The preservation of surface-associated micro-organisms prepared for scanning electron microscopy

Microbial Identification, High-Resolution Microscopy and Spectrometry of the Rhizosphere in Its Native Spatial Context

During the past decades, several stand-alone and combinatorial methods have been developed to investigate the chemistry (i.e., mapping of elemental, isotopic, and molecular composition) and the role of microbes in soil and rhizosphere. However, none of these approaches are currently applicable to characterize soil-root-microbe interactions simultaneously in their spatial arrangement. Here we present a novel approach that allows for simultaneous microbial identification and chemical analysis of the rhizosphere at micro- to nano-meter spatial resolution. Our approach includes (i) a resin embedding and sectioning method suitable for simultaneous correlative characterization of Zea mays rhizosphere, (ii) an analytical work flow that allows up to six instruments/techniques to be used correlatively, and (iii) data and image correlation. Hydrophilic, immunohistochemistry compatible, low viscosity LR white resin was used to embed the rhizosphere sample. We employed waterjet cutting and avoided polishing the surface to prevent smearing of the sample surface at nanoscale. The quality of embedding was analyzed by Helium Ion Microscopy (HIM). Bacteria in the embedded soil were identified by Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH) to avoid interferences from high levels of autofluorescence emitted by soil particles and organic matter. Chemical mapping of the rhizosphere was done by Scanning Electron Microscopy (SEM) with Energy-dispersive X-ray analysis (SEM-EDX), Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS), nano-focused Secondary Ion mass Spectrometry (nanoSIMS), and confocal Raman spectroscopy (μ-Raman). High-resolution correlative characterization by six different techniques followed by image registration shows that this method can meet the demanding requirements of multiple characterization techniques to identify spatial organization of bacteria and chemically map the rhizosphere. Finally, we presented individual and correlative workflows for imaging and image registration to analyze data. We hope this method will be a platform to combine various 2D analytics for an improved understanding of the rhizosphere processes and their ecological significance.

Silicifying biofilm exopolymers on a hot-spring microstromatolite: templating nanometer-thick laminae

Exopolymeric substances (EPS) are an integral component of microbial biofilms; however, few studies have addressed their silicification and preservation in hot-spring deposits. Through comparative analyses with the use of a range of microscopy techniques, we identified abundant EPS significant to the textural development of spicular, microstromatolitic, siliceous sinter at Champagne Pool, Waiotapu, New Zealand. Examination of biofilms coating sinter surfaces by confocal laser scanning microscopy (CLSM), environmental scanning electron microscopy (ESEM), cryo-scanning electron microscopy (cryo-SEM), and transmission electron microscopy (TEM) revealed contraction of the gelatinous EPS matrix into films (approximately 10 nm thick) or fibrillar structures, which is common in conventional SEM analyses and analogous to products of naturally occurring desiccation. Silicification of fibrillar EPS contributed to the formation of filamentous sinter. Matrix surfaces or dehydrated films templated sinter laminae (nanometers to microns thick) that, in places, preserved fenestral voids beneath. Laminae of similar thickness are, in general, common to spicular geyserites. This is the first report to demonstrate EPS templation of siliceous stromatolite laminae. Considering the ubiquity of biofilms on surfaces in hot-spring environments, EPS silicification studies are likely to be important to a better understanding of the origins of laminae in other modern and ancient stromatolitic sinters, and EPS potentially may serve as biosignatures in extraterrestrial rocks.

A balanced technique for preparation of specimens from pathogenicity studies for scanning electron microscopy

This paper reports our experiences with preparing delicate biological specimens for scanning electron microscopy. Three different washing methods were evaluated: One method allowed the analysis of the location of the bacterium Mycoplasma mobile on piscine gill epithelium and the optimal evaluation of histopathologic changes caused by this microbe. These results were achieved when specimens were washed three times in a cacodylic acid buffer after completion of the in vitro infection experiment in gill explant cultures. We also found that of three different concentrations of glutaraldehyde, a fixation with a 1.5% solution was sufficient to achieve excellent structural preservation, even without using post fixation in osmium tetroxide. Furthermore, this study showed that the use of acetone-carbon dioxide in the critical point drying procedure resulted in well-preserved piscine gill epithelium and mycoplasmas. Finally, long-term storage of tissue specimens in 0.1 M cacodylic acid buffer is possible if the buffer is changed on a monthly basis to avoid growth of unwanted microorganisms, such as fungi.

Intestinal, segmented, filamentous bacteria

Segmented, filamentous bacteria (SFBs) are autochthonous, apathogenic bacteria, occurring in the ileum of mice and rats. Although the application of formal taxonomic criteria is impossible due to the lack of an in vitro technique to culture SFBs, microbes with a similar morphology, found in the intestine of a wide range of vertebrate and invertebrate host species, are considered to be related. SFBs are firmly attached to the epithelial cells of the distal ileal mucosa, their preferential ecological niche being the epithelium covering the Peyer's patches. Electron microscopic studies have demonstrated a considerable morphological diversity of SFBs, which may relate to different stages of a life cycle. Determinants of SFB colonization in vivo are host species, genotypical and phenotypical characteristics of the host, diet composition, environmental stress and antimicrobial drugs. SFBs can survive in vitro incubation, but do not multiply. On the basis of their apathogenic character and intimate relationship with the host, it is suggested that SFBs contribute to development and/or maintenance of host resistance to enteropathogens.

