Chapter 10
Classification of
Microorganisms
Terminology
• Taxonomy
– The science of classifying organisms
– Provides universal names for organisms
– Provides a reference for identifying organisms
• Systematics or phylogeny
– The study of the evolutionary history of
organisms
The Study of Phylogenetic
Relationships
• All Species Inventory (2001-2025)
– To identify all species of life on Earth
• Historic Background
– 1735
– 1857
– 1866
– 1937
Plant and Animal Kingdoms
Bacteria & fungi put in the Plant Kingdom
Kingdom Protista proposed for bacteria,
protozoa, algae, & fungi
"Prokaryote" introduced for cells "without
a nucleus"
The Study of Phylogenetic
Relationships
– 1961
– 1959
– 1968
– 1978
– 1979
Prokaryote defined as cells in which
nucleoplasm is not surrounded by a
nuclear membrane
Kingdom Fungi
Kingdom Prokaryotae proposed
Two types of prokaryotic cells found
(sequence in rRNA)
Three domain system proposed (Woese)
above 5 kingdoms (based on the rRNA
nucleotide sequence)
The Three-Domain System
Table 10.1
The Three-Domain System
Figure 10.1
The Three-Domain System
Table 10.2
Endosymbiotic Theory
Figure 10.2
Figure 10.3
A Phylogenetic Hierarchy
• Implies that a group of organisms evolved
from a common ancestor
– Some of the information used to classify comes
from fossils
– Fossil evidence not available for most
prokaryotes
– Phylogeny for prokaryotes based on DNA
hybridization and rRNA sequencing
Classification of Organisms
• Rules for classifying and naming living organisms
– several scientific entities are responsible for
establishing rules
• Scientific nomenclature (binomial nomenclature):
genus and specific epithet (species)
– Used by scientists worldwide
– Bacteria or prokaryotic scientific names taken from
Latin (genus can be taken from Greek) or latinized by
adding suffix “-ales” & “-aceae”.
– If reclassified, old name is often written in parentheses
e.g. Enterococcus (Streptococcus) faecalis
References
•• Bergey’s Manual of Determinative •Morphology, differential
Bacteriology
staining, biochemical tests
•Provides identification schemes for
identifying bacteria and archaea
•• Bergey’s Manual of Systematic
Bacteriology
•Provides phylogenetic information
on bacteria and archaea
•Based on rRNA sequencing
•• Approved Lists of Bacterial
•Based on published articles
Names
•Lists species of known prokaryotes
Scientific Nomenclature
Kbebsiella pneumoniae
Source of Genus
name
Honors Edwin Klebs
Source of
Specific epithet
The disease
Pfiesteria piscicida
Honors Lois Pfiester
Disease in fish
Scientific binomial
Salmonella typhimurium Honors Daniel Salmon
Stupor (typh-) in
mice (muri-)
Forms pus (pyo-)
Streptococcus pyogenes
Chains of cells
(strepto-)
Penicillium notatum
Tuftlike (penicill-)
Trypanosoma cruzi
Corkscrew-like
Honors Oswaldo
(trypano-, borer; soma- Cruz
body)
Spores spread in wind
(nota)
Taxonomic hierarchy
Figure 10.5
Species Definition
• Eukaryotic species: a group of closely related
organisms that breed (interbreed) among
themselves but does not breed with individuals of
another species
• Prokaryotic species: a population of cells with
similar characteristics
– Clone: Population of cells derived from a single cell
– Strain: Genetically different cells within a clone
Domain Eukarya
• 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
Prokaryotes
Figure 10.6
Classification of viruses
• Viral species: population of viruses with
similar characteristics that occupies a
particular ecological niche
• Viruses are not classified as part of the
three-domain system
• Ecological niche of a virus is its specific
host cell
– Viruses may be more closely related to their
hosts than other viruses
Methods of Classifying and
Identifying Microorganisms
• Majority of Bacteria and Archaea have not
been cultured
– Estimate that only 1 % of these microbes have
been discovered
– More than 2,600 species listed in the Approved
Lists of Bacterial Names, but less than 10 %
are human pathogens
Identification Methods
• Morphological
characteristics:
Useful for
identifying
eukaryotes
• Differential staining:
Gram staining,
acid fast staining
• Biochemical tests:
Determines presence
of bacterial enzymes
Figure 10.8
Biochemical test: numerical identification
Figure 10.9
Identification Methods: Serology
• Science that studies blood serum and immune
responses that are evident in serum
– Microorganisms are antigenic (induce/stimulate
formation of antibodies when they enter an
animal’s body)
– Antigen (Ag): any substance that causes
antibody (Ab) formation and reacts only with its
specific Ab; immunogen
– Antibody (Ab): proteins that circulate in the
blood and combine in a highly specific way with
the bacteria that caused their production
Serology
• Combine
known
antiserum +
unknown
bacterium
• Slide
agglutination
• ELISA
• Western blot
Positive result =
