Artificial biofilm model--a useful tool for biofilm research

Genetic mixing and demixing on expanding spherical frontiers

Genetic fluctuation during range expansion is a key process driving evolution. When a bacterial population is expanding on a 2D surface, random fluctuations in the growth of the pioneers at the front line cause a strong demixing of genotypes. Even when there is no selective advantage, sectors of low genetic diversity are formed. Experimental studies of range expansions in surface-attached colonies of fluorescently labelled micro-organisms have contributed significantly to our understanding of fundamental evolutionary dynamics. However, experimental studies on genetic fluctuations in 3D range expansions have been sparse, despite their importance for tumour or biofilm development. We encapsulated populations of two fluorescent Escherichia coli strains in inoculation droplets (volumes [Formula: see text] nl). The confined ensemble of cells grew when embedded in a hydrogel-with nutrients-and developed 3D colonies with well-defined, sector-like regions. Using confocal laser scanning microscopy, we imaged the development of 3D colonies and the emergence of sectors. We characterized how cell concentration in the inoculation droplet controls sectors, growth rate, and the transition from branched colonies to quasi-spherical colonies. We further analysed how sectors on the surface change over time. We complement these experimental results with a modified 3D Eden growth model. The model in 3D spherical growth predicts a phase, where sectors are merging, followed by a steady increase (constant rate), and the experimentally analysed sectors were consistent with this prediction. Therefore, our results demonstrate qualitative differences between radial (2D) and spherical (3D) range expansions and their importance in gene fixation processes.

Motility mediates satellite formation in confined biofilms

Bacteria have spectacular survival capabilities and can spread in many, vastly different environments. For instance, when pathogenic bacteria infect a host, they expand by proliferation and squeezing through narrow pores and elastic matrices. However, the exact role of surface structures-important for biofilm formation and motility-and matrix density in colony expansion and morphogenesis is still largely unknown. Using confocal laser-scanning microscopy, we show how satellite colonies emerge around Escherichia coli colonies embedded in semi-dense hydrogel in controlled in vitro assays. Using knock-out mutants, we tested how extra-cellular structures, (e.g., exo-polysaccharides, flagella, and fimbria) control this morphology. Moreover, we identify the extra-cellular matrix' density, where this morphology is possible. When paralleled with mathematical modelling, our results suggest that satellite formation allows bacterial communities to spread faster. We anticipate that this strategy is important to speed up expansion in various environments, while retaining the close interactions and protection provided by the community.

Hierarchical encapsulation of bacteria in functional hydrogel beads for inter- and intra- species communication

To sequester prokaryotic cells in a biofilm-like niche, the creation of a pertinent and reliable microenvironment that reflects the heterogeneous nature of biological systems is vital for sustenance. Design of a microenvironment that is conducive for growth and survival of organisms, should account for factors such as mass transport, porosity, stability, elasticity, size, functionality, and biochemical characteristics of the organisms in the confined architecture. In this work we present an artificial long-term confinement model fabricated by natural alginate hydrogels that are structurally stable and can host organisms for over 10 days in physiologically relevant conditions. A unique feature of the confinement platform is the development of stratified habitats wherein bacterial cells can be entrapped in the core as well as in the shell layers, wherein the thickness and the number of shell layers are tunable at fabrication. We show that the hydrogel microenvironment in the beads can host complex subpopulations of organisms similar to that in a biofilm. Dynamic interaction of bacterial colonies encapsulated in different beads or within the core and stratified layers of single beads was demonstrated to show intra- species communication. Inter- species communication between probiotic bacteria and human colorectal carcinoma cells was also demonstrated to highlight a possible bidirectional communication between the organisms in the beads and the environment. STATEMENT OF SIGNIFICANCE: Bacteria confinement in a natural soft hydrogel structure has always been a challenge due to the collapse of hydrogel architectures. Alternative methods have been attempted to encapsulate microorganisms by employing various processes to avoid/minimize rupturing of hydrogel structures. However, most of the past approaches have been unfavorable in balancing cell proliferation and functionality upon confinement. Our study addresses the fundamental gap in knowledge necessary to create favorable and complex 3D biofilm mimics utilizing natural hydrogel for microbial colonization for long-term studies. Our approach represents a cornerstone in the development of 3D functional architectures not only to advance studies in microbial communication, host-microbe interaction but also to address basic and fundamental questions in biology.

