Classification of Microorganisms Chapter 10 Classification of Microorganisms

Taxonomy Learning objectives: Define taxonomy, taxon, and phylogeny Discuss the limitations of a 2-kingdom classification system. Taxonomy Taxonomy The science of classifying organisms Provides universal names for organisms Provides a reference for identifying organisms Goal of showing relationships among organisms Taxon Taxonomic categories to show similarities among organisms

Taxonomy Systematics or phylogeny The study of the evolutionary history of organisms and their relationships All Species Inventory (2001-2025) To identify all species of life on Earth Two-kingdom system not based upon natural classification based upon ancestral relationships (e.g., DNA sequencing places fungi closer to animals than plants)

Taxonomy History 1735 Plant and Animal Kingdoms 1857 Bacteria & fungi put in the Plant Kingdom 1866 Kingdom Protista proposed for bacteria, protozoa, algae, & fungi 1937 "Prokaryote" introduced for cells "without a nucleus" 1961 Prokaryote defined as cells in which nucleoplasm is not surrounded by a nuclear membrane 1959 Kingdom Fungi 1968 Kingdom Prokaryotae proposed 1969 Organisms divided into five kingdoms 1978 Two types of prokaryotic cells found

The Three-Domain System Learning objectives: List characteristics of 3-domain system A domain can be divided into kingdoms Classified by cell type, cell wall, rRNA, membrane lipid structure, tRNA, sensitivity to antibiotics Table 10.1

The Three-Domain System Peptidoglycan Unusual cell walls 3-domain recognizes 3 types of cells. Eukarya includes Kingdoms Fungi, Plantae, and Animalia, plus certain protists Figure 10.1

Phylogenetic Hierarchy Organisms grouped into taxa by phylogenetic relationships Some eukaryotic relationships obtained from fossil records Prokaryotic relationships determined by rRNA sequencing Table 10.2

Endosymbiotic Theory Mutualistic symbiosis between eukaryotic host and bacterium – possible precursor to reproductive capability as a unit Similarities in rRNA sequences supporting endosymbiotic theory Figure 10.2 Figure 10.3

Source of Specific epithet Learning objectives: Explain why scientific names are used. Scientific Names Scientific binomial Source of Genus name Source of Specific epithet Kbebsiella pneumoniae Honors Edwin Klebs The disease Pfiesteria piscicida Honors Lois Pfiester Disease in fish Salmonella typhimurium Honors Daniel Salmon Stupor (typh-) in mice (muri-) Streptococcus pyogenes Chains of cells (strepto-) Forms pus (pyo-) Penicillium notatum Tuftlike (penicill-) Spores spread in wind (nota) Trypanosoma cruzi Corkscrew-like (trypano-, borer; soma-body) Honors Oswaldo Cruz Binomials (Genus Species) used by scientists worldwide which enables them to share knowledge efficiently and accurately

Prefer Phylum/ Division Cheese Class Over Order Fried Family Learning objectives: List the major taxa. Differentiate between culture, clone, and strain. Taxonomic Hierarchy Similar species are grouped into a genus; similar genera are grouped into a family, etc. Kids Kingdom Prefer Phylum/ Division Cheese Class Over Order Fried Family Green Genus Spinach Species Figure 10.5

Species Definition Eukaryotic species: A group of closely related organisms that breed among themselves Prokaryotic species: A population of cells with similar characteristics Culture: bacteria grown at a give time in media Clone: Population of cells derived from a single cell Strain: Genetically different cells within a clone Viral species: Population of viruses with similar characteristics that occupies a particular ecological niche

Domain Eukarya Learning objectives: List the major characteristics used to differentiate the three kingdoms of multicellular Eukarya. Define protist. Animalia: Multicellular; no cell walls; chemoheterotrophic Plantae: Multicellular; cellulose cell walls; usually photoautotrophic Fungi: Chemoheterotrophic; unicellular or multicellular; cell walls of chitin; develop from spores or hyphal fragments Protista: A catchall for eukaryotic organisms that do not fit other kingdoms; currently being assigned to kingdoms Viruses not placed in a kingdom (must have host)

