Bacterial survival in biofilms: probes for exopolysaccharide and its hydrolysis, and measurements of intra- and interphase mass fluxes

More than Rotating Flagella: Lipopolysaccharide as a Secondary Receptor for Flagellotropic Phage 7-7-1

Bacteriophage 7-7-1, a member of the family Myoviridae, infects the soil bacterium Agrobacterium sp. strain H13-3. Infection requires attachment to actively rotating bacterial flagellar filaments, with flagellar number, length, and rotation speed being important determinants for infection efficiency. To identify the secondary receptor(s) on the cell surface, we isolated motile, phage-resistant Agrobacterium sp. H13-3 transposon mutants. Transposon insertion sites were pinpointed using arbitrary primed PCR and bioinformatics analyses. Three genes were recognized, whose corresponding proteins had the following computationally predicted functions: AGROH133_07337, a glycosyltransferase; AGROH133_13050, a UDP-glucose 4-epimerase; and AGROH133_08824, an integral cytoplasmic membrane protein. The first two gene products are part of the lipopolysaccharide (LPS) synthesis pathway, while the last is predicted to be a relatively small (13.4-kDa) cytosolic membrane protein with up to four transmembrane helices. The phenotypes of the transposon mutants were verified by complementation and site-directed mutagenesis. Additional characterization of motile, phage-resistant mutants is also described. Given these findings, we propose a model for Agrobacterium sp. H13-3 infection by bacteriophage 7-7-1 where the phage initially attaches to the flagellar filament and is propelled down toward the cell surface by clockwise flagellar rotation. The phage then attaches to and degrades the LPS to reach the outer membrane and ejects its DNA into the host using its syringe-like contractile tail. We hypothesize that the integral membrane protein plays an important role in events following viral DNA ejection or in LPS processing and/or deployment. The proposed two-step attachment mechanism may be conserved among other flagellotropic phages infecting Gram-negative bacteria.IMPORTANCE Flagellotropic bacteriophages belong to the tailed-phage order Caudovirales, the most abundant phages in the virome. While it is known that these viruses adhere to the bacterial flagellum and use flagellar rotation to reach the cell surface, their infection mechanisms are poorly understood. Characterizing flagellotropic-phage-host interactions is crucial to understanding how microbial communities are shaped. Using a transposon mutagenesis approach combined with a screen for motile, phage-resistant mutants, we identified lipopolysaccharides as the secondary cell surface receptor for phage 7-7-1. This is the first cell surface receptor identified for flagellotropic phages. One hypothetical membrane protein was also recognized as essential for infection. These new findings, together with previous results, culminated in an infection model for phage 7-7-1.

First characterization of two C-type lectins of the tubeworm Alaysia sp. from a deep-sea hydrothermal vent

C-type lectins (CTLs) play an important role in innate immune defense. In this study, we identified and characterized two CTLs (Lec1 and Lec2) from the tubeworm Alaysia sp. collected from a hydrothermal vent in Pacmanus. Lec1 and Lec2 possess the typical CTL domain but share low sequence identities (10.8%-20.4%) with known CTLs. Recombinant (r) of Lec1 and Lec2 bound to various PAMPs and a wide arrange of bacteria from neritic and deep-sea environments in a Ca²⁺-independent manner, but only rLec1 caused agglutination of the bound bacteria. The activities of rLec1 and rLec2 were most stable and highest at 4 °C, the ambient temperature of the hydrothermal vent, and decreased at higher temperatures. Both lectins inhibited bacterial growth in a highly selective manner and agglutinated the erythrocytes of fish, rabbit, and chicken in a Ca²⁺-dependent manner. These results provided the first insights into the functional properties of CTLs in deep-sea Alaysia sp.

A three-step method for analysing bacterial biofilm formation under continuous medium flow

For the investigation and comparison of microbial biofilms, a variety of analytical methods have been established, all focusing on different growth stages and application areas of biofilms. In this study, a novel quantitative assay for analysing biofilm maturation under the influence of continuous flow conditions was developed using the interesting biocatalyst Pseudomonas taiwanensis VLB120. In contrast to other tubular-based assay systems, this novel assay format delivers three readouts using a single setup in a total assay time of 40 h. It combines morphotype analysis of biofilm colonies with the direct quantification of biofilm biomass and pellicle formation on an air/liquid interphase. Applying the Tube-Assay, the impact of the second messenger cyclic diguanylate on biofilm formation of P. taiwanensis VLB120 was investigated. To this end, 41 deletions of genes encoding for protein homologues to diguanylate cyclase and phosphodiesterase were generated in the genome of P. taiwanensis VLB120. Subsequently, the biofilm formation of the resulting mutants was analysed using the Tube-Assay. In more than 60 % of the mutants, a significantly altered biofilm formation as compared to the parent strain was detected. Furthermore, the potential of the proposed Tube-Assay was validated by investigating the biofilms of several other bacterial species.

