Atomic force microscopy: A powerful tool for studying bacterial swarming motility

Equations describing semi-confluent cell growth (I) Analytical approximations

A set of differential equations with analytical solutions are presented that can quantitatively account for variable degrees of contact inhibition on cell growth in two- and three-dimensional cultures. The developed equations can be used for comparative purposes when assessing contribution of higher-order effects, such as culture geometry and nutrient depletion, on mean cell growth rate. These equations also offer experimentalists the opportunity to characterize cell culture experiments using a single reductive parameter.

The microbial adhesive arsenal deciphered by atomic force microscopy

Microbes employ a variety of strategies to adhere to abiotic and biotic surfaces, as well as host cells. In addition to their surface physicochemical properties (e.g. charge, hydrophobic balance), microbes produce appendages (e.g. pili, fimbriae, flagella) and express adhesion proteins embedded in the cell wall or cell membrane, with adhesive domains targeting specific ligands or chemical properties. Atomic force microscopy (AFM) is perfectly suited to deciphering the adhesive properties of microbial cells. Notably, AFM imaging has revealed the cell wall topographical organization of live cells at unprecedented resolution, and AFM has a dual capability to probe adhesion at the single-cell and single-molecule levels. AFM is thus a powerful tool for unravelling the molecular mechanisms of microbial adhesion at scales ranging from individual molecular interactions to the behaviours of entire cells. In this review, we cover some of the major breakthroughs facilitated by AFM in deciphering the microbial adhesive arsenal, including the exciting development of anti-adhesive strategies.

Microbial adhesion and ultrastructure from the single-molecule to the single-cell levels by Atomic Force Microscopy

In the last decades, atomic force microscopy (AFM) has evolved towards an accurate and lasting tool to study the surface of living cells in physiological conditions. Through imaging, single-molecule force spectroscopy and single-cell force spectroscopy modes, AFM allows to decipher at multiple scales the morphology and the molecular interactions taking place at the cell surface. Applied to microbiology, these approaches have been used to elucidate biophysical properties of biomolecules and to directly link the molecular structures to their function. In this review, we describe the main methods developed for AFM-based microbial surface analysis that we illustrate with examples of molecular mechanisms unravelled with unprecedented resolution.

Molecular architectures of Pen and Pal: Key enzymes required for CMP-pseudaminic acid biosynthesis in Bacillus thuringiensis

Bacillus thuringiensis is a soil-dwelling Gram positive bacterium that has been utilized as a biopesticide for well over 60 years. It is known to contain flagella that are important for motility. One of the proteins found in flagella is flagellin, which is post-translationally modified by O-glycosylation with derivatives of pseudaminic acid. The biosynthetic pathway for the production of CMP-pseudaminic acid in B. thuringiensis, starting with UDP-N-acetyl-d-glucosamine (UDP-GlcNAc), requires seven enzymes. Here, we report the three-dimensional structures of Pen and Pal, which catalyze the first and second steps, respectively. Pen contains a tightly bound NADP(H) cofactor whereas Pal is isolated with bound NAD(H). For the X-ray analysis of Pen, the site-directed D128N/K129A mutant variant was prepared in order to trap its substrate, UDP-GlcNAc, into the active site. Pen adopts a hexameric quaternary structure with each subunit showing the bilobal architecture observed for members of the short-chain dehydrogenase/reductase superfamily. The hexameric quaternary structure is atypical for most members of the superfamily. The structure of Pal was determined in the presence of UDP. Pal adopts the more typical dimeric quaternary structure. Taken together, Pen and Pal catalyze the conversion of UDP-GlcNAc to UDP-4-keto-6-deoxy-l-N-acetylaltrosamine. Strikingly, in Gram negative bacteria such as Campylobacter jejuni and Helicobacter pylori, only a single enzyme (FlaA1) is required for the production of UDP-4-keto-6-deoxy-l-N-acetylaltrosamine. A comparison of Pen and Pal with FlaA1 reveals differences that may explain why FlaA1 is a bifunctional enzyme whereas Pen and Pal catalyze the individual steps leading to the formation of the UDP-sugar product. This investigation represents the first structural analysis of the enzymes in B. thuringiensis that are required for CMP-pseudaminic acid formation.

