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

RpoN mediates biofilm formation by directly controlling vps gene cluster and c-di-GMP synthetic metabolism in V. alginolyticus

Vibrio alginolyticus is a prevalent pathogen in both humans and marine species, exhibiting high adaptability to various adverse environmental conditions. Our previous studies have shown that ΔrpoN formed three enhanced biofilm types, including spectacular surface-attached biofilm (SB), scattered pellicle biofilm (PB), and colony rugosity. However, the precise mechanism through which rpoN regulates biofilm formation has remained unclear. Based on the critical role of Vibrio exopolysaccharide (VPS) in biofilm formation, several genes related to the production and regulation of VPS were characterized in V. alginolyticus. Our findings from mutant strains indicated that VPS has complete control over the formation of rugose colony morphology and PB, while it only partially contributes to SB formation. Among the four transcriptional regulators of the vps gene cluster, vpsR and VA3545 act as promoters, whereas VA3546 and VA2703 function as repressors. Through transcriptome analysis and c-di-GMP concentration determination, VA0356 and VA3580 which encoded diguanylate cyclase were found to mediate the ΔrpoN biofilm formation. As a central regulator, rpoN governed biofilm formation through two regulatory pathways. Firstly, it directly bound to the upstream region of VA4206 to regulate the expression of the vps gene cluster (VA4206-VA4196). Secondly, it directly and indirectly modulated c-di-GMP synthesis gene VA3580 and VA0356, respectively, thereby affecting c-di-GMP concentration and subsequently influencing the expression of vps transcription activators vpsR and VA3545. Under conditions promoting SB formation, ΔrpoN was unable to thrive below the liquid level due to significantly reduced activities of three catalytic enzymes (ACK, ADH, and ALDH) involved in pyruvate metabolism, but tended to reproduce in air-liquid interface, a high oxygen niche compared to the liquid phase. In conclusion, both exopolysaccharide synthesis and oxygen-related metabolism contributed to ΔrpoN biofilm formation. The role of RpoN-mediated hypoxic metabolism and biofilm formation were crucial for comprehending the colonization and pathogenicity of V. alginolyticus in hosts, providing a novel target for treating V. alginolyticus in aquatic environments and hosts.

Nanomedicines as disruptors or inhibitors of biofilms: Opportunities in addressing antimicrobial resistance

The problem of antimicrobial resistance (AMR) has caused global concern due to its great threat to human health. Evidences are emerging for a critical role of biofilms, one of the natural protective mechanisms developed by bacteria during growth, in resisting commonly used clinical antibiotics. Advances in nanomedicines with tunable physicochemical properties and unique anti-biofilm mechanisms provide opportunities for solving AMR risks more effectively. In this review, we summarize the five "A" stages (adhesion, amplification, alienation, aging and allocation) of biofilm formation and mechanisms through which they protect the internal bacteria. Aimed at the characteristics of biofilms, we emphasize the design "THAT" principles (targeting, hacking, adhering and transport) of nanomedicines in their interactions with biofilms and internal bacteria. Furthermore, recent progresses in multimodal antibacterial nanomedicines, including biofilms disruption and bactericidal activity, and the types of currently available antibiofilm nanomedicines contained organic and inorganic nanomedicines are outlined and highlighted their potential applications in the development of preclinical research. Last but not least, we offer a perspective for the effectiveness of nanomedicines designed to address AMR and challenges associated with their clinical translation.

Novel two-stage expansion of Streptococcus mutans biofilm supports EPS-targeted prevention strategies for early childhood caries

Early childhood caries (ECC) affects nearly half of preschool children worldwide and characterized by rapid progression across multiple teeth. While Streptococcus mutans (S. mutans) is a keystone species in dental caries, its process for rapid biofilm expansion remains unclear. Using an air-solid interface model simulating the oral environment, we uncovered a novel expansion for S. mutans biofilms. Our findings reveal that S. mutans employs a distinct two-step expansion strategy. Through osmotic pressure, extracellular polymeric substances (EPS) spread and transport bacterial clusters to new sites. Subsequently, the hydroxyapatite surface enables new colony formation. Hydroxyapatite's acid-neutralization properties appear critical for bacterial growth and colonization. Despite successful EPS spreading, environments without hydroxyapatite failed to support new colony formation. These results reveal the unique pattern of rapid ECC progression in sugar-rich environments and establish EPS as a promising therapeutic target, advancing understanding of cariogenic biofilm behavior and preventative strategies for ECC prevention.

The role of substrate mechanics in osmotic biofilm spreading

Bacteria invade surfaces by forming dense colonies encased in a polymer matrix. Successful settlement of founder bacteria, early microcolony development and later macroscopic spreading of these biofilms on surfaces rely on complex physical mechanisms. Recent data show that on soft hydrogels, substrate rigidity is an important determinant for biofilm initiation and spreading, through mostly unknown mechanisms. Using a thermodynamically consistent thin-film approach for suspensions on soft elastic surfaces supplemented with biomass production we investigate in silico the role of substrate softness in the osmotic spreading of biofilms. We show that on soft substrates with an imposed osmotic pressure spreading is considerably slowed down and may be completely halted depending on the biomass production rate. We find that the critical slowing down of biofilm spreading on soft surfaces is caused by a reduced osmotic influx of solvent into the biofilm at the edges, which results from the thermodynamic coupling between substrate deformation and interfacial forces. By linking substrate osmotic pressure and mechanical softness through scaling laws, our simple model semi-quantitatively captures a range of experimentally observed biofilm spreading dynamics on hydrogels with different architectures, underscoring the importance of inherent substrate properties in the spreading process.

Stress adaptation under in vitro evolution influences survival and metabolic phenotypes of clinical and environmental strains of Vibrio cholerae El-Tor

Bacterial adaptation to stress can lead to phenotypic variants with diverse levels of niche competitiveness, pathogenicity, and antimicrobial resistance. In this work, we employed experimental evolution to investigate whether exposure to various stress conditions results in new phenotypic and metabolic properties in clinical and environmental strains of Vibrio cholerae. Our findings revealed the emergence of variants with metabolic and genetic variations and enhanced survival under stress compared to the parental isolates. Phenotypic changes in the evolved variants included colony morphology, biofilm formation, and the appearance of proteolytic and hemolytic activities. The variants demonstrated metabolic changes in the preferred use of carbon, nitrogen, phosphorous, and sulfur substrates, while the genetic changes included single nucleotide polymorphisms (SNPs), breakpoints, translocations, and single nucleotide insertions and deletions. Mutations in genes encoding EAL and HD-GYP domain-containing proteins correlated with increased biofilm formation and different colony morphotypes. The combined analysis of the metabolic and genomic data pointed to pathways implicated in stress survival. The environmental strains were generally more pathogenic than the clinical strains in the Galleria mellonella infection model prior to the experimental evolution, and these differences did not change in the evolved variants. This study highlights the contribution of stress conditions as drivers for the evolution of genetic modifications and metabolic adaptation in V. cholerae, which may explain the continuous evolution of El-Tor biotype strains toward variants with improved survival in the environment.IMPORTANCEHow Vibrio cholerae, the causative agent of cholera, survives during the periods between outbreaks remains a critical question. Using experimental evolution based on serial bacterial passages in culture media mimicking diverse environmental stress conditions, we investigated whether clinical and environmental isolates of V. cholerae develop changes in survival and in their metabolism. The evolved variants exhibited alterations in colony morphology, biofilm formation, and metabolism, including changes in the preferred use of carbon, nitrogen, phosphorous, and sulfur substrates. These changes were accompanied by various genetic modifications, notably in genes encoding second messenger molecules that regulate multiple biochemical pathways implicated in stress survival and increased pathogenic potential. Our results suggest a continuous evolution of V. cholerae strains toward variants displaying increased survival under environmental stress conditions that may also be encountered in the human host.