Sprayable biofilm – Agarose hydrogels as 3D matrix for enhanced productivity in bioelectrochemical systems

Bio-based energy production utilizing renewable resources can be realized by exoelectrogenic organisms and their application in bioelectrochemical systems (BES). These organisms catalyze the direct conversion of chemical into electrical energy and are already widely used in bioelectronics and biosensing. However, the biofilm-electrode interaction is a factor that limits sufficient space-time-yields for industrial applications. In this study, a hydrogel matrix consisting of agarose fibers was utilized as a scaffold for S. oneidensis cells to improve anodic processes in BES. This synthetic, scalable biofilm reached a higher current density in BES in comparison to naturally formed biofilms. Complemented with carbon nanofibers and riboflavin, the application of this functionalized hydrogel containing S. oneidensis cells led to an overall 9.1-fold increase in current density to 1324 mA m⁻² in comparison to 145 mA m⁻² for the planktonic control. In addition, the synthetic biofilm can be applied by spraying onto surfaces using a novel spray applicator. The latter allows to apply the biofilm effortless on large surfaces which will facilitate scalability and thus industrial application.

Saliva-derived microcosm biofilms grown on different oral surfaces in vitro

The microbial composition of a specific oral niche could be influenced by initial bacterial adherence, nutrient and physiological property of the local surface. To investigate the influence of nutrient and surface properties on microbial composition, saliva-derived biofilms were grown in agar on three substrata: Reconstructed Human Gingiva (RHG), a hydroxyapatite (HAP) surface, and a titanium (TI) surface. Agar was mixed with either Brain Heart Infusion (BHI) or Thompson (TP) medium. After 1, 3, or 5 days, biofilm viability (by colony forming units) and microbiome profiles (by 16 S rDNA amplicon sequencing) were determined. On RHG, biofilm viability and composition were similar between BHI and TP. However, on the abiotic substrata, biofilm properties greatly depended on the type of medium and substratum. In BHI, the viability of HAP-biofilm first decreased and then increased, whereas that of TI-biofilm decreased in time until a 6-log reduction. In TP, either no or a 2-log reduction in viability was observed for HAP- or TI-biofilms respectively. Furthermore, different bacterial genera (or higher level) were differentially abundant in the biofilms on 3 substrata: Haemophilus and Porphyromonas for RHG; Bacilli for HAP and Prevotella for TI. In conclusion, RHG, the biotic substratum, is able to support a highly viable and diverse microbiome. In contrast, the viability and diversity of the biofilms on the abiotic substrata were influenced by the substrata type, pH of the environment and the richness of the growth media. These results suggest that the host (oral mucosa) plays a vital role in the oral ecology.

Surface-enhanced Raman spectroscopy of microorganisms: limitations and applicability on the single-cell level

Detection and characterization of microorganisms is essential for both clinical diagnostics and environmental studies. An emerging technique to analyse microbes at single-cell resolution is surface-enhanced Raman spectroscopy (surface-enhanced Raman scattering: SERS). Optimised SERS procedures enable fast analytical read-outs with specific molecular information, providing insight into the chemical composition of microbiological samples. Knowledge about the origin of microbial SERS signals and parameter(s) affecting their occurrence, intensity and/or reproducibility is crucial for reliable SERS-based analyses. In this work, we explore the feasibility and limitations of the SERS approach for characterizing microbial cells and investigate the applicability of SERS for single-cell sorting as well as for three-dimensional visualization of microbial communities. Analyses of six different microbial species (an archaeon, two Gram-positive bacteria, three Gram-negative bacteria) showed that for several of these organisms distinct features in their SERS spectra were lacking. As additional confounding factor, the physiological conditions of the cells (as influenced by e.g., storage conditions or deuterium-labelling) were systematically addressed, for which we conclude that the respective SERS signal at the single-cell level is strongly influenced by the metabolic activity of the analysed cells. While this finding complicates the interpretation of SERS data, it may on the other hand enable probing of the metabolic state of individual cells within microbial populations of interest.

