A novel planar flow cell for studies of biofilm heterogeneity and flow-biofilm interactions

Pseudomonas aeruginosa Biofilm Lifecycle: Involvement of Mechanical Constraints and Timeline of Matrix Production

Pseudomonas aeruginosa is an opportunistic pathogen causing acute and chronic infections, especially in immunocompromised patients. Its remarkable adaptability and resistance to various antimicrobial treatments make it difficult to eradicate. Its persistence is enabled by its ability to form a biofilm. Biofilm is a community of sessile micro-organisms in a self-produced extracellular matrix, which forms a scaffold facilitating cohesion, cell attachment, and micro- and macro-colony formation. This lifestyle provides protection against environmental stresses, the immune system, and antimicrobial treatments, and confers the capacity for colonization and long-term persistence, often characterizing chronic infections. In this review, we retrace the events of the life cycle of P. aeruginosa biofilm, from surface perception/contact to cell spreading. We focus on the importance of extracellular appendages, mechanical constraints, and the kinetics of matrix component production in each step of the biofilm life cycle.

Challenges and current advances in in vitro biofilm characterization

Biofilms are structured communities of bacterial cells encased in a self-produced polymeric matrix, which develop over time and exhibit temporal responses to stimuli from internal biological processes or external environmental changes. They can be detrimental, threatening public health and causing economic loss, while they also play beneficial roles in ecosystem health, biotechnology processes, and industrial settings. Biofilms express extreme heterogeneity in their physical properties and structural composition, resulting in critical challenges in understanding them comprehensively. The lack of detailed knowledge of biofilms and their phenotypes has deterred significant progress in developing strategies to control their negative impacts and take advantage of their beneficial applications. A range of in vitro models and characterization tools have been developed and used to study biofilm growth and, specifically, to investigate the impact of environmental and growth factors on their development. This review article discusses the existing knowledge of biofilm properties and explains how external factors, such as flow condition, surface, interface, and host factor, may impact biofilm growth. The limitations of current tools, techniques, and in vitro models that are currently used for biofilms are also presented.

Dynamic Changes in Biofilm Structures under Dynamic Flow Conditions

Detachment is an important process determining the structure and function of bacterial biofilm, which has significant implications for biogeochemical cycling of elements, biofilm application, and infection control in clinical settings. Quantifying the responses of biofilm structure to hydrodynamics is crucial for understanding biofilm detachment mechanisms in aquatic environments.

Quantitative flow chamber system for evaluating in vitro biofilms and the kinetics of S. aureus biofilm formation in human plasma media

Background

It has been well established that biofilm formation on orthopaedic implants is a critical event in the pathogenesis of orthopaedic infections, yet the natural history of this process with respect to bacterial adhesion, proliferation, and glycocalyx matrix production remains poorly understood. Moreover, there are no quantitative methods yet available to assess the differences in biofilm formation between different bacterial strains or implant materials. Consequently, this study aimed to investigate the natural history of S. aureus in in vitro biofilm formation in human plasma media using a flow chamber system. Bioluminescent S. aureus strains were used to better understand the bacterial growth and biofilm formation on orthopaedic materials. Also, the effects of human plasma media were assessed by loading the chamber with Tryptic Soy Broth with 10% human plasma (TSB + HP).

Results

Scanning electron microscopy (SEM) was utilized to assess the morphological appearance of the biofilms, revealing that S. aureus inoculation was required for biofilm formation, and that the phenotypes of biofilm production after 24 h inoculation with three tested strains (SH1000, UAMS-1, and USA300) were markedly different depending on the culture medium. Time course study of the bioluminescence intensity (BLI) and biofilm production on the implants due to the UAMS-1 and USA300 strains revealed different characteristics, whereby UAMS-1 showed increasing BLI and biofilm growth until peaking at 9 h, while USA300 showed a rapid increase in BLI and biofilm formation at 6 h. The kinetics of biofilm formation for both UAMS-1 and USA300 were also supported and confirmed by qRT-PCR analysis of the 16S rRNA gene. Biofilms grown in our flow chamber in the plasma media were also demonstrated to involve an upregulation of the biofilm-forming-related genes icaA, fnbA, and alt. The BLI and SEM results from K-wire experiments revealed that the in vitro growth and biofilm formation by UAMS-1 and USA300 on stainless-steel and titanium surfaces were virtually identical.

Conclusion

We demonstrated a novel in vitro model for S. aureus biofilm formation with quantitative BLI and SEM outcome measures, and then used this model to demonstrate the presence of strain-specific phenotypes and its potential use to evaluate anti-microbial surfaces.

