Liquid transport facilitated by channels in Bacillus subtilis biofilms

Beneficial biofilms: A mini-review of strategies to enhance biofilm formation for biotechnological applications

The capacity of bacteria to form biofilms is an important trait for their survival and persistence. Biofilms occur naturally in soil and aquatic environments, are associated with animals ranging from insects to humans and are also found in built environments. They are typically encountered as a challenge in healthcare, food industry, and water supply ecosystems. In contrast, they are known to play a key role in the industrial production of commercially valuable products, environmental remediation processes, and in microbe-catalysed electrochemical systems for energy and resource recovery from wastewater. While there are many recent articles on biofilm control and removal, review articles on promoting biofilm growth for biotechnological applications are unavailable. Biofilm formation is a tightly regulated response to perturbations in the external environment. The multi-stage process, mediated by an assortment of proteins and signaling systems, involves the attachment of bacterial cells to a surface followed by their aggregation in a matrix of extracellular polymeric substances. Biofilms can be promoted by altering the external environment in a controlled manner, supplying molecules that trigger the aggregation of cells and engineering genes associated with biofilm development. This mini-review synthesizes findings from studies that have described such strategies and highlights areas needing research attention.

Three faces of biofilms: a microbial lifestyle, a nascent multicellular organism, and an incubator for diversity

Biofilms are organised heterogeneous assemblages of microbial cells that are encased within a self-produced matrix. Current estimates suggest that up to 80% of bacterial and archaeal cells reside in biofilms. Since biofilms are the main mode of microbial life, understanding their biology and functions is critical, especially as controlling biofilm growth is essential in industrial, infrastructure and medical contexts. Here we discuss biofilms both as collections of individual cells, and as multicellular biological individuals, and introduce the concept of biofilms as unique incubators of diversity for the microbial world.

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.

Nanotechnology for Targeted Detection and Removal of Bacteria: Opportunities and Challenges

The emergence of nanotechnology has created unprecedented hopes for addressing several unmet industrial and clinical issues, including the growing threat so-termed "antibiotic resistance" in medicine. Over the last decade, nanotechnologies have demonstrated promising applications in the identification, discrimination, and removal of a wide range of pathogens. Here, recent insights into the field of bacterial nanotechnology are examined that can substantially improve the fundamental understanding of nanoparticle and bacteria interactions. A wide range of developed nanotechnology-based approaches for bacterial detection and removal together with biofilm eradication are summarized. The challenging effects of nanotechnologies on beneficial bacteria in the human body and environment and the mechanisms of bacterial resistance to nanotherapeutics are also reviewed.

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.

Mechanisms and Impact of Biofilms and Targeting of Biofilms Using Bioactive Compounds-A Review

Biofilms comprising aggregates of microorganisms or multicellular communities have been a major issue as they cause resistance against antimicrobial agents and biofouling. To date, numerous biofilm-forming microorganisms have been identified, which have been shown to result in major effects including biofouling and biofilm-related infections. Quorum sensing (which describes the cell communication within biofilms) plays a vital role in the regulation of biofilm formation and its virulence. As such, elucidating the various mechanisms responsible for biofilm resistance (including quorum sensing) will assist in developing strategies to inhibit and control the formation of biofilms in nature. Employing biological control measures (such as the use of bioactive compounds) in targeting biofilms is of great interest since they naturally possess antimicrobial activity among other favorable attributes and can also possibly act as potent antibiofilm agents. As an effort to re-establish the current notion and understanding of biofilms, the present review discuss the stages involved in biofilm formation, the factors contributing to its development, the effects of biofilms in various industries, and the use of various bioactive compounds and their strategies in biofilm inhibition.

Bacterial Multicellularity: The Biology of Escherichia coli Building Large-Scale Biofilm Communities

Biofilms are a widespread multicellular form of bacterial life. The spatial structure and emergent properties of these communities depend on a polymeric extracellular matrix architecture that is orders of magnitude larger than the cells that build it. Using as a model the wrinkly macrocolony biofilms of Escherichia coli, which contain amyloid curli fibers and phosphoethanolamine (pEtN)-modified cellulose as matrix components, we summarize here the structure, building, and function of this large-scale matrix architecture. Based on different sigma and other transcription factors as well as second messengers, the underlying regulatory network reflects the fundamental trade-off between growth and survival. It controls matrix production spatially in response to long-range chemical gradients, but it also generates distinct patterns of short-range matrix heterogeneity that are crucial for tissue-like elasticity and macroscopic morphogenesis. Overall, these biofilms confer protection and a potential for homeostasis, thereby reducing maintenance energy, which makes multicellularity an emergent property of life itself. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Review on Recent Progress in Magnetic Nanoparticles: Synthesis, Characterization, and Diverse Applications

Diverse applications of nanoparticles (NPs) have revolutionized various sectors in society. In the recent decade, particularly magnetic nanoparticles (MNPs) have gained enormous interest owing to their applications in specialized areas such as medicine, cancer theranostics, biosensing, catalysis, agriculture, and the environment. Controlled surface engineering for the design of multi-functional MNPs is vital for achieving desired application. The MNPs have demonstrated great efficacy as thermoelectric materials, imaging agents, drug delivery vehicles, and biosensors. In the present review, first we have briefly discussed main synthetic methods of MNPs, followed by their characterizations and composition. Then we have discussed the potential applications of MNPs in different with representative examples. At the end, we gave an overview on the current challenges and future prospects of MNPs. This comprehensive review not only provides the mechanistic insight into the synthesis, functionalization, and application of MNPs but also outlines the limits and potential prospects.

Site-directed mutagenesis of the quorum-sensing transcriptional regulator SinR affects the biosynthesis of menaquinone in Bacillus subtilis

Background

Menaquinone (MK-7) is a highly valuable vitamin K₂ produced by Bacillus subtilis. Common static metabolic engineering approaches for promoting the production of MK-7 have been studied previously. However, these approaches caused an accumulation of toxic substances and reduced product yield. Hence, dynamic regulation by the quorum sensing (QS) system is a promising method for achieving a balance between product synthesis and cell growth.

Results

In this study, the QS transcriptional regulator SinR, which plays a significant role in biofilm formation and MK production simultaneously, was selected, and its site-directed mutants were constructed. Among these mutants, sinR knock out strain (KO-SinR) increased the biofilm biomass by 2.8-fold compared to the wild-type. SinR^quad maximized the yield of MK-7 (102.56 ± 2.84 mg/L). To decipher the mechanism of how this mutant regulates MK-7 synthesis and to find additional potential regulators that enhance MK-7 synthesis, RNA-seq was used to analyze expression changes in the QS system, biofilm formation, and MK-7 synthesis pathway. The results showed that the expressions of tapA, tasA and epsE were up-regulated 9.79-, 0.95-, and 4.42-fold, respectively. Therefore, SinR^quad formed more wrinkly and smoother biofilms than BS168. The upregulated expressions of glpF, glpk, and glpD in this biofilm morphology facilitated the flow of glycerol through the biofilm. In addition, NADH dehydrogenases especially sdhA, sdhB, sdhC and glpD, increased 1.01-, 3.93-, 1.87-, and 1.11-fold, respectively. The increased expression levels of NADH dehydrogenases indicated that more electrons were produced for the electron transport system. Electrical hyperpolarization stimulated the synthesis of the electron transport chain components, such as cytochrome c and MK, to ensure the efficiency of electron transfer. Wrinkly and smooth biofilms formed a network of interconnected channels with a low resistance to liquid flow, which was beneficial for the uptake of glycerol, and facilitated the metabolic flux of four modules of the MK-7 synthesis pathway.

