Spatial patterns of alkaline phosphatase expression within bacterial colonies and biofilms in response to phosphate starvation

Antibiotic Resistant Biofilms and the Quest for Novel Therapeutic Strategies

Antimicrobial resistance (AMR) is one of the major leading causes of death around the globe. Present treatment pipelines are insufficient to overcome the critical situation. Prominent biofilm forming human pathogens which can thrive in infection sites using adaptive features results in biofilm persistence. Considering the present scenario, prudential investigations into the mechanisms of resistance target them to improve antibiotic efficacy is required. Regarding this, developing newer and effective treatment options using edge cutting technologies in medical research is the need of time. The reasons underlying the adaptive features in biofilm persistence have been centred on different metabolic and physiological aspects. The high tolerance levels against antibiotics direct researchers to search for novel bioactive molecules that can help combat the problem. In view of this, the present review outlines the focuses on an opportunity of different strategies which are in testing pipeline can thus be developed into products ready to use.

Effect of Size, Shape and Surface Functionalization on the Antibacterial Activity of Silver Nanoparticles

Silver nanoparticles (AgNPs) are the most investigated antibacterial agents against multidrug resistant (MDR) pathogens. They can lead to cellular death by means of different mechanisms, damaging several cell compartments, from the external membrane, to enzymes, DNA and proteins; this simultaneous attack amplifies the toxic effect on bacteria with respect to traditional antibiotics. The effectiveness of AgNPs against MDR bacteria is strongly correlated with their chemical and morphological properties, which influence the pathways involved in cellular damage. In this review, AgNPs' size, shape and modification by functional groups or other materials are reported, both to investigate the different synthetic pathways correlated with nanoparticles' modifications and to evaluate the related effect on their antibacterial activity. Indeed, understanding the synthetic conditions for obtaining performing antibacterial AgNPs could help to tailor new and improved silver-based agents to combat multidrug resistance.

Serrapeptase impairs biofilm, wall, and phospho-homeostasis of resistant and susceptible Staphylococcus aureus

Staphylococcus aureus biofilms are implicated in hospital infections due to elevated antibiotic and host immune system resistance. Molecular components of cell wall including amyloid proteins, peptidoglycans (PGs), and lipoteichoic acid (LTA) are crucial for biofilm formation and tolerance of methicillin-resistant S. aureus (MRSA). Significance of alkaline phosphatases (ALPs) for biofilm formation has been recorded. Serrapeptase (SPT), a protease of Serratia marcescens, possesses antimicrobial properties similar or superior to those of many antibiotics. In the present study, SPT anti-biofilm activity was demonstrated against S. aureus (ATCC 25923, methicillin-susceptible strain, methicillin-susceptible S. aureus (MSSA)) and MRSA (ST80), with IC₅₀ values of 0.67 μg/mL and 7.70 μg/mL, respectively. SPT affected bacterial viability, causing a maximum inhibition of - 46% and - 27%, respectively. Decreased PGs content at [SPT] ≥ 0.5 μg/mL and ≥ 8 μg/mL was verified for MSSA and MRSA, respectively. In MSSA, LTA levels decreased significantly (up to - 40%) at lower SPT doses but increased at the highest dose of 2 μg/mL, a counter to spectacularly increased cellular and secreted LTA levels in MRSA. SPT also reduced amyloids of both strains. Additionally, intracellular ALP activity decreased in both MSSA and MRSA (up to - 85% and - 89%, respectively), while extracellular activity increased up to + 482% in MSSA and + 267% in MRSA. Altered levels of DING proteins, which are involved in phosphate metabolism, in SPT-treated bacteria, were also demonstrated here, implying impaired phosphorus homeostasis. The differential alterations in the studied molecular aspects underline the differences between MSSA and MRSA and offer new insights in the treatment of resistant bacterial biofilms. KEY POINTS: • SPT inhibits biofilm formation in methicillin-resistant and methicillin-susceptible S. aureus. • SPT treatment decreases bacterial viability, ALP activity, and cell wall composition. • SPT-treated bacteria present altered levels of phosphate-related DING proteins.

Outer Membrane Vesicles: Biogenesis, Functions, and Issues

This review focuses on nonlytic outer membrane vesicles (OMVs), a subtype of bacterial extracellular vesicles (BEVs) produced by Gram-negative organisms focusing on the mechanisms of their biogenesis, cargo, and function. Throughout, we highlight issues concerning the characterization of OMVs and distinguishing them from other types of BEVs. We also highlight the shortcomings of commonly used methodologies for the study of BEVs that impact the interpretation of their functionality and suggest solutions to standardize protocols for OMV studies.

Optimization of Sporulation Conditions for Bacillus subtilis BSNK-5

Bacillus subtilis spores have important biological applications; however, high spore-cell densities and sporulation efficiencies in fermentation is poorly reported. This study systematically analyzed the spore densities and formation efficiency of B. subtilis BSNK-5 in different culture substrates. A response surface regression equation was established based on the results of single factor and Box–Behnken experimental designs. The optimal medium formulation, as predicted from the equation, consisted of soluble starch at 3 g·L−1, soybean flour at 12 g·L−1, and MgSO4 at 5 g·L−1. The spore yield reached 2.43 × 109 CFU·mL−1, and the sporulation rate was 83.3%, which was nearly three times higher than before optimization using an optimized medium at 36 °C and 200 rpm for 60 h.

