Modern microscopy in biofilm research: confocal microscopy and other approaches

Exploring the Biology, Virulence, and General Aspects of Candida dubliniensis

Fungal infections have become a growing public health concern, aggravated by the emergence of new pathogenic species and increasing resistance to antifungal drugs. The most common candidiasis is caused by Candida albicans; however, Candida dubliniensis has become an emerging opportunistic pathogen, and although less prevalent, it can cause superficial and systemic infections, especially in immunocompromised individuals. This yeast can colonize the oral cavity, skin, and other tissues, and has been associated with oral infections in patients with human immunodeficiency virus (HIV) and acquired immunodeficiency syndrome (AIDS), making it difficult to treat. The special interest in the study of this species lies in its ability to evade commonly used antifungal drugs, such as fluconazole, under different concentrations. In addition, it is difficult to identify because it can be confused with the species C. albicans, which could interfere with adequate treatment. Although the study of virulence factors in C. dubliniensis is limited, proteomic comparisons with C. albicans indicate that these virulence factors could be similar between the two species. However, differences could exist considering the evolutionary processes and lifestyle of each species. In this study, a detailed review of the current literature on C. dubliniensis was conducted, considering aspects such as biology, possible virulence factors, immune response, pathogen-host interaction, diagnosis, and treatment.

Resource Recycling, Recovery, and Xenobiotic Remediation from E-wastes Through Biofilm Technology: A Review

Around 50 million tonnes of electronic waste has been generated globally per year, causing an environmental hazard and negative effects on human health, such as infertility and thyroid disorders in adults, endocrine and neurological damage in both animals and humans, and impaired mental and physical development in children. Out of that, only 15% is recycled each year and the remaining is disposed of in a landfill, illegally traded or burned, and treated in a sub-standard way. The processes of recycling are challenged by the presence of brominated flame retardants. The different recycling technologies such as the chemical and mechanical methods have been well studied, while the most promising approach is the biological method. The process of utilizing microbes to decontaminate and degrade a wide range of pollutants into harmless products is known as bioremediation and it is an eco-friendly, cost-effective, and sustainable method. The bioremediation process is significantly aided by biofilm communities attached to electronic waste because they promote substrate bioavailability, metabolite transfer, and cell viability, all of which accelerate bioleaching and biodegradation. Microbes existing in biofilm mode relatable to free-floating planktonic cells are advantageous of bioremediation due to their tolerant ability to environmental stress and pollutants through diverse catabolic pathways. This article discusses the harmful effects of electronic waste and its management using biological strategies especially biofilm-forming communities for resource recovery.

Thermal Effect on Algae, Biofilm and Their Composition Towards Membrane Distillation Unit: A Mini-review

Membrane distillation (MD) has lower operating temperature and potential to recycle waste heat for desalination which catches much attention of the researchers in the recent years. However, the biofouling is still a challenging hurdle to be overcome for such applications. The microbial growth rate, secretion and biofilm formation are sensitive to heat. Membrane distillation is a thermally driven separation, so the increase of temperature in the seawater feed could influence the extent of biofouling on the unit parts. In this review, we present the effect of temperature on algal growth, the range of temperature the microbes, marine algae and planktons able to survive and the changes to those planktons once exceed the critical temperature. Thermal effect on the biofilm, its composition and properties are discussed as well, with association of the biofilm secreting microbes, but the study related to membrane distillation unit seems to be lacking and MD biofouling factors are not fully understood. Characterization of the algae, biofilm and EPS that govern biofouling are discussed. This information not only will help in designing future studies to fill up the knowledge gaps in biofouling of membrane distillation, but also to some extent, assist in pointing out possible fouling factors and predicting the degree of biofouling in the membrane distillation unit.

Tools of the Trade: Image Analysis Programs for Confocal Laser-Scanning Microscopy Studies of Biofilms and Considerations for Their Use by Experimental Researchers

Confocal laser-scanning microscopy (CLSM) is the bedrock of the microscopic visualization of biofilms. Previous applications of CLSM in biofilm studies have largely focused on observations of bacterial or fungal elements of biofilms, often seen as aggregates or mats of cells. However, the field of biofilm research is moving beyond qualitative observations alone, toward the quantitative analysis of the structural and functional features of biofilms, across clinical, environmental, and laboratory conditions. In recent times, several image analysis programs have been developed to extract and quantify biofilm properties from confocal micrographs. These tools not only vary in their scope and relevance to the specific biofilm features under study but also with respect to the user interface, compatibility with operating systems, and raw image requirements. Understanding these considerations is important when selecting tools for quantitative biofilm analysis, including at the initial experimental stages of image acquisition. In this review, we provide an overview of image analysis programs for confocal micrographs of biofilms, with a focus on tool selection and image acquisition parameters that are relevant for experimental researchers to ensure reliability and compatibility with downstream image processing.

Label-free sub-micrometer 3D imaging of ciprofloxacin in native-state biofilms with cryo-time-of-flight secondary ion mass spectrometry

High spatial resolution mass spectrometry imaging has been identified as a key technology needed to improve understanding of the chemical components that influence antibiotic resistance within biofilms, which are communities of micro-organisms that grow attached to a surface. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) offers the unique ability for label-free 3D imaging of organic molecules with sub-micrometer spatial resolution and high sensitivity. Several studies of biofilms have been done with the help of ToF-SIMS, but none of those studies have shown 3D imaging of antibiotics in native-state hydrated biofilms with cell-level resolution. Because ToF-SIMS measurements must be performed in a high-vacuum environment, cryogenic preparation and analysis are necessary to preserve the native biofilm structure and antibiotic spatial distribution during ToF-SIMS measurements. In this study, we have investigated the penetration of the antibiotic ciprofloxacin into Bacillus subtilis biofilms using sub-micrometer resolution 3D imaging cryo-ToF-SIMS. B. subtilis biofilms were exposed to physiologically relevant levels of ciprofloxacin. The treated biofilms were then plunge-frozen in liquid propane and analyzed with ToF-SIMS under cryogenic conditions. Multivariate analysis techniques, including multivariate curve resolution (MCR) and inverse maximum signal factor (iMSF) denoising, were used to aid analysis of the data and facilitate high spatial resolution 3D imaging of the biofilm, providing individually resolved cells and spatially resolved ciprofloxacin intensity at "real world" concentrations.