Conclusions

In this study, we report for the first time that SinR^quad has significant effects on MK-7 synthesis by forming wrinkly and smooth biofilms, upregulating the expression level of most NADH dehydrogenases, and providing higher membrane potential to stimulate the accumulation of the components in the electron transport system.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01603-5.

Collective colony growth is optimized by branching pattern formation in Pseudomonas aeruginosa

Branching pattern formation is common in many microbes. Extensive studies have focused on addressing how such patterns emerge from local cell-cell and cell-environment interactions. However, little is known about whether and to what extent these patterns play a physiological role. Here, we consider the colonization of bacteria as an optimization problem to find the colony patterns that maximize colony growth efficiency under different environmental conditions. We demonstrate that Pseudomonas aeruginosa colonies develop branching patterns with characteristics comparable to the prediction of modeling; for example, colonies form thin branches in a nutrient-poor environment. Hence, the formation of branching patterns represents an optimal strategy for the growth of Pseudomonas aeruginosa colonies. The quantitative relationship between colony patterns and growth conditions enables us to develop a coarse-grained model to predict diverse colony patterns under more complex conditions, which we validated experimentally. Our results offer new insights into branching pattern formation as a problem-solving social behavior in microbes and enable fast and accurate predictions of complex spatial patterns in branching colonies.

Influence of interaction between surface-modified magnetic nanoparticles with infectious biofilm components in artificial channel digging and biofilm eradication by antibiotics in vitro and in vivo

Magnetic targeting of antimicrobial-loaded magnetic nanoparticles to micrometer-sized infectious biofilms is challenging. Bacterial biofilms possess water channels that facilitate transport of nutrient and metabolic waste products, but are insufficient to allow deep penetration of antimicrobials and bacterial killing. Artificial channel digging in infectious biofilms involves magnetically propelling nanoparticles through a biofilm to dig additional channels to enhance antimicrobial penetration. This does not require precise targeting. However, it is not known whether interaction of magnetic nanoparticles with biofilm components impacts the efficacy of antibiotics after artificial channel digging. Here, we functionalized magnetic-iron-oxide-nanoparticles (MIONPs) with polydopamine (PDA) to modify their interaction with staphylococcal pathogens and extracellular-polymeric-substances (EPS) and relate the interaction with in vitro biofilm eradication by gentamicin after magnetic channel digging. PDA-modified MIONPs had less negative zeta potentials than unmodified MIONPs due to the presence of amino groups and accordingly more interaction with negatively charged staphylococcal cell surfaces than unmodified MIONPs. Neither unmodified nor PDA-modified MIONPs interacted with EPS. Concurrently, use of non-interacting unmodified MIONPs for artificial channel digging in in vitro grown staphylococcal biofilms enhanced the efficacy of gentamicin more than the use of interacting, PDA-modified MIONPs. In vivo experiments in mice using a sub-cutaneous infection model confirmed that non-interacting, unmodified MIONPs enhanced eradication by gentamicin of Staphylococcus aureus Xen36 biofilms about 10 fold. Combined with the high biocompatibility of magnetic nanoparticles, these results form an important step in understanding the mechanism of artificial channel digging in infectious biofilms for enhancing antibiotic efficacy in hard-to-treat infectious biofilms in patients.

New Bacterial Surface Display System Development and Application Based on Bacillus subtilis YuaB Biofilm Component as an Anchoring Motif

Bacterial surface display system has been adopted in various biotechnological applications. In the case of Bacillus subtilis, most of the studies have been developed using spore based surface display system utilizing the inherent rigidity of spore against heat, alkali, and shear stress. But, spore harvest, purification and separation need additional cost and labor. To eliminate this procedure and to use the gram-positive nature of B. subtilis, YuaB, which is one of the major B. subtilis biofilm components and locates in the cell wall, based cell surface display system, is developed. P43 promoter driven overexpression of YuaB-His₆ tag does not hamper bacterial cell growth and promoted biofilm formation of recombinant strain. Flow cytometry of recombinant strain and its protoplast using FITC-Anti His₆ antibody, verified that YuaB locate in plasma membrane and protrude to the outside of cell wall, which means YuaB can be used as very efficient anchoring motif. Using surface expressed YuaB-His₆ tag, removal of divalent metal ion, Cu²⁺ and Ni²⁺, was tried to test its possibility for the environmental application of developed system.

Particle Diffusivity and Free-Energy Profiles in Hydrogels from Time-Resolved Penetration Data

A combined experimental and theoretical method to simultaneously determine diffusivity and free-energy profiles of particles that penetrate into inhomogeneous hydrogel systems is presented. As the only input, arbitrarily normalized concentration profiles from fluorescence intensity data of labeled tracer particles for different penetration times are needed. The method is applied to dextran molecules of varying size that penetrate into hydrogels of polyethylene-glycol chains with different lengths that are covalently cross-linked by hyperbranched polyglycerol hubs. Extracted dextran bulk diffusivities agree well with fluorescence correlation spectroscopy data obtained separately. Empirical scaling laws for dextran diffusivities and free energies inside the hydrogel are identified as a function of the dextran mass. An elastic free-volume model that includes dextran as well as polyethylene-glycol linker flexibility quantitively describes the repulsive dextran-hydrogel interaction free energy, which is of steric origin, and furthermore suggests that the hydrogel mesh-size distribution is rather broad and particle penetration is dominated by large hydrogel pores. Particle penetration into hydrogels for steric particle-hydrogel interactions is thus suggested to be governed by an elastic size-filtering mechanism that involves the tail of the hydrogel pore-size distribution.

Hydrodynamics and surface properties influence biofilm proliferation

A biofilm is an interface-associated colloidal dispersion of bacterial cells and excreted polymers in which microorganisms find protection from their environment. Successful colonization of a surface by a bacterial community is typically a detriment to human health and property. Insight into the biofilm life-cycle provides clues on how their proliferation can be suppressed. In this review, we follow a cell through the cycle of attachment, growth, and departure from a colony. Among the abundance of factors that guide the three phases, we focus on hydrodynamics and stratum properties due to the synergistic effect such properties have on bacteria rejection and removal. Cell motion, whether facilitated by the environment via medium flow or self-actuated by use of an appendage, drastically improves the survivability of a bacterium. Once in the vicinity of a stratum, a single cell is exposed to near-surface interactions, such as van der Waals, electrostatic and specific interactions, similarly to any other colloidal particle. The success of the attachment and the potential for detachment is heavily influenced by surface properties such as material type and topography. The growth of the colony is similarly guided by mainstream flow and the convective transport throughout the biofilm. Beyond the growth phase, hydrodynamic traction forces on a biofilm can elicit strongly non-linear viscoelastic responses from the biofilm soft matter. As the colony exhausts the means of survival at a particular location, a set of trigger signals activates mechanisms of bacterial release, a life-cycle phase also facilitated by fluid flow. A review of biofilm-relevant hydrodynamics and startum properties provides insight into future research avenues.

