Taxonomy &

Classification of
Prokaryotes

Chapter 2b

Dr. Caridad D. Garcia

Learning Objectives:
 Define taxonomy, taxon, and phylogeny
 Discuss the limitations of a two-kingdom
classification
 Identify the contributions of von Nageli,
Chatton, Whittaker, and Woese.
 TAXONOMY
 The science of classifying living
organisms
 Provides universal names for organisms
 Provides a reference for identifying
organisms
“Taxonomy is the science that studies
organisms in order to arrange them into
groups; those organisms with similar
properties are grouped together and
separated from those that are different.”
 Taxonomy can be viewed as three separate
but interrelated areas:

 Identification--the process of
characterizing organisms
 Classification--the process of arranging
organisms into similar or related groups,
primarily to provide easy identification
and study
 Nomenclature--the system of assigning
names to organisms
Classification
Classification systems
provide meaningful
groupings of organisms
based on evolutionary
relationships.
 Systematics
 Study of the
evolution of
biological diversity
 We use comparisons
of form and of
genetics classify
living things
 Hierarchical
Classification
 Seven Taxonomic
Categories
 Binomial Nomenclature
 Two part name
(Genus, species) Image: Eric Gaba
Systematics or Pylogeny:
Evolutionary Classification of Organisms
Systematics examines evolution
of biological diversity, and
combines data from the
following areas:
 Fossil record
 Comparative homologies

Similarity of structures
due to shared ancestry
 Comparative sequencing of
DNA/RNA among
organisms

Image: NBII gov, CSS Inc.

 Phylogeny: The Study of Evolutionary
Relationships of Living Organisms
1.5 million different organisms have
been identified to date
Similarities among living organisms:
 Made up of cells surrounded by a
plasma membrane
 Use ATP as energy source
 Store genetic information as DNA
 Ribosomes are the site of protein
synthesis.
 Phylogeny: The Study of Evolutionary
Relationships of Living Organisms
Both differences and similarities
among organisms are caused by
natural selection (Darwin, 1858).

Organisms can be classified into

taxonomic categories (taxa), based
on the differences and similarities
among them.
Phylogeny
Aristotle: categories of living organisms
Plants
Animals

Ancient Greeks classified all living

organisms into two groups
 Kingdom Plantae
 Kingdom Animalia
Phylogeny
1857 (Carl von Nägeli) proposed that bacteria
& fungi be placed in the plant kingdom.

1866 (Ernst Haeckel) Kingdom Protista was

proposed [bacteria, fungi, algae, and protozoa]
but many scientists still classified bacteria and
fungi as plants.

Intense disagreement over classification

of bacteria and fungi persisted over 100 years.
Phylogeny
1930s: electron microscopy --
bacterial cells lacked a nucleus.
The term procaryote was
introduced in 1937 by Edouard
Chatton
1959: Kingdom Fungi
Phylogeny
1961:(Roger Stanier) current
definition of the term
procaryote was established
“cell in which the nuclear
material (nucleoplasm) is NOT
surrounded by a nuclear
membrane”
Phylogeny
1968: Kingdom Procaryotae was
accepted by biologists

1969: Robert Whitaker proposed a

five-kingdom system of
biological classification for all
living organisms.
 Five-Kingdom System of Biological
Classification (1969: Robert Whitaker)
1. Kingdom Procaryotae (Monera): Oldest
known cells (3.5 billion years ago). Lack a
nucleus and membrane bound organelles.
The other four kingdoms are eucaryotes (true nucleus and
membrane bound organelles)
2. Kingdom Protista: Mostly unicellular, lack
tissue organization. Most have flagella during
life.
3. Kingdom Fungi: May be unicellular (yeasts) or
multicellular (molds). Many are saprotrophs.
4. Kingdom Plantae: Multicellular,
photosynthetic.
5. Kingdom Animalia: Multicellular, heterotrophs
that ingest food through a mouth or oral cavity.
Five-Kingdom Classification System
 Differences Between Eucaryotic and Procaryotic Cells

