Direct Comparison of Physical Properties of Bacillus subtilis NCIB 3610 and B-1 Biofilms

Facing Foodborne Pathogen Biofilms with Green Antimicrobial Agents: One Health Approach

Food safety is a significant global and local concern due to the threat of foodborne pathogens to public health and food security. Bacterial biofilms are communities of bacteria adhered to surfaces and represent a persistent contamination source in food environments. Their resistance to conventional antimicrobials exacerbates the challenge of eradication, driving the search for alternative strategies to control biofilms. Unconventional or "green" antimicrobial agents have emerged as promising solutions due to their sustainability and effectiveness. These agents include bacteriophages, phage-derived enzymes, plant extracts, and combinations of natural antimicrobials, which offer novel mechanisms for targeting biofilms. This approach aligns with the "One Health" concept, which underscores the interconnectedness of human, animal, and environmental health and advocates for integrated strategies to address public health challenges. Employing unconventional antimicrobial agents to manage bacterial biofilms can enhance food safety, protect public health, and reduce environmental impacts by decreasing reliance on conventional antimicrobials and mitigating antimicrobial resistance. This review explores the use of unconventional antimicrobials to combat foodborne pathogen biofilms, highlighting their mechanisms of action, antibiofilm activities, and the challenges associated with their application in food safety. By addressing these issues from a "One Health" perspective, we aim to demonstrate how such strategies can promote sustainable food safety, improve public health outcomes, and support environmental health, ultimately fostering a more integrated approach to combating foodborne pathogen biofilms.

Resolving spatiotemporal dynamics in bacterial multicellular populations: approaches and challenges

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

Rapid Stiffness Mapping in Soft Biologic Tissues With Micrometer Resolution Using Optical Multifrequency Time-Harmonic Elastography

Rapid mapping of the mechanical properties of soft biological tissues from light microscopy to macroscopic imaging can transform fundamental biophysical research by providing clinical biomarkers to complement in vivo elastography. This work introduces superfast optical multifrequency time-harmonic elastography (OMTHE) to remotely encode surface and subsurface shear wave fields for generating maps of tissue stiffness with unprecedented detail resolution. OMTHE rigorously exploits the space-time propagation characteristics of multifrequency time-harmonic waves to address current limitations of biomechanical imaging and elastography. Key solutions are presented for stimulation, wave decoding, and stiffness reconstruction of shear waves at multiple harmonic frequencies, all tuned to provide consistent stiffness values across resolutions from microns to millimeters. OMTHE's versatility is demonstrated by simulations, phantoms, Bacillus subtilis biofilms, zebrafish embryos and adult zebrafish, reflecting the diversity of biological systems from a mechanics perspective. By zooming in on stiffness details from coarse to finer scales, OMTHE has the potential to advance mechanobiology and offers a way to perform biomechanics-based tissue histology that consistently matches in vivo time-harmonic elastography in patients.

The Epiphyte Bacillus sp. G2112 Produces a Large Diversity of Nobilamide Peptides That Promote Biofilm Formation in Pseudomonads and Mycobacterium aurum

Bacillus sp. G2112, an isolate from cucumber plants that inhibited plant pathogens, produces not only surfactins, iturins, and fengycins common to many Bacillus spp., but also a large variety of N-acyl-(depsi)peptides related to A-3302-B and nobilamides. Four known and fourteen previously unreported nobilamide peptides were characterized using high-resolution mass spectrometry, tandem mass spectrometry, and NMR. The stereochemistry of the amino acids of nobilamide peptides was determined using Marfey's method. The diversity of nobilamide peptides from Bacillus sp. G2112 resulted from the incorporation of different acyl groups and amino acids in the sequence. The peptides occur in linear or cyclic form. In addition, a truncated N-acetylpentapeptide was produced. Agar diffusion assays with selected nobilamide peptides against plant pathogens and human pathogens revealed that A-3302-B and its N-acyl homologs, A-3302-A and nobilamide J, exhibited powerful antibiotic activity (at 5 µg/hole) against Lysinibacillus sphaericus that can cause severe sepsis and bacteremia in patients. Moreover, nobilamide peptides from Bacillus sp. G2112 strongly promoted biofilm formation in the Gram-positive Mycobacterium aurum and Gram-negative pseudomonads. Structurally diverse nobilamides from Bacillus sp. G2112, whether linear or cyclic, penta and heptapeptides, induced biofilm formation, suggesting that the common N-acetyl-D-Phe-D-Leu-L-Phe-D-allo-Thr-L-Val amino acid sequence motif is important for the biofilm-inducing activity.