TCF-ALP: a fluorescent probe for the selective detection of Staphylococcus bacteria and application in "smart" wound dressings

Alkaline phosphatase (ALP) is an important enzyme-based biomarker present in several bacterial species; however, it is currently undervalued as a strategy to detect pathogenic bacteria. Here, we explore our ALP-responsive colorimetric and fluorescent probe (TCF-ALP) for such applications. TCF-ALP displayed a colorimetric and fluorescence response towards Staphylococcus aureus (S. aureus), with a limit of detection of 3.7 × 106 CFU mL-1 after 24 h incubation. To our surprise, TCF-ALP proved selective towards Staphylococcus bacteria when compared with Enterococcus faecalis (E. faecalis), and Gram-negative P. aeruginosa and E. coli. Selectivity was also seen in clinically relevant S. aureus biofilms. Owing to the high prevalence and surface location of S. aureus in chronic wounds, TCF-ALP was subsequently encapsulated in polyvinyl alcohol (PVA)-based hydrogels as a proof-of-concept "smart" wound dressing. TCF-ALP hydrogels were capable of detecting S. aureus in planktonic and biofilm assays, and displayed a clear colour change from yellow to purple after 24 h incubation using ex vivo porcine skin models. Overall, TCF-ALP is a simple tool that requires no prior knowledge, training, or specialist equipment, and has the potential to overcome issues related to invasive swabbing and tissue biopsy methods. Thus, TCF-ALP could be used as a tool to monitor the early development of infection in a wound and allow for the rapid provision of appropriate treatment for Staphylococcal bacterial infections.

DING Proteins Extend to the Extremophilic World

The DING proteins are ubiquitous in the three domains of life, from mesophiles to thermo- and hyperthermophiles. They belong to a family of more than sixty members and have a characteristic N-terminus, DINGGG, which is considered a "signature" of these proteins. Structurally, they share a highly conserved phosphate binding site, and a three dimensional organization resembling the "Venus Flytrap", both reminding the ones of PstS proteins. They have unusually high sequence conservation, even between distantly related species. Nevertheless despite that the genomes of most of these species have been sequenced, the DING gene has not been reported for all the relative characterized DING proteins. Identity of known DING proteins has been confirmed immunologically and, in some cases, by N-terminal sequence analysis. Only a few of the DING proteins have been purified and biochemically characterized. DING proteins are heterogeneous for their wide range of biological activities and some show different activities not always correlated with each other. Most of them have been originally identified for different biological properties, or rather for binding to phosphate and also to other ligands. Their involvement in pathologies is described. This review is an update of the most recent findings on old and new DING proteins.

Deferasirox (ExJade): An FDA-Approved AIEgen Platform with Unique Photophysical Properties

Deferasirox, ExJade, is an FDA-approved iron chelator used for the treatment of iron overload. In this work, we report several fluorescent deferasirox derivatives that display unique photophysical properties, i.e., aggregation-induced emission (AIE), excited state intramolecular proton transfer, charge transfer, and through-bond and through-space conjugation characteristics in aqueous media. Functionalization of the phenol units on the deferasirox scaffold afforded the fluorescent responsive pro-chelator ExPhos, which enabled the detection of the disease-based biomarker alkaline phosphatase (ALP). The diagnostic potential of these deferasirox derivatives was supported by bacterial biofilm studies.

In vitro and in silico evaluation of the inhibitory effect of a curcumin-based oxovanadium (IV) complex on alkaline phosphatase activity and bacterial biofilm formation

The scientific interest in the development of novel metal-based compounds as inhibitors of bacterial biofilm-related infections and alkaline phosphatase (ALP) deregulating effects is continuous and rising. In the current study, a novel crystallographically defined heteroleptic V(IV)-curcumin-bipyridine (V-Cur) complex with proven bio-activity was studied as a potential inhibitor of ALP activity and bacterial biofilm. The inhibitory effect of V-Cur was evaluated on bovine ALP, with two different substrates: para-nitrophenyl phosphate (pNPP) and adenosine triphosphate (ATP). The obtained results suggested that V-Cur inhibited the ALP activity in a dose-dependent manner (IC₅₀ = 26.91 ± 1.61 μM for ATP, IC₅₀ = 2.42 ± 0.12 μM for pNPP) exhibiting a mixed/competitive type of inhibition with both substrates tested. The evaluation of the potential V-Cur inhibitory effect on bacterial biofilm formation was performed on Gram (+) bacteria Staphylococcus aureus (S. aureus) and Gram (-) Escherichia coli (E. coli) cultures, and it positively correlated with inhibition of bacterial ALP activity. In silico study proved the binding of V-Cur at eukaryotic and bacterial ALP, and its interaction with crucial amino acids of the active sites, verifying complex's inhibitory potential. The findings suggested a specific anti-biofilm activity of V-Cur, offering a further dimension in the importance of metal complexes, with naturally derived products as biological ligands, as therapeutic agents against bacterial infections and ALP-associated diseases. KEY POINTS: • V-Cur inhibits bovine and bacterial alkaline phosphatases and bacterial biofilm formation. • Alkaline phosphatase activity correlates with biofilm formation. • In silico studies prove binding of the complex on alkaline phosphatase.

Nutrient Removal and Uptake by Native Planktonic and Biofilm Bacterial Communities in an Anaerobic Aquifer

Managed aquifer recharge (MAR) offers a collection of water storage and storage options that have been used by resource managers to mitigate the reduced availability of fresh water. One of these technologies is aquifer storage and recovery (ASR), where surface water is treated then recharged into a storage zone within an existing aquifer for later recovery and discharge into a body of water. During the storage phase of ASR, nutrient concentrations in the recharge water have been shown to decrease due, presumably via the uptake by the native aquifer microbial community. In this study, the native microbial community in an anaerobic carbonate aquifer zone targeted for ASR storage was segregated into planktonic and biofilm communities then challenged with NO₃-N, PO₄-P, and acetate as dissolved organic carbon (DOC) to determine their respective removal and uptake rates. The planktonic community removed NO₃-N at a rate of 0.059 mg L^–1d^–1, PO₄-P at 5.73 × 10^–8–1.03 × 10^–7 mg L^–1d^–1 and DOC at 0.015–0.244 mg L^–1d^–1. The biofilm community was significantly more proficient, removing NO₃-N at 0.116 mg L^–1d^–1 (1.6–9.0 μg m^–2d^–1), PO₄-P at 4.20–5.91 × 10^–5 mg L^–1d^–1 (2.47–9.88 ng m^–2d^–1) and DOC at 0.301–0.696 mg L^–1d^–1 (29.0–71.0 μg m^–2d^–1). Additionally, the PO₄-P sorption rate onto the carbonate aquifer matrix ranged from 1.64 × 10^–7 to 9.25 × 10^–7 mg PO₄-P m^–2 day^–1. These rates were applied to field data collected at an ASR facility in central Florida and from the same aquifer storage zone from which the biofilm communities were grown. With only 10% of the available surface area within the storage zone being colonized by biofilms, typical concentrations of NO₃-N, PO4-P, and DOC in the recharged filtered surface waters would be reduced to below detection limits, and by 81.4 and 91.1%, respectively, during a 150 days storage period.

