Mathematical modelling of biofilm structures

Is it selfish to be filamentous in biofilms? Individual-based modeling links microbial growth strategies with morphology using the new and modular iDynoMiCS 2.0

Microbial communities are found in all habitable environments and often occur in assemblages with self-organized spatial structures developing over time. This complexity can only be understood, predicted, and managed by combining experiments with mathematical modeling. Individual-based models are particularly suited if individual heterogeneity, local interactions, and adaptive behavior are of interest. Here we present the completely overhauled software platform, the individual-based Dynamics of Microbial Communities Simulator, iDynoMiCS 2.0, which enables researchers to specify a range of different models without having to program. Key new features and improvements are: (1) Substantially enhanced ease of use (graphical user interface, editor for model specification, unit conversions, data analysis and visualization and more). (2) Increased performance and scalability enabling simulations of up to 10 million agents in 3D biofilms. (3) Kinetics can be specified with any arithmetic function. (4) Agent properties can be assembled from orthogonal modules for pick and mix flexibility. (5) Force-based mechanical interaction framework enabling attractive forces and non-spherical agent morphologies as an alternative to the shoving algorithm. The new iDynoMiCS 2.0 has undergone intensive testing, from unit tests to a suite of increasingly complex numerical tests and the standard Benchmark 3 based on nitrifying biofilms. A second test case was based on the "biofilms promote altruism" study previously implemented in BacSim because competition outcomes are highly sensitive to the developing spatial structures due to positive feedback between cooperative individuals. We extended this case study by adding morphology to find that (i) filamentous bacteria outcompete spherical bacteria regardless of growth strategy and (ii) non-cooperating filaments outcompete cooperating filaments because filaments can escape the stronger competition between themselves. In conclusion, the new substantially improved iDynoMiCS 2.0 joins a growing number of platforms for individual-based modeling of microbial communities with specific advantages and disadvantages that we discuss, giving users a wider choice.

Instabilities in a growing system of active particles: scalar and vectorial systems

The physics of micron-scale biological colonies usually benefits from different out-of-equilibrium sources. In bacterial colonies and cellular tissues, the growth process is among the important active sources that determine the dynamics. In this article, we study the generic dynamical instabilities associated with the growth phenomena that may arise in both scalar and vectorial systems. In vectorial systems, where the rotational degrees of particles play a role, a phenomenological growth-mediated torque can affect the rotational dynamics of individual particles. We show that such a growth-mediated torque can result in active traveling waves in the bulk of a growing system. In addition to the bulk properties, we analyze the instabilities in the shape of growing interfaces in both scalar and vectorial systems.

Unique stratification of biofilm density in heterotrophic membrane-aerated biofilms: An experimental and modeling study

We consistently find a band of high cell density develop within heterotrophic membrane-aerated biofilms. This study reports and attempts to explain this unique behavior. Biofilm density affects volumetric reaction rates, biofilm growth rates, substrate diffusion, and mechanical behavior. Yet the mechanisms and dynamics of biofilm density development are poorly understood. In this study, a membrane-aerated biofilm, where O₂ was supplied from the base of the biofilm and acetate from the bulk liquid, was used to explore spatial and temporal patterns of density development. Biofilm density was assessed by optical coherence tomography. After inoculation, the biofilm quickly increased in thickness, with a low density throughout. However, as the biofilm reached a stable thickness of around 1000 μm, a high-density layer developed in the biofilm interior. The layer slowly expanded over time. Oxygen microprofiles in the biofilm showed this layer coincided with the most metabolically active zone, resulting from counter-diffusing O₂ and acetate. The formation of this dense layer appeared to be related to changes in growth rates. Initially, high growth rates throughout the biofilm presumably led to fast-growing, low-density biofilms. As the biofilm became thicker, and as substrates became limiting in the biofilm interior, growth rates decreased, resulting in new growth at a higher density. A 1-D mathematical model with variable biofilm density was developed by linking the rates of extracellular polymeric substances (EPS) production to the growth rate. The model captured the initial fast growth at a low density, followed by a slower, substrate-limited growth in the biofilm interior, producing a dense band within the biofilm. Together, these results suggest that low growth rates can lead to high-density zones within the interior of counter-diffusional biofilms. These findings should also be relevant to conventional, co-diffusional biofilms, although differences in density may be less obvious.

The biofilm matrix: multitasking in a shared space

The biofilm matrix can be considered to be a shared space for the encased microbial cells, comprising a wide variety of extracellular polymeric substances (EPS), such as polysaccharides, proteins, amyloids, lipids and extracellular DNA (eDNA), as well as membrane vesicles and humic-like microbially derived refractory substances. EPS are dynamic in space and time and their components interact in complex ways, fulfilling various functions: to stabilize the matrix, acquire nutrients, retain and protect eDNA or exoenzymes, or offer sorption sites for ions and hydrophobic substances. The retention of exoenzymes effectively renders the biofilm matrix an external digestion system influencing the global turnover of biopolymers, considering the ubiquitous relevance of biofilms. Physico-chemical and biological interactions and environmental conditions enable biofilm systems to morph into films, microcolonies and macrocolonies, films, ridges, ripples, columns, pellicles, bubbles, mushrooms and suspended aggregates - in response to the very diverse conditions confronting a particular biofilm community. Assembly and dynamics of the matrix are mostly coordinated by secondary messengers, signalling molecules or small RNAs, in both medically relevant and environmental biofilms. Fully deciphering how bacteria provide structure to the matrix, and thus facilitate and benefit from extracellular reactions, remains the challenge for future biofilm research.

