Liquid transport facilitated by channels in Bacillus subtilis biofilms

2018 international consensus meeting on musculoskeletal infection: Summary from the biofilm workgroup and consensus on biofilm related musculoskeletal infections

Biofilm-associated implant-related bone and joint infections are clinically important due to the extensive morbidity, cost of care and socioeconomic burden that they cause. Research in the field of biofilms has expanded in the past two decades, however, there is still an immense knowledge gap related to many clinical challenges of these biofilm-associated infections. This subject was assigned to the Biofilm Workgroup during the second International Consensus Meeting on Musculoskeletal Infection held in Philadelphia USA (ICM 2018) (https://icmphilly.com). The main objective of the Biofilm Workgroup was to prepare a consensus document based on a review of the literature, prepared responses, discussion, and vote on thirteen biofilm related questions. The Workgroup commenced discussing and refining responses prepared before the meeting on day one using Delphi methodology, followed by a tally of responses using an anonymized voting system on the second day of ICM 2018. The Working group derived consensus on information about biofilms deemed relevant to clinical practice, pertaining to: (1) surface modifications to prevent/inhibit biofilm formation; (2) therapies to prevent and treat biofilm infections; (3) polymicrobial biofilms; (4) diagnostics to detect active and dormant biofilm in patients; (5) methods to establish minimal biofilm eradication concentration for biofilm bacteria; and (6) novel anti-infectives that are effective against biofilm bacteria. It was also noted that biomedical research funding agencies and the pharmaceutical industry should recognize these areas as priorities. © 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res.

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.

Self-organization of swimmers drives long-range fluid transport in bacterial colonies

Motile subpopulations in microbial communities are believed to be important for dispersal, quest for food, and material transport. Here, we show that motile cells in sessile colonies of peritrichously flagellated bacteria can self-organize into two adjacent, centimeter-scale motile rings surrounding the entire colony. The motile rings arise from spontaneous segregation of a homogeneous swimmer suspension that mimics a phase separation; the process is mediated by intercellular interactions and shear-induced depletion. As a result of this self-organization, cells drive fluid flows that circulate around the colony at a constant peak speed of ~30 µm s⁻¹, providing a stable and high-speed avenue for directed material transport at the macroscopic scale. Our findings present a unique form of bacterial self-organization that influences population structure and material distribution in colonies.

Motile and non-motile subpopulations often coexist in bacterial communities. Here, Xu et al. show that motile cells in colonies of common flagellated bacteria can self-organize into two adjacent motile rings, driving stable flows of fluid and materials around the colony.

Matrix Production and Sporulation in Bacillus subtilis Biofilms Localize to Propagating Wave Fronts

Bacterial biofilms are surface-attached microbial communities encased in self-produced extracellular polymeric substances. Here we demonstrate that during the development of Bacillus subtilis biofilms, matrix production is localized to an annular front propagating at the periphery and sporulation to a second front at a fixed distance at the interior. We show that within these fronts, cells switch off matrix production and transition to sporulation after a set time delay of ∼100 min. Correlation analyses of fluctuations in fluorescence reporter activity reveal that the fronts emerge from a pair of gene-expression waves of matrix production and sporulation. The localized expression waves travel across cells that are immobilized in the biofilm matrix in contrast to active cell migration or horizontal colony spreading. Our results suggest that front propagation arises via a local developmental program occurring at the level of individual bacterial cells, likely driven by nutrient depletion and metabolic by-product accumulation. A single-length scale and timescale couples the spatiotemporal propagation of both fronts throughout development. As a result, gene expression patterns within the advancing fronts collapse to self-similar expression profiles. Our findings highlight the key role of the localized cellular developmental program associated with the propagating front in describing biofilm growth.

Spatiotemporal establishment of dense bacterial colonies growing on hard agar

The physical interactions of growing bacterial cells with each other and with their surroundings significantly affect the structure and dynamics of biofilms. Here a 3D agent-based model is formulated to describe the establishment of simple bacterial colonies expanding by the physical force of their growth. With a single set of parameters, the model captures key dynamical features of colony growth by non-motile, non EPS-producing E. coli cells on hard agar. The model, supported by experiment on colony growth in different types and concentrations of nutrients, suggests that radial colony expansion is not limited by nutrients as commonly believed, but by mechanical forces. Nutrient penetration instead governs vertical colony growth, through thin layers of vertically oriented cells lifting up their ancestors from the bottom. Overall, the model provides a versatile platform to investigate the influences of metabolic and environmental factors on the growth and morphology of bacterial colonies.

Emergence of evolutionary driving forces in pattern-forming microbial populations

Evolutionary dynamics are controlled by a number of driving forces, such as natural selection, random genetic drift and dispersal. In this perspective article, we aim to emphasize that these forces act at the population level, and that it is a challenge to understand how they emerge from the stochastic and deterministic behaviour of individual cells. Even the most basic steric interactions between neighbouring cells can couple evolutionary outcomes of otherwise unrelated individuals, thereby weakening natural selection and enhancing random genetic drift. Using microbial examples of varying degrees of complexity, we demonstrate how strongly cell-cell interactions influence evolutionary dynamics, especially in pattern-forming systems. As pattern formation itself is subject to evolution, we propose to study the feedback between pattern formation and evolutionary dynamics, which could be key to predicting and potentially steering evolutionary processes. Such an effort requires extending the systems biology approach from the cellular to the population scale.This article is part of the theme issue 'Self-organization in cell biology'.

Mechanical instability and interfacial energy drive biofilm morphogenesis

Surface-attached bacterial communities called biofilms display a diversity of morphologies. Although structural and regulatory components required for biofilm formation are known, it is not understood how these essential constituents promote biofilm surface morphology. Here, using Vibrio cholerae as our model system, we combine mechanical measurements, theory and simulation, quantitative image analyses, surface energy characterizations, and mutagenesis to show that mechanical instabilities, including wrinkling and delamination, underlie the morphogenesis program of growing biofilms. We also identify interfacial energy as a key driving force for mechanomorphogenesis because it dictates the generation of new and the annihilation of existing interfaces. Finally, we discover feedback between mechanomorphogenesis and biofilm expansion, which shapes the overall biofilm contour. The morphogenesis principles that we discover in bacterial biofilms, which rely on mechanical instabilities and interfacial energies, should be generally applicable to morphogenesis processes in tissues in higher organisms.

