Hierarchical transitions and fractal wrinkling drive bacterial pellicle morphogenesis

Exploitative stress within Bacillus subtilis biofilm determines the spatial distribution of pleomorphic cells

Bacteria commonly live in a spatially organized biofilm assemblage. The metabolic activity inside the biofilm leads to segmented physiological microenvironments. In nature, bacteria possess several pleomorphic forms to withstand certain ecological alterations. We hypothesized that pleomorphism also exists within the biofilm, which can be considered as the fundamental niche for bacteria. We report a distinct pattern of cell size variation throughout the biofilm of Bacillus subtilis. Cell size heterogeneity was observed in biofilm development, wherein the frequency of long cells is higher in outer regions, whereas lower in inner regions. Moreover, compared to planktonic cells, bacteria in the biofilm mode reduce their geometric ratio from 8.34 to 3.69 and 2.65 in the outer and inner regions, respectively. There were no significant differences observed in nutrient diffusion from the outer to the inner region, and more than 73 % of cells in the inner region were viable. However, the inner and middle regions were more acidic than the outer of the biofilm. Conclusively, growth rate-independent cell size reduction at low pH suggests that the resulting phenotype switching within biofilm was observed due to the pH gradient of neutral to acidic from the outer to the core of the biofilm. This gradient of H+ ions concentration may create exploitative stress within the biofilm, which could favor specific pleomorphic cells to thrive in their specialized niches. By understanding the cell size variation in response to the local environment, we propose a model of biofilm formation by pleomorphic cells.

Microbes, macrophages, and melanin: a unifying theory of disease as exemplified by cancer

It is widely accepted that cancer mostly arises from random spontaneous mutations triggered by environmental factors. Our theory challenges the idea of the random somatic mutation theory (SMT). The SMT does not fit well with Charles Darwin's theory of evolution in that the same relatively few mutations would occur so frequently and that these mutations would lead to death rather than survival of the fittest. However, it would fit well under the theory of evolution, if we were to look at it from the vantage point of pathogens and their supporting microbial communities colonizing humans and mutating host cells for their own benefit, as it does give them an evolutionary advantage and they are capable of selecting genes to mutate and of inserting their own DNA or RNA into hosts. In this article, we provide evidence that tumors are actually complex microbial communities composed of various microorganisms living within biofilms encapsulated by a hard matrix; that these microorganisms are what cause the genetic mutations seen in cancer and control angiogenesis; that these pathogens spread by hiding in tumor cells and M2 or M2-like macrophages and other phagocytic immune cells and traveling inside them to distant sites camouflaged by platelets, which they also reprogram, and prepare the distant site for metastasis; that risk factors for cancer are sources of energy that pathogens are able to utilize; and that, in accordance with our previous unifying theory of disease, pathogens utilize melanin for energy for building and sustaining tumors and metastasis. We propose a paradigm shift in our understanding of what cancer is, and, thereby, a different trajectory for avenues of treatment and prevention.

Host Material Viscoelasticity Determines Wrinkling of Fungal Films

Microbial organisms react to their environment and are able to change it through biological and physical processes. For example, fungi exhibit various growth morphologies depending on their host material. Here, we show how the rheological properties of the host material influence the fungal wrinkling morphology. Rheological data of the host material was set in relation to the growth morphology. On host material with high storage modulus, the fungal film was flat, whereas on host material with low storage modulus, the fungus showed a morphology made of folds and wrinkles. We combined our findings with mechanical instability theories and found that the formation of wrinkles and folds is dependent on the storage modulus of the host material. The connection between the wrinkling morphology and the storage modulus of the host material is shown with simple scaling theories. The amplitude, number of wrinkles, and wrinkle length follow geometrical laws, and the mechanical properties of the fungal film are expected to increase with increasing host material elasticity. The obtained results show the connection between living biological films, how they react to their surroundings, and the underlying physical mechanisms. They can provide a framework to further design fungal materials with specific surface morphologies.

The Biofilm Lifestyle Shapes the Evolution of β-Lactamases

The evolutionary relationship between the biofilm lifestyle and antibiotic resistance enzymes remains a subject of limited understanding. Here, we investigate how β-lactamases affect biofilm formation in Vibrio cholerae and how selection for a biofilm lifestyle impacts the evolution of these enzymes. Genetically diverse β-lactamases expressed in V. cholerae displayed a strong inhibitory effect on biofilm production. To understand how natural evolution affects this antagonistic pleiotropy, we randomly mutagenized a β-lactamase and selected for elevated biofilm formation. Our results revealed that biofilm evolution selects for β-lactamase variants able to hydrolyze β-lactams without inhibiting biofilms. Mutational analysis of evolved variants demonstrated that restoration of biofilm development was achieved either independently of enzymatic function or by actively leveraging enzymatic activity. Taken together, the biofilm lifestyle can impose a profound selective pressure on antimicrobial resistance enzymes. Shedding light on such evolutionary interplays is of importance to understand the factors driving antimicrobial resistance.