Prokaryotes Phylogenetic relationships of prokaryotes (Kingdom – Phylum) Figure 10.6

References Learning objectives: Compare/contrast classification and identification Explain purpose of Bergey’s Manual • Bergey’s Manual of Determinative Bacteriology (for lab identification) Provides identification schemes for identifying bacteria and archaea Morphology, differential staining, biochemical tests, cell wall composition, oxygen requirements (treatment) • Bergey’s Manual of Systematic Bacteriology Provides phylogenetic information on bacteria and archaea Based on rRNA sequencing • Approved Lists of Bacterial Names Lists species of known prokaryotes Based on published articles

Learning objectives: Describe how staining and biochemical tests are used to identify bacteria

Methods to Classify and Identify Microbes Morphological characteristics (aided by staining) Presence of certain enzymes Serological tests (antigen – antibody response) Phage typing (susceptibility of bacteria to phages) Fatty acid profiles Flow cytometry Percentage of G-C pairs in nucleic acid Number and sizes of DNA fragments (fingerprints) produced by restriction enzymes Sequence of bases in rRNA Polymerase chain reaction (PCR) to detect DNA

Identification Methods Using metabolic characteristics to identify selected genera of enteric (intestinal) bacteria Morphological characteristics: Useful for identifying eukaryotes Differential staining: Gram staining, acid-fast staining Biochemical tests: Determines presence of bacterial enzymes Figure 10.8

Morphology and differential staining important to proper treatment for microbial diseases

Numerical Identification Rapid identification tools for groups of medically important bacteria (e.g., enterics) are designed to perform several biochemical tests simultaneously. The value for each positive test is circled and compared to a computerized listing. In this case a confirma-tory test is advised. Figure 10.9

Serology Combine known antiserum + unknown bacterium Learning objectives: Differentiate Western blotting from Southern blotting. Explain how serological tests and phage typing can be used to identify an unknown bacterium. Combine known antiserum + unknown bacterium Slide agglutination ELISA (enzyme-linked immunosorbent assay) Western blot Left grainy appearance is positive for agglutination – bacteria was mixed with antibodies produced in response to same strain Figure 10.10

Western Blot Proteins separated by electrophoresis can be detected by their reactions with antibodies Figure 10.12

Phage Typing Determining which phages a bacterium is susceptible to: The tested strain was grown over entire plate; known phages are placed in different squares; plaques (areas of lysis) appear dark indicating sensitivity to a specific phage Figure 10.13

Flow Cytometry Uses Used to identify bacteria in a sample without culturing the bacteria Differences in electrical conductivity between species Fluorescence of some species Cells selectively stained with antibody + fluorescent dye Figure 18.11

Genetics DNA base composition Guanine + cytosine moles% (GC) Learning objectives: Describe how newly discovered microbe can be classified by: DNA base composition, rRNA sequencing, DNA fingerprinting, PCR, and nucleic acid hybridization Plasmids from 7 different bacteria digested with same restriction enzyme: none of these bacteria happen to be identical (source of hospital-acquired infections). DNA base composition Guanine + cytosine moles% (GC) DNA fingerprinting Electrophoresis of restriction enzyme digests rRNA sequencing Polymerase Chain Reaction (PCR) Figure 10.14

Nucleic Acid Hybridization Greater degree of hybridization (pairing of two strands of DNA, each from a different microbe) indicates greater similarity Figure 10.15

Nucleic Acid Hybridization: DNA probe Figure 10.16

Nucleic Acid Hybridization: DNA chip Figure 10.17

Dichotomous Key Learning objectives: Differentiate a dichotomous key from a cladogram. Dichotomous key: successive questions with two possible answers.

Cladogram Cladogram: Maps showing evolutionary relationships among organisms. Figure 10.18.1

Cladogram Figure 10.18.2

Figure 10.5