mathematical Model of Quorum Sensing Induced Biofilm Detachment

BACKGROUND

Cell dispersal (or detachment) is part of the developmental cycle of microbial biofilms. It can be externally or internally induced, and manifests itself in discrete sloughing events, whereby many cells disperse in an instance, or in continuous slower dispersal of single cells. One suggested trigger of cell dispersal is quorum sensing, a cell-cell communication mechanism used to coordinate gene expression and behavior in groups based on population densities.

METHOD

To better understand the interplay of colony growth and cell dispersal, we develop a dynamic, spatially extended mathematical model that includes biofilm growth, production of quorum sensing molecules, cell dispersal triggered by quorum sensing molecules, and re-attachment of cells. This is a highly nonlinear system of diffusion-reaction equations that we study in computer simulations.

RESULTS

Our results show that quorum sensing induced cell dispersal can be an efficient mechanism for bacteria to control the size of a biofilm colony, and at the same time enhance its downstream colonization potential. In fact we find that over the lifetime of a biofilm colony the majority of cells produced are lost into the aqueous phase, supporting the notion of biofilms as cell nurseries. We find that a single quorum sensing based mechanism can explain both, discrete dispersal events and continuous shedding of cells from a colony. Moreover, quorum sensing induced cell dispersal affects the structure and architecture of the biofilm, for example it might lead to the formation of hollow inner regions in a biofilm colony.

Strategies of Vibrio parahaemolyticus to acquire nutritional iron during host colonization

Iron is an essential element for the growth and development of virtually all living organisms. As iron acquisition is critical for the pathogenesis, a host defense strategy during infection is to sequester iron to restrict the growth of invading pathogens. To counteract this strategy, bacteria such as Vibrio parahaemolyticus have adapted to such an environment by developing mechanisms to obtain iron from human hosts. This review focuses on the multiple strategies employed by V. parahaemolyticus to obtain nutritional iron from host sources. In these strategies are included the use of siderophores and xenosiderophores, proteases and iron-protein receptor. The host sources used by V. parahaemolyticus are the iron-containing proteins transferrin, hemoglobin, and hemin. The implications of iron acquisition systems in the virulence of V. parahaemolyticus are also discussed.

Bacterial biofilms: a diagnostic and therapeutic challenge

Bacteria have traditionally been regarded as individual organisms growing in homogeneous planktonic populations. However, bacteria in natural environments usually form communities of surface-adherent organisms embedded in an extracellular matrix, called biofilms. Current antimicrobial strategies often fail to control bacteria in the biofilm mode of growth. Treatment failure is particularly frequent in association with intracorporeal or transcutaneous medical devices and compromised host immunity. The rising prevalence of these risk factors over the last decades has paralleled the increase in biofilm infections. This review discusses the shortcomings of current therapies against biofilms both in theory and with clinical examples. Biofilm characteristics are described with a focus on new diagnostic and therapeutic targets.

Targeting quorum sensing in Pseudomonas aeruginosa biofilms: current and emerging inhibitors

Bacterial resistance to conventional antibiotics combined with an increasing acknowledgement of the role of biofilms in chronic infections has led to a growing interest in new antimicrobial strategies that target the biofilm mode of growth. In the aggregated biofilm mode, cell-to-cell communication systems involved in the process known as quorum sensing regulate coordinated expression of virulence with immune shielding mechanisms and antibiotic resistance. For two decades, the potential of interference with quorum sensing by small chemical compounds has been investigated with the aim of developing alternative antibacterial strategies. Here, we review state of the art research of quorum sensing inhibitors against the opportunistic human pathogen Pseudomonas aeruginosa, which is found in a number of biofilm-associated infections and identified as the predominant organism infecting the lungs of cystic fibrosis patients.

