Characterization of nutrient-induced dispersion in Pseudomonas aeruginosa PAO1 biofilm

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.

Engineering global regulator Hha of Escherichia coli to control biofilm dispersal

The global transcriptional regulator Hha of Escherichia coli controls biofilm formation and virulence. Previously, we showed that Hha decreases initial biofilm formation; here, we engineered Hha for two goals: to increase biofilm dispersal and to reduce biofilm formation. Using random mutagenesis, Hha variant Hha13D6 (D22V, L40R, V42I and D48A) was obtained that causes nearly complete biofilm dispersal (96%) by increasing apoptosis without affecting initial biofilm formation. Hha13D6 caused cell death probably by the activation of proteases since Hha‐mediated dispersal was dependent on protease HslV. Hha variant Hha24E9 (K62X) was also obtained that decreased biofilm formation by inducing gadW, glpT and phnF but that did not alter biofilm dispersal. Hence, Hha may be engineered to influence both biofilm dispersal and formation.

Pseudomonas aeruginosa PAO1 virulence factors and poplar tree response in the rhizosphere

Whole-transcriptome analysis was used here for the first time in the rhizosphere to discern the genes involved in the pathogenic response of Pseudomonas aeruginosa PAO1 as well as to discern the response of the poplar tree. Differential gene expression shows that 185 genes of the bacterium and 753 genes of the poplar tree were induced in the rhizosphere. Using the P. aeruginosa transcriptome analysis, isogenic knockout mutants, and two novel plant assays (poplar and barley), seven novel PAO1 virulence genes were identified (PA1385, PA2146, PA2462, PA2463, PA2663, PA4150 and PA4295). The uncharacterized putative haemolysin repressor, PA2463, upon inactivation, resulted in greater poplar virulence and elevated haemolysis while this mutant remained competitive in the rhizosphere. In addition, disruption of the haemolysin gene itself (PA2462) reduced the haemolytic activity of P. aeruginosa, caused less cytotoxicity and reduced barley virulence, as expected. Inactivating PA1385, a putative glycosyl transferase, reduced both poplar and barley virulence. Furthermore, disrupting PA2663, a putative membrane protein, reduced biofilm formation by 20-fold. Inactivation of PA3476 (rhlI) increased virulence with barley as well as haemolytic activity and cytotoxicity, so quorum sensing is important in plant pathogenesis. Hence, this strategy is capable of elucidating virulence genes for an important pathogen.

Engineering a novel c-di-GMP-binding protein for biofilm dispersal

Bacteria prefer to grow attached to themselves or an interface, and it is important for an array of applications to make biofilms disperse. Here we report simultaneously the discovery and protein engineering of BdcA (formerly YjgI) for biofilm dispersal using the universal signal 3,5-cyclic diguanylic acid (c-di-GMP). The bdcA deletion reduced biofilm dispersal, and production of BdcA increased biofilm dispersal to wild-type level. Since BdcA increases motility and extracellular DNA production while decreasing exopolysaccharide, cell length and aggregation, we reasoned that BdcA decreases the concentration of c-di-GMP, the intracellular messenger that controls cell motility through flagellar rotation and biofilm formation through synthesis of curli and cellulose. Consistently, c-di-GMP levels increase upon deleting bdcA, and purified BdcA binds c-di-GMP but does not act as a phosphodiesterase. Additionally, BdcR (formerly YjgJ) is a negative regulator of bdcA. To increase biofilm dispersal, we used protein engineering to evolve BdcA for greater c-di-GMP binding and found that the single amino acid change E50Q causes nearly complete removal of biofilms via dispersal without affecting initial biofilm formation.

Opportunistic respiratory pathogens in the oral cavity of the elderly

The oral cavity of the hospitalized or bedridden elderly is often a reservoir for opportunistic pathogens associated with respiratory diseases. Commensal flora and the host interact in a balanced fashion and oral infections are considered to appear following an imbalance in the oral resident microbiota, leading to the emergence of potentially pathogenic bacteria. The definition of the process involved in colonization by opportunistic respiratory pathogens needs to elucidate the factors responsible for the transition of the microbiota from commensal to pathogenic flora. The regulatory factors influencing the oral ecosystem can be divided into three major categories: the host defense system, commensal bacteria, and external pathogens. In this article, we review the profile of these categories including the intricate cellular interaction between immune factors and commensal bacteria and the disturbance in homeostasis in the oral cavity of hospitalized or bedridden elderly, which facilitates oral colonization by opportunistic respiratory pathogens.

Rhinovirus infection liberates planktonic bacteria from biofilm and increases chemokine responses in cystic fibrosis airway epithelial cells

BACKGROUND

Intermittent viral exacerbations in patients with cystic fibrosis (CF) with chronic Pseudomonas aeruginosa (PA) infection are associated with increased bacterial load. A few clinical studies suggest that rhinoviruses (RV) are associated with the majority of viral-related exacerbations in CF and require prolonged intravenous antibiotic treatment. These observations imply that acute RV infection may increase lower respiratory symptoms by increasing planktonic bacterial load. However, the underlying mechanisms are not known.

METHODS

Primary CF airway epithelial cells differentiated into mucociliary phenotype were infected with mucoid PA (MPA) followed by RV and examined for bacterial density, biofilm mass, levels of chemokines and hydrogen peroxide (H2O2). The need for dual oxidase 2, a component of NADPH oxidase, in RV-induced generation of H2O2 in CF cells was assessed using gene-specific siRNA.

RESULTS

Superinfection with RV increased chemokine responses in CF mucociliary-differentiated airway epithelial cells with pre-existing MPA infection in the form of biofilm. This was associated with the presence of planktonic bacteria at both the apical and basolateral epithelial cell surfaces. Further, RV-induced generation of H2O2 via dual oxidase 2 in CF cells was sufficient for dispersal of planktonic bacteria from the biofilm. Inhibition of NADPH oxidase reduced bacterial transmigration across mucociliary-differentiated CF cells and the interleukin-8 response in MPA- and RV-infected cells.

CONCLUSION

This study shows that acute infection with RV liberates planktonic bacteria from biofilm. Planktonic bacteria, which are more proinflammatory than their biofilm counterparts, stimulate increased chemokine responses in CF airway epithelial cells which, in turn, may contribute to the pathogenesis of CF exacerbations.

Engineering biofilm formation and dispersal

Anywhere water is in the liquid state, bacteria will exist as biofilms, which are complex communities of cells that are cemented together. Although frequently associated with disease and biofouling, biofilms are also important for engineering applications, such as bioremediation, biocatalysis and microbial fuel cells. Here, we review approaches to alter genetic circuits and cell signaling towards controlling biofilm formation, and emphasize utilizing these tools for engineering applications. Based on a better understanding of the genetic basis of biofilm formation, we find that biofilms might be controlled by manipulating extracellular signals, and that they might be dispersed using conserved intracellular signals and regulators. Biofilms could also be formed at specific locations where they might be engineered to make chemicals or treat human disease.