Engineers have long studied how mechanical instabilities cause patterns to form in inanimate materials, and recently more attention has been given to how such forces affect biological systems. For example, stresses can build up within a tissue if one layer grows faster than an adjacent layer. The tissue can release this stress by wrinkling, folding or creasing.

Though ancient and single-celled, bacteria can also develop spectacular patterns when they exist in the lifestyle known as a biofilm: a community of cells adhered to a surface. But do mechanical instabilities drive the patterns seen in biofilms?

To investigate, Yan, Fei, Mao et al. grew biofilms of the bacterium called Vibrio cholerae – which causes the disease cholera – on solid, non-growing ‘substrates’. This work revealed that as the biofilms grow, their expansion is constrained by the substrate, and this situation generates mechanical stresses. To release the stresses, the biofilm initially folds to form wrinkles. Later, as the biofilm expands further, small parts of it detach from the substrate to form blisters. The same forces that keep water droplets spherical (known as interfacial forces) dictate how the blisters evolve, interact, and eventually shape the expanding biofilm. Using these principles, Yan et al. could engineer the biofilm into desired shapes.

Collectively, the results presented by Yan et al. connect the shape of the biofilm surface with its material properties, in particular its stiffness. Understanding this relationship could help researchers to develop new ways to remove harmful biofilms, such as those that cause disease or that damage underwater structures. The stiffness of biofilms is already known to affect how well bacteria can resist antibiotics. Future studies could look for new genes or compounds that change the material properties of a biofilm, thereby altering the biofilm surface.

Efficiency of the flagellar propulsion of Escherichia coli in confined microfluidic geometries

Bacterial movement in confined spaces is routinely encountered either in a natural environment or in artificial structures. Consequently, the ability to understand and predict the behavior of motile bacterial cells in confined geometries is essential to many applications, spanning from the more classical, such as the management complex microbial networks involved in diseases, biomanufacturing, mining, and environment, to the more recent, such as single cell DNA sequencing and computation with biological agents. Fortunately, the development of this understanding can be helped by the decades-long advances in semiconductor microfabrication, which allow the design and the construction of complex confining structures used as test beds for the study of bacterial motility. To this end, here we use microfabricated channels with varying sizes to study the interaction of Escherichia coli with solid confining spaces. It is shown that an optimal channel size exists for which the hydrostatic potential allows the most efficient movement of the cells. The improved understanding of how bacteria move will result in the ability to design better microfluidic structures based on their interaction with bacterial movement.

Drying of channels by evaporation through a permeable medium

We study the drying of isolated channels initially filled with water moulded in a water-permeable polymer (polydimethylsiloxane, PDMS) by pervaporation, when placed in a dry atmosphere. Channel drying is monitored by tracking a meniscus, separating water from air, advancing within the channels. The role of two geometrical parameters, the channel width and the PDMS thickness, is investigated experimentally. All data show that drying displays a truncated exponential dynamics. A fully predictive analytical model, in excellent agreement with the data, is proposed to explain such a dynamics, by solving water diffusion both in the PDMS layer and in the gas inside the channel. This drying process is crucial in geological or biological systems, such as rock disintegration or the drying of plant leaves after cavitation and embolism formation.

Continuous shear stress alters metabolism, mass-transport, and growth in electroactive biofilms independent of surface substrate transport

Electroactive bacteria such as Geobacter sulfurreducens and Shewanella onedensis produce electrical current during their respiration; this has been exploited in bioelectrochemical systems. These bacteria form thicker biofilms and stay more active than soluble-respiring bacteria biofilms because their electron acceptor is always accessible. In bioelectrochemical systems such as microbial fuel cells, corrosion-resistant metals uptake current from the bacteria, producing power. While beneficial for engineering applications, collecting current using corrosion resistant metals induces pH stress in the biofilm, unlike the naturally occurring process where a reduced metal combines with protons released during respiration. To reduce pH stress, some bioelectrochemical systems use forced convection to enhance mass transport of both nutrients and byproducts; however, biofilms’ small pore size limits convective transport, thus, reducing pH stress in these systems remains a challenge. Understanding how convection is necessary but not sufficient for maintaining biofilm health requires decoupling mass transport from momentum transport (i.e. fluidic shear stress). In this study we use a rotating disc electrode to emulate a practical bioelectrochemical system, while decoupling mass transport from shear stress. This is the first study to isolate the metabolic and structural changes in electroactive biofilms due to shear stress. We find that increased shear stress reduces biofilm development time while increasing its metabolic rate. Furthermore, we find biofilm health is negatively affected by higher metabolic rates over long-term growth due to the biofilm’s memory of the fluid flow conditions during the initial biofilm development phases. These results not only provide guidelines for improving performance of bioelectrochemical systems, but also reveal features of biofilm behavior. Results of this study suggest that optimized reactors may initiate operation at high shear to decrease development time before decreasing shear for steady-state operation. Furthermore, this biofilm memory discovered will help explain the presence of channels within biofilms observed in other studies.

Selective Targeting of 4SO4-N-Acetyl-Galactosamine Functionalized Mycobacterium tuberculosis Protein Loaded Chitosan Nanoparticle to Macrophages: Correlation With Activation of Immune System

In the present study, we investigated potential of chitosan-based nanoparticles (CNPs) to deliver loaded therapeutic molecules to pathogen harboring macrophages. We fabricated stable CNPs employing ionic cross-linking method and evaluated their potential to target RAW 264.7 cells. The physicochemical characterization of as-synthesized CNPs was determined using electron microscopy, infrared microscopy and zeta potential measurement. Next, cellular uptake and intracellular localization studies of CNPs were followed in living RAW264.7 cells using confocal microscopy. We found that both Acr-1 loaded (CNP-A) and 4-SO₄-GalNAc ligand harboring (CNP-L) chitosan nanoparticle experience increased cellular uptake by Mycobacterium smegmatis infected RAW cells. Following cellular digestion in model macrophage cell line (RAW), CNPs provide an increased immune response. Further, 4-SO₄-GalNAc bearing CNP-L exhibits high binding affinity as well as antibacterial efficacy toward M. smegmatis. The data of the present study suggest that CNP-based nanoparticle offer a promising delivery strategy to target infected macrophages for prevention and eradication of intracellular pathogens such as M. smegmatis.

