Mathematical modeling of biofilm structure with a hybrid differential-discrete cellular automaton approach

Space biofilms - An overview of the morphology of Pseudomonas aeruginosa biofilms grown on silicone and cellulose membranes on board the international space station

Microorganisms' natural ability to live as organized multicellular communities - also known as biofilms - provides them with unique survival advantages. For instance, bacterial biofilms are protected against environmental stresses thanks to their extracellular matrix, which could contribute to persistent infections after treatment with antibiotics. Bacterial biofilms are also capable of strongly attaching to surfaces, where their metabolic by-products could lead to surface material degradation. Furthermore, microgravity can alter biofilm behavior in unexpected ways, making the presence of biofilms in space a risk for both astronauts and spaceflight hardware. Despite the efforts to eliminate microorganism contamination from spacecraft surfaces, it is impossible to prevent human-associated bacteria from eventually establishing biofilm surface colonization. Nevertheless, by understanding the changes that bacterial biofilms undergo in microgravity, it is possible to identify key differences and pathways that could be targeted to significantly reduce biofilm formation. The bacterial component of Space Biofilms project, performed on the International Space Station in early 2020, contributes to such understanding by characterizing the morphology and gene expression of bacterial biofilms formed in microgravity with respect to ground controls. Pseudomonas aeruginosa was used as model organism due to its relevance in biofilm studies and its ability to cause urinary tract infections as an opportunistic pathogen. Biofilm formation was characterized at one, two, and three days of incubation (37 °C) over six different materials. Materials reported in this manuscript include catheter grade silicone, selected due to its medical relevance in hospital acquired infections, catheter grade silicone with ultrashort pulsed direct laser interference patterning, included to test microtopographies as a potential biofilm control strategy, and cellulose membrane to replicate the column and canopy structure previously reported from a microgravity study. We here present an overview of the biofilm morphology, including 3D images of the biofilms to represent the distinctive morphology observed in each material tested, and some of the key differences in biofilm thickness, mass, and surface area coverage. We also present the impact of the surface microtopography in biofilm formation across materials, incubation time, and gravitational conditions. The Space Biofilms project (bacterial side) is supported by the National Aeronautics and Space Administration under Grant No. 80NSSC17K0036 and 80NSSC21K1950.

Influence of phosphate on bacterial release from activated carbon point-of-use filters and on biofilm characteristics

Point-of-use (POU) filters certified to remove lead are often composed of activated carbon and have been shown to release high concentrations of bacteria, including opportunistic pathogens. In this study, we examine the impacts of the common corrosion inhibitor phosphate on biofilm characteristics and the relationship between biofilm structure and bacterial release from POU filters. This knowledge is essential for understanding how best to use the filters and where these filters fit in a system where other lead contamination prevention measures may be in place. We measured the bacterial release from activated carbon POU filters fed with groundwater - a common source of drinking water - with and without phosphate. We used optical coherence tomography (OCT) to quantitatively characterize biofilm growing on activated carbon filter material in which the biofilms were fed groundwater with and without phosphate. Phosphate filters released significantly less (57-87 %) bacteria than groundwater filters, and phosphate biofilms (median thickness: 82-331 μm) grew to be significantly thicker than groundwater biofilms (median thickness: 122-221 μm). The phosphate biofilm roughness ranged from 97 to 142 % of the groundwater biofilm roughness and was significantly greater in most weeks. Phosphate biofilms also had fewer pores per biofilm volume and shorter channels connecting those pores.

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.

Contrasting morphology and growth habits of Frutexites in Late Devonian reef complexes of the Canning Basin, northwestern Australia

Frutexites-like microstructures are described from the exhumed Late Devonian reef complexes of the northern Canning Basin, Western Australia. Several high-resolution imaging techniques, including X-ray microcomputerised tomography, scanning electron microscopy and X-ray fluorescence microscopy, were used to investigate morphology and composition in two samples. Three types of Frutexites-like microstructures (Types I-III) have been identified. Type I, found lining an early marine cement-filled cavity in fore-reef grainstone facies, consists of dendritic structures formed primarily of coccoid bacteria with filamentous bacteria embedded in sheets of amorphous extracellular polymeric substances (EPS). These ferromanganiferous dendrites have laminated to spheroidal textures. Types II and III are from a toe-of-slope hardground. Type II grew in a crypt between two corals, is also dendritic and composed of bacilliform and filamentous bacteria embedded in an amorphous EPS sheet. The opaqueness of these ferriferous dendrites precludes more detailed description of textures. Type III grew as branching columnar microstromatolites and is composed of entwined filaments of Girvanella, Rothpletzella and Wetheredella with Fe-enriched outer walls that generate Frutexites-like microstructures. Types I and II resemble Frutexites sensu stricto as defined by Maslov (Stromatolites, Trudy Instituta geologicheskikh nauk Akademiya nauk SSR, 1960) and are the result of the consecutive growth and permineralisation of biofilms composed of mixed bacterial communities growing in cryptic habitats. Type III superficially resembles Frutexites sensu stricto based on macroscopic field observations, however, detailed microscopic analysis reveals that it is composed of Fe-enriched tubular walls surrounded by Mn-enriched calcite.

Cooperation in bioluminescence: understanding the role of autoinducers by a stochastic random resistor model

Quorum sensing is a communication mechanism adopted by different bacterial strains for the regulation of gene transcription. It takes place through the exchange of molecules called autoinducers. Bioluminescence is an emergent threshold phenomenon shown by some bacteria strains. Its precise relationship to quorum sensing is a debated topic, particularly regarding the role of the different autoinducers used by bacteria. In this paper, assuming a direct relationship between bioluminescence and quorum sensing, we investigate the role of multiple autoinducers in the bioluminescence response of Vibrio harveyi, considered as a model bioluminescent strain, due to its quorum sensing circuitry involving an array of three different autoinducers. Experiments on mutants of this bacterium, obtained by suppression of one or more autoinducers, reveal their relative non-trivial relevance and cooperative interaction patterns. The proposed analysis is implemented on a regular lattice, whose nodes represent microbial entities equipped with charges, which represent the ability to up/down regulate the gene expression. Quorum sensing results from a Coulomb-type field, produced by the charges. In analogy with random resistor network models, the lattice is permeated by an effective current which accounts for the amount and distribution of the charges. We propose that the presence of different autoinducers correspond to a different up/down regulation of gene expression, i.e., to a different way to account for the charges. Then, by introducing a modulation of the charge dependence into the current flowing within the network, we show that it is able to describe the bioluminescence exhibited by V. harveyi mutants. Furthermore, modulation of the charge dependence allows the interactions between the different autoinducers to be taken into account, providing a prediction regarding the data obtainable under specific growth conditions.