Mechanical interactions between bacteria and hydrogels

Mechanical interactions between bacterial cells and extracellular polymeric substance are essential in determining biofilm assembly and disassembly as well the mechanical characteristics of biofilms. However, the physics of these mechanical interactions in different cell culture conditions are poorly understood. We created typical artificial biofilm consisting of planktonic bacteria and hydrogel, in the absence of metabolic or regulatory effect. We have demonstrated that the cell culture medium can significantly affect the mechanical interactions between bacterial cells and hydrogels. The stiffness of the bacteria-hydrogel artificial biofilm cannot be simply attributed by the summation of the contribution from the bacteria and hydrogel based on the mathematical models and computational models. We have revealed that the tryptone component of Luria-Bertani broth medium plays an important role in stiffening effect of bacteria-hydrogel construct. Such significant stiffening effect can be explained by the following mechanism: the presence of tryptone in cell culture medium may enable the bacteria itself to crosslink the hydrogel polymer chains. Our findings have also demonstrated the synergy of modelling and innovative experiments which would potentially impact the biofilm control strategies.

Development and characterisation of a novel three-dimensional inter-kingdom wound biofilm model

Chronic diabetic foot ulcers are frequently colonised and infected by polymicrobial biofilms that ultimately prevent healing. This study aimed to create a novel in vitro inter-kingdom wound biofilm model on complex hydrogel-based cellulose substrata to test commonly used topical wound treatments. Inter-kingdom triadic biofilms composed of Candida albicans, Pseudomonas aeruginosa, and Staphylococcus aureus were shown to be quantitatively greater in this model compared to a simple substratum when assessed by conventional culture, metabolic dye and live dead qPCR. These biofilms were both structurally complex and compositionally dynamic in response to topical therapy, so when treated with either chlorhexidine or povidone iodine, principal component analysis revealed that the 3-D cellulose model was minimally impacted compared to the simple substratum model. This study highlights the importance of biofilm substratum and inclusion of relevant polymicrobial and inter-kingdom components, as these impact penetration and efficacy of topical antiseptics.

Gel-Entrapped Staphylococcus aureus Bacteria as Models of Biofilm Infection Exhibit Growth in Dense Aggregates, Oxygen Limitation, Antibiotic Tolerance, and Heterogeneous Gene Expression

An experimental model that mimicked the structure and characteristics of in vivo biofilm infections, such as those occurring in the lung or in dermal wounds where no biomaterial surface is present, was developed. In these infections, microbial biofilm forms as cell aggregates interspersed in a layer of mucus or host matrix material. This structure was modeled by filling glass capillary tubes with an agarose gel that had been seeded with Staphylococcus aureus bacteria and then incubating the gel biofilm in medium for up to 30 h. Confocal microscopy showed that the bacteria formed in discrete pockets distributed throughout the gel matrix. These aggregates enlarged over time and also developed a size gradient, with the clusters being larger near the nutrient- and oxygen-supplied interface and smaller at greater depths. Bacteria entrapped in gels for 24 h grew slowly (specific growth rate, 0.06 h(-1)) and were much less susceptible to oxacillin, minocycline, or ciprofloxacin than planktonic cells. Microelectrode measurements showed that the oxygen concentration decreased with depth into the gel biofilm, falling to values less than 3% of air saturation at depths of 500 μm. An anaerobiosis-responsive green fluorescent protein reporter gene for lactate dehydrogenase was induced in the region of the gel where the measured oxygen concentrations were low, confirming biologically relevant hypoxia. These results show that the gel biofilm model captures key features of biofilm infection in mucus or compromised tissue: formation of dense, distinct aggregates, reduced specific growth rates, local hypoxia, and antibiotic tolerance.