The stringent response controls catalases in Pseudomonas aeruginosa and is required for hydrogen peroxide and antibiotic tolerance

Pseudomonas aeruginosa, a human opportunistic pathogen, possesses a number of antioxidant defense enzymes under the control of multiple regulatory systems. We recently reported that inactivation of the P. aeruginosa stringent response (SR), a starvation stress response controlled by the alarmone (p)ppGpp, caused impaired antioxidant defenses and antibiotic tolerance. Since catalases are key antioxidant enzymes in P. aeruginosa, we compared the levels of H2O2 susceptibility and catalase activity in P. aeruginosa wild-type and ΔrelA ΔspoT (ΔSR) mutant cells. We found that the SR was required for optimal catalase activity and mediated H2O2 tolerance during both planktonic and biofilm growth. Upon amino acid starvation, induction of the SR upregulated catalase activity. Full expression of katA and katB also required the SR, and this regulation occurred through both RpoS-independent and RpoS-dependent mechanisms. Furthermore, overexpression of katA was sufficient to restore H2O2 tolerance and to partially rescue the antibiotic tolerance of ΔSR cells. All together, these results suggest that the SR regulates catalases and that this is an important mechanism in protecting nutrient-starved and biofilm bacteria from H2O2- and antibiotic-mediated killing.

The iron-dependent regulator fur controls pheromone signaling systems and luminescence in the squid symbiont Vibrio fischeri ES114

Bacteria often use pheromones to coordinate group behaviors in specific environments. While high cell density is required for pheromones to achieve stimulatory levels, environmental cues can also influence pheromone accumulation and signaling. For the squid symbiont Vibrio fischeri ES114, bioluminescence requires pheromone-mediated regulation, and this signaling is induced in the host to a greater extent than in culture, even at an equivalent cell density. Our goal is to better understand this environment-specific control over pheromone signaling and bioluminescence. Previous work with V. fischeri MJ1 showed that iron limitation induces luminescence, and we recently found that ES114 encounters a low-iron environment in its host. Here we show that ES114 induces luminescence at lower cell density and achieves brighter luminescence in low-iron media. This iron-dependent effect on luminescence required ferric uptake regulator (Fur), which we propose influences two pheromone signaling master regulators, LitR and LuxR. Genetic and bioinformatic analyses suggested that under low-iron conditions, Fur-mediated repression of litR is relieved, enabling more LitR to perform its established role as an activator of luxR. Interestingly, Fur may similarly control the LitR homolog SmcR of Vibrio vulnificus. These results reveal an intriguing regulatory link between low-iron conditions, which are often encountered in host tissues, and pheromone-dependent master regulators.

Multiple virulence factors regulated by quorum sensing may help in establishment and colonisation of urinary tract by Pseudomonas aeruginosa during experimental urinary tract infection

PURPOSE

Damage caused by an organism during infection is attributed to production of virulence factors. Different virulence factors produced by the organism contribute to its pathogenicity, individually. During infectious conditions, role of virulence factors produced by the pathogen is different, depending upon the site of involvement. Pseudomonas aeruginosa is an opportunistic nosocomial pathogen known to cause infections of the respiratory tract, burn wound, urinary tract and eye. Importance of virulence factors produced by P. Aeruginosa during infections such as keratitis, burn wound and respiratory tract is known. The present study was designed to understand the importance of different virulence factors of P. aeruginosa in urinary tract infection in vivo.

MATERIALS AND METHODS

An ascending urinary tract infection model was established in mice using standard parent strain PAO1 and its isogenic mutant, JP2. Mice were sacrificed at different time intervals and renal tissue homogenates were used for estimation of renal bacterial load and virulence factors.

RESULTS

Both parent and mutant strains were able to reach the renal tissue. PAO 1 PAO1 was isolated from renal tissue till day 5 post-infection. However, the mutant strain was unable to colonise the renal tissue. Failure of mutant strain to colonise was attributed to its inability to produce protease, elastase and rhamnolipid.

CONCLUSION

This study suggests that protease, elastase and rhamnolipid contribute to pathogenesis and survival of P. aeruginosa during urinary tract infection.