Collective behavior and virulence arsenal of the fish pathogen Piscirickettsia salmonis in the biofilm realm

Piscirickettsiosis is a fish disease caused by the Gram-negative bacterium Piscirickettsia salmonis. This disease has a high socio-economic impact on the Chilean salmonid aquaculture industry. The bacterium has a cryptic character in the environment and their main reservoirs are yet unknown. Bacterial biofilms represent a ubiquitous mechanism of cell persistence in diverse natural environments and a risk factor for the pathogenesis of several infectious diseases, but their microbiological significance for waterborne veterinary diseases, including piscirickettsiosis, have seldom been evaluated. This study analyzed the in vitro biofilm behavior of P. salmonis LF-89^T (genogroup LF-89) and CA5 (genogroup EM-90) using a multi-method approach and elucidated the potential arsenal of virulence of the P. salmonis LF-89^T type strain in its biofilm state. P. salmonis exhibited a quick kinetics of biofilm formation that followed a multi-step and highly strain-dependent process. There were no major differences in enzymatic profiles or significant differences in cytotoxicity (as tested on the Chinook salmon embryo cell line) between biofilm-derived bacteria and planktonic equivalents. The potential arsenal of virulence of P. salmonis LF-89^T in biofilms, as determined by whole-transcriptome sequencing and differential gene expression analysis, consisted of genes involved in cell adhesion, polysaccharide biosynthesis, transcriptional regulation, and gene mobility, among others. Importantly, the global gene expression profiles of P. salmonis LF-89^T were not enriched with virulence-related genes upregulated in biofilm development stages at 24 and 48 h. An enrichment in virulence-related genes exclusively expressed in biofilms was also undetected. These results indicate that early and mature biofilm development stages of P. salmonis LF-89^T were transcriptionally no more virulent than their planktonic counterparts, which was supported by cytotoxic trials, which, in turn, revealed that both modes of growth induced important and very similar levels of cytotoxicity on the salmon cell line. Our results suggest that the aforementioned biofilm development stages do not represent hot spots of virulence compared with planktonic counterparts. This study provides the first transcriptomic catalogue to select specific genes that could be useful to prevent or control the (in vitro and/or in vivo) adherence and/or biofilm formation by P. salmonis and gain further insights into piscirickettsiosis pathogenesis.

Evaluating the adhesive potential of the newly isolated bacterial strains in research exploitation of plant microbial interaction

Bacterial adhesion potential constitutes the transition of bacteria from the planktonic to the static phase by promoting biofilm formation, which plays a significant role in plant-microbial interaction in the agriculture industry. In present study, the adhesion potential of five soil-borne bacterial strains belonging to different genera was studied. All bacterial strains were capable of forming colonies and biofilms of different levels of firmness on polystyrene. Significant variation was observed in hydrophobicity and motility assays. Among the five bacterial strains (SH-6, SH-8, SH-9, SH-10, and SH-19), SH-19 had a strong hydrophobic force, while SH-10 showed the most hydrophilic property. SH-6 showed great variability in motility; SH-8 had a swimming diffusion diameter of 70 mm, which was three times higher than that of SH-19. In the motility assay, SH-9 and SH-10 showed diffusion diameters of approximately 22 mm and 55 mm, respectively. Furthermore, among the five strains, four are predominately electron donors and one is electron acceptors. Overall, positive correlation was observed among Lewis acid base properties, hydrophobicity, and biofilm forming ability. However, no correlation of motility with bacterial adhesion could be found in present experimental work. Scanning electron microscopy images confirmed the adhesion potential and biofilm ability within extra polymeric substances. Research on the role of adhesion in biofilm formation of bacteria isolated from plants is potentially conducive for developing strategies such as plant-microbial interaction to mitigate the abiotic stress.

On the mechanisms for aerobic granulation - model based evaluation

In this study a mathematical framework was developed to describe aerobic granulation based on 6 main mechanisms: microbial selection, selective wasting, maximizing transport of substrate into the biofilm, selective feeding, substrate type and breakage. A numerical model was developed using four main components; a 1D convection/dispersion model to describe the flow dynamics in a reactor, a reaction/diffusion model describing the essential conversions for granule growth, a setting model to track granules during settling and feeding, and a population model containing up to 100,000 clusters of granules to model the stochastic behaviour of the granulation process. With this approach the model can explain the dynamics of the granulation process observed in practice. This includes the presence of a lag phase and a granulation phase. Selective feeding was identified as an important mechanism that was not yet reported in literature. When aerobic granules are grown from activated sludge flocs, a lag phase occurs, in which not many granules are formed, followed by a granulation phase in which granules rapidly appear. The ratio of granule forming to non-granule forming substrate together with the feast/famine ratio determine if the transition from the lag phase to the granulation phase is successful. The efficiency of selective wasting and selective feeding both determine the rate of this transition. Brake-up of large granules into smaller well settling particles was shown to be an important source for new granules. The granulation process was found to be the combined result from all 6 mechanisms and if conditions for either one are not optimal, other mechanisms can, to some extent, compensate. This model provides a theoretical framework to analyse the different relevant mechanisms for aerobic granular sludge formation and can form the basis for a comprehensive model that includes detailed nutrient removal aspects.

A mathematical model of discrete attachment to a cellulolytic biofilm using random DEs

We propose a new mathematical framework for the addition of stochastic attachment to biofilm models, via the use of random ordinary differential equations. We focus our approach on a spatially explicit model of cellulolytic biofilm growth and formation that comprises a PDE-ODE coupled system to describe the biomass and carbon respectively. The model equations are discretized in space using a standard finite volume method. We introduce discrete attachment events into the discretized model via an impulse function with a standard stochastic process as input. We solve our model with an implicit ODE solver. We provide basic simulations to investigate the qualitative features of our model. We then perform a grid refinement study to investigate the spatial convergence of our model. We investigate model behaviour while varying key attachment parameters. Lastly, we use our attachment model to provide evidence for a stable travelling wave solution to the original PDE-ODE coupled system.

Understanding photosynthetic biofilm productivity and structure through 2D simulation

We present a spatial model describing the growth of a photosynthetic microalgae biofilm. In this 2D-model we consider photosynthesis, cell carbon accumulation, extracellular matrix excretion, and mortality. The rate of each of these mechanisms is given by kinetic laws regulated by light, nitrate, oxygen and inorganic carbon. The model is based on mixture theory and the behaviour of each component is defined on one hand by mass conservation, which takes into account biological features of the system, and on the other hand by conservation of momentum, which expresses the physical properties of the components. The model simulates the biofilm structural dynamics following an initial colonization phase. It shows that a 75 μm thick active region drives the biofilm development. We then determine the optimal harvesting period and biofilm height which maximize productivity. Finally, different harvesting patterns are tested and their effect on biofilm structure are discussed. The optimal strategy differs whether the objective is to recover the total biofilm or just the algal biomass.

Microalgae have many industrial applications, ranging from aquaculture, pharmaceutics, food industry to green energy. Planktonic cultivation of microalgae is energy-consuming. Growing them under a biofilm form is a new trend with attracting promises. Biofilms are complex heterogeneous ecosystems composed of microorganisms embedded within a self-produced extracellular matrix and stuck to a surface. Most of the studies have focused on bacterial biofilms and knowledge about microalgae biofilms is still very limited. In this paper, we propose a mathematical model describing microalgae biofilm development. We simulate in 1D and 2D the impact of harvesting conditions on biofilm productivity. In agreement with available experimental observations, we find that there exist optimal frequencies and patterns that optimize the productivity. We also show that the optimal conditions differ whether for maximizing the productivity of microalgae or of the whole biofilm.