A quantitative framework for understanding complex interactions between competing interfacial processes and in situ biodegradation

In situ bioremediation of contaminated groundwater is made technologically challenging by the physically, chemically, and biologically heterogeneous subsurface environment. Subsurface heterogeneities are important because of influences on interfacial mass transfer processes that impact the availability of substrates to microorganisms. The goal of this study was to perform a "proof-of-concept" evaluation of the utility of a quantitative framework based on a set of dimensionless coefficients for evaluating the effects of competing physicochemical interfacial and biokinetic processes at the field scale. First, three numerical modeling experiments were completed, demonstrating how the framework can be used to identify the rate-limiting process for the overall bioremediation rate, and to predict what engineered enhancements will alleviate the rate-limiting process. Baseline conditions for each scenario were established to examine intrinsic biodegradation with a given rate-limiting process (either dispersion, biokinetics, or sorption). Then different engineering treatments were examined. In each case, the treatment predicted to be appropriate for addressing the overall rate-limiting process based on the quantitative framework alleviated the limitation more successfully, and enhanced the in situ biodegradation rate more than the alternative enhancements. Second, the quantitative framework was applied to a series of large-scale laboratory and field-scale experiments, using reported parameter estimates to calculate the relevant dimensionless coefficients and predict the rate-limiting process(es). Observations from the studies were then used to evaluate those predictions.

Functional characterization of pfm in protein secretion and lung infection of Pseudomonas aeruginosa

Lung infections caused by Pseudomonas aeruginosa in cystic fibrosis (CF) patients cause progressive airway obstruction and tissue damage, which is the predominant cause of morbidity and mortality in patients with CF. This paper describes the functional characterization of the pfm gene (open reading frame PA2950) of P. aeruginosa. Using DNA microarrays, we found that the transcriptional levels of type II secretory system genes were significantly reduced in the pfm mutant strain. The type-II-dependent exoprotein LasB could not be secreted normally. The pfm gene was identified as a gene involved in bacterial protein secretion that was critical for the extracellular release of elastase in P. aeruginosa. The abilities to induce lung injury by wild-type and pfm mutant P. aeruginosa were evaluated in a murine acute lung infection model. The results showed that the pathogenicity and virulence of the pfm mutant strain was significantly reduced compared with that of the wild-type strain. The pfm gene and its expression product, as potential new drug targets against P. aeruginosa infection, have important research significance.

The cyclic-di-GMP phosphodiesterase BinA negatively regulates cellulose-containing biofilms in Vibrio fischeri

Bacteria produce different types of biofilms under distinct environmental conditions. Vibrio fischeri has the capacity to produce at least two distinct types of biofilms, one that relies on the symbiosis polysaccharide Syp and another that depends upon cellulose. A key regulator of biofilm formation in bacteria is the intracellular signaling molecule cyclic diguanylate (c-di-GMP). In this study, we focused on a predicted c-di-GMP phosphodiesterase encoded by the gene binA, located directly downstream of syp, a cluster of 18 genes critical for biofilm formation and the initiation of symbiotic colonization of the squid Euprymna scolopes. Disruption or deletion of binA increased biofilm formation in culture and led to increased binding of Congo red and calcofluor, which are indicators of cellulose production. Using random transposon mutagenesis, we determined that the phenotypes of the DeltabinA mutant strain could be disrupted by insertions in genes in the bacterial cellulose biosynthesis cluster (bcs), suggesting that cellulose production is negatively regulated by BinA. Replacement of critical amino acids within the conserved EAL residues of the EAL domain disrupted BinA activity, and deletion of binA increased c-di-GMP levels in the cell. Together, these data support the hypotheses that BinA functions as a phosphodiesterase and that c-di-GMP activates cellulose biosynthesis. Finally, overexpression of the syp regulator sypG induced binA expression. Thus, this work reveals a mechanism by which V. fischeri inhibits cellulose-dependent biofilm formation and suggests that the production of two different polysaccharides may be coordinated through the action of the cellulose inhibitor BinA.

