Microrheology and Spatial Heterogeneity of Staphylococcus aureus Biofilms Modulated by Hydrodynamic Shear and Biofilm-Degrading Enzymes

Adaptations of Gram-Negative and Gram-Positive Probiotic Bacteria in Engineered Living Materials

Encapsulation of microbes in natural or synthetic matrices is a key aspect of engineered living materials, although the influence of such confinement on microbial behavior is poorly understood. A few recent studies have shown that the spatial confinement and mechanical properties of the encapsulating material significantly influence microbial behavior, including growth, metabolism, and gene expression. However, comparative studies within different bacterial species under identical confinement conditions are limited. In this study, Gram-negative Escherichia coli Nissle 1917 and Gram-positive Lactiplantibacillus plantarum WCFS1 were encapsulated in hydrogel matrices, and their growth, metabolic activity, and recombinant gene expression were examined under varying degrees of hydrogel stiffness, achieved by adjusting the polymer concentration and chemical cross-linking. Both bacteria grow from single cells into confined colonies, but more interestingly, in E. coli gels, mechanical properties influenced colony growth, size, and morphology, whereas this did not occur in L. plantarum gels. However, with both bacteria, increased matrix stiffness led to higher levels of recombinant protein production within the colonies. By measuring metabolic heat from the bacterial gels using the isothermal microcalorimetry technique, it was inferred that E. coli adapts to the mechanical restrictions through multiple metabolic transitions and is significantly affected by the different hydrogel properties. Contrastingly, both of these aspects were not observed with L. plantarum. These results revealed that despite both bacteria being gut-adapted probiotics with similar geometries, mechanical confinement affects them considerably differently. The weaker influence of matrix stiffness on L. plantarum is attributed to its slower growth and thicker cell wall, possibly enabling the generation of higher turgor pressures to overcome restrictive forces under confinement. By providing fundamental insights into the interplay between mechanical forces and bacterial physiology, this work advances our understanding of how matrix properties shape bacterial behavior. The implications of these findings will aid the design of engineered living materials for therapeutic applications.

Resolving spatiotemporal dynamics in bacterial multicellular populations: approaches and challenges

SUMMARYThe development of multicellularity represents a key evolutionary transition that is crucial for the emergence of complex life forms. Although multicellularity has traditionally been studied in eukaryotes, it originates in prokaryotes. Coordinated aggregation of individual cells within the confines of a colony results in emerging, higher-level functions that benefit the population as a whole. During colony differentiation, an almost infinite number of ecological and physiological population-forming forces are at work, creating complex, intricate colony structures with divergent functions. Understanding the assembly and dynamics of such populations requires resolving individual cells or cell groups within such macroscopic structures. Addressing how each cell contributes to the collective action requires pushing the resolution boundaries of key technologies that will be presented in this review. In particular, single-cell techniques provide powerful tools for studying bacterial multicellularity with unprecedented spatial and temporal resolution. These advancements include novel microscopic techniques, mass spectrometry imaging, flow cytometry, spatial transcriptomics, single-bacteria RNA sequencing, and the integration of spatiotemporal transcriptomics with microscopy, alongside advanced microfluidic cultivation systems. This review encourages exploring the synergistic potential of the new technologies in the study of bacterial multicellularity, with a particular focus on individuals in differentiated bacterial biofilms (colonies). It highlights how resolving population structures at the single-cell level and understanding their respective functions can elucidate the overarching functions of bacterial multicellular populations.

Bacterial single-cell RNA sequencing captures biofilm transcriptional heterogeneity and differential responses to immune pressure

Biofilm formation is an important mechanism of survival and persistence for many bacterial pathogens. These multicellular communities contain subpopulations of cells that display metabolic and transcriptional diversity along with recalcitrance to antibiotics and host immune defenses. Here, we present an optimized bacterial single-cell RNA sequencing method, BaSSSh-seq, to study Staphylococcus aureus diversity during biofilm growth and transcriptional adaptations following immune cell exposure. BaSSSh-seq captures extensive transcriptional heterogeneity during biofilm compared to planktonic growth. We quantify and visualize transcriptional regulatory networks across heterogeneous biofilm subpopulations and identify gene sets that are associated with a trajectory from planktonic to biofilm growth. BaSSSh-seq also detects alterations in biofilm metabolism, stress response, and virulence induced by distinct immune cell populations. This work facilitates the exploration of biofilm dynamics at single-cell resolution, unlocking the potential for identifying biofilm adaptations to environmental signals and immune pressure.

