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1.6: Basic Microbiology Principles

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    6977
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    Learning Objectives

    • Describe the nomenclature that is used to classify microorganisms
    • Evaluate the growth of microorganisms
    • Evaluate the structure of microorganisms
    • Describe the classification of microorganisms

    Microorganisms are minute living things that are too small to be seen with the unaided eye. The group includes bacteria, fungi, protozoa, and microscopic algae. It also includes viruses. The majority of microorganisms help to maintain the balance of living organisms and chemicals in the environment. Marine and freshwater microorganisms form the basis of the food chain in oceans, lakes, and rivers. Soil microbes help break down wastes and incorporate nitrogen gas from the air into organic compounds; thereby, recycling chemical elements between the soils, water, life, and air. Certain microbes play important roles in photosynthesis, a food and oxygen-generating process that is critical to life on earth. Humans and animals on earth depend on microbes in their intestines for digestion and the syntheses of the necessary material for life.

    Microorganisms have commercial applications. They are used in the synthesis of chemical products like vitamins, organic acids, enzymes, alcohols, and other drugs. The food industry uses microbes to produce vinegar, sauerkraut, pickles, soy sauce, cheese, yogurt, bread, and alcoholic beverages. In addition, enzymes from microbes can now be manipulated to cause the microbes to produce substances that they normally do not synthesize, including cellulose, digestive aids, and drain cleaner, plus important therapeutic substances like insulin. Microbial enzymes have helped produce jeans as well.

    A minority of microorganisms are pathogenic, disease-producing. Therefore, practical knowledge of microbes is necessary for good health. Microorganisms are found almost everywhere, and they should be studied in order to understand nature and the environment.

    Nomenclature

    The system of nomenclature for microorganisms is broken down into prokaryotic cells and eukaryotic cells. Bacteria and archaea are referred to as prokaryotic cells, and fungi and protozoans are called eukaryotic cells. Bacteria are simple, single-celled organisms. Because their genetic material is not enclosed in a nuclear membrane, bacterial cells are called prokaryotes. Archaea are also called prokaryotes.

    Bacterial cells generally appear in one of several shapes. Bacillus are rod-like, coccus are ovoid, and spirochetes are spiral, corkscrew, or curved. These shapes are among the most common shapes that are encountered. Individual bacteria may form pairs, chains, clusters, or other groupings, such formations usually are characteristic of a particular genus or species.

    Bacteria are enclosed in cell walls that are largely composed of a carbohydrate and protein complex called peptidoglycan. Bacteria generally reproduce by dividing into two equal cells. This process is called binary fission. For nutrition, most bacteria use organic chemicals, which in nature can be derived from dead or living organisms. Some bacteria can manufacture their food through photosynthesis, and some bacteria can derive nutrition from inorganic substances. Many bacteria can move by using appendages called flagella.

    Archaea consist of prokaryotic cells. However, they have cell walls that lack peptidoglycan. Archaea are often found in extreme environments, and they are divided into three primary groups. The methanogens produce methane as a waste product from respiration. The extreme halophiles live in extremely salty environments such as the Great Salt Lake and the Dead Sea. The extreme thermophiles live in hot sulfurous water such as the hot springs at Yellowstone National Park. Archaea are not known to cause disease in humans.

    Fungi are eukaryotes. They are organisms whose cells have a distinct nucleus containing the cell’s genetic material, surrounded by a special envelope called a nuclear membrane. Organisms in this kingdom can be unicellular or multicellular. Fungi cannot carry out photosynthesis. True fungi have cell walls composed of chitin. The unicellular fungi are yeast. They are oval microorganisms that are larger than bacteria. Fungi reproduce sexually and asexually. They obtain nutrients by absorbing them from the environment such as soil, seawater, freshwater, or an animal or plant host.

    Protozoa are unicellular eukaryotic microbes. Protozoa move by pseudopods, flagella, or cilia. Amoebae move by using extensions of their cytoplasm called pseudopods. Other protozoa have long flagella or numerous shorter appendages for locomotion called cilia. Protozoa have a variety of shapes and live as free entities or as parasites that absorb or ingest organic compounds from their environment. Some protozoa, such as Euglena, are photosynthetic. They use light as a source of energy and carbon dioxide as their chief source of carbon to produce sugars. Protozoa can reproduce sexually or asexually.