Staphylococcal biofilms impair wound healing by delaying reepithelialization in a murine cutaneous wound model

Bacterial biofilms have gained increasing visibility in recent years as a ubiquitous form of survival for microorganisms in myriad environments. A number of in vivo models exist for the study of biofilms in the setting of medically relevant implanted foreign bodies. Growing evidence has demonstrated the presence of bacterial biofilms in the setting of a number of chronic wound states including pressure sores, diabetic foot ulcers, and venous stasis ulcers. Here we present a novel murine cutaneous wound system that directly demonstrates delayed reepithelialization caused by the presence of a bacterial biofilm. We established biofilms using either Staphylococcus aureus or Staphylococcus epidermidis in splinted cutaneous punch wounds created on the backs of normal C57Bl6/J mice. Wound reepithelialization was significantly delayed by bacterial biofilms. This effect was specifically dependent on the ability of the bacteria to form biofilms as demonstrated by exogenous administration of biofilm inhibiting peptides and the use of mutant Staphylococcus spp. deficient in biofilm formation. This represents the first direct evidence for the effect of bacterial biofilms on cutaneous wound healing.

In situ bioremediation in heterogeneous porous media: dispersion-limited scenario

A quantitative framework based on a set of dimensionless numbers was developed to capture the effects of competing interfacial and biokinetic processes and define limits on the application of in situ bioremediation. An integrated numerical modeling and experimental approach was utilized to evaluate the quantitative framework. Experiments were conducted to examine the transport and biodegradation of naphthalene in a saturated, heterogeneous intermediate-scale flow cell with two layers of contrasting hydraulic conductivities. The experiments were carried out in two phases: Phase I, simulating intrinsic biodegradation; and Phase II, simulating an engineered in situ bioremediation. In Phase I, dispersion was identified as the overall rate-limiting process based on the proposed quantitative framework. Two engineered perturbations to the system were selected in Phase II to examine their abilities to enhance in situ biodegradation. In the first perturbation, nitrogen and phosphorus were spiked into the influent solution in excess of the required stoichiometric amounts. This perturbation did not have a significant impact because dispersion, not biokinetics, was the overall rate-limiting process. However, in the second perturbation, advection was increased, resulting in increased longitudinal and vertical transverse dispersion, thereby alleviating the rate-limiting process, and enhancing the overall biotransformation rate.

Yersinia pestis biofilm in the flea vector and its role in the transmission of plague

Transmission by fleabite is a relatively recent evolutionary adaptation of Yersinia pestis, the bacterial agent of bubonic plague. To produce a transmissible infection, Y. pestis grows as an attached biofilm in the foregut of the flea vector. Biofilm formation both in the flea foregut and in vitro is dependent on an extracellular matrix (ECM) synthesized by the Yersinia hms gene products. The hms genes are similar to the pga and ica genes of Escherichia coli and Staphylococcus epidermidis, respectively, that act to synthesize a poly-beta-1,6-N-acetyl-d-glucosamine ECM required for biofilm formation. As with extracellular polysaccharide production in many other bacteria, synthesis of the Hms-dependent ECM is controlled by intracellular levels of cyclic-di-GMP. Yersinia pseudotuberculosis, the food- and water-borne enteric pathogen from which Y. pestis evolved recently, possesses identical hms genes and can form biofilm in vitro but not in the flea. The genetic changes in Y. pestis that resulted in adapting biofilm-forming capability to the flea gut environment, a critical step in the evolution of vector-borne transmission, have yet to be identified. During a flea bite, Y. pestis is regurgitated into the dermis in a unique biofilm phenotype, and this has implications for the initial interaction with the mammalian innate immune response.

The yjbEFGH locus in Escherichia coli K-12 is an operon encoding proteins involved in exopolysaccharide production

The RcsCDB phosphorelay was originally identified as the main regulator of colanic acid biosynthesis in Escherichia coli K-12. However, recent transcriptomic analyses have identified more than 150 genes belonging to the Rcs regulon, including yjbE, yjbF, yjbG and yjbH. These genes are clustered on the genome and oriented in the same direction but their function remains unknown. In this work it is shown that yjbE, yjbF, yjbG and yjbH are transcribed as a single operon and it is confirmed that the expression of this operon is controlled by the Rcs phosphorelay, in a manner that is dependent on the auxiliary regulatory protein RcsA. Interestingly, Northern blot analysis revealed that the amount of yjbE transcripts in the cell is higher than the amount of yjbEFGH transcripts and it is proposed that this differential expression is mediated by the presence of a strong stem-loop structure in the yjbE-yjbF intergenic region. Finally, evidence is provided that the overexpression of yjbEFGH affects colony morphology and leads to the production of an extracellular polysaccharide that binds Congo red and toluidine blue-O.