Procaryotes Eucaryotes
Cell size 0.2-2 um in diameter 10-100 um in diameter
Nucleus Absent Present
Membranous
Organelles Absent Present
Cell WallChemically complex When present, simple
Ribosomes Smaller (70S) Larger (80S) in cell
70S in organelles
DNA Single circular Multiple linear
chromosome chromosomes
(histones)
Cell Division Binary fission Mitosis
Summary: 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
(Recap) Learning Objectives:
 Define taxonomy, taxon, and phylogeny
 Discuss the limitations of a two-kingdom
classification
 Identify the contributions of von Nageli,
Chatton, Whittaker, and Woese.
Learning Objectives:
 Discuss the advantages of the
three-domain system
 List the characteristics of Bacteria,
Archae, and Eukarya domains
Three Domain System: 1978, Carl Woese

Domain: level of classification above

kingdom.
Criteria:
 rRNA
 Membrane lipid structure
 tRNA molecules
 Antibiotic sensitivity
 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

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
Figure 10.1
Three-Domain Classification

Line lengths are based on genetic

distances, i.e., longer lines reflect
greater differences.
Three-Domain Classification

Note that majority of genetic diversity is among

single-celled organisms
Three Domain System: 1978, Carl Woese

I. Domain Eubacteria:
“True bacteria”
II. Domain Archaeabacteria:
“Ancient bacteria”
III. Domain Eucarya:
All eucaryotes: Protista,
Fungi, Plantae, and Animalia.
Recap:
Learning Objectives
 Discuss the advantages of the
three-domain system
 List the characteristics of Bacteria,
Archae, and Eukarya domains
Learning Objective:

 Explain why scientific names are

used
 Binomial Nomenclature
 Scientific Nomenclature

 The
system of having 2
names for each organism

 1735:Carl von Linné or

Carolus Linnaeus
 Escherichia coli

Genus Scientific
(pl: genera) Epithet

Genus name: Scientific Epithet:

always capitalized never capitalized
Always a noun Always an
adjective
 Examples: Escherichia coli, E. coli, Escherichia spp.,
and “the genus Escherichia”

The species name (coli) is NEVER

capitalized

The species name is never used

without the genus name (e.g., coli
standing alone, by itself, is a mistake!)
 Examples: Escherichia coli, E. coli, Escherichia spp.,
and “the genus Escherichia”

The genus name may be used without the

species name (e.g., Escherichia may stand
alone, though when doing so it no longer actually
describes a species)

When both genus and species names are

present, the genus name always comes first
(e.g., Escherichia coli, not coli Escherichia)
 Examples: Escherichia coli, E. coli, Escherichia spp.,
and “the genus Escherichia”

Both the genus and species names are

always italicized (or underlined) — always
underline if writing binomials by hand

The first time a binomial is used in a work, it must

be spelled out in its entirety (e.g., E. coli standing
alone in a manuscript is not acceptable unless you
have already written Escherichia coli in the
manuscript)
 Examples: Escherichia coli, E. coli, Escherichia spp.,
and “the genus Escherichia”

The next time a binomial is used it may be

abbreviated (e.g., E. for Escherichia) though this
is done typically only when used in combination
with the species name (e.g., E. coli)

The species name (e.g., coli) is

NEVER abbreviated
 Examples: Escherichia coli, E. coli, Escherichia spp.,
and “the genus Escherichia”

It is a good idea to abbreviate unambiguously if

there is any potential for confusion (e.g.,
Enterococcus vs. Escherichia)

These rules are to be followed when

employing binomial nomenclature even in
your speech. It is proper to refer to
Escherichia coli as E. coli or even as
Escherichia, but it is not proper to call it coli
or E.C.!
 Examples: Escherichia coli, E. coli, Escherichia spp.,
and “the genus Escherichia”

Failure to employ correct binomial nomenclature

on exams will be marked INCORRECT —
don’t let this happen to you!!!!!!

When in doubt, write the whole thing

out (and underline)!
Names are usually derived from Latin (or
Greek) or may have latinized endings.
Examples:
 Homo sapiens (H. sapiens): Human
 Mycobacterium leprae (M. leprae):
etiologic agent of leprosy
 Canis familiaris (C. familiaris): Domestic
dog
Publications
 Rules for the assignment of names to bacteria
are established by the International Committee
on Systematic Bacteriology: Bacteriological Code
International Journal of Systematic Bacteriology
Bergey’s Manual of Systematic Bacteriology
 Fungi & algae: International Code of Botanical
Nomenclature
 Protozoa: International Code of Zoological
Nomenclature
Recap: Learning Objective

 Explain why scientific names are

used
Recap:

