Physical basis for the adaptive flexibility of Bacillus spore coats

Elucidating Antibiotic Permeation through the Escherichia coli Outer Membrane: Insights from Molecular Dynamics

Antibiotic resistance represents a critical public health threat, with an increasing number of Gram-negative pathogens demonstrating resistance to a broad range of clinical drugs. A primary challenge in enhancing antibiotic efficacy is overcoming the robust barrier presented by the bacterial outer membrane. Our research addresses a longstanding question: What is the rate of antibiotic permeation across the outer membrane (OM) of Gram-negative bacteria? Utilizing molecular dynamics (MD) simulations, we assess the passive permeability profiles of four commercially available antibiotics─gentamicin, novobiocin, rifampicin, and tetracycline across an asymmetric atomistic model of the Escherichia coli (E. coli) OM, employing the inhomogeneous solubility-diffusion model. Our examination of the interactions between these drugs and their environmental context during OM permeation reveals that extended hydrogen bond formation and drug-cation interactions significantly hinder the energetics of passive permeation, notably affecting novobiocin. Our MD simulations corroborate well with experimental data and reveal new implications of solvation on drug permeability, overall advancing the possible use of computational prediction of membrane permeability in future antibiotic discovery.

Hydration solids

Hygroscopic biological matter in plants, fungi and bacteria make up a large fraction of Earth's biomass1. Although metabolically inert, these water-responsive materials exchange water with the environment and actuate movement2-5 and have inspired technological uses6,7. Despite the variety in chemical composition, hygroscopic biological materials across multiple kingdoms of life exhibit similar mechanical behaviours including changes in size and stiffness with relative humidity8-13. Here we report atomic force microscopy measurements on the hygroscopic spores14,15 of a common soil bacterium and develop a theory that captures the observed equilibrium, non-equilibrium and water-responsive mechanical behaviours, finding that these are controlled by the hydration force16-18. Our theory based on the hydration force explains an extreme slowdown of water transport and successfully predicts a strong nonlinear elasticity and a transition in mechanical properties that differs from glassy and poroelastic behaviours. These results indicate that water not only endows biological matter with fluidity but also can-through the hydration force-control macroscopic properties and give rise to a 'hydration solid' with unusual properties. A large fraction of biological matter could belong to this distinct class of solid matter.

Water-Content-Dependent Morphologies and Mechanical Properties of Bacillus subtilis Spores' Cortex Peptidoglycan

Peptidoglycan (PG), bacterial spores' major structural component in their cortex layers, was recently found to regulate the spore's water content and deform in response to relative humidity (RH) changes. Here, we report that the cortex PG dominates the Bacillus subtilis spores' water-content-dependent morphological and mechanical properties. When exposed to an environment having RH varied between 10% and 90%, the spores and their cortex PG reversibly expand and contract by 30.7% and 43.2% in volume, which indicates that the cortex PG contributes to 67.3% of a spore's volume change. The spores' and cortex PG's significant volumetric changes also lead to changes in their Young's moduli from 5.7 and 9.0 GPa at 10% RH to 0.62 and 1.2 GPa at 90% RH, respectively. Interestingly, these significant changes in the spores' and cortex PG's morphological and mechanical properties are only caused by a minute amount of the cortex PG's water exchange that occupies 28.0% of the cortex PG's volume. The cortex PG's capability in sensing and responding to environmental RH and effectively changing its structures and properties could provide insight into spores' high desiccation resistance and dormancy mechanisms.

Advances in engineered Bacillus subtilis biofilms and spores, and their applications in bioremediation, biocatalysis, and biomaterials