Fate of sloughed biomass in integrated fixed-film systems

Fate of biofilm sloughing was assessed in a laboratory-scale (LS) integrated fixed-film sequencing batch reactor (IF-SBR) treating synthetic wastewater and in a full-scale (FS) integrated fixed-film activated sludge (IFAS) system treating municipal wastewater. It was observed that the properties of biofilms and flocs, including sludge volume index (SVI), mixed liquor suspended solids (MLSS), effluent suspended solids (ESS), relative hydrophobicity, and composition of extracellular polymeric substance (EPS) were associated with biofilm sloughing and formation of large granular flocs in the LS IF-SBR. In the FS IFAS system, the changes were studied at the molecular level. For example, the extracted EPS content results (the protein to polysaccharide ratio decreased in the flocs and increased in the biofilms, with biofilm sloughing) were complemented with the confocal laser scanning microscopy (CLSM) coupled with molecular specific staining. CLSM analyses revealed that micro-colonies rich in polysaccharides readily sloughed from the carriers. Live-dead staining revealed areas of the biofilm where the viability of biomass was a contributing factor associated with areas of the biofilm susceptible to sloughing. 16S rRNA gene sequencing (Illumina) of FS IFAS samples revealed greater diversity (α-diversity) in biofilms compared to flocs. Biofilm sloughing resulted in a decrease in diversity in biofilms and a corresponding increase in the flocs during sloughing. Microbial population dynamics revealed that bacteria known for denitrification (for example, Comamonadaceae) detached from the biofilms during sloughing, readily associated with the suspended biomass, and were retained in the bioreactors.

Data-driven modeling of heterogeneous viscoelastic biofilms

Biofilms are typically heterogeneous in morphology, structure, and composition, resulting in non-uniform mechanical properties. The distribution of mechanical properties, in turn, determines the biofilm behavior, such as deformation and detachment. Most biofilm models neglect biofilm heterogeneity, especially at the microscale. In this study, an image-based modeling approach was developed to transform two-dimensional optical coherence tomography (OCT) biofilm images to a pixel-scale non-Newtonian viscosity map of the biofilm. The map was calibrated using the bulk viscosity data from rheometer tests, based on assumed maximum and minimum viscosities and a relationship between OCT image intensity signals and non-Newtonian viscosity. While not quantitatively measuring biofilm viscosity for each pixel, it allows a rational spatial allocation of viscosities within the biofilm: areas with lower cell density, e.g., voids, are assigned lower viscosities, and areas with high cell densities are assigned higher viscosities. The spatial distribution of non-Newtonian viscosity was applied in an established Oldroyd-B constitutive model and implemented using the phase-field continuum approach for the deformation and stress analysis. The heterogeneous model was able to predict deformations more accurately than a homogenous one. Stress distribution in the heterogeneous biofilm displayed better characteristics than that in the homogeneous one, because it is highly dependent on the viscosity distribution. This work, using a pixel-scale, image-based approach to map the mechanical heterogeneity of biofilms for computational deformation and stress analysis, provides a novel modeling approach that allows the consideration of biofilm structural and mechanical heterogeneity. Future research should better characterize the relationship between OCT signal and viscosity, and consider other constitutive models for biofilm mechanical behavior. This article is protected by copyright. All rights reserved.

The potentials of biofilm reactor as recourse for the recuperation of rare earth metals/elements from wastewater: a review

Wastewater is nowadays increasingly receiving global attention as a resource much more than a problem due to its potential so serve as a resource recovery channel. In this regard, wastewater is gradually been transformed from being a cesspool to a "treasure pool." Among notable resources in the treasure pool, rare earth metals/elements (REEs) warrant focal investigation, both in terms of environmental abundance and biorecovery, due to their environmental impacts. The ineffectiveness or cost intensiveness of extant physicochemical and advanced wastewater resource recovery techniques warrants the investigation of natural phenomenons in the treasure pools. Bacteria are able to cleverly secrete certain biochemicals to help trap and aggregate nutrients for their metabolism-the biofilms. In this regard, there is increased espousal of biofilm-enabled reactors, especially for the application of the recovery of invaluable feedstock in wastewater as well as other aqueous media due to high production rates and stability of cells. Furthermore, it anticipated that this technology will be translated to recovery of rare earth elements, due to their increased demand across the globe. This piece reiterates the nitty-gritty of biofilm-enhanced biorecovery and also keeps the scientific readership abreast of the multifarious aspects regarding the successful biofilm affected biorecovery of REEs at reactor scale.

Morphogenesis and oxygen dynamics in phototrophic biofilms growing across a gradient of hydraulic conditions

Biofilms are surface-attached and matrix-enclosed microbial communities that dominate microbial life in numerous ecosystems. Using flumes and automated optical coherence tomography, we studied the morphogenesis of phototrophic biofilms along a gradient of hydraulic conditions. Compact and coalescent biofilms formed under elevated bed shear stress, whereas protruding clusters separated by troughs formed under reduced shear stress. This morphological differentiation did not linearly follow the hydraulic gradient, but a break point emerged around a shear stress of ~0.08 Pa. While community composition did not differ between high and low shear environments, our results suggest that the morphological differentiation was linked to biomass displacement and reciprocal interactions between the biofilm structure and hydraulics. Mapping oxygen concentrations within and around biofilm structures, we provide empirical evidence for biofilm-induced alterations of oxygen mass transfer. Our findings suggest that architectural plasticity, efficient mass transfer, and resistance to shear stress contribute to the success of phototrophic biofilms.

Non-Invasive Measurement, Mathematical Simulation and In Situ Detection of Biofilm Evolution in Porous Media: A Review

The development of biofilms and the related changes in porous media in the subsurface cannot be directly observed and evaluated. The primary reason that the mechanism of biofilm clogging in porous media cannot be clearly demonstrated is due to the opacity and structural complexity of three-dimensional pore space. Interest in exploring methods to overcome this limitation has been increasing. In the first part of this review, we introduce the underlying characteristics of biofilm in porous media. Then, we summarize two approaches, non-invasive measurement methods and mathematical simulation strategies, for studying fluid–biofilm–porous medium interaction with spatiotemporal resolution. We also discuss the advantages and limitations of these approaches. Lastly, we provide a perspective on opportunities for in situ monitoring at the field site.