Substrate stiffness modulates collective colony expansion of the social bacterium Myxococcus xanthus

Many cellular functions depend on the physical properties of the cell's environment. Many bacteria have different types of surface appendages to enable adhesion and motion on various surfaces. Myxococcus xanthus is a social soil bacterium with two distinctly regulated modes of surface motility, termed the social motility mode, driven by type IV pili, and the adventurous motility mode, based on focal adhesion complexes. How bacteria sense different surfaces and subsequently coordinate their collective motion remains largely unclear. Using polyacrylamide hydrogels of tunable stiffness, we found that wild type M. xanthus spreads faster on stiffer substrates. Here, we show that using motility mutants that disrupt adventurous motility suppresses this substrate stiffness response, suggesting focal adhesion-based adventurous motility is substrate stiffness dependent. We also show that modifying surface adhesion by adding adhesive ligands, chitosan, increases the amount of M. xanthus flairs, a characteristic feature of adventurous motility. Taken together, we hypothesize a central role of M. xanthus adventurous motility as a driving mechanism for surface and surface stiffness sensing.

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

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

Disentangling the feedback loops driving spatial patterning in microbial communities

The properties of multispecies biofilms are determined by how species are arranged in space. How these patterns emerge is a complex and largely unsolved problem. Here, we synthesize the known factors affecting pattern formation, identify the interdependencies and feedback loops coupling them, and discuss approaches to disentangle their effects. Finally, we propose an interdisciplinary research program that could create a predictive understanding of pattern formation in microbial communities.

Morphogenesis of confined biofilms: how mechanical interactions determine cellular patterning and global geometry

Biofilms are surface-attached bacterial communities encased within extracellular matrices that play significant roles in health and society and serve as prototypical examples of proliferating active nematics. Recent advances in fluorescence microscopy have facilitated an unprecedented view of biofilm development at the single-cell level, thus providing the opportunity to develop a mechanistic understanding of how biofilm development is influenced by mechanical interactions with the environment. Here, we review recent studies that examined the morphogenesis of Vibrio cholerae biofilms under confinement at both single-cell and continuum levels. We describe how biofilms under different confinement modes-embedded and interstitial-can acquire various global geometries and forms of cell orientational ordering different from those in unconfined biofilms, and we demonstrate how these properties arise from the mechanical interplay between the biofilm and its confining medium. We also discuss how this interplay is fundamentally governed by the extracellular matrix, which facilitates the transmission of mechanical stress from the medium into the biofilm via adhesion and friction, and serves as the key feature that distinguishes biofilms from classical bacterial colonies. These studies lay the groundwork for many potential future directions, all of which will contribute to the establishment of a new "developmental biology" of biofilms.

Surface remodeling and inversion of cell-matrix interactions underlie community recognition and dispersal in Vibrio cholerae biofilms

Biofilms are ubiquitous surface-associated bacterial communities embedded in an extracellular matrix. It is commonly assumed that biofilm cells are glued together by the matrix; however, how the specific biochemistry of matrix components affects the cell-matrix interactions and how these interactions vary during biofilm growth remain unclear. Here, we investigate cell-matrix interactions in Vibrio cholerae, the causative agent of cholera. We combine genetics, microscopy, simulations, and biochemical analyses to show that V. cholerae cells are not attracted to the main matrix component (Vibrio polysaccharide, VPS), but can be attached to each other and to the VPS network through surface-associated VPS and crosslinks formed by the protein Bap1. Downregulation of VPS production and surface trimming by the polysaccharide lyase RbmB cause surface remodeling as biofilms age, shifting the nature of cell-matrix interactions from attractive to repulsive and facilitating cell dispersal as aggregated groups. Our results shed light on the dynamics of diverse cell-matrix interactions as drivers of biofilm development.

Bacteria Colonies Modify Their Shear and Compressive Mechanical Properties in Response to Different Growth Substrates

Bacteria build multicellular communities termed biofilms, which are often encased in a self-secreted extracellular matrix that gives the community mechanical strength and protection against harsh chemicals. How bacteria assemble distinct multicellular structures in response to different environmental conditions remains incompletely understood. Here, we investigated the connection between bacteria colony mechanics and the colony growth substrate by measuring the oscillatory shear and compressive rheology of bacteria colonies grown on agar substrates. We found that bacteria colonies modify their own mechanical properties in response to shear and uniaxial compression in a manner that depends on the concentration of agar in their growth substrate. These findings highlight that mechanical interactions between bacteria and their microenvironments are an important element in bacteria colony development, which can aid in developing strategies to disrupt or reduce biofilm growth.

Nutrient availability influences E. coli biofilm properties and the structure of purified curli amyloid fibers

Bacterial biofilms are highly adaptable and resilient to challenges. Nutrient availability can induce changes in biofilm growth, architecture and mechanical properties. Their extracellular matrix plays an important role in achieving biofilm stability under different environmental conditions. Curli amyloid fibers are critical for the architecture and stiffness of E. coli biofilms, but how this major matrix component adapts to different environmental cues remains unclear. We investigated, for the first time, the effect of nutrient availability both on biofilm material properties and on the structure and properties of curli amyloid fibers extracted from similar biofilms. Our results show that biofilms grown on low nutrient substrates are stiffer, contain more curli fibers, and these fibers present higher β-sheet content and chemical stability. Our multiscale study sheds new light on the relationship between bacterial matrix molecular structure and biofilm macroscopic properties. This knowledge will benefit the development of both anti-biofilm strategies and biofilm-based materials.

Bacterial-host adhesion dominated by collagen subtypes remodelled by osmotic pressure

Environmental osmolarity plays a crucial role in regulating the functions and behaviors of both host cells and pathogens. However, it remains unclear whether and how environmental osmotic stimuli modulate bacterial‒host interfacial adhesion. Using single-cell force spectroscopy, we revealed that the interfacial adhesion force depended nonlinearly on the osmotic prestimulation of host cells but not bacteria. Quantitatively, the adhesion force increased dramatically from 25.98 nN under isotonic conditions to 112.45 or 93.10 nN after the host cells were treated with the hypotonic or hypertonic solution. There was a strong correlation between the adhesion force and the number of host cells harboring adherent/internalized bacteria. We further revealed that enhanced overexpression levels of collagen XV and II were responsible for the increases in interfacial adhesion under hypotonic and hypertonic conditions, respectively. This work provides new opportunities for developing host-directed antibacterial strategies related to interfacial adhesion from a mechanobiological perspective.