Development and Quantitation of Pseudomonas aeruginosa Biofilms after in vitro Cultivation in Flow-reactors

Characterization of biofilm formation and metabolic activities is critical to investigating biofilm interactions with environmental factors and illustrating biofilm regulatory mechanisms. An appropriate in vitro model that mimics biofilm in vivo habitats therefore demands accurate quantitation and investigation of biofilm-associated activities. Current methodologies commonly involve static biofilm setups (such as biofilm assays in microplates, bead biofilms, or biofilms on glass-slides) and fluidic flow biofilm systems (such as drip-flow biofilm reactors, 3-channel biofilm reactors, or tubing biofilm reactors). Continuous flow systems take into consideration the contribution of hydrodynamic shear forces, nutrient supply, and physical transport of dispersed cells, which define the habitat for biofilm development in most natural and engineered systems. This protocol describes the assembly of 3 flow-system setups to cultivate Pseudomonas aeruginosa PAO1 and Shewanella oneidensis MR-1 model biofilms, including the respective quantitation and observation approaches. The standardized flow systems promise productive and reproducible biofilm experimental results, which can be further modified according to specific research projects.

Engineered topographies and hydrodynamics in relation to biofouling control-a review

Biofouling, the unwanted growth of microorganisms on submerged surfaces, has appeared as a significant impediment for underwater structures, water vessels, and medical devices. For fixing the biofouling issue, modification of the submerged surface is being experimented as a non-toxic approach worldwide. This technique necessitated altering the surface topography and roughness and developing a surface with a nano- to micro-structured pattern. The main objective of this study is to review the recent advancements in surface modification and hydrodynamic analysis concerning biofouling control. This study described the occurrence of the biofouling process, techniques suitable for biofouling control, and current state of research advancements comprehensively. Different biofilms under various hydrodynamic conditions have also been outlined in this study. Scenarios of biomimetic surfaces and underwater super-hydrophobicity, locomotion of microorganisms, nano- and micro-hydrodynamics on various surfaces around microorganisms, and material stiffness were explained thoroughly. The review also documented the approaches to inhibit the initial settlement of microorganisms and prolong the subsequent biofilm formation process for patterned surfaces. Though it is well documented that biofouling can be controlled to various degrees with different nano- and micro-structured patterned surfaces, the understanding of the underlying mechanism is still imprecise. Therefore, this review strived to present the possibilities of implementing the patterned surfaces as a physical deterrent against the settlement of fouling organisms and developing an active microfluidic environment to inhibit the initial bacterial settlement process. In general, microtopography equivalent to that of bacterial cells influences attachment via hydrodynamics, topography-induced cell placement, and air-entrapment, whereas nanotopography influences physicochemical forces through macromolecular conditioning.

Occurrence of Potentially Pathogenic Bacteria in Epilithic Biofilm Forming Bacteria isolated from Porter Brook River-stones, Sheffield, UK

Biofilms in aquatic ecosystems develop on wet benthic surfaces and are primarily comprised of various allochthonous microorganisms, including bacteria embedded within a self-produced matrix of extracellular polymeric substances (EPS). In such environment, where there is a continuous flow of water, attachment of microbes to surfaces prevents cells being washed out of a suitable habitat with the added benefits of the water flow and the surface itself providing nutrients for growth of attached cells. When watercourses are contaminated with pathogenic bacteria, these can become incorporated into biofilms. This study aimed to isolate and identify the bacterial species within biofilms retrieved from river-stones found in the Porter Brook, Sheffield based on morphological, biochemical characteristics and molecular characteristics, such as 16S rDNA sequence phylogeny analysis. Twenty-two bacterial species were identified. Among these were 10 gram-negative pathogenic bacteria, establishing that potential human pathogens were present within the biofilms. Klebsiella pneumoniae MBB9 isolate showed the greatest ability to form a biofilm using a microtiter plate-based crystal violet assay. Biofilm by K. pneumoniae MBB9 formed rapidly (within 6 h) under static conditions at 37 °C and then increased up to 24 h of incubation before decreasing with further incubation (48 h), whereas the applied shear forces (horizontal orbital shaker; diameter of 25 mm at 150 rpm) had no effect on K. pneumoniae MBB9 biofilm formation.