Bacillus subtilis is a commonly used commercial specie with broad applications in the fields of bioengineering and biotechnology. B. subtilis is capable of producing both biofilms and spores. Biofilms are matrix-encased multicellular communities that comprise various components including exopolysaccharides, proteins, extracellular DNA, and poly-γ-glutamic acid. These biofilms resist environmental conditions such as oxidative stress and hence have applications in bioremediation technologies. Furthermore, biofilms and spores can be engineered through biotechnological techniques for environmentally-friendly and safe production of bio-products such as enzymes. The ability to withstand with harsh conditions and producing spores makes Bacillus a suitable candidate for surface display technology. In recent years, the spores of such specie are widely used as it is generally regarded as safe to use. Advances in synthetic biology have enabled the reprogramming of biofilms to improve their functions and enhance the production of value-added products. Globally, there is increased interest in the production of engineered biosensors, biocatalysts, and biomaterials. The elastic modulus and gel properties of B. subtilis biofilms have been utilized to develop living materials. This review outlines the formation of B. subtilis biofilms and spores. Biotechnological engineering processes and their increasing application in bioremediation and biocatalysis, as well as the future directions of B. subtilis biofilm engineering, are discussed. Furthermore, the ability of B. subtilis biofilms and spores to fabricate functional living materials with self-regenerating, self-regulating and environmentally responsive characteristics has been summarized. This review aims to resume advances in biological engineering of B. subtilis biofilms and spores and their applications.

Bacterial Spore-Based Hygromorphs: A Novel Active Material with Potential for Architectural Applications

This paper introduces a new active material which responds to changes in environmental humidity. There has been growing interest in active materials which are able to respond to their environment, creating dynamic architectural systems without the need for energy input or complex systems of sensors and actuators. A subset of these materials are hygromorphs, which respond to changes in relative humidity (RH) and wetting through shape change. Here, we introduce a novel hygromorphic material in the context of architectural design, composed of multiple monolayers of microbial spores of Bacillus subtilis and latex sheets. Methods of fabrication and testing for this new material are described, showing that small actuators made from this material demonstrate rapid, reversible and repeatable deflection in response to changes in RH. It is demonstrated that the hygromorphic actuators are able to lift at least 150% of their own mass. Investigations are also extended to understanding this new biomaterial in terms of meaningful work.

Structural, Metabolic and Evolutionary Comparison of Bacterial Endospore and Exospore Formation

Sporulation is a specialized developmental program employed by a diverse set of bacteria which culminates in the formation of dormant cells displaying increased resilience to stressors. This represents a major survival strategy for bacteria facing harsh environmental conditions, including nutrient limitation, heat, desiccation, and exposure to antimicrobial compounds. Through dispersal to new environments via biotic or abiotic factors, sporulation provides a means for disseminating genetic material and promotes encounters with preferable environments thus promoting environmental selection. Several types of bacterial sporulation have been characterized, each involving numerous morphological changes regulated and performed by non-homologous pathways. Despite their likely independent evolutionary origins, all known modes of sporulation are typically triggered by limited nutrients and require extensive membrane and peptidoglycan remodeling. While distinct modes of sporulation have been observed in diverse species, two major types are at the forefront of understanding the role of sporulation in human health, and microbial population dynamics and survival. Here, we outline endospore and exospore formation by members of the phyla Firmicutes and Actinobacteria, respectively. Using recent advances in molecular and structural biology, we point to the regulatory, genetic, and morphological differences unique to endo- and exospore formation, discuss shared characteristics that contribute to the enhanced environmental survival of spores and, finally, cover the evolutionary aspects of sporulation that contribute to bacterial species diversification.

Spore-adsorption: Mechanism and applications of a non-recombinant display system

Surface display systems have been developed to express target molecules on almost all types of biological entities from viruses to mammalian cells and on a variety of synthetic particles. Various approaches have been developed to achieve the display of many different target molecules, aiming at several technological and biomedical applications. Screening of libraries, delivery of drugs or antigens, bio-catalysis, sensing of pollutants and bioremediation are commonly considered as fields of potential application for surface display systems. In this review, the non-recombinant approach to display antigens and enzymes on the surface of bacterial spores is discussed. Examples of molecules displayed on the spore surface and their potential applications are summarized and a mechanism of display is proposed.