Surface remodeling and inversion of cell-matrix interactions underlies community recognition and dispersal in Vibrio cholerae biofilms

Biofilms are ubiquitous surface-associated bacterial communities embedded in an extracellular matrix. While it is commonly assumed that biofilm-dwelling cells are glued together by the matrix, how the cell-matrix interaction depends on the specific biochemistry of the matrix components and how this interaction varies during biofilm growth remains unclear. Here, we investigated cell-matrix interactions in Vibrio cholerae ( Vc ), the causative agent of cholera. We combine genetics, microscopy, simulation, and biochemical tools to show that Vc cells are not attractive to V ibrio p oly s accharide (VPS), the main matrix component, but they can be bridged with each other and to the VPS network through crosslinking by Bap1. Downregulation of VPS and surface trimming by the polysaccharide lyase RbmB cause surface remodeling as biofilms age, shifting the nature of cell-matrix interactions from attractive to repulsive and facilitating cell dispersal as aggregated groups. Our results suggest a new conceptual model in understanding the intricate cell-matrix interaction as the major driver for biofilm development, which is potentially generalizable to certain other biofilm-forming species and exopolysaccharides.

Biofilm dispersal patterns revealed using far-red fluorogenic probes

Bacteria frequently colonize niches by forming multicellular communities called biofilms. To explore new territories, cells exit biofilms through an active process called dispersal. Biofilm dispersal is essential for bacteria to spread between infection sites, yet how the process is executed at the single-cell level remains mysterious due to the limitations of traditional fluorescent proteins, which lose functionality in large, oxygen-deprived biofilms. To overcome this challenge, we developed a cell-labeling strategy utilizing fluorogen-activating proteins (FAPs) and cognate far-red dyes, which remain functional throughout biofilm development, enabling long-term imaging. Using this approach, we characterize dispersal at unprecedented resolution for the global pathogen Vibrio cholerae. We reveal that dispersal initiates at the biofilm periphery and approximately 25% of cells never disperse. We define novel micro-scale patterns that occur during dispersal, including biofilm compression during cell departure and regional heterogeneity in cell motions. These patterns are attenuated in mutants that reduce overall dispersal or that increase dispersal at the cost of homogenizing local mechanical properties. Collectively, our findings provide fundamental insights into the mechanisms of biofilm dispersal, advancing our understanding of how pathogens disseminate. Moreover, we demonstrate the broad applicability of FAPs as a powerful tool for high-resolution studies of microbial dynamics in complex environments.

How bacteria actively use passive physics to make biofilms

Modern molecular microbiology elucidates the organizational principles of bacterial biofilms via detailed examination of the interplay between signaling and gene regulation. A complementary biophysical approach studies the mesoscopic dependencies at the cellular and multicellular levels with a distinct focus on intercellular forces and mechanical properties of whole biofilms. Here, motivated by recent advances in biofilm research and in other, seemingly unrelated fields of biology and physics, we propose a perspective that links the biofilm, a dynamic multicellular organism, with the physical processes occurring in the extracellular milieu. Using Bacillus subtilis as an illustrative model organism, we specifically demonstrate how such a rationale explains biofilm architecture, differentiation, communication, and stress responses such as desiccation tolerance, metabolism, and physiology across multiple scales-from matrix proteins and polysaccharides to macroscopic wrinkles and water-filled channels.

Combinatorial control of Pseudomonas aeruginosa biofilm development by quorum-sensing and nutrient-sensing regulators

The human pathogen Pseudomonas aeruginosa, a leading cause of hospital-acquired infections, inhabits and forms sessile antibiotic-resistant communities called biofilms in a wide range of biotic and abiotic environments. In this study, we examined how two global sensory signaling pathways-the RhlR quorum-sensing system and the CbrA/CbrB nutritional adaptation system-intersect to control biofilm development. Previous work has shown that individually these two systems repress biofilm formation. Here, we used biofilm analyses, RNA-seq, and reporter assays to explore the combined effect of information flow through RhlR and CbrA on biofilm development. We find that the ΔrhlRΔcbrA double mutant exhibits a biofilm morphology and an associated transcriptional response distinct from wildtype and the parent ΔrhlR and ΔcbrA mutants indicating codominance of each signaling pathway. The ΔrhlRΔcbrA mutant gains suppressor mutations that allow biofilm expansion; these mutations map to the crc gene resulting in loss of function of the carbon catabolite repression protein Crc. Furthermore, the combined absence of RhlR and CbrA leads to a drastic reduction in the abundance of the Crc antagonist small RNA CrcZ. Thus, CrcZ acts as the molecular convergence point for quorum- and nutrient-sensing cues. We find that in the absence of antagonism by CrcZ, Crc promotes the expression of biofilm matrix components-Pel exopolysaccharide, and CupB and CupC fimbriae. Therefore, this study uncovers a regulatory link between nutritional adaption and quorum sensing with potential implications for anti-biofilm targeting strategies.IMPORTANCEBacteria often form multicellular communities encased in an extracytoplasmic matrix called biofilms. Biofilm development is controlled by various environmental stimuli that are decoded and converted into appropriate cellular responses. To understand how information from two distinct stimuli is integrated, we used biofilm formation in the human pathogen Pseudomonas aeruginosa as a model and studied the intersection of two global sensory signaling pathways-quorum sensing and nutritional adaptation. Global transcriptomics on biofilm cells and reporter assays suggest parallel regulation of biofilms by each pathway that converges on the abundance of a small RNA antagonist of the carbon catabolite repression protein, Crc. We find a new role of Crc as it modulates the expression of biofilm matrix components in response to the environment. These results expand our understanding of the genetic regulatory strategies that allow P. aeruginosa to successfully develop biofilm communities.

The biophysical basis of bacterial colony growth

Bacteria often attach to surfaces and grow densely-packed communities called biofilms. As biofilms grow, they expand across the surface, increasing their surface area and access to nutrients. Thus, the overall growth rate of a biofilm is directly dependent on its "range expansion" rate. One factor that limits the range expansion rate is vertical growth; at the biofilm edge there is a direct trade-off between horizontal and vertical growth-the more a biofilm grows up, the less it can grow out. Thus, the balance of horizontal and vertical growth impacts the range expansion rate and, crucially, the overall biofilm growth rate. However, the biophysical connection between horizontal and vertical growth remains poorly understood, due in large part to difficulty in resolving biofilm shape with sufficient spatial and temporal resolution from small length scales to macroscopic sizes. Here, we experimentally show that the horizontal expansion rate of bacterial colonies is strongly coupled to vertical expansion via the contact angle at the biofilm edge. Using white light interferometry, we measure the three-dimensional surface morphology of growing colonies, and find that small colonies are surprisingly well-described as spherical caps. At later times, nutrient diffusion and uptake prevent the tall colony center from growing exponentially. However, the colony edge always has a region short enough to grow exponentially; the size and shape of this region, characterized by its contact angle, along with cellular doubling time, determines the range expansion rate. We found that the geometry of the exponentially growing biofilm edge is well-described as a spherical-cap-napkin-ring, i.e., a spherical cap with a cylindrical hole in its center (where the biofilm is too tall to grow exponentially). We derive an exact expression for the spherical-cap-napkin-ring-based range expansion rate; further, to first order, the expansion rate only depends on the colony contact angle, the thickness of the exponentially growing region, and the cellular doubling time. We experimentally validate both of these expressions. In line with our theoretical predictions, we find that biofilms with long cellular doubling times and small contact angles do in fact grow faster than biofilms with short cellular doubling times and large contact angles. Accordingly, sensitivity analysis shows that biofilm growth rates are more sensitive to their contact angles than to their cellular growth rates. Finally, we show that a simple biophysical model connecting vertical and horizontal growth dynamics can reproduce the above phenomena, suggesting that the spherical cap and spherical cap napkin ring shapes emerge due to the biophysical consequences of diffusion-limited growth. Thus, to understand the fitness of a growing biofilm, one must account for its shape, not just its cellular doubling time.