Ultrastructure of filamentous microorganisms associated with zebra cyathostomes

Filamentous microorganisms were observed colonizing the cuticle of cyathostomes (Nematoda: Strongylidae) collected from the large intestine of Burchell's zebra (Equus burchelli antiquorum). Scanning (SEM) and transmission (TEM) electron microscopy revealed three filamentous microorganisms, designated as segmented, continuous multicellular, and helical. The segmented and continuous multicellular morphotypes each revealed a process of segmentation in their developmental stages, and those of the segmented filaments are demonstrated in this report. In contrast, the helical types of filaments appeared to be complexes of spiraling rodshaped organisms. In addition to these filaments, the cyathostome cuticle was also colonized by other smaller microorganisms.

Pathogenesis of corneal lesions caused by Moraxella bovis in gnotobiotic calves

Moraxella bovis was instilled into the conjunctival sac of gnotobiotic calves and corneas were sampled serially after infection. Lesions developed in seven of eight infected calves, but were absent in a noninfected control calf. Histologically, M. bovis was first seen in foci of swollen epithelium and within basal epithelial cells adjacent to ulcers. Corneal ulcers were severe in later stages of infection; fibrin deposits, neutrophils, and bacteria were present in the stromas. Examination of early lesions by scanning electron microscopy showed M. bovis in pits on the surfaces of dark epithelial cells, enmeshed in degenerate epithelial cells and within erosions and an ulcer; in later samples, bacteria were rare. Ultrastructurally, M. bovis was seen in surface pits in superficial epithelial cell processes and within swollen epithelial cells. In stroma, M. bovis was frequently seen among collagen fibrils, within neutrophil phagosomes, and associated with cellular debris. This study demonstrates that a virulent strain of M. bovis can invade bovine corneal epithelial cells and can cause keratitis in the absence of injurious ultraviolet irradiation or other known predisposing environmental factors.

Colonization of the gut of the blue crab (Callinectes sapidus) by Vibrio cholerae

Attachment of Vibrio cholerae to the mucosal surface of the intestine is considered to be an important virulence characteristic. Vibrio cholerae, an autochthonous member of brackish water and estuarine bacterial communities, also attaches to crustacea, a significant factor in multiplication and survival of V. cholerae in nature. The ability of V. cholerae to attach to the gut wall of the blue crab (Callinectes sapidus) was examined, and attachment was observed only in the hindgut and not the midgut of crabs, confirming a requirement for chitin in the attachment of V. cholerae to invertebrate and zooplankton surfaces. The new finding of attachment of V. cholerae to the hindgut of crabs may be correlated with the epidemiology and transmission of cholera in the aquatic environment. The crab model may also prove useful in elucidating the mechanism(s) of ion transport in crustacea.

The bacterial biota on crustose (nonarticulated) coralline algae from Tasmanian waters

The bacterial biota associated with the cuticle surface of healthy benthic samples of crustose nonarticulated coralline algae from the east coast of Tasmania (Australia) was examined by bacteriological cultivation and electron microscopy. In 32 samples studied, the viable count on Zobell's marine agar (supplemented with vitamins) was 3.3×10(6) bacteria g(-1) wet wt. (range 2.9×10(4)-2.7×10(7)). Of 732 strains isolated from 16 out of 32 samples and identified to genus level,Moraxella was the predominant genus (66%). In contrast,Moraxella comprised only 11% of 217 strains isolated from benthic seawater samples collected at the same time as coralline algae. In 22 out of 32 algal samples examined by scanning electron microscopy, the total count was 1.6 × 10(7) bacteria g(-1) wet wt. (range 5.1× 10(6)-3.8×107); the major morphotype was cocco-bacilli (80%). Several environmental factors did not significantly influence the viable count or generic distribution, or the total count or morphotypic distribution of bacteria on the cuticle. These factors included geographical site, season, storage of samples in aquarium conditions, and the presence or absence of abalone from shells that the coralline algae encrusted. The microbiota, consisting mostly of the nonmotile bacterial genusMoraxella, appeared to be highly adapted to its calcerous plant host.

Scanning electron microscope studies on preparations of bovine cornea exposed to Moraxella bovis

Preparations of bovine cornea were studied by scanning electron microscopy before and after in vitro exposure to Moraxella bovis. The bacteria were observed in association with the surface of the corneal epithelium; they showed a predilection for dark cells relatively devoid of surface structure. Pit-like depressions related to the presence of individual bacteria were produced in these cells. An evident association with corneal epithelium was shown by 2 strains known to be pathogenic experimentally in cattle but not by 2 non-pathogenic strains.