Spatial distribution of mechanical properties in Pseudomonas aeruginosa biofilms, and their potential impacts on biofilm deformation

The mechanical properties of biofilms can be used to predict biofilm deformation under external forces, for example, under fluid flow. We used magnetic tweezers to spatially map the compliance of Pseudomonas aeruginosa biofilms at the microscale, then applied modeling to assess its effects on biofilm deformation. Biofilms were grown in capillary flow cells with Reynolds numbers (Re) ranging from 0.28 to 13.9, bulk dissolved oxygen (DO) concentrations from 1 mg/L to 8 mg/L, and bulk calcium ion (Ca²⁺ ) concentrations of 0 and 100 mg CaCl₂ /L. Higher Re numbers resulted in more uniform biofilm morphologies. The biofilm was stiffer at the center of the flow cell than near the walls. Lower bulk DO led to more stratified biofilms. Higher Ca²⁺ concentrations led to increased stiffness and more uniform mechanical properties. Using the experimental mechanical properties, fluid-structure interaction models predicted up to 64% greater deformation for heterogeneous biofilms, compared with a homogeneous biofilms with the same average properties. However, the deviation depended on the biofilm morphology and flow regime. Our results show significant spatial mechanical variability exists at the microscale, and that this variability can potentially affect biofilm deformation. The average biofilm mechanical properties, provided in many studies, should be used with caution when predicting biofilm deformation.

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.

Differential Effects of Heated Perfusate on Morphology, Viability, and Dissemination of Staphylococcus epidermidis Biofilms

Bacterial biofilms are a leading cause of medical device infections. Staphylococcus epidermidis is commonly responsible for these types of infections. With increasing occurrences of antibacterial resistance, there has been a new push to explore treatment options that augment traditional antibiotic therapies. Here, we show how thermal treatment can be applied to both degrade bacterial biofilms on substrates and impede the proliferation of cells that detach from them. Understanding the response of both surface-adhered and dispersed bacterial cells under thermal stress conditions is a foundational step toward the development of an in situ treatment/remediation method for biofilm growth in medical devices; such an application could use oscillatory flow of heated fluid in a catheter as an adjuvant to antibiotic treatment. The work furthermore provides new insight into the viability of disseminated biofilm material.

The biofilm phenotype offers bacterial communities protection from environmental factors, as evidenced by its role in the viability, persistence, and virulence of cells under conditions in which flow is present, such as in riverbeds, industrial piping networks, and the human circulatory system. Here, we examined the hypothesis that temperature—an environmental factor that affects the growth of the Gram-positive bacterium Staphylococcus epidermidis—controls, through dual mechanisms, persistence of this bacterial strain in a shear environment characteristic of the human circulatory system. We demonstrated that temperature and antibiotics impact the surface-adhered biofilm and material disseminated downstream in different ways. Specifically, by means of three-dimensional (3D) confocal and scanning electron microscopy, an increase in surface-adhered biofilm heterogeneity was observed with increasing temperature. Additionally, we found a 4-log decrease in cell viability at the biofilm surface as the perfusate temperature was increased from 37°C to 50°C. Finally, the viability of cell-containing fragments that were disseminated from the substrate was assessed by downstream sampling, culture, and optical density measurement. We found that although temperature decreased the viability of the surface-adhered biofilm, the downstream material remained viable. And yet, in the presence of antibiotics, the growth of disseminated material was nearly completely inhibited, even though the addition of antibiotics had no significant impact on the viability of the surface-adhered biofilm. The mechanism involves both biofilm structural damage, as quantified by morphology of debrided material, and reduced cell viability, as quantified by assay of bacterial cells present in the surface-adherent biofilm and in the downstream effluent. The results potentially identify parameter ranges in which elevated temperature could augment current antibiotic treatment regimens.

IMPORTANCE Bacterial biofilms are a leading cause of medical device infections. Staphylococcus epidermidis is commonly responsible for these types of infections. With increasing occurrences of antibacterial resistance, there has been a new push to explore treatment options that augment traditional antibiotic therapies. Here, we show how thermal treatment can be applied to both degrade bacterial biofilms on substrates and impede the proliferation of cells that detach from them. Understanding the response of both surface-adhered and dispersed bacterial cells under thermal stress conditions is a foundational step toward the development of an in situ treatment/remediation method for biofilm growth in medical devices; such an application could use oscillatory flow of heated fluid in a catheter as an adjuvant to antibiotic treatment. The work furthermore provides new insight into the viability of disseminated biofilm material.

Non-antibiotic antimicrobial agents to combat biofilm-forming bacteria

Biofilms can be produced by multiple species or by a single strain of bacteria. The biofilm state enhances the resistance of the resident microorganisms to antimicrobial agents by producing extracellular polymeric substances. Typically, antibiotics are used to stop the growth of bacteria, but emerging resistance has limited their effectiveness. Bacteria in biofilms are less susceptible to antibiotics compared with their free-floating state, as biofilms impair antibiotic penetration. To obviate this challenge, non-antibiotic antimicrobial agents are needed. This review describes two classes of these agents, namely antimicrobial nanoparticles and antimicrobial peptides. Applications of these antimicrobials in the food industry and medical applications are discussed, and the directions for future research are highlighted.

Burst statistics in an early biofilm quorum sensing model: the role of spatial colony-growth heterogeneity

Quorum-sensing bacteria in a growing colony of cells send out signalling molecules (so-called “autoinducers”) and themselves sense the autoinducer concentration in their vicinity. Once—due to increased local cell density inside a “cluster” of the growing colony—the concentration of autoinducers exceeds a threshold value, cells in this clusters get “induced” into a communal, multi-cell biofilm-forming mode in a cluster-wide burst event. We analyse quantitatively the influence of spatial disorder, the local heterogeneity of the spatial distribution of cells in the colony, and additional physical parameters such as the autoinducer signal range on the induction dynamics of the cell colony. Spatial inhomogeneity with higher local cell concentrations in clusters leads to earlier but more localised induction events, while homogeneous distributions lead to comparatively delayed but more concerted induction of the cell colony, and, thus, a behaviour close to the mean-field dynamics. We quantify the induction dynamics with quantifiers such as the time series of induction events and burst sizes, the grouping into induction families, and the mean autoinducer concentration levels. Consequences for different scenarios of biofilm growth are discussed, providing possible cues for biofilm control in both health care and biotechnology.