Glyphosate effects on growth and biofilm formation in bee gut symbionts and diverse associated bacteria

Biofilm formation is a common adaptation enabling bacteria to thrive in various environments and withstand external pressures. In the context of host-microbe interactions, biofilms play vital roles in establishing microbiomes associated with animals and plants and are used by opportunistic microbes to facilitate survival within hosts. Investigating biofilm dynamics, composition, and responses to environmental stressors is crucial for understanding microbial community assembly and biofilm regulation in health and disease. In this study, we explore in vivo colonization and in vitro biofilm formation abilities of core members of the honey bee (Apis mellifera) gut microbiota. Additionally, we assess the impact of glyphosate, a widely used herbicide with antimicrobial properties, and a glyphosate-based herbicide formulation on growth and biofilm formation in bee gut symbionts as well as in other biofilm-forming bacteria associated with diverse animals and plants. Our results demonstrate that several strains of core bee gut bacterial species can colonize the bee gut, which probably depends on their ability to form biofilms. Furthermore, glyphosate exposure elicits variable effects on bacterial growth and biofilm formation. In some instances, the effects correlate with the bacteria's ability to encode a susceptible or tolerant version of the enzyme inhibited by glyphosate in the shikimate pathway. However, in other instances, no such correlation is observed. Testing the herbicide formulation further complicates comparisons, as results often diverge from glyphosate exposure alone, suggesting that co-formulants influence bacterial growth and biofilm formation. These findings highlight the nuanced impacts of environmental stressors on microbial biofilms, with both ecological and host health-related implications.

IMPORTANCE

Biofilms are essential for microbial communities to establish and thrive in diverse environments. In the honey bee gut, the core microbiota member Snodgrassella alvi forms biofilms, potentially aiding the establishment of other members and promoting interactions with the host. In this study, we show that specific strains of other core members, including Bifidobacterium, Bombilactobacillus, Gilliamella, and Lactobacillus, also form biofilms in vitro. We then examine the impact of glyphosate, a widely used herbicide that can disrupt the bee microbiota, on bacterial growth and biofilm formation. Our findings demonstrate the diverse effects of glyphosate on biofilm formation, ranging from inhibition to enhancement, reflecting observations in other beneficial or pathogenic bacteria associated with animals and plants. Thus, glyphosate exposure may influence bacterial growth and biofilm formation, potentially shaping microbial establishment on host surfaces and impacting health outcomes.

Inhalable Polymeric Microparticles for Phage and Photothermal Synergistic Therapy of Methicillin-Resistant Staphylococcus aureus Pneumonia

Acute methicillin-resistant Staphylococcus aureus (MRSA) pneumonia is a common and serious lung infection with high morbidity and mortality rates. Due to the increasing antibiotic resistance, toxicity, and pathogenicity of MRSA, there is an urgent need to explore effective antibacterial strategies. In this study, we developed a dry powder inhalable formulation which is composed of porous microspheres prepared from poly(lactic-co-glycolic acid) (PLGA), internally loaded with indocyanine green (ICG)-modified, heat-resistant phages that we screened for their high efficacy against MRSA. This formulation can deliver therapeutic doses of ICG-modified active phages to the deep lung tissue infection sites, avoiding rapid clearance by alveolar macrophages. Combined with the synergistic treatment of phage therapy and photothermal therapy, the formulation demonstrates potent bactericidal effects in acute MRSA pneumonia. With its long-term stability at room temperature and inhalable characteristics, this formulation has the potential to be a promising drug for the clinical treatment of MRSA pneumonia.

Biofilm dispersal patterns revealed using far-red fluorogenic probes

Bacteria frequently colonize niches by forming multicellular communities called biofilms. To explore new territories, cells exit biofilms through an active process called dispersal. Biofilm dispersal is essential for bacteria to spread between infection sites, yet how the process is executed at the single-cell level remains mysterious. Here, we characterize dispersal at unprecedented resolution for the global pathogen Vibrio cholerae. To do so, we first developed a far-red cell-labeling strategy that overcomes pitfalls of fluorescent protein-based approaches. We reveal that dispersal initiates at the biofilm periphery and ~25% of cells never disperse. We define novel micro-scale patterns that occur during dispersal, including biofilm compression and the formation of dynamic channels. These patterns are attenuated in mutants that reduce overall dispersal or that increase dispersal at the cost of homogenizing local mechanical properties. Collectively, our findings provide fundamental insights into the mechanisms of biofilm dispersal, advancing our understanding of how pathogens disseminate.

The dynamic hypoosmotic response of Vibrio cholerae relies on the mechanosensitive channel MscS

Vibrio cholerae adapts to osmotic down-shifts by releasing metabolites through two mechanosensitive (MS) channels, low-threshold MscS and high-threshold MscL. To investigate each channel's contribution to the osmotic response, we generated ΔmscS, ΔmscL, and double ΔmscL ΔmscS mutants in V. cholerae O395. We characterized their tension-dependent activation in patch-clamp, and the millisecond-scale osmolyte release kinetics using a stopped-flow light scattering technique. We additionally generated numerical models describing osmolyte and water fluxes. We illustrate the sequence of events and define the parameters that characterize discrete phases of the osmotic response. Survival is correlated to the extent of cell swelling, the rate of osmolyte release, and the completeness of post-shock membrane resealing. Not only do the two channels interact functionally, but there is also an up-regulation of MscS in the ΔmscL strain, suggesting transcriptional crosstalk. The data reveal the role of MscS in the termination of the osmotic permeability response in V. cholerae.

Colonization and spreading dynamics of Lactiplantibacillus plantarum spoilage isolates on wet surfaces

The role of lactic acid bacteria, including Lactiplantibacillus plantarum, in food spoilage is well recognized, while the behavior of these non-motile bacteria on wet surfaces, such as those encountered in food processing environments has gained relatively little attention. Here, we observed a fast colony spreading of non-motile L. plantarum spoilage isolates on wet surfaces via passive sliding using solid BHI agar media as a model. We investigated the effect of physical properties of agar hydrogel substrate on the surface spreading of six L. plantarum food isolates FBR1-6 and a model strain WCFS1, using increasing concentrations of agar from 0.25 up to 1.5% (w/v). Our results revealed that L. plantarum strain FBR2 spreads significantly on low agar concentration plates compared to the other strains studied here (with a factor of 50-60 folds higher surface coverage), due to the formation of very soft biofilms with high water content that can float on the surface. The fast-spreading of FBR2 colonies is accompanied by an increased number of cells, elongated cell morphology, and a higher amount of extracellular components. Our finding highlights colonization dynamics and the spreading capacity of non-motile bacteria on surfaces that are relatively wet, thereby revealing an additional hitherto unnoticed parameter for non-motile bacteria that may contribute to contamination of foods by fast surface spreading of these bacteria in food processing environments.