agglutination
(clumping)
Figure 10.10
Western Blot
Figure 10.12
Identification Methods:
Phage typing
• Looks for similarities among bacteria
– bacteriophages infect only specific host bacteria
and usually causes lysis fo the bacterial host
cells they infect
• Useful in tracing the origin and course of a
disease outbreak
– Can trace sources of food-associated infections
– Also useful for locating the source of hospital
acquired (nosocomial) infection
Phage Typing
Figure 10.13
Identification Methods: Flow cytometry
• Differences in
electrical
conductivity
between species
• Fluorescence of
some species
• Cells selectively
stained with
antibody +
fluorescent dye
Figure 18.11
Genetics
• DNA base composition (Classification)
– Comparison of the Guanine + cytosine (GC)
moles % in different species can reveal the
degree of species relatedness
• rRNA sequencing (Classification)
– Used to determine the diversity of organisms
and the phylogenetic relationships among them
• Polymerase Chain Reaction (PCR)
– Amplification of DNA; Detect microbes that
cannot be cultured by conventional methods
– Used for classification & identification
Identification Methods: Genetics
• DNA fingerprinting
– Electrophoresis of
restriction enzyme
digests
– The more similar the
patterns, the more
closely related
– Can be used to find
sources of
nosocomial
infections
Figure 10.14
Nucleic Acid Hybridization
• Measures the ability of DNA strands from
one organism to hybridize with the DNA
strands of another organism
– The greater the degree of hybridization, the
greater the degree of relatedness (classification)
– DNA-RNA hybridization can also be used
– Can be used for identification (Southern
blotting, DNA probe, & DNA chip)
Nucleic Acid Hybridization
Figure 10.15
Nucleic Acid Hybridization: DNA probe
Figure 10.16
Nucleic Acid Hybridization: DNA chip
Figure 10.17
Figure 10.5
Dichotomous Key
• Widely used for
identification
purposes
Chap. 10, p. 287
Cladogram
• Maps that show evolutionary relationships
among organisms
• Made primarily using rRNA sequence
Figure 10.18.1
Cladogram
• Each branch point is defined by a feature
shared by various species on that branch
Figure 10.18.2
Chapter Review
• Taxonomy: the science of classifying
organisms
– Provides universal names for organisms
– Show degree of similarities among organisms
– Provides a common reference for identifying
organisms already classified
• Systematics or phylogeny: the study of the
evolutionary history of organisms
• Provides tools for clarifying the evolution of
organisms as well as their interrelationships
The Three-Domain System
• Proposed by Carl R. Woese in 1978
• Based on the nucleotide sequences of
rRNA; a universal ancestor split into 3
lineages (endosynbiotic theory)
• Eukarya: animals, fungi, plants, & protists
– Eukaryotic species: a group of closely related
organisms that breed (interbreed) among
themselves but does not breed with individuals
of another species
Domain Eukarya
• 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
The Three-Domain System
• Bacteria: all the prokaryotes with
peptidoglycan cell wall (pathogenic &
nonpathogenic)
• Archaea: prokaryotes that do not have
peptidiglycan in their cell walls
(methanogens, extreme halophiles, 7
hyperthermophiles)
The Three-Domain System
• Prokaryotic species: a population of cells
with similar characteristics
– Clone: Population of cells derived from a single
cell
– Strain: Genetically different cells within a clone
• Phylogenetic Hierarchy
– Eukaryotic evidence comes from fossils
– Prokaryotic evidence comes from DNA
hybridization & rRNA sequencing
Viruses
• Not a part of the three-domain system
• Viral species: population of viruses with
similar characteristics that occupies a
particular ecological niche
• Ecological niche of a virus is its specific
host cell
– Viruses may be more closely related to their
hosts than other viruses
Methods of Classifying and
Identifying Microorganisms
• Majority of Bacteria and Archaea have not
been cultured
– Estimate that only 1 % of these microbes have
been discovered
– More than 2,600 species listed in the Approved
Lists of Bacterial Names, but less than 10 %
are human pathogens
Chapter Review
• Know these terms: taxonomy, phylogeny
(systematics), eukaryotic species,
prokaryotic species, viral species, clone,
and strain.
• Know how phylogenetic hierarchy was
determined (fossil evidence, rRNA
sequence & DNA hybridization)
Chapter Review
• Know the three-domain system
• Know the classifications of eukaryotes,
prokaryotes, and virus.
• Classification and Identification part of this
chapter (some techniques are applicable to
Chapter 9, too) will be tested as a take home
exam (due on Friday, Oct. 17). Ten
questions (matching) for the take home exam
will be posted on the web and given in the
class by Monday.