Opportunities for the application of real-time bacterial cell analysis using flow cytometry for the advancement of sterilization microbiology

Medical devices provide critical care and diagnostic applications through patient contact. Sterility assurance level (SAL) may be defined as the probability of a single viable micro-organism occurring on an item after a sterilization process. Sterilization microbiology often relies upon using an overkill validation method where a 12-log reduction in recalcitrant bacterial endospore population occurs during the process that exploits conventional laboratory-based culture media for enumeration. This timely review explores key assumptions underpinning use of conventional culture-based methods in sterilization microbiology. Consideration is given to how such methods may limit the ability to fully appreciate the inactivation kinetics of a sterilization process such as vaporized hydrogen peroxide (VH2O2) sterilization, and consequently design efficient sterilization processes. Specific use of the real-time flow cytometry (FCM) is described by way of elucidating the practical relevance of these limitation factors with implications and opportunities for the sterilization industry discussed. Application of FCM to address these culture-based limitation factors will inform real-time kinetic inactivation modelling and unlock potential to embrace emerging opportunities for pharma, medical device and sterilization industries including potentially disruptive applications that may involve reduced usage of sterilant.

Identifying different types of microorganisms with terahertz spectroscopy

Most microbial detection techniques require pretreatment, such as fluorescent labeling and cultivation processes. Here, we propose novel tools for classifying and identifying microorganisms such as molds, yeasts, and bacteria based on their intrinsic dielectric constants in the THz frequency range. We first measured the dielectric constant of films that consisted of a wide range of microbial species, and extracted the values for the individual microbes using the effective medium theory. The dielectric constant of the molds was 1.24-1.85, which was lower than that of bacteria ranging from 2.75-4.11. The yeasts exhibited particularly high dielectric constants reaching 5.63-5.97, which were even higher than that of water. These values were consistent with the results of low-density measurements in an aqueous environment using microfluidic metamaterials. In particular, a blue shift in the metamaterial resonance occurred for molds and bacteria, whereas the molds have higher contrast relative to bacteria in the aqueous environment. By contrast, the deposition of the yeasts induced a red shift because their dielectric constant was higher than that of water. Finally, we measured the dielectric constants of peptidoglycan and polysaccharides such as chitin, α-glucan, and β-glucans (with short and long branches), and confirmed that cell wall composition was the main cause of the observed differences in dielectric constants for different types of microorganisms.

Resilient living materials built by printing bacterial spores

Materials can be made multifunctional by embedding them with living cells that perform sensing, synthesis, energy production, and physical movement. A challenge is that the conditions needed for living cells are not conducive to materials processing and require continuous water and nutrients. Here, we present a three dimensional (3D) printer that can mix material and cell streams to build 3D objects. Bacillus subtilis spores were printed within the material and germinated on its exterior surface, including spontaneously in new cracks. The material was resilient to extreme stresses, including desiccation, solvents, osmolarity, pH, ultraviolet light, and γ-radiation. Genetic engineering enabled the bacteria to respond to stimuli or produce chemicals on demand. As a demonstration, we printed custom-shaped hydrogels containing bacteria that can sense or kill Staphylococcus aureus, a causative agent of infections. This work demonstrates materials endued with living functions that can be used in applications that require storage or exposure to environmental stresses.

Terahertz vibrational signature of bacterial spores arising from nanostructure decorated endospore surface

This theoretical effort is the first to explore the possible hypothesis that terahertz optical activity of Bacillus spores arises from normal vibrational modes of spore coat subcomponents in the terahertz frequency range. Bacterial strains like Bacillus and Clostridium form spores with a hardened coating made of peptidoglycan to protect its genetic material in harsh conditions. In recent years, electron microscopy and atomic force microscopy has revealed that bacterial spore surfaces are decorated with nanocylinders and honeycomb nanostructures. In this article, a simple elastic continuum model is used to describe the vibration of these nanocylinders mainly in Bacillus subtilis, which also leads to the conclusion that the terahertz signature of these spores arises from the vibration of these nanostructures. Three vibrating modes: radial/longitudinal, torsional and flexural, have been identified and discussed for the nanocylinders. The effect of bound water, which shifts the vibration frequency, is also discussed. The peptidoglycan molecule consists of polar and charged amino acids; hence, the sporal surface local vibrations interact strongly with the terahertz radiation.

