TORTORA FUNKE

CASE

Microbiology
AN INTRODUCTION
EIGHTH EDITION

B.E Pruitt & Jane J. Stein

Chapter 10
Classification of Microorganisms

PowerPoint Lecture Slide Presentation prepared by Christine L. Case

Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Learning objectives:
Define taxonomy, taxon, and phylogeny
Discuss the limitations of a 2-kingdom classification system.

Taxonomy
Taxonomy
The science of classifying organisms
Provides universal names for organisms
Provides a reference for identifying organisms
Goal of showing relationships among organisms
Taxon
Taxonomic categories to show similarities
among organisms
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Taxonomy
Systematics or phylogeny
The study of the evolutionary history of
organisms and their relationships
All Species Inventory (2001-2025)
To identify all species of life on Earth
Two-kingdom system not based upon natural
classification based upon ancestral
relationships (e.g., DNA sequencing places
fungi closer to animals than plants)

Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Taxonomy History
1735

Plant and Animal Kingdoms

1857

Bacteria & fungi put in the Plant Kingdom

1866
Kingdom Protista proposed for bacteria,
protozoa, algae, & fungi
1937
"Prokaryote" introduced for cells "without a
nucleus"
1961
Prokaryote defined as cells in which
nucleoplasm is not surrounded by a nuclear
membrane
1959

Kingdom Fungi

1968

Kingdom Prokaryotae proposed

1969

Organisms divided into five kingdoms

1978

Two types of prokaryotic cells found

Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Learning objectives:
List characteristics
of 3-domain system

The Three-Domain System

A domain can be divided into kingdoms

Classified by cell type,

cell wall, rRNA,
membrane lipid
structure, tRNA,
sensitivity to antibiotics

Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Table 10.1

The Three-Domain System

Peptidoglycan

Unusual cell walls

3-domain recognizes 3
types of cells. Eukarya
includes Kingdoms
Fungi, Plantae, and
Animalia, plus certain
protists
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Figure 10.1

Phylogenetic Hierarchy
Organisms grouped into taxa by phylogenetic relationships
Some eukaryotic relationships obtained from fossil records
Prokaryotic relationships determined by rRNA sequencing

Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Table 10.2

Endosymbiotic Theory

Similarities in rRNA
sequences supporting
endosymbiotic theory
Figure 10.2
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Mutualistic symbiosis
between eukaryotic host
and bacterium possible
precursor to
reproductive capability
Figure 10.3
as a unit

Learning objectives:
Explain why
scientific names are
used.
Scientific binomial

Scientific Names
Source of Genus name

Source of
Specific epithet

Kbebsiella 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 notatum

Tuftlike (penicill-)

Spores spread in wind

(nota)

Trypanosoma cruzi

Corkscrew-like (trypano-, Honors Oswaldo Cruz

borer; soma-body)

Binomials (Genus Species) used by scientists worldwide which

enables them to share knowledge efficiently and accurately
Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Learning objectives: List the major taxa.

Taxonomic Hierarchy

Differentiate between culture, clone, and strain.

Similar species are

grouped into a
genus; similar
genera are grouped
into a family, etc.
Kids

Kingdom

Prefer
Phylum/
Division
Cheese

Class

Over

Order

Fried

Family

Green

Genus

Spinach Species

Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Figure 10.5

Species Definition
Eukaryotic species:
A group of closely related organisms that breed
among themselves
Prokaryotic species:
A population of cells with similar characteristics
Culture: bacteria grown at a give time in media
Clone: Population of cells derived from a single cell
Strain: Genetically different cells within a clone
Viral species:
Population of viruses with similar characteristics that
occupies a particular ecological niche
Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Domain Eukarya
Learning objectives: List the major characteristics used to
differentiate the three kingdoms of multicellular Eukarya.
Define protist.