Mass transfer in heterogeneous biofilms: Key issues in biofilm reactors and AI-driven performance prediction

Biofilm reactors, known for utilizing biofilm formation for cell immobilization, offer enhanced biomass concentration and operational stability over traditional planktonic systems. However, the dense nature of biofilms poses challenges for substrate accessibility to cells and the efficient release of products, making mass transfer efficiency a critical issue in these systems. Recent advancements have unveiled the intricate, heterogeneous architecture of biofilms, contradicting the earlier view of them as uniform, porous structures with consistent mass transfer properties. In this review, we explore six biofilm reactor configurations and their potential combinations, emphasizing how the spatial arrangement of biofilms within reactors influences mass transfer efficiency and overall reactor performance. Furthermore, we discuss how to apply artificial intelligence in processing biofilm measurement data and predicting reactor performance. This review highlights the role of biofilm reactors in environmental and energy sectors, paving the way for future innovations in biofilm-based technologies and their broader applications.

Effect of biofilm physical characteristics on their susceptibility to antibiotics: impacts of low-frequency ultrasound

Biofilms are highly resistant to antimicrobials, often causing chronic infections. Combining antimicrobials with low-frequency ultrasound (LFU) enhances antimicrobial efficiency, but little is known about the underlying mechanisms. Biofilm physical characteristics, which depend on factors such as growth conditions and age, can have significant effects on inactivation efficiency. In this study, we investigated the susceptibility of Pseudomonas aeruginosa biofilms to tobramycin, with and without LFU treatment. The biofilms were grown under low and high fluid shear to provide different characteristics. Low-shear biofilms exhibited greater thickness, roughness, and porosity and lower density, compared to high-shear biofilms. The biofilm matrix of the high-shear biofilms had a three times higher protein-to-polysaccharide ratio, suggesting greater biofilm stiffness. This was supported by microrheology measurements of biofilm creep compliance. For the low-shear biofilms without LFU, the viability of the biofilms in their inner regions was largely unaffected by the antibiotic after a 2-hour treatment. However, when tobramycin was combined with LFU, the inactivation for the entire biofilm increased to 80% after 2 h. For the high-shear biofilms without LFU, higher LFU intensities were needed to achieve similar inactivation results. Microrheology measurements revealed that changes in biofilm inactivation profiles were closely related to changes in biofilm mechanical properties. Modeling suggests that LFU changes antibiotic diffusivity within the biofilm, probably due to a "decohesion" effect. Overall, this research suggests that biofilm physical characteristics (e.g., compliance, morphology) are linked to antimicrobial efficiency. LFU weakens the biofilm while increasing its diffusivity for antibiotics.

A review of chemical signaling mechanisms underlying quorum sensing and its inhibition in Staphylococcus aureus

Staphylococcus aureus is a significant bacterium responsible for multiple infections and is a primary cause of fatalities among patients in hospital environments. The advent of pathogenic bacteria such as methicillin-resistant S. aureus revealed the shortcomings of employing antibiotics to treat bacterial infectious diseases. Quorum sensing enhances S. aureus's survivability through signaling processes. Targeting the key components of quorum sensing has drawn much interest nowadays as a promising strategy for combating infections caused by bacteria. Concentrating on the accessory gene regulator quorum-sensing mechanism is the most commonly suggested anti-virulence approach for S.aureus. Quorum quenching is a common strategy for controlling illnesses triggered by microorganisms since it reduces the pathogenicity of bacteria and improves bacterial biofilm susceptibility to antibiotics, thus providing an intriguing prospect for drug discovery. Quorum sensing inhibition reduces selective stresses and constrains the emergence of antibiotic resistance while limiting bacterial pathogenicity. This review examines the quorum sensing mechanisms involved in S. aureus, quorum sensing targets and gene regulation, environmental factors affecting quorum sensing, quorum sensing inhibition, natural products as quorum sensing inhibitory agents and novel therapeutical strategies to target quorum sensing in S. aureus as drug developing technique to augment conventional antibiotic approaches.