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.

Titanium complexes affect Bacillus subtilis biofilm formation

Biofilms are surface or interface-associated communities of bacterial cells, embedded in a self-secreted extracellular matrix (ECM). Cells in biofilms are 100-1000 times more resistant to antibiotic treatment relative to planktonic cells due to various reasons, including the ECM acting as a diffusion barrier to antibiotic molecules, the presence of persister cells that divide slowly and are less susceptible to cell-wall targeting drugs, and the activation of efflux pumps in response to antibiotic stress. In this study we tested the effect of two titanium(iv) complexes that have been previously reported as potent and non-toxic anticancer chemotherapeutic agents on Bacillus subtilis cells in culture and in biofilm forming conditions. The Ti(iv) complexes tested, a hexacoordinate diaminobis(phenolato)-bis(alkoxo) complex (phenolaTi) and a bis(isopropoxo) complex of a diaminobis(phenolato) "salan"-type ligand (salanTi), did not affect the growth rate of cells in shaken cultures, however they did affect biofilm formation. Surprisingly, while phenolaTi inhibited biofilm formation, the presence of salanTi induced the formation of more mechanically robust biofilms. Optical microscopy images of biofilm samples in the absence and presence of Ti(iv) complexes suggest that Ti(iv) complexes affect cell-cell and/or cell-matrix adhesion, and that these are interfered with phenolaTi and enhanced by salanTi. Our results highlight the possible effect of Ti(iv) complexes on bacterial biofilms, which is gaining interest in light of the emerging relations between bacteria and cancerous tumors.

Experimental challenges in determining the rheological properties of bacterial biofilms

Bacterial biofilms are communities living in a matrix consisting of self-produced, hydrated extracellular polymeric substances. Most microorganisms adopt the biofilm lifestyle since it protects by conferring resistance to antibiotics and physico-chemical stress factors. Consequently, mechanical removal is often necessary but rendered difficult by the biofilm's complex, viscoelastic response, and adhesive properties. Overall, the mechanical behaviour of biofilms also plays a role in the spreading, dispersal and subsequent colonization of new surfaces. Therefore, the characterization of the mechanical properties of biofilms plays a crucial role in controlling and combating biofilms in industrial and medical environments. We performed in situ shear rheological measurements of Bacillus subtilis biofilms grown between the plates of a rotational rheometer under well-controlled conditions relevant to many biofilm habitats. We investigated how the mechanical history preceding rheological measurements influenced biofilm mechanics and compared these results to the techniques commonly used in the literature. We also compare our results to measurements using interfacial rheology on bacterial pellicles formed at the air-water interface. This work aims to help understand how different growth and measurement conditions contribute to the large variability of mechanical properties reported in the literature and provide a new tool for the rigorous characterization of matrix components and biofilms.

Ultra-lightweight living structural material for enhanced stiffness and environmental sensing

Natural materials such as bone, wood, and bamboo can inspire the fabrication of stiff, lightweight structural materials. Biofilms are one of the most dominant forms of life in nature. However, little is known about their physical properties as a structural material. Here we report an Escherichia coli biofilm having a Young's modulus close to 10 ​GPa with ultra-low density, indicating a high-performance structural material. The mechanical and structural characterization of the biofilm and its components illuminates its adaptable bottom-up design, consisting of lightweight microscale cells covered by a dense network of amyloid nanofibrils on the surface. We engineered E. coli such that 1) carbon nanotubes assembled on the biofilm, enhancing its stiffness to over 30 ​GPa, or that 2) the biofilm sensitively detected heavy metal as an example of an environmental toxin. These demonstrations offer new opportunities for developing responsive living structural materials to serve many real-world applications.