Scaffolds in the microbial resistant era: Fabrication, materials, properties and tissue engineering applications

Due to microbial infections dramatically affect cell survival and increase the risk of implant failure, scaffolds produced with antimicrobial materials are now much more likely to be successful. Multidrug-resistant infections without suitable prevention strategies are increasing at an alarming rate. The ability of cells to organize, develop, differentiate, produce a functioning extracellular matrix (ECM) and create new functional tissue can all be controlled by careful control of the extracellular microenvironment. This review covers the present state of advanced strategies to develop scaffolds with antimicrobial properties for bone, oral tissue, skin, muscle, nerve, trachea, cardiac and other tissue engineering applications. The review focuses on the development of antimicrobial scaffolds against bacteria and fungi using a wide range of materials, including polymers, biopolymers, glass, ceramics and antimicrobials agents such as antibiotics, antiseptics, antimicrobial polymers, peptides, metals, carbon nanomaterials, combinatorial strategies, and includes discussions on the antimicrobial mechanisms involved in these antimicrobial approaches. The toxicological aspects of these advanced scaffolds are also analyzed to ensure future technological transfer to clinics. The main antimicrobial methods of characterizing scaffolds' antimicrobial and antibiofilm properties are described. The production methods of these porous supports, such as electrospinning, phase separation, gas foaming, the porogen method, polymerization in solution, fiber mesh coating, self-assembly, membrane lamination, freeze drying, 3D printing and bioprinting, among others, are also included in this article. These important advances in antimicrobial materials-based scaffolds for regenerative medicine offer many new promising avenues to the material design and tissue-engineering communities.

Bacterial Biofilm Growth on 3D-Printed Materials

Recent advances in 3D printing have led to a rise in the use of 3D printed materials in prosthetics and external medical devices. These devices, while inexpensive, have not been adequately studied for their ability to resist biofouling and biofilm buildup. Bacterial biofilms are a major cause of biofouling in the medical field and, therefore, hospital-acquired, and medical device infections. These surface-attached bacteria are highly recalcitrant to conventional antimicrobial agents and result in chronic infections. During the COVID-19 pandemic, the U.S. Food and Drug Administration and medical officials have considered 3D printed medical devices as alternatives to conventional devices, due to manufacturing shortages. This abundant use of 3D printed devices in the medical fields warrants studies to assess the ability of different microorganisms to attach and colonize to such surfaces. In this study, we describe methods to determine bacterial biofouling and biofilm formation on 3D printed materials. We explored the biofilm-forming ability of multiple opportunistic pathogens commonly found on the human body including Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus to colonize eight commonly used polylactic acid (PLA) polymers. Biofilm quantification, surface topography, digital optical microscopy, and 3D projections were employed to better understand the bacterial attachment to 3D printed surfaces. We found that biofilm formation depends on surface structure, hydrophobicity, and that there was a wide range of antimicrobial properties among the tested polymers. We compared our tested materials with commercially available antimicrobial PLA polymers.

Microsystems for biofilm characterization and sensing - A review

Biofilms are the primary cause of clinical bacterial infections and are impervious to typical amounts of antibiotics, necessitating very high doses for elimination. Therefore, it is imperative to have suitable methods for characterization to develop novel methods of treatment that can complement or replace existing approaches using significantly lower doses of antibiotics. This review presents some of the current developments in microsystems for characterization and sensing of bacterial biofilms. Initially, we review current standards for studying biofilms that are based on invasive and destructive end-point biofilm characterization. Additionally, biofilm formation and growth is extremely sensitive to various growth and environmental parameters that cause large variability in biofilms between repeated experiments, making it very difficult to compare experimental repeats and characterize the temporal characteristics of these organisms. To address these challenges, recent developments in the field have moved toward systems and miniature devices that can aid in the non-invasive characterization of bacterial biofilms. Our review focuses on several types of microsystems for biofilm evaluation including optical, electrochemical, and mechanical systems. This review will show how these devices can lead to better understanding of the physiology and function of these communities of bacteria, which can eventually lead to the development of novel treatments that do not rely on high-dosage antibiotics.

A Technological Understanding of Biofilm Detection Techniques: A Review

Biofouling is a persistent problem in almost any water-based application in several industries. To eradicate biofouling-related problems in bioreactors, the detection of biofilms is necessary. The current literature does not provide clear supportive information on selecting biofilm detection techniques that can be applied to detect biofouling within bioreactors. Therefore, this research aims to review all available biofilm detection techniques and analyze their characteristic properties to provide a comparative assessment that researchers can use to find a suitable biofilm detection technique to investigate their biofilms. In addition, it discusses the confluence of common bioreactor fabrication materials in biofilm formation.