The preservation of mucus and surface-associated microorganisms using acrolein vapour fixation

Three fixation schedules were devised and compared in terms of their influence on the preservation of mucus and surface-associated microorganisms contained within it. Different mucus-secreting epithelial tissues from normal and spoiled oysters and normal rats were examined by scanning and transmission electron microscopy and light microscopy. On all tissues, mucus was best preserved in specimens fixed by 10% acrolein vapour for 1 h then immersed in 3% glutaraldehyde--3% formaldehyde fixative containing 0.05% ruthenium red, cacodylate buffer pH 7.4, for at least 3 h. This fixation schedule also greatly increased the preservation of microorganisms in mucus in specimens from spoiled oysters and normal rats. In contrast, the retention of mucus and surface-associated microorganisms was poor in tissues fixed either by 1% OsO4 vapour for 1 h followed by immersion in combined aldehyde fixative, or by direct immersion. The quality of preservation of the mucus layer, epithelium and sub-epithelium was also noted by transmission electron microscopy in tissues prepared by the different fixation schedules. Cellular preservation was satisfactory in directly immersed tissues but poor in vapour fixed specimens.

Absence of surface-associated microorganisms in adult oysters (Crassostrea gigas)

Healthy, actively feeding intertidal oysters were removed from an estuarine environment (Pipeclay Lagoon, Tasmania). The epithelial surfaces of various organs of the mantle cavity and alimentary tract were explored by scanning and transmission electron microscopy. All epithelial tissues examined were ciliated, and nearly all were partly covered with secreted mucus. However, microorganisms were seen rarely in the adhesive mucus and never attached to the epithelium. Electron microscopy also failed to demonstrate a surface microflora in emersed oysters which had been incubated at 5 to 25 degrees C for 6 or 24 h. The absence of an internal surface microflora did not vary on a seasonal basis. In laboratory experiments, oysters were allowed to filter feed from seawater containing diverse types of marine bacteria at concentrations of 10(3) to 10(7)/mL. However, no surface microflora could be found within actively feeding oysters or in emersed animals incubated at 20 degrees C for 6 or 24 h. In contrast, surface-associated microorganisms were detected readily by scanning electron microscopy on the external shell of healthy oysters and on various internal tissues in spoiled oysters. It is suggested that the major mechanisms restricting microbial growth within oysters are ciliary movement and mucus secretion.

Segmented filamentous bacteria in the rodent small intestine: Their colonization of growing animals and possible role in host resistance toSalmonella

The establishment and proliferation of a model population of autochthonous surface-associated microorganisms in the small bowel of growing rats (2-12 weeks of age) was studied. Segmented filamentous bacteria on the distal ileal villi were examined by scanning electron microscopy (SEM) and countedin situ by transect line analysis. In young animals, these bacteria first colonized the villous base, but occupied all areas on the villus by adult age. Their distribution on Peyer's patches was also noted.In growing animals, colonization of the ileal villi by filamentous bacteria was significantly correlated to the development of host resistance to fatal infection by orally-dosedSalmonella enteritidis. In animals givenSalmonella and examined by SEM and transmission EM (TEM), the pathogen was seen only on ileal tissue surfaces, predominantly the villous base, from which the autochthonous population was absent. Conversely, in animals with filamentous bacteria,Salmonella surface colonization was not observed. The results suggest a possible protective role for the surface flora in the small bowel.

Scanning electron microscope observation of the swarming phenomenon of Vibrio parahaemolyticus

Scanning electron microscopy was used to study the production of lateral flagella and the swarming phenomenon in Vibrio parahaemolyticus. Differences in the size and diameter of the sheathed, polar flagellum and lateral flagella were apparent in these preparations. Swarming of V. parahaemolyticus was found to be similar to the swarming of Proteus spp. in that swarm cells which are heavily flagellated and elongated are formed.

Improved handling of structural fragile cell-biological specimens during electron microscopic preparation by the exchange method

An exact method of preparation of soft biological specimens for electron microscopic analysis of surface fine structures is described. It allows routine preparations of fragile specimens for SEM and TEM imaging modes. With this procedure physical preparation parameters such as mechanical loads on the specimen surface or changes of temperature are controlled. The wet specimens are premounted in cheap disposable BEEM-containers or glass boats and are constantly kept under liquid in a closed system. The exchange of preparation media is performed continuously and, if necessary, over gradients. For comparative investigations with different EM-modes, at each step of the procedure parts of the specimens may be removed for individual processing. Conventionally prepared critical-point dried specimens are compared to those processed by the exchange technique and preservation of surface fine structures is demonstrated. Shadow-casted clathrin cages and stereo-replicas of virus infected cell cultures are shown in TEM preparations. For SEM, coverslip cell cultures and isolated glomerulus basement membranes are prepared and an additional flat embedding for TEM ultrathin sections is demonstrated.