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.

Morphogenesis of Biofilms in Porous Media and Control on Hydrodynamics

The functioning of natural and engineered porous media, like soils and filters, depends in many cases on the interplay between biochemical processes and hydrodynamics. In such complex environments, microorganisms often form surface-attached communities known as biofilms. Biofilms can take the shape of clusters, which alter the distribution of fluid flow velocities within the porous medium, subsequently influencing biofilm growth. Despite numerous experimental and numerical efforts, the control of the biofilm clustering process and the resulting heterogeneity in biofilm permeability is not well understood, limiting our predictive abilities for biofilm-porous medium systems. Here, we use a quasi-2D experimental model of a porous medium to characterize biofilm growth dynamics for different pore sizes and flow rates. We present a method to obtain the time-resolved biofilm permeability field from experimental images and use the obtained permeability field to compute the flow field through a numerical model. We observe a biofilm cluster size distribution characterized by a spectrum slope evolving in time between -2 and -1, a fundamental measure that can be used to create spatio-temporal distributions of biofilm clusters for upscaled models. We find a previously undescribed biofilm permeability distribution, which can be used to stochastically generate permeability fields within biofilms. An increase in velocity variance for a decrease in physical heterogeneity shows that the bioclogged porous medium behaves differently than expected from studies on heterogeneity in abiotic porous media.

Active layer dynamics drives a transition to biofilm fingering

The emergence of spatial organisation in biofilm growth is one of the most fundamental topics in biofilm biophysics and microbiology. It has long been known that growing biofilms can adopt smooth or rough interface morphologies, depending on the balance between nutrient supply and microbial growth; this 'fingering' transition has been linked with the average width of the 'active layer' of growing cells at the biofilm interface. Here we use long-time individual-based simulations of growing biofilms to investigate in detail the driving factors behind the biofilm-fingering transition. We show that the transition is associated with dynamical changes in the active layer. Fingering happens when gaps form in the active layer, which can cause local parts of the biofilm interface to pin, or become stationary relative to the moving front. Pinning can be transient or permanent, leading to different biofilm morphologies. By constructing a phase diagram for the transition, we show that the controlling factor is the magnitude of the relative fluctuations in the active layer thickness, rather than the active layer thickness per se. Taken together, our work suggests a central role for active layer dynamics in controlling the pinning of the biofilm interface and hence biofilm morphology.

Collective polarization dynamics in bacterial colonies signify the occurrence of distinct subpopulations

Membrane potential in bacterial systems has been shown to be dynamic and tightly related to survivability at the single-cell level. However, little is known about spatiotemporal patterns of membrane potential in bacterial colonies and biofilms. Here, we discovered a transition from uncorrelated to collective dynamics within colonies formed by the human pathogen Neisseria gonorrhoeae. In freshly assembled colonies, polarization is heterogeneous with instances of transient and uncorrelated hyper- or depolarization of individual cells. As colonies reach a critical size, the polarization behavior transitions to collective dynamics: A hyperpolarized shell forms at the center, travels radially outward, and halts several micrometers from the colony periphery. Once the shell has passed, we detect an influx of potassium correlated with depolarization. Transient hyperpolarization also demarks the transition from volume to surface growth. By combining simulations and the use of an alternative electron acceptor for the respiratory chain, we provide strong evidence that local oxygen gradients shape the collective polarization dynamics. Finally, we show that within the hyperpolarized shell, tolerance against aminoglycoside antibiotics increases. These findings highlight that the polarization pattern can signify the differentiation into distinct subpopulations with different growth rates and antibiotic tolerance.

Peaks, pores, and dragon eggs: Uncovering and quantifying the heterogeneity of treatment wetland biofilm matrices

Biofilms serve to house diverse microbial communities, which are responsible for the majority of wastewater constituent degradation and transformation in treatment wetlands (TWs). TW biofilm has been generally conceptualized as a relatively uniform film covering available surfaces. However, no studies attaining direct visual 3D representations of biofilm morphology have been conducted. This study focuses on imaging the morphology of detached, gravel-associated, and rhizospheric (Phalaris arundinacea) biofilms from subsurface TW mesocosms. Images obtained through both traditional light microscopy, environmental scanning electron microscopy (E-SEM) and Wet-SEM revealed that TW biofilms are structurally heterogeneous ranging from corrugated films to clusters of aggregates. Features such as water channels and pores were observed suggesting that pollutant transport inside biofilms is complex, and that the interfacial surface area between water and biofilm is much larger than previously understood. Biofilm thickness generally ranged between 170 and 240 μm, with internal biofilm porosities estimated as 34 ± 10 %, reaching a maximum of 50 %. Internal biofilm matrix pore diameters ranged from 1 to 205.2 μm, with a distribution that favored pores and channels smaller than 10 μm, and a mean equivalent spherical diameter of 8.6 μm. Based on the large variation in pore and channel sizes it is expected that a variety of flow regimes and therefore pollutant dynamics are likely to occur inside TW biofilm matrices. Based on the visual evidence and analysis, a new conceptual model was created to reflect the microscale TW biofilm dynamics and morphology. This new conceptual model will serve to inform future biokinetic modelling, microscale hydrology, microbial community assessment, and pollutant treatment studies.