Raman spectroscopic signatures of carotenoids and polyenes enable label-free visualization of microbial distributions within pink biofilms

Pink biofilms are multispecies microbial communities that are commonly found in moist household environments. The development of this pink stain is problematic from an aesthetic point of view, but more importantly, it raises hygienic concerns because they may serve as a potential reservoir of opportunistic pathogens. Although there have been several studies of pink biofilms using molecular analysis and confocal laser scanning microscopy, little is known about the spatial distributions of constituent microorganisms within pink biofilms, a crucial factor associated with the characteristics of pink biofilms. Here we show that Raman spectroscopic signatures of intracellular carotenoids and polyenes enable us to visualize pigmented microorganisms within pink biofilms in a label-free manner. We measured space-resolved Raman spectra of a pink biofilm collected from a bathroom, which clearly show resonance Raman bands of carotenoids. Multivariate analysis of the Raman hyperspectral imaging data revealed the presence of typical carotenoids and structurally similar but different polyenes, whose spatial distributions within the pink biofilm were found to be mutually exclusive. Raman measurements on individual microbial cells isolated from the pink biofilm confirmed that these distributions probed by carotenoid/polyene Raman signatures are attributable to different pigmented microorganisms. The present results suggest that Raman microspectroscopy with a focus on microbial pigments such as carotenoids is a powerful nondestructive method for studying multispecies biofilms in various environments.

Streptococcus mutans Biofilm Formation and Cell Viability on Polymer-infiltrated Ceramic and Yttria-stabilized Polycrystalline Zirconium Dioxide Ceramic

OBJECTIVE

The aim of this study was to investigate the biofilm formation and cell viability of a polymer-infiltrated ceramic (PIC) and an yttria-stabilized polycrystalline zirconium dioxide ceramic (Y-TZP). The null hypothesis was that there would be no difference in biofilm formation and cell viability between the materials.

METHODS AND MATERIALS

Streptococcus mutans biofilm was analyzed with scanning electron microscopy (SEM), confocal laser scanning microscopy, and colony counting (colony-forming units/mL). The cell viability (fibroblasts) of both materials was measured with 3-(4,5-dimethylthiazol-2yl)-2,5-diphenyl tetrazolium) (MTT) test. Roughness measurements were also performed.

RESULTS

The PIC displayed higher roughness but showed similar colony-forming units and biovolume values to those of Y-TZP. SEM showed a higher amount of adhered fibroblasts on the PIC surface on the first day and similar amounts on both materials after seven days. Moreover, the materials were biocompatible with human fibroblasts.

CONCLUSION

PIC and Y-TZP are biocompatible and present the same characteristics for biofilm formation; therefore, they are indicated for indirect restorations and implant abutments.

Manganese dioxide coating reduces bacterial adhesion and infection in silicon implants in animal model

PURPOSE

To propose a new coating to silicone implants using Manganese dioxide. We present bacterial adhesion and proliferation when implants are challenged with Escherichia coli.

METHODS

Coated and control silicon implants were placed in two independent subcutaneous pouches in the dorsum of Wistar rats. After skin closure, 0.5 ml of E. coli solution was injected in each incision. The animals were euthanized at 7 and 28 days. Extracted material was cultured and analyzed by confocal microscopy.

RESULTS

At 1 week, uncoated implants had a 17-fold higher infection rate (p < 0.001). Coated samples showed a mean bacterial count of 28,700 CFU/ml, while the control ones 503,000 CFU/ml, with a significant mean difference of 474,300 CFU/ml (95% CI 165,900-782,600). At 4 weeks, the mean bacterial growth in coated group was 7600; while in control one was 53,890. The mean difference between groups was 46,200 (95% CI 21,100-71,400). Confocal microscopy presented the percentage of implant's surface with attached bacteria: at 7 days, coated implants had 6.85% and controls 10.9% and the difference was not significant (p =0.32). At 4 weeks, the coated group showed 0.98% of the surface with attached bacteria, while control group showed 7.64%, which resulted in a significant 11-fold difference (p = 0.004).

CONCLUSIONS

Manganese dioxide coating inhibits bacterial proliferation and adhesion in subcutaneous silicon implants in an animal model. These findings can be useful to improve development of biomaterials.

Unveiling the role of Gardnerella vaginalis in polymicrobial Bacterial Vaginosis biofilms: the impact of other vaginal pathogens living as neighbors

Bacterial vaginosis (BV) is characterized by a highly structured polymicrobial biofilm, which is strongly adhered to the vaginal epithelium and primarily consists of the bacterium Gardnerella vaginalis. However, despite the presence of other BV-associated bacteria, little is known regarding the impact of other species on BV development. To gain insight into BV progress, we analyzed the ecological interactions between G. vaginalis and 15 BV-associated microorganisms using a dual-species biofilm model. Bacterial populations were quantified using a validated peptide nucleic acid fluorescence in situ hybridization approach. Furthermore, biofilm structure was analyzed by confocal laser scanning microscopy. In addition, bacterial coaggregation ability was determined as well as the expression of key virulence genes. Remarkably, our results revealed distinct biofilm structures between each bacterial consortium, leading to at least three unique dual-species biofilm morphotypes. Furthermore, our transcriptomic findings seem to indicate that Enterococcus faecalis and Actinomyces neuii had a higher impact on the enhancement of G. vaginalis virulence, while the other tested species had a lower or no impact on G. vaginalis virulence. This study casts a new light on how BV-associated species can modulate the virulence aspects of G. vaginalis, contributing to a better understanding of the development of BV-associated biofilms.

Flexible Platform for In Situ Impedimetric Detection and Bioelectric Effect Treatment of Escherichia Coli Biofilms

GOAL

This paper reports a platform for real-time monitoring and treatment of biofilm formation on three-dimensional biomedical device surfaces.

METHODS

We utilize a flexible platform consisting of gold interdigitated electrodes patterned on a polyimide substrate. The device was integrated onto the interior of a urinary catheter and characterization was performed in a custom-developed flow system. Biofilm growth was monitored via impedance change at 100 Hz ac with a 50 mV signal amplitude.