High copper concentration reduces biofilm formation in Acidithiobacillus ferrooxidans by decreasing production of extracellular polymeric substances and its adherence to elemental sulfur

Acidithiobacillus ferrooxidans is an acidophilic bacterium able to grow in environments with high concentrations of metals. It is a chemolithoautotroph able to form biofilms on the surface of solid minerals to obtain its energy. The response of both planktonic and sessile cells of A. ferrooxidans ATCC 23270 grown in elemental sulfur and adapted to high copper concentration was analyzed by quantitative proteomics. It was found that 137 proteins varied their abundance when comparing both lifestyles. Copper effllux proteins, some subunits of the ATP synthase complex, porins, and proteins involved in cell wall modification increased their abundance in copper-adapted sessile lifestyle cells. On the other hand, planktonic copper-adapted cells showed increased levels of proteins such as: cupreredoxins involved in copper cell sequestration, some proteins related to sulfur metabolism, those involved in biosynthesis and transport of lipopolysaccharides, and in assembly of type IV pili. During copper adaptation a decreased formation of biofilms was measured as determined by epifluorescence microscopy. This was apparently due not only to a diminished number of sessile cells but also to their exopolysaccharides production. This is the first study showing that copper, a prevalent metal in biomining environments causes dispersion of A. ferrooxidans biofilms. SIGNIFICANCE: Copper is a metal frequently found in high concentrations at mining environments inhabitated by acidophilic microorganisms. Copper resistance determinants of A. ferrooxidans have been previously studied in planktonic cells. Although biofilms are recurrent in these types of environments, the effect of copper on their formation has not been studied so far. The results obtained indicate that high concentrations of copper reduce the capacity of A. ferrooxidans ATCC 23270 to form biofilms on sulfur. These findings may be relevant to consider for a bacterium widely used in copper bioleaching processes.

Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis biofilms

Stochastic pulsing of gene expression can generate phenotypic diversity in a genetically identical population of cells, but it is unclear whether it has a role in the development of multicellular systems. Here, we show how stochastic pulsing of gene expression enables spatial patterns to form in a model multicellular system, Bacillus subtilis bacterial biofilms. We use quantitative microscopy and time-lapse imaging to observe pulses in the activity of the general stress response sigma factor σ^B in individual cells during biofilm development. Both σ^B and sporulation activity increase in a gradient, peaking at the top of the biofilm, even though σ^B represses sporulation. As predicted by a simple mathematical model, increasing σ^B expression shifts the peak of sporulation to the middle of the biofilm. Our results demonstrate how stochastic pulsing of gene expression can play a key role in pattern formation during biofilm development.

Stochastic pulsing of gene expression can generate phenotypic diversity in a genetically identical population of cells. Here, the authors show that stochastic pulsing in the expression of a sigma factor enables the formation of spatial patterns in a multicellular system, Bacillus subtilis bacterial biofilms.

Single microcolony diffusion analysis in Pseudomonas aeruginosa biofilms

The influence of the biofilm matrix on molecular diffusion is commonly hypothesized to be responsible for emergent characteristics of biofilms such as nutrient trapping, signal accumulation and antibiotic tolerance. Hence quantifying the molecular diffusion coefficient is important to determine whether there is an influence of biofilm microenvironment on the mobility of molecules. Here, we use single plane illumination microscopy fluorescence correlation spectroscopy (SPIM-FCS) to obtain 3D diffusion coefficient maps with micrometre spatial and millisecond temporal resolution of entire Pseudomonas aeruginosa microcolonies. We probed how molecular properties such as size and charge as well as biofilm properties such as microcolony size and depth influence diffusion of fluorescently labelled dextrans inside biofilms. The 2 MDa dextran showed uneven penetration and a reduction in diffusion coefficient suggesting that the biofilm acts as a molecular sieve. Its diffusion coefficient was negatively correlated with the size of the microcolony. Positively charged dextran molecules and positively charged antibiotic tobramycin preferentially partitioned into the biofilm and remained mobile inside the microcolony, albeit with a reduced diffusion coefficient. Lastly, we measured changes of diffusion upon induction of dispersal and detected an increase in diffusion coefficient inside the biofilm before any loss of biomass. Thus, the change in diffusion is a proxy to detect early stages of dispersal. Our work shows that 3D diffusion maps are very sensitive to physiological changes in biofilms, viz. dispersal. However, this study also shows that diffusion, as mediated by the biofilm matrix, does not account for the high level of antibiotic tolerance associated with biofilms.

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.

Rapid detection of Escherichia coli in beverages using genetically engineered bacteriophage T7

Foodborne illness due to bacterial contamination is a significant issue impacting public health that demands new technology which is practical to implement by food industry. Detection of bacteria in food products and production facilities is a crucial strategy supporting food safety assessments. Bacteriophages were investigated as a tool for bacterial detection due to their ability to infect specific strain of host bacteria in order to improve sensitivity, specificity, and rapidity of bacterial detection. The results of this investigation reveal a novel method for rapid detection. The method employs a genetically engineered bacteriophage, phage T7-ALP, which expresses alkaline phosphatase. Upon infection of Escherichia coli, overexpression of alkaline phosphatase provides an opportunity for rapid sensitive detection of a signal indicative of bacterial presence in model beverage samples as low as 100 bacteria per gram. The method employs a fluorescent precipitated substrate, ELF-97, as a substrate for alkaline phosphatase activity coupled with fluorescence imaging and image analysis allowing single-cell imaging results in high detection sensitivity. The method is easily completed within less than 6 h enabling it to be deployed within most large industrial food processing facilities that have routine 8-h operational shifts.

