Conventional Scanning Electron Microscopy of Bacteria Miloslav Kaláb, Ann-Fook Yang, Denise Chabot Scanning electron microscopy (SEM) is one of the best suited out of a variety of procedures to visualise the external appearance of bacteria. Bacteria live in various environments and their preparation for SEM thus takes their nature into consideration. The basic principles of isolation, fixation, dehydration, drying, mounting, and photographing have many variations, some of which are discussed in this article. Bacteria are present everywhere: in the soil, deep in the rocks, in all bodies of water, in the atmosphere, including the clouds, and also on and inside other living organisms. Introduction bacteria visualised by TEM are shown to distinguish Bacteria are present everywhere: in the soil, deep in them from images obtained by SEM. the rocks, in all bodies of water, in the atmosphere, including the clouds, and also on and inside other In negative staining, a dilute suspension of unfixed living organisms. Their effects on higher life forms bacteria is applied on a Formvar film followed by are known for only a limited number of bacterial addition of a dilute heavy metal salt solution (e.g., species. Some are harmful - pathogenic - causing uranyl acetate, ammonium molybdate, or sodium diseases in plants or in animals including humans, phosphotungstate). When the dried specimen is and some are useful to humans either as “probiotic” placed into the path of an electron beam in the bacteria protecting health (Karpa, 2006), or TEM, the electrons are absorbed by the heavy metal industrially by participating in the production of but they pass through the bacteria and form their various commodities. The effects of most bacteria images on a fluorescent screen. This procedure is are not known. A new trend is in progress (Sachs, excellent to show bacterial fimbriae, flagella, etc. 2008) not to exterminate harmful bacteria in human (see Figure 2). and animal environments but to replace them with beneficial ones. Bacteria which are genetically Embedding bacteria in a resin and staining thin programmed to die after their mission has been sections of the resulting bloc with heavy metals accomplished in humans or animals are part of the such as uranyl acetate and lead citrate (Reynolds new trend. These minute microorganisms have far- 1963) reveals the internal structure of the bacteria reaching macroscopic consequences. They are of (Figure 3). interest to agriculture because they may harm or improve the production of foods, either animal or One of the most elaborate TEM techniques consists plant, and thus affect human civilisation. of rapidly freezing the bacteria, freeze-fracturing them, replicating the newly developed surfaces with Electron microscopy is one of a limited number platinum and carbon, and examining the replicas. of techniques suitable to show bacteria in great Haggis & Bond (1979) developed a replication detail in their natural environment. There are two procedure for dried specimens which was later used basic modes, scanning electron microscopy (SEM) by Kalab (1980) to visualise bacteria in cultured milk and transmission electron microscopy (TEM), and products (Figure 4). each of them uses specially designed microscopes. SEM is relatively easy to perform and the results Scanning electron microscopy are easy to interpret, because the specimens are Like TEM, SEM also consists of different techniques. shown as three-dimensional objects (Figure 1). TEM Conventional SEM is used to visualise bacteria produces different kinds of images based on the fact which had been fixed, dehydrated, and dried. Rapidly that the electron beam passes through the specimen frozen (cryofixed) bacteria may be examined and forms a shadow-like image on a fluorescent at very low temperatures (below –120°C) by screen which is photographed. Several examples of cryo-SEM. Both techniques are carried out with 44 ISSUE 10 JUNE 2008 Fig. 1. SEM of a cluster of Bifidobacterium breve bacteria on a bacterial filter. Bifidobacteria are gram-positive, anaerobic, branched rod-shaped probiotic bacteria with a very wide variety of species. Bar: 2 µm. 45 Fig. 2. Negative staining of a Gluconoacetobacter spp. bacterium with phosphotungstic acid reveals the flagella. Bar: 1 µm. Fig. 3. Thin section of Pseudomonas fluorescens bacteria. P. fluorescens are gram-negative, rod-shaped bacteria with multiple flagella. Bar: 1 µm. 46 ISSUE 10 JUNE 2008 the specimen placed in a high vacuum chamber. contain proteins and a high proportion of water in There, the specimen must not release any volatile their cells. It is essential to fix them first in order substances. Drying or freezing at a very low to preserve their structure while they are being temperature meets this requirement. Environmental further prepared for SEM. To accomplish such SEM (ESEM) makes it possible to examine hydrated steps in reasonable time, the specimens should specimens by not exposing them to high vacuum. A be relatively thin (<2 mm) and small (only a few sophisticated technical design keeps the specimen mm). Large solid materials which contain bacteria at a temperature several degrees above the on their surfaces such as contaminated meat, skin, freezing point of water in a small area inside the vegetables, composted materials, or agar gel plates microscope where a low partial pressure of water with bacterial colonies are first excised and trimmed vapour provides ions at a concentration sufficient to approximately 10 mm x 10 mm specimens as thin to neutralise electrons and thus to prevent charging as possible (1 - 2 mm), and fixed before they are artifacts (Kalab 1984). Cryo-SEM and ESEM have further reduced into smaller (approx. 