Classification of Microorganisms: Taxonomy, Phylogeny, and Scientific Nomenclature, Exams of Systematics

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Classification of Microorganisms By Dr. Carmen Rexach Mt San Antonio College Microbiology Taxonomy • Science of classification of organisms – Aids in categorizing organisms not yet studied in detail – Aids in identifying already classified organisms – Provides common frame of reference when organisms are discussed • 1735 Plant & Animal Kingdoms • 1857 Bacteria & fungi put in the Plant Kingdom • 1866 Kingdom Protista proposed for bacteria, protozoa, algae, and fungi • 1937 Prokaryote introduced for cells "without a nucleus" • 1961 Prokaryote = cells in which nucleoplasm is not surrounded by a nuclear membrane • 1959 Kingdom Fungi • 1968 Kingdom Prokaryotae proposed • 1978 Two types of prokaryotic cells found Timeline The Three-Domain Cell Type Cell Wall Membrane Lipids First Amino Acid in Protein Synthesis Antibiotic Sensitivity rRNA Loop* Common Arm of tRNA’ Archaea Methanosarcina bo | Prokaryotic Varies in composition; contains no peptidoglycan Composed of branched carbon chains attached to glycerol by ether linkage Methionine No Lacking Lacking *Binds to ribosomal protein; found in all bacteria. TA sequence of bases in tRNA found in all eukaryotes and bacteria: guanine thymine pseudouridine-cytosine-guanine. Bacteria Prokaryotic Contains peptidoglycan Composed of straight carbon chains attached to glycerol by ester linkage Formylmethionine Yes Present Present Eukarya Amoeba a | 1Cum Eukaryotic Varies in composition; contains carbohydrates Composed of straight carbon chains atlached to glycerol by ester linkage Methionine No Lacking Present Table 10.1 The Three-Domain EUKARYA Fungi Animals Cellular Mitochondrion slime molds Oomycotes Plants Cyanobacteria Amoeba Gram-negative Extreme Ciliates bacteria halophiles | Chloroplast Methanogens Chromista | Euglenozoa e Plasmodial Brampositive Hyperthermophiles eine acide Microspora Thermotoga Archaezoa Mitochondrion degenerates Nucleoplasm grows larger Universal ancestor Figure 10.1 Kingdom Bacteria • Prokaryotes • Peptidoglycan cell walls • Binary fission • Energy source: organic chemicals, inorganic chemicals, or photosynthesis H. influenza Kingdom Archaea • Extreme living conditions • Unusual metabolism • No peptidoglycan in cell walls • Examples – Methanogens – Halophiles – thermoacidophiles methanosarcinae Anamox Kingdom Protista • Primarily unicellular eukaryotes • Protozoa, algae, slime molds, water molds Kingdom Animalia • Sponges, worms, insects, chordates • Heterotrophic • multicellular Algae • Some unicellular, some multicellular • Kingdom Protista, Kingdom Archaea, and Kingdom Plantae! • photoautotrophs Tropical red algae Viruses • Acellular • DNA or RNA, not both at same time • Protein capsid • Some have envelope and other external structures • Obligate intracellular parasites Scientific Nomenclature • Carolus Linnaeus • Binomial nomenclature: genus + species – italicized or underlined. – genus is capitalized – specific epithet (species) is lower case. • “Latinized” • used worldwide Scientific nomenclature • Naming bacteria – Names can describe characteristics or honor pioneer in field – Rules established by International Committee on Systemic Bacteriology = Bacteriological Code – Bergey’s Manual contains description and rules • Compiled from publications in International Journal of Systemic Bacteriology • Change as new techniques disclose similarities and differences Examples • Staphylococcus aureus – Describes the clustered arrangement of the cells (staphylo-) and the golden color of the colonies (aur-). • Escherichia coli – Honors the discoverer, Theodor Escherich, and describes the bacterium’s habitat–the large intestine or colon. • After first use, can be abbreviated as: “S. aureus” and “E. coli” What is a species? • Eukaryotic species: A group of closely related organisms that breed among themselves • Prokaryotic species: A population of cells with similar characteristics – 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 How to determine phylogenetic heirarchy • Generally determined by fossil records for higher organisms • Not available for most microbes with following exceptions – White Cliffs of Dover in England • Fossilized remains of marine protists – Stromalites • Fossilized microbial communities up to 2 billion years old – Cyanobacterial fossils • Found in Australia • 3-3.5 billion years old Stromalites: Hamilin Bay, Australia Classifying