Nonthermal Plasma Jet Treatment Negatively Affects the Viability and Structure of Candida albicans SC5314 Biofilms

Microorganisms are predominantly organized in biofilms, where cells live in dense communities and are more resistant to external stresses than are their planktonic counterparts. With in vitro experiments, the susceptibility of Candida albicans biofilms to a nonthermal plasma treatment (plasma source, kINPen09) in terms of growth, survival, and cell viability was investigated. C. albicans strain SC5314 (ATCC MYA-2876) was plasma treated for different time periods (30 s, 60 s, 120 s, 180 s, 300 s). The results of the experiments, encompassing CFU, fluorescence Live/Dead, and 2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide salt (XTT) assays, revealed a negative influence of the plasma treatment on the proliferation ability, vitality, and metabolism of C. albicans biofilms, respectively. Morphological analysis of plasma-treated biofilms using atomic force microscopy supported the indications for lethal plasma effects concomitant with membrane disruptions and the loss of intracellular fluid. Yielding controversial results compared to those of other publications, fluorescence and confocal laser scanning microscopic inspection of plasma-treated biofilms indicated that an inactivation of cells appeared mainly on the bottom of the biofilms. If this inactivation leads to a detachment of the biofilms from the overgrown surface, it might offer completely new approaches in the plasma treatment of biofilms. Because of plasma's biochemical-mechanical mode of action, resistance of microbial cells against plasma is unknown at this state of research.IMPORTANCE Microbial communities are an increasing problem in medicine but also in industry. Thus, an efficient and rapid removal of biofilms is becoming increasingly important. With the aid of the kINPen09, a radiofrequency plasma jet (RFPJ) instrument, decisive new findings on the effects of plasma on C. albicans biofilms were obtained. This work showed that the inactivation of biofilms takes place mainly on the bottom, which in turn offers new possibilities for the removal of biofilms by other strategies, e.g., mechanical treatment. This result demonstrated that nonthermal atmospheric pressure plasma is well suited for biofilm decontamination.

Periprosthetic bacterial biofilm and quorum sensing

Periprosthetic joint infection (PJI) is a common complication after total joint arthroplasty leading to severe morbidity and mortality. With an aging population and increasing prevalence of total joint replacement procedures, the burden of PJI will be felt not only by individual patients, but in increased healthcare costs. Current treatment of PJI is inadequate resulting in incredibly high failure rates. This is believed to be largely mediated by the presence of bacterial biofilms. These polymicrobial bacterial colonies form within secreted extracellular matrices, adhering to the implant surface and local tissue. The biofilm architecture is believed to play a complex and critical role in a variety of bacterial processes including nutrient supplementation, metabolism, waste management, and antibiotic and immune resistance. The establishment of these biofilms relies heavily on the quorum sensing communication systems utilized by bacteria. Early stage research into disrupting bacterial communication by targeting quorum sensing show promise for future clinical applications. However, prevention of the biofilm formation via early forced induction of the biofilm forming process remains yet unexplored. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:2331-2339, 2018.

Programmable wettability on photocontrolled graphene film

Surface materials with specific wettability play important roles in a wide variety of areas from science to industry. We present a novel paraffin-infused porous graphene film (PIPGF) with programmable wettability. Because of graphene's photothermal property, the paraffin in the PIPGF was in transition between liquid and solid in response to near-infrared (NIR) light irradiation. Thus, we imparted the film with a dynamic and reversible transition between a slippery and a rough surface as the remotely tunable wettability. In addition, with the integration of NIR masks, the paraffin could melt at corresponding patterns on the PIPGF, which formed special flow pathways for the slipping droplets. Therefore, the PIPGF could provide programmable wettability pathways for the spatiotemporal droplet manipulation by flexibly changing the NIR masks. We demonstrated these programmable wettability pathways to not only simplify liquid handling in the microplates and droplet microarrays technology but also to provide distinctly microfluidic microreactors for different purposes, such as practical blood grouping diagnosis. These features indicated that the photocontrollable PIPGF would be amenable to a variety of applications, such as microfluidic systems, laboratory-on-a-chip settings, and droplet manipulations.

FINITE ELEMENT SIMULATION OF BIOFILM VISCOELASTIC BEHAVIOR UNDER VARIOUS LOADINGS

Experiments showed that biofilms exhibit viscoelasticity under both displacement and stress loadings, irrespective of pellicles at liquid–air interface or biofilms at solid–liquid interface. However, the general theoretical models are lacking inuniformly and quantitatively describing biofilms’ viscoelastic behavior under various loading conditions. We use the linear viscoelastic theory — Generalized Maxwell model to describe the viscoelastic mechanical properties of biofilms, and study the responses of biofilms under different loadings, including various strain/stress loading rates and cyclic loadings, by finite element method. The results can capture the typical viscoelastic characteristics of biofilms, such as creep, hysteresis, energy dissipation and loading rate-dependent behavior. Our work provides a simple viscoelastic model not only for bacterial biofilms but also for other biological materials.

A universal growth limit for circular lichens

Lichens fix carbon dioxide from the air to build biomass. Crustose and foliose lichens grow as nearly flat, circular disks. Smaller individuals grow slowly, but with small, steady increases in radial growth rate over time. Larger individuals grow more quickly and with a roughly constant radial velocity maintained over the lifetime of the lichen. We translate the coffee drop effect to model lichen growth and demonstrate that growth patterns follow directly from the diffusion of carbon dioxide in the air around a lichen. When a lichen is small, carbon dioxide is fixed across its surface, and the entire thallus contributes to radial growth, but when a lichen is larger carbon dioxide is disproportionately fixed at the edges of an individual, which are the primary drivers of growth. Tests of the model against data suggest it provides an accurate, robust, and universal framework for understanding the growth dynamics of both large and small lichens in nature.

Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation

Rhizosphere-associated Pseudomonas fluorescens are known plant growth promoting (PGP) and mycorrhizal helper bacteria (MHB) of many plants and ectomycorrhizal fungi. We investigated the spatial and temporal dynamics of colonization of mycorrhizal and non-mycorrhizal Aspen seedlings roots by the P. fluorescens strains SBW25, WH6, Pf0-1, and the P. protegens strain Pf-5. Seedlings were grown in laboratory vertical plates systems, inoculated with a fluorescently labeled Pseudomonas strain, and root colonization was monitored over a period of 5 weeks. We observed unexpected diversity of bacterial assemblies on seedling roots that changed over time and were strongly affected by root mycorrhization. P. fluorescens SBW25 and WH6 stains developed highly structured biofilms with internal void spaces forming channels. On mycorrhizal roots bacteria appeared encased in a mucilaginous substance in which they aligned side by side in parallel arrangements. The different phenotypic classes of bacterial assemblies observed for the four Pseudomonas strains were summarized in a single model describing transitions between phenotypic classes. Our findings also reveal that bacterial assembly phenotypes are driven by interactions with mucilaginous materials present at roots.

Local growth rules can maintain metabolically efficient spatial structure throughout growth

A ubiquitous feature of bacterial communities is the existence of spatial structures. These are often coupled to metabolism, whereby the spatial organization can improve chemical reaction efficiency. However, it is not clear whether or how a desired colony configuration, for example, one that optimizes some overall global objective, could be achieved by individual cells that do not have knowledge of their positions or of the states of all other cells. By using a model which consists of cells producing enzymes that catalyze coupled metabolic reactions, we show that simple, local rules can be sufficient for achieving a global, community-level goal. In particular, even though the optimal configuration varies with colony size, we demonstrate that cells regulating their relative enzyme levels based solely on local metabolite concentrations can maintain the desired overall spatial structure during colony growth. We also show that these rules can be very simple and hence easily implemented by cells. Our framework also predicts scenarios where additional signaling mechanisms may be required.

Cell death as a trigger for morphogenesis

The complex morphologies observed in many biofilms play a critical role in the survival of these microbial communities. Recently, the formation of wrinkles has been the focus of many studies aimed at finding fundamental information on morphogenesis during development. While the underlying genetic mechanisms of wrinkling are not well-understood, recent discoveries have led to the counterintuitive idea that wrinkle formation is triggered by localized cell death. This work examines the hypothesis that the material properties of a biofilm both power and control wrinkle formation within biofilms in response to localized cell death. Using an agent-based model and a high-performance platform (Biocellion), we built a model that qualitatively reproduced wrinkle formation in biofilms due to cell death. Through the use of computational simulations, we determined important relationships between cellular level mechanical interactions and changes in colony morphology. These simulations were also used to identify significant cellular interactions that are required for wrinkle formation. These results are a first step towards more comprehensive models that, in combination with experimental observations, will improve our understanding of the morphological development of bacterial biofilms.

Role of red cells and plasma composition on blood sessile droplet evaporation

The morphology of dried blood droplets derives from the deposition of red cells, the main components of their solute phase. Up to now, evaporation-induced convective flows were supposed to be at the base of red cell distribution in blood samples. Here, we present a direct visualization by videomicroscopy of the internal dynamics in desiccating blood droplets, focusing on the role of cell concentration and plasma composition. We show that in diluted suspensions, the convection is promoted by the rich molecular composition of plasma, whereas it is replaced by an outward red blood cell displacement front at higher hematocrits. We also evaluate by ultrasounds the effect of red cell deposition on the temporal evolution of sample rigidity and adhesiveness.

Rapid in situ imaging and whole genome sequencing of biofilm in neonatal feeding tubes: A clinical proof of concept

The bacterial flora of nasogastric feeding tubes and faecal samples were analysed for a low-birth weight (725 g) neonate EGA 25 weeks in intensive care. Samples were collected at age 6 and 8 weeks of life. Optical coherence tomography (OCT) was used to visualise bacterial biofilms inside the nasogastric feeding tubes. The biofilm was heterogeneously distributed along the tube lumen wall, and had a depth of up to 500 µm. The bacterial biofilm and faecal samples included Enterococcus faecalis and Enterobacter hormaechei. Representative strains, recovered from both feeding tubes and faecal samples, were whole genome sequenced using Illumina, Mi-Seq, which revealed indistinguishable strains, each with less than 28 SNP differences, of E. faecalis and E. hormaechei. The E. faecalis strains were from two sequence types (ST191 and ST211) and encoded for a number of traits related to biofilm formation (BopD), adherence (Epb pili), virulence (cps loci, gelatinase, SprE) and antibiotic resistances (IsaA, tetM). The E. hormaechei were all ST106, and encoded for blaACT-15 β–lactamase and fosfomycin resistance (fosA). This proof of concept study demonstrates that bacterial flora within the neonatal feeding tubes may influence the bacterial colonisation of the intestinal tract and can be visualised non-destructively using OCT.