5 mm x 5 their own specific features which in some aspects mm) particles. differ from conventional SEM. If the bacteria are inside a specimen such as set- Every specimen destined style yogurt, cheese, kefir grains and other materials which may easily be cut, it is advantageous to for conventional SEM trim them into prisms 10 to 15 mm long and less must be dry. than 1.5 mm x 1.5 mm in cross section. Viscous specimens such as stirred yogurt and cream are Each of the electron microscopy modes mentioned best encapsulated in agar gel tubes in the form of has advantages and disadvantages. Conventional 10 to 15 mm long columns (Allan-Wojtas & Kaláb, SEM is a relatively simple and rapid technique and 1984a), whereas heat-sensitive foods such as raw the images are easy to interpret, but it does not egg yolk may be encapsulated in calcium alginate gel provide as high resolution as TEM. In principle, the tubes (Veliky & Kaláb, 1990). Bacterial colonies on preparation for SEM consists of isolating the bacteria agar gel plates are excised with up to 1 mm of a or trimming the specimen where they are present, clear agar gel rim. If possible, the bacteria destined fixing them, dehydrating in ethanol, critical-point for SEM should be grown on thin plates (<2 mm) to drying, mounting on an SEM stub, sputter-coating make the excision easier. with gold, and recording images at an appropriate accelerating voltage. Solid specimens are fixed in a buffered (0.1 M, pH 6.5-7.0) fixative such as 2-3% glutaraldehyde Dehydration and critical-point drying may disturb for periods ranging from 5 min to 24 h (Glauert, bacterial flagella. Sputter coating the fixed and dried 1975a). If specimen constituents not based on bacteria with a 20 nm thick layer gold obscures fine protein such as lipids (fat globules in food products) structures such as pili and fimbriae. However, such or polysaccharides (mucus in the intestines) are structures may be visualised by TEM using negative also present, postfixation using osmium tetroxide staining or shadowing with platinum. (OsO4) or Ruthenium Red, respectively, is used. Although double bonds (–C=C–) in unsaturated fatty acids react with osmium tetroxide, osmium SEM Preparation Procedures is easily removed by subsequent spontaneous Every specimen destined for conventional SEM hydrolysis. It results in the formation of a diol and must be dry. As living microorganisms, bacteria the release of free osmium trioxide (OsO3) (Greyer 47 Fig. 4. Replica of a lactic acid bacterium in Cottage cheese. The specimen had been fixed, dehydrated in ethanol, freeze-fractured, thawed, critical- point dried, and replicated with platinum and carbon. Bar: 1µm. 1977). No hydrolysis takes places, however, if a fixative. Our own experiments on chicken intestines heterocyclic base such as pyridine or imidazole is (not yet published) indicate that the intestinal wall present in the fixative (Angermüller & Fahimi, 1982). specimens need to be freeze-fractured and viewed Imidazole-buffered OsO4 preserves the fat and oil sideways in order to see the bacteria which are particles for SEM in specimens such as cheese, below the mucus. yogurt (Allan-Wojtas & Kaláb, 1984b), hard-boiled eggs, and comminuted meat products. Fixed specimens are washed with the corresponding buffer and dehydrated in a graded ethanol series. The need to fix intestinal mucus to visualise bacteria Foods may be considerably denser than the sources attached to the intestinal walls was encountered by from which they had been produced. For example, Allan-Wojtas et al. (1997). Conventional preparation cheeses are very dense, particularly low-fat cheeses of intestinal specimens, however, may fail to retain and processed cheeses, ham is considerably denser the bacteria because they are washed off from the than muscle. Such specimens thus require longer intestines along with the mucus covering them. The periods for both fixation and dehydration. The mucus may be fixed using Ruthenium Red or Alcian fixative and dehydrating solutions must penetrate Blue (Erdos, 1986) added to the glutaraldehyde the entire specimens to make the SEM examination 48 ISSUE 10 JUNE 2008 relevant. There is a relatively easy test to check void spaces. Naturally, bacteria present in the area osmium tetroxide fixation of yogurt and cheese.