Competition between growth and shear stress drives intermittency in preferential flow paths in porous medium biofilms

Bacteria in porous media, such as soils, aquifers, and filters, often form surface-attached communities known as biofilms. Biofilms are affected by fluid flow through the porous medium, for example, for nutrient supply, and they, in turn, affect the flow. A striking example of this interplay is the strong intermittency in flow that can occur when biofilms nearly clog the porous medium. Intermittency manifests itself as the rapid opening and slow closing of individual preferential flow paths (PFPs) through the biofilm-porous medium structure, leading to continual spatiotemporal rearrangement. The drastic changes to the flow and mass transport induced by intermittency can affect the functioning and efficiency of natural and industrial systems. Yet, the mechanistic origin of intermittency remains unexplained. Here, we show that the mechanism driving PFP intermittency is the competition between microbial growth and shear stress. We combined microfluidic experiments quantifying Bacillus subtilis biofilm formation and behavior in synthetic porous media for different pore sizes and flow rates with a mathematical model accounting for flow through the biofilm and biofilm poroelasticity to reveal the underlying mechanisms. We show that the closing of PFPs is driven by microbial growth, controlled by nutrient mass flow. Opposing this, we find that the opening of PFPs is driven by flow-induced shear stress, which increases as a PFP becomes narrower due to microbial growth, causing biofilm compression and rupture. Our results demonstrate that microbial growth and its competition with shear stresses can lead to strong temporal variability in flow and transport conditions in bioclogged porous media.

Probing the growth and mechanical properties of Bacillus subtilis biofilms through genetic mutation strategies

Bacterial communities form biofilms on various surfaces by synthesizing a cohesive and protective extracellular matrix, and these biofilms protect microorganisms against harsh environmental conditions. Bacillus subtilis is a widely used experimental species, and its biofilms are used as representative models of beneficial biofilms. Specifically, B. subtilis biofilms are known to be rich in extracellular polymeric substances (EPS) and other biopolymers such as DNA and proteins like the amyloid protein TasA and the hydrophobic protein BslA. These materials, which form an interconnected, cohesive, three-dimensional polymer network, provide the mechanical stability of biofilms and mediate their adherence to surfaces among other functional contributions. Here, we explored how genetically-encoded components specifically contribute to regulate the growth status, mechanical properties, and antibiotic resistance of B. subtilis biofilms, thereby establishing a solid empirical basis for understanding how various genetic engineering efforts are likely to affect the structure and function of biofilms. We noted discrete contributions to biofilm morphology, mechanical properties, and survival from major biofilm components such as EPS, TasA and BslA. For example, EPS plays an important role in maintaining the stability of the mechanical properties and the antibiotic resistance of biofilms, whereas BslA has a significant impact on the resolution that can be obtained for printing applications. This work provides a deeper understanding of the internal interactions of biofilm components through systematic genetic manipulations. It thus not only broadens the application prospects of beneficial biofilms, but also serves as the basis of future strategies for targeting and effectively removing harmful biofilms.

Systems view of Bacillus subtilis pellicle development

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

Applications of Antimicrobial Photodynamic Therapy against Bacterial Biofilms

Antimicrobial photodynamic therapy and allied photodynamic antimicrobial chemotherapy have shown remarkable activity against bacterial pathogens in both planktonic and biofilm forms. There has been little or no resistance development against antimicrobial photodynamic therapy. Furthermore, recent developments in therapies that involve antimicrobial photodynamic therapy in combination with photothermal hyperthermia therapy, magnetic hyperthermia therapy, antibiotic chemotherapy and cold atmospheric pressure plasma therapy have shown additive and synergistic enhancement of its efficacy. This paper reviews applications of antimicrobial photodynamic therapy and non-invasive combination therapies often used with it, including sonodynamic therapy and nanozyme enhanced photodynamic therapy. The antimicrobial and antibiofilm mechanisms are discussed. This review proposes that these technologies have a great potential to overcome the bacterial resistance associated with bacterial biofilm formation.