Bactericidal Effect and Cytotoxicity of Graphene Oxide/Silver Nanocomposites

To tackle the proliferation of pathogenic microorganisms without relying on antibiotics, innovative materials boasting antimicrobial properties have been engineered. This study focuses on the development of graphene oxide/silver (GO/Ag) nanocomposites, derived from partially reduced graphene oxide adorned with silver nanoparticles. Various nanocomposites with different amounts of silver (GO/Ag-1, GO/Ag-2, GO/Ag-3, and GO/Ag-4) were synthesized, and their antibacterial efficacy was systematically studied. The silver nanoparticles were uniformly deposited on the partially reduced graphene oxide surface, exhibiting spherical morphologies with an average size of 25 nm. The nanocomposites displayed potent antibacterial properties against both gram-positive bacteria (S. aureus and B. subtilis) and gram-negative bacteria (E. coli and S. enterica) as confirmed by minimum inhibition concentration (MIC) studies and time-dependent experiments. The optimal MIC for Gram-positive bacteria was 62.5 μg/mL and for Gram-negative bacteria was 125 μg/mL for the GO/Ag nanocomposites. Bacterial cells that encountered the nanocomposite films exhibited significantly greater inhibitory effects compared to those exposed to conventional antibacterial materials. Furthermore, the cytotoxicity of these nanocomposites was assessed using human epithelial cells (HEC), revealing that GO/Ag-1 and GO/Ag-2 exhibited lower toxicity levels toward HEC and remained compatible even at higher dilution rates. This study underscores the potential of GO/Ag-based nanocomposites as versatile materials for antibacterial applications, particularly as biocompatible wound dressings, offering promising prospects for wound healing and infection control.

Curli Amyloid Fibers in Escherichia coli Biofilms: The Influence of Water Availability on their Structure and Functional Properties

Escherichia coli biofilms consist of bacteria embedded in a self-produced matrix mainly made of protein fibers and polysaccharides. The curli amyloid fibers found in the biofilm matrix are promising versatile building blocks to design sustainable bio-sourced materials. To exploit this potential, it is crucial to understand i) how environmental cues during biofilm growth influence the molecular structure of these amyloid fibers, and ii) how this translates at higher length scales. To explore these questions, the effect of water availability during biofilm growth on the conformation and functions of curli is studied. Microscopy and spectroscopy are used to characterize the amyloid fibers purified from biofilms grown on nutritive substrates with different water contents, and micro-indentation to measure the rigidity of the respective biofilms. The purified curli amyloid fibers present differences in the yield, structure, and functional properties upon biofilm growth conditions. Fiber packing and β-sheets content correlate with their hydrophobicity and chemical stability, and with the rigidity of the biofilms. This study highlights how E. coli biofilm growth conditions impact curli structure and functions contributing to macroscopic materials properties. These fundamental findings infer an alternative strategy to tune curli structure, which will ultimately benefit engineering hierarchical and functional curli-based materials.

Analysis of biofilm expansion rate of Bacillus subtilis (MTC871) on agar substrates with different stiffness

The surface morphology of mature biofilms is heterogeneous and can be divided into concentric rings wrinkles (I), labyrinthine networks wrinkles (II), radial ridges wrinkles (III), and branches wrinkles (IV), according to surface wrinkle structure and distribution characteristics. Due to the wrinkle structures, channels are formed between the biofilm and substrate and transport nutrients, water, metabolic products, etc. We find that expansion rate variations of biofilms growing on substrates with high and low agar concentrations (1.5, 2.0, 2.5 wt.%) are not in the same phase. In the first 3 days' growth, the interaction stress between biofilm and each agar substrate increases, which makes the biofilm expansion rate decreases before wrinkle pattern IV (branches) comes up. After 3 days, in the later growth stage after wrinkle pattern IV appears, the biofilm has larger expansion rate growing on 2.0 wt.% agar concentration, which has the larger wrinkle distance in wrinkle pattern IV reducing energy consumption. Our study shows that the stiff substrate does not always inhibit the biofilm expansion, although it does in the earlier stage; after that, mature biofilms acquire larger expansion rate by adjusting the growth mode through the wrinkle evolution even in nutrient extremely depletion.

Dynamic response of the cell traction force to osmotic shock

Osmotic pressure is vital to many physiological activities, such as cell proliferation, wound healing and disease treatment. However, how cells interact with the extracellular matrix (ECM) when subjected to osmotic shock remains unclear. Here, we visualize the mechanical interactions between cells and the ECM during osmotic shock by quantifying the dynamic evolution of the cell traction force. We show that both hypertonic and hypotonic shocks induce continuous and large changes in cell traction force. Moreover, the traction force varies with cell volume: the traction force increases as cells shrink and decreases as cells swell. However, the direction of the traction force is independent of cell volume changes and is always toward the center of the cell-substrate interface. Furthermore, we reveal a mechanical mechanism in which the change in cortical tension caused by osmotic shock leads to the variation in traction force, which suggests a simple method for measuring changes in cell cortical tension. These findings provide new insights into the mechanical force response of cells to the external environment and may provide a deeper understanding of how the ECM regulates cell structure and function. Traction force exerted by cells under hypertonic and hypotonic shocks. Scale bar, 200 Pa. Color bar, Pa. The black arrows represent the tangential traction forces.

Microstructural and Rheological Transitions in Bacterial Biofilms

Biofilms are aggregated bacterial communities structured within an extracellular matrix (ECM). ECM controls biofilm architecture and confers mechanical resistance against shear forces. From a physical perspective, biofilms can be described as colloidal gels, where bacterial cells are analogous to colloidal particles distributed in the polymeric ECM. However, the influence of the ECM in altering the cellular packing fraction (ϕ) and the resulting viscoelastic behavior of biofilm remains unexplored. Using biofilms of Pantoea sp. (WT) and its mutant (ΔUDP), the correlation between biofilm structure and its viscoelastic response is investigated. Experiments show that the reduction of exopolysaccharide production in ΔUDP biofilms corresponds with a seven-fold increase in ϕ, resulting in a colloidal glass-like structure. Consequently, the rheological signatures become altered, with the WT behaving like a weak gel, whilst the ΔUDP displayed a glass-like rheological signature. By co-culturing the two strains, biofilm ϕ is modulated which allows us to explore the structural changes and capture a change in viscoelastic response from a weak to a strong gel, and to a colloidal glass-like state. The results reveal the role of exopolysaccharide in mediating a structural transition in biofilms and demonstrate a correlation between biofilm structure and viscoelastic response.

Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines

BACKGROUND

Climate change threatens Earth's ice-based ecosystems which currently offer archives and eco-evolutionary experiments in the extreme. Arctic cryopeg brine (marine-derived, within permafrost) and sea ice brine, similar in subzero temperature and high salinity but different in temporal stability, are inhabited by microbes adapted to these extreme conditions. However, little is known about their viruses (community composition, diversity, interaction with hosts, or evolution) or how they might respond to geologically stable cryopeg versus fluctuating sea ice conditions.