Magnetic resonance imaging of pathogenic protozoan parasite Entamoeba histolytica labeled with superparamagnetic iron oxide nanoparticles

OBJECTIVES

The aim of this study was to establish a noninvasive tracking of the pathogenic parasite Entamoeba histolytica (Eh) after superparamagnetic iron oxide (SPIO) labeling by magnetic resonance imaging (MRI) on a single-cell level in vitro and in vivo in a mouse model for amebic liver abscess (ALA).

MATERIALS AND METHODS

Local institutional review committee on animal care approved all animal experiments. Entamoeba histolytica trophozoites were labeled with SPIO nanoparticles (SPIO-Eh). The uptake of SPIO by Eh was optimized using flow cytometry and visualized by bright field, fluorescence, and transmission electron microscopy. The viability of SPIO-Eh was assessed in vitro by determination of growth and ingestion rate of red blood cells. Migration of SPIO-Eh was proven by in vitro MRI in a preclinical 7 T MRI system using continually repeated MRI scans. In vivo distribution of SPIO-Eh within the mouse liver was assessed qualitatively and quantitatively by serial respiration-triggered T2*-weighted MRI, T2-weighted MRI, and R2* MR relaxometry up to 5 days after injection and correlated with immunohistology of the liver sections after removal.

RESULTS

Entamoeba histolytica can be efficiently labeled with SPIO without influence on parasite growth rate or phagocytic capacity. In vitro dynamic MRI allowed real-time migration monitoring and determination of velocity of single SPIO-Eh. In vivo SPIO-Eh showed signal decrease in T2*-weighted and increase of R2* in ALA formations. Motility of SPIO-Eh was necessary to induce ALA formations.

CONCLUSIONS

The present study demonstrates the feasibility of an efficient magnetic labeling and a noninvasive in vitro and in vivo MR tracking of the pathogenic protozoan Eh in a mouse model for ALA, thus representing in future a noninvasive imaging tool to study parasite, as well as on host-specific pathomechanisms.

Swimming performance of Bradyrhizobium diazoefficiens is an emergent property of its two flagellar systems

Many bacterial species use flagella for self-propulsion in aqueous media. In the soil, which is a complex and structured environment, water is found in microscopic channels where viscosity and water potential depend on the composition of the soil solution and the degree of soil water saturation. Therefore, the motility of soil bacteria might have special requirements. An important soil bacterial genus is Bradyrhizobium, with species that possess one flagellar system and others with two different flagellar systems. Among the latter is B. diazoefficiens, which may express its subpolar and lateral flagella simultaneously in liquid medium, although its swimming behaviour was not described yet. These two flagellar systems were observed here as functionally integrated in a swimming performance that emerged as an epistatic interaction between those appendages. In addition, each flagellum seemed engaged in a particular task that might be required for swimming oriented toward chemoattractants near the soil inner surfaces at viscosities that may occur after the loss of soil gravitational water. Because the possession of two flagellar systems is not general in Bradyrhizobium or in related genera that coexist in the same environment, there may be an adaptive tradeoff between energetic costs and ecological benefits among these different species.

Influence of lysogeny of Tectiviruses GIL01 and GIL16 on Bacillus thuringiensis growth, biofilm formation, and swarming motility