Extreme heterogeneity in the microrheology of lamellar surfactant gels analyzed with neural networks

The heterogeneity of the viscoelasticity of a lamellar gel network based on cetyl-trimethylammonium chloride and cetostearyl alcohol was studied using particle-tracking microrheology. A recurrent neural network (RNN) architecture was used for estimating the Hurst exponent, H, on small sections of tracks of probe spheres moving with fractional Brownian motion. Thus, dynamic segmentation of tracks via neural networks was used in microrheology and it is significantly more accurate than using mean square displacements (MSDs). An ensemble of 414 particles produces a MSD that is subdiffusive in time, t, with a power law of the form t^{0.74±0.02}, indicating power law viscoelasticity. RNN analysis of the probability distributions of H, combined with detailed analysis of the time-averaged MSDs of individual tracks, revealed diverse diffusion processes belied by the simple scaling of the ensemble MSD, such as caging phenomena, which give rise to the complex viscoelasticity of lamellar gels.

In Vivo Microrheology Reveals Local Elastic and Plastic Responses Inside 3D Bacterial Biofilms

Bacterial biofilms are highly abundant 3D living materials capable of performing complex biomechanical and biochemical functions, including programmable growth, self-repair, filtration, and bioproduction. Methods to measure internal mechanical properties of biofilms in vivo with spatial resolution on the cellular scale have been lacking. Here, thousands of cells are tracked inside living 3D biofilms of the bacterium Vibrio cholerae during and after the application of shear stress, for a wide range of stress amplitudes, periods, and biofilm sizes, which revealed anisotropic elastic and plastic responses of both cell displacements and cell reorientations. Using cellular tracking to infer parameters of a general mechanical model, spatially-resolved measurements of the elastic modulus inside the biofilm are obtained, which correlate with the spatial distribution of the polysaccharides within the biofilm matrix. The noninvasive microrheology and force-inference approach introduced here provides a general framework for studying mechanical properties with high spatial resolution in living materials.

Bacterial single-cell RNA sequencing captures biofilm transcriptional heterogeneity and differential responses to immune pressure

Biofilm formation is an important mechanism of survival and persistence for many bacterial pathogens. These multicellular communities contain subpopulations of cells that display vast metabolic and transcriptional diversity along with high recalcitrance to antibiotics and host immune defenses. Investigating the complex heterogeneity within biofilm has been hindered by the lack of a sensitive and high-throughput method to assess stochastic transcriptional activity and regulation between bacterial subpopulations, which requires single-cell resolution. We have developed an optimized bacterial single-cell RNA sequencing method, BaSSSh-seq, to study Staphylococcus aureus diversity during biofilm growth and transcriptional adaptations following immune cell exposure. We validated the ability of BaSSSh-seq to capture extensive transcriptional heterogeneity during biofilm compared to planktonic growth. Application of new computational tools revealed transcriptional regulatory networks across the heterogeneous biofilm subpopulations and identification of gene sets that were associated with a trajectory from planktonic to biofilm growth. BaSSSh-seq also detected alterations in biofilm metabolism, stress response, and virulence that were tailored to distinct immune cell populations. This work provides an innovative platform to explore biofilm dynamics at single-cell resolution, unlocking the potential for identifying biofilm adaptations to environmental signals and immune pressure.

Staphylococcus aureus biofilm: Formulation, regulatory, and emerging natural products-derived therapeutics

Staphylococcus aureus can readily form biofilm which enhances the drug-resistance, resulting in life-threatening infections involving different organs. Biofilm formation occurs due to a series of developmental events including bacterial adhesion, aggregation, biofilm maturation, and dispersion, which are controlled by multiple regulatory systems. Rapidly increasing research and development outcomes on natural products targeting S. aureus biofilm formation and/or regulation led to an emergent application of active phytochemicals and combinations. This review aimed at providing an in-depth understanding of biofilm formation and regulation mechanisms for S. aureus, outlining the most important antibiofilm strategies and potential targets of natural products, and summarizing the latest progress in combating S. aureus biofilm with plant-derived natural products. These findings provided further evidence for novel antibiofilm drugs research and clinical therapies.