    Algae are photosynthetic eukaryotes with a variety of shapes and sexual and asexual reproductive forms. The algae of interest to biologists are unicellular. The cell walls of many algae are composed of a carbohydrate called cellulose. Algae are abundant in freshwater and salt water, in soil, and in association with plants. Algae need light, water, and carbon dioxide for food production and growth. They receive their energy from sunlight. They do not generally require organic compounds from the environment. As a result of photosynthesis, algae produce oxygen and carbohydrates that are utilized by other organisms, including animals. They play an important role in the balance of nature.

    Viruses are different from the other microorganisms. They are so small that most can be seen only with an electron microscope. They are considered to be acellular. Structurally virus particles contain a core made of one type of nucleic acid, either RNA or DNA. This core is surrounded by a protein coat, which is sometimes encased by a lipid membrane called an envelope. All living cells have RNA and DNA, carry out chemical reactions, and reproduce as self-sufficient units. Viruses can reproduce by using the cellular machinery of other organisms. Viruses are considered to be living when they multiply within the host cells that they infect. In this sense, viruses are parasites of other forms of life. On the other hand, viruses are not considered to be living because they are inert outside living hosts.

    The Growth of Microorganisms

    The requirements for microbial growth are divided into two primary categories. Physical and chemical requirements exist for microorganisms to grow and reproduce. Physical aspects include temperature, pH, and osmotic pressure. Chemical requirements include sources of carbon, nitrogen, sulfur, phosphorus, oxygen, trace elements, and organic growth factors.

    Physical Factors

    Differing temperatures are required for different microorganisms. These organisms are classified into three groups on the basis of their preferred range of temperatures. Psychrophilic microorganisms are cold-loving microbes, mesophilic microorganisms are moderate temperature microbes, and thermophiles are microbes that are considered to be heat-loving microbes. Most bacteria grow only within a limited range of temperatures, and their maximum and minimum growth temperatures are about 30oC apart. They grow poorly at the high and low-temperature extremes within their range.

    Each bacterial species grows at particular minimum, optimum, and maximum temperatures. The minimum growth temperature is the lowest temperature at which the organism will grow. The optimum growth temperature is the temperature at which the species grows best. The maximum growth temperatures are the highest temperature at which growth is possible. The rate of growth diminishes rapidly as the maximum temperature of growth is approached because the high temperature inactivates necessary enzymatic system in the cell.

    Refrigeration is the most common method of preserving organic materials. It is based on the principle that microbial reproductive rates decrease at low temperatures. Microbes can survive subfreezing temperatures, they become dormant and their numbers gradually decline in low temperatures. Some species decline faster than other species. Pyschrotrophs do not grow well at low temperatures, except in comparison with other organisms. However, over time, they are able to slowly degrade organic material. The temperature inside a properly set refrigerator will slow the growth of organisms and will prevent the growth of mesophilic organisms.

    Mesophilic organisms have an optimum growth temperature of 25 to 40oC. This group is the most common of the microbes. These organisms that have adapted to live in the bodies of animals have an optimum temperature close to that of the host. The optimum temperature for pathogenic bacteria is about 37oC. The mesophiles include most of the common spoilage and disease-causing organisms.

    Thermophiles are microorganisms capable of growth at high temperatures. These organisms have an optimum growth temperature of 50 to 60oC. These temperatures can be reached in sunlit soil and in thermal water such as hot springs and hot water taps. Many thermophiles cannot grow at temperatures below about 45oC. Endospores formed by thermophilic bacteria are heat resistant and can survive the usual heat treatment given canned goods. Elevated storage temperatures can cause surviving endospore to germinate and grow; thereby, spoiling food. Thermophilic bacteria are not considered a public health problem. Thermophiles are important in organic compost piles, where temperatures can rise to 50 to 60oC.

    Members of the Archaea have an optimum growth temperature of 80oC or higher. These organisms are called hyperthermophiles or extreme thermophiles. They live in hot springs associated with volcanic activity; sulfur is usually important in their metabolic activity.