Exploring flow-biofilm-sediment interactions: Assessment of current status and future challenges

Biofilm activities and their interactions with physical, chemical and biological processes are of great importance for a variety of ecosystem functions, impacting hydrogeomorphology, water quality and aquatic ecosystem health. Effective management of water bodies requires advancing our understanding of how flow influences biofilm-bound sediment and ecosystem processes and vice-versa. However, research on this triangle of flow-biofilm-sediment is still at its infancy. In this Review, we summarize the current state of the art and methodological approaches in the flow-biofilm-sediment research with an emphasis on biostabilization and fine sediment dynamics mainly in the benthic zone of lotic and lentic environments. Example studies of this three-way interaction across a range of spatial scales from cell (nm - µm) to patch scale (mm - dm) are highlighted in view of the urgent need for interdisciplinary approaches. As a contribution to the review, we combine a literature survey with results of a pilot experiment that was conducted in the framework of a joint workshop to explore the feasibility of asking interdisciplinary questions. Further, within this workshop various observation and measuring approaches were tested and the quality of the achieved results was evaluated individually and in combination. Accordingly, the paper concludes by highlighting the following research challenges to be considered within the forthcoming years in the triangle of flow-biofilm-sediment: i) Establish a collaborative work among hydraulic and sedimentation engineers as well as ecologists to study mutual goals with appropriate methods. Perform realistic experimental studies to test hypotheses on flow-biofilm-sediment interactions as well as structural and mechanical characteristics of the bed. ii) Consider spatially varying characteristics of flow at the sediment-water interface. Utilize combinations of microsensors and non-intrusive optical methods, such as particle image velocimetry and laser scanner to elucidate the mechanism behind biofilm growth as well as mass and momentum flux exchanges between biofilm and water. Use molecular approaches (DNA, pigments, staining, microscopy) for sophisticated community analyses. Link varying flow regimes to microbial communities (and processes) and fine sediment properties to explore the role of key microbial players and functions in enhancing sediment stability (biostabilization). iii) Link laboratory-scale observations to larger scales relevant for management of water bodies. Conduct field experiments to better understand the complex effects of variable flow and sediment regimes on biostabilization. Employ scalable and informative observation techniques (e.g., hyperspectral imaging, particle tracking) that can support predictions on the functional aspects, such as metabolic activity, bed stability, nutrient fluxes under variable regimes of flow-biofilm-sediment.

Studying the Impact of Wall Shear Stress on the Development and Performance of Electrochemically Active Biofilms

A laminar flow reactor was designed that provides constant and reproducible growth conditions for the bioelectrochemical observation of electroactive bacteria (EAB). Experiments were performed using four reactors in parallel to enable the comparison of EAB growth behavior and bioelectrochemical performance under different hydrodynamic conditions while simultaneously keeping biological conditions identical. With regard to the moderate flow conditions found in wastewater treatment applications, the wall shear stress was adjusted to a range between 0.4 mPa to 2.9 mPa. Chronoamperometric data indicate that early stage current densities are improved by a moderate increase of the wall shear stress. In the same way, current onset times were increasing slightly towards higher values of the applied wall shear stress. Long-term observations of EAB performance showed a decrease in current density and a leveling of the trend observed for the early stages of biofilm growth.

Three-dimensional biofilm image reconstruction for assessing structural parameters

Parameters representing three-dimensional (3D) biofilm structure are quantified from confocal laser-scanning microscope (CLSM) images. These 3D parameters describe the distribution of biomass pixels within the space occupied by a biofilm; however, they lack a direct connection to biofilm activity. As a result, researchers choose a handful of parameters without there being a consensus on a standard set of parameters. We hypothesized that a select 3D parameter set could be used to reconstruct a biofilm image and that the reconstructed and original biofilm images would have similar activities. To test this hypothesis, an algorithm was developed to reconstruct a biofilm image with parameters identical to those of the original CLSM image. We introduced an objective method to assess the reconstruction algorithm by comparing the activities of the original and reconstructed biofilm images. We found that biofilm images with identical structural parameters showed nearly identical activities and substrate concentration profiles. This implies that the set containing all common structural parameters can successfully describe biofilm structure. This finding is significant, as it opens the door to the next step, of finding a smaller standard set of biofilm structural parameters that can be used to compare biofilm structure.

The role of flow in bacterial biofilm morphology and wetting properties

Biofilms are bacterial communities embedded in an extracellular matrix, able to adhere to surfaces. Different experimental set-ups are widely used for in vitro biofilm cultivation; however, a well-defined comparison among different culture conditions, especially suited to interfacial characterization, is still lacking in the literature. The main objective of this work is to study the role of flow on biofilm formation, morphology and interfacial properties. Three different in vitro setups, corresponding to stagnant, shaking, and laminar flow conditions (custom-made flow cell), are used in this work to grow single strain biofilms of Pseudomonas fluorescens AR 11 on glass coupons. Results show that flow conditions significantly influenced biofilm formation kinetics, affecting mass transfer and cell attachment/detachment processes. Distinct morphological patterns are found under different flow regimes. Static contact angle data do not depend significantly on biofilm growth conditions in the parametric range investigated in this work.