Analysis of killing of growing cells and dormant and germinated spores of Bacillus species by black silicon nanopillars

Black silicon (bSi) wafers with a high density of high-aspect ratio nanopillars have recently been suggested to have mechanical bactericidal activity. However, it remains unclear whether bSi with the nanopillars can kill only growing bacterial cells or also dormant spores that are harder to kill. We have reexamined the cidal activity of bSi on growing cells, dormant and germinated spores of B. subtilis, and dormant spores of several other Bacillus species by incubation on bSi wafers with and without nanopillars. We found that the bSi wafers with nanopillars were indeed very effective in rupturing and killing the growing bacterial cells, while wafers without nanopillars had no bactericidal effect. However, bSi wafers with or without nanopillars gave no killing or rupture of dormant spores of B. subtilis, Bacillus cereus or Bacillus megaterium, although germinated B. subtilis spores were rapidly killed. This work lays a foundation for novel bactericidal applications of bSi by elucidating the limits of mechanical bactericidal approaches.

Incorporating germination-induction into decontamination strategies for bacterial spores

Bacterial spores resist environmental extremes and protect key spore macromolecules until more supportive conditions arise. Spores germinate upon sensing specific molecules, such as nutrients. Germination is regulated by specialized mechanisms or structural features of the spore that limit contact with germinants and enzymes that regulate germination. Importantly, germination renders spores more susceptible to inactivating processes such as heat, desiccation, and ultraviolet radiation, to which they are normally refractory. Thus, germination can be intentionally induced through a process called germination-induction and subsequent treatment of these germinated spores with common disinfectants or gentle heat will inactivate them. However, while the principle of germination-induction has been shown effective in the laboratory, this strategy has not yet been fully implemented in real-word scenarios. Here, we briefly review the mechanisms of bacterial spore germination and discuss the evolution of germination-induction as a decontamination strategy. Finally, we examine progress towards implementing germination-induction in three contexts: biodefense, hospital settings and food manufacture.

SIGNIFICANCE AND IMPACT

This article reviews implementation of germination-induction as part of a decontamination strategy for the cleanup of bacterial spores. To our knowledge this is the first time that germination-induction studies have been reviewed in this context. This article will provide a resource which summarizes the mechanisms of germination in Clostridia and Bacillus species, challenges and successes in germination-induction, and potential areas where this strategy may be implemented.

The Spore Coat

Spores of Clostridiales and Bacillales are encased in a complex series of concentric shells that provide protection, facilitate germination, and mediate interactions with the environment. Analysis of diverse spore-forming species by thin-section transmission electron microscopy reveals that the number and morphology of these encasing shells vary greatly. In some species, they appear to be composed of a small number of discrete layers. In other species, they can comprise multiple, morphologically complex layers. In addition, spore surfaces can possess elaborate appendages. For all their variability, there is a consistent architecture to the layers encasing the spore. A hallmark of all Clostridiales and Bacillales spores is the cortex, a layer made of peptidoglycan. In close association with the cortex, all species examined possess, at a minimum, a series of proteinaceous layers, called the coat. In some species, including Bacillus subtilis, only the coat is present. In other species, including Bacillus anthracis, an additional layer, called the exosporium, surrounds the coat. Our goals here are to review the present understanding of the structure, composition, assembly, and functions of the coat, primarily in the model organism B. subtilis, but also in the small but growing number of other spore-forming species where new data are showing that there is much to be learned beyond the relatively well-developed basis of knowledge in B. subtilis. To help summarize this large field and define future directions for research, we will focus on key findings in recent years.

Surviving Between Hosts: Sporulation and Transmission

To survive adverse conditions, some bacterial species are capable of developing into a cell type, the "spore," which exhibits minimal metabolic activity and remains viable in the presence of multiple environmental challenges. For some pathogenic bacteria, this developmental state serves as a means of survival during transmission from one host to another. Spores are the highly infectious form of these bacteria. Upon entrance into a host, specific signals facilitate germination into metabolically active replicating organisms, resulting in disease pathogenesis. In this article, we will review spore structure and function in well-studied pathogens of two genera, Bacillus and Clostridium, focusing on Bacillus anthracis and Clostridium difficile, and explore current data regarding the lifestyles of these bacteria outside the host and transmission from one host to another.