RESULTS

A 30% impedance decrease over 24 h corresponded to Escherichia coli biofilm formation. The platform also enabled removal of the biofilm through the bioelectric effect; a low concentration of antibiotic combined with the applied ac voltage signal led to a synergistic reduction in biofilm resulting in a 12% increase in impedance. Biomass characterization via crystal violet staining confirmed that the impedance detection results correlate with changes in the amount of biofilm biomass on the sensor. We also demonstrated integration with a chip-based impedance converter to enable miniaturization and allow in situ wireless implementation. A 5% impedance decrease measured with the impedance converter corresponded to biofilm growth, replicating the trend measured with the potentiostat.

CONCLUSION

This platform represents a promising solution for biofilm infection management in diverse vulnerable environments.

SIGNIFICANCE

Biofilms are the dominant mode of growth for microorganisms, where bacterial cells colonize hydrated surfaces and lead to recurring infections. Due to the inaccessible nature of the environments where biofilms grow and their increased tolerance of antimicrobials, identification, and removal on medical devices poses a challenge.

A Sensitive Thresholding Method for Confocal Laser Scanning Microscope Image Stacks of Microbial Biofilms

Biofilms are surface-attached microbial communities whose architecture can be captured with confocal microscopy. Manual or automatic thresholding of acquired images is often needed to help distinguish biofilm biomass from background noise. However, manual thresholding is subjective and current automatic thresholding methods can lead to loss of meaningful data. Here, we describe an automatic thresholding method designed for confocal fluorescent signal, termed the biovolume elasticity method (BEM). We evaluated BEM using confocal image stacks of oral biofilms grown in pooled human saliva. Image stacks were thresholded manually and automatically with three different methods; Otsu, iterative selection (IS), and BEM. Effects on biovolume, surface area, and number of objects detected indicated that the BEM was the least aggressive at removing signal, and provided the greatest visual and quantitative acuity of single cells. Thus, thresholding with BEM offers a sensitive, automatic, and tunable method to maintain biofilm architectural properties for subsequent analysis.

Characterization and Transcriptome Analysis of Acinetobacter baumannii Persister Cells

Acinetobacter baumannii is a nonfermenting Gram-negative bacillus. A. baumannii resistance is a significant obstacle to clinical infection treatment. The existence of persister cells (persisters) might represent the reason for therapy failure and relapse, and such cells may be the driving force behind rising resistance rates. In this study, A. baumannii ATCC 19606 was used as a target to explore the essential features of A. baumannii persisters. Antibiotic treatment of A. baumannii cultures at 50-fold the minimum inhibitory concentration resulted in a distinct plateau of surviving drug-tolerant persisters. The sensitive bacteria were lysed with ceftazidime, and the nonreplicating bacteria were isolated for transcriptome analysis using RNA sequencing. We analyzed the transcriptome of A. baumannii persisters and identified significantly differentially expressed genes, as well as their enriched pathways. The results showed that both the GP49 (HigB)/Cro (HigA) and DUF1044/RelB toxin/antitoxin systems were significantly increased during the persister incubation period. In addition, the activities of certain metabolic pathways (such as electron transport, adenosine triphosphate [ATP], and the citrate cycle) decreased sharply after antibiotic treatment and remained low during the persister period, while aromatic compound degradation genes were only upregulated in persisters. These results suggest the involvement of aromatic compound degradation genes in persister formation and maintenance. They further provide the first insight into the mechanism of persister formation in A. baumannii.

Mechanism of bacterial adhesion on ultrafiltration membrane modified by natural antimicrobial polymers (chitosan) and combination with activated carbon (PAC)

Bacterial adhesion to surfaces is related to several factors, such as surface charge, surface energy, and substrate characteristics (leading to the formation of biofilms). Organisms are dominant in most environmental, industrial, and medical problems and processes that are of interest to microbiologists. Biofilm cells are at least 500 times more resistant to antibacterial agents compared to planktonic cells. The usage of ultrafiltration membranes is fast becoming popular for water treatment. Membrane lifetime and permeate flux are primarily affected by the phenomena of microbial accumulation and fouling at the membrane’s surface. This review intends to understand the mechanism of membrane fouling by bacterial attachment on polymeric ultrafiltration membrane modified by natural antimicrobial polymers (chitosan) combined with powder activated carbon. Also, to guide future research on membrane water treatment processes, adhesion prediction using the extended Derjaguin-Landau-Verwey-Overbeek theory is discussed.

Image analysis driven single-cell analytics for systems microbiology

BACKGROUND

Time-lapse microscopy is an essential tool for capturing and correlating bacterial morphology and gene expression dynamics at single-cell resolution. However state-of-the-art computational methods are limited in terms of the complexity of cell movies that they can analyze and lack of automation. The proposed Bacterial image analysis driven Single Cell Analytics (BaSCA) computational pipeline addresses these limitations thus enabling high throughput systems microbiology.

RESULTS

BaSCA can segment and track multiple bacterial colonies and single-cells, as they grow and divide over time (cell segmentation and lineage tree construction) to give rise to dense communities with thousands of interacting cells in the field of view. It combines advanced image processing and machine learning methods to deliver very accurate bacterial cell segmentation and tracking (F-measure over 95%) even when processing images of imperfect quality with several overcrowded colonies in the field of view. In addition, BaSCA extracts on the fly a plethora of single-cell properties, which get organized into a database summarizing the analysis of the cell movie. We present alternative ways to analyze and visually explore the spatiotemporal evolution of single-cell properties in order to understand trends and epigenetic effects across cell generations. The robustness of BaSCA is demonstrated across different imaging modalities and microscopy types.

CONCLUSIONS

BaSCA can be used to analyze accurately and efficiently cell movies both at a high resolution (single-cell level) and at a large scale (communities with many dense colonies) as needed to shed light on e.g. how bacterial community effects and epigenetic information transfer play a role on important phenomena for human health, such as biofilm formation, persisters' emergence etc. Moreover, it enables studying the role of single-cell stochasticity without losing sight of community effects that may drive it.