Diffusion profiles in L. lactis biofilms under different conditions

Despite being an important topic in biofilm research, we still know little about diffusion in biofilms. Emerging biofilms of Lactococcus lactis growing in custom-made flow-cells were monitored and diffusion constants across the height of the biofilms recorded. The biofilms showed different diffusional behavior with regard to flow rate and pH variations, despite growing to similar thickness. At a higher flow rate, the biofilm exhibits slower diffusion compared to the reference cultivation at lower flow rate. By increasing pH, the biofilm exhibited fast growth and little difference in diffusion compared to the reference cultivation. Furthermore, the diffusion inside of the biofilms differed depending on the position in the flow-cell. The present study reveals new insights in how external factors can affect structure and density of biofilms. The method can be reliably used for L. lactis biofilms with a thickness up to 120 μm.

Topography and Expansion Patterns at the Biofilm-Agar Interface in Bacillus subtilis Biofilms

Bacterial biofilms are complex microbial communities that are formed on various natural and synthetic surfaces. In contrast to bacteria in their planktonic form, biofilms are characterized by their relatively low susceptibility to anti-microbial treatments, in part due to limited diffusion throughout the biofilm and the complex distribution of bacterial cells within. The virulence of biofilms is therefore a combination of the structural properties and patterns of adhesion that anchor them to their host surface. In this paper, we analyze the topographical properties of Bacillus subtilis' biofilm-agar interface across different growth conditions. B. subtilis colonies were grown to maturity on biofilm-promoting agar-based media (LBGM), under standard and stress-inducing growth conditions. The biofilm-agar interface of the colony-type biofilms was modeled using confocal microscopy and computational analysis. Profilometry data were obtained from the macrocolonies and used for the analysis of the surface topography as it relates to the adhesion modes present at the biofilm-agar interface. Fluorescent microspheres were utilized to monitor the expansion patterns present at the interface between the macrocolonies and the solid growth medium. Contact surface analysis revealed topographical changes that could have a direct effect on the adhesion strength of the biofilm to its host surface, thus affecting its potential susceptibility to anti-microbial agents. The topographical characteristics of the biofilm-agar interface partially define the macrocolony structure and may have significant effects on bacterial survival and virulence.

Effects of noise and harmonic excitation on the growth of Bacillus subtilis biofilm

We study the dynamic growth behaviors of Bacillus subtilis biofilms by using a stochastic delay differential equation similar to the Mackey-Glass equation. We observe a wealth of dynamic behavior from a mathematical perspective. Firstly, the change of the time delay (i.e. the time that the growth state of the periphery to affect the stress of the interior cells needs and the time required for the stress signal coming from the interior to reach the peripheral cells) and the external excitation (i.e. the change in temperature) frequency will influence the size of Bacillus subtilis biofilm and the collective growth of the cell community. We also found the resonance phenomena in mathematics, which is of great help in understanding the behavior of stress levels in the biofilm periphery. Secondly, the direction of the Hopf bifurcation and the stability of the bifurcating periodic solutions are derived by using the normal form theory and the center manifold reduction. Numerical simulations are carried out to ensure theoretical results. Finally, the effects of noise on stress levels in the biofilm periphery are analyzed and reveal more complex dynamics of the system.

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

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

Emerging Roles of Functional Bacterial Amyloids in Gene Regulation, Toxicity, and Immunomodulation

Bacteria often reside in multicellular communities, called biofilms, held together by an extracellular matrix. In many bacteria, the major proteinaceous component of the biofilm are amyloid fibers. Amyloids are highly stable and structured protein aggregates which were known mostly to be associated with neurodegenerative diseases, such as Alzheimer's, Parkinson's, and Huntington's diseases. In recent years, microbial amyloids were identified also in other species and shown to play major roles in microbial physiology and virulence. For example, amyloid fibers assemble on the bacterial cell surface as a part of the extracellular matrix and are extremely important to the scaffolding and structural integrity of biofilms, which contribute to microbial resilience and resistance. Furthermore, microbial amyloids play fundamental nonscaffold roles that contribute to the development of biofilms underlying numerous persistent infections. Here, we review several nonscaffold roles of bacterial amyloid proteins, including bridging cells during collective migration, acting as regulators of cell fate, as toxins against other bacteria or against host immune cells, and as modulators of the hosts' immune system. These overall points on the complexity of the amyloid fold in encoding numerous activities, which offer approaches for the development of a novel repertoire of antivirulence therapeutics.

Biofilms deform soft surfaces and disrupt epithelia

During chronic infections and in microbiota, bacteria predominantly colonize their hosts as multicellular structures called biofilms. A common assumption is that biofilms exclusively interact with their hosts biochemically. However, the contributions of mechanics, while being central to the process of biofilm formation, have been overlooked as a factor influencing host physiology. Specifically, how biofilms form on soft, tissue-like materials remains unknown. Here, we show that biofilms of the pathogens Vibrio cholerae and Pseudomonas aeruginosa can induce large deformations of soft synthetic hydrogels. Biofilms buildup internal mechanical stress as single cells grow within the elastic matrix. By combining mechanical measurements and mutations in matrix components, we found that biofilms deform by buckling, and that adhesion transmits these forces to their substrates. Finally, we demonstrate that V. cholerae biofilms can generate sufficient mechanical stress to deform and even disrupt soft epithelial cell monolayers, suggesting a mechanical mode of infection.

Intra-colony channels in E. coli function as a nutrient uptake system

The ability of microorganisms to grow as aggregated assemblages has been known for many years, however their structure has remained largely unexplored across multiple spatial scales. The development of the Mesolens, an optical system which uniquely allows simultaneous imaging of individual bacteria over a 36 mm2 field of view, has enabled the study of mature Escherichia coli macro-colony biofilm architecture like never before. The Mesolens enabled the discovery of intra-colony channels on the order of 10 μm in diameter, that are integral to E. coli macro-colony biofilms and form as an emergent property of biofilm growth. These channels have a characteristic structure and re-form after total mechanical disaggregation of the colony. We demonstrate that the channels are able to transport particles and play a role in the acquisition of and distribution of nutrients through the biofilm. These channels potentially offer a new route for the delivery of dispersal agents for antimicrobial drugs to biofilms, ultimately lowering their impact on public health and industry.