Modulation of Pseudomonas aeruginosa biofilm dispersal by a cyclic-Di-GMP phosphodiesterase with a putative hypoxia-sensing domain

Pseudomonas aeruginosa encodes many enzymes that are potentially associated with the synthesis or degradation of the widely conserved second messenger cyclic-di-GMP (c-di-GMP). In this study, we show that mutation of rbdA, which encodes a fusion protein consisting of PAS-PAC-GGDEF-EAL multidomains, results in decreased biofilm dispersal. RbdA contains a highly conserved GGDEF domain and EAL domain, which are involved in the synthesis and degradation of c-di-GMP, respectively. However, in vivo and in vitro analyses show that the full-length RbdA protein only displays phosphodiesterase activity, causing c-di-GMP degradation. Further analysis reveals that the GGDEF domain of RbdA plays a role in activating the phosphodiesterase activity of the EAL domain in the presence of GTP. Moreover, we show that deletion of the PAS domain or substitution of the key residues implicated in sensing low-oxygen stress abrogates the functionality of RbdA. Subsequent study showed that RbdA is involved in positive regulation of bacterial motility and production of rhamnolipids, which are associated with biofilm dispersal, and in negative regulation of production of exopolysaccharides, which are required for biofilm formation. These data indicate that the c-di-GMP-degrading regulatory protein RbdA promotes biofilm dispersal through its two-pronged effects on biofilm development, i.e., downregulating biofilm formation and upregulating production of the factors associated with biofilm dispersal.

The novel two-component regulatory system BfiSR regulates biofilm development by controlling the small RNA rsmZ through CafA

The formation of biofilms by the opportunistic pathogen Pseudomonas aeruginosa is a developmental process governed by a novel signal transduction system composed of three two-component regulatory systems (TCSs), BfiSR, BfmSR, and MifSR. Here, we show that BfiSR-dependent arrest of biofilm formation coincided with reduced expression of genes involved in virulence, posttranslational/transcriptional modification, and Rhl quorum sensing but increased expression of rhlAB and the small regulatory RNAs rsmYZ. Overexpression of rsmZ, but not rsmY, coincided with impaired biofilm development similar to inactivation of bfiS and retS. We furthermore show that BfiR binds to the 5' untranslated region of cafA encoding RNase G. Lack of cafA expression coincided with impaired biofilm development and increased rsmYZ levels during biofilm growth compared to the wild type. Overexpression of cafA restored ΔbfiS biofilm formation to wild-type levels and reduced rsmZ abundance. Moreover, inactivation of bfiS resulted in reduced virulence, as revealed by two plant models of infection. This work describes the regulation of a committed biofilm developmental step following attachment by the novel TCS BfiSR through the suppression of sRNA rsmZ via the direct regulation of RNase G in a biofilm-specific manner, thus underscoring the importance of posttranscriptional mechanisms in controlling biofilm development and virulence.

Quorum sensing affects biofilm formation through lipopolysaccharide synthesis in Klebsiella pneumoniae

Biofilm formation by Klebsiella pneumoniae is modulated by quorum sensing through the synthesis of interspecies AI-2 autoinducers. We characterized in K. pneumoniae the genes homologous to those described in Escherichia coli involved in AI-2 transport, and created two isogenic mutants deleted of lsrCD and tqsA. The levels of extracellular AI-2 with lsrCD and tqsA knockout mutants showed increased and lowered concentrations of AI-2, respectively. The level of transcripts of luxS, the gene responsible for AI-2 synthesis, was increased in sessile cells of the tqsA mutant. In contrast, the expression of the AI-2 import regulator genes lsrR and lsrK was decreased. In addition, the two mutants lsrCD and tqsA formed biofilms with greater biomass but impaired architecture. Since exopolysaccharides play a main role in K. pneumoniae biofilm formation, we investigated their relationship with AI-2 synthesis. None of the mutations in luxS and the AI-2 transport systems affected the expression of three capsule polysaccharide-related genes (wzi, wza and wzx), but all induced an increase in the expression of two lipopolysaccharide (LPS)-synthesis-related genes, wbbM and wzm. AI-2 therefore seems to act as a regulator of biofilm formation and LPS synthesis in sessile K. pneumoniae cells.

Coupling metabolism and chemotaxis-dependent behaviours by energy taxis receptors

Bacteria have evolved the ability to monitor changes in various physico-chemical parameters and to adapt their physiology and metabolism by implementing appropriate cellular responses to these changes. Energy taxis is a metabolism-dependent form of taxis and is the directed movement of motile bacteria in gradients of physico-chemical parameters that affect metabolism. Energy taxis has been described in diverse bacterial species and several dedicated energy sensors have been identified. The molecular mechanism of energy taxis has not been studied in as much detail as chemotaxis, but experimental evidence indicates that this behaviour differs from metabolism-independent taxis only by the presence of dedicated energy taxis receptors. Energy taxis receptors perceive changes in energy-related parameters, including signals related to the redox and/or intracellular energy status of the cell. The best-characterized energy taxis receptors are those that sense the redox state of the electron transport chain via non-covalently bound FAD cofactors. Other receptors shown to mediate energy taxis lack any recognizable redox cofactor or conserved energy-sensing motif, and some have been suggested to monitor changes in the proton motive force. The exact energy-sensing mechanism(s) involved are yet to be elucidated for most of these energy sensors. By monitoring changes in energy-related parameters, energy taxis receptors allow cells to couple motility behaviour with metabolism under diverse environmental conditions. Energy taxis receptors thus provide fruitful models to decipher how cells integrate sensory behaviours with metabolic activities.

Biological 'glue' and 'Velcro': molecular tools for adhesion and biofilm formation in the hairy and gluey bug Pseudomonas aeruginosa

Pseudomonas aeruginosa contains an extraordinarily large number of loci encoding systems facilitating a communal lifestyle and binding to supports of various natures. These P. aeruginosa systems are reviewed here and may be categorized as classical or non-classical systems. They highlight the panoply of strategies that this hairy and gluey bacterium has developed for dealing with the diverse environments with which it is faced during various types of infection, involving complex regulatory networks that have not yet been fully elucidated but several aspects of which are discussed here.