Coordination of the arc regulatory system and pheromone-mediated positive feedback in controlling the Vibrio fischeri lux operon

Bacterial pheromone signaling is often governed both by environmentally responsive regulators and by positive feedback. This regulatory combination has the potential to coordinate a group response among distinct subpopulations that perceive key environmental stimuli differently. We have explored the interplay between an environmentally responsive regulator and pheromone-mediated positive feedback in intercellular signaling by Vibrio fischeri ES114, a bioluminescent bacterium that colonizes the squid Euprymna scolopes. Bioluminescence in ES114 is controlled in part by N-(3-oxohexanoyl)-L-homoserine lactone (3OC6), a pheromone produced by LuxI that together with LuxR activates transcription of the luxICDABEG operon, initiating a positive feedback loop and inducing luminescence. The lux operon is also regulated by environmentally responsive regulators, including the redox-responsive ArcA/ArcB system, which directly represses lux in culture. Here we show that inactivating arcA leads to increased 3OC6 accumulation to initiate positive feedback. In the absence of positive feedback, arcA-mediated control of luminescence was only ∼2-fold, but luxI-dependent positive feedback contributed more than 100 fold to the net induction of luminescence in the arcA mutant. Consistent with this overriding importance of positive feedback, 3OC6 produced by the arcA mutant induced luminescence in nearby wild-type cells, overcoming their ArcA repression of lux. Similarly, we found that artificially inducing ArcA could effectively repress luminescence before, but not after, positive feedback was initiated. Finally, we show that 3OC6 produced by a subpopulation of symbiotic cells can induce luminescence in other cells co-colonizing the host. Our results suggest that even transient loss of ArcA-mediated regulation in a sub-population of cells can induce luminescence in a wider community. Moreover, they indicate that 3OC6 can communicate information about both cell density and the state of ArcA/ArcB.

A dynamic and intricate regulatory network determines Pseudomonas aeruginosa virulence

Pseudomonas aeruginosa is a metabolically versatile bacterium that is found in a wide range of biotic and abiotic habitats. It is a major human opportunistic pathogen causing numerous acute and chronic infections. The critical traits contributing to the pathogenic potential of P. aeruginosa are the production of a myriad of virulence factors, formation of biofilms and antibiotic resistance. Expression of these traits is under stringent regulation, and it responds to largely unidentified environmental signals. This review is focused on providing a global picture of virulence gene regulation in P. aeruginosa. In addition to key regulatory pathways that control the transition from acute to chronic infection phenotypes, some regulators have been identified that modulate multiple virulence mechanisms. Despite of a propensity for chaotic behaviour, no chaotic motifs were readily observed in the P. aeruginosa virulence regulatory network. Having a ‘birds-eye’ view of the regulatory cascades provides the forum opportunities to pose questions, formulate hypotheses and evaluate theories in elucidating P. aeruginosa pathogenesis. Understanding the mechanisms involved in making P. aeruginosa a successful pathogen is essential in helping devise control strategies.

Monitoring bacterial twitter: does quorum sensing determine the behavior of water and wastewater treatment biofilms?

Bacteria have their own form of "twitter" communication, described as quorum sensing (QS), where bacteria emit and sense chemical signal molecules as a means to gauge population density and control gene expression. Many QS-controlled genes relate to biofilm formation and function and may be important for some water and wastewater treatment biofilms. There is a need to better understand bacterial QS, the bacteria biofilm aspects influenced by QS in engineered reactors, and to assess how designs and operations might be improved by taking this signaling into account. This paper provides a critical review of QS and how it relates to biofilms in engineered water and wastewater treatment systems and identifies needs for future research.

Quorum sensing: regulating the regulators

Many bacteria use 'quorum sensing' (QS) as a mechanism to regulate gene induction in a population-dependent manner. In its simplest sense this involves the accumulation of a signaling metabolite during growth; the binding of this metabolite to a regulator or multiple regulators activates induction or repression of gene expression. However QS regulation is seldom this simple, because other inputs are usually involved. In this review we have focussed on how those other inputs influence QS regulation and as implied by the title, this often occurs by environmental or physiological effects regulating the expression or activity of the QS regulators. The rationale of this review is to briefly introduce the main QS signals used in Gram-negative bacteria and then introduce one of the earliest understood mechanisms of regulation of the regulator, namely the plant-mediated control of expression of the TraR QS regulator in Agrobacterium tumefaciens. We then describe how in several species, multiple QS regulatory systems can act as integrated hierarchical regulatory networks and usually this involves the regulation of QS regulators. Such networks can be influenced by many different physiological and environmental inputs and we describe diverse examples of these. In the final section, we describe different examples of how eukaryotes can influence QS regulation in Gram-negative bacteria.