    Most bacteria grow best in a narrow pH range near neutrality, between pH 6.5 and 7.5. Few bacteria grow at an acidity below pH 4. For this reason, a number of foods prevent spoilage by using acids produced by bacterial fermentation. Although some bacteria are referred to as acidophiles, and they are tolerant of acidity. The chemoautotrophic bacteria, which are found in the drainage water from coal mines, oxidize sulfur to form sulfuric acid, and they can survive at a pH value of 1.

    Molds and yeast grow over a greater pH range than bacteria. However, the optimum pH for molds and yeast is generally below that of bacteria, usually about pH 5 to 6. Alkalinity also inhibits microbial growth. When bacteria are cultured in the laboratory, they often produce acids that eventually interfere with their growth. To neutralize the acids and maintain the proper pH, chemical buffers are included in the growth medium. Peptones and amino acids in some media act as buffers, and many media also contain phosphate salts. Phosphate salts have the advantage of exhibiting a buffering effect in the pH growth range of most bacteria. They are non-toxic, and they provide phosphorus, which is an essential nutrient.

    Microorganisms obtain their nutrients in solution from the surrounding water. They require water for growth, and their composition is 80 to 90-percent water. High osmotic pressures have the effect of removing necessary water from cells. When microbial cells are in a solution whose concentration of solutes is higher than in the cell (hypertonic) cellular water passes out of the cell through the plasma membrane to the high solute concentration. This osmotic loss of water causes plasmolysis, or shrinkage, of the cell’s cytoplasm.

    The growth of the cell is inhibited as the plasma membrane pulls away from the cell wall. The addition of salts to a solution, and the resulting increase in osmotic pressure, can be used to preserve foods. The effects of osmotic pressure are related to the number of dissolved molecules and ions in a volume of solution.

    Some organisms, extreme halophiles, have adapted to high salt concentrations, and they require high salt concentrations for growth. They are called obligate halophiles. Organisms from such saline water often require nearly 30-percent salt, and the inoculation loop used to transfer them must first be dipped into a saturated salt solution. More common are facultative halophiles, which do not require high salt concentration; however, they are able to grow at salt concentrations of up to 2-percent which is a concentration that inhibits the growth of many organisms. A few species of facultative halophiles can tolerate 15-percent salt.

    Most microorganisms grow in a medium that is nearly all water. If the osmotic pressure is unusually low, hypotonic, water tends to enter a cell. Some microbes that have a relatively weak cell wall can be lysed by such an environment.

    Chemical Factors

    Besides water, an important requirement for the growth of microorganisms is carbon. Carbon is the structural backbone of living matter. It is needed for organic compounds that make up a living cell. Carbon makes up half of the weight of bacterial cells. Chemoheterotrophs receive their carbon from their source of energy, organic materials such as proteins, carbohydrates, and lipids. Chemoautotrophs and photoautotrophs, derive their carbon from carbon dioxide.

    Microorganisms need other elements to synthesize cellular material. Protein synthesis requires considerable amounts of nitrogen as well as some sulfur. The synthesis of DNA and RNA also require nitrogen and some phosphorus, as does the synthesis of ATP, the molecule that is important for the storage and transfer of chemical energy within cells. Nitrogen makes up about 14-percent of the weight of a bacterial cell, and sulfur and phosphorus together constitute about 4-percent of the weight of the cell.

    Many microorganisms have metabolic systems that require oxygen for aerobic respiration. Hydrogen atoms that have been stripped from organic compounds combine with oxygen to form water. This process yields vast amounts of energy while neutralizing a potentially toxic gas. Microbes that use molecular oxygen, aerobes, extract more energy from nutrients than microbes that do not use oxygen, anaerobes. Organisms that require oxygen to live are called obligate aerobes.

    Obligate aerobes are at a disadvantage because oxygen is poorly soluble in water. Therefore, aerobic bacteria have developed, or retained, the ability to continue to grow in the absence of oxygen. Such organisms are called facultative anaerobes. Facultative anaerobes can use oxygen when it is present; however, they are able to continue to grow by using fermentation or anaerobic respiration when oxygen is not available. Their efficiency in producing energy decreases in the absence of oxygen. Escherichia coli is a facultative anaerobe that is found in the human intestinal tract. Many yeasts are also facultative anaerobes. Some microbes are able to substitute other electron acceptors and utilize aerobic respiration. These molecules are nitrate ions and sulfate ions.