A Dimensionally Reduced Model of Biofilm Growth Within a Flow Cell

Biofilms are colonies of bacteria attached to surfaces. They play a critical role in many engineering and medical applications. Scientists study biofilm growth in flow cells but often have limited direct knowledge of the environmental conditions in the apparatus. Using fully resolved, numerical simulations to estimate conditions within a flow cell is computationally expensive. In this paper, we use asymptotic analysis to create a simulation of a biofilm system that has one growth-limiting substrate, and we show that this method runs quickly while maintaining similar accuracy to prior models. These equations can provide a better understanding of the environmental conditions in experiments and can establish the boundary conditions for further smaller-scale numerical simulations.

Microfluidic bioanalytical flow cells for biofilm studies: a review

Bacterial biofilms are among the oldest and most prevalent multicellular life forms on Earth and are increasingly relevant in research areas related to industrial fouling, medicine and biotechnology. The main hurdles to obtaining definitive experimental results include time-varying biofilm properties, structural and chemical heterogeneity, and especially their strong sensitivity to environmental cues. Therefore, in addition to judicious choice of measurement tools, a well-designed biofilm study requires strict control over experimental conditions, more so than most chemical studies. Due to excellent control over a host of physiochemical parameters, microfluidic flow cells have become indispensable in microbiological studies. Not surprisingly, the number of lab-on-chip studies focusing on biofilms and other microbiological systems with expanded analytical capabilities has expanded rapidly in the past decade. In this paper, we comprehensively review the current state of microfluidic bioanalytical research applied to bacterial biofilms and offer a perspective on new approaches that are expected to drive continued advances in this field.

Real-time Imaging and Quantification of Fungal Biofilm Development Using a Two-Phase Recirculating Flow System

In oropharyngeal candidiasis, members of the genus Candida must adhere to and grow on the oral mucosal surface while under the effects of salivary flow. While models for the growth under flow have been developed, many of these systems are expensive, or do not allow imaging while the cells are under flow. We have developed a novel apparatus that allows us to image the growth and development of Candida albicans cells under flow and in real-time. Here, we detail the protocol for the assembly and use of this flow apparatus, as well as the quantification of data that are generated. We are able to quantify the rates that the cells attach to and detach from the slide, as well as to determine a measure of the biomass on the slide over time. This system is both economical and versatile, working with many types of light microscopes, including inexpensive benchtop microscopes, and is capable of extended imaging times compared to other flow systems. Overall, this is a low-throughput system that can provide highly detailed real-time information on the biofilm growth of fungal species under flow.

Dynamic Flow Characteristics and Design Principles of Laminar Flow Microbial Fuel Cells

Laminar flow microbial fuel cells (MFCs) are used to understand the role of microorganisms, and their interactions with electrodes in microbial bioelectrochemical systems. In this study, we reported the flow characteristics of laminar flow in a typical MFC configuration in a non-dimensional form, which can serve as a guideline in the design of such microfluidic systems. Computational fluid dynamics simulations were performed to examine the effects of channel geometries, surface characteristics, and fluid velocity on the mixing dynamics in microchannels with a rectangular cross-section. The results showed that decreasing the fluid velocity enhances mixing but changing the angle between the inlet channels, only had strong effects when the angle was larger than 135°. Furthermore, different mixing behaviors were observed depending on the angle of the channels, when the microchannel aspect ratio was reduced. Asymmetric growth of microbial biofilm on the anode side skewed the mixing zone and wall roughness due to the bacterial attachment, which accelerated the mixing process and reduced the efficiency of the laminar flow MFC. Finally, the magnitude of mass diffusivity had a substantial effect on mixing behavior. The results shown here provided both design guidelines, as well as better understandings of the MFCs due to microbial growth.

Polyester-based particles to overcome the obstacles of mucus and biofilms in the lung for tobramycin application under static and dynamic fluidic conditions

Pulmonary infections with Pseudomonas aeruginosa and Burkholderia cepacia complex (Bcc) are difficult to treat and related with high mortality in some diseases like cystic fibrosis due to the recurrent formation of biofilms. The biofilm formation hinders efficient treatment with inhaled antibiotics due to a low penetration of the antibiotics through the polyanionic biofilm matrix and increased antimicrobial resistance of the biofilm-embedded bacteria. In this study, tobramycin (Tb) was encapsulated in particles based on poly(d,l,-lactide-co-glycolide) (PLGA) and poly(ethylene glycol)-co-poly(d,l,-lactide-co-glycolide) diblock (PEG-PLGA) to overcome the biofilm barrier with particle sizes of 225-231 nm (nanoparticles) and 896-902 nm (microparticles), spherical shape and negative zeta potentials. The effectiveness against biofilms of P. aeruginosa and B. cepacia was strongly enhanced by the encapsulation under fluidic experimental condition as well as under static conditions in artificial mucus. The biofilm-embedded bacteria were killed by less than 0.77 mg/l encapsulated Tb, whereas 1,000 mg/l of free Tb or the bulk mixtures of Tb and the particles were ineffective against the biofilms. Moreover, encapsulated Tb was even effective against biofilms of the intrinsically aminoglycoside-resistant B. cepacia, indicating a supportive effect of PEG and PLGA on Tb. No cytotoxicity was detected in vitro in human lung epithelial cells with any formulation.

