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

Biofilm Maintenance as an Active Process: Evidence that Biofilms Work Hard to Stay Put

Biofilm formation represents a critical strategy whereby bacteria can tolerate otherwise damaging environmental stressors and antimicrobial insults. While the mechanisms bacteria use to establish a biofilm and disperse from these communities have been well-studied, we have only a limited understanding of the mechanisms required to maintain these multicellular communities. Indeed, until relatively recently, it was not clear that maintaining a mature biofilm could be considered an active, regulated process with dedicated machinery. Using Pseudomonas aeruginosa as a model system, we review evidence from recent studies that support the model that maintenance of these persistent, surface-attached communities is indeed an active process. Biofilm maintenance mechanisms include transcriptional regulation and second messenger signaling (including the production of extracellular polymeric substances). We also discuss energy-conserving pathways that play a key role in the maintenance of these communities. We hope to highlight the need for further investigation to uncover novel biofilm maintenance pathways and suggest the possibility that such pathways can serve as novel antibiofilm targets.

Spreading rates of bacterial colonies depend on substrate stiffness and permeability

The ability of bacteria to colonize and grow on different surfaces is an essential process for biofilm development. Here, we report the use of synthetic hydrogels with tunable stiffness and porosity to assess physical effects of the substrate on biofilm development. Using time-lapse microscopy to track the growth of expanding Serratia marcescens colonies, we find that biofilm colony growth can increase with increasing substrate stiffness, unlike what is found on traditional agar substrates. Using traction force microscopy-based techniques, we find that biofilms exert transient stresses correlated over length scales much larger than a single bacterium, and that the magnitude of these forces also increases with increasing substrate stiffness. Our results are consistent with a model of biofilm development in which the interplay between osmotic pressure arising from the biofilm and the poroelastic response of the underlying substrate controls biofilm growth and morphology.

The many faces of the unusual biofilm activator RemA

Biofilms can be viewed as tissue-like structures in which microorganisms are organized in a spatial and functional sophisticated manner. Biofilm formation requires the orchestration of a highly integrated network of regulatory proteins to establish cell differentiation and production of a complex extracellular matrix. Here, we discuss the role of the essential Bacillus subtilis biofilm activator RemA. Despite intense research on biofilms, RemA is a largely underappreciated regulatory protein. RemA forms donut-shaped octamers with the potential to assemble into dimeric superstructures. The presumed DNA-binding mode suggests that RemA organizes its target DNA into nucleosome-like structures, which are the basis for its role as transcriptional activator. We discuss how RemA affects gene expression in the context of biofilm formation, and its regulatory interplay with established components of the biofilm regulatory network, such as SinR, SinI, SlrR, and SlrA. We emphasize the additional role of RemA played in nitrogen metabolism and osmotic-stress adjustment.

Chemotactic smoothing of collective migration

Collective migration-the directed, coordinated motion of many self-propelled agents-is a fascinating emergent behavior exhibited by active matter with functional implications for biological systems. However, how migration can persist when a population is confronted with perturbations is poorly understood. Here, we address this gap in knowledge through studies of bacteria that migrate via directed motion, or chemotaxis, in response to a self-generated nutrient gradient. We find that bacterial populations autonomously smooth out large-scale perturbations in their overall morphology, enabling the cells to continue to migrate together. This smoothing process arises from spatial variations in the ability of cells to sense and respond to the local nutrient gradient-revealing a population-scale consequence of the manner in which individual cells transduce external signals. Altogether, our work provides insights to predict, and potentially control, the collective migration and morphology of cellular populations and diverse other forms of active matter.

Materials science and mechanosensitivity of living matter

Living systems are composed of molecules that are synthesized by cells that use energy sources within their surroundings to create fascinating materials that have mechanical properties optimized for their biological function. Their functionality is a ubiquitous aspect of our lives. We use wood to construct furniture, bacterial colonies to modify the texture of dairy products and other foods, intestines as violin strings, bladders in bagpipes, and so on. The mechanical properties of these biological materials differ from those of other simpler synthetic elastomers, glasses, and crystals. Reproducing their mechanical properties synthetically or from first principles is still often unattainable. The challenge is that biomaterials often exist far from equilibrium, either in a kinetically arrested state or in an energy consuming active state that is not yet possible to reproduce de novo. Also, the design principles that form biological materials often result in nonlinear responses of stress to strain, or force to displacement, and theoretical models to explain these nonlinear effects are in relatively early stages of development compared to the predictive models for rubberlike elastomers or metals. In this Review, we summarize some of the most common and striking mechanical features of biological materials and make comparisons among animal, plant, fungal, and bacterial systems. We also summarize some of the mechanisms by which living systems develop forces that shape biological matter and examine newly discovered mechanisms by which cells sense and respond to the forces they generate themselves, which are resisted by their environment, or that are exerted upon them by their environment. Within this framework, we discuss examples of how physical methods are being applied to cell biology and bioengineering.

A DNase-mimetic artificial enzyme for the eradication of drug-resistant bacterial biofilm infections

The construction of multifunctional nano-enzymes is a feasible strategy for fighting multi-drug resistant (MDR) bacterial biofilm-associated infections. Extracellular DNA (eDNA) is an important functional part of biofilm formation, including the initial adherence of bacteria to subsequent development and eventual maturation. A nano-enzyme platform of graphene oxide-based nitrilotriacetic acid-cerium(IV) composite (GO-NTA-Ce) against bacterial biofilm infection has been developed. When located at the site of bacteria-associated infection, GO-NTA-Ce could inhibit the biofilm formation and effectively disperse the formed biofilm by degrading the eDNA. In addition to Ce-mediated deoxyribonuclease (DNase)-like activity, near-infrared laser irradiation of GO-NTA-Ce could produce local hyperthermia to kill the bacteria that lost the protection by the biofilm matrix. In addition, graphene is also a new green broad-spectrum antimicrobial material that can exert its antimicrobial effects through physical damage and chemical damage. In short, our GO-NTA-Ce nano-enzyme platform is capable of effectively eradicating drug-resistant bacterial biofilm infections through the triple action of DNase-like enzyme properties, photothermal therapy, and graphene-based antimicrobial activity, and the nano-composite has excellent potential for the treatment of MDR bacterial biofilm infections.

Osmotic stress induces long-term biofilm survival in Liberibacter crescens

Citrus greening, also known as Huanglongbing (HLB), is a devastating citrus plant disease caused predominantly by Liberibacter asiaticus. While nearly all Liberibacter species remain uncultured, here we used the culturable L. crescens BT-1 as a model to examine physiological changes in response to the variable osmotic conditions and nutrient availability encountered within the citrus host. Similarly, physiological responses to changes in growth temperature and dimethyl sulfoxide concentrations were also examined, due to their use in many of the currently employed therapies to control the spread of HLB. Sublethal heat stress was found to induce the expression of genes related to tryptophan biosynthesis, while repressing the expression of ribosomal proteins. Osmotic stress induces expression of transcriptional regulators involved in expression of extracellular structures, while repressing the biosynthesis of fatty acids and aromatic amino acids. The effects of osmotic stress were further evaluated by quantifying biofilm formation of L. crescens in presence of increasing sucrose concentrations at different stages of biofilm formation, where sucrose-induced osmotic stress delayed initial cell attachment while enhancing long-term biofilm viability. Our findings revealed that exposure to osmotic stress is a significant contributing factor to the long term survival of L. crescens and, possibly, to the pathogenicity of other Liberibacter species.