Nutrients determine the spatial architecture of Paracoccus sp. biofilm

Bacterial biofilms adapt and shape their structure in response to varied environmental conditions. A statistical methodology was adopted in this study to empirically investigate the influence of nutrients on biofilm structural parameters deduced from confocal scanning laser microscope images of Paracoccus sp.W1b, a denitrifying bacterium. High concentrations of succinate, Mg(++), Ca(++), and Mn(++) were shown to enhance biofilm formation whereas higher concentration of iron decreased biofilm formation. Biofilm formed at high succinate was uneven with high surface to biovolume ratio. Higher Mg(++) or Ca(++) concentrations induced cohesion of biofilm cells, but contrasting biofilm architectures were detected. Biofilm with subpopulation of pillar-like protruding cells was distributed on a mosaic form of monolayer cells in medium with 10 mM Mg(++). 10 mM Ca(++) induced a dense confluent biofilm. Denitrification activity was significantly increased in the Mg(++)- and Ca(++)-induced biofilms. Chelator treatment of various biofilm ages indicated that divalent cations are important in the initial stages of biofilm formation.

Biofilm formation by the human pathogen Neisseria meningitidis

The past decade has seen an increasing interest in biofilm formation by Neisseria meningitidis, a human facultative pathogen causing life-threatening childhood disease commencing from asymptomatic nasopharyngeal colonization. Studying the biology of in vitro biofilm formation improves the understanding of inter-bacterial processes in asymptomatic carriage, of bacterial aggregate formation on host cells, and of meningococcal population biology. This paper reviews publications referring to meningococcal biofilm formation with an emphasis on the role of motility and of extracellular DNA. The theory of sub-dividing the meningococcal population in settler and spreader lineages is discussed, which provides a mechanistic framework for the assumed balance of colonization efficacy and transmission frequency.

Planktonic cell yield is linked to biofilm development

We report on the ability of surface-associated microbes to produce and release single planktonic cells to the bulk liquid as early as 6 h after attachment, with pure culture and mixed-species biofilms yielding up to approximately 1 x 10(6) cells/cm(2) of attachment area per hour to the effluent after 24 h. Planktonic cell production typically increased as the biofilm developed and levelled off after the biofilm reached steady-state dimensions. Microscopic observations of continuous-flow cultured biofilms revealed independent cell movement within the biofilm microenvironment compared with flow-dependent movement of mostly single cells in the bulk-liquid phase. These results indicate that the prevailing concept of detachment occurring only after the biofilm has matured is incomplete. Instead, we show that biofilms yield cells to the environment soon after initial surface contact; the extent of this yield is dependent on biofilm development, which in turn is influenced by environmental parameters such as bulk-liquid flow rates and nutrient availability. The observation that biofilms yield significant numbers of cells throughout development should lead to a greater understanding of pathogen dissemination, biofouling of products or facilities, and the role that biofilms play in microbial proliferation in the environment.

Extracellular enzymes affect biofilm formation of mucoid Pseudomonas aeruginosa

Pseudomonas aeruginosa secretes a variety of hydrolases, many of which contribute to virulence or are thought to play a role in the nutrition of the bacterium. As most studies concerning extracellular enzymes have been performed on planktonic cultures of non-mucoid P. aeruginosa strains, knowledge of the potential role of these enzymes in biofilm formation in mucoid (alginate-producing) P. aeruginosa remains limited. Here we show that mucoid P. aeruginosa produces extracellular hydrolases during biofilm growth. Overexpression of the extracellular lipases LipA and LipC, the esterase EstA and the proteolytic elastase LasB from plasmids revealed that some of these hydrolases affected the composition and physicochemical properties of the extracellular polymeric substances (EPS). While no influence of LipA was observed, the overexpression of estA and lasB led to increased concentrations of extracellular rhamnolipids with enhanced levels of mono-rhamnolipids, elevated amounts of total carbohydrates and decreased alginate concentrations, resulting in increased EPS hydrophobicity and viscosity. Moreover, we observed an influence of the enzymes on cellular motility. Overexpression of estA resulted in a loss of twitching motility, although it enhanced the ability to swim and swarm. The lasB-overexpression strain showed an overall enhanced motility compared with the parent strain. Moreover, the EstA- and LasB-overproduction strains completely lost the ability to form 3D biofilms, whereas the overproduction of LipC increased cell aggregation and the heterogeneity of the biofilms formed. Overall, these findings indicate that directly or indirectly, the secreted enzymes EstA, LasB and LipC can influence the formation and architecture of mucoid P. aeruginosa biofilms as a result of changes in EPS composition and properties, as well as the motility of the cells.

Dispersion as an important step in the Candida albicans biofilm developmental cycle

Biofilms are dynamic microbial communities in which transitions between planktonic and sessile modes of growth occur interchangeably in response to different environmental cues. In the last decade, early events associated with C. albicans biofilm formation have received considerable attention. However, very little is known about C. albicans biofilm dispersion or the mechanisms and signals that trigger it. This is important because it is precisely C. albicans cells dispersed from biofilms that are the main culprits associated with candidemia and establishment of disseminated invasive disease, two of the gravest forms of candidiasis. Using a simple flow biofilm model recently developed by our group, we have performed initial investigations into the phenomenon of C. albicans biofilm dispersion, as well as the phenotypic characteristics associated with dispersed cells. Our results indicate that C. albicans biofilm dispersion is dependent on growing conditions, including carbon source and pH of the media used for biofilm development. C. albicans dispersed cells are mostly in the yeast form and display distinct phenotypic properties compared to their planktonic counterparts, including enhanced adherence, filamentation, biofilm formation and, perhaps most importantly, increased pathogenicity in a murine model of hematogenously disseminated candidiasis, thus indicating that dispersed cells are armed with a complete arsenal of “virulence factors” important for seeding and establishing new foci of infection. In addition, utilizing genetically engineered strains of C. albicans (tetO-UME6 and tetO-PES1) we demonstrate that C. albicans biofilm dispersion can be regulated by manipulating levels of expression of these key genes, further supporting the evidence for a strong link between biofilms and morphogenetic conversions at different stages of the C. albicans biofilm developmental cycle. Overall, our results offer novel and important insight into the phenomenon of C. albicans biofilm dispersion, a key part of the biofilm developmental cycle, and provide the basis for its more detailed analysis.

Candida albicans is the main causative agent of candidiasis, a difficult-to-treat infection that occurs mostly in severely immunosuppressed and other at-risk patients. Candidiasis is often associated with the formation of biofilms (attached microbial communities encapsulated within a protective matrix) on host surfaces and/or implantable medical devices, most notably intravascular catheters. In recent years, for C. albicans, the process of biofilm formation has received much attention. However, the same is not true for biofilm dispersion (the release of cells from the biofilm). This is important since these dispersed cells are responsible for the subsequent establishment of disseminated candidiasis at distal organs. Here we have taken advantage of a model of biofilm formation under conditions of flow recently described by our group to study and characterize the phenomenon of C. albicans biofilm dispersion. Rather than an end-stage process, our results indicate that dispersion occurs at all different stages of the biofilm developmental cycle and is influenced by nutritional and other physiochemical conditions. In addition, our findings provide initial insights into how this process is regulated at the molecular level. We also demonstrate that dispersed cells display distinct phenotypic properties that are associated with increased virulence, with important clinical repercussions.