1. __________________ system of giving 2 names to

organisms
2. The system of naming mentioned in #1 was first proposed
in the 1700s by Swedish scientist __________.
3. It provides a “u_ _ _ _ _ s _ _ language” for scientists to
use when classifying organisms.
Example: Clostridium botulinum
4. Specie name: ________________
5. Genus: _____________________
6. Genus names are always capitalized
7. species names are lower case
8. The _______ name is always written first.
9. The _______ name is NEVER capitalized.
10. The language used is generally __________.
The Taxonomic Hierarchy
Learning Objectives
 List the major taxa
 Differentiate between culture, clone, &
strain
Classification of Organisms
Hierarchy of Taxonomic Categories
DOMAIN
Kingdom
 Phylum or Division (Bacteria)
 Class
 Order
 Family
 Genus
species
Learning objectives: List the major taxa.
Differentiate between culture, clone, and
strain. Taxonomic Hierarchy

 Similar species are

grouped into a genus;
similar genera are
grouped into a family,
etc.
 King Kingdom
 Philip Phylum/
David Division
 Came Class
 Over Order
 For Family
 Good Genus
 Spaghetti Species

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
Prokaryotes
Phylogenetic
relationships of
prokaryotes (Kingdom –
Phylum)
Classification of Bacteria: Scientific Nomenclature

Bergey’s Manual: Provides a reference for

identifying and classifying bacteria.
 Classification initially based on cell
morphology, staining, metabolism,
biochemistry, serology, etc.
 More recently, DNA, RNA, and protein
sequence analysis are being used to study
evolutionary relationships.
Taxonomic Rank

Strain O157:H7
One difficulty is deciding how different two isolates must be
before one describes them as different species rather than as
different strains.
 Note that not all groupings of
microorganisms have taxonomic meaning:
Taxonomic Rank
e.g., lactic acid bacteria, endospore-formers, or
enteric pathogens. These are examples of
classifying “mistakes” due to phenotypic
similarity that results from convergent evolution.

Strain O157:H7

One difficulty is deciding how different two isolates must be

before one describes them as different species rather than as
different strains.
Taxonomy: Nomenclature
Nomenclature: “Bacterial
names may originate from
any language, but they
must be given a Latin
suffix.” (i.e., they must be
Latinized).

Strain O157:H7

Recall Binomial Nomenclature.

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

 Kingdom Fungi: Chemoheterotrophic;

unicellular or multicellular; cell walls of chitin;
develop from spores or hyphal fragments
 Kingdom Plantae: Multicellular; cellulose cell
walls; usually photoautotrophic
some algae, all mossess, ferns,
conifers, & flowering plants
 Kingdom Animalia: Multicellular; no cell
walls; chemoheterotrophic
sponges, various worms, insects, &
animals with backbones (vertebrates)
Domain Eukarya

 Protista: A catchall for eukaryotic

organisms that do not fit other
kingdoms; currently being assigned to
kingdoms; mostly unicellular
Classification of Viruses

Viruses are not considered living organisms by most

biologists, because they lack cells and their own
anabolic machinery.
Obligate intracellular parasites. Must have evolved
after their host cell evolved.
Viral species: Population of viruses with similar
characteristics that occupies a particular
ecological niche.
 Morphology
 Genes
 Enzymes
But aren’t we talking about microbes
in this class?

Prokaryotes
__________ Bacteria & Archaea
Cellular
Microorganisms
Everything else! (Yes,
Eukaryotes
__________ everything!)
But when studying
microbes, includes:
Acellular Fungi, Protozoa &
Particles Viruses Algae
____________
Phylogenetic Relationships of Procaryotes
Domain: Archaea
 Prokaryotic
 Lack peptidoglycan
 Often live in extreme
environments
 Not known to cause disease in
humans or animals
 Had been considered bacteria
until examination of their
unique rRNA sequences.
 Archaea appear to be more
closely related to Deinococcus radiodurans,
___________ than to an Extremophile
Bacteria.

Image: US gov, pub domain

Archaeabacteria: 3 Kingdoms
1. Methanogens:
Strict anaerobes; produce methane
2. Extreme Halophiles:
Require high salt concentrations
3. Thermoacidophiles:
Live in hot, acidic environments
ARCHAEA: Extremophiles (X-trem’-o-files)

Require extreme conditions of

temperature, salinity or pH to
survive.