Slow expanders invade by forming dented fronts in microbial colonies

Living organisms never cease to evolve, so there is a significant interest in predicting and controlling evolution in all branches of life sciences. The most basic question is whether a trait should increase or decrease in a given environment. The answer seems to be trivial for traits such as the growth rate in a bioreactor or the expansion rate of a tumor. Yet, it has been suggested that such traits can decrease, rather than increase, during evolution. Here, we report a mutant that outcompeted the ancestor despite having a slower expansion velocity when in isolation. To explain this observation, we developed and validated a theory that describes spatial competition between organisms with different expansion rates and arbitrary competitive interactions.

Most organisms grow in space, whether they are viruses spreading within a host tissue or invasive species colonizing a new continent. Evolution typically selects for higher expansion rates during spatial growth, but it has been suggested that slower expanders can take over under certain conditions. Here, we report an experimental observation of such population dynamics. We demonstrate that mutants that grow slower in isolation nevertheless win in competition, not only when the two types are intermixed, but also when they are spatially segregated into sectors. The latter was thought to be impossible because previous studies focused exclusively on the global competitions mediated by expansion velocities, but overlooked the local competitions at sector boundaries. Local competition, however, can enhance the velocity of either type at the sector boundary and thus alter expansion dynamics. We developed a theory that accounts for both local and global competitions and describes all possible sector shapes. In particular, the theory predicted that a slower on its own, but more competitive, mutant forms a dented V-shaped sector as it takes over the expansion front. Such sectors were indeed observed experimentally, and their shapes matched quantitatively with the theory. In simulations, we further explored several mechanisms that could provide slow expanders with a local competitive advantage and showed that they are all well-described by our theory. Taken together, our results shed light on previously unexplored outcomes of spatial competition and establish a universal framework to understand evolutionary and ecological dynamics in expanding populations.

Thin-film lubrication model for biofilm expansion under strong adhesion

Understanding microbial biofilm growth is important to public health because biofilms are a leading cause of persistent clinical infections. In this paper, we develop a thin-film model for microbial biofilm growth on a solid substratum to which it adheres strongly. We model biofilms as two-phase viscous fluid mixtures of living cells and extracellular fluid. The model explicitly tracks the movement, depletion, and uptake of nutrients and incorporates cell proliferation via a nutrient-dependent source term. Notably, our thin-film reduction is two dimensional and includes the vertical dependence of cell volume fraction. Numerical solutions show that this vertical dependence is weak for biologically feasible parameters, reinforcing results from previous models in which this dependence was neglected. We exploit this weak dependence by writing and solving a simplified one-dimensional model that is computationally more efficient than the full model. We use both the one- and two-dimensional models to predict how model parameters affect expansion speed and biofilm thickness. This analysis reveals that expansion speed depends on cell proliferation, nutrient availability, cell-cell adhesion on the upper surface, and slip on the biofilm-substratum interface. Our numerical solutions provide a means to qualitatively distinguish between the extensional flow and lubrication regimes, and quantitative predictions that can be tested in future experiments.

Adaptation of Escherichia coli Biofilm Growth, Morphology, and Mechanical Properties to Substrate Water Content

Biofilms are complex living materials that form as bacteria become embedded in a matrix of self-produced protein and polysaccharide fibers. In addition to their traditional association with chronic infections or clogging of pipelines, biofilms currently gain interest as a potential source of functional material. On nutritive hydrogels, micron-sized Escherichia coli cells can build centimeter-large biofilms. During this process, bacterial proliferation, matrix production, and water uptake introduce mechanical stresses in the biofilm that are released through the formation of macroscopic delaminated buckles in the third dimension. To clarify how substrate water content could be used to tune biofilm material properties, we quantified E. coli biofilm growth, delamination dynamics, and rigidity as a function of water content of the nutritive substrates. Time-lapse microscopy and computational image analysis revealed that softer substrates with high water content promote biofilm spreading kinetics, while stiffer substrates with low water content promote biofilm delamination. The delaminated buckles observed on biofilm cross sections appeared more bent on substrates with high water content, while they tended to be more vertical on substrates with low water content. Both wet and dry biomass, accumulated over 4 days of culture, were larger in biofilms cultured on substrates with high water content, despite extra porosity within the matrix layer. Finally, microindentation analysis revealed that substrates with low water content supported the formation of stiffer biofilms. This study shows that E. coli biofilms respond to substrate water content, which might be used for tuning their material properties in view of further applications.

Phenotypic Switching of Staphylococcus aureus Mu50 Into a Large Colony Variant Enhances Heritable Resistance Against β-Lactam Antibiotics

Phenotypic heterogeneity within a bacterial population may confer new functionality and allow microorganisms to adapt to fluctuating environments. Previous work has suggested that Staphylococcus aureus could form small colony variants to avoid elimination by therapeutic antibiotics and host immunity systems. Here we show that a reversible non-pigment large colony morphology (Mu50∆lcpA-LC) was observed in S. aureus Mu50 after knocking out lcpA, coding for the LytR-CpsA-Psr family A protein. Mu50∆lcpA-LC increased resistance to β-lactam antibiotics, in addition, the enlarged cell size, enhanced spreading ability on solid medium, and reduced biofilm formation, suggesting better abilities for bacterial expansion. Moreover, the expression of spa encoding protein A was significantly increased in Mu50∆lcpA-LC. This study shows that besides the small colony variants, S. aureus could fight against antibiotics and host immunity through phenotype switching into a large colony variant.

The Diguanylate Cyclase YfiN of Pseudomonas aeruginosa Regulates Biofilm Maintenance in Response to Peroxide

Pseudomonas aeruginosa forms surface-attached communities that persist in the face of antimicrobial agents and environmental perturbation. Published work has found extracellular polysaccharide (EPS) production, regulation of motility and induction of stress response pathways as contributing to biofilm tolerance during such insults. However, little is known regarding the mechanism(s) whereby biofilm maintenance is regulated when exposed to such environmental challenges. Here, we provide evidence that the diguanylate cyclase YfiN is important for the regulation of biofilm maintenance when exposed to peroxide. We find that, compared to the wild type (WT), static biofilms of the ΔyfiN mutant exhibit a maintenance defect, which can be further exacerbated by exposure to peroxide (H₂O₂); this defect can be rescued through genetic complementation. Additionally, we found that the ΔyfiN mutant biofilms produce less c-di-GMP than WT, and that H₂O₂ treatment enhanced motility of surface-associated bacteria and increased cell death for the ΔyfiN mutant grown as a biofilm compared to WT biofilms. These data provide evidence that YfiN is required for biofilm maintenance by P. aeruginosa, via c-di-GMP signaling, to limit motility and protect viability in response to peroxide stress. These findings add to the growing recognition that biofilm maintenance by P. aeruginosa is an actively regulated process that is controlled, at least in part, by the wide array of c-di-GMP metabolizing enzymes found in this microbe. Importance We build on previous findings that suggest that P. aeruginosa utilizes c-di-GMP metabolizing enzymes to actively maintain a mature biofilm. Here, we explore how the diguanylate cyclase YfiN contributes to the regulation of biofilm maintenance during peroxide exposure. We find that mature P. aeruginosa biofilms require YfiN to synthesize c-di-GMP, regulate motility and to insure viability during peroxide stress. These findings provide further evidence that the modulation of c-di-GMP in response to environmental signals is an important mechanism by which biofilms are maintained.