Pseudomonas aeruginosa biofilm infections in cystic fibrosis: insights into pathogenic processes and treatment strategies

IMPORTANCE OF THE FIELD

CF airway mucus can be infected by opportunistic microorganisms, notably Pseudomonas aeruginosa. Once organisms are established as biofilms, even the most potent antibiotics have little effect on their viability, especially during late-stage chronic infections. Better understanding of the mechanisms used by P. aeruginosa to circumvent host defenses and therapeutic intervention strategies is critical for advancing novel treatment strategies.

AREAS COVERED IN THIS REVIEW

Inflammatory injury in CF lung, role of neutrophils in pathogenesis, P. aeruginosa biofilms, mucoidy and its relationship with poor airway oxygenation, mechanisms by which P. aeruginosa biofilms in the CF airway can be killed.

WHAT THE READER WILL GAIN

An understanding of the processes that P. aeruginosa undergoes during CF airway disease and clues to better treat such infections in future.

TAKE HOME MESSAGE

The course of CF airway disease is a process involving host and microbial factors that often dictate frequency of pulmonary exacerbations, thus affecting the overall course. In the past decade significant discoveries have been made regarding the pathogenic processes used by P. aeruginosa to bypass the immune system. Many new and exciting features of P. aeruginosa now illuminate weaknesses in the organism that may render it susceptible to inexpensive compounds that force its own destruction.

Molecular mechanisms of compounds affecting bacterial biofilm formation and dispersal

Bacteria can switch between planktonic forms (single cells) and biofilms, i.e., bacterial communities growing on solid surfaces and embedded in a matrix of extracellular polymeric substance. Biofilm formation by pathogenic bacteria often results in lower susceptibility to antibiotic treatments and in the development of chronic infections; thus, biofilm formation can be considered an important virulence factor. In recent years, much attention has been directed towards understanding the biology of biofilms and towards searching for inhibitors of biofilm development and of biofilm-related cellular processes. In this report, we review selected examples of target-based screening for anti-biofilm agents: We focus on inhibitors of quorum sensing, possibly the most characterized target for molecules with anti-biofilm activity, and on compounds interfering with the metabolism of the signal molecule cyclic di-GMP metabolism and on inhibitors of DNA and nucleotide biosynthesis, which represent a novel and promising class of biofilm inhibitors. Finally, we discuss the activation of biofilm dispersal as a novel mode of action for anti-biofilm compounds.

Pseudomonas aeruginosa cystic fibrosis isolates of similar RAPD genotype exhibit diversity in biofilm forming ability in vitro

BACKGROUND

Pseudomonas aeruginosa is considered to grow in a biofilm in cystic fibrosis (CF) chronic lung infections. Bacterial cell motility is one of the main factors that have been connected with P. aeruginosa adherence to both biotic and abiotic surfaces. In this investigation, we employed molecular and microscopic methods to determine the presence or absence of motility in P. aeruginosa CF isolates, and statistically correlated this with their biofilm forming ability in vitro.

RESULTS

Our investigations revealed a wide diversity in the production, architecture and control of biofilm formation. Of 96 isolates, 49% possessed swimming motility, 27% twitching and 52% swarming motility, while 47% were non-motile. Microtitre plate assays for biofilm formation showed a range of biofilm formation ability from biofilm deficient phenotypes to those that formed very thick biofilms. A comparison of the motility and adherence properties of individual strains demonstrated that the presence of swimming and twitching motility positively affected biofilm biomass. Crucially, however, motility was not an absolute requirement for biofilm formation, as 30 non-motile isolates actually formed thick biofilms, and three motile isolates that had both flagella and type IV pili attached only weakly. In addition, CLSM analysis showed that biofilm-forming strains of P. aeruginosa were in fact capable of entrapping non-biofilm forming strains, such that these 'non-biofilm forming' cells could be observed as part of the mature biofilm architecture.

CONCLUSIONS

Clinical isolates that do not produce biofilms in the laboratory must have the ability to survive in the patient lung. We propose that a synergy exists between isolates in vivo, which allows "non biofilm-forming" isolates to be incorporated into the biofilm. Therefore, there is the potential for strains that are apparently non-biofilm forming in vitro to participate in biofilm-mediated pathogenesis in the CF lung.

Biofilm dispersal: mechanisms, clinical implications, and potential therapeutic uses

Like all sessile organisms, surface-attached communities of bacteria known as biofilms must release and disperse cells into the environment to colonize new sites. For many pathogenic bacteria, biofilm dispersal plays an important role in the transmission of bacteria from environmental reservoirs to human hosts, in horizontal and vertical cross-host transmission, and in the exacerbation and spread of infection within a host. The molecular mechanisms of bacterial biofilm dispersal are only beginning to be elucidated. Biofilm dispersal is a promising area of research that may lead to the development of novel agents that inhibit biofilm formation or promote biofilm cell detachment. Such agents may be useful for the prevention and treatment of biofilms in a variety of industrial and clinical settings. This review describes the current status of research on biofilm dispersal, with an emphasis on studies aimed to characterize dispersal mechanisms, and to identify environmental cues and inter- and intracellular signals that regulate the dispersal process. The clinical implications of biofilm dispersal and the potential therapeutic applications of some of the most recent findings will also be discussed.

Biofilms correlate with TH1 inflammation in the sinonasal tissue of patients with chronic rhinosinusitis

OBJECTIVE

Determine the prevalence of bacterial biofilms in surgical chronic rhinosinusitis (CRS) patients and characterize the inflammatory response associated with biofilm CRS.

STUDY DESIGN

Cross-sectional.

SETTING

Tertiary care academic center.

SUBJECTS AND METHODS

Sinonasal mucosa and peripheral blood were collected from 60 CRS patients. Mucosal biofilms were demonstrated by scanning electron microscopy. Leukocyte subpopulations were determined by flow cytometry. Cytokines were identified with a luminex-based assay on the lysate of homogenized tissue or plasma.

RESULTS

Of the 60 samples, 17 were determined to be positive for the presence of biofilms. Oral steroid-naive CRS patients with biofilm demonstrated a local T(H)1 inflammatory response with significantly elevated levels of interferon-gamma (INF-gamma), granulocyte colony-stimulating factor, macrophage inflammatory protein-1 beta, and neutrophils in the sinonasal mucosa. No differences were present at the systemic level.

CONCLUSION

Sinonasal bacterial biofilms correlate to a T(H)1 skewed local but not systemic inflammatory response in CRS. This difference is abrogated by the use of oral steroids.

