Chapter 10 - Classification of Microorganisms



-orderly arrangement
-science of classifying organisms
-provides universal names for organisms
-provides a reference for identifying organisms


evolutionary history of a group of organisms

Stanier defined prokaryote as

a cell in which nucleoplasm is not surrounded by a nuclear membrane


-proposed 5 kingdom system
-believed prokaryotes were ancestors of eukaryotes
-prokaryotes were placed in kingdom Monera
-Eukaryotes were placed in the other 4 kingdoms

What did scientists determine the difference between eukaryotes and prokaryotes was in?

ribosome and rRNA nucleotide sequences

how many types of prokaryotic cells vs eukaryotic cells?

two types of prokaryotic cells and one type of eukaryotic cell

What are the three domains?

-established by Carl Woese
1. Eukarya
2. Bacteria
3. Archaea

How many kingdoms does eukarya have?

4 kingdoms
1. fungi
2. protista
3. plantae
4. animalia

How many kingdoms does archaea have?

3 kingdoms (no peptidoglycan)
1. Methanogens
--> strict anaerobe
--> generates methane
2. Halophiles
--> need high salt
3. Hyperthermophiles
--> grow in hot, acidic environment

Archaea characteristics:

Cell type: prokaryotic
Cell wall: varies in composition - no peptidoglycan
Membrane lipids: branched carbon chains attached to glycerol by ether linkage
First AA in protein synthesis: Methionine
Antibiotic sensitivity: No
rRNA loop: lacking
Common arm of

Bacteria characteristics:

Cell type: prokaryotic
Cell wall: peptidoglycan
Membrane lipids: straight carbon chains attached to glycerol by ester linkage
First AA in protein synthesis: Formylmethionine
Antibiotic sensitivity: Yes
rRNA loop: present
Common arm of tRNA: present

Eukarya characteristics:

Cell type: eukaryotic
Cell wall: varies - contains carbohydrates
Membrane lipids:
First AA in protein synthesis: straight carbon chains attached to glycerol by ester linkage
Antibiotic sensitivity: no
rRNA loop: lacking
Common arm of tRNA: present

Endosymbiotic theory

theory that eukaryotic cells formed from a symbiosis among several different prokaryotic organisms

Evidence of a common ancestor comes from:

-fossils --> not available for prokaryotes

Paul Cano

isolated a Bacillus (25-40 million years old) embedded in amber
--> viable

Binomial nomenclature:

each organism is assigned two names
-specific epithet (species)
should be written in italic or be underlined
Genus is always capitalized
Only genus can be abbreviated

Taxonomic hierarchy


Prokaryotic species

not based on interbreeding but on similar characteristics
(clone, strain, viral species)


Population (colony) of cells derived from a single cell
considered a pure culture


Pure cultures of same bacteria are not always genetically identical

Viral Species

population of viruses with similar characteristics that occupies a particular ecological niche
-NOT classified in any of 3 domains
-NOT composed of cells
-obligatory intracellular parasites

Eukaryotic species

A group of closely related organisms that breed among themselves

Animalia kingdom

no cell walls

Plantae kingdom

fern, some algae, cellulose cell walls
Have chlorophylls
Usually photoautotrophic

Fungi kingdom

unicellular or multicellular
cell walls of chitin
developed from spores of hyphal fragments, mushrooms

Protista kingdom

A kingdom for mostly unicellular eukaryotic organisms
-divided into two clades based on homologous features of a common ancestor

Methods of identifying bacteria

Morphological characteristics, differential staining, biochemical tests

Morphological characteristics identification

microbes can look very similar
cocci, bacillus

differential staining identification

gram staining, acid-fast staining
first step

biochemical tests identification

1. enzymatic activity (ability to ferment sugars)
2. Selective media: contains ingredients that suppresses growth of undesirable organisms
3. Differential media: bacteria generate a distinct morphology
4. Rapid system: used for medically important organis

Dichotomous Key

population is divided into two

Numerical Identification

1. One tube containing media for 15 biochemical tests is inoculated with an unknown enteric bacterium
2. After incubation, the tube is observed for results
3. The value for each positive test is circled, and the numbers from each group of tests are added


Combine known antiserum plus unknown bacterium
Slide agglutination test


an example of a serological test
-Enzyme-linked immunosorbent assay
-known antibodies
-unknown type of bacterium
-antibodies linked to enzyme
-enzyme substrate

Positive direct ELISA

-detects antigens
-enzyme's substrate is added, and reaction produces a product that causes a visible color change

Positive indirect ELISA

-detects antibodies
-Enzyme's substrate is added, and reaction produces a product that causes a visible color change

Western Blot steps

1. electrophoresis is used to separate proteins in the serum --> proteins move at different rates based on their charge and size when the gel is exposed to an electric current
2. bands are transferred to a nitrocellulose filter by blotting --> each band c

What charge is DNA

negatively charged


a virus that infects bacteria --> viruses are host specific

Flow Cytometry

-no need to culture bacteria
-fluorescence of some species
-cells selectively stained with antibody plus fluorescent dye
-detects Listeria in milk

What is DNA fingerprinting?

Electrophoresis of restriction enzyme digests

Nucleic Acid hybridization steps

1. Take two organism's DNA
2. Heat to separate strands
3. combine single strands of opposite DNA's
4. Cool to allow renaturation of double-stranded DNA
5. Determine degree of hybridization

Complete hybridization

Organisms are identical

Partial hybridization

organisms are related

no hybridization

organisms are unrelated

DNA Chip Technology

1. A DNA chip can be manufactured to contain hundreds of thousands of synthetic single-stranded DNA sequences --> Assume that each DNA sequence was unique to a different gene
2.Unknown DNA from a patient is separated into single strands, enzymatically cut


Fluorescent In Situ Hybridization
-Add DNA probe for S. aureus


shows evolutionary relationship

How to build a cladogram

1. Determine the sequence of bases in an rRNA molecule for each organism
2. Calculate the percentage of similarity in the nucleotide bases between pairs of species
3. Construct a cladogram --> lengths of horizontal lines corresponds to the percent similar