Soil pH has a stronger effect than arsenic content on shaping plastisphere bacterial communities in soil

Microplastic (MP) pollution is widespread in various ecosystems and is colonized by microbes that form biofilms with compositions and functions. However, compared with aquatic environments, the soil environment has been poorly studied in terms of the taxonomic composition of microbial communities and the factors influencing the community structure of microbes in the plastisphere. In the present study, a microcosm experiment was conducted to investigate the plastisphere bacterial communities of MP (polyvinyl chloride, PVC) in soils with different pH (4.62, 6.5, and 7.46) and arsenic (As) contents (13 and 74 mg kg^-1). Bacterial communities in the plastisphere were dominated by Proteobacteria and Firmicutes, with distinct compositions and structures compared with soil bacterial communities. Soil pH and As content significantly affected the plastisphere bacterial communities. Constrained analysis of principal coordinates and a structural equation model demonstrated that soil pH had a stronger influence on the dissimilarity and diversity of bacterial communities than did soil As content. Soil pH affected As speciation in soil and on MP. The concentration of dimethylarsinic acid (DMA) was significantly higher on MP than that in soil, indicating that As methylation occurred on MP. These results suggest that environmental fluctuations govern plastisphere bacterial communities with cascading effects on biogeochemical cycling of As in the soil ecosystems.

Evidence for biosurfactant-induced flow in corners and bacterial spreading in unsaturated porous media

The spread of pathogenic bacteria in unsaturated porous media, where air and liquid coexist in pore spaces, is the major cause of soil contamination by pathogens, soft rot in plants, food spoilage, and many pulmonary diseases. However, visualization and fundamental understanding of bacterial transport in unsaturated porous media are currently lacking, limiting the ability to address the above contamination- and disease-related issues. Here, we demonstrate a previously unreported mechanism by which bacterial cells are transported in unsaturated porous media. We discover that surfactant-producing bacteria can generate flows along corners through surfactant production that changes the wettability of the solid surface. The corner flow velocity is on the order of several millimeters per hour, which is the same order of magnitude as bacterial swarming, one of the fastest known modes of bacterial surface translocation. We successfully predict the critical corner angle for bacterial corner flow to occur based on the biosurfactant-induced change in the contact angle of the bacterial solution on the solid surface. Furthermore, we demonstrate that bacteria can indeed spread by producing biosurfactants in a model soil, which consists of packed angular grains. In addition, we demonstrate that bacterial corner flow is controlled by quorum sensing, the cell-cell communication process that regulates biosurfactant production. Understanding this previously unappreciated bacterial transport mechanism will enable more accurate predictions of bacterial spreading in soil and other unsaturated porous media.

Structure formation in a conserved mass model of a set of individuals interacting with attractive and repulsive forces

We study a set of interacting individuals that conserve their total mass. In order to describe its dynamics we resort to mesoscopic equations of reaction diffusion including currents driven by attractive and repulsive forces. For the mass conservation we consider a linear response parameter that maintains the mass in the vicinity of a optimal value which is determined by the set. We use the reach and intensity of repulsive forces as control parameters. When sweeping a wide range of parameter space we find a great diversity of localized structures, stationary as well as other ones with cyclical and chaotic dynamics. We compare our results with real situations.

Water in bacterial biofilms: pores and channels, storage and transport functions

Bacterial biofilms occur in many natural and industrial environments. Besides bacteria, biofilms comprise over 70 wt% water. Water in biofilms occurs as bound- or free-water. Bound-water is adsorbed to bacterial surfaces or biofilm (matrix) structures and possesses different Infra-red and Nuclear-Magnetic-Resonance signatures than free-water. Bound-water is different from intra-cellularly confined-water or water confined within biofilm structures and bacteria are actively involved in building water-filled structures by bacterial swimmers, dispersion or lytic self-sacrifice. Water-filled structures can be transient due to blocking, resulting from bacterial growth, compression or additional matrix formation and are generally referred to as "channels and pores." Channels and pores can be distinguished based on mechanism of formation, function and dimension. Channels allow transport of nutrients, waste-products, signalling molecules and antibiotics through a biofilm provided the cargo does not adsorb to channel walls and channels have a large length/width ratio. Pores serve a storage function for nutrients and dilute waste-products or antimicrobials and thus should have a length/width ratio close to unity. The understanding provided here on the role of water in biofilms, can be employed to artificially engineer by-pass channels or additional pores in industrial and environmental biofilms to increase production yields or enhance antimicrobial penetration in infectious biofilms.

Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities

The metabolic capabilities of the species and the local environment shape the microbial interactions in a community either through the exchange of metabolic products or the competition for the resources. Cells are often arranged in close proximity to each other, creating a crowded environment that unevenly reduce the diffusion of nutrients. Herein, we investigated how the crowding conditions and metabolic variability among cells shape the dynamics of microbial communities. For this, we developed CROMICS, a spatio-temporal framework that combines techniques such as individual-based modeling, scaled particle theory, and thermodynamic flux analysis to explicitly incorporate the cell metabolism and the impact of the presence of macromolecular components on the nutrients diffusion. This framework was used to study two archetypical microbial communities (i) Escherichia coli and Salmonella enterica that cooperate with each other by exchanging metabolites, and (ii) two E. coli with different production level of extracellular polymeric substances (EPS) that compete for the same nutrients. In the mutualistic community, our results demonstrate that crowding enhanced the fitness of cooperative mutants by reducing the leakage of metabolites from the region where they are produced, avoiding the resource competition with non-cooperative cells. Moreover, we also show that E. coli EPS-secreting mutants won the competition against the non-secreting cells by creating less dense structures (i.e. increasing the spacing among the cells) that allow mutants to expand and reach regions closer to the nutrient supply point. A modest enhancement of the relative fitness of EPS-secreting cells over the non-secreting ones were found when the crowding effect was taken into account in the simulations. The emergence of cell-cell interactions and the intracellular conflicts arising from the trade-off between growth and the secretion of metabolites or EPS could provide a local competitive advantage to one species, either by supplying more cross-feeding metabolites or by creating a less dense neighborhood.

