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Taxonomy:
Naming, Classifying, and Identifying Microorganisms

Taxonomy: The science of classifying living beings.

Carl von Linné (also known as Carolus Linnaeus; 1701-1778), a Swedish botanist. He introduced a formal
system of classification dividing living organisms into two kingdoms Plantae and Animalia.

Nomenclature is the assignment of scientific names to the various taxonomic categories and individual organisms.

Classification attempts the orderly arrangement of organisms into a hierarchy of taxa.

Identification is the process of discovering and recording the traits of organisms so they may be recognized or
named and placed in an overall taxonomic scheme.

The Origin and Evolution of Microorganisms

To understand the natural history of and the relatedness among organisms, we must understand some fundamentals
of the process of evolution. Evolution is an important theme that underlies all of biology, including the biology of
microorganisms.

Natural Selection: The process of evolution is selective in that those changes that most favor the survival of a
particular organism or group of organisms tend to be retained whereas those that are less beneficial to survival tend
to be lost. (Charles Darwin)

Evolution is founded on the two preconceptions that

(1) all new species originate from preexisting species and
(2) closely related organisms have similar features because they emerged by divergence.

Three Domain System

By: Carl R. Woese & George Fox

• Domain Eukarya
– Plants, animals, protists and fungi
• Domain Bacteria
– All pathogenic and nonpathogenic prokaryotes found in soil and water
• Domain Archaea
– Prokaryotes w/o peptidoglycan in their cell walls
– Extreme halophiles, methanogens, and hyperthermophiles

Five–Kingdom System
- Proposed by Robert H. Whittaker in 1969, which considers prokaryotes to be the ancestors of all
eukaryotes.
Kingdom Prokaryotae (Monera)
- all prokaryotes
Kingdom Protista
- includes simple eukaryotic organisms such as alga and protozoa, mostly unicellular
Kingdom Fungi
- includes unicellular yeast, multicellular molds, and macroscopic mushrooms
Kingdom Plantae
- (plants) include some plants, algae, mosses, ferns; undergo photosynthesis
Kingdom Animalia
- includes multicellular organisms which obtain nutrient and energy by ingesting organic matter

The Levels of Classification: Taxonomic Hierarchy

The taxonomic categories from top to bottom are:

Domain
- also known as superkingdom or empire, is the highest taxonomic rank of organisms, higher than a
kingdom.
Kingdom
- constitutes a group of related divisions or phyla
Division or Phylum
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- made up of related classes

Class
- consists of similar orders
Order
- constitutes a group of similar families
Family
- made up of related genus
Genus
- consists of related species
Species
- a group of closely related organisms that breed among themselves

Assigning Specific Names: Binomial Nomenclature

The method of assigning scientific or specific name is called the binomial (two-name) system of nomenclature. The
scientific name is always a combination of the generic (genus) name followed by the species name (specific epithet).
The generic part of the scientific name is capitalized, and the species part begins with a lowercase letter. Both should
be italicized (or underlined if italics are not available), as follows:
Staphylococcus aureus

Some species have been named in honor of a microbiologist who originally discovered the microbe or how has made
outstanding contributions to the field.

Other names may designate a characteristic of the microbe (shape, color), a location where it was found, or a
disease it causes. Some examples of specific names and their origins are:
• Staphylococcus aureus
o Gr. staphule, bunch of grapes, kokkus, berry, and Gr. aureus, golden. A common bacterial
pathogen of humans.
• Campylobacter jejuni
o Gr. kampylos, curved, bakterion, little rod, and jejunum, a section of the intestine. One of the most
important causes of intestinal infection worldwide.
• Lactobacillus sanfrancisco
o L. lacto, milk, and bacillus, little rod. A bacterial species used to make sourdough bread.
• Vampirovibrio chlorellavirus
o F. vampire; L. vibrio, curved cell; Chlorella, a genus of green algae; and vorus, to devour. A small,
curved bacterium that sucks out the cell juices of Chlorella.
• Giardia lamblia
o for Alfred Giard, a French microbiologist, and Vilen Lambl, a Bohemian physician, both of whom
worked on the organism, a protozoan that causes severe intestinal infection.