Experimental and visual research on the microbial induced carbonate precipitation by Pseudomonas aeruginosa

Microbial induced carbonate precipitation (MICP) is a common occurrence of geochemistry influences in many fields, such as biological, geographical, and engineering systems. However, the processes that control interactions between carbonate biomineralization and biofilm properties are poorly understood. We develop a method for real time, in situ and nondestructive imaging with confocal scanning microscopy. This method provides a possible way to observe biomineralization process and the morphology of biomineralized deposits within biofilms. We use this method to show calcite biominerals produced by Pseudomonas aeruginosa biofilms which extremely change biofilm structures. The distribution of calcite precipitation produced in situ biomineralization is highly heterogeneous in biofilms and also to occur primarily on the bottom of biofilms. It is distinct from those usual expectations that mineral started to precipitate from surface of biofilm. Our results reveal that biomineralization plays a comprehensive regulation function on biofilm architecture and properties.

A new look at bubbles during biofilm inoculation reveals pronounced effects on growth and patterning

Specially designed microfluidic bioflow cells were used to temporarily trap microbubbles during different inoculation stages of Pseudomonas sp. biofilms. Despite being eliminated many hours before biofilm appearance, templated growth could occur at former bubble positions. Bubble-templated growth was either continuous or in ring patterns, depending on the stage of inoculation when the bubbles were introduced. Templated biofilms were strongly enhanced in terms of their growth kinetics and structural homogeneity. High resolution confocal imaging showed two separate bubble-induced bacterial trapping modes, which were responsible for the altered biofilm development. It is concluded that static bubbles can be exploited for fundamental improvements to bioreactor performance, as well as open new avenues to study isolated bacteria and small colonies.

Development of a flow chamber system for the reproducible in vitro analysis of biofilm formation on implant materials

Since the introduction of modern dental implants in the 1980s, the number of inserted implants has steadily increased. Implant systems have become more sophisticated and have enormously enhanced patients’ quality of life. Although there has been tremendous development in implant materials and clinical methods, bacterial infections are still one of the major causes of implant failure. These infections involve the formation of sessile microbial communities, called biofilms. Biofilms possess unique physical and biochemical properties and are hard to treat conventionally. There is a great demand for innovative methods to functionalize surfaces antibacterially, which could be used as the basis of new implant technologies. Present, there are few test systems to evaluate bacterial growth on these surfaces under physiological flow conditions. We developed a flow chamber model optimized for the assessment of dental implant materials. As a result it could be shown that biofilms of the five important oral bacteria Streptococcus gordonii, Streptococcus oralis, Streptococcus salivarius, Porphyromonas gingivalis, and Aggregatibacter actinomycetemcomitans, can be reproducibly formed on the surface of titanium, a frequent implant material. This system can be run automatically in combination with an appropriate microscopic device and is a promising approach for testing the antibacterial effect of innovative dental materials.

Biofilm development of an opportunistic model bacterium analysed at high spatiotemporal resolution in the framework of a precise flow cell

Life of bacteria is governed by the physical dimensions of life in microscales, which is dominated by fast diffusion and flow at low Reynolds numbers. Microbial biofilms are structurally and functionally heterogeneous and their development is suggested to be interactively related to their microenvironments. In this study, we were guided by the challenging requirements of precise tools and engineered procedures to achieve reproducible experiments at high spatial and temporal resolutions. Here, we developed a robust precise engineering approach allowing for the quantification of real-time, high-content imaging of biofilm behaviour under well-controlled flow conditions. Through the merging of engineering and microbial ecology, we present a rigorous methodology to quantify biofilm development at resolutions of single micrometre and single minute, using a newly developed flow cell. We designed and fabricated a high-precision flow cell to create defined and reproducible flow conditions. We applied high-content confocal laser scanning microscopy and developed image quantification using a model biofilm of a defined opportunistic strain, Pseudomonas putida OUS82. We observed complex patterns in the early events of biofilm formation, which were followed by total dispersal. These patterns were closely related to the flow conditions. These biofilm behavioural phenomena were found to be highly reproducible, despite the heterogeneous nature of biofilm.