The effect of light intensity on microalgae biofilm structures and physiology under continuous illumination

The interest by biofilm-based microalgae technologies has increased lately due to productivity improvement, energy consumption reduction and easy harvesting. However, the effect of light, one key factor for system's operation, received less attention than for planktonic cultures. This work assessed the impact of Photon Flux Density (PFD) on Chlorella vulgaris biofilm dynamics (structure, physiology, activity). Microalgae biofilms were cultivated in a flow-cell system with PFD from 100 to 500 [Formula: see text]. In the first stage of biofilm development, uniform cell distribution was observed on the substratum exposed to 100 [Formula: see text] while cell clusters were formed under 500 [Formula: see text]. Though similar specific growth rate in exponential phase (ca. 0.3 [Formula: see text]) was obtained under all light intensities, biofilm cells at 500 [Formula: see text] seem to be ultimately photoinhibited (lower final cell density). Data confirm that Chlorella vulgaris showed a remarkable capability to cope with high light. This was marked for sessile cells at 300 [Formula: see text], which reduce very rapidly (in 2 days) their chlorophyll-a content, most probably to reduce photodamage, while maintaining a high final cell density. Besides cellular physiological adjustments, our data demonstrate that cellular spatial organization is light-dependent.

Heterogeneous anomalous transport in cellular and molecular biology

It is well established that a wide variety of phenomena in cellular and molecular biology involve anomalous transport e.g. the statistics for the motility of cells and molecules are fractional and do not conform to the archetypes of simple diffusion or ballistic transport. Recent research demonstrates that anomalous transport is in many cases heterogeneous in both time and space. Thus single anomalous exponents and single generalised diffusion coefficients are unable to satisfactorily describe many crucial phenomena in cellular and molecular biology. We consider advances in the field ofheterogeneous anomalous transport(HAT) highlighting: experimental techniques (single molecule methods, microscopy, image analysis, fluorescence correlation spectroscopy, inelastic neutron scattering, and nuclear magnetic resonance), theoretical tools for data analysis (robust statistical methods such as first passage probabilities, survival analysis, different varieties of mean square displacements, etc), analytic theory and generative theoretical models based on simulations. Special emphasis is made on high throughput analysis techniques based on machine learning and neural networks. Furthermore, we consider anomalous transport in the context of microrheology and the heterogeneous viscoelasticity of complex fluids. HAT in the wavefronts of reaction-diffusion systems is also considered since it plays an important role in morphogenesis and signalling. In addition, we present specific examples from cellular biology including embryonic cells, leucocytes, cancer cells, bacterial cells, bacterial biofilms, and eukaryotic microorganisms. Case studies from molecular biology include DNA, membranes, endosomal transport, endoplasmic reticula, mucins, globular proteins, and amyloids.

Wip1 inhibits neutrophil extracellular traps to promote abscess formation in mice by directly dephosphorylating Coronin-1a

Neutrophil extracellular traps (NETs) participate in the rapid inhibition and clearance of pathogens during infection; however, the molecular regulation of NET formation remains poorly understood. In the current study, we found that inhibition of the wild-type p53-induced phosphatase 1 (Wip1) significantly suppressed the activity of Staphylococcus aureus (S. aureus) and accelerated abscess healing in S. aureus-induced abscess model mice by enhancing NET formation. A Wip1 inhibitor significantly enhanced NET formation in mouse and human neutrophils in vitro. High-resolution mass spectrometry and biochemical assays demonstrated that Coro1a is a substrate of Wip1. Further experiments also revealed that Wip1 preferentially and directly interacts with phosphorylated Coro1a than compared to unphosphorylated inactivated Coro1a. The phosphorylated Ser426 site of Coro1a and the 28-90 aa domain of Wip1 are essential for the direct interaction of Coro1a and Wip1 and for Wip1 dephosphorylation of p-Coro1a Ser426. Wip1 deletion or inhibition in neutrophils significantly upregulated the phosphorylation of Coro1a-Ser426, which activated phospholipase C and subsequently the calcium pathway, the latter of which promoted NET formation after infection or lipopolysaccharide stimulation. This study revealed Coro1a to be a novel substrate of Wip1 and showed that Wip1 is a negative regulator of NET formation during infection. These results support the potential application of Wip1 inhibitors to treat bacterial infections.