Glycerol conversion by aerobic granular sludge

Glycerol is abundantly present in wastewater from industries such as biodiesel production facilities. Glycerol is also a potential carbon source for microbes that are involved in wastewater nutrient removal processes. The conversion of glycerol in biological phosphorus removal of aerobic granular sludge processes has not been explored to date. The current study describes glycerol utilization by aerobic granular sludge and enhanced biological phosphorus removal (EBPR). Robust granules with good phosphorus removal capabilities were formed in an aerobic granular sludge sequencing batch reactor fed with glycerol. The interaction between the fermentative conversion of glycerol and product uptake by polyphosphate accumulating organisms (PAO) was studied using stoichiometric and microbial community analysis. Metagenomic, metaproteomic and microscopic analysis identified a community dominated by Actinobacteria (Tessaracoccus and Micropruina) and a typical PAO known as Ca. Accumulibacter. Glycerol uptake facilitator (glpF) and glycerol kinase (glpK), two proteins involved in the transport of glycerol into the cellular metabolism, were only observed in the genome of the Actinobacteria. The anaerobic conversion appeared to be a combination of a substrate fermentation and product uptake-type reaction. Initially, glycerol fermentation led mainly to the production of 1,3-propanediol (1,3-PDO) which was not taken up under anaerobic conditions. Despite the aerobic conversion of 1,3-PDO stable granulation was observed. Over time, 1,3-PDO production decreased and complete anaerobic COD uptake was observed. The results demonstrate that glycerol-containing wastewater can effectively be treated by the aerobic granular sludge process and that fermentative and polyphosphate accumulating organisms can form a food chain in glycerol-based EBPR processes.

Probing patterning in microbial consortia with a cellular automaton for spatial organisation

Microbial consortia exhibit spatial patterning across diverse environments. Since probing the self-organization of natural microbial communities is limited by their inherent complexity, synthetic models have emerged as attractive alternatives. In this study, we develop novel frameworks of bacterial communication and explore the emergent spatiotemporal organization of microbes. Specifically, we built quorum sensing-mediated models of microbial growth that are utilized to characterize the dynamics of communities from arbitrary initial configurations and establish the effectiveness of our communication strategies in coupling the growth rates of microbes. Our simulations indicate that the behavior of quorum sensing-coupled consortia can be most effectively modulated by the rates of secretion of acyl homoserine lactones. Such a mechanism of control enables the construction of desired relative populations of constituent species in spatially organized populations. Our models accurately recapitulate previous experiments that have investigated pattern formation in synthetic multi-cellular systems. Additionally, our software tool enables the easy implementation and analysis of our frameworks for a variety of initial configurations and simplifies the development of sophisticated gene circuits facilitating distributed computing. Overall, we demonstrate the potential of spatial organization as a tunable parameter in synthetic biology by introducing a communication paradigm based on the location and strength of coupling of microbial strains.

Homogeneously and heterogeneously structured biofilm models for wastewater treatment

Biofilm, a layer comprising extracellular polymeric substances, is the platform where the embedded living cells degrade the substances in the wastewaters. Biofilm models have been developed as part of the comprehensive models for the wastewater treatment process. This review summarizes the biofilm models applied in contemporary literature based on the spatial dimensions adopted for model build-up. The most commonly applied biofilm models are null-dimensional, considering the biofilm active biomass for the substrate sink's biological reaction. The one-dimensional, multi-species models are the second standard models for contemporary studies, providing transport and reaction resistances of substrates in the biofilm matrix and the interactions of competing or collaborating strains in the biofilm. The structural homogeneity of the biofilm challenges the validity of the uniformly structured models, highlighting the need to re-examine the validity of the uniformly structured models. The challenges and prospects of biofilm model developments and applications are outlined.

Lineage dynamics in growing biofilms: Spatial patterns of standing vs. de novo diversity

Microbial biofilms show high phenotypic and genetic diversity, yet the mechanisms underlying diversity generation and maintenance remain unclear. Here, we investigate how spatial patterns of growth activity within a biofilm lead to spatial patterns of genetic diversity. Using individual-based computer simulations, we show that the active layer of growing cells at the biofilm interface controls the distribution of lineages within the biofilm, and therefore the patterns of standing and de novo diversity. Comparing biofilms of equal size, those with a thick active layer retain more standing diversity, while de novo diversity is more evenly distributed within the biofilm. In contrast, equal-sized biofilms with a thin active layer retain less standing diversity, and their de novo diversity is concentrated at the top of the biofilm, and in fewer lineages. In the context of antimicrobial resistance, biofilms with a thin active layer may be more prone to generate lineages with multiple resistance mutations, and to seed new resistant biofilms via sloughing of resistant cells from the upper layers. Our study reveals fundamental "baseline" mechanisms underlying the patterning of diversity within biofilms.

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.

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.

Enhanced aerobic granulation for treating low-strength wastewater in an anaerobic-aerobic-anoxic sequencing batch reactor by selecting slow-growing organisms and adding carriers

The aerobic granular sludge (AGS) process is a promising technology for wastewater treatment. However, a long start-up period for granulation and instability during long-term operation still hinder the application of AGS technology, especially for low-strength wastewater. To solve these two problems, this study tested a novel strategy involving the selection of slow-growing organisms and the addition of carriers in an anaerobic-aerobic-anoxic sequencing batch reactor (AN/O/AX_SBR). Three identical AN/O/AX_SBRs (R_Ctrl, R_CCM, and R_GAC), fed with low-strength wastewater, were operated for 120 days. R_Ctrl had no carriers, R_CCM contained cell culture microcarriers (CCM), and R_GAC contained granular activated carbon (GAC). Mature AGS was achieved within 80 days in all reactors. The carriers could reduce the maturation period of AGS by approximately 10 days (76, 66, and 69 days in R_Ctrl, R_CCM, and R_GAC, respectively) and improve the physical strength of the AGS. AGS showed a strong structure without excessive proliferation of filamentous bacteria, full-grown size (900-1100 μm), and good settleability (SVI₅ was 15.4-19.4 mL/g). Microbiological analysis showed that AN/O/AX_SBRs can provide a metabolic selective pressure to select slow-growing organisms such as nitrifying bacteria (norank_f__NS9_marine_group, Ellin6067, and Nitrospira), glycogen and phosphorus accumulating organisms (GAOs: Candidatus_Competibacter and Defluviicoccus; PAOs: Candidatus_Accumulibacter and Flavobacterium). All reactors showed good performance for simultaneous nitrification, endogenous denitrification, and phosphorus removal. The removal efficiencies of total nitrogen and total phosphorous were above 70% and 80%, respectively. The cycle test showed intermediate PAO-GAO metabolism prevailed in the system, and endogenous denitrification was primarily carried out by denitrifying GAOs.