RESULTS

We used long- and short-read viromics and metatranscriptomics to study viruses in Arctic cryopeg brine, sea ice brine, and underlying seawater, recovering 11,088 vOTUs (~species-level taxonomic unit), a 4.4-fold increase of known viruses in these brines. More specifically, the long-read-powered viromes doubled the number of longer (≥25 kb) vOTUs generated and recovered more hypervariable regions by >5-fold compared to short-read viromes. Distribution assessment, by comparing to known viruses in public databases, supported that cryopeg brine viruses were of marine origin yet distinct from either sea ice brine or seawater viruses, while 94% of sea ice brine viruses were also present in seawater. A virus-encoded, ecologically important exopolysaccharide biosynthesis gene was identified, and many viruses (~half of metatranscriptome-inferred "active" vOTUs) were predicted as actively infecting the dominant microbial genera Marinobacter and Polaribacter in cryopeg and sea ice brines, respectively. Evolutionarily, microdiversity (intra-species genetic variations) analyses suggested that viruses within the stable cryopeg brine were under significantly lower evolutionary pressures than those in the fluctuating sea ice environment, while many sea ice brine virus-tail genes were under positive selection, indicating virus-host co-evolutionary arms races.

CONCLUSIONS

Our results confirmed the benefits of long-read-powered viromics in understanding the environmental virosphere through significantly improved genomic recovery, expanding viral discovery and the potential for biological inference. Evidence of viruses actively infecting the dominant microbes in subzero brines and modulating host metabolism underscored the potential impact of viruses on these remote and underexplored extreme ecosystems. Microdiversity results shed light on different strategies viruses use to evolve and adapt when extreme conditions are stable versus fluctuating. Together, these findings verify the value of long-read-powered viromics and provide foundational data on viral evolution and virus-microbe interactions in Earth's destabilized and rapidly disappearing cryosphere. Video Abstract.

Diffusiophoretic Particle Penetration into Bacterial Biofilms

Bacterial biofilms are communities of cells adhered to surfaces. These communities represent a predominant form of bacterial life on Earth. A defining feature of a biofilm is the three-dimensional extracellular polymer matrix that protects resident cells by acting as a mechanical barrier to the penetration of chemicals, such as antimicrobials. Beyond being recalcitrant to antibiotic treatment, biofilms are notoriously difficult to remove from surfaces. A promising, but relatively underexplored, approach to biofilm control is to disrupt the extracellular polymer matrix by enabling penetration of particles to increase the susceptibility of biofilms to antimicrobials. In this work, we investigate externally imposed chemical gradients as a mechanism to transport polystyrene particles into bacterial biofilms. We show that preconditioning the biofilm with a prewash step using deionized (DI) water is essential for altering the biofilm so it takes up the micro- and nanoparticles by the application of a further chemical gradient created by an electrolyte. Using different particles and chemicals, we document the transport behavior that leads to particle motion into the biofilm and its further reversal out of the biofilm. Our results demonstrate the importance of chemical gradients in disrupting the biofilm matrix and regulating particle transport in crowded macromolecular environments, and suggest potential applications of particle transport and delivery in other physiological systems.

Mechanobiology as a tool for addressing the genotype-to-phenotype problem in microbiology

The central hypothesis of the genotype-phenotype relationship is that the phenotype of a developing organism (i.e., its set of observable attributes) depends on its genome and the environment. However, as we learn more about the genetics and biochemistry of living systems, our understanding does not fully extend to the complex multiscale nature of how cells move, interact, and organize; this gap in understanding is referred to as the genotype-to-phenotype problem. The physics of soft matter sets the background on which living organisms evolved, and the cell environment is a strong determinant of cell phenotype. This inevitably leads to challenges as the full function of many genes, and the diversity of cellular behaviors cannot be assessed without wide screens of environmental conditions. Cellular mechanobiology is an emerging field that provides methodologies to understand how cells integrate chemical and physical environmental stress and signals, and how they are transduced to control cell function. Biofilm forming bacteria represent an attractive model because they are fast growing, genetically malleable and can display sophisticated self-organizing developmental behaviors similar to those found in higher organisms. Here, we propose mechanobiology as a new area of study in prokaryotic systems and describe its potential for unveiling new links between an organism's genome and phenome.

Density measurements of aerobic granular sludge

Granular sludge processes are frequently used in domestic and industrial wastewater treatment. The granule buoyant density and biomass density are important parameters for the design and operation of granular sludge reactors. Different methods to measure the granule density include the pycnometer method, the Percoll density gradient method, the dextran blue method, and the settling velocity method. In this study, a comparison was made between these four methods to measure granule density for granules from a full-scale granular sludge plant treating domestic sewage. The effect of salinity on granule density was assessed as well. Three out of the four evaluated methods yielded comparable results, with granule buoyant densities between 1025.7 and 1028.1 kg/m³ and granule biomass densities between 71.1 and 71.5 g/L (based on volatile suspended solids (VSS)). The settling velocity method clearly underestimated the granule density, due to the complex relation between granule properties and settling velocity. The pycnometer method was the most precise method, but it was also quite susceptible to bias. The granule buoyant density increased proportionally with salinity, to 1049.2 kg/m³ at 36 g/L salinity. However, the granule biomass density, based on VSS, remained constant. This showed that the granule volume was not affected by salinity and that the buoyant density increase was the result of diffusion of salts into the granule pores. Overall, the granule density can be measured reliably with most methods, as long as the effect of salinity is considered. The results are discussed in light of operational aspects for full-scale granular sludge plants.

Protection of electroactive biofilms against hypersaline shock by quorum sensing

Quorum sensing (QS) is an ideal strategy for boosting the operating performance of electroactive biofilms (EABs), but its potential effects on the protection of electroactive biofilms against environmental shocks (e.g., hypersaline shock) have been rarely revealed. In this study, a QS signaling molecule, the N-(3-oxo-dodecanoyl)-L-homoserine lactone, was employed to promote the anti-shock property of the EABs against extreme saline shock. The maximum current density of the QS-regulated biofilm recovered to 0.17 mA/cm² after 10% salinity exposure, which was much higher than those of its counterparts. The laser scanning confocal microscope confirmed a thicker and more compact biofilm with the presence of the QS signaling molecule. The extracellular polymeric substances (EPS) might play a crucial role in the anti-shocking behaviors, as the polysaccharides in EPS of QS-biofilm had doubled compared to the groups with acylase (the QS quencher). The microbial community analysis indicated that the QS molecule enriched the relative abundance of key species including Pseudomonas sp. and Geobacter sp., which were both beneficial to the stability and electroactivity of the biofilms. The functional genes related to the bacterial community were also up-regulated with the presence of the QS molecule. These results highlight the importance of QS effects in protecting electroactive biofilm under extreme environmental shock, which provides effective and feasible strategies for the future development of microbial electrochemical technologies.