Antifouling activity of enzyme-functionalized silica nanobeads

The amelioration of biofouling in industrial processing equipment is critical for performance and reliability. While conventional biocides are effective in biofouling control, they are potentially hazardous to the environment and in some cases corrosive to materials. Enzymatic approaches have been shown to be effective and can overcome the disadvantages of traditional biocides, however they are typically uneconomic for routine biofouling control. The aim of this study was to design a robust and reusable enzyme-functionalized nano-bead system having biofilm dispersion properties. This work describes the biochemical covalent functionalization of silica-based nanobeads (hereafter referred to as Si-NanoB) with Proteinase K (PK). Results showed that PK-functionalized Si-NanoB are effective in dispersing both protein-based model biofilms and structurally altering Pseudomonas fluorescens biofilms, with significant decreases in surface coverage and thickness of 30.1% and 38.85%, respectively, while increasing surface roughness by 19 % following 24 h treatments on bacterial biofilms. This study shows that enzyme-functionalized nanobeads may potentially be an environmentally friendly and cost effective alternative to pure enzyme and chemical treatments.

Biological noise abatement: coordinating the responses of autonomous bacteria in a synthetic biofilm to a fluctuating environment using a stochastic bistable switch

Noise is inherent to single cell behavior. Its origins can be traced to the stochasticity associated with a few copies of genes and low concentrations of protein and ligands. We have studied the mechanisms by which the response of noisy elements can be entrained for biological signal processing. To elicit predictable biological function, we have engineered a gene environment that incorporates a gene regulatory network with the stringently controlled microenvironment found in a synthetic biofilm. The regulatory network leverages the positive feedback found in quorum-sensing regulatory components of the lux operon, which is used to coordinate cellular responses to environmental fluctuations. Accumulation of the Lux receptor in cells, resulting from autoregulation, confers a rapid response and enhanced sensitivity to the quorum-sensing molecule that is retained after cell division as epigenetic memory. The memory of the system channels stochastic noise into a coordinated response among quorum-sensing signal receivers in a synthetic biofilm in which the noise diminishes with repeated exposure to noisy transmitters on the input of a signaling cascade integrated into the same biofilm. Thus, gene expression in the receivers, which are autonomous and do not communicate with each other, is synchronized to fluctuations in the environment.

Assessment of the working range and effect of sodium dichloroisocyanurate on Pseudomonas aeruginosa biofilms and planktonic cells

Sodium dichloroisocyanurate (NaDCC) is a chemical agent that acts against microorganisms in a manner similar to that of sodium hypochlorite by releasing free available chlorine. NaDCC has been approved by the WHO for the emergency treatment of water and by the US EPA for routine treatment of water. Previous studies assessing the effectiveness of NaDCC for the treatment of water implied that NaDCC should have a wide array of disinfecting effects beyond the treatment of planktonic cells in potable water. In this study the biocidal effects of NaDCC against Pseudomonas aeruginosa cells in different growth modes including planktonic cells and biofilms were explored. The data showed that a 60% dilution of the standard NaDCC solution was effective in the treatment of both P. aeruginosa planktonic cells and biofilms.

A three-phase in-vitro system for studying Pseudomonas aeruginosa adhesion and biofilm formation upon hydrogel contact lenses

Background

Pseudomonas aeruginosa is commonly associated with contact lens (CL) -related eye infections, for which bacterial adhesion and biofilm formation upon hydrogel CLs is a specific risk factor. Whilst P. aeruginosa has been widely used as a model organism for initial biofilm formation on CLs, in-vitro models that closely reproduce in-vivo conditions have rarely been presented.

Results

In the current investigation, a novel in-vitro biofilm model for studying the adherence of P. aeruginosa to hydrogel CLs was established. Nutritional and interfacial conditions similar to those in the eye of a CL wearer were created through the involvement of a solid:liquid and a solid:air interface, shear forces and a complex artificial tear fluid. Bioburdens varied depending on the CL material and biofilm maturation occurred after 72 h incubation. Whilst a range of biofilm morphologies were visualised including dispersed and adherent bacterial cells, aggregates and colonies embedded in extracellular polymer substances (EPS), EPS fibres, mushroom-like formations, and crystalline structures, a compact and heterogeneous biofilm morphology predominated on all CL materials.

Conclusions

In order to better understand the process of biofilm formation on CLs and to test the efficacy of CL care solutions, representative in-vitro biofilm models are required. Here, we present a three-phase biofilm model that simulates the environment in the eye of a CL wearer and thus generates biofilms which resemble those commonly observed in-situ.