Evaluation of the polyphenolic profile of native Ecuadorian stingless bee honeys (Tribe: Meliponini) and their antibiofilm activity on susceptible and multidrug-resistant pathogens: An exploratory analysis

Biofilms are associated with infections that are resistant to conventional therapies, contributing to the antimicrobial resistance crisis. The need for alternative approaches against biofilms is well-known. Although natural products like stingless bee honeys (tribe: Meliponini) constitute an alternative treatment, much is still unknown. Our main goal was to evaluate the antibiofilm activity of stingless bee honey samples against multidrug-resistant (MDR) pathogens through biomass assays, fluorescence (cell count and viability), and scanning electron (structural composition) microscopy. We analyzed thirty-five honey samples at 15% (v/v) produced by ten different stingless bee species (Cephalotrigona sp., Melipona sp., M. cramptoni, M. fuscopilosa, M. grandis, M. indecisa, M. mimetica, M. nigrifacies, Scaptotrigona problanca, and Tetragonisca angustula) from five provinces of Ecuador (Tungurahua, Pastaza, El Oro, Los Ríos, and Loja) against 24-h biofilms of Staphylococcus aureus, Klebsiella pneumoniae, Candida albicans, and Candida tropicalis. The present honey set belonged to our previous study, where the samples were collected in 2018-2019 and their physicochemical parameters, chemical composition, mineral elements, and minimal inhibitory concentration (MIC) were screened. However, the polyphenolic profile and their antibiofilm activity on susceptible and multidrug-resistant pathogens were still unknown. According to polyphenolic profile of the honey samples, significant differences were observed according to their geographical origin in terms of the qualitative profiles. The five best honey samples (OR24.1, LR34, LO40, LO48, and LO53) belonging to S. problanca, Melipona sp., and M. indecisa were selected for further analysis due to their high biomass reduction values, identification of the stingless bee specimens, and previously reported physicochemical parameters. This subset of honey samples showed a range of 63-80% biofilm inhibition through biomass assays. Fluorescence microscopy (FM) analysis evidenced statistical log reduction in the cell count of honey-treated samples in all pathogens (P <0.05), except for S. aureus ATCC 25923. Concerning cell viability, C. tropicalis, K. pneumoniae ATCC 33495, and K. pneumoniae KPC significantly decreased (P <0.01) by 21.67, 25.69, and 45.62%, respectively. Finally, scanning electron microscopy (SEM) analysis demonstrated structural biofilm disruption through cell morphological parameters (such as area, size, and form). In relation to their polyphenolic profile, medioresinol was only found in the honey of Loja, while scopoletin, kaempferol, and quercetin were only identified in honey of Los Rios, and dihydrocaffeic and dihydroxyphenylacetic acids were only detected in honey of El Oro. All the five honey samples showed dihydrocoumaroylhexose, luteolin, and kaempferol rutinoside. To the authors' best knowledge, this is the first study to analyze stingless bees honey-treated biofilms of susceptible and/or MDR strains of S. aureus, K. pneumoniae, and Candida species.

Proliferating active matter

The fascinating patterns of collective motion created by autonomously driven particles have fuelled active-matter research for over two decades. So far, theoretical active-matter research has often focused on systems with a fixed number of particles. This constraint imposes strict limitations on what behaviours can and cannot emerge. However, a hallmark of life is the breaking of local cell number conservation by replication and death. Birth and death processes must be taken into account, for example, to predict the growth and evolution of a microbial biofilm, the expansion of a tumour, or the development from a fertilized egg into an embryo and beyond. In this Perspective, we argue that unique features emerge in these systems because proliferation represents a distinct form of activity: not only do the proliferating entities consume and dissipate energy, they also inject biomass and degrees of freedom capable of further self-proliferation, leading to myriad dynamic scenarios. Despite this complexity, a growing number of studies document common collective phenomena in various proliferating soft-matter systems. This generality leads us to propose proliferation as another direction of active-matter physics, worthy of a dedicated search for new dynamical universality classes. Conceptual challenges abound, from identifying control parameters and understanding large fluctuations and nonlinear feedback mechanisms to exploring the dynamics and limits of information flow in self-replicating systems. We believe that, by extending the rich conceptual framework developed for conventional active matter to proliferating active matter, researchers can have a profound impact on quantitative biology and reveal fascinating emergent physics along the way.

