Classification of Microorganisms Chapter 10 Classification of Microorganisms

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?

The Study of Phylogenetic Relationships 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.

Taxonomy The science of classifying organisms Provides universal names for organisms Provides a reference for identifying organisms

Systematics, or Phylogeny The study of the evolutionary history of organisms All Species Inventory (2001–2025) To identify all species of life on Earth

Of what value is taxonomy and systematics? 10-1 Why shouldn’t bacteria be placed in the plant kingdom? 10-2, 10-3

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

The Three-Domain System Figure 10.1

Table 10.1

A Model of the Origin of Eukaryotes Figure 10.2

Endosymbiotic Theory Figures 10.2, 10.3

Fossilized Prokaryotes Figure 10.4a

Fossilized Prokaryotes Figure 10.4b

Fossilized Prokaryotes Figure 10.4c

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 rRNA

What evidence supports classifying organisms into three domains? 10-4 Compare Archaea and Bacteria; Bacteria and Eukarya; and Archaea and Eukarya. 10-5

Classification of Organisms 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 the three kingdoms of multicellular Eukarya. 10-10 Define protist. 10-11 Differentiate eukaryotic, prokaryotic, and viral species.

Scientific Nomenclature Common names Vary with languages Vary with geography Binomial Nomenclature (genus + specific epithet) Used worldwide Escherichia coli Homo sapiens

Source of Specific Epithet 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 typhimurium Honors Daniel Salmon Stupor (typh-) in mice (muri-) Streptococcus pyogenes Chains of cells (strepto-) Forms pus (pyo-) Penicillium chrysogenum Tuftlike (penicill-) Produces a yellow (chryso-) pigment Trypanosoma cruzi Corkscrew-like (trypano-, borer; soma-, body) Honors Oswaldo Cruz

Taxonomic Hierarchy Domain Kingdom Phylum Class Order Family Genus Species

The Taxonomic Hierarchy Figure 10.5

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 Find the gram-positive bacteria Staphylococcus in Appendix F. To which bacteria is this genus most closely related: Gemella or Streptococcus? 10-7

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

Phylogenetic Relationships of Prokaryotes Figure 10.6

Classification of Eukaryotes Eukaryotic species: A group of closely related organisms that breed among themselves

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 rRNA

Classification of Viruses Viral species: Population of viruses with similar characteristics that occupies a particular ecological niche

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

Identifying Bacteria Applications, p. 283

Use the terms species, culture, clone, and strain in one sentence to describe growing methicillin-resistant Staphylococcus aureus (MRSA). 10-8 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 Write your own definition of protist. 10-10 Why wouldn’t the definition of a viral species work for a bacterial species? 10-11

Classifying & Identifying Microorganisms 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.

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

Identifying Klebsiella doesn’t tell you it’s classified as gammaproteobacteria 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 Bacteriology Provides phylogenetic information on bacteria and archaea Based on rRNA sequencing

What is in Bergey’s Manual? 10-13

A Clinical Microbiology Lab Report Form 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

Identifying a Gram – Negative, Oxidase – Negative Rod Figure 10.8

Numerical Identification Figure 10.9

Design a rapid test for a Staphylococcus aureus. 10-14 Figure 6.10

Serology Combine known antiserum plus unknown bacterium Slide agglutination test Figure 10.10

ELISA Enzyme-linked immunosorbent assay Known antibodies Unknown type of bacterium Antibodies linked to enzyme Enzyme substrate Figure 18.14

An ELISA Test Figure 10.11

The Western Blot Figure 10.12

Phage Typing of Salmonella enterica Figure 10.13

Flow Cytometry Uses differences in electrical conductivity between species Fluorescence of some species Cells selectively stained with antibody plus fluorescent dye Figure 18.12

Genetics DNA base composition DNA fingerprinting rRNA sequencing Guanine + cytosine moles% (GC) DNA fingerprinting Electrophoresis of restriction enzyme digests rRNA sequencing Polymerase chain reaction (PCR) Figure 10.14

Nucleic Acid Hybridization Figure 10.15

A DNA Probe Used to Identify Bacteria Figure 10.16

DNA Chip Technology Figure 10.17

DNA Chip Technology Figure 10.17

FISH Fluorescent in situ hybridization Add DNA probe for S. aureus Figure 10.18

Dichotomous Key Figure 10.8

Dichotomous Key ANIMATION Dichotomous Keys: Overview ANIMATION Dichotomous Keys: Sample with Flowchart ANIMATION Dichotomous Keys: Practice

Building a Cladogram Figure 10.19

Building a Cladogram Figure 10.19

Building a Cladogram Figure 10.19

What is tested in Western blotting and Southern blotting? 10-15 What is identified by phage typing? 10-16 Why does PCR identify a microbe? 10-17 Which techniques involve nucleic acid hybridization? 10-18 Is a cladogram used for identification or classification? 10-12, 10-19