A novel signaling network essential for regulating Pseudomonas aeruginosa biofilm development

The important human pathogen Pseudomonas aeruginosa has been linked to numerous biofilm-related chronic infections. Here, we demonstrate that biofilm formation following the transition to the surface attached lifestyle is regulated by three previously undescribed two-component systems: BfiSR (PA4196-4197) harboring an RpoD-like domain, an OmpR-like BfmSR (PA4101-4102), and MifSR (PA5511-5512) belonging to the family of NtrC-like transcriptional regulators. These two-component systems become sequentially phosphorylated during biofilm formation. Inactivation of bfiS, bfmR, and mifR arrested biofilm formation at the transition to the irreversible attachment, maturation-1 and -2 stages, respectively, as indicated by analyses of biofilm architecture, and protein and phosphoprotein patterns. Moreover, discontinuation of bfiS, bfmR, and mifR expression in established biofilms resulted in the collapse of biofilms to an earlier developmental stage, indicating a requirement for these regulatory systems for the development and maintenance of normal biofilm architecture. Interestingly, inactivation did not affect planktonic growth, motility, polysaccharide production, or initial attachment. Further, we demonstrate the interdependency of this two-component systems network with GacS (PA0928), which was found to play a dual role in biofilm formation. This work describes a novel signal transduction network regulating committed biofilm developmental steps following attachment, in which phosphorelays and two sigma factor-dependent response regulators appear to be key components of the regulatory machinery that coordinates gene expression during P. aeruginosa biofilm development in response to environmental cues.

Biofilms are complex communities of microorganisms encased in a matrix and attached to surfaces. It is well recognized that biofilm cells differ from their free swimming counterparts with respect to gene expression, protein production, and resistance to antibiotics and the human immune system. However, little is known about the underlying regulatory events that lead to the formation of biofilms, the primary cause of many chronic and persistent human infections. By mapping the phosphoproteome over the course of P. aeruginosa biofilm development, we identified three novel two-component regulatory systems that were required for the development and maturation of P. aeruginosa biofilms. Activation (phosphorylation) of these three regulatory systems occurred in a sequential manner and inactivation arrested biofilm formation at three distinct developmental stages. Discontinuation of bfiS, bfmR, or mifR expression after biofilms had already matured resulted in disaggregation/collapse of biofilms. Furthermore, this regulatory cascade appears to be linked via BfiS-dependent GacS-phosphorylation to the previously identified LadS/RetS/GacAS/RsmA network that reciprocally regulates virulence and surface attachment. Our data thus indicate the existence of a previously unidentified regulatory program of biofilm development once P. aeruginosa cells have committed to a surface associated lifestyle, and may provide new targets for controlling the programmed differentiation process of biofilm formation.

Nitric oxide signaling in Pseudomonas aeruginosa biofilms mediates phosphodiesterase activity, decreased cyclic di-GMP levels, and enhanced dispersal

Bacteria in biofilms often undergo active dispersal events and revert to a free-swimming, planktonic state to complete the biofilm life cycle. The signaling molecule nitric oxide (NO) was previously found to trigger biofilm dispersal in the opportunistic pathogen Pseudomonas aeruginosa at low, nontoxic concentrations (N. Barraud, D. J. Hassett, S. H. Hwang, S. A. Rice, S. Kjelleberg, and J. S. Webb, J. Bacteriol. 188:7344-7353, 2006). NO was further shown to increase cell motility and susceptibility to antimicrobials. Recently, numerous studies revealed that increased degradation of the secondary messenger cyclic di-GMP (c-di-GMP) by specific phosphodiesterases (PDEs) triggers a planktonic mode of growth in eubacteria. In this study, the potential link between NO and c-di-GMP signaling was investigated by performing (i) PDE inhibitor studies, (ii) enzymatic assays to measure PDE activity, and (iii) direct quantification of intracellular c-di-GMP levels. The results suggest a role for c-di-GMP signaling in triggering the biofilm dispersal event induced by NO, as dispersal requires PDE activity and addition of NO stimulates PDE and induces the concomitant decrease in intracellular c-di-GMP levels in P. aeruginosa. Furthermore, gene expression studies indicated global responses to low, nontoxic levels of NO in P. aeruginosa biofilms, including upregulation of genes involved in motility and energy metabolism and downregulation of adhesins and virulence factors. Finally, site-directed mutagenesis of candidate genes and physiological characterization of the corresponding mutant strains uncovered that the chemotaxis transducer BdlA is involved in the biofilm dispersal response induced by NO.

SiaA and SiaD are essential for inducing autoaggregation as a specific response to detergent stress in Pseudomonas aeruginosa

Cell aggregation is a stress response and serves as a survival strategy for Pseudomonas aeruginosa strain PAO1 during growth with the toxic detergent Na-dodecylsulfate (SDS). This process involves the psl operon and is linked to c-di-GMP signalling. The induction of cell aggregation in response to SDS was studied. Transposon and site-directed mutagenesis revealed that the cupA-operon and the co-transcribed genes siaA (PA0172) and siaD (PA0169) were essential for SDS-induced aggregation. While siaA encodes a putative membrane protein with a HAMP and a PP2C-like phosphatase domain, siaD encodes a putative diguanylate cyclase involved in the biosynthesis of c-di-GMP. Complementation studies uncovered that the loss of SDS-induced aggregation in the formerly isolated spontaneous mutant strain N was caused by a non-functional siaA allele. DNA-microarray analysis of SDS-grown cells revealed consistent activation of eight genes, including cupA1, with known or presumptive important functions in cell aggregation in the parent strain compared with non-aggregating siaA and siaD mutants. A siaAD-dependent increase of cupA1 mRNA levels in SDS-grown cells was also shown by Northern blots. These results clearly demonstrate that SiaAD are essential for inducing cell aggregation as a specific response to SDS and suggest that they are responsible for perceiving and transducing SDS-related stress.

Signals, regulatory networks, and materials that build and break bacterial biofilms

Biofilms are communities of microorganisms that live attached to surfaces. Biofilm formation has received much attention in the last decade, as it has become clear that virtually all types of bacteria can form biofilms and that this may be the preferred mode of bacterial existence in nature. Our current understanding of biofilm formation is based on numerous studies of myriad bacterial species. Here, we review a portion of this large body of work including the environmental signals and signaling pathways that regulate biofilm formation, the components of the biofilm matrix, and the mechanisms and regulation of biofilm dispersal.