Temperature-specific adaptations and genetic requirements in a biofilm formed by Pseudomonas aeruginosa

Pseudomonas aeruginosa is a gram-negative opportunistic pathogen often associated with nosocomial infections that are made more severe by this bacterium's ability to form robust biofilms. A biofilm is a microbial community encompassing cells embedded within an extracellular polymeric substrate (EPS) matrix that is typically secreted by the encased microbial cells. Biofilm formation is influenced by several environmental cues, and temperature fluctuations are likely to be an important stimulus in the lifecycle of P. aeruginosa as it transitions between life in aquatic or soil environments to sites of infection in the human host. Previous work has demonstrated that human body temperature can induce a shift in the biofilm EPS relative to room temperature growth, resulting in an incorporation of a filamentous phage coat protein into the biofilm EPS. In this study, we sought to identify adaptations enabling biofilm formation at room temperature or temperatures mimicking the natural environment of P. aeruginosa (23°C and 30°C) relative to temperatures mimicking life in the human host (37°C and 40°C). We identified higher biofilm: biomass ratios at lower temperatures on certain substrates, which correlated with a higher relative abundance of apparent polysaccharide EPS content. However, the known genes for EPS polysaccharide production in P. aeruginosa PA14 did not appear to be specifically important for temperature-dependent biofilm adaptation, with the pelB gene appearing to be generally important and the algD gene being generally expendable in all conditions tested. Instead, we were able to identify two previously uncharacterized hypothetical proteins (PA14_50070 and PA14_67550) specifically required for biofilm formation at 23°C and/or 30°C relative to temperatures associated with the human host. These unstudied contributors to biofilm integrity may have been previously overlooked since most P. aeruginosa biofilm studies tend to use 37°C growth temperatures. Overall, our study demonstrates that temperature shifts can have dramatic impacts on biofilm structure and highlights the importance of studying environment-specific adaptations in biofilm physiology.

New Insights into Vibrio cholerae Biofilms from Molecular Biophysics to Microbial Ecology

With the discovery that 48% of cholera infections in rural Bangladesh villages could be prevented by simple filtration of unpurified waters and the detection of Vibrio cholerae aggregates in stools from cholera patients it was realized V. cholerae biofilms had a central function in cholera pathogenesis. We are currently in the seventh cholera pandemic, caused by O1 serotypes of the El Tor biotypes strains, which initiated in 1961. It is estimated that V. cholerae annually causes millions of infections and over 100,000 deaths. Given the continued emergence of cholera in areas that lack access to clean water, such as Haiti after the 2010 earthquake or the ongoing Yemen civil war, increasing our understanding of cholera disease remains a worldwide public health priority. The surveillance and treatment of cholera is also affected as the world is impacted by the COVID-19 pandemic, raising significant concerns in Africa. In addition to the importance of biofilm formation in its life cycle, V. cholerae has become a key model system for understanding bacterial signal transduction networks that regulate biofilm formation and discovering fundamental principles about bacterial surface attachment and biofilm maturation. This chapter will highlight recent insights into V. cholerae biofilms including their structure, ecological role in environmental survival and infection, regulatory systems that control them, and biomechanical insights into the nature of V. cholerae biofilms.

Evolutionary rescue of resistant mutants is governed by a balance between radial expansion and selection in compact populations

Mutation-mediated treatment resistance is one of the primary challenges for modern antibiotic and anti-cancer therapy. Yet, many resistance mutations have a substantial fitness cost and are subject to purifying selection. How emerging resistant lineages may escape purifying selection via subsequent compensatory mutations is still unclear due to the difficulty of tracking such evolutionary rescue dynamics in space and time. Here, we introduce a system of fluorescence-coupled synthetic mutations to show that the probability of evolutionary rescue, and the resulting long-term persistence of drug resistant mutant lineages, is dramatically increased in dense microbial populations. By tracking the entire evolutionary trajectory of thousands of resistant lineages in expanding yeast colonies we uncover an underlying quasi-stable equilibrium between the opposing forces of radial expansion and natural selection, a phenomenon we term inflation-selection balance. Tailored computational models and agent-based simulations corroborate the fundamental nature of the observed effects and demonstrate the potential impact on drug resistance evolution in cancer. The described phenomena should be considered when predicting multi-step evolutionary dynamics in any mechanically compact cellular population, including pathogenic microbial biofilms and solid tumors. The insights gained will be especially valuable for the quantitative understanding of response to treatment, including emerging evolution-based therapy strategies.

Extracellular Vesicles Contribute to Mixed-Fungal Species Competition during Biofilm Initiation

Extracellular vesicles commonly modulate interactions among cellular communities. Recent studies demonstrate that biofilm maturation features, including matrix production, drug resistance, and dispersion, require the delivery of a core protein and carbohydrate vesicle cargo in Candida species. The function of the vesicle cargo for these advanced-phase biofilm characteristics appears to be conserved across Candida species. Mixed-species interactions in mature biofilms indicate that vesicle cargo serves a cooperative role in preserving the community. Here, we define the function of biofilm-associated vesicles for biofilm initiation both within and among five species across the Candida genus. We found similar vesicle cargo functions for several conserved proteins across species, based on the behavior of mutants. Repletion of the adhesion environment with wild-type vesicles returned the community phenotype toward reference levels in intraspecies experiments. However, cross-species vesicle complementation did not restore the wild-type biology and in fact drove the phenotype in the opposite direction for most cross-species interactions. Further study of mixed-species biofilm adhesion and exogenous wild-type vesicle administration similarly demonstrated competitive interactions. Our studies indicate that similar vesicle cargoes contribute to biofilm initiation. However, vesicles from disparate species serve an interference competitive role in mixed-Candida species scenarios. IMPORTANCE Candida species commonly form mixed-species biofilms with other Candida species and bacteria. In the established biofilm state, vesicle cargo delivers public goods to support the mature community. At biofilm initiation, however, vesicles play a negative role in cross-species interactions, presumably to allow species to gain a survival advantage. These observations and recent reports reveal that vesicle cargo has both cooperative and competitive roles among Candida species, depending on the needs of the community biofilm formation.

Density and temperature controlled fluid extraction in a bacterial biofilm is determined by poly-γ-glutamic acid production

A hallmark of microbial biofilms is the self-production of an extracellular molecular matrix that encases the resident cells. The matrix provides protection from the environment, while spatial heterogeneity of gene expression influences the structural morphology and colony spreading dynamics. Bacillus subtilis is a model bacterial system used to uncover the regulatory pathways and key building blocks required for biofilm growth and development. In this work, we report on the emergence of a highly active population of bacteria during the early stages of biofilm formation, facilitated by the extraction of fluid from the underlying agar substrate. We trace the origin of this fluid extraction to the production of poly-γ-glutamic acid (PGA). The flagella-dependent activity develops behind a moving front of fluid that propagates from the boundary of the biofilm towards the interior. The extent of fluid proliferation is controlled by the presence of extracellular polysaccharides (EPS). We also find that PGA production is positively correlated with higher temperatures, resulting in high-temperature mature biofilm morphologies that are distinct from the rugose colony biofilm architecture typically associated with B. subtilis. Although previous reports have suggested that PGA production does not play a major role in biofilm morphology in the undomesticated isolate NCIB 3610, our results suggest that this strain produces distinct biofilm matrices in response to environmental conditions.