Challenges of biofilm control and utilization: lessons from mathematical modelling

This article reviews modern applications of mathematical descriptions of biofilm formation. The focus is on theoretically obtained results which have implications for areas including the medical sector, food industry and wastewater treatment. Examples are given as to how models have contributed to the overall knowledge on biofilms and how they are used to predict biofilm behaviour. We conclude that the use of mathematical models of biofilms has demonstrated over the years the ability to significantly contribute to the vast field of biofilm research. Among other things, they have been used to test various hypotheses on the nature of interspecies interactions, viability of biofilm treatment methods or forces behind observed biofilm pattern formations. Mathematical models can also play a key role in future biofilm research. Many models nowadays are analysed through computer simulations and continue to improve along with computational capabilities. We predict that models will keep on providing answers to important challenges involving biofilm formation. However, further strengthening of the ties between various disciplines is necessary to fully use the tools of collective knowledge in tackling the biofilm phenomenon.

Modelling anaerobic, aerobic and partial nitritation-anammox granular sludge reactors - A review

Wastewater treatment processes with granular sludge are compact and are becoming increasingly popular. Interest has been accompanied by the development of mathematical models. This contribution simultaneously reviews available models in the scientific literature for anaerobic, aerobic and partial nitritation-anammox granular sludge reactors because they comprise common phenomena (e.g. liquid, gas and granule transport) and thus pose similar challenges. Many of the publications were found to have no clearly defined goal. The importance of a goal is stressed because it determines the appropriate model complexity and helps other potential users to find a suitable model in the vast amount of literature. Secondly, a wide variety was found in the model features. This review explains the chosen modelling assumptions based on the different reactor types and goals wherever possible, but some assumptions appeared to be habitual within fields of research, without clear reason. We therefore suggest further research to more clearly define the range of operational conditions and goals for which certain simplifying assumptions can be made, e.g. when intragranule solute transport can be lumped in apparent kinetics and when biofilm models are needed, which explicitly calculate substrate concentration gradients inside granules. Furthermore, research is needed to better mechanistically understand detachment, removal of influent particulate matter and changes in the mixing behaviour inside anaerobic systems, before these phenomena can be adequately incorporated in models. Finally, it is suggested to perform full-scale model validation studies for aerobic and anammox reactors. A spreadsheet in the supplementary information provides an overview of the features in the 167 reviewed models.

Hypoxia arising from concerted oxygen consumption by neutrophils and microorganisms in biofilms

Infections associated with microbial biofilms are often found to involve hypoxic or anoxic conditions within the biofilm or its vicinity. To shed light on the phenomenon of local oxygen depletion, mathematical reaction-diffusion models were derived that integrated the two principal oxygen sinks, microbial respiration and neutrophil consumption. Three simple one-dimensional problems were analyzed approximating biofilm near an air interface as in a dermal wound or mucus layer, biofilm on an implanted medical device, or biofilm aggregates dispersed in mucus or tissue. In all three geometries considered, hypoxia at the biofilm-neutrophil interface or within the biofilm was predicted for a subset of plausible parameter values. The finding that oxygen concentration at the biofilm-neutrophil juncture can be diminished to hypoxic levels is biologically relevant because oxygen depletion will reduce neutrophil killing ability. The finding that hypoxia can readily establish in the interior of the biofilm is biologically relevant because this change will alter microbial metabolism and persistence.

Dynamics of Pseudomonas putida biofilms in an upscale experimental framework

Exploitation of biofilms for industrial processes requires them to adopt suitable physical structures for rendering them efficient and predictable. While hydrodynamics could be used to control material features of biofilms of the platform strain Pseudomonas putida KT2440 there is a dearth of experimental data on surface-associated growth behavior in such settings. Millimeter scale biofilm patterns formed by its parental strain P. putida mt-2 under different Reynolds numbers (Re) within laminar regime were analyzed using an upscale experimental continuous cultivation assembly. A tile-scan image acquisition process combined with a customized image analysis revealed patterns of dense heterogeneous structures at Re = 1000, but mostly flattened coverings sparsely patched for Re < 400. These results not only fix the somewhat narrow hydrodynamic regime under which P. putida cells form stable coatings on surfaces destined for large-scale processes, but also provide useful sets of parameters for engineering catalytic biofilms based on this important bacterium as a cell factory.

Simulation-Based Exploration of Quorum Sensing Triggered Resistance of Biofilms to Antibiotics

We present a mathematical model of biofilm response to antibiotics, controlled by a quorum sensing system that confers increased resistance. The model is a highly nonlinear system of partial differential equations that we investigate in computer simulations. Our results suggest that an adaptive, quorum sensing-controlled, mechanism to switch between modes of fast growth with little protection and protective modes of slow growth may confer benefits to biofilm populations. It enhances the formation of micro-niches in the inner regions of the biofilm in which bacteria are not easily reached by antibiotics. Whereas quorum sensing inhibitors can delay the onset of increased resistance, their advantage is lost after up-regulation. This emphasizes the importance of timing for treatment of biofilms with antibiotics.

Modeling of methane formation in gravity sewer system: the impact of microorganism and hydraulic condition

Sewer system is an important source of methane formation and emission. Although some models were developed to predict methane production in sewers, the impact of microorganism amount was indicated indirectly. Here, seven laboratory scale sewers with varied wall-shear stresses were established. The biofilm thickness, microorganism amount, DO distribution, microorganism community in the biofilms and methane production in the sewers were measured. Based on experimental data, an empirical model was developed to directly describe the relationship between methane production, microorganism amount and wall-shear stress. The results showed that DO concentration decreased significantly along the biofilm depth under varied wall-shear stress, and the DO reduction rate was positively related to the intensity of wall-shear stress. The dominant archaea species in mature biofilms were similar whereas the proportions showed remarkable differences. The abundance of Methanospirillum in biofilms cultured at 2.0 Pa wall-shear stress was 53.08% more than that at 1.29 Pa. The maximum methane production rate, 2.04 mg/L wastewater day, was obtained when the wall-shear stress kept at 1.45 Pa, which was 1.2-fold higher than the minimum in sewer at 0.5 Pa. The R² value of the established model was 0.95, the difference between the measurement and simulation was in the rage of 1.5–13.0%.

