CHAPTER 9

AN INTRODUCTION TO TAXONOMY: THE BACTERIA

FChapter Overview

Taxonomy has changed quite a bit. The same dichotomous keys are still there, the kingdoms are still there, the phyla, classes, and families are mostly still there, but the methods used in taxonomy have vastly changed. Physical characteristics are still used, but taxonomy also incorporates such techniques as genetic homology, DNA hybridization, protein profiles, and immunology. Scientists use more than just morphological characteristics to identify organisms and speculate on evolutionary relationships between organisms.

FChapter Objectives

  • Discuss how and why microorganisms are named.
  • Describe the contributions of Linnaeus to taxonomy.
  • Describe how a dichotomous taxonomic key is used to identify organisms.
  • List and describe two major problems in creating a taxonomic system; note several important taxonomic developments since Linnaeus's time.
  • List at least four major characteristics for each of the five kingdoms in the current system of taxonomy.
  • Provide rationale for the need of the Three-Domain Classification System
  • List and describe the characteristics currently used in classifying viruses.
  • Provide several reasons why special methods are needed to determine evolutionary relationships among prokaryotes; list the major methods currently used.

Note the convention of writing microbe names with a capitalized Genus first, and a lowercase species second and either underlined or italicised. Example: Proteus mirabilis

1.Videos and animations – online

  1. General videos on biological classification from BioEd online -
  2. Annenberg Foundation (registration required) video on Microbial Evolution -

 Web Destinations


  • This site provides scientific names of all organisms in specific genetic databases

This site is maintained by the American Type Culture Collection. The ATCC collects and maintains living specimens of bacteria, viruses, protists and fungi and provides cultures to scientists for research


  • A fun bacterial identification activity

This site, produced at the Museum of Paleontology at the University of California, Berkeley, provides links to the fossil record and information about the three domains.

Bacterial systematics from the University of California, Berkely

A short guide to bacterial genera by Harold Eddleman

Classification, nomenclature and key making

Wastewater organisms, filamentous bacteria dichotomous key

Stephen Abedon’s taxonomy site from Ohio State University

University of Wisconsin Microbiology textbook on dichotomous keys

Website on bacterial diversity with many different links

 Discussion Topics (aka. potential essay questions)

  • Should viruses or the Archaea be placed in a sixth kingdom of life? If not, why not?
  • Why is evolution of interest to taxonomists?
  • If a new bacterium was discovered, what criteria would you use to classify it in the current Bergey’s system of taxonomy?
  • An unusual genus, Deinococcus, which was placed with the Micrococcaceae, has some very important properties. What are they and what effects do they have on the environment?
  • It was discovered that a mycoplasma-like organism was affecting the royal palm trees of Florida (see National Geographic, July 1988). What evidence suggests that it is a mycoplasma, and how is it transmitted?

FChapter Outline

I.TaxonomyThe Science of Classification

A.Linnaeusthe father of taxonomy

1Binomial nomenclature

a.Genus

b.Specific epithet

c.Species

d.Strain

2.Taxonomic hierarchy

B.Using a taxonomic key

1.Dichotomous key

2.Bacterial dichotomous key

C.Problems in taxonomy

D.Developments since Linnaeus's time

1.Contributions by Haeckel

2.Bergey's Manual of Determinative Bacteriology

3. Contributions by Margulis and Copeland

4. Contributions by Whittaker

II.The FiveKingdom Classification System

A.General features

B.Kingdom Monera

1.True bacteria

2.Cyanobacteria

3.Archaea

C.Kingdom Protista

D.Kingdom Fungi

E.Kingdom Plantae

F.Kingdom Animalia

III.The Three-Domain Classification System

  1. The evolution of prokaryotic organisms
  2. Stromatolites
  3. Domain

B.The tree of life is replaced by a shrub

C.The Archaea

1.Methanogens

2.Extreme halophiles

3.Extreme thermoacidophiles

IV.Classification of Viruses

V.The Search for Evolutionary Relationships

A.Special methods needed for prokaryotes

B.Numerical taxonomy

C.Genetic homology

1.Base composition

2.DNA and RNA sequencing

3.DNA hybridization

4.Protein profiles and amino acid sequences

a.Protein profile

b.Polyacrylamide gel electrophoresis (PAGE)

D.Other techniques

1.Properties of ribosomes

2.Immunological reactions

3.Phage typing

E.Significance of findings

1.Major significance

  1. Divergent evolution

VI.Bacterial Taxonomy and Nomenclature

A.Criteria for classifying bacteria

  1. Type strain
  2. ATCC

B.The history and significance of Bergey’s Manual

C.Problems associated with bacterial taxonomy

D.Bacterial nomenclature

E.Bacteria – unusual groups

F.Bacterial taxonomy and you

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