Lecture II: Classification of Microorganisms PDF

9/21/2023 Lecture II. Classification of Microorganisms MTN Cabasan 1 Outline: 1. Taxonomy and characteristics used in taxonomy 2. The Bergey’s Manual 3. Methods used in identifying and classifying microorganisms 4....

9/21/2023 Lecture II. Classification of Microorganisms MTN Cabasan 1 Outline: 1. Taxonomy and characteristics used in taxonomy 2. The Bergey’s Manual 3. Methods used in identifying and classifying microorganisms 4. Prokaryotic, eukaryotic and viral species 2 1  9/21/2023 Objectives: 1) Define taxonomy, taxon and phylogeny 2) Discuss the classification systems 3) Explain the purpose of Bergey’s Manual 4) Identify the methods used in identifying and classifying microorganisms 5) Differentiate prokaryotic, eukaryotic and viral species 3 Classification Attempts to Catalog Organisms Carolus Linnaeus 4 2  9/21/2023 Classification Attempts to Catalog Organisms 5 Classification Attempts to Catalog Organisms Haeckel, Pasteur, Koch, and their associates 6 3  9/21/2023 Classification Attempts to Catalog Organisms Edouard Chatton- proposed that there was a fundamental dichotomy among the Protista 7 Classification Attempts to Catalog Organisms Bacteria- separated from all other protists “which have eukaryotic cells Herbert Copland- suggested bacteria be placed in a fourth kingdom, the Monera 8 4  9/21/2023 Classification Attempts to Catalog Organisms Carl Woese- (late 1970s), - molecularly analyze nucleotide sequences of genes coding for the small subunit ribosomal RNA (rRNA) found in all organisms. Another dichotomy among the prokaryotes- (1990) kingdom Monera contained 2 unrelated groups: Bacteria and Archaebacteria 9 Organisms historically were grouped by shared characteristics 10 5  9/21/2023 Systematics studying the diversity of life and its evolutionary relationships. Systematic biologists or systematists— identify, describe, name, and classify organisms Goal: to reconstruct the phylogeny (phylo = “tribe”; geny = “production”), the evolutionary history of a species or group of species 11 Phylogenetic trees- identify inferred relationships among species Carl Woese – introduced the three-domain system, one branch of the phylogenetic tree includes the former archaebacteria: called the domain Archaea 12 6  9/21/2023 13 Nomenclature The system of nomenclature (naming) for organisms - established in 1735 by Carolus Linnaeus Scientific names – in Latin was the language Scientific nomenclature assigns each organism two names— genus (plural: genera) is the first name; capitalized specific epithet (species name) follows; not capitalized 14 7  9/21/2023 Scientific names - describe an organism, - honor a researcher - identify the habitat of a species. Genera Named after Individuals Escherichia coli: named after Theodore Escherich who isolated the bacterial cells from infant feces in 1885. Being in feces, it commonly is found in the colon. Neisseria gonorrhoeae: named after Albert Neisser who discovered the bacterial organism in 1879. As the specific epithet points out, the disease it causes is gonorrhea. 15 Naming Names Genera Named for a Microbe’s Shape Vibrio cholerae: vibrio means “comma-shaped,” which describes the shape of the bacterial cells that cause cholera. Staphylococcus epidermidis: staphylo means “cluster” and coccus means “spheres.” So, these bacterial cells form clusters of spheres that are found on the skin surface (epidermis). 16 8  9/21/2023 Naming Names Genera Named after an Attribute of the Microbe Saccharomyces cerevisiae: in 1837, Theodor Schwann observed yeast cells and called them Saccharomyces (saccharo = “sugar”; myce = “fungus”) because the yeast converted grape juice (sugar) into alcohol; cerevisiae (from cerevisia = “beer”) refers to the use of yeast since ancient times to make beer. Myxococcus xanthus: myxo means “slime,” so these are slime-producing spheres that grow as yellow (xantho = “yellow”) colonies on agar 17 18 9  9/21/2023 In prokaryotes, an organism may belong to a rank below the species level - a special characteristic exists within a subgroup of the species. - Useful in identifying organisms. For example, two biotypes of the cholera bacterium, Vibrio cholerae, are known: Vibrio cholerae classic and Vibrio cholerae El Tor. Other designations of ranks include subspecies, serotype, strain, and morphotype. 19 David Hendricks Bergey devised one of the first systems of classification for the bacterial species in 1923. Taxonomic classification for the Bacteria and Archaea can be found in the Bergey’s Manual of Systematic Bacteriology. 20 10  9/21/2023 Classification system most widely accepted by microbiologists is that of Bergey’s Manual of Systematic Bacteriology, a major taxonomic treatment of Bacteria and Archaea 21 22 11  9/21/2023 23 Methods to Identify and Classify Microorganisms 1) Physical Characteristics – include differential staining reactions to help determine the organism’s shape (morphology), and the size and arrangement of cells. - Other characteristics can include oxygen, pH, and growth temperature requirements. - Spore-forming ability and motility are additional determinants. (Note: there are many bacterial and archaeal organisms that have the same physical characteristics, so other distinguishing features are needed) 24 12  9/21/2023 Methods to Identify and Classify Microorganisms 2) Biochemical Tests - In bacterial physiology, there were certain metabolic properties that were present only in certain groups. Common tests: -fermentation of carbohydrates - the use of a specific substrate - the production of specific products or waste products. (But, as with the physical characteristics, often several biochemical tests are needed to differentiate between species) 25 Methods to Identify and Classify Microorganisms 3) Serological Tests - Microorganisms are antigenic - capable of triggering the production of antibodies. - Solutions of collected antibodies, called antisera, are commercially available for many medically important pathogens. - For example, mixing a Salmonella antiserum with Salmonella cells will cause the cells to clump together or agglutinate. - If a foodborne illness occurs, the antiserum may be useful in identifying if Salmonella is the pathogen. 