Biofilms in chronic rhinosinusitis: Pathophysiology and therapeutic strategies

BACKGROUND

There is increasing evidence that biofilms are critical to the pathophysiology of chronic infections including chronic rhinosinusitis (CRS). Until relatively recently, our understanding of biofilms was limited. Recent advances in methods for biofilm identification and molecular biology have offered new insights into the role of biofilms in CRS. With these insights, investigators have begun to investigate novel therapeutic strategies that may disrupt or eradicate biofilms in CRS.

OBJECTIVE

This review seeks to explore the evidence implicating biofilms in CRS, discuss potential anti-biofilm therapeutic strategies, and suggest future directions for research.

RESULTS

The existing evidence strongly supports the role of biofilms in the pathogenesis of CRS. Several anti-biofilm therapies have been investigated for use in CRS and these are at variable stages of development. Generally, these strategies: 1) neutralize biofilm microbes; 2) disperse existing biofilms; or 3) disrupt quorum sensing. Several of the most promising anti-biofilm therapeutic strategies are reviewed.

CONCLUSIONS

A better understanding of biofilm function and their contribution to the CRS disease process will be pivotal to the development of novel treatments that may augment and, potentially, redefine the CRS treatment paradigm. There is tremendous potential for future research.

Nanoscopic Cellular Imaging: Confinement Broadens Understanding

In recent years, single-molecule fluorescence imaging has been reconciling a fundamental mismatch between optical microscopy and subcellular biophysics. However, the next step in nanoscale imaging in living cells can be accessed only by optical excitation confinement geometries. Here, we review three methods of confinement that can enable nanoscale imaging in living cells: excitation confinement by laser illumination with beam shaping; physical confinement by micron-scale geometries in bacterial cells; and nanoscale confinement by nanophotonics.

Environmental factors that shape biofilm formation

Cells respond to the environment and alter gene expression. Recent studies have revealed the social aspects of bacterial life, such as biofilm formation. Biofilm formation is largely affected by the environment, and the mechanisms by which the gene expression of individual cells affects biofilm development have attracted interest. Environmental factors determine the cell's decision to form or leave a biofilm. In addition, the biofilm structure largely depends on the environment, implying that biofilms are shaped to adapt to local conditions. Second messengers such as cAMP and c-di-GMP are key factors that link environmental factors with gene regulation. Cell-to-cell communication is also an important factor in shaping the biofilm. In this short review, we will introduce the basics of biofilm formation and further discuss environmental factors that shape biofilm formation. Finally, the state-of-the-art tools that allow us investigate biofilms under various conditions are discussed.

Quantitative analysis of biofilm formation by oropharyngeal Candida albicans isolates under static conditions by confocal

Candida albicans may colonize natural or artificial surfaces, leading to formation of the biofilm. Infections associated with the biofilm formation are important therapeutic problem. In this paper, we present data concerning the biofilm formation under static conditions by oropharyngeal isolates of C. albicans on a glass surface using confocal scanning laser microscopy (CSLM). The areal parameters describing the architecture of biofilm and its development, i.e. the areal porosity, the length of edge line, the length of skeleton line, were calculated. The changes in values of these parameters during the biofilm formation by C. albicans were similar for biofilm consisting of only blastospores as well as the biofilm consisting of blastospores and filamentous elements (hyphae or/and pseudohyphae). However, the thickness of C. albicans biofilm consisting of blastospores and filamentous elements was much higher than that consisting of only blastospores. The heterogeneity may be regarded as an important feature of the yeast biofilm including C. albicans.

Combination of synchrotron radiation-based Fourier transforms infrared microspectroscopy and confocal laser scanning microscopy to understand spatial heterogeneity in aquatic multispecies biofilms

Understanding the spatial heterogeneity within environmental biofilms can provide an insight into compartmentalization of different functions in biofilm communities. We used a non-destructive and label-free method by combining Synchrotron Radiation-based Fourier Transform Infrared Microspectroscopy (SR-FTIR) with Confocal Laser Scanning Microscopy (CLSM) to distinguish the spatial chemical changes within multispecies biofilms grown from natural storm waters in flow cells. Among the different surfaces tested for biofilm growth and optimal imaging, mylar membranes were most suited and it enabled successful spatial infrared imaging of natural biofilms for obtaining reliable and interpretable FTIR spectra. Time series analysis of biofilm growth showed that influx of water during biofilm growth, results in significant changes in biofilm formation. Early biofilms showed active nutrient acquisition and desiccation tolerance mechanisms corresponding with accumulation of secreted proteins. Statistical approach used for the evaluation of chemical spectra allowed for clustering and classification of various regions of the biofilm. Microheterogeneity was observed in the polymeric components of the biofilm matrix, including cellulose, glycocalyx and dextran-like molecules. Fructan and glycan-rich regions were distinguishable and glycocalyx was abundant in the strongly adhering peripheral regions of biofilms. Inner core showed coexistence of oxygen dimers and ferrihydrite that will likely support growth of Fe (II)-oxidising bacteria. The combined SR-FTIR microspectroscopy and CSLM approach for complex natural biofilms described here will be useful both in understanding heterogeneity of matrix components and in correlating functions of juxtaposed microbial species in complex natural biofilms with physicochemical microenvironment to which they are exposed.