Calcium carbonate precipitation by cyanobacterial polysaccharides

Cyanobacteria have been recognized as key players in the precipitation of calcium carbonate in marine and freshwater systems. These bacteria increase pH, (as a result of photosynthetic activity) and also produce extracellular polysaccharides, which act as binding sites for Ca2+ and CO32−. Both processes influence the morphology and the mineralogy of the carbonate minerals. In order to clarify the role of polysaccharides of picocyanobacteria upon calcium carbonate precipitation, both their buffering capacity and ability to induce precipitation need to be investigated. In this experimental study, we characterized the polysaccharides of three unicellular autotrophic picocyanobacterial Synechococcus-type strains by potentiometric titration and infrared spectroscopy. Potentiometric titrations were conducted to determine the total buffering capacity. The nature and concentration of active sites of the polysaccharides was clarified with the aid of potentiometric titration and spectral analysis of an aqueous cellular suspension. Precipitation experiments with polysaccharides of different strains allowed an estimation of their potential to precipitate calcium carbonate. The results presented here indicate that polysaccharides from cyanobacteria have a strong potential to exchange protons with their surrounding environment. Precipitation experiments demonstrated that extracellular polysaccharides of all the strains studied able to precipitate calcium carbonate.

Towards chemical analysis of nanostructures in biofilms I: imaging of biological nanostructures

Due to their direct influence on the stability of bacterial biofilms, a better insight into the nanoscopic spatial arrangement of the different extracellular polymeric substances (EPS), e.g., polysaccharides and proteins, is important for the improvement of biocides and for process optimization in wastewater treatment and biofiltration. Here, the first application of a combination of confocal laser-scanning microscopy (CLSM) and atomic force microscopy (AFM) to the investigation of river-water biofilms and related biopolymers is presented. AFM images collected at selected areas of CLS micrographs dramatically demonstrate the heterogeneity of biofilms at the nanometer scale and the need for a chemical imaging method with nanoscale resolution. The nanostructures (e.g., pili, flagella, hydrocolloids, and EPS) found in the extracellular matrix are classified according to shape and size, which is typically 50-150 nm in width and 1-10 nm in thickness, and sets the demands regarding spatial resolution of a potential chemical imaging method. Additionally, thin layers of the polysaccharide alginate were investigated. We demonstrate that calcium alginate is a good model for the EPS architecture at the nanometer scale, because of its similar network-like structure.

Short-duration low-direct-current electrical field treatment is a practical tool for considerably reducing counts of gram-negative bacteria entrapped in gel beads

Application of a direct-current electrical field for very short times can serve as a practical nonthermal procedure to reduce or modify the microbial distribution in gel beads. The viability of Escherichia coli and Serratia marcescens entrapped in alginate and agarose beads decreases as the field intensity and duration of electrical field increase.

Unexpected distribution of immobilized microorganisms within alginate beads

Immobilization refers to the prevention of free cell movement by natural or artificial means. It has always been assumed that immediately after an immobilization procedure is performed, cells are distributed homogeneously in the beads that entrap them. However, in this study, Escherichia coli and Trichoderma asperellum distribution in alginate-gel beads was found to be nonhomogeneous. In fact, there was a greater presence of cells on the surface of the alginate beads than in their cores.

How to build an adapted and bioactive cell microenvironment? A chemical interaction study of the structure of Ca-alginate matrices and their repercussion on confined cells

Alginates are increasingly being used as medical materials (matrices for tissue regeneration, surgical sponges, hemostatic bandages, microbial and cell encapsulation, artificial bacterial biofilms, etc.). The constitution of alginate gel networks is a complex phenomenon. A great number of different kinds of polysaccharidic frameworks can come to existence depending on the conditions used for their attainment. For instance, the degree of heterogeneity and porosity of Ca-alginate beads rely on this molecular organization. The formation of structural irregularities (superficial crust, cavities, shafts, dense or light gel frameworks, ordered or chaotic domains, etc.) within the alginate gel beads are inherent to this skeletal design. Several specific staining molecules (e.g. calcon carboxylic acid, murexide, methylene blue) that are negatively or positively charged interact with the gel network. These molecules allowed us to reveal a great variety of chemical interactions shown by the pattern coloration of the internal structure of the gel. The results observed are very different for the several matrices analyzed, which could explain to a great extent the singular behavior that cells confined in these kind of matrices exhibit.