26 13  9/21/2023 Methods to Identify and Classify Microorganisms 4) Nucleic Acid Analysis - analysis and sequencing of nucleic acids - new era of molecular taxonomy - Molecular taxonomy - RNAs in the ribosome, called ribosomal RNA (rRNA) - Genes for rRNA are the most accurate measure for precise bacterial classification in all taxonomic classes. - Other techniques, including the polymerase chain reaction and nucleic acid hybridization 27 28 14  9/21/2023 Dichotomous key widely used technique construction is a flow chart where a series of positive or negative test procedures are listed down based on the dichotomous nature of the test (always a positive or negative result), the flow chart immediately leads to the next test result. The result is the identification of a specific organism. 29 Try this! In this simplified scenario, an unknown bacterium has been cultured and several tests run. The test results are shown in the box. Using the test results and the flow chart, identify the bacterial species that has been cultured. 30 15  9/21/2023 31 Types of Microorganisms 1) Bacteria(singular: bacterium) simple, single celled (unicellular) organisms genetic material is not enclosed in a special nuclear membrane= bacterial cells - prokaryotes Prokaryotes include both bacteria and archaea. Bacterial cells generally appear in one of several shapes: Bacillus (rodlike}, coccus (spherical or ovoid), and spiral (corkscrew or curved) Individual bacteria may form pairs, chains, clusters, or other groupings 32 16  9/21/2023 Types of Microorganisms 1) Bacteria(singular: bacterium) enclosed in cell walls - composed of a carbohydrate and protein complex = peptidoglycan generally reproduce by dividing into two equal cells = binary fission Nutrition - most bacteria use organic chemicals, can be derived from either dead or living organisms. Some bacteria can manufacture their own food by photosynthesis Some can derive nutrition from inorganic substances. Many bacteria can “swim” by using moving appendages = flagella. 33 Types of Microorganisms 2) Archaea Like bacteria, archaea consist of prokaryotic cells, but if they have cell walls, the walls lack peptidoglycan. often found in extreme environments Divided into three main groups: 1)methanogens - produce methane as a waste product from respiration 2) extreme halophiles- live in extremely salty environments 3) extreme thermophiles - live in hot sulfurous water; not known to cause disease in humans. 34 17  9/21/2023 Types of Microorganisms 3) Fungi (singular: fungus) are eukaryotes organisms whose cells have a distinct nucleus containing the cell’s genetic material (DNA), surrounded by a special envelope = nuclear membrane. may be unicellular or multicellular have cell walls composed primarily of a substance called chitin. The unicellular forms of fungi, yeasts, are oval microorganisms that are larger than bacteria. 35 Types of Microorganisms 3) Fungi (singular: fungus) The most typical fungi are molds. Molds form visible masses called mycelia, which are composed of long filaments (hyphae) that branch and intertwine. The cottony growths sometimes found on bread and fruit are mold mycelia. Fungi can reproduce sexually or asexually. They obtain nourishment by absorbing organic material from their environment 36 18  9/21/2023 Types of Microorganisms 4) Protozoa (singular: protozoan) are unicellular eukaryotic microbes move by pseudopods, flagella, or cilia. Amebae move by using extensions of their cytoplasm called pseudopods (false feet). Other protozoa have long flagella or numerous shorter appendages for locomotion called cilia. Protozoa have a variety of shapes and live either as free entities or as parasites Some protozoa, such as Euglena, are photosynthetic. 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 37 Types of Microorganisms 5) Algae (singular: alga) photosynthetic eukaryotes with a wide variety of shapes and both sexual and asexual reproductive forms cell walls of many algae are composed of a carbohydrate called cellulose. Algae are abundant in freshwater and saltwater, in soil, and in association with plants. As photosynthesizers, algae need light, water, and carbon dioxide for food production and growth, but they do not generally require organic compounds 38 19  9/21/2023 Types of Microorganisms 5) Viruses different from the other microbial groups so small that most can be seen only with an electron microscope acellular (that is, they are not cells). Structurally very simple; contains a core made of only one type of nucleic acid, either DNA or RNA. The core is surrounded by a protein coat, which is sometimes encased by a lipid membrane called an envelope. Viruses can reproduce only by using the cellular machinery of other organisms; considered to be living only when they multiply within host cells they infect. 39 40 20  9/21/2023 References: Brock, T. D., Madigan, M. T., Martinko, J. M., & Parker, J. (2015). Brock biology of microorganisms. Upper Saddle River (NJ): Prentice-Hall, 2003. Pommerville, J. C. (2012). Alcamo's fundamentals of microbiology: Body systems. Jones & Bartlett Publishers. Tortora, G. J., Funke, B. R., & Case, C. L. (2015). Microbiology: An Introduction, Books a la Carte Edition. Benjamin-Cummings. 41 21