Microbiology Part 2 PDF

SECTION 1: Part 2 Monerans and Protists  MONERANS Bacteria and archaea are in the Kingdom Procaryotae (or Monera) Algae and protozoa are in the Kingdom Protista (organisms in this kingdom are referred to as protists)  TAXONOMY According to Bergey...

SECTION 1: Part 2 Monerans and Protists  MONERANS Bacteria and archaea are in the Kingdom Procaryotae (or Monera) Algae and protozoa are in the Kingdom Protista (organisms in this kingdom are referred to as protists)  TAXONOMY According to Bergey’s Manual of Systematic Bacteriology taxonomy (the science of classification of living organisms) consists of three separate but interrelated areas: classification, nomenclature, and identification. Classification - is the arrangement of organisms into taxonomic groups (known as taxa [sing., taxon]) on the basis of similarities or relationships. Taxa include kingdoms or domains, divisions or phyla, classes, orders,  TAXONOMY Nomenclature - is the assignment of names to the various taxa according to international rules. Identification - is the process of determining whether an isolate belongs to one of the established, named taxa or represents a previously unidentified species.  Microbial Classification the science of taxonomy was established, based on the binomial system of nomenclature developed in the 18th century by the Swedish scientist, Carolus Linnaeus.  Microbial Classification In the binomial system, each organism is given two names: The first name is the genus (pl., genera), and the second name is the specific epithet. The first and second names together are referred to as the species.  Cell Morphology Bacteria vary greatly in size, usually ranging from spheres measuring about 0.2 µm in diameter to 10.0 µm–long spiral- shaped bacteria, to even longer filamentous bacteria.  Cell Morphology There are three basic shapes of bacteria:  round or spherical bacteria (cocci)  rectangular or rod-shaped bacteria (bacilli)  curved and spiral-shaped bacteria (sometimes referred to as spirilla). Bacteria reproduce by binary fission. The time it takes for one bacterial cell to split into two cells is referred to as that organism’s generation time.  COCCI IN PAIRS (diplococci) CHAINS (streptococci) CLUSTER (staphylococci) PACKETS OF FOUR (tetrad) PACKETS OF EIGHT (octads) COCCI Photo courtesy: https://www.toppr.com/guides/biology/mic roorganisms/cocci-or-cocus-bacteria/  BACILLI PAIRS (diplobacilli) CHAINS (streptobacilli) SOME RODS ARE QUITE SHORT, RESEMBLING ELONGATED COCCI (coccobacilli)  BACILLI Curved and spiral-shaped bacilli are placed into a third morphologic grouping. Spiral-shaped bacteria are referred to as spirochetes.  Some bacteria may lose their characteristic shape because adverse growth conditions (e.g., the presence of certain antibiotics) prevent the production of normal cell walls.  Some CWD bacteria revert to their original shape when placed in favorable growth conditions, whereas others do not. Bacteria in the genus Mycoplasma do not have cell walls; thus, when examined microscopically, they  Bacteria in the genus Mycoplasma do not have cell walls; thus, when examined microscopically, they appear in various shapes. Bacteria that exist in a variety of shapes are described as being pleomorphic; the ability to exist in a variety of shapes is known as pleomorphism.  Staining Procedures In preparation for staining, the bacteria are smeared onto a glass microscope slide (resulting in what is known as a “smear”), air-dried, and then “fixed.”  Staining Procedures TO MOST COMMON METHODS OF FIXATION:  HEAT FIXATION -is usually accomplished by passing the smear through a Bunsen burner flame. If not performed properly, excess heat can distort the morphology of the cells.  METHANOL FIXATION- which is accomplished by flooding the smear with absolute methanol for 30 seconds, is a more satisfactory fixation technique.  Staining Procedures Specific stains and staining techniques are used to observe bacterial cell morphology (e.g., size, shape, morphologic arrangement, composition of cell wall, capsules, flagella, endospores).  Staining Procedures In 1883, Dr. Hans Christian Gram developed a staining technique that bears his name—the Gram stain or Gram staining procedure. The Gram stain has become the most important staining procedure in the bacteriology laboratory, because it differentiates between “Gram-positive” and “Gram-  Staining Procedures The color of the bacteria at the end of the Gram staining procedure depends on the chemical composition of their cell wall. If the bacteria were not decolorized during the decolorization step, they will be blue to purple at the conclusion of the Gram staining procedure; such bacteria are said to be “Gram-positive.” The thick layer of peptidoglycan in the cell walls of Gram-positive bacteria makes it difficult to remove the crystal violet–iodine  Staining Procedures If, on the other hand, the crystal violet was removed from the cells during the decolorization step, and the cells were subsequently stained by the safranin (a red dye), they will be pink to red at the conclusion of the Gram staining procedure; such bacteria are said to be “Gram- negative.” The thin layer of peptidoglycan in the cell walls of Gram-negative bacteria makes it easier to remove the crystal violet–iodine complex during decolorization.  