Polyamines are essential for the formation of plague biofilm

We provide the first evidence for a link between polyamines and biofilm levels in Yersinia pestis, the causative agent of plague. Polyamine-deficient mutants of Y. pestis were generated with a single deletion in speA or speC and a double deletion mutant. The genes speA and speC code for the biosynthetic enzymes arginine decarboxylase and ornithine decarboxylase, respectively. The level of the polyamine putrescine compared to the parental speA+ speC+ strain (KIM6+) was depleted progressively, with the highest levels found in the Y. pestis DeltaspeC mutant (55% reduction), followed by the DeltaspeA mutant (95% reduction) and the DeltaspeA DeltaspeC mutant (>99% reduction). Spermidine, on the other hand, remained constant in the single mutants but was undetected in the double mutant. The growth rates of mutants with single deletions were not altered, while the DeltaspeA DeltaspeC mutant grew at 65% of the exponential growth rate of the speA+ speC+ strain. Biofilm levels were assayed by three independent measures: Congo red binding, crystal violet staining, and confocal laser scanning microscopy. The level of biofilm correlated to the level of putrescine as measured by high-performance liquid chromatography-mass spectrometry and as observed in a chemical complementation curve. Complementation of the DeltaspeA DeltaspeC mutant with speA showed nearly full recovery of biofilm to levels observed in the speA+ speC+ strain. Chemical complementation of the double mutant and recovery of the biofilm defect were only observed with the polyamine putrescine.

The phosphodiesterase activity of the HmsP EAL domain is required for negative regulation of biofilm formation in Yersinia pestis

In Yersinia pestis, biofilm formation is stimulated by HmsT, a GGDEF-domain containing protein that synthesizes cyclic-di-GMP (c-di-GMP), and inhibited by HmsP, an EAL-domain protein. Only the EAL-domain portion of HmsP is required to inhibit biofilm formation. The EAL domain of HmsP was purified as a 6XHis-tag fusion protein and demonstrated to have phosphodiesterase activity using bis(p-nitrophenyl) phosphate (bis-pNPP) as a substrate. This enzymatic activity was strictly manganese dependent. A critical residue (E506) of HmsP within the EAL domain, that is required for inhibition of biofilm formation, is also essential for this phosphodiesterase activity. While the proposed function of EAL-domain proteins is to linearize c-di-GMP, this is a direct demonstration of the required phosphodiesterase activity of a purified EAL-domain protein.

Novel mouse model of chronic Pseudomonas aeruginosa lung infection mimicking cystic fibrosis

Pseudomonas aeruginosa causes a chronic infection in the lungs of cystic fibrosis (CF) patients by establishing an alginate-containing biofilm. The infection has been studied in several animal models; however, most of the models required artificial embedding of the bacteria. We present here a new pulmonary mouse model without artificial embedding. The model is based on a stable mucoid CF sputum isolate (NH57388A) with hyperproduction of alginate due to a deletion in mucA and functional N-acylhomoserine lactone (AHL)-based quorum-sensing systems. Chronic lung infection could be established in both CF mice (Cftr(tmlUnc-/-)) and BALB/c mice, as reflected by the detection of a high number of P. aeruginosa organisms in the lung homogenates at 7 days postinfection and alginate biofilms, surrounded by polymorphonuclear leukocytes in the alveoli. In comparison, both an AHL-producing nonmucoid revertant (NH57388C) from the mucoid isolate (NH57388A) and a nonmucoid isolate (NH57388B) deficient in AHL were almost cleared from the lungs of the mice. This model, in which P. aeruginosa is protected against the defense system of the lung by alginate, is similar to the clinical situation. Therefore, the mouse model provides an improved method for evaluating the interaction between mucoid P. aeruginosa, the host, and antibacterial therapy.

HmsP, a putative phosphodiesterase, and HmsT, a putative diguanylate cyclase, control Hms-dependent biofilm formation in Yersinia pestis