Reversible adhesives with controlled wrinkling patterns for programmable integration and discharging

Switchable and minimally invasive tissue adhesives have great potential for medical applications. However, on-demand adherence to and detachment from tissue surfaces remain difficult. We fabricated a switchable hydrogel film adhesive by designing pattern-tunable wrinkles to control adhesion. When adhered to a substrate, the compressive stress generated from the bilayer system leads to self-similar wrinkling patterns at short and long wavelengths, regulating the interfacial adhesion. To verify the concept and explore its application, we established a random skin flap model, which is a crucial strategy for repairing severe or large-scale wounds. Our hydrogel adhesive provides sufficient adhesion for tissue sealing and promotes neovascularization at the first stage, and then gradually detaches from the tissue while a dynamic wrinkling pattern transition happens. The gel film can be progressively ejected out from the side margins after host-guest integration. Our findings provide insights into tunable bioadhesion by manipulating the wrinkling pattern transition.

The role of biofilm matrix composition in controlling colony expansion and morphology

Biofilms are biological viscoelastic gels composed of bacterial cells embedded in a self-secreted polymeric extracellular matrix (ECM). In environmental settings, such as in the rhizosphere and phyllosphere, biofilm colonization occurs at the solid-air interface. The biofilms' ability to colonize and expand over these surfaces depends on the formation of osmotic gradients and ECM viscoelastic properties. In this work, we study the influence of biofilm ECM components on its viscoelasticity and expansion, using the model organism Bacillus subtilis and deletion mutants of its three major ECM components, TasA, EPS and BslA. Using a multi-scale approach, we quantified macro-scale viscoelasticity and expansion dynamics. Furthermore, we used a microsphere assay to visualize the micro-scale expansion patterns. We find that the viscoelastic phase angle Φ is likely the best viscoelastic parameter correlating to biofilm expansion dynamics. Moreover, we quantify the sensitivity of the biofilm to changes in substrate water potential as a function of ECM composition. Finally, we find that the deletion of ECM components significantly increases the coherence of micro-scale colony expansion patterns. These results demonstrate the influence of ECM viscoelasticity and substrate water potential on the expansion of biofilm colonies on wet surfaces at the air-solid interface, commonly found in natural environments.

Quorum-sensing control of matrix protein production drives fractal wrinkling and interfacial localization of Vibrio cholerae pellicles

Bacterial cells at fluid interfaces can self-assemble into collective communities with stunning macroscopic morphologies. Within these soft, living materials, called pellicles, constituent cells gain group-level survival advantages including increased antibiotic resistance. However, the regulatory and structural components that drive pellicle self-patterning are not well defined. Here, using Vibrio cholerae as our model system, we report that two sets of matrix proteins and a key quorum-sensing regulator jointly orchestrate the sequential mechanical instabilities underlying pellicle morphogenesis, culminating in fractal patterning. A pair of matrix proteins, RbmC and Bap1, maintain pellicle localization at the interface and prevent self-peeling. A single matrix protein, RbmA, drives a morphogenesis program marked by a cascade of ever finer wrinkles with fractal scaling in wavelength. Artificial expression of rbmA restores fractal wrinkling to a ΔrbmA mutant and enables precise tuning of fractal dimensions. The quorum-sensing regulatory small RNAs Qrr1-4 first activate matrix synthesis to launch pellicle primary wrinkling and ridge instabilities. Subsequently, via a distinct mechanism, Qrr1-4 suppress fractal wrinkling to promote fine modulation of pellicle morphology. Our results connect cell-cell signaling and architectural components to morphogenic patterning and suggest that manipulation of quorum-sensing regulators or synthetic control of rbmA expression could underpin strategies to engineer soft biomaterial morphologies on demand.