In Situ Biomineralization and Particle Deposition Distinctively Mediate Biofilm Susceptibility to Chlorine

Microbial biofilms and mineral precipitation commonly co-occur in engineered water systems, such as cooling towers and water purification systems, and both decrease process performance. Microbial biofilms are extremely challenging to control and eradicate. We previously showed that in situ biomineralization and the precipitation and deposition of abiotic particles occur simultaneously in biofilms under oversaturated conditions. Both processes could potentially alter the essential properties of biofilms, including susceptibility to biocides. However, the specific interactions between mineral formation and biofilm processes remain poorly understood. Here we show that the susceptibility of biofilms to chlorination depends specifically on internal transport processes mediated by biomineralization and the accumulation of abiotic mineral deposits. Using injections of the fluorescent tracer Cy5, we show that Pseudomonas aeruginosa biofilms are more permeable to solutes after in situ calcite biomineralization and are less permeable after the deposition of abiotically precipitated calcite particles. We further show that biofilms are more susceptible to chlorine killing after biomineralization and less susceptible after particle deposition. Based on these observations, we found a strong correlation between enhanced solute transport and chlorine killing in biofilms, indicating that biomineralization and particle deposition regulate biofilm susceptibility by altering biocide penetration into the biofilm. The distinct effects of in situ biomineralization and particle deposition on biocide killing highlight the importance of understanding the mechanisms and patterns of biomineralization and scale formation to achieve successful biofilm control.

Methods for characterizing the co-development of biofilm and habitat heterogeneity

Biofilms are surface-attached microbial communities that have complex structures and produce significant spatial heterogeneities. Biofilm development is strongly regulated by the surrounding flow and nutritional environment. Biofilm growth also increases the heterogeneity of the local microenvironment by generating complex flow fields and solute transport patterns. To investigate the development of heterogeneity in biofilms and interactions between biofilms and their local micro-habitat, we grew mono-species biofilms of Pseudomonas aeruginosa and dual-species biofilms of P. aeruginosa and Escherichia coli under nutritional gradients in a microfluidic flow cell. We provide detailed protocols for creating nutrient gradients within the flow cell and for growing and visualizing biofilm development under these conditions. We also present protocols for a series of optical methods to quantify spatial patterns in biofilm structure, flow distributions over biofilms, and mass transport around and within biofilm colonies. These methods support comprehensive investigations of the co-development of biofilm and habitat heterogeneity.

Pseudomonas aeruginosa promotes Escherichia coli biofilm formation in nutrient-limited medium

Biofilms have been implicated as an important reservoir for pathogens and commensal enteric bacteria such as Escherichia coli in natural and engineered water systems. However, the processes that regulate the survival of E. coli in aquatic biofilms have not been thoroughly studied. We examined the effects of hydrodynamic shear and nutrient concentrations on E. coli colonization of pre-established Pseudomonas aeruginosa biofilms, co-inoculation of E. coli and P. aeruginosa biofilms, and P. aeruginosa colonization of pre-established E. coli biofilms. In nutritionally-limited R2A medium, E. coli dominated biofilms when co-inoculated with P. aeruginosa, and successfully colonized and overgrew pre-established P. aeruginosa biofilms. In more enriched media, P. aeruginosa formed larger clusters, but E. coli still extensively overgrew and colonized the interior of P. aeruginosa clusters. In mono-culture, E. coli formed sparse and discontinuous biofilms. After P. aeruginosa was introduced to these biofilms, E. coli growth increased substantially, resulting in patterns of biofilm colonization similar to those observed under other sequences of organism introduction, i.e., E. coli overgrew P. aeruginosa and colonized the interior of P. aeruginosa clusters. These results demonstrate that E. coli not only persists in aquatic biofilms under depleted nutritional conditions, but interactions with P. aeruginosa can greatly increase E. coli growth in biofilms under these experimental conditions.

The influence of shear on the metabolite yield of Lactobacillus rhamnosus biofilms

A tubular recycle bioreactor was employed to ensure homogeneous shear conditions on the biofilm surface. Superficial liquid velocities of 0.19 ms(-1), 0.37 ms(-1), 0.55 ms(-1) and 3.65 ms(-1) were used. The highest velocity resulted in negligible cell attachment (chemostat) while the ratio of attached-to-total cell mass escalated as the superficial velocity decreased. The lactic acid yield on glucose increased from 0.75 g g(-1) to 0.90 g g(-1) with declining shear while the corresponding acetoin yield on glucose decreased from 0.074 g g(-1) to 0.017 g g(-1). Redox analysis of the catabolites revealed a net consumption of NADH in the anabolism, while the extent of NADH consumption decreased when shear was reduced. This was attributed to the formation of more extracellular polymeric substance (EPS) at low shear conditions. A simplified metabolic flux model was used to estimate the EPS content of the biomass as a function of the shear velocity. Rate data supported the notion of increased EPS at lower shear.