A novel two-component system BqsS-BqsR modulates quorum sensing-dependent biofilm decay in Pseudomonas aeruginosa

Pseudomonas aeruginosa can grow either as planktonic- or biofilm-form in response to environmental changes. Recent studies show that switching from biofilm to planktonic lifestyle requires rhamnolipids. Here we report the identification of a novel twocomponent system BqsS-BqsR that regulates biofilm decay in P. aeruginosa. BqsS is a multidomain sensor kinase and BqsR is an OmpR-like response regulator. Deletion of either bqsS or bqsR in P. aeruginosa mPAO1 resulted in a significant increase in biofilm formation. Time course analysis showed that the bqsS-bqsR mutants were defective in biofilm dispersal and in rhamnolipid production. Mutation of the BqsS-BqsR two-component system did not affect the biosynthesis of long chain quorum sensing (QS) signal N-3-oxo-dodecanoyl-homoserine lactone (3OC12HSL) but resulted in reduced production of the short chain QS signal N-butyryl-L-homoserine lactone (C4HSL) and the Pseudomonas quinolone signal (PQS). Exogenous addition of C4HSL, PQS or rhamnolipids to the bqsS mutant reduced the biofilm formation to the wild-type level. Evidence suggests that the BqsS-BqsR two-component system might promote conversion of anthranilate to PQS. Taken together, these results establish BqsS-BqsR as a novel two-component system that regulates biofilm decay in P. aeruginosa by modulating biosynthesis of QS signals and rhamnolipids.

The contribution of cell-cell signaling and motility to bacterial biofilm formation

Many bacteria grow attached to a surface as biofilms. Several factors dictate biofilm formation, including responses by the colonizing bacteria to their environment. Here we review how bacteria use cell-cell signaling (also called quorum sensing) and motility during biofilm formation. Specifically, we describe quorum sensing and surface motility exhibited by the bacterium Pseudomonas aeruginosa, a ubiquitous environmental organism that acts as an opportunistic human pathogen in immunocompromised individuals. P. aeruginosa uses acyl-homoserine lactone signals during quorum sensing to synchronize gene expression important to the production of polysaccharides, rhamnolipid, and other virulence factors. Surface motility affects the assembly and architecture of biofilms, and some aspects of motility are also influenced by quorum sensing. While some genes and their function are specific to P. aeruginosa, many aspects of biofilm development can be used as a model system to understand how bacteria differentially colonize surfaces.

A histidine-kinase cheA gene of Pseudomonas pseudoalcaligens KF707 not only has a key role in chemotaxis but also affects biofilm formation and cell metabolism

A histidine-kinase cheA gene in Pseudomonas pseudoalcaligenes KF707 plays a central role in the regulation of metabolic responses as well as in chemotaxis. Non-chemotactic mutants harboring insertions into the cheA gene were screened for their ability to form biofilms in the Calgary biofilm device. Notably, ≥95% decrease in the number of cells attached to the polystyrene surface was observed in cheA mutants compared to the KF707 wild-type biofilm phenotype. The ability to form mature biofilms was restored to wild-type levels, providing functional copies of the KF707 cheA gene to the mutants. In addition, phenotype micro-arrays and proteomic analyses revealed that several basic metabolic activities and a few periplasmic binding proteins of cheA mutant cells differed compared to those of wild-type cells. These results are interpreted as evidence of a strong integration between chemotactic and metabolic pathways in the process of biofilm development by P. pseudoalcaligenes KF707.