The Hms(+) phenotype of Yersinia pestis promotes the binding of haemin or Congo red (CR) to the cell surface at temperatures below 34 degrees C. We previously demonstrated that temperature regulation of the Hms(+) phenotype is not controlled at the level of transcription. Instead, HmsH, HmsR and HmsT are degraded upon a temperature shift from 26 degrees C to 37 degrees C. We used random transposon mutagenesis to identify new genes involved in the temperature-regulated expression of the Hms phenotype. One of these genes, which we designated hmsP, encodes a putative phosphodiesterase with a conserved EAL motif. Mutations in hmsP caused formation of red colonies on CR plates at 26 degrees C and 37 degrees C. Strains complemented with hmsP(+) on a plasmid form white colonies at both temperatures. We used a crystal violet assay and confocal laser scanning microscopy to demonstrate Hms-dependent biofilm formation by Y. pestis cells. Y. pestis Hms(+) strains grown at 26 degrees C but not at 37 degrees C form a biofilm on borosilicate glass surfaces. Strains that either overexpress HmsT (a GGDEF domain protein) or have a mutation in hmsP produced an extremely thick biofilm. Alanine substitutions for each of the GGEE residues (amino acids 296-299) of HmsT as well as the E506 and L508 residues of HmsP caused a loss of function. We propose that HmsT and HmsP together control the amount of biofilm produced in Y. pestis. Degradation of HmsT at 37 degrees C may be a critical factor in controlling the temperature-dependent expression of the Hms biofilm.

Biofilm formation at the air-liquid interface by the Pseudomonas fluorescens SBW25 wrinkly spreader requires an acetylated form of cellulose

The wrinkly spreader (WS) genotype of Pseudomonas fluorescens SBW25 colonizes the air-liquid interface of spatially structured microcosms resulting in formation of a thick biofilm. Its ability to colonize this niche is largely due to overproduction of a cellulosic polymer, the product of the wss operon. Chemical analysis of the biofilm matrix shows that the cellulosic polymer is partially acetylated cellulose, which is consistent with predictions of gene function based on in silico analysis of wss. Both polar and non-polar mutations in the sixth gene of the wss operon (wssF ) or adjacent downstream genes (wssGHIJ ) generated mutants that overproduce non-acetylated cellulose, thus implicating WssFGHIJ in acetylation of cellulose. WssGHI are homologues of AlgFIJ from P. aeruginosa, which together are necessary and sufficient to acetylate alginate polymer. WssF belongs to a newly established Pfam family and is predicted to provide acyl groups to WssGHI. The role of WssJ is unclear, but its similarity to MinD-like proteins suggests a role in polar localization of the acetylation complex. Fluorescent microscopy of Calcofluor-stained biofilms revealed a matrix structure composed of networks of cellulose fibres, sheets and clumped material. Quantitative analyses of biofilm structure showed that acetylation of cellulose is important for effective colonization of the air-liquid interface: mutants identical to WS, but defective in enzymes required for acetylation produced biofilms with altered physical properties. In addition, mutants producing non-acetylated cellulose were unable to spread rapidly across solid surfaces. Inclusion in these assays of a WS mutant with a defect in the GGDEF regulator (WspR) confirmed the requirement for this protein in expression of both acetylated cellulose polymer and bacterial attachment. These results suggest a model in which WspR regulation of cellulose expression and attachment plays a role in the co-ordination of surface colonization.

Structure and carbohydrate analysis of the exopolysaccharide capsule of Pseudomonas putida G7

The aromatic hydrocarbon-degrading bacterium, Pseudomonas putida G7, produces exopolymers of potential interest in biotechnological applications. These exopolymers have been shown to have significant metal-binding ability. To initiate the study of the metal-polymer interactions, we explored the physical and chemical nature of the P. putida G7 exopolysaccharide, a major component of the exopolymer. A capsular structure was observed by light microscopy surrounding both planktonic and attached cells in biofilms after immunofluorescence staining with polyclonal antiserum raised against planktonic cells. Further work with planktonic cells showed that the immunostained capsule remained associated with young (log phase) cells, whereas older (stationary phase) cells lost their capsular material to the external milieu. Visualization of frozen, hydrated stationary phase cells by cryo-field emission scanning electron microscopy (cryoFESEM) revealed highly preserved extracellular material. In contrast, conventional scanning electron microscopy (SEM) of stationary phase cells showed rope-like material that most probably results from dehydrated and collapsed exopolymer. Both capsular and released exopolymers were separated from cells, and the released extracellular polysaccharide (EPS) was purified. Deoxycholate-polyacrylamide gel electrophoresis (PAGE) and silver/alcian blue staining of the partially purified material showed that it contained both EPS and lipopolysaccharide (LPS). Further purification of the EPS using a differential solubilization technique to remove LPS yielded highly purified EPS. Gas chromatography-mass spectrometry revealed that the purified EPS contained the monosaccharides, glucose, rhamnose, ribose, N-acetylgalactosamine and glucuronic acid. The structural and chemical properties of the P. putida EPS described here increase our understanding of the mechanisms of toxic metal binding by this well-known Proteobacterium.