Exercise 3C: Microscopic Characteristics Group 5: Quilang, Aleia Sharisse F. Quinto, Thea Marie Dolores N. Recio, Jose Angelo G. Refuerzo, Jirah Angelica M. Robles, Andreu Vinzent F. Rodriguez, Joanne Claire E. Romero, Mavourneen Tracy Chanel V. Samonte, Muriel Fay D. Introduction All bacteria, both pathogenic and saprophytic, are unicellular organisms that reproduce by binary fission. Most bacteria are capable of independent metabolic existence and growth, but species of Chlamydia and Rickettsia are obligately intracellular organisms. Bacterial cells are extremely small and are most conveniently measured in microns (10-6 m). They range in size from large cells such as Bacillus anthracis (1.0 to 1.3 µm X 3 to 10 µm) to very small cells such as Pasteurella tularensis (0.2 X 0.2 to 0.7 µm). Mycoplasmas (atypical pneumonia group) are even smaller, measuring 0.1 to 0.2 µm in diameter. Bacteria therefore have a surface-to-volume ratio that is very high: about 100,000. Bacteria have characteristic shapes. The common microscopic morphologies are cocci (round or ellipsoidal cells, such as Staphylococcus aureus or Streptococcus, respectively); rods, such as Bacillus and Clostridium species; long, filamentous branched cells, such as Actinomyces species; and comma-shaped and spiral cells, such as Vibrio cholerae and Treponema pallidum, respectively. The arrangement of cells is also typical of various species or groups of bacteria. Some rods or cocci characteristically grow in chains; some, such as Staphylococcus aureus, form grapelike clusters of spherical cells; some round cocci form cubic packets. Bacterial cells of other species grow separately. The microscopic appearance is therefore valuable in classification and diagnosis. The higher resolving power of the electron microscope not only magnifies the typical shape of a bacterial cell but also clearly resolves its prokaryotic organization. Typical Shapes and Arrangements of Bacterial Cells Bacteria are microscopic organisms that cannot be seen with unaided eye. They can be seen even in unstained preparations such as a wet mount or hanging drop preparation but the morphology is not clear. Bacteria are colorless and when suspended in saline they don’t offer any contrast. Besides, bacterial motility makes it difficult to observe the morphology clearly. Hence, bacteria have to be stained to observe them. The dyes often used are toxic chemicals that kill the bacteria. The process of smearing, fixing and drying often kill the bacteria. This process fixes the bacteria to the slide and their position on slide remains unaltered. Objectives To know the different staining methods and how to execute them. To be able to identify the different characteristics of bacteria. To know why it’s important to fix bacteria on the slide. To know the unknown bacteria. Results We we’re not able to perfectly culture all eight bacteria but we were able to get 5. These are what we think the identities of those 5 bacteria: CR_9 A_21 A_1 CR_8 A_22 Unknown Shape Arrangement Color A_1 (BA) coccus staphylococcus Blue A_21 (NA) coccus staphylococcus red A_22 (NA) coccus staphylococcus violet S_CR8 (BA) rods - colorless S_CR9 (NA) coccus streptococcus Blue cell wall Discussion Bacteria display a wide diversity of shapes and sizes, called morphologies. Bacterial cells are about one-tenth the size of eukaryotic cells and are typically 0.5–5.0 micrometres in length. However, a few species — for example,Thiomargarita namibiensis and Epulopiscium fishelsoni — are up to half a millimetre long and are visible to the unaided eye; E. fishelsoni reaches 0.7 mm. Among the smallest bacteria are members of the genusMycoplasma, which measure only 0.3 micrometres, as small as the largest viruses. Some bacteria may be even smaller, but these ultramicrobacteria are not well-studied. Most bacterial species are either spherical, called cocci (sing. coccus, from Greek kókkos, grain, seed), or rod-shaped, called bacilli (sing. bacillus, from Latin baculus, stick). Elongation is associated with swimming. Some bacteria, called vibrio, are shaped like slightly curved rods or comma-shaped; others can be spiral-shaped, called spirilla, or tightly coiled, called spirochaetes. A small number of species even have tetrahedral or cuboidal shapes. More recently, bacteria were discovered deep under Earth's crust that grows as branching filamentous types with a star-shaped cross-section. The large surface area to volume ratio of this morphology may give these bacteria an advantage in nutrient-poor environments. This