Bacillus thuringiensis is an entomopathogenic bacterium that has been used as an efficient biopesticide worldwide. Despite the fact that this bacterium is usually described as an insect pathogen, its life cycle in the environment is still largely unknown. B. thuringiensis belongs to the Bacillus cereus group of bacteria, which has been associated with many mobile genetic elements, such as species-specific temperate or virulent bacteriophages (phages). Temperate (lysogenic) phages are able to establish a long-term relationship with their host, providing, in some cases, novel ecological traits to the bacterial lysogens. Therefore, this work focuses on evaluating the potential influence of temperate tectiviruses GIL01 and GIL16 on the development of different life traits of B. thuringiensis. For this purpose, a B. thuringiensis serovar israelensis plasmid-cured (nonlysogenic) strain was used to establish bacterial lysogens for phages GIL01 and GIL16, and, subsequently, the following life traits were compared among the strains: kinetics of growth, metabolic profiles, antibiotics susceptibility, biofilm formation, swarming motility, and sporulation. The results revealed that GIL01 and GIL16 lysogeny has a significant influence on the bacterial growth, sporulation rate, biofilm formation, and swarming motility of B. thuringiensis. No changes in metabolic profiles or antibiotic susceptibilities were detected. These findings provide evidence that tectiviruses have a putative role in the B. thuringiensis life cycle as adapters of life traits with ecological advantages.

Applications of microscopy in Salmonella research

Salmonella enterica is a Gram-negative enteropathogen that can cause localized infections, typically resulting in gastroenteritis, or systemic infection, e.g., typhoid fever, in humans and many other animals. Understanding the mechanisms by which Salmonella induces disease has been the focus of intensive research. This has revealed that Salmonella invasion requires dynamic cross-talk between the microbe and host cells, in which bacterial adherence rapidly leads to a complex sequence of cellular responses initiated by proteins translocated into the host cell by a type 3 secretion system. Once these Salmonella-induced responses have resulted in bacterial invasion, proteins translocated by a second type 3 secretion system initiate further modulation of cellular activities to enable survival and replication of the invading pathogen. Elucidation of the complex and highly dynamic pathogen-host interactions ultimately requires analysis at the level of single cells and single infection events. To achieve this goal, researchers have applied a diverse range of microscopy techniques to analyze Salmonella infection in models ranging from whole animal to isolated cells and simple eukaryotic organisms. For example, electron microscopy and high-resolution light microscopy techniques such as confocal microscopy can reveal the precise location of Salmonella and its relationship to cellular components. Widefield light microscopy is a simpler approach with which to study the interaction of bacteria with host cells and often has advantages for live cell imaging, enabling detailed analysis of the dynamics of infection and cellular responses. Here we review the use of imaging techniques in Salmonella research and compare the capabilities of different classes of microscope to address specific types of research question. We also provide protocols and notes on some microscopy techniques used routinely in our own research.

Phages preying on Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis: past, present and future

Many bacteriophages (phages) have been widely studied due to their major role in virulence evolution of bacterial pathogens. However, less attention has been paid to phages preying on bacteria from the Bacillus cereus group and their contribution to the bacterial genetic pool has been disregarded. Therefore, this review brings together the main information for the B. cereus group phages, from their discovery to their modern biotechnological applications. A special focus is given to phages infecting Bacillus anthracis, B. cereus and Bacillus thuringiensis. These phages belong to the Myoviridae, Siphoviridae, Podoviridae and Tectiviridae families. For the sake of clarity, several phage categories have been made according to significant characteristics such as lifestyles and lysogenic states. The main categories comprise the transducing phages, phages with a chromosomal or plasmidial prophage state, γ-like phages and jumbo-phages. The current genomic characterization of some of these phages is also addressed throughout this work and some promising applications are discussed here.

Atomic Force Microscopy and pharmacology: from microbiology to cancerology

BACKGROUND

Atomic Force Microscopy (AFM) has been extensively used to study biological samples. Researchers take advantage of its ability to image living samples to increase our fundamental knowledge (biophysical properties/biochemical behavior) on living cell surface properties, at the nano-scale.

SCOPE OF REVIEW

AFM, in the imaging modes, can probe cells morphological modifications induced by drugs. In the force spectroscopy mode, it is possible to follow the nanomechanical properties of a cell and to probe the mechanical modifications induced by drugs. AFM can be used to map single molecule distribution at the cell surface. We will focus on a collection of results aiming at evaluating the nano-scale effects of drugs, by AFM. Studies on yeast, bacteria and mammal cells will illustrate our discussion. Especially, we will show how AFM can help in getting a better understanding of drug mechanism of action.