A Multi-Skilled Mathematical Model of Bacterial Attachment in Initiation of Biofilms

The initial step of biofilm formation is bacteria attachment to biotic or abiotic surfaces and other bacteria through intra or interspecies interactions. Adhesion can be influenced by physicochemical conditions of the environment, such as iron. There is no available mathematical model of bacterial attachment giving realistic initiation rather than random adhesion. We describe a simple stochastic attachment model, from the simplest case in two dimensions with one bacterial species attaching on a homogeneous flat surface to more complex situations, with either several bacterial species, inhomogeneous or non-flat surfaces, or in three dimensions. The model depends on attachment probabilities (on the surface, laterally, or vertically on bacteria). Effects of each of these parameters were analyzed. This mathematical model is then applied to experimental oral microcolonies of Porphyromonas gingivalis, Streptococcus gordonii, and Treponema denticola, either as mono-, two, or three species, under different iron concentrations. The model allows to characterize the adhesion of three bacterial species and explore the effect of iron on attachment. This model appears as a powerful tool for initial attachment analysis of bacterial species. It will enable further modeling of biofilm formation in later steps with biofilm initialization more relevant to real-life subgingival biofilms.

A Game Theoretic Analysis of the Dual Function of Antibiotics

There are two major views toward the role of antibiotics in microbial social interactions. The classical view is that antibiotics serve as weapons, produced by a bacterial species, at a significant cost, to inhibit the growth of its competitors. This view is supported by observations that antibiotics are usually upregulated by stress responses that infer the intensity of ecological competition, such as nutrient limitation and cellular damage, which point out to a competitive role for antibiotics. The other ecological function frequently assigned to antibiotics is that they serve as signaling molecules which regulate the collective behavior of a microbial community. Here, we investigate the conditions at which a weapon can serve as a signal in the context of microbial competition. We propose that an antibiotic will serve as a signal whenever a potential alteration of the growth behavior of the signal receiver, in response to a subinhibitory concentration (SIC) of the antibiotic, reduces the competitive pressure on the signal producer. This in turn would lead to avoiding triggering the stress mechanisms of the signal producer responsible for further antibiotics production. We show using individual-based modeling that this reduction of competitive pressure on the signal producer can happen through two main classes of responses by the signal recipient: competition tolerance, where the recipient reduces its competitive impact on the signal producer by switching to a low growth rate/ high yield strategy, and niche segregation, where the recipient reduces the competitive pressure on the signal producer by reducing their niche overlap. Our hypothesis proposes that antibiotics serve as signals out of their original function as weapons in order to reduce the chances of engaging in fights that would be costly to both the antibiotic producer as well as to its competitors.

Dishonest Signaling in Microbial Conflicts

Quorum sensing is a cell-cell communication system that bacteria use to express social phenotypes, such as the production of extracellular enzymes or toxins, at high cell densities when these phenotypes are most beneficial. However, many bacterial strains are known to lack a sensing mechanism for quorum signals, despite having the gene responsible for releasing the signals to the environment. The aim of this article is 2-fold. First, we utilize mathematical modeling and signaling theory to elucidate the advantage that a bacterial species can gain by releasing quorum signals, while not being able to sense them, in the context of ecological competition with a focal quorum sensing species, by reducing the focal species' ability to optimize the timing of expression of the quorum sensing regulated phenotype. Additionally, the consequences of such “dishonest signaling,” signaling that has evolved to harm the signal's receiver, on the focal quorum sensing species are investigated. It is found that quorum sensing bacteria would have to incur an additional, strategic, signaling cost in order to not suffer a reduction in fitness against dishonest signaling strains. Also, the concept of the Least Expensive Reliable Signal is introduced and applied to study how the properties of the regulated phenotype affect the metabolic investment in signaling needed by the quorum sensing bacteria to withstand dishonest signaling.

Biofilm viscoelasticity and nutrient source location control biofilm growth rate, migration rate, and morphology in shear flow

We present a numerical model to simulate the growth and deformation of a viscoelastic biofilm in shear flow under different nutrient conditions. The mechanical interaction between the biofilm and the fluid is computed using the Immersed Boundary Method with viscoelastic parameters determined a priori from measurements reported in the literature. Biofilm growth occurs at the biofilm-fluid interface by a stochastic rule that depends on the local nutrient concentration. We compare the growth, migration, and morphology of viscoelastic biofilms with a common relaxation time of 18 min over the range of elastic moduli 10-1000 Pa in different nearby nutrient source configurations. Simulations with shear flow and an upstream or a downstream nutrient source indicate that soft biofilms grow more if nutrients are downstream and stiff biofilms grow more if nutrients are upstream. Also, soft biofilms migrate faster than stiff biofilms toward a downstream nutrient source, and although stiff biofilms migrate toward an upstream nutrient source, soft biofilms do not. Simulations without nutrients show that on the time scale of several hours, soft biofilms develop irregular structures at the biofilm-fluid interface, but stiff biofilms deform little. Our results agree with the biophysical principle that biofilms can adapt to their mechanical and chemical environment by modulating their viscoelastic properties. We also compare the behavior of a purely elastic biofilm to a viscoelastic biofilm with the same elastic modulus of 50 Pa. We find that the elastic biofilm underestimates growth rates and downstream migration rates if the nutrient source is downstream, and it overestimates growth rates and upstream migration rates if the nutrient source is upstream. Future modeling can use our comparison to identify errors that can occur by simulating biofilms as purely elastic structures.

Anaerobic hydrolysis of complex substrates in full-scale aerobic granular sludge: enzymatic activity determined in different sludge fractions

Abstract

Complex substrates, like proteins, carbohydrates, and lipids, are major components of domestic wastewater, and yet their degradation in biofilm-based wastewater treatment technologies, such as aerobic granular sludge (AGS), is not well understood. Hydrolysis is considered the rate-limiting step in the bioconversion of complex substrates, and as such, it will impact the utilization of a large wastewater COD (chemical oxygen demand) fraction by the biofilms or granules. To study the hydrolysis of complex substrates within these types of biomass, this paper investigates the anaerobic activity of major hydrolytic enzymes in the different sludge fractions of a full-scale AGS reactor. Chromogenic substrates were used under fully mixed anaerobic conditions to determine lipase, protease, α-glucosidase, and β-glucosidase activities in large granules (>1 mm in diameter), small granules (0.2–1 mm), flocculent sludge (0.045–0.2 mm), and bulk liquid. Furthermore, composition and hydrolytic activity of influent wastewater samples were determined. Our results showed an overcapacity of the sludge to hydrolyze wastewater soluble and colloidal polymeric substrates. The highest specific hydrolytic activity was associated with the flocculent sludge fraction (1.5–7.5 times that of large and smaller granules), in agreement with its large available surface area. However, the biomass in the full-scale reactor consisted of 84% large granules, making the large granules account for 55–68% of the total hydrolytic activity potential in the reactor. These observations shine a new light on the contribution of large granules to the conversion of polymeric COD and suggest that large granules can hydrolyze a significant amount of this influent fraction. The anaerobic removal of polymeric soluble and colloidal substrates could clarify the stable granule formation that is observed in full-scale installations, even when those are fed with complex wastewaters.