Microbial communities play a key role in biogeochemical cycles, bioremediation, and human health. In crowded microbial systems such as biofilms and cellular aggregates, the close proximity between individual cells reduces the free space for the nutrients diffusion. To model the heterogeneous nature of these microbial systems, we developed CROMICS, a framework that integrates the information about the metabolic capabilities of each individual cell as well as the size and location of cells and macromolecules in the medium. The interactions among the individuals arise naturally through competition for or the exchange of metabolites. We show how the presence of mutants and a reduced diffusion in crowded environments can perturb the local availability of nutrients and therefore modify the dynamics of a microbial community. The discovered mechanisms underlying the microbial interactions in crowded systems together with the developed framework represent a valuable starting point for future studies of the interplay of human microbiome and host metabolism, the pathogen invasion, and the evaluation of antibiotic effectiveness.

The effectiveness of divalent cation addition for highly saline activated sludge cultures: Influence of monovalent/divalent ratio and specific cations

Saline wastewaters are prevalent in various industries and pose challenges to stable biological treatment. Increasing monovalent cation concentrations are commonly reported to deteriorate treatment and settling performance, while divalent cations can enhance flocculation and settling. However, many previous studies were performed at relatively low salinities and reports conflict on whether concentrations of monovalent cations, divalent cations, or their ratio (M/D) are most critical. This study investigates whether addition of divalent cations shows the same benefits at high salinity (∼40 g NaCl.L^-1) and whether divalent ion concentration or M/D is a better predictor of enhancement. Nine sequencing batch reactors were operated at 0.8 M NaCl or KCl monovalent salt concentration, and the concentration of divalent cations (Ca²⁺ and Mg²⁺) was varied. M/D was found to be the critical factor that consistently influenced sludge characteristics. It was particularly important in describing hydrophobicity, sludge volume index (SVI) and specific oxygen uptake rate (SOUR), with r_partial of -0.879, 0.971 and 0.966 respectively in models that had an r²_adj greater than 0.93. Lower M/D also increased biomass concentrations and reduced extracellular polysaccharides, the latter which in turn correlated strongly with many shape and surface charge measures. The specific monovalent salt (Na⁺ or K⁺) influenced treatment performance, biomass concentrations, hydrophobicity, SOUR, extracellular protein and SVI. The specific divalent cation was only important in describing SVI, where Mg²⁺ was beneficial. Overall, this study shows that addition of divalent cations can greatly benefit high salinity activated sludge systems by improving the sludge structure, settling and organic removal.

Near-Infrared Light Enhanced Peroxidase-Like Activity of PEGylated Palladium Nanozyme for Highly Efficient Biofilm Eradication

The overall eradication of biofilm-mode growing bacteria holds significant key to the answer of a series of infection-related health problems. However, the extracellular matrix of bacteria biofilms disables the traditional antimicrobials and, more unfortunately, hampers the development of the anti-infectious alternatives. Therefore, highly effective antimicrobial agents are an urgent need for biofilm-infection control. Herein, a PEGylated palladium nanozyme (Pd-PEG) with peroxidase (POD)-like activity for highly efficient biofilm infection control is reported. Pd-PEG also shows the intrinsic photothermal effect as well as near-infrared (NIR) light-enhanced POD-like activity in the acidic environment, thereby massively destroying the biofilm matrix and killing the adhering bacteria. Importantly, the antimicrobial mechanism of the synergistic treatment based on Pd-PEG+H₂O₂+NIR combination was disclosed. In vitro and in vivo results illustrated the designed Pd-PEG+H₂O₂ +NIR treatment reagent possessed outstanding antibacterial and biofilms elimination effects with negligible biotoxicity. This work hopefully facilitates the development of metal-based nanozymes in biofilm related infectious diseases.

The ups and downs of ectoine: structural enzymology of a major microbial stress protectant and versatile nutrient

Ectoine and its derivative 5-hydroxyectoine are compatible solutes and chemical chaperones widely synthesized by Bacteria and some Archaea as cytoprotectants during osmotic stress and high- or low-growth temperature extremes. The function-preserving attributes of ectoines led to numerous biotechnological and biomedical applications and fostered the development of an industrial scale production process. Synthesis of ectoines requires the expenditure of considerable energetic and biosynthetic resources. Hence, microorganisms have developed ways to exploit ectoines as nutrients when they are no longer needed as stress protectants. Here, we summarize our current knowledge on the phylogenomic distribution of ectoine producing and consuming microorganisms. We emphasize the structural enzymology of the pathways underlying ectoine biosynthesis and consumption, an understanding that has been achieved only recently. The synthesis and degradation pathways critically differ in the isomeric form of the key metabolite N-acetyldiaminobutyric acid (ADABA). γ-ADABA serves as preferred substrate for the ectoine synthase, while the α-ADABA isomer is produced by the ectoine hydrolase as an intermediate in catabolism. It can serve as internal inducer for the genetic control of ectoine catabolic genes via the GabR/MocR-type regulator EnuR. Our review highlights the importance of structural enzymology to inspire the mechanistic understanding of metabolic networks at the biological scale.

Environmental Stress Selects for Innovations That Drive Vibrio Symbiont Diversity

Symbiotic bacteria in the Vibrionaceae are a dynamic group of γ-Proteobacteria that are commonly found throughout the world. Although they primarily are free-living in the environment, they can be commonly found associated with various Eukarya, either as beneficial or pathogenic symbionts. Interestingly, this dual lifestyle (free-living or in symbiosis) enables the bacteria to have enormous ecological breadth, where they can accommodate a variety of stresses in both stages. Here, we discuss some of the most common stressors that Vibrio bacteria encounter when in their free-living state or associated with an animal host, and how some of the mechanisms that are used to cope with these stressors can be used as an evolutionary advantage that increases their diversity both in the environment and within their specific hosts.

Biophysical determinants of biofilm formation in the gut

The gastrointestinal (GI) tract harbors the most complex microbial ecosystem in the human body. The mucosal layer that covers the GI tract serves as a polymer-based defensive barrier that prevents the microbiome from reaching the epithelium and disseminating inside the body. Colonization of the mucus may result in the formation of structured polymicrobial communities or biofilms, a hallmark in pathologies such as colorectal cancer, inflammatory bowel disease, and chronic gut wounds. However, the mechanisms by which multispecies biofilms establish on the gut mucosa is unknown. Whether mucus-associated biofilms exist as part of a healthy mucosal barrier is still debated. Here, we discuss the impact that diet and microbial-derived polymers has on mucus structure and microcolony formation and highlight relevant biophysical forces that further shape nascent biofilms.

Spatiotemporal Measurement of Osmotic Pressures by FRET Imaging

Osmotic pressures (OPs) play essential roles in biological processes and numerous technological applications. However, the measurement of OP in situ with spatiotemporal resolution has not been achieved so far. Herein, we introduce a novel kind of OP sensor based on liposomes loaded with water-soluble fluorescent dyes exhibiting resonance energy transfer (FRET). The liposomes experience volume changes in response to OP due to water outflux. The FRET efficiency depends on the average distance between the entrapped dyes and thus provides a direct measure of the OP surrounding each liposome. The sensors exhibit high sensitivity to OP in the biologically relevant range of 0-0.3 MPa in aqueous solutions of salt, small organic molecules, and macromolecules. With the help of FRET microscopy, we demonstrate the feasibility of spatiotemporal OP imaging, which can be a promising new tool to investigate phenomena involving OPs and their dynamics in biology and technology.