Topography quantifications allow for identifying the contribution of parental strains to physical properties of co-cultured biofilms

Most biofilm research has so far focused on investigating biofilms generated by single bacterial strains. However, such single-species biofilms are rare in nature where bacteria typically coexist with other microorganisms. Although, from a biological view, the possible interactions occurring between different bacteria are well studied, little is known about what determines the material properties of a multi-species biofilm. Here, we ask how the co-cultivation of two B. subtilis strains affects certain important biofilm properties such as surface topography and wetting behavior. We find that, even though each daughter colony typically resembles one of the parent colonies in terms of morphology and wetting, it nevertheless exhibits a significantly different surface topography. Yet, this difference is only detectable via a quantitative metrological analysis of the biofilm surface. Furthermore, we show that this difference is due to the presence of bacteria belonging to the 'other' parent strain, which does not dominate the biofilm features. The findings presented here may pinpoint new strategies for how biofilms with hybrid properties could be generated from two different bacterial strains. In such engineered biofilms, it might be possible to combine desired properties from two strains by co-cultivation.

Machine Learning Approach to Analyze the Surface Properties of Biological Materials

Similar to how CRISPR has revolutionized the field of molecular biology, machine learning may drastically boost research in the area of materials science. Machine learning is a fast-evolving method that allows for analyzing big data and unveiling correlations that otherwise would remain undiscovered. It may hold invaluable potential to engineer novel functional materials with desired properties, a field, which is currently limited by time-consuming trial and error approaches and our limited understanding of how different material properties depend on each other. Here, we apply machine learning algorithms to classify complex biological materials based on their microtopography. With this approach, the surfaces of different variants of biofilms and plant leaves can not only be distinguished but also correctly classified according to their wettability. Furthermore, an importance ranking provided by one of the algorithms allows us to identify those surface features that are critical for a successful sample classification. Our study exemplifies how machine learning can contribute to the analysis and categorization of complex surfaces, a tool, which can be highly useful for other areas of materials science, such as damage assessment as well as adhesion or friction studies.

Biofilm hydrophobicity in environmental isolates of Bacillus subtilis

Biofilms are communities of bacteria that are attached to a surface and surrounded by an extracellular matrix. The extracellular matrix protects the community from stressors in the environment, making biofilms robust. The Gram-positive soil bacterium Bacillus subtilis, particularly the isolate NCIB 3610, is widely used as a model for studying biofilm formation. B. subtilis NCIB 3610 forms colony biofilms that are architecturally complex and highly hydrophobic. The hydrophobicity is linked, in part, to the localisation of the protein BslA at the surface of the biofilm, which provides the community with increased resistance to biocides. As most of our knowledge about B. subtilis biofilm formation comes from one isolate, it is unclear if biofilm hydrophobicity is a widely distributed feature of the species. To address this knowledge gap, we collated a library of B. subtilis soil isolates and acquired their whole genome sequences. We used our novel isolates to examine biofilm hydrophobicity and found that, although BslA is encoded and produced by all isolates in our collection, hydrophobicity is not a universal feature of B. subtilis colony biofilms. To test whether the matrix exopolymer poly γ-glutamic acid could be masking hydrophobicity in our hydrophilic isolates, we constructed deletion mutants and found, contrary to our hypothesis, that the presence of poly γ-glutamic acid was not the reason for the observed hydrophilicity. This study highlights the natural variation in the properties of biofilms formed by different isolates and the importance of using a more diverse range of isolates as representatives of a species.

Bacillus subtilis biofilm formation and social interactions

Biofilm formation is a process in which microbial cells aggregate to form collectives that are embedded in a self-produced extracellular matrix. Bacillus subtilis is a Gram-positive bacterium that is used to dissect the mechanisms controlling matrix production and the subsequent transition from a motile planktonic cell state to a sessile biofilm state. The collective nature of life in a biofilm allows emergent properties to manifest, and B. subtilis biofilms are linked with novel industrial uses as well as probiotic and biocontrol processes. In this Review, we outline the molecular details of the biofilm matrix and the regulatory pathways and external factors that control its production. We explore the beneficial outcomes associated with biofilms. Finally, we highlight major advances in our understanding of concepts of microbial evolution and community behaviour that have resulted from studies of the innate heterogeneity of biofilms.