Role of Wall Shear Stress in Cryptosporidium parvum Oocyst Attachment to Environmental Biofilms

This study investigated Cryptosporidium parvum oocyst deposition onto biofilms as a function of shear stress under laminar or turbulent flow. Annular rotating bioreactors were used to grow stabilized stream biofilms at shear stresses ranging from 0.038 to 0.46 Pa. These steady-state biofilms were then used to assess the impact of hydrodynamic conditions on C. parvum oocyst attachment. C. parvum deposition onto biofilms followed a pseudo-second-order model under both laminar (after a lag phase) and turbulent flows. The total number of oocysts attached to the biofilm at steady state decreased as the hydrodynamic wall shear stress increased. The oocyst deposition rate constant increased with shear stress but decreased at high shear, suggesting that increasing wall shear stress results in faster attachment of Cryptosporidium due to higher mass transport until the shear forces exceed a critical limit that prevents oocyst attachment. These data show that oocyst attachment in the short and long term are impacted differently by shear: higher shear (to a certain limit) may be associated with faster initial oocyst attachment, but lower shear is associated with greater numbers of oocysts attached at equilibrium.IMPORTANCE This research provides experimental evidence to demonstrate that shear stress plays a critical role in protozoan-pathogen transport and deposition in environmental waters. The data presented in this work expand scientific understanding of Cryptosporidium attachment and fate, which will further influence the development of timely and accurate sampling strategies, as well as advanced water treatment technologies, to target protozoan pathogens in surface waters that serve as municipal drinking water sources.

Visualisation study on Pseudomonas migulae AN-1 transport in saturated porous media

Influence of granular size and groundwater flow rate on transport of Pseudomonas migulae AN-1 in saturated porous media was non-invasively and visually investigated with a novel imaging technique based on our previously established green fluorescent protein-tagging approach. AN-1 was transported faster than water was. The finer the media were, the greater the enhancement of bacterial velocity was. Mass recovery (MR) increased, while deposition rate coefficient (K_c) decreased, with increasing granular size. Similar and linear trends of MR and K_c, respectively, were quantitatively observed with increasing water flow rate. The images revealed that the initial shape of bacterial plume after injection was a narrow strip along the injection well and an ellipsoid in the lower part of the injection well in medium and coarse sand, respectively. Bacterial plume migrated horizontally in medium sand, but shifted slightly downward in coarse sand. Under similar conditions, the fluorescent area carrying AN-1 in medium sand was larger than that carrying AN-1 in coarse sand during the same period. The visualisation method of this study captured both the movement of free-state and retained bacteria that adhered to sediments. A continuous biological zone composed of planktonic and retained AN-1 was observed. These findings are significant for actual bioremediation.

Continuum and discrete approach in modeling biofilm development and structure: a review

The scientific community has recognized that almost 99% of the microbial life on earth is represented by biofilms. Considering the impacts of their sessile lifestyle on both natural and human activities, extensive experimental activity has been carried out to understand how biofilms grow and interact with the environment. Many mathematical models have also been developed to simulate and elucidate the main processes characterizing the biofilm growth. Two main mathematical approaches for biomass representation can be distinguished: continuum and discrete. This review is aimed at exploring the main characteristics of each approach. Continuum models can simulate the biofilm processes in a quantitative and deterministic way. However, they require a multidimensional formulation to take into account the biofilm spatial heterogeneity, which makes the models quite complicated, requiring significant computational effort. Discrete models are more recent and can represent the typical multidimensional structural heterogeneity of biofilm reflecting the experimental expectations, but they generate computational results including elements of randomness and introduce stochastic effects into the solutions.

Agent-based modelling in synthetic biology

Biological systems exhibit complex behaviours that emerge at many different levels of organization. These span the regulation of gene expression within single cells to the use of quorum sensing to co-ordinate the action of entire bacterial colonies. Synthetic biology aims to make the engineering of biology easier, offering an opportunity to control natural systems and develop new synthetic systems with useful prescribed behaviours. However, in many cases, it is not understood how individual cells should be programmed to ensure the emergence of a required collective behaviour. Agent-based modelling aims to tackle this problem, offering a framework in which to simulate such systems and explore cellular design rules. In this article, I review the use of agent-based models in synthetic biology, outline the available computational tools, and provide details on recently engineered biological systems that are amenable to this approach. I further highlight the challenges facing this methodology and some of the potential future directions.

Hydrodynamic Effects on Biofilms at the Biointerface Using a Microfluidic Electrochemical Cell: Case Study of Pseudomonas sp

The anchoring biofilm layer is expected to exhibit a different response to environmental stresses than for portions in the bulk, due to the protection from other strata and the proximity to the attachment surface. The effect of hydrodynamic stress on surface-adhered biofilm layers was tested using a specially designed microfluidic bio flow cell with an embedded three-electrode detection system. In situ electrochemical impedance spectroscopy (EIS) measurements of biocapacitance and bioresistance of Pseudomonas sp. biofilms were conducted during the growth phase and under different shear flow conditions with verification by other surface sensitive techniques. Distinct, but reversible changes to the amount of biofilm and its structure at the attachment surface were observed during the application of elevated shear stress. In contrast, regular microscopy revealed permanent distortion to the biofilm bulk, in the form of streamers and ripples. Following the application of extreme shear stresses, complete removal of significant portions of biofilm outer layers occurred, but this did not change the measured quantity of biofilm at the electrode attachment surface. The structure of the remaining biofilm, however, appeared to be modified and susceptible to further changes following application of shear stress directly to the unprotected biofilm layers at the attachment surface.

Patterned SLIPS for the Formation of Arrays of Biofilm Microclusters with Defined Geometries

Biofilms represent an immense problem in medicine due to their strong drug-resistant properties and inherent stress-response activities. Due to the inhomogeneous and very complex architectures of large biofilm aggregates, biofilm studies often suffer from low reproducibility. In this study, an approach to form arrays of homogeneous biofilm microclusters with defined 2D geometries is presented. The method is based on the formation of water-infused hydrophilic porous polymer areas with precise geometries separated by "slippery" lubricant-infused porous surface (SLIPS). Due to the SLIPS' biofilm repellent properties, multiple identical 3D biofilm clusters are formed in the hydrophilic patches that can be used for biofilm screening. Formation of biofilm microcluster arrays of different bacterial strains of Pseudomonas aeruginosa on the SLIPS micropatterns is investigated. Critical parameters influencing minimal adhesive regions for biofilm attachment and minimal SLIPS dimensions to avoid biofilm adhesion are studied. The ability to produce arrays of biofilm microclusters with highly uniform, well-defined shapes opens an opportunity to study interactions of biofilms with various medically relevant factors with a better reproducibility and to investigate the complex biofilm architecture, heterogeneity, and interactions between biofilm subpopulations.