Phosphate deficiency induced biofilm formation of Burkholderia on insoluble phosphate granules plays a pivotal role for maximum release of soluble phosphate

Involvement of biofilm formation process during phosphate (P) solubilization by rhizobacterial strains is not clearly understood. Scanning electron microscopic observations revealed prominent biofilm development on tricalcium phosphate as well as on four different rock phosphate granules by two P solubilizing rhizobacteria viz. Burkholderia tropica P4 and B. unamae P9. Variation in the biofilm developments were also observed depending on the total P content of insoluble P used. Biofilm quantification suggested a strong correlation between the amounts of available P and degrees of biofilm formation. Lower concentrations of soluble P directed both the organisms towards compact biofilm development with maximum substratum coverage. Variation in the production of extracellular polymeric substances (EPS) in the similar pattern also suggested its close relationship with biofilm formation by the isolates. Presence of BraI/R quorum sensing (QS) system in both the organisms were detected by PCR amplification and sequencing of two QS associated genes viz. braR and rsaL, which are probably responsible for biofilm formation during P solubilization process. Overall observations help to hypothesize for the first time that, biofilm on insoluble P granules creates a close environment for better functioning of organic acids secreted by Burkholderia strains for maximum P solubilization during P deficient conditions.

Mineral Ecology: Surface Specific Colonization and Geochemical Drivers of Biofilm Accumulation, Composition, and Phylogeny

This study tests the hypothesis that surface composition influences microbial community structure and growth of biofilms. We used laboratory biofilm reactors (inoculated with a diverse subsurface community) to explore the phylogenetic and taxonomic variability in microbial communities as a function of surface type (carbonate, silicate, aluminosilicate), media pH, and carbon and phosphate availability. Using high-throughput pyrosequencing, we found that surface type significantly controlled ~70–90% of the variance in phylogenetic diversity regardless of environmental pressures. Consistent patterns also emerged in the taxonomy of specific guilds (sulfur-oxidizers/reducers, Gram-positives, acidophiles) due to variations in media chemistry. Media phosphate availability was a key property associated with variation in phylogeny and taxonomy of whole reactors and was negatively correlated with biofilm accumulation and α-diversity (species richness and evenness). However, mineral-bound phosphate limitations were correlated with less biofilm. Carbon added to the media was correlated with a significant increase in biofilm accumulation and overall α-diversity. Additionally, planktonic communities were phylogenetically distant from those in biofilms. All treatments harbored structurally (taxonomically and phylogenetically) distinct microbial communities. Selective advantages within each treatment encouraged growth and revealed the presence of hundreds of additional operational taxonomix units (OTU), representing distinct consortiums of microorganisms. Ultimately, these results provide evidence that mineral/rock composition significantly influences microbial community structure, diversity, membership, phylogenetic variability, and biofilm growth in subsurface communities.

The Stringent Response Promotes Antibiotic Resistance Dissemination by Regulating Integron Integrase Expression in Biofilms

Class 1 integrons are genetic systems that enable bacteria to capture and express gene cassettes. These integrons, when isolated in clinical contexts, most often carry antibiotic resistance gene cassettes. They play a major role in the dissemination of antibiotic resistance among Gram-negative bacteria. The key element of integrons is the integrase, which allows gene cassettes to be acquired and shuffled. Planktonic culture experiments have shown that integrase expression is regulated by the bacterial SOS response. In natural settings, however, bacteria generally live in biofilms, which are characterized by strong antibiotic resilience and by increased expression of stress-related genes. Here, we report that under biofilm conditions, the stringent response, which is induced upon starvation, (i) increases basal integrase and SOS regulon gene expression via induction of the SOS response and (ii) exerts biofilm-specific regulation of the integrase via the Lon protease. This indicates that biofilm environments favor integron-mediated acquisition of antibiotic resistance and other adaptive functions encoded by gene cassettes.

Multidrug-resistant bacteria are becoming a worldwide health problem. Integrons are bacterial genetic platforms that allow the bacteria to capture and express gene cassettes. In clinical settings, integrons play a major role in the dissemination of antibiotic resistance gene cassettes among Gram-negative bacteria. Cassette capture is catalyzed by the integron integrase, whose expression is induced by DNA damage and controlled by the bacterial SOS response in laboratory planktonic cultures. In natural settings, bacteria usually grow in heterogeneous environments known as biofilms, which have very different conditions than planktonic cultures. Integrase regulation has not been investigated in biofilms. Our results showed that in addition to the SOS response, the stringent response (induced upon starvation) is specifically involved in the regulation of class 1 integron integrases in biofilms. This study shows that biofilms are favorable environments for integron-mediated acquisition/exchange of antibiotic resistance genes by bacteria and for the emergence of multidrug-resistant bacteria.

Colonization of Abiotic Surfaces

E. coli is a relevant model organism for the study of the molecular mechanisms underlying surface colonization. This process requires two essential steps: adhesion to a surface, followed by cell-cell adhesion counteracting the shear forces of the environment, with both steps contributing to the formation of a biofilm. This review provides an overview of the current knowledge of the genetic analyses aiming at identifying factors involved in both of these two highly related biological processes, with a particular emphasis on studies performed in Escherichia coli K-12. Bacterial adhesion to abiotic surfaces is likely to be highly dependent on the physicochemical and electrostatic interactions between the bacterial envelope and the substrate, which is itself often conditioned by the fluids to which it is exposed. Genetic analyses have revealed the diversity of genetic factors in E. coli that participate in colonization and biofilm formation on abiotic surfaces. The study of surface colonization and biofilm formation represents a rapidly expanding field of investigation. The use of E. coli K-12 to investigate the genetic basis of bacterial interactions with surfaces has led to the identification of a large repertoire of adhesins whose expression is subject to a complex interplay between regulatory networks. Understanding how E. coli K-12 behaves in complex biofilm communities will certainly contribute to an understanding of how natural commensal and pathogenic E. coli isolates develop.

Biofilm-related infections: bridging the gap between clinical management and fundamental aspects of recalcitrance toward antibiotics

Surface-associated microbial communities, called biofilms, are present in all environments. Although biofilms play an important positive role in a variety of ecosystems, they also have many negative effects, including biofilm-related infections in medical settings. The ability of pathogenic biofilms to survive in the presence of high concentrations of antibiotics is called "recalcitrance" and is a characteristic property of the biofilm lifestyle, leading to treatment failure and infection recurrence. This review presents our current understanding of the molecular mechanisms of biofilm recalcitrance toward antibiotics and describes how recent progress has improved our capacity to design original and efficient strategies to prevent or eradicate biofilm-related infections.

