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