Mechanisms driving spatial distribution of residents in colony biofilms: an interdisciplinary perspective

Biofilms are consortia of microorganisms that form collectives through the excretion of extracellular matrix compounds. The importance of biofilms in biological, industrial and medical settings has long been recognized due to their emergent properties and impact on surrounding environments. In laboratory situations, one commonly used approach to study biofilm formation mechanisms is the colony biofilm assay, in which cell communities grow on solid-gas interfaces on agar plates after the deposition of a population of founder cells. The residents of a colony biofilm can self-organize to form intricate spatial distributions. The assay is ideally suited to coupling with mathematical modelling due to the ability to extract a wide range of metrics. In this review, we highlight how interdisciplinary approaches have provided deep insights into mechanisms causing the emergence of these spatial distributions from well-mixed inocula.

Responses of Salmonella biofilms to oxidizing biocides: Evidence of spatial clustering

The spatial organization of biofilm bacterial communities can be influenced by several factors, including growth conditions and challenge with antimicrobials. Differential survival of clusters of cells within biofilms has been observed. In this work, we present a variety of methods to identify, quantify and statistically analyse clusters of live cells from images of two Salmonella strains with differential biofilm forming capacity exposed to three oxidizing biocides. With a support vector machine approach, we showed spatial separation between the two strains, and, using statistical testing and high-performance computing (HPC), we determined conditions which possess an inherent cluster structure. Our results indicate that there is a relationship between biocide potency and inherent biofilm formation capacity with the tendency to select for spatial clusters of survivors. There was no relationship between positions of clusters of live or dead cells within stressed biofilms. This work identifies an approach to robustly quantify clusters of physiologically distinct cells within biofilms and suggests work to understand how clusters form and survive is needed. SIGNIFICANCE STATEMENT: Control of biofilm growth remains a major challenge and there is considerable uncertainty about how bacteria respond to disinfection within a biofilm and how clustering of cells impacts survival. We have developed a methodological approach to identify and statistically analyse clusters of surviving cells in biofilms after biocide challenge. This approach can be used to understand bacterial behaviour within biofilms under stress and is widely applicable.

Dynamic Changes in Biofilm Structures under Dynamic Flow Conditions

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

SARS-CoV-2 Spike Protein and Mouse Coronavirus Inhibit Biofilm Formation by Streptococcus pneumoniae and Staphylococcus aureus

The presence of co-infections or superinfections with bacterial pathogens in COVID-19 patients is associated with poor outcomes, including increased morbidity and mortality. We hypothesized that SARS-CoV-2 and its components interact with the biofilms generated by commensal bacteria, which may contribute to co-infections. This study employed crystal violet staining and particle-tracking microrheology to characterize the formation of biofilms by Streptococcus pneumoniae and Staphylococcus aureus that commonly cause secondary bacterial pneumonia. Microrheology analyses suggested that these biofilms were inhomogeneous soft solids, consistent with their dynamic characteristics. Biofilm formation by both bacteria was significantly inhibited by co-incubation with recombinant SARS-CoV-2 spike S1 subunit and both S1 + S2 subunits, but not with S2 extracellular domain nor nucleocapsid protein. Addition of spike S1 and S2 antibodies to spike protein could partially restore bacterial biofilm production. Furthermore, biofilm formation in vitro was also compromised by live murine hepatitis virus, a related beta-coronavirus. Supporting data from LC-MS-based proteomics of spike-biofilm interactions revealed differential expression of proteins involved in quorum sensing and biofilm maturation, such as the AI-2E family transporter and LuxS, a key enzyme for AI-2 biosynthesis. Our findings suggest that these opportunistic pathogens may egress from biofilms to resume a more virulent planktonic lifestyle during coronavirus infections. The dispersion of pathogens from biofilms may culminate in potentially severe secondary infections with poor prognosis. Further detailed investigations are warranted to establish bacterial biofilms as risk factors for secondary pneumonia in COVID-19 patients.