Functional gene diversity of oolitic sands from Great Bahama Bank

Despite the importance of oolitic depositional systems as indicators of climate and reservoirs of inorganic C, little is known about the microbial functional diversity, structure, composition, and potential metabolic processes leading to precipitation of carbonates. To fill this gap, we assess the metabolic gene carriage and extracellular polymeric substance (EPS) development in microbial communities associated with oolitic carbonate sediments from the Bahamas Archipelago. Oolitic sediments ranging from high-energy 'active' to lower energy 'non-active' and 'microbially stabilized' environments were examined as they represent contrasting depositional settings, mostly influenced by tidal flows and wave-generated currents. Functional gene analysis, which employed a microarray-based gene technology, detected a total of 12,432 of 95,847 distinct gene probes, including a large number of metabolic processes previously linked to mineral precipitation. Among these, gene-encoding enzymes for denitrification, sulfate reduction, ammonification, and oxygenic/anoxygenic photosynthesis were abundant. In addition, a broad diversity of genes was related to organic carbon degradation, and N2 fixation implying these communities has metabolic plasticity that enables survival under oligotrophic conditions. Differences in functional genes were detected among the environments, with higher diversity associated with non-active and microbially stabilized environments in comparison with the active environment. EPS showed a gradient increase from active to microbially stabilized communities, and when combined with functional gene analysis, which revealed genes encoding EPS-degrading enzymes (chitinases, glucoamylase, amylases), supports a putative role of EPS-mediated microbial calcium carbonate precipitation. We propose that carbonate precipitation in marine oolitic biofilms is spatially and temporally controlled by a complex consortium of microbes with diverse physiologies, including photosynthesizers, heterotrophs, denitrifiers, sulfate reducers, and ammonifiers.

Biofilm responses to smooth flow fields and chemical gradients in novel microfluidic flow cells

We present two novel microfluidic flow cells developed to provide reliable control of flow distributions and chemical gradients in biofilm studies. We developed a single-inlet microfluidic flow cell to support biofilm growth under a uniform velocity field, and a double-inlet flow cell to provide a very smooth transverse concentration gradient. Both flow cells consist of a layer of polydimethylsiloxane (PDMS) bonded to glass cover slips and were fabricated using the replica molding technique. We demonstrate the capabilities of the flow cells by quantifying flow patterns before and after growth of Pseudomonas aeruginosa biofilms through particle imaging velocimetry, and by evaluating concentration gradients within the double-inlet microfluidic flow cell. Biofilm growth substantially increased flow complexity by diverting flow around biomass, creating high- and low-velocity regions and surface friction. Under a glucose gradient in the double-inlet flow cell, P. aeruginosa biofilms grew in proportion to the local glucose concentration, producing distinct spatial patterns in biofilm biomass relative to the imposed glucose gradient. When biofilms were subjected to a ciprofloxacin gradient, spatial patterns of fractions of dead cells were also in proportion to the local antibiotic concentration. These results demonstrate that the microfluidic flow cells are suitable for quantifying flow complexities resulting from flow-biofilm interactions and investigating spatial patterns of biofilm growth under chemical gradients. These novel microfluidic flow cells will facilitate biofilm research that requires flow control and in situ imaging, particularly investigations of biofilm-environment interactions.

Biophysical controls on cluster dynamics and architectural differentiation of microbial biofilms in contrasting flow environments

Ecology, with a traditional focus on plants and animals, seeks to understand the mechanisms underlying structure and dynamics of communities. In microbial ecology, the focus is changing from planktonic communities to attached biofilms that dominate microbial life in numerous systems. Therefore, interest in the structure and function of biofilms is on the rise. Biofilms can form reproducible physical structures (i.e. architecture) at the millimetre-scale, which are central to their functioning. However, the spatial dynamics of the clusters conferring physical structure to biofilms remains often elusive. By experimenting with complex microbial communities forming biofilms in contrasting hydrodynamic microenvironments in stream mesocosms, we show that morphogenesis results in ‘ripple-like’ and ‘star-like’ architectures – as they have also been reported from monospecies bacterial biofilms, for instance. To explore the potential contribution of demographic processes to these architectures, we propose a size-structured population model to simulate the dynamics of biofilm growth and cluster size distribution. Our findings establish that basic physical and demographic processes are key forces that shape apparently universal biofilm architectures as they occur in diverse microbial but also in single-species bacterial biofilms.