Pseudomonas aeruginosa PAO1 preferentially grows as aggregates in liquid batch cultures and disperses upon starvation

In both natural and artificial environments, bacteria predominantly grow in biofilms, and bacteria often disperse from biofilms as freely suspended single-cells. In the present study, the formation and dispersal of planktonic cellular aggregates, or ‘suspended biofilms’, by Pseudomonas aeruginosa in liquid batch cultures were closely examined, and compared to biofilm formation on a matrix of polyester (PE) fibers as solid surface in batch cultures. Plankton samples were analyzed by laser-diffraction particle-size scanning (LDA) and microscopy of aggregates. Interestingly, LDA indicated that up to 90% of the total planktonic biomass consisted of cellular aggregates in the size range of 10–400 µm in diameter during the growth phase, as opposed to individual cells. In cultures with PE surfaces, P. aeruginosa preferred to grow in biofilms, as opposed to planktonicly. However, upon carbon, nitrogen or oxygen limitation, the planktonic aggregates and PE-attached biofilms dispersed into single cells, resulting in an increase in optical density (OD) independent of cellular growth. During growth, planktonic aggregates and PE-attached biofilms contained densely packed viable cells and extracellular DNA (eDNA), and starvation resulted in a loss of viable cells, and an increase in dead cells and eDNA. Furthermore, a release of metabolites and infective bacteriophage into the culture supernatant, and a marked decrease in intracellular concentration of the second messenger cyclic di-GMP, was observed in dispersing cultures. Thus, what traditionally has been described as planktonic, individual cell cultures of P. aeruginosa, are in fact suspended biofilms, and such aggregates have behaviors and responses (e.g. dispersal) similar to surface associated biofilms. In addition, we suggest that this planktonic biofilm model system can provide the basis for a detailed analysis of the synchronized biofilm life cycle of P. aeruginosa.

Environmental proteomics: applications of proteome profiling in environmental microbiology and biotechnology

In this review, we present the use of proteomics to advance knowledge in the field of environmental biotechnology, including studies of bacterial physiology, metabolism and ecology. Bacteria are widely applied in environmental biotechnology for their ability to catalyze dehalogenation, methanogenesis, denitrification and sulfate reduction, among others. Their tolerance to radiation and toxic compounds is also of importance. Proteomics has an important role in helping uncover the pathways behind these cellular processes. Environmental samples are often highly complex, which makes proteome studies in this field especially challenging. Some of these challenges are the lack of genome sequences for the vast majority of environmental bacteria, difficulties in isolating bacteria and proteins from certain environments, and the presence of complex microbial communities. Despite these challenges, proteomics offers a unique dynamic view into cellular function. We present examples of environmental proteomics of model organisms, and then discuss metaproteomics (microbial community proteomics), which has the potential to provide insights into the function of a community without isolating organisms. Finally, the environmental proteomics literature is summarized as it pertains to the specific application areas of wastewater treatment, metabolic engineering, microbial ecology and environmental stress responses.

Quorum sensing in Pseudomonas aeruginosa biofilms

In nature, the bulk of bacterial biomass is believed to exist as an adherent community of cells called a biofilm. Pseudomonas aeruginosa has become a model organism for studying this mode of growth. Over the past decade, significant strides have been made towards understanding biofilm development in P. aeruginosa and we now have a clearer picture of the mechanisms involved. Available evidence suggests that construction of these sessile communities proceeds by many different pathways, rather than a specific programme of biofilm development. A cell-to-cell communication mechanism known as quorum sensing (QS) has been found to play a role in P. aeruginosa biofilm formation. Because both QS and biofilms are impacted by the surrounding environment, understanding the full involvement of cell-to-cell signalling in establishing these complex communities represents a challenge. Nevertheless, under set conditions, several links between QS and biofilm formation have been recognized, which is the focus of this review. A role for antibiotics as alternative QS signalling molecules influencing biofilm development is also discussed.

A Candida albicans early stage biofilm detachment event in rich medium

BACKGROUND

Dispersal from Candida albicans biofilms that colonize catheters is implicated as a primary factor in the link between contaminated catheters and life threatening blood stream infections (BSI). Appropriate in vitro C. albicans biofilm models are needed to probe factors that induce detachment events.

RESULTS

Using a flow through system to culture C. albicans biofilms we characterized a detachment process which culminates in dissociation of an entire early stage biofilm from a silicone elastomer surface. We analyzed the transcriptome response at time points that bracketed an abrupt transition in which a strong adhesive association with the surface is weakened in the initial stages of the process, and also compared batch and biofilm cultures at relevant time points. K means analysis of the time course array data revealed categories of genes with similar patterns of expression that were associated with adhesion, biofilm formation and glycoprotein biosynthesis. Compared to batch cultures the biofilm showed a pattern of expression of metabolic genes that was similar to the C. albicans response to hypoxia. However, the loss of strong adhesion was not obviously influenced by either the availability of oxygen in the medium or at the silicone elastomer surface. The detachment phenotype of mutant strains in which selected genes were either deleted or overexpressed was characterized. The microarray data indicated that changes associated with the detachment process were complex and, consistent with this assessment, we were unable to demonstrate that transcriptional regulation of any single gene was essential for loss of the strong adhesive association.

CONCLUSION

The massive dispersal of the early stage biofilm from a biomaterial surface that we observed is not orchestrated at the level of transcriptional regulation in an obvious manner, or is only regulated at this level by a small subpopulation of cells that mediate adhesion to the surface.

5-Fluorouracil reduces biofilm formation in Escherichia coli K-12 through global regulator AriR as an antivirulence compound

The uracil analog, 5-fluorouracil (5-FU), reduces virulence and biofilm formation for Pseudomonas aeruginosa PA14 without affecting its growth. As 5-FU is an approved anticancer drug, its antivirulence attributes in P. aeruginosa prompted us to examine the effect of this compound on three different Escherichia coli K-12 strains and its effect on virulence genes in E. coli O157:H7 (EHEC); the mechanism by which it functions was also examined. 5-FU decreased biofilm formation in a dose-dependent manner in E. coli K-12 and repressed the expression of virulence genes in EHEC. Five other uracil analogs were also tested for their effects on biofilm formation, and none of these compounds affected the biofilm formation in E. coli K-12. Whole-transcriptome analysis revealed that 5-FU induced the expression of 157 genes and repressed the expression of 19 genes. Biofilm formation with the addition of 5-FU was checked in 21 isogenic knockout mutants whose gene expression was induced in the microarray data; we found that 5-FU does not decrease biofilm formation of the cells that lack AriR, a global DNA regulator that controls acid resistance in E. coli. Hence, 5-FU represses biofilm formation of E. coli K-12 through AriR and is a novel antivirulence compound for this strain.