Key points

• Large and small granules contain >70% of the hydrolysis potential in an AGS reactor.

• Flocculent sludge has high hydrolytic activity but constitutes <10% VS in AGS.

• AGS has an overcapacity to hydrolyze complex substrates in domestic wastewater.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11443-3.

Lattice Boltzmann Method in Modeling Biofilm Formation, Growth and Detachment

Biofilms are a complex and heterogeneous aggregation of multiple populations of microorganisms linked together by their excretion of extracellular polymer substances (EPS). Biofilms can cause many serious problems, such as chronic infections, food contamination and equipment corrosion, although they can be useful for constructive purposes, such as in wastewater treatment, heavy metal removal from hazardous waste sites, biofuel production, power generation through microbial fuel cells and microbially enhanced oil recovery; however, biofilm formation and growth are complex due to interactions among physicochemical and biological processes under operational and environmental conditions. Advanced numerical modeling techniques using the lattice Boltzmann method (LBM) are enabling the prediction of biofilm formation and growth and microbial community structures. This study is the first attempt to perform a general review on major contributions to LBM-based biofilm models, ranging from pioneering efforts to more recent progress. We present our understanding of the modeling of biofilm formation, growth and detachment using LBM-based models and present the fundamental aspects of various LBM-based biofilm models. We describe how the LBM couples with cellular automata (CA) and individual-based model (IbM) approaches and discuss their applications in assessing the spatiotemporal distribution of biofilms and their associated parameters and evaluating bioconversion efficiency. Finally, we discuss the main features and drawbacks of LBM-based biofilm models from ecological and biotechnological perspectives and identify current knowledge gaps and future research priorities.

Cellular Automata in Chemistry and Chemical Engineering

We review the modern state of cellular automata (CA) applications for solving practical problems in chemistry and chemical technology. We consider the problems of material structure modeling and prediction of materials' morphology-dependent properties. We review the use of the CA approach for modeling diffusion, crystallization, dissolution, erosion, corrosion, adsorption, and hydration processes. We also consider examples of hybrid CA-based models, which are combinations of various CA with other computational approaches and modeling methods. Finally, we discuss the use of high-performance parallel computing to increase the efficiency of CA.

Aerobic Granular Sludge-Membrane BioReactor (AGS-MBR) as a Novel Configuration for Wastewater Treatment and Fouling Mitigation: A Mini-Review

This mini-review reports the effect of aerobic granular sludge (AGS) on performance and membrane-fouling in combined aerobic granular sludge-membrane bioreactor (AGS-MBR) systems. Membrane-fouling represents a major drawback hampering the wider application of membrane bioreactor (MBR) technology. Fouling can be mitigated by applying aerobic granular sludge technology, a novel kind of biofilm technology characterized by high settleability, strong microbial structure, high resilience to toxic/recalcitrant compounds of industrial wastewater, and the possibility to simultaneously remove organic matter and nutrients. Different schemes can be foreseen for the AGS-MBR process. However, an updated literature review reveals that in the AGS-MBR process, granule breakage represents a critical problem in all configurations, which often causes an increase of pore-blocking. Therefore, to date, the objective of research in this sector has been to develop a stable AGS-MBR through multiple operational strategies, including the cultivation of AGS directly in an AGS-MBR reactor, the occurrence of an anaerobic-feast/aerobic-famine regime in continuous-flow reactors, maintenance of average granule dimensions far from critical values, and proper management of AGS scouring, which has been recently recognized as a crucial factor in membrane-fouling mitigation.

Coupled flow and biomass-nutrient growth at pore-scale with permeable biofilm, adaptive singularity and multiple species

In this paper we describe a coupled model for flow and microbial growth as well as nutrient utilization. These processes occur within and outside the biofilm phase formed by the microbes. The primary challenge is to address the volume constraint of maximum cell density but also to allow some microbial presence outside the contiguous biofilm phase. Our model derives from the continuum analogues of the mechanism of cell shoving introduced in discrete biomass models, and in particular from the models exploiting singular diffusivity as well as from models of variational inequality type which impose explicit constraints. We blend these approaches and propose a new idea to adapt the magnitude of the diffusivity automatically so as to ensure the volume constraint without affecting the reactions; this construction can be implemented in many variants without deteriorating the overall efficiency. The second challenge is to account for the flow and transport in the bulk fluid phase adjacent to the biofilm phase. We use the Brinkman flow model with a spatially variable permeability depending on biomass amount. The fluid flow allows some advection of the nutrient within the biofilm phase as well as for the flow even when the pores are close to being plugged up. Our entire model is monolithic and computationally robust even in complex pore-scale geometries, and extends to multiple species. We provide illustrations of our model and of related approaches. The results of the model can be easily post-processed to provide Darcy scale properties of the porous medium, e.g., one can predict how the permeability changes depending on the biomass growth in many realistic scenarios.

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.

Hydrodynamics and surface properties influence biofilm proliferation

A biofilm is an interface-associated colloidal dispersion of bacterial cells and excreted polymers in which microorganisms find protection from their environment. Successful colonization of a surface by a bacterial community is typically a detriment to human health and property. Insight into the biofilm life-cycle provides clues on how their proliferation can be suppressed. In this review, we follow a cell through the cycle of attachment, growth, and departure from a colony. Among the abundance of factors that guide the three phases, we focus on hydrodynamics and stratum properties due to the synergistic effect such properties have on bacteria rejection and removal. Cell motion, whether facilitated by the environment via medium flow or self-actuated by use of an appendage, drastically improves the survivability of a bacterium. Once in the vicinity of a stratum, a single cell is exposed to near-surface interactions, such as van der Waals, electrostatic and specific interactions, similarly to any other colloidal particle. The success of the attachment and the potential for detachment is heavily influenced by surface properties such as material type and topography. The growth of the colony is similarly guided by mainstream flow and the convective transport throughout the biofilm. Beyond the growth phase, hydrodynamic traction forces on a biofilm can elicit strongly non-linear viscoelastic responses from the biofilm soft matter. As the colony exhausts the means of survival at a particular location, a set of trigger signals activates mechanisms of bacterial release, a life-cycle phase also facilitated by fluid flow. A review of biofilm-relevant hydrodynamics and startum properties provides insight into future research avenues.