THE EVOLVING WRINKLE PATTERN OF THE BACILLUS SUBTILIS BIOFILM PROVIDING MORE LIVING SPACE FOR CELLS

The biofilm wrinkle evolution is the growth mechanism by which bacteria regulate their physiological state in response to the environmental change. We use the parameter of surface complexity to describe different wrinkle patterns. The surface complexity is defined that the biofilm surface area contact with the air is divided by the projected area of the biofilm. We find that the biofilm surface complexity variation is positively proportional to the number of spores. Although each wrinkle pattern has various wrinkle thickness and width, surface complexities of some patterns are almost same, which guarantees cells have enough living space. Through the observation of the growth of the damaged biofilm, we further find that the biofilm expansion along the circumferential direction is faster than that along radial direction, which means that the internal stress along the circumferential direction contributes the wrinkle formation. Our work provides a new perspective to study biofilm morphologies, and relates the morphology evolution with phenotypes in the Bacillus subtilis biofilm.

A Microscopically Motivated Model for Particle Penetration into Swollen Biological Networks

Biological gels (bio-gels) are hydrated polymer networks that serve diverse biological functions, which often lead to intentional or unintentional exposure to particulate matter. In this work, we derive a microscopically motivated framework that enables the investigation of penetration mechanisms into bio-gels. We distinguish between two types of mechanisms: spontaneous (unforced) penetration and forced penetration. Using experimental data available in the literature, we exploit the proposed model to characterize and compare between the microstructures of respiratory, intestinal, and cervicovaginal mucus and two types of biofilms. Next, we investigate the forced penetration process of spherical and ellipsoidal particles into a locally quadrilateral network. The proposed framework can be used to improve and complement the analysis of experimental findings in vitro, ex vivo, and in vivo. Additionally, the insights from this work pave the way towards enhanced designs of nano-medicines and allow the assessment of risk factors related to the nano-pollutants exposure.

Characterizing the structure of aerobic granular sludge using ultra-high field magnetic resonance

Despite aerobic granular sludge wastewater treatment plants operating around the world, our understanding of internal granule structure and its relation to treatment efficiency remains limited. This can be attributed in part to the drawbacks of time-consuming, labor-intensive, and invasive microscopy protocols which effectively restrict samples sizes and may introduce artefacts. Time-domain nuclear magnetic resonance (NMR) allows non-invasive measurements which describe internal structural features of opaque, complex materials like biofilms. NMR was used to image aerobic granules collected from five full-scale wastewater treatment plants in the Netherlands and United States, as well as laboratory granules and control beads. T₁ and T₂ relaxation-weighted images reveal heterogeneous structures that include high- and low-density biofilm regions, water-like voids, and solid-like inclusions. Channels larger than approximately 50 μm and connected to the bulk fluid were not visible. Both cluster and ring-like structures were observed with each granule source having a characteristic structural type. These structures, and their NMR relaxation behavior, were stable over several months of storage. These observations reveal the complex structures within aerobic granules from a range of sources and highlight the need for non-invasive characterization methods like NMR to be applied in the ongoing effort to correlate structure and function.

Bacillus subtilis biofilms characterized as hydrogels. Insights on water uptake and water binding in biofilms

Biofilms are aggregates of cells that form on surfaces or at the air-water interface. Cells in a biofilm are encased in a self-secreted extracellular matrix (ECM) that provides them with mechanical stability and protects them from antibiotic treatment. From a soft matter perspective, biofilms are regarded as colloidal hydrogels, with the cells playing the role of colloids and the ECM compared with a cross-linked hydrogel. Here, we examined whole biofilms of the soil bacterium Bacillus subtilis utilizing methods that are commonly used to characterize hydrogels in order to evaluate the uptake of water and the water properties in the biofilms. Specifically, we studied wild-type as well ECM mutants, lacking the protein TasA and the exopolysaccharide (EPS). We characterized the morphology and mesh size of biofilms using electron microscopy, studied the state of water in the biofilms using differential scanning calorimetry, and finally, we tested the biofilms' swelling properties. Our study revealed that Bacillus subtilis biofilms resemble cross-linked hydrogels in their morphology and swelling properties. Strikingly, we discovered that all the water in biofilms was bound water and there was no free water in the biofilms. Water binding was mostly related with the presence of solutes and much less so with the major ECM components, the protein TasA and the polysaccharide EPS. This study sheds light on water uptake and water binding in biofilms and it is therefore important for the understanding of solute transport and enzymatic function inside biofilms.

Acid soluble extracellular matrix confers structural stability to marine Bacillus haynesii pellicle biofilms

In natural and engineered settings, bacteria predominantly thrive in biofilms, which are complex microbial communities embedded in a self-produced extracellular polymeric substances (EPSs) matrix. Pellicles are complex macroscopic biofilms floating at air-water interface. Though pellicle formation has been studied in detail in Bacillus subtilis, a soil bacterium, it is not reported in aquatic bacteria, which may use pellicle-growth as survival-strategy. This study shows that Bacillus haynesii isolated from a marine environment forms robust pellicle biofilms at air-water interface. B. haynesii pellicles showed complex architecture, involving dense cell-aggregates with interconnecting thread-like structures in an extracellular matrix. In situ staining by Alcian blue, Concanavalin A and ThioflavinT (ThT), respectively, localized acidic polymers, glycoconjugates and amyloid-like fibers in the pellicle. The pellicle was rigid and not disrupted by common EPS extraction protocols. Hence, a set of reagents and conditions were evaluated for solubilizing the EPS and pellicle. Acetic acid was able to effectively solubilize the structural EPS and pellicle structure. Acid soluble structural EPS contained chemical signatures for both proteins and carbohydrates, as revealed by elemental analysis, Fourier Transform Infrared Spectroscopy and Raman Spectroscopy. Ex situ staining of acid soluble EPS by ThT showed recovery of amyloid-forming proteins from pellicle. Results show that structural stability of the pellicle is mainly conferred by amyloid-like fibers of the EPS matrix. The robust pellicle-growth reported here may represent a survival-strategy in the aquatic bacterium. The findings reported here can support future research on biofilm structure, EPS matrix and its formation, which are critical for understanding how microbes thrive in natural and engineered settings.

Exploiting geometric similarity for statistical quantification of fluorescence spatial patterns in bacterial colonies

Background

Currently the combination of molecular tools, imaging techniques and analysis software offer the possibility of studying gene activity through the use of fluorescent reporters and infer its distribution within complex biological three-dimensional structures. For example, the use of Confocal Scanning Laser Microscopy (CSLM) is a regularly-used approach to visually inspect the spatial distribution of a fluorescent signal. Although a plethora of generalist imaging software is available to analyze experimental pictures, the development of tailor-made software for every specific problem is still the most straightforward approach to perform the best possible image analysis. In this manuscript, we focused on developing a simple methodology to satisfy one particular need: automated processing and analysis of CSLM image stacks to generate 3D fluorescence profiles showing the average distribution detected in bacterial colonies grown in different experimental conditions for comparison purposes.

