Chapter 10 Classification of Microorganisms Copyright 2010 Pearson

Chapter 10 Classification of Microorganisms Copyright © 2010 Pearson Education, Inc. Lectures prepared by Christine L.

Q&A § Pneumocystis jirovecii was thought to be a protozoan until DNA analysis showed it is a fungus. Why does it matter whether an organism is classified as a protozoan or a fungus? Copyright © 2010 Pearson Education, Inc.

The Study of Phylogenetic Relationships Learning Objectives 10 -1 Define taxonomy, taxon, and phylogeny. 10 -2 Discuss the limitations of a two-kingdom classification system. 10 -3 Identify the contributions of Linnaeus, von Nägeli, Chatton, Whittaker, and Woese. 10 -4 Discuss the advantages of the three-domain system. 10 -5 List the characteristics of the Bacteria, Archaea, and Eukarya domains. Copyright © 2010 Pearson Education, Inc.

Taxonomy § The science of classifying organisms § Provides universal names for organisms § Provides a reference for identifying organisms Copyright © 2010 Pearson Education, Inc.

Systematics, or Phylogeny § The study of the evolutionary history of organisms § All Species Inventory (2001– 2025) § To identify all species of life on Earth Copyright © 2010 Pearson Education, Inc.

Check Your Understanding ü Of what value is taxonomy and systematics? 10 -1 ü Why shouldn’t bacteria be placed in the plant kingdom? 10 -2, 10 -3 Copyright © 2010 Pearson Education, Inc.

Placing Bacteria 1735 Kingdoms Plantae and Animalia 1857 Bacteria and fungi put in the Kingdom Plantae – “Flora” 1866 Kingdom Protista proposed for bacteria, protozoa, algae, and fungi 1937 Prokaryote introduced for cells "without a nucleus" 1961 Prokaryote defined as cell in which nucleoplasm is not surrounded by a nuclear membrane 1959 Kingdom Fungi 1968 Kingdom Prokaryotae proposed 1978 Two types of prokaryotic cells found Copyright © 2010 Pearson Education, Inc.

The Three-Domain System Copyright © 2010 Pearson Education, Inc. Figure 10. 1

Copyright © 2010 Pearson Education, Inc. Table 10. 1

A Model of the Origin of Eukaryotes Copyright © 2010 Pearson Education, Inc. Figure 10. 2

Endosymbiotic Theory Copyright © 2010 Pearson Education, Inc. Figures 10. 2, 10. 3

Fossilized Prokaryotes Copyright © 2010 Pearson Education, Inc. Figure 10. 4 a

Fossilized Prokaryotes Copyright © 2010 Pearson Education, Inc. Figure 10. 4 b

Fossilized Prokaryotes Copyright © 2010 Pearson Education, Inc. Figure 10. 4 c

Phylogenetics § Each species retains some characteristics of its ancestor § Grouping organisms according to common properties implies that a group of organisms evolved from a common ancestor § Anatomy § Fossils § r. RNA Copyright © 2010 Pearson Education, Inc.

Check Your Understanding ü What evidence supports classifying organisms into three domains? 10 -4 ü Compare Archaea and Bacteria; Bacteria and Eukarya; and Archaea and Eukarya. 10 -5 Copyright © 2010 Pearson Education, Inc.

Classification of Organisms Learning Objectives 10 -6 Explain why scientific names are used. 10 -7 List the major taxa. 10 -8 Differentiate culture, clone, and strain. 10 -9 List the major characteristics used to differentiate three kingdoms of multicellular Eukarya. 10 -10 Define protist. 10 -11 Differentiate eukaryotic, prokaryotic, and viral species. Copyright © 2010 Pearson Education, Inc.

Scientific Nomenclature § Common names § Vary with languages § Vary with geography § Binomial Nomenclature (genus + specific epithet) § Used worldwide § Escherichia coli § Homo sapiens Copyright © 2010 Pearson Education, Inc.

Scientific Names Scientific Binomial Source of Genus Name Source of Specific Epithet Klebsiella pneumoniae Honors Edwin Klebs The disease Pfiesteria piscicida Honors Lois Pfiester Disease in fish Salmonella Honors Daniel Salmon typhimurium Streptococcus pyogenes Chains of cells (strepto -) Penicillium Tuftlike (penicill-) chrysogenum Trypanosoma cruzi Corkscrew-like (trypano-, borer; soma -, body) Copyright © 2010 Pearson Education, Inc. Stupor (typh-) in mice (muri-) Forms pus (pyo-) Produces a yellow (chryso-) pigment Honors Oswaldo Cruz

Taxonomic Hierarchy Domain Kingdom Phylum Class Order Family Genus Species Copyright © 2010 Pearson Education, Inc.

The Taxonomic Hierarchy Copyright © 2010 Pearson Education, Inc. Figure 10. 5

Check Your Understanding ü Using Escherichia coli and Entamoeba coli as examples, explain why the genus name must always be written out for the first use. Why is binomial nomenclature preferable to the use of common names? 10 -6 ü Find the gram-positive bacteria Staphylococcus in Appendix F. To which bacteria is this genus most closely related: Gemella or Streptococcus? 10 -7 Copyright © 2010 Pearson Education, Inc.

Classification of Prokaryotes § Prokaryotic species: A population of cells with similar characteristics § Culture: Grown in laboratory media § Clone: Population of cells derived from a single cell § Strain: Genetically different cells within a clone Copyright © 2010 Pearson Education, Inc.

Phylogenetic Relationships of Prokaryotes Copyright © 2010 Pearson Education, Inc. Figure 10. 6

Classification of Eukaryotes § Eukaryotic species: A group of closely related organisms that breed among themselves Copyright © 2010 Pearson Education, Inc.