Bacillus subtilis Biofilm Development - A Computerized Study of Morphology and Kinetics

Biofilm is commonly defined as accumulation of microbes, embedded in a self-secreted extra-cellular matrix, on solid surfaces or liquid interfaces. In this study, we analyze several aspects of Bacillus subtilis biofilm formation using tools from the field of image processing. Specifically, we characterize the growth kinetics and morphological features of B. subtilis colony type biofilm formation and compare these in colonies grown on two different types of solid media. Additionally, we propose a model for assessing B. subtilis biofilm complexity across different growth conditions. GFP-labeled B. subtilis cells were cultured on agar surfaces over a 4-day period during which microscopic images of developing colonies were taken at equal time intervals. The images were used to perform a computerized analysis of few aspects of biofilm development, based on features that characterize the different phenotypes of B. subtilis colonies. Specifically, the analysis focused on the segmented structure of the colonies, consisting of two different regions of sub-populations that comprise the biofilm – a central “core” region and an “expanding” region surrounding it. Our results demonstrate that complex biofilm of B. subtillis grown on biofilm-promoting medium [standard lysogeny broth (LB) supplemented with manganese and glycerol] is characterized by rapidly developing three-dimensional complex structure observed at its core compared to biofilm grown on standard LB. As the biofilm develops, the core size remains largely unchanged during development and colony expansion is mostly attributed to the expansion in area of outer cell sub-populations. Moreover, when comparing the bacterial growth on biofilm-promoting agar to that of colonies grown on LB, we found a significant decrease in the GFP production of colonies that formed a more complex biofilm. This suggests that complex biofilm formation has a diminishing effect on cell populations at the biofilm core, likely due to a combination of reduced metabolic rate and increased levels of cell death within this region.

Experimental and theoretical studies on the morphogenesis of bacterial biofilms

Biofilm morphogenesis not only reflects the physiological state of bacteria but also serves as a strategy to sustain bacterial survival. In this paper, we take the Bacillus subtilis colony as a model system to explore the morphomechanics of growing biofilms confined in a defined geometry. We find that the growth-induced stresses may drive the occurrence of both surface wrinkling and interface delamination in the biofilm, leading to the formation of a labyrinthine network on its surface. The wrinkles are perpendicular to the boundary of the constraint region. The variation in the surface undulations is attributed to the spatial stress field, which is isotropic in the inner regime but anisotropic in the vicinity of the boundary. Our experiments show that the directional surface wrinkles can confer biofilms with anisotropic wetting properties. This study not only highlights the role of mechanics in sculpturing organisms within the morphogenetic context but also suggests a promising route toward desired surfaces at the interface between synthetic biology and materials sciences.

Lysinibacillus fusiformis M5 Induces Increased Complexity in Bacillus subtilis 168 Colony Biofilms via Hypoxanthine

In recent years, biofilms have become a central subject of research in the fields of microbiology, medicine, agriculture, and systems biology, among others. The sociomicrobiology of multispecies biofilms, however, is still poorly understood. Here, we report a screening system that allowed us to identify soil bacteria which induce architectural changes in biofilm colonies when cocultured with Bacillus subtilis We identified the soil bacterium Lysinibacillus fusiformis M5 as an inducer of wrinkle formation in B. subtilis colonies mediated by a diffusible signaling molecule. This compound was isolated by bioassay-guided chromatographic fractionation. The elicitor was identified to be the purine hypoxanthine using mass spectrometry and nuclear magnetic resonance (NMR) spectroscopy. We show that the induction of wrinkle formation by hypoxanthine is not dependent on signal recognition by the histidine kinases KinA, KinB, KinC, and KinD, which are generally involved in phosphorylation of the master regulator Spo0A. Likewise, we show that hypoxanthine signaling does not induce the expression of biofilm matrix-related operons epsABCDEFGHIJKLMNO and tasA-sipW-tapA Finally, we demonstrate that the purine permease PbuO, but not PbuG, is necessary for hypoxanthine to induce an increase in wrinkle formation of B. subtilis biofilm colonies. Our results suggest that hypoxanthine-stimulated wrinkle development is not due to a direct induction of biofilm-related gene expression but rather is caused by the excess of hypoxanthine within B. subtilis cells, which may lead to cell stress and death.IMPORTANCE Biofilms are a bacterial lifestyle with high relevance regarding diverse human activities. Biofilms can be beneficial, for instance, in crop protection. In nature, biofilms are commonly found as multispecies communities displaying complex social behaviors and characteristics. The study of interspecies interactions will thus lead to a better understanding and use of biofilms as they occur outside laboratory conditions. Here, we present a screening method suitable for the identification of multispecies interactions and showcase L. fusiformis as a soil bacterium that is able to live alongside B. subtilis and modify the architecture of its biofilms.

Recent advances in studying single bacteria and biofilm mechanics

Bacterial biofilms correspond to surface-associated bacterial communities embedded in hydrogel-like matrix, in which high cell density, reduced diffusion and physico-chemical heterogeneity play a protective role and induce novel behaviors. In this review, we present recent advances on the understanding of how bacterial mechanical properties, from single cell to high-cell density community, determine biofilm tri-dimensional growth and eventual dispersion and we attempt to draw a parallel between these properties and the mechanical properties of other well-studied hydrogels and living systems.

Extracellular-matrix-mediated osmotic pressure drives Vibrio cholerae biofilm expansion and cheater exclusion

Biofilms, surface-attached communities of bacteria encased in an extracellular matrix, are a major mode of bacterial life. How the material properties of the matrix contribute to biofilm growth and robustness is largely unexplored, in particular in response to environmental perturbations such as changes in osmotic pressure. Here, using Vibrio cholerae as our model organism, we show that during active cell growth, matrix production enables biofilm-dwelling bacterial cells to establish an osmotic pressure difference between the biofilm and the external environment. This pressure difference promotes biofilm expansion on nutritious surfaces by physically swelling the colony, which enhances nutrient uptake, and enables matrix-producing cells to outcompete non-matrix-producing cheaters via physical exclusion. Osmotic pressure together with crosslinking of the matrix also controls the growth of submerged biofilms and their susceptibility to invasion by planktonic cells. As the basic physicochemical principles of matrix crosslinking and osmotic swelling are universal, our findings may have implications for other biofilm-forming bacterial species.Most bacteria live in biofilms, surface-attached communities encased in an extracellular matrix. Here, Yan et al. show that matrix production in Vibrio cholerae increases the osmotic pressure within the biofilm, promoting biofilm expansion and physical exclusion of non-matrix producing cheaters.