    Obligate anaerobes are bacteria that are unable to use molecular oxygen for energy-yielding reactions. These organisms are harmed by the presence of oxygen. Clostridium contains the species that cause tetanus and botulism. These organisms are harmed by the presence of oxygen. They do not use oxygen atoms present in cellular materials, instead they obtain oxygen atoms from water.

    Toxic forms of oxygen include singlet oxygen which is a high energy state of normal oxygen and is highly reactive. Superoxide radicals or superoxide anions are formed during the normal respiration of organisms that use oxygen as a final electron acceptor forming water. In the presence of oxygen, obligate anaerobes appear to form superoxide radicals which are toxic to cellular components. Organisms attempting to grow in atmospheric oxygen must produce an enzyme, superoxide dismutase, to neutralize them. Their toxicity is caused by their instability which leads them to steal electrons. Aerobic bacteria and facultative anaerobes growing aerobically, and aerotolerant anaerobes produce superoxide dismutase with which they convert the superoxide radical to molecular oxygen and hydrogen peroxide. Hydrogen peroxide contains the peroxide anion which is also toxic. Because the hydrogen peroxide produced during normal aerobic respiration is toxic, microbes have developed enzymes, catalase, to neutralize hydrogen peroxide. Catalase and another enzyme, peroxidase, are used by microbes to neutralize peroxide. Another important form of reactive oxygen is ozone. The hydroxyl radical is another intermediate form of oxygen and is the most reactive. It is formed in the cellular cytoplasm by ionizing radiation. Most aerobic respiration produces traces of hydroxyl radicals but they are transient.

    Obligate anaerobes produce neither superoxide dismutase nor catalase. Because aerobic conditions lead to an accumulation of superoxide radicals in the cytoplasm, obligate anaerobes are sensitive to oxygen.

    Aerotolerant anaerobes cannot use oxygen for growth, but they tolerate it. On the surface of a solid medium, they will grow without the use of special techniques. Many of the aerotolerant bacteria characteristically ferment carbohydrates to lactic acid. As lactic acid accumulates, it inhibits the growth of aerobic competitors and establishes a favorable ecological niche for lactic acid producers. Lactobacilli are an example.

    Essential organic compounds an organism is unable to synthesize are known as organic growth factors. These growth factors are obtained from the environment. Some of these growth factors are amino acids, purines, and pyrimidines.

    Classifying Microbes

    The classification of organisms into progressively more inclusive groups is based on phylogeny and phenotype. The nomenclature is the process of applying formal rules in the naming of organisms.

    Domains

    Organisms are classified by cell type in the three domain systems. Animals, plants, and fungi are kingdoms in the Domain Eukarya. The Domain Bacteria includes the pathogenic prokaryotes as well as many of the nonpathogenic prokaryotes found in soil and water. The photoautotrophic prokaryotes are also in this domain.

    The Domain Archaea includes prokaryotes that do not have peptidoglycan in their cell walls. They often live in extreme environments and carry out unusual metabolic processes. Archaea include three major groups:

    • The methanogens—Strict anaerobes that produce methane from carbon dioxide and hydrogen
    • Extreme halophiles—Require high concentrations of salt for survival
    • Hyperthermophiles—Normally grow in extremely hot environments
     The trunk of the phylogenetic tree is a universal ancestor. The tree forms two branches. One branch leads to the domain bacteria, which includes the phyla proteobacteria, chlamydias, spirochetes, cyanobacteria, and Gram-positive bacteria. The other branch branches again, into the eukarya and archaea domains. Domain archaea includes the phyla euryarchaeotes, crenarchaeotes, nanoarchaeotes, and korarchaeotea.
    Figure \(\PageIndex{1}\): Three Domain system – image by OpenStax is licensed under CC BY 4.0

    Bacteria are classified into five groups based on their basic shapes. These shapes include spherical (cocci), spiral (spirilla), rod (bacilli), comma (vibrios), or corkscrew (spirochaetes). These cells can exist as single cells, in pairs, chains, or in clusters.