Effect of flow rate on growth and oxygen consumption of biofilm in gravity sewer

The function of sewer as reactors must rely on the biofilm in it. In this paper, the formation, structure, oxygen transfer, and activity of the biofilm under different hydraulic conditions were studied by the microelectrode technology, oxygen uptake rate (OUR) technology, and 454 high-throughput pyrosequencing technology. Results showed that when the wall-shear stresses were 1.12, 1.29, and 1.45 Pa, the porosity of the steady-state biofilm were 69.1, 64.4, and 55.1 %, respectively. The maximum values of OUR were 0.033, 0.027, and 0.022 mg/(L*s), respectively, and the COD removal efficiency in the sewers reached 40, 35, and 32 %, respectively. The research findings had an important significance on how to improve the treatment efficiency of the sewers. Fig. a Graphical Abstract.

Modeling of Mesoscale Variability in Biofilm Shear Behavior

Formation of bacterial colonies as biofilm on the surface/interface of various objects has the potential to impact not only human health and disease but also energy and environmental considerations. Biofilms can be regarded as soft materials, and comprehension of their shear response to external forces is a key element to the fundamental understanding. A mesoscale model has been presented in this article based on digitization of a biofilm microstructure. Its response under externally applied shear load is analyzed. Strain stiffening type behavior is readily observed under high strain loads due to the unfolding of chains within soft polymeric substrate. Sustained shear loading of the biofilm network results in strain localization along the diagonal direction. Rupture of the soft polymeric matrix can potentially reduce the intercellular interaction between the bacterial cells. Evolution of stiffness within the biofilm network under shear reveals two regimes: a) initial increase in stiffness due to strain stiffening of polymer matrix, and b) eventual reduction in stiffness because of tear in polymeric substrate.

Physical Forces Shape Group Identity of Swimming Pseudomonas putida Cells

The often striking macroscopic patterns developed by motile bacterial populations on agar plates are a consequence of the environmental conditions where the cells grow and spread. Parameters such as medium stiffness and nutrient concentration have been reported to alter cell swimming behavior, while mutual interactions among populations shape collective patterns. One commonly observed occurrence is the mutual inhibition of clonal bacteria when moving toward each other, which results in a distinct halt at a finite distance on the agar matrix before having direct contact. The dynamics behind this phenomenon (i.e., intolerance to mix in time and space with otherwise identical others) has been traditionally explained in terms of cell-to-cell competition/cooperation regarding nutrient availability. In this work, the same scenario has been revisited from an alternative perspective: the effect of the physical mechanics that frame the process, in particular the consequences of collisions between moving bacteria and the semi-solid matrix of the swimming medium. To this end, we set up a simple experimental system in which the swimming patterns of Pseudomonas putida were tested with different geometries and agar concentrations. A computational analysis framework that highlights cell-to-medium interactions was developed to fit experimental observations. Simulated outputs suggested that the medium is compressed in the direction of the bacterial front motion. This phenomenon generates what was termed a compression wave that goes through the medium preceding the swimming population and that determines the visible high-level pattern. Taken together, the data suggested that the mechanical effects of the bacteria moving through the medium created a factual barrier that impedes to merge with neighboring cells swimming from a different site. The resulting divide between otherwise clonal bacteria is thus brought about by physical forces—not genetic or metabolic programs.

An integrated mathematical model for chemical oxygen demand (COD) removal in moving bed biofilm reactors (MBBR) including predation and hydrolysis

An integrated mathematical model is proposed for modelling a moving bed biofilm reactor (MBBR) for removal of chemical oxygen demand (COD) under aerobic conditions. The composite model combines the following: (i) a one-dimensional biofilm model, (ii) a bulk liquid model, and (iii) biological processes in the bulk liquid and biofilm considering the interactions among autotrophic, heterotrophic and predator microorganisms. Depending on the values for the soluble biodegradable COD loading rate (SCLR), the model takes into account a) the hydrolysis of slowly biodegradable compounds in the bulk liquid, and b) the growth of predator microorganisms in the bulk liquid and in the biofilm. The integration of the model and the SCLR allows a general description of the behaviour of COD removal by the MBBR under various conditions. The model is applied for two in-series MBBR wastewater plant from an integrated cellulose and viscose production and accurately describes the experimental concentrations of COD, total suspended solids (TSS), nitrogen and phosphorous obtained during 14 months working at different SCLRs and nutrient dosages. The representation of the microorganism group distribution in the biofilm and in the bulk liquid allow for verification of the presence of predator microorganisms in the second reactor under some operational conditions.

Shaping the Growth Behaviour of Biofilms Initiated from Bacterial Aggregates

Bacterial biofilms are usually assumed to originate from individual cells deposited on a surface. However, many biofilm-forming bacteria tend to aggregate in the planktonic phase so that it is possible that many natural and infectious biofilms originate wholly or partially from pre-formed cell aggregates. Here, we use agent-based computer simulations to investigate the role of pre-formed aggregates in biofilm development. Focusing on the initial shape the aggregate forms on the surface, we find that the degree of spreading of an aggregate on a surface can play an important role in determining its eventual fate during biofilm development. Specifically, initially spread aggregates perform better when competition with surrounding unaggregated bacterial cells is low, while initially rounded aggregates perform better when competition with surrounding unaggregated cells is high. These contrasting outcomes are governed by a trade-off between aggregate surface area and height. Our results provide new insight into biofilm formation and development, and reveal new factors that may be at play in the social evolution of biofilm communities.

Conservation of acquired morphology and community structure in aged biofilms after facing environmental stress

The influence of growth history on biofilm morphology and microbial community structure is poorly studied despite its important role for biofilm development. Here, biofilms were exposed to a change in hydrodynamic conditions at different growth stages and we observed how biofilm age affected the change in morphology and bacterial community structure. Biofilms were developed in two bubble column reactors, one operated under constant shear stress and one under variable shear stress. Biofilms were transferred from one reactor to the other at different stages in their development by withdrawing and inserting the support medium from one reactor to the other. The developments of morphology and microbial community structure were followed by image analysis and molecular tools. When transferred early in biofilm development, biofilms adapted to the new hydrodynamic conditions and adopted features of the biofilm already developed in the receiving reactor. Biofilms transferred at a late state of biofilm development continued their initial trajectories of morphology and community development even in a new environment. These biofilms did not immediately adapt to their new environment and kept features acquired during their early growth phase, a property we called memory effect.