Swarming bacteria undergo localized dynamic phase transition to form stress-induced biofilms

Self-organized multicellular behaviors enable cells to adapt and tolerate stressors to a greater degree than isolated cells. However, whether and how cellular communities alter their collective behaviors adaptively upon exposure to stress is largely unclear. Here, we investigate this question using Bacillus subtilis, a model system for bacterial multicellularity. We discover that, upon exposure to a spatial gradient of kanamycin, swarming bacteria activate matrix genes and transit to biofilms. The initial stage of this transition is underpinned by a stress-induced multilayer formation, emerging from a biophysical mechanism reminiscent of motility-induced phase separation (MIPS). The physical nature of the process suggests that stressors which suppress the expansion of swarms would induce biofilm formation. Indeed, a simple physical barrier also induces a swarm-to-biofilm transition. Based on the gained insight, we propose a strategy of antibiotic treatment to inhibit the transition from swarms to biofilms by targeting the localized phase transition.

The Exo-Polysaccharide Component of Extracellular Matrix is Essential for the Viscoelastic Properties of Bacillus subtilis Biofilms

Bacteria are known to form biofilms on various surfaces. Biofilms are multicellular aggregates, held together by an extracellular matrix, which is composed of biological polymers. Three principal components of the biofilm matrix are exopolysaccharides (EPS), proteins, and nucleic acids. The biofilm matrix is essential for biofilms to remain organized under mechanical stress. Thanks to their polymeric nature, biofilms exhibit both elastic and viscous mechanical characteristics; therefore, an accurate mechanical description needs to take into account their viscoelastic nature. Their viscoelastic properties, including during their growth dynamics, are crucial for biofilm survival in many environments, particularly during infection processes. How changes in the composition of the biofilm matrix affect viscoelasticity has not been thoroughly investigated. In this study, we used interfacial rheology to study the contribution of the EPS component of the matrix to viscoelasticity of Bacillus subtilis biofilms. Two strategies were used to specifically deplete the EPS component of the biofilm matrix, namely (i) treatment with sub-lethal doses of vitamin C and (ii) seamless inactivation of the eps operon responsible for biosynthesis of the EPS. In both cases, the obtained results suggest that the EPS component of the matrix is essential for maintaining the viscoelastic properties of bacterial biofilms during their growth. If the EPS component of the matrix is depleted, the mechanical stability of biofilms is compromised and the biofilms become more susceptible to eradication by mechanical stress.

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.

Nonlinear rheological characteristics of single species bacterial biofilms

Bacterial biofilms in natural and artificial environments perform a wide array of beneficial or detrimental functions and exhibit resistance to physical as well as chemical perturbations. In dynamic environments, where periodic or aperiodic flows over surfaces are involved, biofilms can be subjected to large shear forces. The ability to withstand these forces, which is often attributed to the resilience of the extracellular matrix. This attribute of the extracellular matrix is referred to as viscoelasticity and is a result of self-assembly and cross-linking of multiple polymeric components that are secreted by the microbes. We aim to understand the viscoelastic characteristic of biofilms subjected to large shear forces by performing Large Amplitude Oscillatory Shear (LAOS) experiments on four species of bacterial biofilms: Bacillus subtilis, Comamonas denitrificans, Pseudomonas fluorescens and Pseudomonas aeruginosa. We find that nonlinear viscoelastic measures such as intracycle strain stiffening and intracycle shear thickening for each of the tested species, exhibit subtle or distinct differences in the plot of strain amplitude versus frequency (Pipkin diagram). The biofilms also exhibit variability in the onset of nonlinear behaviour and energy dissipation characteristics, which could be a result of heterogeneity of the extracellular matrix constituents of the different biofilms. The results provide insight into the nonlinear rheological behaviour of biofilms as they are subjected to large strains or strain rates; a situation that is commonly encountered in nature, but rarely investigated.

Chelate chemistry governs ion-specific stiffening of Bacillus subtilis B-1 and Azotobacter vinelandii biofilms

Unwanted formation of bacterial biofilms can cause problems in both the medical sector and industrial settings. However, removing them from surfaces remains an ongoing challenge since biofilm bacteria efficiently protect themselves from external influences such as mechanical shear forces by embedding themselves into a matrix of extracellular polymeric substances. Here, we discuss microscopic principles, which are responsible for alterations in the viscoelastic properties of biofilms upon contact with metal ions. We suggest that it is a combination of mainly two parameters, that decides if biofilm stiffening occurs or not: the ion size and the detailed configuration of polyanionic macromolecules from the biofilm matrix. Our results provide new insights in the molecular mechanisms that govern the mechanical properties of biofilms. Also, they indicate that hydrogels comprising purified biopolymers can serve as suitable model systems to reproduce certain aspects of biofilm mechanics - provided that the correct biopolymer is chosen.