Determination of the regulon and identification of novel mRNA targets of Pseudomonas aeruginosa RsmA

One of the prokaryotic post-transcriptional regulatory mechanisms involves the CsrA/RsmA family of proteins that act by modulating translation initiation at target mRNAs. In this study, we identified the regulon of RsmA of the Pseudomonas aeruginosa PAK strain by using cultures in the stationary phase of growth. The RsmA regulon includes over 500 genes, of which approximately one-third were affected by an rsmA mutation negatively, while the rest were affected positively. By isolating RsmA/mRNA complexes, analysing transcriptional and translational fusions, and performing gel-shift analyses, we identified 40 genes in six operons that are regulated by RsmA directly at the level of translation. All of these genes were affected by RsmA negatively and include genes encoding the type VI secretion system HSI-I, which has been implicated in the P. aeruginosa chronic infections. On the other hand, we were unable to demonstrate a direct interaction of RsmA with transcripts that are positively affected by this protein, including mRNAs encoding the type III secretion system and the type IV pili genes. Our work supports a model in which RsmA acts as a negative translational regulator, and where its positive effects are achieved indirectly by RsmA-mediated interference with translation of specific regulatory factors.

In situ monitoring of antibiotic susceptibility of bacterial biofilms in a microfluidic device

Antibiotic resistance of biofilms is a growing public health concern due to overuse and improper use of antibiotics. Thus, determining an effective minimal concentration of antibiotics to eradicate bacterial biofilms is crucial. Here we present a simple, novel one-pot assay for the analysis of antibiotic susceptibility of bacterial biofilms using a microfluidics system where continuous concentration gradients of antibiotics are generated. The results of minimal biofilm eradication concentration (MBEC) clearly confirm that the concentration required to eradicate biofilm-grown Pseudomonas aeruginosa is higher than the minimal inhibitory concentration (MIC) that has been widely used to determine the lowest concentration of antibiotics against planktonically grown bacteria.

Parasitic growth of Pseudomonas aeruginosa in co-culture with the chitinolytic bacterium Aeromonas hydrophila

Polymer-degrading bacteria face exploitation by opportunistic bacteria that grow with the degradation products without investing energy into production of extracellular hydrolytic enzymes. This scenario was investigated with a co-culture of Aeromonas hydrophila and Pseudomonas aeruginosa with chitin as carbon, nitrogen and energy source. In single cultures, A. hydrophila could grow with chitin, while P. aeruginosa could not. Co-cultures with both strains had a biphasic course. In the first phase, P. aeruginosa grew along with A. hydrophila without affecting it. The second phase was initiated by a rapid inactivation of and a massive acetate release by A. hydrophila. Both processes coincided and were dependent on quorum sensing-regulated production of secondary metabolites by P. aeruginosa. Among these the redox-active phenazine compound pyocyanin caused the release of acetate by A. hydrophila by blocking the citric acid cycle through inhibition of aconitase. Thus, A. hydrophila was forced into an incomplete oxidation of chitin with acetate as end-product, which supported substantial growth of P. aeruginosa in the second phase of the co-culture. In conclusion, P. aeruginosa could profit from a substrate that was originally not bioavailable to it by influencing the metabolism and viability of A. hydrophila in a parasitic way.

Interactions of Botryococcus braunii cultures with bacterial biofilms

Unicellular microalgae generally grow in the presence of bacteria, particularly when they are farmed massively. This study analyzes the bacteria associated with mass culture of Botryococcus braunii: both the planktonic bacteria in the water column and those forming biofilms adhered to the surface of the microalgal cells (∼10⁷-10⁸ culturable cells per gram microalgae). Furthermore, we identified the culturable bacteria forming a biofilm in the microalgal cells by 16S rDNA sequencing. At least eight different culturable species of bacteria were detected in the biofilm and were evaluated for the presence of quorum-sensing signals in these bacteria. Few studies have considered the implications of this phenomenon as regards the interaction between bacteria and microalgae. Production of C4-AHL and C6-AHL were detected in two species, Pseudomonas sp. and Rhizobium sp., which are present in the bacterial biofilm associated with B. braunii. This type of signal was not detected in the planktonic bacteria isolated from the water. We also noted that the bacterium, Rhizobium sp., acted as a probiotic bacterium and significantly encouraged the growth of B. braunii. A direct application of these beneficial bacteria associated with B. braunii could be, to use them like inoculants for large-scale microalgal cultures. They could optimize biomass production by enhancing growth, particularly in this microalga that has a low growth rate.