How Physical Interactions Shape Bacterial Biofilms

Biofilms are structured communities formed by a single or multiple microbial species. Within biofilms, bacteria are embedded into extracellular matrix, allowing them to build macroscopic objects. Biofilm structure can respond to environmental changes such as the presence of antibiotics or predators. By adjusting expression levels of surface and extracellular matrix components, bacteria tune cell-to-cell interactions. One major challenge in the field is the fact that these components are very diverse among different species. Deciphering how physical interactions within biofilms are affected by changes in gene expression is a promising approach to obtaining a more unified picture of how bacteria modulate biofilms. This review focuses on recent advances in characterizing attractive and repulsive forces between bacteria in correlation with biofilm structure, dynamics, and spreading. How bacteria control physical interactions to maximize their fitness is an emerging theme.

Three-dimensional biofilm colony growth supports a mutualism involving matrix and nutrient sharing

Life in a three-dimensional biofilm is typical for many bacteria, yet little is known about how strains interact in this context. Here, we created essential gene CRISPR interference knockdown libraries in biofilm-forming Bacillus subtilis and measured competitive fitness during colony co-culture with wild type. Partial knockdown of some translation-related genes reduced growth rates and led to out-competition. Media composition led some knockdowns to compete differentially as biofilm versus non-biofilm colonies. Cells depleted for the alanine racemase AlrA died in monoculture but survived in a biofilm colony co-culture via nutrient sharing. Rescue was enhanced in biofilm colony co-culture with a matrix-deficient parent due to a mutualism involving nutrient and matrix sharing. We identified several examples of mutualism involving matrix sharing that occurred in three-dimensional biofilm colonies but not when cultured in two dimensions. Thus, growth in a three-dimensional colony can promote genetic diversity through sharing of secreted factors and may drive evolution of mutualistic behavior.

Influence of interspecies interactions on the spatial organization of dual species bacterial communities

Interspecies interactions in bacterial biofilms have important impacts on the composition and function of communities in natural and engineered systems. To investigate these interactions, synthetic communities provide experimentally tractable systems. Biofilms grown on agar-surfaces have been used for investigating the eco-evolutionary and biophysical forces that determine community composition and spatial distribution of bacteria. Prior studies have used genetically identical bacterial strains and strains with specific mutations, that express different fluorescent proteins, to investigate intraspecies interactions. Here, we investigated interspecies interactions and, specifically, determined the community composition and spatial distribution in synthetic communities of Pseudomonas aeruginosa, Pseudomonas protegens and Klebsiella pneumoniae. Using quantitative microscopic imaging, we found that interspecies interactions in multispecies colonies were influenced by type IV pilus mediated motility, extracellular matrix secretion, environmental parameters, and these effects were also influenced by the specific partner in the dual species combinations. These results indicate that the patterns observable in mixed species colonies can be used to understand the mechanisms that drive interspecies interactions, which are dependent on the interplay between specific species’ physiology and environmental conditions.

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Spatial patterns in bacterial colonies are species and interaction dependent.

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Surface motility and extracellar matrix production affect interspecies interactions.

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Agar surface colonies show how bacteria interact in biofilms.

Theoretical modelling of competitive microbial range expansion with heterogeneous mechanical interactions

Microbial range expansion experiments provide insight into the complex link between dynamic structure, pattern formation and evolutionary dynamics of growing populations. In this work, we develop a theoretical model in order to investigate the interplay of growth statistics and mechanical interactions which are implemented as division driven pushing and swapping of cells. For the case of the competitive growth of a strongly and a weakly interacting strain we investigate the influence of different mean division times, as well as different mechanical interactions on the development of the colony. Our results show that the susceptibility to cell division induced pushing has a much stronger influence on the structure of the colony than cell sorting towards the colony's perimeter. Motivated by microbial range expansion experiments of Neisseria gonorrhoeae bacteria, we also consider the influence of mutating cells on the structure of the colony. We show that the outgrowth of the three different strains is strongly influenced by the relative strengths of their mechanical interaction. The experimentally observed patterns are reproduced for mechanical interactions of the mutants, which range between those of the strongly and weakly interacting strain.

Ways to control harmful biofilms: prevention, inhibition, and eradication

Biofilms are complex microbial architectures that encase microbial cells in a matrix comprising self-produced extracellular polymeric substances. Microorganisms living in biofilms are much more resistant to hostile environments than their planktonic counterparts and exhibit enhanced resistance against the microbicides. From the human perspective, biofilms can be classified into beneficial, neutral, and harmful. Harmful biofilms impact food safety, cause plant and animal diseases, and threaten medical fields, making it urgent to develop effective and robust strategies to control harmful biofilms. In this review, we discuss various strategies to control biofilm formation on infected tissues, implants, and medical devices. We classify the current strategies into three main categories: (i) changing the properties of susceptible surfaces to prevent biofilm formation; (ii) regulating signalling pathways to inhibit biofilm formation; (iii) applying external forces to eradicate the biofilm. We hope this review would motivate the development of innovative and effective strategies for controlling harmful biofilms.

Mechanics of biofilms formed of bacteria with fimbriae appendages

Gram-negative bacteria, as well as some Gram-positive bacteria, possess hair-like appendages known as fimbriae, which play an important role in adhesion of the bacteria to surfaces or to other bacteria. Unlike the sex pili or flagellum, the fimbriae are quite numerous, with of order 1000 fimbriae appendages per bacterial cell. In this paper, a recently developed hybrid model for bacterial biofilms is used to examine the role of fimbriae tension force on the mechanics of bacterial biofilms. Each bacterial cell is represented in this model by a spherocylindrical particle, which interact with each other through collision, adhesion, lubrication force, and fimbrial force. The bacterial cells absorb water and nutrients and produce extracellular polymeric substance (EPS). The flow of water and EPS, and nutrient diffusion within these substances, is computed using a continuum model that accounts for important effects such as osmotic pressure gradient, drag force on the bacterial cells, and viscous shear. The fimbrial force is modeled using an outer spherocylinder capsule around each cell, which can transmit tensile forces to neighboring cells with which the fimbriae capsule collides. We find that the biofilm structure during the growth process is dominated by a balance between outward drag force on the cells due to the EPS flow away from the bacterial colony and the inward tensile fimbrial force acting on chains of cells connected by adhesive fimbriae appendages. The fimbrial force also introduces a large rotational motion of the cells and disrupts cell alignment caused by viscous torque imposed by the EPS flow. The current paper characterizes the competing effects of EPS drag and fimbrial force using a series of computations with different values of the ratio of EPS to bacterial cell production rate and different numbers of fimbriae per cell.