Influence of biofilm lubricity on shear-induced transmission of staphylococcal biofilms from stainless steel to silicone rubber

In real-life situations, bacteria are often transmitted from biofilms growing on donor surfaces to receiver ones. Bacterial transmission is more complex than adhesion, involving bacterial detachment from donor and subsequent adhesion to receiver surfaces. Here, we describe a new device to study shear-induced bacterial transmission from a (stainless steel) pipe to a (silicone rubber) tube and compare transmission of EPS-producing and non-EPS-producing staphylococci. Transmission of an entire biofilm from the donor to the receiver tube did not occur, indicative of cohesive failure in the biofilm rather than of adhesive failure at the donor-biofilm interface. Biofilm was gradually transmitted over an increasing length of receiver tube, occurring mostly to the first 50 cm of the receiver tube. Under high-shearing velocity, transmission of non-EPS-producing bacteria to the second half decreased non-linearly, likely due to rapid thinning of the lowly lubricious biofilm. Oppositely, transmission of EPS-producing strains to the second tube half was not affected by higher shearing velocity due to the high lubricity and stress relaxation of the EPS-rich biofilms, ensuring continued contact with the receiver. The non-linear decrease of ongoing bacterial transmission under high-shearing velocity is new and of relevance in for instance, high-speed food slicers and food packaging.

Structural damage of Bacillus subtilis biofilms using pulsed laser interaction with gold thin films

There is a huge interest in developing strategies to effectively eliminate biofilms due to their negative impact in both industrial and clinical settings. In this study, structural damage was induced on two day-old B. subtilis biofilms using the interaction of 532 nm pulsed laser with gold thin films. Radiant exposure of 225 mJ/cm² induced distinct changes on the surface structure and overall morphology of the matured biofilms after laser irradiation. Moreover, at the radiant exposure used, changes in the colour and viscosity of the biofilm were observed which may indicate a compromised extracellular matrix. Irradiated biofilms in the presence of gold film also showed strong propidium iodide signal which implies an increase in the number of dead bacterial cells after laser treatment. Thus, this laser-based technique is a promising approach in targeting and eradicating matured biofilms attached on surfaces such as medical implants.

Morphologies of Bacillus subtilis communities responding to environmental variation

Bacterial communities exhibit a variety of growth morphologies in constructing robust systems under different environmental conditions. We review the diverse morphologies of Bacillus subtilis communities and their mechanisms of self-organization. B. subtilis uses different cell types to suit environmental conditions and cell density. The subpopulation of each cell type exhibits various environment-sensitive properties. Furthermore, division of labor among the subpopulations results in flexible development for the community as a whole. We review how B. subtilis community morphologies and growth strategies respond to environmental perturbations.

The particle in the spider's web: transport through biological hydrogels

Biological hydrogels such as mucus, extracellular matrix, biofilms, and the nuclear pore have diverse functions and compositions, but all act as selectively permeable barriers to the diffusion of particles. Each barrier has a crosslinked polymeric mesh that blocks penetration of large particles such as pathogens, nanotherapeutics, or macromolecules. These polymeric meshes also employ interactive filtering, in which affinity between solutes and the gel matrix controls permeability. Interactive filtering affects the transport of particles of all sizes including peptides, antibiotics, and nanoparticles and in many cases this filtering can be described in terms of the effects of charge and hydrophobicity. The concepts described in this review can guide strategies to exploit or overcome gel barriers, particularly for applications in diagnostics, pharmacology, biomaterials, and drug delivery.

Biofilms: an emergent form of bacterial life

Bacterial biofilms are formed by communities that are embedded in a self-produced matrix of extracellular polymeric substances (EPS). Importantly, bacteria in biofilms exhibit a set of 'emergent properties' that differ substantially from free-living bacterial cells. In this Review, we consider the fundamental role of the biofilm matrix in establishing the emergent properties of biofilms, describing how the characteristic features of biofilms - such as social cooperation, resource capture and enhanced survival of exposure to antimicrobials - all rely on the structural and functional properties of the matrix. Finally, we highlight the value of an ecological perspective in the study of the emergent properties of biofilms, which enables an appreciation of the ecological success of biofilms as habitat formers and, more generally, as a bacterial lifestyle.

Mechanism of signal propagation in Physarum polycephalum

Complex behaviors are typically associated with animals, but the capacity to integrate information and function as a coordinated individual is also a ubiquitous but poorly understood feature of organisms such as slime molds and fungi. Plasmodial slime molds grow as networks and use flexible, undifferentiated body plans to forage for food. How an individual communicates across its network remains a puzzle, but Physarum polycephalum has emerged as a novel model used to explore emergent dynamics. Within P. polycephalum, cytoplasm is shuttled in a peristaltic wave driven by cross-sectional contractions of tubes. We first track P. polycephalum's response to a localized nutrient stimulus and observe a front of increased contraction. The front propagates with a velocity comparable to the flow-driven dispersion of particles. We build a mathematical model based on these data and in the aggregate experiments and model identify the mechanism of signal propagation across a body: The nutrient stimulus triggers the release of a signaling molecule. The molecule is advected by fluid flows but simultaneously hijacks flow generation by causing local increases in contraction amplitude as it travels. The molecule is initiating a feedback loop to enable its own movement. This mechanism explains previously puzzling phenomena, including the adaptation of the peristaltic wave to organism size and P. polycephalum's ability to find the shortest route between food sources. A simple feedback seems to give rise to P. polycephalum's complex behaviors, and the same mechanism is likely to function in the thousands of additional species with similar behaviors.

Exploiting Self-organization in Bioengineered Systems: A Computational Approach

The productivity of bioengineered cell factories is limited by inefficiencies in nutrient delivery and waste and product removal. Current solution approaches explore changes in the physical configurations of the bioreactors. This work investigates the possibilities of exploiting self-organizing vascular networks to support producer cells within the factory. A computational model simulates de novo vascular development of endothelial-like cells and the resultant network functioning to deliver nutrients and extract product and waste from the cell culture. Microbial factories with vascular networks are evaluated for their scalability, robustness, and productivity compared to the cell factories without a vascular network. Initial studies demonstrate that at least an order of magnitude increase in production is possible, the system can be scaled up, and the self-organization of an efficient vascular network is robust. The work suggests that bioengineered multicellularity may offer efficiency improvements difficult to achieve with physical engineering approaches.