wide variety of shapes is determined by the bacterialcell wall and cytoskeleton, and is important because it can influence the ability of bacteria to acquire nutrients, attach to surfaces, swim through liquids and escape predators. Many bacterial species exist simply as single cells, others associate in characteristic patterns: Neisseria form diploids (pairs), Streptococcus form chains, and Staphylococcus group together in "bunch of grapes" clusters. Bacteria can also be elongated to form filaments, for example the Actinobacteria. Filamentous bacteria are often surrounded by a sheath that contains many individual cells. Certain types, such as species of the genus Nocardia, even form complex, branched filaments, similar in appearance to fungal mycelia. Classification seeks to describe the diversity of bacterial species by naming and grouping organisms based on similarities. Bacteria can be classified on the basis of cell structure, cellular metabolism or on differences in cell components such as DNA, fatty acids, pigments, antigens and quinones. While these schemes allowed the identification and classification of bacterial strains, it was unclear whether these differences represented variation between distinct species or between strains of the same species. This uncertainty was due to the lack of distinctive structures in most bacteria, as well as lateral gene transfer between unrelated species. Due to lateral gene transfer, some closely related bacteria can have very different morphologies and metabolisms. To overcome this uncertainty, modern bacterial classification emphasizes molecular systematics, using genetic techniques such as guanine cytosine ratio determination, genome-genome hybridization, as well as sequencing genes that have not undergone extensive lateral gene transfer, such as the rRNA gene. Classification of bacteria is determined by publication in the International Journal of Systematic Bacteriology, and Bergey's Manual of Systematic Bacteriology. The International Committee on Systematic Bacteriology (ICSB) maintains international rules for the naming of bacteria and taxonomic categories and for the ranking of them in the International Code of Nomenclature of Bacteria The term "bacteria" was traditionally applied to all microscopic, single-cell prokaryotes. However, molecular systematics showed prokaryotic life to consist of two separate domains, originally called Eubacteria and Archaebacteria, but now called Bacteria and Archaea that evolved independently from an ancient common ancestor. The archaea and eukaryotes are more closely related to each other than either is to the bacteria. These two domains, along with Eukarya, are the basis of the three-domain system, which is currently the most widely used classification system in microbiology. However, due to the relatively recent introduction of molecular systematics and a rapid increase in the number of genome sequences that are available, bacterial classification remains a changing and expanding field. For example, a few biologists argue that the Archaea and Eukaryotes evolved from Gram-positive bacteria. Identification of bacteria in the laboratory is particularly relevant in medicine, where the correct treatment is determined by the bacterial species causing an infection. Consequently, the need to identify human pathogens was a major impetus for the development of techniques to identify bacteria. The Gram stain, developed in 1884 by Hans Christian Gram, characterizes bacteria based on the structural characteristics of their cell walls. The thick layers of peptidoglycan in the "Gram-positive" cell wall stain purple, while the thin "Gram-negative" cell wall appears pink. By combining morphology and Gram-staining, most bacteria can be classified as belonging to one of four groups (Gram-positive cocci, Gram-positive bacilli, Gram-negative cocci and Gramnegative bacilli). Some organisms are best identified by stains other than the Gram stain, particularly mycobacteria or Nocardia, which show acid-fastness on Ziehl–Neelsen or similar stains. Other organisms may need to be identified by their growth in special media, or by other techniques, such as serology. Culture techniques are designed to promote the growth and identify particular bacteria, while restricting the growth of the other bacteria in the sample. Often these techniques are designed for specific specimens; for example, a sputum sample will be treated to identify organisms that cause pneumonia, while stool specimens are cultured on selective media to identify organisms