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 for eukaryotic organisms that do not
fit other kingdoms; currently being assigned to
kingdoms
Viruses not placed in a kingdom (must have host)
Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Prokaryotes
Phylogenetic
relationships of
prokaryotes (Kingdom
Phylum)

Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Figure 10.6

References
Learning objectives:
Compare/contrast classification and identification
Explain purpose of Bergeys Manual
Bergeys Manual of Determinative
Bacteriology (for lab identification)
Provides identification schemes for
identifying bacteria and archaea

Morphology, differential
staining, biochemical tests, cell
wall composition, oxygen
requirements (treatment)

Bergeys Manual of Systematic

Bacteriology
Provides phylogenetic information
on bacteria and archaea

Based on rRNA sequencing

Approved Lists of Bacterial Names

Lists species of known prokaryotes

Based on published articles

Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Learning objectives:
Describe how staining and
biochemical tests are used to
identify bacteria
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Methods to Classify and Identify Microbes

Morphological characteristics (aided by staining)
Presence of certain enzymes
Serological tests (antigen antibody response)
Phage typing (susceptibility of bacteria to phages)
Fatty acid profiles
Flow cytometry
Percentage of G-C pairs in nucleic acid
Number and sizes of DNA fragments (fingerprints)
produced by restriction enzymes
Sequence of bases in rRNA
Polymerase chain reaction (PCR) to detect DNA
Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Identification Methods
Morphological
characteristics:
Useful for
identifying
eukaryotes

Using metabolic characteristics to

identify selected genera of enteric
(intestinal) bacteria

Differential
staining: Gram
staining, acid-fast
staining
Biochemical
tests: Determines
presence of
bacterial
enzymes
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Figure 10.8

Morphology and
differential staining
important to proper
treatment for microbial
diseases
Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Numerical Identification
Rapid identification
tools for groups of
medically important
bacteria (e.g., enterics)
are designed to perform
several biochemical tests
simultaneously.
The value for each
positive test is circled
and compared to a
computerized listing.
In this case a confirmatory test is advised.

Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Figure 10.9

Serology
Learning objectives:
Differentiate Western blotting from Southern blotting.
Explain how serological tests and phage typing can be used
to identify an unknown bacterium.

Combine known
antiserum +
unknown
bacterium

Left grainy appearance is positive for agglutination

bacteria was mixed with antibodies produced in
response to same strain

Slide
agglutination
ELISA (enzymelinked
immunosorbent
assay)
Western blot

Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Figure 10.10

Western Blot

Proteins separated by electrophoresis

can be detected by their reactions with
antibodies
Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Figure 10.12

Phage Typing
Determining which
phages a bacterium is
susceptible to:
The tested strain was
grown over entire plate;
known phages are
placed in different
squares; plaques (areas
of lysis) appear dark
indicating sensitivity to a
specific phage

Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Figure 10.13

Flow Cytometry Uses

Used to identify
bacteria in a sample
without culturing the
bacteria
Differences in electrical
conductivity between
species
Fluorescence of some
species
Cells selectively stained
with antibody +
fluorescent dye
Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Figure 18.11

Genetics
Learning objectives:
Describe how newly discovered microbe can be classified by:
DNA base composition, rRNA sequencing, DNA fingerprinting,
PCR, and nucleic acid hybridization

DNA base composition

Guanine + cytosine
moles% (GC)

Plasmids from 7 different bacteria digested

with same restriction enzyme: none of these
bacteria happen to be identical (source of
hospital-acquired infections).

DNA fingerprinting
Electrophoresis of
restriction enzyme
digests
rRNA sequencing
Polymerase Chain
Reaction (PCR)

Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Figure 10.14

Nucleic Acid Hybridization

Greater degree of hybridization (pairing of two strands of DNA, each
from a different microbe) indicates greater similarity

Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Figure 10.15

Nucleic Acid Hybridization: DNA probe

Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Figure 10.16

Nucleic Acid Hybridization: DNA chip

Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Figure 10.17

Dichotomous Key
Learning objectives:
Differentiate a
dichotomous key
from a cladogram.
Dichotomous key:
successive questions
with two possible
answers.

Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Cladogram
Cladogram:
Maps showing evolutionary relationships among
organisms.

Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Figure 10.18.1

Cladogram

Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Figure 10.18.2

Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings

Figure 10.5