An overview on the reactors to study drinking water biofilms

The development of biofilms in drinking water distribution systems (DWDS) can cause pipe degradation, changes in the water organoleptic properties but the main problem is related to the public health. Biofilms are the main responsible for the microbial presence in drinking water (DW) and can be reservoirs for pathogens. Therefore, the understanding of the mechanisms underlying biofilm formation and behavior is of utmost importance in order to create effective control strategies. As the study of biofilms in real DWDS is difficult, several devices have been developed. These devices allow biofilm formation under controlled conditions of physical (flow velocity, shear stress, temperature, type of pipe material, etc), chemical (type and amount of nutrients, type of disinfectant and residuals, organic and inorganic particles, ions, etc) and biological (composition of microbial community - type of microorganism and characteristics) parameters, ensuring that the operational conditions are similar as possible to the DWDS conditions in order to achieve results that can be applied to the real scenarios. The devices used in DW biofilm studies can be divided essentially in two groups, those usually applied in situ and the bench top laboratorial reactors. The selection of a device should be obviously in accordance with the aim of the study and its advantages and limitations should be evaluated to obtain reproducible results that can be transposed into the reality of the DWDS. The aim of this review is to provide an overview on the main reactors used in DW biofilm studies, describing their characteristics and applications, taking into account their main advantages and limitations.

Quantification of confocal images of biofilms grown on irregular surfaces

Bacterial biofilms grow on many types of surfaces, including flat surfaces such as glass and metal and irregular surfaces such as rocks, biological tissues and polymers. While laser scanning confocal microscopy can provide high-resolution images of biofilms grown on any surface, quantification of biofilm-associated bacteria is currently limited to bacteria grown on flat surfaces. This can limit researchers studying irregular surfaces to qualitative analysis or quantification of only the total bacteria in an image. In this work, we introduce a new algorithm called modified connected volume filtration (MCVF) to quantify bacteria grown on top of an irregular surface that is fluorescently labeled or reflective. Using the MCVF algorithm, two new quantification parameters are introduced. The modified substratum coverage parameter enables quantification of the connected-biofilm bacteria on top of the surface and on the imaging substratum. The utility of MCVF and the modified substratum coverage parameter were shown with Pseudomonas aeruginosa and Staphylococcus aureus biofilms grown on human airway epithelial cells. A second parameter, the percent association, provides quantified data on the colocalization of the bacteria with a labeled component, including bacteria within a labeled tissue. The utility of quantifying the bacteria associated with the cell cytoplasm was demonstrated with Neisseria gonorrhoeae biofilms grown on cervical epithelial cells. This algorithm provides more flexibility and quantitative ability to researchers studying biofilms grown on a variety of irregular substrata.

Contribution of confocal laser scanning microscopy in deciphering biofilm tridimensional structure and reactivity

Confocal laser scanning microscopy (CLSM) became in last years an invaluable technique to study biofilms since it enables researchers to explore noninvasively the dynamic architecture and the reactivity of these biological edifices. The constant development of fluorescent markers and genetic tools along with the improvement of spatial, spectral, and temporal resolution of imaging facilities offers new opportunities to better decipher microbial biofilm properties. In this contribution, we proposed to describe the contribution of CLSM to the study of biofilm architecture and reactivity throughout two different illustrative approaches.

Advanced techniques for in situ analysis of the biofilm matrix (structure, composition, dynamics) by means of laser scanning microscopy

The extracellular constituents in bioaggregates and biofilms can be imaged four dimensionally by using laser scanning microscopy. In this protocol we provide guidance on how to examine the various extracellular compartments in between microbial cells and communities associated with interfaces. The current options for fluorescence staining of matrix compounds and extracellular microhabitats are presented. Furthermore, practical aspects are discussed and useful notes are added. The chapter ends with a brief introduction to other approaches for EPS analysis and an outlook for future needs.

Investigation of microbial biofilm structure by laser scanning microscopy

Microbial bioaggregates and biofilms are hydrated three-dimensional structures of cells and extracellular polymeric substances (EPS). Microbial communities associated with interfaces and the samples thereof may come from natural, technical, and medical habitats. For imaging such complex microbial communities confocal laser scanning microscopy (CLSM) is the method of choice. CLSM allows flexible mounting and noninvasive three-dimensional sectioning of hydrated, living, as well as fixed samples. For this purpose a broad range of objective lenses is available having different working distance and resolution. By means of CLSM the signals detected may originate from reflection, autofluorescence, reporter genes/fluorescence proteins, fluorochromes binding to specific targets, or other probes conjugated with fluorochromes. Recorded datasets can be used not only for visualization but also for semiquantitative analysis. As a result CLSM represents a very useful tool for imaging of microbiological samples in combination with other analytical techniques.

Macroscale versus microscale methods for physiological analysis of biofilms formed in 96-well microtiter plates

Microtiter plates with 96 wells have become one of the preferred platforms for biofilm studies mainly because they enable high-throughput assays. In this work, macroscale and microscale methods were used to study the impact of hydrodynamic conditions on the physiology and location of Escherichia coli JM109(DE3) biofilms formed in microtiter plates. Biofilms were formed in shaking and static conditions, and two macroscale parameters were assayed: the total amount of biofilm was measured by the crystal violet assay and the metabolic activity was determined by the resazurin assay. From the macroscale point of view, there were no statistically significant differences between the biofilms formed in static and shaking conditions. However, at a microscale level, the differences between both conditions were revealed using scanning electron microscopy (SEM). It was observed that biofilm morphology and spatial distribution along the wall were different in these conditions. Simulation of the hydrodynamic conditions inside the wells at a microscale was performed by computational fluid dynamics (CFD). These simulations showed that the shear strain rate was unevenly distributed on the walls during shaking conditions and that regions of higher shear strain rate were obtained closer to the air/liquid interface. Additionally, it was shown that wall regions subjected to higher shear strain rates were associated with the formation of biofilms containing cells of smaller size. Conversely, regions with lower shear strain rate were prone to have a more uniform spatial distribution of adhered cells of larger size. The results presented on this work highlight the wealth of information that may be gathered by complementing macroscale approaches with a microscale analysis of the experiments.