that cause diarrhea, while preventing growth of non-pathogenic bacteria. Specimens that are normally sterile, such as blood, urine or spinal fluid, are cultured under conditions designed to grow all possible organisms. Once a pathogenic organism has been isolated, it can be further characterized by its morphology, growth patterns such as (aerobic or anaerobic growth, patterns of hemolysis) and staining. As with bacterial classification, identification of bacteria is increasingly using molecular methods. Diagnostics using such DNA-based tools, such as polymerase chain reaction, are increasingly popular due to their specificity and speed, compared to culture-based methods. These methods also allow the detection and identification of "viable but nonculturable" cells that are metabolically active but non-dividing. However, even using these improved methods, the total number of bacterial species is not known and cannot even be estimated with any certainty. Following present classification, there are a little less than 9,300 known species of prokaryotes, which includes bacteria and archaea; but attempts to estimate the true number of bacterial diversity have ranged from 107 to 109 total species – and even these diverse estimates may be off by many orders of magnitude. Answers to Questions Different Staining Methods Direct Stain Microbial cells are small and transparent. Stains are often used to increase contrast between the cells and the background, making them easier to see under the microscope. Since many of the cell components are negatively charged, stains with positively charged chromophores (the colored ion of the dye) will attach to the cells. Examples of such stains include methylene blue, crystal violet, and carbol fuchsin. Steps: Make a heat-fixed smear, taking care not to use too much culture if working from an agar culture. Place the slide on a staining rack over a sink or catch basin. Add a drop of dye to the smear. You need enough stain to just cover the smear, not the whole slide. Allow the dye to act. (One minute is generally adequate.) Gently rinse the dye from the slide with water from a squirt bottle. Gently blot the slide and observe under the microscope. Negative Staining This is an established method, often used in diagnostic microscopy, for contrasting a thin specimen with an optically opaque fluid. In this technique, the background is stained, leaving the actual specimen untouched, and thus visible. This contrasts with 'positive staining', in which the actual specimen is stained. Steps: Place a very small drop (more than a loop full--less than a free falling drop from the dropper) of nigrosin near one end of a well-cleaned and flamed slide. Remove a small amount of the culture from the slant with an inoculating loop and disperse it in the drop of stain without spreading the drop. Use another clean slide to spread the drop of stain containing the organism using the following technique. Rest one end of the clean slide on the center of the slide with the stain. Tilt the clean slide toward the drop forming an acute angle and draw that slide toward the drop until it touches the drop and causes it to spread along the edge of the spreader slide. Maintaining a small acute angle between the slides, push the spreader slide toward the clean end of the slide being stained dragging the drop behind the spreader slide and producing a broad, even, thin smear. Allow the smear to dry without heating. Focus a thin area under oil immersion and observe the unstained cells surrounded by the gray stain. Gram Staining This is a method of differentiating bacterial species into two large groups (grampositive and gram-negative). The name comes from its inventor, Hans Christian Gram. Gram staining differentiates bacteria by the chemical and physical properties of their cell walls by detecting peptidoglycan, which is present in a thick layer in gram-positive bacteria. In a Gram stain test, gram-positive bacteria retain the crystal violet dye, while a counterstain (commonly safranin or fuchsin) added after the crystal violet gives all gramnegative bacteria a red or pink coloring. The Gram stain is almost always the first step in the identification of a bacterial organism. While Gram staining is a valuable diagnostic tool in both clinical and research settings, not all bacteria can be definitively classified by this technique. This gives rise to gram-variable and gram-indeterminate groups as well. The reagents used are Crystal violet, Gram's iodine solution, acetone/ethanol (50:50 v:v), 0.1% basic