Biofilm architecture: An emerging synthetic biology target

Synthetic biologists are exploiting biofilms as an effective mechanism for producing various outputs. Metabolic optimization has become commonplace as a method of maximizing system output. In addition to production pathways, the biofilm itself contributes to the efficacy of production. The purpose of this review is to highlight opportunities that might be leveraged to further enhance production in preexisting biofilm production systems. These opportunities may be used with previously established production systems as a method of improving system efficiency further. This may be accomplished through the reduction in the cost of establishing and maintaining biofilms, and maintenance of the enhancement of product yield per unit of time, per unit of area, or per unit of required input.

ABC transporter genes ABC-C6 and ABC-G33 alter plant-microbe-parasite interactions in the rhizosphere

Plants are master regulators of rhizosphere ecology, secreting a complex mixture of compounds into the soil, collectively termed plant root exudate. Root exudate composition is highly dynamic and functional, mediating economically important interactions between plants and a wide range of soil organisms. Currently we know very little about the molecular basis of root exudate composition, which is a key hurdle to functional exploitation of root exudates for crop improvement. Root expressed transporters modulate exudate composition and could be manipulated to develop beneficial plant root exudate traits. Using Virus Induced Gene silencing (VIGS), we demonstrate that knockdown of two root-expressed ABC transporter genes in tomato cv. Moneymaker, ABC-C6 and ABC-G33, alters the composition of semi-volatile compounds in collected root exudates. Root exudate chemotaxis assays demonstrate that knockdown of each transporter gene triggers the repulsion of economically relevant Meloidogyne and Globodera spp. plant parasitic nematodes, which are attracted to control treatment root exudates. Knockdown of ABC-C6 inhibits egg hatching of Meloidogyne and Globodera spp., relative to controls. Knockdown of ABC-G33 has no impact on egg hatching of Meloidogyne spp. but has a substantial inhibitory impact on egg hatching of G. pallida. ABC-C6 knockdown has no impact on the attraction of the plant pathogen Agrobacterium tumefaciens, or the plant growth promoting Bacillus subtilis, relative to controls. Silencing ABC-G33 induces a statistically significant reduction in attraction of B. subtilis, with no impact on attraction of A. tumefaciens. By inoculating selected differentially exuded compounds into control root exudates, we demonstrate that hexadecaonic acid and pentadecane are biologically relevant parasite repellents. ABC-C6 represents a promising target for breeding or biotechnology intervention strategies as gene knockdown leads to the repulsion of economically important plant parasites and retains attraction of the beneficial rhizobacterium B. subtilis. This study exposes the link between ABC transporters, root exudate composition, and ex planta interactions with agriculturally and economically relevant rhizosphere organisms, paving the way for new approaches to rhizosphere engineering and crop protection.

Biopolymer-enriched B. subtilis NCIB 3610 biofilms exhibit increased erosion resistance

The erosion resistance of bacterial biofilms can be a double-edged sword: it hampers the removal of undesired biofilms in biomedical settings, but it is necessary for beneficial biofilms to be used in aqueous environments for biotechnological applications. Whether or not a bacterial biofilm exhibits this material property depends on the bacterial species and the detailed composition of the biofilm matrix. Here, we demonstrate how the erosion resistance of B. subtilis NCIB 3610 biofilms can be enhanced by integrating foreign (bio)polymers into the matrix during biofilm growth. As a result of this artificial macromolecule addition, the engineered biofilm colonies show changes in their surface topography which, in turn, cause an alteration in the mode of surface superhydrophobicity. Surprisingly, the viscoelastic properties and permeability of the biofilms towards antibiotics remain unaffected. The method introduced here may present a promising strategy for engineering beneficial biofilms such, that they become more stable towards shear forces caused by flowing water but, at the same time, remain permeable to nutrients or other molecules.

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.

Testing Anti-Biofilm Polymeric Surfaces: Where to Start?