Shear stress affects the architecture and cohesion of Chlorella vulgaris biofilms

The architecture of microalgae biofilms has been poorly investigated, in particular with respect to shear stress, which is a crucial factor in biofilm-based reactor design and operation. To investigate how microalgae biofilms respond to different hydrodynamic regimes, the architecture and cohesion of Chlorella vulgaris biofilms were studied in flow-cells at three shear stress: 1.0, 6.5 and 11.0 mPa. Biofilm physical properties and architecture dynamics were monitored using a set of microscopic techniques such as, fluorescence recovery after photobleaching (FRAP) and particle tracking. At low shear, biofilms cohesion was heterogeneous resulting in a strong basal (close to the substrate) layer and in more loose superficial ones. Higher shear (11.0 mPa) significantly increased the cohesion of the biofilms allowing them to grow thicker and to produce more biomass, likely due to a biological response to resist the shear stress. Interestingly, an acclimation strategy seemed also to occur which allowed the biofilms to preserve their growth rate at the different hydrodynamic regimes. Our results are in accordance with those previously reported for bacteria biofilms, revealing some general physical/mechanical rules that govern microalgae life on substrates. These results may bring new insights about how to improve productivity and stability of microalgae biofilm-based systems.

Spatial Correlations and Distribution of Competence Gene Expression in Biofilms of Streptococcus mutans

Streptococcus mutans is an important pathogen in the human oral biofilm. It expresses virulent behaviors that are linked to its genetic competence regulon, which is controlled by comX. Expression of comX is modulated by two diffusible signaling peptides, denoted CSP and XIP, and by other environmental cues such as pH and oxidative stress. The sensitivity of S. mutans competence to environmental inputs that may vary on microscopic length scales raises the question of whether the biofilm environment creates microniches where competence and related phenotypes are concentrated, leading to spatial clustering of S. mutans virulence behaviors. We have used two-photon microscopy to characterize the spatial distribution of comX expression among individual S. mutans cells in biofilms. By analyzing correlations in comX activity, we test for spatial clustering that may suggest localized competence microenvironments. Our data indicate that both competence-signaling peptides diffuse efficiently through the biofilm. XIP elicits a population-wide response. CSP triggers a Poisson-like, spatially random comX response from a subpopulation of cells that is homogeneously dispersed. Our data indicate that competence microenvironments if they exist are small enough that the phenotypes of individual cells are not clustered or correlated to any greater extent than occurs in planktonic cultures.

Biofilm and swarming emergent behaviours controlled through the aid of biophysical understanding and tools

Bacteria can organise themselves into communities in the forms of biofilms and swarms. Through chemical and physical interactions between cells, these communities exhibit emergent properties that individual cells alone do not have. While bacterial communities have been mainly studied in the context of biochemistry and molecular biology, recent years have seen rapid advancements in the biophysical understanding of emergent phenomena through physical interactions in biofilms and swarms. Moreover, new technologies to control bacterial emergent behaviours by physical means are emerging in synthetic biology. Such technologies are particularly promising for developing engineered living materials (ELM) and devices and controlling contamination and biofouling. In this minireview, we overview recent studies unveiling physical and mechanical cues that trigger and affect swarming and biofilm development. In particular, we focus on cell shape, motion and density as the key parameters for mechanical cell-cell interactions within a community. We then showcase recent studies that use physical stimuli for patterning bacterial communities, altering collective behaviours and preventing biofilm formation. Finally, we discuss the future potential extension of biophysical and bioengineering research on microbial communities through computational modelling and deeper investigation of mechano-electrophysiological coupling.