MAJOR CONCLUSIONS

This review demonstrates that AFM is a versatile tool, useful in pharmacology. In microbiology, it has been used to study the drugs fighting Candida albicans or Pseudomonas aeruginosa. The major conclusions are a better understanding of the microbes' cell wall and of the drugs mechanism of action. In cancerology, AFM has been used to explore the effects of cytotoxic drugs or as an innovative diagnostic technology. AFM has provided original results on cultured cells, cells extracted from patient and directly on patient biopsies.

GENERAL SIGNIFICANCE

This review enhances the interest of AFM technologies for pharmacology. The applications reviewed range from microbiology to cancerology.

Observation of multicellular spinning behavior of Proteus mirabilis by atomic force microscopy and multifunctional microscopy

This study aimed to observe the multicellular spinning behavior of Proteus mirabilis by atomic force microscopy (AFM) and multifunctional microscopy in order to understand the mechanism underlying this spinning movement and its biological significance. Multifunctional microscopy with charge-coupled device (CCD) and real-time AFM showed changes in cell structure and shape of P. mirabilis during multicellular spinning movement. Specifically, the morphological characteristics of P. mirabilis, multicellular spinning dynamics, and unique movement were observed. Our findings indicate that the multicellular spinning behavior of P. mirabilis may be used to collect nutrients, perform colonization, and squeeze out competitors. The movement characteristics of P. mirabilis are vital to the organism's biological adaptability to the surrounding environment.

Bacillus thuringiensis colonises plant roots in a phylogeny-dependent manner

Although much is known about the pathology of Bacillus thuringiensis against invertebrates, current understanding of its natural ecology is limited. This study evaluated the biodiversity of B. thuringiensis in relation to its interaction with plants. Phylogenetic relationships between 44 reference and field-collected strains, determined using 16S rRNA and gyrB gene sequences, revealed a high degree of variability, similar to that found in databases. An Arabidopsis thaliana in vitro inoculation model was developed to screen the ability of B. thuringiensis to colonise roots. Significant colonisation differences up to 91-fold were observed between strains, and correlation between strain phylogeny and colonisation was found. The genetics and biochemistry of auxin production; presence of the gene encoding indole pyruvate decarboxylase; and the abilities of Bt strains to swarm, grow in rich/minimal media and affect root growth differed between the strains, but only auxin production correlated significantly with ability to colonise roots. Co-inoculation with Burkholderia phytofirmans PsJN or Pseudomonas fluorescens SBW25 produced no effect on B. thuringiensis colonisation levels, regardless of the co-inoculant. Similarly, root colonisation of A. thaliana mutants impaired in plant defences was not significantly higher compared with controls. This is the first systematic and phylogenetic evaluation of B. thuringiensis interaction with plants.

Nanoscopic analysis on pH induced morphological changes of flagella in Escherichia coli

BACKGROUND AND PURPOSE

Flagella contribute to the virulence of pathogenic bacteria through chemotaxis, motility, and adhesion. Understanding the various functions of flagella may provide insight into mechanisms of bacterial infection and transmission. The objectives of our study were to apply biophysical and biochemical methods to investigate the mechanisms of pH-dependent changes in flagella functions.

METHODS

Atomic force microscopy (AFM) was used to analyze the flagellum morphology of Escherichia coli cultured in various pH conditions. The swarming plate method was used to identify pH-dependent changes in bacterial motility. Western blot analysis and attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) were also carried out to study pH-dependent expression and structural changes of flagellin C.

RESULTS

E coli cultured at pH 7 produced the flagella with the greatest average length and diameter. When the bacteria were grown at pH 6 or pH 8, shorter and thinner forms of flagella were produced. The morphology of the flagella was correlated to the bacterial motility. While western blot analysis showed only a slight change in the expression of the flagellin C protein in response to changes in the pH of the culture medium, ATR-FTIR showed significant pH-dependent changes in the secondary structure of the flagellin C assembled in sheared flagella.

CONCLUSION

Our results show that both acidification and alkalization of the culture medium restricted bacterial motility, and indicate that the reduced motility may be caused by incorrect assembly of the flagellum proteins.