TOPIC 5

BACTERIAL TAXONOMY
KALAIVANI NADARAJAH
ROOM 4114, 4
TH
FLOOR
BIOLOGY BUILDING
Email: vani@pkrisc.cc.ukm.my

TAXONOMY
Comes from the Greek word
taxis arrangement;
nomos - rules
Is a science of organismal classification
It is a system that creates an universal name
for an organism
Presents a reference point to classify
organisms
Taxonomy is made up of
i. classification
ii. nomenclature and
iii. identification

TAXONOMY
Classification is the arrangement of
organisms into groups (taxa) according to
similarities and evolutionary connections
Nomenclature is a branch that is involved
in the processing of naming a taxonomical
group according to a series of rules
Identification determines taxa for organism
that were isolated
THE HISTORY OF TAXONOMY
1735 Plant and animal Kingdom
1857 Fungus and bacteria classified under plant
kingdom
1866 bacteria, protozoa, algae, and fungi makes up
the Kingdom Protista
1937 "Prokaryote" terminology used for organisms
without nucleus
1961 cells with non membrane nucleoplasm are
Prokaryote
1959 Kingdom Fungi
1968 Prokaryote Kingdom suggested
1978 Two types of prokaryotic cells found
Table 5.1
TAXONOMY
Systematic or phylogeny
- Is the study of the evolutionary history of an
organism
All Species Inventory (2001-2025)
Was formed to identify all species on Earth
Binomial Nomenclature was proposed by Carolus
Linnaeus in the18 Century. This system introduced
Genus
Specific epithet
Strain is the subgroup of species
Strain can be written as a name, nomber or an alphabet
There are several rules that need to be observed in
writing a scientific name (see Table 5.2)

Carolus Linnaeus
Scientific Name
Scientific binomial
Source of Genus
name
Source of
Specific epithet
Klebsiella 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-, borer;
soma-body)
Honors Oswaldo
Cruz
Table 5.2
Taxonomic key
Linnaeus suggested a taxonomical hierarchy
All organisms that are from the same species are classified under
one genus
Genus with the same traits will be classified into the same family
and the list goes on
He classified all living organisms under two kingdoms, animal and
plant
Figure 5.1 The classification of human, dog, wolf and bacterium
DICHOTOMOUS KEYS
The taxonomy keys are
used to identify
characteristics of an
organism
We hope that the
classification of organisms
can be conducted based
on phylogenic connections
and evolutionary ties
between organism.
Figure 5.2 The dichotomous key generated
for classification of main bacterial groups
Problems in taxonomy
Problems that crop up in taxonomy studies are
i. To determine members in a species
ii.To identify members of a kingdom and
kingdoms that are in a domain
In an advanced organism such as plants and
animals, classification is conducted according to
the ability to reproduce, morphology and
geography
genetic transfer and changes in morphology can
not be used in the classification of bacteria
Problems in taxonomy

Bacteria is classified according to
i. chemical reaction
ii. Chemical composition
iii. Cell structure
iv. Genetic characteristic and
v. Immunological characteristic
Development since LINNAEUS
1866- Ernst H.Haeckel created the third kingdom
PROTISTA which contains algae,
protozoa,bacteria,fungi and sponge
1956- Lynn Marguilis and H.F Copeland
introduced the 4 kingdoms classification scheme
for prokaryote and eukaryote
i. Monera inclu. all prokaryotes i.e. true bacteria
and blue green algae
ii. Protoctista- all eukaryotes as algae, fungi and
protozoa
iii. Plantae- all green plants
iv. Animalia all animals created from zygotes
Development since LINNAEUS
R.H. Whittaker does not accept the theory of
endosymbiosis for eukaryotic and prokaryotic
diversity
Suggested a means of classification according
to the dietary requirements
1969- Whittaker suggested the division of
Protoctista to Prostista and Fungi

5 Kingdom Classification System
From Whittaker and other
taxonomist suggestion
and observations the 5
Kingdom classification
system was formed
All prokaryotes were
classified as Monera no
cells nucleus
Unicellular Eukaryotes
with nucleus were
classified as Protista

Figure 5.3 The 5 Kingdom Classification
See Table 5.3 for characteristic
of all 5 kingdoms
Table 5.3 Characteristics of the 5kingdom classification
Kingdom Monera
All prokaryotes including
eubacteria, cyanobacteria
and archaebacteria

Kingdom Monera
characteristics:

Unicellular; no nuclei, no
membranous organelles
DNA contains little or no
protein
Binary fission
Rajah 5.4 Ahli kingdom Monera
Kingdom Monera
Type of organisms:
Eubacteria is important in the area of health
science
Cyanobacteria are important in maintaining
balance in environment
Archaebacteria are primitive prokaryotic
organism that have formed adaptation to
extreme environments
* Methanogen
* Termoacidophiles
* Halophiles