Microbial Biofilms and Chronic Wounds

Background is provided on biofilms, including their formation, tolerance mechanisms, structure, and morphology within the context of chronic wounds. The features of biofilms in chronic wounds are discussed in detail, as is the impact of biofilm on wound chronicity. Difficulties associated with the use of standard susceptibility tests (minimum inhibitory concentrations or MICs) to determine appropriate treatment regimens for, or develop new treatments for use in, chronic wounds are discussed, with alternate test methods specific to biofilms being recommended. Animal models appropriate for evaluating biofilm treatments are also described. Current and potential future therapies for treatment of biofilm-containing chronic wounds, including probiotic therapy, virulence attenuation, biofilm phenotype expression attenuation, immune response suppression, and aggressive debridement combined with antimicrobial dressings, are described.

The antimicrobial activity of nanoparticles: present situation and prospects for the future

Nanoparticles (NPs) are increasingly used to target bacteria as an alternative to antibiotics. Nanotechnology may be particularly advantageous in treating bacterial infections. Examples include the utilization of NPs in antibacterial coatings for implantable devices and medicinal materials to prevent infection and promote wound healing, in antibiotic delivery systems to treat disease, in bacterial detection systems to generate microbial diagnostics, and in antibacterial vaccines to control bacterial infections. The antibacterial mechanisms of NPs are poorly understood, but the currently accepted mechanisms include oxidative stress induction, metal ion release, and non-oxidative mechanisms. The multiple simultaneous mechanisms of action against microbes would require multiple simultaneous gene mutations in the same bacterial cell for antibacterial resistance to develop; therefore, it is difficult for bacterial cells to become resistant to NPs. In this review, we discuss the antibacterial mechanisms of NPs against bacteria and the factors that are involved. The limitations of current research are also discussed.

Patterns in Saccharomyces cerevisiae yeast colonies via magnetic resonance imaging

We report the use of high-resolution magnetic resonance imaging methods to observe pattern formation in colonies of Saccharomyces cerevisiae. Our results indicate substantial signal loss localized in specific regions of the colony rendering useful imaging contrast. This imaging contrast is recognizable as being due to discontinuities in magnetic susceptibility (χ) between different spatial regions. At the microscopic pixel level, the local variations in the magnetic susceptibility (Δχ) induce a loss in the NMR signal, which was quantified via T₂ and T₂* maps, permitting estimation of Δχ values for different regions of the colony. Interestingly the typical petal/wrinkling patterns present in the colony have a high degree of correlation with the estimated susceptibility distribution. We conclude that the presence of magnetic susceptibility inclusions, together with their spatial arrangement within the colony, may be a potential cause of the susceptibility distribution and therefore the contrast observed on the images.

An oxygen-sensitive toxin-antitoxin system

The Hha and TomB proteins from Escherichia coli form an oxygen-dependent toxin–antitoxin (TA) system. Here we show that YmoB, the Yersinia orthologue of TomB, and its single cysteine variant [C117S]YmoB can replace TomB as antitoxins in E. coli. In contrast to other TA systems, [C117S]YmoB transiently interacts with Hha (rather than forming a stable complex) and enhances the spontaneous oxidation of the Hha conserved cysteine residue to a -SO_xH-containing species (sulfenic, sulfinic or sulfonic acid), which destabilizes the toxin. The nuclear magnetic resonance structure of [C117S]YmoB and the homology model of TomB show that the two proteins form a four-helix bundle with a conserved buried cysteine connected to the exterior by a channel with a diameter comparable to that of an oxygen molecule. The Hha interaction site is located on the opposite side of the helix bundle.

Classical toxin–antitoxin systems in bacteria are based on silencing of a toxin by an antitoxin that, when inactivated, releases the toxin, resulting in a change in metabolism. Here, the authors characterize an oxygen-sensitive toxin–antitoxin system and discuss the implications for the role of the Hha antitoxin.

EPS-Then and Now

“Slime” played a brief and spectacular role in the 19th century founded by the theory of primordial slime by Ernst Haeckel. However, that substance was never found and eventually abandoned. Further scientific attention slowly began in the 1930s referring to slime as a microbial product and then was inspired by “How bacteria stick” by Costerton et al. in 1978, and the matrix material was considered to be polysaccharides. Later, it turned out that proteins, nucleic acids and lipids were major other constituents of the extracellular polymeric substances (EPS), an acronym which was highly discussed. The role of the EPS matrix turns out to be fundamental for biofilms, in terms of keeping cells in proximity and allowing for extended interaction, resource capture, mechanical strength and other properties, which emerge from the life of biofilm organisms, including enhanced tolerance to antimicrobials and other stress. The EPS components are extremely complex and dynamic and fulfil many functional roles, turning biofilms into the most ubiquitous and successful form of life on Earth.

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.

A variational approach to the growth dynamics of pre-stressed actin filament networks

In order to model the growth dynamics of elastic bodies with residual stresses a thermodynamically consistent approach is needed such that the cross-coupling between growth and mechanics can be correctly described. In the present work we apply a variational principle to the formulation of the interfacial growth dynamics of dendritic actin filament networks growing from biomimetic beads, an experimentally well studied system, where the buildup of residual stresses governs the network growth. We first introduce the material model for the network via a strain energy density for an isotropic weakly nonlinear elastic material and then derive consistently from this model the dynamic equations for the interfaces, i.e. for a polymerizing internal interface in contact with the bead and a depolymerizing external interface directed towards the solvent. We show that (i) this approach automatically preserves thermodynamic symmetry-properties, which is not the case for the often cited 'rubber-band-model' (Sekimoto et al 2004 Eur. Phys. J. E 13 247-59, Plastino et al 2004 Eur. Biophys. J. 33 310-20) and (ii) leads to a robust morphological instability of the treadmilling network interfaces. The nature of the instability depends on the interplay of the two dynamic interfaces. Depending on the biochemical conditions the network envelope evolves into a comet-like shape (i.e. the actin envelope thins out at one side and thickens on the opposite side of the bead) via a varicose instability or it breaks the symmetry via higher order zigzag modes. We conclude that morphological instabilities due to mechano-chemical coupling mechanisms and the presences of mechancial pre-stresses can play a major role in locally organizing the cytoskeleton of living cells.