Results

The presented method processes batches of CSLM stacks containing three-dimensional images of an arbitrary number of colonies. Quasi-circular colonies are identified, filtered and projected onto a normalized orthogonal coordinate system, where a numerical interpolation is performed to obtain fluorescence values within a spatially fixed grid. A statistically representative three-dimensional fluorescent pattern is then generated from this data, allowing for standardized fluorescence analysis regardless of variability in colony size. The proposed methodology was evaluated by analyzing fluorescence from GFP expression subject to regulation by a stress-inducible promoter.

Conclusions

This method provides a statistically reliable spatial distribution profile of fluorescence detected in analyzed samples, helping the researcher to establish general correlations between gene expression and spatial allocation under differential experimental regimes. The described methodology was coded into a MATLAB script and shared under an open source license to make it accessible to the whole community.

Cave bacteria-induced amorphous calcium carbonate formation

Amorphous calcium carbonate (ACC) is a precursor of crystalline calcium carbonates that plays a key role in biomineralization and polymorph evolution. Here, we show that several bacterial strains isolated from a Hungarian cave produce ACC and their extracellular polymeric substance (EPS) shields ACC from crystallization. The findings demonstrate that bacteria-produced ACC forms in water-rich environment at room temperature and is stable for at least half year, which is in contrast to laboratory-produced ACC that needs to be stored in a desiccator and kept below 10 °C for avoiding crystallization. The ACC-shielding EPS consists of lipids, proteins, carbohydrates and nucleic acids. In particular, we identified large amount of long-chain fatty acid components. We suggest that ACC could be enclosed in a micella-like formula within the EPS that inhibits water infiltration. As the bacterial cells lyse, the covering protective layer disintegrates, water penetrates and the unprotected ACC grains crystallize to calcite. Our study indicates that bacteria are capable of producing ACC, and we estimate its quantity in comparison to calcite presumably varies up to 20% depending on the age of the colony. Since diverse bacterial communities colonize the surface of cave sediments in temperate zone, we presume that ACC is common in these caves and its occurrence is directly linked to bacterial activity and influences the geochemical signals recorded in speleothems.

Bioinspired Multiscale Wrinkling Patterns on Curved Substrates: An Overview

The surface wrinkling of biological tissues is ubiquitous in nature. Accumulating evidence suggests that the mechanical force plays a significant role in shaping the biological morphologies. Controlled wrinkling has been demonstrated to be able to spontaneously form rich multiscale patterns, on either planar or curved surfaces. The surface wrinkling on planar substrates has been investigated thoroughly during the past decades. However, most wrinkling morphologies in nature are based on the curved biological surfaces and the research of controllable patterning on curved substrates still remains weak. The study of wrinkling on curved substrates is critical for understanding the biological growth, developing three-dimensional (3D) or four-dimensional (4D) fabrication techniques, and creating novel topographic patterns. In this review, fundamental wrinkling mechanics and recent advances in both fabrications and applications of the wrinkling patterns on curved substrates are summarized. The mechanics behind the wrinkles is compared between the planar and the curved cases. Beyond the film thickness, modulus ratio, and mismatch strain, the substrate curvature is one more significant parameter controlling the surface wrinkling. Curved substrates can be both solid and hollow with various 3D geometries across multiple length scales. Up to date, the wrinkling morphologies on solid/hollow core-shell spheres and cylinders have been simulated and selectively produced. Emerging applications of the curved topographic patterns have been found in smart wetting surfaces, cell culture interfaces, healthcare materials, and actuators, which may accelerate the development of artificial organs, stimuli-responsive devices, and micro/nano fabrications with higher dimensions.

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.

Diffusion maps of Bacillus subtilis biofilms via magnetic resonance imaging highlight a complex network of channels

Bacillus subtilis microorganism when cultivated under chemically-defined conditions developed a biofilm with an unusual pattern of wrinkles on the surface. Some questions were raised about whether there was a special function of these wrinkles for the biofilm itself, since they resembled microchannels that could be involved in the transport of nutrients within the biofilm. Since the diffusion is the main mechanism for nutrient transport to biofilm from the medium, the role of these wrinkled structures in the whole diffusion within the biofilm was investigated using diffusion-weighted magnetic resonance imaging (DW-MRI). Data from these diffusion images was used to generate 2D diffusion maps which highlighted the striking channel features of the biofilm surface. The diffusion maps revealed a network of interconnected channels, with self-diffusion coefficients higher in the microchannels than in other regions of the biofilms. Polar plots made from 2D diffusion maps obtained from the plane of the biofilm show an anisotropy of the diffusion inside the microchannels, with the diffusion higher when along the principal direction of the microchannels. These results agree with the model, that the buckling of the biofilm surface from the B. subtilis creates microchannels that can enhance diffusion throughout the biofilm.

Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis biofilms

Stochastic pulsing of gene expression can generate phenotypic diversity in a genetically identical population of cells, but it is unclear whether it has a role in the development of multicellular systems. Here, we show how stochastic pulsing of gene expression enables spatial patterns to form in a model multicellular system, Bacillus subtilis bacterial biofilms. We use quantitative microscopy and time-lapse imaging to observe pulses in the activity of the general stress response sigma factor σ^B in individual cells during biofilm development. Both σ^B and sporulation activity increase in a gradient, peaking at the top of the biofilm, even though σ^B represses sporulation. As predicted by a simple mathematical model, increasing σ^B expression shifts the peak of sporulation to the middle of the biofilm. Our results demonstrate how stochastic pulsing of gene expression can play a key role in pattern formation during biofilm development.

Stochastic pulsing of gene expression can generate phenotypic diversity in a genetically identical population of cells. Here, the authors show that stochastic pulsing in the expression of a sigma factor enables the formation of spatial patterns in a multicellular system, Bacillus subtilis bacterial biofilms.

Incorporating Cellular Stochasticity in Solid-Fluid Mixture Biofilm Models

The dynamics of cellular aggregates is driven by the interplay of mechanochemical processes and cellular activity. Although deterministic models may capture mechanical features, local chemical fluctuations trigger random cell responses, which determine the overall evolution. Incorporating stochastic cellular behavior in macroscopic models of biological media is a challenging task. Herein, we propose hybrid models for bacterial biofilm growth, which couple a two phase solid/fluid mixture description of mechanical and chemical fields with a dynamic energy budget-based cellular automata treatment of bacterial activity. Thin film and plate approximations for the relevant interfaces allow us to obtain numerical solutions exhibiting behaviors observed in experiments, such as accelerated spread due to water intake from the environment, wrinkle formation, undulated contour development, and the appearance of inhomogeneous distributions of differentiated bacteria performing varied tasks.