LuxR family transcriptional repressor YjjQ modulates the biofilm formation and motility of avian pathogenic Escherichia coli

Avian pathogenic Escherichia coli (APEC) can cause the acute and sudden death of poultry, which leads to serious economic losses in the poultry industry. Biofilm formation contributes to the persistence of bacterial infection, drug resistance, and resistance to diverse environmental stress. Many transcription regulators in APEC play an essential role in the formation of biofilm and could provide further insights into APEC pathogenesis. YjjQ has an important role in the pathogenicity of bacteria by regulating the expression of virulence factors, such as flagellar and iron uptake. However, YjjQ regulates other virulence factors, and their role in the overall regulatory network is unclear. Here, we further evaluate the function of YjjQ on APEC biofilm formation and motility. In this study, we successfully constructed mutant (AE27∆yjjQ) and complement (AE27ΔyjjQ-comp) strains of the wild-type strain AE27. Inactivation of the yjjQ gene significantly increased biofilm-forming ability in APEC. Scanning electron microscopy showed that the biofilm formation of the AE27 was single-layered and flat, whereas that of the AE27∆yjjQ had a porous three-dimensional structure. Moreover, the deletion of the yjjQ gene inhibited the motility of APEC. RNA-sequencing was used to further investigate the regulatory mechanism of YjjQ in APEC. The results indicate that YjjQ regulates biofilm formation and flagellar genes in AE27∆yjjQ. RT-qPCR shows that YjjQ affects the transcriptional levels of genes, including flagella genes (flhD, flhC and flgE), and biofilm formation genes (pstA, uhpC, nikD, and ygcS). These results confirm that the transcription regulator YjjQ is involved in APEC biofilm formation and motility, and provide new evidence for the prevention and control of APEC.

The CRISPR-Cas System Differentially Regulates Surface-Attached and Pellicle Biofilm in Salmonella enterica Serovar Typhimurium

The CRISPR-Cas mediated regulation of biofilm by Salmonella enterica serovar Typhimurium was investigated by deleting CRISPR-Cas components ΔcrisprI, ΔcrisprII, ΔΔcrisprI crisprII, and Δcas op. We determined that the system positively regulates surface biofilm while inhibiting pellicle biofilm formation. Results of real-time PCR suggest that the flagellar (fliC, flgK) and curli (csgA) genes were repressed in knockout strains, causing reduced surface biofilm. The mutants displayed altered pellicle biofilm architecture. They exhibited bacterial multilayers and a denser extracellular matrix with enhanced cellulose and less curli, ergo weaker pellicles than those of the wild type. The cellulose secretion was more in the knockout strains due to the upregulation of bcsC, which is necessary for cellulose export. We hypothesized that the secreted cellulose quickly integrates into the pellicle, leading to enhanced pellicular cellulose in the knockout strains. We determined that crp is upregulated in the knockout strains, thereby inhibiting the expression of csgD and, hence, also of csgA and bcsA. The conflicting upregulation of bcsC, the last gene of the bcsABZC operon, could be caused by independent regulation by the CRISPR-Cas system owing to a partial match between the CRISPR spacers and bcsC gene. The cAMP-regulated protein (CRP)-mediated regulation of the flagellar genes in the knockout strains was probably circumvented through the regulation of yddx governing the availability of the sigma factor σ²⁸ that further regulates class 3 flagellar genes (fliC, fljB, and flgK). Additionally, the variations in the lipopolysaccharide (LPS) profile and expression of LPS-related genes (rfaC, rfbG, and rfbI) in knockout strains could also contribute to the altered pellicle architecture. Collectively, we establish that the CRISPR-Cas system differentially regulates the formation of surface-attached and pellicle biofilm.

IMPORTANCE In addition to being implicated in bacterial immunity and genome editing, the CRISPR-Cas system has recently been demonstrated to regulate endogenous gene expression and biofilm formation. While the function of individual cas genes in controlling Salmonella biofilm has been explored, the regulatory role of CRISPR arrays in biofilm is less studied. Moreover, studies have focused on the effects of the CRISPR-Cas system on surface-associated biofilms, and comprehensive studies on the impact of the system on pellicle biofilm remain an unexplored niche. We demonstrate that the CRISPR array and cas genes modulate the expression of various biofilm genes in Salmonella, whereby surface and pellicle biofilm formation is distinctively regulated.