Classification of phenotypic subpopulations in isogenic bacterial cultures by triple promoter probing at single cell level

Phenotypic heterogeneity, defined as the unequal behavior of individuals in an isogenic population, is prevalent in microorganisms. It has a significant impact both on industrial bioprocesses and microbial ecology. We introduce a new versatile reporter system designed for simultaneous monitoring of the activities of three different promoters, where each promoter is fused to a dedicated fluorescent reporter gene (cerulean, mCherry, and mVenus). The compact 3.1 kb triple reporter cassette can either be carried on a replicating plasmid or integrated into the genome avoiding artifacts associated with variation in copy number of plasmid-borne reporter constructs. This construct was applied to monitor promoter activities related to quorum sensing (sinI promoter) and biosynthesis of the exopolysaccharide galactoglucan (wgeA promoter) at single cell level in colonies of the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti growing in a microfluidics system. The T5-promoter served as a constitutive and homogeneously active control promoter indicating cell viability. wgeA promoter activity was heterogeneous over the whole period of colony development, whereas sinI promoter activity passed through a phase of heterogeneity before becoming homogeneous at late stages. Although quorum sensing-dependent regulation is a major factor activating galactoglucan production, activities of both promoters did not correlate at single cell level. We developed a novel mathematical strategy for classification of the gene expression status in cell populations based on the increase in fluorescence over time in each individual. With respect to galactoglucan biosynthesis, cells in the population were classified into non-contributors, weak contributors, and strong contributors.

Successional change in microbial communities of benthic Phormidium-dominated biofilms

Benthic cyanobacterial blooms are increasing worldwide and can be harmful to human and animal health if they contain toxin-producing species. Microbial interactions are important in the formation of benthic biofilms and can lead to increased dominance and/or toxin production of one or few taxa. This study investigated how microbial interactions contribute to proliferation of benthic blooms dominated by the neurotoxin-producing Phormidium autumnale. Following a rainfall event that cleared the substrate, biofilm succession was characterised at a site on the Hutt River (New Zealand) by sampling every 2-3 days over 32 days. A combination of morphological and molecular community analyses (automated ribosomal intergenic spacer analysis and Illumina™ MiSeq sequencing) identified three distinct phases of succession in both the micro-algal and bacterial communities within P. autumnale-dominated biofilms. Bacterial composition shifted between the phases, and these changes occurred several days before those of the micro-algal community. Alphaproteobacteria and Betaproteobacteria dominate in the early phase; Alphaproteobacteria, Betaproteobacteria, Sphingobacteria and Flavobacteria in the mid-phase; and Sphingobacteria and Flavobacteria in the late phase. Collectively, the results suggest that succession is driven by bacteria in the early stages but becomes dependent on micro-algae in the mid- and late stages of biofilm formation.

Fabrication of biomimetically patterned surfaces and their application to probing plant-bacteria interactions

We have developed a two-step replica molding method for rapid fabrication of biomimetically patterned plant surfaces (BPS) using polydimethylsiloxane (PDMS-BPS) and agarose (AGAR-BPS). Beyond providing multiple identical specimens that faithfully reproduce leaf surface microstructure, this approach also offers unique chemical, physical, and biological features. PDMS-BPS provide good structural durability for SEM examination, have surface wettability comparable to plant surfaces for coating development, and allow for real-time monitoring of biosynthesis through incorporation into microfluidic devices. AGAR-BPS are compatible with bacterial growth, recovery, and quantification, and enable investigation of the effects of surface topography on spatially varying survival and inactivation of Escherichia coli cells during biocide treatment. Further development and application of these biomimetically patterned surfaces to study (and possibly modify) other aspects of plant-bacteria interactions can provide insight into controlling pathogen contamination in a wide range of applications.

The behavior of organic phosphorus under non-point source wastewater in the presence of phototrophic periphyton

To understand the role of ubiquitous phototrophic periphyton in aquatic ecosystem on the biogeochemical cycling of organic phosphorus, the conversion and removal kinetic characteristics of organic phosphorus (Porg) such as adenosine triphosphate (ATP) were investigated in the presence of the periphyton cultured in artificial non-point source wastewater. The preliminary results showed that the periphyton was very powerful in converting P_org evidenced by the fact that inorganic phosphorus (P_inorg) content in solution increased from about 0.7 to 14.3 mg P L⁻¹ in 48 hours in the presence of 0.6 g L⁻¹ periphyton. This was because the periphyton could produce abundant phosphatases that benefited the conversion of P_org to P_inrog. Moreover, this conversion process was described more suitable by the pseudo-first-order kinetic model. The periphyton was also effective in removing P_org, which showed that the P_org can be completely removed even when the initial P_org concentration was as high as 13 mg P L⁻¹ in 48 hours in the presence of 1.6 g L⁻¹ periphyton. Furthermore, it was found that biosorption dominated the P_org removal process and exhibited the characteristics of physical adsorption. However, this biosorption process by the periphyton was significantly influenced by biomass (absorbent dosage) and temperature. This work provides insights into P_org biogeochemical circulation of aquatic ecosystem that contained the periphyton or similar microbial aggregates.

Rapid evolution of culture-impaired bacteria during adaptation to biofilm growth

Biofilm growth increases the fitness of bacteria in harsh conditions. However, bacteria from clinical and environmental biofilms can exhibit impaired growth in culture, even when the species involved are readily culturable and permissive conditions are used. Here, we show that culture-impaired variants of Pseudomonas aeruginosa arise rapidly and become abundant in laboratory biofilms. The culture-impaired phenotype is caused by mutations that alter the outer-membrane lipopolysaccharide structure. Within biofilms, the lipopolysaccharide mutations markedly increase bacterial fitness. However, outside the protected biofilm environment, the mutations sensitize the variants to killing by a self-produced antimicrobial agent. Thus, a biofilm-mediated adaptation produces a stark fitness trade-off that compromises bacterial survival in culture. Trade-offs like this could limit the ability of bacteria to transition between biofilm growth and the free-living state and produce bacterial populations that escape detection by culture-based sampling.