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.

Damage Repair versus Aging in an Individual-Based Model of Biofilms

Damage is an inevitable consequence of life. For unicellular organisms, this leads to a trade-off between allocating resources into damage repair or into growth coupled with segregation of damage upon cell division, i.e., aging and senescence. Few studies considered repair as an alternative to senescence. None considered biofilms, where the majority of unicellular organisms live, although fitness advantages in well-mixed systems often turn into disadvantages in spatially structured systems such as biofilms. We compared the fitness consequences of aging versus an adaptive repair mechanism based on sensing damage, using an individual-based model of a generic unicellular organism growing in biofilms. We found that senescence is not beneficial provided that growth is limited by substrate availability. Instead, it is useful as a stress response to deal with damage that failed to be repaired when (i) extrinsic mortality was high; (ii) a degree of multicellularity was present; and (iii) damage segregation was effective.

The extent of senescence due to damage accumulation—or aging—is evidently evolvable as it differs hugely between species and is not universal, suggesting that its fitness advantages depend on life history and environment. In contrast, repair of damage is present in all organisms studied. Despite the fundamental trade-off between investing resources into repair or into growth, repair and segregation of damage have not always been considered alternatives. For unicellular organisms, unrepaired damage could be divided asymmetrically between daughter cells, leading to senescence of one and rejuvenation of the other. Repair of “unicells” has been predicted to be advantageous in well-mixed environments such as chemostats. Most microorganisms, however, live in spatially structured systems, such as biofilms, with gradients of environmental conditions and cellular physiology as well as a clonal population structure. To investigate whether this clonal structure might favor senescence by damage segregation (a division-of-labor strategy akin to the germline-soma division in multicellular organisms), we used an individual-based computational model and developed an adaptive repair strategy where cells respond to their current intracellular damage levels by investing into repair machinery accordingly. Our simulations showed that the new adaptive repair strategy was advantageous provided that growth was limited by substrate availability, which is typical for biofilms. Thus, biofilms do not favor a germline-soma-like division of labor between daughter cells in terms of damage segregation. We suggest that damage segregation is beneficial only when extrinsic mortality is high, a degree of multicellularity is present, and an active mechanism makes segregation effective.

IMPORTANCE Damage is an inevitable consequence of life. For unicellular organisms, this leads to a trade-off between allocating resources into damage repair or into growth coupled with segregation of damage upon cell division, i.e., aging and senescence. Few studies considered repair as an alternative to senescence. None considered biofilms, where the majority of unicellular organisms live, although fitness advantages in well-mixed systems often turn into disadvantages in spatially structured systems such as biofilms. We compared the fitness consequences of aging versus an adaptive repair mechanism based on sensing damage, using an individual-based model of a generic unicellular organism growing in biofilms. We found that senescence is not beneficial provided that growth is limited by substrate availability. Instead, it is useful as a stress response to deal with damage that failed to be repaired when (i) extrinsic mortality was high; (ii) a degree of multicellularity was present; and (iii) damage segregation was effective.

Modeling of Biofilm Growth on Fine Spherical Particles with the Use of Cellular Automata: The Influence of Cell Death and Lysis on the Biofilm Structure

The paper concerns the modeling of heterogeneous biofilm growth on fine spherical particles of such biofilm forms as, e.g., fluidized-bed bioreactors. Three discrete mathematical models based on cellular automata theory were proposed. The double-substrate kinetics of biomass growth, biomass displacement, internal and external mass transfer resistances, death and lysis of microbiological cells and biofilm detachment were taken into account. It was shown that there are no significant qualitative and quantitative differences between biofilm growth on flat and spherical particles of different radii. Computer simulations were compared with experimental observations. Qualitative and quantitative agreement areachieved if both cell death and lysis aretaken into consideration and a proper algorithm of biomass displacement is used. The value of the bacteria lysis rate coefficient was estimated.

Not Just Numbers: Mathematical Modelling and Its Contribution to Anaerobic Digestion Processes

Mathematical modelling of bioprocesses has a long and notable history, with eminent contributions from fields including microbiology, ecology, biophysics, chemistry, statistics, control theory and mathematical theory. This richness of ideas and breadth of concepts provide great motivation for inquisitive engineers and intrepid scientists to try their hand at modelling, and this collaboration of disciplines has also delivered significant milestones in the quality and application of models for both theoretical and practical interrogation of engineered biological systems. The focus of this review is the anaerobic digestion process, which, as a technology that has come in and out of fashion, remains a fundamental process for addressing the global climate emergency. Whether with conventional anaerobic digestion systems, biorefineries, or other anaerobic technologies, mathematical models are important tools that are used to design, monitor, control and optimise the process. Both highly structured, mechanistic models and data-driven approaches have been used extensively over half a decade, but recent advances in computational capacity, scientific understanding and diversity and quality of process data, presents an opportunity for the development of new modelling paradigms, augmentation of existing methods, or even incorporation of tools from other disciplines, to ensure that anaerobic digestion research can remain resilient and relevant in the face of emerging and future challenges.

Stable granulation of seawater-adapted aerobic granular sludge with filamentous Thiothrix bacteria

Many sources of wastewater contain sulfides, which can cause excessive growth of filamentous bacteria such as Thiothrix sp. resulting in bulking sludge in conventional activated sludge systems. Granular sludge systems could potentially also suffer from the growth of filamentous bacteria. Uptake of easily degradable COD by the relatively slow growing Ca. Accumulibacter phosphatis bacteria and the absence of strong diffusion gradients due to plug flow feeding through the settled granular sludge bed are assumed to be the dominant factors for successful granulation. Sulfides will remain after this anaerobic phase and cause growth of sulfide-consuming bacteria such as Thiothrix sp. Here we observed the impact of growth of Thiothrix sp bacteria in a laboratory aerobic granular sludge reactor by feeding a mixture of acetate and thiosulfate in the influent. Thiothrix sp, proliferated when 18% of the influent COD was due to thiosulfate, forming 51.4 ± 8.3% of the total granular biomass. Despite the strong presence of these filamentous bacteria a well settling sludge was maintained (SVI₁₀ equal to 13.3 mL/g). These results confirm that sludge morphology is not necessarily a reflection of the cell morphology of the bacteria, but is highly influence by reactor operation. It also reiterates the fact that compact biofilms are formed when the substrate consumption rate is lower than the substrate transport rate.