Peculiarities of biofilm formation by Paracoccus denitrificans

Most bacteria form biofilms, which are thick multicellular communities covered in extracellular matrix. Biofilms can become thick enough to be even observed by the naked eye, and biofilm formation is a tightly regulated process. Paracoccus denitrificans is a non-motile, Gram-negative bacterium that forms a very thin, unique biofilm. A key factor in the biofilm formed by this bacterium is a large surface protein named biofilm-associated protein A (BapA), which was recently reported to be regulated by cyclic diguanosine monophosphate (cyclic-di-GMP or c-di-GMP). Cyclic-di-GMP is a major second messenger involved in biofilm formation in many bacteria. Though cyclic-di-GMP is generally reported as a positive regulatory factor in biofilm formation, it represses biofilm formation in P. denitrificans. Furthermore, quorum sensing (QS) represses biofilm formation in this bacterium, which is also reported as a positive regulator of biofilm formation in most bacteria. The QS signal used in P. denitrificans is hydrophobic and is delivered through membrane vesicles. Studies on QS show that P. denitrificans can potentially form a thick biofilm but maintains a thin biofilm under normal growth conditions. In this review, we discuss the peculiarities of biofilm formation by P. denitrificans with the aim of deepening the overall understanding of bacterial biofilm formation and functions.

Flower-like patterns in multi-species bacterial colonies

Diverse interactions among species within bacterial colonies lead to intricate spatiotemporal dynamics, which can affect their growth and survival. Here, we describe the emergence of complex structures in a colony grown from mixtures of motile and non-motile bacterial species on a soft agar surface. Time-lapse imaging shows that non-motile bacteria 'hitchhike' on the motile bacteria as the latter migrate outward. The non-motile bacteria accumulate at the boundary of the colony and trigger an instability that leaves behind striking flower-like patterns. The mechanism of the front instability governing this pattern formation is elucidated by a mathematical model for the frictional motion of the colony interface, with friction depending on the local concentration of the non-motile species. A more elaborate two-dimensional phase-field model that explicitly accounts for the interplay between growth, mechanical stress from the motile species, and friction provided by the non-motile species, fully reproduces the observed flower-like patterns.

The Adaptive Morphology of Bacillus subtilis Biofilms: A Defense Mechanism against Bacterial Starvation

Biofilms are commonly defined as accumulations of microbes, embedded in a self-secreted, polysaccharide-rich extra-cellular matrix. This study aimed to characterize specific morphological changes that occur in Bacillus subtilis biofilms under nutrient-limiting growth conditions. Under varying levels of nutrient depletion, colony-type biofilms were found to exhibit different rates of spatial expansion and green fluorescent protein production. Specifically, colony-type biofilms grown on media with decreased lysogeny broth content exhibited increased spatial expansion and more stable GFP production over the entire growth period. By modeling the surface morphology of colony-type biofilms using confocal and multiphoton microscopy, we analyzed the appearance of distinctive folds or "wrinkles" that form as a result of lysogeny broth content reduction in the solid agar growth media. When subjected to varying nutritional conditions, the channel-like folds were shown to alter their morphology; growth on nutrient-depleted media was found to trigger the formation of large and straight wrinkles connecting the colony core to its periphery. To test a possible functional role of the formed channels, a fluorescent analogue of glucose was used to demonstrate preferential native uptake of the molecules into the channels' interiors which supports their possible role in the transport of molecules throughout biofilm structures.

Characterization of interface properties of fluids by evaporation of a capillary bridge

The surface properties between two non-miscible fluids are key elements to understand mass transfer, chemistry and bio-chemistry at interfaces. In this paper, surface properties are investigated in evaporating and non-evaporating conditions. A capillary bridge between two large plates (similar to a Hele-Shaw cell) is considered. The temporal evolution of surface forces and mass transfers due to evaporation of the liquid are measured. The force depends on surface properties of the substrate. It is adhesive in the wetting case and repulsive in the non-wetting case. The force is also shown to depend linearly on the volume of the capillary bridge F ∝ V ₀ and inversely to the height of the bridge. Modelling is performed to characterize both surface force and evaporation properties of the capillary bridge. The evaporation is shown to be diffusion driven and is decoupled from the bridge mechanics.

RNA-Dependent Regulation of Virulence in Pathogenic Bacteria

During infection, bacterial pathogens successfully sense, respond and adapt to a myriad of harsh environments presented by the mammalian host. This exquisite level of adaptation requires a robust modulation of their physiological and metabolic features. Additionally, virulence determinants, which include host invasion, colonization and survival despite the host's immune responses and antimicrobial therapy, must be optimally orchestrated by the pathogen at all times during infection. This can only be achieved by tight coordination of gene expression. A large body of evidence implicate the prolific roles played by bacterial regulatory RNAs in mediating gene expression both at the transcriptional and post-transcriptional levels. This review describes mechanistic and regulatory aspects of bacterial regulatory RNAs and highlights how these molecules increase virulence efficiency in human pathogens. As illustrative examples, Staphylococcus aureus, Listeria monocytogenes, the uropathogenic strain of Escherichia coli, Helicobacter pylori, and Pseudomonas aeruginosa have been selected.

Luminescent Nanosensors for Ratiometric Monitoring of Three-Dimensional Oxygen Gradients in Laboratory and Clinical Pseudomonas aeruginosa Biofilms

Bacterial biofilms can form persistent infections on wounds and implanted medical devices and are associated with many chronic diseases, such as cystic fibrosis. These infections are medically difficult to treat, as biofilms are more resistant to antibiotic attack than their planktonic counterparts. An understanding of the spatial and temporal variation in the metabolism of biofilms is a critical component toward improved biofilm treatments. To this end, we developed oxygen-sensitive luminescent nanosensors to measure three-dimensional (3D) oxygen gradients, an application of which is demonstrated here with Pseudomonas aeruginosa biofilms. The method was applied here and improves on traditional one-dimensional (1D) methods of measuring oxygen profiles by investigating the spatial and temporal variation of oxygen concentration when biofilms are challenged with antibiotic attack. We observed an increased oxygenation of biofilms that was consistent with cell death from comparisons with antibiotic kill curves for PAO1. Due to the spatial and temporal nature of our approach, we also identified spatial and temporal inhomogeneities in the biofilm metabolism that are consistent with previous observations. Clinical strains of P. aeruginosa subjected to similar interrogation showed variations in resistance to colistin and tobramycin, which are two antibiotics commonly used to treat P. aeruginosa infections in cystic fibrosis patients.IMPORTANCE Biofilm infections are more difficult to treat than planktonic infections for a variety of reasons, such as decreased antibiotic penetration. Their complex structure makes biofilms challenging to study without disruption. To address this limitation, we developed and demonstrated oxygen-sensitive luminescent nanosensors that can be incorporated into biofilms for studying oxygen penetration, distribution, and antibiotic efficacy-demonstrated here with our sensors monitoring antibiotic impacts on metabolism in biofilms formed from clinical isolates. The significance of our research is in demonstrating not only a nondisruptive method for imaging and measuring oxygen in biofilms but also that this nanoparticle-based sensing platform can be modified to measure many different ions and small molecule analytes.