A Mixed-Culture Biofilm Model with Cross-Diffusion

We propose a deterministic continuum model for mixed-culture biofilms. A crucial aspect is that movement of one species is affected by the presence of the other. This leads to a degenerate cross-diffusion system that generalizes an earlier single-species biofilm model. Two derivations of this new model are given. One, like cellular automata biofilm models, starts from a discrete in space lattice differential equation where the spatial interaction is described by microscopic rules. The other one starts from the same continuous mass balances that are the basis of other deterministic biofilm models, but it gives up a simplifying assumption of these models that has recently been criticized as being too restrictive in terms of ecological structure. We show that both model derivations lead to the same PDE model, if corresponding closure assumptions are introduced. To investigate the role of cross-diffusion, we conduct numerical simulations of three biofilm systems: competition, allelopathy and a mixed system formed by an aerobic and an anaerobic species. In all cases, we find that accounting for cross-diffusion affects local distribution of biomass, but it does not affect overall lumped quantities such as the total amount of biomass in the system.

Mechanical properties of a mature biofilm from a wastewater system: from microscale to macroscale level

A fundamental understanding of biofilm mechanical stability is critical in order to describe detachment and develop biofouling control strategies. It is thus important to characterise the elastic deformation and flow behaviour of the biofilm under different modes of applied force. In this study, the mechanical properties of a mature wastewater biofilm were investigated with methods including macroscale compression and microscale indentation using atomic force microscopy (AFM). The mature biofilm was found to be mechanically isotropic at the macroscale level as its mechanical properties did not depend on the scales and modes of loading. However, the biofilm showed a tendency for mechanical inhomogeneity at the microscale level as indentation progressed deeper into the matrix. Moreover, it was observed that the adhesion force had a significant influence on the elastic properties of the biofilm at the surface, subjected to microscale tensile loading. These results are expected to inform a damage-based model for biofilm detachment.

Biofilm architecture in a novel pressurized biofilm reactor

A novel pure-oxygen pressurized biofilm reactor was operated at different organic loading, mechanical shear and hydrodynamic conditions to understand the relationships between biofilm architecture and its operation. The ultimate goal was to improve the performance of the biofilm reactor. The biofilm was labeled with seven stains and observed with confocal laser scanning microscopy. Unusual biofilm architecture of a ribbon embedded between two surfaces with very few points of attachment was observed. As organic loading increased, the biofilm morphology changed from a moderately rough layer into a locally smoother biomass with significant bulging protuberances, although the chemical oxygen demand (COD) removal efficiency remained unchanged at about 75%. At higher organic loadings, biofilms contained a larger fraction of active cells distributed uniformly within a proteinaceous matrix with decreasing polysaccharide content. Higher hydrodynamic shear in combination with high organic loading resulted in the collapse of biofilm structure and a substantial decrease in reactor performance (a COD removal of 16%). Moreover, the important role of proteins for the spatial distribution of active cells was demonstrated quantitatively.

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.

An automated method for the quantification of moving predators such as rotifers in biofilms by image analysis

In natural environments as well as in industrial processes, microorganisms form biofilms. Eukaryotic microorganisms, like metazoans and protozoans, can shape the microbial communities because of their grazing activity. However, their influence on biofilm structure is often neglected because of the lack of appropriate methods to quantify their presence. In the present work, a method has been developed to quantify moving population of rotifers within a biofilm. We developed an automated approach to characterize the rotifer population density. Two time lapse images are recorded per biofilm location at an interval of 1s. By subtracting the two images from each other, rotifer displacements that occurred between the two images acquisition can be quantified. A comparison of the image analysis approach with manually counted rotifers showed a correlation of R(2)=0.90, validating the automated method. We verified our method with two biofilms of different superficial and community structures and measured rotifer densities of up to 1700 per cm(2). The method can be adapted for other types of moving organisms in biofilms like nematodes and ciliates.

Morphological optimization for access to dual oxidants in biofilms

A major theme driving research in biology is the relationship between form and function. In particular, a longstanding goal has been to understand how the evolution of multicellularity conferred fitness advantages. Here we show that biofilms of the bacterium Pseudomonas aeruginosa produce structures that maximize cellular reproduction. Specifically, we develop a mathematical model of resource availability and metabolic response within colony features. This analysis accurately predicts the measured distribution of two types of electron acceptors: oxygen, which is available from the atmosphere, and phenazines, redox-active antibiotics produced by the bacterium. Using this model, we demonstrate that the geometry of colony structures is optimal with respect to growth efficiency. Because our model is based on resource dynamics, we also can anticipate shifts in feature geometry based on changes to the availability of electron acceptors, including variations in the external availability of oxygen and genetic manipulation that renders the cells incapable of phenazine production.

Life under flow: A novel microfluidic device for the assessment of anti-biofilm technologies

In the current study, we have developed and fabricated a novel lab-on-a-chip device for the investigation of biofilm responses, such as attachment kinetics and initial biofilm formation, to different hydrodynamic conditions. The microfluidic flow channels are designed using computational fluid dynamic simulations so as to have a pre-defined, homogeneous wall shear stress in the channels, ranging from 0.03 to 4.30 Pa, which are relevant to in-service conditions on a ship hull, as well as other man-made marine platforms. Temporal variations of biofilm formation in the microfluidic device were assessed using time-lapse microscopy, nucleic acid staining, and confocal laser scanning microscopy (CLSM). Differences in attachment kinetics were observed with increasing shear stress, i.e., with increasing shear stress there appeared to be a delay in bacterial attachment, i.e., at 55, 120, 150, and 155 min for 0.03, 0.60, 2.15, and 4.30 Pa, respectively. CLSM confirmed marked variations in colony architecture, i.e.,: (i) lower shear stresses resulted in biofilms with distinctive morphologies mainly characterised by mushroom-like structures, interstitial channels, and internal voids, and (ii) for the higher shear stresses compact clusters with large interspaces between them were formed. The key advantage of the developed microfluidic device is the combination of three architectural features in one device, i.e., an open-system design, channel replication, and multiple fully developed shear stresses.