Present day awareness of biofilm colonization on polymeric surfaces has prompted the scientific community to develop an ever-increasing number of new materials with anti-biofilm features. However, compared to the large amount of work put into discovering potent biofilm inhibitors, only a small number of papers deal with their validation, a critical step in the translation of research into practical applications. This is due to the lack of standardized testing methods and/or of well-controlled in vivo studies that show biofilm prevention on polymeric surfaces; furthermore, there has been little correlation with the reduced incidence of material deterioration. Here an overview of the most common methods for studying biofilms and for testing the anti-biofilm properties of new surfaces is provided.

Viscoelastic response of Escherichia coli biofilms to genetically altered expression of extracellular matrix components

How the viscoelastic properties of the extracellular matrix affect the various biological functions conferred by biofilms is an important question in microbiology. In this study, the viscoelastic response of Escherichia coli biofilms to the genetically altered expression of extracellular matrix components was studied. Biofilms of the wild type E. coli MG1655 and its mutant strains producing different amounts of extracellular matrix components (curli, colanic acid, and poly-β-1,6-N-acetyl-d-glucosamine) were used to examine the viscoelastic behavior of biofilms grown at the solid-atmosphere interface. The results suggest that the presence of curli proteins dominates biofilm mechanical behavior. The rheological data indicate that the cohesive energy of the biofilm was the highest in the wild type strain. The results demonstrate the importance of extracellular matrix composition for biofilm mechanical properties. We propose that by genetically altering the expression of extracellular matrix polymers, bacteria are able to modulate the mechanical properties of their local environment in accordance with bulk environmental conditions.

Importance of the biofilm matrix for the erosion stability of Bacillus subtilis NCIB 3610 biofilms

Erosion of bacterial biofilms is dependent on the composition of the biofilm matrix and the surrounding chemical environment.

Topographical alterations render bacterial biofilms susceptible to chemical and mechanical stress

Treatment with concentrated ethanol, saline or glucose solutions smoothens biofilm surface topography and initially superhydrophobic/omniphobic biofilms are rendered hydrophilic.

Programmable and printable Bacillus subtilis biofilms as engineered living materials

Bacterial biofilms can be programmed to produce living materials with self-healing and evolvable functionalities. However, the wider use of artificial biofilms has been hindered by limitations on processability and functional protein secretion capacity. We describe a highly flexible and tunable living functional materials platform based on the TasA amyloid machinery of the bacterium Bacillus subtilis. We demonstrate that genetically programmable TasA fusion proteins harboring diverse functional proteins or domains can be secreted and can assemble into diverse extracellular nano-architectures with tunable physicochemical properties. Our engineered biofilms have the viscoelastic behaviors of hydrogels and can be precisely fabricated into microstructures having a diversity of three-dimensional (3D) shapes using 3D printing and microencapsulation techniques. Notably, these long-lasting and environmentally responsive fabricated living materials remain alive, self-regenerative, and functional. This new tunable platform offers previously unattainable properties for a variety of living functional materials having potential applications in biomaterials, biotechnology, and biomedicine.

Evolution of exploitative interactions during diversification in Bacillus subtilis biofilms

Microbial biofilms are tightly packed, heterogeneous structures that serve as arenas for social interactions. Studies on Gram negative models reveal that during evolution in structured environments like biofilms, isogenic populations commonly diversify into phenotypically and genetically distinct variants. These variants can settle in alternative biofilm niches and develop new types of interactions that greatly influence population productivity. Here, we explore the evolutionary diversification of pellicle biofilms of the Gram positive, spore-forming bacterium Bacillus subtilis. We discovered that-similarly to other species-B. subtilis diversifies into distinct colony variants. These variants dramatically differ in biofilm formation abilities and expression of biofilm-related genes. In addition, using a quantitative approach, we reveal striking differences in surface complexity and hydrophobicity of the evolved colony types. Interestingly, one of the morphotypes completely lost the ability of independent biofilm formation and evolved to hitchhike with other morphotypes with improved biofilm forming abilities. Genome comparison suggests that major phenotypic transformations between the morphotypes can be triggered by subtle genetic differences. Our work demonstrates how positive complementarity effects and exploitative interactions intertwine during evolutionary diversification in biofilms.