Factors Controlling Floc Formation and Structure in the Cyanobacterium Synechocystis sp. Strain PCC 6803

Motile strains of the unicellular cyanobacterium Synechocystis sp. strain PCC 6803 readily aggregate into flocs, or floating multicellular assemblages, when grown in liquid culture. As described here, we used confocal imaging to probe the structure of these flocs, and we developed a quantitative assay for floc formation based on fluorescence imaging of 6-well plates. The flocs are formed from strands of linked cells, sometimes packed into dense clusters but also containing voids with very few cells. Cells within the dense clusters show signs of nutrient stress, as judged by the subcellular distribution of green fluorescent protein (GFP)-tagged Vipp1 protein. We analyzed the effects on flocculation of a series of mutations that alter piliation and motility, including Δhfq, ΔpilB1, ΔpilT1, and ΔushA mutations and deletion mutations affecting major and minor pilins. The extent of flocculation is increased in the hyperpiliated ΔpilT1 mutant, but active cycles of pilus extension and retraction are not required for flocculation. Deletion of PilA1, the major subunit of type IV pili, has no effect on flocculation; however, flocculation is lost in mutants lacking an operon coding for the minor pilins PilA9 to -11. Therefore, minor pilins appear crucial for flocculation. We show that flocculation is a tightly regulated process that is promoted by blue light perception by the cyanobacteriochrome Cph2. Floc formation also seems to be a highly cooperative process. A proportion of nonflocculating Δhfq cells can be incorporated into wild-type flocs, but the presence of a high proportion of Δhfq cells disrupts the large-scale architecture of the floc.IMPORTANCE Some bacteria form flocs, which are multicellular floating assemblages of many thousands of cells. Flocs have been relatively little studied compared to surface-adherent biofilms, but flocculation could play many physiological roles, be a crucial factor in marine carbon burial, and enable more efficient biotechnological cell harvesting. We studied floc formation and architecture in the model cyanobacterium Synechocystis sp. strain PCC 6803, using mutants to identify specific cell surface structures required for floc formation. We show that floc formation is regulated by blue and green light perceived by the photoreceptor Cph2. The flocs have a characteristic structure based on strands of linked cells aggregating into dense clusters. Cells within the dense clusters show signs of nutrient stress, pointing to a disadvantage of floc formation.

STUDYING THE INTERNAL STRESS HETEROGENEITY OF THE GROWING BIOFILM BY THE MICROPILLAR DEFORMATION OF THE GROWING SUBSTRATE

The bacterial biofilm is a microbial community in which bacteria are embedded in the extracellular matrix and can also be used as a solid composite. It was found that internal stresses are generated during pellicle growth, which exists between the air and the liquid. But we do not know if there is the internal stress in the biofilm, which exists between the air and the solid, and how does the internal stress evolve and distribute in the growing biofilm. So, in this paper, we make the growing substrate into the micropillar array to grow biofilms, each micropillar has the deformation due to the growing heterogeneity of the biofilm around the micropillar, and we can get the internal stress by measuring each micropillar’s deformation. First, we find that the direction of the internal stress is approximately along the biofilm expansion at the early time, colonies are formed in the biofilm at the later time, which cause the internal stress locally along the expansion of the colony. Second, the internal stress is proportional to the biofilm thickness. Finally, we find that the matrix producing cells contribute more the internal stress, and the internal stress evolving is closely related to the secretion of the extracellular matrix. Form our work, we obtain the distribution of the internal stress direction, we also can use the biofilm thickness, which is easy to measure, express the internal stress approximately, by doing so, we can further study other phenomena of biofilms, such as self-healing and mechanical resistance.

Artificial Channels in an Infectious Biofilm Created by Magnetic Nanoparticles Enhanced Bacterial Killing by Antibiotics

The poor penetrability of many biofilms contributes to the recalcitrance of infectious biofilms to antimicrobial treatment. Here, a new application for the use of magnetic nanoparticles in nanomedicine to create artificial channels in infectious biofilms to enhance antimicrobial penetration and bacterial killing is proposed. Staphylococcus aureus biofilms are exposed to magnetic-iron-oxide nanoparticles (MIONPs), while magnetically forcing MIONP movement through the biofilm. Confocal laser scanning microscopy demonstrates artificial channel digging perpendicular to the substratum surface. Artificial channel digging significantly (4-6-fold) enhances biofilm penetration and bacterial killing efficacy by gentamicin in two S. aureus strains with and without the ability to produce extracellular polymeric substances. Herewith, this work provides a simple, new, and easy way to enhance the eradication of infectious biofilms using MIONPs combined with clinically applied antibiotic therapies.

A Dual-Species Biofilm with Emergent Mechanical and Protective Properties

Many microbes coexist within biofilms, or multispecies communities of cells encased in an extracellular matrix. However, little is known about the microbe-microbe interactions relevant for creating these structures. In this study, we explored a striking dual-species biofilm between Bacillus subtilis and Pantoea agglomerans that exhibited characteristics that were not predictable from previous work examining monoculture biofilms. Coculture wrinkle formation required a P. agglomerans exopolysaccharide as well as the B. subtilis amyloid-like protein TasA. Unexpectedly, other B. subtilis matrix components essential for monoculture biofilm formation were not necessary for coculture wrinkling (e.g., the exopolysaccharide EPS, the hydrophobin BslA, and cell chaining). In addition, B. subtilis cell chaining prevented coculture wrinkling, even though chaining was previously associated with more robust monoculture biofilms. We also observed that increasing the relative proportion of P. agglomerans (which forms completely featureless monoculture colonies) increased coculture wrinkling. Using microscopy and rheology, we observed that these two bacteria assemble into an organized layered structure that reflects the physical properties of both monocultures. This partitioning into distinct regions negatively affected the survival of P. agglomerans while also serving as a protective mechanism in the presence of antibiotic stress. Taken together, these data indicate that studying cocultures is a productive avenue to identify novel mechanisms that drive the formation of structured microbial communities.IMPORTANCE In the environment, many microbes form biofilms. However, the interspecies interactions underlying bacterial coexistence within these biofilms remain understudied. Here, we mimic environmentally relevant biofilms by studying a dual-species biofilm formed between Bacillus subtilis and Pantoea agglomerans and subjecting the coculture to chemical and physical stressors that it may experience in the natural world. We determined that both bacteria contribute structural elements to the coculture, which is reflected in its overall viscoelastic behavior. Existence within the coculture can be either beneficial or detrimental depending on the context. Many of the features and determinants of the coculture biofilm appear distinct from those identified in monoculture biofilm studies, highlighting the importance of characterizing multispecies consortia to understand naturally occurring bacterial interactions.