fuchsin solution Steps: 1. Prepare a Slide Smear: A. Transfer a drop of the suspended culture to be examined on a slide with an inoculation loop. If the culture is to be taken from a Petri dish or a slant culture tube, first add a drop or a few loopful of water on the slide and aseptically transfer a minute amount of a colony from the Petri dish. Note that only a very small amount of culture is needed; a visual detection of the culture on an inoculation loop already indicates that too much is taken. If staining a clinical specimen, smear a very thin layer onto the slide, using a wooden stick. Do not use a cotton swab, if at all possible, as the cotton fibers may appear as artifacts. The smear should be thin enough to dry completely within a few seconds. Stain does not penetrate thickly applied specimens, making interpretation very difficult. B. Spread the culture with an inoculation loop to an even thin film over a circle of 1.5 cm in diameter, approximately the size of a dime. Thus, a typical slide can simultaneously accommodate 3 to 4 small smears if more than one culture is to be examined. C. Air-dry the culture and fix it or over a gentle flame, while moving the slide in a circular fashion to avoid localized overheating. The applied heat helps the cell adhesion on the glass slide to make possible the subsequent rinsing of the smear with water without a significant loss of the culture. Heat can also be applied to facilitate drying the smear. However, ring patterns can form if heating is not uniform, e.g. taking the slide in and out of the flame. 2. Gram Staining: A. Add crystal violet stain over the fixed culture. Let stand for 10 to 60 seconds; for thinly prepared slides, it is usually acceptable to pour the stain on and off immediately. Pour off the stain and gently rinse the excess stain with a stream of water from a faucet or a plastic water bottle. Note that the objective of this step is to wash off the stain, not the fixed culture. B. Add the iodine solution on the smear, enough to cover the fixed culture. Let stand for 10 to 60 seconds. Pour off the iodine solution and rinse the slide with running water. Shake off the excess water from the surface. C. Add a few drops of decolorizer so the solution trickles down the slide. Rinse it off with water after 5 seconds. The exact time to stop is when the solvent is no longer colored as it flows over the slide. Further delay will cause excess decolorization in the gram-positive cells, and the purpose of staining will be defeated. D. Counterstain with basic fuchsin solution for 40 to 60 seconds. Wash off the solution with water. Blot with bibulous paper to remove the excess water. Alternatively, the slide may shake to remove most of the water and air-dried. Acid Fast Staining Mycobacterium and many Nocardia species are called acid-fast because during an acid-fast staining procedure they retain the primary dye carbol fuchsin despite decolorization with the powerful solvent acid-alcohol. Nearly all other genera of bacteria are nonacid-fast. The acid-fast genera have lipoidal mycolic acid in their cell walls. It is assumed that mycolic acid prevents acid-alcohol from decolorizing protoplasm. The acid-fast stain is a differential stain. Ziehl Neelsen Acid-fast stain ACID-FAST STAIN Cell Color Cell Color Procedure Reagent Acid-fast Bacteria Nonacid-fast Bacteria Primary dye Carbolfuchsin RED RED Decolorizer Acid-alcohol RED COLORLESS RED BLUE Counterstain Methylene blue Step 1: Smear Preparation Add one loopful of sterile water to a microscope slide. Make a heavy smear of Mycobacterium smegmatis. Mix thoroughly with your loop. Then transfer a small amount of Staphylococcus epidermidis to the same drop of water. You will now have a mixture of M. smegmatis and S. epidermidis. Air dry and heat fix. Step 2: Cover the smear with carbolfuchsin dye. Carbolfuchsin a potential carcinogen. Please wear gloves and work with the stain in the hood. Place a piece of paper towel on top of the dye. Be sure the paper towel is saturated with the dye. Step 3: Dry heat for 2 minutes. Step 4: Cool and rinse with water. Decolorize with acid-alcohol for 15-20 seconds. Step 5: Wash the top and bottom of slide with water and clean the slide bottom well. Step 6: Counterstain with Methylene Blue for 30 seconds to 1 minute. Wash and blot the slide with bibulous paper. Focus 10X - then use oil immersion. Spore Staining The primary dye malachite green is a relatively weakly binding dye to the cell wall and spore wall. In fact, if washed well with water, the dye comes right out of the cell wall, however not from the spore wall once the dye is locked in. That is why there is no need for a decolorizer in this stain: it is based on the binding of the malachite green and the permeability of the spore vs. cell wall. The steaming helps the malachite green to permeate the spore wall. Steps: 1. Make a smear of the Bacillus species---air-dry and heat-fix. 2. Put a beaker of water on the hot plate and boil until steam is coming up from the water. Then turn the hot plate down so that the water is barely boiling. 