Spatial distribution and expression of intracellular and extracellular acid phosphatases of cluster roots at different developmental stages in white lupin

Acid phosphatases (APases) play a key role in phosphorus (P) acquisition and recycling in plants. White lupin (Lupinus albus L.) forms cluster roots (CRs) and produces large amounts of APases under P deficiency. However, the relationships between the activity of intracellular and extracellular APases (EC 3.1.3.2) and CR development are not fully understood. Here, comparative studies were conducted to examine the spatial variation pattern of APase activity during CR development using the enzyme-labelled fluorescence-97 (ELF-97) and the p-nitrophenyl phosphate methods. The activity of intracellular and extracellular APases was significantly enhanced under P deficiency in the non-CRs and CRs at different developmental stages. These two APases exhibited different spatial distribution patterns during CR development, and these distribution patterns were highly modified by P deficiency. The activity of extracellular APase increased steadily with CR development from meristematic, juvenile, mature to senescent stages under P deficiency. In comparison, P deficiency-induced increase in the activity of intracellular APase remained relatively constant during CR development. Increased activity of intracellular and extracellular APases was associated with enhanced expression of LaSAP1 encoding intracellular APase and LaSAP2 encoding extracellular APase. The expression levels of these two genes were significantly higher at transcriptional level in both mature and senescent CRs. Taken together, these findings demonstrate that both activity and gene expression of intracellular or extracellular APases exhibit a differential response pattern during CR development, depending on root types, CR developmental stages and P supply. Simultaneous in situ determination of intracellular and extracellular APase activity has proved to be an effective approach for studying spatial variation of APases during CR development.

Heterogeneity in Pseudomonas aeruginosa biofilms includes expression of ribosome hibernation factors in the antibiotic-tolerant subpopulation and hypoxia-induced stress response in the metabolically active population

Bacteria growing in biofilms are physiologically heterogeneous, due in part to their adaptation to local environmental conditions. Here, we characterized the local transcriptome responses of Pseudomonas aeruginosa growing in biofilms by using a microarray analysis of isolated biofilm subpopulations. The results demonstrated that cells at the top of the biofilms had high mRNA abundances for genes involved in general metabolic functions, while mRNA levels for these housekeeping genes were low in cells at the bottom of the biofilms. Selective green fluorescent protein (GFP) labeling showed that cells at the top of the biofilm were actively dividing. However, the dividing cells had high mRNA levels for genes regulated by the hypoxia-induced regulator Anr. Slow-growing cells deep in the biofilms had little expression of Anr-regulated genes and may have experienced long-term anoxia. Transcripts for ribosomal proteins were associated primarily with the metabolically active cell fraction, while ribosomal RNAs were abundant throughout the biofilms, indicating that ribosomes are stably maintained even in slowly growing cells. Consistent with these results was the identification of mRNAs for ribosome hibernation factors (the rmf and PA4463 genes) at the bottom of the biofilms. The dormant biofilm cells of a P. aeruginosa Δrmf strain had decreased membrane integrity, as shown by propidium iodide staining. Using selective GFP labeling and cell sorting, we show that the dividing cells are more susceptible to killing by tobramycin and ciprofloxacin. The results demonstrate that in thick P. aeruginosa biofilms, cells are physiologically distinct spatially, with cells deep in the biofilm in a viable but antibiotic-tolerant slow-growth state.

Anti-cariogenic effect of a cetylpyridinium chloride-containing nanoemulsion

OBJECTIVES

The aim of this pilot study was to investigate the anticaries activity of a nanoemulsion composed of soybean oil, water, Triton X-100 and cetylpyridinium chloride.

METHODS

Tooth blocks (3 mm length x 3 mm width x 2 mm thickness) were cut from smooth surfaces of selected molar teeth using a water-cooled diamond wire saw. The blocks were randomly assigned to three experimental groups: (A) nanoemulsion, (B) 0.12% chlorhexidine gluconate, and (C) no treatment. The formation of dental caries in human tooth enamel was tested using a continuous flow dual-organism (Streptococcus mutans and Lactobacillus casei), biofilm model, which acts as an artificial mouth and simulates the biological and physiological activities observed within the oral environment. Experimental groups A and B were treated with their respective solutions once daily for 30 s on each occasion, while group C received no treatment. 10% sucrose was supplied every 6 h for 6 min to simulate meals and pH cycling. The experiment lasted for 5 days, and the tooth blocks were harvested and processed for demineralization assessment using transverse microradiography (TMR).

RESULTS

For both lesion depth and mineral loss, statistical analysis indicated that Emulsion was significantly lower than Control and Chlorhexidine, and Chlorhexidine was significantly lower than Control.

CONCLUSIONS

We conclude that cetylpyridinium-containing nanoemulsions appear to present a feasible means of preventing the occurrence of early caries.

Transient alginate gene expression by Pseudomonas putida biofilm residents under water-limiting conditions reflects adaptation to the local environment

Under water-limiting conditions Pseudomonas putida produces the exopolysaccharide alginate, which influences biofilm development and facilitates maintaining a hydrated microenvironment. Since alginate is a minor biofilm matrix component it is important to determine whether alginate production occurs by all or a subset of residents, and when and to what extent cells contribute to alginate production. To address these questions we employed stable and unstable fluorescent reporters to measure alginate biosynthesis (algD) operon expression and metabolic activity in vivo quantitatively by flow cytometry and visually by microscopy. Here we report that during growth under water-limiting conditions and when biofilms become dehydrated most residents transiently express the alginate biosynthesis genes leading to distinct spatial patterns as the biofilm ages. Transient alginate gene expression was not a consequence of decreased metabolic activity, since metabolic reporters were still expressed, nor was it likely due to transient cytosolic availability of the alternative sigma factor AlgT, based on qRT-PCR. Our findings also indicate that one or more biofilm attribute, other than alginate, provides protection from desiccation stress. Collectively, our findings suggest that differentiated cells dedicated to alginate production are not part of the P. putida biofilm lifestyle under water-limiting conditions. Alternatively, P. putida biofilm cells may be responding to their own local environment, producing alginate because of the fitness advantage it confers under those particular conditions.