Time-Dependent Changes in Morphostructural Properties and Relative Abundances of Contributors in Pleurotus ostreatus/Pseudomonas alcaliphila Mixed Biofilms

Pleurotus ostreatus dual biofilms with bacteria are known to be involved in rock phosphate solubilization, endophytic colonization, and even in nitrogen fixation. Despite these relevant implications, no information is currently available on the architecture of P. ostreatus-based dual biofilms. In addition to this, there is a limited amount of information regarding the estimation of the temporal changes in the relative abundances of the partners in such binary systems. To address these issues, a dual biofilm model system with this fungus was prepared by using Pseudomonas alcaliphila 34 as the bacterial partner due to its very fast biofilm-forming ability. The application of the bacterial inoculum to already settled fungal biofilm on a polystyrene surface coated with hydroxyapatite was the most efficient approach to the production of the mixed system the ultrastructure of which was investigated by a multi-microscopy approach. Transmission electron microscopy analysis showed that the adhesion of bacterial cells onto the mycelial cell wall appeared to be mediated by the presence of an abundant layer of extracellular matrix (ECM). Scanning electron microscopy analysis showed that ECM filaments of bacterial origin formed initially a reticular structure that assumed a tabular semblance after 72 h, thus overshadowing the underlying mycelial network. Across the thickness of the mixed biofilms, the presence of an extensive network of channels with large aggregates of viable bacteria located on the edges of their lumina was found by confocal laser scanning microscopy; on the outermost biofilm layer, a significant fraction of dead bacterial cells was evident. Albeit with tangible differences, similar results regarding the estimation of the temporal shifts in the relative abundances of the two partners were obtained by two independent methods, the former relying on qPCR targeting of 16S and 18S rRNA genes and the latter on ester-linked fatty acid methyl esters analysis.

Chemical Transfers Occurring Through Oenococcus oeni Biofilm in Different Enological Conditions

Chardonnay wine malolactic fermentations were carried out to evaluate the chemical transfers occurring at the wood/wine interface in the presence of two different bacterial lifestyles. To do this, Oenococcus oeni was inoculated into must and wine in its planktonic and biofilm lifestyles, whether adhering or not to oak chips, leading to three distinct enological conditions: (i) post-alcoholic fermentation inoculation in wine in the absence of oak chips, (ii) post-alcoholic fermentation inoculation in wine in the presence of oak chips, and (iii) co-inoculation of both Saccharomyces cerevisiae and O. oeni directly in Chardonnay musts in the presence of oak chips. Classical microbiological and physico-chemical parameters analyzed during the fermentation processes confirmed that alcoholic fermentation was completed identically regardless of the enological conditions, and that once O. oeni had acquired a biofilm lifestyle in the presence or absence of oak, malolactic fermentation occurred faster and with better reproducibility compared to planktonic lifestyles. Analyses of volatile components (higher alcohols and wood aromas) and non-volatile components (Chardonnay grape polyphenols) carried out in the resulting wines revealed chemical differences, particularly when bacterial biofilms were present at the wood interface. This study revealed the non-specific trapping activity of biofilm networks in the presence of wood and grape compounds regardless of the enological conditions. Changes of concentrations in higher alcohols reflected the fermentation bioactivity of bacterial biofilms on wood surfaces. These chemical transfers were statistically validated by an untargeted approach using Excitation Emission Matrices of Fluorescence combined with multivariate analysis to discriminate innovative enological practices during winemaking and to provide winemakers with an optical tool for validating the biological and chemical differentiations occurring in wine that result from their decisions.

Effects of food waste addition on biofilm formation and sulfide production in a gravity sewer

The conversion of food waste (FW) into the sewage system is regarded as a promising method of relieving the burden of solid waste management. However, knowledge about its effects on sewer processes is limited, particularly in terms of biofilm formation and sulfide production. In this study, a gravity sewer system was set up to investigate the effects of the addition of FW on biofilm formation, the sulfate-reducing bacteria (SRB) population, and the sulfide production potential. The sewer biofilm characteristics changed with long-term FW addition, and a greater thickness (by 32%), an increased dry density (by 13%), and more extracellular polymeric substance (by 141%) were observed. The thicker and denser biofilm limited oxygen diffusion, enlarged the anaerobic area in the sewer biofilm, promoted an increase in the SRB population, and enhanced the sulfide production potential in the gravity sewer. Substantial differences in the H₂S profiles in the biofilm samples with and without the addition of FW were observed via microelectrode analysis. A model-based investigation of sewer biofilm formation with and without the addition of FW was conducted with a dynamic sewer biofilm model to gain further insights into sewer biofilm processes. The results suggest that the addition of FW can promote sulfide production and SRB growth in a sewer biofilm, which can be significantly affected by the ratio of FW to sewage. It is worth further investigations of the impacts of FW addition on the potential sulfide production in pressure sewers.

Agent-Based Modeling Demonstrates How Local Chemotactic Behavior Can Shape Biofilm Architecture

Bacteria are often found living in aggregated multicellular communities known as biofilms. Biofilms are three-dimensional structures that confer distinct physical and biological properties to the collective of cells living within them. We used agent-based modeling to explore whether local cellular interactions were sufficient to give rise to global structural features of biofilms. Specifically, we asked whether chemorepulsion from a self-produced quorum-sensing molecule, autoinducer-2 (AI-2), was sufficient to recapitulate biofilm growth and cellular organization observed for biofilms of Helicobacter pylori, a common bacterial resident of human stomachs. To carry out this modeling, we modified an existing platform, Individual-based Dynamics of Microbial Communities Simulator (iDynoMiCS), to incorporate three-dimensional chemotaxis, planktonic cells that could join or leave the biofilm structure, and cellular production of AI-2. We simulated biofilm growth of previously characterized H. pylori strains with various AI-2 production and sensing capacities. Using biologically plausible parameters, we were able to recapitulate both the variation in biofilm mass and cellular distributions observed with these strains. Specifically, the strains that were competent to chemotax away from AI-2 produced smaller and more heterogeneously spaced biofilms, whereas the AI-2 chemotaxis-defective strains produced larger and more homogeneously spaced biofilms. The model also provided new insights into the cellular demographics contributing to the biofilm patterning of each strain. Our analysis supports the idea that cellular interactions at small spatial and temporal scales are sufficient to give rise to larger-scale emergent properties of biofilms.IMPORTANCE Most bacteria exist in aggregated, three-dimensional structures called biofilms. Although biofilms play important ecological roles in natural and engineered settings, they can also pose societal problems, for example, when they grow in plumbing systems or on medical implants. Understanding the processes that promote the growth and disassembly of biofilms could lead to better strategies to manage these structures. We had previously shown that Helicobacter pylori bacteria are repulsed by high concentrations of a self-produced molecule, AI-2, and that H. pylori mutants deficient in AI-2 sensing form larger and more homogeneously spaced biofilms. Here, we used computer simulations of biofilm formation to show that local H. pylori behavior of repulsion from high AI-2 could explain the overall architecture of H. pylori biofilms. Our findings demonstrate that it is possible to change global biofilm organization by manipulating local cell behaviors, which suggests that simple strategies targeting cells at local scales could be useful for controlling biofilms in industrial and medical settings.