Mechanical limitation of bacterial motility mediated by growing cell chains

Contrasting most known bacterial motility mechanisms, a bacterial sliding motility discovered in at least two gram-positive bacterial families does not depend on designated motors. Instead, the cells maintain end-to-end connections following cell divisions to form long chains and exploit cell growth and division to push the cells forward. To investigate the dynamics of this motility mechanism, we constructed a mechanical model that depicts the interplay of the forces acting on and between the cells comprising the chain. Due to the exponential growth of individual cells, the tips of the chains can, in principle, accelerate to speeds faster than any known single-cell motility mechanism can achieve. However, analysis of the mechanical model shows that the exponential acceleration comes at the cost of an exponential buildup in mechanical stress in the chain, making overly long chains prone to breakage. Additionally, the mechanical model reveals that the dynamics of the chain expansion hinges on a single non-dimensional parameter. Perturbation analysis of the mechanical model further predicts the critical stress leading to chain breakage and its dependence on the non-dimensional parameter. Finally, we developed a simplistic population-expansion model that uses the predicted breaking behavior to estimate the physical limit of chain-mediated population expansion. Predictions from the models provide critical insights into how this motility depends on key physical properties of the cell and the substrate. Overall, our models present a generically applicable theoretical framework for cell-chain-mediated bacterial sliding motility and provide guidance for future experimental studies on such motility.

The role of surface adhesion on the macroscopic wrinkling of biofilms

Biofilms, bacterial communities of cells encased by a self-produced matrix, exhibit a variety of three-dimensional structures. Specifically, channel networks formed within the bulk of the biofilm have been identified to play an important role in the colonies' viability by promoting the transport of nutrients and chemicals. Here, we study channel formation and focus on the role of the adhesion of the biofilm matrix to the substrate in Pseudomonas aeruginosa biofilms grown under constant flow in microfluidic channels. We perform phase contrast and confocal laser scanning microscopy to examine the development of the biofilm structure as a function of the substrates' surface energy. The formation of the wrinkles and folds is triggered by a mechanical buckling instability, controlled by biofilm growth rate and the film's adhesion to the substrate. The three-dimensional folding gives rise to hollow channels that rapidly increase the effective volume occupied by the biofilm and facilitate bacterial movement inside them. The experiments and analysis on mechanical instabilities for the relevant case of a bacterial biofilm grown during flow enable us to predict and control the biofilm morphology.

Groovy and Gnarly: Surface Wrinkles as a Multifunctional Motif for Terrestrial and Marine Environments

From large ventral pleats of humpback whales to nanoscale ridges on flower petals, wrinkled structures are omnipresent, multifunctional, and found at hugely diverse scales. Depending on the particulars of the biological system-its environment, morphology, and mechanical properties-wrinkles may control adhesion, friction, wetting, or drag; promote interfacial exchange; act as flow channels; or contribute to stretching, mechanical integrity, or structural color. Undulations on natural surfaces primarily arise from stress-induced instabilities of surface layers (e.g., buckling) during growth or aging. Variation in the material properties of surface layers and in the magnitude and orientation of intrinsic stresses during growth lead to a variety of wrinkling morphologies and patterns which, in turn, reflect the wide range of biophysical challenges wrinkled surfaces can solve. Therefore, investigating how surface wrinkles vary and are implemented across biological systems is key to understanding their structure-function relationships. In this work, we synthesize the literature in a metadata analysis of surface wrinkling in various terrestrial and marine organisms to review important morphological parameters and classify functional aspects of surface wrinkles in relation to the size and ecology of organisms. Building on our previous and current experimental studies, we explore case studies on nano/micro-scale wrinkles in biofilms, plant surfaces, and basking shark filter structures to compare developmental and structure-vs-function aspects of wrinkles with vastly different size scales and environmental demands. In doing this and by contrasting wrinkle development in soft and hard biological systems, we provide a template of structure-function relationships of biological surface wrinkles and an outlook for functionalized wrinkled biomimetic surfaces.

Systems view of Bacillus subtilis pellicle development

In this study, we link pellicle development at the water-air interface with the vertical distribution and viability of the individual B. subtilis PS-216 cells throughout the water column. Real-time interfacial rheology and time-lapse confocal laser scanning microscopy were combined to correlate mechanical properties with morphological changes (aggregation status, filament formation, pellicle thickness, spore formation) of the growing pellicle. Six key events were identified in B. subtilis pellicle formation that are accompanied by a major change in viscoelastic and morphology behaviour of the pellicle. The results imply that pellicle development is a multifaceted response to a changing environment induced by bacterial growth that causes population redistribution within the model system, reduction of the viable habitat to the water-air interface, cell development, and morphogenesis. The outcome is a build-up of mechanical stress supporting structure that eventually, due to nutrient deprivation, reaches the finite thickness. After prolonged incubation, the formed pellicle collapses, which correlates with the spore releasing process. The pellicle loses the ability to support mechanical stress, which marks the end of the pellicle life cycle and entry of the system into the dormant state.