Combining Biofilm-Controlling Compounds and Antibiotics as a Promising New Way to Control Biofilm Infections

Many bacteria grow on surfaces forming biofilms. In this structure, they are well protected and often high dosages of antibiotics cannot clear infectious biofilms. The formation and stabilization of biofilms are mediated by diffusible autoinducers (e.g. N-acyl homoserine lactones, small peptides, furanosyl borate diester). Metabolites interfering with this process have been identified in plants, animals and microbes, and synthetic analogues are known. Additionally, this seems to be not the only way to control biofilms. Enzymes capable of cleaving essential components of the biofilm matrix, e.g. polysaccharides or extracellular DNA, and thus weakening the biofilm architecture have been identified. Bacteria also have mechanisms to dissolve their biofilms and return to planktonic lifestyle. Only a few compounds responsible for the signalling of these processes are known, but they may open a completely novel line of biofilm control. All these approaches lead to the destruction of the biofilm but not the killing of the pathogens. Therefore, a combination of biofilm-destroying compounds and antibiotics to handle biofilm infections is proposed. In this article, different approaches to combine biofilm-controlling compounds and antibiotics to fight biofilm infections are discussed, as well as the balance between biofilm formation and virulence.

Homeostatic interplay between bacterial cell-cell signaling and iron in virulence

Pathogenic bacteria use interconnected multi-layered regulatory networks, such as quorum sensing (QS) networks to sense and respond to environmental cues and external and internal bacterial cell signals, and thereby adapt to and exploit target hosts. Despite the many advances that have been made in understanding QS regulation, little is known regarding how these inputs are integrated and processed in the context of multi-layered QS regulatory networks. Here we report the examination of the Pseudomonas aeruginosa QS 4-hydroxy-2-alkylquinolines (HAQs) MvfR regulatory network and determination of its interaction with the QS acyl-homoserine-lactone (AHL) RhlR network. The aim of this work was to elucidate paradigmatically the complex relationships between multi-layered regulatory QS circuitries, their signaling molecules, and the environmental cues to which they respond. Our findings revealed positive and negative homeostatic regulatory loops that fine-tune the MvfR regulon via a multi-layered dependent homeostatic regulation of the cell-cell signaling molecules PQS and HHQ, and interplay between these molecules and iron. We discovered that the MvfR regulon component PqsE is a key mediator in orchestrating this homeostatic regulation, and in establishing a connection to the QS rhlR system in cooperation with RhlR. Our results show that P. aeruginosa modulates the intensity of its virulence response, at least in part, through this multi-layered interplay. Our findings underscore the importance of the homeostatic interplay that balances competition within and between QS systems via cell-cell signaling molecules and environmental cues in the control of virulence gene expression. Elucidation of the fine-tuning of this complex relationship offers novel insights into the regulation of these systems and may inform strategies designed to limit infections caused by P. aeruginosa and related human pathogens.

Bacterial cells can communicate with one another about their surrounding environment. This information can be in the form of small self-secreted molecules acting as signals to activate or inhibit the expression of genes. Pseudomonas aeruginosa is an environmental bacterium that infects diverse organisms from plants to humans. Our results show that this pathogen uses two highly sensitive networks, namely MvfR and LasR/RhlR pathways, to modulate its virulence functions by titrating the concentration of the small molecules HHQ and PQS in a manner that depends upon the presence or absence of iron. Via negative and positive feedback loops, this bacterium processes the signaled information to regulate its virulence functions and homeostatically balance the production of the small molecules required for the activation of the MvfR virulence network. Our study sheds light on paradigmatic complex networks that maintain a homeostatic bacterial virulence response.