Pulse-based non-thermal plasma (NTP) disrupts the structural characteristics of bacterial biofilms

Bacterial biofilms were constructed in vitro with two pathogenic strains of Pseudomonas aeruginosa and Staphylococcus aureus using a modified, novel sequential bioreactor system. The structure and stability of bacterial biofilms were evaluated following exposure to non-thermal plasma (NTP) discharge. Mathematical software was used to determine structural changes as biofilms grew over the course of 7 days. Statistical modeling was also performed to assess the ability of NTP to affect the development of the biofilms over different periods of time. Several structural characteristics were significantly affected by NTP discharge whereas others were unaffected. Changes in the three-dimensional structure of the biofilm following introduction of NTP was not limited to one period of development. The mechanism for this phenomenon is not understood but is likely to be a dual, synergistic effect due to the composition of the reactive species and other plasma-associated molecules isolated previously in the NTP discharge used in this study.

Continuous live cell imaging of cellulose attachment by microbes under anaerobic and thermophilic conditions using confocal microscopy

Live cell imaging methods provide important insights into the dynamics of cellular processes that cannot be derived easily from population-averaged datasets. In the bioenergy field, much research is focused on fermentation of cellulosic biomass by thermophilic microbes to produce biofuels; however, little effort is dedicated to the development of imaging tools to monitor this dynamic biological process. This is, in part, due to the experimental challenges of imaging cells under both anaerobic and thermophilic conditions. Here an imaging system is described that integrates confocal microscopy, a flow cell device, and a lipophilic dye to visualize cells. Solutions to technical obstacles regarding suitable fluorescent markers, photodamage during imaging, and maintenance of environmental conditions during imaging are presented. This system was utilized to observe cellulose colonization by Clostridium thermocellum under anaerobic conditions at 60 degrees C. This method enables live cell imaging of bacterial growth under anaerobic and thermophilic conditions and should be widely applicable to visualizing different cell types or processes in real time.

Biofouling of water treatment membranes: a review of the underlying causes, monitoring techniques and control measures

Biofouling is a critical issue in membrane water and wastewater treatment as it greatly compromises the efficiency of the treatment processes. It is difficult to control, and significant economic resources have been dedicated to the development of effective biofouling monitoring and control strategies. This paper highlights the underlying causes of membrane biofouling and provides a review on recent developments of potential monitoring and control methods in water and wastewater treatment with the aim of identifying the remaining issues and challenges in this area.

Bacterial colony from two-dimensional division to three-dimensional development

On agar surface, bacterial daughter cells form a 4-cell array after the first two rounds of division, and this phenomenon has been previously attributed to a balancing of interactions among the daughter bacteria and the underneath agar. We studied further the organization and development of colony after additional generations. By confocal laser scanning microscopy and real-time imaging, we observed that bacterial cells were able to self-organize and resulted in a near circular micro-colony consisting of monolayer cells. After continuous dividing, bacteria transited from two-dimensional expansion into three-dimensional growth and formed two to multi-layers in the center but retained a monolayer in the outer ring of the circular colony. The transverse width of this outer ring appeared to be approximately constant once the micro-colony reached a certain age. This observation supports the notion that balanced interplays of the forces involved lead to a gross morphology as the bacteria divide into offspring on agar surface. In this case, the result is due to a balance between the expansion force of the dividing bacteria, the non-covalent force among bacterial offspring and that between bacteria and substratum.

Pathophysiology, favoring factors, and associated disorders in otorhinosinusology

The pathogenesis of rhinosinusitis (RS) is related to inflammation, caused by infections in the acute form of the disease but also by other agents in the chronic forms. Cytology allows to evaluate the defensive components, such as hair cells and muciparous cells, while the presence in the nasal mucosa of eosinophils, mast cells, bacteria and/or fungal hyphae, or spores indicates the nasal pathology. The anatomic and physiologic characteristics of the otorhinosinusal system account for the frequent concomitant involvement of the different components. The pivotal pathophysiologic sites are the ostiomeatal complex, the spheno-ethmoidal recess, and the Eustachian tube. The latter is the link with acute otitis media (AOM), which is the most common disease in infants and children and has major medical, social, and economic effects. Moreover, because of the strict relationship between upper and lower airways, nasal sinus disease may contribute to asthma and sinusitis may be considered as an independent factor associated with frequent severe asthma exacerbations. Concerning the role of allergy, the available data do not permit to attribute a central role to atopy in sinusitis and thus allergy testing should not be a routine procedure, while an allergologic evaluation may be indicated in children with OM, especially when they have concomitant rhinitis.

Evaluation of methods to assess the biofilm-forming ability of Listeria monocytogenes

The contamination of ready-to-eat products with Listeria monocytogenes has been related to the presence of biofilms in production lines, as biofilms protect cells from chemical sanitizers. The ability of L. monocytogenes to produce biofilms is often evaluated using in vitro methodologies. This work aims to compare the most frequently used methodologies, including high-throughput screening methods based on microplates (crystal violet and the Calgary Biofilm Device) and methods based on CFU enumeration and microscopy after growth on stainless steel. Thirty isolates with diverse origins and genetic characteristics were evaluated. No (or low) correlations between methods were observed. The only significant correlation was found between the methods using stainless steel. No statistically significant correlation (P > 0.05) was detected among genetic lineage, serovar, and biofilm-forming ability. Because results indicate that biofilm formation is influenced by the surface material, the extrapolation of results from high-throughput methods using microplates to more industrially relevant surfaces should be undertaken with caution.