KINGDOM PROTISTA
Is unicellular; contains
nucleus with
membrane
Lives in freshwater,
sea water and also in
soil
Figure 5.5 Member of the Kingdom Protista
Members are mostly
multicellular with
some that are
unicellular
Obtains nutrients via
absorption
Produces spores
Figure 5.6 Members of the Fungal Kingdom
KINGDOM FUNGI
Are animals that are
produced by zygote
formation
Members are
macroscopic or
microscopic
Includes many types
of animals including
Helminths and
Arthropods
Figure 5.7 Members of the Animal Kingdom
KINGDOM ANIMALIA
PROCESS OF PROKAROTIC
EVOLUTION
Figure 5.8 Evolutionary Model since the
identification of archaebacteria
Carl Woese, G.E.Fox 1970s
The proof that was
obtained from research
on Archaebacteria and
stromatolites suggested
that there are three
branches to the tree of
life that was produced in
Age of Microorganism
Each of this branch
produces a different
group of organism
Tree of life
PROCESS OF PROKAROTIC
EVOLUTION
1977- T.Cavalier suggested that the archaebacteria
emerged after the eubacteria as a result of evolution of the
Gram positive bacteria that are actinomycetes

1988- J.A.Lake proposed a two branch model; one branch
produces the eubacteria and 2 groups of archaebacteria
and the other branch is divided into eukaryote and one
group of archaebacteria

1990- Woese suggested the domain category
Domain is above the kingdom
The three branch theory was not received by all.
THREE DOMAIN THEORY OF WOESE
Before the three domain theory was proposed by
Woese in 1998; there were 3 views held by
taxonomist
1
st
view- from a general ancestor it branched out to
bacteria and archae, and the archae branched into
eukaryote
2
nd
view all three domains existed together and this
allowed for the exchange of genetic content between
all universal genetic code
3
rd
view there are 4 domains and the members of
the 4th domain that produced the eukaryote; this
domain has become extinct
ENDOSYMBIOSIS THEORY
Figure 5.9
THREE DOMAIN THEORY OF WOESE
Figure 5.10
This diagram explains the three domain theory of Woese
THE DIFFERENCES BETWEEN BACTERIA, ARCHAE AND
EUKARYOTE
Table 5.4
Three Domain
WOESES THREE DOMAINS
Kingdom
Monera
All eucaryotes
Table 5.11
Figure 5.12 The Shrub of life
Proposed by W Ford Doolittle
Has more than one ancestor
The interlinked and
intertwined
interactions show
that there is a lateral
gene transfer
between genomes
Lateral gene transfer
The different colored line that comes from different ancestors shows that
there is lateral gene transfer from one cell to another. When genes from
different sources are united, a new cell with ancestral diversity will be
Generated.
Figure 5.13
Three Domain System
Table5.5
Figure 5.14 Evolution Tree Generated
through Numerical Taxonomy


Numerical Taxonomy more
traits observed in an organism
will increase the accuracy by
which the similarities between
organism is determined

When two organism have 90%
similarities in all traits that are
observed therefore both
organisms can be assumed to
be in the same species

Figure 5.14
NUMERICAL IDENTIFICATION
Figure 5.15
Genetic Homology
Can be studied by :
i. studying the base composition
ii. Sequencing of DNA and RNA
iii. Through the hybridization of DNA
iv. Studying protein profile
DNA base composition
Guanine + cytosine
mol % (GC)
DNA fingerprinting
Electrophoresis of
restriction enzyme
digested product
rRNA sequencing
Polymerase Chain
Reaction (PCR)
Base composition, fingerprinting and PCR
Acid nucleic hybridization:DNA probes
Figure 5.16
Acid nucleic hybridization: DNA Chip
Figure 5.17
Western Blotting
Figure 5.18
Other methods used
The difference in the
flow of electric between
species
Cells are stained
selectively with
Antibodies and
fluorescent stain
Flow cytometry
antiserum mixture
that is known with
unknown bacteria
Agglutination
slide
ELISA
Western blot
Serology
Figure 5.19
Phage Typing
Figure 5.20
Table 5.6
Differential evolution
When a group of organism that are
connected is identified, it is presumed
that both have the same ancestor and
any differences observed is present
due to differential evolution
(divergent evolution)
Divergent evolution happens when a
subgroup of organism have
experienced mutation where the two
organisms are differentiated into two
groups.
Eubacteria can produce Gram
positive and Gram negative
Figure 5.21 divergent evolution
Characteristics used in classifying
bacteria
Table 5.7
Biochemical Test used in identification and
classification of bacteria
Table 5.8
Characteristics of bacteria that have
medical importance
Table 5.9
Characteristics of bacteria that have medical
importance
Table 5.10