Classification of Eukaryotes § 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 kingdom for eukaryotic organisms that do not fit other kingdoms § Grouped into clades based on r. RNA Copyright © 2010 Pearson Education, Inc.

Classification of Viruses § Viral species: Population of viruses with similar characteristics that occupies a particular ecological niche Copyright © 2010 Pearson Education, Inc.

References International Journal of Systematic and Evolutionary Microbiology Articles with evidence of new species or classification Bergey’s Manual of Systematic Bacteriology Provides phylogenetic and identification information on bacteria and archaea Approved Lists of Bacterial Names Lists species of known prokaryotes Based on published articles Copyright © 2010 Pearson Education, Inc.

Identifying Bacteria Copyright © 2010 Pearson Education, Inc. Applications, p. 283

Check Your Understanding ü Use the terms species, culture, clone, and strain in one sentence to describe growing methicillin-resistant Staphylococcus aureus (MRSA). 10 -8 ü Assume you discovered a new organism: it is multicellular, is nucleated, is heterotrophic, and has cell walls. To what kingdom does it belong? 10 -9 ü Write your own definition of protist. 10 -10 ü Why wouldn’t the definition of a viral species work for a bacterial species? 10 -11 Copyright © 2010 Pearson Education, Inc.

Classifying & Identifying Microorganisms Learning Objectives 10 -12 Compare and contrast classification and identification. 10 -13 Explain the purpose of Bergey’s Manual. 10 -14 Describe how staining and biochemical tests are used to identify bacteria. Copyright © 2010 Pearson Education, Inc.

Classification and Identification § Classification: Placing organisms in groups of related species. Lists of characteristics of known organisms. § Identification: Matching characteristics of an “unknown” organism to lists of known organisms. § Clinical lab identification Copyright © 2010 Pearson Education, Inc.

§ Identifying Klebsiella doesn’t tell you it’s classified as gammaproteobacteria Copyright © 2010 Pearson Education, Inc. Applications, p. 283

References Bergey’s Manual of Determinative Bacteriology Provides identification schemes for identifying bacteria and archaea Morphology, differential staining, biochemical tests Bergey’s Manual of Systematic Based on r. RNA sequencing Bacteriology Provides phylogenetic information on bacteria and archaea Copyright © 2010 Pearson Education, Inc.

Check Your Understanding ü What is in Bergey’s Manual? 10 -13 Copyright © 2010 Pearson Education, Inc.

A Clinical Microbiology Lab Report Form Copyright © 2010 Pearson Education, Inc. Figure 10. 7

Identification Methods § Morphological characteristics: Useful for identifying eukaryotes § Differential staining: Gram staining, acid-fast staining § Biochemical tests: Determines presence of bacterial enzymes Copyright © 2010 Pearson Education, Inc.

Identifying a Gram – Negative, Oxidase – Negative Rod Copyright © 2010 Pearson Education, Inc. Figure 10. 8

Numerical Identification Copyright © 2010 Pearson Education, Inc. Figure 10. 9

Check Your Understanding ü Design a rapid test for a Staphylococcus aureus. 10 -14 Copyright © 2010 Pearson Education, Inc. Figure 6. 10

Serology § Combine known antiserum plus unknown bacterium § Slide agglutination test Copyright © 2010 Pearson Education, Inc. Figure 10. 10

ELISA § § § Enzyme-linked immunosorbent assay Known antibodies Unknown type of bacterium Antibodies linked to enzyme Enzyme substrate Copyright © 2010 Pearson Education, Inc. Figure 18. 14

An ELISA Test Copyright © 2010 Pearson Education, Inc. Figure 10. 11

The Western Blot Copyright © 2010 Pearson Education, Inc. Figure 10. 12

Phage Typing of Salmonella enterica Copyright © 2010 Pearson Education, Inc. Figure 10. 13

Flow Cytometry § Uses differences in electrical conductivity between species § Fluorescence of some species § Cells selectively stained with antibody plus fluorescent dye Copyright © 2010 Pearson Education, Inc. Figure 18. 12

Genetics § DNA base composition § Guanine + cytosine moles% (GC) § DNA fingerprinting § Electrophoresis of restriction enzyme digests § r. RNA sequencing § Polymerase chain reaction (PCR) Copyright © 2010 Pearson Education, Inc. Figure 10. 14

Nucleic Acid Hybridization Copyright © 2010 Pearson Education, Inc. Figure 10. 15

A DNA Probe Used to Identify Bacteria Copyright © 2010 Pearson Education, Inc. Figure 10. 16

DNA Chip Technology Copyright © 2010 Pearson Education, Inc. Figure 10. 17

DNA Chip Technology Copyright © 2010 Pearson Education, Inc. Figure 10. 17

FISH § Fluorescent in situ hybridization § Add DNA probe for S. aureus Copyright © 2010 Pearson Education, Inc. Figure 10. 18

Dichotomous Key Copyright © 2010 Pearson Education, Inc. Figure 10. 8

Dichotomous Key ANIMATION Dichotomous Keys: Overview ANIMATION Dichotomous Keys: Sample with Flowchart ANIMATION Dichotomous Keys: Practice Copyright © 2010 Pearson Education, Inc.

Building a Cladogram Copyright © 2010 Pearson Education, Inc. Figure 10. 19

Building a Cladogram Copyright © 2010 Pearson Education, Inc. Figure 10. 19

Building a Cladogram Copyright © 2010 Pearson Education, Inc. Figure 10. 19

Check Your Understanding ü What is tested in Western blotting and Southern blotting? 10 -15 ü What is identified by phage typing? 10 -16 ü Why does PCR identify a microbe? 10 -17 ü Which techniques involve nucleic acid hybridization? 10 -18 ü Is a cladogram used for identification or classification? 10 -12, 10 -19 Copyright © 2010 Pearson Education, Inc.