bacteria: Bergey’s Manual of Systematic Bacteriology • 4 divisions – Distinguished by cell wall structure • 7 classes – 3 eubacterial – 4 archaeobacterial • Bacterial species – Population of cells with similar characteristics • Strain – Variation within a species – Race, clade (ex) E. coli 0157:H7 Using Bergey’s Manual • Approx 1800 bacteria classified, <200 human pathogens • Four volumes – 1. Wall-less eubacteria and some gram-negative eubacteria – 2. Gram positive eubacteria – 3. Gram negative eubacteria • Photosynthetic, chemolithotropic, sheathed, budding, appendaged, gliding, and fruiting bacteria • archaeobacteria – 4. Actinomycetes Morphology • Not as dominant in classification as in higher organisms because few shapes • Many biochemical differences • Structures that occasionally help in identification – Spore formation – Orientation of flagella, etc. Differential staining • Distinguish between gram positive & gram negative, acid fast & non-acid fast • Very general • Refers only to cell wall structure • Some bacteria have no cell wall, or unusual ones SOP 13 02 253 eXIaOLsVd 5 $ "ete E “~ 30 : f & O40 ’ 1 ge Ec ai : 4 > Latex agglutination (a) Positive test (b) Negative test Western Blot • Electrophoresis separates proteins in patient’s serum • Transfer proteins onto nitrocellulose filter by blotting • Wash filter with antibodies tagged with dye • Presence of antigen appears as colored band Phage typing ia) a) “6 Oa ere ct a Amino acid sequencing • More similar indicates closer phylogenetic relationship • Farther apart = more distant • Compare the amino acid sequence of same protein in two organisms to determine the degree of similarity • Can only be used when organisms have common proteins • Possibility exists that two unrelated organisms can produce same protein with same code Sequencer Base composition of nucleic acids • Compare the percentage of certain bases in nucleic acids of two organisms • Calculate the common ratio of: – G+C/A+T+G+C PCR= polymerase chain reaction • Amplify DNA • Especially useful in microbes that cannot be cultured • Also where limited amount of DNA is available DNA fingerprinting • Amplify specific regions of DNA using PCR, or cut DNA from organism with restriction enzymes • Compare number and size of fragments after separation by gel electrophoresis DNA is denatured =] by heating Renaturation on cooling ” SECRET I (c) RNA et IMI MIMI iy 3 GCAU 5 Hybridization DNA/RNA hybrid ia RNA strand DNA strand http: f fwuw.accessexcellence.org/468/GG/nucleic.html Nucleic Acid Hybridization Hybridization + Probe Plasmid Salmonella DNA fragment 8 Unknown bacteria are collected on a filter. € Vv é a The cells are lysed, and the DNA is released, © The DNA is separated into single strands. Fluorescent probe Salmoneila DNA DNA from other bacteria Flow cytometry • Run cells through narrow tube in liquid medium so that only one cell moves through at at time • Hit each cell with laser – Determines shape, size, surface, density, fluorescence, etc. • Results recorded by computer • Determine similarity Dichotomous Key Gram reaction? Sf \t Glucose fermentation? Morphology Acid if “yee and gas af = Plesiomonas Motile at 37°C? Erysipelothrix Staphylococcus shigelloides rhusiopathiae aureus No J = Urea hydrolyzed? Aeromonas hydrophila No Lo NG Indole produced? Citrate utilized? No Lo xy No vA Yy Mannheimia Pasteurella Yersinia Klebsiella haemolytica multocida enterocolitica pneumoniae UN 10.2 Cladogram @ Determine the sequence of bases in an rRNA molecule for Lactobacillus brevis AGUCCAGAGC each organism. Only a short L. sanfranciscensis GUAAAAGAGC sequence of bases is shown for L. acidophilus AGCGGAGAGC this example. L. plantarum ACGUUAGAGC Percent similarity 6 Calculate the percentage of similarity in the nucleotide bases between L. brevis—~ L. sanfranciscensis 50% each species. For example, L. brevis—~ L. acidophilus 70% there is a 70% similarity L. brevis— L. plantarum 60% between the sequences for L. L. sanfranciscensis—- L. acidophilus 50% brevis and L. acidophilus. L. sanfranciscensis— L. plantarum 50% L. plantarum—~ L. acidophilus 60% @ Construct a cladogram. The length of the horizontal lines % similarity corresponds to the percent 100 50 similarity values. Each ah branch point, or node, in the cladogram represents an L. brevis ancestor common to all species beyond that node. Each node is defined by a similarity in L. ee eS rRNA present in all species L. sanfranciscensis beyond that branch point. 70% node L. acidophilus eS Figure 10.19, steps 1-2