Complex microbial systems across different levels of description

Complex biological systems offer a variety of interesting phenomena at the different physical scales. With increasing abstraction, details of the microscopic scales can often be extrapolated to average or typical macroscopic properties. However, emergent properties and cross-scale interactions can impede naïve abstractions and necessitate comprehensive investigations of these complex systems. In this review paper, we focus on microbial communities, and first, summarize a general hierarchy of relevant scales and description levels to understand these complex systems: (1) genetic networks, (2) single cells, (3) populations, and (4) emergent multi-cellular properties. Second, we employ two illustrating examples, microbial competition and biofilm formation, to elucidate how cross-scale interactions and emergent properties enrich the observed multi-cellular behavior in these systems. Finally, we conclude with pointing out the necessity of multi-scale investigations to understand complex biological systems and discuss recent investigations.

The Role of Functional Amyloids in Multicellular Growth and Development of Gram-Positive Bacteria

Amyloid fibrils play pivotal roles in all domains of life. In bacteria, these fibrillar structures are often part of an extracellular matrix that surrounds the producing organism and thereby provides protection to harsh environmental conditions. Here, we discuss the role of amyloid fibrils in the two distant Gram-positive bacteria, Streptomyces coelicolor and Bacillus subtilis. We describe how amyloid fibrils contribute to a multitude of developmental processes in each of these systems, including multicellular growth and community development. Despite this variety of tasks, we know surprisingly little about how their assembly is organized to fulfill all these roles.

An improved protocol for harvesting Bacillus subtilis colony biofilms

Bacterial biofilms cause severe problems in medicine and industry due to the high resistance to disinfectants and environmental stress of organisms within biofilms. Addressing challenges caused by biofilms requires full understanding of the underlying mechanisms for bacterial resistance and survival in biofilms. However, such work is hampered by a relative lack of systems for biofilm cultivation that are practical and reproducible. To address this problem, we developed a readily applicable method to culture Bacillus subtilis biofilms on a membrane filter. The method results in biofilms with highly reproducible characteristics, and which can be readily analyzed by a variety of methods with little further manipulation. This biofilm preparation method simplifies routine generation of B. subtilis biofilms for molecular and cellular analysis, and could be applicable to other microbial systems.

Modulation of the mechanical properties of bacterial biofilms in response to environmental challenges

In this review, we highlight recent research on the relationship between biofilm matrix composition, biofilm mechanics and environmental stimuli.

Matrix composition determines the dimensions of Bacillus subtilis NCIB 3610 biofilm colonies grown on LB agar

Exopolymeric substances secreted by biofilm formingBacillus subtilisNCIB 3610 bacteria influence the growth and final dimensions of these biofilms.

Just in case it rains: building a hydrophobic biofilm the Bacillus subtilis way

Over the millennia, diverse species of bacteria have evolved multiple independent mechanisms to structure sessile biofilm communities that confer protection and stability to the inhabitants. The Gram-positive soil bacterium Bacillus subtilis biofilm presents as an architecturally complex, highly hydrophobic community that resists wetting by water, solvents, and biocides. This remarkable property is conferred by a small secreted protein called BslA, which self-assembles into an organized lattice at an interface. In the biofilm, production of BslA is tightly regulated and the resultant protein is secreted into the extracellular environment where it forms a very effective communal barrier allowing the resident B. subtilis cells to shelter under the protection of a protein raincoat.

Mechanical signatures of microbial biofilms in micropillar-embedded growth chambers

Biofilms are surface-attached communities of microorganisms embedded in an extracellular matrix and are essential for the cycling of organic matter in natural and engineered environments. They are also the leading cause of many infections, for example, those associated with chronic wounds and implanted medical devices. The extracellular matrix is a key biofilm component that determines its architecture and defines its physical properties. Herein, we used growth chambers embedded with micropillars to study the net mechanical forces (differential pressure) exerted during biofilm formation in situ. Pressure from the biofilm is transferred to the micropillars via the extracellular matrix, and reduction of major matrix components decreases the magnitude of micropillar deflections. The spatial arrangement of micropillar deflections caused by pressure differences in the different biofilm strains may potentially be used as mechanical signatures for biofilm characterization. Hence, we submit that micropillar-embedded growth chambers provide insights into the mechanical properties and dynamics of the biofilm and its matrix.