Nasal cytology: the "infectious spot", an expression of a morphological-chromatic biofilm

The purpose of this study was to describe some "morphological-chromatic" patterns (i.e. spots of cyan colour) identified during the study of nasal cytology in patients with both bacterial and fungal infectious rhinological disorders. These peculiar aspects strongly suggest the presence of a microscopic biofilm. We retrospectively examined 1,410 nasal cytology specimens from subjects who underwent clinical-instrumental investigations (history, ENT visit, nasal endoscopy and nasal cytology) from January to August 2010. The control samples were represented by 30 subjects not suffering from infectious rhinological diseases. The presence of particular spots of "cyan" was found in colour in 107/1,410 rhinocytograms (7.6%), within which bacterial colonies and/or fungal spores were found. We called these coloured spot formations "infectious spots" (IS). The positivity to periodic acid Schiff (PAS) staining confirmed the polysaccharide nature of the coloured spots and allowed us to relate them to biofilms. This study demonstrates, for the first time, that nasal cytology performed by optical microscope can play an important role in detecting biofilms.

Confocal Laser Microscopic Analysis of Biofilm on Newer Feldspar Ceramic

When the glazed surface of glass ceramics is submitted to chairside preparation, polishing with rubber points followed by felt disks impregnated with a fine-aluminum oxide particle appears be a good option to polish the surface of the glass ceramic, since this finishing-polishing method results in biofilm formation similar to the glazed ceramic surface.

Biofilms in chronic suppurative otitis media and cholesteatoma: scanning electron microscopy findings

BACKGROUND

Biofilms play a role in the pathogenesis of a variety of otorhinolaryngologic diseases, including otitis media and cholesteatoma. Despite this, relatively few studies have undertaken to demonstrate the presence of biofilms tissues from patients with chronic otitis media or infected cholesteatoma.

OBJECTIVE/HYPOTHESIS

Our objective is to detect evidence of biofilms human chronic ear infections with scanning electron microscopy (SEM). We hypothesized that bacterial biofilms are present in patients with chronic otitis media.

STUDY DESIGN

We performed prospective collection of tissue collected during middle ear surgery from 16 patients undergoing middle ear or mastoid surgery with chronic ear infections.

METHODS

A total of 31 middle and mastoid tissue samples were harvested at the time of surgery and processed with critical point drying for SEM analysis. Samples were then searched for evidence of biofilms.

RESULTS

Bacterial-shaped objects were identified that displayed both surface binding and the presence of a glycocalyx in 4 patients, findings consistent with bacterial biofilms. Most of these (3 of 4) were in patients with infected cholesteatoma, and biofims were identified in 60% of cholesteatoma cases (3 of 5). On the other hand, only 1 of 7 cases with chronic suppurative otitis media had evidence of biofilms.

CONCLUSION

SEM supports the hypothesis that bacterial biofilms are common in chronic infections associated with cholesteatoma and are present in some cases of chronic suppurative otitis media without cholesteatoma.

Targeted imaging modality selection for bacterial biofilms in chronic rhinosinusitis

OBJECTIVES/HYPOTHESIS

Biofilms are increasingly recognized as having an etiological role in chronic rhinosinusitis (CRS). Research into biofilms in CRS currently relies on microscopic imaging techniques, none of which are universally accepted. This study compares LIVE/DEAD BacLight (Invitrogen Corp., Carlsbad, CA) staining and fluorescence in situ hybridization (FISH), both utilizing the confocal scanning laser microscope (CSLM) for biofilm determination and characterization in CRS patients.

STUDY DESIGN

Prospective study.

METHODS

Twenty CRS patients undergoing endoscopic sinus surgery were recruited for the study. Sinus mucosal tissue harvested at the time of surgery underwent both the BacLight/CSLM and FISH/CSLM protocols for biofilm determination and characterization.

RESULTS

Combining the results of both protocols, 18/20 (90%) patients had bacterial biofilms demonstrable on at least one modality. The high biofilm detection rate combining the two techniques suggests the prevalence of biofilms in CRS may be greater than previously reported. The protocols had equivalent results in 15/20 patients. Using the differences observed in the remaining five patients, we can highlight the most appropriate use for each technique.

CONCLUSIONS

BacLight/CSLM and FISH/CSLM are complementary techniques for biofilm determination and characterization. Both protocols are suited to different research areas and the selection of technique used should be based on the specific objectives of the research protocol. In this way we can utilize the advantages of each technique to facilitate effective research.

Functional tomographic fluorescence imaging of pH microenvironments in microbial biofilms by use of silica nanoparticle sensors

Attached bacterial communities can generate three-dimensional (3D) physicochemical gradients that create microenvironments where local conditions are substantially different from those in the surrounding solution. Given their ubiquity in nature and their impacts on issues ranging from water quality to human health, better tools for understanding biofilms and the gradients they create are needed. Here we demonstrate the use of functional tomographic imaging via confocal fluorescence microscopy of ratiometric core-shell silica nanoparticle sensors (C dot sensors) to study the morphology and temporal evolution of pH microenvironments in axenic Escherichia coli PHL628 and mixed-culture wastewater biofilms. Testing of 70-, 30-, and 10-nm-diameter sensor particles reveals a critical size for homogeneous biofilm staining, with only the 10-nm-diameter particles capable of successfully generating high-resolution maps of biofilm pH and distinct local heterogeneities. Our measurements revealed pH values that ranged from 5 to >7, confirming the heterogeneity of the pH profiles within these biofilms. pH was also analyzed following glucose addition to both suspended and attached cultures. In both cases, the pH became more acidic, likely due to glucose metabolism causing the release of tricarboxylic acid cycle acids and CO(2). These studies demonstrate that the combination of 3D functional fluorescence imaging with well-designed nanoparticle sensors provides a powerful tool for in situ characterization of chemical microenvironments in complex biofilms.