A genomic analysis of osmotolerance in Staphylococcus aureus

A key phenotypic characteristic of the Gram-positive bacterial pathogen, Staphylococcus aureus, is its ability to grow in low a_w environments. A homology transfer based approach, using the well characterised osmotic stress response systems of Bacillus subtilis and Escherichia coli, was used to identify putative osmotolerance loci in Staphylococcus aureus ST772-MRSA-V. A total of 17 distinct putative hyper and hypo-osmotic stress response systems, comprising 78 genes, were identified. The ST772-MRSA-V genome exhibits significant degeneracy in terms of the osmotic stress response; with three copies of opuD, two copies each of nhaK and mrp/mnh, and five copies of opp. Furthermore, regulation of osmotolerance in ST772-MRSA-V appears to be mediated at the transcriptional, translational, and post-translational levels.

Privatization of Biofilm Matrix in Structurally Heterogeneous Biofilms

The self-produced biofilm provides beneficial protection for the enclosed cells, but the costly production of matrix components makes producer cells susceptible to cheating by nonproducing individuals. Despite detrimental effects of nonproducers, biofilms can be heterogeneous, with isogenic nonproducers being a natural consequence of phenotypic differentiation processes. For instance, in Bacillus subtilis biofilm cells differ in production of the two major matrix components, the amyloid fiber protein TasA and exopolysaccharides (EPS), demonstrating different expression levels of corresponding matrix genes. This raises questions regarding matrix gene expression dynamics during biofilm development and the impact of phenotypic nonproducers on biofilm robustness. Here, we show that biofilms are structurally heterogeneous and can be separated into strongly and weakly associated clusters. We reveal that spatiotemporal changes in structural heterogeneity correlate with matrix gene expression, with TasA playing a key role in biofilm integrity and timing of development. We show that the matrix remains partially privatized by the producer subpopulation, where cells tightly stick together even when exposed to shear stress. Our results support previous findings on the existence of "weak points" in seemingly robust biofilms as well as on the key role of linkage proteins in biofilm formation. Furthermore, we provide a starting point for investigating the privatization of common goods within isogenic populations.IMPORTANCE Biofilms are communities of bacteria protected by a self-produced extracellular matrix. The detrimental effects of nonproducing individuals on biofilm development raise questions about the dynamics between community members, especially when isogenic nonproducers exist within wild-type populations. We asked ourselves whether phenotypic nonproducers impact biofilm robustness, and where and when this heterogeneity of matrix gene expression occurs. Based on our results, we propose that the matrix remains partly privatized by the producing subpopulation, since producing cells stick together when exposed to shear stress. The important role of linkage proteins in robustness and development of the structurally heterogeneous biofilm provides an entry into studying the privatization of common goods within isogenic populations.

Biofilm Matrixome: Extracellular Components in Structured Microbial Communities

Biofilms consist of microbial communities embedded in a 3D extracellular matrix. The matrix is composed of a complex array of extracellular polymeric substances (EPS) that contribute to the unique attributes of biofilm lifestyle and virulence. This ensemble of chemically and functionally diverse biomolecules is termed the 'matrixome'. The composition and mechanisms of EPS matrix formation, and its role in biofilm biology, function, and microenvironment are being revealed. This perspective article highlights recent advances about the multifaceted role of the 'matrixome' in the development, physical-chemical properties, and virulence of biofilms. We emphasize that targeting biofilm-specific conditions such as the matrixome could lead to precise and effective antibiofilm approaches. We also discuss the limited knowledge in the context of polymicrobial biofilms, and the need for more in-depth analyses of the EPS matrix in mixed communities that are associated with many human infectious diseases.

Highly Efficient 2D NIR-II Photothermal Agent with Fenton Catalytic Activity for Cancer Synergistic Photothermal-Chemodynamic Therapy

Photothermal therapy (PTT) has emerged as a promising cancer therapeutic modality with high therapeutic specificity, however, its therapeutic effectiveness is limited by available high-efficiency photothermal agents (PTAs), especially in the second near-infrared (NIR-II) biowindow. Here, based on facile liquid-exfoliated FePS3 nanosheets, a highly efficient NIR-II PTA with its photothermal conversion efficiency of up to 43.3% is demonstrated, which is among the highest reported levels in typical PTAs. More importantly, such Fe-based 2D nanosheets also show superior Fenton catalytic activity facilitated by their ultrahigh specific surface area, simultaneously enabling cancer chemodynamic therapy (CDT). Impressively, the efficiency of CDT could be further remarkably enhanced by its photothermal effect, leading to cancer synergistic PTT/CDT. Both in vitro and in vivo studies reveal a highly efficient tumor ablation under NIR-II light irradiation. This work provides a paradigm for cancer CDT and PTT in the NIR-II biowindow via a single 2D nanoplatform with desired therapeutic effect. Furthermore, with additional possibilities for magnetic resonance imaging, photoacoustic tomography, as well as drug loading, this Fe-based 2D material could potentially serve as a 2D "all-in-one" theranostic nanoplatform.

Nonuniform growth and surface friction determine bacterial biofilm morphology on soft substrates

During development, organisms acquire three-dimensional (3D) shapes with important physiological consequences. While basic mechanisms underlying morphogenesis are known in eukaryotes, it is often difficult to manipulate them in vivo. To circumvent this issue, here we present a study of developing Vibrio cholerae biofilms grown on agar substrates in which the spatiotemporal morphological patterns were altered by varying the agar concentration. Expanding biofilms are initially flat but later undergo a mechanical instability and become wrinkled. To gain mechanistic insights into this dynamic pattern-formation process, we developed a model that considers diffusion of nutrients and their uptake by bacteria, bacterial growth/biofilm matrix production, mechanical deformation of both the biofilm and the substrate, and the friction between them. Our model shows quantitative agreement with experimental measurements of biofilm expansion dynamics, and it accurately predicts two distinct spatiotemporal patterns observed in the experiments-the wrinkles initially appear either in the peripheral region and propagate inward (soft substrate/low friction) or in the central region and propagate outward (stiff substrate/high friction). Our results, which establish that nonuniform growth and friction are fundamental determinants of stress anisotropy and hence biofilm morphology, are broadly applicable to bacterial biofilms with similar morphologies and also provide insight into how other bacterial biofilms form distinct wrinkle patterns. We discuss the implications of forming undulated biofilm morphologies, which may enhance the availability of nutrients and signaling molecules and serve as a "bet hedging" strategy.