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.

Modeling cell aggregate morphology during aerobic granulation in activated sludge processes reveals the combined effect of substrate and shear

Past research on AGS (aerobic granular sludge technology) has mainly focused on macro-environment factors, such as settling time, feeding pattern, OLR (organic loading rate), SRT (sludge retention time), among others, and their effects on the granulation process. The biomass granulation process, however, is significantly affected by the micro-environment surrounding these biomass aggregates. In this research, an in silico computational approach was adopted to study the impact of the micro-environment on the biomass granulation process. A 2-D biofilm model based on the cellular automata algorithm and computational fluid dynamics was used to simulate the development of an individual biomass aggregate under specific hydrodynamic and substrate availability conditions. The simulation results indicated that shear and bulk substrate concentration combined to create the optimal conditions for aerobic granule formation. This process can be characterized by the RT (reversed Thiele) modulus value, which is the ratio of the maximum substrate transport over the maximum substrate reaction rate and an indicator of substrate availability. For AGS formation, the RT value should be greater than 0.1. Many common strategies, such as the application of batch reactors, selection for slow-growing microorganism, F/M (food/mass) ratio adjustment, feast and famine condition, and short settling time, for biomass granulation production can be explained by the RT value. The results suggest that rethinking unit process configurations in wastewater treatment facilities will be required to achieve reliable AGS formation.

Hybrid Model of Bacterial Biofilm Growth

Bacterial biofilms play a critical role in environmental processes, water treatment, human health, and food processing. They exhibit highly complex dynamics due to the interactions between the bacteria and the extracellular polymeric substance (EPS), water, and nutrients and minerals that make up the biofilm. We present a hybrid computational model in which the dynamics of discrete bacterial cells are simulated within a multiphase continuum, consisting of EPS and water as separate interacting phases, through which nutrients and minerals diffuse. Bacterial cells in our model consume water and nutrients in order to grow, divide, and produce EPS. Consequently, EPS flows outward from the bacterial colony, while water flows inward. The model predicts bacterial colony formation as a treelike structure. The distribution of bacterial growth and EPS production is found to be sensitive to the pore spacing between bacteria and the consumption of nutrients within the bacterial colony. Forces that are sometimes neglected in biofilm simulations, such as lubrication force between nearby bacterial cells and osmotic (swelling) pressure force resulting from gradients in EPS concentration, are observed to have an important effect on biofilm growth via their influence on bacteria pore spacing and associated water/nutrient percolation into the bacterial colony.

Influence of operation mode and wastewater strength on aerobic granulation at pilot scale: Startup period, granular sludge characteristics, and effluent quality

This study attempted to investigate the influence of operation mode and wastewater strength on startup period, aerobic granular sludge (AGS) characteristics, and system effluent quality at pilot scale. Granulation was monitored in three pilot-scale granular sequencing batch reactors (GSBRs). Comparative evaluation of AN/O/AX/O_SBR and O_SBR, fed with wastewater of the same composition but run with completely different SBR reaction phase arrangements (alternating vs. purely aerobic), revealed the effect of SBR operation mode. Comparative study of the GSBRs operated with alternating SBR reaction phases (AN/O/AX/O_SBR and AN/O_SBR) and fed with wastewater of different strength (high- vs. medium-strength) determined the effect of wastewater composition. Granulation time and granule size were regulated by wastewater strength and the resulting organic and sludge loading conditions. Whereas, AGS morphology, granule structure, and floccular proportion of AGS were attributed to SBR operation mode. Effluent clarity in terms of suspended solid concentration depended on wastewater strength. Subtle but distinct microbial selection strategies were in effect during granulation which were also imposed by wastewater strength. Due to strong correlation between the effluent and AGS microbial structures, demonstrated by biodiversity analysis, differences in the microbial composition of effluent biomass and washout patterns of the GSBRs could be explained by wastewater strength as well. Limited nutrient removal efficiencies, restricted by organic matter concentration, could be due to involvement of unorthodox nutrient removal pathways which warrants further investigation.

A thin-film extensional flow model for biofilm expansion by sliding motility

In the presence of glycoproteins, bacterial and yeast biofilms are hypothesized to expand by sliding motility. This involves a sheet of cells spreading as a unit, facilitated by cell proliferation and weak adhesion to the substratum. In this paper, we derive an extensional flow model for biofilm expansion by sliding motility to test this hypothesis. We model the biofilm as a two-phase (living cells and an extracellular matrix) viscous fluid mixture, and model nutrient depletion and uptake from the substratum. Applying the thin-film approximation simplifies the model, and reduces it to one-dimensional axisymmetric form. Comparison with Saccharomyces cerevisiae mat formation experiments reveals good agreement between experimental expansion speed and numerical solutions to the model withO ( 1 ) parameters estimated from experiments. This confirms that sliding motility is a possible mechanism for yeast biofilm expansion. Having established the biological relevance of the model, we then demonstrate how the model parameters affect expansion speed, enabling us to predict biofilm expansion for different experimental conditions. Finally, we show that our model can explain the ridge formation observed in some biofilms. This is especially true if surface tension is low, as hypothesized for sliding motility.

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.

Mechanistic Morphogenesis of Organo-Sedimentary Structures Growing Under Geochemically Stressed Conditions: Keystone to Proving the Biogenicity of Some Archaean Stromatolites?

