Tortora Chapter 10

TORTORA • FUNKE

• CASE

Microbiology AN INTRODUCTION EIGHTH EDITION

B.E Pruitt & Jane J. Stein

Chapter 10 Classification of Microorganisms

PowerPoint® Lecture Slide Presentation prepared by Christine L. Case Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings

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 Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings

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)

Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings

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


Learning objectives: List characteristics of 3-domain system

The Three-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 Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings

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

Similarities in rRNA sequences supporting endosymbiotic theory Figure 10.2 Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Mutualistic symbiosis between eukaryotic host and bacterium – possible precursor to reproductive capability Figure 10.3 as a unit

Learning objectives: Explain why scientific names are used. Scientific binomial

Scientific Names 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-, Honors Oswaldo Cruz borer; soma-body)

Binomials (Genus Species) used by scientists worldwide which enables them to share knowledge efficiently and accurately Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Learning objectives: List the major taxa.

Taxonomic Hierarchy

Differentiate between culture, clone, and strain.

• 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 Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings

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) Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings

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 Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings

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 Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Identification Methods • Morphological characteristics: Useful for identifying eukaryotes

Using metabolic characteristics to identify selected genera of enteric (intestinal) bacteria

• Differential staining: Gram staining, acid-fast staining • Biochemical tests: Determines presence of bacterial enzymes Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Figure 10.8

Morphology and differential staining important to proper treatment for microbial diseases Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings

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 confirmatory test is advised.


Figure 10.9

Serology 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

Left grainy appearance is positive for agglutination – bacteria was mixed with antibodies produced in response to same strain

• Slide agglutination • ELISA (enzymelinked immunosorbent assay) • Western blot


Figure 10.10

Western Blot

Proteins separated by electrophoresis can be detected by their reactions with antibodies Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings

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 Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Figure 18.11

Genetics Learning objectives: Describe how newly discovered microbe can be classified by: DNA base composition, rRNA sequencing, DNA fingerprinting, PCR, and nucleic acid hybridization

• DNA base composition • Guanine + cytosine moles% (GC)

Plasmids from 7 different bacteria digested with same restriction enzyme: none of these bacteria happen to be identical (source of hospital-acquired infections).

• 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

Tortora Chapter 10

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