Neutral super-oxidised solutions are effective in killing P. aeruginosa biofilms

Bacteria growing in biofilms can become up to 1000-fold more resistant to antibiotics and biocides as compared to their planktonic counterparts. As a result of this increased resistance, biofilms and biofilm-related infections cannot be effectively treated with conventional antibiotic therapy. The goal of this study was to determine the efficacy of three neutral pH, super-oxidised solutions (nSOSs, OIS-80, OIS-125, OIS-200, Microcyn Technology) varying in oxychlorine concentration (80, 125 and 200 ppm) against P. aeruginosa grown planktonically and as biofilms. Exposure for 20 s of exponential phase cells to any of the three solutions was sufficient to reduce viability by more than five logs. However, only exposure for 10 min to OIS-125 and OIS-200 for 10 min was sufficient to eradicate stationary phase P. aeruginosa cells. The efficacy of nSOSs on P. aeruginosa biofilms, grown to maturity in continuous flow tube reactors, was determined upon treatment up to 60 min. Viability pre- and post-treatment was determined by CFU counts. The effect of these solutions on P. aeruginosa biofilms and biofilm architecture was further visualised by confocal scanning laser microscopy and quantitatively analysed by COMSTAT. Under these experimental conditions, only OIS-125 and OIS-200 achieved a >3-log reduction and biofilm disaggregation within 30 min of exposure. Because OIS-125 and OIS-200 enhance the disaggregation of biofilms, their use in the treatment of surface-related biofilm infections deserves further investigation.

Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa

Pseudomonas aeruginosa isolates have a highly conserved core genome representing up to 90% of the total genomic sequence with additional variable accessory genes, many of which are found in genomic islands or islets. The identification of the Liverpool Epidemic Strain (LES) in a children's cystic fibrosis (CF) unit in 1996 and its subsequent observation in several centers in the United Kingdom challenged the previous widespread assumption that CF patients acquire only unique strains of P. aeruginosa from the environment. To learn about the forces that shaped the development of this important epidemic strain, the genome of the earliest archived LES isolate, LESB58, was sequenced. The sequence revealed the presence of many large genomic islands, including five prophage clusters, one defective (pyocin) prophage cluster, and five non-phage islands. To determine the role of these clusters, an unbiased signature tagged mutagenesis study was performed, followed by selection in the chronic rat lung infection model. Forty-seven mutants were identified by sequencing, including mutants in several genes known to be involved in Pseudomonas infection. Furthermore, genes from four prophage clusters and one genomic island were identified and in direct competition studies with the parent isolate; four were demonstrated to strongly impact on competitiveness in the chronic rat lung infection model. This strongly indicates that enhanced in vivo competitiveness is a major driver for maintenance and diversifying selection of these genomic prophage genes.

Interplay between cyclic AMP-cyclic AMP receptor protein and cyclic di-GMP signaling in Vibrio cholerae biofilm formation

Vibrio cholerae is a facultative human pathogen. The ability of V. cholerae to form biofilms is crucial for its survival in aquatic habitats between epidemics and is advantageous for host-to-host transmission during epidemics. Formation of mature biofilms requires the production of extracellular matrix components, including Vibrio polysaccharide (VPS) and matrix proteins. Biofilm formation is positively controlled by the transcriptional regulators VpsR and VpsT and is negatively regulated by the quorum-sensing transcriptional regulator HapR, as well as the cyclic AMP (cAMP)-cAMP receptor protein (CRP) regulatory complex. Transcriptome analysis of cyaA (encoding adenylate cyclase) and crp (encoding cAMP receptor protein) deletion mutants revealed that cAMP-CRP negatively regulates transcription of both VPS biosynthesis genes and genes encoding biofilm matrix proteins. Further mutational and expression analysis revealed that cAMP-CRP negatively regulates transcription of vps genes indirectly through its action on vpsR transcription. However, negative regulation of the genes encoding biofilm matrix proteins by cAMP-CRP can also occur independent of VpsR. Transcriptome analysis also revealed that cAMP-CRP regulates the expression of a set of genes encoding diguanylate cyclases (DGCs) and phosphodiesterases. Mutational and phenotypic analysis of the differentially regulated DGCs revealed that a DGC, CdgA, is responsible for the increase in biofilm formation in the Deltacrp mutant, showing the connection between of cyclic di-GMP and cAMP signaling in V. cholerae.

Prevalence of biofilm-forming bacteria in chronic rhinosinusitis

BACKGROUND

Recently, biofilms have been implicated in the pathogenesis of recalcitrant chronic rhinosinusitis (CRS). We sought to determine the prevalence of biofilm-forming cultures obtained from patients with CRS and clinical factors that may contribute to biofilm formation.

METHODS

Endoscopically guided sinonasal cultures were obtained in duplicate from CRS patients with evidence of mucopurulence. Bacterial swabs were sent for microbiological characterization and were simultaneously evaluated for biofilm-forming capacity by a modified Calgary Biofilm Detection Assay. Biofilm formation was based on concomitant values of biofilm-forming Pseudomonas aeruginosa O1 (PAO1) (positive control) and non-biofilm-forming mutants sad-31 (type IV pili) and sad-36 (flagella K; negative control). Samples, with growth greater than the sad-31 mutant, were designated as biofilm formers.

RESULTS

Sinonasal cultures were obtained from 157 consecutive patients (83 female patients) over a 4-month period. Forty-five samples (28.6%) showed biofilm formation. Among patients with a prior history of functional endoscopic sinus surgery (FESS), 30.7% (n = 42) showed biofilm growth. For patients naive to surgical intervention (n = 20), only 15% showed biofilm formation. A positive, statistically significant correlation existed between biofilm formation and number of prior FESS procedures. Polymicrobial cultures, Pseudomonas aeruginosa, and/or Staphylococcus aureus comprised 71% of samples. Chi-squared analysis showed an association with prior infections, but not with any pharmacologic therapy or comorbidies.

CONCLUSION

We show a high percentage of CRS patients (28.6%) whose sinonasal mucopurulence has biofilm-forming capacity. Postsurgical patients had a high prevalence of biofilm-forming bacteria, a possible reflection of the severe nature of their disease. Additional studies are warranted.

Medical biofilms

For more than two decades, Biotechnology and Bioengineering has documented research focused on natural and engineered microbial biofilms within aquatic and subterranean ecosystems, wastewater and waste-gas treatment systems, marine vessels and structures, and industrial bioprocesses. Compared to suspended culture systems, intentionally engineered biofilms are heterogeneous reaction systems that can increase reactor productivity, system stability, and provide inherent cell:product separation. Unwanted biofilms can create enormous increases in fluid frictional resistances, unacceptable reductions in heat transfer efficiency, product contamination, enhanced material deterioration, and accelerated corrosion. Missing from B&B has been an equivalent research dialogue regarding the basic molecular microbiology, immunology, and biotechnological aspects of medical biofilms. Presented here are the current problems related to medical biofilms; current concepts of biofilm formation, persistence, and interactions with the host immune system; and emerging technologies for controlling medical biofilms.