Protein Synthesis during Germination: Shedding New Light on a Classical Question

Despite over a century of research into the mystery of bacterial spore dormancy and germination, a key question remains unresolved: is protein synthesis required for germination? The development of more sophisticated techniques for assessing and preventing protein synthesis has renewed interest in this long-standing question in recent years. In this issue, Korza et al. (G. Korza, B. Setlow, L. Rao, Q. Li, and P. Setlow, J. Bacteriol 198:3254-3264, 2016, http://dx.doi.org/10.1128/JB.00583-16) address this with a novel approach. We discuss their results in the context of recently published data.

Nanomechanical Characterization of Bacillus anthracis Spores by Atomic Force Microscopy

The study of structures and properties of bacterial spores is important to understanding spore formation and biological responses to environmental stresses. While significant progress has been made over the years in elucidating the multilayer architecture of spores, the mechanical properties of the spore interior are not known. Here, we present a thermal atomic force microscopy (AFM) study of the nanomechanical properties of internal structures of Bacillus anthracis spores. We developed a nanosurgical sectioning method in which a stiff diamond AFM tip was used to cut an individual spore, exposing its internal structure, and a soft AFM tip was used to image and characterize the spore interior on the nanometer scale. We observed that the elastic modulus and adhesion force, including their thermal responses at elevated temperatures, varied significantly in different regions of the spore section. Our AFM images indicated that the peptidoglycan (PG) cortex of Bacillus anthracis spores consisted of rod-like nanometer-sized structures that are oriented in the direction perpendicular to the spore surface. Our findings may shed light on the spore architecture and properties.

IMPORTANCE

A nanosurgical AFM method was developed that can be used to probe the structure and properties of the spore interior. The previously unknown ultrastructure of the PG cortex of Bacillus anthracis spores was observed to consist of nanometer-sized rod-like structures that are oriented in the direction perpendicular to the spore surface. The variations in the nanomechanical properties of the spore section were largely correlated with its chemical composition. Different components of the spore materials showed different thermal responses at elevated temperatures.

High-precision fitting measurements of the kinetics of size changes during germination of individual Bacillus spores

High-precision measurements of size changes of individual bacterial spores based on ellipse fitting to bright-field images recorded with a digital camera were employed to monitor the germination of Bacillus spores with a precision of ~5 nm. To characterize the germination of individual spores, we recorded bright-field and phase-contrast images and found that the timing of changes in their normalized intensities coincided, so the bright-field images can be used to characterize spore size and refractility changes during germination. The major conclusions from this work were as follows. (i) The sizes of germinating B. cereus spores were nearly unchanged until Trelease, the time of the completion of CaDPA (a 1:1 chelate of Ca(2+) and dipicolinic acid [DPA]) release after addition of nutrient germinants. (ii) The minor axis of germinating B. cereus spores rapidly increased by ~50 nm in a few seconds right after Trelease, while the major axis was slightly decreased or unchanged. Both the minor and major axes remained unchanged for a further 30 to 45 s and then increased by 100 to 200 nm by Tlys, the time of completion of cortex lysis. (iii) Individual spores in a population showed significant heterogeneity in the timing of germination events, such as Trelease and Tlys, but also variation in size changes during germination. (iv) Bacillus subtilis wild-type spores, B. subtilis spores lacking the cortex-lytic enzyme CwlJ, and wild-type Bacillus megaterium spores showed similar kinetics of size changes during nutrient germination. The size increases in germinating spores probably result from uptake of water and cortex lysis after completion of CaDPA release.