Vibrio parahaemolyticus Isolates from Asian Green Mussel: Molecular Characteristics, Virulence and Their Inhibition by Chitooligosaccharide-Tea Polyphenol Conjugates

Fifty isolates of Vibrio parahaemolyticus were tested for pathogenicity, biofilm formation, motility, and antibiotic resistance. Antimicrobial activity of chitooligosaccharide (COS)-tea polyphenol conjugates against all isolates was also studied. Forty-three isolates were randomly selected from 520 isolates from Asian green mussel (Perna viridis) grown on CHROMagarTM Vibrio agar plate. Six isolates were acquired from stool specimens of diarrhea patients. One laboratory strain was V. parahaemolyticus PSU.SCB.16S.14. Among all isolates tested, 12% of V. parahaemolyticus carried the tdh+trh- gene and were positive toward Kanagawa phenomenon test. All of V. parahaemolyticus isolates could produce biofilm and showed relatively strong motile ability. When COS-catechin conjugate (COS-CAT) and COS-epigallocatechin-3-gallate conjugate (COS-EGCG) were examined for their inhibitory effect against V. parahaemolyticus, the former showed the higher bactericidal activity with the MBC value of 1.024 mg/mL against both pathogenic and non-pathogenic strains. Most of the representative Asian green mussel V. parahaemolyticus isolates exhibited high sensitivity to all antibiotics, whereas one isolate showed the intermediate resistance to cefuroxime. However, the representative clinical isolates were highly resistant to nine types of antibiotics and had multiple antibiotic resistance (MAR) index of 0.64. Thus, COS-CAT could be used as potential antimicrobial agent for controlling V. parahaemolyticus-causing disease in Asian green mussel.

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

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

Multispecies biofilm architecture determines bacterial exposure to phages

Numerous ecological interactions among microbes-for example, competition for space and resources, or interaction among phages and their bacterial hosts-are likely to occur simultaneously in multispecies biofilm communities. While biofilms formed by just a single species occur, multispecies biofilms are thought to be more typical of microbial communities in the natural environment. Previous work has shown that multispecies biofilms can increase, decrease, or have no measurable impact on phage exposure of a host bacterium living alongside another species that the phages cannot target. The reasons underlying this variability are not well understood, and how phage-host encounters change within multispecies biofilms remains mostly unexplored at the cellular spatial scale. Here, we study how the cellular scale architecture of model 2-species biofilms impacts cell-cell and cell-phage interactions controlling larger scale population and community dynamics. Our system consists of dual culture biofilms of Escherichia coli and Vibrio cholerae under exposure to T7 phages, which we study using microfluidic culture, high-resolution confocal microscopy imaging, and detailed image analysis. As shown previously, sufficiently mature biofilms of E. coli can protect themselves from phage exposure via their curli matrix. Before this stage of biofilm structural maturity, E. coli is highly susceptible to phages; however, we show that these bacteria can gain lasting protection against phage exposure if they have become embedded in the bottom layers of highly packed groups of V. cholerae in co-culture. This protection, in turn, is dependent on the cell packing architecture controlled by V. cholerae biofilm matrix secretion. In this manner, E. coli cells that are otherwise susceptible to phage-mediated killing can survive phage exposure in the absence of de novo resistance evolution. While co-culture biofilm formation with V. cholerae can confer phage protection to E. coli, it comes at the cost of competing with V. cholerae and a disruption of normal curli-mediated protection for E. coli even in dual species biofilms grown over long time scales. This work highlights the critical importance of studying multispecies biofilm architecture and its influence on the community dynamics of bacteria and phages.

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.

A Torsion-Based Rheometer for Measuring Viscoelastic Material Properties

Rheology and the study of viscoelastic materials are an integral part of engineering and the study of biophysical systems. Tissue rheology is even used in the study of cancer and other diseases. However, the cost of a rheometer is feasible only for colleges, universities, and research laboratories. Even if a rheometer can be purchased, it is bulky and delicately calibrated, limiting its usefulness to the laboratory itself. The design presented here is less than a tenth of the cost of a professional rheometer. The design is also portable, making it the ideal solution to introduce viscoelasticity to high school students as well as for use in the field for obtaining rheological data.

Sequence Polymorphisms in Vibrio cholerae HapR Affect Biofilm Formation under Aerobic and Anaerobic Conditions

We investigated the influence of hapR sequence mutations on the biofilm formation of Vibrio cholerae. In this study, hapR sequences from 85 V. cholerae strains belonging to both pandemic and nonpandemic serogroup were investigated through phylogenetic and sequence analyses. Biofilm formation assays under aerobic and anaerobic conditions were also performed. Sequence variations include single point mutations and insertions/deletions (indels) leading to either truncated or frameshifted HapR. Population structure analysis revealed two major hapR haplogroups, hapR1 and hapR2. Phylogenetic reconstruction displayed a hypothetical ancestral hapR sequence located within the hapR1 haplogroup. Higher numbers of single nucleotide polymorphisms and genetic diversity indices were observed in hapR1, while indels occurred dominantly in hapR2. Aerobic conditions supported more robust biofilms compared to anaerobic conditions. Strains with frameshifted HapR produced the largest amount of biofilm under both oxygen conditions. Quantitative real-time PCR assay confirmed that strains with truncated and frameshifted HapR resulted in a nonfunctional regulator as exhibited by the significantly low hapA gene expression. The present study shows that HapR mutations had a strong influence on biofilm formation and that sequence polymorphisms leading to the disruption of DNA-binding sites or dimerization of the HapR will result in more-robust V. cholerae biofilms. IMPORTANCE Our study revealed an ancestral hapR sequence from a phylogenetic reconstruction that displayed the evolutionary lineage of the nonpandemic to the pandemic strains. Here, we established hapR1 and hapR2 as major hapR haplogroups. The association of the O1 and O139 serogroups with the hapR2 haplogroup demonstrated the distinction of hapR2 in causing cholera infection. Moreover, mutations in this regulator that could lead to the disruption of transcription factor-binding sites or dimerization of the HapR can significantly affect the biofilm formation of V. cholerae. These observations on the relationship of the hapR polymorphism and V. cholerae biofilm formation will provide additional considerations for future biofilm studies and insights into the epidemiology of the pathogen that could ultimately help in the surveillance and mitigation of future cholera disease outbreaks.

Mechanisms Underlying Vibrio cholerae Biofilm Formation and Dispersion

Biofilms are a widely observed growth mode in which microbial communities are spatially structured and embedded in a polymeric extracellular matrix. Here, we focus on the model bacterium Vibrio cholerae and summarize the current understanding of biofilm formation, including initial attachment, matrix components, community dynamics, social interactions, molecular regulation, and dispersal. The regulatory network that orchestrates the decision to form and disperse from biofilms coordinates various environmental inputs. These cues are integrated by several transcription factors, regulatory RNAs, and second-messenger molecules, including bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP). Through complex mechanisms, V. cholerae weighs the energetic cost of forming biofilms against the benefits of protection and social interaction that biofilms provide. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The Xanthomonas citri Reverse Fitness Deficiency by Activating a Novel β-Glucosidase Under Low Osmostress

Bacteria can withstand various types of environmental osmostress. A sudden rise in osmostress affects bacterial cell growth that is countered by activating special genes. The change of osmostress is generally a slow process under the natural environment. However, the collective response of bacteria to low osmostress remains unknown. This study revealed that the deletion of phoP (ΔphoP) from X. citri significantly compromised the growth and virulence as compared to the wild-type strain. Interestingly, low osmostress reversed physiological deficiencies of X. citri phoP mutant related to bacterial growth and virulence. The results also provided biochemical and genetic evidence that the physiological deficiency of phoP mutant can be reversed by low osmostress induced β-glucosidase (BglS) expression. Based on the data, this study proposes a novel regulatory mechanism of a novel β-glucosidase activation in X. citri through low osmostress to reverse the fitness deficiency.