    Common Prokaryotic Cell Shapes. The term Coccus (plural: cocci) is the name given to round, spherical shapes. The term bacillus (plural: bacilli) is the name given to rod shaped cells. These cells are shaped like long rounded rectangles. The term vibrio (plural vibrios) is the name given to curved rods, these cells have a shape like a long comma. The term coccobacillus (plural coccobacilli) is the name for short rods; these cells look like ovals. The term spirillum (plural spirilla) is the name for long spiral cells; these look like cork screws. The term spirochete (plural spirochetes) is the name for long, loose helical spiral shaped cells. These look similar to the spirillum but are more floppy.
    Figure \(\PageIndex{2}\): Basic Shapes of Bacteria – Image by OpenStax is licensed under CC BY 4.0

    Nomenclature

    Scientific Nomenclature is a binomial nomenclature so that every organism has a unique binomial identification that indicates the individual and its taxonomic placement among other organisms. Taxonomy is the science of classification. Almost 2 million organisms have been identified so far, and the estimate is that 10-100 million total organisms occupy the earth. All cellular organisms evolved from a common ancestor:

    • Similar plasma membrane
    • Use ATP for energy
    • Use DNA for genetic storage

    The differences observed between organisms are due to random mutation and natural selection. Organisms are organized into taxonomic categories by relatedness. Systematics/Phylogeny are the studies of the evolutionary history and relatedness of organisms. Modern taxonomy is based on genetic sequence information or molecular biology.

    Classification of living organisms
    Figure \(\PageIndex{3}\): Hierarchal system of scientific nomenclature for the classification of living organisms – image by Pengo is in the public domain

    Of all the different classification systems, the Gram stain has withstood the test of time. The Gram stain remains an important and useful technique. It allows a large proportion of clinically important bacteria to be classified as Gram positive or negative based on their morphology and differential staining properties.

    Microorganisms can be grouped on the basis of their need for oxygen as well. Facultative anaerobic bacteria can grow in high oxygen or low oxygen content and are among the more versatile bacteria. In contrast, strictly anaerobic bacteria grow only in conditions, where minimal or no oxygen is present in the environment. Bacteria such as bacteroides found in the large bowel are examples of anaerobes. Strict aerobes only grow in the presence of significant quantities of oxygen. Pseudomonas aeruginosa, an opportunistic pathogen, is an example of a strict aerobe. Microaerophilic bacteria grow under conditions of reduced oxygen and sometimes require increased levels of carbon dioxide.

    Phylogenetic Tree

    A universal Phylogenetic Tree has been developed for living organisms that establishes a tripartite division of all living organisms– bacteria, archaea, and eucarya. The classification is based on a comparison of 16s ribosomal RNA sequences. These sequences are highly conserved and undergo change at a slow, gradual and consistent rate. They are therefore useful for making comparisons among different living organisms.

    This phylogenetic tree shows that the three domains of life, bacteria, archaea and eukarya, all arose from a common ancestor.
    Figure \(\PageIndex{4}\): Phylogenetic Tree for microorganisms. - image by OpenStax is licensed under CC BY 4.0

    Ribosomal RNA (rRNA) sequence analysis has emerged as a major method for classification. It has been used to establish a phylogenetic tree. In addition, it is also used to rapidly diagnose pathogens responsible for infections, to help select appropriate therapy, and to identify non-cultivatable microorganisms.

    Molecular subtyping is necessary to determine whether strains from the same species are the same or different. Clues can be obtained by examining the biochemical studies or the antibiotic susceptibility profile, but a more reliable method is by molecular analysis. Pulsed Field Gel Electrophoresis (PFGE) is the most frequently used molecular technique. Chromosomal DNA is digested with a restriction enzyme that makes relatively infrequent cuts in the DNA and as a result creates large DNA fragments. The DNA fragments from the different strains are then run on a gel and compared.

    • Eukaryotes (animals, plants, fungi, protists)
    • Bacteria
    • Archaea (prior to sequencing, Bacteria and Archaea had been grouped together in the kingdom Monera)

    Taxonomic/Phylogenetic Hierarchy groups are based on similarities. The groups begin very general and become more restricted. DNA hybridization and rRNA sequencing are used to determine evolutionary relationships and classification. Organisms that are grouped together are based on relatedness; very general relatedness at the top, followed by more and more specific and restricted subgroups where genus is all related species, and species is a single unique organism group.