Morphologically diverse organo-sedimentary structures (including microbial mats and stromatolites) provide a palaeobiological record through more than three billion years of Earth history. Since understanding much of the Archaean fossil record is contingent upon proving the biogenicity of such structures, mechanistic interpretations of well-preserved fossil microbialites can reinforce our understanding of their biogeochemistry and distinguish unambiguous biological characteristics in these structures, which represent some of the earliest records of life. Mechanistic morphogenetic understanding relies upon the analysis of geomicrobiological experiments. Herein, we report morphological-biogeochemical comparisons between micromorphologies observed in growth experiments using photosynthetic mats built by the cyanobacterium Coleofasciculus chthonoplastes (formerly Microcoleus) and green anoxygenic phototrophic Chloroflexus spp. (i.e., Coleofasciculus–Chloroflexus mats), and Precambrian organo-sedimentary structures, demonstrating parallels between them. In elevated ambient concentrations of Cu (toxic to Coleofasciculus), Coleofasciculus–Chloroflexus mats respond by forming centimetre-scale pinnacle-like structures (supra-lamina complexities) associated with large quantities of EPS at their surfaces. µPIXE mapping shows that Cu and other metals become concentrated within surficial sheath-EPS-Chloroflexus-rich layers, producing density-differential micromorphologies with distinct fabric orientations that are detectable using X-ray computed micro-tomography (X-ray µCT). Similar micromorphologies are also detectable in stromatolites from the 3.481 Ga Dresser Formation (Pilbara, Western Australia). The cause and response link between the presence of toxic elements (geochemical stress) and the development of multi-layered topographical complexities in organo-sedimentary structures may thus be considered an indicator of biogenicity, being an indisputably biological and predictable morphogenetic response reflecting, in this case, the differential responses of Coleofasciculus and Chloroflexus to Cu. Growth models for microbialite morphogenesis rely upon linking morphology to intrinsic (biological) and extrinsic (environmental) influences. Since the pinnacles of Coleofasciculus–Chloroflexus mats have an unambiguously biological origin linked to extrinsic geochemistry, we suggest that similar micromorphologies observed in ancient organo-sedimentary structures are indicative of biogenesis. An identical Coleofasciculus–Chloroflexus community subjected to salinity stress also produced supra-lamina complexities (tufts) but did not produce identifiable micromorphologies in three dimensions since salinity seems not to negatively impact either organism, and therefore cannot be used as a morphogenetic tool for the interpretation of density-homogeneous micro-tufted mats—for example, those of the 3.472 Ga Middle Marker horizon. Thus, although correlative microscopy is the keystone to confirming the biogenicity of certain Precambrian stromatolites, it remains crucial to separately interrogate each putative trace of ancient life, ideally using three-dimensional analyses, to determine, where possible, palaeoenvironmental influences on morphologies. Widespread volcanism and hydrothermal effusion into the early oceans likely concentrated toxic elements in early biomes. Morphological diversity in fossil microbialites could, therefore, reflect either (or both of) differential exposure to ambient fluids enriched in toxic elements and/or changing ecosystem structure and tolerance to elements through evolutionary time—for example, after incorporation into enzymes. Proof of biogenicity by deducing morphogenesis (i.e., a process preserved in the fossil record) overcomes many of the shortcomings inherent to the proof of biogenicity by descriptions of morphology alone.

From molecules to multispecies ecosystems: the roles of structure in bacterial biofilms

Biofilms are communities of sessile microbes that are bound to each other by a matrix made of biopolymers and proteins. Spatial structure is present in biofilms on many lengthscales. These range from the nanometer scale of molecular motifs to the hundred-micron scale of multicellular aggregates. Spatial structure is a physical property that impacts the biology of biofilms in many ways. The molecular structure of matrix components controls their interaction with each other (thereby impacting biofilm mechanics) and with diffusing molecules such as antibiotics and immune factors (thereby impacting antibiotic tolerance and evasion of the immune system). The size and structure of multicellular aggregates, combined with microbial consumption of growth substrate, give rise to differentiated microenvironments with different patterns of metabolism and gene expression. Spatial association of more than one species can benefit one or both species, while distances between species can both determine and result from the transport of diffusible factors between species. Thus, a widespread theme in the biological importance of spatial structure in biofilms is the effect of structure on transport. We survey what is known about this and other effects of spatial structure in biofilms, from molecules up to multispecies ecosystems. We conclude with an overview of what experimental approaches have been developed to control spatial structure in biofilms and how these and other experiments can be complemented with computational work.

Unraveling the biophysical underpinnings to the success of multispecies biofilms in porous environments

Biofilms regulate critical processes in porous ecosystems. However, the biophysical underpinnings of the ecological success of these biofilms are poorly understood. Combining experiments with fluidic devices, sequencing and modeling, we reveal that architectural plasticity enhances space exploitation by multispecies biofilms in porous environments. Biofilms consistently differentiated into an annular base biofilm coating the grains and into streamers protruding from the grains into the pore space. Although different flow-related processes governed the differentiation of these architectures, both BB and streamers were composed of similar bacterial assemblages. This is evidence for architectural plasticity. Architectural plasticity allowed for complementary use of the space provided by the grain–pore complexes, which increased biofilm carrying capacity at the larger scale of the porous system. This increase comes potentially at the cost of a tradeoff. Contrasting time scales of oxygen replenishment and consumption, we show that streamers locally inhibit the growth of the BB downstream from the grains. Our study provides first insights into the biophysical underpinnings to the success of multispecies biofilms in porous environments.

Modeling Oral Multispecies Biofilm Recovery After Antibacterial Treatment

Recovery of multispecies oral biofilms is investigated following treatment by chlorhexidine gluconate (CHX), iodine-potassium iodide (IPI) and Sodium hypochlorite (NaOCl) both experimentally and theoretically. Experimentally, biofilms taken from two donors were exposed to the three antibacterial solutions (irrigants), respectively, for 10 minutes. We observe that (a) live bacterial cell ratios decline for a week after the exposure and the trend then reverses beyond the week; after fifteen weeks, live bacterial cell ratios in biofilms fully return to their pretreatment levels; (b) NaOCl is shown as the strongest antibacterial agent for the oral biofilms; (c) multispecies oral biofilms from different donors showed no difference in their susceptibility to all the bacterial solutions. Guided by the experiment, a mathematical model for biofilm dynamics is developed, accounting for multiple bacterial phenotypes, quorum sensing, and growth factor proteins, to describe the nonlinear time evolutionary behavior of the biofilms. The model captures time evolutionary dynamics of biofilms before and after antibacterial treatment very well. It reveals the important role played by quorum sensing molecules and growth factors in biofilm recovery and verifies that the source of biofilms has a minimal effect to their recovery. The model is also applied to describe the state of biofilms of various ages treated respectively by CHX, IPI and NaOCl, taken from different donors. Good agreement with experimental data predicted by the model is obtained as well, confirming its applicability to modeling biofilm dynamics in general.

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.