Microbial Community Drivers in Anaerobic Granulation at High Salinity

In the recent years anaerobic sludge granulation at elevated salinities in upflow anaerobic sludge blanket (UASB) reactors has been investigated in few engineering based studies, never addressing the microbial community structural role in driving aggregation and keeping granules stability. In this study, the combination of different techniques was applied in order to follow the microbial community members and their structural dynamics in granules formed at low (5 g/L Na⁺) and high (20 g/L Na⁺) salinity conditions. Experiments were carried out in four UASB reactors fed with synthetic wastewater, using two experimental set-ups. By applying 16S rRNA gene analysis, the comparison of granules grown at low and high salinity showed that acetotrophic Methanosaeta harundinacea was the dominant methanogen at both salinities, while the dominant bacteria changed. At 5 g/L Na⁺, cocci chains of Streptoccoccus were developing, while at 20 g/L Na⁺ members of the family Defluviitaleaceae formed long filaments. By means of Fluorescence in Situ Hybridization (FISH) and Scanning Electron Microscopy (SEM), it was shown that aggregation of Methanosaeta in compact clusters and the formation of filaments of Streptoccoccus and Defluviitaleaceae during the digestion time were the main drivers for the granulation at low and high salinity. Interestingly, when the complex protein substrate (tryptone) in the synthetic wastewater was substituted with single amino acids (proline, leucine and glutamic acid), granules at high salinity (20 g/L Na⁺) were not formed. This corresponded to a decrease of Methanosaeta relative abundance and a lack of compact clustering, together with disappearance of Defluviitaleaceae and consequent absence of bacterial filaments within the dispersed biomass. In these conditions, a biofilm was growing on the glass wall of the reactor instead, highlighting that a complex protein substrate such as tryptone can contribute to granules formation at elevated salinity.

Breakdown of Vibrio cholerae biofilm architecture induced by antibiotics disrupts community barrier function

Bacterial cells in nature are frequently exposed to changes in their chemical environment1,2. The response mechanisms of isolated cells to such stimuli have been investigated in great detail. By contrast, little is known about the emergent multicellular responses to environmental changes, such as antibiotic exposure3-7, which may hold the key to understanding the structure and functions of the most common type of bacterial communities: biofilms. Here, by monitoring all individual cells in Vibrio cholerae biofilms during exposure to antibiotics that are commonly administered for cholera infections, we found that translational inhibitors cause strong effects on cell size and shape, as well as biofilm architectural properties. We identified that single-cell-level responses result from the metabolic consequences of inhibition of protein synthesis and that the community-level responses result from an interplay of matrix composition, matrix dissociation and mechanical interactions between cells. We further observed that the antibiotic-induced changes in biofilm architecture have substantial effects on biofilm population dynamics and community assembly by enabling invasion of biofilms by bacteriophages and intruder cells of different species. These mechanistic causes and ecological consequences of biofilm exposure to antibiotics are an important step towards understanding collective bacterial responses to environmental changes, with implications for the effects of antimicrobial therapy on the ecological succession of biofilm communities.

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

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

In situ characterisation of biofilms formed by psychrotrophic meat spoilage pseudomonads

Psychrotrophic Pseudomonas species form biofilms on meat during refrigerated and temperature abuse conditions. Biofilm growth leads to slime formation on meat which is a key organoleptic degradation characteristic. Limited research has been undertaken characterising biofilms grown on meat during chilled aerobic storage. In this work, biofilms formed by two key meat spoilage organisms, Pseudomonas fragi and Pseudomonas lundensis were studied in situ using five strains from each species. Biofilm structures were studied using confocal microscope images, cellular arrangement, cell counts and biomass quantifications. This work demonstrated that highly dense, compact biofilms are a characteristic of P. fragi strains. P. lundensis formed biofilms with loosely arranged cells. The cells in P. fragi biofilm appear to be vertically oriented whereas this characteristic was absent in P. lundensis biofilms formed under identical conditions. Despite the continued access to nutrients, biofilms formed on meat by proteolytic Pseudomonas species dispersed after a population maximum was reached.

Rivalry in Bacillus subtilis colonies: enemy or family?

Two colonies of Bacillus subtilis of identical strains growing adjacent to each other on an agar plate exhibit two distinct types of interactions: they either merge as they grow or demarcation occurs leading to formation of a line of demarcation at the colony fronts. The nature of this interaction depends on the agar concentration in the growth medium and the initial separation between the colonies. When the agar concentration was 0.67% or lower, the two sibling colonies were found to always merge. At 1% or higher concentrations, the colonies formed a demarcation line only when their initial separation was 20 mm or higher. Interactions of a colony with solid structures and liquid drops have indicated that biochemical factors rather than the presence of physical obstacles are responsible for the demarcation line formation. A reaction diffusion model has been formulated to predict if two sibling colonies will form a demarcation line under given agar concentration and initial separation. The model prediction agrees well with experimental findings and generates a dimensionless phase diagram containing merging and demarcation regimes. The phase diagram is in terms of a dimensionless initial separation, d[combining macron], and a dimensionless diffusion coefficient, D[combining macron], of the colonies. The phase boundary between the two interaction regimes can be described by a power law relation between d[combining macron] and D[combining macron].

Responses of Microorganisms to Osmotic Stress

The cytoplasm of bacterial cells is a highly crowded cellular compartment that possesses considerable osmotic potential. As a result, and owing to the semipermeable nature of the cytoplasmic membrane and the semielastic properties of the cell wall, osmotically driven water influx will generate turgor, a hydrostatic pressure considered critical for growth and viability. Both increases and decreases in the external osmolarity inevitably trigger water fluxes across the cytoplasmic membrane, thus impinging on the degree of cellular hydration, molecular crowding, magnitude of turgor, and cellular integrity. Here, we assess mechanisms that permit the perception of osmotic stress by bacterial cells and provide an overview of the systems that allow them to genetically and physiologically cope with this ubiquitous environmental cue. We highlight recent developments implicating the secondary messenger c-di-AMP in cellular adjustment to osmotic stress and the role of osmotic forces in the life of bacteria-assembled in biofilms.

Virulence Factors Produced by Staphylococcus aureus Biofilms Have a Moonlighting Function Contributing to Biofilm Integrity

Staphylococcus aureus is the causative agent of various biofilm-associated infections in humans causing major healthcare problems worldwide. This type of infection is inherently difficult to treat because of a reduced metabolic activity of biofilm-embedded cells and the protective nature of a surrounding extracellular matrix (ECM). However, little is known about S. aureus biofilm physiology and the proteinaceous composition of the ECM. Thus, we cultivated S. aureus biofilms in a flow system and comprehensively profiled intracellular and extracellular (ECM and flow-through (FT)) biofilm proteomes, as well as the extracellular metabolome compared with planktonic cultures. Our analyses revealed the expression of many pathogenicity factors within S. aureus biofilms as indicated by a high abundance of capsule biosynthesis proteins along with various secreted virulence factors, including hemolysins, leukotoxins, and lipases as a part of the ECM. The activity of ECM virulence factors was confirmed in a hemolysis assay and a Galleria mellonella pathogenicity model. In addition, we uncovered a so far unacknowledged moonlighting function of secreted virulence factors and ribosomal proteins trapped in the ECM: namely their contribution to biofilm integrity. Mechanistically, it was revealed that this stabilizing effect is mediated by the strong positive charge of alkaline virulence factors and ribosomal proteins in an acidic ECM environment, which is caused by the release of fermentation products like formate, lactate, and acetate because of oxygen limitation in biofilms. The strong positive charge of these proteins most likely mediates electrostatic interactions with anionic cell surface components, eDNA, and anionic metabolites. In consequence, this leads to strong cell aggregation and biofilm stabilization. Collectively, our study identified a new molecular mechanism during S. aureus biofilm formation and thus significantly widens the understanding of biofilm-associated S. aureus infections - an essential prerequisite for the development of novel antimicrobial therapies.