    • Kingdom Protista (unicellular eukaryotes) are algae and protozoa and they are nutritionally diverse: autotrophs, heterotrophs, and intracellular parasite
    • Kingdom Fungi are yeasts, molds, and mushrooms that absorb organic material through their plasma membrane
    • Kingdom Animalia are multicellular animals that ingest organic food through a mouth and have cells organized into tissues
    • Kingdom Plantae are multicellular plants that undergo photosynthesis to convert carbon dioxide and water into organic molecules, and this Kingdom has cells organized into tissues

    Prokaryotic Classification-prokaryotes have two domains:

    1. Bacteria are all pathogenic prokaryotes, many non-pathogenic prokaryotes, and all photoautotrophic prokaryotes
    2. Archaea are all prokaryotes with walls that are not peptidoglycan, that carry out unusual metabolism and live in extreme environments, and are groupings based entirely on gene sequencing since most look similar

    Prokaryotic species are defined as a population of cells with similar characteristics that do not demonstrate sexual reproduction. Pure cultures are clones because they are populations derived from a single cell. They are genetically identical. Strains are cells of the same species that are not genetically identical.

    Viral Classification

    Viruses do not fit into a domain system because they are acellular. They are usually only classified by Family and Genus. Viral species are defined as a population of viruses with similar characteristics (including morphology, genes, and enzymes) that occupy a particular ecological niche. Viruses are obligate intracellular parasites that have evolved to infect cells, and they usually only infect one type of cell which is the one that best supports viral replication. Viruses tend to be very specific about their niche.

    Structure

    Prokaryotes–Structure/Function

    Prokaryotes are distinguished from eukaryotes by their smaller size (0.2- 10µm), their lack of internal organelles (mitochondria), the presence of a cell wall, and their cell division by binary fission rather than mitosis. They lack introns, are not capable of endo/exocytosis, and have single-stranded circular DNA rather than multiple discrete chromosomes.

    Bacteria share a number of common structures such as:

    • Slime (extracellular polysaccharide) is an extracellular material, loosely associated with the bacteria, that is elaborated by some bacterial species that facilitate colonization of smooth surfaces
    • Capsule is polysaccharide outer coating of the bacterial surface often plays a role in preventing phagocytosis of bacteria
    • Peptidoglycan (cell wall) provides bacterial shape and rigidity. The cell wall consists of alternating units of N-acetylglucosamine and N-acetylmuramic acid. The polysaccharide chains are cross-linked by a peptide bridge. It is a primary target of antimicrobial therapy because it is specific to prokaryotes.
    • Cytoplasmic membrane is a phospholipid bilayer that assumes many of the functions of eukaryotic organelles such as the biosynthetic processes
    • Flagella provide bacteria with the capacity for locomotion. They vary in number and location.
    • Pili are structures that project from the cell surface enabling bacteria to adhere to host tissue surfaces. Based on their amino acid structure, their affinity for particular host tissue surfaces can be remarkably specific.
    • Secreted products are a variety of products that includes exotoxins that are proteins grouped into A-B toxins, such as those elaborated by vibrio that causes cholera

    Distinguishing Features between Gram Positive and Negative Bacteria

    Gram positive bacteria have a large peptidoglycan structure. This structure accounts for the differential staining with Gram stain. Some Gram positive bacteria are also capable of forming spores under stressful environmental conditions such as when there is limited availability of carbon and nitrogen. Spores, therefore, allow bacteria to survive exposure to extreme conditions.

    Gram negative bacteria have a small peptidoglycan layer but have an additional membrane, the outer cytoplasmic membrane. This membrane creates an additional permeability barrier and results in the need for transport mechanisms across it. A major component of the cytoplasmic membrane that is unique to Gram negatives is endotoxin.

    Gram staining of bacterial cell for identification
    Figure \(\PageIndex{5}\): Gram staining of bacterial cell for identification – Image by Michigan State University. Microbiology 301-702 Summer 2016 is licensed under CC BY-SA 4.0

    Microorganism Identification

    The classification is based on morphological characteristics that refer to size, shape, cellular characteristics (capsule, flagella, endospores), differential staining (Gram stain, Acid fast stain), and biochemical tests that probe for specific enzyme activities that lead to carbohydrate fermentation, nitrogen fixation, sulfur oxidation, gas production, acid production, and nitrate reduction.