3. Place the wire stain rack over the beaker which now has steam coming up from the boiled water. 4. Cut a small piece of paper towel and place it on top of the smear on the slide. The towel will keep the dye from evaporating too quickly, thereby giving more contact time between the dye and the bacterial walls. 5. Flood the smear with the primary dye, malachite green, and leave for 5 minutes. Keep the paper towel moist with the malachite green. DO NOT let the dye dry on the towel. 6. Remove and discard the small paper towel piece. 7. Wash really WELL with water. 8. Place the smear over the sink and flood the smear with the counterstain dye, safranin, and leave for 1 minute. Flagella Staining Bacterial flagella are fine, threadlike organelles of locomotion. They are slender (about 10 to 30 nm in diameter) and can only be seen directly using the electron microscope. In order to observe them with the light microscope, the thickness of the flagella are increased by coating them with mordants like tannic acid and potassium alum, and staining them with basic fuchsin (Gray method), pararosaniline (Leifson method), silver nitrate West method), or crystal violet (Difco's method). Although flagella staining procedures are difficult to carry out, they often provide information about the presence and location of flagella, which is of great value in bacterial identification. Difco's Spot Test Flagella stain employs an alcoholic solution of crystal violet as the primary stain, and tannic acid and aluminum potassium sulfate as mordants. As the alcohol evaporates during the staining procedure, the crystal violet forms a precipitate around the flagella, thereby increasing their apparent size. Procedure (West): 1. With a wax pencil, mark the left-hand comer of a clean glass slide with the name of the bacterium. 2. Aseptically transfer the bacterium with an inoculating loop from the turbid liquid at the bottom of the slant to 3 small drops of distilled water in the center of a clean slide that has been carefully wiped off with clean lens paper. Gently spread the diluted bacterial suspension over a 3 cm area using the inoculating needle. 3. Let the slide air dry for 15 minutes. 4. Cover the dry smear with solution A (the mordant) for 4 minutes. 5. Rinse thoroughly with distilled water. 6. Place a piece of paper toweling on the smear and soak it with solution B (the stain). Heat the slide in a boiling water bath for 5 minutes in an exhaust hood with the fan on. Add more stain to keep the slide from drying out. 7. Remove the toweling and rinse off excess solution B with distilled water. Flood the slide with distilled water and allow it to sit for 1 minute while more silver nitrate residue floats to the surface. 8. Then, rinse gently with water once more and carefully shake excess water off the slide. 9. Allow the slide to air dry at room temperature. 10. Examine the slide with the oil immersion objective. The best specimens will probably be seen at the edge of the smear where bacteria are less dense. Record your results in the report. Procedure (Difco): 1. Draw a border around the clear portion of a frosted microscope slide with a wax pencil. 2. Place a drop of distilled water on the slide, approximately I cm from the frosted edge. 3. Gently touch a colony of the culture being tested with an inoculating loop and then lightly touch the drop of water without touching the slide. Do not mix. 4. Tilt the slide at a slight angle to allow the drop preparation to flow to the opposite end of the slide. 5. Let the slide air-dry at room temperature. Do not heat-fix. 6. Flood the slide with the contents of the Difco Spot Test Flagella stain ampule. 7. Allow the stain to remain on the slide for approximately 4 minutes. (Note: The staining time may need to be adjusted from 2 to 8 minutes depending on the age of the culture, the age of the stain, the temperature, and the depth of staining solution over the culture.) 