A bacterial spore model of pulsed electric fields on spore morphology change revealed by simulation and SEM

A two-layered spore model was proposed to analyze morphological change of bacterial spores subjected under pulsed electric fields. The outer layer, i.e. spore coat, was defined by Mooney-Rivlin hyper-elastic material model. The inner layer, i.e. peptidoglycan and spore core, was modeled by applying additional adhesion forces. The effect of pulsed electric fields on surface displacement was simulated in COMSOL Multiphysics and verified by SEM. The electro-mechanical theory, considering spore coat as a capacitor, was used to explain concavity; and the thin viscoelastic film theory, considering membrane bilayer as fluctuating surfaces, was used to explain leakage forming. Mutual interaction of external electric fields, charged spores, adhesion forces and ions movement were all predicted to contribute to concavity and leakage.

Nanoscale chemical imaging of Bacillus subtilis spores by combining tip-enhanced Raman scattering and advanced statistical tools

Tip-enhanced Raman Scattering (TERS) has recently emerged as a powerful spectroscopic technique capable of providing subdiffraction morphological and chemical information on samples. In this work, we apply TERS spectroscopy for surface analysis of the Bacillus subtilis spore, a very attractive biosystem for a wide range of applications regulated by the spore surface properties. The observed spectra reflect the complex and heterogeneous environment explored by the plasmonic tip, therefore exhibiting significant point-to-point variations at the nanoscale. Herein, we demonstrate that TERS data processing via principal component analysis allows handling such spectral changes, thus enabling an unbiased correlative imaging based on TERS. Our experimental outcomes suggest a denser arrangement of both proteins and carbohydrates on specific spore surface regions simultaneously revealed by AFM phase imaging. Successful TERS analysis of spores' surface is useful for bacterial surface-display systems and drug delivery applications.

Life cycle and spore resistance of spore-forming Bacillus atrophaeus

Bacillus endospores have a wide variety of important medical and industrial applications. This is an overview of the fundamental aspects of the life cycle, spore structure and factors that influence the spore resistance of spore-forming Bacillus. Bacillus atrophaeus was used as reference microorganism for this review because their spores are widely used to study spore resistance and morphology. Understanding the mechanisms involved in the cell cycle and spore survival is important for developing strategies for spore killing; producing highly resistant spores for biodefense, food and pharmaceutical applications; and developing new bioactive molecules and methods for spore surface display.

Bacillus spores as building blocks for stimuli-responsive materials and nanogenerators

Materials that respond mechanically to external chemical stimuli have applications in biomedical devices, adaptive architectural systems, robotics and energy harvesting. Inspired by biological systems, stimuli-responsive materials have been created that can oscillate, transport fluid, provide homeostasis and undergo complex changes in shape. However, the effectiveness of synthetic stimuli-responsive materials in generating work is limited when compared with mechanical actuators. Here, we show that the mechanical response of Bacillus spores to water gradients exhibits an energy density of more than 10 MJ m(-3), which is two orders of magnitude higher than synthetic water-responsive materials. We also identified mutations that can approximately double the energy density of the spores and found that they can self-assemble into dense, submicrometre-thick monolayers on substrates such as silicon microcantilevers and elastomer sheets, creating bio-hybrid hygromorph actuators. To illustrate the potential applications of the spores, we used them to build an energy-harvesting device that can remotely generate electrical power from an evaporating body of water.

Thermal effects on surface structures and properties of Bacillus anthracis spores on nanometer scales

Bacterial spores, one of the hardiest forms of life known, can survive severe environmental stresses such as high temperature. Using thermal atomic force microscopy (AFM), we show that the surface structures and properties of Bacillus anthracis spores when exposed to elevated temperatures undergo substantial changes on nanometer scales. Thermal-blister-like nanostructures, which grow in size with increasing temperature, are formed on the spore surface when it is heated by a thermal tip. Although thermal damage to the spore surface is persistent upon cooling heat-treated spores to room temperature, thermal effects on surface properties of the spores are complex. The thermally induced nanostructures show a lower surface-tip adhesion and a higher modulus than the surrounding spore surface. The overall trend is for the adhesion to decrease with increasing temperature. However, the adhesion of heat-treated spores may be smaller than, equal to, or larger than that of untreated spores, depending upon the degree of surface damage induced by heat. Although the overall spore dimensions show few changes during and after heat treatment, the size of the spore substructures decreases significantly. In addition, we demonstrate a nanoscratch AFM method for imaging the subsurface structures of spores.