Staining Procedures Some strains of bacteria are neither consistently blue to purple nor pink to red after Gram staining; they are referred to as Gram-variable bacteria. Examples of Gram- variable bacteria are members of the genus Mycobacterium, such as M. tuberculosis and M. leprae. Staining Procedures The diversity of microorganisms we see today is the result of nearly 4 billion years of evolution. Microbial diversity can be seen in many ways besides phylogeny, including cell size and morphology (shape), physiology, motility, mechanism of cell division, pathogenicity, developmental biology, adaptation to  MOTILITY Bacterial motility is most If a bacterium Bacteria often associated with the presence of flagella or is able to axial filaments, although unable to some bacteria exhibit a “swim,” it is type of gliding motility on swim are said secreted slime. Bacteria said to be never possess cilia. to be motile. Most spiral-shaped bacteria nonmotile monotrichous, Various terms (e.g., and about one half of the bacilli are motile by means of amphitrichous, flagella, but cocci are lophotrichous, generally nonmotile. A flagella stain can be used to peritrichous) are used to demonstrate the presence, describe the number and number, and location of location of flagella on flagella on bacterial cells. bacterial cell  Metabolic Diversity All cells require an energy source and a metabolic strategy for conserving energy from it to drive energy- consuming life processes. As far as is known, energy can be tapped from three sources in nature: organic  Chemolithotrophs This form of metabolism is called chemolithotrophy and was discovered by the Russian microbiologist Winogradsky. Organisms that carry out chemolithotrophic reactions are called chemolithotrophs. Chemolithotrophy occurs only in prokaryotes and is widely distributed among species of Bacteria and  Phototrophs Phototrophic microorganisms contain pigments that allow them to convert light energy into chemical energy, and thus their cells appear colored. Unlike chemotrophic organisms, then, phototrophs do not require chemicals as a source of energy. This is a significant metabolic advantage because competition with chemotrophic organisms for energy sources is not an issue and sunlight is  Heterotrophs and Autotrophs All cells require carbon in large amounts and can be considered either heterotrophs, which require organic compounds as their carbon source, or autotrophs, which use carbon dioxide (CO2) as their carbon source.  BACTERIA The domain Bacteria contains an enormous variety of prokaryotes. All known disease-causing (pathogenic) prokaryotes are Bacteria, as are thousands of nonpathogenic species. A large variety of morphologies and physiologies are also observed in this domain.  BACTERIA The Proteobacteria make up the largest phylum of Bacteria.  Atmospheric Requirements With respect to oxygen, a bacterial isolate can be classified into one of five major groups:  Obligate aerobes  Microaerophilic aerobes (microaerophiles)  Facultative anaerobes  Aerotolerant anaerobes  Obligate anaerobes  Atmospheric Requirements  Obligate aerobes - To grow and multiply, obligate aerobes require an atmosphere containing molecular oxygen in concentrations comparable to that found in room air (i.e., 20%–21% O2) EXAMPLES: Mycobacteria and certain fungi are examples of microorganisms that are obligate aerobes.  Atmospheric Requirements  Microaerophiles (microaerophilic aerobes) - Microaerophiles (microaerophilic aerobes) also require oxygen for multiplication, but in concentrations lower than that found in room air. EXAMPLE: Neisseria gonorrhoeae (the causative agent of gonorrhea) and Campylobacter spp. (which are major causes of bacterial diarrhea) are examples of microaerophilic bacteria  Atmospheric Requirements  Microaerophiles (microaerophilic aerobes) - Microaerophiles (microaerophilic aerobes) also require oxygen for multiplication, but in concentrations lower than that found in room air. EXAMPLE: Neisseria gonorrhoeae (the causative agent of gonorrhea) and Campylobacter spp. (which are major causes of bacterial diarrhea) are examples of microaerophilic bacteria  Atmospheric Requirements  Obligate anaerobe - is an anaerobe that can only grow in an anaerobic environment (i.e., an environment containing no oxygen).  Aerotolerant anaerobe - does not require oxygen, grows better in the absence of oxygen, but can survive in atmospheres containing molecular oxygen (such as air and a CO2  Atmospheric Requirements  Facultative anaerobes - are capable of surviving in either the presence or absence of oxygen; anywhere from 0% O2 to 20% to 21% O2. EXAMPLE: Many of the bacteria routinely isolated from clinical specimens are facultative anaerobes (e.g., members of the family Enterobacteriaceae, most streptococci, most staphylococci)  Habitats and Extreme Environments Some microbial habitats are ones in which humans could not survive, being too hot or too cold, too acidic or too caustic, or too salty. Although such environments would pose challenges to any life forms, they are often teeming with microorganisms. Organisms inhabiting such extreme environments are called extremophiles, a remarkable group of microorganisms that collectively define the physiochemical limits to life.  Habitats and Extreme Environments Extremophiles abound in such harsh environments as volcanic hot springs; on or in the ice covering lakes, glaciers, or the polar seas; in extremely salty bodies of water; in soils and waters having a pH as low as 0 or as high as 12; and in the deep sea, where hydrostatic pressure can exceed 1000 times atmospheric. Interestingly, these prokaryotes do not just tolerate their particular environmental extreme, they actually Habitats and Extreme Environments ARCHAEA Procaryotic organisms in the Domain Archaea were discovered in 1977. Archae means “ancient,” and the name archaea was originally assigned when it was thought that these procaryotes evolved earlier than bacteria. Now, there is considerable debate as to whether bacteria or archaea came first. Genetically, even though they are procaryotes, archaea are more closely related to eucaryotes than they are to bacteria; some possess genes otherwise found only in eucaryotes. Many scientists believe that bacteria and archaea diverged from a common ancestor relatively soon after life began on this planet. Later, the eucaryotes split off Many, but not all, archaea are “extremophiles,” in the sense that they live in extreme environments, such as extremely acidic, alkaline, hot, cold, or salty environments, or environments where there is extremely high pressure. Some live at the bottom of the ocean in and near thermal vents, where, in addition to heat and salinity, there is extreme pressure. Other archaea, called methanogens, produce methane,