8. Carefully rinse the stain by adding water from a faucet or wash bottle to the slide while it remains on the staining rack. Do not tip the slide before this is done. 9. After rinsing, gently tilt the slide to allow excess water to run off and let the slide airdry at room temperature or place on a slide warmer. 10. Examine the slide microscopically with the oil immersion objective. Begin examination at thinner areas of the preparation and move toward the center. Look for fields which contain several isolated bacteria, rather than fields which contain clumps of many bacteria. Bacteria and their flagella should stain purple. Capsule Staining Many bacteria have a slimy layer surrounding them, which is usually referred to as a capsule. The capsule's composition, as well as its thickness, varies with individual bacterial species. Polysaccharides, polypeptides, and glycoproteins have all been found in capsules. Often, a pathogenic bacterium with a thick capsule will be more virulent than a strain with little or no capsule since the capsule protects the bacterium against the phagocytic activity of the host's phagocytic cells. The capsule stain is of some importance in clinical microbiology (e.g., in the diagnosis of bacterial pneumonia and the fungus Cryptococcus neoformans). However, one cannot always determine if a capsule is present by simple staining procedures, such as using negative staining and India ink. An unstained area around a bacterial cell may be due to the separation of the cell from the surrounding stain upon drying. Two convenient procedures for determining the presence of a capsule are Anthony's capsule staining method and the Graham and Evans procedure. Anthony's procedure employs two reagents. The primary stain is crystal violet, which gives the bacterial cell and its capsular material a dark purple color. Unlike the cell, the capsule is nonionic and the primary stain cannot adhere. Copper sulfate is the decolorizing agent. It removes excess primary stain as well as color from the capsule. At the same time, the copper sulfate acts as a counterstain by being absorbed into the capsule and turning it a light blue. In this procedure, smears should not be heat-fixed since shrinkage is likely to occur and create a clear zone around the bacterium, which can be mistaken for a capsule. Procedure: Capsule Staining (Anthony): 1. With a wax pencil, label the left-hand comer of a clean glass slide with the name of the bacterium that will be stained. 2. As shown in figure 15.3, aseptically transfer a loopful of culture with an inoculating loop to the slide. Allow the slide to air dry. Do not heat-fix! 3. Place the slide on a staining rack. Flood the slide with crystal violet and let stand for 4 to 7 minutes. 4. Rinse the slide thoroughly with 20% copper sulfate. 5. Blot dry with bibulous paper. 6. Examine under oil immersion (a coverslip is not necessary) and draw the respective bacteria in the report for exercise 12. Capsules appear as faint blue halos around dark blue to purple cells. Modified Capsule Stain (Graham and Evans): 1. Thoroughly clean the slide to be used with Bon Ami and alcohol. 2. Mix two loopfuls of culture with a small amount (1 to 2 drops) of India ink at one end of the slide. 3. Spread out the drop using a second slide in the same way one prepares a thin smear. 4. Dry the smear. 5. GENTLY rinse with distilled water. 6. Stain for 1 minute with Gram's crystal violet. 7. Rinse again with water. 8. Stain for 1.5 minutes with safranin stain. 9. Rinse with water and blot dry. 10. If a capsule is present, the pink to red bacteria are surrounded by a clear zone. The background is blue-black Importance of Fixing Bacteria on the Slide and How It’s Done Fixation terminates any ongoing biochemical reactions, and may also increase the mechanical strength or stability of the treated tissues. The purpose of fixing a slide that is to be stained is to kill the organism, make it adhere to the slide, and alter the organism so that they more readily accept stains (dyes). In order to heat fix a bacterial smear, it is necessary to first let the bacterial sample air dry. Then either place the slide in the slide holder of a micro incinerator, or pass the dried slide through the flame of a Bunsen burner 3 or 4 times, smear side facing up. Once the slide is heat fixed, it can then be stained. Conclusion Therefore, I conclude that bacteria have different characteristics (shapes and sizes). The different staining techniques make it easy to view these characteristics under the microscope and to differentiate them from one another. 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