    Bacteria shapes: Cocci, Bacilli, and Spirilla
    Figure \(\PageIndex{6}\): Classification of bacteria by shape and environmental appearance – Image by CKRobinson is licensed under CC BY-SA 4.0

    Rapid determination tools include:

    • Selective media-inhibits the growth of one group while allowing another group to flourish such as salt tolerance broth selects for organisms that are tolerant of 6.5% NaCl (Staph and Streps)
    • Differential media which allows organisms to grow but causes one group to appear different
    • Multi-test systems/numerical ID such as Enterotube API test systems

    Serology is another method to identify microorganisms where the science of serum and immune responses are the evidence that identifies an organism. The process involves the use of antibodies to detect specific microbe antigens (foreign proteins) that are used to detect proteins in samples. Antibodies are special proteins, produced by animals, to bind to a specific target (antigen/epitope, protein). The immune response of an animal can produce antibodies to any molecule (antigen) that is foreign to that animal, and these diagnostic antibodies can be produced to detect particular microbes and identify them. Agglutination tests are used to identify specific antibodies by producing antigen clumps when injected.

    Phage typing/Plaque assay are bacterial viruses. Each phage is specific, and it infects only one species or even strain of bacteria. When phages infect a microorganism, it causes lysis of the bacteria. By applying known phages to unknown bacteria and looking for bacterial cell death, bacteria can be identified.

    FISH (Fluorescent In Situ Hybridization) uses a fluorescent dye labeled DNA probes that are mixed with a sample (biopsy, environment sample), hybridization tags cells with the DNA sequence, and cells are observed using UV light.

    Bacterial morphology diagram
    Figure \(\PageIndex{7}\): Morphology of bacterial cells – Image by LadyofHats is in the public domain

    Review Questions

    1. Name the two major types of cells found in nature.
    2. List and define the various types of living microorganisms.
    3. List the classifications in descending order for the hierarchal system of scientific nomenclature for the classification of living organisms.
    4. Distinguish the features between gram positive and gram negative bacteria.
    5. Describe how serology is used to identify microorganisms.

    Chapter Quiz

    1. Microorganisms that are disease-producing are called ___________.
      1. Pathogenic
      2. Streptococcus
      3. Staphylococcus
      4. Gram negative
    2. Bacteria and archaea are referred to as ___________ cells.
      1. Eukaryotic
      2. Prokaryotic
      3. Gram negative
      4. Gram positive
    3. Cells with cell walls that lack peptidoglycan are ___________.
      1. Bacteria
      2. Algae
      3. Protozans
      4. Archaea
    4. ___________ are eukaryotes. They are organisms whose cells have a distinct nucleus containing the cell’s genetic material, surrounded by a special envelope called a nuclear membrane.
      1. Archaea
      2. Bacteria
      3. Viruses
      4. Fungii
    5. ___________ bacteria have a large peptidoglycan structure.
      1. Streptococcus
      2. Staphylococcus
      3. Gram negative
      4. Gram positive
    6. Most bacteria grow best in a narrow pH range near neutrality, between ___________.
      1. 2.0 to 6.5
      2. 6.5 to 7.5
      3. 8.0 to 10.0
      4. 11.0 to 14.0
    7. In Taxonomic/Phylogenetic Hierarchy, groups are based on similarities. The groups begin very general and become more restricted. ___________ are used to determine evolutionary relationships and classification. Organisms that are grouped together are based on relatedness; very general relatedness at the top, followed by more and more specific and restricted subgroups where genus is all related species, and species is a single unique organism group.
      1. Gram staining techniques
      2. DNA hybridization and rRNA sequencing
      3. Serologic tests
      4. Morphological examinations
    8. A major component of the cytoplasmic membrane that is unique to Gram negatives is ___________.
      1. Peptidoglycan
      2. Exotoxins
      3. Chlorophyll
      4. Endotoxins
    9. ___________ is a binomial nomenclature so that every organism has a unique binomial identification that indicates the individual and its taxonomic placement among other organisms.
      1. Taxonomy
      2. Scientific nomenclature
      3. DNA hybridization
      4. Genus species
    10. ___________ is the science of classification.
      1. Taxonomy
      2. Scientific nomenclature
      3. DNA hybridization
      4. Genus species

    This page titled 1.6: Basic Microbiology Principles is shared under a not declared license and was authored, remixed, and/or curated by John Rowe (ZTC Textbooks) .

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