Biofilm formation in Pseudoalteromonas lipolytica is related to IS5-like insertions in the capsular polysaccharide operon

Bacterial capsular polysaccharides (CPSs) participate in environmental adaptation in diverse bacteria species. However, the role and regulation of CPS production in marine bacteria have remained largely unexplored. We previously reported that both wrinkled and translucent Pseudoalteromonas lipolytica variants with altered polysaccharide production were generated in pellicle biofilm-associated cells. In this study, we observed that translucent variants were generated at a rate of ∼20% in colony biofilms of P. lipolytica cultured on HSLB agar plates for 12 days. The DNA sequencing results revealed that nearly 90% of these variants had an IS5-like element inserted within the coding or promoter regions of nine genes in the cps operon. In contrast, IS5 insertion into the cps operon was not detected in planktonic cells. Furthermore, we demonstrated that the IS5 insertion event inactivated CPS production, which leads to a translucent colony morphology. The CPS-deficient variants showed an increased ability to form attached biofilms but exhibited reduced resistance to sublethal concentrations of antibiotics. Moreover, deleting the DNA repair gene recA significantly decreased the frequency of occurrence of CPS-deficient variants during biofilm formation. Thus, IS insertion into the cps operon is an important mechanism for the production of genetic variants during biofilm formation of marine bacteria.

Rechargeable Antibacterial N-Halamine Films with Antifouling Function for Food Packaging Applications

Pathogenic microbial contamination from microbial adhesion and subsequent formation of the biofilm on surfaces of plastic food packaging materials, especially with robust resistance to antimicrobial agents, is a major reason for the outbreak of foodborne infections. Conventional strategies in controlling the contaminations are significantly limited either by biofouling or by the irreversible consumption of antimicrobial agents. Herein, we report a robust methodology to create rechargeable biocidal poly(vinyl alcohol- co-ethylene) films (SBMA@HAF films) with antifouling function via chemically incorporating both N-halamine (HAF) and zwitterionic moieties [[2-(methacryloyloxy)ethyl]dimethyl-(3-sulfopropyl)ammonium hydroxide (SBMA)]. The promise of the design exhibits three features to defeat bacterial contaminations: (i) zwitterionic moieties can effectively reduce bacterial attachment onto the films, (ii) N-halamine with robust rechargeable biocidal activity can rapidly kill any attached bacteria, and (iii) any inactivated bacterial debris can be easily released to avoid biofilm formation due to the superhydrophilicity of the zwitterions. The resulting SBMA@HAF films exhibit integrated properties of high transparency, robust mechanical property, great hydrophilicity, ease of chlorine recharging (>250 ppm), long-term stability, high biocidal efficacy (>99.9999% via contact killing), and promising antifouling functions, which enable the SBMA@HAF films to serve as a biocidal material in food packaging applications.

A multiphase theory for spreading microbial swarms and films

Bacterial swarming and biofilm formation are collective multicellular phenomena through which diverse microbial species colonize and spread over water-permeable tissue. During both modes of surface translocation, fluid uptake and transport play a key role in shaping the overall morphology and spreading dynamics. Here we develop a generalized two-phase thin-film model that couples bacterial growth, extracellular matrix swelling, fluid flow, and nutrient transport to describe the expansion of both highly motile bacterial swarms, and sessile bacterial biofilms. We show that swarm expansion corresponds to steady-state solutions in a nutrient-rich, capillarity dominated regime. In contrast, biofilm colony growth is described by transient solutions associated with a nutrient-limited, extracellular polymer stress driven limit. We apply our unified framework to explain a range of recent experimental observations of steady and unsteady expansion of microbial swarms and biofilms. Our results demonstrate how the physics of flow and transport in slender geometries serve to constrain biological organization in microbial communities.

Bacteria can grow and thrive in many different environments. Although we usually think of bacteria as single-celled organisms, they are not always solitary; they can also form groups containing large numbers of individuals. These aggregates work together as one super-colony, allowing the bacteria to feed and protect themselves more efficiently than they could as isolated cells.

These colonies move and grow in characteristic patterns as they respond to their environment. They can form swarms, like insects, or biofilms, which are thin, flat structures containing both cells and a film-like substance that the cells secrete. Availability of food and water influences the way colonies spread; however, since movement and growth are accompanied by mechanical forces, physical constraints are also important. These include the ability of the bacteria to change the water balance and their local mechanical environment, and the forces they create as they grow and move.

Previous research has used a variety of experimental and theoretical approaches to explain the dynamics of bacterial swarms and biofilms as separate phenomena. However, while they do differ biologically, they also share many physical characteristics.

Srinivasan et al. wanted to exploit these similarities, and use them to predict the growth and shape of biofilms and bacterial swarms under different conditions. To do this, a unified mathematical model for the growth of both swarms and biofilms was created. The model accounted for various factors, such as the transport of nutrients into the colony, the movement of water between the colony and the surface on which it grew, and mechanical changes in the environment (e.g. swelling/softening). The theoretical results were then compared with results from experimental measurements of different bacterial aggregates grown on a soft, hydrated gel. For both swarms and biofilms, the model correctly predicted how fast the colony expanded overall, as well as the shape and location of actively growing regions.

Biofilms and other bacterial aggregates can cause diseases and increase inflammation in tissues, and also hinder industrial processes by damage to submerged surfaces, such as ships and waterpipes. The results described here may open up new approaches to restrict the spreading of bacterial aggregates by focusing on their physical constraints.

Phenotypic Heterogeneity in Bacterial Quorum Sensing Systems

Quorum sensing is usually thought of as a collective behavior in which all members of a population partake. However, over the last decade, several reports of phenotypic heterogeneity in quorum sensing-related gene expression have been put forward, thus challenging this view. In the respective systems, cells of isogenic populations did not contribute equally to autoinducer production or target gene activation, and in some cases, the fraction of contributing cells was modulated by environmental factors. Here, we look into potential origins of these incidences and into how initial cell-to-cell variations might be amplified to establish distinct phenotypic heterogeneity. We furthermore discuss potential functions heterogeneity in bacterial quorum sensing systems could serve: as a preparation for environmental fluctuations (bet hedging), as a more cost-effective way of producing public goods (division of labor), as a loophole for genotypic cooperators when faced with non-contributing mutants (cheat protection), or simply as a means to fine-tune the output of the population as a whole (output modulation). We illustrate certain aspects of these recent developments with the model organisms Sinorhizobium meliloti, Sinorhizobium fredii and Bacillus subtilis, which possess quorum sensing systems of different complexity, but all show phenotypic heterogeneity therein.

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'.