Specific Bacillus subtilis 168 variants form biofilms on nutrient-rich medium

Bacillus subtilis is an intensively studied Gram-positive bacterium that has become one of the models for biofilm development. B. subtilis 168 is a well-known domesticated strain that has been suggested to be deficient in robust biofilm formation. Moreover, the diversity of available B. subtilis laboratory strains and their derivatives have made it difficult to compare independent studies related to biofilm formation. Here, we analysed numerous 168 stocks from multiple laboratories for their ability to develop biofilms in different set-ups and media. We report a wide variation among the biofilm-forming capabilities of diverse stocks of B. subtilis 168, both in architecturally complex colonies and liquid-air interface pellicles, as well as during plant root colonization. Some 168 variants are indeed unable to develop robust biofilm structures, while others do so as efficiently as the non-domesticated NCIB 3610 strain. In all cases studied, the addition of glucose to the medium dramatically improved biofilm development of the laboratory strains. Furthermore, the expression of biofilm matrix component operons, epsA-O and tapA-sipW-tasA, was monitored during colony biofilm formation. We found a lack of direct correlation between the expression of these genes and the complexity of wrinkles in colony biofilms. However, the presence of a single mutation in the exopolysaccharide-related gene epsC correlates with the ability of the stocks tested to form architecturally complex colonies and pellicles, and to colonize plant roots.

Characterization of the diffusive dynamics of particles with time-dependent asymmetric microscopy intensity profiles

We put forth an algorithm to track isolated micron-size solid and liquid particles that produce time-dependent asymmetric intensity patterns. This method quantifies the displacement of a particle in the image plane from the peak of a spatial cross-correlation function with a reference image. The peak sharpness results in subpixel resolution. We demonstrate the utility of the method for tracking liquid droplets with changing shapes and micron-size particles producing images with exaggerated asymmetry. We compare the accuracy of diffusivity determination with particles of known size by this method to that by common tracking techniques and demonstrate that our algorithm is superior. We address several open questions on the characterization of diffusive behaviors. We show that for particles, diffusing with a root-mean-square displacement of 0.6 pixel widths in the time between two successive recorded frames, more accurate diffusivity determinations result from mean squared displacement (MSD) for lag times up to 5 time intervals and that MSDs determined from non-overlapping displacements do not yield more accurate diffusivities. We discuss the optimal length of image sequences and demonstrate that lower frame rates do not affect the accuracy of the estimated diffusivity.

Self-Driven Jamming in Growing Microbial Populations

In natural settings, microbes tend to grow in dense populations [1-4] where they need to push against their surroundings to accommodate space for new cells. The associated contact forces play a critical role in a variety of population-level processes, including biofilm formation [5-7], the colonization of porous media [8, 9], and the invasion of biological tissues [10-12]. Although mechanical forces have been characterized at the single cell level [13-16], it remains elusive how collective pushing forces result from the combination of single cell forces. Here, we reveal a collective mechanism of confinement, which we call self-driven jamming, that promotes the build-up of large mechanical pressures in microbial populations. Microfluidic experiments on budding yeast populations in space-limited environments show that self-driven jamming arises from the gradual formation and sudden collapse of force chains driven by microbial proliferation, extending the framework of driven granular matter [17-20]. The resulting contact pressures can become large enough to slow down cell growth, to delay the cell cycle in the G1 phase, and to strain or even destroy the microenvironment through crack propagation. Our results suggest that self-driven jamming and build-up of large mechanical pressures is a natural tendency of microbes growing in confined spaces, contributing to microbial pathogenesis and biofouling [21-26].

Just in case it rains: building a hydrophobic biofilm the Bacillus subtilis way

Over the millennia, diverse species of bacteria have evolved multiple independent mechanisms to structure sessile biofilm communities that confer protection and stability to the inhabitants. The Gram-positive soil bacterium Bacillus subtilis biofilm presents as an architecturally complex, highly hydrophobic community that resists wetting by water, solvents, and biocides. This remarkable property is conferred by a small secreted protein called BslA, which self-assembles into an organized lattice at an interface. In the biofilm, production of BslA is tightly regulated and the resultant protein is secreted into the extracellular environment where it forms a very effective communal barrier allowing the resident B. subtilis cells to shelter under the protection of a protein raincoat.

Simulation of Bacillus subtilis biofilm growth on agar plate by diffusion-reaction based continuum model

Various species of bacteria form highly organized spatially-structured aggregates known as biofilms. To understand how microenvironments impact biofilm growth dynamics, we propose a diffusion-reaction continuum model to simulate the formation of Bacillus subtilis biofilm on an agar plate. The extended finite element method combined with level set method are employed to perform the simulation, numerical results show the quantitative relationship between colony morphologies and nutrient depletion over time. Considering that the production of polysaccharide in wild-type cells may enhance biofilm spreading on the agar plate, we inoculate mutant colony incapable of producing polysaccharide to verify our results. Predictions of the glutamate source biofilm's shape parameters agree with the experimental mutant colony better than that of glycerol source biofilm, suggesting that glutamate is rate limiting nutrient for Bacillus subtilis biofilm growth on agar plate, and the diffusion-limited is a better description to the experiment. In addition, we find that the diffusion time scale is of the same magnitude as growth process, and the common-employed quasi-steady approximation is not applicable here.

Multi-layer composite mechanical modeling for the inhomogeneous biofilm mechanical behavior

Experiments showed that bacterial biofilms are heterogeneous, for example, the density, the diffusion coefficient, and mechanical properties of the biofilm are different along the biofilm thickness. In this paper, we establish a multi-layer composite model to describe the biofilm mechanical inhomogeneity based on unified multiple-component cellular automaton (UMCCA) model. By using our model, we develop finite element simulation procedure for biofilm tension experiment. The failure limit and biofilm extension displacement obtained from our model agree well with experimental measurements. This method provides an alternative theory to study the mechanical inhomogeneity in biological materials.