Agr-mediated dispersal of Staphylococcus aureus biofilms

The agr quorum-sensing system of Staphylococcus aureus modulates the expression of virulence factors in response to autoinducing peptides (AIPs). Recent studies have suggested a role for the agr system in S. aureus biofilm development, as agr mutants exhibit a high propensity to form biofilms, and cells dispersing from a biofilm have been observed displaying an active agr system. Here, we report that repression of agr is necessary to form a biofilm and that reactivation of agr in established biofilms through AIP addition or glucose depletion triggers detachment. Inhibitory AIP molecules did not induce detachment and an agr mutant was non-responsive, indicating a dependence on a functional, active agr system for dispersal. Biofilm detachment occurred in multiple S. aureus strains possessing divergent agr systems, suggesting it is a general S. aureus phenomenon. Importantly, detachment also restored sensitivity of the dispersed cells to the antibiotic rifampicin. Proteinase K inhibited biofilm formation and dispersed established biofilms, suggesting agr-mediated detachment occurred in an ica-independent manner. Consistent with a protease-mediated mechanism, increased levels of serine proteases were detected in detaching biofilm effluents, and the serine protease inhibitor PMSF reduced the degree of agr-mediated detachment. Through genetic analysis, a double mutant in the agr-regulated Aur metalloprotease and the SplABCDEF serine proteases displayed minimal extracellular protease activity, improved biofilm formation, and a strongly attenuated detachment phenotype. These findings indicate that induction of the agr system in established S. aureus biofilms detaches cells and demonstrate that the dispersal mechanism requires extracellular protease activity.

A biofilm is a surface-attached community of cells bound together by an extracellular matrix. In a bacterial infection, biofilm-encased cells are protected from antibiotic therapy and host immune response, and these encased cells can develop into a chronic infection. Staphylococcus aureus is a prominent bacterial pathogen known to form biofilms on many medical implants and host tissues. In this report, we demonstrate that repression of the S. aureus quorum-sensing system is required to form a biofilm, and quorum-sensing reactivation in established biofilms disperses the cells. Genetic and molecular analysis demonstrates that quorum-sensing is activated before and required for the detachment mechanism. Detachment is protease-mediated, as established biofilms are sensitive to a non-specific protease and quorum-sensing activation increases the production of extracellular proteases. Using mutations in the protease genes, we show that these secreted enzymes are required for the detachment mechanism. These findings denote that S. aureus quorum-sensing can function as a dispersal mechanism to colonize new sites, and our results suggest this mechanism could be modulated to treat recalcitrant biofilms.

Proteomic, microarray, and signature-tagged mutagenesis analyses of anaerobic Pseudomonas aeruginosa at pH 6.5, likely representing chronic, late-stage cystic fibrosis airway conditions

Patients suffering from cystic fibrosis (CF) commonly harbor the important pathogen Pseudomonas aeruginosa in their airways. During chronic late-stage CF, P. aeruginosa is known to grow under reduced oxygen tension and is even capable of respiring anaerobically within the thickened airway mucus, at a pH of approximately 6.5. Therefore, proteins involved in anaerobic metabolism represent potentially important targets for therapeutic intervention. In this study, the clinically relevant "anaerobiome" or "proteogenome" of P. aeruginosa was assessed. First, two different proteomic approaches were used to identify proteins differentially expressed under anaerobic versus aerobic conditions. Microarray studies were also performed, and in general, the anaerobic transcriptome was in agreement with the proteomic results. However, we found that a major portion of the most upregulated genes in the presence of NO(3)(-) and NO(2)(-) are those encoding Pf1 bacteriophage. With anaerobic NO(2)(-), the most downregulated genes are those involved postglycolytically and include many tricarboxylic acid cycle genes and those involved in the electron transport chain, especially those encoding the NADH dehydrogenase I complex. Finally, a signature-tagged mutagenesis library of P. aeruginosa was constructed to further screen genes required for both NO(3)(-) and NO(2)(-) respiration. In addition to genes anticipated to play important roles in the anaerobiome (anr, dnr, nar, nir, and nuo), the cysG and dksA genes were found to be required for both anaerobic NO(3)(-) and NO(2)(-) respiration. This study represents a major step in unraveling the molecular machinery involved in anaerobic NO(3)(-) and NO(2)(-) respiration and offers clues as to how we might disrupt such pathways in P. aeruginosa to limit the growth of this important CF pathogen when it is either limited or completely restricted in its oxygen supply.

Environmental influences on biofilm development

Bacterial biofilms are found under diverse environmental conditions, from sheltered and specialized environments found within mammalian hosts to the extremes of biological survival. The process of forming a biofilm and the eventual return of cells to the planktonic state involve the coordination of vast amounts of genetic information. Nevertheless, the prevailing evidence suggests that the overall progression of this cycle within a given species or strain of bacteria responds to environmental conditions via a finite number of key regulatory factors and pathways, which affect enzymatic and structural elements that are needed for biofilm formation and dispersal. Among the conditions that affect biofilm development are temperature, pH, O2 levels, hydrodynamics, osmolarity, the presence of specific ions, nutrients, and factors derived from the biotic environment. The integration of these influences ultimately determines the pattern of behavior of a given bacterium with respect to biofilm development. This chapter will present examples of how environmental conditions affect biofilm development, most of which come from studies of species that have mammalian hosts.

PA2663 (PpyR) increases biofilm formation in Pseudomonas aeruginosa PAO1 through the psl operon and stimulates virulence and quorum-sensing phenotypes

Previously, we identified the uncharacterized predicted membrane protein PA2663 of Pseudomonas aeruginosa PAO1 as a virulence factor using a poplar tree model; PA2663 was induced in the poplar rhizosphere and, upon inactivation, it caused 20-fold lower biofilm formation (Attila et al., Microb Biotechnol, 2008). Here, we confirmed that PA2663 is related to biofilm formation by restoring the wild-type phenotype by complementing the PA2663 mutation in trans and investigated the genetic basis of its influence on biofilm formation through whole-transcriptome and -phenotype studies. Upon inactivating PA2663 by transposon insertion, the psl operon that encodes a galactose- and mannose-rich exopolysaccharide was highly repressed (verified by RT-PCR). The inactivation of PA2663 also repressed 13 pyoverdine genes, which eliminated the production of the virulence factor pyoverdine in P. aeruginosa. The inactivation of PA2663 also affected other quorum-sensing-related phenotypes in that it repressed the Pseudomonas quinolone signal (PQS) genes, which abolished PQS production, and repressed lasB, which decreased elastase activity sevenfold. Genes were also induced for motility and attachment (PA0499, PA0993, PA2130, and PA4549) and for small molecule transport (PA0326, PA1541, PA1632, PA1971, PA2214, PA2215, PA2678, and PA3407). Phenotype arrays also showed that PA2663 represses growth on D: -gluconic acid, D: -mannitol, and N-phthaloyl-L: -glutamic acid. Hence, the PA2663 gene product increases biofilm formation by increasing the psl-operon-derived exopolysaccharides and increases pyoverdine synthesis, PQS production, and elastase activity while reducing swarming and swimming motility. We speculate that PA2663 performs these myriad functions as a novel membrane sensor.