A novel approach to determine the efficacy of patterned surfaces for biofouling control in relation to its microfluidic environment

Biofouling, the unwanted growth of sessile microorganisms on submerged surfaces, presents a serious problem for underwater structures. While biofouling can be controlled to various degrees with different microstructure-based patterned surfaces, understanding of the underlying mechanism is still imprecise. Researchers have long speculated that microtopographies might influence near-surface microfluidic conditions, thus microhydrodynamically preventing the settlement of microorganisms. It is therefore very important to identify the microfluidic environment developed on patterned surfaces and its relation with the antifouling behaviour of those surfaces. This study considered the wall shear stress distribution pattern as a significant aspect of this microfluidic environment. In this study, patterned surfaces with microwell arrays were assessed experimentally with a real-time biofilm development monitoring system using a novel microchannel-based flow cell reactor. Finally, computational fluid dynamics simulations were carried out to show how the microfluidic conditions were affecting the initial settlement of microorganisms.

Effects of fluid flow conditions on interactions between species in biofilms

Most microorganisms live in complex communities, where they interact both synergistically and competitively. To explore the relationship between environmental heterogeneity and the spatial structure of well-defined biofilms, single- and mixed-species biofilms of Pseudomonas aeruginosa PAO1 and Flavobacterium sp. CDC-65 was grown in a planar flow cell under highly controlled flow gradients. Both organisms behaved differently in mixed cultures than in single-species cultures due to inter-species interactions, and these interactions were significantly affected by external flow conditions. Pseudomonas and Flavobacterium showed a competitive relationship under slow inflow conditions, where the supply of growth medium was limited. Under such competitive conditions, the faster- specific growth rate of Flavobacterium allowed it to secure access to favorable regions of the biofilm by overgrowing Pseudomonas. In contrast, Pseudomonas was restricted to nutritionally depleted habitat near the base of the biofilm, and its growth was significantly inhibited. Conversely, under higher inflow conditions providing greater influx of growth medium, both organisms accumulated greater biomass in mixed biofilms than in single-species biofilms. Spatial segregation of the two organisms within the biofilms contributed to enhanced overall exploitation of available nutrients and substrates, while morphological changes favored better adherence to the surface under high hydrodynamic shear. These results indicate that synergy and competition in biofilms vary with flow conditions. Limited resource replenishment favors competition under low-flow conditions, while high flow reduces competition and favors synergy by providing greater resources and simultaneously imposing increased hydrodynamic shear that makes it more difficult to accumulate biomass on the surface. Ecological interactions that produce mechanically stronger and more robust biofilms will support more extensive growth on surfaces subject to high hydrodynamic shear, but these interactions are difficult to predict from observations of the behavior of individual organisms.

Biofilms 2012: new discoveries and significant wrinkles in a dynamic field

The ASM 6th Conference on Biofilms was held in Miami, Florida, 29 September to 4 October, 2012. The conference provided an opportunity for the exchange of new findings and ideas with regard to biofilm research. A wide range of findings, spanning applied biology, evolution, ecology, physiology, and molecular biology, were presented at the conference. This review summarizes the presentations with regard to emerging biofilm-related themes.

Biofilms as living catalysts in continuous chemical syntheses

Biofilms are resilient to a wide variety of environmental stresses. This inherited robustness has been exploited mainly for bioremediation. With a better understanding of their physiology, the application of these living catalysts has been extended to the production of bulk and fine chemicals as well as towards biofuels, biohydrogen, and electricity production in microbial fuel cells. Numerous challenges call for novel solutions and concepts of analytics, biofilm reactor design, product recovery, and scale-up strategies. In this review, we highlight recent advancements in spatiotemporal biofilm characterization and new biofilm reactor developments for the production of value-added fine chemicals as well as current challenges and future scenarios.

Mini-review: convection around biofilms

Water that flows around a biofilm influences the transport of solutes into and out of the biofilm and applies forces to the biofilm that can cause it to deform and detach. Engineering approaches to quantifying and understanding these phenomena are reviewed in the context of biofilm systems. The slow-moving fluid adjacent to the biofilm acts as an insulator for diffusive exchange. External mass transfer resistance is important because it can exacerbate oxygen or nutrient limitation in biofilms, worsen product inhibition, affect quorum sensing, and contribute to the development of tall, fingerlike biofilm clusters. Measurements of fluid motion around biofilms by particle velocimetry and magnetic resonance imaging indicate that water flows around, but not through biofilm cell clusters. Moving fluid applies forces to biofilms resulting in diverse outcomes including viscoelastic deformation, rolling, development of streamers, oscillatory movement, and material failure or detachment. The primary force applied to the biofilm is a shear force in the main direction of fluid flow, but complex hydrodynamics including eddies, vortex streets, turbulent wakes, and turbulent bursts result in additional force components.