Enzymatic substrates in microbiology

Enzymatic substrates are powerful tools in biochemistry. They are widely used in microbiology to study metabolic pathways, to monitor metabolism and to detect, enumerate and identify microorganisms. Synthetic enzymatic substrates have been customized for various microbial assays, to detect an expanding range of both new enzymatic activities and target microorganisms. Recent developments in synthetic enzymatic substrates with new spectral, chemical and biochemical properties allow improved detection, enumeration and identification of food-borne microorganisms, clinical pathogens and multi-resistant bacteria in various sample types. In the past 20 years, the range of synthetic enzymatic substrates used in microbiology has been markedly extended supporting the development of new multi-test systems (e.g., Microscan, Vitek 2, Phoenix) and chromogenic culture media. The use of such substrates enables an improvement in time to detection and specificity over conventional tests that employ natural substrates. In the era of intense developments in molecular biology, phenotypic tests involving enzymatic substrates remain useful to analyse both simple and complex samples. Such tests are applicable to diagnostic and research laboratories all over the world.

Localized expression profiles of rpoS in Escherichia coli biofilms

Although importance of the rpoS gene on biofilm formation by Escherichia coli has been suggested, there has not been any report showing where the rpoS is expressed during biofilm formation process. Since physiological state of the cells in the biofilms is considerably heterogeneous, the expression of the rpoS gene must be heterogeneous. In this study, in situ spatial expression of the rpoS gene during biofilm formation was investigated with an rpoS-gfp transcriptional fusion mutant strain. A ribosomal binding site and a gene encoding a green fluorescent protein were introduced into the downstream of the rpoS gene, which enabled us to observe the in situ spatial expression of the rpoS gene during biofilm formation processes without any disturbance of the rpoS expression. In the early stages of the biofilm formation process, the rpoS gene was expressed in the most of the cells. On the other hand, the rpoS expression was observed only at the outside of the biofilms during the late stages of the biofilm formation process. The in situ spatial expression of the rpoS gene in the biofilm was verified by quantifying the expression levels of the rpoS at the outside and the inside of the biofilms with the real time RT-PCR. In addition, global gene expression analysis was performed with DNA microarray to investigate physiological difference between the outside and the inside of the biofilms. This heterogeneous rpoS expression profile suggested that the cells at the outside of the biofilm need to express the rpoS to shift the physiological state to the stationary growth mode such as induction of various stress responses and suppression of the motility.

Long-distance delivery of bacterial virulence factors by Pseudomonas aeruginosa outer membrane vesicles

Bacteria use a variety of secreted virulence factors to manipulate host cells, thereby causing significant morbidity and mortality. We report a mechanism for the long-distance delivery of multiple bacterial virulence factors, simultaneously and directly into the host cell cytoplasm, thus obviating the need for direct interaction of the pathogen with the host cell to cause cytotoxicity. We show that outer membrane-derived vesicles (OMV) secreted by the opportunistic human pathogen Pseudomonas aeruginosa deliver multiple virulence factors, including beta-lactamase, alkaline phosphatase, hemolytic phospholipase C, and Cif, directly into the host cytoplasm via fusion of OMV with lipid rafts in the host plasma membrane. These virulence factors enter the cytoplasm of the host cell via N-WASP-mediated actin trafficking, where they rapidly distribute to specific subcellular locations to affect host cell biology. We propose that secreted virulence factors are not released individually as naked proteins into the surrounding milieu where they may randomly contact the surface of the host cell, but instead bacterial derived OMV deliver multiple virulence factors simultaneously and directly into the host cell cytoplasm in a coordinated manner.

Laser desorption 7.87 eV postionization mass spectrometry of antibiotics in Staphylococcus epidermidis bacterial biofilms

This paper describes the development of laser desorption 7.87 eV vacuum UV (VUV) postionization MS to detect antibiotics within intact bacterial colony biofilms. As >99% of the molecules ejected by laser desorption are neutrals, VUV photoionization of these neutrals can provide significantly increased signal as compared to the detection of directly emitted ions. Postionization with VUV radiation from the molecular fluorine laser single photon ionizes laser desorbed neutrals with ionization potentials below the 7.87 eV photon energy. Antibiotics with structures indicative of sub-7.87 eV ionization potentials were examined for their ability to be detected by 7.87 eV laser desorption postionization MS. Tetracycline, sulfadiazine, and novobiocin were successfully detected neat as dried films physisorbed on porous silicon oxide substrates. Tetracycline and sulfadiazine were then detected within intact Staphylococcus epidermidis colony biofilms, the former with LOD in the micromolar concentration range.

Anti-biofilm properties of chitosan-coated surfaces

Surfaces coated with the naturally-occurring polysaccharide chitosan (partially deacetylated poly N-acetyl glucosamine) resisted biofilm formation by bacteria and yeast. Reductions in biofilm viable cell numbers ranging from 95% to 99.9997% were demonstrated for Staphylococcus epidermidis, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa and Candida albicans on chitosan-coated surfaces over a 54-h experiment in comparison to controls. For instance, chitosan-coated surfaces reduced S. epidermidis surface-associated growth more than 5.5 (10)log units (99.9997%) compared to a control surface. As a comparison, coatings containing a combination of the antibiotics minocycline and rifampin reduced S. epidermidis growth by 3.9 (10)log units (99.99%) and coatings containing the antiseptic chlorhexidine did not significantly reduce S. epidermidis surface associated growth as compared to controls. The chitosan effects were confirmed with microscopy. Using time-lapse fluorescence microscopy and fluorescent-dye-loaded S. epidermidis, the permeabilization of these cells was observed as they alighted on chitosan-coated surfaces. This suggests chitosan disrupts cell membranes as microbes settle on the surface. Chitosan offers a flexible, biocompatible platform for designing coatings to protect surfaces from infection.