______________ (Therm’-o- Thermophiles produce some of the

files) bright colors of Grand Prismatic
Spring, Yellowstone National Park
Require temperatures > 45oC
(113oF) to survive.

_____________ (Hal’-o-files)
Colonize extremely saline
environments.
Require salinity > 9% to maintain
integrity of cell walls.
The Great Salt Lake.
Red areas color due to
halophiles.
ARCHAEA: _____________
(Meth-ann’-o-jens)

Largest group of
Archaea.

Produce methane as a
metabolic byproduct.

Common in wetlands
(responsible for marsh
gas)

In the guts of animals

such as ruminants and
humans (where they
are responsible for
flatulence)
Images:
Cow Face, Andrew Duffell_wikimedia
Methanogen Diagram,
microimm.queensu.ca/.../methanogens.htm
 Methods of Identification
Note existence of other methods of visualization beyond Gram stain...

Note Phenotype- vs.

Genotype-based classification.
Phenotypic Characteristics  Microscopy: Gram stain, acid-fast stain, cell
morphology, cell arrangements.
 Colony morphology: size, color, border
shape, etc.
 Growth on Differential media: blood agar,
MacConkey agar, etc.
 Growth on Selective/Differential media:
MacConkey agar, EMB agar, etc.
 Biochemical tests: “Most biochemical tests
rely on a pH indicator or chemical reaction
that results in a color change [or gas
production] when a [specific] compound is
degraded.”
Gas Generation: Catalase Test
Durham Tube: Gas Production
Color Change: Urease Test
Commercial Biochemical Test Kits
 Don’t worry about the
specific details of this
key but do keep in
Dichotomous Key

mind how it is
organized.
 Typing of Strains
Biovar, Biotype (syn)

Serovar, Serotype (syn)

Typing via RFLP analysis

Ribotype (RFLP of rRNA) Also Phage Type

Polymorphism (RFLP) Analysis Genomic DNA is
1 2 3 4 5
Restriction Fragment Length

isolated, cut using

specific restriction
enzymes, run out on a
gel, and then Southern
Blotted with specific
DNA probes.

Can you tell me

which lanes contain
bacteria that are
clonally related?
What is an RFLP?
 What is an RFLP? (fig. 9.9)
Different strains have Note resulting
recognition sites in differences in
different places due restriction fragment
to genotypic length.
differences.
 RFLP generation.
Southern Blotting
Gels separate DNA
by size.

This is a post-
probe detection
blot.
 Ribotyping

Clonally related These are two strains

strains should have that have been
same RFLP type (i.e., differentiated based
same band pattern). on RFLP analysis.

Why care about clonal relatedness? Is a contamination

problem due to fault in your aseptic technique? Or is
there just a particularly invasive bug making the rounds?
Phages are
viruses of Phage Typing The clear
bacteria. spots are due
This is a “Soft-Agar to bacteria
Overlay.” killing (lysis).

“Phage” = “Bacteriophage”
The disks are
impregnated Antibiogram The streaks
make up a
with specific bacterial
antibiotics. “lawn”.

These two strains have different

antibiotic-resistance patterns.
  Numerical Taxonomy is a method of classification
Numerical Taxonomy that pools phenotypic characteristics.
 The key to numerical taxonomy is that no one trait
(e.g., ability to ferment glucose) is elevated in
importance above any other trait (e.g., Gram
staining characteristics).
 Instead, all traits are weighted equally.
 Classification in numerical taxonomy is expressed
in terms of a Similarity Coefficient found between
two compared strains. It is equal to:
 [# pos both strains]/[# pos one or both strains]
 by “pos” I mean that the characteristic is
present, e.g., ferments glucose or has pili, etc.
 Greater similarity coefficient, closer relatedness is
inferred. Greater than ~70% and inference is that
two compared bacteria are of the same species.
Numerical Taxonomy
Similarity Coefficients

Rearranged into two distinct species...

G-C Content (DNA Base Ratio) dsDNA is
distinguished
from ssDNA
based on UV
absorbance.

Different
species have
different DNA
melting temps.
G-C Content (DNA Base Ratio) Helix has higher
stability with
greater fraction G-
C vs. A-T pairing.

Higher melting
points therefore
correspond to
greater G-C content
DNA-DNA Hybridization
DNA-DNA Hybridization

Similarity is in terms of
nucleotide sequence
between the two compared
organisms.
16S rRNA Sequence Comparison
16S rRNA