Localized gene expression in Pseudomonas aeruginosa biofilms

Gene expression in biofilms is dependent on bacterial responses to the local environmental conditions. Most techniques for studying bacterial gene expression in biofilms characterize average values across the entire population. Here, we describe the use of laser capture microdissection microscopy (LCMM) combined with multiplex quantitative real-time reverse transcriptase PCR (qRT-PCR) to isolate and quantify RNA transcripts from small groups of cells at spatially resolved sites within biofilms. The approach was first tested and analytical parameters were determined for Pseudomonas aeruginosa containing an isopropyl-beta-D-thiogalactopyranoside-inducible gene for the green fluorescent protein (gfp). The results show that the amounts of gfp mRNA were greatest in the top zones of the biofilms, and that gfp mRNA levels correlated with the zone of active green fluorescent protein fluorescence. The method then was used to quantify transcripts from wild-type P. aeruginosa biofilms for a housekeeping gene, acpP; the 16S rRNA; and two genes regulated by quorum sensing, phzA1 and aprA. The results demonstrated that the amount of acpP mRNA was greatest in the top 30 microm of the biofilm, with little or no mRNA for this gene at the base of the biofilms. In contrast, 16S rRNA amounts were relatively uniform throughout biofilm strata. Using this strategy, the RNA amounts of individual genes were determined, and therefore the results are dependent on both gene expression and the half-life of the transcripts. Therefore, the uniform amount of rRNA throughout the biofilms likely is due to the stability of the rRNA within ribosomes. The levels of aprA mRNA showed stratification, with the largest amounts in the upper 30-microm zone of these biofilms. The results demonstrate that mRNA levels for individual genes are not uniformly distributed throughout biofilms but may vary by orders of magnitude over small distances. The LCMM/qRT-PCR technique can be used to resolve and quantify this RNA variability at high spatial resolution.

Phosphatase activity in anaerobic bioreactors for wastewater treatment

Phosphatase (PO4ase) activity was investigated in continuous and fed-batch anaerobic bioreactors for wastewater treatment. PO4ase levels were high in continuously fed reactors (880-2632 micromol/L/h), compared to a fed-batch reactor (FBR) (540-1249 micromol/L/h). Alkaline and acid PO4ases were present in all the reactors, but in varying magnitudes and total PO4ase activity exhibited a 10-30% variation even at steady-state reactor conditions. The PO4ase activity was not affected by the inorganic phosphate (Pi) level in the reactors, but biomass level and wastewater type, including specific PO4ases (either alkaline or acid), strongly influenced the PO4ase activity in a reactor. Both flocculated and suspended cells produced PO4ase, and 60-65% of the enzyme was cell bound, remaining entrapped in the extracellular matrix and in cell-free form. Batch studies with anaerobic sludge showed a negative correlation between Pi and PO4ase activity. An increase in PO4ase activity was observed under starvation and higher salinity (above 15 g/L). Glucose and propionate (at 10 mM level) induced PO4ase activity, whereas acetate and butyrate (10 mM) addition had no response. This study also reveals that Archaea and bacteria contributed 45% and 55%, respectively, of total PO4ase activity in anaerobic sludge.

Characterizing the dynamic nature of the Yersinia pestis periplasmic proteome in response to nutrient exhaustion and temperature change

The periplasmic proteome of Yersinia pestis strain KIM6+ was characterized using differential 2-DE display of proteins isolated from several subcellular fractions. Circa 160 proteins were designated as periplasmic, including 62 (putative) solute-binding proteins of ATP-binding cassette (ABC) transporters (SBPs) and 46 (putative) metabolic enzymes. More than 30 SBPs were significantly increased in abundance during stationary phase cell growth, compared to the exponential phase. The data suggest that nutrient exhaustion in the stationary phase triggers cellular responses resulting in the induced expression of numerous ABC transporters, which are responsible for the import of solutes/nutrients. Limited availability of inorganic phosphate (P(i)) also caused dramatic proteomic changes. Nine proteins were functionally linked to the mobilization and import of three small molecules (P(i), phosphonate and glycerol-3-phosphate) and accounted for nearly half of the total protein mass in the periplasm of P(i)-starved cells. When cells were grown at 26 degrees C versus 37 degrees C, corresponding to ambient temperatures in the flea vector and mammalian hosts, respectively, several periplasmic proteins with no known roles in the Y. pestis life cycle were strongly altered in abundance. This included a putative nitrate/sulfonate/bicarbonate-specific SBP (Y1004), encoded by the virulence-associated plasmid pMT1 and increased in abundance at 37 degrees C.

Physiological heterogeneity in biofilms

Biofilms contain bacterial cells that are in a wide range of physiological states. Within a biofilm population, cells with diverse genotypes and phenotypes that express distinct metabolic pathways, stress responses and other specific biological activities are juxtaposed. The mechanisms that contribute to this genetic and physiological heterogeneity include microscale chemical gradients, adaptation to local environmental conditions, stochastic gene expression and the genotypic variation that occurs through mutation and selection. Here, we discuss the processes that generate chemical gradients in biofilms, the genetic and physiological responses of the bacteria as they adapt to these gradients and the techniques that can be used to visualize and measure the microscale physiological heterogeneities of bacteria in biofilms.

Escherichia coli biofilms

Escherichia coli is a predominant species among facultative anaerobic bacteria of the gastrointestinal tract. Both its frequent community lifestyle and the availability of a wide array of genetic tools contributed to establish E. coli as a relevant model organism for the study of surface colonization. Several key factors, including different extracellular appendages, are implicated in E. coli surface colonization and their expression and activity are finely regulated, both in space and time, to ensure productive events leading to mature biofilm formation. This chapter will present known molecular mechanisms underlying biofilm development in both commensal and pathogenic E. coli.

Multimetal resistance and tolerance in microbial biofilms

Geochemical cycling and industrial pollution have made toxic metal ions a pervasive environmental pressure throughout the world. Biofilm formation is a strategy that microorganisms might use to survive a toxic flux in these inorganic compounds. Evidence in the literature suggests that biofilm populations are protected from toxic metals by the combined action of chemical, physical and physiological phenomena that are, in some instances, linked to phenotypic variation among the constituent biofilm cells. Here, we propose a multifactorial model by which biofilm populations can withstand metal toxicity by a process of cellular diversification.